Nonsense-Mediated Decay of Alternative Precursor mRNA Splicing Variants Is a Major Determinant of the Arabidopsis Steady State Transcriptome
Drechsel, Gabriele, Kahles, André, Kesarwani, Anil K., Stauffer, Eva, Behr, Jonas, Drewe, Philipp, Rätsch, Gunnar, Wachter, Andreas
Published in The Plant cell (01.10.2013)
Published in The Plant cell (01.10.2013)
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Journal Article
Mutational interactions define novel cancer subgroups
Kuipers, Jack, Thurnherr, Thomas, Moffa, Giusi, Suter, Polina, Behr, Jonas, Goosen, Ryan, Christofori, Gerhard, Beerenwinkel, Niko
Published in Nature communications (19.10.2018)
Published in Nature communications (19.10.2018)
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Journal Article
Accurate splice site prediction using support vector machines
Sonnenburg, Sören, Schweikert, Gabriele, Philips, Petra, Behr, Jonas, Rätsch, Gunnar
Published in BMC bioinformatics (01.01.2007)
Published in BMC bioinformatics (01.01.2007)
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Journal Article
Multi-omics data integration reveals novel drug targets in hepatocellular carcinoma
Dimitrakopoulos, Christos, Hindupur, Sravanth Kumar, Colombi, Marco, Liko, Dritan, Ng, Charlotte K. Y, Piscuoglio, Salvatore, Behr, Jonas, Moore, Ariane L, Singer, Jochen, Ruscheweyh, Hans-Joachim, Matter, Matthias S, Mossmann, Dirk, Terracciano, Luigi M, Hall, Michael N, Beerenwinkel, Niko
Published in BMC genomics (04.08.2021)
Published in BMC genomics (04.08.2021)
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Journal Article
Detailed simulation of cancer exome sequencing data reveals differences and common limitations of variant callers
Hofmann, Ariane L, Behr, Jonas, Singer, Jochen, Kuipers, Jack, Beisel, Christian, Schraml, Peter, Moch, Holger, Beerenwinkel, Niko
Published in BMC bioinformatics (03.01.2017)
Published in BMC bioinformatics (03.01.2017)
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Journal Article
Assessment of transcript reconstruction methods for RNA-seq
Steijger, Tamara, Abril, Josep F, Engström, Pär G, Kokocinski, Felix, Hubbard, Tim J, Guigó, Roderic, Harrow, Jennifer, Bertone, Paul
Published in Nature methods (01.12.2013)
Published in Nature methods (01.12.2013)
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Journal Article
Systematic evaluation of spliced alignment programs for RNA-seq data
Engström, Pär G, Steijger, Tamara, Sipos, Botond, Grant, Gregory R, Kahles, André, Rätsch, Gunnar, Goldman, Nick, Hubbard, Tim J, Harrow, Jennifer, Guigó, Roderic, Bertone, Paul
Published in Nature methods (01.12.2013)
Published in Nature methods (01.12.2013)
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Journal Article
Multiple reference genomes and transcriptomes for Arabidopsis thaliana
Gan, Xiangchao, Stegle, Oliver, Behr, Jonas, Steffen, Joshua G., Drewe, Philipp, Hildebrand, Katie L., Lyngsoe, Rune, Schultheiss, Sebastian J., Osborne, Edward J., Sreedharan, Vipin T., Kahles, André, Bohnert, Regina, Jean, Géraldine, Derwent, Paul, Kersey, Paul, Belfield, Eric J., Harberd, Nicholas P., Kemen, Eric, Toomajian, Christopher, Kover, Paula X., Clark, Richard M., Rätsch, Gunnar, Mott, Richard
Published in Nature (London) (22.09.2011)
Published in Nature (London) (22.09.2011)
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Journal Article
MITIE: Simultaneous RNA-Seq-based transcript identification and quantification in multiple samples
Behr, Jonas, Kahles, André, Zhong, Yi, Sreedharan, Vipin T, Drewe, Philipp, Rätsch, Gunnar
Published in Bioinformatics (15.10.2013)
Published in Bioinformatics (15.10.2013)
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Journal Article
Alternative Splicing Substantially Diversifies the Transcriptome during Early Photomorphogenesis and Correlates with the Energy Availability in Arabidopsis
Hartmann, Lisa, Drewe-Boß, Philipp, Wießner, Theresa, Wagner, Gabriele, Geue, Sascha, Lee, Hsin-Chieh, Obermüller, Dominik M., Kahles, André, Behr, Jonas, Sinz, Fabian H., Rätsch, Gunnar, Wachter, Andreas
Published in The Plant cell (01.11.2016)
Published in The Plant cell (01.11.2016)
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Journal Article
mGene: accurate SVM-based gene finding with an application to nematode genomes
Schweikert, Gabriele, Zien, Alexander, Zeller, Georg, Behr, Jonas, Dieterich, Christoph, Ong, Cheng Soon, Philips, Petra, De Bona, Fabio, Hartmann, Lisa, Bohlen, Anja, Krüger, Nina, Sonnenburg, Sören, Rätsch, Gunnar
Published in Genome research (01.11.2009)
Published in Genome research (01.11.2009)
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Journal Article
Next generation genome annotation with mGene.ngs
Behr, Jonas, Bohnert, Regina, Zeller, Georg, Schweikert, Gabriele, Hartmann, Lisa, Rätsch, Gunnar
Published in BMC bioinformatics (07.12.2010)
Published in BMC bioinformatics (07.12.2010)
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Journal Article
Oqtans: a Galaxy-integrated workflow for quantitative transcriptome analysis from NGS Data
Schultheiss, Sebastian J, Jean, Géraldine, Behr, Jonas, Bohnert, Regina, Drewe, Philipp, Görnitz, Nico, Kahles, André, Mudrakarta, Pramod, Sreedharan, Vipin T, Zeller, Georg, Rätsch, Gunnar
Published in BMC Bioinformatics (21.11.2011)
Published in BMC Bioinformatics (21.11.2011)
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Journal Article
Conference Proceeding
mGene.web: a web service for accurate computational gene finding
Schweikert, Gabriele, Behr, Jonas, Zien, Alexander, Zeller, Georg, Ong, Cheng Soon, Sonnenburg, Sören, Rätsch, Gunnar
Published in Nucleic acids research (01.07.2009)
Published in Nucleic acids research (01.07.2009)
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Journal Article
Methods for processing next-generation sequencing genomic data
Hernandez, David, Behr, Jonas, Song, Lin, Novak, Adam, Steijger, Tamara, Xu, Zhenyu
Year of Publication 05.03.2024
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Year of Publication 05.03.2024
Patent
METHODS FOR PROCESSING NEXT-GENERATION SEQUENCING GENOMIC DATA
XU, Zhenyu, NOVAK, Adam, SONG, Lin, HERNANDEZ, David, STEIJGER, Tamara, BEHR, Jonas
Year of Publication 06.12.2023
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Year of Publication 06.12.2023
Patent
METHODS FOR PROCESSING NEXT-GENERATION SEQUENCING GENOMIC DATA
XU, Zhenyu, NOVAK, Adam, SONG, Lin, HERNANDEZ, David, STEIJGER, Tamara, BEHR, Jonas
Year of Publication 04.07.2019
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Year of Publication 04.07.2019
Patent