Publications

S. Haydar, R. Bednarz, P. Laurette, I. Sobitov, N. Díaz i Pedrosa, P. Videm, T. Lueneburg, S. Kuß, H. Lahm, M. Dreßen, M. Krane, C. Schmidt, B. A. Grüning, N. Voigt, K. Streckfuss-Bömeke, R. Gilsbach.

Nature Communications, 17(1), 117, 2026.

DOI BIB

Comprehensive analysis of CRISPR array repeat mutations reveals subtype-specific patterns and links to spacer dynamics

Alexander Mitrofanov, Chase L Beisel, Franz Baumdicker, Omer S Alkhnbashi, Rolf Backofen.

microLife, 7, uqaf050, 2026.

DOI BIB

CoMPaseD: advanced planning of proteomic experiments aiming to identify small proteins

Jürgen Bartel, Philipp T Kaulich, Borja Ferrero-Bordera, Rick Gelhausen, Rolf Backofen, Andreas Tholey, Sandra Maaß.

microLife, 7, uqaf043, 2026.

DOI BIB

The complexity of multiple CRISPR arrays in strains with (co-occurring) CRISPR systems

Axel Fehrenbach, Alexander Mitrofanov, Rolf Backofen, Franz Baumdicker.

microLife, 7, uqaf042, 2026.

DOI BIB

LiraSearch—ultrafast ligand shape and electrostatic matching server

Rinaldo W Montalvão, Simon Bray, Marcos Veríssimo-Alves, Elena Cubero, Björn Grüning, Vitor B Pinheiro.

Bioinformatics Advances, 6(1), vbag139, 2026.

DOI BIB

The Spirogyra pratensis genome illuminates the evolution of developmental programs and spiral chloroplast biology

Elisa S Goldbecker, Deepti Varshney, Anja Holzhausen, Tatyana Darienko, Hong Zhou, Armin Dadras, Lukas Pfeifer, Thomas Pröschold, Enrique Lopez-Gomez, Elke Woelken, Charlotte Permann, Tassilo Erik Wollenweber, Kerstin Becker, Stefanie König, Franz Hadacek, Fay-Wei Li, Ivo Feussner, Noe Fernandez-Pozo, Andreas Holzinger, Florian Maumus, André Marques, Henrik Buschmann, Klaus von Schwartzenberg, Jan de Vries, Stefan A Rensing.

The Plant Cell, 38(8), koag224, 2026.

DOI BIB

Galaxy for accessible, reproducible, and collaborative data analyses: 2026 update

The Galaxy Community, Enis Afgan, Najat Amoukou, Rafael Andrade Buono, Mihail Anton, Christophe Antoniewski, Patrick Austin, Ahmed Hamid Awan, Rolf Backofen, Wendi Anne Bacon, Dannon Baker, Arthur Barreau, Bérénice Batut, Matthias Bernt, Daniel Blankenberg, Anthony Bretaudeau, Catherine Joan Bromhead, Richard Burhans, Melissa Burke, Scott Cain, Danielle Callan, Martin Cech, María Chavero-Díez, Haswane Chei, Ying Chen, Diana Chiang, John M Chilton, Tyler James Collins, Frederik Coppens, Nate Coraor, Charles Coulombe, Michael R Crusoe, Fabio Cumbo, Triskell Cumunel, Michael D'Silva, Armin Dadras, Céline Dalle, Khai Dang, John Y Davis, Paul De Geest, Willem de Koning, Giuseppe Defazio, Boris Depoortere, Katherine Do, José Manuel Domínguez Begines, Bert Droesbeke, Erick Nicolas Duarte, Enol Fernández-del-Castillo, Jeremy Fix, Giulio Formenti, Julian Frey, Melanie Christine Föll, Carol Gauthier, Kilian Gerberding, Franck Giacomoni, Jeremy Goecks, Nuwan A Goonasekera, Nadia Goué, Timothy J Griffin, Björn Andreas Grüning, Aysam Guerler, Yann Guitton, Ove Johan Ragnar Gustafsson, Kristína Gömöryová, Magdalena Harakalova, Helge Hecht, Alireza Heidari, Florian Heyl, Jennifer Hillman-Jackson, Saskia Hiltemann, Mina Hojat Ansari, Hans-Rudolf Hotz, Cameron John Hyde, Pierre-Étienne Jacques, Pratik Dilip Jagtap, Jayadev Joshi, Marie Jossé, Khaled Moahmmad Ahmad Jumah, Arash Kadkhodaei Elyaderani, Katarzyna Kamieniecka, Teja Kattenborn, Markus Konkol, Leonid Kostrykin, Natalie Kucher, Anup Kumar, Mira Kuntz, Bradley William Langhorst, Delphine Lariviere, Yvan Le Bras, Gildas Le Corguillé, Jean Le Cras, Justin Lee, Jan Leendertse, Hugo Lefeuvre, Brane Leskošek, Leandro Miguel Liborio, Romane Libouban, Marisa Loach, Jose David Lopez Tabernero, Lucille Lopez-Delisle, Daniel Lusk, Alexandru Mahmoud, Molène Mahé, Wolfgang Maier, Igor Makunin, Kirsty McCaffrey, Jack A Medico, Subina Mehta, Hailiang Mei, Mirela Minkova, Saim Momin, Paulo Cilas Morais Lyra Junior, Teresa Müller, Amirhossein Naghsh Nilchi, Tannistha Nandi, Engy Mohamed Taha Nasr, Anton Nekrutenko, Tiffanie Nelson, Johannes Nussbaum, Asime James Oba, Łukasz Opioła, Kevin Payet, Melanie Petera, Polina V Polunina, Sergei Pond, Krzysztof Poterlowicz, Gareth Robert Price, Junhao Qiu, Helena Rasche, Bryan Raubenolt, Tristan N Reynolds, Dave Rogers, Karl Rohr, Gabriel Ferreira Saudade, Michelle Terese Savage, Volodymyr Savchenko, Michael C Schatz, Isabelle Schmitz, Daniela Schneider, Pauline Seguineau, Beatriz Serrano-Solano, Clea Siguret, Patrik Smeds, Marco Sollitto, Nicola Soranzo, Sanjay Kumar Srikakulam, Lieven Sterck, Nikolaos Strepis, Andrew Stubbs, Keith Suderman, Anna Syme, Marco Antonio Tangaro, Reyhaneh Tavakoli Koopaei, Jonathan Andrew Tedds, Mehmet Tekman, Wai Cheng (Mike) Thang, Anil S Thanki, Michael Uhl, Janusch Vajna-Jehle, Marius van den Beek, Deepti Varshney, Nikolay Alexandrov Vazov, Jennifer Vessio, Pavankumar Videm, Tomas Vondrak, Reid Wagner, Gregory R Watson, Ralf J M Weber, Natalie Whitaker-Allen, Federico Zambelli, Paul Zierep, Rand Zoabi.

Nucleic Acids Research, 54(W1), W105-W116, 2026.

DOI BIB

Community-curated Galaxy interfaces with the Galaxy Labs Engine

Cameron J Hyde, Anna Syme, Bérénice Batut, Paul F Zierep, Winnie Mok, Wendi A Bacon, Gareth R Price.

GigaScience, 15, giag041, 2026.

DOI BIB

Ten common misconceptions about Galaxy (and why they are wrong!)

Wendi Anne Bacon, Bérénice Batut, Sanjay Kumar Srikakulam, Paul Zierep, Anthony Bretaudeau, Björn Grüning, Gildas Le Corguillé, Helge Hecht, John Y. Davis, Hans-Rudolf Hotz, Beatriz Serrano-Solano.

PLOS Computational Biology, 22(2), e1013869, 2026.

DOI BIB

RSEc-Atlas

Alireza Heidari, Arash Kadkhodaei, Paul Zierep, Björn Grüning, Saurabh Dome, Mihail Anton.

2026.

DOI BIB

Enhancing multi-omic analyses through a federated microbiome analysis service

Alexander Rogers, Famke Bäuerle, Martin Beracochea, Alireza Heidari, Matt Burridge, Benedikt Osterholz, Alexander Sczyrba, Mahfouz Shehu, Tom Tubbesing, Anil Wipat.

2025.

DOI BIB

A searchable atlas of pathogen-sensitive lncRNA networks in human macrophages

Nils Schmerer, Harshavardhan Janga, Michelle Aillaud, Janina Hoffmann, Marina Aznaourova, Sarah Wende, Henrike Steding, Luke D Halder, Michael Uhl, Fabian Boldt, others.

Nature Communications, 16(1), 1--17, 2025.

DOI BIB

RAPDOR: Using Jensen-Shannon Distance for the computational analysis of complex proteomics datasets

Luisa Hemm, Dominik Rabsch, Halie Rae Ropp, Viktoria Reimann, Philip Gerth, Jürgen Bartel, Manuel Brenes-Álvarez, Sandra Maaß, Dörte Becher, Wolfgang R Hess, others.

Nature Communications, 16(1), 8527, 2025.

DOI BIB

StahlDigital: Ontology‐Based Workflows for the Steel Industry

Franz Roters, Ahmed Aslam, Yang Bai, Matthias Büschelberger, Kirill Bulert, Alexander Butz, Tilmann Hickel, Tushar Jogi, Silke Klitschke, Michael Martin, Lars‐Peter Meyer, Lukas Morand, Yoav Nahshon, Norman Radtke, Ujjal Saikia, Andreas Trondl, Alexander Wessel, Paul Zierep, Dirk Helm.

Advanced Engineering Materials, 27(8), 2402148, 2025.

DOI BIB

Semantic Orchestration and Exploitation of Material Data: A Dataspace Solution Demonstrated on Steel and Copper Applications

Yoav Nahshon, Lukas Morand, Matthias Büschelberger, Dirk Helm, Kiran Kumaraswamy, Paul Zierep, Matthias Weber, Pablo de Andrés.

Advanced Engineering Materials, 27(8), 2401448, 2025.

DOI BIB

Open-Source and FAIR Research Software for Proteomics

Yasset Perez-Riverol, Wout Bittremieux, William S. Noble, Lennart Martens, Aivett Bilbao, Michael R. Lazear, Bjorn Grüning, Daniel S. Katz, Michael J. MacCoss, Chengxin Dai, Jimmy K. Eng, Robbin Bouwmeester, Michael R. Shortreed, Enrique Audain, Timo Sachsenberg, Jeroen Van Goey, Georg Wallmann, Bo Wen, Lukas Käll, William E. Fondrie.

Journal of Proteome Research, 24(5), 2222-2234, 2025.

DOI BIB

Galaxy single-cell & spatial omics community update: Navigating new frontiers in 2025

Marisa Loach, Amirhossein Naghsh Nilchi, Diana Chiang, Morgan Howells, Florian Heyl, Helena Rasche, Julia Jakiela, Mehmet Tekman, Menna Gamal, Pablo Moreno, Saskia Hiltemann, Timon Schlegel, Björn Grüning, Rolf Backofen, Pavankumar Videm, Wendi Bacon.

Cell Genomics, 5(10), 101005, 2025.

DOI BIB

Interventional real-time molecular MRI for targeting early myocardial injury in a pig model

Timo Heidt, Simon Reiss, Julien Thielmann, Christian Weber, Alexander Maier, Thomas Lottner, Heidi R. Cristina-Schmitz, Timon Bühler, Diana Chiang, Claus Jülicher, Carolin Wadle, Ingo Hilgendorf, Dennis Wolf, Gavin Tumlinson, Luis Hortells, Dirk Westermann, Michael Bock, Constantin von zur Mühlen.

npj Imaging, 3(1), 7, 2025.

DOI BIB

Modulation of bone marrow haematopoietic stem cell activity as a therapeutic strategy after myocardial infarction: a preclinical study

Jasmin Rettkowski, Mari Carmen Romero-Mulero, Indranil Singh, Carolin Wadle, Jan Wrobel, Diana Chiang, Natalie Hoppe, Julian Mess, Katharina Schönberger, Maria-Eleni Lalioti, Karin Jäcklein, Beatriz SilvaRego, Timon Bühler, Noémie Karabacz, Mirijam Egg, Helen Demollin, Nadine Obier, Yu Wei Zhang, Claus Jülicher, Anne Hetkamp, Martin Czerny, Michael-Jason Jones, Hana Seung, Ritika Jain, Constantin von zur Mühlen, Alexander Maier, Achim Lother, Ingo Hilgendorf, Peter van Galen, Antonia Kreso, Dirk Westermann, Alejo E. Rodriguez-Fraticelli, Timo Heidt, Nina Cabezas-Wallscheid.

Nature Cell Biology, 27(4), 591-604, 2025.

DOI BIB

Fibroblast growth factor signaling induces a chondrocyte-like state of peripheral nerve fibroblast during aging

Dragana Stefanovska, Eliza Sassu, Mehmet Tekman, Amirhossein Naghsh Nilchi, Severin Haider, Claudia Domisch, Madelon Hossfeld, Stefanie Perez-Feliz, Lauritz Miarka, Franziska Schneider-Warme, Sebastian J. Arnold, Marco Prinz, Björn Grüning, Sebastian Preissl, Luis Hortells.

Nature Communications, 16(1), 10020, 2025.

DOI BIB

Flexynesis: A deep learning toolkit for bulk multi-omics data integration for precision oncology and beyond

Bora Uyar, Taras Savchyn, Amirhossein Naghsh Nilchi, Ahmet Sarigun, Ricardo Wurmus, Mohammed Maqsood Shaik, Björn Grüning, Vedran Franke, Altuna Akalin.

Nature Communications, 16(1), 8261, 2025.

DOI BIB

Analysis of tracrRNAs reveals subgroup V2 of type V-K CAST systems

Marcus Ziemann, Alexander Mitrofanov, Richard Stöckl, Omer S Alkhnbashi, Rolf Backofen, Wolfgang R Hess.

microLife, 6, uqaf020, 2025.

DOI BIB

Disparate mechanisms counteract extraneous CRISPR RNA production in type II-C CRISPR-Cas systems

Maximilian Feussner, Angela Migur, Alexander Mitrofanov, Omer S Alkhnbashi, Rolf Backofen, Chase L Beisel, Zasha Weinberg.

microLife, 6, uqaf007, 2025.

DOI BIB

Evaluating discrepancies in dimensionality reduction for time-series single-cell RNA-sequencing data

Maren Hackenberg, Laia Canal Guitart, Rolf Backofen, Harald Binder.

Briefings in Bioinformatics, 26(3), bbaf287, 2025.

DOI BIB

Importin-9 and a TPR domain protein MpH drive periodic patterning of ciliary arrays in Tetrahymena

Anushi Suwaneththiya Deraniyagala, Wolfgang Maier, Mireya Parra, Elise Nanista, Deborah Oluwabukola Sowunmi, Michael Hassan, Nathan Chasen, Sunita Sharma, Karl F. Lechtreck, Eric S. Cole, Natalia Bernardes, Yuh Min Chook, Jacek Gaertig.

Journal of Cell Biology, 224(6), e202409057, 2025.

DOI BIB

The lincRNA Pantr1 is a FOXG1 target gene conferring site-specific chromatin binding of FOXG1

Fabian Gather, Tudor Rauleac, Ipek Akol, Ganeshkumar Arumugam, Camila L Fullio, Teresa Müller, Dimitrios Kleidonas, Ruth Geiss-Friedlander, Andre Fischer, Andreas Vlachos, Rolf Backofen, Tanja Vogel.

Nucleic Acids Research, 53(12), gkaf539, 2025.

DOI BIB

Structural determinants of inverted Alu-mediated backsplicing revealed by -MaP and -JuMP

Justin M Waldern, Colin Taylor, Catherine A Giannetti, Patrick S Irving, Scott R Allen, Mingyi Zhu, Rolf Backofen, David H Mathews, Kevin M Weeks, Alain Laederach.

Nucleic Acids Research, 53(9), gkaf433, 2025.

DOI BIB

HVSeeker: a deep-learning-based method for identification of host and viral DNA sequences

Abdullatif Al-Najim, Sven Hauns, Van Dinh Tran, Rolf Backofen, Omer S Alkhnbashi.

GigaScience, 14, giaf037, 2025.

DOI BIB

PathoGFAIR: a collection of FAIR and adaptable (meta)genomics workflows for (foodborne) pathogens detection and tracking

Engy Nasr, Anna Henger, Björn Grüning, Paul Zierep, Bérénice Batut.

GigaScience, 14, giaf017, 2025.

DOI BIB

Galaxy as a gateway to bioinformatics: Multi-Interface Galaxy Hands-on Training Suite (MIGHTS) for scRNA-seq

Camila L Goclowski, Julia Jakiela, Tyler Collins, Saskia Hiltemann, Morgan Howells, Marisa Loach, Jonathan Manning, Pablo Moreno, Alex Ostrovsky, Helena Rasche, Mehmet Tekman, Graeme Tyson, Pavankumar Videm, Wendi Bacon.

GigaScience, 14, giae107, 2025.

DOI BIB

Open Science in the Humanities: Galaxy as a Flexible and yet Reproducible Platform

European Galaxy Team.

Heidelberg University Library, 2025.

DOI BIB

Open Science in den Humanities: Mehr Spielräume und Nachvollziehbarkeit durch Galaxy

Daniela Schneider, Jan Leendertse.

E-Science-Tage 2025, 2025.

DOI BIB

Enhanced sensitivity of TAPscan v4 enables comprehensive analysis of streptophyte transcription factor evolution

Romy Petroll, Deepti Varshney, Saskia Hiltemann, Hermann Finke, Mona Schreiber, Jan de Vries, Stefan A. Rensing.

The Plant Journal, 121(1), e17184, 2025.

DOI BIB

MaveDB 2024: a curated community database with over seven million variant effects from multiplexed functional assays

Alan F. Rubin, Jeremy Stone, Aisha Haley Bianchi, Benjamin J. Capodanno, Estelle Y. Da, Mafalda Dias, Daniel Esposito, Jonathan Frazer, Yunfan Fu, Sally B. Grindstaff, Matthew R. Harrington, Iris Li, Abbye E. McEwen, Joseph K. Min, Nick Moore, Olivia G. Moscatelli, Jesslyn Ong, Polina V. Polunina, Joshua E. Rollins, Nathan J. Rollins, Ashley E. Snyder, Amy Tam, Matthew J. Wakefield, Shenyi Sunny Ye, Lea M. Starita, Vanessa L. Bryant, Debora S. Marks, Douglas M. Fowler.

Genome Biology, 26(1), 13, 2025.

DOI BIB

Ten Common Misconceptions About Galaxy (and Why They Are Wrong!)

Wendi Anne Bacon, Sanjay Kumar Srikakulam, Bérénice Batut, Paul Zierep, Anthony Bretaudeau, Björn Grüning, Gildas Le Corguillé, Helge Hecht, John Y. Davis, Hans-Rudolf Hotz, Beatriz Serrano-Solano.

2025.

DOI BIB

Community-Curated Galaxy Interfaces with the Galaxy Labs Engine

Cameron J. Hyde, Anna Syme, Bérénice Batut, Paul F. Zierep, Winnie Mok, Wendi A. Bacon, Gareth R. Price.

2025.

DOI BIB

Left-right cortical interactions drive intracellular pattern formation in the ciliate Tetrahymena

Chinkyu Lee, Ewa Joachimiak, Wolfgang Maier, Yu-Yang Jiang, Mireya Parra, Karl F. Lechtreck, Eric S. Cole, Jacek Gaertig.

PLOS Genetics, 21(6), e1011735, 2025.

DOI BIB

FAIR Digital Objects for Seamless Research Data Management for Researchers and Higher Education Institutions

Markus Stocker, Björn Grüning, Tomasz Miksa, Claudia Biniossek, Dirk Betz.

Open Conference Proceedings, 5, 2025.

DOI BIB

Approaching Digital History with the Open Source Platform Galaxy

Daniela Schneider.

Zenodo, 2025.

DOI BIB

Scaling Scientific Workflows in Europe: Architecture and Deployment of the Galaxy-Pulsar Computational Network

Marco Antonio Tangaro, Stefano Nicotri, Björn Grüning, Sanjay Kumar Srikakulam, Armin Dadras, Oana Kaiser, Mira Kuntz, Anthony Bretaudeau, Paul De Geest, Sebastian Luna-Valero, María Chavero Díez, José María Fernández González, Salvador Capella-Gutierrez, Josep Lluís Gelpí, Jan Astalos, Boris Jurič, Miroslav Ruda, Łukasz Opioła, Hakan Bayındır, SILVIA GIOIOSA, Gaetanomaria De Sanctis, Federico Zambelli.

2025.

DOI BIB

Scaling Scientific Workflows in Europe: Architecture and Deployment of the Galaxy-Pulsar Computational Network

Marco Antonio Tangaro, Stefano Nicotri, Björn Grüning, Sanjay Kumar Srikakulam, Armin Dadras, Oana Kaiser, Mira Kuntz, Anthony Bretaudeau, Paul De Geest, Sebastian Luna-Valero, María Chavero Díez, José María Fernández González, Salvador Capella-Gutierrez, Josep Lluís Gelpí, Jan Astalos, Boris Jurič, Miroslav Ruda, Łukasz Opioła, Hakan Bayındır, SILVIA GIOIOSA, Gaetanomaria De Sanctis, Federico Zambelli.

2025.

DOI BIB

Advancing Interdisciplinary Research using Galaxy

Saim Momin, Wolfgang Maier, Daniela Schneider, Björn Grüning.

2025.

DOI BIB

The Open Source Platform Galaxy: A Gateway to Digital Humanities and Research Data Management

Daniela Schneider.

2025.

DOI BIB

Interactive Galaxy Tools: Combining real-time user interaction with scientific workflows

Paul Zierep, Mira Kuntz, Sanjay Kumar Srikakulam, Björn Grüning.

2025.

DOI BIB

Dynamic meta-scheduling in Galaxy with TPV Broker for smarter workload distribution

Sanjay Kumar Srikakulam, Abdulrahman Azab, Paul De Geest, Tomáš Vondrák, Mira Kuntz, Sebastian Luna-Valero, Björn Grüning.

Zenodo, 2025.

DOI BIB

Publication on the smart job scheduler implementation

Abdulrahman Azab, Sanjay Kumar Srikakulam, Paul De Geest, Tomáš Vondrák, Björn Grüning, Mira Kuntz, Enol Fernandez-del-Castillo, Sebastian Luna-Valero.

Zenodo, 2025.

DOI BIB

Optimized meta-scheduling in Galaxy using TPV Broker

Abdulrahman Azab, Paul De Geest, Sanjay Kumar Srikakulam, Tomáš Vondra, Mira Kuntz, Björn Grüning.

2025.

DOI BIB

Simple and secure credential handling for tools in Galaxy

Alireza Heidari, Arash Kadkhodaei, David Lopez, Bjoern Gruening.

2025.

DOI BIB

Serving locally hosted LLMs with Galaxy

Arash Kadkhodaei.

2025.

DOI BIB

Broadening the Galaxy: Introducing digital humanities in Galaxy

Daniela Schneider.

2025.

DOI BIB

Introducing a new notification system in Galaxy

Alireza Heidari, David Lopez Albert.

2024.

DOI BIB

Migrating from Vuex to Pinia

Alireza Heidari, Marius van den Beek, Laila Los, Ahmed Awan, Dannon Baker, Aysam Guerler.

2024.

DOI BIB

Instant data gathering across multiple histories

Alireza Heidari, Laila Los, Aysam Guerler.

2024.

DOI BIB

Uncovering the small proteome of Methanosarcina mazei using Ribo-seq and peptidomics under different nitrogen conditions

Muhammad Aammar Tufail, Britta Jordan, Lydia Hadjeras, Rick Gelhausen, Liam Cassidy, Tim Habenicht, Miriam Gutt, Lisa Hellwig, Rolf Backofen, Andreas Tholey, Cynthia M. Sharma, Ruth A. Schmitz.

Nature Communications, 15(1), 2024.

DOI BIB

CheRRI—Accurate classification of the biological relevance of putative RNA–RNA interaction sites

Teresa Müller, Stefan Mautner, Pavankumar Videm, Florian Eggenhofer, Martin Raden, Rolf Backofen.

GigaScience, 13, giae022, 2024.

DOI BIB

The challenges of research data management in cardiovascular science: a DGK and DZHK position paper—executive summary

Sabine Steffens, Katrin Schröder, Martina Krüger, Christoph Maack, Katrin Streckfuss-Bömeke, Johannes Backs, Rolf Backofen, Bettina Baeßler, Yvan Devaux, Ralf Gilsbach, Jordi Heijman, Jochen Knaus, Rafael Kramann, Dominik Linz, Allyson L. Lister, Henrike Maatz, Lars Maegdefessel, Manuel Mayr, Benjamin Meder, Sara Y. Nussbeck, Eva A. Rog-Zielinska, Marcel H. Schulz, Albert Sickmann, Gökhan Yigit, Peter Kohl.

Clinical Research in Cardiology, 113(5), 672-679, 2024.

DOI BIB

How to do RNA-RNA Interaction Prediction? A Use-Case Driven Handbook Using IntaRNA

Martin Raden, Milad Miladi.

Methods in Molecular Biology, 209-234, 2024.

DOI BIB

Convert-Pheno: A software toolkit for the interconversion of standard data models for phenotypic data

Manuel Rueda, Ivo C. Leist, Ivo G. Gut.

Journal of Biomedical Informatics, 149, 104558, 2024.

DOI BIB

Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy

Delphine Larivière, Linelle Abueg, Nadolina Brajuka, Cristóbal Gallardo-Alba, Bjorn Grüning, Byung June Ko, Alex Ostrovsky, Marc Palmada-Flores, Brandon D. Pickett, Keon Rabbani, Agostinho Antunes, Jennifer R. Balacco, Mark J. P. Chaisson, Haoyu Cheng, Joanna Collins, Melanie Couture, Alexandra Denisova, Olivier Fedrigo, Guido Roberto Gallo, Alice Maria Giani, Grenville MacDonald Gooder, Kathleen Horan, Nivesh Jain, Cassidy Johnson, Heebal Kim, Chul Lee, Tomas Marques-Bonet, Brian O’Toole, Arang Rhie, Simona Secomandi, Marcella Sozzoni, Tatiana Tilley, Marcela Uliano-Silva, Marius van den Beek, Robert W. Williams, Robert M. Waterhouse, Adam M. Phillippy, Erich D. Jarvis, Michael C. Schatz, Anton Nekrutenko, Giulio Formenti.

Nature Biotechnology, 42(3), 367-370, 2024.

DOI BIB

Near telomere-to-telomere genome of the model plant Physcomitrium patens

Guiqi Bi, Shijun Zhao, Jiawei Yao, Huan Wang, Mengkai Zhao, Yuanyuan Sun, Xueren Hou, Fabian B. Haas, Deepti Varshney, Michael Prigge, Stefan A. Rensing, Yuling Jiao, Yingxin Ma, Jianbin Yan, Junbiao Dai.

Nature Plants, 10(2), 327-343, 2024.

DOI BIB

Partial RNA design

Frederic Runge, Jörg Franke, Daniel Fertmann, Rolf Backofen, Frank Hutter.

Bioinformatics, 40(Supplement_1), i437-i445, 2024.

DOI BIB

blast2galaxy: a CLI and Python API for BLAST+ and DIAMOND searches on Galaxy servers

Patrick König, Anne Fiebig, Thomas Münch, Björn Grüning, Uwe Scholz.

Bioinformatics Advances, 4(1), vbae185, 2024.

DOI BIB

The role of the 5’ sensing function of ribonuclease E in cyanobacteria

Ute A. Hoffmann, Elisabeth Lichtenberg, Said N. Rogh, Raphael Bilger, Viktoria Reimann, Florian Heyl, Rolf Backofen, Claudia Steglich, Wolfgang R. Hess, Annegret Wilde.

RNA Biology, 21(1), 373-390, 2024.

DOI BIB

Mobilisation and analyses of publicly available SARS-CoV-2 data for pandemic responses

Nadim Rahman, Colman O'Cathail, Ahmad Zyoud, Alexey Sokolov, Bas Oude Munnink, Björn Grüning, Carla Cummins, Clara Amid, David F. Nieuwenhuijse, Dávid Visontai, David Yu Yuan, Dipayan Gupta, Divyae K. Prasad, Gábor Máté Gulyás, Gabriele Rinck, Jasmine McKinnon, Jeena Rajan, Jeff Knaggs, Jeffrey Edward Skiby, József Stéger, Judit Szarvas, Khadim Gueye, Krisztián Papp, Maarten Hoek, Manish Kumar, Marianna A. Ventouratou, Marie-Catherine Bouquieaux, Martin Koliba, Milena Mansurova, Muhammad Haseeb, Nathalie Worp, Peter W. Harrison, Rasko Leinonen, Ross Thorne, Sandeep Selvakumar, Sarah Hunt, Sundar Venkataraman, Suran Jayathilaka, Timothée Cezard, Wolfgang Maier, Zahra Waheed, Zamin Iqbal, Frank Møller Aarestrup, Istvan Csabai, Marion Koopmans, Tony Burdett, Guy Cochrane.

Microbial Genomics, 10(2), 2024.

DOI BIB

Clusters of mammalian conserved RNA structures in UTRs associate with RBP binding sites

Veerendra P Gadekar, Alexander Welford Munk, Milad Miladi, Alexander Junge, Rolf Backofen, Stefan E Seemann, Jan Gorodkin.

NAR Genomics and Bioinformatics, 6(3), lqae089, 2024.

DOI BIB

SpacerPlacer: ancestral reconstruction of CRISPR arrays reveals the evolutionary dynamics of spacer deletions

Axel Fehrenbach, Alexander Mitrofanov, Omer S Alkhnbashi, Rolf Backofen, Franz Baumdicker.

Nucleic Acids Research, 52(18), 10862-10878, 2024.

DOI BIB

The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update

The Galaxy Community, Linelle Ann L Abueg, Enis Afgan, Olivier Allart, Ahmed H Awan, Wendi A Bacon, Dannon Baker, Madeline Bassetti, Bérénice Batut, Matthias Bernt, Daniel Blankenberg, Aureliano Bombarely, Anthony Bretaudeau, Catherine J Bromhead, Melissa L Burke, Patrick K Capon, Martin Čech, María Chavero-Díez, John M Chilton, Tyler J Collins, Frederik Coppens, Nate Coraor, Gianmauro Cuccuru, Fabio Cumbo, John Davis, Paul F De Geest, Willem de Koning, Martin Demko, Assunta DeSanto, José Manuel Domínguez Begines, Maria A Doyle, Bert Droesbeke, Anika Erxleben-Eggenhofer, Melanie C Föll, Giulio Formenti, Anne Fouilloux, Rendani Gangazhe, Tanguy Genthon, Jeremy Goecks, Alejandra N Gonzalez Beltran, Nuwan A Goonasekera, Nadia Goué, Timothy J Griffin, Björn A Grüning, Aysam Guerler, Sveinung Gundersen, Ove Johan Ragnar Gustafsson, Christina Hall, Thomas W Harrop, Helge Hecht, Alireza Heidari, Tillman Heisner, Florian Heyl, Saskia Hiltemann, Hans-Rudolf Hotz, Cameron J Hyde, Pratik D Jagtap, Julia Jakiela, James E Johnson, Jayadev Joshi, Marie Jossé, Khaled Jum’ah, Matúš Kalaš, Katarzyna Kamieniecka, Tunc Kayikcioglu, Markus Konkol, Leonid Kostrykin, Natalie Kucher, Anup Kumar, Mira Kuntz, Delphine Lariviere, Ross Lazarus, Yvan Le Bras, Gildas Le Corguillé, Justin Lee, Simone Leo, Leandro Liborio, Romane Libouban, David López Tabernero, Lucille Lopez-Delisle, Laila S Los, Alexandru Mahmoud, Igor Makunin, Pierre Marin, Subina Mehta, Winnie Mok, Pablo A Moreno, François Morier-Genoud, Stephen Mosher, Teresa Müller, Engy Nasr, Anton Nekrutenko, Tiffanie M Nelson, Asime J Oba, Alexander Ostrovsky, Polina V Polunina, Krzysztof Poterlowicz, Elliott J Price, Gareth R Price, Helena Rasche, Bryan Raubenolt, Coline Royaux, Luke Sargent, Michelle T Savage, Volodymyr Savchenko, Denys Savchenko, Michael C Schatz, Pauline Seguineau, Beatriz Serrano-Solano, Nicola Soranzo, Sanjay Kumar Srikakulam, Keith Suderman, Anna E Syme, Marco Antonio Tangaro, Jonathan A Tedds, Mehmet Tekman, Wai Cheng (Mike) Thang, Anil S Thanki, Michael Uhl, Marius van den Beek, Deepti Varshney, Jenn Vessio, Pavankumar Videm, Greg Von Kuster, Gregory R Watson, Natalie Whitaker-Allen, Uwe Winter, Martin Wolstencroft, Federico Zambelli, Paul Zierep, Rand Zoabi.

Nucleic Acids Research, 52(W1), W83-W94, 2024.

DOI BIB

Improved discovery of RNA-binding protein binding sites in eCLIP data using DEWSeq

Thomas Schwarzl, Sudeep Sahadevan, Benjamin Lang, Milad Miladi, Rolf Backofen, Wolfgang Huber, Matthias W Hentze, Gian Gaetano Tartaglia.

Nucleic Acids Research, 52(1), e1-e1, 2024.

DOI BIB

Interrogating two extensively self-targeting Type I CRISPR-Cas systems in Xanthomonas albilineans reveals distinct anti-CRISPR proteins that block DNA degradation

Franziska Wimmer, Frank Englert, Katharina G Wandera, Omer S Alkhnbashi, Scott P Collins, Rolf Backofen, Chase L Beisel.

Nucleic Acids Research, 52(2), 769-783, 2024.

DOI BIB

Deepdefense: annotation of immune systems in prokaryotes using deep learning

Sven Hauns, Omer S Alkhnbashi, Rolf Backofen.

GigaScience, 13, giae062, 2024.

DOI BIB

Pheno-Ranker: a toolkit for comparison of phenotypic data stored in GA4GH standards and beyond

Ivo C. Leist, María Rivas-Torrubia, Marta E. Alarcón-Riquelme, Guillermo Barturen, PRECISESADS Clinical Consortium, Ivo G. Gut, Manuel Rueda.

BMC Bioinformatics, 25(1), 373, 2024.

DOI BIB

How sensor Amt-like proteins integrate ammonium signals

Tobias Pflüger, Mathias Gschell, Lin Zhang, Volodymyr Shnitsar, Annas J. Zabadné, Paul Zierep, Stefan Günther, Oliver Einsle, Susana L. A. Andrade.

Science Advances, 10(23), eadm9441, 2024.

DOI BIB

Global and local functions of the Fused kinase ortholog CdaH in intracellular patterning in Tetrahymena

Chinkyu Lee, Wolfgang Maier, Yu-Yang Jiang, Kentaro Nakano, Karl F. Lechtreck, Jacek Gaertig.

Journal of Cell Science, 137(5), jcs261256, 2024.

DOI BIB

Heterogenous nuclear ribonucleoprotein D-like controls endothelial cell functions

Sandra Fischer, Chiara Lichtenthaeler, Anastasiya Stepanenko, Florian Heyl, Daniel Maticzka, Katrin Kemmerer, Melina Klostermann, Rolf Backofen, Kathi Zarnack, Julia E. Weigand.

Biological Chemistry, 405(4), 229-239, 2024.

DOI BIB

Enhancing the image analysis community in Galaxy

Leonid Kostrykin, Tatiana Woller, Matúš Kalaš, Bugra Özdemir, Rafael Andrade Buono, Yi Sun, Anup Kumar, Nadia Goué, Björn Grüning, Beatriz Serrano-Solano, Anne Fouilloux.

2024.

DOI BIB

How to improve the annotation of Galaxy resources? Outcomes of an online hackathon for improving the annotation of Galaxy resources for microbial data resources

Bérénice Batut, Matthias Bernt, Mina Hojat Ansari, Matúš Kalaš, Paul Klemm, Romane Libouban, Engy Nasr, Claire Rioualen, Wai Cheng Thang, Rand Zoabi, Paul Zierep.

2024.

DOI BIB

How to increase the findability, visibility, and impact of Galaxy tools for your scientific community

Paul Zierep, Bérénice Batut, Matúš Kalaš, Tunc Kayikcioglu, Engy Nasr, Nicola Soranzo, Wai Cheng Thang, Joseph Wang, Ove Johan Ragnar Gustafsson.

2024.

DOI BIB

Recommendations for Uniform Variant Calling of SARS-CoV-2 Genome Sequence across Bioinformatic Workflows

Ryan Connor, Migun Shakya, David A. Yarmosh, Wolfgang Maier, Ross Martin, Rebecca Bradford, J. Rodney Brister, Patrick S. G. Chain, Courtney A. Copeland, Julia di Iulio, Bin Hu, Philip Ebert, Jonathan Gunti, Yumi Jin, Kenneth S. Katz, Andrey Kochergin, Tré LaRosa, Jiani Li, Po-E Li, Chien-Chi Lo, Sujatha Rashid, Evguenia S. Maiorova, Chunlin Xiao, Vadim Zalunin, Lisa Purcell, Kim D. Pruitt.

Viruses, 16(3), 430, 2024.

DOI BIB

Workflow recommendations using deep learning and machine learning tools for exploratory and predictive data analysis in Galaxy

Anup Kumar.

2024.

DOI BIB

London and British Hong Kong, 1940: Colonial press censorship

Daniela Schneider.

2024.

DOI BIB

Quantifying Visible Censorship in Da gong bao Hong Kong Edition 1938-41

Daniela Schneider.

2024.

DOI BIB

Navigating the variant landscape: integrating MAVE data analysis into Galaxy

Polina Polunina.

2024.

DOI BIB

Galaxy social

Arash Kadkhodaei.

2024.

DOI BIB

Galaxy social

Arash Kadkhodaei.

2024.

DOI BIB

WALL·E: Prevent abuse of interactive research environments

Mira Kuntz.

2024.

DOI BIB

Community-driven standards development for reference genome generation

Tom Brown, Diego De Panis, Romane Libouban, Saim Momin, Arash Kadkhodaei, Anthony Bretaudeau, Björn Grüning, Camila Mazzoni.

2024.

DOI BIB

Community-driven standards development for reference genome generation

Tom Brown, Diego De Panis, Romane Libouban, Saim Momin, Arash Kadkhodaei, Anthony Bretaudeau, Björn Grüning, Camila Mazzoni.

2024.

DOI BIB

Revolutionizing search in Galaxy: New features for improved data and tool discovery

Ahmed Awan, Dannon Baker, Marius van den Beek, Tyler Collins, Aysam Guerler, Alireza Heidari, Cameron Hyde, David Lopez, Laila Los, Michelle Savage.

2023.

DOI BIB

Ribosome profiling reveals the fine-tuned response of Escherichia coli to mild and severe acid stress

Kilian Schumacher, Rick Gelhausen, Willow Kion-Crosby, Lars Barquist, Rolf Backofen, Kirsten Jung.

mSystems, 8(6), e01037-23, 2023.

DOI BIB

Unraveling the small proteome of the plant symbiont Sinorhizobium meliloti by ribosome profiling and proteogenomics

Lydia Hadjeras, Benjamin Heiniger, Sandra Maaß, Robina Scheuer, Rick Gelhausen, Saina Azarderakhsh, Susanne Barth-Weber, Rolf Backofen, Dörte Becher, Christian H. Ahrens, Cynthia M. Sharma, Elena Evguenieva-Hackenberg.

Microlife, 4, uqad012, 2023.

DOI BIB

Revealing the small proteome of Haloferax volcanii by combining ribosome profiling and small-protein optimized mass spectrometry

Lydia Hadjeras, Jürgen Bartel, Lisa-Katharina Maier, Sandra Maaß, Verena Vogel, Sarah L. Svensson, Florian Eggenhofer, Rick Gelhausen, Teresa Müller, Omer S. Alkhnbashi, Rolf Backofen, Dörte Becher, Cynthia M. Sharma, Anita Marchfelder.

Microlife, 4, uqad001, 2023.

DOI BIB

The Planemo toolkit for developing, deploying, and executing scientific data analyses in Galaxy and beyond

Simon Bray, John Chilton, Matthias Bernt, Nicola Soranzo, Marius van den Beek, Bérénice Batut, Helena Rasche, Martin Cech, Peter J. A. Cock, Björn Grüning, Anton Nekrutenko.

Genome Res, 33(2), 261-268, 2023.

DOI BIB

Plant-Associated Bacteria in Ecosystems Functioning and Sustainability

Akanksha Jaiswar, Deepti Varshney, Vineeta Kaushik, Neha Sharma, Ashish Bedi.

Microbial Bioremediation, 265-281, 2023.

DOI BIB

A comparative gene expression matrix in Apoe-deficient mice identifies unique and atherosclerotic disease stage-specific gene regulation patterns in monocytes and macrophages

Carmen Härdtner, Anup Kumar, Carolin A. Ehlert, Tamara Antonela Vico, Christopher Starz, Alexander von Ehr, Katja Krebs, Bianca Dufner, Natalie Hoppe, Peter Stachon, Timo Heidt, Dennis Wolf, Constantin von zur Mühlen, Björn Grüning, Clinton S. Robbins, Lars Maegdefessel, Dirk Westermann, Tsai-Sang Dederichs, Ingo Hilgendorf.

Atherosclerosis, 371, 1-13, 2023.

DOI BIB

Taxonomically Restricted Genes inBacillusmay Form Clusters of Homologs and Can be Traced to a Large Reservoir of Noncoding Sequences

Wojciech M Karlowski, Deepti Varshney, Andrzej Zielezinski.

Genome Biology and Evolution, 15(3), evad023, 2023.

DOI BIB

RNA interaction format: a general data format for RNA interactions

Richard A Schäfer, Dominik Rabsch, Guillaume E Scholz, Peter F Stadler, Wolfgang R Hess, Rolf Backofen, Jörg Fallmann, Björn Voß.

Bioinformatics, 39(11), btad665, 2023.

DOI BIB

Transformer-based tool recommendation system in Galaxy

Anup Kumar, Björn Grüning, Rolf Backofen.

BMC Bioinformatics, 24(1), 446, 2023.

DOI BIB

Michael Ng, Political Censorship in British Hong Kong. Freedom of Expression and the Law (1842–1997). Cambridge, Cambridge University Press 2022

Daniela Schneider.

Historische Zeitschrift, 316(2), 499-500, 2023.

DOI BIB

Meta-Analysis of Mechano-Sensitive Ion Channels in Human Hearts: Chamber- and Disease-Preferential mRNA Expression

Elisa Darkow, Dilmurat Yusuf, Sridharan Rajamani, Rolf Backofen, Peter Kohl, Ursula Ravens, Rémi Peyronnet.

International Journal of Molecular Sciences, 24(13), 10961, 2023.

DOI BIB

New Insights into the Roles of the Hippo Signaling Pathway in Stem Cell Biology

Amirhossein Naghsh Nilchi, Fariba Dehghanian, Sheyda Khalilian, Seyedeh Zahra Hosseini Imani.

Jentashapir Journal of Cellular and Molecular Biology, 14(3), 2023.

DOI BIB

Galaxy and RDM

Sebastian Schaaf, Anika Erxleben-Eggenhofer, Bjoern Gruening.

Proceedings of the Conference on Research Data Infrastructure, 1, 2023.

DOI BIB

Conda, Container and Bots

Paul Zierep, Sanjay Kumar Srikakulam, Sebastian Schaaf, Björn Grüning.

Proceedings of the Conference on Research Data Infrastructure, 1, 2023.

DOI BIB

EOSC-Life Workflow Collaboratory for the Life Sciences

Carole Goble, Finn Bacall, Stian Soiland-Reyes, Stuart Owen, Ignacio Eguinoa, Bert Droesbeke, Hervé Ménager, Laura Rodriguez-Navas, José M. Fernández, Björn Grüning, Simone Leo, Luca Pireddu, Michael Crusoe, Johan Gustafsson, Salvador Capella-Gutierrez, Frederik Coppens.

Proceedings of the Conference on Research Data Infrastructure, 1, 2023.

DOI BIB

Critical Assessment of Metagenome Interpretation: the second round of challenges

Fernando Meyer, Adrian Fritz, Zhi-Luo Deng, David Koslicki, Till Robin Lesker, Alexey Gurevich, Gary Robertson, Mohammed Alser, Dmitry Antipov, Francesco Beghini, Denis Bertrand, Jaqueline J. Brito, C. Titus Brown, Jan Buchmann, Aydin Buluç, Bo Chen, Rayan Chikhi, Philip T. L. C. Clausen, Alexandru Cristian, Piotr Wojciech Dabrowski, Aaron E. Darling, Rob Egan, Eleazar Eskin, Evangelos Georganas, Eugene Goltsman, Melissa A. Gray, Lars Hestbjerg Hansen, Steven Hofmeyr, Pingqin Huang, Luiz Irber, Huijue Jia, Tue Sparholt Jørgensen, Silas D. Kieser, Terje Klemetsen, Axel Kola, Mikhail Kolmogorov, Anton Korobeynikov, Jason Kwan, Nathan LaPierre, Claire Lemaitre, Chenhao Li, Antoine Limasset, Fabio Malcher-Miranda, Serghei Mangul, Vanessa R. Marcelino, Camille Marchet, Pierre Marijon, Dmitry Meleshko, Daniel R. Mende, Alessio Milanese, Niranjan Nagarajan, Jakob Nissen, Sergey Nurk, Leonid Oliker, Lucas Paoli, Pierre Peterlongo, Vitor C. Piro, Jacob S. Porter, Simon Rasmussen, Evan R. Rees, Knut Reinert, Bernhard Renard, Espen Mikal Robertsen, Gail L. Rosen, Hans-Joachim Ruscheweyh, Varuni Sarwal, Nicola Segata, Enrico Seiler, Lizhen Shi, Fengzhu Sun, Shinichi Sunagawa, Søren Johannes Sørensen, Ashleigh Thomas, Chengxuan Tong, Mirko Trajkovski, Julien Tremblay, Gherman Uritskiy, Riccardo Vicedomini, Zhengyang Wang, Ziye Wang, Zhong Wang, Andrew Warren, Nils Peder Willassen, Katherine Yelick, Ronghui You, Georg Zeller, Zhengqiao Zhao, Shanfeng Zhu, Jie Zhu, Ruben Garrido-Oter, Petra Gastmeier, Stephane Hacquard, Susanne Häußler, Ariane Khaledi, Friederike Maechler, Fantin Mesny, Simona Radutoiu, Paul Schulze-Lefert, Nathiana Smit, Till Strowig, Andreas Bremges, Alexander Sczyrba, Alice Carolyn McHardy.

Nature Methods, 19(4), 429-440, 2022.

DOI BIB

RiboReport - benchmarking tools for ribosome profiling-based identification of open reading frames in bacteria

Rick Gelhausen, Teresa Müller, Sarah L Svensson, Omer S Alkhnbashi, Cynthia M Sharma, Florian Eggenhofer, Rolf Backofen.

Briefings in Bioinformatics, 2022.

DOI BIB

Loop detection using Hi-C data with HiCExplorer

Joachim Wolff, Rolf Backofen, Björn Grüning.

Gigascience, 11, 2022.

DOI BIB

Distinct SARS-CoV-2 RNA fragments activate Toll-like receptors 7 and 8 and induce cytokine release from human macrophages and microglia

Thomas Wallach, Martin Raden, Lukas Hinkelmann, Mariam Brehm, Dominik Rabsch, Hannah Weidling, Christina Kruger, Helmut Kettenmann, Rolf Backofen, Seija Lehnardt.

Front Immunol, 13, 1066456, 2022.

DOI BIB

Anti-CRISPR prediction using deep learning reveals an inhibitor of Cas13b nucleases

Katharina G. Wandera, Omer S. Alkhnbashi, Harris v.I. Bassett, Alexander Mitrofanov, Sven Hauns, Anzhela Migur, Rolf Backofen, Chase L. Beisel.

Molecular Cell, 82(14), 2714-2726.e4, 2022.

DOI BIB

Expanding the Galaxy's reference data

Nagampalli VijayKrishna, Jayadev Joshi, Nate Coraor, Jennifer Hillman-Jackson, Dave Bouvier, Marius van den Beek, Ignacio Eguinoa, Frederik Coppens, John Davis, Michal Stolarczyk, Nathan C. Sheffield, Simon Gladman, Gianmauro Cuccuru, Björn Grüning, Nicola Soranzo, Helena Rasche, Bradley W. Langhorst, Matthias Bernt, Dan Fornika, David Anderson de Lima Morais, Michel Barrette, Peter van Heusden, Mauro Petrillo, Antonio Puertas-Gallardo, Alex Patak, Hans-Rudolf Hotz, Daniel Blankenberg.

Bioinform Adv, 2(1), vbac030, 2022.

DOI BIB

Peakhood: individual site context extraction for CLIP-seq peak regions

Michael Uhl, Dominik Rabsch, Florian Eggenhofer, Rolf Backofen.

Bioinformatics, 38(4), 1139-1140, 2022.

DOI BIB

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update

Galaxy Team.

NAR, 50(W1), W345-W351, 2022.

DOI BIB

Genome wide CRISPR screen for Pasteurella multocida toxin (PMT) binding proteins reveals LDL Receptor Related Protein 1 (LRP1) as crucial cellular receptor

Julian Schöllkopf, Thomas Mueller, Lena Hippchen, Teresa Müller, Raphael Reuten, Rolf Backofen, Joachim Orth, Gudula Schmidt.

PLoS Pathog, 18(12), e1010781, 2022.

DOI BIB

Temporal annotation of high-resolution intra-annual wood density information of Eucalyptus urophylla and its correlation with hydroclimatic conditions

Gleice Gomes Rodrigues, Martin Raden, Luciana Duque Silva, Hans-Peter Kahle.

Dendrochronologia, 74, 125978, 2022.

DOI BIB

MaxQuant and MSstats in Galaxy Enable Reproducible Cloud-Based Analysis of Quantitative Proteomics Experiments for Everyone

Niko Pinter, Damian Glatzer, Matthias Fahrner, Klemens Frohlich, James Johnson, Björn Andreas Grüning, Bettina Warscheid, Friedel Drepper, Oliver Schilling, Melanie Christine Foll.

J Proteome Res, 21(6), 1558-1565, 2022.

DOI BIB

High detection rate for disease-causing variants in a cohort of 30 Iranian pediatric steroid resistant nephrotic syndrome cases

Maryam Najafi, Korbinian M. Riedhammer, Aboulfazl Rad, Paria Najarzadeh Torbati, Riccardo Berutti, Isabel Schule, Sophie Schroda, Thomas Meitinger, Jasmina Comic, Simin Sadeghi Bojd, Tayebeh Baranzehi, Azadeh Shojaei, Anoush Azarfar, Mahmood Reza Khazaei, Anna Kottgen, Rolf Backofen, Ehsan Ghayoor Karimiani, Julia Hoefele, Miriam Schmidts.

Front Pediatr, 10, 974840, 2022.

DOI BIB

Gut microbiota drives age-related oxidative stress and mitochondrial damage in microglia via the metabolite N(6)-carboxymethyllysine

Omar Mossad, Bérénice Batut, Bahtiyar Yilmaz, Nikolaos Dokalis, Charlotte Mezo, Elisa Nent, Lara Susann Nabavi, Melanie Mayer, Feres Jose Mocayar Maron, Joerg M. Buescher, Mercedes Gomez de Aguero, Antal Szalay, Tim Lammermann, Andrew J. Macpherson, Stephanie C. Ganal-Vonarburg, Rolf Backofen, Daniel Erny, Marco Prinz, Thomas Blank.

Nat Neurosci, 25(3), 295-305, 2022.

DOI BIB

CRISPRtracrRNA: robust approach for CRISPR tracrRNA detection

Alexander Mitrofanov, Marcus Ziemann, Omer S. Alkhnbashi, Wolfgang R. Hess, Rolf Backofen.

Bioinformatics, 38(Suppl_2), ii42-ii48, 2022.

DOI BIB

The antileukemic activity of decitabine upon PML/RARA-negative AML blasts is supported by all-trans retinoic acid: in vitro and in vivo evidence for cooperation

Ruth Meier, Gabriele Greve, Dennis Zimmer, Helena Bresser, Bettina Berberich, Ralitsa Langova, Julia Stomper, Anne Rubarth, Lars Feuerbach, Daniel B. Lipka, Joschka Hey, Björn Grüning, Benedikt Brors, Justus Duyster, Christoph Plass, Heiko Becker, Michael Lubbert.

Blood Cancer J, 12(8), 122, 2022.

DOI BIB

Catching the Wave: Detecting Strain-Specific SARS-CoV-2 Peptides in Clinical Samples Collected during Infection Waves from Diverse Geographical Locations

Subina Mehta, Valdemir M. Carvalho, Andrew T. Rajczewski, Olivier Pible, Björn A. Grüning, James E. Johnson, Reid Wagner, Jean Armengaud, Timothy J. Griffin, Pratik D. Jagtap.

Viruses, 14(10), 2022.

DOI BIB

Spacer prioritization in CRISPR-Cas9 immunity is enabled by the leader RNA

Chunyu Liao, Sahil Sharma, Sarah L. Svensson, Anuja Kibe, Zasha Weinberg, Omer S. Alkhnbashi, Thorsten Bischler, Rolf Backofen, Neva Caliskan, Cynthia M. Sharma, Chase L. Beisel.

Nat Microbiol, 7(4), 530-541, 2022.

DOI BIB

An accessible infrastructure for artificial intelligence using a Docker-based JupyterLab in Galaxy

Anup Kumar, Gianmauro Cuccuru, Björn Grüning, Rolf Backofen.

Gigascience, 12, 2022.

DOI BIB

The long noncoding RNA mimi scaffolds neuronal granules to maintain nervous system maturity

Dominika Grzejda, Jana Mach, Johanna Aurelia Schweizer, Barbara Hummel, Andrew Mischa Rezansoff, Florian Eggenhofer, Amol Panhale, Maria-Eleni Lalioti, Nina Cabezas Wallscheid, Rolf Backofen, Johannes Felsenberg, Valerie Hilgers.

Sci Adv, 8(39), eabo5578, 2022.

DOI BIB

Pluripotency factors determine gene expression repertoire at zygotic genome activation

Meijiang Gao, Marina Veil, Marcus Rosenblatt, Aileen Julia Riesle, Anna Gebhard, Helge Hass, Lenka Buryanova, Lev Y. Yampolsky, Björn Grüning, Sergey V. Ulianov, Jens Timmer, Daria Onichtchouk.

Nature Communications, 13(1), 788, 2022.

DOI BIB

Democratizing data-independent acquisition proteomics analysis on public cloud infrastructures via the Galaxy framework

Matthias Fahrner, Melanie Christine Foll, Björn A. Grüning, Matthias Bernt, Hannes Rost, Oliver Schilling.

Gigascience, 11, 2022.

DOI BIB

Galaxy workflows for fragment-based virtual screening: a case study on the SARS-CoV-2 main protease

Simon Bray, Tim Dudgeon, Rachael Skyner, Rolf Backofen, Björn Grüning, Frank von Delft.

J Cheminform, 14(1), 22, 2022.

DOI BIB

Ten simple rules for making a software tool workflow-ready

Paul Brack, Peter Crowther, Stian Soiland-Reyes, Stuart Owen, Douglas Lowe, Alan R. Williams, Quentin Groom, Mathias Dillen, Frederik Coppens, Björn Grüning, Ignacio Eguinoa, Philip Ewels, Carole Goble.

PLoS Comput Biol, 18(3), e1009823, 2022.

DOI BIB

Spectrum of Genetic Variants in a Cohort of 37 Laterality Defect Cases

Dinu Antony, Elif Gulec Yilmaz, Alper Gezdirici, Lennart Slagter, Zeineb Bakey, Helen Bornaun, Ibrahim Cansaran Tanidir, Tran Van Dinh, Han G. Brunner, Peter Walentek, Sebastian J. Arnold, Rolf Backofen, Miriam Schmidts.

Front Genet, 13, 861236, 2022.

DOI BIB

P2Y12-dependent activation of hematopoietic stem and progenitor cells promotes emergency hematopoiesis after myocardial infarction

Hana Seung, Jan Wrobel, Carolin Wadle, Timon Bühler, Diana Chiang, Jasmin Rettkowski, Nina Cabezas-Wallscheid, Béatrice Hechler, Peter Stachon, Alexander Maier, Christian Weber, Dennis Wolf, Daniel Duerschmied, Marco Idzko, Christoph Bode, Constantin von zur Mühlen, Ingo Hilgendorf, Timo Heidt.

Basic Research in Cardiology, 117(1), 16, 2022.

DOI BIB

Selection Analysis Identifies Clusters of Unusual Mutational Changes in Omicron Lineage BA.1 That Likely Impact Spike Function

Darren P. Martin, Spyros Lytras, Alexander G. Lucaci, Wolfgang Maier, Björn Grüning, Stephen D. Shank, Steven Weaver, Oscar A. MacLean, Richard J. Orton, Philippe Lemey, Maciej F. Boni, Houriiyah Tegally, Gordon W. Harkins, Cathrine Scheepers, Jinal N. Bhiman, Josie Everatt, Daniel G. Amoako, James Emmanuel San, Jennifer Giandhari, Alex Sigal, Carolyn Williamson, Nei-yuan Hsiao, Anne von Gottberg, Arne De Klerk, Robert W. Shafer, David L. Robertson, Robert J. Wilkinson, B. Trevor Sewell, Richard Lessells, Anton Nekrutenko, Allison J. Greaney, Tyler N. Starr, Jesse D. Bloom, Ben Murrell, Eduan Wilkinson, Ravindra K. Gupta, Tulio de Oliveira, Sergei L. Kosakovsky Pond.

Molecular Biology and Evolution, 39(4), msac061, 2022.

DOI BIB

Association between gut colonization of vancomycin‐resistant enterococci and liver transplant outcomes

Diana Chiang, Tanis C. Dingle, Sara Belga, Dima Kabbani, Rahima A. Bhanji, Jens Walter, Juan G. Abraldes, Carlos Cervera.

Transplant Infectious Disease, 24(3), e13821, 2022.

DOI BIB

Construction of miRNA‐lncRNA‐mRNA co‐expression network affecting EMT‐mediated cisplatin resistance in ovarian cancer

Amirhosein Naghsh‐Nilchi, Laleh Ebrahimi Ghahnavieh, Fariba Dehghanian.

Journal of Cellular and Molecular Medicine, 26(16), 4530-4547, 2022.

DOI BIB

Community-driven ELIXIR activities in single-cell omics

Paulo Czarnewski, Ahmed Mahfouz, Raffaele A. Calogero, Patricia M. Palagi, Laura Portell-Silva, Asier Gonzalez-Uriarte, Charlotte Soneson, Tony Burdett, Barbara Szomolay, Pavankumar Videm, Hans-Rudolf Hotz, Irene Papatheodorou, John M. Hancock, Björn Grüning, Wilfried Haerty, Roland Krause, Salvador Capella-Gutierrez, Brane Leskošek, Luca Alessandri, Maddalena Arigoni, Tadeja Rezen, Alexander Botzki, Polonca Ferk, Jessica Lindvall, Katharina F. Heil, Naveed Ishaque, Eija Korpelainen.

F1000Research, 11, 869, 2022.

DOI BIB

A novel membrane complex is required for docking and regulated exocytosis of lysosome-related organelles in Tetrahymena thermophila

Aarthi Kuppannan, Yu-Yang Jiang, Wolfgang Maier, Chang Liu, Charles F. Lang, Chao-Yin Cheng, Mark C. Field, Minglei Zhao, Martin Zoltner, Aaron P. Turkewitz.

PLOS Genetics, 18(5), e1010194, 2022.

DOI BIB

Towards the prediction of non-peptidic epitopes

Paul F. Zierep, Randi Vita, Nina Blazeska, Aurélien F. A. Moumbock, Jason A. Greenbaum, Bjoern Peters, Stefan Günther.

PLOS Computational Biology, 18(2), e1009151, 2022.

DOI BIB

Packaging research artefacts with RO-Crate

Stian Soiland-Reyes, Peter Sefton, Mercè Crosas, Leyla Jael Castro, Frederik Coppens, José M. Fernández, Daniel Garijo, Björn Grüning, Marco La Rosa, Simone Leo, Eoghan Ó Carragáin, Marc Portier, Ana Trisovic, RO-Crate Community, Paul Groth, Carole Goble.

Data Science, 5(2), 97-138, 2022.

DOI BIB

Hippo Signaling Pathway and Cancer: Molecular Regulation and Therapeutic Targets

Fariba Dehghanian, Seyedeh Zahra Hosseini Imani, Amirhosein Naghsh-Nilchi, Sheyda Khalilian.

Precision Medicine and Clinical OMICS, 2(1), 2022.

DOI BIB

Haploflow: strain-resolved de novo assembly of viral genomes

Adrian Fritz, Andreas Bremges, Zhi-Luo Deng, Till Robin Lesker, Jasper Götting, Tina Ganzenmueller, Alexander Sczyrba, Alexander Dilthey, Frank Klawonn, Alice Carolyn McHardy.

Genome Biology, 22(1), 212, 2021.

DOI BIB

Tutorial: assessing metagenomics software with the CAMI benchmarking toolkit

Fernando Meyer, Till-Robin Lesker, David Koslicki, Adrian Fritz, Alexey Gurevich, Aaron E. Darling, Alexander Sczyrba, Andreas Bremges, Alice C. McHardy.

Nature Protocols, 16(4), 1785-1801, 2021.

DOI BIB

Robust and efficient single-cell Hi-C clustering with approximate k-nearest neighbor graphs

Joachim Wolff, Rolf Backofen, Björn Grüning.

Bioinformatics, 37(22), 4006-4013, 2021.

DOI BIB

MicroRNA-100-5p and microRNA-298-5p released from apoptotic cortical neurons are endogenous Toll-like receptor 7/8 ligands that contribute to neurodegeneration

Thomas Wallach, Zoe Mossmann, Michal Szczepek, Max Wetzel, Rui Machado, Martin Raden, Milad Miladi, Gunnar Kleinau, Christina Krüger, Paul Dembny, Drew Adler, Yuanyuan Zhai, Omar Dzaye, Matthias Futschik, Rolf Backofen, Patrick Scheerer, Seija Lehnardt.

Molecular Neurodegeneration, 16(80), 2021.

DOI BIB

ChiRA: an integrated framework for chimeric read analysis from RNA-RNA interactome and RNA structurome data

Pavankumar Videm, Anup Kumar, Oleg Zharkov, Björn Andreas Grüning, Rolf Backofen.

Gigascience, 10(2), 2021.

DOI BIB

RNAProt: an efficient and feature-rich RNA binding protein binding site predictor

Michael Uhl, Van Dinh Tran, Florian Heyl, Rolf Backofen.

Gigascience, 10(8), 2021.

DOI BIB

Effects of intra-seasonal drought on kinetics of tracheid differentiation and seasonal growth dynamics of Norway spruce along an elevational gradient

Dominik F. Stangler, Hans-Peter Kahle, Martin Raden, Elena Larysch, Thomas Seifert, Heinrich Spiecker.

Forests, 12(3), 274, 2021.

DOI BIB

Structure-aware machine learning identifies microRNAs operating as Toll-like receptor 7/8 ligands

Martin Raden, Thomas Wallach, Milad Miladi, Yuanyuan Zhai, Christina Kruger, Zoe J. Mossmann, Paul Dembny, Rolf Backofen, Seija Lehnardt.

RNA Biol, 18(sup1), 268-277, 2021.

DOI BIB

Structure-aware machine learning classification of oligonucleotide-induced immune response identifies microRNAs operating as Toll-like receptor 7/8 ligands

Martin Raden, Thomas Wallach, Milad Miladi, Yuanyuan Zhai, Christina Krüger, Zoe J. Mossmann, Paul Dembny, Rolf Backofen, Seija Lehnardt.

RNA Biology, 18(sup1), 268-277, 2021.

DOI BIB

Galaxy-ML: An accessible, reproducible, and scalable machine learning toolkit for biomedicine

Qiang Gu, Anup Kumar, Simon Bray, Allison Creason, Alireza Khanteymoori, Vahid Jalili, Björn Grüning, Jeremy Goecks.

PLOS Computational Biology, 17(6), 1-11, 2021.

DOI BIB

An integrated database of small RNAs and their interplay with transcriptional gene regulatory networks in corynebacteria

Mariana T.D. Parise, Doglas Parise, Flavia F. Aburjaile, Anne C.P. Gomide, Rodrigo B. Kato, Martin Raden, Rolf Backofen, Vasco A. de Carvalho Azevedo, Jan Baumbach.

Frontiers in Microbiology, 2021.

DOI BIB

The temperature-regulated DEAD-box RNA helicase CrhR interactome: Autoregulation and photosynthesis-related transcripts

Anzhela Migur, Florian Heyl, Janina Fuss, Afshan Srikumar, Bruno Huettel, Claudia Steglich, Jogadhenu S. S. Prakash, Richard Reinhardt, Rolf Backofen, George W. Owttrim, Wolfgang R. Hess.

J Exp Bot, 2021.

DOI BIB

A distinct CD38+CD45RA+ population of CD4+, CD8+, and double-negative T cells is controlled by FAS

Maria Elena Maccari, Sebastian Fuchs, Patrick Kury, Geoffroy Andrieux, Simon Volkl, Bertram Bengsch, Myriam Ricarda Lorenz, Maximilian Heeg, Jan Rohr, Sabine Jagle, Carla N. Castro, Miriam Gross, Ursula Warthorst, Christoph Konig, Ilka Fuchs, Carsten Speckmann, Julian Thalhammer, Friedrich G. Kapp, Markus G. Seidel, Gregor Duckers, Stefan Schonberger, Catharina Schutz, Marita Fuhrer, Robin Kobbe, Dirk Holzinger, Christian Klemann, Petr Smisek, Stephen Owens, Gerd Horneff, Reinhard Kolb, Nora Naumann-Bartsch, Maurizio Miano, Julian Staniek, Marta Rizzi, Tomas Kalina, Pascal Schneider, Anika Erxleben, Rolf Backofen, Arif Ekici, Charlotte M. Niemeyer, Klaus Warnatz, Bodo Grimbacher, Hermann Eibel, Andreas Mackensen, Andreas Philipp Frei, Klaus Schwarz, Melanie Boerries, Stephan Ehl, Anne Rensing-Ehl.

J Exp Med, 218(2), 2021.

DOI BIB

CdrS Is a Global Transcriptional Regulator Influencing Cell Division in Haloferax volcanii

Yan Liao, Verena Vogel, Sabine Hauber, Jurgen Bartel, Omer S. Alkhnbashi, Sandra Maaß, Thandi S. Schwarz, Rolf Backofen, Dörte Becher, Iain G. Duggin, Anita Marchfelder.

mBio, 12(4), e0141621, 2021.

DOI BIB

Tool recommender system in Galaxy using deep learning

Anup Kumar, Helena Rasche, Björn A. Grüning, Rolf Backofen.

GigaScience, 10(1), 2021.

DOI BIB

Transcriptome-wide in vivo mapping of cleavage sites for the compact cyanobacterial ribonuclease E reveals insights into its function and substrate recognition

Ute A. Hoffmann, Florian Heyl, Said N. Rogh, Thomas Wallner, Rolf Backofen, Wolfgang R. Hess, Claudia Steglich, Annegret Wilde.

NAR, 49(22), 13075-13091, 2021.

DOI BIB

StoatyDive: Evaluation and classification of peak profiles for sequencing data

Florian Heyl, Rolf Backofen.

Gigascience, 10(6), 2021.

DOI BIB

A SARS-CoV-2 sequence submission tool for the European Nucleotide Archive

Miguel Roncoroni, Bert Droesbeke, Ignacio Eguinoa, Kim De Ruyck, Flora D'Anna, Dilmurat Yusuf, Björn Grüning, Rolf Backofen, Frederik Coppens.

Bioinformatics, 2021.

DOI BIB

Chemotherapy-induced transposable elements activate MDA5 to enhance haematopoietic regeneration

Thomas Clapes, Aikaterini Polyzou, Pia Prater, Sagar, Antonio Morales-Hernandez, Mariana Galvao Ferrarini, Natalie Kehrer, Stylianos Lefkopoulos, Veronica Bergo, Barbara Hummel, Nadine Obier, Daniel Maticzka, Anne Bridgeman, Josip S. Herman, Ibrahim Ilik, Lheanna Klaeyle, Jan Rehwinkel, Shannon McKinney-Freeman, Rolf Backofen, Asifa Akhtar, Nina Cabezas-Wallscheid, Ritwick Sawarkar, Rita Rebollo, Dominic Grun, Eirini Trompouki.

Nat Cell Biol, 23(7), 704-717, 2021.

DOI BIB

CRISPRloci: comprehensive and accurate annotation of CRISPR-Cas system

Omer S. Alkhnbashi, Alexander Mitrofanov, Robson Bonidia, Martin Raden, Tran Van Dinh, Florian Eggenhofer, Shiraz A. Shah, Ekrem Öztürk, Victor A. Padilha, Danilo S. Sanches, Andre C.P.L.F. de Carvalho, Rolf Backofen.

NAR, 2021.

DOI BIB

Leukoencephalopathy with calcifications and cysts: Genetic and phenotypic spectrum

Yanick J Crow, Heather Marshall, Gillian I Rice, Luis Seabra, Emma M Jenkinson, Kristin Baranano, Roberta Battini, Andrea Berger, Edward Blair, Thomas Blauwblomme, Francois Bolduc, Natalie Boddaert, Johannes Buckard, Heather Burnett, Sophie Calvert, Roseline Caumes, Andy Cheuk‐Him Ng, Diana Chiang, David B Clifford, Duccio M Cordelli, Anna de Burca, Natasha Demic, Isabelle Desguerre, Liesbeth De Waele, Alessio Di Fonzo, S. Richard Dunham, Sarah Dyack, Frances Elmslie, Mickaël Ferrand, Gemma Fisher, Ehsan Ghayoor Karimiani, Jamal Ghoumid, Frances Gibbon, Himanshu Goel, Hilde T Hilmarsen, Imelda Hughes, Anu Jacob, Elizabeth A Jones, Ram Kumar, Richard J Leventer, Shelley MacDonald, Reza Maroofian, Sarju G Mehta, Imke Metz, Edoardo Monfrini, Daniela Neumann, Michael Noetzel, Mary O'Driscoll, Katrin Õunap, Axel Panzer, Sumit Parikh, Prab Prabhakar, Francis Ramond, Richard Sandford, Russell Saneto, Calvin Soh, Chloe A Stutterd, Gopinath M Subramanian, Kevin Talbot, Rhys H Thomas, Camilo Toro, Renaud Touraine, Emma Wakeling, Evangeline Wassmer, Andrea Whitney, John H Livingston, Raymond T O'Keefe, Andrew P Badrock.

American Journal of Medical Genetics Part A, 185(1), 15-25, 2021.

DOI BIB

BioContainers Registry: Searching Bioinformatics and Proteomics Tools, Packages, and Containers

Jingwen Bai, Chakradhar Bandla, Jiaxin Guo, Roberto Vera Alvarez, Mingze Bai, Juan Antonio Vizcaíno, Pablo Moreno, Björn Grüning, Olivier Sallou, Yasset Perez-Riverol.

Journal of Proteome Research, 20(4), 2056-2061, 2021.

DOI BIB

Metaproteomics Analysis of SARS-CoV-2-Infected Patient Samples Reveals Presence of Potential Coinfecting Microorganisms

Peter S. Thuy-Boun, Subina Mehta, Bjoern Gruening, Thomas McGowan, An Nguyen, Andrew T. Rajczewski, James. E Johnson, Timothy J. Griffin, Dennis W. Wolan, Pratik D. Jagtap.

Journal of Proteome Research, 20(2), 1451-1454, 2021.

DOI BIB

Ready-to-use public infrastructure for global SARS-CoV-2 monitoring

Wolfgang Maier, Simon Bray, Marius van den Beek, Dave Bouvier, Nathan Coraor, Milad Miladi, Babita Singh, Jordi Rambla De Argila, Dannon Baker, Nathan Roach, Simon Gladman, Frederik Coppens, Darren P. Martin, Andrew Lonie, Björn Grüning, Sergei L. Kosakovsky Pond, Anton Nekrutenko.

Nature Biotechnology, 39(10), 1178-1179, 2021.

DOI BIB

The secreted endoribonuclease ENDU-2 from the soma protects germline immortality in C. elegans

Wenjing Qi, Erika D. V. Gromoff, Fan Xu, Qian Zhao, Wei Yang, Dietmar Pfeifer, Wolfgang Maier, Lijiang Long, Ralf Baumeister.

Nature Communications, 12(1), 1262, 2021.

DOI BIB

Donor Graft Cytomegalovirus Serostatus and the Risk of Arterial and Venous Thrombotic Events in Seronegative Recipients After Non-Thoracic Solid Organ Transplantation

Sara Belga, Clayton MacDonald, Diana Chiang, Dima Kabbani, Soroush Shojai, Juan G Abraldes, Carlos Cervera.

Clinical Infectious Diseases, 72(5), 845-852, 2021.

DOI BIB

Mechnetor: a web server for exploring protein mechanism and the functional context of genetic variants

Juan Carlos González-Sánchez, Mustafa F R Ibrahim, Ivo C Leist, Kyle R Weise, Robert B Russell.

Nucleic Acids Research, 49(W1), W366-W374, 2021.

DOI BIB

StreptomeDB 3.0: an updated compendium of streptomycetes natural products

Aurélien F A Moumbock, Mingjie Gao, Ammar Qaseem, Jianyu Li, Pascal A Kirchner, Bakoh Ndingkokhar, Boris D Bekono, Conrad V Simoben, Smith B Babiaka, Yvette I Malange, Florian Sauter, Paul Zierep, Fidele Ntie-Kang, Stefan Günther.

Nucleic Acids Research, 49(D1), D600-D604, 2021.

DOI BIB

Computational Applications in Secondary Metabolite Discovery (CAiSMD): an online workshop

Fidele Ntie-Kang, Kiran K. Telukunta, Serge A. T. Fobofou, Victor Chukwudi Osamor, Samuel A. Egieyeh, Marilia Valli, Yannick Djoumbou-Feunang, Maria Sorokina, Conrad Stork, Neann Mathai, Paul Zierep, Ana L. Chávez-Hernández, Miquel Duran-Frigola, Smith B. Babiaka, Romuald Tematio Fouedjou, Donatus B. Eni, Simeon Akame, Augustine B. Arreyetta-Bawak, Oyere T. Ebob, Jonathan A. Metuge, Boris D. Bekono, Mustafa A. Isa, Raphael Onuku, Daniel M. Shadrack, Thommas M. Musyoka, Vaishali M. Patil, Justin J. J. van der Hooft, Vanderlan da Silva Bolzani, José L. Medina-Franco, Johannes Kirchmair, Tilmann Weber, Özlem Tastan Bishop, Marnix H. Medema, Ludger A. Wessjohann, Jutta Ludwig-Müller.

Journal of Cheminformatics, 13(1), 64, 2021.

DOI BIB

A constructivist-based proposal for bioinformatics teaching practices during lockdown

Cristóbal Gallardo-Alba, Björn Grüning, Beatriz Serrano-Solano.

PLOS Computational Biology, 17(5), e1008922, 2021.

DOI BIB

Modelling of Protein Complexes Involved in Signalling Pathway for Non-small Cell Lung Cancer

Sanket Bapat, Saim Momin, Renu Vyas.

Advances in Bioengineering, 3-28, 2020.

DOI BIB

Scool: a new data storage format for single-cell Hi-C data

Joachim Wolff, Nezar Abdennur, Rolf Backofen, Björn Grüning.

Bioinformatics, 2020.

DOI BIB

Galaxy HiCExplorer 3: a web server for reproducible Hi-C, capture Hi-C and single-cell Hi-C data analysis, quality control and visualization

Joachim Wolff, Leily Rabbani, Ralf Gilsbach, Gautier Richard, Thomas Manke, Rolf Backofen, Björn A Grüning.

Nucleic Acids Research, 48(W1), W177-W184, 2020.

DOI BIB

A global data-driven census of Salmonella small proteins and their potential functions in bacterial virulence

Elisa Venturini, Sarah L Svensson, Sandra Maass, Rick Gelhausen, Florian Eggenhofer, Lei Li, Amy K Cain, Julian Parkhill, Dörte Becher, Rolf Backofen, Lars Barquist, Cynthia M Sharma, Alexander J Westermann, Jörg Vogel.

microLife, 1(1), 2020.

DOI BIB

Improving CLIP-seq data analysis by incorporating transcript information

Michael Uhl, Van Dinh Tran, Rolf Backofen.

BMC genomics, 21(1), 1--8, 2020.

DOI BIB

pyGenomeTracks: reproducible plots for multivariate genomic data sets

Lucille Lopez-Delisle, Leily Rabbani, Joachim Wolff, Vivek Bhardwaj, Rolf Backofen, Björn Grüning, Fidel Ramirez, Thomas Manke.

Bioinformatics, 2020.

DOI BIB

Casboundary: automated definition of integral Cas cassettes

Victor A Padilha, Omer S Alkhnbashi, Van Dinh Tran, Shiraz A Shah, André C P L F Carvalho, Rolf Backofen.

Bioinformatics, 2020.

DOI BIB

HRIBO: high-throughput analysis of bacterial ribosome profiling data

Rick Gelhausen, Sarah L Svensson, Kathrin Froschauer, Florian Heyl, Lydia Hadjeras, Cynthia M Sharma, Florian Eggenhofer, Rolf Backofen.

Bioinformatics, 2020.

DOI BIB

Generation of pure monocultures of human microglia-like cells from induced pluripotent stem cells

Poulomi Banerjee, Evdokia Paza, Emma M Perkins, Owen G James, Boyd Kenkhuis, Amy F Lloyd, Karen Burr, David Story, Dilmurat Yusuf, Xin He, Rolf Backofen, Owen Dando, Siddharthan Chandran, Josef Priller.

Stem Cell Res., 49, 102046, 2020.

DOI BIB

Temporospatial distribution and transcriptional profile of retinal microglia in the oxygen-induced retinopathy mouse model

Myriam Boeck, Adrian Thien, Julian Wolf, Nora Hagemeyer, Yannik Laich, Dilmurat Yusuf, Rolf Backofen, Peipei Zhang, Stefaniya Boneva, Andreas Stahl, Ingo Hilgendorf, Hansjürgen Agostini, Marco Prinz, Peter Wieghofer, Günther Schlunck, Anja Schlecht, Clemens Lange.

Glia, 68(9), 1859--1873, 2020.

DOI BIB

Heterogeneous networks integration for disease-gene prioritization with node kernels

Van Dinh Tran, Alessandro Sperduti, Rolf Backofen, Fabrizio Costa.

Bioinformatics, 36(9), 2649-2656, 2020.

DOI BIB

A single-cell RNA-sequencing training and analysis suite using the Galaxy framework

Mehmet Tekman, Bérénice Batut, Alexander Ostrovsky, Christophe Antoniewski, Dave Clements, Fidel Ramirez, Graham J Etherington, Hans-Rudolf Hotz, Jelle Scholtalbers, Jonathan R Manning, Lea Bellenger, Maria A Doyle, Mohammad Heydarian, Ni Huang, Nicola Soranzo, Pablo Moreno, Stefan Mautner, Irene Papatheodorou, Anton Nekrutenko, James Taylor, Daniel Blankenberg, Rolf Backofen, Björn Grüning.

GigaScience, 9(10), 2020.

DOI BIB

Adaptation induced by self-targeting in a type I-B CRISPR-Cas system

Aris-Edda Stachler, Julia Wortz, Omer S. Alkhnbashi, Israela Turgeman-Grott, Rachel Smith, Thorsten Allers, Rolf Backofen, Uri Gophna, Anita Marchfelder.

JBC, 295(39), 13502-13515, 2020.

DOI BIB

The potential of intra-annual density information for crossdating of short tree-ring series

Martin Raden, Alexander Mattheis, Hans-Peter Kahle, Heinrich Spiecker, Rolf Backofen.

Dendrochronologia, 60, 125679, 2020.

DOI BIB

The impact of various seed, accessibility and interaction constraints on sRNA target prediction - a systematic assessment

Martin Raden, Teresa Müller, Stefan Mautner, Rick Gelhausen, Rolf Backofen.

BMC Bioinformatics, 21, 15, 2020.

DOI BIB

CopomuS - ranking compensatory mutations to guide RNA-RNA interaction verification experiments

Martin Raden, Fabio Gutmann, Michael Uhl, Rolf Backofen.

International Journal of Molecular Sciences, 21(11), 3852, 2020.

DOI BIB

CRISPRcasIdentifier: Machine learning for accurate identification and classification of CRISPR-Cas systems

Victor A. Padilha, Omer S. Alkhnbashi, Shiraz A. Shah, Andre C. P. L. F. de Carvalho, Rolf Backofen.

Gigascience, 9(6), 2020.

DOI BIB

The locality dilemma of Sankoff-like RNA alignments

Teresa Müller, Milad Miladi, Frank Hutter, Ivo Hofacker, Sebastian Will, Rolf Backofen.

Bioinformatics, 2020.

DOI BIB

CRISPRidentify: identification of CRISPR arrays using machine learning approach

Alexander Mitrofanov, Omer S. Alkhnbashi, Sergey A. Shmakov, Kira S. Makarova, Eugene V. Koonin, Rolf Backofen.

NAR, 2020.

DOI BIB

NanoGalaxy: Nanopore long-read sequencing data analysis in Galaxy

Willem de Koning, Milad Miladi, Saskia Hiltemann, Astrid Heikema, John P Hays, Stephan Flemming, Marius van den Beek, Dana A. Mustafa, Rolf Backofen, Björn Grüning, Andrew P. Stubbs.

GigaScience, 9(10), 2020.

DOI BIB

MutaRNA: analysis and visualization of mutation-induced changes in RNA structure

Milad Miladi, Martin Raden, Sven Diederichs, Rolf Backofen.

Nucleic Acids Research, 2020.

DOI BIB

Nephronophthisis gene products display RNA-binding properties and are recruited to stress granules

Luisa Estrada Mallarino, Christina Engel, Ibrahim Avsar Ilik, Daniel Maticzka, Florian Heyl, Barbara Müller, Toma A Yakulov, Jörn Dengjel, Rolf Backofen, Asifa Akhtar.

Scientific reports, 10(1), 1--14, 2020.

DOI BIB

Evolutionary classification of CRISPR-Cas systems: a burst of class 2 and derived variants

Kira S. Makarova, Yuri I. Wolf, Jaime Iranzo, Sergey A. Shmakov, Omer S. Alkhnbashi, Stan J. J. Brouns, Emmanuelle Charpentier, David Cheng, Daniel H. Haft, Philippe Horvath, Sylvain Moineau, Francisco J. M. Mojica, David Scott, Shiraz A. Shah, Virginijus Siksnys, Michael P. Terns, Ceslovas Venclovas, Malcolm F. White, Alexander F. Yakunin, Winston Yan, Feng Zhang, Roger A. Garrett, Rolf Backofen, John van der Oost, Rodolphe Barrangou, Eugene V. Koonin.

Nat Rev Microbiol, 18(2), 67-83, 2020.

DOI BIB

pourRNA - a time- and memory-efficient approach for the guided exploration of RNA energy landscapes

Gregor Entzian, Martin Raden.

Bioinformatics, 36(2), 462-469, 2020.

DOI BIB

Intuitive, reproducible high-throughput molecular dynamics in Galaxy: a tutorial

Simon A. Bray, Tharindu Senapathi, Christopher B. Barnett, Björn A. Grüning.

Journal of Cheminformatics, 12(1), 2020.

DOI BIB

The ChemicalToolbox: reproducible, user-friendly cheminformatics analysis on the Galaxy platform

Simon A. Bray, Xavier Lucas, Anup Kumar, Björn A. Grüning.

Journal of Cheminformatics, 12(1), 2020.

DOI BIB

Engineering proton conductivity in melanin using metal doping

A. Bernardus Mostert, Shermiyah B. Rienecker, Margarita Sheliakina, Paul Zierep, Graeme R. Hanson, Jeffrey R. Harmer, Gerhard Schenk, Paul Meredith.

Journal of Materials Chemistry B, 8(35), 8050-8060, 2020.

DOI BIB

Ewastools: Infinium Human Methylation BeadChip pipeline for population epigenetics integrated into Galaxy

Katarzyna Murat, Björn Grüning, Paulina Wiktoria Poterlowicz, Gillian Westgate, Desmond J Tobin, Krzysztof Poterlowicz.

GigaScience, 9(5), giaa049, 2020.

DOI BIB

Galaxy CLIP-Explorer: a web server for CLIP-Seq data analysis

Florian Heyl, Daniel Maticzka, Michael Uhl, Rolf Backofen.

GigaScience, 9(11), giaa108, 2020.

DOI BIB

The de.NBI / ELIXIR-DE training platform - Bioinformatics training in Germany and across Europe within ELIXIR

Daniel Wibberg, Bérénice Batut, Peter Belmann, Jochen Blom, Frank Oliver Glöckner, Björn Grüning, Nils Hoffmann, Nils Kleinbölting, René Rahn, Maja Rey, Uwe Scholz, Malvika Sharan, Andreas Tauch, Ulrike Trojahn, Björn Usadel, Oliver Kohlbacher.

F1000Research, 8, 1877, 2020.

DOI BIB

Fast and accurate structure probability estimation for simultaneous alignment and folding of RNAs with Markov chains

Milad Miladi, Martin Raden, Sebastian Will, Rolf Backofen.

Algorithms for Molecular Biology, 15(1), 19, 2020.

DOI BIB

No more business as usual: Agile and effective responses to emerging pathogen threats require open data and open analytics

Dannon Baker, Marius van den Beek, Daniel Blankenberg, Dave Bouvier, John Chilton, Nate Coraor, Frederik Coppens, Ignacio Eguinoa, Simon Gladman, Björn Grüning, Nicholas Keener, Delphine Larivière, Andrew Lonie, Sergei Kosakovsky Pond, Wolfgang Maier, Anton Nekrutenko, James Taylor, Steven Weaver.

PLOS Pathogens, 16(8), e1008643, 2020.

DOI BIB

Survey of metaproteomics software tools for functional microbiome analysis

Ray Sajulga, Caleb Easterly, Michael Riffle, Bart Mesuere, Thilo Muth, Subina Mehta, Praveen Kumar, James Johnson, Bjoern Andreas Gruening, Henning Schiebenhoefer, Carolin A. Kolmeder, Stephan Fuchs, Brook L. Nunn, Joel Rudney, Timothy J. Griffin, Pratik D. Jagtap.

PLOS ONE, 15(11), e0241503, 2020.

DOI BIB

SeMPI 2.0—A Web Server for PKS and NRPS Predictions Combined with Metabolite Screening in Natural Product Databases

Paul F. Zierep, Adriana T. Ceci, Ilia Dobrusin, Sinclair C. Rockwell-Kollmann, Stefan Günther.

Metabolites, 11(1), 13, 2020.

DOI BIB

uORF-Tools - Workflow for the determination of translation-regulatory upstream open reading frames

Anica Scholz, Florian Eggenhofer, Rick Gelhausen, Björn Grüning, Kathi Zarnack, Bernhard Brüne, Rolf Backofen, Tobias Schmid.

PLOS ONE, 14, e0222459, 2019.

DOI BIB

Universal readout for graph convolutional neural networks

Nicolò Navarin, Dinh Van Tran, Alessandro Sperduti.

2019 International Joint Conference on Neural Networks (IJCNN), 1--7, 2019.

DOI BIB

Progress Towards Graph Optimization: Efficient Learning of Vector to Graph Space Mappings

Stefan Mautner, Rolf Backofen, Fabrizio Costa.

ESANN 2019 - Proceedings, 2019.

BIB

The RNA workbench 2.0: next generation RNA data analysis

Jörg Fallmann, Pavankumar Videm, Andrea Bagnacani, Bérénice Batut, Maria A Doyle, Tomas Klingstrom, Florian Eggenhofer, Peter F Stadler, Rolf Backofen, Björn Grüning.

Nucleic Acids Research, 2019.

DOI BIB

The RNA workbench 2.0: next generation RNA data analysis

Jörg Fallmann, Pavankumar Videm, Andrea Bagnacani, Bérénice Batut, Maria A Doyle, Tomas Klingstrom, Florian Eggenhofer, Peter F Stadler, Rolf Backofen, Björn Grüning.

Nucleic Acids Research, 2019.

DOI BIB

Noncoding deletions reveal a gene that is critical for intestinal function

Danit Oz-Levi, Tsviya Olender, Ifat Bar-Joseph, Yiwen Zhu, Dina Marek-Yagel, Iros Barozzi, Marco Osterwalder, Anna Alkelai, Elizabeth K Ruzzo, Yujun Han.

Nature, 571(7763), 107--111, 2019.

DOI BIB

A pan-cancer analysis of synonymous mutations

Yogita Sharma, Milad Miladi, Sandeep Dukare, Karine Boulay, Maiwen Caudron-Herger, Matthias Gross, Rolf Backofen, Sven Diederichs.

Nature communications, 10(1), 2569, 2019.

DOI BIB

Comprehensive search for accessory proteins encoded with archaeal and bacterial type III CRISPR-cas gene cassettes reveals 39 new cas gene families

Shiraz A. Shah, Omer S. Alkhnbashi, Juliane Behler, Wenyuan Han, Qunxin She, Wolfgang R. Hess, Roger A. Garrett, Rolf Backofen.

RNA Biol, 16(4), 530-542, 2019.

DOI BIB

Cross-cleavage activity of Cas6b in crRNA processing of two different CRISPR-Cas systems in Methanosarcina mazei Go1

Lisa Nickel, Andrea Ulbricht, Omer S. Alkhnbashi, Konrad U. Forstner, Liam Cassidy, Katrin Weidenbach, Rolf Backofen, Ruth A. Schmitz.

RNA Biol, 16(4), 492-503, 2019.

DOI BIB

Fast and Accurate Structure Probability Estimation for Simultaneous Alignment and Folding of RNAs

Milad Miladi, Martin Raden, Sebastian Will, Rolf Backofen.

19th International Workshop on Algorithms in Bioinformatics (WABI 2019), 143, 14:1--14:13, 2019.

DOI BIB

GraphClust2: Annotation and discovery of structured RNAs with scalable and accessible integrative clustering

Milad Miladi, Eteri Sokhoyan, Torsten Houwaart, Steffen Heyne, Fabrizio Costa, Björn Grüning, Rolf Backofen.

GigaScience, 8(12), 2019.

DOI BIB

Integration of accessibility data from structure probing into RNA-RNA interaction prediction

Milad Miladi, Soheila Montaseri, Rolf Backofen, Martin Raden.

Bioinformatics, 35(16), 2862-2864, 2019.

DOI BIB

ShaKer: RNA SHAPE prediction using graph kernel

Stefan Mautner, Soheila Montaseri, Milad Miladi, Martin Raden, Fabrizio Costa, Rolf Backofen.

Bioinformatics, 35(14), i354-i359, 2019.

DOI BIB

The nuts and bolts of the Haloferax CRISPR-Cas system I-B

Lisa-Katharina Maier, Aris-Edda Stachler, Jutta Brendel, Britta Stoll, Susan Fischer, Karina A. Haas, Thandi S. Schwarz, Omer S. Alkhnbashi, Kundan Sharma, Henning Urlaub, Rolf Backofen, Uri Gophna, Anita Marchfelder.

RNA Biol, 16(4), 469-480, 2019.

DOI BIB

FLASH: ultra-fast protocol to identify RNA–protein interactions in cells

Ibrahim Avsar Ilik, Tugce Aktas, Daniel Maticzka, Rolf Backofen, Asifa Akhtar.

Nucleic Acids Research, 48(3), e15-e15, 2019.

DOI BIB

CRISPR-Cas systems in multicellular cyanobacteria

Shengwei Hou, Manuel Brenes-Alvarez, Viktoria Reimann, Omer S. Alkhnbashi, Rolf Backofen, Alicia M. Muro-Pastor, Wolfgang R. Hess.

RNA Biol, 16(4), 518-529, 2019.

DOI BIB

Constraint Maximal Inter-molecular Helix Lengths within RNA-RNA Interaction Prediction Improves Bacterial sRNA Target Prediction

Rick Gelhausen, Sebastian Will, Ivo L. Hofacker, Rolf Backofen, Martin Raden.

Proceedings of the 12th International Joint Conference on Biomedical Engineering Systems and Technologies - Volume 3: BIOINFORMATICS, 131-140, 2019.

DOI BIB

IntaRNAhelix - Composing RNA-RNA interactions from stable inter-molecular helices boosts bacterial sRNA target prediction

Rick Gelhausen, Sebastian Will, Ivo L. Hofacker, Rolf Backofen, Martin Raden.

Journal of Bioinformatics and Computational Biology, 17(5), 1940009, 2019.

DOI BIB

The RNA workbench 2.0: next generation RNA data analysis

Jörg Fallmann, Pavankumar Videm, Andrea Bagnacani, Bérénice Batut, Maria A. Doyle, Tomas Klingstrom, Florian Eggenhofer, Peter F. Stadler, Rolf Backofen, Björn Grüning.

NAR, 47(W1), W511-W515, 2019.

DOI BIB

Biomolecular Reaction and Interaction Dynamics Global Environment (BRIDGE)

Tharindu Senapathi, Simon Bray, Christopher B Barnett, Björn Grüning, Kevin J Naidoo.

Bioinformatics, 35(18), 3508-3509, 2019.

DOI BIB

CRISPR-Cas bioinformatics

Omer S. Alkhnbashi, Tobias Meier, Alexander Mitrofanov, Rolf Backofen, Björn Voss.

Methods, 2019.

DOI BIB

Tissue specific long non-coding RNAs are involved in aroma formation of black tea

Deepti Varshney, Hukam C. Rawal, Himanshu Dubey, Tanoy Bandyopadhyay, Biswajit Bera, P. Mohan Kumar, Nagendra Kumar Singh, Tapan Kumar Mondal.

Industrial Crops and Products, 133, 79-89, 2019.

DOI BIB

Impact of angiogenic activation and inhibition on miRNA profiles of human retinal endothelial cells

Johanna M. Walz, Thomas Wecker, Pei Pei Zhang, Bertan Cakir, Bjoern Gruening, Hansjuergen Agostini, Tristan Reuer, Franziska Ludwig, Stefaniya Boneva, Lothar Faerber, Clemens Lange, Guenther R. Schlunck, Andreas Stahl.

Experimental Eye Research, 181, 98-104, 2019.

DOI BIB

Update on the moFF Algorithm for Label-Free Quantitative Proteomics

Andrea Argentini, An Staes, Björn Grüning, Subina Mehta, Caleb Easterly, Timothy J. Griffin, Pratik Jagtap, Francis Impens, Lennart Martens.

Journal of Proteome Research, 18(2), 728-731, 2019.

DOI BIB

The direct and indirect effects of vancomycin-resistant enterococci colonization in liver transplant candidates and recipients

Sara Belga, Diana Chiang, Dima Kabbani, Juan G. Abraldes, Carlos Cervera.

Expert Review of Anti-infective Therapy, 17(5), 363-373, 2019.

DOI BIB

Accessible and reproducible mass spectrometry imaging data analysis in Galaxy

Melanie Christine Föll, Lennart Moritz, Thomas Wollmann, Maren Nicole Stillger, Niklas Vockert, Martin Werner, Peter Bronsert, Karl Rohr, Björn Andreas Grüning, Oliver Schilling.

GigaScience, 8(12), giz143, 2019.

DOI BIB

Software engineering for scientific big data analysis

Björn A Grüning, Samuel Lampa, Marc Vaudel, Daniel Blankenberg.

GigaScience, 8(5), giz054, 2019.

DOI BIB

Faecal microbiota from patients with cirrhosis has a low capacity to ferment non‐digestible carbohydrates into short‐chain fatty acids

Mingliang Jin, Sylvia Kalainy, Nami Baskota, Diana Chiang, Edward C. Deehan, Chelsea McDougall, Puneeta Tandon, Inés Martínez, Carlos Cervera, Jens Walter, Juan G. Abraldes.

Liver International, 39(8), 1437-1447, 2019.

DOI BIB

Pou5f3, SoxB1, and Nanog remodel chromatin on high nucleosome affinity regions at zygotic genome activation

Marina Veil, Lev Y. Yampolsky, Björn Grüning, Daria Onichtchouk.

Genome Research, 29(3), 383-395, 2019.

DOI BIB

The de.NBI / ELIXIR-DE training platform - Bioinformatics training in Germany and across Europe within ELIXIR

Daniel Wibberg, Bérénice Batut, Peter Belmann, Jochen Blom, Frank Oliver Glöckner, Björn Grüning, Nils Hoffmann, Nils Kleinbölting, René Rahn, Maja Rey, Uwe Scholz, Malvika Sharan, Andreas Tauch, Ulrike Trojahn, Björn Usadel, Oliver Kohlbacher.

F1000Research, 8, 1877, 2019.

DOI BIB

Recommendations for the packaging and containerizing of bioinformatics software

Bjorn Gruening, Olivier Sallou, Pablo Moreno, Felipe da Veiga Leprevost, Hervé Ménager, Dan Søndergaard, Hannes Röst, Timo Sachsenberg, Brian O'Connor, Fábio Madeira, Victoria Dominguez Del Angel, Michael R. Crusoe, Susheel Varma, Daniel Blankenberg, Rafael C. Jimenez, BioContainers Community, Yasset Perez-Riverol.

F1000Research, 7, 742, 2019.

DOI BIB

Reproducible inference of transcription factor footprints in ATAC-seq and DNase-seq datasets using protocol-specific bias modeling

Aslıhan Karabacak Calviello, Antje Hirsekorn, Ricardo Wurmus, Dilmurat Yusuf, Uwe Ohler.

Genome Biology, 20(1), 42, 2019.

DOI BIB

Two Antagonistic Hippo Signaling Circuits Set the Division Plane at the Medial Position in the CiliateTetrahymena

Yu-Yang Jiang, Wolfgang Maier, Ralf Baumeister, Ewa Joachimiak, Zheng Ruan, Natarajan Kannan, Diamond Clarke, Panagiota Louka, Mayukh Guha, Joseph Frankel, Jacek Gaertig.

Genetics, 211(2), 651-663, 2019.

DOI BIB

LF4/MOK and a CDK-related kinase regulate the number and length of cilia in Tetrahymena

Yu-Yang Jiang, Wolfgang Maier, Ralf Baumeister, Gregory Minevich, Ewa Joachimiak, Dorota Wloga, Zheng Ruan, Natarajan Kannan, Stephen Bocarro, Anoosh Bahraini, Krishna Kumar Vasudevan, Karl Lechtreck, Eduardo Orias, Jacek Gaertig.

PLOS Genetics, 15(7), e1008099, 2019.

DOI BIB

bgruening/galaxy-rna-workbench: 19.01 release

Björn Grüning, Bérénice Batut, Andrea Bagnacani, Joerg Fallmann, Dilmurat Yusuf, Florian Eggenhofer, Youri Hoogstrate, Mwolfien, Sebastian Will, Cameron Smith, Torsten Houwaart, Pavankumar Videm, Jasper, Colin Davenport.

2019.

DOI BIB

bgruening/galaxy-rna-workbench: 19.01 release

Björn Grüning, Bérénice Batut, Andrea Bagnacani, Joerg Fallmann, Dilmurat Yusuf, Florian Eggenhofer, Youri Hoogstrate, Mwolfien, Sebastian Will, Cameron Smith, Torsten Houwaart, Pavankumar Videm, Jasper, Colin Davenport.

2019.

DOI BIB

DOT1L promotes progenitor proliferation and primes neuronal layer identity in the developing cerebral cortex

Henriette Franz, Alejandro Villarreal, Stefanie Heidrich, Pavankumar Videm, Fabian Kilpert, Ivan Mestres, Federico Calegari, Rolf Backofen, Thomas Manke, Tanja Vogel.

Nucleic Acids Research, 47(1), 168-183, 2018.

DOI BIB

DOT1L promotes progenitor proliferation and primes neuronal layer identity in the developing cerebral cortex

Henriette Franz, Alejandro Villarreal, Stefanie Heidrich, Pavankumar Videm, Fabian Kilpert, Ivan Mestres, Federico Calegari, Rolf Backofen, Thomas Manke, Tanja Vogel.

Nucleic Acids Research, 47(1), 168-183, 2018.

DOI BIB

Analysis of the androgen receptor-regulated lncRNA landscape identifies a role for ARLNC1 in prostate cancer progression

Yajia Zhang, Sethuramasundaram Pitchiaya, Marcin Cieslik, Yashar S. Niknafs, Jean C-Y Tien, Yasuyuki Hosono, Matthew K. Iyer, Sahr Yazdani, Shruthi Subramaniam, Sudhanshu K. Shukla, Xia Jiang, Lisha Wang, Tzu-Ying Liu, Michael Uhl, Alexander R. Gawronski, Yuanyuan Qiao, Lanbo Xiao, Saravana M. Dhanasekaran, Kristin M. Juckette, Lakshmi P. Kunju, Xuhong Cao, Utsav Patel, Mona Batish, Girish C. Shukla, Michelle T. Paulsen, Mats Ljungman, Hui Jiang, Rohit Mehra, Rolf Backofen, Cenk S. Sahinalp, Susan M. Freier, Andrew T. Watt, Shuling Guo, John T. Wei, Felix Y. Feng, Rohit Malik, Arul M. Chinnaiyan.

Nat Genet, 50(6), 814-824, 2018.

DOI BIB

Workflow for a Computational Analysis of an sRNA Candidate in Bacteria

Patrick R. Wright, Jens Georg.

Methods Mol Biol, 1737, 3-30, 2018.

DOI BIB

Structure and interaction prediction in prokaryotic RNA biology

Patrick R. Wright, Martin Mann, Rolf Backofen.

Microbiol Spectrum, 6(2), 2018.

DOI BIB

FOXG1 Regulates PRKAR2B Transcriptionally and Posttranscriptionally via miR200 in the Adult Hippocampus

Stefan C. Weise, Ganeshkumar Arumugam, Alejandro Villarreal, Pavankumar Videm, Stefanie Heidrich, Nils Nebel, Verónica I. Dumit, Farahnaz Sananbenesi, Viktoria Reimann, Madeline Craske, Oliver Schilling, Wolfgang R. Hess, Andre Fischer, Rolf Backofen, Tanja Vogel.

Molecular Neurobiology, 2018.

DOI BIB

On filter size in graph convolutional networks

Dinh V Tran, Nicolò Navarin, Alessandro Sperduti.

2018 IEEE Symposium Series on Computational Intelligence (SSCI), 1534--1541, 2018.

Link BIB

Combinatorial Omics Analysis Reveals Perturbed Lysosomal Homeostasis in Collagen VII-deficient Keratinocytes

Kerstin Thriene, Björn Andreas Grüning, Olivier Bornert, Anika Erxleben, Juna Leppert, Ioannis Athanasiou, Ekkehard Weber, Dimitra Kiritsi, Alexander Nystrom, Thomas Reinheckel, Rolf Backofen, Cristina Has, Leena Bruckner-Tuderman, Jorn Dengjel.

Mol Cell Proteomics, 17(4), 565-579, 2018.

DOI BIB

In vitro iCLIP-based modeling uncovers how the splicing factor U2AF2 relies on regulation by cofactors

F. X. Reymond Sutandy, Stefanie Ebersberger, Lu Huang, Anke Busch, Maximilian Bach, Hyun-Seo Kang, Jörg Fallmann, Daniel Maticzka, Rolf Backofen, Peter F. Stadler, Kathi Zarnack, Michael Sattler, Stefan Legewie, Julian Konig.

Genome Res, 2018.

DOI BIB

The RNA-binding protein ARPP21 controls dendritic branching by functionally opposing the miRNA it hosts

Frederick Rehfeld, Daniel Maticzka, Sabine Grosser, Pina Knauff, Murat Eravci, Imre Vida, Rolf Backofen, F. Gregory Wulczyn.

Nat Commun, 9(1), 1235, 2018.

DOI BIB

Freiburg RNA tools: a central online resource for RNA-focused research and teaching

Martin Raden, Syed M Ali, Omer S Alkhnbashi, Anke Busch, Fabrizio Costa, Jason A Davis, Florian Eggenhofer, Rick Gelhausen, Jens Georg, Steffen Heyne, Michael Hiller, Kousik Kundu, Robert Kleinkauf, Steffen C Lott, Mostafa M Mohamed, Alexander Mattheis, Milad Miladi, Andreas S Richter, Sebastian Will, Joachim Wolff, Patrick R Wright, Rolf Backofen.

Nucleic Acids Research, 46(W1), W25-W29, 2018.

DOI BIB

Interactive implementations of thermodynamics-based RNA structure and RNA-RNA interaction prediction approaches for example-driven teaching

Martin Raden, Mostafa M Mohamed, Syed M Ali, Rolf Backofen.

PLOS Comput. Biol, 14(8), e1006341, 2018.

DOI BIB

uvCLAP is a fast and non-radioactive method to identify in vivo targets of RNA-binding proteins

Daniel Maticzka, Ibrahim Avsar Ilik, Tugce Aktas, Rolf Backofen, Asifa Akhtar.

Nat Commun, 9(1), 1142, 2018.

DOI BIB

MICA: Multiple interval-based curve alignment

Martin Mann, Hans-Peter Kahle, Matthias Beck, Bela Johannes Bender, Heinrich Spiecker, Rolf Backofen.

SoftwareX, 7, 53-58, 2018.

DOI BIB

The nuts and bolts of the Haloferax CRISPR-Cas system I-B

Lisa-Katharina Maier, Aris-Edda Stachler, Jutta Brendel, Britta Stoll, Susan Fischer, Karina Haas, Thandi Schwarz, Omer S. Alkhnbashi, Kundan Sharma, Henning Urlaub, Rolf Backofen, Uri Gophna, Anita Marchfelder.

RNA Biol, 1-39, 2018.

DOI BIB

Bioconda: sustainable and comprehensive software distribution for the life sciences

Björn Grüning, Ryan Sjödin Andreas Dale, Brad A. Chapman, Jillian Rowe, Christopher H. Tomkins-Tinch, Renan Valieris, Bioconda Team, Johannes Köster.

Nature Methods, 15(7), 475-476, 2018.

DOI BIB

Distinct epigenetic programs regulate cardiac myocyte development and disease in the human heart in vivo

Ralf Gilsbach, Martin Schwaderer, Sebastian Preissl, Björn A. Grüning, David Kranzhofer, Pedro Schneider, Thomas G. Nuhrenberg, Sonia Mulero-Navarro, Dieter Weichenhan, Christian Braun, Martina Dressen, Adam R. Jacobs, Harald Lahm, Torsten Doenst, Rolf Backofen, Markus Krane, Bruce D. Gelb, Lutz Hein.

Nat Commun, 9(1), 391, 2018.

DOI BIB

GLASSgo - Automated and reliable detection of sRNA homologs from a single input sequences

Steffen C. Lott, Richard A. Schäfer, Martin Mann, Rolf Backofen, Wolfgang R. Hess, Björn Voss, Jens Georg.

Frontiers in Genetics, 9, 124, 2018.

DOI BIB

MechRNA: prediction of lncRNA mechanisms from RNA-RNA and RNA-protein interactions

Alexander R. Gawronski, Michael Uhl, Yajia Zhang, Yen-Yi Lin, Yashar S. Niknafs, Varune R. Ramnarine, Rohit Malik, Felix Feng, Arul M. Chinnaiyan, Colin C. Collins, S. Cenk Sahinalp, Rolf Backofen.

Bioinformatics, 2018.

DOI BIB

CMV - Visualization for RNA and Protein family models and their comparisons

Florian Eggenhofer, Ivo L. Hofacker, Rolf Backofen, Christian Honer Zu Siederdissen.

Bioinformatics, 2018.

DOI BIB

GraphDDP: a graph-embedding approach to detect differentiation pathways in single-cell-data using prior class knowledge

Fabrizio Costa, Dominic Grun, Rolf Backofen.

Nat Commun, 9(1), 3685, 2018.

DOI BIB

hnRNP R and its main interactor, the noncoding RNA 7SK, coregulate the axonal transcriptome of motoneurons

Michael Briese, Lena Saal-Bauernschubert, Changhe Ji, Mehri Moradi, Hanaa Ghanawi, Michael Uhl, Silke Appenzeller, Rolf Backofen, Michael Sendtner.

PNAS, 115(12), E2859-E2868, 2018.

DOI BIB

Comparative RNA Genomics

Rolf Backofen, Jan Gorodkin, Ivo L. Hofacker, Peter F. Stadler.

Methods Mol Biol, 1704, 363-400, 2018.

DOI BIB

Community-Driven Data Analysis Training for Biology

Bérénice Batut, Saskia Hiltemann, Andrea Bagnacani, Dannon Baker, Vivek Bhardwaj, Clemens Blank, Anthony Bretaudeau, Loraine Brillet-Guéguen, Martin Čech, John Chilton, Dave Clements, Olivia Doppelt-Azeroual, Anika Erxleben, Mallory Ann Freeberg, Simon Gladman, Youri Hoogstrate, Hans-Rudolf Hotz, Torsten Houwaart, Pratik Jagtap, Delphine Larivière, Gildas Le Corguillé, Thomas Manke, Fabien Mareuil, Fidel Ramírez, Devon Ryan, Florian Christoph Sigloch, Nicola Soranzo, Joachim Wolff, Pavankumar Videm, Markus Wolfien, Aisanjiang Wubuli, Dilmurat Yusuf, James Taylor, Rolf Backofen, Anton Nekrutenko, Björn Grüning.

Cell Systems, 6(6), 752-758.e1, 2018.

DOI BIB

Draft genome sequence of first monocot-halophytic species Oryza coarctata reveals stress-specific genes

Tapan Kumar Mondal, Hukam Chand Rawal, Soni Chowrasia, Deepti Varshney, Alok Kumar Panda, Abhishek Mazumdar, Harmeet Kaur, Kishor Gaikwad, Tilak Raj Sharma, Nagendra Kumar Singh.

Scientific Reports, 8(1), 13698, 2018.

DOI BIB

High-resolution TADs reveal DNA sequences underlying genome organization in flies

Fidel Ramírez, Vivek Bhardwaj, Laura Arrigoni, Kin Chung Lam, Björn A. Grüning, José Villaveces, Bianca Habermann, Asifa Akhtar, Thomas Manke.

Nature Communications, 9(1), 189, 2018.

DOI BIB

Managing recurrent urinary tract infections in kidney transplant patients

Marta Bodro, Laura Linares, Diana Chiang, Asuncion Moreno, Carlos Cervera.

Expert Review of Anti-infective Therapy, 16(9), 723-732, 2018.

DOI BIB

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update

Enis Afgan, Dannon Baker, Bérénice Batut, Marius van den Beek, Dave Bouvier, Martin Čech, John Chilton, Dave Clements, Nate Coraor, Björn A Grüning, Aysam Guerler, Jennifer Hillman-Jackson, Saskia Hiltemann, Vahid Jalili, Helena Rasche, Nicola Soranzo, Jeremy Goecks, James Taylor, Anton Nekrutenko, Daniel Blankenberg.

Nucleic Acids Research, 46(W1), W537-W544, 2018.

DOI BIB

Recommendations for the packaging and containerizing of bioinformatics software

Bjorn Gruening, Olivier Sallou, Pablo Moreno, Felipe da Veiga Leprevost, Hervé Ménager, Dan Søndergaard, Hannes Röst, Timo Sachsenberg, Brian O'Connor, Fábio Madeira, Victoria Dominguez Del Angel, Michael R. Crusoe, Susheel Varma, Daniel Blankenberg, Rafael C. Jimenez, BioContainers Community, Yasset Perez-Riverol.

F1000Research, 7, 742, 2018.

DOI BIB

Small RNA profiling of low biomass samples: identification and removal of contaminants

Anna Heintz-Buschart, Dilmurat Yusuf, Anne Kaysen, Alton Etheridge, Joëlle V. Fritz, Patrick May, Carine de Beaufort, Bimal B. Upadhyaya, Anubrata Ghosal, David J. Galas, Paul Wilmes.

BMC Biology, 16(1), 52, 2018.

DOI BIB

Do environmentally induced DNA variations mediate adaptation in Aspergillus flavus exposed to chromium stress in tannery sludge?

Akanksha Jaiswar, Deepti Varshney, Alok Adholeya, Pushplata Prasad.

BMC Genomics, 19(1), 868, 2018.

DOI BIB

Additional file 5: of Small RNA profiling of low biomass samples: identification and removal of contaminants

Anna Heintz-Buschart, Dilmurat Yusuf, Anne Kaysen, Alton Etheridge, Joëlle Fritz, Patrick May, Carine de Beaufort, Bimal Upadhyaya, Anubrata Ghosal, David Galas, Paul Wilmes.

figshare, 2018.

DOI BIB

Additional file 4: of Small RNA profiling of low biomass samples: identification and removal of contaminants

Anna Heintz-Buschart, Dilmurat Yusuf, Anne Kaysen, Alton Etheridge, JoĂŤlle Fritz, Patrick May, Carine de Beaufort, Bimal Upadhyaya, Anubrata Ghosal, David Galas, Paul Wilmes.

figshare, 2018.

DOI BIB

Additional file 3: of Small RNA profiling of low biomass samples: identification and removal of contaminants

Anna Heintz-Buschart, Dilmurat Yusuf, Anne Kaysen, Alton Etheridge, JoĂŤlle Fritz, Patrick May, Carine de Beaufort, Bimal Upadhyaya, Anubrata Ghosal, David Galas, Paul Wilmes.

figshare, 2018.

DOI BIB

Additional file1: of Small RNA profiling of low biomass samples: identification and removal of contaminants

Anna Heintz-Buschart, Dilmurat Yusuf, Anne Kaysen, Alton Etheridge, JoĂŤlle Fritz, Patrick May, Carine de Beaufort, Bimal Upadhyaya, Anubrata Ghosal, David Galas, Paul Wilmes.

figshare, 2018.

DOI BIB

bgruening/galaxytools: September release 2019

Björn Grüning, Dilmurat Yusuf, Torsten Houwaart, Anika, Milad Miladi, Qiang Gu, Bérénice Batut, Nicola Soranzo, Hassan Gamaleldin, Greg Von Kuster, Zwanli, Joerg Fallmann, Cameron Smith, Pkohvaei, Florian Eggenhofer, M Bernt, DamCorreia, Youri Hoogstrate, Scott Ouellette, Clemens Blank, Eteri Sokhoyan, Bithiah Yuan, Sebastian Will, Brad Langhorst, Mblue9, Devon Ryan, H. F., Annkatrin Göpfert, Lucille Delisle, Gianluca Corrado.

2018.

DOI BIB

MiModD - Mutation Identification in Model Organism Genomes

Wolfgang Maier.

2018.

DOI BIB

MetSV, a novel archaeal lytic virus targeting Methanosarcina strains

Katrin Weidenbach, Lisa Nickel, Horst Neve, Omer S. Alkhnbashi, Sven Kunzel, Anne Kupczok, Thorsten Bauersachs, Liam Cassidy, Andreas Tholey, Rolf Backofen, Ruth A. Schmitz.

J Virol, 2017.

DOI BIB

Computational analysis of CLIP-seq data

Michael Uhl, Torsten Houwaart, Gianluca Corrado, Patrick R. Wright, Rolf Backofen.

Methods, 118-119, 60-72, 2017.

DOI BIB

Structural constraints and enzymatic promiscuity in the Cas6-dependent generation of crRNAs

Viktoria Reimann, Omer S. Alkhnbashi, Sita J. Saunders, Ingeborg Scholz, Stephanie Hein, Rolf Backofen, Wolfgang R. Hess.

NAR, 45(2), 915-925, 2017.

DOI BIB

sRNA154 a newly identified regulator of nitrogen fixation in Methanosarcina mazei strain Go1

Daniela Prasse, Konrad U. Förstner, Dominik Jäger, Rolf Backofen, Ruth A. Schmitz.

RNA Biol, 13(11), 1544-58, 2017.

DOI BIB

Mechanism of beta-actin mRNA Recognition by ZBP1

Giuseppe Nicastro, Adela M. Candel, Michael Uhl, Alain Oregioni, David Hollingworth, Rolf Backofen, Stephen R. Martin, Andres Ramos.

Cell Rep, 18(5), 1187-1199, 2017.

DOI BIB

Differentiation of ncRNAs from small mRNAs in Escherichia coli O157:H7 EDL933 (EHEC) by combined RNAseq and RIBOseq - ryhB encodes the regulatory RNA RyhB and a peptide, RyhP

Klaus Neuhaus, Richard Landstorfer, Svenja Simon, Steffen Schober, Patrick R. Wright, Cameron Smith, Rolf Backofen, Romy Wecko, Daniel A. Keim, Siegfried Scherer.

BMC Genomics, 18(1), 216, 2017.

DOI BIB

RNAscClust: clustering RNA sequences using structure conservation and graph based motifs

Milad Miladi, Alexander Junge, Fabrizio Costa, Stefan E Seemann, Jakob Hull Havgaard, Jan Gorodkin, Rolf Backofen.

Bioinformatics, 33(14), 2089-2096, 2017.

DOI BIB

IntaRNA 2.0: enhanced and customizable prediction of RNA-RNA interactions

Martin Mann, Patrick R. Wright, Rolf Backofen.

NAR, 45(W1), W435-W439, 2017.

DOI BIB

CRISPR and Salty: CRISPR-Cas Systems in Haloarchaea

Lisa-Katharina Maier, Omer S. Alkhnbashi, Rolf Backofen, Anita Marchfelder.

RNA Metabolism and Gene Expression in Archaea, 243--269, 2017.

DOI BIB

An Efficient Semi-supervised Learning Approach to Predict SH2 Domain Mediated Interactions

Kousik Kundu, Rolf Backofen.

Methods Mol Biol, 1555, 83-97, 2017.

DOI BIB

A mutually exclusive stem-loop arrangement in roX2 RNA is essential for X-chromosome regulation in Drosophila

Ibrahim Avsar Ilik, Daniel Maticzka, Plamen Georgiev, Noel Marie Gutierrez, Rolf Backofen, Asifa Akhtar.

Genes Dev, 31(19), 1973-1987, 2017.

DOI BIB

Jupyter and Galaxy: Easing entry barriers into complex data analyses for biomedical researchers

Björn A. Grüning, Eric Rasche, Boris Rebolledo-Jaramillo, Carl Eberhard, Torsten Houwaart, John Chilton, Nate Coraor, Rolf Backofen, James Taylor, Anton Nekrutenko.

PLoS Comput Biol, 13(5), e1005425, 2017.

DOI BIB

The RNA workbench: best practices for RNA and high-throughput sequencing bioinformatics in Galaxy

Björn A. Grüning, Jörg Fallmann, Dilmurat Yusuf, Sebastian Will, Anika Erxleben, Florian Eggenhofer, Torsten Houwaart, Bérénice Batut, Pavankumar Videm, Andrea Bagnacani, Markus Wolfien, Steffen C. Lott, Youri Hoogstrate, Wolfgang R. Hess, Olaf Wolkenhauer, Steve Hoffmann, Altuna Akalin, Uwe Ohler, Peter F. Stadler, Rolf Backofen.

NAR, 45(W1), W560-W566, 2017.

DOI BIB

Recent advances in RNA folding

Jörg Fallmann, Sebastian Will, Jan Engelhardt, Björn Grüning, Rolf Backofen, Peter F. Stadler.

J Biotechnol, 261, 97-104, 2017.

DOI BIB

Combinatorial ensemble miRNA target prediction of co-regulation networks with non-prediction data

Jason A. Davis, Sita J. Saunders, Martin Mann, Rolf Backofen.

NAR, 45(15), 8745-8757, 2017.

DOI BIB

RIP-Seq Suggests Translational Regulation by L7Ae in Archaea

Michael Daume, Michael Uhl, Rolf Backofen, Lennart Randau.

MBio, 8(4), 2017.

DOI BIB

RNA-bioinformatics: Tools, services and databases for the analysis of RNA-based regulation

Rolf Backofen, Jan Engelhardt, Anika Erxleben, Jorg Fallmann, Björn Grüning, Uwe Ohler, Nikolaus Rajewsky, Peter F. Stadler.

J Biotechnol, 261, 76-84, 2017.

DOI BIB

DHX9 suppresses RNA processing defects originating from the Alu invasion of the human genome

Tugce Aktas, Ibrahim Avsar Ilik, Daniel Maticzka, Vivek Bhardwaj, Cecilia Pessoa Rodrigues, Gerhard Mittler, Thomas Manke, Rolf Backofen, Asifa Akhtar.

Nature, 544(7648), 115-119, 2017.

DOI BIB

GRIN3Bmissense mutation as an inherited risk factor for schizophrenia: whole-exome sequencing in a family with a familiar history of psychotic disorders

TOBIAS HORNIG, BJÖRN GRÜNING, KOUSIK KUNDU, TORSTEN HOUWAART, ROLF BACKOFEN, KNUT BIBER, CLAUS NORMANN.

Genetics Research, 99, e1, 2017.

DOI BIB

BioContainers: an open-source and community-driven framework for software standardization

Felipe da Veiga Leprevost, Björn A Grüning, Saulo Alves Aflitos, Hannes L Röst, Julian Uszkoreit, Harald Barsnes, Marc Vaudel, Pablo Moreno, Laurent Gatto, Jonas Weber, Mingze Bai, Rafael C Jimenez, Timo Sachsenberg, Julianus Pfeuffer, Roberto Vera Alvarez, Johannes Griss, Alexey I Nesvizhskii, Yasset Perez-Riverol.

Bioinformatics, 33(16), 2580-2582, 2017.

DOI BIB

SeMPI: a genome-based secondary metabolite prediction and identification web server

Paul F. Zierep, Natàlia Padilla, Dimitar G. Yonchev, Kiran K. Telukunta, Dennis Klementz, Stefan Günther.

Nucleic Acids Research, 45(W1), W64-W71, 2017.

DOI BIB

RCAS: an RNA centric annotation system for transcriptome-wide regions of interest

Bora Uyar, Dilmurat Yusuf, Ricardo Wurmus, Nikolaus Rajewsky, Uwe Ohler, Altuna Akalin.

Nucleic Acids Research, 45(10), e91-e91, 2017.

DOI BIB

Four simple recommendations to encourage best practices in research software

Rafael C. Jiménez, Mateusz Kuzak, Monther Alhamdoosh, Michelle Barker, Bérénice Batut, Mikael Borg, Salvador Capella-Gutierrez, Neil Chue Hong, Martin Cook, Manuel Corpas, Madison Flannery, Leyla Garcia, Josep Ll. Gelpí, Simon Gladman, Carole Goble, Montserrat González Ferreiro, Alejandra Gonzalez-Beltran, Philippa C. Griffin, Björn Grüning, Jonas Hagberg, Petr Holub, Rob Hooft, Jon Ison, Daniel S. Katz, Brane Leskošek, Federico López Gómez, Luis J. Oliveira, David Mellor, Rowland Mosbergen, Nicola Mulder, Yasset Perez-Riverol, Robert Pergl, Horst Pichler, Bernard Pope, Ferran Sanz, Maria V. Schneider, Victoria Stodden, Radosław Suchecki, Radka Svobodová Vařeková, Harry-Anton Talvik, Ilian Todorov, Andrew Treloar, Sonika Tyagi, Maarten van Gompel, Daniel Vaughan, Allegra Via, Xiaochuan Wang, Nathan S. Watson-Haigh, Steve Crouch.

F1000Research, 6, 876, 2017.

DOI BIB

ENASearch: A Python library for interacting with ENA's API

Bérénice Batut, Björn Grüning.

The Journal of Open Source Software, 2(18), 418, 2017.

DOI BIB

RCAS

Bora Uyar [Aut, Cre], Dilmurat Yusuf [Aut], Ricardo Wurmus[Aut], Altuna Akalin [Aut].

2017.

DOI BIB

The Hippo Pathway Maintains the Equatorial Division Plane in the CiliateTetrahymena

Yu-Yang Jiang, Wolfgang Maier, Ralf Baumeister, Gregory Minevich, Ewa Joachimiak, Zheng Ruan, Natarajan Kannan, Diamond Clarke, Joseph Frankel, Jacek Gaertig.

Genetics, 206(2), 873-888, 2017.

DOI BIB

EBF1 binds to EBNA2 and promotes the assembly of EBNA2 chromatin complexes in B cells

Laura V. Glaser, Simone Rieger, Sybille Thumann, Sophie Beer, Cornelia Kuklik-Roos, Dietmar E. Martin, Kerstin C. Maier, Marie L. Harth-Hertle, Björn Grüning, Rolf Backofen, Stefan Krebs, Helmut Blum, Ralf Zimmer, Florian Erhard, Bettina Kempkes.

PLOS Pathogens, 13(10), e1006664, 2017.

DOI BIB

bgruening/galaxy-rna-workbench: 17.09 release

Björn Grüning, Bérénice Batut, Andrea Bagnacani, Joerg Fallmann, Dilmurat Yusuf, Youri, Mwolfien, Sebastian Will, Cameron Smith, Torsten Houwaart, Florian Eggenhofer, Pavankumar Videm, Colin Davenport.

2017.

DOI BIB

Training Data For 'From Peaks To Gene' Tutorial (Galaxy Training Material)

Björn Grüning, Bérénice Batut, Clemens Blank, Anne Pajon, Nicola Soranzo, Dilmurat Yusuf.

2017.

DOI BIB

Data from: Phylogenetic analyses reveal molecular signatures associated with functional divergence among Subtilisin like Serine Proteases are linked to lifestyle transitions in Hypocreales

Deepti Varshney, Akanksha Jaiswar, Alok Adholeya, Pushplata Singh.

2016.

DOI BIB

SnoReport 2.0: new features and a refined Support Vector Machine to improve snoRNA identification

Joao Victor de Araujo Oliveira, Fabrizio Costa, Rolf Backofen, Peter Florian Stadler, Maria Emilia Machado Telles Walter, Jana Hertel.

BMC Bioinformatics, 17(Suppl 18), 464, 2016.

DOI BIB

MicroRNA Profiling in Aqueous Humor of Individual Human Eyes by Next-Generation Sequencing

Thomas Wecker, Klaus Hoffmeier, Anne Plotner, Björn Andreas Grüning, Ralf Horres, Rolf Backofen, Thomas Reinhard, Gunther Schlunck.

Invest Ophthalmol Vis Sci, 57(4), 1706-13, 2016.

DOI BIB

Plasticity of archaeal C/D box sRNA biogenesis

Vanessa Tripp, Roman Martin, Alvaro Orell, Omer S. Alkhnbashi, Rolf Backofen, Lennart Randau.

Mol Microbiol, 103(1), 151-164, 2016.

DOI BIB

Photorhabdus-nematode symbiosis is dependent on hfq-mediated regulation of secondary metabolites

Nicholas J. Tobias, Antje K. Heinrich, Helena Eresmann, Patrick R. Wright, Nick Neubacher, Rolf Backofen, Helge B. Bode.

Environ Microbiol, 19(1), 119-129, 2016.

DOI BIB

Spatiotemporal alignment of radial tracheid diameter profiles of submontane Norway spruce

D.F. Stangler, M. Mann, H.-P. Kahle, E. Rosskopf, S. Fink, H. Spiecker.

Dendrochronologia, 37, 33-45, 2016.

DOI BIB

Structural constraints and enzymatic promiscuity in the Cas6-dependent generation of crRNAs

Viktoria Reimann, Omer S. Alkhnbashi, Sita J. Saunders, Ingeborg Scholz, Stephanie Hein, Rolf Backofen, Wolfgang R. Hess.

NAR, 2016.

DOI BIB

The lncRNA landscape of breast cancer reveals a role for DSCAM-AS1 in breast cancer progression

Yashar S. Niknafs, Sumin Han, Teng Ma, Corey Speers, Chao Zhang, Kari Wilder-Romans, Matthew K. Iyer, Sethuramasundaram Pitchiaya, Rohit Malik, Yasuyuki Hosono, John R. Prensner, Anton Poliakov, Udit Singhal, Lanbo Xiao, Steven Kregel, Ronald F. Siebenaler, Shuang G. Zhao, Michael Uhl, Alexander Gawronski, Daniel F. Hayes, Lori J. Pierce, Xuhong Cao, Colin Collins, Rolf Backofen, Cenk S. Sahinalp, James M. Rae, Arul M. Chinnaiyan, Felix Y. Feng.

Nat Commun, 7, 12791, 2016.

DOI BIB

GenToS: Use of Orthologous Gene Information to Prioritize Signals from Human GWAS

Anselm S. Hoppmann, Pascal Schlosser, Rolf Backofen, Ekkehart Lausch, Anna Kottgen.

PLoS One, 11(9), e0162466, 2016.

DOI BIB

Differential transcriptional responses to Ebola and Marburg virus infection in bat and human cells

Martin Holzer, Verena Krahling, Fabian Amman, Emanuel Barth, Stephan H. Bernhart, Victor A. O. Carmelo, Maximilian Collatz, Gero Doose, Florian Eggenhofer, Jan Ewald, Jörg Fallmann, Lasse M. Feldhahn, Markus Fricke, Juliane Gebauer, Andreas J. Gruber, Franziska Hufsky, Henrike Indrischek, Sabina Kanton, Jorg Linde, Nelly Mostajo, Roman Ochsenreiter, Konstantin Riege, Lorena Rivarola-Duarte, Abdullah H. Sahyoun, Sita J. Saunders, Stefan E. Seemann, Andrea Tanzer, Bertram Vogel, Stefanie Wehner, Michael T. Wolfinger, Rolf Backofen, Jan Gorodkin, Ivo Grosse, Ivo Hofacker, Steve Hoffmann, Christoph Kaleta, Peter F. Stadler, Stephan Becker, Manja Marz.

Sci Rep, 6, 34589, 2016.

DOI BIB

Global RNA recognition patterns of post-transcriptional regulators Hfq and CsrA revealed by UV crosslinking in vivo

Erik Holmqvist, Patrick R. Wright, Lei Li, Thorsten Bischler, Lars Barquist, Richard Reinhardt, Rolf Backofen, Jörg Vogel.

EMBO J, 35(9), 991-1011, 2016.

DOI BIB

RNA-binding protein HuR and the members of the miR-200 family play an unconventional role in the regulation of c-Jun mRNA

Giorgia Del Vecchio, Francesca De Vito, Sita J. Saunders, Adele Risi, Cecilia Mannironi, Irene Bozzoni, Carlo Presutti.

RNA, 22(10), 1510-21, 2016.

DOI BIB

Characterizing leader sequences of CRISPR loci

Omer S. Alkhnbashi, Shiraz A. Shah, Roger A. Garrett, Sita J. Saunders, Fabrizio Costa, Rolf Backofen.

Bioinformatics, 32(17), i576-i585, 2016.

DOI BIB

DOT1L Activity Promotes Proliferation and Protects Cortical Neural Stem Cells from Activation of ATF4-DDIT3-Mediated ER Stress In Vitro

Deborah Roidl, Nicole Hellbach, Patrick P. Bovio, Alejandro Villarreal, Stefanie Heidrich, Sigrun Nestel, Björn A. Grüning, Ulrike Boenisch, Tanja Vogel.

Stem Cells, 34(1), 233-245, 2016.

DOI BIB

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update

Enis Afgan, Dannon Baker, Marius van den Beek, Daniel Blankenberg, Dave Bouvier, Martin Čech, John Chilton, Dave Clements, Nate Coraor, Carl Eberhard, Björn Grüning, Aysam Guerler, Jennifer Hillman-Jackson, Greg Von Kuster, Eric Rasche, Nicola Soranzo, Nitesh Turaga, James Taylor, Anton Nekrutenko, Jeremy Goecks.

Nucleic Acids Research, 44(W1), W3-W10, 2016.

DOI BIB

deepTools2: a next generation web server for deep-sequencing data analysis

Fidel Ramírez, Devon P Ryan, Björn Grüning, Vivek Bhardwaj, Fabian Kilpert, Andreas S Richter, Steffen Heyne, Friederike Dündar, Thomas Manke.

Nucleic Acids Research, 44(W1), W160-W165, 2016.

DOI BIB

Tools and data services registry: a community effort to document bioinformatics resources

Jon Ison, Kristoffer Rapacki, Hervé Ménager, Matúš Kalaš, Emil Rydza, Piotr Chmura, Christian Anthon, Niall Beard, Karel Berka, Dan Bolser, Tim Booth, Anthony Bretaudeau, Jan Brezovsky, Rita Casadio, Gianni Cesareni, Frederik Coppens, Michael Cornell, Gianmauro Cuccuru, Kristian Davidsen, Gianluca Della Vedova, Tunca Dogan, Olivia Doppelt-Azeroual, Laura Emery, Elisabeth Gasteiger, Thomas Gatter, Tatyana Goldberg, Marie Grosjean, Björn Grüning, Manuela Helmer-Citterich, Hans Ienasescu, Vassilios Ioannidis, Martin Closter Jespersen, Rafael Jimenez, Nick Juty, Peter Juvan, Maximilian Koch, Camille Laibe, Jing-Woei Li, Luana Licata, Fabien Mareuil, Ivan Mičetić, Rune Møllegaard Friborg, Sebastien Moretti, Chris Morris, Steffen Möller, Aleksandra Nenadic, Hedi Peterson, Giuseppe Profiti, Peter Rice, Paolo Romano, Paola Roncaglia, Rabie Saidi, Andrea Schafferhans, Veit Schwämmle, Callum Smith, Maria Maddalena Sperotto, Heinz Stockinger, Radka Svobodová Vařeková, Silvio C.E. Tosatto, Victor de la Torre, Paolo Uva, Allegra Via, Guy Yachdav, Federico Zambelli, Gert Vriend, Burkhard Rost, Helen Parkinson, Peter Løngreen, Søren Brunak.

Nucleic Acids Research, 44(D1), D38-D47, 2016.

DOI BIB

Echinocandin B biosynthesis: a biosynthetic cluster from Aspergillus nidulans NRRL 8112 and reassembly of the subclusters Ecd and Hty from Aspergillus pachycristatus NRRL 11440 reveals a single coherent gene cluster

Wolfgang Hüttel, Loubna Youssar, Björn A. Grüning, Stefan Günther, Katharina G. Hugentobler.

BMC Genomics, 17(1), 570, 2016.

DOI BIB

5'-Hydroxymethylcytosine Precedes Loss of CpG Methylation in Enhancers and Genes Undergoing Activation in Cardiomyocyte Maturation

David K. Kranzhöfer, Ralf Gilsbach, Björn A. Grüning, Rolf Backofen, Thomas G. Nührenberg, Lutz Hein.

PLOS ONE, 11(11), e0166575, 2016.

DOI BIB

PubMedPortable: A Framework for Supporting the Development of Text Mining Applications

Kersten Döring, Björn A. Grüning, Kiran K. Telukunta, Philippe Thomas, Stefan Günther.

PLOS ONE, 11(10), e0163794, 2016.

DOI BIB

galaxytools: July 2016 release

Björn Grüning, Anika, Torsten Houwaart, Nicola Soranzo, Greg Von Kuster, Bérénice Batut, Cameron Smith, Pkohvaei, DamCorreia, Yhoogstrate, Dilmurat Yusuf, Eric Rasche, Annkatrin Göpfert, Gianluca Corrado, Peter Cock, Bernhardlutz, John Chilton, Rémi Marenco, B. Dave, Pvanheus, Jan Kanis, Daniel Blankenberg, Shaun Jackman, Rekado, Hans-Rudolf Hotz, Ira Cooke, Brad Langhorst, Cche, Tiffany Fernandez, Scholtalbers.

2016.

DOI BIB

SPARSE: quadratic time simultaneous alignment and folding of RNAs without sequence-based heuristics

Sebastian Will, Christina Otto, Milad Miladi, Mathias Möhl, Rolf Backofen.

Bioinformatics, 31(15), 2489-2496, 2015.

DOI BIB

A stress-induced small RNA modulates alpha-rhizobial cell cycle progression

Marta Robledo, Benjamin Frage, Patrick R. Wright, Anke Becker.

PLoS Genet, 11(4), e1005153, 2015.

DOI BIB

SimiRa: A tool to identify coregulation between microRNAs and RNA-binding proteins

Martin Preusse, Carsten Marr, Sita Saunders, Daniel Maticzka, Heiko Lickert, Rolf Backofen, Fabian Theis.

RNA Biology, 12(9), 998-1009, 2015.

DOI BIB

Deciphering the Epigenetic Code of Cardiac Myocyte Transcription

Sebastian Preissl, Martin Schwaderer, Alexandra Raulf, Michael Hesse, Björn A. Grüning, Claudia Kobele, Rolf Backofen, Bernd K. Fleischmann, Lutz Hein, Ralf Gilsbach.

Circ Res, 117, 413-423, 2015.

DOI BIB

RC3H1 post-transcriptionally regulates A20 mRNA and modulates the activity of the IKK/NF-kappaB pathway

Yasuhiro Murakawa, Michael Hinz, Janina Mothes, Anja Schuetz, Michael Uhl, Emanuel Wyler, Tomoharu Yasuda, Guido Mastrobuoni, Caroline C. Friedel, Lars Dolken, Stefan Kempa, Marc Schmidt-Supprian, Nils Bluthgen, Rolf Backofen, Udo Heinemann, Jana Wolf, Claus Scheidereit, Markus Landthaler.

Nat Commun, 6, 7367, 2015.

DOI BIB

An updated evolutionary classification of CRISPR-Cas systems

Kira S. Makarova, Yuri I. Wolf, Omer S. Alkhnbashi, Fabrizio Costa, Shiraz A. Shah, Sita J. Saunders, Rodolphe Barrangou, Stan J. J. Brouns, Emmanuelle Charpentier, Daniel H. Haft, Philippe Horvath, Sylvain Moineau, Francisco J. M. Mojica, Rebecca M. Terns, Michael P. Terns, Malcolm F. White, Alexander F. Yakunin, Roger A. Garrett, John van der Oost, Rolf Backofen, Eugene V. Koonin.

Nat Rev Microbiol, 13(11), 722-736, 2015.

DOI BIB

An active immune defense with a minimal CRISPR (clustered regularly interspaced short palindromic repeats) RNA and without the Cas6 protein

Lisa-Katharina Maier, Aris-Edda Stachler, Sita J. Saunders, Rolf Backofen, Anita Marchfelder.

JBC, 290(7), 4192-201, 2015.

DOI BIB

Cell type specific gene expression analysis of prostate needle biopsies resolves tumor tissue heterogeneity

Malte Kronig, Max Walter, Vanessa Drendel, Martin Werner, Cordula A. Jilg, Andreas S. Richter, Rolf Backofen, David McGarry, Marie Follo, Wolfgang Schultze-Seemann, Roland Schule.

Oncotarget, 6(2), 1302-14, 2015.

DOI BIB

Computational Prediction of Modular Domain-Peptide Interactions

Kousik Kundu, Fabrizio Costa, Rolf Backofen.

Poster Proceedings of ISMB'15, 2015.

BIB

antaRNA - Ant Colony Based RNA Sequence Design

R. Kleinkauf, M. Mann, R. Backofen.

Bioinformatics, 31(19), 3114-3121, 2015.

DOI BIB

antaRNA - Multi-objective inverse folding of pseudoknot RNA using ant-colony optimization

R. Kleinkauf, T. Houwaart, R. Backofen, M. Mann.

BMC Bioinformatics, 16(1), 1-7, 2015.

DOI BIB

Comparative analysis of the antioxidant properties of Icelandic and Hawaiian lichens

Kehau Hagiwara, Patrick R. Wright, Nicole K. Tabandera, Dovi Kelman, Rolf Backofen, Sesselja Omarsdottir, Anthony D. Wright.

Environ Microbiol, 18(8), 2319-2325, 2015.

DOI BIB

Towards an Automated Annotation of CRISPR-Cas systems

F Costa, O. S. Alkhnbashi, S. A. Shah, S. J. Saunders, R Barrangou, SJJ Brouns, E Charpentier, DH Haft, P Horvath, EV Koonin, KS Makarova, S Moineau, FJM Mojica, RM Terns, MA Terns, J van der Oost, MF White, YI Wolf, AF Yakunin, RA Garrett, R. Backofen.

Poster, CRISPR Conference 2015, 2015.

BIB

Towards an Automated Annotation of CRISPR-Cas systems

F. Costa, O. S. Alkhnbashi, S. A. Shah, S. J. Saunders, R. Barrangou, S. J. J. Brouns, E. Charpentier, D. H. Haft, P. Horvath, E. V. Koonin, K. S. Makarova, S. Moineau, F. J. M. Mojica, R. M. Terns, M. A. Terns, J van der Oost, M. F. White, YI Wolf, A. F. Yakunin, R. A. Garrett, R. Backofen.

Poster, CRISPR Conference'15, 2015.

BIB

The role of Cas8 in type I CRISPR interference

Simon D. B. Cass, Karina A. Haas, Britta Stoll, Omer Alkhnbashi, Kundan Sharma, Henning Urlaub, Rolf Backofen, Anita Marchfelder, Edward L. Bolt.

Biosci Rep, 35(4), e00197, 2015.

DOI BIB

CRISPRloci: Comprehensive and accurate annotation of CRISPR-Cas systems

Omer S. Alkhnbashi, Shiraz A. Shah, Fabrizio Costa, Martin Mann, Xu Peng, Roger A. Garrett, Rolf Backofen.

Poster, CRISPR Conference'15, 2015.

BIB

The Purchasable Chemical Space: A Detailed Picture

Xavier Lucas, Björn A. Grüning, Stefan Bleher, Stefan Günther.

Journal of Chemical Information and Modeling, 55(5), 915-924, 2015.

DOI BIB

NCBI BLAST+ integrated into Galaxy

Peter J. A. Cock, John M. Chilton, Björn Grüning, James E. Johnson, Nicola Soranzo.

Gigascience, 4(1), s13742-015-0080-7, 2015.

DOI BIB

An NGS Workflow Blueprint for DNA Sequencing Data and Its Application in Individualized Molecular Oncology

Jian Li, Aarif Mohamed Nazeer Batcha, Björn Gaining, Ulrich R. Mansmann.

Cancer Informatics, 14s5, CIN.S30793, 2015.

DOI BIB

Anatomy of BioJS, an open source community for the life sciences

Guy Yachdav, Tatyana Goldberg, Sebastian Wilzbach, David Dao, Iris Shih, Saket Choudhary, Steve Crouch, Max Franz, Alexander García, Leyla J García, Björn A Grüning, Devasena Inupakutika, Ian Sillitoe, Anil S Thanki, Bruno Vieira, José M Villaveces, Maria V Schneider, Suzanna Lewis, Steve Pettifer, Burkhard Rost, Manuel Corpas.

eLife, 4, e07009, 2015.

DOI BIB

Local Exact Pattern Matching for Non-Fixed RNA Structures.

Mika Amit, Rolf Backofen, Steffen Heyne, Gad M. Landau, Mathias Möhl, Christina Otto, Sebastian Will.

IEEE/ACM Trans. Comput. Biology Bioinform., 11(1), 219-230, 2014.

DOI BIB

CopraRNA and IntaRNA: predicting small RNA targets, networks and interaction domains

Patrick R. Wright, Jens Georg, Martin Mann, Dragos A. Sorescu, Andreas S. Richter, Steffen Lott, Robert Kleinkauf, Wolfgang R. Hess, Rolf Backofen.

NAR, 42(Web Server issue), W119-23, 2014.

DOI BIB

Simultaneous Alignment and Folding of Protein Sequences

Jerome Waldispuhl, Charles W. O'Donnell, Sebastian Will, Srinivas Devadas, Rolf Backofen, Bonnie Berger.

JCB, 21(7), 477-491, 2014.

DOI BIB

BlockClust: efficient clustering and classification of non-coding RNAs from short read RNA-seq profiles

Pavankumar Videm, Dominic Rose, Fabrizio Costa, Rolf Backofen.

Bioinformatics, 30(12), i274-i282, 2014.

DOI BIB

Autosomal dominant immune dysregulation syndrome in humans with CTLA4 mutations

Desiree Schubert, Claudia Bode, Rupert Kenefeck, Tie Zheng Hou, James B. Wing, Alan Kennedy, Alla Bulashevska, Britt-Sabina Petersen, Alejandro A. Schaffer, Björn A. Grüning, Susanne Unger, Natalie Frede, Ulrich Baumann, Torsten Witte, Reinhold E. Schmidt, Gregor Dueckers, Tim Niehues, Suranjith Seneviratne, Maria Kanariou, Carsten Speckmann, Stephan Ehl, Anne Rensing-Ehl, Klaus Warnatz, Mirzokhid Rakhmanov, Robert Thimme, Peter Hasselblatt, Florian Emmerich, Toni Cathomen, Rolf Backofen, Paul Fisch, Maximilian Seidl, Annette May, Annette Schmitt-Graeff, Shinji Ikemizu, Ulrich Salzer, Andre Franke, Shimon Sakaguchi, Lucy S. K. Walker, David M. Sansom, Bodo Grimbacher.

Nat Med, 20(12), 1410-1416, 2014.

DOI BIB

Graph-distance distribution of the Boltzmann ensemble of RNA secondary structures

Jing Qin, Markus Fricke, Manja Marz, Peter F. Stadler, Rolf Backofen.

Algorithms Mol Biol, 9, 19, 2014.

DOI BIB

Two separate modules of the conserved regulatory RNA AbcR1 address multiple target mRNAs in and outside of the translation initiation region

Aaron Overloeper, Alexander Kraus, Rosemarie Gurski, Patrick R. Wright, Jens Georg, Wolfgang R. Hess, Franz Narberhaus.

RNA Biol, 11(5), 624-40, 2014.

DOI BIB

ExpaRNA-P: simultaneous exact pattern matching and folding of RNAs

Christina Otto, Mathias Möhl, Steffen Heyne, Mika Amit, Gad M. Landau, Rolf Backofen, Sebastian Will.

BMC Bioinformatics, 15(1), 6602, 2014.

DOI BIB

GraphProt: modeling binding preferences of RNA-binding proteins

Daniel Maticzka, Sita J. Lange, Fabrizio Costa, Rolf Backofen.

Genome Biol, 15(1), R17, 2014.

DOI BIB

Memory efficient RNA energy landscape exploration

Martin Mann, Marcel Kucharik, Christoph Flamm, Michael T. Wolfinger.

Bioinformatics, 30(18), 2584-2591, 2014.

DOI BIB

Atom Mapping with Constraint Programming

Martin Mann, Feras Nahar, Norah Schnorr, Rolf Backofen, Peter F. Stadler, Christoph Flamm.

BMC Algorithms for Molecular Biology, 9(1), 23, 2014.

DOI BIB

Exact methods for lattice protein models

Martin Mann, Rolf Backofen.

Bio-Algorithms and Med-Systems, 10(4), 213-225, 2014.

DOI BIB

An Active Immune Defence with a Minimal CRISPR (clustered regularly interspaced short palindromic repeats) RNA and Without the Cas6 Protein

Lisa-Katharina Maier, Aris-Edda Stachler, Sita J. Saunders, Rolf Backofen, Anita Marchfelder.

JBC, 290(7), 4192-4201, 2014.

DOI BIB

Activation of a GPCR leads to eIF4G phosphorylation at the 5' cap and to IRES-dependent translation

Kelly Leon, Thomas Boulo, Astrid Musnier, Julia Morales, Christophe Gauthier, Laurence Dupuy, Steffen Heyne, Rolf Backofen, Anne Poupon, Patrick Cormier, Eric Reiter, Pascale Crepieux.

J Mol Endocrinol, 52(3), 373-82, 2014.

DOI BIB

MoDPepInt: An interactive webserver for prediction of modular domain-peptide interactions

Kousik Kundu, Martin Mann, Fabrizio Costa, Rolf Backofen.

Bioinformatics, 2014.

DOI BIB

MoDPepInt: an interactive web server for prediction of modular domain-peptide interactions

Kousik Kundu, Martin Mann, Fabrizio Costa, Rolf Backofen.

Bioinformatics, 30(18), 2668-2669, 2014.

DOI BIB

Cluster based prediction of PDZ-peptide interactions

Kousik Kundu, Rolf Backofen.

BMC Genomics, 15(Suppl 1), S5, 2014.

DOI BIB

Dynamic DNA methylation orchestrates cardiomyocyte development, maturation and disease

Ralf Gilsbach, Sebastian Preissl, Björn A. Grüning, Tilman Schnick, Lukas Burger, Vladimir Benes, Andreas Wurch, Ulrike Bonisch, Stefan Gunther, Rolf Backofen, Bernd K. Fleischmann, Dirk Schubeler, Lutz Hein.

Nat Commun, 5, 5288, 2014.

DOI BIB

Lineage-specific splicing of a brain-enriched alternative exon promotes glioblastoma progression

Roberto Ferrarese, Griffith R. 4th Harsh, Ajay K. Yadav, Eva Bug, Daniel Maticzka, Wilfried Reichardt, Stephen M. Dombrowski, Tyler E. Miller, Anie P. Masilamani, Fangping Dai, Hyunsoo Kim, Michael Hadler, Denise M. Scholtens, Irene L. Y. Yu, Jurgen Beck, Vinodh Srinivasasainagendra, Fabrizio Costa, Nicoleta Baxan, Dietmar Pfeifer, Dominik V. Elverfeldt, Rolf Backofen, Astrid Weyerbrock, Christine W. Duarte, Xiaolin He, Marco Prinz, James P. Chandler, Hannes Vogel, Arnab Chakravarti, Jeremy N. Rich, Maria S. Carro, Markus Bredel.

J Clin Invest, 124(7), 2861-2876, 2014.

DOI BIB

MOF-associated complexes ensure stem cell identity and Xist repression

Tomasz Chelmicki, Friederike Dundar, Matthew Turley, Tasneem Khanam, Tugce Aktas, Fidel Ramirez, Anne-Valerie Gendrel, Patrick R. Wright, Pavankumar Videm, Rolf Backofen, Edith Heard, Thomas Manke, Asifa Akhtar.

Elife, 3, e02024, 2014.

DOI BIB

A complex of Cas proteins 5, 6, and 7 is required for the biogenesis and stability of crRNAs in Haloferax volcanii

Jutta Brendel, Britta Stoll, Sita J. Lange, Kundan Sharma, Christof Lenz, Aris-Edda Stachler, Lisa-Katharina Maier, Hagen Richter, Lisa Nickel, Ruth A. Schmitz, Lennart Randau, Thorsten Allers, Henning Urlaub, Rolf Backofen, Anita Marchfelder.

JBC, 289(10), 7164-77, 2014.

DOI BIB

Biological and bioinformatical approaches to study crosstalk of long-non-coding RNAs and chromatin-modifying proteins

Rolf Backofen, Tanja Vogel.

Cell Tissue Res, 356(3), 507-26, 2014.

DOI BIB

Bioinformatics of prokaryotic RNAs

Rolf Backofen, Fabian Amman, Fabrizio Costa, Sven Findeiss, Andreas S. Richter, Peter F. Stadler.

RNA Biol, 11(5), 2014.

DOI BIB

Computational Prediction of RNA-RNA Interactions

Rolf Backofen.

Methods Mol Biol, 1097, 417-35, 2014.

DOI BIB

CRISPRstrand: predicting repeat orientations to determine the crRNA-encoding strand at CRISPR loci

Omer S. Alkhnbashi, Fabrizio Costa, Shiraz A. Shah, Roger A. Garrett, Sita J. Saunders, Rolf Backofen.

Bioinformatics, 30(17), i489-i496, 2014.

DOI BIB

Regio- and Stereoselective Intermolecular Oxidative Phenol Coupling in Streptomyces

Andreas Präg, Björn A. Grüning, Matthias Häckh, Steffen Lüdeke, Marcel Wilde, Andriy Luzhetskyy, Michael Richter, Marta Luzhetska, Stefan Günther, Michael Müller.

Journal of the American Chemical Society, 136(17), 6195-6198, 2014.

DOI BIB

PyWATER: a PyMOL plug-in to find conserved water molecules in proteins by clustering

Hitesh Patel, Björn A. Grüning, Stefan Günther, Irmgard Merfort.

Bioinformatics, 30(20), 2978-2980, 2014.

DOI BIB

Electron paramagnetic resonance study of ZnO varistor material

Raschid Baraki, Paul Zierep, Emre Erdem, Stefan Weber, Torsten Granzow.

Journal of Physics: Condensed Matter, 26(11), 115801, 2014.

DOI BIB

deepTools: a flexible platform for exploring deep-sequencing data

Fidel Ramírez, Friederike Dündar, Sarah Diehl, Björn A. Grüning, Thomas Manke.

Nucleic Acids Research, 42(W1), W187-W191, 2014.

DOI BIB

Dynamic information system for small molecules

Kiran K Telukunta, Xavier Lucas, Kersten Döring, Björn A Grüning, Stefan Günther.

Journal of Cheminformatics, 6(S1), P28, 2014.

DOI BIB

Automated peptide mapping and protein-topographical annotation of proteomics data

Pavankumar Videm, Deepika Gunasekaran, Bernd Schröder, Bettina Mayer, Martin L Biniossek, Oliver Schilling.

BMC Bioinformatics, 15(1), 207, 2014.

DOI BIB

Neonicotinoids Interfere with Specific Components of Navigation in Honeybees

Johannes Fischer, Teresa Müller, Anne-Kathrin Spatz, Uwe Greggers, Bernd Grünewald, Randolf Menzel.

PLoS ONE, 9(3), e91364, 2014.

DOI BIB

Distribution of Graph-Distances in Boltzmann Ensembles of RNA Secondary Structures

Rolf Backofen, Markus Fricke, Manja Marz, Jing Qin, Peter F. Stadler.

Algorithms in Bioinformatics, 8126, 112-125, 2013.

DOI BIB

Comparative genomics boosts target prediction for bacterial small RNAs

Patrick R. Wright, Andreas S. Richter, Kai Papenfort, Martin Mann, Jorg Vogel, Wolfgang R. Hess, Rolf Backofen, Jens Georg.

PNAS, 110(37), E3487-96, 2013.

DOI BIB

Freiburg RNA Tools webserver

Patrick R. Wright, Martin Mann, Dragos A. Sorescu, Sita J. Lange, Omer S. Alkhnbashi, Dominic Rose, Steffen Heyne, Andreas S. Richter, Wolfgang R. Hess, Jens Georg, Anke Busch, Sebastian Will, Rolfs Backofen.

Poster, 3rd Conference on Regulating with RNA in Bacteria, 2013.

BIB

SPARSE: Quadratic Time Simultaneous Alignment and Folding of RNAs Without Sequence-Based Heuristics

Sebastian Will, Christina Schmiedl, Milad Miladi, Mathias Möhl, Rolf Backofen.

Proceedings of the 17th International Conference on Research in Computational Molecular Biology (RECOMB 2013), 7821, 289-290, 2013.

DOI BIB

Structure-based whole genome realignment reveals many novel non-coding RNAs

Sebastian Will, Michael Yu, Bonnie Berger.

Genome Res, [Epub ahead of print], 2013.

DOI BIB

LocARNAscan: Incorporating thermodynamic stability in sequence and structure-based RNA homology search

Sebastian Will, Michael F. Siebauer, Steffen Heyne, Jan Engelhardt, Peter F. Stadler, Kristin Reiche, Rolf Backofen.

Algorithms Mol Biol, 8(1), 14, 2013.

DOI BIB

Requirements for a successful defence reaction by the CRISPR-Cas subtype I-B system

Britta Stoll, Lisa-Katharina Maier, Sita J. Lange, Jutta Brendel, Susan Fischer, Rolf Backofen, Anita Marchfelder.

Biochem Soc Trans, 41(6), 1444-8, 2013.

DOI BIB

CRISPR-Cas Systems in the Cyanobacterium Synechocystis sp. PCC6803 Exhibit Distinct Processing Pathways Involving at Least Two Cas6 and a Cmr2 Protein

Ingeborg Scholz, Sita J. Lange, Stephanie Hein, Wolfgang R. Hess, Rolf Backofen.

PLoS One, 8(2), e56470, 2013.

DOI BIB

Comparative analysis of Cas6b processing and CRISPR RNA stability

Hagen Richter, Sita J. Lange, Rolf Backofen, Lennart Randau.

RNA Biology, 10(5), 700-707, 2013.

DOI BIB

Evaluation and cross-comparison of lexical entities of biological interest (LexEBI)

Dietrich Rebholz-Schuhmann, Jee-Hyub Kim, Ying Yan, Abhishek Dixit, Caroline Friteyre, Robert Hoehndorf, Rolf Backofen, Ian Lewin.

PLoS One, 8(10), e75185, 2013.

DOI BIB

Evaluating gold standard corpora against gene/protein tagging solutions and lexical resources

Dietrich Rebholz-Schuhmann, Senay Kafkas, Jee-Hyub Kim, Chen Li, Antonio Jimeno Yepes, Robert Hoehndorf, Rolf Backofen, Ian Lewin.

J Biomed Semantics, 4(1), 28, 2013.

DOI BIB

A case study: semantic integration of gene-disease associations for type 2 diabetes mellitus from literature and biomedical data resources

Dietrich Rebholz-Schuhmann, Christoph Grabmuller, Silvestras Kavaliauskas, Samuel Croset, Peter Woollard, Rolf Backofen, Wendy Filsell, Dominic Clark.

Drug Discov Today, 19(7), 882–889, 2013.

DOI BIB

Regulatory RNAs in archaea: first target identification in Methanoarchaea

Daniela Prasse, Claudia Ehlers, Rolf Backofen, Ruth A. Schmitz.

Biochem Soc Trans, 41(1), 344-9, 2013.

DOI BIB

Two CRISPR-Cas systems in Methanosarcina mazei strain Go1 display common processing features despite belonging to different types I and III

Lisa Nickel, Katrin Weidenbach, Dominik Jager, Rolf Backofen, Sita J. Lange, Nadja Heidrich, Ruth A. Schmitz.

RNA Biol, 10(5), 779-791, 2013.

DOI BIB

Kekule structure enumeration yields unique SMILES

Martin Mann, Bernhard Thiel.

Proceedings of the Workshop on Constraint Based Methods for Bioinformatics (WCB 2013), 1-9, 2013.

Link BIB

Atom Mapping with Constraint Programming

Martin Mann, Feras Nahar, Heinz Ekker, Rolf Backofen, Peter F. Stadler, Christoph Flamm.

Proc. of the 19th International Conference on Principles and Practice of Constraint Programming (CP'13), 8124, 805-822, 2013.

DOI BIB

The Graph Grammar Library - a generic framework for chemical graph rewrite systems

Martin Mann, Heinz Ekker, Christoph Flamm.

Theory and Practice of Model Transformations, Proc. of ICMT 2013, 7909, 52-53, 2013.

DOI BIB

Essential requirements for the detection and degradation of invaders by the Haloferax volcanii CRISPR/Cas system I-B

Lisa-Katharina Maier, Sita J. Lange, Britta Stoll, Karina A. Haas, Susan Fischer, Eike Fischer, Elke Duchardt-Ferner, Jens Wohnert, Rolf Backofen, Anita Marchfelder.

RNA Biology, 10(5), 865-874, 2013.

DOI BIB

CRISPRmap: an automated classification of repeat conservation in prokaryotic adaptive immune systems

Sita J. Lange, Omer S. Alkhnbashi, Dominic Rose, Sebastian Will, Rolf Backofen.

NAR, 41(17), 8034-44, 2013.

DOI BIB

Semi-Supervised Prediction of SH2-Peptide Interactions from Imbalanced High-Throughput Data

Kousik Kundu, Fabrizio Costa, Michael Huber, Michael Reth, Rolf Backofen.

PLoS One, 8(5), e62732, 2013.

DOI BIB

A graph kernel approach for alignment-free domain-peptide interaction prediction with an application to human SH3 domains

Kousik Kundu, Fabrizio Costa, Rolf Backofen.

Bioinformatics, 29(13), i335-i343, 2013.

DOI BIB

Tandem Stem-Loops in roX RNAs Act Together to Mediate X Chromosome Dosage Compensation in Drosophila

Ibrahim Avsar Ilik, Jeffrey J. Quinn, Plamen Georgiev, Filipe Tavares-Cadete, Daniel Maticzka, Sarah Toscano, Yue Wan, Robert C. Spitale, Nicholas Luscombe, Rolf Backofen, Howard Y. Chang, Asifa Akhtar.

Mol Cell, 51(2), 156-73, 2013.

DOI BIB

Salimabromide: Unexpected Chemistry from the Obligate Marine Myxobacterium Enhygromxya salina

Stephan Felder, Sandra Dreisigacker, Stefan Kehraus, Edith Neu, Gabriele Bierbaum, Patrick R. Wright, Dirk Menche, Till F. Schaberle, Gabriele M. Konig.

Chemistry, 19(28), 9319-24, 2013.

DOI BIB

StreptomeDB: a resource for natural compounds isolated from Streptomyces species

X. Lucas, C. Senger, A. Erxleben, B. A. Gruning, K. Doring, J. Mosch, S. Flemming, S. Gunther.

Nucleic Acids Research, 41(D1), D1130-D1136, 2013.

DOI BIB

Draft Genome Sequence of Streptomyces viridochromogenes Strain Tü57, Producer of Avilamycin

Björn A. Grüning, Anika Erxleben, Anna Hähnlein, Stefan Günther.

Genome Announcements, 1(3), e00384-13, 2013.

DOI BIB

Characterization and Phylogenetic Analysis of the Mitochondrial Genome of Glarea lozoyensis Indicates High Diversity within the Order Helotiales

Loubna Youssar, Björn Andreas Grüning, Stefan Günther, Wolfgang Hüttel.

PLoS ONE, 8(9), e74792, 2013.

DOI BIB

Galaxy tools and workflows for sequence analysis with applications in molecular plant pathology

Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz, Leighton Pritchard.

PeerJ, 1, e167, 2013.

DOI BIB

Impact of the Energy Model on the Complexity of RNA Folding with Pseudoknots

Saad Sheikh, Rolf Backofen, Yann Ponty.

Combinatorial Pattern Matching - 23rd Annual Symposium, CPM 2012, Helsinki, Finland, July 3-5, 2012. Proceedings, 321--333, 2012.

DOI BIB

LocARNA-P: Accurate boundary prediction and improved detection of structural RNAs

Sebastian Will, Tejal Joshi, Ivo L. Hofacker, Peter F. Stadler, Rolf Backofen.

RNA, 18(5), 900-14, 2012.

DOI BIB

Structure-based Whole Genome Realignment Reveals Many Novel Non-coding RNAs

Sebastian Will, Michael Yu, Bonnie Berger.

Proceedings of the 16th International Conference on Research in Computational Molecular Biology (RECOMB 2012), 7262, 341, 2012.

DOI BIB

Computational analysis of noncoding RNAs

Stefan Washietl, Sebastian Will, David A. Hendrix, Loyal A. Goff, John L. Rinn, Bonnie Berger, Manolis Kellis.

Wiley Interdiscip Rev RNA, 3(6), 759-78, 2012.

DOI BIB

CARNA - alignment of RNA structure ensembles

Dragos A. Sorescu, Mathias Möhl, Martin Mann, Rolf Backofen, Sebastian Will.

Nucleic Acids Res, 40(W1), W49-W53, 2012.

DOI BIB

Exact Pattern Matching for RNA Structure Ensembles

Christina Schmiedl, Mathias Möhl, Steffen Heyne, Mika Amit, Gad M. Landau, Sebastian Will, Rolf Backofen.

Proceedings of the 16th International Conference on Research in Computational Molecular Biology (RECOMB 2012), 7262, 245-260, 2012.

DOI BIB

Characterization of CRISPR RNA processing in Clostridium thermocellum and Methanococcus maripaludis

Hagen Richter, Judith Zoephel, Jeanette Schermuly, Daniel Maticzka, Rolf Backofen, Lennart Randau.

NAR, 40(19), 9887-96, 2012.

DOI BIB

Accessibility and conservation: General features of bacterial small RNA-mRNA interactions?

Andreas S. Richter, Rolf Backofen.

RNA Biol, 9(7), 954-65, 2012.

DOI BIB

MicroRNAs in Cancer Translational Research: The Microcosm of Cancer Diagnosis, Prognosis and Therapy

Dominic Rose.

Frontiers in Genetics, 3(42), 2012.

DOI BIB

The SH2-domain of SHIP1 interacts with the SHIP1 C-terminus: Impact on SHIP1/Ig-alpha interaction

Oindrilla Mukherjee, Lars Weingarten, Inken Padberg, Catrin Pracht, Rileen Sinha, Thomas Hochdorfer, Stephan Kuppig, Rolf Backofen, Michael Reth, Michael Huber.

Biochim Biophys Acta, 1823(2), 206-14, 2012.

DOI BIB

Navigating the unexplored seascape of pre-miRNA candidates in single-genome approaches

Nuno D. Mendes, Steffen Heyne, Ana T. Freitas, Marie-France Sagot, Rolf Backofen.

Bioinformatics, 28(23), 3034-41, 2012.

DOI BIB

Navigating the unexplored seascape of pre-miRNA candidates in single-genome approaches

Nuno D. Mendes, Steffen Heyne, Ana T. Freitas, Marie-France Sagot, Rolf Backofen.

Bioinformatics, 2012.

DOI BIB

Atom Mapping with Constraint Programming

Martin Mann, Heinz Ekker, Peter F. Stadler, Christoph Flamm.

Proceedings of the Workshop on Constraint Based Methods for Bioinformatics (WCB 2012), 23-29, 2012.

Link BIB

Producing high-accuracy lattice models from protein atomic co-ordinates including side chains

Martin Mann, Rhodri Saunders, Cameron Smith, Rolf Backofen, Charlotte M. Deane.

Advances in Bioinformatics, 2012(Article ID 148045), 6, 2012.

DOI BIB

Global or local? Predicting secondary structure and accessibility in mRNAs

Sita J. Lange, Daniel Maticzka, Mathias Möhl, Joshua N. Gagnon, Chris M. Brown, Rolf Backofen.

NAR, 40(12), 5215-26, 2012.

DOI BIB

Antioxidant activity of Hawaiian marine algae

Dovi Kelman, Ellen Kromkowski Posner, Karla J. McDermid, Nicole K. Tabandera, Patrick R. Wright, Anthony D. Wright.

Mar Drugs, 10(2), 403-16, 2012.

DOI BIB

An archaeal sRNA targeting cis- and trans-encoded mRNAs via two distinct domains

Dominik Jäger, Sandy R. Pernitzsch, Andreas S. Richter, Rolf Backofen, Cynthia M. Sharma, Ruth A. Schmitz.

NAR, 40(21), 10964-79, 2012.

DOI BIB

Abstract folding space analysis based on helices

Jiabin Huang, Rolf Backofen, Björn Voss.

RNA, 18(12), 2135-47, 2012.

DOI BIB

GraphClust: alignment-free structural clustering of local RNA secondary structures

Steffen Heyne, Fabrizio Costa, Dominic Rose, Rolf Backofen.

Bioinformatics, 28(12), i224-i232, 2012.

DOI BIB

Microstructure Alignment of Wood Density Profiles: an Approach to Equalize Radial Differences in Growth Rate

Bela Bender, Martin Mann, Rolf Backofen, Heinrich Spiecker.

Trees - Structure and Function, 26(4), 1267-1274, 2012.

DOI BIB

Local Exact Pattern Matching for Non-fixed RNA Structures

Mika Amit, Rolf Backofen, Steffen Heyne, Gad M. Landau, Mathias Möhl, Christina Schmiedl, Sebastian Will.

Proceedings of the 23th Annual Symposium on Combinatorial Pattern Matching (CPM 2012), 7354, 306-320, 2012.

DOI BIB

Small-molecule conversion of toxic oligomers to nontoxic β-sheet–rich amyloid fibrils

Jan Bieschke, Martin Herbst, Thomas Wiglenda, Ralf P Friedrich, Annett Boeddrich, Franziska Schiele, Daniela Kleckers, Juan Miguel Lopez del Amo, Björn A Grüning, Qinwen Wang, Michael R Schmidt, Rudi Lurz, Roger Anwyl, Sigrid Schnoegl, Marcus Fändrich, Ronald F Frank, Bernd Reif, Stefan Günther, Dominic M Walsh, Erich E Wanker.

Nature Chemical Biology, 8(1), 93-101, 2012.

DOI BIB

Mining and evaluation of molecular relationships in literature

Christian Senger, Björn A. Grüning, Anika Erxleben, Kersten Döring, Hitesh Patel, Stephan Flemming, Irmgard Merfort, Stefan Günther.

Bioinformatics, 28(5), 709-714, 2012.

DOI BIB

Genome Sequence of the Fungus Glarea lozoyensis: the First Genome Sequence of a Species from the Helotiaceae Family

Loubna Youssar, Björn Andreas Grüning, Anika Erxleben, Stefan Günther, Wolfgang Hüttel.

Eukaryotic Cell, 11(2), 250-250, 2012.

DOI BIB

Lattice model refinement of protein structures

Martin Mann, Alessandro Dal Palù.

WCB10. Workshop on Constraint Based Methods for Bioinformatics, 4, 67-74, 2012.

DOI BIB

Fast RNA Structure Alignment for Crossing Input Structures

Rolf Backofen, Gad M. Landau, Mathias Möhl, Dekel Tsur, Oren Weimann.

Journal of Discrete Algorithms, 9(1), 2-11, 2011.

DOI BIB

Sparse RNA folding: Time and space efficient algorithms

Rolf Backofen, Dekel Tsur, Shay Zakov, Michal Ziv-Ukelson.

J. Discrete Algorithms, 9(1), 12-31, 2011.

DOI BIB

Bioinformatics of Bacterial sRNAs and Their Targets

Rolf Backofen.

Regulatory RNAs in Prokaryotes, 221-239, 2011.

Link BIB

The small RNA PhrS stimulates synthesis of the Pseudomonas aeruginosa quinolone signal

Elisabeth Sonnleitner, Nicolas Gonzalez, Theresa Sorger-Domenigg, Stephan Heeb, Andreas S. Richter, Rolf Backofen, Paul Williams, Alexander Huttenhofer, Dieter Haas, Udo Blasi.

Mol Microbiol, 80(4), 868-85, 2011.

DOI BIB

PETcofold: predicting conserved interactions and structures of two multiple alignments of RNA sequences

Stefan E. Seemann, Andreas S. Richter, Tanja Gesell, Rolf Backofen, Jan Gorodkin.

Bioinformatics, 27(2), 211-219, 2011.

DOI BIB

The PETfold and PETcofold web servers for intra- and intermolecular structures of multiple RNA sequences

S. E. Seemann, P. Menzel, R. Backofen, J. Gorodkin.

NAR, 39, W107-11, 2011.

DOI BIB

Signatures of Co-translational Folding

Rhodri Saunders, Martin Mann, Charlotte Deane.

Biotechnology Journal, Special issue: Protein folding in vivo, 6(6), 742-751, 2011.

DOI BIB

Molecular evolution of the non-coding eosinophil granule ontogeny transcript

Dominic Rose, Peter F. Stadler.

Front Genet, 2, 69, 2011.

DOI BIB

Computational discovery of human coding and non-coding transcripts with conserved splice sites

Dominic Rose, Michael Hiller, Katharina Schutt, Jorg Hackermuller, Rolf Backofen, Peter F. Stadler.

Bioinformatics, 27(14), 1894-900, 2011.

DOI BIB

Molecular Evolution of the non-coding Eosinophil Granule Ontogeny Transcript

Dominic Rose, Peter F. Stadler.

Frontiers in Genetics, 2(0), 2011.

DOI BIB

Computational discovery of human coding and non-coding transcripts with conserved splice sites

Dominic Rose, Michael Hiller, Katharina Schutt, Jörg Hackermüller, Rolf Backofen, Peter F. Stadler.

Bioinformatics, 2011.

DOI BIB

Accessibility and conservation in bacterial small RNA-mRNA interactions and implications for genome-wide target predictions

Andreas S. Richter, Rolf Backofen.

Proceedings of the German Conference on Bioinformatics (GCB 2011), 2011.

BIB

Sparsification in Algebraic Dynamic Programming

Mathias Möhl, Christina Schmiedl, Shay Zakov.

Proceedings of the German Conference on Bioinformatics (GCB 2011), 2011.

Link BIB

Structator: fast index-based search for RNA sequence-structure patterns

Fernando Meyer, Stefan Kurtz, Rolf Backofen, Sebastian Will, Michael Beckstette.

BMC Bioinformatics, 12(1), 214, 2011.

DOI BIB

LatFit - Producing high accuracy lattice models from protein atomic co-ordinates including side chains

Martin Mann, Rhodri Saunders, Cameron Smith, Rolf Backofen, Charlotte Deane.

Adv Bioinformatics, 9, 2011.

DOI BIB

Efficient exploration of discrete energy landscapes

Martin Mann, Konstantin Klemm.

Phys. Rev. E, 83(1), online, 2011.

DOI BIB

CRISPR revisited: structure prediction of CRISPR repeats

Sita Lange, Omer S. Alkhnbashi, Dominic Rose, Ingeborg Scholz, Wolfgang R. Hess, Rolf Backofen.

Poster Proceedings of the 62th Mosbach Colloquium, 2011.

BIB

Identification of SH2-peptide interactions using machine learning approaches

Kousik Kundu, Fabrizio Costa, Michael Reth, Michael Huber, Rolf Backofen.

Poster Proceedings of ISMB'11, 2011.

BIB

Data fusion of Fourier transform infrared spectra and powder X-ray diffraction patterns for pharmaceutical mixtures

Rahul V. Haware, Patrick R. Wright, Kenneth R. Morris, Mazen L. Hamad.

J Pharm Biomed Anal, 56(5), 944-9, 2011.

DOI BIB

Compounds In Literature (CIL): screening for compounds and relatives in PubMed

Björn A. Grüning, Christian Senger, Anika Erxleben, Stephan Flemming, Stefan Günther.

Bioinformatics, 27(9), 1341-1342, 2011.

DOI BIB

Cyclic stretch increases splicing noise rate in cultured human fibroblasts

Michael Uhl, Kevin Mellert, Britta Striegl, Martin Deibler, Markus Lamla, Joachim P Spatz, Ralf Kemkemer, Dieter Kaufmann.

BMC Research Notes, 4(1), 470, 2011.

DOI BIB

Genome Sequence of Streptomyces sp. Strain Tü6071

Anika Erxleben, Julia Wunsch-Palasis, Björn A. Grüning, Marta Luzhetska, Andreas Bechthold, Stefan Günther.

Journal of Bacteriology, 193(16), 4278-4279, 2011.

DOI BIB

Animal snoRNAs and scaRNAs with exceptional structures

Manja Marz, Andreas R. Gruber, Christian Höner zu Siederdissen, Fabian Amman, Stefan Badelt, Sebastian Bartschat, Stephan H. Bernhart, Wolfgang Beyer, Stephanie Kehr, Ronny Lorenz, Andrea Tanzer, Dilmurat Yusuf, Hakim Tafer, Ivo L. Hofacker, Peter F. Stadler.

RNA Biology, 8(6), 938-946, 2011.

DOI BIB

Aberrant Single Exon Skipping is not Altered by Age in Exons of NF1, RABAC1, AATF or PCGF2 in Human Blood Cells and Fibroblasts

Kevin Mellert, Michael Uhl, Josef Högel, Markus Lamla, Ralf Kemkemer, Dieter Kaufmann.

Genes, 2(3), 562-577, 2011.

DOI BIB

Computational Methods for Lattice Protein Models

Martin Mann.

2011.

DOI BIB

Alignnment of RNA with Structures of Unlimited Complexity

Alessandro Dal Palu, Mathias Möhl, Sebastian Will.

Proceedings of the Workshop on Constraint Based Methods for Bioinformatics (WCB 2010), 7, 2010.

Link BIB

A Propagator for Maximum Weight String Alignment with Arbitrary Pairwise Dependencies

Alessandro Dal Palu, Mathias Möhl, Sebastian Will.

Proceedings of the 16th International Conference on Principles and Practice of Constraint Programming (CP-2010), 8, 2010.

Link BIB

Sparsification of RNA Structure Prediction Including Pseudoknots

Mathias Möhl, Raheleh Salari, Sebastian Will, Rolf Backofen, S. Cenk Sahinalp.

Proc. of the 10th Workshop on Algorithms in Bioinformatics (WABI), 6293, 40-51, 2010.

DOI BIB

Identifikation von Targetmolekülen kleiner regulatorischer RNAs

Rolf Backofen.

Laborwelt, 11(1), 29-30, 2010.

BIB

Partitioning biological data with transitivity clustering

Tobias Wittkop, Dorothea Emig, Sita Lange, Sven Rahmann, Mario Albrecht, John H. Morris, Sebastian Bocker, Jens Stoye, Jan Baumbach.

Nat Methods, 7(6), 419-20, 2010.

DOI BIB

Freiburg RNA Tools: a web server integrating IntaRNA, ExpaRNA and LocARNA

Cameron Smith, Steffen Heyne, Andreas S. Richter, Sebastian Will, Rolf Backofen.

NAR, 38 Suppl, W373-7, 2010.

DOI BIB

Identification and characterization of NAGNAG alternative splicing in the moss Physcomitrella patens

Rileen Sinha, Andreas D. Zimmer, Kathrin Bolte, Daniel Lang, Ralf Reski, Matthias Platzer, Stefan A. Rensing, Rolf Backofen.

BMC Plant Biol, 10, 76, 2010.

DOI BIB

TassDB2 - A comprehensive database of subtle alternative splicing events

Rileen Sinha, Thorsten Lenser, Niels Jahn, Ulrike Gausmann, Swetlana Friedel, Karol Szafranski, Klaus Huse, Philip Rosenstiel, Jochen Hampe, Stefan Schuster, Michael Hiller, Rolf Backofen, Matthias Platzer.

BMC Bioinformatics, 11, 216, 2010.

DOI BIB

Hierarchical folding of multiple sequence alignments for the prediction of structures and RNA-RNA interactions

Stefan E. Seemann, Andreas S. Richter, Jan Gorodkin, Rolf Backofen.

Algorithms Mol Biol, 5, 22, 2010.

DOI BIB

The small RNA Aar in Acinetobacter baylyi: a putative regulator of amino acid metabolism

Dominik Schilling, Sven Findeiss, Andreas S. Richter, Jennifer A. Taylor, Ulrike Gerischer.

Arch Microbiol, 192(9), 691-702, 2010.

DOI BIB

Time and Space Efficient RNA-RNA Interaction Prediction via Sparse Folding

Raheleh Salari, Mathias Möhl, Sebastian Will, S. Cenk Sahinalp, Rolf Backofen.

Proc. of RECOMB 2010, 6044, 473-490, 2010.

DOI BIB

Fast prediction of RNA-RNA interaction

Raheleh Salari, Rolf Backofen, S. Cenk Sahinalp.

Algorithms Mol Biol, 5, 5, 2010.

DOI BIB

Identification of functional elements and regulatory circuits by Drosophila modENCODE

Sushmita Roy, Jason Ernst, Peter V. Kharchenko, Pouya Kheradpour, Nicolas Negre, Matthew L. Eaton, Jane M. Landolin, Christopher A. Bristow, Lijia Ma, Michael F. Lin, Stefan Washietl, Bradley I. Arshinoff, Ferhat Ay, Patrick E. Meyer, Nicolas Robine, Nicole L. Washington, Luisa Di Stefano, Eugene Berezikov, Christopher D. Brown, Rogerio Candeias, Joseph W. Carlson, Adrian Carr, Irwin Jungreis, Daniel Marbach, Rachel Sealfon, Michael Y. Tolstorukov, Sebastian Will, Artyom A. Alekseyenko, Carlo Artieri, Benjamin W. Booth, Angela N. Brooks, Qi Dai, Carrie A. Davis, Michael O. Duff, Xin Feng, Andrey A. Gorchakov, Tingting Gu, Jorja G. Henikoff, Philipp Kapranov, Renhua Li, Heather K. MacAlpine, John Malone, Aki Minoda, Jared Nordman, Katsutomo Okamura, Marc Perry, Sara K. Powell, Nicole C. Riddle, Akiko Sakai, Anastasia Samsonova, Jeremy E. Sandler, Yuri B. Schwartz, Noa Sher, Rebecca Spokony, David Sturgill, Marijke van Baren, Kenneth H. Wan, Li Yang, Charles Yu, Elise Feingold, Peter Good, Mark Guyer, Rebecca Lowdon, Kami Ahmad, Justen Andrews, Bonnie Berger, Steven E. Brenner, Michael R. Brent, Lucy Cherbas, Sarah C. R. Elgin, Thomas R. Gingeras, Robert Grossman, Roger A. Hoskins, Thomas C. Kaufman, William Kent, Mitzi I. Kuroda, Terry Orr-Weaver, Norbert Perrimon, Vincenzo Pirrotta, James W. Posakony, Bing Ren, Steven Russell, Peter Cherbas, Brenton R. Graveley, Suzanna Lewis, Gos Micklem, Brian Oliver, Peter J. Park, Susan E. Celniker, Steven Henikoff, Gary H. Karpen, Eric C. Lai, David M. MacAlpine, Lincoln D. Stein, Kevin P. White, Manolis Kellis.

Science, 330(6012), 1787-97, 2010.

DOI BIB

Seed-based IntaRNA prediction combined with GFP-reporter system identifies mRNA targets of the small RNA Yfr1

Andreas S. Richter, Christian Schleberger, Rolf Backofen, Claudia Steglich.

Bioinformatics, 26(1), 1-5, 2010.

DOI BIB

Lifting prediction to alignment of RNA pseudoknots

Mathias Möhl, Sebastian Will, Rolf Backofen.

JCB, 17(3), 429-42, 2010.

DOI BIB

Sparsification of RNA structure prediction including pseudoknots

Mathias Möhl, Raheleh Salari, Sebastian Will, Rolf Backofen, S. Cenk Sahinalp.

Algorithms Mol Biol, 5(1), 39, 2010.

DOI BIB

Lattice model refinement of protein structures

Martin Mann, Alessandro Dal Palu.

Proceedings of the Workshop on Constraint Based Methods for Bioinformatics (WCB 2010), 7, 2010.

DOI BIB

High accuracy on-lattice side chain models of PDB protein structures

Martin Mann, Rhodri Saunders, Cameron Smith, Rolf Backofen, Charlotte Deane.

Poster Proceedings of ISMB'10, 2010.

BIB

Machine learning approaches for prediction of SH2-peptide interactions

Kousik Kundu, Rileen Sinha, Michael Reth, Michael Huber, Rolf Backofen.

Poster Proceedings of ISMB'10, 2010.

BIB

In silico modelling of human lipoprotein metabolism

Martin Jansen, Karl Winkler, Gerhard Puetz, Peter Pfaffelhuber, Martin Mann.

Poster Proceedings of SBMC'10, (conference for system biology in mammalian cells), 2010.

BIB

Evolution of Metabolic Networks: A Computational Framework

Christoph Flamm, Alexander Ullrich, Heinz Ekker, Martin Mann, Daniel Hoegerl, Markus Rohrschneider, Sebastian Sauer, Gerik Scheuermann, Konstantin Klemm, Ivo L. Hofacker, Peter F. Stadler.

Journal of Systems Chemistry, 1(1), 4, 2010.

DOI BIB

Shape-based barrier estimation for RNAs

Sergiy Bogomolov, Martin Mann, Björn Voss, Andreas Podelski, Rolf Backofen.

In Proceedings of German Conference on Bioinformatics GCB'10, 173, 42-51, 2010.

Link BIB

Computational prediction of sRNAs and their targets in bacteria

Rolf Backofen, Wolfgang R. Hess.

RNA Biol, 7(1), 33-42, 2010.

DOI BIB

COMPUTATIONAL STUDIES OF NON-CODING RNAS - Session Introduction

R. Backofen, H. Chitsaz, I. Hofacker, S. C. Sahinalp, P. F. Stadler.

PSB10, 15, 54-56, 2010.

DOI BIB

Bcheck: a wrapper tool for detecting RNase P RNA genes

Dilmurat Yusuf, Manja Marz, Peter F Stadler, Ivo L Hofacker.

BMC Genomics, 11(1), 432, 2010.

DOI BIB

Fast prediction of RNA-RNA Interaction

Raheleh Salari, Rolf Backofen, S. Cenk Sahinalp.

Proc. of the 9th Workshop on Algorithms in Bioinformatics (WABI), 5724, 261-272, 2009.

DOI BIB

Fast Feature Subset Selection in Biological Sequence Analysis

Rainer Pudimat, Rolf Backofen, Ernst-Günter Schukat-Talamazzini.

International Journal of Pattern Recognition and Artificial Intelligence, 23(2), 191 -- 207, 2009.

DOI BIB

biRNA: Fast RNA-RNA Binding Sites Prediction

Hamidreza Chitsaz, Rolf Backofen, S. Cenk Sahinalp.

Proc. of the 9th Workshop on Algorithms in Bioinformatics (WABI), 5724, 25-36, 2009.

DOI BIB

Sparse RNA Folding: Time and Space Efficient Algorithms

Rolf Backofen, Dekel Tsur, Shay Zakov, Michal Ziv-Ukelson.

Proc. 20th Symp. Combinatorial Pattern Matching, 5577, 249-262, 2009.

DOI BIB

Fast RNA Structure Alignment for Crossing Input Structures

Rolf Backofen, Gad M. Landau, Mathias Möhl, Dekel Tsur, Oren Weimann.

Proc. 20th Symp. Combinatorial Pattern Matching, 5577, 236-248, 2009.

DOI BIB

Simultaneous Alignment and Folding of Protein Sequences

Jérôme Waldispühl, Charles W. O'Donnell, Sebastian Will, Srinivas Devadas, Rolf Backofen, Bonnie Berger.

RECOMB09, 5541, 339--355, 2009.

DOI BIB

Protein Folding Simulation by Two-Stage Optimization

Abu Dayem Ullah, Leonidas Kapsokalivas, Martin Mann, Kathleen Steinhöfel.

Proc. of ISICA'09, 51, 138-145, 2009.

DOI BIB

Accurate prediction of NAGNAG alternative splicing

Rileen Sinha, Swetlana Nikolajewa, Karol Szafranski, Michael Hiller, Niels Jahn, Klaus Huse, Matthias Platzer, Rolf Backofen.

NAR, 37(11), 3569-79, 2009.

DOI BIB

Lifting Prediction to Alignment of RNA Pseudoknots

Mathias Möhl, Sebastian Will, Rolf Backofen.

RECOMB09, 5541, 285--301, 2009.

DOI BIB

CPSP-web-tools: a server for 3D lattice protein studies

Martin Mann, Cameron Smith, Mohamad Rabbath, Marlien Edwards, Sebastian Will, Rolf Backofen.

Bioinformatics, 25(5), 676-7, 2009.

DOI BIB

Constraint-based Local Move Definitions for Lattice Protein Models Including Side Chains

Martin Mann, Mohamed Abou Hamra, Kathleen Steinhöfel, Rolf Backofen.

Proceedings of the Fifth Workshop on Constraint Based Methods for Bioinformatics (WCB09), 2009.

DOI BIB

Equivalence Classes of Optimal Structures in HP~Protein Models Including Side Chains

Martin Mann, Rolf Backofen, Sebastian Will.

Proceedings of the Fifth Workshop on Constraint Based Methods for Bioinformatics (WCB09), 2009.

Link BIB

Statement of Ongoing Work:Extending Boolean Satisfiability Techniques for Haplotype Inference by Pure Parsimony

Eric I. Hsu, Sheila A. McIlraith.

WCB09, 2009.

BIB

Conserved introns reveal novel transcripts in Drosophila melanogaster

Michael Hiller, Sven Findeiss, Sandro Lein, Manja Marz, Claudia Nickel, Dominic Rose, Christine Schulz, Rolf Backofen, Sonja J. Prohaska, Gunter Reuter, Peter F. Stadler.

Genome Res, 19(7), 1289-300, 2009.

DOI BIB

Lightweight Comparison of RNAs Based on Exact Sequence-Structure Matches

Steffen Heyne, Sebastian Will, Michael Beckstette, Rolf Backofen.

Bioinformatics, 25(16), 2095-2102, 2009.

DOI BIB

Non-coding RNA annotation of the genome of Trichoplax adhaerens

Jana Hertel, Danielle de Jong, Manja Marz, Dominic Rose, Hakim Tafer, Andrea Tanzer, Bernd Schierwater, Peter F. Stadler.

NAR, 37(5), 1602-15, 2009.

DOI BIB

Haplotype Inference Combining Pedigreesand Unrelated Individuals

Ana Graca, Ines Lynce, Joao Marques-Silva, Arlindo L. Oliveira.

WCB09, 2009.

BIB

Homology-based annotation of non-coding RNAs in the genomes of Schistosoma mansoni and Schistosoma japonicum

Claudia S. Copeland, Manja Marz, Dominic Rose, Jana Hertel, Paul J. Brindley, Clara Bermudez Santana, Stephanie Kehr, Camille Stephan-Otto Attolini, Peter F. Stadler.

BMC Genomics, 10, 464, 2009.

DOI BIB

A Constraint Model for Constrained Hidden Markov Models: a first Biological Application

Henning Christiansen, Christian Theil Have, Ole Torp Lassen, Matthieu Petit.

WCB09, 2009.

Link BIB

A partition function algorithm for interacting nucleic acid strands

Hamidreza Chitsaz, Raheleh Salari, S. Cenk Sahinalp, Rolf Backofen.

Bioinformatics, 25(12), i365-73, 2009.

DOI BIB

Constraint Based Languages for Biological Reactions

Stefano Bistarelli, Marco Bottalico.

WCB09, 2009.

Link BIB

Tagsnp selection using Weighted CSP and Russian Doll Search with Tree Decomposition

D. Allouche, S. de Givry, M. Sanchez, T. Schiex.

WCB09, 2009.

Link BIB

Qupe--a Rich Internet Application to take a step forward in the analysis of mass spectrometry-based quantitative proteomics experiments

S. P. Albaum, H. Neuweger, B. Franzel, S. Lange, D. Mertens, C. Trotschel, D. Wolters, J. Kalinowski, T. W. Nattkemper, A. Goesmann.

Bioinformatics, 25(23), 3128-3134, 2009.

DOI BIB

RHYTHM--a server to predict the orientation of transmembrane helices in channels and membrane-coils

A. Rose, S. Lorenzen, A. Goede, B. Gruening, P. W. Hildebrand.

Nucleic Acids Research, 37(Web Server), W575-W580, 2009.

DOI BIB

SuperLooper--a prediction server for the modeling of loops in globular and membrane proteins

P. W. Hildebrand, A. Goede, R. A. Bauer, B. Gruening, J. Ismer, E. Michalsky, R. Preissner.

Nucleic Acids Research, 37(Web Server), W571-W574, 2009.

DOI BIB

SuperToxic: a comprehensive database of toxic compounds

U. Schmidt, S. Struck, B. Gruening, J. Hossbach, I. S. Jaeger, R. Parol, U. Lindequist, E. Teuscher, R. Preissner.

Nucleic Acids Research, 37(Database), D295-D299, 2009.

DOI BIB

Voronoia: analyzing packing in protein structures

K. Rother, P. W. Hildebrand, A. Goede, B. Gruening, R. Preissner.

Nucleic Acids Research, 37(Database), D393-D395, 2009.

DOI BIB

SuperScent--a database of flavors and scents

M. Dunkel, U. Schmidt, S. Struck, L. Berger, B. Gruening, J. Hossbach, I. S. Jaeger, U. Effmert, B. Piechulla, R. Eriksson, J. Knudsen, R. Preissner.

Nucleic Acids Research, 37(Database), D291-D294, 2009.

DOI BIB

Techniques de Décomposition pour l'Isomorphisme de Sous-Graphe

Stephane Zampelli, Martin Mann, Yves Deville, R. Backofen.

Proc. of the 4th Journées Francophones de Programmation par Contraintes (JFPC'08), 2008.

Link BIB

Efficient Sequence Alignment with Side-Constraints by Cluster Tree Elimination

Sebastian Will, Anke Busch, Rolf Backofen.

Constraints Journal, 13(1), 110-129, 2008.

DOI BIB

Improved identification of conserved cassette exons using Bayesian networks

R. Sinha, M. Hiller, R. Pudimat, U. Gausmann, M. Platzer, R. Backofen.

BMC Bioinformatics, 9(1), 477, 2008.

DOI BIB

Unifying evolutionary and thermodynamic information for RNA folding of multiple alignments

Stefan E. Seemann, Jan Gorodkin, Rolf Backofen.

NAR, 36(20), 6355-62, 2008.

DOI BIB

Alternative splicing at NAGNAG acceptors in Arabidopsis thaliana SR and SR-related protein-coding genes

Stefanie Schindler, Karol Szafranski, Michael Hiller, Gul Shad Ali, Saiprasad G. Palusa, Rolf Backofen, Matthias Platzer, Anireddy S. N. Reddy.

BMC Genomics, 9, 159, 2008.

DOI BIB

Duplicated RNA genes in teleost fish genomes

Dominic Rose, Julian Joris, Jörg Hackermüller, Kristin Reiche, Qiang Li, Peter F. Stadler.

J Bioinform Comput Biol, 6(6), 1157-75, 2008.

DOI BIB

NcDNAlign: plausible multiple alignments of non-protein-coding genomic sequences

Dominic Rose, Jana Hertel, Kristin Reiche, Peter F. Stadler, Jörg Hackermüller.

Genomics, 92(1), 65-74, 2008.

DOI BIB

A Sampling Approach for the Exploration of Biopolymer Energy Landscapes

Andreas S. Richter, Sebastian Will, Rolf Backofen.

Proceedings of the European Conference on Metallobiolomics (HMI Berlin, Germany, 2007), 27-38, 2008.

BIB

Structure Local Multiple Alignment of RNA

Otto Wolfgang, Will Sebastian, Backofen Rolf.

Proceedings of German Conference on Bioinformatics (GCB'2008), P-136, 178-188, 2008.

Link BIB

Fixed Parameter Tractable Alignment of RNA Structures Including Arbitrary Pseudoknots

Mathias Möhl, Sebastian Will, Rolf Backofen.

Proceedings of the 19th Annual Symposium on Combinatorial Pattern Matching (CPM 2008), 69-81, 2008.

Link BIB

Classifying protein-like sequences in arbitrary lattice protein models using LatPack

Martin Mann, Daniel Maticzka, Rhodri Saunders, Rolf Backofen.

HFSP Journal, 2(6), 396-404, 2008.

DOI BIB

CPSP-tools - Exact and Complete Algorithms for High-throughput 3D Lattice Protein Studies

Martin Mann, Sebastian Will, Rolf Backofen.

BMC Bioinformatics, 9, 230, 2008.

DOI BIB

Genetic Variants of the Copy Number Polymorphic beta-Defensin Locus Are Associated with Sporadic Prostate Cancer

K. Huse, S. Taudien, M. Groth, P. Rosenstiel, K. Szafranski, M. Hiller, J. Hampe, K. Junker, J. Schubert, S. Schreiber, G. Birkenmeier, M. Krawczak, M. Platzer.

Tumour Biol, 29(2), 83-92, 2008.

DOI BIB

Widespread and subtle: alternative splicing at short-distance tandem sites

Michael Hiller, Matthias Platzer.

TIG, 24(5), 246-55, 2008.

DOI BIB

Selection against tandem splice sites affecting structured protein regions

Michael Hiller, Karol Szafranski, Klaus Huse, Rolf Backofen, Matthias Platzer.

BMC Evolutionary Biology, 8, 89, 2008.

DOI BIB

Assessing the fraction of short-distance tandem splice sites under purifying selection

Michael Hiller, Karol Szafranski, Rileen Sinha, Klaus Huse, Swetlana Nikolajewa, Philip Rosenstiel, Stefan Schreiber, Rolf Backofen, Matthias Platzer.

RNA, 14, 616-29, 2008.

DOI BIB

Lightweight comparison of RNAs based on exact sequence-structure matches

Steffen Heyne, Sebastian Will, Michael Beckstette, Rolf Backofen.

Proceedings of the German Conference on Bioinformatics (GCB'2008), P-136, 189-198, 2008.

BIB

IntaRNA: efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions

Anke Busch, Andreas S. Richter, Rolf Backofen.

Bioinformatics, 24(24), 2849-56, 2008.

DOI BIB

Variations on RNA folding and alignment: lessons from Benasque

Athanasius F. Bompfünewerer, Rolf Backofen, Stephan H. Bernhart, Jana Hertel, Ivo L. Hofacker, Peter F. Stadler, Sebastian Will.

Journal of Mathematical Biology, 56(1-2), 129-144, 2008.

DOI BIB

RNAalifold: improved consensus structure prediction for RNA alignments

Stephan H. Bernhart, Ivo L. Hofacker, Sebastian Will, Andreas R. Gruber, Peter F. Stadler.

BMC Bioinformatics, 9, 474, 2008.

DOI BIB

Constraint-based Methods for Bioinformatics

Alessandro Dal Palù, Agostino Dovier, François Fages, Sebastian Will.

Trends in Constraint Programming, 129--150, 2007.

BIB

The string-generative capacity of regular dependency languages

Marco Kuhlmann, Mathias Möhl.

Twelfth Conference on Formal Grammar (FG), 2007.

BIB

Mildly Context-Sensitive Dependency Languages

Marco Kuhlmann, Mathias Möhl.

45th Annual Meeting of the Association for Computational Linguistics (ACL), 2007.

Link BIB

BioBayesNet: a web server for feature extraction and Bayesian network modeling of biological sequence data

Swetlana Nikolajewa, Rainer Pudimat, Michael Hiller, Matthias Platzer, Rolf Backofen.

NAR, 35(Web Server issue), W688-93, 2007.

DOI BIB

Inferring Non-Coding RNA Families and Classes by Means of Genome-Scale Structure-Based Clustering

Sebastian Will, Kristin Reiche, Ivo L. Hofacker, Peter F. Stadler, Rolf Backofen.

PLoS Comput Biol, 3(4), e65, 2007.

DOI BIB

Violating the splicing rules: TG dinucleotides function as alternative 3' splice sites in U2-dependent introns

K. Szafranski, S. Schindler, S. Taudien, M. Hiller, K. Huse, N. Jahn, S. Schreiber, R. Backofen, M. Platzer.

Genome Biol, 8(8), R154, 2007.

DOI BIB

A dynamic programming approach for finding common patterns in RNAs

Sven Siebert, Rolf Backofen.

JCB, 14(1), 33-44, 2007.

DOI BIB

Methods for multiple alignment and consensus structure prediction of RNAs implemented in MARNA

Sven Siebert, Rolf Backofen.

Methods Mol Biol, 395, 489-502, 2007.

DOI BIB

Computational RNomics of drosophilids

Dominic Rose, Jorg Hackermuller, Stefan Washietl, Kristin Reiche, Jana Hertel, Sven Findeiss, Peter F. Stadler, Sonja J. Prohaska.

BMC Genomics, 8, 406, 2007.

DOI BIB

GenColors: annotation and comparative genomics of prokaryotes made easy

Alessandro Romualdi, Marius Felder, Dominic Rose, Ulrike Gausmann, Markus Schilhabel, Gernot Glockner, Matthias Platzer, Jurgen Suhnel.

Methods Mol Biol, 395, 75-96, 2007.

Link BIB

The Energy Landscape Library - A Platform for Generic Algorithms

Martin Mann, Sebastian Will, Rolf Backofen.

BIRD'07 - 1st international Conference on Bioinformatics Research and Development, 217, 83-86, 2007.

BIB

The Energy Landscape Library - A Platform for Generic Algorithms

Martin Mann, Sebastian Will, Rolf Backofen.

BIRD'07 - 1st international Conference on Bioinformatics Research and Development, 217, 83-86, 2007.

BIB

HPdesign: Inverse Folding of Proteins

Martin Mann, Sebastian Will, Rolf Backofen.

ISMB/ECCB, 2007.

BIB

TassDB: a database of alternative tandem splice sites

Michael Hiller, Swetlana Nikolajewa, Klaus Huse, Karol Szafranski, Philip Rosenstiel, Stefan Schuster, Rolf Backofen, Matthias Platzer.

NAR, 35(Database issue), D188-92, 2007.

DOI BIB

Pre-mRNA Secondary Structures Influence Exon Recognition

Michael Hiller, Zhaiyi Zhang, Rolf Backofen, Stefan Stamm.

PLoS Genet, 3(11), e204, 2007.

DOI BIB

INFO-RNA--a server for fast inverse RNA folding satisfying sequence constraints

Anke Busch, Rolf Backofen.

NAR, 35(Web Server issue), W310-3, 2007.

DOI BIB

RNAs everywhere: genome-wide annotation of structured RNAs

Athanasius F. Bompfünewerer Consortium, Rolf Backofen, Stephan H. Bernhart, Christoph Flamm, Claudia Fried, Guido Fritzsch, Jörg Hackermüller, Jana Hertel, Ivo L. Hofacker, Kristin Missal, Axel Mosig, Sonja J. Prohaska, Dominic Rose, Peter F. Stadler, Andrea Tanzer, Stefan Washietl, Sebastian Will.

J Exp Zoolog B Mol Dev Evol, 308B(1), 1-25, 2007.

DOI BIB

IMS2 -- An integrated medical software system for early lung cancer detection using ion mobility spectrometry data of human breath

Jan Baumbach, Alexander Bunkowski, Sita Lange, Timm Oberwahrenbrock, Nils Kleinbölting, Sven Rahmann, Jörg Ingo Baumbach.

Journal of Integrative Bioinformatics, 4(3), 75, 2007.

DOI BIB

Fast Detection of Common Sequence Structure Patterns in RNAs

Rolf Backofen, Sven Siebert.

Journal of Discrete Algorithms, 5(2), 212-228, 2007.

DOI BIB

Locality and gaps in RNA comparison

Rolf Backofen, Shihyen Chen, Danny Hermelin, Gad M. Landau, Mikhail A. Roytberg, Oren Weimann, Kaizhong Zhang.

JCB, 14(8), 1074-87, 2007.

DOI BIB

Index-based algorithms for motif search and their integration in a system for differential genome analysis

M. Beckstette.

2007.

Link BIB

Extended cross-serial dependencies in Tree Adjoining Grammars

Marco Kuhlmann, Mathias Möhl.

Eighth International Workshop on Tree Adjoining Grammars and Related Formalisms (TAG+8), 2006.

Link BIB

Local Alignment of RNA Sequences with Arbitrary Scoring Schemes

Rolf Backofen, Danny Hermelin, Gad M. Landau, Oren Weimann.

CPM06, 4009, 246-257, 2006.

DOI BIB

A Bottom-up approach to Grid-Computing at a University: the Black-Forest-Grid Initiative

R. Backofen, H.-G. Borrmann, W. Deck, A. Dedner, L. De Raedt, K. Desch, M. Diesmann, M. Geier, A. Greiner, W. R. Hess, J. Honerkamp, St. Jamkowski, I. Krossing, A. W. Liehr, A. Karwath, R. Kloefkorn, R. Pesche, T. Potjans, M. C. Roettger, L. Schmiedt-Thieme, G. Schneider, B. Voss, B. Wiebelt, P. Wienemann, and V.-H. Winterer.

PIK, 29(2), 81-87, 2006.

DOI BIB

Bioinformatics and Constraints

Rolf Backofen, David Gilbert.

Handbook of Constraint Programming, 905-944, 2006.

DOI BIB

Exploring the lower part of discrete polymer model energy landscapes

Michael T. Wolfinger, Sebastian Will, Ivo L. Hofacker, Rolf Backofen, Peter F. Stadler.

Europhysics Letters, 74(4), 725-732, 2006.

DOI BIB

Counting Protein Structures by DFS with Dynamic Decomposition

Sebastian Will, Martin Mann.

Proc. of the Workshop on Constraint Based Methods for Bioinformatics. http://www.dimi.uniud.it/dovier/WCB06/WCB06_proceedings.pdf, 83-90, 2006.

Link BIB

Constrained Alignment Using Cluster Tree Elimination

Sebastian Will, Anke Busch, Rolf Backofen.

14th Annual International conference on Intelligent Systems for Molecular Biology (ISMB'06), 2006.

BIB

Sequencing errors or SNPs at splice-acceptor guanines in dbSNP?

Matthias Platzer, Michael Hiller, Karol Szafranski, Niels Jahn, Jochen Hampe, Stefan Schreiber, Rolf Backofen, Klaus Huse.

Nat Biotechnol, 24(9), 1068-70, 2006.

DOI BIB

Prediction of structured non-coding RNAs in the genomes of the nematodes Caenorhabditis elegans and Caenorhabditis briggsae

Kristin Missal, Xiaopeng Zhu, Dominic Rose, Wei Deng, Geir Skogerbo, Runsheng Chen, Peter F. Stadler.

J Exp Zool B Mol Dev Evol, 306(4), 379-92, 2006.

DOI BIB

Alternative Splicing at NAGNAG Acceptors: Simply Noise or Noise and More?

Michael Hiller, Karol Szafranski, Rolf Backofen, Matthias Platzer.

PLoS Genet, 2(11), e207, 2006.

DOI BIB

Using RNA secondary structures to guide sequence motif finding towards single-stranded regions

Michael Hiller, Rainer Pudimat, Anke Busch, Rolf Backofen.

NAR, 34(17), e117, 2006.

DOI BIB

Phylogenetically widespread alternative splicing at unusual GYNGYN donors

M. Hiller, K. Huse, K. Szafranskzi, P. Rosenstiel, S. Schreiber, R. Backofen, M. Platzer.

Genome Biol, 7(7), R65, 2006.

DOI BIB

Single-Nucleotide Polymorphisms in NAGNAG Acceptors Are Highly Predictive for Variations of Alternative Splicing

Michael Hiller, Klaus Huse, Karol Szafranski, Niels Jahn, Jochen Hampe, Stefan Schreiber, Rolf Backofen, Matthias Platzer.

Am J Hum Genet, 78(2), 291-302, 2006.

DOI BIB

INFO-RNA--a fast approach to inverse RNA folding

Anke Busch, Rolf Backofen.

Bioinformatics, 22(15), 1823-31, 2006.

DOI BIB

Fast index based algorithms and software for matching position specific scoring matrices

Michael Beckstette, Robert Homann, Robert Giegerich, Stefan Kurtz.

BMC Bioinformatics, 7, 389, 2006.

DOI BIB

A Constraint-Based Approach to Fast and Exact Structure Prediction in Three-Dimensional Protein Models

Rolf Backofen, Sebastian Will.

Journal of Constraints, 11(1), 5--30, 2006.

DOI BIB

A Posteriori Modelling of Sequence Motif Arrangements

Rolf Backofen, Rainer Pudimat.

GCB, 2005.

BIB

A multiple-feature framework for modelling and predicting transcription factor binding sites

Rainer Pudimat, E.G. Schukat-Talamazzini, Rolf Backofen.

Bioinformatics, 21(14), 3082-8, 2005.

DOI BIB

Lexicalised Configuration Grammars

Robert Grabowski, Marco Kuhlmann, Mathias Möhl.

Second International Workshop on Constraint Solving and Language Processing (CSLP 2005), 2005.

BIB

INFO-RNA - A Fast Approach of the Inverse RNA Folding

Anke Busch, Rolf Backofen.

ECCB, 2005.

BIB

Well-Nested Drawings as Models of Syntactic Structure

Manuel Bodirsky, Marco Kuhlmann, Mathias Möhl.

10th Conference on Formal Grammar and 9th Meeting on Mathematics of Language, 2005.

Link BIB

Efficient Constraint-based Sequence Alignment by Cluster Tree Elimination

Sebastian Will, Anke Busch, Rolf Backofen.

Proceedings of the Workshop on Constraint Based Methods in Bioinformatics (WCB05), 66-74, 2005.

BIB

A new distance measure of RNA ensembles and its application to phylogenetic tree construction

Sven Siebert, Rolf Backofen.

IEEE 2005 Symposium on Computational Intelligence in Bioinformatics and Computational Biology, 150-157, 2005.

Link BIB

MARNA: multiple alignment and consensus structure prediction of RNAs based on sequence structure comparisons

Sven Siebert, Rolf Backofen.

Bioinformatics, 21(16), 3352-9, 2005.

DOI BIB

XenDB: Full Length cDNA Prediction and Cross Species Mapping in Xenopus laevis

M. Beckstette, A. Sczyrba, A.H. Brivanlou, R. Giegerich, C.R. Altmann.

BMC Genomics, 6(123), 2005.

DOI BIB

Non-coding RNAs in Ciona intestinalis

Kristin Missal, Dominic Rose, Peter F. Stadler.

Bioinformatics, 21 Suppl 2, ii77-ii78, 2005.

DOI BIB

The origin of bilateral animals. A multigene approach.

P. Martinez, K. Malde, M. Beckstette, J. Baguna.

Comparative Biochemistry and Physiology. Abstracts of the Society for Experimental Biology Annual Main Meeting, 141, 2005.

BIB

Non-EST based prediction of exon skipping and intron retention events using Pfam information

Michael Hiller, Klaus Huse, Matthias Platzer, Rolf Backofen.

NAR, 33(17), 5611-21, 2005.

DOI BIB

Creation and disruption of protein features by alternative splicing -- a novel mechanism to modulate function

Michael Hiller, Klaus Huse, Matthias Platzer, Rolf Backofen.

Genome Biology, 6(7), R58, 2005.

DOI BIB

SECISDesign: a server to design SECIS-elements within the coding sequence

Anke Busch, Sebastian Will, Rolf Backofen.

Bioinformatics, 21(15), 3312-3, 2005.

DOI BIB

Normalized Similarity of RNA Sequences

Rolf Backofen, Danny Hermelin, Gad M. Landau, Oren Weimann.

Proc. 12th Symposium on String Processing and Information Retrieval (SPIRE 2005), 3772, 360-369, 2005.

Link BIB

Prediction of Transcription Factor Binding Sites by Modeling Multiple Features

Rainer Pudimat, Rolf Backofen.

ISMB-ECCB, 2004.

BIB

Feature Based Representation and Detection of Transcription Factor Binding Sites

Rainer Pudimat, E. G. Schukat-Talamazzini, Rolf Backofen.

GCB, 53, 43-52, 2004.

Link BIB

MODERNA - Design of New and Recombinant Selenoproteins

Anke Busch, Rolf Backofen.

ISMB/ECCB, 2004.

BIB

Fast Detection of Common Sequence Structure Patterns in RNAs

Rolf Backofen, Sven Siebert.

Symposium on String Processing and Information Retrieval (SPIRE 2004), 3246, 79-92, 2004.

Link BIB

A Polynomial Time Upper Bound for the Number of Contacts in the HP-Model on the Face-Centered-Cubic Lattice (FCC)

Rolf Backofen.

Journal of Discrete Algorithms, 2(2), 161-206, 2004.

DOI BIB

Identification of 10,500 Xenopus laevis Full Length Clones through EST Clustering and Sequence Analysis

A. Sczyrba, M. Beckstette, R. Giegerich, C.A. Altmann.

Proceedings of the German Conference on Bioinformatics (GCB). Discovery Notes, P-53, 6-7, 2004.

BIB

Widespread occurrence of alternative splicing at NAGNAG acceptors contributes to proteome plasticity

Michael Hiller, Klaus Huse, Karol Szafranski, Niels Jahn, Jochen Hampe, Stefan Schreiber, Rolf Backofen, Matthias Platzer.

Nat Genet, 36(12), 1255-7, 2004.

DOI BIB

Efficient prediction of alternative splice forms using protein domain homology

Michael Hiller, Rolf Backofen, Stephan Heymann, Anke Busch, Timo Mika Glaesser, Johann-Christoph Freytag.

In Silico Biol, 4(2), 0017, 2004.

BIB

Using protein secondary structure to build structural template

Y. He, S. Qin, X. M. Pan, M. Beckstette, R. Giegerich.

CASP6 method paper, 2004.

BIB

Constraint Based Protein Structure Prediction Exploiting Secondary Structure Information

Alessandro Dal Palu, Sebastian Will, Rolf Backofen, Agostino Dovier.

Convegno Italiano di Logica Computazionale 2004 (CILC 2004), 16-17, 2004.

BIB

Local Sequence-Structure Motifs in RNA

Rolf Backofen, Sebastian Will.

Journal of Bioinformatics and Computational Biology (JBCB), 2(4), 681-698, 2004.

DOI BIB

Computational Design of New and Recombinant Selenoproteins

Rolf Backofen, Anke Busch.

Proc. of the 15th Annual Symposium on Combinatorial Pattern Matching (CPM2004), 3109, 270-284, 2004.

Link BIB

PoSSuMsearch: Fast and Sensitive Matching of Position Specific Scoring Matrices using Enhanced Suffix Arrays

M. Beckstette, D. Strothmann, R. Homann, R. Giegerich, S. Kurtz.

Proc. of the German Conference on Bioinformatics, P-53, 53-64, 2004.

Link BIB

Genlight: An Interactive System for High-throughput sequence analysis and Comparative Genomics

M. Beckstette, A. Sczyrba, P. M. Selzer.

Proc. of the German Conference on Bioinformatics, P-53, 2004.

DOI BIB

Genlight: Interactive High-Throughput Sequence Analysis and comparative genomics

M. Beckstette, J.T. Mailänder, R.J. Marhöfer, A. Sczyrba, E. Ohlebusch, R. Giegerich, P.M. Selzer.

Yearbook Bioinformatics, 79-94, 2004.

BIB

Genlight: Interactive High-Throughput Sequence Analysis and comparative genomics

M. Beckstette, J.T. Mailaennder, R.J. Marhoefer, A. Sczyrba, E. Ohlebusch, R. Giegerich, P.M. Selzer.

Journal of Integrative Bioinformatics, 1(8), 2004.

DOI BIB

Breaking of Partial Symmetries in the Photo and Alignment Problem

Sebastian Will, Rolf Backofen.

Proceedings of the Third International Workshop on Symmetry in Constraint Satisfaction Problems (SymCon 2003), 187--194, 2003.

BIB

Multiple Local Sequence Structure Alignment of RNA Sequences

Sven Siebert, Rolf Backofen.

RECOMB 2003, 2003.

BIB

MARNA: A Server for Multiple Alignment of RNAs

Sven Siebert, Rolf Backofen.

GCB, 135-140, 2003.

Link BIB

A Constraint-Based Approach to Structure Prediction for Simplified Protein Models that Outperforms Other Existing Methods

Rolf Backofen, Sebastian Will.

Proceedings of the 19th International Conference on Logic Programming (ICLP 2003), 2916, 49--71, 2003.

Link BIB

Constraint-based Hydrophobic Core Construction for Protein Structure Prediction in the Face-Centered-Cubic Lattice

Sebastian Will.

Proceedings of the Pacific Symposium on Biocomputing 2002 (PSB 2002), 661--672, 2002.

Link BIB

Protein Structure Prediction in the Face-Centered Cubic Lattice

Sebastian Will, Rolf Backofen.

European Conference on Computational Biology 2002, 2002.

BIB

Multiple Local Sequence Structure Alignment of RNA Sequences

Sven Siebert.

European Conference on Computational Biology 2002, 2002.

BIB

Structural Infectomics: Identification and Characterization of Potential Virulence Factors in Legionella pneumophila

Steffen Heyne, Martin Mann, Debnath Pal, Aida Baharuddin, Andreas Vogel, Rolf Hilgenfeld.

ECCB'02, 2002.

BIB

Protein similarity search under mRNA structural constraints: application to targeted selenocysteine insertion

Rolf Backofen, N. S. Narayanaswamy, Firas Swidan.

In Silico Biology, 2(3), 275-90, 2002.

Link BIB

Excluding symmetries in constraint-based search

Rolf Backofen, Sebastian Will.

Constraints, 7(3), 333-349, 2002.

Link BIB

On the Complexity of Protein Similarity Search under mRNA Structure Constraints

Rolf Backofen, N. S. Narayanaswamy, Firas Swidan.

Proc. of 19th International Symposium on Theoretical Aspects of Computer Science (STACS2002), 2285, 274--286, 2002.

Link BIB

Introduction to Bioinformatics

Rolf Backofen.

Companion Volume to the Proceedings of the 39th Annual Meeting of the Association for Computational Linguistic (ACL), 2001.

Link BIB

Introduction to the Special Issue on Bioinformatics

David Gilbert, Rolf Backofen, Roland H. C. Yap.

Constraints, 6(2/3), 139, 2001.

Link BIB

RNA-Sequence-Structure Properties and Selenocysteine Insertion

Rolf Backofen.

Proc. of the Fourth International Symposium on Intelligent Data Analysis, 2189, 187--197, 2001.

Link BIB

Bioinformatics and Constraints

Rolf Backofen, David Gilbert.

Constraints, 6, 141-156, 2001.

Link BIB

The Protein Structure Prediction Problem: A Constraint Optimisation Approach using a New Lower Bound

Rolf Backofen.

Constraints, 6, 223-255, 2001.

DOI BIB

Optimally Compact Finite Sphere Packings --- Hydrophobic Cores in the FCC

Rolf Backofen, Sebastian Will.

Proc. of the 12th Annual Symposium on Combinatorial Pattern Matching (CPM2001), 2089, 257--272, 2001.

Link BIB

Fast, Constraint-based Threading of HP-Sequences to Hydrophobic Cores

Rolf Backofen, Sebastian Will.

Proc. of the 7th International Conference on Principle and Practice of Constraint Programming (CP'2001), 2239, 494--508, 2001.

Link BIB

Protein similarity search under mRNA structural constraints: application to selenocysteine incorporation

Rolf Backofen, N. S. Narayanaswamy, Swidan Firas.

Proc. of German Conference on Bioinformatics (GCB2001), 135-140, 2001.

Link BIB

Computational Molecular Biology: An Introduction

Peter Clote, Rolf Backofen.

2000.

BIB

An Upper Bound for Number of Contacts in the HP-Model on the Face-Centered-Cubic Lattice (FCC)

Rolf Backofen.

Proceedings of the 11th Annual Symposium on Combinatorial Pattern Matching (CPM 2000), 1848, 277--292, 2000.

Link BIB

Algorithmic approach to quantifying the hydrophobic force contribution in protein folding

Rolf Backofen, Sebastian Will, Peter Clote.

Proceedings of the Pacific Symposium on Biocomputing (PSB 2000), 5, 92--103, 2000.

DOI BIB

Classroom Assignment using Constraint Logic Programming

Slim Abdennadher, Matthias Saft, Sebastian Will.

Proceedings of the Second International Conference and Exhibition on The Practical Application of Constraint Technologies and Logic Programming (PACLP 2000), 2000.

Link BIB

Algorithmic approach to quantifying the hydrophobic force contribution in protein folding

Rolf Backofen, Sebastian Will, Peter Clote.

Proceedings of the German Conference on Bioinformatics (GCB'99), 93-106, 1999.

Link BIB

Excluding Symmetries in Constraint-Based Search

Rolf Backofen, Sebastian Will.

Proceedings of 5th International Conference on Principle and Practice of Constraint Programming (CP'99), 1713, 73-87, 1999.

Link BIB

Application of Constraint Programming Techniques for Structure Prediction of Lattice Proteins with Extended Alphabets

Rolf Backofen, Sebastian Will, Erich Bornberg-Bauer.

Bioinformatics, 15(3), 234-242, 1999.

DOI BIB

Aktuelles Schlagwort Bioinformatik

Rolf Backofen, François Bry, Peter Clote, Hans-Peter Kriegel, Thomas Seidl, Klaus Schulz.

Informatik Spektrum, 22(5), 376-378, 1999.

DOI BIB

Using Constraint Programming for lattice Protein Folding

Rolf Backofen.

Proceedings of the Pacific Symposium on Biocomputing (PSB'98), 3, 387-398, 1998.

Link BIB

Constraint Techniques for Solving the Protein Structure Prediction Problem

Rolf Backofen.

Proceedings of 4th International Conference on Principle and Practice of Constraint Programming (CP'98), 1520, 72-86, 1998.

Link BIB

Excluding Symmetries in Concurrent Constraint Programming

Rolf Backofen, Sebastian Will.

Workshop on Modeling and Computing with Concurrent Constraint Programming, 1998.

Link BIB

Structure Prediction in an HP-type Lattice with an Extended Alphabet

Rolf Backofen, Sebastian Will.

Proc of German Conference on Bioinformatics (GCB'98), 1998.

Link BIB

How to Win a Game with Features

Rolf Backofen, Ralf Treinen.

Information and Computation, 142(1), 76--101, 1998.

DOI BIB

Using Constraint Programming for lattice Protein Folding

Rolf Backofen.

Workshop on Constraints and Bioinformatics/Biocomputing, 1997.

Link BIB

Evolution as a Computational Engine

Rolf Backofen, Peter Clote.

Proc. of Annual Conference of the European Association for Computer Science Logic (CSL'97), 1414, 35--55, 1997.

Link BIB

Controlling Functional Uncertainty

Rolf Backofen.

Proceedings of 12th European Conference on Artificial Intelligence, 557--561, 1996.

BIB

A Complete Axiomatization of a Theory with Feature and Arity Constraints

Rolf Backofen.

Journal of Logic Programming, 24, 37-72, 1995.

DOI BIB

A Complete and Recursive Feature Theory

Rolf Backofen, Gert Smolka.

tcs, 146(1--2), 243--268, 1995.

DOI BIB

A First-Order Axiomatization of the Theory of Finite Trees

Rolf Backofen, James Rogers, K. Vijay-Shanker.

Journal of Logic, Language and Information, 4(1), 5-39, 1995.

Link BIB

DISCO -- An HPSG-Based NLP System and its Application for Appointment Scheduling

Hans Uszkoreit, Rolf Backofen, Stephan Busemann, Abdel Kader Diagne, Elizabeth A. Hinkleman, Walter Kasper, Bernd Kiefer, Hans-Ulrich Krieger, Klaus Netter, Günter Neumann, Stephan Oepen, Stephen P. Spackman.

Proceedings of the 15th International Conference on Computational Linguistics (COLING'94), 436--440, 1994.

DOI BIB

How to Win a Game with Features

Rolf Backofen, Ralf Treinen.

1st International Conference on Constraints in Computational Logics, 845, 320--335, 1994.

DOI BIB

Regular Path Expressions in Feature Logic

Rolf Backofen.

Journal of Symbolic Computation, 17, 412--455, 1994.

DOI BIB

On the Decidability of Functional Uncertainty

Rolf Backofen.

Proc. of the 31st ACL, 201--208, 1993.

Link BIB

Regular Path Expressions in Feature Logic

Rolf Backofen.

Proc. of the RTA'93, 690, 121--135, 1993.

Link BIB

The TDL/UDiNe system

Rolf Backofen, Hans-Ulrich Krieger.

Report of the EAGLES Workshop on Implemented Formalisms at DFKI, Saarbrücken, 67--74, 1993.

BIB

A Complete and Recursive Feature Theory

Rolf Backofen, Gert Smolka.

Proc. of the 31st ACL, 193--200, 1993.

DOI BIB

Distributed Disjunktions For LIFE

Rolf Backofen, Lutz Euler, Günther Görz.

Proc. of the Inter. Workshop on Processing Declarative Knowledge (PDK'91), 567, 161-170, 1991.

Link BIB

Linking Typed Feature Formalisms and Terminological Knowledge Representation Languages in Natural Language Front-Ends

Rolf Backofen, Harald Trost, Hans Uszkoreit.

Proceedings of the GI Congress, Knowledge-Based Systems 1991, 291, 375-384, 1991.

Link BIB

Towards the Integration of Functions, Relations and Types in an AI Programming Language

Rolf Backofen, Lutz Euler, Günther Görz.

Proc. of the 14th German Workshop on Artificial Intelligence, 251, 297--306, 1990.

Link BIB