The PD-(D/E)XK superfamily revisited: identification of new members among proteins involved in DNA metabolism and functional predictions for domains of (hitherto) unknown function. - Jan Kosinski; Marcin Feder; Janusz M. Bujnicki (BMC Bioinform., 2005)

REPAIRtoire - a database of DNA repair pathways. - Kaja Milanowska; Joanna Krwawicz; Grzegorz Papaj; Jan Kosinski; Katarzyna Poleszak; Justyna Lesiak; Ewelina Osinska; Kristian Rother; Janusz M. Bujnicki (Nucleic Acids Res., 2011)

Improving your target-template alignment with MODalign. - Alessandro Barbato; Pascal Benkert; Torsten Schwede; Anna Tramontano; Jan Kosinski (Bioinform., 2012)

MODexplorer: an integrated tool for exploring protein sequence, structure and function relationships. - Jan Kosinski; Alessandro Barbato; Anna Tramontano (Bioinform., 2013)

RetrogeneDB-a database of plant and animal retrocopies. - Wojciech Rosikiewicz; Michal Kabza; Jan Kosinski; Joanna Ciomborowska-Basheer; Magdalena R. Kubiak; Izabela Makalowska (Database J. Biol. Databases Curation, 2017)

AlphaPulldown - a python package for protein-protein interaction screens using AlphaFold-Multimer. - Dingquan Yu; Grzegorz Chojnowski; Maria Rosenthal; Jan Kosinski (Bioinform., 2023)

AGouTI-Flexible Annotation of Genomic and Transcriptomic Intervals. - Jan Kosinski; Marek Zywicki (PLoS Comput. Biol., 2023)

PyTME (Python Template Matching Engine): A fast, flexible, and multi-purpose template matching library for cryogenic electron microscopy data. - Valentin J. Maurer; Marc Siggel; Jan Kosinski (SoftwareX, 2024)