BlockClust: efficient clustering and classification of non-coding RNAs from short read RNA-seq profiles. - Pavankumar Videm; Dominic Rose; Fabrizio Costa; Rolf Backofen (Bioinform., 2014)

Automated peptide mapping and protein-topographical annotation of proteomics data. - Pavankumar Videm; Deepika Gunasekaran; Bernd Schröder; Bettina Mayer; Martin L. Biniossek; Oliver Schilling (BMC Bioinform., 2014)

The RNA workbench: best practices for RNA and high-throughput sequencing bioinformatics in Galaxy. - Björn A. Grüning; Jörg Fallmann; Dilmurat Yusuf; Sebastian Will; Anika Erxleben; Florian Eggenhofer; Torsten Houwaart; Bérénice Batut; Pavankumar Videm; Andrea Bagnacani; Markus Wolfien; Steffen Lott; et al. (Nucleic Acids Res., 2017)

The RNA workbench 2.0: next generation RNA data analysis. - Jörg Fallmann; Pavankumar Videm; Andrea Bagnacani; Bérénice Batut; Maria A. Doyle; Tomas Klingström; Florian Eggenhofer; Peter F. Stadler; Rolf Backofen; Björn A. Grüning (Nucleic Acids Res., 2019)

Analysis of high-throughput sequencing data related to small non-coding RNAs biogenesis and function - Pavankumar Videm (2021)

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update. - Enis Afgan; Anton Nekrutenko; Björn A. Grüning; Daniel J. Blankenberg; Jeremy Goecks; Michael C. Schatz; Alexander E. Ostrovsky; Alexandru Mahmoud; Andrew J. Lonie; Anna Syme; Anne Fouilloux; Anthony Bretaudeau; et al. (Nucleic Acids Res., 2022)