Publications

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

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

Nature Communications , 15 (1) , 2024.

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

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

GigaScience , 13 , giae022 , 2024.

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

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

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

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

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

Microlife , 4 , uqad012 , 2023.

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

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

Microlife , 4 , uqad001 , 2023.

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

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

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

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

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

Briefings in Bioinformatics , 2022.

Loop detection using Hi-C data with HiCExplorer

Joachim Wolff, Rolf Backofen, Björn Grüning.

Gigascience , 11 , 2022.

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

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

Front Immunol , 13 , 1066456 , 2022.

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

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

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

Expanding the Galaxy's reference data

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

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

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

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

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

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

Galaxy Team.

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

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

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

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

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

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

Dendrochronologia , 74 , 125978 , 2022.

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, Melanie Christine Foll.

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

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

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

Front Pediatr , 10 , 974840 , 2022.

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

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

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

CRISPRtracrRNA: robust approach for CRISPR tracrRNA detection

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

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

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

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

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

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, Pratik D. Jagtap.

Viruses , 14 (10) , 2022.

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

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

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

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

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

Gigascience , 12 , 2022.

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

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

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

Pluripotency factors determine gene expression repertoire at zygotic genome activation

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

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

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, Oliver Schilling.

Gigascience , 11 , 2022.

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

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

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

Ten simple rules for making a software tool workflow-ready

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

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

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, Miriam Schmidts.

Front Genet , 13 , 861236 , 2022.

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

Joachim Wolff, Rolf Backofen, Björn Grüning.

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

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

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

Molecular Neurodegeneration , 16 (80) , 2021.

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

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

Gigascience , 10 (2) , 2021.

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

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

Gigascience , 10 (8) , 2021.

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

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

Forests , 12 (3) , 274 , 2021.

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

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

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

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

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

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

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

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

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

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

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

Frontiers in Microbiology , 2021.

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

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

J Exp Bot , 2021.

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

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

J Exp Med , 218 (2) , 2021.

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

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

mBio , 12 (4) , e0141621 , 2021.

Tool recommender system in Galaxy using deep learning

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

GigaScience , 10 (1) , 2021.

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

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

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

StoatyDive: Evaluation and classification of peak profiles for sequencing data

Florian Heyl, Rolf Backofen.

Gigascience , 10 (6) , 2021.

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

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

Bioinformatics , 2021.

Chemotherapy-induced transposable elements activate MDA5 to enhance haematopoietic regeneration

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

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

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, Rolf Backofen.

NAR , 2021.

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

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

Bioinformatics , 2020.

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

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

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

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

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

microLife , 1 (1) , 2020.

Improving CLIP-seq data analysis by incorporating transcript information

Michael Uhl, Van Dinh Tran, Rolf Backofen.

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

pyGenomeTracks: reproducible plots for multivariate genomic data sets

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

Bioinformatics , 2020.

Casboundary: automated definition of integral Cas cassettes

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

Bioinformatics , 2020.

HRIBO: high-throughput analysis of bacterial ribosome profiling data

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

Bioinformatics , 2020.

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

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

Stem Cell Res. , 49 , 102046 , 2020.

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

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

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

Heterogeneous networks integration for disease-gene prioritization with node kernels

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

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

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

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

GigaScience , 9 (10) , 2020.

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

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

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

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

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

Dendrochronologia , 60 , 125679 , 2020.

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

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

BMC Bioinformatics , 21 , 15 , 2020.

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

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

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

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

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

Gigascience , 9 (6) , 2020.

The locality dilemma of Sankoff-like RNA alignments

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

Bioinformatics , 2020.

CRISPRidentify: identification of CRISPR arrays using machine learning approach

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

NAR , 2020.

NanoGalaxy: Nanopore long-read sequencing data analysis in Galaxy

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

GigaScience , 9 (10) , 2020.

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

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

Nucleic Acids Research , 2020.

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

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

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

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

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

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

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

Gregor Entzian, Martin Raden.

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

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

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

Journal of Cheminformatics , 12 (1) , 2020.

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

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

Journal of Cheminformatics , 12 (1) , 2020.

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

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

PLOS ONE , 14 , e0222459 , 2019.

Universal readout for graph convolutional neural networks

Nicolò Navarin, Van Dinh Tran, Alessandro Sperduti.

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

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

Stefan Mautner, Rolf Backofen, Fabrizio Costa.

ESANN 2019 - Proceedings , 2019.

The RNA workbench 2.0: next generation RNA data analysis

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

Nucleic Acids Research , 2019.

The RNA workbench 2.0: next generation RNA data analysis

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

Nucleic Acids Research , 2019.

Noncoding deletions reveal a gene that is critical for intestinal function

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

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

A pan-cancer analysis of synonymous mutations

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

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

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

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

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

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

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

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

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

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

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

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

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

GigaScience , 8 (12) , 2019.

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

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

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

ShaKer: RNA SHAPE prediction using graph kernel

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

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

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

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

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

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

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

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

CRISPR-Cas systems in multicellular cyanobacteria

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

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

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

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

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

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

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

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

The RNA workbench 2.0: next generation RNA data analysis

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

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

Biomolecular Reaction and Interaction Dynamics Global Environment (BRIDGE)

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

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

CRISPR-Cas bioinformatics

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

Methods , 2019.

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

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

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

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

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

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

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

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

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

Workflow for a Computational Analysis of an sRNA Candidate in Bacteria

Patrick R. Wright, Jens Georg.

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

Structure and interaction prediction in prokaryotic RNA biology

Patrick R. Wright, Martin Raden, Rolf Backofen.

Microbiol Spectrum , 6 (2) , 2018.

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

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

Molecular Neurobiology , 2018.

On filter size in graph convolutional networks

Van Dinh Tran, Nicolò Navarin, Alessandro Sperduti.

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

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, Jorn Dengjel.

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

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

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

Genome Res , 2018.

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

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

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

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

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

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

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

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

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

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

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

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

MICA: Multiple interval-based curve alignment

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

SoftwareX , 7 , 53-58 , 2018.

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

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

RNA Biol , 1-39 , 2018.

Bioconda: sustainable and comprehensive software distribution for the life sciences

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

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

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, Lutz Hein.

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

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, Jens Georg.

Frontiers in Genetics , 9 , 124 , 2018.

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

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

Bioinformatics , 2018.

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

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

Bioinformatics , 2018.

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

Fabrizio Costa, Dominic Grun, Rolf Backofen.

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

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

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

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

Comparative RNA Genomics

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

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

MetSV, a novel archaeal lytic virus targeting Methanosarcina strains

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

J Virol , 2017.

Computational analysis of CLIP-seq data

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

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

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

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

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

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

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

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

Mechanism of beta-actin mRNA Recognition by ZBP1

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

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

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

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

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

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

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

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

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

Martin Raden, Patrick R. Wright, Rolf Backofen.

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

CRISPR and Salty: CRISPR-Cas Systems in Haloarchaea

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

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

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

Kousik Kundu, Rolf Backofen.

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

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

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

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

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, Anton Nekrutenko.

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

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, Rolf Backofen.

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

Recent advances in RNA folding

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

J Biotechnol , 261 , 97-104 , 2017.

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

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

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

RIP-Seq Suggests Translational Regulation by L7Ae in Archaea

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

MBio , 8 (4) , 2017.

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

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

J Biotechnol , 261 , 76-84 , 2017.

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

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

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

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

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

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

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, Gunther Schlunck.

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

Plasticity of archaeal C/D box sRNA biogenesis

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

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

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

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

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

Spatiotemporal alignment of radial tracheid diameter profiles of submontane Norway spruce

D.F. Stangler, Martin Raden, H.-P. Kahle, E. Rosskopf, S. Fink, H. Spiecker.

Dendrochronologia , 37 , 33-45 , 2016.

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

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

NAR , 2016.

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

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

Nat Commun , 7 , 12791 , 2016.

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

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

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

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

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

Sci Rep , 6 , 34589 , 2016.

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

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

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

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

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

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

Characterizing leader sequences of CRISPR loci

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

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

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

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

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

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

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

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

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

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

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

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, Ralf Gilsbach.

Circ Res , 117 , 413-423 , 2015.

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

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

Nat Commun , 6 , 7367 , 2015.

An updated evolutionary classification of CRISPR-Cas systems

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

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

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

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

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

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

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

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

Computational Prediction of Modular Domain-Peptide Interactions

Kousik Kundu, Fabrizio Costa, Rolf Backofen.

Poster Proceedings of ISMB'15 , 2015.

antaRNA - Ant Colony Based RNA Sequence Design

R. Kleinkauf, Martin Raden, Rolf Backofen.

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

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

R. Kleinkauf, T. Houwaart, Rolf Backofen, Martin Raden.

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

Comparative analysis of the antioxidant properties of Icelandic and Hawaiian lichens

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

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

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, Rolf Backofen.

Poster, CRISPR Conference 2015 , 2015.

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, Rolf Backofen.

Poster, CRISPR Conference'15 , 2015.

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, Edward L. Bolt.

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

CRISPRloci: Comprehensive and accurate annotation of CRISPR-Cas systems

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

Poster, CRISPR Conference'15 , 2015.

Local Exact Pattern Matching for Non-Fixed RNA Structures.

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

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

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, Rolf Backofen.

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

Simultaneous Alignment and Folding of Protein Sequences

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

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

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

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

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

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, Bodo Grimbacher.

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

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

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

Algorithms Mol Biol , 9 , 19 , 2014.

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

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

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

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

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

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

GraphProt: modeling binding preferences of RNA-binding proteins

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

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

Memory efficient RNA energy landscape exploration

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

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

Atom Mapping with Constraint Programming

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

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

Exact methods for lattice protein models

Martin Raden, Rolf Backofen.

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

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

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

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

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

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

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

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

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

Bioinformatics , 2014.

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

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

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

Cluster based prediction of PDZ-peptide interactions

Kousik Kundu, Rolf Backofen.

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

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, Lutz Hein.

Nat Commun , 5 , 5288 , 2014.

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

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

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

MOF-associated complexes ensure stem cell identity and Xist repression

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

Elife , 3 , e02024 , 2014.

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, Anita Marchfelder.

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

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

Rolf Backofen, Tanja Vogel.

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

Bioinformatics of prokaryotic RNAs

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

RNA Biol , 11 (5) , 2014.

Computational Prediction of RNA-RNA Interactions

Rolf Backofen.

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

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

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

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

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

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

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

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, Jens Georg.

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

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, Rolfs Backofen.

Poster, 3rd Conference on Regulating with RNA in Bacteria , 2013.

SPARSE: Quadratic Time Simultaneous Alignment and Folding of RNAs Without Sequence-Based Heuristics

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

Proceedings of the 17th International Conference on Research in Computational Molecular Biology (RECOMB 2013) , 7821 , 289-290 , 2013.

Structure-based whole genome realignment reveals many novel non-coding RNAs

Sebastian Will, Michael Yu, Bonnie Berger.

Genome Res , [Epub ahead of print] , 2013.

LocARNAscan: Incorporating thermodynamic stability in sequence and structure-based RNA homology search

Sebastian Will, Michael F. Siebauer, Steffen Heyne, Jan Engelhardt, Peter F. Stadler, Kristin Reiche, Rolf Backofen.

Algorithms Mol Biol , 8 (1) , 14 , 2013.

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, Anita Marchfelder.

Biochem Soc Trans , 41 (6) , 1444-8 , 2013.

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, Rolf Backofen.

PLoS One , 8 (2) , e56470 , 2013.

Comparative analysis of Cas6b processing and CRISPR RNA stability

Hagen Richter, Sita J. Saunders, Rolf Backofen, Lennart Randau.

RNA Biology , 10 (5) , 700-707 , 2013.

Evaluation and cross-comparison of lexical entities of biological interest (LexEBI)

Dietrich Rebholz-Schuhmann, Jee-Hyub Kim, Ying Yan, Abhishek Dixit, Caroline Friteyre, Robert Hoehndorf, Rolf Backofen, Ian Lewin.

PLoS One , 8 (10) , e75185 , 2013.

Evaluating gold standard corpora against gene/protein tagging solutions and lexical resources

Dietrich Rebholz-Schuhmann, Senay Kafkas, Jee-Hyub Kim, Chen Li, Antonio Jimeno Yepes, Robert Hoehndorf, Rolf Backofen, Ian Lewin.

J Biomed Semantics , 4 (1) , 28 , 2013.

A case study: semantic integration of gene-disease associations for type 2 diabetes mellitus from literature and biomedical data resources

Dietrich Rebholz-Schuhmann, Christoph Grabmuller, Silvestras Kavaliauskas, Samuel Croset, Peter Woollard, Rolf Backofen, Wendy Filsell, Dominic Clark.

Drug Discov Today , 19 (7) , 882–889 , 2013.

Regulatory RNAs in archaea: first target identification in Methanoarchaea

Daniela Prasse, Claudia Ehlers, Rolf Backofen, Ruth A. Schmitz.

Biochem Soc Trans , 41 (1) , 344-9 , 2013.

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, Ruth A. Schmitz.

RNA Biol , 10 (5) , 779-791 , 2013.

Kekule structure enumeration yields unique SMILES

Martin Raden, Bernhard Thiel.

Proceedings of the Workshop on Constraint Based Methods for Bioinformatics (WCB 2013) , 1-9 , 2013.

Atom Mapping with Constraint Programming

Martin Raden, Feras Nahar, Heinz Ekker, Rolf Backofen, Peter F. Stadler, Christoph Flamm.

Proc. of the 19th International Conference on Principles and Practice of Constraint Programming (CP'13) , 8124 , 805-822 , 2013.

The Graph Grammar Library - a generic framework for chemical graph rewrite systems

Martin Raden, Heinz Ekker, Christoph Flamm.

Theory and Practice of Model Transformations, Proc. of ICMT 2013 , 7909 , 52-53 , 2013.

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, Anita Marchfelder.

RNA Biology , 10 (5) , 865-874 , 2013.

CRISPRmap: an automated classification of repeat conservation in prokaryotic adaptive immune systems

Sita J. Saunders, Omer S. Alkhnbashi, Dominic Rose, Sebastian Will, Rolf Backofen.

NAR , 41 (17) , 8034-44 , 2013.

Semi-Supervised Prediction of SH2-Peptide Interactions from Imbalanced High-Throughput Data

Kousik Kundu, Fabrizio Costa, Michael Huber, Michael Reth, Rolf Backofen.

PLoS One , 8 (5) , e62732 , 2013.

A graph kernel approach for alignment-free domain-peptide interaction prediction with an application to human SH3 domains

Kousik Kundu, Fabrizio Costa, Rolf Backofen.

Bioinformatics , 29 (13) , i335-i343 , 2013.

Tandem Stem-Loops in roX RNAs Act Together to Mediate X Chromosome Dosage Compensation in Drosophila

Ibrahim Avsar Ilik, Jeffrey J. Quinn, Plamen Georgiev, Filipe Tavares-Cadete, Daniel Maticzka, Sarah Toscano, Yue Wan, Robert C. Spitale, Nicholas Luscombe, Rolf Backofen, Howard Y. Chang, Asifa Akhtar.

Mol Cell , 51 (2) , 156-73 , 2013.

Salimabromide: Unexpected Chemistry from the Obligate Marine Myxobacterium Enhygromxya salina

Stephan Felder, Sandra Dreisigacker, Stefan Kehraus, Edith Neu, Gabriele Bierbaum, Patrick R. Wright, Dirk Menche, Till F. Schaberle, Gabriele M. Konig.

Chemistry , 19 (28) , 9319-24 , 2013.

Impact of the Energy Model on the Complexity of RNA Folding with Pseudoknots

Saad Sheikh, Rolf Backofen, Yann Ponty.

Combinatorial Pattern Matching - 23rd Annual Symposium, CPM 2012, Helsinki, Finland, July 3-5, 2012. Proceedings , 321--333 , 2012.

LocARNA-P: Accurate boundary prediction and improved detection of structural RNAs

Sebastian Will, Tejal Joshi, Ivo L. Hofacker, Peter F. Stadler, Rolf Backofen.

RNA , 18 (5) , 900-14 , 2012.

Structure-based Whole Genome Realignment Reveals Many Novel Non-coding RNAs

Sebastian Will, Michael Yu, Bonnie Berger.

Proceedings of the 16th International Conference on Research in Computational Molecular Biology (RECOMB 2012) , 7262 , 341 , 2012.

Computational analysis of noncoding RNAs

Stefan Washietl, Sebastian Will, David A. Hendrix, Loyal A. Goff, John L. Rinn, Bonnie Berger, Manolis Kellis.

Wiley Interdiscip Rev RNA , 3 (6) , 759-78 , 2012.

CARNA - alignment of RNA structure ensembles

Dragos A. Sorescu, Mathias Möhl, Martin Raden, Rolf Backofen, Sebastian Will.

Nucleic Acids Res , 40 (W1) , W49-W53 , 2012.

Exact Pattern Matching for RNA Structure Ensembles

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

Proceedings of the 16th International Conference on Research in Computational Molecular Biology (RECOMB 2012) , 7262 , 245-260 , 2012.

Characterization of CRISPR RNA processing in Clostridium thermocellum and Methanococcus maripaludis

Hagen Richter, Judith Zoephel, Jeanette Schermuly, Daniel Maticzka, Rolf Backofen, Lennart Randau.

NAR , 40 (19) , 9887-96 , 2012.

Accessibility and conservation: General features of bacterial small RNA-mRNA interactions?

Andreas S. Richter, Rolf Backofen.

RNA Biol , 9 (7) , 954-65 , 2012.

MicroRNAs in Cancer Translational Research: The Microcosm of Cancer Diagnosis, Prognosis and Therapy

Dominic Rose.

Frontiers in Genetics , 3 (42) , 2012.

The SH2-domain of SHIP1 interacts with the SHIP1 C-terminus: Impact on SHIP1/Ig-alpha interaction

Oindrilla Mukherjee, Lars Weingarten, Inken Padberg, Catrin Pracht, Rileen Sinha, Thomas Hochdorfer, Stephan Kuppig, Rolf Backofen, Michael Reth, Michael Huber.

Biochim Biophys Acta , 1823 (2) , 206-14 , 2012.

Navigating the unexplored seascape of pre-miRNA candidates in single-genome approaches

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

Bioinformatics , 28 (23) , 3034-41 , 2012.

Navigating the unexplored seascape of pre-miRNA candidates in single-genome approaches

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

Bioinformatics , 2012.

Atom Mapping with Constraint Programming

Martin Raden, Heinz Ekker, Peter F. Stadler, Christoph Flamm.

Proceedings of the Workshop on Constraint Based Methods for Bioinformatics (WCB 2012) , 23-29 , 2012.

Producing high-accuracy lattice models from protein atomic co-ordinates including side chains

Martin Raden, Rhodri Saunders, Cameron Smith, Rolf Backofen, Charlotte M. Deane.

Advances in Bioinformatics , 2012 (Article ID 148045) , 6 , 2012.

Global or local? Predicting secondary structure and accessibility in mRNAs

Sita J. Saunders, Daniel Maticzka, Mathias Möhl, Joshua N. Gagnon, Chris M. Brown, Rolf Backofen.

NAR , 40 (12) , 5215-26 , 2012.

Antioxidant activity of Hawaiian marine algae

Dovi Kelman, Ellen Kromkowski Posner, Karla J. McDermid, Nicole K. Tabandera, Patrick R. Wright, Anthony D. Wright.

Mar Drugs , 10 (2) , 403-16 , 2012.

An archaeal sRNA targeting cis- and trans-encoded mRNAs via two distinct domains

Dominik Jäger, Sandy R. Pernitzsch, Andreas S. Richter, Rolf Backofen, Cynthia M. Sharma, Ruth A. Schmitz.

NAR , 40 (21) , 10964-79 , 2012.

Abstract folding space analysis based on helices

Jiabin Huang, Rolf Backofen, Björn Voss.

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

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

Steffen Heyne, Fabrizio Costa, Dominic Rose, Rolf Backofen.

Bioinformatics , 28 (12) , i224-i232 , 2012.

Microstructure Alignment of Wood Density Profiles: an Approach to Equalize Radial Differences in Growth Rate

Bela Bender, Martin Raden, Rolf Backofen, Heinrich Spiecker.

Trees - Structure and Function , 26 (4) , 1267-1274 , 2012.

Local Exact Pattern Matching for Non-fixed RNA Structures

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

Proceedings of the 23th Annual Symposium on Combinatorial Pattern Matching (CPM 2012) , 7354 , 306-320 , 2012.

Fast RNA Structure Alignment for Crossing Input Structures

Rolf Backofen, Gad M. Landau, Mathias Möhl, Dekel Tsur, Oren Weimann.

Journal of Discrete Algorithms , 9 (1) , 2-11 , 2011.

Sparse RNA folding: Time and space efficient algorithms

Rolf Backofen, Dekel Tsur, Shay Zakov, Michal Ziv-Ukelson.

J. Discrete Algorithms , 9 (1) , 12-31 , 2011.

Bioinformatics of Bacterial sRNAs and Their Targets

Rolf Backofen.

Regulatory RNAs in Prokaryotes , 221-239 , 2011.

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

Elisabeth Sonnleitner, Nicolas Gonzalez, Theresa Sorger-Domenigg, Stephan Heeb, Andreas S. Richter, Rolf Backofen, Paul Williams, Alexander Huttenhofer, Dieter Haas, Udo Blasi.

Mol Microbiol , 80 (4) , 868-85 , 2011.

PETcofold: predicting conserved interactions and structures of two multiple alignments of RNA sequences

Stefan E. Seemann, Andreas S. Richter, Tanja Gesell, Rolf Backofen, Jan Gorodkin.

Bioinformatics , 27 (2) , 211-219 , 2011.

The PETfold and PETcofold web servers for intra- and intermolecular structures of multiple RNA sequences

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

NAR , 39 , W107-11 , 2011.

Signatures of Co-translational Folding

Rhodri Saunders, Martin Raden, Charlotte Deane.

Biotechnology Journal, Special issue: Protein folding in vivo , 6 (6) , 742-751 , 2011.

Molecular evolution of the non-coding eosinophil granule ontogeny transcript

Dominic Rose, Peter F. Stadler.

Front Genet , 2 , 69 , 2011.

Computational discovery of human coding and non-coding transcripts with conserved splice sites

Dominic Rose, Michael Hiller, Katharina Schutt, Jorg Hackermuller, Rolf Backofen, Peter F. Stadler.

Bioinformatics , 27 (14) , 1894-900 , 2011.

Molecular Evolution of the non-coding Eosinophil Granule Ontogeny Transcript

Dominic Rose, Peter F. Stadler.

Frontiers in Genetics , 2 (0) , 2011.

Computational discovery of human coding and non-coding transcripts with conserved splice sites

Dominic Rose, Michael Hiller, Katharina Schutt, Jörg Hackermüller, Rolf Backofen, Peter F. Stadler.

Bioinformatics , 2011.

Accessibility and conservation in bacterial small RNA-mRNA interactions and implications for genome-wide target predictions

Andreas S. Richter, Rolf Backofen.

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

Sparsification in Algebraic Dynamic Programming

Mathias Möhl, Christina Schmiedl, Shay Zakov.

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

Structator: fast index-based search for RNA sequence-structure patterns

Fernando Meyer, Stefan Kurtz, Rolf Backofen, Sebastian Will, Michael Beckstette.

BMC Bioinformatics , 12 (1) , 214 , 2011.

LatFit - Producing high accuracy lattice models from protein atomic co-ordinates including side chains

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

Adv Bioinformatics , 9 , 2011.

Efficient exploration of discrete energy landscapes

Martin Raden, Konstantin Klemm.

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

CRISPR revisited: structure prediction of CRISPR repeats

Sita Lange, Omer S. Alkhnbashi, Dominic Rose, Ingeborg Scholz, Wolfgang R. Hess, Rolf Backofen.

Poster Proceedings of the 62th Mosbach Colloquium , 2011.

Identification of SH2-peptide interactions using machine learning approaches

Kousik Kundu, Fabrizio Costa, Michael Reth, Michael Huber, Rolf Backofen.

Poster Proceedings of ISMB'11 , 2011.

Data fusion of Fourier transform infrared spectra and powder X-ray diffraction patterns for pharmaceutical mixtures

Rahul V. Haware, Patrick R. Wright, Kenneth R. Morris, Mazen L. Hamad.

J Pharm Biomed Anal , 56 (5) , 944-9 , 2011.

Alignnment of RNA with Structures of Unlimited Complexity

Alessandro Dal Palu, Mathias Möhl, Sebastian Will.

Proceedings of the Workshop on Constraint Based Methods for Bioinformatics (WCB 2010) , 7 , 2010.

A Propagator for Maximum Weight String Alignment with Arbitrary Pairwise Dependencies

Alessandro Dal Palu, Mathias Möhl, Sebastian Will.

Proceedings of the 16th International Conference on Principles and Practice of Constraint Programming (CP-2010) , 8 , 2010.

Sparsification of RNA Structure Prediction Including Pseudoknots

Mathias Möhl, Raheleh Salari, Sebastian Will, Rolf Backofen, S. Cenk Sahinalp.

Proc. of the 10th Workshop on Algorithms in Bioinformatics (WABI) , 6293 , 40-51 , 2010.

Identifikation von Targetmolekülen kleiner regulatorischer RNAs

Rolf Backofen.

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

Partitioning biological data with transitivity clustering

Tobias Wittkop, Dorothea Emig, Sita Lange, Sven Rahmann, Mario Albrecht, John H. Morris, Sebastian Bocker, Jens Stoye, Jan Baumbach.

Nat Methods , 7 (6) , 419-20 , 2010.

Freiburg RNA Tools: a web server integrating IntaRNA, ExpaRNA and LocARNA

Cameron Smith, Steffen Heyne, Andreas S. Richter, Sebastian Will, Rolf Backofen.

NAR , 38 Suppl , W373-7 , 2010.

Identification and characterization of NAGNAG alternative splicing in the moss Physcomitrella patens

Rileen Sinha, Andreas D. Zimmer, Kathrin Bolte, Daniel Lang, Ralf Reski, Matthias Platzer, Stefan A. Rensing, Rolf Backofen.

BMC Plant Biol , 10 , 76 , 2010.

TassDB2 - A comprehensive database of subtle alternative splicing events

Rileen Sinha, Thorsten Lenser, Niels Jahn, Ulrike Gausmann, Swetlana Friedel, Karol Szafranski, Klaus Huse, Philip Rosenstiel, Jochen Hampe, Stefan Schuster, Michael Hiller, Rolf Backofen, Matthias Platzer.

BMC Bioinformatics , 11 , 216 , 2010.

Hierarchical folding of multiple sequence alignments for the prediction of structures and RNA-RNA interactions

Stefan E. Seemann, Andreas S. Richter, Jan Gorodkin, Rolf Backofen.

Algorithms Mol Biol , 5 , 22 , 2010.

The small RNA Aar in Acinetobacter baylyi: a putative regulator of amino acid metabolism

Dominik Schilling, Sven Findeiss, Andreas S. Richter, Jennifer A. Taylor, Ulrike Gerischer.

Arch Microbiol , 192 (9) , 691-702 , 2010.

Time and Space Efficient RNA-RNA Interaction Prediction via Sparse Folding

Raheleh Salari, Mathias Möhl, Sebastian Will, S. Cenk Sahinalp, Rolf Backofen.

Proc. of RECOMB 2010 , 6044 , 473-490 , 2010.

Fast prediction of RNA-RNA interaction

Raheleh Salari, Rolf Backofen, S. Cenk Sahinalp.

Algorithms Mol Biol , 5 , 5 , 2010.

Identification of functional elements and regulatory circuits by Drosophila modENCODE

Sushmita Roy, Jason Ernst, Peter V. Kharchenko, Pouya Kheradpour, Nicolas Negre, Matthew L. Eaton, Jane M. Landolin, Christopher A. Bristow, Lijia Ma, Michael F. Lin, Stefan Washietl, Bradley I. Arshinoff, Ferhat Ay, Patrick E. Meyer, Nicolas Robine, Nicole L. Washington, Luisa Di Stefano, Eugene Berezikov, Christopher D. Brown, Rogerio Candeias, Joseph W. Carlson, Adrian Carr, Irwin Jungreis, Daniel Marbach, Rachel Sealfon, Michael Y. Tolstorukov, Sebastian Will, Artyom A. Alekseyenko, Carlo Artieri, Benjamin W. Booth, Angela N. Brooks, Qi Dai, Carrie A. Davis, Michael O. Duff, Xin Feng, Andrey A. Gorchakov, Tingting Gu, Jorja G. Henikoff, Philipp Kapranov, Renhua Li, Heather K. MacAlpine, John Malone, Aki Minoda, Jared Nordman, Katsutomo Okamura, Marc Perry, Sara K. Powell, Nicole C. Riddle, Akiko Sakai, Anastasia Samsonova, Jeremy E. Sandler, Yuri B. Schwartz, Noa Sher, Rebecca Spokony, David Sturgill, Marijke van Baren, Kenneth H. Wan, Li Yang, Charles Yu, Elise Feingold, Peter Good, Mark Guyer, Rebecca Lowdon, Kami Ahmad, Justen Andrews, Bonnie Berger, Steven E. Brenner, Michael R. Brent, Lucy Cherbas, Sarah C. R. Elgin, Thomas R. Gingeras, Robert Grossman, Roger A. Hoskins, Thomas C. Kaufman, William Kent, Mitzi I. Kuroda, Terry Orr-Weaver, Norbert Perrimon, Vincenzo Pirrotta, James W. Posakony, Bing Ren, Steven Russell, Peter Cherbas, Brenton R. Graveley, Suzanna Lewis, Gos Micklem, Brian Oliver, Peter J. Park, Susan E. Celniker, Steven Henikoff, Gary H. Karpen, Eric C. Lai, David M. MacAlpine, Lincoln D. Stein, Kevin P. White, Manolis Kellis.

Science , 330 (6012) , 1787-97 , 2010.

Seed-based IntaRNA prediction combined with GFP-reporter system identifies mRNA targets of the small RNA Yfr1

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

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

Lifting prediction to alignment of RNA pseudoknots

Mathias Möhl, Sebastian Will, Rolf Backofen.

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

Sparsification of RNA structure prediction including pseudoknots

Mathias Möhl, Raheleh Salari, Sebastian Will, Rolf Backofen, S. Cenk Sahinalp.

Algorithms Mol Biol , 5 (1) , 39 , 2010.

Lattice model refinement of protein structures

Martin Raden, Alessandro Dal Palu.

Proceedings of the Workshop on Constraint Based Methods for Bioinformatics (WCB 2010) , 7 , 2010.

High accuracy on-lattice side chain models of PDB protein structures

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

Poster Proceedings of ISMB'10 , 2010.

Machine learning approaches for prediction of SH2-peptide interactions

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

Poster Proceedings of ISMB'10 , 2010.

In silico modelling of human lipoprotein metabolism

Martin Jansen, Karl Winkler, Gerhard Puetz, Peter Pfaffelhuber, Martin Raden.

Poster Proceedings of SBMC'10, (conference for system biology in mammalian cells) , 2010.

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, Peter F. Stadler.

Journal of Systems Chemistry , 1 (1) , 4 , 2010.

Shape-based barrier estimation for RNAs

Sergiy Bogomolov, Martin Raden, Björn Voss, Andreas Podelski, Rolf Backofen.

In Proceedings of German Conference on Bioinformatics GCB'10 , 173 , 42-51 , 2010.

Computational prediction of sRNAs and their targets in bacteria

Rolf Backofen, Wolfgang R. Hess.

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

COMPUTATIONAL STUDIES OF NON-CODING RNAS - Session Introduction

Rolf Backofen, H. Chitsaz, I. Hofacker, S. C. Sahinalp, P. F. Stadler.

PSB10 , 15 , 54-56 , 2010.

Fast prediction of RNA-RNA Interaction

Raheleh Salari, Rolf Backofen, S. Cenk Sahinalp.

Proc. of the 9th Workshop on Algorithms in Bioinformatics (WABI) , 5724 , 261-272 , 2009.

Fast Feature Subset Selection in Biological Sequence Analysis

Rainer Pudimat, Rolf Backofen, Ernst-Günter Schukat-Talamazzini.

International Journal of Pattern Recognition and Artificial Intelligence , 23 (2) , 191 -- 207 , 2009.

biRNA: Fast RNA-RNA Binding Sites Prediction

Hamidreza Chitsaz, Rolf Backofen, S. Cenk Sahinalp.

Proc. of the 9th Workshop on Algorithms in Bioinformatics (WABI) , 5724 , 25-36 , 2009.

Sparse RNA Folding: Time and Space Efficient Algorithms

Rolf Backofen, Dekel Tsur, Shay Zakov, Michal Ziv-Ukelson.

Proc. 20th Symp. Combinatorial Pattern Matching , 5577 , 249-262 , 2009.

Fast RNA Structure Alignment for Crossing Input Structures

Rolf Backofen, Gad M. Landau, Mathias Möhl, Dekel Tsur, Oren Weimann.

Proc. 20th Symp. Combinatorial Pattern Matching , 5577 , 236-248 , 2009.

Simultaneous Alignment and Folding of Protein Sequences

Jérôme Waldispühl, Charles W. O'Donnell, Sebastian Will, Srinivas Devadas, Rolf Backofen, Bonnie Berger.

RECOMB09 , 5541 , 339--355 , 2009.

Protein Folding Simulation by Two-Stage Optimization

Abu Dayem Ullah, Leonidas Kapsokalivas, Martin Raden, Kathleen Steinhöfel.

Proc. of ISICA'09 , 51 , 138-145 , 2009.

Accurate prediction of NAGNAG alternative splicing

Rileen Sinha, Swetlana Nikolajewa, Karol Szafranski, Michael Hiller, Niels Jahn, Klaus Huse, Matthias Platzer, Rolf Backofen.

NAR , 37 (11) , 3569-79 , 2009.

Lifting Prediction to Alignment of RNA Pseudoknots

Mathias Möhl, Sebastian Will, Rolf Backofen.

RECOMB09 , 5541 , 285--301 , 2009.

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

Martin Raden, Cameron Smith, Mohamad Rabbath, Marlien Edwards, Sebastian Will, Rolf Backofen.

Bioinformatics , 25 (5) , 676-7 , 2009.

Constraint-based Local Move Definitions for Lattice Protein Models Including Side Chains

Martin Raden, Mohamed Abou Hamra, Kathleen Steinhöfel, Rolf Backofen.

Proceedings of the Fifth Workshop on Constraint Based Methods for Bioinformatics (WCB09) , 2009.

Equivalence Classes of Optimal Structures in HP~Protein Models Including Side Chains

Martin Raden, Rolf Backofen, Sebastian Will.

Proceedings of the Fifth Workshop on Constraint Based Methods for Bioinformatics (WCB09) , 2009.

Statement of Ongoing Work:Extending Boolean Satisfiability Techniques for Haplotype Inference by Pure Parsimony

Eric I. Hsu, Sheila A. McIlraith.

WCB09 , 2009.

Conserved introns reveal novel transcripts in Drosophila melanogaster

Michael Hiller, Sven Findeiss, Sandro Lein, Manja Marz, Claudia Nickel, Dominic Rose, Christine Schulz, Rolf Backofen, Sonja J. Prohaska, Gunter Reuter, Peter F. Stadler.

Genome Res , 19 (7) , 1289-300 , 2009.

Lightweight Comparison of RNAs Based on Exact Sequence-Structure Matches

Steffen Heyne, Sebastian Will, Michael Beckstette, Rolf Backofen.

Bioinformatics , 25 (16) , 2095-2102 , 2009.

Non-coding RNA annotation of the genome of Trichoplax adhaerens

Jana Hertel, Danielle de Jong, Manja Marz, Dominic Rose, Hakim Tafer, Andrea Tanzer, Bernd Schierwater, Peter F. Stadler.

NAR , 37 (5) , 1602-15 , 2009.

Haplotype Inference Combining Pedigreesand Unrelated Individuals

Ana Graca, Ines Lynce, Joao Marques-Silva, Arlindo L. Oliveira.

WCB09 , 2009.

Homology-based annotation of non-coding RNAs in the genomes of Schistosoma mansoni and Schistosoma japonicum

Claudia S. Copeland, Manja Marz, Dominic Rose, Jana Hertel, Paul J. Brindley, Clara Bermudez Santana, Stephanie Kehr, Camille Stephan-Otto Attolini, Peter F. Stadler.

BMC Genomics , 10 , 464 , 2009.

A Constraint Model for Constrained Hidden Markov Models: a first Biological Application

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

WCB09 , 2009.

A partition function algorithm for interacting nucleic acid strands

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

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

Constraint Based Languages for Biological Reactions

Stefano Bistarelli, Marco Bottalico.

WCB09 , 2009.

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

D. Allouche, S. de Givry, M. Sanchez, T. Schiex.

WCB09 , 2009.

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, A. Goesmann.

Bioinformatics , 25 (23) , 3128-3134 , 2009.

Techniques de Décomposition pour l'Isomorphisme de Sous-Graphe

Stephane Zampelli, Martin Raden, Yves Deville, Rolf Backofen.

Proc. of the 4th Journées Francophones de Programmation par Contraintes (JFPC'08) , 2008.

Efficient Sequence Alignment with Side-Constraints by Cluster Tree Elimination

Sebastian Will, Anke Busch, Rolf Backofen.

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

Improved identification of conserved cassette exons using Bayesian networks

R. Sinha, M. Hiller, R. Pudimat, U. Gausmann, M. Platzer, Rolf Backofen.

BMC Bioinformatics , 9 (1) , 477 , 2008.

Unifying evolutionary and thermodynamic information for RNA folding of multiple alignments

Stefan E. Seemann, Jan Gorodkin, Rolf Backofen.

NAR , 36 (20) , 6355-62 , 2008.

Alternative splicing at NAGNAG acceptors in Arabidopsis thaliana SR and SR-related protein-coding genes

Stefanie Schindler, Karol Szafranski, Michael Hiller, Gul Shad Ali, Saiprasad G. Palusa, Rolf Backofen, Matthias Platzer, Anireddy S. N. Reddy.

BMC Genomics , 9 , 159 , 2008.

Duplicated RNA genes in teleost fish genomes

Dominic Rose, Julian Joris, Jörg Hackermüller, Kristin Reiche, Qiang Li, Peter F. Stadler.

J Bioinform Comput Biol , 6 (6) , 1157-75 , 2008.

NcDNAlign: plausible multiple alignments of non-protein-coding genomic sequences

Dominic Rose, Jana Hertel, Kristin Reiche, Peter F. Stadler, Jörg Hackermüller.

Genomics , 92 (1) , 65-74 , 2008.

A Sampling Approach for the Exploration of Biopolymer Energy Landscapes

Andreas S. Richter, Sebastian Will, Rolf Backofen.

Proceedings of the European Conference on Metallobiolomics (HMI Berlin, Germany, 2007) , 27-38 , 2008.

Structure Local Multiple Alignment of RNA

Otto Wolfgang, Will Sebastian, Backofen Rolf.

Proceedings of German Conference on Bioinformatics (GCB'2008) , P-136 , 178-188 , 2008.

Fixed Parameter Tractable Alignment of RNA Structures Including Arbitrary Pseudoknots

Mathias Möhl, Sebastian Will, Rolf Backofen.

Proceedings of the 19th Annual Symposium on Combinatorial Pattern Matching (CPM 2008) , 69-81 , 2008.

Classifying protein-like sequences in arbitrary lattice protein models using LatPack

Martin Raden, Daniel Maticzka, Rhodri Saunders, Rolf Backofen.

HFSP Journal , 2 (6) , 396-404 , 2008.

CPSP-tools - Exact and Complete Algorithms for High-throughput 3D Lattice Protein Studies

Martin Raden, Sebastian Will, Rolf Backofen.

BMC Bioinformatics , 9 , 230 , 2008.

Genetic Variants of the Copy Number Polymorphic beta-Defensin Locus Are Associated with Sporadic Prostate Cancer

K. Huse, S. Taudien, M. Groth, P. Rosenstiel, K. Szafranski, M. Hiller, J. Hampe, K. Junker, J. Schubert, S. Schreiber, G. Birkenmeier, M. Krawczak, M. Platzer.

Tumour Biol , 29 (2) , 83-92 , 2008.

Widespread and subtle: alternative splicing at short-distance tandem sites

Michael Hiller, Matthias Platzer.

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

Selection against tandem splice sites affecting structured protein regions

Michael Hiller, Karol Szafranski, Klaus Huse, Rolf Backofen, Matthias Platzer.

BMC Evolutionary Biology , 8 , 89 , 2008.

Assessing the fraction of short-distance tandem splice sites under purifying selection

Michael Hiller, Karol Szafranski, Rileen Sinha, Klaus Huse, Swetlana Nikolajewa, Philip Rosenstiel, Stefan Schreiber, Rolf Backofen, Matthias Platzer.

RNA , 14 , 616-29 , 2008.

Lightweight comparison of RNAs based on exact sequence-structure matches

Steffen Heyne, Sebastian Will, Michael Beckstette, Rolf Backofen.

Proceedings of the German Conference on Bioinformatics (GCB'2008) , P-136 , 189-198 , 2008.

IntaRNA: efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions

Anke Busch, Andreas S. Richter, Rolf Backofen.

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

Variations on RNA folding and alignment: lessons from Benasque

Athanasius F. Bompfünewerer, Rolf Backofen, Stephan H. Bernhart, Jana Hertel, Ivo L. Hofacker, Peter F. Stadler, Sebastian Will.

Journal of Mathematical Biology , 56 (1-2) , 129-144 , 2008.

RNAalifold: improved consensus structure prediction for RNA alignments

Stephan H. Bernhart, Ivo L. Hofacker, Sebastian Will, Andreas R. Gruber, Peter F. Stadler.

BMC Bioinformatics , 9 , 474 , 2008.

Constraint-based Methods for Bioinformatics

Alessandro Dal Palù, Agostino Dovier, François Fages, Sebastian Will.

Trends in Constraint Programming , 129--150 , 2007.

The string-generative capacity of regular dependency languages

Marco Kuhlmann, Mathias Möhl.

Twelfth Conference on Formal Grammar (FG) , 2007.

Mildly Context-Sensitive Dependency Languages

Marco Kuhlmann, Mathias Möhl.

45th Annual Meeting of the Association for Computational Linguistics (ACL) , 2007.

BioBayesNet: a web server for feature extraction and Bayesian network modeling of biological sequence data

Swetlana Nikolajewa, Rainer Pudimat, Michael Hiller, Matthias Platzer, Rolf Backofen.

NAR , 35 (Web Server issue) , W688-93 , 2007.

Inferring Non-Coding RNA Families and Classes by Means of Genome-Scale Structure-Based Clustering

Sebastian Will, Kristin Reiche, Ivo L. Hofacker, Peter F. Stadler, Rolf Backofen.

PLoS Comput Biol , 3 (4) , e65 , 2007.

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, M. Platzer.

Genome Biol , 8 (8) , R154 , 2007.

A dynamic programming approach for finding common patterns in RNAs

Sven Siebert, Rolf Backofen.

JCB , 14 (1) , 33-44 , 2007.

Methods for multiple alignment and consensus structure prediction of RNAs implemented in MARNA

Sven Siebert, Rolf Backofen.

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

Computational RNomics of drosophilids

Dominic Rose, Jorg Hackermuller, Stefan Washietl, Kristin Reiche, Jana Hertel, Sven Findeiss, Peter F. Stadler, Sonja J. Prohaska.

BMC Genomics , 8 , 406 , 2007.

GenColors: annotation and comparative genomics of prokaryotes made easy

Alessandro Romualdi, Marius Felder, Dominic Rose, Ulrike Gausmann, Markus Schilhabel, Gernot Glockner, Matthias Platzer, Jurgen Suhnel.

Methods Mol Biol , 395 , 75-96 , 2007.

The Energy Landscape Library - A Platform for Generic Algorithms

Martin Raden, Sebastian Will, Rolf Backofen.

BIRD'07 - 1st international Conference on Bioinformatics Research and Development , 217 , 83-86 , 2007.

The Energy Landscape Library - A Platform for Generic Algorithms

Martin Raden, Sebastian Will, Rolf Backofen.

BIRD'07 - 1st international Conference on Bioinformatics Research and Development , 217 , 83-86 , 2007.

HPdesign: Inverse Folding of Proteins

Martin Raden, Sebastian Will, Rolf Backofen.

ISMB/ECCB , 2007.

TassDB: a database of alternative tandem splice sites

Michael Hiller, Swetlana Nikolajewa, Klaus Huse, Karol Szafranski, Philip Rosenstiel, Stefan Schuster, Rolf Backofen, Matthias Platzer.

NAR , 35 (Database issue) , D188-92 , 2007.

Pre-mRNA Secondary Structures Influence Exon Recognition

Michael Hiller, Zhaiyi Zhang, Rolf Backofen, Stefan Stamm.

PLoS Genet , 3 (11) , e204 , 2007.

INFO-RNA--a server for fast inverse RNA folding satisfying sequence constraints

Anke Busch, Rolf Backofen.

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

RNAs everywhere: genome-wide annotation of structured RNAs

Athanasius F. Bompfünewerer Consortium, Rolf Backofen, Stephan H. Bernhart, Christoph Flamm, Claudia Fried, Guido Fritzsch, Jörg Hackermüller, Jana Hertel, Ivo L. Hofacker, Kristin Missal, Axel Mosig, Sonja J. Prohaska, Dominic Rose, Peter F. Stadler, Andrea Tanzer, Stefan Washietl, Sebastian Will.

J Exp Zoolog B Mol Dev Evol , 308B (1) , 1-25 , 2007.

IMS2 -- An integrated medical software system for early lung cancer detection using ion mobility spectrometry data of human breath

Jan Baumbach, Alexander Bunkowski, Sita Lange, Timm Oberwahrenbrock, Nils Kleinbölting, Sven Rahmann, Jörg Ingo Baumbach.

Journal of Integrative Bioinformatics , 4 (3) , 75 , 2007.

Fast Detection of Common Sequence Structure Patterns in RNAs

Rolf Backofen, Sven Siebert.

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

Locality and gaps in RNA comparison

Rolf Backofen, Shihyen Chen, Danny Hermelin, Gad M. Landau, Mikhail A. Roytberg, Oren Weimann, Kaizhong Zhang.

JCB , 14 (8) , 1074-87 , 2007.

Index-based algorithms for motif search and their integration in a system for differential genome analysis

M. Beckstette.

2007.

Extended cross-serial dependencies in Tree Adjoining Grammars

Marco Kuhlmann, Mathias Möhl.

Eighth International Workshop on Tree Adjoining Grammars and Related Formalisms (TAG+8) , 2006.

Local Alignment of RNA Sequences with Arbitrary Scoring Schemes

Rolf Backofen, Danny Hermelin, Gad M. Landau, Oren Weimann.

CPM06 , 4009 , 246-257 , 2006.

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 V.-H. Winterer.

PIK , 29 (2) , 81-87 , 2006.

Bioinformatics and Constraints

Rolf Backofen, David Gilbert.

Handbook of Constraint Programming , 905-944 , 2006.

Exploring the lower part of discrete polymer model energy landscapes

Michael T. Wolfinger, Sebastian Will, Ivo L. Hofacker, Rolf Backofen, Peter F. Stadler.

Europhysics Letters , 74 (4) , 725-732 , 2006.

Counting Protein Structures by DFS with Dynamic Decomposition

Sebastian Will, Martin Raden.

Proc. of the Workshop on Constraint Based Methods for Bioinformatics. http://www.dimi.uniud.it/dovier/WCB06/WCB06_proceedings.pdf , 83-90 , 2006.

Constrained Alignment Using Cluster Tree Elimination

Sebastian Will, Anke Busch, Rolf Backofen.

14th Annual International conference on Intelligent Systems for Molecular Biology (ISMB'06) , 2006.

Sequencing errors or SNPs at splice-acceptor guanines in dbSNP?

Matthias Platzer, Michael Hiller, Karol Szafranski, Niels Jahn, Jochen Hampe, Stefan Schreiber, Rolf Backofen, Klaus Huse.

Nat Biotechnol , 24 (9) , 1068-70 , 2006.

Prediction of structured non-coding RNAs in the genomes of the nematodes Caenorhabditis elegans and Caenorhabditis briggsae

Kristin Missal, Xiaopeng Zhu, Dominic Rose, Wei Deng, Geir Skogerbo, Runsheng Chen, Peter F. Stadler.

J Exp Zool B Mol Dev Evol , 306 (4) , 379-92 , 2006.

Alternative Splicing at NAGNAG Acceptors: Simply Noise or Noise and More?

Michael Hiller, Karol Szafranski, Rolf Backofen, Matthias Platzer.

PLoS Genet , 2 (11) , e207 , 2006.

Using RNA secondary structures to guide sequence motif finding towards single-stranded regions

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

NAR , 34 (17) , e117 , 2006.

Phylogenetically widespread alternative splicing at unusual GYNGYN donors

M. Hiller, K. Huse, K. Szafranskzi, P. Rosenstiel, S. Schreiber, Rolf Backofen, M. Platzer.

Genome Biol , 7 (7) , R65 , 2006.

Single-Nucleotide Polymorphisms in NAGNAG Acceptors Are Highly Predictive for Variations of Alternative Splicing

Michael Hiller, Klaus Huse, Karol Szafranski, Niels Jahn, Jochen Hampe, Stefan Schreiber, Rolf Backofen, Matthias Platzer.

Am J Hum Genet , 78 (2) , 291-302 , 2006.

INFO-RNA--a fast approach to inverse RNA folding

Anke Busch, Rolf Backofen.

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

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

Michael Beckstette, Robert Homann, Robert Giegerich, Stefan Kurtz.

BMC Bioinformatics , 7 , 389 , 2006.

A Constraint-Based Approach to Fast and Exact Structure Prediction in Three-Dimensional Protein Models

Rolf Backofen, Sebastian Will.

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

A Posteriori Modelling of Sequence Motif Arrangements

Rolf Backofen, Rainer Pudimat.

GCB , 2005.

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

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

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

Lexicalised Configuration Grammars

Robert Grabowski, Marco Kuhlmann, Mathias Möhl.

Second International Workshop on Constraint Solving and Language Processing (CSLP 2005) , 2005.

INFO-RNA - A Fast Approach of the Inverse RNA Folding

Anke Busch, Rolf Backofen.

ECCB , 2005.

Well-Nested Drawings as Models of Syntactic Structure

Manuel Bodirsky, Marco Kuhlmann, Mathias Möhl.

10th Conference on Formal Grammar and 9th Meeting on Mathematics of Language , 2005.

Efficient Constraint-based Sequence Alignment by Cluster Tree Elimination

Sebastian Will, Anke Busch, Rolf Backofen.

Proceedings of the Workshop on Constraint Based Methods in Bioinformatics (WCB05) , 66-74 , 2005.

A new distance measure of RNA ensembles and its application to phylogenetic tree construction

Sven Siebert, Rolf Backofen.

IEEE 2005 Symposium on Computational Intelligence in Bioinformatics and Computational Biology , 150-157 , 2005.

MARNA: multiple alignment and consensus structure prediction of RNAs based on sequence structure comparisons

Sven Siebert, Rolf Backofen.

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

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

M. Beckstette, A. Sczyrba, A.H. Brivanlou, R. Giegerich, C.R. Altmann.

BMC Genomics , 6 (123) , 2005.

Non-coding RNAs in Ciona intestinalis

Kristin Missal, Dominic Rose, Peter F. Stadler.

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

The origin of bilateral animals. A multigene approach.

P. Martinez, K. Malde, M. Beckstette, J. Baguna.

Comparative Biochemistry and Physiology. Abstracts of the Society for Experimental Biology Annual Main Meeting , 141 , 2005.

Non-EST based prediction of exon skipping and intron retention events using Pfam information

Michael Hiller, Klaus Huse, Matthias Platzer, Rolf Backofen.

NAR , 33 (17) , 5611-21 , 2005.

Creation and disruption of protein features by alternative splicing -- a novel mechanism to modulate function

Michael Hiller, Klaus Huse, Matthias Platzer, Rolf Backofen.

Genome Biology , 6 (7) , R58 , 2005.

SECISDesign: a server to design SECIS-elements within the coding sequence

Anke Busch, Sebastian Will, Rolf Backofen.

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

Normalized Similarity of RNA Sequences

Rolf Backofen, Danny Hermelin, Gad M. Landau, Oren Weimann.

Proc. 12th Symposium on String Processing and Information Retrieval (SPIRE 2005) , 3772 , 360-369 , 2005.

Prediction of Transcription Factor Binding Sites by Modeling Multiple Features

Rainer Pudimat, Rolf Backofen.

ISMB-ECCB , 2004.

Feature Based Representation and Detection of Transcription Factor Binding Sites

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

GCB , 53 , 43-52 , 2004.

MODERNA - Design of New and Recombinant Selenoproteins

Anke Busch, Rolf Backofen.

ISMB/ECCB , 2004.

Fast Detection of Common Sequence Structure Patterns in RNAs

Rolf Backofen, Sven Siebert.

Symposium on String Processing and Information Retrieval (SPIRE 2004) , 3246 , 79-92 , 2004.

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

Rolf Backofen.

Journal of Discrete Algorithms , 2 (2) , 161-206 , 2004.

Identification of 10,500 Xenopus laevis Full Length Clones through EST Clustering and Sequence Analysis

A. Sczyrba, M. Beckstette, R. Giegerich, C.A. Altmann.

Proceedings of the German Conference on Bioinformatics (GCB). Discovery Notes , P-53 , 6-7 , 2004.

Widespread occurrence of alternative splicing at NAGNAG acceptors contributes to proteome plasticity

Michael Hiller, Klaus Huse, Karol Szafranski, Niels Jahn, Jochen Hampe, Stefan Schreiber, Rolf Backofen, Matthias Platzer.

Nat Genet , 36 (12) , 1255-7 , 2004.

Efficient prediction of alternative splice forms using protein domain homology

Michael Hiller, Rolf Backofen, Stephan Heymann, Anke Busch, Timo Mika Glaesser, Johann-Christoph Freytag.

In Silico Biol , 4 (2) , 0017 , 2004.

Using protein secondary structure to build structural template

Y. He, S. Qin, X. M. Pan, M. Beckstette, R. Giegerich.

CASP6 method paper , 2004.

Constraint Based Protein Structure Prediction Exploiting Secondary Structure Information

Alessandro Dal Palu, Sebastian Will, Rolf Backofen, Agostino Dovier.

Convegno Italiano di Logica Computazionale 2004 (CILC 2004) , 16-17 , 2004.

Local Sequence-Structure Motifs in RNA

Rolf Backofen, Sebastian Will.

Journal of Bioinformatics and Computational Biology (JBCB) , 2 (4) , 681-698 , 2004.

Computational Design of New and Recombinant Selenoproteins

Rolf Backofen, Anke Busch.

Proc. of the 15th Annual Symposium on Combinatorial Pattern Matching (CPM2004) , 3109 , 270-284 , 2004.

PoSSuMsearch: Fast and Sensitive Matching of Position Specific Scoring Matrices using Enhanced Suffix Arrays

M. Beckstette, D. Strothmann, R. Homann, R. Giegerich, S. Kurtz.

Proc. of the German Conference on Bioinformatics , P-53 , 53-64 , 2004.

Genlight: An Interactive System for High-throughput sequence analysis and Comparative Genomics

M. Beckstette, A. Sczyrba, P. M. Selzer.

Proc. of the German Conference on Bioinformatics , P-53 , 2004.

Genlight: Interactive High-Throughput Sequence Analysis and comparative genomics

M. Beckstette, J.T. Mailänder, R.J. Marhöfer, A. Sczyrba, E. Ohlebusch, R. Giegerich, P.M. Selzer.

Yearbook Bioinformatics , 79-94 , 2004.

Genlight: Interactive High-Throughput Sequence Analysis and comparative genomics

M. Beckstette, J.T. Mailaennder, R.J. Marhoefer, A. Sczyrba, E. Ohlebusch, R. Giegerich, P.M. Selzer.

Journal of Integrative Bioinformatics , 1 (8) , 2004.

Breaking of Partial Symmetries in the Photo and Alignment Problem

Sebastian Will, Rolf Backofen.

Proceedings of the Third International Workshop on Symmetry in Constraint Satisfaction Problems (SymCon 2003) , 187--194 , 2003.

Multiple Local Sequence Structure Alignment of RNA Sequences

Sven Siebert, Rolf Backofen.

RECOMB 2003 , 2003.

MARNA: A Server for Multiple Alignment of RNAs

Sven Siebert, Rolf Backofen.

GCB , 135-140 , 2003.

A Constraint-Based Approach to Structure Prediction for Simplified Protein Models that Outperforms Other Existing Methods

Rolf Backofen, Sebastian Will.

Proceedings of the 19th International Conference on Logic Programming (ICLP 2003) , 2916 , 49--71 , 2003.

Constraint-based Hydrophobic Core Construction for Protein Structure Prediction in the Face-Centered-Cubic Lattice

Sebastian Will.

Proceedings of the Pacific Symposium on Biocomputing 2002 (PSB 2002) , 661--672 , 2002.

Protein Structure Prediction in the Face-Centered Cubic Lattice

Sebastian Will, Rolf Backofen.

European Conference on Computational Biology 2002 , 2002.

Multiple Local Sequence Structure Alignment of RNA Sequences

Sven Siebert.

European Conference on Computational Biology 2002 , 2002.

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

Steffen Heyne, Martin Raden, Debnath Pal, Aida Baharuddin, Andreas Vogel, Rolf Hilgenfeld.

ECCB'02 , 2002.

Protein similarity search under mRNA structural constraints: application to targeted selenocysteine insertion

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

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

Excluding symmetries in constraint-based search

Rolf Backofen, Sebastian Will.

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

On the Complexity of Protein Similarity Search under mRNA Structure Constraints

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

Proc. of 19th International Symposium on Theoretical Aspects of Computer Science (STACS2002) , 2285 , 274--286 , 2002.

Introduction to Bioinformatics

Rolf Backofen.

Companion Volume to the Proceedings of the 39th Annual Meeting of the Association for Computational Linguistic (ACL) , 2001.

Introduction to the Special Issue on Bioinformatics

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

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

RNA-Sequence-Structure Properties and Selenocysteine Insertion

Rolf Backofen.

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

Bioinformatics and Constraints

Rolf Backofen, David Gilbert.

Constraints , 6 , 141-156 , 2001.

The Protein Structure Prediction Problem: A Constraint Optimisation Approach using a New Lower Bound

Rolf Backofen.

Constraints , 6 , 223-255 , 2001.

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

Rolf Backofen, Sebastian Will.

Proc. of the 12th Annual Symposium on Combinatorial Pattern Matching (CPM2001) , 2089 , 257--272 , 2001.

Fast, Constraint-based Threading of HP-Sequences to Hydrophobic Cores

Rolf Backofen, Sebastian Will.

Proc. of the 7th International Conference on Principle and Practice of Constraint Programming (CP'2001) , 2239 , 494--508 , 2001.

Protein similarity search under mRNA structural constraints: application to selenocysteine incorporation

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

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

Computational Molecular Biology: An Introduction

Peter Clote, Rolf Backofen.

2000.

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

Rolf Backofen.

Proceedings of the 11th Annual Symposium on Combinatorial Pattern Matching (CPM 2000) , 1848 , 277--292 , 2000.

Algorithmic approach to quantifying the hydrophobic force contribution in protein folding

Rolf Backofen, Sebastian Will, Peter Clote.

Proceedings of the Pacific Symposium on Biocomputing (PSB 2000) , 5 , 92--103 , 2000.

Classroom Assignment using Constraint Logic Programming

Slim Abdennadher, Matthias Saft, Sebastian Will.

Proceedings of the Second International Conference and Exhibition on The Practical Application of Constraint Technologies and Logic Programming (PACLP 2000) , 2000.

Algorithmic approach to quantifying the hydrophobic force contribution in protein folding

Rolf Backofen, Sebastian Will, Peter Clote.

Proceedings of the German Conference on Bioinformatics (GCB'99) , 93-106 , 1999.

Excluding Symmetries in Constraint-Based Search

Rolf Backofen, Sebastian Will.

Proceedings of 5th International Conference on Principle and Practice of Constraint Programming (CP'99) , 1713 , 73-87 , 1999.

Application of Constraint Programming Techniques for Structure Prediction of Lattice Proteins with Extended Alphabets

Rolf Backofen, Sebastian Will, Erich Bornberg-Bauer.

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

Aktuelles Schlagwort Bioinformatik

Rolf Backofen, François Bry, Peter Clote, Hans-Peter Kriegel, Thomas Seidl, Klaus Schulz.

Informatik Spektrum , 22 (5) , 376-378 , 1999.

Using Constraint Programming for lattice Protein Folding

Rolf Backofen.

Proceedings of the Pacific Symposium on Biocomputing (PSB'98) , 3 , 387-398 , 1998.

Constraint Techniques for Solving the Protein Structure Prediction Problem

Rolf Backofen.

Proceedings of 4th International Conference on Principle and Practice of Constraint Programming (CP'98) , 1520 , 72-86 , 1998.

Excluding Symmetries in Concurrent Constraint Programming

Rolf Backofen, Sebastian Will.

Workshop on Modeling and Computing with Concurrent Constraint Programming , 1998.

Structure Prediction in an HP-type Lattice with an Extended Alphabet

Rolf Backofen, Sebastian Will.

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

How to Win a Game with Features

Rolf Backofen, Ralf Treinen.

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

Using Constraint Programming for lattice Protein Folding

Rolf Backofen.

Workshop on Constraints and Bioinformatics/Biocomputing , 1997.

Evolution as a Computational Engine

Rolf Backofen, Peter Clote.

Proc. of Annual Conference of the European Association for Computer Science Logic (CSL'97) , 1414 , 35--55 , 1997.

Controlling Functional Uncertainty

Rolf Backofen.

Proceedings of 12th European Conference on Artificial Intelligence , 557--561 , 1996.

A Complete Axiomatization of a Theory with Feature and Arity Constraints

Rolf Backofen.

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

A Complete and Recursive Feature Theory

Rolf Backofen, Gert Smolka.