Publications

Lisa Fiedler, Matthias Bernt, Martin Middendorf, and Peter F. Stadler. Detecting gene breakpoints in noisy genome sequences using position-annotated colored de-Bruijn graphs. BMC Bioinformatics, (24)1Springer Science and Business Media LLC, June 2023. [PUMA: Zno breakpoints de-Bruijn gene genome graphs noisy position-annotated] URL

David Schaller, Marc Hellmuth, and Peter F. Stadler. AsymmeTree: A Flexible Python Package for the Simulation of Complex Gene Family Histories. Software, (1)3:276–298, MDPI AG, August 2022. [PUMA: AsymmeTree Family Gene Histories Package Python Simulation zno] URL

Johannes R. Schmidt, Janine Haupt, Sina Riemschneider, Christoph Kämpf, Dennis Löffler, Conny Blumert, Kristin Reiche, Ulrike Koehl, Stefan Kalkhof, and Jörg Lehmann. Transcriptomic signatures reveal a shift towards an anti-inflammatory gene expression profile but also the induction of type I and type II interferon signaling networks through aryl hydrocarbon receptor activation in murine macrophages. Frontiers in Immunology, (14)Frontiers Media SA, May 2023. [PUMA: Transcriptomic Zno activation anti-inflammatory aryl expression gene hydrocarbon induction interferon macrophages murine networks profile receptor signaling signatures through] URL

Michael Rade, Sebastian Böhlen, Vanessa Neuhaus, Dennis Löffler, Conny Blumert, Maximilian Merz, Ulrike Köhl, Susann Dehmel, Katherina Sewald, and Kristin Reiche. A time-resolved meta-analysis of consensus gene expression profiles during human T-cell activation. Genome Biology, (24)1Springer Science and Business Media LLC, December 2023. [PUMA: T-cell Yaff activation consensus expression gene human meta-analysis] URL

Qinghe Zeng, Christophe Klein, Stefano Caruso, Pascale Maille, Narmin Ghaffari Laleh, Daniele Sommacale, Alexis Laurent, Giuliana Amaddeo, David Gentien, Audrey Rapinat, Hélène Regnault, Cécile Charpy, Cong Trung Nguyen, Christophe Tournigand, Raffaele Brustia, Jean Michel Pawlotsky, Jakob Nikolas Kather, Maria Chiara Maiuri, Nicolas Loménie, and Julien Calderaro. Artificial intelligence predicts immune and inflammatory gene signatures directly from hepatocellular carcinoma histology. J. Hepatol., (77)1:116--127, Elsevier BV, July 2022. [PUMA: topic_lifescience artificial deep gene image immune intelligence; learning; pathology; signatures; slide whole]

Martin Pippel, David Jebb, Franziska Patzold, Sylke Winkler, Heiko Vogel, Gene Myers, Michael Hiller, and Anna K Hundsdoerfer. A highly contiguous genome assembly of the bat hawkmoth Hyles vespertilio (Lepidoptera: Sphingidae). Gigascience, (9)1Oxford University Press (OUP), January 2020. [PUMA: PacBio annotation; assembly; comparison gene genome hawkmoth-silk long moth reads; topic_lifescience]

Sonja J Prohaska, Sarah J Berkemer, Fabian Gärtner, Thomas Gatter, Nancy Retzlaff, Students of the Graphs and Biological Networks Lab 2017, Christian Höner Zu Siederdissen, and Peter F Stadler. Expansion of gene clusters, circular orders, and the shortest Hamiltonian path problem. J. Math. Biol., (77)2:313--341, August 2018. [PUMA: Evolution Hamiltonian Kalmanson Non-homologous Phylogenetic Unequal clusters; combinatorics; crossing gene metrics; of over path problems; recombination;]

Sebastian Rosch, Karl-Philipp Rommel, Markus Scholz, Holger Thiele, and Philipp Lurz. Transcriptomic research in heart failure with preserved ejection fraction: Current state and future perspectives. Card. Fail. Rev., (6):e24, Radcliffe Group Ltd, March 2020. [PUMA: Heart LIFE-Heart; RNA; blood cells; ejection expression; failure fraction; gene mononuclear peripheral preserved transcriptome with]

Jirina Zackova Suchanova, Gust Bilcke, Beata Romanowska, Ali Fatlawi, Martin Pippel, Alastair Skeffington, Michael Schroeder, Wim Vyverman, Klaas Vandepoele, Nils Kröger, and Nicole Poulsen. Diatom adhesive trail proteins acquired by horizontal gene transfer from bacteria serve as primers for marine biofilm formation. New Phytol., (240)2:770--783, Wiley, October 2023. [PUMA: topic_lifescience bioadhesion; biofilm; diatom; gene gliding horizontal motility; unit_transfer]