Publications

Prediction of plant organismal complexity based on transcription factor annotation: an AI approach

Preprint

Deepti Varshney, Mustafa Hisham Tajjar, Jan de Vries, Frank Hutter, Stefan A. Rensing.

2026.

DOI BIB

FAIRyMAGs - a series of FAIR Galaxy workflows for the generation of metagenome assembled genomes

Preprint

Paul Zierep, Mina Hojat Ansari, Patrick Bühler, Santino Faack, Bruno Fosso, Giuseppe Defazio, Martin Beracochea, Santiago Sanchez, Alexandra Hottmann, Bérénice Batut.

2026.

DOI BIB

Machine learning-based prediction of memory requirements for metagenomic assembly in high-performance computing environments

Preprint

Santiago Sanchez, Santino Faack, Martin Beracochea, Robert D. Finn, Björn Grüning, Bérénice Batut, Paul Zierep.

2026.

DOI BIB

DisGeneFormer: Precise Disease Gene Prioritization by Integrating Local and Global Graph Attention

Preprint

Ryan Koeksal, Adrian Fritz, Anup Kumar, Miriam Schmidts, Van Dinh Tran, Rolf Backofen.

2026.

DOI BIB

Structural variation landscape of Middle Eastern and North African individuals from long-read nanopore sequencing reveals medically relevant variants

Preprint

Talal AL Yazeedi, Sophie Tandonnet, Sven Hauns, Sumaya Almansoori, Philip Davis, Rolf Backofen, Ahmed Abou Tayoun, Omer Alkhnbashi.

2026.

DOI BIB

Biological Foundation Models Enable CRISPR Array Detection Without Metagenomic Assembly

Preprint

Lukas Daugaard Schröder, Ryan Köksal, Alexander Mitrofanov, Michael Uhl, Rolf Backofen.

2026.

DOI BIB

Prioritizing DNA methylation biomarkers using graph neural networks and explainable AI

Preprint

Anup Kumar, Ton Anh Do, Björn Grüning, Heiko Becker, Rolf Backofen.

2026.

DOI BIB

Enhanced IGFL1 translation in response to IL-1β is controlled by distinct 3’UTR elements

Preprint

Giulia Cardamone, Melanie Flohr, Rebecca Raue, Irina Bode, Sofie P. Meyer, Sven Hauns, Rolf Backofen, Tobias Schmid.

2026.

DOI BIB

A revised genome annotation of the model cyanobacterium Synechocystis based on start and stop codon-enriched ribosome profiling and proteogenomics

Preprint

Wolfgang Hess, Vanessa Krauspe, Viktoria Reimann, Paul Minges, Raphael Bilger, Maren Gerstner, Rick Gelhausen, Rolf Backofen, Benjamin Heiniger, Garance Jaques, Christian Ahrens, Philipp Spät, Boris Macek, Cynthia Sharma, Lydia Hadjeras.

2026.

DOI BIB

Tree-aware conditional language modeling recovers mutational patterns of viral evolution

Preprint

Polina V Polunina, Wolfgang Maier, Alan F Rubin.

2026.

DOI BIB

Hi-cGAN: Prediction of Hi-C interaction matrices with conditional generative adversarial networks

Preprint

Ralf Krauth, Anup Kumar, Joachim Wolff.

2026.

DOI BIB

Evolving FAIR Image Analysis in Galaxy for Cross-domain and AI-ready Applications

Preprint

Diana Chiang, Pavankumar Videm, David Lopez Tabernero, Maarten W. Paul, Alireza Heidari, Martin Etzrodt, Beatriz Serrano-Solano, Leonid Kostrykin.

2026.

DOI BIB

Optimized Meta-Scheduling in Galaxy Using TPV Broker

Book

Abdulrahman Azab, Paul De Geest, Sanjay K. Srikakulam, Tomáš Vondrák, Mira Kuntz, Björn Grüning.

Smart Innovation, Systems and Technologies, 499-509, 2026.

DOI BIB

VEFill: accurate and generalizable deep mutational scanning score imputation across protein domains

Journal

Polina V Polunina, Wolfgang Maier, Alan F Rubin.

Molecular Systems Biology, 22(6), 979-1002, 2026.

DOI BIB

A leader-repeat hairpin blocks extraneous CRISPR RNA production in diverse CRISPR-Cas13 systems

Journal

Angela Migur, Maximilian Feussner, Chunyu Liao, Omer S Alkhnbashi, Adrien Chauvier, Nils G Walter, Rolf Backofen, Zasha Weinberg, Chase L Beisel.

The EMBO Journal, 45(10), 3396-3415, 2026.

DOI BIB

Chamber-specific chromatin architecture guides functional interpretation of disease-associated Cis-regulatory elements in human cardiomyocytes

Journal

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

Journal

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

Journal

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

Journal

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

microLife, 7, uqaf042, 2026.

DOI BIB

LiraSearch—ultrafast ligand shape and electrostatic matching server

Journal

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

Journal

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

Journal

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

Journal

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!)

Journal

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

Other

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

2026.

DOI BIB

A revised genome annotation of the model cyanobacterium Synechocystis based on start and stop codon-enriched ribosome profiling and proteogenomics

Preprint

Lydia Hadjeras, Vanessa Krauspe, Rick Gelhausen, Benjamin Heiniger, Philipp Spät, Viktoria Reimann, Garance Jaques, Paul Minges, Raphael Bilger, Maren Gerstner, Boris Maček, Christian H. Ahrens, Rolf Backofen, Cynthia M. Sharma, Wolfgang R. Hess.

2025.

DOI BIB

The Spirogyra genome: signatures of shared and divergent division and differentiation

Preprint

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.

2025.

DOI BIB

AVDB: The Arab Variation and Disease Burden Database

Preprint

Omer S. Alkhnbashi, Ruchi Jain, Sathishkumar Ramaswamy, Costerwell Khyriem, Sven Hauns, Rasheed Mohammad, Rolf Backofen, Ahmad Abou Tayoun.

2025.

DOI BIB

VEFill: a model for accurate and generalizable deep mutational scanning score imputation across protein domains

Preprint

Polina V Polunina, Wolfgang Maier, Alan F Rubin.

2025.

DOI BIB

An evolutionary approach to predict the orientation of CRISPR arrays

Preprint

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

2025.

DOI BIB

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

Preprint

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

2025.

DOI BIB

Comprehensive Analysis of CRISPR Array Repeat Mutations Reveals Subtype-Specific Patterns and Links to Spacer Dynamics

Preprint

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

2025.

DOI BIB

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

Preprint

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

2025.

DOI BIB

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

Preprint

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

2025.

DOI BIB

Enhancing multi-omic analyses through a federated microbiome analysis service

Preprint

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

Journal

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

Journal

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

Journal

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

Journal

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

Journal

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

Journal

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

Journal

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

Journal

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

Journal

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

Journal

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

Journal

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

Journal

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

Journal

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

Journal

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

Journal

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

Journal

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

Journal

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

Journal

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

Journal

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

Journal

European Galaxy Team.

Heidelberg University Library, 2025.

DOI BIB

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

Journal

Daniela Schneider, Jan Leendertse.

E-Science-Tage 2025, 2025.

DOI BIB

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

Journal

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

Journal

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!)

Preprint

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

Preprint

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

Journal

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

Journal

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

Journal

Daniela Schneider.

Zenodo, 2025.

DOI BIB

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

Journal

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

Journal

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

Other

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

Other

Daniela Schneider.

2025.

DOI BIB

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

Other

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

2025.

DOI BIB

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

Journal

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

Journal

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

Journal

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

2025.

DOI BIB

Microbiology Galaxy Lab: The first community-driven gateway for reproducible and FAIR analysis of microbial data

Preprint

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

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RNAformer: A Simple yet Effective Model for Homology-Aware RNA Secondary Structure Prediction

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

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

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

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

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

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

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

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

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

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

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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.

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

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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.

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

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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.

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

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

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

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

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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.

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StreptomeDB 3.0: an updated compendium of streptomycetes natural products

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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.

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

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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.

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A constructivist-based proposal for bioinformatics teaching practices during lockdown

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

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

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Improving CLIP-seq data analysis by incorporating transcript information

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Michael Uhl, Van Dinh Tran, Rolf Backofen.

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Improving CLIP-Seq Data Analysis by Incorporating Transcript Information

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Michael Uhl, Dinh Van Tran, Rolf Backofen.

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The importance of incorporating transcript information in CLIP-seq data analysis

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Michael Uhl, Dinh Van Tran, Rolf Backofen.

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Adding software to package management systems can increase their citation by 280%

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Vahid Jalili, Dave Clements, Björn Grüning, Daniel Blankenberg, Jeremy Goecks.

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CRISPRidentify: identification of CRISPR arrays using machine learning approach

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

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Training Infrastructure as a Service

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Helena Rasche, Björn Grüning.

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BioContainers Registry: searching for bioinformatics tools, packages and containers

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

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The landscape of SARS-CoV-2 RNA modifications

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Milad Miladi, Jonas Fuchs, Wolfgang Maier, Sebastian Weigang, Núria Díaz i Pedrosa, Lisa Weiss, Achim Lother, Anton Nekrutenko, Zsolt Ruzsics, Marcus Panning, Georg Kochs, Ralf Gilsbach, Björn Grüning.

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Accessible, Reproducible, and Scalable Machine Learning for Biomedicine

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

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

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

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

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

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HRIBO - High-throughput analysis of bacterial ribosome profiling data

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

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Pluripotency factors determine gene expression repertoire at zygotic genome activation

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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.

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Survey of metaproteomics software tools for functional microbiome analysis

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R. Sajulga, C. Easterly, M. Riffle, B. Mesuere, T. Muth, S. Mehta, P. Kumar, J. Johnson, B. Gruening, H. Schiebenhoefer, C. A. Kolmeder, S. Fuchs, B. L. Nunn, J. Rudney, T. J. Griffin, P. D. Jagtap.

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

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Sanket Bapat, Saim Momin, Renu Vyas.

Advances in Bioengineering, 3-28, 2020.

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

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

Bioinformatics, 2020.

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

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

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

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

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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.

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Improving CLIP-seq data analysis by incorporating transcript information

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Michael Uhl, Van Dinh Tran, Rolf Backofen.

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

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pyGenomeTracks: reproducible plots for multivariate genomic data sets

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

Bioinformatics, 2020.

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Casboundary: automated definition of integral Cas cassettes

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

Bioinformatics, 2020.

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HRIBO: high-throughput analysis of bacterial ribosome profiling data

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

Bioinformatics, 2020.

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

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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.

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

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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.

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Heterogeneous networks integration for disease-gene prioritization with node kernels

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

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

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

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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.

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

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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.

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

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

Dendrochronologia, 60, 125679, 2020.

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

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

BMC Bioinformatics, 21, 15, 2020.

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

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

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

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

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

Gigascience, 9(6), 2020.

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The locality dilemma of Sankoff-like RNA alignments

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

Bioinformatics, 2020.

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CRISPRidentify: identification of CRISPR arrays using machine learning approach

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

NAR, 2020.

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NanoGalaxy: Nanopore long-read sequencing data analysis in Galaxy

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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.

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

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

Nucleic Acids Research, 2020.

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

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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.

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

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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.

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

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Gregor Entzian, Martin Raden.

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

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

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

Journal of Cheminformatics, 12(1), 2020.

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

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

Journal of Cheminformatics, 12(1), 2020.

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Engineering proton conductivity in melanin using metal doping

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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.

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

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

GigaScience, 9(5), giaa049, 2020.

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

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

GigaScience, 9(11), giaa108, 2020.

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

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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.

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

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

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

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

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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.

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Survey of metaproteomics software tools for functional microbiome analysis

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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.

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

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

Metabolites, 11(1), 13, 2020.

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GraphProt2: A graph neural network-based method for predicting binding sites of RNA-binding proteins

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

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Accessible and reproducible mass spectrometry imaging data analysis in Galaxy

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

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Empowering the annotation and discovery of structured RNAs with scalable and accessible integrative clustering

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

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

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

PLOS ONE, 14, e0222459, 2019.

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Universal readout for graph convolutional neural networks

Conference

Nicolò Navarin, Dinh Van Tran, Alessandro Sperduti.

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

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

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Stefan Mautner, Rolf Backofen, Fabrizio Costa.

ESANN 2019 - Proceedings, 2019.

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The RNA workbench 2.0: next generation RNA data analysis

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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.

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The RNA workbench 2.0: next generation RNA data analysis

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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.

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Noncoding deletions reveal a gene that is critical for intestinal function

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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.

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A pan-cancer analysis of synonymous mutations

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

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

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

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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.

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

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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.

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

Conference

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

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

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

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

GigaScience, 8(12), 2019.

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

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

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

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ShaKer: RNA SHAPE prediction using graph kernel

Journal

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

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

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

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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.

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

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

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

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CRISPR-Cas systems in multicellular cyanobacteria

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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.

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

Conference

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.

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

Journal

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

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

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The RNA workbench 2.0: next generation RNA data analysis

Journal

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.

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Biomolecular Reaction and Interaction Dynamics Global Environment (BRIDGE)

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

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

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CRISPR-Cas bioinformatics

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

Methods, 2019.

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

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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.

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

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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.

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Update on the moFF Algorithm for Label-Free Quantitative Proteomics

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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.

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

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

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

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Accessible and reproducible mass spectrometry imaging data analysis in Galaxy

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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.

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Software engineering for scientific big data analysis

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

GigaScience, 8(5), giz054, 2019.

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

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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.

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

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

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

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

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

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Plasticity of archaeal C/D box sRNA biogenesis

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

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

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

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

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Spatiotemporal alignment of radial tracheid diameter profiles of submontane Norway spruce

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Dendrochronologia, 37, 33-45, 2016.

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

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Nat Commun, 7, 12791, 2016.

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

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

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

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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.

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

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

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

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

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Characterizing leader sequences of CRISPR loci

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

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

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

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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

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

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

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

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

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

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galaxytools: July 2016 release

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

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

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

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

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Deciphering the Epigenetic Code of Cardiac Myocyte Transcription

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Circ Res, 117, 413-423, 2015.

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Nat Commun, 6, 7367, 2015.

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An updated evolutionary classification of CRISPR-Cas systems

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

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

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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.

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Computational Prediction of Modular Domain-Peptide Interactions

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

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Comparative analysis of the antioxidant properties of Icelandic and Hawaiian lichens

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

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Towards an Automated Annotation of CRISPR-Cas systems

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CRISPRloci: Comprehensive and accurate annotation of CRISPR-Cas systems

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The Purchasable Chemical Space: A Detailed Picture

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

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

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

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eLife, 4, e07009, 2015.

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Local Exact Pattern Matching for Non-Fixed RNA Structures.

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

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

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

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Simultaneous Alignment and Folding of Protein Sequences

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

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

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

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

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Autosomal dominant immune dysregulation syndrome in humans with CTLA4 mutations

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

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

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

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GraphProt: modeling binding preferences of RNA-binding proteins

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Memory efficient RNA energy landscape exploration

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

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

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Atom Mapping with Constraint Programming

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Exact methods for lattice protein models

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

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

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

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

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

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Bioinformatics, 2014.

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

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

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Cluster based prediction of PDZ-peptide interactions

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

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Dynamic DNA methylation orchestrates cardiomyocyte development, maturation and disease

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Nat Commun, 5, 5288, 2014.

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

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Elife, 3, e02024, 2014.

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

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

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Regio- and Stereoselective Intermolecular Oxidative Phenol Coupling in Streptomyces

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Electron paramagnetic resonance study of ZnO varistor material

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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

Journal

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

Book

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

Journal

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

Conference

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

Conference

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

Journal

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

Journal

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

Journal

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

Journal

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

Journal

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)

Journal

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

Journal

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

Journal

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

Journal

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

Journal

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

Conference

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

Conference

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

Conference

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

Journal

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

Journal

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

Journal

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

Journal

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

Journal

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

Journal

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

Journal

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

Journal

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

Journal

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

Journal

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

Conference

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

Journal

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

Conference

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

Journal

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

Journal

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

Conference

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

Journal

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?

Journal

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

Journal

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

Journal

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

Journal

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

Journal

Nuno D. Mendes, Steffen Heyne, Ana T. Freitas, Marie-France Sagot, Rolf Backofen.

Bioinformatics, 2012.

DOI BIB

Atom Mapping with Constraint Programming

Conference

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

Journal

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

Journal

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

Journal

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

Journal

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

Journal

Jiabin Huang, Rolf Backofen, Björn Voss.

RNA, 18(12), 2135-47, 2012.

DOI BIB

GraphClust: alignment-free structural clustering of local RNA secondary structures

Journal

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

Journal

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

Conference

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

Journal

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

Journal

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

Journal

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

Conference

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

Journal

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

Journal

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

Book

Rolf Backofen.

Regulatory RNAs in Prokaryotes, 221-239, 2011.

Link BIB

The small RNA PhrS stimulates synthesis of the Pseudomonas aeruginosa quinolone signal

Journal

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

Journal

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

Journal

S. E. Seemann, P. Menzel, R. Backofen, J. Gorodkin.

NAR, 39, W107-11, 2011.

DOI BIB

Signatures of Co-translational Folding

Journal

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

Journal

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

Journal

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

Journal

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

Journal

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

Conference

Andreas S. Richter, Rolf Backofen.

Proceedings of the German Conference on Bioinformatics (GCB 2011), 2011.

BIB

Sparsification in Algebraic Dynamic Programming

Conference

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

Journal

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

Journal

Martin Mann, Rhodri Saunders, Cameron Smith, Rolf Backofen, Charlotte Deane.

Adv Bioinformatics, 9, 2011.

DOI BIB

Efficient exploration of discrete energy landscapes

Journal

Martin Mann, Konstantin Klemm.

Phys. Rev. E, 83(1), online, 2011.

DOI BIB

CRISPR revisited: structure prediction of CRISPR repeats

Conference

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

Conference

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

Journal

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

Journal

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

Journal

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

Journal

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

Journal

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

Journal

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

Journal

Martin Mann.

2011.

DOI BIB

Alignnment of RNA with Structures of Unlimited Complexity

Conference

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

Conference

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

Conference

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

Journal

Rolf Backofen.

Laborwelt, 11(1), 29-30, 2010.

BIB

Partitioning biological data with transitivity clustering

Journal

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

Journal

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

Journal

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

Journal

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

Journal

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

Journal

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

Conference

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

Journal

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

Journal

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

Journal

Andreas S. Richter, Christian Schleberger, Rolf Backofen, Claudia Steglich.

Bioinformatics, 26(1), 1-5, 2010.

DOI BIB

Lifting prediction to alignment of RNA pseudoknots

Journal

Mathias Möhl, Sebastian Will, Rolf Backofen.

JCB, 17(3), 429-42, 2010.

DOI BIB

Sparsification of RNA structure prediction including pseudoknots

Journal

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

Conference

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

Conference

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

Conference

Kousik Kundu, Rileen Sinha, Michael Reth, Michael Huber, Rolf Backofen.

Poster Proceedings of ISMB'10, 2010.

BIB

In silico modelling of human lipoprotein metabolism

Conference

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

Journal

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

Conference

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

Journal

Rolf Backofen, Wolfgang R. Hess.

RNA Biol, 7(1), 33-42, 2010.

DOI BIB

COMPUTATIONAL STUDIES OF NON-CODING RNAS - Session Introduction

Conference

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

Journal

Dilmurat Yusuf, Manja Marz, Peter F Stadler, Ivo L Hofacker.

BMC Genomics, 11(1), 432, 2010.

DOI BIB

Fast prediction of RNA-RNA Interaction

Conference

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

Journal

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

Conference

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

Conference

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

Conference

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

Conference

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

Conference

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

Journal

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

Conference

Mathias Möhl, Sebastian Will, Rolf Backofen.

RECOMB09, 5541, 285--301, 2009.

DOI BIB

CPSP-web-tools: a server for 3D lattice protein studies

Journal

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

Conference

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

Conference

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

Conference

Eric I. Hsu, Sheila A. McIlraith.

WCB09, 2009.

BIB

Conserved introns reveal novel transcripts in Drosophila melanogaster

Journal

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

Journal

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

Journal

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

Conference

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

Journal

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

Conference

Henning Christiansen, Christian Theil Have, Ole Torp Lassen, Matthieu Petit.

WCB09, 2009.

Link BIB

A partition function algorithm for interacting nucleic acid strands

Journal

Hamidreza Chitsaz, Raheleh Salari, S. Cenk Sahinalp, Rolf Backofen.

Bioinformatics, 25(12), i365-73, 2009.

DOI BIB

Constraint Based Languages for Biological Reactions

Conference

Stefano Bistarelli, Marco Bottalico.

WCB09, 2009.

Link BIB

Tagsnp selection using Weighted CSP and Russian Doll Search with Tree Decomposition

Conference

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

Journal

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

Journal

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

Journal

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

Journal

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

Journal

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

Journal

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

Conference

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

Journal

Sebastian Will, Anke Busch, Rolf Backofen.

Constraints Journal, 13(1), 110-129, 2008.

DOI BIB

Improved identification of conserved cassette exons using Bayesian networks

Journal

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

Journal

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

Journal

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

Journal

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

Journal

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

Conference

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

Conference

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

Conference

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

Journal

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

Journal

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

Journal

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

Journal

Michael Hiller, Matthias Platzer.

TIG, 24(5), 246-55, 2008.

DOI BIB

Selection against tandem splice sites affecting structured protein regions

Journal

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

Journal

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

Conference

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

Journal

Anke Busch, Andreas S. Richter, Rolf Backofen.

Bioinformatics, 24(24), 2849-56, 2008.

DOI BIB

Variations on RNA folding and alignment: lessons from Benasque

Journal

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

Journal

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

Book

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

Conference

Marco Kuhlmann, Mathias Möhl.

Twelfth Conference on Formal Grammar (FG), 2007.

BIB

Mildly Context-Sensitive Dependency Languages

Conference

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

Journal

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

Journal

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

Journal

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

Journal

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

Journal

Sven Siebert, Rolf Backofen.

Methods Mol Biol, 395, 489-502, 2007.

DOI BIB

Computational RNomics of drosophilids

Journal

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

Journal

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

Conference

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

Conference

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

Conference

Martin Mann, Sebastian Will, Rolf Backofen.

ISMB/ECCB, 2007.

BIB

TassDB: a database of alternative tandem splice sites

Journal

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

Journal

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

Journal

Anke Busch, Rolf Backofen.

NAR, 35(Web Server issue), W310-3, 2007.

DOI BIB

RNAs everywhere: genome-wide annotation of structured RNAs

Journal

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

Journal

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

Journal

Rolf Backofen, Sven Siebert.

Journal of Discrete Algorithms, 5(2), 212-228, 2007.

DOI BIB

Locality and gaps in RNA comparison

Journal

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

Book

M. Beckstette.

2007.

Link BIB

Extended cross-serial dependencies in Tree Adjoining Grammars

Conference

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

Conference

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

Journal

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

Book

Rolf Backofen, David Gilbert.

Handbook of Constraint Programming, 905-944, 2006.

DOI BIB

Exploring the lower part of discrete polymer model energy landscapes

Journal

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

Conference

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

Conference

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?

Journal

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

Journal

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?

Journal

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

Journal

Michael Hiller, Rainer Pudimat, Anke Busch, Rolf Backofen.

NAR, 34(17), e117, 2006.

DOI BIB

Phylogenetically widespread alternative splicing at unusual GYNGYN donors

Journal

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

Journal

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

Journal

Anke Busch, Rolf Backofen.

Bioinformatics, 22(15), 1823-31, 2006.

DOI BIB

Fast index based algorithms and software for matching position specific scoring matrices

Journal

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

Journal

Rolf Backofen, Sebastian Will.

Journal of Constraints, 11(1), 5--30, 2006.

DOI BIB

A Posteriori Modelling of Sequence Motif Arrangements

Conference

Rolf Backofen, Rainer Pudimat.

GCB, 2005.

BIB

A multiple-feature framework for modelling and predicting transcription factor binding sites

Journal

Rainer Pudimat, E.G. Schukat-Talamazzini, Rolf Backofen.

Bioinformatics, 21(14), 3082-8, 2005.

DOI BIB

Lexicalised Configuration Grammars

Conference

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

Conference

Anke Busch, Rolf Backofen.

ECCB, 2005.

BIB

Well-Nested Drawings as Models of Syntactic Structure

Conference

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

Conference

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

Conference

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

Journal

Sven Siebert, Rolf Backofen.

Bioinformatics, 21(16), 3352-9, 2005.

DOI BIB

XenDB: Full Length cDNA Prediction and Cross Species Mapping in Xenopus laevis

Journal

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

Journal

Kristin Missal, Dominic Rose, Peter F. Stadler.

Bioinformatics, 21 Suppl 2, ii77-ii78, 2005.

DOI BIB

The origin of bilateral animals. A multigene approach.

Journal

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

Journal

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

Journal

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

Journal

Anke Busch, Sebastian Will, Rolf Backofen.

Bioinformatics, 21(15), 3312-3, 2005.

DOI BIB

Normalized Similarity of RNA Sequences

Conference

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

Conference

Rainer Pudimat, Rolf Backofen.

ISMB-ECCB, 2004.

BIB

Feature Based Representation and Detection of Transcription Factor Binding Sites

Conference

Rainer Pudimat, E. G. Schukat-Talamazzini, Rolf Backofen.

GCB, 53, 43-52, 2004.

Link BIB

MODERNA - Design of New and Recombinant Selenoproteins

Conference

Anke Busch, Rolf Backofen.

ISMB/ECCB, 2004.

BIB

Fast Detection of Common Sequence Structure Patterns in RNAs

Conference

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)

Journal

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

Conference

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

Journal

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

Journal

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

Journal

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

Conference

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

Journal

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

Conference

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

Conference

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

Conference

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

Book

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

Journal

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

Conference

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

Conference

Sven Siebert, Rolf Backofen.

RECOMB 2003, 2003.

BIB

MARNA: A Server for Multiple Alignment of RNAs

Conference

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

Conference

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

Conference

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

Conference

Sebastian Will, Rolf Backofen.

European Conference on Computational Biology 2002, 2002.

BIB

Multiple Local Sequence Structure Alignment of RNA Sequences

Conference

Sven Siebert.

European Conference on Computational Biology 2002, 2002.

BIB

Structural Infectomics: Identification and Characterization of Potential Virulence Factors in Legionella pneumophila

Conference

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

Journal

Rolf Backofen, N. S. Narayanaswamy, Firas Swidan.

In Silico Biology, 2(3), 275-90, 2002.

Link BIB

Excluding symmetries in constraint-based search

Journal

Rolf Backofen, Sebastian Will.

Constraints, 7(3), 333-349, 2002.

Link BIB

On the Complexity of Protein Similarity Search under mRNA Structure Constraints

Conference

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

Conference

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

Journal

David Gilbert, Rolf Backofen, Roland H. C. Yap.

Constraints, 6(2/3), 139, 2001.

Link BIB

RNA-Sequence-Structure Properties and Selenocysteine Insertion

Conference

Rolf Backofen.

Proc. of the Fourth International Symposium on Intelligent Data Analysis, 2189, 187--197, 2001.

Link BIB

Bioinformatics and Constraints

Journal

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

Journal

Rolf Backofen.

Constraints, 6, 223-255, 2001.

DOI BIB

Optimally Compact Finite Sphere Packings --- Hydrophobic Cores in the FCC

Conference

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

Conference

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

Conference

Rolf Backofen, N. S. Narayanaswamy, Swidan Firas.

Proc. of German Conference on Bioinformatics (GCB2001), 135-140, 2001.

Link BIB

Computational Molecular Biology: An Introduction

Book

Peter Clote, Rolf Backofen.

2000.

BIB

An Upper Bound for Number of Contacts in the HP-Model on the Face-Centered-Cubic Lattice (FCC)

Conference

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

Conference

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

Conference

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

Conference

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

Conference

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

Journal

Rolf Backofen, Sebastian Will, Erich Bornberg-Bauer.

Bioinformatics, 15(3), 234-242, 1999.

DOI BIB

Aktuelles Schlagwort Bioinformatik

Journal

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

Conference

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

Conference

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

Conference

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

Conference

Rolf Backofen, Sebastian Will.

Proc of German Conference on Bioinformatics (GCB'98), 1998.

Link BIB

How to Win a Game with Features

Journal

Rolf Backofen, Ralf Treinen.

Information and Computation, 142(1), 76--101, 1998.

DOI BIB

Using Constraint Programming for lattice Protein Folding

Conference

Rolf Backofen.

Workshop on Constraints and Bioinformatics/Biocomputing, 1997.

Link BIB

Evolution as a Computational Engine

Conference

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

Conference

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

Journal

Rolf Backofen.

Journal of Logic Programming, 24, 37-72, 1995.

DOI BIB

A Complete and Recursive Feature Theory

Journal

Rolf Backofen, Gert Smolka.

tcs, 146(1--2), 243--268, 1995.

DOI BIB

A First-Order Axiomatization of the Theory of Finite Trees

Journal

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

Conference

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