Publications | Scibiome

Otto Richter, Uwe Drewitz, Reinhold Haux, Stefan Heuser, Tim Kacprowski, Jochen Steil (2025). Zusammenwirken von natürlicher und künstlicher Intelligenz: Beurteilen – Messen – Bewerten. Springer.

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Corinna Thoben, Boas Pucker, Stephan Winter, Bethany Fallon Econopouly, Samar Sheat (2025). The haplotype-resolved assembly of COL40, a cassava (Manihot esculenta) line with broad-spectrum resistance against viruses causing Cassava brown streak disease, unveils a region of highly repeated elements on chromosome 12. G3 Genes|Genomes|Genetics, 15(6).

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Pranab Rudra, Wolf-Tilo Balke, Tim Kacprowski, Frank Ursin, Sabine Salloch (2025). Large language models for surgical informed consent: An ethical perspective on simulated empathy. Journal of Medical Ethics, 52(2).

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Nadia Khaveh, Jan Berghöfer, Ralph Brehm, René Buschow, Karsten Cirksena, Cord Drögemüller, Abeera Fatima, Gordon Grabert, Gisa Gerold, Alexander Grahofer, Ralf Herwig, Klaus Jung, Tim Kacprowski, Bai-Wei Lo, Roya Shiasi Sardoabi, Martin Vingron, Stefan Mundlos, Julia Metzger (2025). Integrative multi-omics analysis of growth plate regulation underlying body size in miniature pigs. Research Square (preprint, under review).

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(2025). Domain Specific Transfer Learning and Classifier Chains in Alzheimer's Disease Detection using 3D Convolutional Neural Networks. Informatics in Medicine Unlocked, 59.

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Moana Witte, Carlos Oltmanns, Jan Tauwaldt, Hagen Schmaus, Jasmin Mischke, Gordon Grabert, Mara Bretthauer, Lennart M. Roesner, Thomas Werfel, Katja Deterding, Benjamin Maasoumy, Heiner Wedemeyer, Tim Kacprowski, Anke R. M. Kraft, Markus Cornberg (2025). Distinct inflammatory imprint in non-cirrhotic and cirrhotic patients before and after direct-acting antiviral therapy. Clinical and Molecular Hepatology, 31.

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Elias Albrecht, Konstantin Pelz, Alexander Gress, Hieu Nguyen Trung, Olga v. Kalinina, Tim Kacprowski, Jan Baumbach, Markus List, Olga Tsoy (2025). DIGGER 2.0: digging into the functional impact of differential splicing on human and mouse disorders. Nucleic Acids Research, 53(W1).

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Daniel Dehncke, Vinzenz Fiebach, Lennart Kinzel, Knut Baumann, Tim Kacprowski (2024). VISPER—Visualization System for Interactions between Proteins and Drugs for Exploratory Research. VCBM 2024: Eurographics Workshop on Visual Computing for Biology and Medicine.

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Hannah Benedictine Maier, Alexandra Neyazi, Gabriel L. Bundies, Fiona Meyer-Bockenkamp, Stefan Bleich, Hansi Pathak, Yvonne Ziert, Barbara Neuhaus, Franz-Josef Müller, Iris Pollmann, Thomas Illig, Stefanie Mücke, Meike Müller, Brinja Kira Möller, Steffen Oeltze-Jafra, Tim Kacprowski, Jan Voges, Fabian Müntefering, Josef Scheiber, Andreas Reif, Mareike Aichholzer, Christine Reif-Leonhard, Maren Schmidt-Kassow, Ulrich Hegerl, Hanna Reich, Stefan Unterecker, Heike Weber, Jürgen Deckert, Nicole Bössel-Debbert, Hans J. Grabe, Michael Lucht, Helge Frieling (2024). Validation of the predictive value of BDNF -87 methylation for antidepressant treatment success in severely depressed patients—a randomized rater-blinded trial. Trials, 25.

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Moana Witte, Carlos Oltmanns, Jan Tauwaldt, Hagen Schmaus, Jasmin Mischke, Leon Kalix, Gordon Grabert, Mara Bretthauer, Katja Deterding, Benjamin Maasoumy, Heiner Wedemeyer, Tim Kacprowski, Anke R. M. Kraft, Markus Cornberg (2024). SAT-363 Hepatocellular carcinoma development post hepatitis C virus cure is associated with distinct changes in the dynamics of the soluble inflammatory milieu. Journal of Hepatology, 80(Suppl. 1).

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Olga Tsoy, Sabine Ameling, Sören Franzenburg, Markus Hoffmann, Lina Liv-Willuth, Hye Kyung Lee, Ludwig Knabl, Priscilla A. Furth, Uwe Völker, Lothar Hennighausen, Jan Baumbach, Tim Kacprowski, Markus List (2024). RNA sequencing depth guidelines for the study of alternative splicing. bioRxiv (preprint).

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Willi Schüler, Lisa-Marie Bente, Thomas M. Deserno, Tim Kacprowski (2024). Real-time ECG-monitoring in virtual reality. Medical Imaging 2024: Imaging Informatics for Healthcare, Research, and Applications.

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Antonio Jesus Diaz-Honrubia, Philipp D. Rohde, Emetis Niazmand, Ernestina Menasalvas, Maria-Esther Vidal (2024). PALADIN: A process-based constraint language for data validation. Information Fusion, 112.

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Monica S. Matchado, Malte Rühlemann, Sandra Reitmeier, Tim Kacprowski, Fabian Frost, Dirk Haller, Jan Baumbach, Markus List (2024). On the limits of 16S rRNA gene-based metagenome prediction and functional profiling. Microbial Genomics, 10(2).

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Markus Hoffmann, Julian M. Poschenrieder, Massimiliano Incudini, Sylvie Baier, Amelie Fritz, Andreas Maier, Michael Hartung, Christian Hoffmann, Nico Trummer, Klaudia Adamowicz, Mario Picciani, Evelyn Scheibling, Maximilian v. Harl, Ingmar Lesch, Hunor Frey, Simon Kayser, Paul Wissenberg, Leon Schwartz, Leon Hafner, Aakriti Acharya, Lena Hackl, Gordon Grabert, Sung-Gwon Lee, Gyuhyeok Cho, Matthew E. Cloward, Jakub Jankowski, Hye K. Lee, Olga Tsoy, Nina Wenke, Anders G. Pedersen, Klaus Bønnelykke, Antonio Mandarino, Federico Melograna, Laura Schulz, Héctor Climente-González, Mathias Wilhelm, Luigi Iapichino, Lars Wienbrandt, David Ellinghaus, Kristel Van Steen, Michele Grossi, Priscilla A. Furth, Lothar Hennighausen, Alessandra Di Pierro, Jan Baumbach, Tim Kacprowski, Markus List, David B. Blumenthal (2024). Network medicine-based epistasis detection in complex diseases: ready for quantum computing. Nucleic Acids Research, 52(17).

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Gordon Grabert, Daniel Dehncke, Tushar More, Markus List, Anke R. M. Kraft, Markus Cornberg, Karsten Hiller, Tim Kacprowski (2024). MeTEor: an R Shiny app for exploring longitudinal metabolomics data. Bioinformatics Advances, 4(1).

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Moana Witte, Carlos Oltmanns, Jan Tauwaldt, Hagen Schmaus, Jasmin Mischke, Gordon Grabert, Mara Bretthauer, Katja Deterding, Benjamin Maasoumy, Heiner Wedemeyer, Tim Kacprowski, Anke Kraft, Markus Cornberg (2024). Inflammatory milieu alterations associated with carcinogenesis persist in cirrhotic patients despite HCV cure. Zeitschrift für Gastroenterologie, 62.

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Gihanna Galindez, Markus List, Jan Baumbach, Uwe Völker, Ulrike Mäder, David B. Blumenthal, Tim Kacprowski (2024). Inference of differential gene regulatory networks using boosted differential trees. Bioinformatics Advances, 4(1).

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Hayder Radhi Hussein Mzedawee, Rasoul Kowsar, Reza Moradi-Hajidavaloo, Roya Shiasi Sardoabi, Khaled Sadeghi, Mohammad Hossein Nasr-Esfahani, Mehdi Hajian (2024). Heat shock interferes with the amino acid metabolism of bovine cumulus-oocyte complexes in vitro: a multistep analysis. Amino Acids, 56.

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Jonathan Wittau, Serkan Celik, Tim Kacprowski, Thomas M. Deserno, Roland Seifert (2024). Fake paper identification in the pool of withdrawn and rejected manuscripts submitted to Naunyn–Schmiedeberg's Archives of Pharmacology. Naunyn-Schmiedeberg’s Archives of Pharmacology, 397.

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Francescapaola Mattias, Olga Tsoy, Elke Hammer, Alexander Gress, Stefan Simm, Chit Tong Lio, Sabine Ameling, Kerstin Amann, Leonie Dreher, Ulrich Wenzel, Tim Kacprowski, Markus List, Olga Kalinina, Karlhans Endlich, Jan Baumbach, Uwe Völker, Nicole Endlich, Felix Kliewe (2024). Alternative splicing in mechanically stretched podocytes as a model of glomerular hypertension. Journal of the American Society of Nephrology, 36.

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Hendrik Fokken, Julian Waclawski, Nadine Kattre, Arnold Kloos, Sebastian Müller, Max Ettinger, Tim Kacprowski, Michael Heuser, Tobias Maetzig, Adrian Schwarzer (2024). A 19-color single-tube full spectrum flow cytometry assay for the detection of measurable residual disease in acute myeloid leukemia. Cytometry Part A, 105(3).

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Moana Witte, Carlos Oltmanns, Jan Tauwaldt, Hagen Schmaus, Jasmin Mischke, Gordon Grabert, Leon Kalix, Daniel Dehncke, Mara Bretthauer, Katja Deterding, Benjamin Maasoumy, Heiner Wedemeyer, Tim Kacprowski, Anke R. M. Kraft, Markus Cornberg (2023). The impact of cirrhosis on the inflammatory milieu before and long-term after hepatitis C virus elimination by direct-acting antiviral therapy. medRxiv (preprint).

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Julian Matschinske, Julian Späth, Mohammad Bakhtiari, Niklas Probul, Mohammad M. K. Majdabadi, Reza Nasirigerdeh, Reihaneh Torkzadehmahani, Anne Hartebrodt, Balazs-Attila Orban, Sándor-József Fejér, Olga Zolotareva, Supratim Das, Linda Baumbach, Josch K. Pauling, Olivera Tomašević, Béla Bihari, Marcus Bloice, Nina C. Donner, Walid Fdhila, Tobias Frisch, Anne-Christin Hauschild, Dominik Heider, Andreas Holzinger, Walter Hötzendorfer, Jan Hospes, Tim Kacprowski, Markus Kastelitz, Markus List, Rudolf Mayer, Mónika Moga, Heimo Müller, Anastasia Pustozerova, Richard Röttger, Christina C. Saak, Anna Saranti, Harald H. H. W. Schmidt, Christof Tschohl, Nina K. Wenke, Jan Baumbach (2023). The FeatureCloud Platform for Federated Learning in Biomedicine: Unified Approach. Journal of Medical Internet Research, 25.

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Lasse Benzinger, Frank Ursin, Wolf-Tilo Balke, Tim Kacprowski, Sabine Salloch (2023). Should Artificial Intelligence be used to support clinical ethical decision-making? A systematic review of reasons. BMC Medical Ethics, 24.

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Zsolt Illes, Malene Møller Jørgensen, Rikke Bæk, Lisa-Marie Bente, Jørgen T. Lauridsen, Kirsten H. Hyrlov, Christopher Aboo, Jan Baumbach, Tim Kacprowski, Francois Cotton, Charles R. G. Guttmann, Allan Stensballe (2023). New Enhancing MRI Lesions Associate with IL-17, Neutrophil Degranulation and Integrin Microparticles: Multi-Omics Combined with Frequent MRI in Multiple Sclerosis. Biomedicines, 11.

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Gihanna Galindez, Sepideh Sadegh, Jan Baumbach, Tim Kacprowski, Markus List (2023). Network-based approaches for modeling disease regulation and progression. Computational and Structural Biotechnology Journal, 21.

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Philip Gemke, Theresa Bender, Ennio Idrobo-Avila, Henning Dathe, Dagmar Krefting, Tim Kacprowski, Nicolai Spicher (2023). Measurement of Individual Alteration in Perioperative ECGs During Elective Percutaneous Coronary Intervention. arXiv (preprint).

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Sepideh Sadegh, James Skelton, Elisa Anastasi, Andreas Maier, Klaudia Adamowicz, Anna Möller, Nils M. Kriege, Jaanika Kronberg, Toomas Haller, Tim Kacprowski, Anil Wipat, Jan Baumbach, David B. Blumenthal (2023). Lacking mechanistic disease definitions and corresponding association data hamper progress in network medicine and beyond. Nature Communications, 14.

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Ahmad Sakor, Samaneh Jozashoori, Emetis Niazmand, Ariam Rivas, Konstantinos Bougiatiotis, Fotis Aisopos, Enrique Iglesias, Philipp D. Rohde, Trupti Padiya, Anastasia Krithara, Georgios Paliouras, Maria-Esther Vidal (2023). Knowledge4COVID-19: A semantic-based approach for constructing a COVID-19 related knowledge graph from various sources and analyzing treatments' toxicities. Journal of Web Semantics, 75.

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Fabian Stögbauer, Barbara Geß, Christine Brambs, Manuela Lautizi, Tim Kacprowski, Iordanis Ourailidis, Holger Bronger, Marion Kiechle, Aurelia Noske, Gisela Keller, Moritz Jesinghaus, Christopher Poremba, Wilko Weichert, Melanie Boxberg (2023). Independent Tissue-Based Biomarkers in Endometrioid Endometrial Cancer: Tumor Budding in Microsatellite Instability and WHO Grading in Copy-Number-Low Patients. Cancers, 15(15).

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Felix Erne, Daniel Dehncke, Steven C. Herath, Fabian Springer, Nico Pfeifer, Ralf Eggeling, Markus A. Küper (2023). Deep Learning in the Detection of Rare Fractures—Development of a ``Deep Learning Convolutional Network'' Model for Detecting Acetabular Fractures. Zeitschrift für Orthopädie und Unfallchirurgie, 161(1).

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Corinna Thoben, Boas Pucker (2023). Automatic annotation of the bHLH gene family in plants. BMC Genomics.

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Olivia I. Coleman, Adam Sorbie, Alessandra Riva, Miriam Von Stern, Stephanie Kuhls, Denise M. Selegato, Nikolai Köhler, Jakob Wirbel, Tim Kacprowski, Andreas Dunkel, Josh K. Pauling, Johannes Plagge, Diego Mediel-Cuadra, Sophia Wagner, Ines Chadly, Sandra Bierwith, Tingying Peng, Thomas Metzler, Clemens Schafmayer, Sebastian Hinz, Christian Röder, Christoph Röcken, Michael Zimmermann, Philip Rosenstiel, Katja Steiger, Moritz Jesinghaus, Gerhard Liebisch, Josef Ecker, Christina Schmidt, Georg Zeller, Klaus-Peter Janssen, Dirk Haller (2023). ATF6 activation alters colonic lipid metabolism causing tumor-associated microbial adaptation. bioRxiv (preprint).

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Lena Hackl, Amit Fenn, Zakaria Louadi, Jan Baumbach, Tim Kacprowski, Markus List, Olga Tsoy (2023). Alternative splicing impacts microRNA regulation within coding regions. NAR Genomics and Bioinformatics, 5(3).

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Amit Fenn, Olga Tsoy, Tim Faro, Fanny Rößler, Alexander Dietrich, Johannes Kersting, Zakaria Louadi, Chit Tong Lio, Uwe Völker, Jan Baumbach, Tim Kacprowski, Markus List (2023). Alternative splicing analysis benchmark with DICAST. NAR Genomics and Bioinformatics, 5(2).

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Sandra Klawitter, Tim Kacprowski (2023). A visualization tool for continuous reference intervals based on GAMLSS. Journal of Laboratory Medicine, 47(4).

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Fabian Stögbauer, Manuela Lautizi, Mark Kriegsmann, Hauke Winter, Thomas Muley, Katharina Kriegsmann, Moritz Jesinghaus, Jan Baumbach, Peter Schüffler, Wilko Weichert, Tim Kacprowski, Melanie Boxberg (2022). Tumour cell budding and spread through air spaces in squamous cell carcinoma of the lung—Determination and validation of optimal prognostic cut-offs. Lung Cancer, 169.

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Manuela Lautizi, Jan Baumbach, Wilko Weichert, Katja Steiger, Markus List, Nicole Pfarr, Tim Kacprowski (2022). The Limits of Molecular Signatures for Pancreatic Ductal Adenocarcinoma Subtyping. NAR Cancer, 4(4).

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Chit Tong Lio, Zakaria Louadi, Amit Fenn, Jan Baumbach, Tim Kacprowski, Markus List, Olga Tsoy (2022). Systematic analysis of alternative splicing in time course data using Spycone. Bioinformatics, 39(1).

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Reza Nasirigerdeh, Reihaneh Torkzadehmahani, Julian Matschinske, Tobias Frisch, Markus List, Julian Späth, Stefan Weiss, Uwe Völker, Esa Pitkänen, Dominik Heider, Nina K. Wenke, Georgios Kaissis, Daniel Rueckert, Tim Kacprowski, Jan Baumbach (2022). sPLINK: a hybrid federated tool as a robust alternative to meta-analysis in genome-wide association studies. Genome Biology, 23.

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Chit Tong Lio, Tim Kacprowski, Maik Klaedtke, Lars R. Jensen, Yvonne Bouter, Thomas A. Bayer, Andreas W. Kuss (2022). Small RNA Sequencing in the Tg4–42 Mouse Model Suggests the Involvement of snoRNAs in the Etiology of Alzheimer's Disease. Journal of Alzheimer’s Disease, 87(4).

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Judith Bernett, Dominik Krupke, Sepideh Sadegh, Jan Baumbach, Sándor P. Fekete, Tim Kacprowski, Markus List, David B. Blumenthal (2022). Robust disease module mining via enumeration of diverse prize-collecting Steiner trees. Bioinformatics, 38(6).

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Reihaneh Torkzadehmahani, Reza Nasirigerdeh, David B. Blumenthal, Tim Kacprowski, Markus List, Julian Matschinske, Julian Spaeth, Nina Kerstin Wenke, Jan Baumbach (2022). Privacy-Preserving Artificial Intelligence Techniques in Biomedicine. Methods of Information in Medicine, 61(S01).

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Hendrik Fokken, Nadine Kattre, Arnold Kloos, Michael Heuser, Tim Kacprowski, Tobias Maetzig, Adrian Schwarzer (2022). P401: Next-generation flow cytometry to detect measurable residual disease in acute myeloid leukemia using a 19-color full spectrum flow cytometry panel. HemaSphere, 6.

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Sandra Bierwirth, Adam Sorbie, Olivia I. Coleman, Elena M. Reuß, Philipp Weber, Nikolai Köhler, Tim Kacprowski, Andreas Dunkel, Josch K. Pauling, Josef Ecker, Jan Baumbach, Philip Rosenstiel, Katja Steiger, Jakob Wirbel, Georg Zeller, Klaus-Peter Janssen, Dirk Haller (2022). P057 Mucosal microbiota adapts to ATF6-induced alterations in host lipid metabolism with prognostic value in colorectal cancer. Journal of Crohn’s and Colitis, 16(Supplement_1).

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Zakaria Louadi, Olga Tsoy, Jan Baumbach, Tim Kacprowski, Markus List (2022). Not Quite the Same: How Alternative Splicing Affects Protein Interactions. Protein Interactions: The Molecular Basis of Interactomics, Ch. 16.

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Sepideh Sadegh, James Skelton, Elisa Anastasi, David B. Blumenthal, Andreas Maier, Gihanna Galindez, Cristian Nogales, Ana I. Casas, Harald H. H. W. Schmidt, Anil Wipat, Tim Kacprowski, Jan Baumbach (2022). NeDRex—an integrative and interactive network medicine platform for drug repurposing. International Conference on Systems Medicine, AI & Drug Repurposing.

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Anne Hartebrodt, Reza Nasirigerdeh, Jan Baumbach, David B. Blumenthal, Tim Kacprowski, Richard Röttger (2022). Medical data safety via federated machine learning. International Conference on Systems Medicine, AI & Drug Repurposing.

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Maria L. Elkjaer, Lukas Simon, Tobias Frisch, Lisa-Marie Bente, Tim Kacprowski, Mads Thomassen, Richard Reynolds, Jan Baumbach, Richard Röttger, Zsolt Illes (2022). Hypothesis of a potential BrainBiota and its relation to CNS autoimmune inflammation. Frontiers in Immunology, 13.

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Aniket Mishra, Cécile Duplaà, Dina Vojinovic, Hideaki Suzuki, Muralidharan Sargurupremraj, Nuno R. Zilhão, Shuo Li, Traci M. Bartz, Xueqiu Jian, Wei Zhao, Edith Hofer, Katharina Wittfeld, Sarah E. Harris, Sandra Van Der Auwera-Palitschka, Michelle Luciano, Joshua C. Bis, Hieab H. H. Adams, Claudia L. Satizabal, Rebecca F. Gottesman, Piyush G. Gampawar, Robin Bülow, Stefan Weiss, Miao Yu, Mark E. Bastin, Oscar L. Lopez, Meike W. Vernooij, Alexa S. Beiser, Uwe Völker, Tim Kacprowski, Aicha Soumare, Jennifer A. Smith, David S. Knopman, Zoe Morris, Yicheng Zhu, Jerome I. Rotter, Carole Dufouil, Maria Valdés Hernández, Susana Muñoz Maniega, Mark Lathrop, Erik Boerwinkle, Reinhold Schmidt, Masafumi Ihara, Bernard Mazoyer, Qiong Yang, Anne Joutel, Elizabeth Tournier-Lasserve, Lenore J. Launer, Ian J. Deary, Thomas H. Mosley, Philippe Amouyel, Charles S. DeCarli, Bruce M. Psaty, Christophe Tzourio, Sharon L. R. Kardia, Hans J. Grabe, Alexander Teumer, Cornelia M. Van Duijn, Helena Schmidt, Joanna M. Wardlaw, Mohammad A. Ikram, Myriam Fornage, Vilmundur Gudnason, Sudha Seshadri, Paul M. Matthews, William T. Longstreth, Thierry Couffinhal, Stephanie Debette (2022). Gene-mapping study of extremes of cerebral small vessel disease reveals TRIM47 as a strong candidate. Brain, 145(6).

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Jan Wolff, Ansgar Klimke, Michael Marschollek, Tim Kacprowski (2022). Forecasting admissions in psychiatric hospitals before and during Covid-19: a retrospective study with routine data. Scientific Reports, 12.

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Emetis Niazmand, Gezim Sejdiu, Damien Graux, Maria-Esther Vidal (2022). Efficient semantic summary graphs for querying large knowledge graphs. arXiv (preprint).

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Sandra Klawitter, Georg Hoffmann, Stefan Holdenrieder, Tim Kacprowski, Frank Klawonn (2022). A zlog-based algorithm and tool for plausibility checks of reference intervals. Clinical Chemistry and Laboratory Medicine (CCLM), 61(2).

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Mary L. Kromrey, Anne Röhnert, Sophia Blum, Robert Winzer, Ralf T. Hoffman, Henry Völzke, Tim Kacprowski, Jens-Peter Kühn (2021). Whole-body R2* mapping to quantify tissue iron in iron storage organs: reference values and a genotype. Clinical Radiology, 76.

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June Feliciano F. Ordoñez, Gihanna Galindez, Karina Therese Gulay, Rachel Ravago-Gotanco (2021). Transcriptome analysis of growth variation in early juvenile stage sandfish Holothuria scabra. Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, 40.

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Julian Matschinske, Julian Späth, Reza Nasirigerdeh, Reihaneh Torkzadehmahani, Anne Hartebrodt, Balázs Orbán, Sándor Fejér, Olga Zolotareva, Mohammad Bakhtiari, Béla Bihari, Marcus Bloice, Nina C. Donner, Walid Fdhila, Tobias Frisch, Anne-Christin Hauschild, Dominik Heider, Andreas Holzinger, Walter Hötzendorfer, Jan Hospes, Tim Kacprowski, Markus Kastelitz, Markus List, Rudolf Mayer, Mónika Moga, Heimo Müller, Anastasia Pustozerova, Richard Röttger, Anna Saranti, Harald H. H. W. Schmidt, Christof Tschohl, Nina K. Wenke, Jan Baumbach (2021). The FeatureCloud AI Store for Federated Learning in Biomedicine and Beyond. arXiv (preprint).

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Monica Steffi Matchado, Michael Lauber, Sandra Reitmeier, Tim Kacprowski, Jan Baumbach, Dirk Haller, Markus List (2021). Network analysis methods for studying microbial communities: A mini review. Computational and Structural Biotechnology Journal, 19.

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Alexander G. B. Grønning, Tim Kacprowski, Camilla Schéele (2021). MultiPep: a hierarchical deep learning approach for multi-label classification of peptide bioactivities. Biology Methods and Protocols, 6(1).

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Gihanna Galindez, Julian Matschinske, Tim Daniel Rose, Sepideh Sadegh, Marisol Salgado-Albarrán, Julian Späth, Jan Baumbach, Josch Konstantin Pauling (2021). Lessons from the COVID-19 pandemic for advancing computational drug repurposing strategies. Nature Computational Science, 1.

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Ryan J. Longchamps, Stephanie Y. Yang, Christina A. Castellani, Wen Shi, John Lane, Megan L. Grove, Tracy M. Bartz, Chloé Sarnowski, Chunyu Liu, Kimberly Burrows, Anne L. Guyatt, Tom R. Gaunt, Tim Kacprowski, Jing Yang, Philip L. De Jager, Lz Yu, Aviv Bergman, Rui Xia, Myriam Fornage, Mary F. Feitosa, Mary K. Wojczynski, Aldi T. Kraja, Michael A. Province, Naseer Amin, Fanny Rivadeneira, Henning Tiemeier, André G. Uitterlinden, Linda Broer, Joyce B. J. Van Meurs, Cornelia M. Van Duijn, Laura M. Raffield, Leslie Lange, Stephen S. Rich, Rozenn N. Lemaitre, Mark O. Goodarzi, Colleen M. Sitlani, Angel C. Y. Mak, David A. Bennett, Santiago Rodriguez, J. M. Murabito, Kathryn L. Lunetta, N. Sotoodehnia, Gil Atzmon, Kenny Ye, Nir Barzilai, Jennifer A. Brody, Bruce M. Psaty, Kent D. Taylor, Jerome I. Rotter, Eric Boerwinkle, Nathan Pankratz, Dan E. Arking (2021). Genome-wide analysis of mitochondrial DNA copy number reveals loci implicated in nucleotide metabolism, platelet activation, and megakaryocyte proliferation. Human Genetics, 141.

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Zakaria Louadi, Maria L. Elkjaer, Melissa Klug, Chit Tong Lio, Amit Fenn, Zsolt Illes, Dario Bongiovanni, Jan Baumbach, Tim Kacprowski, Markus List, Olga Tsoy (2021). Functional enrichment of alternative splicing events with NEASE reveals insights into tissue identity and diseases. Genome Biology, 22.

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Alexander G. B. Grønning, Mhaned Oubounyt, Kristiyan Kanev, Jesper Lund, Tim Kacprowski, Dietmar Zehn, Richard Röttger, Jan Baumbach (2021). Enabling single-cell trajectory network enrichment. Nature Computational Science, 1.

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Roya Shiasi Sardoabi, Malihe Alikhani, Farzad Hashemzadeh, M. Khorvash, Masoud Mirzaei, J. K. Drackley (2021). Effects of different planes of milk feeding and milk total solids concentration on growth, ruminal fermentation, health, and behavior of late weaned dairy calves during summer. Journal of Animal Science and Biotechnology, 12(96).

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Zakaria Louadi, Kevin Yuan, Alexander Gress, Olga Tsoy, Olga v. Kalinina, Jan Baumbach, Tim Kacprowski, Markus List (2021). DIGGER: exploring the functional role of alternative splicing in protein interactions. Nucleic Acids Research, 49(D1).

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Fabian Frost, Tim Kacprowski, Malte Rühlemann, Stefan Weiss, Corinna Bang, Andre Franke, Maik Pietzner, Ali A. Aghdassi, Matthias Sendler, Uwe Völker, Henry Völzke, Julia Mayerle, Frank U. Weiss, Georg Homuth, Markus M. Lerch (2021). Carrying asymptomatic gallstones is not associated with changes in intestinal microbiota composition and diversity but cholecystectomy with significant dysbiosis. Scientific Reports, 11.

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Olga Lazareva, Stefan Canzar, Kevin Yuan, Jan Baumbach, David B. Blumenthal, Paolo Tieri, Tim Kacprowski, Markus List (2021). BiCoN: network-constrained biclustering of patients and omics data. Bioinformatics, 37(16).

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Quirin Manz, Olga Tsoy, Amit Fenn, Jan Baumbach, Uwe Völker, Markus List, Tim Kacprowski (2021). ASimulatoR: splice-aware RNA-Seq data simulation. Bioinformatics, 37(12).

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David B. Blumenthal, Jan Baumbach, Markus Hoffmann, Tim Kacprowski, Markus List (2021). A framework for modeling epistatic interaction. Bioinformatics, 37(12).

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Ming-Huei Chen, Laura M. Raffield, Abdou Mousas, Saori Sakaue, Jennifer E. Huffman, Arden Moscati, Bhavi Trivedi, Tao Jiang, Parsa Akbari, Dragana Vuckovic, Erik L. Bao, Xue Zhong, Regina Manansala, Véronique Laplante, Minhui Chen, Ken Sin Lo, Huijun Qian, Caleb A. Lareau, Mélissa Beaudoin, Karen A. Hunt, Masato Akiyama, Traci M. Bartz, Yoav Ben-Shlomo, Andrew Beswick, Jette Bork-Jensen, Erwin P. Bottinger, Jennifer A. Brody, Frank J. A. Van Rooij, Kumaraswamynaidu Chitrala, Kelly Cho, Hélène Choquet, Adolfo Correa, John Danesh, Emanuele Di Angelantonio, Niki Dimou, Jingzhong Ding, Paul Elliott, Tõnu Esko, Michele K. Evans, James S. Floyd, Linda Broer, Niels Grarup, Michael H. Guo, Andreas Greinacher, Jeff Haessler, Torben Hansen, Joanna M. M. Howson, Qin Qin Huang, Wei Huang, Eric Jorgenson, Tim Kacprowski, Mika Kähönen, Yoichiro Kamatani, Masahiro Kanai, Savita Karthikeyan, Fotis Koskeridis, Leslie A. Lange, Terho Lehtimäki, Markus M. Lerch, Allan Linneberg, Yongmei Liu, Leo-Pekka Lyytikäinen, Ani Manichaikul, Hilary C. Martin, Koichi Matsuda, Karen L. Mohlke, Nina Mononen, Yoshinori Murakami, Girish N. Nadkarni, Matthias Nauck, Kjell Nikus, Willem H. Ouwehand, Nathan Pankratz, Oluf Pedersen, Michael Preuss, Bruce M. Psaty, Olli T. Raitakari, David J. Roberts, Stephen S. Rich, Benjamin A. T. Rodriguez, Jonathan D. Rosen, Jerome I. Rotter, Petra Schubert, Cassandra N. Spracklen, Praveen Surendran, Hua Tang, Jean-Claude Tardif, Richard C. Trembath, Mohsen Ghanbari, Uwe Völker, Henry Völzke, Nicholas A. Watkins, Alan B. Zonderman, Peter W. F. Wilson, Yun Li, Adam S. Butterworth, Jean-François Gauchat, Charleston W. K. Chiang, Bingshan Li, Ruth J. F. Loos, William J. Astle, Evangelos Evangelou, David A. Van Heel, Vijay G. Sankaran, Yukinori Okada, Nicole Soranzo, Andrew D. Johnson, Alexander P. Reiner, Paul L. Auer, Guillaume Lettre (2020). Trans-ethnic and Ancestry-Specific Blood-Cell Genetics in 746,667 Individuals from 5 Global Populations. Cell, 182(5).

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Dragana Vuckovic, Erik L. Bao, Parsa Akbari, Caleb A. Lareau, Abdou Mousas, Tao Jiang, Ming-Huei Chen, Laura M. Raffield, Manuel Tardaguila, Jennifer E. Huffman, Scott C. Ritchie, Karyn Megy, Hannes Ponstingl, Christopher J. Penkett, Patrick K. Albers, Emilie M. Wigdor, Saori Sakaue, Arden Moscati, Regina Manansala, Ken Sin Lo, Huijun Qian, Masato Akiyama, Traci M. Bartz, Yoav Ben-Shlomo, Andrew Beswick, Jette Bork-Jensen, Erwin P. Bottinger, Jennifer A. Brody, Frank J. A. Van Rooij, Kumaraswamy N. Chitrala, Peter W. F. Wilson, Hélène Choquet, John Danesh, Emanuele Di Angelantonio, Niki Dimou, Jingzhong Ding, Paul Elliott, Tõnu Esko, Michele K. Evans, Stephan B. Felix, James S. Floyd, Linda Broer, Niels Grarup, Michael H. Guo, Qi Guo, Andreas Greinacher, Jeff Haessler, Torben Hansen, Joanna M. M. Howson, Wei Huang, Eric Jorgenson, Tim Kacprowski, Mika Kähönen, Yoichiro Kamatani, Masahiro Kanai, Savita Karthikeyan, Fotios Koskeridis, Leslie A. Lange, Terho Lehtimäki, Allan Linneberg, Yongmei Liu, Leo-Pekka Lyytikäinen, Ani Manichaikul, Koichi Matsuda, Karen L. Mohlke, Nina Mononen, Yoshinori Murakami, Girish N. Nadkarni, Kjell Nikus, Nathan Pankratz, Oluf Pedersen, Michael Preuss, Bruce M. Psaty, Olli T. Raitakari, Stephen S. Rich, Benjamin A. T. Rodriguez, Jonathan D. Rosen, Jerome I. Rotter, Petra Schubert, Cassandra N. Spracklen, Praveen Surendran, Hua Tang, Jean-Claude Tardif, Mohsen Ghanbari, Uwe Völker, Henry Völzke, Nicholas A. Watkins, Stefan Weiss, Na Cai, Kousik Kundu, Stephen B. Watt, Klaudia Walter, Alan B. Zonderman, Kelly Cho, Yun Li, Ruth J. F. Loos, Julian C. Knight, Michel Georges, Oliver Stegle, Evangelos Evangelou, Yukinori Okada, David J. Roberts, Michael Inouye, Andrew D. Johnson, Paul L. Auer, William J. Astle, Alexander P. Reiner, Adam S. Butterworth, Willem H. Ouwehand, Guillaume Lettre, Vijay G. Sankaran, Nicole Soranzo (2020). The Polygenic and Monogenic Basis of Blood Traits and Diseases. Cell, 182(5).

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Fabian Frost, Frank U. Weiss, Matthias Sendler, Tim Kacprowski, Malte Rühlemann, Corinna Bang, Andre Franke, Uwe Völker, Henry Völzke, Georg Lamprecht, Julia Mayerle, Ali A. Aghdassi, Georg Homuth, Markus M. Lerch (2020). The Gut Microbiome in Patients With Chronic Pancreatitis Is Characterized by Significant Dysbiosis and Overgrowth by Opportunistic Pathogens. Clinical and Translational Gastroenterology, 11(9).

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Ming Wu, Tim Kacprowski, Dietmar Zehn (2020). PySCNet: A tool for reconstructing and analyzing gene regulatory network from single-cell RNA-Seq data. bioRxiv (preprint).

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Tobias Frisch, Maria L. Elkjaer, Richard Reynolds, Tanja Maria Michel, Tim Kacprowski, Mark Burton, Torben A. Kruse, Mads Thomassen, Jan Baumbach, Zsolt Illes (2020). Multiple Sclerosis Atlas: A Molecular Map of Brain Lesion Stages in Progressive Multiple Sclerosis. Network and Systems Medicine, 3(1).

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Yvonne Bouter, Tim Kacprowski, Fanny Rößler, Lars R. Jensen, Andreas W. Kuss, Thomas A. Bayer (2020). miRNA Alterations Elicit Pathways Involved in Memory Decline and Synaptic Function in the Hippocampus of Aged Tg4-42 Mice. Frontiers in Neuroscience, 14.

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Katharina Messerer, Tim Kacprowski, Horst Kolo, Jan Baumbach, Thomas Knoke (2020). Importance of considering the growth response after partial harvesting and economic risk of discounted net revenues when optimizing uneven-aged forest management. Canadian Journal of Forest Research, 50(5).

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Pascal Schlosser, Yong Li, Peggy Sekula, Johannes Raffler, Franziska Grundner-Culemann, Maik Pietzner, Yurong Cheng, Matthias Wuttke, Inga Steinbrenner, Ulla T. Schultheiss, Fruzsina Kotsis, Tim Kacprowski, Lukas Forer, Birgit Hausknecht, Arif B. Ekici, Matthias Nauck, Uwe Völker, Gerd Walz, Peter J. Oefner, Florian Kronenberg, Robert P. Mohney, Michael Köttgen, Karsten Suhre, Kai-Uwe Eckardt, Gabi Kastenmüller, Anna Köttgen (2020). Genetic studies of urinary metabolites illuminate mechanisms of detoxification and excretion in humans. Nature Genetics, 52.

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Hanieh Yaghootkar, Yiying Zhang, Cassandra N. Spracklen, Tugce Karaderi, Lam Opal Huang, Jonathan Bradfield, Claudia Schurmann, Rebecca S. Fine, Michael H. Preuss, Zoltan Kutalik, Laura B. L. Wittemans, Yingchang Lu, Sophia Metz, Sara M. Willems, Ruifang Li-Gao, Niels Grarup, Shuai Wang, Sophie Molnos, América A. Sandoval-Zárate, Mike A. Nalls, Leslie A. Lange, Jeffrey Haesser, Xiuqing Guo, Leo-Pekka Lyytikäinen, Mary F. Feitosa, Colleen M. Sitlani, Cristina Venturini, Anubha Mahajan, Tim Kacprowski, Carol A. Wang, Daniel I. Chasman, Najaf Amin, Linda Broer, Neil Robertson, Kristin L. Young, Matthew Allison, Paul L. Auer, Matthias Blüher, Judith B. Borja, Jette Bork-Jensen, Germán D. Carrasquilla, Paraskevi Christofidou, Ayse Demirkan, Claudia A. Doege, Melissa E. Garcia, Mariaelisa Graff, Kaiying Guo, Hakon Hakonarson, Jaeyoung Hong, Yii-Der Ida Chen, Rebecca Jackson, Hermina Jakupović, Pekka Jousilahti, Anne E. Justice, Mika Kähönen, Jorge R. Kizer, Jennifer Kriebel, Charles A. LeDuc, Jin Li, Lars Lind, Jian'an Luan, David A. Mackey, Massimo Mangino, Satu Männistö, Jayne F. Martin Carli, Carolina Medina-Gomez, Dennis O. Mook-Kanamori, Andrew P. Morris, Renée De Mutsert, Matthias Nauck, Ivana Prokic, Craig E. Pennell, Arund D. Pradhan, Bruce M. Psaty, Olli T. Raitakari, Robert A. Scott, Tea Skaaby, Konstantin Strauch, Kent D. Taylor, Alexander Teumer, Andre G. Uitterlinden, Ying Wu, Jie Yao, Mark Walker, Kari E. North, Peter Kovacs, M. Arfan Ikram, Cornelia M. Van Duijn, Paul M. Ridker, Stephen Lye, Georg Homuth, Erik Ingelsson, Tim D. Spector, Barbara McKnight, Michael A. Province, Terho Lehtimäki, Linda S. Adair, Jerome I. Rotter, Alexander P. Reiner, James G. Wilson, Tamara B. Harris, Samuli Ripatti, Harald Grallert, James B. Meigs, Veikko Salomaa, Torben Hansen, Ko Willems Van Dijk, Nicholas J. Wareham, Struan F. A. Grant, Claudia Langenberg, Timothy M. Frayling, Cecilia M. Lindgren, Karen L. Mohlke, Rudolph L. Leibel, Ruth J. F. Loos, Tuomas O. Kilpeläinen (2020). Genetic Studies of Leptin Concentrations Implicate Leptin in the Regulation of Early Adiposity. Diabetes, 69(12).

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David B. Blumenthal, Lorenzo Viola, Markus List, Jan Baumbach, Paolo Tieri, Tim Kacprowski (2020). EpiGEN: an epistasis simulation pipeline. Bioinformatics, 36(19).

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Alexander G. B. Grønning, Mhaned Oubounyt, Kristiyan Kanev, Jesper Lund, Tim Kacprowski, Dietmar Zehn, Richard Röttger, Jan Baumbach (2020). Comparative single-cell trajectory network enrichment identifies pseudo-temporal systems biology patterns in hematopoiesis and CD8 T-cell development. bioRxiv (preprint).

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Manuela Gesell Salazar, Sophie Neugebauer, Tim Kacprowski, Stephan Michalik, Peter Ahnert, Petra Creutz, Maciej Rosolowski, Markus Löffler, Michael Bauer, Norbert Suttorp, Michael Kiehntopf, Uwe Völker (2020). Association of proteome and metabolome signatures with severity in patients with community-acquired pneumonia. Journal of Proteomics, 214.

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