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The Planemo toolkit for developing, deploying, and executing scientific data analyses in Galaxy and beyond
Simon Bray, John Chilton, Matthias Bernt, Nicola Soranzo, Marius van den Beek, Bérénice Batut, Helena Rasche, Martin Cech, Peter J. A. Cock, Björn Grüning and Anton Nekrutenko
Genome Res, 2023
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Revealing the small proteome of Haloferax volcanii by combining ribosome profiling and small-protein optimized mass spectrometry
Lydia Hadjeras, Jürgen Bartel, Lisa-Katharina Maier, Sandra Maaß, Verena Vogel, Sarah L. Svensson, Florian Eggenhofer, Rick Gelhausen, Teresa Müller, Omer S. Alkhnbashi, Rolf Backofen, Dörte Becher, Cynthia M. Sharma and Anita Marchfelder
Microlife, 2023
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Unraveling the small proteome of the plant symbiont Sinorhizobium meliloti by ribosome profiling and proteogenomics
Lydia Hadjeras, Benjamin Heiniger, Sandra Maaß, Robina Scheuer, Rick Gelhausen, Saina Azarderakhsh, Susanne Barth-Weber, Rolf Backofen, Dörte Becher, Christian H. Ahrens, Cynthia M. Sharma and Elena Evguenieva-Hackenberg
Microlife, 2023
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Spectrum of Genetic Variants in a Cohort of 37 Laterality Defect Cases
Dinu Antony, Elif Gulec Yilmaz, Alper Gezdirici, Lennart Slagter, Zeineb Bakey, Helen Bornaun, Ibrahim Cansaran Tanidir, Van Dinh Tran, Han G. Brunner, Peter Walentek, Sebastian J. Arnold, Rolf Backofen and Miriam Schmidts
Front Genet, 2022
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Ten simple rules for making a software tool workflow-ready
Paul Brack, Peter Crowther, Stian Soiland-Reyes, Stuart Owen, Douglas Lowe, Alan R. Williams, Quentin Groom, Mathias Dillen, Frederik Coppens, Björn Grüning, Ignacio Eguinoa, Philip Ewels and Carole Goble
PLoS Comput Biol, 2022
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Galaxy workflows for fragment-based virtual screening: a case study on the SARS-CoV-2 main protease
Simon Bray, Tim Dudgeon, Rachael Skyner, Rolf Backofen, Björn Grüning and Frank von Delft
J Cheminform, 2022
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Democratizing data-independent acquisition proteomics analysis on public cloud infrastructures via the Galaxy framework
Matthias Fahrner, Melanie Christine Foll, Björn Grüning, Matthias Bernt, Hannes Rost and Oliver Schilling
Gigascience, 2022
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Pluripotency factors determine gene expression repertoire at zygotic genome activation
Meijiang Gao, Marina Veil, Marcus Rosenblatt, Aileen Julia Riesle, Anna Gebhard, Helge Hass, Lenka Buryanova, Lev Y. Yampolsky, Björn Grüning, Sergey V. Ulianov, Jens Timmer and Daria Onichtchouk
Nature Communications, 2022
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RiboReport - benchmarking tools for ribosome profiling-based identification of open reading frames in bacteria
Rick Gelhausen, Teresa Müller, Sarah L Svensson, Omer S. Alkhnbashi, Cynthia M Sharma, Florian Eggenhofer and Rolf Backofen
Briefings in Bioinformatics, 2022
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The long noncoding RNA mimi scaffolds neuronal granules to maintain nervous system maturity
Dominika Grzejda, Jana Mach, Johanna Aurelia Schweizer, Barbara Hummel, Andrew Mischa Rezansoff, Florian Eggenhofer, Amol Panhale, Maria-Eleni Lalioti, Nina Cabezas Wallscheid, Rolf Backofen, Johannes Felsenberg and Valerie Hilgers
Sci Adv, 2022
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Anti-CRISPR prediction using deep learning reveals an inhibitor of Cas13b nucleases
Katharina G. Wandera, Omer S. Alkhnbashi, Harris v.I. Bassett, Alexander Mitrofanov, Sven Hauns, Anzhela Migur, Rolf Backofen and Chase L. Beisel
Molecular Cell, 2022
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An accessible infrastructure for artificial intelligence using a Docker-based JupyterLab in Galaxy
Anup Kumar, Gianmauro Cuccuru, Björn Grüning and Rolf Backofen
Gigascience, 2022
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Spacer prioritization in CRISPR-Cas9 immunity is enabled by the leader RNA
Chunyu Liao, Sahil Sharma, Sarah L. Svensson, Anuja Kibe, Zasha Weinberg, Omer S. Alkhnbashi, Thorsten Bischler, Rolf Backofen, Neva Caliskan, Cynthia M. Sharma and Chase L. Beisel
Nat Microbiol, 2022
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Catching the Wave: Detecting Strain-Specific SARS-CoV-2 Peptides in Clinical Samples Collected during Infection Waves from Diverse Geographical Locations
Subina Mehta, Valdemir M. Carvalho, Andrew T. Rajczewski, Olivier Pible, Björn Grüning, James E. Johnson, Reid Wagner, Jean Armengaud, Timothy J. Griffin and Pratik D. Jagtap
Viruses, 2022
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The antileukemic activity of decitabine upon PML/RARA-negative AML blasts is supported by all-trans retinoic acid: in vitro and in vivo evidence for cooperation
Ruth Meier, Gabriele Greve, Dennis Zimmer, Helena Bresser, Bettina Berberich, Ralitsa Langova, Julia Stomper, Anne Rubarth, Lars Feuerbach, Daniel B. Lipka, Joschka Hey, Björn Grüning, Benedikt Brors, Justus Duyster, Christoph Plass, Heiko Becker and Michael Lubbert
Blood Cancer J, 2022
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CRISPRtracrRNA: robust approach for CRISPR tracrRNA detection
Alexander Mitrofanov, Marcus Ziemann, Omer S. Alkhnbashi, Wolfgang R. Hess and Rolf Backofen
Bioinformatics, 2022
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Gut microbiota drives age-related oxidative stress and mitochondrial damage in microglia via the metabolite N(6)-carboxymethyllysine
Omar Mossad, Bérénice Batut, Bahtiyar Yilmaz, Nikolaos Dokalis, Charlotte Mezo, Elisa Nent, Lara Susann Nabavi, Melanie Mayer, Feres Jose Mocayar Maron, Joerg M. Buescher, Mercedes Gomez de Aguero, Antal Szalay, Tim Lammermann, Andrew J. Macpherson, Stephanie C. Ganal-Vonarburg, Rolf Backofen, Daniel Erny, Marco Prinz and Thomas Blank
Nat Neurosci, 2022
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High detection rate for disease-causing variants in a cohort of 30 Iranian pediatric steroid resistant nephrotic syndrome cases
Maryam Najafi, Korbinian M. Riedhammer, Aboulfazl Rad, Paria Najarzadeh Torbati, Riccardo Berutti, Isabel Schule, Sophie Schroda, Thomas Meitinger, Jasmina Comic, Simin Sadeghi Bojd, Tayebeh Baranzehi, Azadeh Shojaei, Anoush Azarfar, Mahmood Reza Khazaei, Anna Kottgen, Rolf Backofen, Ehsan Ghayoor Karimiani, Julia Hoefele and Miriam Schmidts
Front Pediatr, 2022
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MaxQuant and MSstats in Galaxy Enable Reproducible Cloud-Based Analysis of Quantitative Proteomics Experiments for Everyone
Niko Pinter, Damian Glatzer, Matthias Fahrner, Klemens Frohlich, James Johnson, Björn Grüning, Bettina Warscheid, Friedel Drepper, Oliver Schilling and Melanie Christine Foll
J Proteome Res, 2022
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Temporal annotation of high-resolution intra-annual wood density information of Eucalyptus urophylla and its correlation with hydroclimatic conditions
Gleice Gomes Rodrigues, Martin Raden, Luciana Duque Silva and Hans-Peter Kahle
Dendrochronologia, 2022
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Genome wide CRISPR screen for Pasteurella multocida toxin (PMT) binding proteins reveals LDL Receptor Related Protein 1 (LRP1) as crucial cellular receptor
Julian Schöllkopf, Thomas Mueller, Lena Hippchen, Teresa Müller, Raphael Reuten, Rolf Backofen, Joachim Orth and Gudula Schmidt
PLoS Pathog, 2022
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The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update
Galaxy Team
NAR, 2022
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Peakhood: individual site context extraction for CLIP-seq peak regions
Michael Uhl, Dominik Rabsch, Florian Eggenhofer and Rolf Backofen
Bioinformatics, 2022
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Expanding the Galaxy's reference data
Nagampalli VijayKrishna, Jayadev Joshi, Nate Coraor, Jennifer Hillman-Jackson, Dave Bouvier, Marius van den Beek, Ignacio Eguinoa, Frederik Coppens, John Davis, Michal Stolarczyk, Nathan C. Sheffield, Simon Gladman, Gianmauro Cuccuru, Björn Grüning, Nicola Soranzo, Helena Rasche, Bradley W. Langhorst, Matthias Bernt, Dan Fornika, David Anderson de Lima Morais, Michel Barrette, Peter van Heusden, Mauro Petrillo, Antonio Puertas-Gallardo, Alex Patak, Hans-Rudolf Hotz and Daniel Blankenberg
Bioinform Adv, 2022
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Distinct SARS-CoV-2 RNA fragments activate Toll-like receptors 7 and 8 and induce cytokine release from human macrophages and microglia
Thomas Wallach, Martin Raden, Lukas Hinkelmann, Mariam Brehm, Dominik Rabsch, Hannah Weidling, Christina Kruger, Helmut Kettenmann, Rolf Backofen and Seija Lehnardt
Front Immunol, 2022
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Loop detection using Hi-C data with HiCExplorer
Joachim Wolff, Rolf Backofen and Björn Grüning
Gigascience, 2022
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CRISPRloci: comprehensive and accurate annotation of CRISPR-Cas system
Omer S. Alkhnbashi, Alexander Mitrofanov, Robson Bonidia, Martin Raden, Van Dinh Tran, Florian Eggenhofer, Shiraz A. Shah, Ekrem Öztürk, Victor A. Padilha, Danilo S. Sanches, Andre C.P.L.F. de Carvalho and Rolf Backofen
NAR, 2021
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Chemotherapy-induced transposable elements activate MDA5 to enhance haematopoietic regeneration
Thomas Clapes, Aikaterini Polyzou, Pia Prater, Sagar, Antonio Morales-Hernandez, Mariana Galvao Ferrarini, Natalie Kehrer, Stylianos Lefkopoulos, Veronica Bergo, Barbara Hummel, Nadine Obier, Daniel Maticzka, Anne Bridgeman, Josip S. Herman, Ibrahim Ilik, Lheanna Klaeyle, Jan Rehwinkel, Shannon McKinney-Freeman, Rolf Backofen, Asifa Akhtar, Nina Cabezas-Wallscheid, Ritwick Sawarkar, Rita Rebollo, Dominic Grun and Eirini Trompouki
Nat Cell Biol, 2021
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Galaxy-ML: An accessible, reproducible, and scalable machine learning toolkit for biomedicine
Qiang Gu, Anup Kumar, Simon Bray, Allison Creason, Alireza Khanteymoori, Vahid Jalili, Björn Grüning and Jeremy Goecks
PLOS Computational Biology, 2021
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StoatyDive: Evaluation and classification of peak profiles for sequencing data
Florian Heyl and Rolf Backofen
Gigascience, 2021
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Transcriptome-wide in vivo mapping of cleavage sites for the compact cyanobacterial ribonuclease E reveals insights into its function and substrate recognition
Ute A. Hoffmann, Florian Heyl, Said N. Rogh, Thomas Wallner, Rolf Backofen, Wolfgang R. Hess, Claudia Steglich and Annegret Wilde
NAR, 2021
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Tool recommender system in Galaxy using deep learning
Anup Kumar, Helena Rasche, Björn Grüning and Rolf Backofen
GigaScience, 2021
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CdrS Is a Global Transcriptional Regulator Influencing Cell Division in Haloferax volcanii
Yan Liao, Verena Vogel, Sabine Hauber, Jurgen Bartel, Omer S. Alkhnbashi, Sandra Maaß, Thandi S. Schwarz, Rolf Backofen, Dörte Becher, Iain G. Duggin and Anita Marchfelder
mBio, 2021
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A distinct CD38+CD45RA+ population of CD4+, CD8+, and double-negative T cells is controlled by FAS
Maria Elena Maccari, Sebastian Fuchs, Patrick Kury, Geoffroy Andrieux, Simon Volkl, Bertram Bengsch, Myriam Ricarda Lorenz, Maximilian Heeg, Jan Rohr, Sabine Jagle, Carla N. Castro, Miriam Gross, Ursula Warthorst, Christoph Konig, Ilka Fuchs, Carsten Speckmann, Julian Thalhammer, Friedrich G. Kapp, Markus G. Seidel, Gregor Duckers, Stefan Schonberger, Catharina Schutz, Marita Fuhrer, Robin Kobbe, Dirk Holzinger, Christian Klemann, Petr Smisek, Stephen Owens, Gerd Horneff, Reinhard Kolb, Nora Naumann-Bartsch, Maurizio Miano, Julian Staniek, Marta Rizzi, Tomas Kalina, Pascal Schneider, Anika Erxleben, Rolf Backofen, Arif Ekici, Charlotte M. Niemeyer, Klaus Warnatz, Bodo Grimbacher, Hermann Eibel, Andreas Mackensen, Andreas Philipp Frei, Klaus Schwarz, Melanie Boerries, Stephan Ehl and Anne Rensing-Ehl
J Exp Med, 2021
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The temperature-regulated DEAD-box RNA helicase CrhR interactome: Autoregulation and photosynthesis-related transcripts
Anzhela Migur, Florian Heyl, Janina Fuss, Afshan Srikumar, Bruno Huettel, Claudia Steglich, Jogadhenu S. S. Prakash, Richard Reinhardt, Rolf Backofen, George W. Owttrim and Wolfgang R. Hess
J Exp Bot, 2021
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An integrated database of small RNAs and their interplay with transcriptional gene regulatory networks in corynebacteria
Mariana T.D. Parise, Doglas Parise, Flavia F. Aburjaile, Anne C.P. Gomide, Rodrigo B. Kato, Martin Raden, Rolf Backofen, Vasco A. de Carvalho Azevedo and Jan Baumbach
Frontiers in Microbiology, 2021
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Structure-aware machine learning classification of oligonucleotide-induced immune response identifies microRNAs operating as Toll-like receptor 7/8 ligands
Martin Raden, Thomas Wallach, Milad Miladi, Yuanyuan Zhai, Christina Krüger, Zoe J. Mossmann, Paul Dembny, Rolf Backofen and Seija Lehnardt
RNA Biology, 2021
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Structure-aware machine learning identifies microRNAs operating as Toll-like receptor 7/8 ligands
Martin Raden, Thomas Wallach, Milad Miladi, Yuanyuan Zhai, Christina Kruger, Zoe J. Mossmann, Paul Dembny, Rolf Backofen and Seija Lehnardt
RNA Biol, 2021
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A SARS-CoV-2 sequence submission tool for the European Nucleotide Archive
Miguel Roncoroni, Bert Droesbeke, Ignacio Eguinoa, Kim De Ruyck, Flora D'Anna, Dilmurat Yusuf, Björn Grüning, Rolf Backofen and Frederik Coppens
Bioinformatics, 2021
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Effects of intra-seasonal drought on kinetics of tracheid differentiation and seasonal growth dynamics of Norway spruce along an elevational gradient
Dominik F. Stangler, Hans-Peter Kahle, Martin Raden, Elena Larysch, Thomas Seifert and Heinrich Spiecker
Forests, 2021
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RNAProt: an efficient and feature-rich RNA binding protein binding site predictor
Michael Uhl, Van Dinh Tran, Florian Heyl and Rolf Backofen
Gigascience, 2021
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ChiRA: an integrated framework for chimeric read analysis from RNA-RNA interactome and RNA structurome data
Pavankumar Videm, Anup Kumar, Oleg Zharkov, Björn Grüning and Rolf Backofen
Gigascience, 2021
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MicroRNA-100-5p and microRNA-298-5p released from apoptotic cortical neurons are endogenous Toll-like receptor 7/8 ligands that contribute to neurodegeneration
Thomas Wallach, Zoe Mossmann, Michal Szczepek, Max Wetzel, Rui Machado, Martin Raden, Milad Miladi, Gunnar Kleinau, Christina Krüger, Paul Dembny, Drew Adler, Yuanyuan Zhai, Omar Dzaye, Matthias Futschik, Rolf Backofen, Patrick Scheerer and Seija Lehnardt
Molecular Neurodegeneration, 2021
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Robust and efficient single-cell Hi-C clustering with approximate k-nearest neighbor graphs
Joachim Wolff, Rolf Backofen and Björn Grüning
Bioinformatics, 2021
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Generation of pure monocultures of human microglia-like cells from induced pluripotent stem cells
Poulomi Banerjee, Evdokia Paza, Emma M Perkins, Owen G James, Boyd Kenkhuis, Amy F Lloyd, Karen Burr, David Story, Dilmurat Yusuf, Xin He, Rolf Backofen, Owen Dando, Siddharthan Chandran and Josef Priller
Stem Cell Res., 2020
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Temporospatial distribution and transcriptional profile of retinal microglia in the oxygen-induced retinopathy mouse model
Myriam Boeck, Adrian Thien, Julian Wolf, Nora Hagemeyer, Yannik Laich, Dilmurat Yusuf, Rolf Backofen, Peipei Zhang, Stefaniya Boneva, Andreas Stahl, Ingo Hilgendorf, Hansjürgen Agostini, Marco Prinz, Peter Wieghofer, Günther Schlunck, Anja Schlecht and Clemens Lange
Glia, 2020
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The ChemicalToolbox: reproducible, user-friendly cheminformatics analysis on the Galaxy platform
Simon A. Bray, Xavier Lucas, Anup Kumar and Björn Grüning
Journal of Cheminformatics, 2020
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Intuitive, reproducible high-throughput molecular dynamics in Galaxy: a tutorial
Simon A. Bray, Tharindu Senapathi, Christopher B. Barnett and Björn Grüning
Journal of Cheminformatics, 2020
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pourRNA - a time- and memory-efficient approach for the guided exploration of RNA energy landscapes
Gregor Entzian and Martin Raden
Bioinformatics, 2020
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HRIBO: high-throughput analysis of bacterial ribosome profiling data
Rick Gelhausen, Sarah L Svensson, Kathrin Froschauer, Florian Heyl, Lydia Hadjeras, Cynthia M Sharma, Florian Eggenhofer and Rolf Backofen
Bioinformatics, 2020
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pyGenomeTracks: reproducible plots for multivariate genomic data sets
Lucille Lopez-Delisle, Leily Rabbani, Joachim Wolff, Vivek Bhardwaj, Rolf Backofen, Björn Grüning, Fidel Ramirez and Thomas Manke
Bioinformatics, 2020
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Evolutionary classification of CRISPR-Cas systems: a burst of class 2 and derived variants
Kira S. Makarova, Yuri I. Wolf, Jaime Iranzo, Sergey A. Shmakov, Omer S. Alkhnbashi, Stan J. J. Brouns, Emmanuelle Charpentier, David Cheng, Daniel H. Haft, Philippe Horvath, Sylvain Moineau, Francisco J. M. Mojica, David Scott, Shiraz A. Shah, Virginijus Siksnys, Michael P. Terns, Ceslovas Venclovas, Malcolm F. White, Alexander F. Yakunin, Winston Yan, Feng Zhang, Roger A. Garrett, Rolf Backofen, John van der Oost, Rodolphe Barrangou and Eugene V. Koonin
Nat Rev Microbiol, 2020
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Nephronophthisis gene products display RNA-binding properties and are recruited to stress granules
Luisa Estrada Mallarino, Christina Engel, Ibrahim Avsar Ilik, Daniel Maticzka, Florian Heyl, Barbara Müller, Toma A Yakulov, Jörn Dengjel, Rolf Backofen and Asifa Akhtar
Scientific reports, 2020
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MutaRNA: analysis and visualization of mutation-induced changes in RNA structure
Milad Miladi, Martin Raden, Sven Diederichs and Rolf Backofen
Nucleic Acids Research, 2020
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CRISPRidentify: identification of CRISPR arrays using machine learning approach
Alexander Mitrofanov, Omer S. Alkhnbashi, Sergey A. Shmakov, Kira S. Makarova, Eugene V. Koonin and Rolf Backofen
NAR, 2020
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The locality dilemma of Sankoff-like RNA alignments
Teresa Müller, Milad Miladi, Frank Hutter, Ivo Hofacker, Sebastian Will and Rolf Backofen
Bioinformatics, 2020
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CRISPRcasIdentifier: Machine learning for accurate identification and classification of CRISPR-Cas systems
Victor A. Padilha, Omer S. Alkhnbashi, Shiraz A. Shah, Andre C. P. L. F. de Carvalho and Rolf Backofen
Gigascience, 2020
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Casboundary: automated definition of integral Cas cassettes
Victor A Padilha, Omer S. Alkhnbashi, Van Dinh Tran, Shiraz A Shah, André C P L F Carvalho and Rolf Backofen
Bioinformatics, 2020
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CopomuS - ranking compensatory mutations to guide RNA-RNA interaction verification experiments
Martin Raden, Fabio Gutmann, Michael Uhl and Rolf Backofen
International Journal of Molecular Sciences , 2020
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The impact of various seed, accessibility and interaction constraints on sRNA target prediction - a systematic assessment
Martin Raden, Teresa Müller, Stefan Mautner, Rick Gelhausen and Rolf Backofen
BMC Bioinformatics, 2020
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The potential of intra-annual density information for crossdating of short tree-ring series
Martin Raden, Alexander Mattheis, Hans-Peter Kahle, Heinrich Spiecker and Rolf Backofen
Dendrochronologia, 2020
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Adaptation induced by self-targeting in a type I-B CRISPR-Cas system
Aris-Edda Stachler, Julia Wortz, Omer S. Alkhnbashi, Israela Turgeman-Grott, Rachel Smith, Thorsten Allers, Rolf Backofen, Uri Gophna and Anita Marchfelder
JBC, 2020
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A single-cell RNA-sequencing training and analysis suite using the Galaxy framework
Mehmet Tekman, Bérénice Batut, Alexander Ostrovsky, Christophe Antoniewski, Dave Clements, Fidel Ramirez, Graham J Etherington, Hans-Rudolf Hotz, Jelle Scholtalbers, Jonathan R Manning, Lea Bellenger, Maria A Doyle, Mohammad Heydarian, Ni Huang, Nicola Soranzo, Pablo Moreno, Stefan Mautner, Irene Papatheodorou, Anton Nekrutenko, James Taylor, Daniel Blankenberg, Rolf Backofen and Björn Grüning
GigaScience, 2020
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Heterogeneous networks integration for disease-gene prioritization with node kernels
Van Dinh Tran, Alessandro Sperduti, Rolf Backofen and Fabrizio Costa
Bioinformatics, 2020
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Improving CLIP-seq data analysis by incorporating transcript information
Michael Uhl, Van Dinh Tran and Rolf Backofen
BMC genomics, 2020
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A global data-driven census of Salmonella small proteins and their potential functions in bacterial virulence
Elisa Venturini, Sarah L Svensson, Sandra Maass, Rick Gelhausen, Florian Eggenhofer, Lei Li, Amy K Cain, Julian Parkhill, Dörte Becher, Rolf Backofen, Lars Barquist, Cynthia M Sharma, Alexander J Westermann and Jörg Vogel
microLife, 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
Joachim Wolff, Leily Rabbani, Ralf Gilsbach, Gautier Richard, Thomas Manke, Rolf Backofen and Björn Grüning
Nucleic Acids Research, 2020
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Scool: a new data storage format for single-cell Hi-C data
Joachim Wolff, Nezar Abdennur, Rolf Backofen and Björn Grüning
Bioinformatics, 2020
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NanoGalaxy: Nanopore long-read sequencing data analysis in Galaxy
Willem de Koning, Milad Miladi, Saskia Hiltemann, Astrid Heikema, John P Hays, Stephan Flemming, Marius van den Beek, Dana A. Mustafa, Rolf Backofen, Björn Grüning and Andrew P. Stubbs
GigaScience, 2020
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CRISPR-Cas bioinformatics
Omer S. Alkhnbashi, Tobias Meier, Alexander Mitrofanov, Rolf Backofen and Björn Voss
Methods, 2019
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The RNA workbench 2.0: next generation RNA data analysis
Jörg Fallmann, Pavankumar Videm, Andrea Bagnacani, Bérénice Batut, Maria A. Doyle, Tomas Klingstrom, Florian Eggenhofer, Peter F. Stadler, Rolf Backofen and Björn Grüning
NAR, 2019
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The RNA workbench 2.0: next generation RNA data analysis
Jörg Fallmann, Pavankumar Videm, Andrea Bagnacani, Bérénice Batut, Maria A Doyle, Tomas Klingstrom, Florian Eggenhofer, Peter F Stadler, Rolf Backofen and Björn Grüning
Nucleic Acids Research, 2019
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The RNA workbench 2.0: next generation RNA data analysis
Jörg Fallmann, Pavankumar Videm, Andrea Bagnacani, Bérénice Batut, Maria A Doyle, Tomas Klingstrom, Florian Eggenhofer, Peter F Stadler, Rolf Backofen and Björn Grüning
Nucleic Acids Research, 2019
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IntaRNAhelix - Composing RNA-RNA interactions from stable inter-molecular helices boosts bacterial sRNA target prediction
Rick Gelhausen, Sebastian Will, Ivo L. Hofacker, Rolf Backofen and Martin Raden
Journal of Bioinformatics and Computational Biology, 2019
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Constraint Maximal Inter-molecular Helix Lengths within RNA-RNA Interaction Prediction Improves Bacterial sRNA Target Prediction
Rick Gelhausen, Sebastian Will, Ivo L. Hofacker, Rolf Backofen and Martin Raden
Proceedings of the 12th International Joint Conference on Biomedical Engineering Systems and Technologies - Volume 3: BIOINFORMATICS, 2019
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CRISPR-Cas systems in multicellular cyanobacteria
Shengwei Hou, Manuel Brenes-Alvarez, Viktoria Reimann, Omer S. Alkhnbashi, Rolf Backofen, Alicia M. Muro-Pastor and Wolfgang R. Hess
RNA Biol, 2019
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FLASH: ultra-fast protocol to identify RNA–protein interactions in cells
Ibrahim Avsar Ilik, Tugce Aktas, Daniel Maticzka, Rolf Backofen and Asifa Akhtar
Nucleic Acids Research, 2019
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The nuts and bolts of the Haloferax CRISPR-Cas system I-B
Lisa-Katharina Maier, Aris-Edda Stachler, Jutta Brendel, Britta Stoll, Susan Fischer, Karina A. Haas, Thandi S. Schwarz, Omer S. Alkhnbashi, Kundan Sharma, Henning Urlaub, Rolf Backofen, Uri Gophna and Anita Marchfelder
RNA Biol, 2019
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ShaKer: RNA SHAPE prediction using graph kernel
Stefan Mautner, Soheila Montaseri, Milad Miladi, Martin Raden, Fabrizio Costa and Rolf Backofen
Bioinformatics, 2019
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Progress Towards Graph Optimization: Efficient Learning of Vector to Graph Space Mappings
Stefan Mautner, Rolf Backofen and Fabrizio Costa
ESANN 2019 - Proceedings, 2019
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Integration of accessibility data from structure probing into RNA-RNA interaction prediction
Milad Miladi, Soheila Montaseri, Rolf Backofen and Martin Raden
Bioinformatics, 2019
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GraphClust2: Annotation and discovery of structured RNAs with scalable and accessible integrative clustering
Milad Miladi, Eteri Sokhoyan, Torsten Houwaart, Steffen Heyne, Fabrizio Costa, Björn Grüning and Rolf Backofen
GigaScience, 2019
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Fast and Accurate Structure Probability Estimation for Simultaneous Alignment and Folding of RNAs
Milad Miladi, Martin Raden, Sebastian Will and Rolf Backofen
19th International Workshop on Algorithms in Bioinformatics (WABI 2019), 2019
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Universal readout for graph convolutional neural networks
Nicolò Navarin, Van Dinh Tran and Alessandro Sperduti
2019 International Joint Conference on Neural Networks (IJCNN), 2019
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Cross-cleavage activity of Cas6b in crRNA processing of two different CRISPR-Cas systems in Methanosarcina mazei Go1
Lisa Nickel, Andrea Ulbricht, Omer S. Alkhnbashi, Konrad U. Forstner, Liam Cassidy, Katrin Weidenbach, Rolf Backofen and Ruth A. Schmitz
RNA Biol, 2019
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Noncoding deletions reveal a gene that is critical for intestinal function
Danit Oz-Levi, Tsviya Olender, Ifat Bar-Joseph, Yiwen Zhu, Dina Marek-Yagel, Iros Barozzi, Marco Osterwalder, Anna Alkelai, Elizabeth K Ruzzo and Yujun Han
Nature, 2019
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uORF-Tools - Workflow for the determination of translation-regulatory upstream open reading frames
Anica Scholz, Florian Eggenhofer, Rick Gelhausen, Björn Grüning, Kathi Zarnack, Bernhard Brüne, Rolf Backofen and Tobias Schmid
PLOS ONE, 2019
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Biomolecular Reaction and Interaction Dynamics Global Environment (BRIDGE)
Tharindu Senapathi, Simon Bray, Christopher B Barnett, Björn Grüning and Kevin J Naidoo
Bioinformatics, 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
Shiraz A. Shah, Omer S. Alkhnbashi, Juliane Behler, Wenyuan Han, Qunxin She, Wolfgang R. Hess, Roger A. Garrett and Rolf Backofen
RNA Biol, 2019
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A pan-cancer analysis of synonymous mutations
Yogita Sharma, Milad Miladi, Sandeep Dukare, Karine Boulay, Maiwen Caudron-Herger, Matthias Gross, Rolf Backofen and Sven Diederichs
Nature communications, 2019
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Comparative RNA Genomics
Rolf Backofen, Jan Gorodkin, Ivo L. Hofacker and Peter F. Stadler
Methods Mol Biol, 2018
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hnRNP R and its main interactor, the noncoding RNA 7SK, coregulate the axonal transcriptome of motoneurons
Michael Briese, Lena Saal-Bauernschubert, Changhe Ji, Mehri Moradi, Hanaa Ghanawi, Michael Uhl, Silke Appenzeller, Rolf Backofen and Michael Sendtner
PNAS, 2018
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GraphDDP: a graph-embedding approach to detect differentiation pathways in single-cell-data using prior class knowledge
Fabrizio Costa, Dominic Grun and Rolf Backofen
Nat Commun, 2018
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CMV - Visualization for RNA and Protein family models and their comparisons
Florian Eggenhofer, Ivo L. Hofacker, Rolf Backofen and Christian Honer Zu Siederdissen
Bioinformatics, 2018
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DOT1L promotes progenitor proliferation and primes neuronal layer identity in the developing cerebral cortex
Henriette Franz, Alejandro Villarreal, Stefanie Heidrich, Pavankumar Videm, Fabian Kilpert, Ivan Mestres, Federico Calegari, Rolf Backofen, Thomas Manke and Tanja Vogel
Nucleic Acids Research, 2018
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DOT1L promotes progenitor proliferation and primes neuronal layer identity in the developing cerebral cortex
Henriette Franz, Alejandro Villarreal, Stefanie Heidrich, Pavankumar Videm, Fabian Kilpert, Ivan Mestres, Federico Calegari, Rolf Backofen, Thomas Manke and Tanja Vogel
Nucleic Acids Research, 2018
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MechRNA: prediction of lncRNA mechanisms from RNA-RNA and RNA-protein interactions
Alexander R. Gawronski, Michael Uhl, Yajia Zhang, Yen-Yi Lin, Yashar S. Niknafs, Varune R. Ramnarine, Rohit Malik, Felix Feng, Arul M. Chinnaiyan, Colin C. Collins, S. Cenk Sahinalp and Rolf Backofen
Bioinformatics, 2018
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Distinct epigenetic programs regulate cardiac myocyte development and disease in the human heart in vivo
Ralf Gilsbach, Martin Schwaderer, Sebastian Preissl, Björn Grüning, David Kranzhofer, Pedro Schneider, Thomas G. Nuhrenberg, Sonia Mulero-Navarro, Dieter Weichenhan, Christian Braun, Martina Dressen, Adam R. Jacobs, Harald Lahm, Torsten Doenst, Rolf Backofen, Markus Krane, Bruce D. Gelb and Lutz Hein
Nat Commun, 2018
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Bioconda: sustainable and comprehensive software distribution for the life sciences
Björn Grüning, Ryan Sjödin Andreas Dale, Brad A. Chapman, Jillian Rowe, Christopher H. Tomkins-Tinch, Renan Valieris, Bioconda Team and Johannes Köster
Nature Methods, 2018
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GLASSgo - Automated and reliable detection of sRNA homologs from a single input sequences
Steffen C. Lott, Richard A. Schäfer, Martin Raden, Rolf Backofen, Wolfgang R. Hess, Björn Voss and Jens Georg
Frontiers in Genetics, 2018
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The nuts and bolts of the Haloferax CRISPR-Cas system I-B
Lisa-Katharina Maier, Aris-Edda Stachler, Jutta Brendel, Britta Stoll, Susan Fischer, Karina Haas, Thandi Schwarz, Omer S. Alkhnbashi, Kundan Sharma, Henning Urlaub, Rolf Backofen, Uri Gophna and Anita Marchfelder
RNA Biol, 2018
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MICA: Multiple interval-based curve alignment
Martin Raden, Hans-Peter Kahle, Matthias Beck, Bela Johannes Bender, Heinrich Spiecker and Rolf Backofen
SoftwareX, 2018
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uvCLAP is a fast and non-radioactive method to identify in vivo targets of RNA-binding proteins
Daniel Maticzka, Ibrahim Avsar Ilik, Tugce Aktas, Rolf Backofen and Asifa Akhtar
Nat Commun, 2018
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Interactive implementations of thermodynamics-based RNA structure and RNA-RNA interaction prediction approaches for example-driven teaching
Martin Raden, Mostafa M Mohamed, Syed M Ali and Rolf Backofen
PLOS Comput. Biol, 2018
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Freiburg RNA tools: a central online resource for RNA-focused research and teaching
Martin Raden, Syed M Ali, Omer S. Alkhnbashi, Anke Busch, Fabrizio Costa, Jason A Davis, Florian Eggenhofer, Rick Gelhausen, Jens Georg, Steffen Heyne, Michael Hiller, Kousik Kundu, Robert Kleinkauf, Steffen C Lott, Mostafa M Mohamed, Alexander Mattheis, Milad Miladi, Andreas S Richter, Sebastian Will, Joachim Wolff, Patrick R Wright and Rolf Backofen
Nucleic Acids Research, 2018
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The RNA-binding protein ARPP21 controls dendritic branching by functionally opposing the miRNA it hosts
Frederick Rehfeld, Daniel Maticzka, Sabine Grosser, Pina Knauff, Murat Eravci, Imre Vida, Rolf Backofen and F. Gregory Wulczyn
Nat Commun, 2018
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In vitro iCLIP-based modeling uncovers how the splicing factor U2AF2 relies on regulation by cofactors
F. X. Reymond Sutandy, Stefanie Ebersberger, Lu Huang, Anke Busch, Maximilian Bach, Hyun-Seo Kang, Jörg Fallmann, Daniel Maticzka, Rolf Backofen, Peter F. Stadler, Kathi Zarnack, Michael Sattler, Stefan Legewie and Julian Konig
Genome Res, 2018
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Combinatorial Omics Analysis Reveals Perturbed Lysosomal Homeostasis in Collagen VII-deficient Keratinocytes
Kerstin Thriene, Björn Grüning, Olivier Bornert, Anika Erxleben, Juna Leppert, Ioannis Athanasiou, Ekkehard Weber, Dimitra Kiritsi, Alexander Nystrom, Thomas Reinheckel, Rolf Backofen, Cristina Has, Leena Bruckner-Tuderman and Jorn Dengjel
Mol Cell Proteomics, 2018
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On filter size in graph convolutional networks
Van Dinh Tran, Nicolò Navarin and Alessandro Sperduti
2018 IEEE Symposium Series on Computational Intelligence (SSCI), 2018
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FOXG1 Regulates PRKAR2B Transcriptionally and Posttranscriptionally via miR200 in the Adult Hippocampus
Stefan C. Weise, Ganeshkumar Arumugam, Alejandro Villarreal, Pavankumar Videm, Stefanie Heidrich, Nils Nebel, Verónica I. Dumit, Farahnaz Sananbenesi, Viktoria Reimann, Madeline Craske, Oliver Schilling, Wolfgang R. Hess, Andre Fischer, Rolf Backofen and Tanja Vogel
Molecular Neurobiology, 2018
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Structure and interaction prediction in prokaryotic RNA biology
Patrick R. Wright, Martin Raden and Rolf Backofen
Microbiol Spectrum, 2018
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Workflow for a Computational Analysis of an sRNA Candidate in Bacteria
Patrick R. Wright and Jens Georg
Methods Mol Biol, 2018
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Analysis of the androgen receptor-regulated lncRNA landscape identifies a role for ARLNC1 in prostate cancer progression
Yajia Zhang, Sethuramasundaram Pitchiaya, Marcin Cieslik, Yashar S. Niknafs, Jean C-Y Tien, Yasuyuki Hosono, Matthew K. Iyer, Sahr Yazdani, Shruthi Subramaniam, Sudhanshu K. Shukla, Xia Jiang, Lisha Wang, Tzu-Ying Liu, Michael Uhl, Alexander R. Gawronski, Yuanyuan Qiao, Lanbo Xiao, Saravana M. Dhanasekaran, Kristin M. Juckette, Lakshmi P. Kunju, Xuhong Cao, Utsav Patel, Mona Batish, Girish C. Shukla, Michelle T. Paulsen, Mats Ljungman, Hui Jiang, Rohit Mehra, Rolf Backofen, Cenk S. Sahinalp, Susan M. Freier, Andrew T. Watt, Shuling Guo, John T. Wei, Felix Y. Feng, Rohit Malik and Arul M. Chinnaiyan
Nat Genet, 2018
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DHX9 suppresses RNA processing defects originating from the Alu invasion of the human genome
Tugce Aktas, Ibrahim Avsar Ilik, Daniel Maticzka, Vivek Bhardwaj, Cecilia Pessoa Rodrigues, Gerhard Mittler, Thomas Manke, Rolf Backofen and Asifa Akhtar
Nature, 2017
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RNA-bioinformatics: Tools, services and databases for the analysis of RNA-based regulation
Rolf Backofen, Jan Engelhardt, Anika Erxleben, Jorg Fallmann, Björn Grüning, Uwe Ohler, Nikolaus Rajewsky and Peter F. Stadler
J Biotechnol, 2017
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RIP-Seq Suggests Translational Regulation by L7Ae in Archaea
Michael Daume, Michael Uhl, Rolf Backofen and Lennart Randau
MBio, 2017
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Combinatorial ensemble miRNA target prediction of co-regulation networks with non-prediction data
Jason A. Davis, Sita J. Saunders, Martin Raden and Rolf Backofen
NAR, 2017
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Recent advances in RNA folding
Jörg Fallmann, Sebastian Will, Jan Engelhardt, Björn Grüning, Rolf Backofen and Peter F. Stadler
J Biotechnol, 2017
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The RNA workbench: best practices for RNA and high-throughput sequencing bioinformatics in Galaxy
Björn Grüning, Jörg Fallmann, Dilmurat Yusuf, Sebastian Will, Anika Erxleben, Florian Eggenhofer, Torsten Houwaart, Bérénice Batut, Pavankumar Videm, Andrea Bagnacani, Markus Wolfien, Steffen C. Lott, Youri Hoogstrate, Wolfgang R. Hess, Olaf Wolkenhauer, Steve Hoffmann, Altuna Akalin, Uwe Ohler, Peter F. Stadler and Rolf Backofen
NAR, 2017
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Jupyter and Galaxy: Easing entry barriers into complex data analyses for biomedical researchers
Björn Grüning, Eric Rasche, Boris Rebolledo-Jaramillo, Carl Eberhard, Torsten Houwaart, John Chilton, Nate Coraor, Rolf Backofen, James Taylor and Anton Nekrutenko
PLoS Comput Biol, 2017
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A mutually exclusive stem-loop arrangement in roX2 RNA is essential for X-chromosome regulation in Drosophila
Ibrahim Avsar Ilik, Daniel Maticzka, Plamen Georgiev, Noel Marie Gutierrez, Rolf Backofen and Asifa Akhtar
Genes Dev, 2017
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An Efficient Semi-supervised Learning Approach to Predict SH2 Domain Mediated Interactions
Kousik Kundu and Rolf Backofen
Methods Mol Biol, 2017
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CRISPR and Salty: CRISPR-Cas Systems in Haloarchaea
Lisa-Katharina Maier, Omer S. Alkhnbashi, Rolf Backofen and Anita Marchfelder
RNA Metabolism and Gene Expression in Archaea, 2017
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IntaRNA 2.0: enhanced and customizable prediction of RNA-RNA interactions
Martin Raden, Patrick R. Wright and Rolf Backofen
NAR, 2017
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RNAscClust: clustering RNA sequences using structure conservation and graph based motifs
Milad Miladi, Alexander Junge, Fabrizio Costa, Stefan E Seemann, Jakob Hull Havgaard, Jan Gorodkin and Rolf Backofen
Bioinformatics, 2017
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Differentiation of ncRNAs from small mRNAs in Escherichia coli O157:H7 EDL933 (EHEC) by combined RNAseq and RIBOseq - ryhB encodes the regulatory RNA RyhB and a peptide, RyhP
Klaus Neuhaus, Richard Landstorfer, Svenja Simon, Steffen Schober, Patrick R. Wright, Cameron Smith, Rolf Backofen, Romy Wecko, Daniel A. Keim and Siegfried Scherer
BMC Genomics, 2017
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Mechanism of beta-actin mRNA Recognition by ZBP1
Giuseppe Nicastro, Adela M. Candel, Michael Uhl, Alain Oregioni, David Hollingworth, Rolf Backofen, Stephen R. Martin and Andres Ramos
Cell Rep, 2017
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sRNA154 a newly identified regulator of nitrogen fixation in Methanosarcina mazei strain Go1
Daniela Prasse, Konrad U. Förstner, Dominik Jäger, Rolf Backofen and Ruth A. Schmitz
RNA Biol, 2017
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Structural constraints and enzymatic promiscuity in the Cas6-dependent generation of crRNAs
Viktoria Reimann, Omer S. Alkhnbashi, Sita J. Saunders, Ingeborg Scholz, Stephanie Hein, Rolf Backofen and Wolfgang R. Hess
NAR, 2017
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Computational analysis of CLIP-seq data
Michael Uhl, Torsten Houwaart, Gianluca Corrado, Patrick R. Wright and Rolf Backofen
Methods, 2017
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MetSV, a novel archaeal lytic virus targeting Methanosarcina strains
Katrin Weidenbach, Lisa Nickel, Horst Neve, Omer S. Alkhnbashi, Sven Kunzel, Anne Kupczok, Thorsten Bauersachs, Liam Cassidy, Andreas Tholey, Rolf Backofen and Ruth A. Schmitz
J Virol, 2017
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Characterizing leader sequences of CRISPR loci
Omer S. Alkhnbashi, Shiraz A. Shah, Roger A. Garrett, Sita J. Saunders, Fabrizio Costa and Rolf Backofen
Bioinformatics, 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
Giorgia Del Vecchio, Francesca De Vito, Sita J. Saunders, Adele Risi, Cecilia Mannironi, Irene Bozzoni and Carlo Presutti
RNA, 2016
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Global RNA recognition patterns of post-transcriptional regulators Hfq and CsrA revealed by UV crosslinking in vivo
Erik Holmqvist, Patrick R. Wright, Lei Li, Thorsten Bischler, Lars Barquist, Richard Reinhardt, Rolf Backofen and Jörg Vogel
EMBO J, 2016
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Differential transcriptional responses to Ebola and Marburg virus infection in bat and human cells
Martin Holzer, Verena Krahling, Fabian Amman, Emanuel Barth, Stephan H. Bernhart, Victor A. O. Carmelo, Maximilian Collatz, Gero Doose, Florian Eggenhofer, Jan Ewald, Jörg Fallmann, Lasse M. Feldhahn, Markus Fricke, Juliane Gebauer, Andreas J. Gruber, Franziska Hufsky, Henrike Indrischek, Sabina Kanton, Jorg Linde, Nelly Mostajo, Roman Ochsenreiter, Konstantin Riege, Lorena Rivarola-Duarte, Abdullah H. Sahyoun, Sita J. Saunders, Stefan E. Seemann, Andrea Tanzer, Bertram Vogel, Stefanie Wehner, Michael T. Wolfinger, Rolf Backofen, Jan Gorodkin, Ivo Grosse, Ivo Hofacker, Steve Hoffmann, Christoph Kaleta, Peter F. Stadler, Stephan Becker and Manja Marz
Sci Rep, 2016
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GenToS: Use of Orthologous Gene Information to Prioritize Signals from Human GWAS
Anselm S. Hoppmann, Pascal Schlosser, Rolf Backofen, Ekkehart Lausch and Anna Kottgen
PLoS One, 2016
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The lncRNA landscape of breast cancer reveals a role for DSCAM-AS1 in breast cancer progression
Yashar S. Niknafs, Sumin Han, Teng Ma, Corey Speers, Chao Zhang, Kari Wilder-Romans, Matthew K. Iyer, Sethuramasundaram Pitchiaya, Rohit Malik, Yasuyuki Hosono, John R. Prensner, Anton Poliakov, Udit Singhal, Lanbo Xiao, Steven Kregel, Ronald F. Siebenaler, Shuang G. Zhao, Michael Uhl, Alexander Gawronski, Daniel F. Hayes, Lori J. Pierce, Xuhong Cao, Colin Collins, Rolf Backofen, Cenk S. Sahinalp, James M. Rae, Arul M. Chinnaiyan and Felix Y. Feng
Nat Commun, 2016
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Structural constraints and enzymatic promiscuity in the Cas6-dependent generation of crRNAs
Viktoria Reimann, Omer S. Alkhnbashi, Sita J. Saunders, Ingeborg Scholz, Stephanie Hein, Rolf Backofen and Wolfgang R. Hess
NAR, 2016
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Spatiotemporal alignment of radial tracheid diameter profiles of submontane Norway spruce
D.F. Stangler, Martin Raden, H.-P. Kahle, E. Rosskopf, S. Fink and H. Spiecker
Dendrochronologia, 2016
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Photorhabdus-nematode symbiosis is dependent on hfq-mediated regulation of secondary metabolites
Nicholas J. Tobias, Antje K. Heinrich, Helena Eresmann, Patrick R. Wright, Nick Neubacher, Rolf Backofen and Helge B. Bode
Environ Microbiol, 2016
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Plasticity of archaeal C/D box sRNA biogenesis
Vanessa Tripp, Roman Martin, Alvaro Orell, Omer S. Alkhnbashi, Rolf Backofen and Lennart Randau
Mol Microbiol, 2016
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MicroRNA Profiling in Aqueous Humor of Individual Human Eyes by Next-Generation Sequencing
Thomas Wecker, Klaus Hoffmeier, Anne Plotner, Björn Grüning, Ralf Horres, Rolf Backofen, Thomas Reinhard and Gunther Schlunck
Invest Ophthalmol Vis Sci, 2016
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SnoReport 2.0: new features and a refined Support Vector Machine to improve snoRNA identification
Joao Victor de Araujo Oliveira, Fabrizio Costa, Rolf Backofen, Peter Florian Stadler, Maria Emilia Machado Telles Walter and Jana Hertel
BMC Bioinformatics, 2016
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The role of Cas8 in type I CRISPR interference
Simon D. B. Cass, Karina A. Haas, Britta Stoll, Omer S. Alkhnbashi, Kundan Sharma, Henning Urlaub, Rolf Backofen, Anita Marchfelder and Edward L. Bolt
Biosci Rep, 2015
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Towards an Automated Annotation of CRISPR-Cas systems
F. Costa, O. S. Alkhnbashi, S. A. Shah, Sita J. Saunders, R. Barrangou, S. J. J. Brouns, E. Charpentier, D. H. Haft, P. Horvath, E. V. Koonin, K. S. Makarova, S. Moineau, F. J. M. Mojica, R. M. Terns, M. A. Terns, J van der Oost, M. F. White, YI Wolf, A. F. Yakunin, R. A. Garrett and Rolf Backofen
Poster, CRISPR Conference'15, 2015
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Towards an Automated Annotation of CRISPR-Cas systems
F Costa, O. S. Alkhnbashi, S. A. Shah, Sita J. Saunders, R Barrangou, SJJ Brouns, E Charpentier, DH Haft, P Horvath, EV Koonin, KS Makarova, S Moineau, FJM Mojica, RM Terns, MA Terns, J van der Oost, MF White, YI Wolf, AF Yakunin, RA Garrett and Rolf Backofen
Poster, CRISPR Conference 2015, 2015
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Comparative analysis of the antioxidant properties of Icelandic and Hawaiian lichens
Kehau Hagiwara, Patrick R. Wright, Nicole K. Tabandera, Dovi Kelman, Rolf Backofen, Sesselja Omarsdottir and Anthony D. Wright
Environ Microbiol, 2015
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antaRNA - Multi-objective inverse folding of pseudoknot RNA using ant-colony optimization
R. Kleinkauf, T. Houwaart, Rolf Backofen and Martin Raden
BMC Bioinformatics, 2015
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antaRNA - Ant Colony Based RNA Sequence Design
R. Kleinkauf, Martin Raden and Rolf Backofen
Bioinformatics, 2015
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Computational Prediction of Modular Domain-Peptide Interactions
Kousik Kundu, Fabrizio Costa and Rolf Backofen
Poster Proceedings of ISMB'15, 2015
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Cell type specific gene expression analysis of prostate needle biopsies resolves tumor tissue heterogeneity
Malte Kronig, Max Walter, Vanessa Drendel, Martin Werner, Cordula A. Jilg, Andreas S. Richter, Rolf Backofen, David McGarry, Marie Follo, Wolfgang Schultze-Seemann and Roland Schule
Oncotarget, 2015
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An active immune defense with a minimal CRISPR (clustered regularly interspaced short palindromic repeats) RNA and without the Cas6 protein
Lisa-Katharina Maier, Aris-Edda Stachler, Sita J. Saunders, Rolf Backofen and Anita Marchfelder
JBC, 2015
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An updated evolutionary classification of CRISPR-Cas systems
Kira S. Makarova, Yuri I. Wolf, Omer S. Alkhnbashi, Fabrizio Costa, Shiraz A. Shah, Sita J. Saunders, Rodolphe Barrangou, Stan J. J. Brouns, Emmanuelle Charpentier, Daniel H. Haft, Philippe Horvath, Sylvain Moineau, Francisco J. M. Mojica, Rebecca M. Terns, Michael P. Terns, Malcolm F. White, Alexander F. Yakunin, Roger A. Garrett, John van der Oost, Rolf Backofen and Eugene V. Koonin
Nat Rev Microbiol, 2015
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RC3H1 post-transcriptionally regulates A20 mRNA and modulates the activity of the IKK/NF-kappaB pathway
Yasuhiro Murakawa, Michael Hinz, Janina Mothes, Anja Schuetz, Michael Uhl, Emanuel Wyler, Tomoharu Yasuda, Guido Mastrobuoni, Caroline C. Friedel, Lars Dolken, Stefan Kempa, Marc Schmidt-Supprian, Nils Bluthgen, Rolf Backofen, Udo Heinemann, Jana Wolf, Claus Scheidereit and Markus Landthaler
Nat Commun, 2015
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CRISPRloci: Comprehensive and accurate annotation of CRISPR-Cas systems
Omer S. Alkhnbashi, Shiraz A. Shah, Fabrizio Costa, Martin Raden, Xu Peng, Roger A. Garrett and Rolf Backofen
Poster, CRISPR Conference'15, 2015
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CRISPRloci: Comprehensive and accurate annotation of CRISPR-Cas systems
Omer S. Alkhnbashi, Shiraz A. Shah, Fabrizio Costa, Martin Raden, Xu Peng, Roger A. Garrett and Rolf Backofen
Poster, CRISPR Conference 2015, 2015
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Deciphering the Epigenetic Code of Cardiac Myocyte Transcription
Sebastian Preissl, Martin Schwaderer, Alexandra Raulf, Michael Hesse, Björn Grüning, Claudia Kobele, Rolf Backofen, Bernd K. Fleischmann, Lutz Hein and Ralf Gilsbach
Circ Res, 2015
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SimiRa: A tool to identify coregulation between microRNAs and RNA-binding proteins
Martin Preusse, Carsten Marr, Sita Saunders, Daniel Maticzka, Heiko Lickert, Rolf Backofen and Fabian Theis
RNA Biology, 2015
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A stress-induced small RNA modulates alpha-rhizobial cell cycle progression
Marta Robledo, Benjamin Frage, Patrick R. Wright and Anke Becker
PLoS Genet, 2015
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SPARSE: quadratic time simultaneous alignment and folding of RNAs without sequence-based heuristics
Sebastian Will, Christina Otto, Milad Miladi, Mathias Möhl and Rolf Backofen
Bioinformatics, 2015
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CRISPRstrand: predicting repeat orientations to determine the crRNA-encoding strand at CRISPR loci
Omer S. Alkhnbashi, Fabrizio Costa, Shiraz A. Shah, Roger A. Garrett, Sita J. Saunders and Rolf Backofen
Bioinformatics, 2014
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CRISPRstrand: Predicting repeat orientations to determine the crRNA-encoding strand at CRISPR loci
Omer S. Alkhnbashi, Fabrizio Costa, Shiraz A. Shah, Roger A. Garrett, Sita J. Saunders and Rolf Backofen
Bioinformatics, 2014
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Local Exact Pattern Matching for Non-Fixed RNA Structures.
Mika Amit, Rolf Backofen, Steffen Heyne, Gad M. Landau, Mathias Möhl, Christina Otto and Sebastian Will
IEEE/ACM Trans. Comput. Biology Bioinform., 2014
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Computational Prediction of RNA-RNA Interactions
Rolf Backofen
Methods Mol Biol, 2014
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Bioinformatics of prokaryotic RNAs
Rolf Backofen, Fabian Amman, Fabrizio Costa, Sven Findeiss, Andreas S. Richter and Peter F. Stadler
RNA Biol, 2014
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Biological and bioinformatical approaches to study crosstalk of long-non-coding RNAs and chromatin-modifying proteins
Rolf Backofen and Tanja Vogel
Cell Tissue Res, 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
Jutta Brendel, Britta Stoll, Sita J. Saunders, Kundan Sharma, Christof Lenz, Aris-Edda Stachler, Lisa-Katharina Maier, Hagen Richter, Lisa Nickel, Ruth A. Schmitz, Lennart Randau, Thorsten Allers, Henning Urlaub, Rolf Backofen and Anita Marchfelder
JBC, 2014
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MOF-associated complexes ensure stem cell identity and Xist repression
Tomasz Chelmicki, Friederike Dundar, Matthew Turley, Tasneem Khanam, Tugce Aktas, Fidel Ramirez, Anne-Valerie Gendrel, Patrick R. Wright, Pavankumar Videm, Rolf Backofen, Edith Heard, Thomas Manke and Asifa Akhtar
Elife, 2014
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Lineage-specific splicing of a brain-enriched alternative exon promotes glioblastoma progression
Roberto Ferrarese, Griffith R. 4th Harsh, Ajay K. Yadav, Eva Bug, Daniel Maticzka, Wilfried Reichardt, Stephen M. Dombrowski, Tyler E. Miller, Anie P. Masilamani, Fangping Dai, Hyunsoo Kim, Michael Hadler, Denise M. Scholtens, Irene L. Y. Yu, Jurgen Beck, Vinodh Srinivasasainagendra, Fabrizio Costa, Nicoleta Baxan, Dietmar Pfeifer, Dominik V. Elverfeldt, Rolf Backofen, Astrid Weyerbrock, Christine W. Duarte, Xiaolin He, Marco Prinz, James P. Chandler, Hannes Vogel, Arnab Chakravarti, Jeremy N. Rich, Maria S. Carro and Markus Bredel
J Clin Invest, 2014
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Dynamic DNA methylation orchestrates cardiomyocyte development, maturation and disease
Ralf Gilsbach, Sebastian Preissl, Björn Grüning, Tilman Schnick, Lukas Burger, Vladimir Benes, Andreas Wurch, Ulrike Bonisch, Stefan Gunther, Rolf Backofen, Bernd K. Fleischmann, Dirk Schubeler and Lutz Hein
Nat Commun, 2014
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Cluster based prediction of PDZ-peptide interactions
Kousik Kundu and Rolf Backofen
BMC Genomics, 2014
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MoDPepInt: an interactive web server for prediction of modular domain-peptide interactions
Kousik Kundu, Martin Raden, Fabrizio Costa and Rolf Backofen
Bioinformatics, 2014
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MoDPepInt: An interactive webserver for prediction of modular domain-peptide interactions
Kousik Kundu, Martin Raden, Fabrizio Costa and Rolf Backofen
Bioinformatics, 2014
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Activation of a GPCR leads to eIF4G phosphorylation at the 5' cap and to IRES-dependent translation
Kelly Leon, Thomas Boulo, Astrid Musnier, Julia Morales, Christophe Gauthier, Laurence Dupuy, Steffen Heyne, Rolf Backofen, Anne Poupon, Patrick Cormier, Eric Reiter and Pascale Crepieux
J Mol Endocrinol, 2014
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An Active Immune Defence with a Minimal CRISPR (clustered regularly interspaced short palindromic repeats) RNA and Without the Cas6 Protein
Lisa-Katharina Maier, Aris-Edda Stachler, Sita J. Saunders, Rolf Backofen and Anita Marchfelder
JBC, 2014
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Exact methods for lattice protein models
Martin Raden and Rolf Backofen
Bio-Algorithms and Med-Systems, 2014
DOI
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Atom Mapping with Constraint Programming
Martin Raden, Feras Nahar, Norah Schnorr, Rolf Backofen, Peter F. Stadler and Christoph Flamm
BMC Algorithms for Molecular Biology, 2014
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Memory efficient RNA energy landscape exploration
Martin Raden, Marcel Kucharik, Christoph Flamm and Michael T. Wolfinger
Bioinformatics, 2014
DOI
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GraphProt: modeling binding preferences of RNA-binding proteins
Daniel Maticzka, Sita J. Saunders, Fabrizio Costa and Rolf Backofen
Genome Biol, 2014
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ExpaRNA-P: simultaneous exact pattern matching and folding of RNAs
Christina Otto, Mathias Möhl, Steffen Heyne, Mika Amit, Gad M. Landau, Rolf Backofen and Sebastian Will
BMC Bioinformatics, 2014
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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
Aaron Overloeper, Alexander Kraus, Rosemarie Gurski, Patrick R. Wright, Jens Georg, Wolfgang R. Hess and Franz Narberhaus
RNA Biol, 2014
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Graph-distance distribution of the Boltzmann ensemble of RNA secondary structures
Jing Qin, Markus Fricke, Manja Marz, Peter F. Stadler and Rolf Backofen
Algorithms Mol Biol, 2014
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Autosomal dominant immune dysregulation syndrome in humans with CTLA4 mutations
Desiree Schubert, Claudia Bode, Rupert Kenefeck, Tie Zheng Hou, James B. Wing, Alan Kennedy, Alla Bulashevska, Britt-Sabina Petersen, Alejandro A. Schaffer, Björn Grüning, Susanne Unger, Natalie Frede, Ulrich Baumann, Torsten Witte, Reinhold E. Schmidt, Gregor Dueckers, Tim Niehues, Suranjith Seneviratne, Maria Kanariou, Carsten Speckmann, Stephan Ehl, Anne Rensing-Ehl, Klaus Warnatz, Mirzokhid Rakhmanov, Robert Thimme, Peter Hasselblatt, Florian Emmerich, Toni Cathomen, Rolf Backofen, Paul Fisch, Maximilian Seidl, Annette May, Annette Schmitt-Graeff, Shinji Ikemizu, Ulrich Salzer, Andre Franke, Shimon Sakaguchi, Lucy S. K. Walker, David M. Sansom and Bodo Grimbacher
Nat Med, 2014
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BlockClust: efficient clustering and classification of non-coding RNAs from short read RNA-seq profiles
Pavankumar Videm, Dominic Rose, Fabrizio Costa and Rolf Backofen
Bioinformatics, 2014
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Simultaneous Alignment and Folding of Protein Sequences
Jerome Waldispuhl, Charles W. O'Donnell, Sebastian Will, Srinivas Devadas, Rolf Backofen and Bonnie Berger
JCB, 2014
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CopraRNA and IntaRNA: predicting small RNA targets, networks and interaction domains
Patrick R. Wright, Jens Georg, Martin Raden, Dragos A. Sorescu, Andreas S. Richter, Steffen Lott, Robert Kleinkauf, Wolfgang R. Hess and Rolf Backofen
NAR, 2014
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Distribution of Graph-Distances in Boltzmann Ensembles of RNA Secondary Structures
Rolf Backofen, Markus Fricke, Manja Marz, Jing Qin and Peter F. Stadler
Algorithms in Bioinformatics, 2013
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Salimabromide: Unexpected Chemistry from the Obligate Marine Myxobacterium Enhygromxya salina
Stephan Felder, Sandra Dreisigacker, Stefan Kehraus, Edith Neu, Gabriele Bierbaum, Patrick R. Wright, Dirk Menche, Till F. Schaberle and Gabriele M. Konig
Chemistry, 2013
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Tandem Stem-Loops in roX RNAs Act Together to Mediate X Chromosome Dosage Compensation in Drosophila
Ibrahim Avsar Ilik, Jeffrey J. Quinn, Plamen Georgiev, Filipe Tavares-Cadete, Daniel Maticzka, Sarah Toscano, Yue Wan, Robert C. Spitale, Nicholas Luscombe, Rolf Backofen, Howard Y. Chang and Asifa Akhtar
Mol Cell, 2013
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A graph kernel approach for alignment-free domain-peptide interaction prediction with an application to human SH3 domains
Kousik Kundu, Fabrizio Costa and Rolf Backofen
Bioinformatics, 2013
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Semi-Supervised Prediction of SH2-Peptide Interactions from Imbalanced High-Throughput Data
Kousik Kundu, Fabrizio Costa, Michael Huber, Michael Reth and Rolf Backofen
PLoS One, 2013
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CRISPRmap: an automated classification of repeat conservation in prokaryotic adaptive immune systems
Sita J. Saunders, Omer S. Alkhnbashi, Dominic Rose, Sebastian Will and Rolf Backofen
NAR, 2013
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Essential requirements for the detection and degradation of invaders by the Haloferax volcanii CRISPR/Cas system I-B
Lisa-Katharina Maier, Sita J. Saunders, Britta Stoll, Karina A. Haas, Susan Fischer, Eike Fischer, Elke Duchardt-Ferner, Jens Wohnert, Rolf Backofen and Anita Marchfelder
RNA Biology, 2013
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The Graph Grammar Library - a generic framework for chemical graph rewrite systems
Martin Raden, Heinz Ekker and Christoph Flamm
Theory and Practice of Model Transformations, Proc. of ICMT 2013, 2013
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Atom Mapping with Constraint Programming
Martin Raden, Feras Nahar, Heinz Ekker, Rolf Backofen, Peter F. Stadler and Christoph Flamm
Proc. of the 19th International Conference on Principles and Practice of Constraint Programming (CP'13), 2013
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Kekule structure enumeration yields unique SMILES
Martin Raden and Bernhard Thiel
Proceedings of the Workshop on Constraint Based Methods for Bioinformatics (WCB 2013), 2013
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Two CRISPR-Cas systems in Methanosarcina mazei strain Go1 display common processing features despite belonging to different types I and III
Lisa Nickel, Katrin Weidenbach, Dominik Jager, Rolf Backofen, Sita J. Saunders, Nadja Heidrich and Ruth A. Schmitz
RNA Biol, 2013
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Regulatory RNAs in archaea: first target identification in Methanoarchaea
Daniela Prasse, Claudia Ehlers, Rolf Backofen and Ruth A. Schmitz
Biochem Soc Trans, 2013
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A case study: semantic integration of gene-disease associations for type 2 diabetes mellitus from literature and biomedical data resources
Dietrich Rebholz-Schuhmann, Christoph Grabmuller, Silvestras Kavaliauskas, Samuel Croset, Peter Woollard, Rolf Backofen, Wendy Filsell and Dominic Clark
Drug Discov Today, 2013
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Evaluating gold standard corpora against gene/protein tagging solutions and lexical resources
Dietrich Rebholz-Schuhmann, Senay Kafkas, Jee-Hyub Kim, Chen Li, Antonio Jimeno Yepes, Robert Hoehndorf, Rolf Backofen and Ian Lewin
J Biomed Semantics, 2013
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Evaluation and cross-comparison of lexical entities of biological interest (LexEBI)
Dietrich Rebholz-Schuhmann, Jee-Hyub Kim, Ying Yan, Abhishek Dixit, Caroline Friteyre, Robert Hoehndorf, Rolf Backofen and Ian Lewin
PLoS One, 2013
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Comparative analysis of Cas6b processing and CRISPR RNA stability
Hagen Richter, Sita J. Saunders, Rolf Backofen and Lennart Randau
RNA Biology, 2013
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CRISPR-Cas Systems in the Cyanobacterium Synechocystis sp. PCC6803 Exhibit Distinct Processing Pathways Involving at Least Two Cas6 and a Cmr2 Protein
Ingeborg Scholz, Sita J. Saunders, Stephanie Hein, Wolfgang R. Hess and Rolf Backofen
PLoS One, 2013
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Requirements for a successful defence reaction by the CRISPR-Cas subtype I-B system
Britta Stoll, Lisa-Katharina Maier, Sita J. Saunders, Jutta Brendel, Susan Fischer, Rolf Backofen and Anita Marchfelder
Biochem Soc Trans, 2013
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LocARNAscan: Incorporating thermodynamic stability in sequence and structure-based RNA homology search
Sebastian Will, Michael F. Siebauer, Steffen Heyne, Jan Engelhardt, Peter F. Stadler, Kristin Reiche and Rolf Backofen
Algorithms Mol Biol, 2013
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Structure-based whole genome realignment reveals many novel non-coding RNAs
Sebastian Will, Michael Yu and Bonnie Berger
Genome Res, 2013
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SPARSE: Quadratic Time Simultaneous Alignment and Folding of RNAs Without Sequence-Based Heuristics
Sebastian Will, Christina Schmiedl, Milad Miladi, Mathias Möhl and Rolf Backofen
Proceedings of the 17th International Conference on Research in Computational Molecular Biology (RECOMB 2013), 2013
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Freiburg RNA Tools webserver
Patrick R. Wright, Martin Raden, Dragos A. Sorescu, Sita J. Saunders, Omer S. Alkhnbashi, Dominic Rose, Steffen Heyne, Andreas S. Richter, Wolfgang R. Hess, Jens Georg, Anke Busch, Sebastian Will and Rolfs Backofen
Poster, 3rd Conference on Regulating with RNA in Bacteria, 2013
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Comparative genomics boosts target prediction for bacterial small RNAs
Patrick R. Wright, Andreas S. Richter, Kai Papenfort, Martin Raden, Jorg Vogel, Wolfgang R. Hess, Rolf Backofen and Jens Georg
PNAS, 2013
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Local Exact Pattern Matching for Non-fixed RNA Structures
Mika Amit, Rolf Backofen, Steffen Heyne, Gad M. Landau, Mathias Möhl, Christina Schmiedl and Sebastian Will
Proceedings of the 23th Annual Symposium on Combinatorial Pattern Matching (CPM 2012), 2012
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Microstructure Alignment of Wood Density Profiles: an Approach to Equalize Radial Differences in Growth Rate
Bela Bender, Martin Raden, Rolf Backofen and Heinrich Spiecker
Trees - Structure and Function, 2012
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GraphClust: alignment-free structural clustering of local RNA secondary structures
Steffen Heyne, Fabrizio Costa, Dominic Rose and Rolf Backofen
Bioinformatics, 2012
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Abstract folding space analysis based on helices
Jiabin Huang, Rolf Backofen and Björn Voss
RNA, 2012
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An archaeal sRNA targeting cis- and trans-encoded mRNAs via two distinct domains
Dominik Jäger, Sandy R. Pernitzsch, Andreas S. Richter, Rolf Backofen, Cynthia M. Sharma and Ruth A. Schmitz
NAR, 2012
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Antioxidant activity of Hawaiian marine algae
Dovi Kelman, Ellen Kromkowski Posner, Karla J. McDermid, Nicole K. Tabandera, Patrick R. Wright and Anthony D. Wright
Mar Drugs, 2012
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Global or local? Predicting secondary structure and accessibility in mRNAs
Sita J. Saunders, Daniel Maticzka, Mathias Möhl, Joshua N. Gagnon, Chris M. Brown and Rolf Backofen
NAR, 2012
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Producing high-accuracy lattice models from protein atomic co-ordinates including side chains
Martin Raden, Rhodri Saunders, Cameron Smith, Rolf Backofen and Charlotte M. Deane
Advances in Bioinformatics, 2012
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Atom Mapping with Constraint Programming
Martin Raden, Heinz Ekker, Peter F. Stadler and Christoph Flamm
Proceedings of the Workshop on Constraint Based Methods for Bioinformatics (WCB 2012), 2012
DOI
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Navigating the unexplored seascape of pre-miRNA candidates in single-genome approaches
Nuno D. Mendes, Steffen Heyne, Ana T. Freitas, Marie-France Sagot and Rolf Backofen
Bioinformatics, 2012
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Navigating the unexplored seascape of pre-miRNA candidates in single-genome approaches
Nuno D. Mendes, Steffen Heyne, Ana T. Freitas, Marie-France Sagot and Rolf Backofen
Bioinformatics, 2012
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The SH2-domain of SHIP1 interacts with the SHIP1 C-terminus: Impact on SHIP1/Ig-alpha interaction
Oindrilla Mukherjee, Lars Weingarten, Inken Padberg, Catrin Pracht, Rileen Sinha, Thomas Hochdorfer, Stephan Kuppig, Rolf Backofen, Michael Reth and Michael Huber
Biochim Biophys Acta, 2012
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Accessibility and conservation: General features of bacterial small RNA-mRNA interactions?
Andreas S. Richter and Rolf Backofen
RNA Biol, 2012
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Characterization of CRISPR RNA processing in Clostridium thermocellum and Methanococcus maripaludis
Hagen Richter, Judith Zoephel, Jeanette Schermuly, Daniel Maticzka, Rolf Backofen and Lennart Randau
NAR, 2012
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MicroRNAs in Cancer Translational Research: The Microcosm of Cancer Diagnosis, Prognosis and Therapy
Dominic Rose
Frontiers in Genetics, 2012
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Exact Pattern Matching for RNA Structure Ensembles
Christina Schmiedl, Mathias Möhl, Steffen Heyne, Mika Amit, Gad M. Landau, Sebastian Will and Rolf Backofen
Proceedings of the 16th International Conference on Research in Computational Molecular Biology (RECOMB 2012), 2012
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Impact of the Energy Model on the Complexity of RNA Folding with Pseudoknots
Saad Sheikh, Rolf Backofen and Yann Ponty
Combinatorial Pattern Matching - 23rd Annual Symposium, CPM 2012, Helsinki, Finland, July 3-5, 2012. Proceedings, 2012
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CARNA - alignment of RNA structure ensembles
Dragos A. Sorescu, Mathias Möhl, Martin Raden, Rolf Backofen and Sebastian Will
Nucleic Acids Res, 2012
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Computational analysis of noncoding RNAs
Stefan Washietl, Sebastian Will, David A. Hendrix, Loyal A. Goff, John L. Rinn, Bonnie Berger and Manolis Kellis
Wiley Interdiscip Rev RNA, 2012
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Structure-based Whole Genome Realignment Reveals Many Novel Non-coding RNAs
Sebastian Will, Michael Yu and Bonnie Berger
Proceedings of the 16th International Conference on Research in Computational Molecular Biology (RECOMB 2012), 2012
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LocARNA-P: Accurate boundary prediction and improved detection of structural RNAs
Sebastian Will, Tejal Joshi, Ivo L. Hofacker, Peter F. Stadler and Rolf Backofen
RNA, 2012
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Bioinformatics of Bacterial sRNAs and Their Targets
Rolf Backofen
Regulatory RNAs in Prokaryotes, 2011
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Sparse RNA folding: Time and space efficient algorithms
Rolf Backofen, Dekel Tsur, Shay Zakov and Michal Ziv-Ukelson
J. Discrete Algorithms, 2011
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Fast RNA Structure Alignment for Crossing Input Structures
Rolf Backofen, Gad M. Landau, Mathias Möhl, Dekel Tsur and Oren Weimann
Journal of Discrete Algorithms, 2011
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Data fusion of Fourier transform infrared spectra and powder X-ray diffraction patterns for pharmaceutical mixtures
Rahul V. Haware, Patrick R. Wright, Kenneth R. Morris and Mazen L. Hamad
J Pharm Biomed Anal, 2011
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Identification of SH2-peptide interactions using machine learning approaches
Kousik Kundu, Fabrizio Costa, Michael Reth, Michael Huber and Rolf Backofen
Poster Proceedings of ISMB'11, 2011
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Efficient exploration of discrete energy landscapes
Martin Raden and Konstantin Klemm
Phys. Rev. E, 2011
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LatFit - Producing high accuracy lattice models from protein atomic co-ordinates including side chains
Martin Raden, Rhodri Saunders, Cameron Smith, Rolf Backofen and Charlotte Deane
Adv Bioinformatics, 2011
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Structator: fast index-based search for RNA sequence-structure patterns
Fernando Meyer, Stefan Kurtz, Rolf Backofen, Sebastian Will and Michael Beckstette
BMC Bioinformatics, 2011
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Sparsification in Algebraic Dynamic Programming
Mathias Möhl, Christina Schmiedl and Shay Zakov
Proceedings of the German Conference on Bioinformatics (GCB 2011), 2011
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Accessibility and conservation in bacterial small RNA-mRNA interactions and implications for genome-wide target predictions
Andreas S. Richter and Rolf Backofen
Proceedings of the German Conference on Bioinformatics (GCB 2011), 2011
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Computational discovery of human coding and non-coding transcripts with conserved splice sites
Dominic Rose, Michael Hiller, Katharina Schutt, Jörg Hackermüller, Rolf Backofen and Peter F. Stadler
Bioinformatics, 2011
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Molecular Evolution of the non-coding Eosinophil Granule Ontogeny Transcript
Dominic Rose and Peter F. Stadler
Frontiers in Genetics, 2011
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Computational discovery of human coding and non-coding transcripts with conserved splice sites
Dominic Rose, Michael Hiller, Katharina Schutt, Jorg Hackermuller, Rolf Backofen and Peter F. Stadler
Bioinformatics, 2011
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Molecular evolution of the non-coding eosinophil granule ontogeny transcript
Dominic Rose and Peter F. Stadler
Front Genet, 2011
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Signatures of Co-translational Folding
Rhodri Saunders, Martin Raden and Charlotte Deane
Biotechnology Journal, Special issue: Protein folding in vivo, 2011
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The PETfold and PETcofold web servers for intra- and intermolecular structures of multiple RNA sequences
S. E. Seemann, P. Menzel, Rolf Backofen and J. Gorodkin
NAR, 2011
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PETcofold: predicting conserved interactions and structures of two multiple alignments of RNA sequences
Stefan E. Seemann, Andreas S. Richter, Tanja Gesell, Rolf Backofen and Jan Gorodkin
Bioinformatics, 2011
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CRISPR revisited: structure prediction of CRISPR repeats
Sita Lange, Omer S. Alkhnbashi, Dominic Rose, Ingeborg Scholz, Wolfgang R. Hess and Rolf Backofen
Poster Proceedings of the 62th Mosbach Colloquium, 2011
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The small RNA PhrS stimulates synthesis of the Pseudomonas aeruginosa quinolone signal
Elisabeth Sonnleitner, Nicolas Gonzalez, Theresa Sorger-Domenigg, Stephan Heeb, Andreas S. Richter, Rolf Backofen, Paul Williams, Alexander Huttenhofer, Dieter Haas and Udo Blasi
Mol Microbiol, 2011
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Computational prediction of sRNAs and their targets in bacteria
Rolf Backofen and Wolfgang R. Hess
RNA Biol, 2010
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Identifikation von Targetmolekülen kleiner regulatorischer RNAs
Rolf Backofen
Laborwelt, 2010
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Shape-based barrier estimation for RNAs
Sergiy Bogomolov, Martin Raden, Björn Voss, Andreas Podelski and Rolf Backofen
In Proceedings of German Conference on Bioinformatics GCB'10, 2010
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A Propagator for Maximum Weight String Alignment with Arbitrary Pairwise Dependencies
Alessandro Dal Palu, Mathias Möhl and Sebastian Will
Proceedings of the 16th International Conference on Principles and Practice of Constraint Programming (CP-2010), 2010
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Alignnment of RNA with Structures of Unlimited Complexity
Alessandro Dal Palu, Mathias Möhl and Sebastian Will
Proceedings of the Workshop on Constraint Based Methods for Bioinformatics (WCB 2010), 2010
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Evolution of Metabolic Networks: A Computational Framework
Christoph Flamm, Alexander Ullrich, Heinz Ekker, Martin Raden, Daniel Hoegerl, Markus Rohrschneider, Sebastian Sauer, Gerik Scheuermann, Konstantin Klemm, Ivo L. Hofacker and Peter F. Stadler
Journal of Systems Chemistry, 2010
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In silico modelling of human lipoprotein metabolism
Martin Jansen, Karl Winkler, Gerhard Puetz, Peter Pfaffelhuber and Martin Raden
Poster Proceedings of SBMC'10, (conference for system biology in mammalian cells), 2010
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Machine learning approaches for prediction of SH2-peptide interactions
Kousik Kundu, Rileen Sinha, Michael Reth, Michael Huber and Rolf Backofen
Poster Proceedings of ISMB'10, 2010
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Lattice model refinement of protein structures
Martin Raden and Alessandro Dal Palu
Proceedings of the Workshop on Constraint Based Methods for Bioinformatics (WCB 2010), 2010
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High accuracy on-lattice side chain models of PDB protein structures
Martin Raden, Rhodri Saunders, Cameron Smith, Rolf Backofen and Charlotte Deane
Poster Proceedings of ISMB'10, 2010
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Sparsification of RNA structure prediction including pseudoknots
Mathias Möhl, Raheleh Salari, Sebastian Will, Rolf Backofen and S. Cenk Sahinalp
Algorithms Mol Biol, 2010
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Lifting prediction to alignment of RNA pseudoknots
Mathias Möhl, Sebastian Will and Rolf Backofen
JCB, 2010
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Sparsification of RNA Structure Prediction Including Pseudoknots
Mathias Möhl, Raheleh Salari, Sebastian Will, Rolf Backofen and S. Cenk Sahinalp
Proc. of the 10th Workshop on Algorithms in Bioinformatics (WABI), 2010
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COMPUTATIONAL STUDIES OF NON-CODING RNAS - Session Introduction
Rolf Backofen, H. Chitsaz, I. Hofacker, S. C. Sahinalp and P. F. Stadler
PSB10, 2010
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Seed-based IntaRNA prediction combined with GFP-reporter system identifies mRNA targets of the small RNA Yfr1
Andreas S. Richter, Christian Schleberger, Rolf Backofen and Claudia Steglich
Bioinformatics, 2010
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Identification of functional elements and regulatory circuits by Drosophila modENCODE
Sushmita Roy, Jason Ernst, Peter V. Kharchenko, Pouya Kheradpour, Nicolas Negre, Matthew L. Eaton, Jane M. Landolin, Christopher A. Bristow, Lijia Ma, Michael F. Lin, Stefan Washietl, Bradley I. Arshinoff, Ferhat Ay, Patrick E. Meyer, Nicolas Robine, Nicole L. Washington, Luisa Di Stefano, Eugene Berezikov, Christopher D. Brown, Rogerio Candeias, Joseph W. Carlson, Adrian Carr, Irwin Jungreis, Daniel Marbach, Rachel Sealfon, Michael Y. Tolstorukov, Sebastian Will, Artyom A. Alekseyenko, Carlo Artieri, Benjamin W. Booth, Angela N. Brooks, Qi Dai, Carrie A. Davis, Michael O. Duff, Xin Feng, Andrey A. Gorchakov, Tingting Gu, Jorja G. Henikoff, Philipp Kapranov, Renhua Li, Heather K. MacAlpine, John Malone, Aki Minoda, Jared Nordman, Katsutomo Okamura, Marc Perry, Sara K. Powell, Nicole C. Riddle, Akiko Sakai, Anastasia Samsonova, Jeremy E. Sandler, Yuri B. Schwartz, Noa Sher, Rebecca Spokony, David Sturgill, Marijke van Baren, Kenneth H. Wan, Li Yang, Charles Yu, Elise Feingold, Peter Good, Mark Guyer, Rebecca Lowdon, Kami Ahmad, Justen Andrews, Bonnie Berger, Steven E. Brenner, Michael R. Brent, Lucy Cherbas, Sarah C. R. Elgin, Thomas R. Gingeras, Robert Grossman, Roger A. Hoskins, Thomas C. Kaufman, William Kent, Mitzi I. Kuroda, Terry Orr-Weaver, Norbert Perrimon, Vincenzo Pirrotta, James W. Posakony, Bing Ren, Steven Russell, Peter Cherbas, Brenton R. Graveley, Suzanna Lewis, Gos Micklem, Brian Oliver, Peter J. Park, Susan E. Celniker, Steven Henikoff, Gary H. Karpen, Eric C. Lai, David M. MacAlpine, Lincoln D. Stein, Kevin P. White and Manolis Kellis
Science, 2010
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Fast prediction of RNA-RNA interaction
Raheleh Salari, Rolf Backofen and S. Cenk Sahinalp
Algorithms Mol Biol, 2010
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Time and Space Efficient RNA-RNA Interaction Prediction via Sparse Folding
Raheleh Salari, Mathias Möhl, Sebastian Will, S. Cenk Sahinalp and Rolf Backofen
Proc. of RECOMB 2010, 2010
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The small RNA Aar in Acinetobacter baylyi: a putative regulator of amino acid metabolism
Dominik Schilling, Sven Findeiss, Andreas S. Richter, Jennifer A. Taylor and Ulrike Gerischer
Arch Microbiol, 2010
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Hierarchical folding of multiple sequence alignments for the prediction of structures and RNA-RNA interactions
Stefan E. Seemann, Andreas S. Richter, Jan Gorodkin and Rolf Backofen
Algorithms Mol Biol, 2010
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TassDB2 - A comprehensive database of subtle alternative splicing events
Rileen Sinha, Thorsten Lenser, Niels Jahn, Ulrike Gausmann, Swetlana Friedel, Karol Szafranski, Klaus Huse, Philip Rosenstiel, Jochen Hampe, Stefan Schuster, Michael Hiller, Rolf Backofen and Matthias Platzer
BMC Bioinformatics, 2010
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Identification and characterization of NAGNAG alternative splicing in the moss Physcomitrella patens
Rileen Sinha, Andreas D. Zimmer, Kathrin Bolte, Daniel Lang, Ralf Reski, Matthias Platzer, Stefan A. Rensing and Rolf Backofen
BMC Plant Biol, 2010
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Freiburg RNA Tools: a web server integrating IntaRNA, ExpaRNA and LocARNA
Cameron Smith, Steffen Heyne, Andreas S. Richter, Sebastian Will and Rolf Backofen
NAR, 2010
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Partitioning biological data with transitivity clustering
Tobias Wittkop, Dorothea Emig, Sita Lange, Sven Rahmann, Mario Albrecht, John H. Morris, Sebastian Bocker, Jens Stoye and Jan Baumbach
Nat Methods, 2010
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Fast RNA Structure Alignment for Crossing Input Structures
Rolf Backofen, Gad M. Landau, Mathias Möhl, Dekel Tsur and Oren Weimann
Proc. 20th Symp. Combinatorial Pattern Matching, 2009
DOI
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Sparse RNA Folding: Time and Space Efficient Algorithms
Rolf Backofen, Dekel Tsur, Shay Zakov and Michal Ziv-Ukelson
Proc. 20th Symp. Combinatorial Pattern Matching, 2009
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A partition function algorithm for interacting nucleic acid strands
Hamidreza Chitsaz, Raheleh Salari, S. Cenk Sahinalp and Rolf Backofen
Bioinformatics, 2009
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A Constraint Model for Constrained Hidden Markov Models: a first Biological Application
Henning Christiansen, Christian Theil Have, Ole Torp Lassen and Matthieu Petit
WCB09, 2009
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Homology-based annotation of non-coding RNAs in the genomes of Schistosoma mansoni and Schistosoma japonicum
Claudia S. Copeland, Manja Marz, Dominic Rose, Jana Hertel, Paul J. Brindley, Clara Bermudez Santana, Stephanie Kehr, Camille Stephan-Otto Attolini and Peter F. Stadler
BMC Genomics, 2009
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Tagsnp selection using Weighted CSP and Russian Doll Search with Tree Decomposition
D. Allouche, S. de Givry, M. Sanchez and T. Schiex
WCB09, 2009
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Haplotype Inference Combining Pedigreesand Unrelated Individuals
Ana Graca, Ines Lynce, Joao Marques-Silva and Arlindo L. Oliveira
WCB09, 2009
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biRNA: Fast RNA-RNA Binding Sites Prediction
Hamidreza Chitsaz, Rolf Backofen and S. Cenk Sahinalp
Proc. of the 9th Workshop on Algorithms in Bioinformatics (WABI), 2009
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Non-coding RNA annotation of the genome of Trichoplax adhaerens
Jana Hertel, Danielle de Jong, Manja Marz, Dominic Rose, Hakim Tafer, Andrea Tanzer, Bernd Schierwater and Peter F. Stadler
NAR, 2009
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Lightweight Comparison of RNAs Based on Exact Sequence-Structure Matches
Steffen Heyne, Sebastian Will, Michael Beckstette and Rolf Backofen
Bioinformatics, 2009
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Conserved introns reveal novel transcripts in Drosophila melanogaster
Michael Hiller, Sven Findeiss, Sandro Lein, Manja Marz, Claudia Nickel, Dominic Rose, Christine Schulz, Rolf Backofen, Sonja J. Prohaska, Gunter Reuter and Peter F. Stadler
Genome Res, 2009
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Statement of Ongoing Work:Extending Boolean Satisfiability Techniques for Haplotype Inference by Pure Parsimony
Eric I. Hsu and Sheila A. McIlraith
WCB09, 2009
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Equivalence Classes of Optimal Structures in HP~Protein Models Including Side Chains
Martin Raden, Rolf Backofen and Sebastian Will
Proceedings of the Fifth Workshop on Constraint Based Methods for Bioinformatics (WCB09), 2009
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Constraint-based Local Move Definitions for Lattice Protein Models Including Side Chains
Martin Raden, Mohamed Abou Hamra, Kathleen Steinhöfel and Rolf Backofen
Proceedings of the Fifth Workshop on Constraint Based Methods for Bioinformatics (WCB09), 2009
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CPSP-web-tools: a server for 3D lattice protein studies
Martin Raden, Cameron Smith, Mohamad Rabbath, Marlien Edwards, Sebastian Will and Rolf Backofen
Bioinformatics, 2009
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Lifting Prediction to Alignment of RNA Pseudoknots
Mathias Möhl, Sebastian Will and Rolf Backofen
RECOMB09, 2009
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Fast Feature Subset Selection in Biological Sequence Analysis
Rainer Pudimat, Rolf Backofen and Ernst-Günter Schukat-Talamazzini
International Journal of Pattern Recognition and Artificial Intelligence, 2009
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Qupe--a Rich Internet Application to take a step forward in the analysis of mass spectrometry-based quantitative proteomics experiments
S. P. Albaum, H. Neuweger, B. Franzel, Sita J. Saunders, D. Mertens, C. Trotschel, D. Wolters, J. Kalinowski, T. W. Nattkemper and A. Goesmann
Bioinformatics, 2009
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Fast prediction of RNA-RNA Interaction
Raheleh Salari, Rolf Backofen and S. Cenk Sahinalp
Proc. of the 9th Workshop on Algorithms in Bioinformatics (WABI), 2009
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Accurate prediction of NAGNAG alternative splicing
Rileen Sinha, Swetlana Nikolajewa, Karol Szafranski, Michael Hiller, Niels Jahn, Klaus Huse, Matthias Platzer and Rolf Backofen
NAR, 2009
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Constraint Based Languages for Biological Reactions
Stefano Bistarelli and Marco Bottalico
WCB09, 2009
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Protein Folding Simulation by Two-Stage Optimization
Abu Dayem Ullah, Leonidas Kapsokalivas, Martin Raden and Kathleen Steinhöfel
Proc. of ISICA'09, 2009
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Simultaneous Alignment and Folding of Protein Sequences
Jérôme Waldispühl, Charles W. O'Donnell, Sebastian Will, Srinivas Devadas, Rolf Backofen and Bonnie Berger
RECOMB09, 2009
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RNAalifold: improved consensus structure prediction for RNA alignments
Stephan H. Bernhart, Ivo L. Hofacker, Sebastian Will, Andreas R. Gruber and Peter F. Stadler
BMC Bioinformatics, 2008
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Variations on RNA folding and alignment: lessons from Benasque
Athanasius F. Bompfünewerer, Rolf Backofen, Stephan H. Bernhart, Jana Hertel, Ivo L. Hofacker, Peter F. Stadler and Sebastian Will
Journal of Mathematical Biology, 2008
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IntaRNA: efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions
Anke Busch, Andreas S. Richter and Rolf Backofen
Bioinformatics, 2008
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Lightweight comparison of RNAs based on exact sequence-structure matches
Steffen Heyne, Sebastian Will, Michael Beckstette and Rolf Backofen
Proceedings of the German Conference on Bioinformatics (GCB'2008), 2008
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Assessing the fraction of short-distance tandem splice sites under purifying selection
Michael Hiller, Karol Szafranski, Rileen Sinha, Klaus Huse, Swetlana Nikolajewa, Philip Rosenstiel, Stefan Schreiber, Rolf Backofen and Matthias Platzer
RNA, 2008
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Selection against tandem splice sites affecting structured protein regions
Michael Hiller, Karol Szafranski, Klaus Huse, Rolf Backofen and Matthias Platzer
BMC Evolutionary Biology, 2008
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Widespread and subtle: alternative splicing at short-distance tandem sites
Michael Hiller and Matthias Platzer
TIG, 2008
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Genetic Variants of the Copy Number Polymorphic beta-Defensin Locus Are Associated with Sporadic Prostate Cancer
K. Huse, S. Taudien, M. Groth, P. Rosenstiel, K. Szafranski, M. Hiller, J. Hampe, K. Junker, J. Schubert, S. Schreiber, G. Birkenmeier, M. Krawczak and M. Platzer
Tumour Biol, 2008
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CPSP-tools - Exact and Complete Algorithms for High-throughput 3D Lattice Protein Studies
Martin Raden, Sebastian Will and Rolf Backofen
BMC Bioinformatics, 2008
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Classifying protein-like sequences in arbitrary lattice protein models using LatPack
Martin Raden, Daniel Maticzka, Rhodri Saunders and Rolf Backofen
HFSP Journal, 2008
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Fixed Parameter Tractable Alignment of RNA Structures Including Arbitrary Pseudoknots
Mathias Möhl, Sebastian Will and Rolf Backofen
Proceedings of the 19th Annual Symposium on Combinatorial Pattern Matching (CPM 2008), 2008
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Structure Local Multiple Alignment of RNA
Otto Wolfgang, Will Sebastian and Backofen Rolf
Proceedings of German Conference on Bioinformatics (GCB'2008), 2008
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A Sampling Approach for the Exploration of Biopolymer Energy Landscapes
Andreas S. Richter, Sebastian Will and Rolf Backofen
Proceedings of the European Conference on Metallobiolomics (HMI Berlin, Germany, 2007), 2008
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NcDNAlign: plausible multiple alignments of non-protein-coding genomic sequences
Dominic Rose, Jana Hertel, Kristin Reiche, Peter F. Stadler and Jörg Hackermüller
Genomics, 2008
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Duplicated RNA genes in teleost fish genomes
Dominic Rose, Julian Joris, Jörg Hackermüller, Kristin Reiche, Qiang Li and Peter F. Stadler
J Bioinform Comput Biol, 2008
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Alternative splicing at NAGNAG acceptors in Arabidopsis thaliana SR and SR-related protein-coding genes
Stefanie Schindler, Karol Szafranski, Michael Hiller, Gul Shad Ali, Saiprasad G. Palusa, Rolf Backofen, Matthias Platzer and Anireddy S. N. Reddy
BMC Genomics, 2008
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Unifying evolutionary and thermodynamic information for RNA folding of multiple alignments
Stefan E. Seemann, Jan Gorodkin and Rolf Backofen
NAR, 2008
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Improved identification of conserved cassette exons using Bayesian networks
R. Sinha, M. Hiller, R. Pudimat, U. Gausmann, M. Platzer and Rolf Backofen
BMC Bioinformatics, 2008
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Techniques de Décomposition pour l'Isomorphisme de Sous-Graphe
Stephane Zampelli, Martin Raden, Yves Deville and Rolf Backofen
Proc. of the 4th Journées Francophones de Programmation par Contraintes (JFPC'08), 2008
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Efficient Sequence Alignment with Side-Constraints by Cluster Tree Elimination
Sebastian Will, Anke Busch and Rolf Backofen
Constraints Journal, 2008
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RNAs everywhere: genome-wide annotation of structured RNAs
Athanasius F. Bompfünewerer Consortium, Rolf Backofen, Stephan H. Bernhart, Christoph Flamm, Claudia Fried, Guido Fritzsch, Jörg Hackermüller, Jana Hertel, Ivo L. Hofacker, Kristin Missal, Axel Mosig, Sonja J. Prohaska, Dominic Rose, Peter F. Stadler, Andrea Tanzer, Stefan Washietl and Sebastian Will
J Exp Zoolog B Mol Dev Evol, 2007
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Locality and gaps in RNA comparison
Rolf Backofen, Shihyen Chen, Danny Hermelin, Gad M. Landau, Mikhail A. Roytberg, Oren Weimann and Kaizhong Zhang
JCB, 2007
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Fast Detection of Common Sequence Structure Patterns in RNAs
Rolf Backofen and Sven Siebert
Journal of Discrete Algorithms, 2007
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IMS2 -- An integrated medical software system for early lung cancer detection using ion mobility spectrometry data of human breath
Jan Baumbach, Alexander Bunkowski, Sita Lange, Timm Oberwahrenbrock, Nils Kleinbölting, Sven Rahmann and Jörg Ingo Baumbach
Journal of Integrative Bioinformatics, 2007
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Index-based algorithms for motif search and their integration in a system for differential genome analysis
M. Beckstette
, 2007
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INFO-RNA--a server for fast inverse RNA folding satisfying sequence constraints
Anke Busch and Rolf Backofen
NAR, 2007
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Constraint-based Methods for Bioinformatics
Alessandro Dal Palù, Agostino Dovier, François Fages and Sebastian Will
Trends in Constraint Programming, 2007
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Pre-mRNA Secondary Structures Influence Exon Recognition
Michael Hiller, Zhaiyi Zhang, Rolf Backofen and Stefan Stamm
PLoS Genet, 2007
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TassDB: a database of alternative tandem splice sites
Michael Hiller, Swetlana Nikolajewa, Klaus Huse, Karol Szafranski, Philip Rosenstiel, Stefan Schuster, Rolf Backofen and Matthias Platzer
NAR, 2007
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Mildly Context-Sensitive Dependency Languages
Marco Kuhlmann and Mathias Möhl
45th Annual Meeting of the Association for Computational Linguistics (ACL), 2007
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The string-generative capacity of regular dependency languages
Marco Kuhlmann and Mathias Möhl
Twelfth Conference on Formal Grammar (FG), 2007
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HPdesign: Inverse Folding of Proteins
Martin Raden, Sebastian Will and Rolf Backofen
ISMB/ECCB, 2007
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The Energy Landscape Library - A Platform for Generic Algorithms
Martin Raden, Sebastian Will and Rolf Backofen
BIRD'07 - 1st international Conference on Bioinformatics Research and Development, 2007
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The Energy Landscape Library - A Platform for Generic Algorithms
Martin Raden, Sebastian Will and Rolf Backofen
BIRD'07 - 1st international Conference on Bioinformatics Research and Development, 2007
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BioBayesNet: a web server for feature extraction and Bayesian network modeling of biological sequence data
Swetlana Nikolajewa, Rainer Pudimat, Michael Hiller, Matthias Platzer and Rolf Backofen
NAR, 2007
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GenColors: annotation and comparative genomics of prokaryotes made easy
Alessandro Romualdi, Marius Felder, Dominic Rose, Ulrike Gausmann, Markus Schilhabel, Gernot Glockner, Matthias Platzer and Jurgen Suhnel
Methods Mol Biol, 2007
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Computational RNomics of drosophilids
Dominic Rose, Jorg Hackermuller, Stefan Washietl, Kristin Reiche, Jana Hertel, Sven Findeiss, Peter F. Stadler and Sonja J. Prohaska
BMC Genomics, 2007
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Methods for multiple alignment and consensus structure prediction of RNAs implemented in MARNA
Sven Siebert and Rolf Backofen
Methods Mol Biol, 2007
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A dynamic programming approach for finding common patterns in RNAs
Sven Siebert and Rolf Backofen
JCB, 2007
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Violating the splicing rules: TG dinucleotides function as alternative 3' splice sites in U2-dependent introns
K. Szafranski, S. Schindler, S. Taudien, M. Hiller, K. Huse, N. Jahn, S. Schreiber, Rolf Backofen and M. Platzer
Genome Biol, 2007
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Inferring Non-Coding RNA Families and Classes by Means of Genome-Scale Structure-Based Clustering
Sebastian Will, Kristin Reiche, Ivo L. Hofacker, Peter F. Stadler and Rolf Backofen
PLoS Comput Biol, 2007
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A Constraint-Based Approach to Fast and Exact Structure Prediction in Three-Dimensional Protein Models
Rolf Backofen and Sebastian Will
Journal of Constraints, 2006
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Bioinformatics and Constraints
Rolf Backofen and David Gilbert
Handbook of Constraint Programming, 2006
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Local Alignment of RNA Sequences with Arbitrary Scoring Schemes
Rolf Backofen, Danny Hermelin, Gad M. Landau and Oren Weimann
CPM06, 2006
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Fast index based algorithms and software for matching position specific scoring matrices
Michael Beckstette, Robert Homann, Robert Giegerich and Stefan Kurtz
BMC Bioinformatics, 2006
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INFO-RNA--a fast approach to inverse RNA folding
Anke Busch and Rolf Backofen
Bioinformatics, 2006
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Single-Nucleotide Polymorphisms in NAGNAG Acceptors Are Highly Predictive for Variations of Alternative Splicing
Michael Hiller, Klaus Huse, Karol Szafranski, Niels Jahn, Jochen Hampe, Stefan Schreiber, Rolf Backofen and Matthias Platzer
Am J Hum Genet, 2006
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Phylogenetically widespread alternative splicing at unusual GYNGYN donors
M. Hiller, K. Huse, K. Szafranskzi, P. Rosenstiel, S. Schreiber, Rolf Backofen and M. Platzer
Genome Biol, 2006
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Using RNA secondary structures to guide sequence motif finding towards single-stranded regions
Michael Hiller, Rainer Pudimat, Anke Busch and Rolf Backofen
NAR, 2006
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Alternative Splicing at NAGNAG Acceptors: Simply Noise or Noise and More?
Michael Hiller, Karol Szafranski, Rolf Backofen and Matthias Platzer
PLoS Genet, 2006
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Extended cross-serial dependencies in Tree Adjoining Grammars
Marco Kuhlmann and Mathias Möhl
Eighth International Workshop on Tree Adjoining Grammars and Related Formalisms (TAG+8), 2006
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Prediction of structured non-coding RNAs in the genomes of the nematodes Caenorhabditis elegans and Caenorhabditis briggsae
Kristin Missal, Xiaopeng Zhu, Dominic Rose, Wei Deng, Geir Skogerbo, Runsheng Chen and Peter F. Stadler
J Exp Zool B Mol Dev Evol, 2006
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Sequencing errors or SNPs at splice-acceptor guanines in dbSNP?
Matthias Platzer, Michael Hiller, Karol Szafranski, Niels Jahn, Jochen Hampe, Stefan Schreiber, Rolf Backofen and Klaus Huse
Nat Biotechnol, 2006
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A Bottom-up approach to Grid-Computing at a University: the Black-Forest-Grid Initiative
Rolf 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 and V.-H. Winterer
PIK, 2006
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Constrained Alignment Using Cluster Tree Elimination
Sebastian Will, Anke Busch and Rolf Backofen
14th Annual International conference on Intelligent Systems for Molecular Biology (ISMB'06), 2006
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Counting Protein Structures by DFS with Dynamic Decomposition
Sebastian Will and Martin Raden
Proc. of the Workshop on Constraint Based Methods for Bioinformatics. http://www.dimi.uniud.it/dovier/WCB06/WCB06_proceedings.pdf, 2006
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Exploring the lower part of discrete polymer model energy landscapes
Michael T. Wolfinger, Sebastian Will, Ivo L. Hofacker, Rolf Backofen and Peter F. Stadler
Europhysics Letters, 2006
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Normalized Similarity of RNA Sequences
Rolf Backofen, Danny Hermelin, Gad M. Landau and Oren Weimann
Proc. 12th Symposium on String Processing and Information Retrieval (SPIRE 2005), 2005
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A Posteriori Modelling of Sequence Motif Arrangements
Rolf Backofen and Rainer Pudimat
GCB, 2005
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XenDB: Full Length cDNA Prediction and Cross Species Mapping in Xenopus laevis
M. Beckstette, A. Sczyrba, A.H. Brivanlou, R. Giegerich and C.R. Altmann
BMC Genomics, 2005
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Well-Nested Drawings as Models of Syntactic Structure
Manuel Bodirsky, Marco Kuhlmann and Mathias Möhl
10th Conference on Formal Grammar and 9th Meeting on Mathematics of Language, 2005
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SECISDesign: a server to design SECIS-elements within the coding sequence
Anke Busch, Sebastian Will and Rolf Backofen
Bioinformatics, 2005
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INFO-RNA - A Fast Approach of the Inverse RNA Folding
Anke Busch and Rolf Backofen
ECCB, 2005
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Lexicalised Configuration Grammars
Robert Grabowski, Marco Kuhlmann and Mathias Möhl
Second International Workshop on Constraint Solving and Language Processing (CSLP 2005), 2005
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Creation and disruption of protein features by alternative splicing -- a novel mechanism to modulate function
Michael Hiller, Klaus Huse, Matthias Platzer and Rolf Backofen
Genome Biology, 2005
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Non-EST based prediction of exon skipping and intron retention events using Pfam information
Michael Hiller, Klaus Huse, Matthias Platzer and Rolf Backofen
NAR, 2005
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The origin of bilateral animals. A multigene approach.
P. Martinez, K. Malde, M. Beckstette and J. Baguna
Comparative Biochemistry and Physiology. Abstracts of the Society for Experimental Biology Annual Main Meeting, 2005
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Non-coding RNAs in Ciona intestinalis
Kristin Missal, Dominic Rose and Peter F. Stadler
Bioinformatics, 2005
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A multiple-feature framework for modelling and predicting transcription factor binding sites
Rainer Pudimat, E.G. Schukat-Talamazzini and Rolf Backofen
Bioinformatics, 2005
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MARNA: multiple alignment and consensus structure prediction of RNAs based on sequence structure comparisons
Sven Siebert and Rolf Backofen
Bioinformatics, 2005
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A new distance measure of RNA ensembles and its application to phylogenetic tree construction
Sven Siebert and Rolf Backofen
IEEE 2005 Symposium on Computational Intelligence in Bioinformatics and Computational Biology, 2005
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Efficient Constraint-based Sequence Alignment by Cluster Tree Elimination
Sebastian Will, Anke Busch and Rolf Backofen
Proceedings of the Workshop on Constraint Based Methods in Bioinformatics (WCB05), 2005
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Computational Design of New and Recombinant Selenoproteins
Rolf Backofen and Anke Busch
Proc. of the 15th Annual Symposium on Combinatorial Pattern Matching (CPM2004), 2004
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Local Sequence-Structure Motifs in RNA
Rolf Backofen and Sebastian Will
Journal of Bioinformatics and Computational Biology (JBCB), 2004
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A Polynomial Time Upper Bound for the Number of Contacts in the HP-Model on the Face-Centered-Cubic Lattice (FCC)
Rolf Backofen
Journal of Discrete Algorithms, 2004
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Fast Detection of Common Sequence Structure Patterns in RNAs
Rolf Backofen and Sven Siebert
Symposium on String Processing and Information Retrieval (SPIRE 2004), 2004
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Genlight: Interactive High-Throughput Sequence Analysis and comparative genomics
M. Beckstette, J.T. Mailaennder, R.J. Marhoefer, A. Sczyrba, E. Ohlebusch, R. Giegerich and P.M. Selzer
Journal of Integrative Bioinformatics, 2004
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Genlight: Interactive High-Throughput Sequence Analysis and comparative genomics
M. Beckstette, J.T. Mailänder, R.J. Marhöfer, A. Sczyrba, E. Ohlebusch, R. Giegerich and P.M. Selzer
Yearbook Bioinformatics, 2004
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Genlight: An Interactive System for High-throughput sequence analysis and Comparative Genomics
M. Beckstette, A. Sczyrba and P. M. Selzer
Proc. of the German Conference on Bioinformatics, 2004
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PoSSuMsearch: Fast and Sensitive Matching of Position Specific Scoring Matrices using Enhanced Suffix Arrays
M. Beckstette, D. Strothmann, R. Homann, R. Giegerich and S. Kurtz
Proc. of the German Conference on Bioinformatics, 2004
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MODERNA - Design of New and Recombinant Selenoproteins
Anke Busch and Rolf Backofen
ISMB/ECCB, 2004
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Constraint Based Protein Structure Prediction Exploiting Secondary Structure Information
Alessandro Dal Palu, Sebastian Will, Rolf Backofen and Agostino Dovier
Convegno Italiano di Logica Computazionale 2004 (CILC 2004), 2004
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Using protein secondary structure to build structural template
Y. He, S. Qin, X. M. Pan, M. Beckstette and R. Giegerich
CASP6 method paper, 2004
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Efficient prediction of alternative splice forms using protein domain homology
Michael Hiller, Rolf Backofen, Stephan Heymann, Anke Busch, Timo Mika Glaesser and Johann-Christoph Freytag
In Silico Biol, 2004
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Widespread occurrence of alternative splicing at NAGNAG acceptors contributes to proteome plasticity
Michael Hiller, Klaus Huse, Karol Szafranski, Niels Jahn, Jochen Hampe, Stefan Schreiber, Rolf Backofen and Matthias Platzer
Nat Genet, 2004
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Feature Based Representation and Detection of Transcription Factor Binding Sites
Rainer Pudimat, E. G. Schukat-Talamazzini and Rolf Backofen
GCB, 2004
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Prediction of Transcription Factor Binding Sites by Modeling Multiple Features
Rainer Pudimat and Rolf Backofen
ISMB-ECCB, 2004
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Identification of 10,500 Xenopus laevis Full Length Clones through EST Clustering and Sequence Analysis
A. Sczyrba, M. Beckstette, R. Giegerich and C.A. Altmann
Proceedings of the German Conference on Bioinformatics (GCB). Discovery Notes, 2004
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A Constraint-Based Approach to Structure Prediction for Simplified Protein Models that Outperforms Other Existing Methods
Rolf Backofen and Sebastian Will
Proceedings of the 19th International Conference on Logic Programming (ICLP 2003), 2003
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MARNA: A Server for Multiple Alignment of RNAs
Sven Siebert and Rolf Backofen
GCB, 2003
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Multiple Local Sequence Structure Alignment of RNA Sequences
Sven Siebert and Rolf Backofen
RECOMB 2003, 2003
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Breaking of Partial Symmetries in the Photo and Alignment Problem
Sebastian Will and Rolf Backofen
Proceedings of the Third International Workshop on Symmetry in Constraint Satisfaction Problems (SymCon 2003), 2003
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On the Complexity of Protein Similarity Search under mRNA Structure Constraints
Rolf Backofen, N. S. Narayanaswamy and Firas Swidan
Proc. of 19th International Symposium on Theoretical Aspects of Computer Science (STACS2002), 2002
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Excluding symmetries in constraint-based search
Rolf Backofen and Sebastian Will
Constraints, 2002
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Protein similarity search under mRNA structural constraints: application to targeted selenocysteine insertion
Rolf Backofen, N. S. Narayanaswamy and Firas Swidan
In Silico Biology, 2002
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Structural Infectomics: Identification and Characterization of Potential Virulence Factors in Legionella pneumophila
Steffen Heyne, Martin Raden, Debnath Pal, Aida Baharuddin, Andreas Vogel and Rolf Hilgenfeld
ECCB'02, 2002
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Multiple Local Sequence Structure Alignment of RNA Sequences
Sven Siebert
European Conference on Computational Biology 2002, 2002
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Protein Structure Prediction in the Face-Centered Cubic Lattice
Sebastian Will and Rolf Backofen
European Conference on Computational Biology 2002, 2002
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Constraint-based Hydrophobic Core Construction for Protein Structure Prediction in the Face-Centered-Cubic Lattice
Sebastian Will
Proceedings of the Pacific Symposium on Biocomputing 2002 (PSB 2002), 2002
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Protein similarity search under mRNA structural constraints: application to selenocysteine incorporation
Rolf Backofen, N. S. Narayanaswamy and Swidan Firas
Proc. of German Conference on Bioinformatics (GCB2001), 2001
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Fast, Constraint-based Threading of HP-Sequences to Hydrophobic Cores
Rolf Backofen and Sebastian Will
Proc. of the 7th International Conference on Principle and Practice of Constraint Programming (CP'2001), 2001
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Optimally Compact Finite Sphere Packings --- Hydrophobic Cores in the FCC
Rolf Backofen and Sebastian Will
Proc. of the 12th Annual Symposium on Combinatorial Pattern Matching (CPM2001), 2001
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The Protein Structure Prediction Problem: A Constraint Optimisation Approach using a New Lower Bound
Rolf Backofen
Constraints, 2001
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Bioinformatics and Constraints
Rolf Backofen and David Gilbert
Constraints, 2001
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RNA-Sequence-Structure Properties and Selenocysteine Insertion
Rolf Backofen
Proc. of the Fourth International Symposium on Intelligent Data Analysis, 2001
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Introduction to Bioinformatics
Rolf Backofen
Companion Volume to the Proceedings of the 39th Annual Meeting of the Association for Computational Linguistic (ACL), 2001
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Introduction to the Special Issue on Bioinformatics
David Gilbert, Rolf Backofen and Roland H. C. Yap
Constraints, 2001
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Algorithmic approach to quantifying the hydrophobic force contribution in protein folding
Rolf Backofen, Sebastian Will and Peter Clote
Proceedings of the Pacific Symposium on Biocomputing (PSB 2000), 2000
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An Upper Bound for Number of Contacts in the HP-Model on the Face-Centered-Cubic Lattice (FCC)
Rolf Backofen
Proceedings of the 11th Annual Symposium on Combinatorial Pattern Matching (CPM 2000), 2000
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Computational Molecular Biology: An Introduction
Peter Clote and Rolf Backofen
, 2000
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Classroom Assignment using Constraint Logic Programming
Slim Abdennadher, Matthias Saft and Sebastian Will
Proceedings of the Second International Conference and Exhibition on The Practical Application of Constraint Technologies and Logic Programming (PACLP 2000), 2000
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Aktuelles Schlagwort Bioinformatik
Rolf Backofen, François Bry, Peter Clote, Hans-Peter Kriegel, Thomas Seidl and Klaus Schulz
Informatik Spektrum, 1999
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Application of Constraint Programming Techniques for Structure Prediction of Lattice Proteins with Extended Alphabets
Rolf Backofen, Sebastian Will and Erich Bornberg-Bauer
Bioinformatics, 1999
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Excluding Symmetries in Constraint-Based Search
Rolf Backofen and Sebastian Will
Proceedings of 5th International Conference on Principle and Practice of Constraint Programming (CP'99), 1999
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Algorithmic approach to quantifying the hydrophobic force contribution in protein folding
Rolf Backofen, Sebastian Will and Peter Clote
Proceedings of the German Conference on Bioinformatics (GCB'99), 1999
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How to Win a Game with Features
Rolf Backofen and Ralf Treinen
Information and Computation, 1998
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Structure Prediction in an HP-type Lattice with an Extended Alphabet
Rolf Backofen and Sebastian Will
Proc of German Conference on Bioinformatics (GCB'98), 1998
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Excluding Symmetries in Concurrent Constraint Programming
Rolf Backofen and Sebastian Will
Workshop on Modeling and Computing with Concurrent Constraint Programming, 1998
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Constraint Techniques for Solving the Protein Structure Prediction Problem
Rolf Backofen
Proceedings of 4th International Conference on Principle and Practice of Constraint Programming (CP'98), 1998
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Using Constraint Programming for lattice Protein Folding
Rolf Backofen
Proceedings of the Pacific Symposium on Biocomputing (PSB'98), 1998
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Evolution as a Computational Engine
Rolf Backofen and Peter Clote
Proc. of Annual Conference of the European Association for Computer Science Logic (CSL'97), 1997
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Using Constraint Programming for lattice Protein Folding
Rolf Backofen
Workshop on Constraints and Bioinformatics/Biocomputing, 1997
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Controlling Functional Uncertainty
Rolf Backofen
Proceedings of 12th European Conference on Artificial Intelligence, 1996
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A First-Order Axiomatization of the Theory of Finite Trees
Rolf Backofen, James Rogers and K. Vijay-Shanker
Journal of Logic, Language and Information, 1995
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A Complete and Recursive Feature Theory
Rolf Backofen and Gert Smolka
tcs, 1995
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A Complete Axiomatization of a Theory with Feature and Arity Constraints
Rolf Backofen
Journal of Logic Programming, 1995
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Regular Path Expressions in Feature Logic
Rolf Backofen
Journal of Symbolic Computation, 1994
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How to Win a Game with Features
Rolf Backofen and Ralf Treinen
1st International Conference on Constraints in Computational Logics, 1994
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DISCO -- An HPSG-Based NLP System and its Application for Appointment Scheduling
Hans Uszkoreit, Rolf Backofen, Stephan Busemann, Abdel Kader Diagne, Elizabeth A. Hinkleman, Walter Kasper, Bernd Kiefer, Hans-Ulrich Krieger, Klaus Netter, Günter Neumann, Stephan Oepen and Stephen P. Spackman
Proceedings of the 15th International Conference on Computational Linguistics (COLING'94), 1994
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A Complete and Recursive Feature Theory
Rolf Backofen and Gert Smolka
Proc. of the 31st ACL, 1993
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The TDL/UDiNe system
Rolf Backofen and Hans-Ulrich Krieger
Report of the EAGLES Workshop on Implemented Formalisms at DFKI, Saarbrücken, 1993
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Regular Path Expressions in Feature Logic
Rolf Backofen
Proc. of the RTA'93, 1993
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On the Decidability of Functional Uncertainty
Rolf Backofen
Proc. of the 31st ACL, 1993
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Linking Typed Feature Formalisms and Terminological Knowledge Representation Languages in Natural Language Front-Ends
Rolf Backofen, Harald Trost and Hans Uszkoreit
Proceedings of the GI Congress, Knowledge-Based Systems 1991, 1991
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Distributed Disjunktions For LIFE
Rolf Backofen, Lutz Euler and Günther Görz
Proc. of the Inter. Workshop on Processing Declarative Knowledge (PDK'91), 1991
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Towards the Integration of Functions, Relations and Types in an AI Programming Language
Rolf Backofen, Lutz Euler and Günther Görz
Proc. of the 14th German Workshop on Artificial Intelligence, 1990
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