Hierarchical Multitask Structured Output Learning for Large-scale Sequence Segmentation. - Nico Görnitz; Christian Widmer; Georg Zeller; André Kahles; Sören Sonnenburg; Gunnar Rätsch (NIPS, 2011)

Oqtans: a Galaxy-integrated workflow for quantitative transcriptome analysis from NGS Data. - Sebastian J. Schultheiß; Géraldine Jean; Jonas Behr; Regina Bohnert; Philipp Drewe; Nico Görnitz; André Kahles; Pramod Mudrakarta; Vipin T. Sreedharan; Georg Zeller; Gunnar Rätsch (BMC Bioinform., 2011)

MITIE: Simultaneous RNA-Seq-based transcript identification and quantification in multiple samples. - Jonas Behr; André Kahles; Yi Zhong; Vipin T. Sreedharan; Philipp Drewe; Gunnar Rätsch (Bioinform., 2013)

Oqtans: the RNA-seq workbench in the cloud for complete and reproducible quantitative transcriptome analysis. - Vipin T. Sreedharan; Sebastian J. Schultheiß; Géraldine Jean; André Kahles; Regina Bohnert; Philipp Drewe; Pramod Mudrakarta; Nico Görnitz; Georg Zeller; Gunnar Rätsch (Bioinform., 2014)

Oqtans: a multifunctional workbench for RNA-seq data analysis. - Vipin T. Sreedharan; Sebastian J. Schultheiß; Géraldine Jean; André Kahles; Regina Bohnert; Philipp Drewe; Pramod Mudrakarta; Nico Görnitz; Georg Zeller; Gunnar Rätsch (BMC Bioinform., 2014)

Integrative Genome-wide Analysis of the Determinants of RNA Splicing in Kidney Renal Clear Cell Carcinoma. - Kjong-Van Lehmann; André Kahles; Cyriac Kandoth; William Lee; Nikolaus Schultz; Oliver Stegle; Gunnar Rätsch (Pacific Symposium on Biocomputing, 2015)

MMR: a tool for read multi-mapper resolution. - André Kahles; Jonas Behr; Gunnar Rätsch (Bioinform., 2016)

SplAdder: identification, quantification and testing of alternative splicing events from RNA-Seq data. - André Kahles; Cheng Soon Ong; Yi Zhong; Gunnar Rätsch (Bioinform., 2016)

Dynamic compression schemes for graph coloring. - Harun Mustafa; Ingo Schilken; Mikhail Karasikov; Carsten Eickhoff; Gunnar Rätsch; André Kahles (Bioinform., 2019)

AStarix: Fast and Optimal Sequence-to-Graph Alignment. - Pesho Ivanov; Benjamin Bichsel; Harun Mustafa; André Kahles; Gunnar Rätsch; Martin T. Vechev (RECOMB, 2020)

Sparse Binary Relation Representations for Genome Graph Annotation. - Mikhail Karasikov; Harun Mustafa; Amir Joudaki; Sara Javadzadeh-No; Gunnar Rätsch; André Kahles (J. Comput. Biol., 2020)

Genomic basis for RNA alterations in cancer. - Claudia Calabrese; Natalie R. Davidson; Deniz Demircioglu; Nuno A. Fonseca; Yao He; André Kahles; Kjong-Van Lehmann; Fenglin Liu; Yuichi Shiraishi; Cameron M. Soulette; Lara Urban; Liliana Greger; et al. (Nat., 2020)

Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. - Esther Rheinbay; Morten Muhlig Nielsen; Federico Abascal; Jeremiah Wala; Ofer Shapira; Grace Tiao; Henrik Hornshøj; Julian M. Hess; Randi Istrup Juul; Ziao Lin; Lars Feuerbach; Radhakrishnan Sabarinathan; et al. (Nat., 2020)

Topology-based sparsification of graph annotations. - Daniel Danciu; Mikhail Karasikov; Harun Mustafa; André Kahles; Gunnar Rätsch (Bioinform., 2021)

Lossless Indexing with Counting de Bruijn Graphs. - Mikhail Karasikov; Harun Mustafa; Gunnar Rätsch; André Kahles (RECOMB, 2022)

SECEDO: SNV-based subclone detection using ultra-low coverage single-cell DNA sequencing. - Hana Rozhonová; Daniel Danciu; Stefan Stark; Gunnar Rätsch; André Kahles; Kjong-Van Lehmann (Bioinform., 2022)

RNA Instant Quality Check: Alignment-Free RNA-Degradation Detection. - Kjong-Van Lehmann; André Kahles; Magdalena Murr; Gunnar Rätsch (J. Comput. Biol., 2022)

Probabilistic pathway-based multimodal factor analysis. - Alexander Immer; Stefan G. Stark; Francis Jacob; Ximena Bonilla; Tinu Thomas; André Kahles; Sandra Götze; Emanuela S. Milani; Bernd Wollscheid; Tumor Profiler Consortium; Gunnar Rätsch; Kjong-Van Lehmann (Bioinform., 2024)

Label-guided seed-chain-extend alignment on annotated De Bruijn graphs. - Harun Mustafa; Mikhail Karasikov; Nika Mansouri-Ghiasi; Gunnar Rätsch; André Kahles (Bioinform., 2024)