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)

Visualization and analysis of gene expression data using freeware and GPL-Software. - E. W. Wolski; Christoph K. Wierling; Thomas Kreitler; Szymon M. Kielbasa; U. Schneider; Johan Gobom; Hans Lehrach; Holger Eickhoff (German Conference on Bioinformatics, 2001)

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)

Modeling the G1/S transition in mammals -Bifurcation an alysis of elementary modules. - Maciej Swat; Alexander E. Kel; Szymon M. Kielbasa; Hanspeter Herzel (German Conference on Bioinformatics, 2003)

Genome-wide Analysis of Functions Regulated by Sets of Transcription Factors. - Szymon M. Kielbasa; Nils Blüthgen; Hanspeter Herzel (German Conference on Bioinformatics, 2004)

HOMGL - comparing genelists across species and with different accession numbers. - Nils Blüthgen; Szymon M. Kielbasa; Branka Cajavec; Hanspeter Herzel (Bioinform., 2004)

SeqVISTA: a new module of integrated computational tools for studying transcriptional regulation. - Zhenjun Hu; Yutao Fu; Anason S. Halees; Szymon M. Kielbasa; Zhiping Weng (Nucleic Acids Res., 2004)

Measuring similarities between transcription factor binding sites. - Szymon M. Kielbasa; Didier Gonze; Hanspeter Herzel (BMC Bioinform., 2005)

HuSiDa - the human siRNA database: an open-access database for published functional siRNA sequences and technical details of efficient transfer into recipient cells. - Matthias Truss; Maciej Swat; Szymon M. Kielbasa; Reinhold Schäfer; Hanspeter Herzel; Christian Hagemeier (Nucleic Acids Res., 2005)

Targetfinder.org: a resource for systematic discovery of transcription factor target genes. - Szymon M. Kielbasa; Nils Blüthgen; Michael Fähling; Ralf Mrowka (Nucleic Acids Res., 2010)

TransFind - predicting transcriptional regulators for gene sets. - Szymon M. Kielbasa; Holger Klein; Helge G. Roider; Martin Vingron; Nils Blüthgen (Nucleic Acids Res., 2010)

BIOPET: towards Scalable, Maintainable, User-friendly, Robust and Flexible NGS data analysis pipelines. - Peter van't Hof; Szymon M. Kielbasa; Wibowo Arindrarto; Jeroen F. J. Laros; Sander Bollen; Hailiang Mei (CCGrid, 2017)

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)