Finding Transcription Factor Binding Sites in Coregulated Genes by Exhaustive Sequence Search. - Szymon M. Kielbasa; Jan O. Korbel; Dieter Beule; Johannes Schuchhardt; Hanspeter Herzel (German Conference on Bioinformatics, 2000)

Combining frequency and positional information to predict transcription factor binding sites. - Szymon M. Kielbasa; Jan O. Korbel; Dieter Beule; Johannes Schuchhardt; Hanspeter Herzel (Bioinform., 2001)

The Helmholtz Network for Bioinformatics: an integrative web portal for bioinformatics resources. - Torsten Crass; Iris Antes; Rico Basekow; Peer Bork; Christian Buning; Maik Christensen; Holger Claussen 002; Christian Ebeling; Peter Ernst; Valérie Gailus-Durner; Karl-Heinz Glatting; Rolf Gohla; et al. (Bioinform., 2004)

A supervised hidden markov model framework for efficiently segmenting tiling array data in transcriptional and chIP-chip experiments: systematically incorporating validated biological knowledge. - Jiang Du 003; Joel S. Rozowsky; Jan O. Korbel; Zhengdong D. Zhang; Thomas E. Royce; Martin H. Schultz; Michael Snyder 001; Mark Gerstein (Bioinform., 2006)

Systematic Inference of Copy-Number Genotypes from Personal Genome Sequencing Data Reveals Extensive Olfactory Receptor Gene Content Diversity. - Sebastian M. Waszak; Yehudit Hasin; Thomas Zichner; Tsviya Olender; Ifat Keydar; Miriam Khen; Adrian M. Stütz; Andreas Schlattl; Doron Lancet; Jan O. Korbel (PLoS Comput. Biol., 2010)

DELLY: structural variant discovery by integrated paired-end and split-read analysis. - Tobias Rausch; Thomas Zichner; Andreas Schlattl; Adrian M. Stütz; Vladimir Benes; Jan O. Korbel (Bioinform., 2012)

Data analysis: Create a cloud commons. - Lincoln D. Stein; Bartha M. Knoppers; Peter Campbell; Gad Getz; Jan O. Korbel (Nat., 2015)

Active medulloblastoma enhancers reveal subgroup-specific cellular origins. - Charles Y. Lin; Serap Erkek; Yiai Tong; Linlin Yin; Alexander J. Federation; Marc Zapatka; Parthiv Haldipur; Daisuke Kawauchi; Thomas Risch; Hans-Jörg Warnatz; Barbara C. Worst; Bensheng Ju; et al. (Nat., 2016)

Strand-seq enables reliable separation of long reads by chromosome via expectation maximization. - Maryam Ghareghani; David Porubsky; Ashley D. Sanders; Sascha Meiers; Evan E. Eichler; Jan O. Korbel; Tobias Marschall (Bioinform., 2018)

Alfred: interactive multi-sample BAM alignment statistics, feature counting and feature annotation for long- and short-read sequencing. - Tobias Rausch; Markus Hsi-Yang Fritz; Jan O. Korbel; Vladimir Benes (Bioinform., 2019)

12 Grand Challenges in Single-Cell Data Science. - David Laehnemann; Johannes Köster; Ewa Szczurek; Davis J. McCarthy; Stephanie C. Hicks; Mark D. Robinson; Catalina A. Vallejos; Niko Beerenwinkel; Kieran R. Campbell; Ahmed Mahfouz; Luca Pinello; Pavel Skums; et al. (PeerJ Prepr., 2019)

InTAD: chromosome conformation guided analysis of enhancer target genes. - Konstantin Okonechnikov; Serap Erkek; Jan O. Korbel; Stefan M. Pfister; Lukas Chavez (BMC Bioinform., 2019)

VISOR: a versatile haplotype-aware structural variant simulator for short- and long-read sequencing. - Davide Bolognini; Ashley D. Sanders; Jan O. Korbel; Alberto Magi; Vladimir Benes; Tobias Rausch (Bioinform., 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)

ASHLEYS: automated quality control for single-cell Strand-seq data. - Christina Gros; Ashley D. Sanders; Jan O. Korbel; Tobias Marschall; Peter Ebert (Bioinform., 2021)