Publikationen

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2024

Anokian, Ezequiel; Bernett, Judith; Freeman, Adrian; List, Markus; Santamaría, Lucía Prieto; Tanoli, Ziaurrehman; Bonnin, Sarah: Machine Learning and Artificial Intelligence in Drug Repurposing—Challenges and Perspectives. Drug Repurposing 1 (1), 2024 mehr… BibTeX Volltext ( DOI )
Bernett, Judith; Blumenthal, David B.; Grimm, Dominik G.; Haselbeck, Florian; Joeres, Roman; Kalinina, Olga V.; List, Markus: Guiding questions to avoid data leakage in biological machine learning applications. Nature Methods 21 (8), 2024, 1444-1453 mehr… BibTeX Volltext ( DOI )
Bernett, Judith; Blumenthal, David B; List, Markus: Cracking the black box of deep sequence-based protein–protein interaction prediction. Briefings in Bioinformatics 25 (2), 2024 mehr… BibTeX Volltext ( DOI )
Dill, Veronika; Kirmes, Kilian; Han, Jiaying; Klug, Melissa; Rosenbaum, Marc; Viggiani, Giacomo; von Scheidt, Moritz; List, Markus; Herhaus, Peter; Ruland, Jürgen; Bassermann, Florian; Laugwitz, Karl-Ludwig; Götze, Katharina S.; Jost, Philipp J.; Jilg, Stefanie; Bloxham, Conor J.; Raake, Philip W.J.; Bernlochner, Isabell; Bongiovanni, Dario: Platelet mass cytometry reveals dysregulation of prothrombotic pathways in essential thrombocythemia. Platelets 35 (1), 2024 mehr… BibTeX Volltext ( DOI )
Galindez, Gihanna; List, Markus; Baumbach, Jan; Völker, Uwe; Mäder, Ulrike; Blumenthal, David B; Kacprowski, Tim: Inference of differential gene regulatory networks using boosted differential trees. Bioinformatics Advances, 2024 mehr… BibTeX Volltext ( DOI )
Grabert, Gordon; Dehncke, Daniel; More, Tushar; List, Markus; Kraft, Anke R M; Cornberg, Markus; Hiller, Karsten; Kacprowski, Tim: MeTEor - an R Shiny app for Exploring Longitudinal Metabolomics Data. Bioinformatics Advances, 2024 mehr… BibTeX Volltext ( DOI )
Heppner, Nina; Reitmeier, Sandra; Heddes, Marjolein; Merino, Michael Vig; Schwartz, Leon; Dietrich, Alexander; List, Markus; Gigl, Michael; Meng, Chen; van der Veen, Daan R.; Schirmer, Melanie; Kleigrewe, Karin; Omer, Hélène; Kiessling, Silke; Haller, Dirk: Diurnal rhythmicity of infant fecal microbiota and metabolites: A randomized controlled interventional trial with infant formula. Cell Host & Microbe 32 (4), 2024, 573-587.e5 mehr… BibTeX Volltext ( DOI )
Hoelz, Hannes; Faro, Tim; Frank, Marie-Luise; Forné, Ignasi; Kugelmann, Daniela; Jurk, Anja; Buehler, Simon; Siebert, Kolja; Matchado, Monica; Straub, Tobias; Hering, Annett; Piontek, Guido; Mueller, Susanna; Koletzko, Sibylle; List, Markus; Steiger, Katja; Rudelius, Martina; Waschke, Jens; Schwerd, Tobias: Persistent desmoglein-1 downregulation and periostin accumulation in histologic remission of eosinophilic esophagitis. Journal of Allergy and Clinical Immunology, 2024 mehr… BibTeX Volltext ( DOI )
Hoffmann, Markus; Poschenrieder, Julian M; Incudini, Massimiliano; Baier, Sylvie; Fritz, Amelie; Maier, Andreas; Hartung, Michael; Hoffmann, Christian; Trummer, Nico; Adamowicz, Klaudia; Picciani, Mario; Scheibling, Evelyn; Harl, Maximilian V; Lesch, Ingmar; Frey, Hunor; Kayser, Simon; Wissenberg, Paul; Schwartz, Leon; Hafner, Leon; Acharya, Aakriti; Hackl, Lena; Grabert, Gordon; Lee, Sung-Gwon; Cho, Gyuhyeok; Cloward, Matthew E; Jankowski, Jakub; Lee, Hye Kyung; Tsoy, Olga; Wenke, Nina; Pedersen, Anders Gorm; Bønnelykke, Klaus; Mandarino, Antonio; Melograna, Federico; Schulz, Laura; Climente-González, Héctor; Wilhelm, Mathias; Iapichino, Luigi; Wienbrandt, Lars; Ellinghaus, David; Van Steen, Kristel; Grossi, Michele; Furth, Priscilla A; Hennighausen, Lothar; Di Pierro, Alessandra; Baumbach, Jan; Kacprowski, Tim; List, Markus; Blumenthal, David B: Network medicine-based epistasis detection in complex diseases: ready for quantum computing. Nucleic Acids Research, 2024 mehr… BibTeX Volltext ( DOI )
Hoffmann, Markus; Willruth, Lina-Liv; Dietrich, Alexander; Lee, Hye Kyung; Knabl, Ludwig; Trummer, Nico; Baumbach, Jan; Furth, Priscilla A.; Hennighausen, Lothar; List, Markus: Blood transcriptomics analysis offers insights into variant-specific immune response to SARS-CoV-2. Scientific Reports 14 (1), 2024 mehr… BibTeX Volltext ( DOI )
Hysenaj, Franc; Lauber, Michael; Bast-Habersbrunner, Andrea; List, Markus; Klingenspor, Martin: Single-cell transcriptome analysis reveals secretin as a hallmark of human enteroendocrine cell maturation. Scientific Reports 14 (1), 2024 mehr… BibTeX Volltext ( DOI )
Häcker, Deborah; Siebert, Kolja; Smith, Byron J.; Köhler, Nikolai; Riva, Alessandra; Mahapatra, Aritra; Heimes, Helena; Nie, Jiatong; Metwaly, Amira; Hölz, Hannes; Manz, Quirin; De Zen, Federica; Heetmeyer, Jeannine; Socas, Katharina; Le Thi, Giang; Meng, Chen; Kleigrewe, Karin; Pauling, Josch K.; Neuhaus, Klaus; List, Markus; Pollard, Katherine S.; Schwerd, Tobias; Haller, Dirk: Exclusive enteral nutrition initiates individual protective microbiome changes to induce remission in pediatric Crohn’s disease. Cell Host & Microbe, 2024 mehr… BibTeX Volltext ( DOI )
Maier, Andreas; Hartung, Michael; Abovsky, Mark; Adamowicz, Klaudia; Bader, Gary D; Baier, Sylvie; Blumenthal, David B; Chen, Jing; Elkjaer, Maria L; Garcia-Hernandez, Carlos; Helmy, Mohamed; Hoffmann, Markus; Jurisica, Igor; Kotlyar, Max; Lazareva, Olga; Levi, Hagai; List, Markus; Lobentanzer, Sebastian; Loscalzo, Joseph; Malod-Dognin, Noel; Manz, Quirin; Matschinske, Julian; Mee, Miles; Oubounyt, Mhaned; Pastrello, Chiara; Pico, Alexander R; Pillich, Rudolf T; Poschenrieder, Julian M; Pratt, Dexter; Pržulj, Nataša; Sadegh, Sepideh; Saez-Rodriguez, Julio; Sarkar, Suryadipto; Shaked, Gideon; Shamir, Ron; Trummer, Nico; Turhan, Ugur; Wang, Rui-Sheng; Zolotareva, Olga; Baumbach, Jan: Drugst.One — a plug-and-play solution for online systems medicine and network-based drug repurposing. Nucleic Acids Research, 2024 mehr… BibTeX Volltext ( DOI )
Matchado, Monica Steffi; Rühlemann, Malte; Reitmeier, Sandra; Kacprowski, Tim; Frost, Fabian; Haller, Dirk; Baumbach, Jan; List, Markus: On the limits of 16S rRNA gene-based metagenome prediction and functional profiling. Microbial Genomics 10 (2), 2024 mehr… BibTeX Volltext ( DOI )
Merotto, Lorenzo; Sturm, Gregor; Dietrich, Alexander; List, Markus; Finotello, Francesca: Making mouse transcriptomics deconvolution accessible with immunedeconv. Bioinformatics Advances 4 (1), 2024 mehr… BibTeX Volltext ( DOI )
Probul, Niklas; Huang, Zihua; Saak, Christina Caroline; Baumbach, Jan; List, Markus: <scp>AI</scp> in microbiome‐related healthcare. Microbial Biotechnology 17 (11), 2024 mehr… BibTeX Volltext ( DOI )

2023

Boniolo, Fabio; Hoffmann, Markus; Roggendorf, Norman; Tercan, Bahar; Baumbach, Jan; Castro, Mauro A A; Robertson, A Gordon; Saur, Dieter; List, Markus: spongEffects: ceRNA modules offer patient-specific insights into the miRNA regulatory landscape. Bioinformatics 39 (5), 2023 mehr… BibTeX Volltext ( DOI )
Fenn, Amit; Tsoy, Olga; Faro, Tim; Rößler, Fanny L M; Dietrich, Alexander; Kersting, Johannes; Louadi, Zakaria; Lio, Chit Tong; Völker, Uwe; Baumbach, Jan; Kacprowski, Tim; List, Markus: Alternative splicing analysis benchmark with DICAST. NAR Genomics and Bioinformatics 5 (2), 2023 mehr… BibTeX Volltext ( DOI )
Galindez, Gihanna; Sadegh, Sepideh; Baumbach, Jan; Kacprowski, Tim; List, Markus: Network-based approaches for modeling disease regulation and progression. Computational and Structural Biotechnology Journal 21, 2023, 780-795 mehr… BibTeX Volltext ( DOI )
Hackl, Lena Maria; Fenn, Amit; Louadi, Zakaria; Baumbach, Jan; Kacprowski, Tim; List, Markus; Tsoy, Olga: Alternative splicing impacts microRNA regulation within coding regions. NAR Genomics and Bioinformatics 5 (3), 2023 mehr… BibTeX Volltext ( DOI )
Hecker, Dennis; Lauber, Michael; Behjati Ardakani, Fatemeh; Ashrafiyan, Shamim; Manz, Quirin; Kersting, Johannes; Hoffmann, Markus; Schulz, Marcel H.; List, Markus: Computational tools for inferring transcription factor activity. PROTEOMICS, 2023 mehr… BibTeX Volltext ( DOI )
Henao, Juan D; Lauber, Michael; Azevedo, Manuel; Grekova, Anastasiia; Theis, Fabian; List, Markus; Ogris, Christoph; Schubert, Benjamin: Multi-omics regulatory network inference in the presence of missing data. Briefings in Bioinformatics 24 (5), 2023 mehr… BibTeX Volltext ( DOI )
Hoffmann, Markus; Schwartz, Leon; Ciora, Octavia-Andreea; Trummer, Nico; Willruth, Lina-Liv; Jankowski, Jakub; Lee, Hye Kyung; Baumbach, Jan; Furth, Priscilla A; Hennighausen, Lothar; List, Markus: circRNA-sponging: a pipeline for extensive analysis of circRNA expression and their role in miRNA sponging. Bioinformatics Advances 3 (1), 2023 mehr… BibTeX Volltext ( DOI )
Hoffmann, Markus; Trummer, Nico; Schwartz, Leon; Jankowski, Jakub; Lee, Hye Kyung; Willruth, Lina-Liv; Lazareva, Olga; Yuan, Kevin; Baumgarten, Nina; Schmidt, Florian; Baumbach, Jan; Schulz, Marcel H; Blumenthal, David B; Hennighausen, Lothar; List, Markus: TF-Prioritizer: a Java pipeline to prioritize condition-specific transcription factors. GigaScience 12, 2023 mehr… BibTeX Volltext ( DOI )
Lio, Chit Tong; Grabert, Gordon; Louadi, Zakaria; Fenn, Amit; Baumbach, Jan; Kacprowski, Tim; List, Markus; Tsoy, Olga: Systematic analysis of alternative splicing in time course data using Spycone. Bioinformatics 39 (1), 2023 mehr… BibTeX Volltext ( DOI )
Matschinske, Julian; Späth, Julian; Bakhtiari, Mohammad; Probul, Niklas; Kazemi Majdabadi, Mohammad Mahdi; Nasirigerdeh, Reza; Torkzadehmahani, Reihaneh; Hartebrodt, Anne; Orban, Balazs-Attila; Fejér, Sándor-József; Zolotareva, Olga; Das, Supratim; Baumbach, Linda; Pauling, Josch K; Tomašević, Olivera; Bihari, Béla; Bloice, Marcus; Donner, Nina C; Fdhila, Walid; Frisch, Tobias; Hauschild, Anne-Christin; Heider, Dominik; Holzinger, Andreas; Hötzendorfer, Walter; Hospes, Jan; Kacprowski, Tim; Kastelitz, Markus; List, Markus; Mayer, Rudolf; Moga, Mónika; Müller, Heimo; Pustozerova, Anastasia; Röttger, Richard; Saak, Christina C; Saranti, Anna; Schmidt, Harald H H W; Tschohl, Christof; Wenke, Nina K; Baumbach, Jan: The FeatureCloud Platform for Federated Learning in Biomedicine: Unified Approach. Journal of Medical Internet Research 25, 2023, e42621 mehr… BibTeX Volltext ( DOI )
Sarkar, Suryadipto; Lucchetta, Marta; Maier, Andreas; Abdrabbou, Mohamed M; Baumbach, Jan; List, Markus; Schaefer, Martin H; Blumenthal, David B: Online bias-aware disease module mining with ROBUST-Web. Bioinformatics 39 (6), 2023 mehr… BibTeX Volltext ( DOI )

2022

Bernett, Judith; Krupke, Dominik; Sadegh, Sepideh; Baumbach, Jan; Fekete, Sándor P; Kacprowski, Tim; List, Markus; Blumenthal, David B: Robust disease module mining via enumeration of diverse prize-collecting Steiner trees. Bioinformatics 38 (6), 2022, 1600-1606 mehr… BibTeX Volltext ( DOI )
Casas, Ana I.; Hassan, Ahmed A.; Manz, Quirin; Wiwie, Christian; Kleikers, Pamela; Egea, Javier; López, Manuela G.; List, Markus; Baumbach, Jan; Schmidt, Harald H. H. W.: Un-biased housekeeping gene panel selection for high-validity gene expression analysis. Scientific Reports 12 (1), 2022 mehr… BibTeX Volltext ( DOI )
Dietrich, Alexander; Matchado, Monica Steffi; Zwiebel, Maximilian; Ölke, Benjamin; Lauber, Michael; Lagkouvardos, Ilias; Baumbach, Jan; Haller, Dirk; Brandl, Beate; Skurk, Thomas; Hauner, Hans; Reitmeier, Sandra; List, Markus: Namco: a microbiome explorer. Microbial Genomics 8 (8), 2022 mehr… BibTeX Volltext ( DOI )
Dietrich, Alexander; Sturm, Gregor; Merotto, Lorenzo; Marini, Federico; Finotello, Francesca; List, Markus: <i>SimBu</i>: bias-aware simulation of bulk RNA-seq data with variable cell-type composition. Bioinformatics 38 (Supplement_2), 2022, ii141-ii147 mehr… BibTeX Volltext ( DOI )
Hartung, Michael; Anastasi, Elisa; Mamdouh, Zeinab M; Nogales, Cristian; Schmidt, Harald H H W; Baumbach, Jan; Zolotareva, Olga; List, Markus: Cancer driver drug interaction explorer. Nucleic Acids Research 50 (W1), 2022, W138-W144 mehr… BibTeX Volltext ( DOI )
Hernández-Lorenzo, Laura; Hoffmann, Markus; Scheibling, Evelyn; List, Markus; Matías-Guiu, Jordi A.; Ayala, Jose L.: On the limits of graph neural networks for the early diagnosis of Alzheimer’s disease. Scientific Reports 12 (1), 2022 mehr… BibTeX Volltext ( DOI )
Lautizi, Manuela; Baumbach, Jan; Weichert, Wilko; Steiger, Katja; List, Markus; Pfarr, Nicole; Kacprowski, Tim: The limits of molecular signatures for pancreatic ductal adenocarcinoma subtyping. NAR Cancer 4 (4), 2022 mehr… BibTeX Volltext ( DOI )
Maurer, H. Carlo; Schult, David; Koyumdzhieva, Plamena; Reitmeier, Sandra; Middelhoff, Moritz; Rasch, Sebastian; List, Markus; Janssen, Klaus-Peter; Steiger, Katja; Protzer, Ulrike; Schmid, Roland M.; Neuhaus, Klaus; Haller, Dirk; Quante, Michael; Lahmer, Tobias: Gut Microbial Disruption in Critically Ill Patients with COVID-19-Associated Pulmonary Aspergillosis. Journal of Fungi 8 (12), 2022, 1265 mehr… BibTeX Volltext ( DOI )
Mechteridis, Konstantinos; Lauber, Michael; Baumbach, Jan; List, Markus: KeyPathwayMineR: De Novo Pathway Enrichment in the R Ecosystem. Frontiers in Genetics 12, 2022 mehr… BibTeX Volltext ( DOI )
Nasirigerdeh, Reza; Torkzadehmahani, Reihaneh; Matschinske, Julian; Frisch, Tobias; List, Markus; Späth, Julian; Weiss, Stefan; Völker, Uwe; Pitkänen, Esa; Heider, Dominik; Wenke, Nina Kerstin; Kaissis, Georgios; Rueckert, Daniel; Kacprowski, Tim; Baumbach, Jan: sPLINK: a hybrid federated tool as a robust alternative to meta-analysis in genome-wide association studies. Genome Biology 23 (1), 2022 mehr… BibTeX Volltext ( DOI )
Nogales, Cristian; Mamdouh, Zeinab M.; List, Markus; Kiel, Christina; Casas, Ana I.; Schmidt, Harald H.H.W.: Network pharmacology: curing causal mechanisms instead of treating symptoms. Trends in Pharmacological Sciences 43 (2), 2022, 136-150 mehr… BibTeX Volltext ( DOI )
Torkzadehmahani, Reihaneh; Nasirigerdeh, Reza; Blumenthal, David B.; Kacprowski, Tim; List, Markus; Matschinske, Julian; Spaeth, Julian; Wenke, Nina Kerstin; Baumbach, Jan: Privacy-Preserving Artificial Intelligence Techniques in Biomedicine. Methods of Information in Medicine 61 (S 01), 2022, e12-e27 mehr… BibTeX Volltext ( DOI )

2021

Abellan-Schneyder, Isabel; Matchado, Monica S.; Reitmeier, Sandra; Sommer, Alina; Sewald, Zeno; Baumbach, Jan; List, Markus; Neuhaus, Klaus: Primer, Pipelines, Parameters: Issues in 16S rRNA Gene Sequencing. mSphere 6 (1), 2021 mehr… BibTeX Volltext ( DOI )
Bongiovanni, Dario; Klug, Melissa; Lazareva, Olga; Weidlich, Simon; Biasi, Marina; Ursu, Simona; Warth, Sarah; Buske, Christian; Lukas, Marina; Spinner, Christoph D.; Scheidt, Moritz von; Condorelli, Gianluigi; Baumbach, Jan; Laugwitz, Karl-Ludwig; List, Markus; Bernlochner, Isabell: SARS-CoV-2 infection is associated with a pro-thrombotic platelet phenotype. Cell Death & Disease 12 (1), 2021 mehr… BibTeX Volltext ( DOI )
Hoffmann, Markus; Pachl, Elisabeth; Hartung, Michael; Stiegler, Veronika; Baumbach, Jan; Schulz, Marcel H; List, Markus: SPONGEdb: a pan-cancer resource for competing endogenous RNA interactions. NAR Cancer 3 (1), 2021 mehr… BibTeX Volltext ( DOI )
Klug, Melissa; Lazareva, Olga; Kirmes, Kilian; Rosenbaum, Marc; Lukas, Marina; Weidlich, Simon; Spinner, Christoph D.; von Scheidt, Moritz; Gosetti, Rosanna; Baumbach, Jan; Ruland, Jürgen; Condorelli, Gianluigi; Laugwitz, Karl-Ludwig; List, Markus; Bernlochner, Isabell; Bongiovanni, Dario: Platelet Surface Protein Expression and Reactivity upon TRAP Stimulation after BNT162b2 Vaccination. Thrombosis and Haemostasis 122 (10), 2021, 1706-1711 mehr… BibTeX Volltext ( DOI )
Lazareva, Olga; Baumbach, Jan; List, Markus; Blumenthal, David B: On the limits of active module identification. Briefings in Bioinformatics 22 (5), 2021 mehr… BibTeX Volltext ( DOI )
Louadi, Zakaria; Elkjaer, Maria L.; Klug, Melissa; Lio, Chit Tong; Fenn, Amit; Illes, Zsolt; Bongiovanni, Dario; Baumbach, Jan; Kacprowski, Tim; List, Markus; Tsoy, Olga: Functional enrichment of alternative splicing events with NEASE reveals insights into tissue identity and diseases. Genome Biology 22 (1), 2021 mehr… BibTeX Volltext ( DOI )
Manz, Quirin; Tsoy, Olga; Fenn, Amit; Baumbach, Jan; Völker, Uwe; List, Markus; Kacprowski, Tim: ASimulatoR: splice-aware RNA-Seq data simulation. Bioinformatics 37 (18), 2021, 3008-3010 mehr… BibTeX Volltext ( DOI )
Matchado, Monica Steffi; Lauber, Michael; Reitmeier, Sandra; Kacprowski, Tim; Baumbach, Jan; Haller, Dirk; List, Markus: Network analysis methods for studying microbial communities: A mini review. Computational and Structural Biotechnology Journal 19, 2021, 2687-2698 mehr… BibTeX Volltext ( DOI )
Matschinske, Julian; Alcaraz, Nicolas; Benis, Arriel; Golebiewski, Martin; Grimm, Dominik G.; Heumos, Lukas; Kacprowski, Tim; Lazareva, Olga; List, Markus; Louadi, Zakaria; Pauling, Josch K.; Pfeifer, Nico; Röttger, Richard; Schwämmle, Veit; Sturm, Gregor; Traverso, Alberto; Van Steen, Kristel; de Freitas, Martiela Vaz; Villalba Silva, Gerda Cristal; Wee, Leonard; Wenke, Nina K.; Zanin, Massimiliano; Zolotareva, Olga; Baumbach, Jan; Blumenthal, David B.: The AIMe registry for artificial intelligence in biomedical research. Nature Methods 18 (10), 2021, 1128-1131 mehr… BibTeX Volltext ( DOI )
Parise, Doglas; Parise, Mariana Teixeira Dornelles; Kataka, Evans; Kato, Rodrigo Bentes; List, Markus; Tauch, Andreas; Azevedo, Vasco Ariston de Carvalho; Baumbach, Jan: On the Consistency between Gene Expression and the Gene Regulatory Network of <i>Corynebacterium glutamicum</i>. Network and Systems Medicine 4 (1), 2021, 51-59 mehr… BibTeX Volltext ( DOI )
Sarno, Federica; ; Benincasa, Giuditta; List, Markus; Barabasi, Albert-Lazlo; Baumbach, Jan; Ciardiello, Fortunato; Filetti, Sebastiano; Glass, Kimberly; Loscalzo, Joseph; Marchese, Cinzia; Maron, Bradley A.; Paci, Paola; Parini, Paolo; Petrillo, Enrico; Silverman, Edwin K.; Verrienti, Antonella; Altucci, Lucia; Napoli, Claudio: Clinical epigenetics settings for cancer and cardiovascular diseases: real-life applications of network medicine at the bedside. Clinical Epigenetics 13 (1), 2021 mehr… BibTeX Volltext ( DOI )
Scherer, Michael; Schmidt, Florian; Lazareva, Olga; Walter, Jörn; Baumbach, Jan; Schulz, Marcel H.; List, Markus: Machine learning for deciphering cell heterogeneity and gene regulation. Nature Computational Science 1 (3), 2021, 183-191 mehr… BibTeX Volltext ( DOI )
Sturm, Gregor; List, Markus; Zhang, Jitao David: Tissue heterogeneity is prevalent in gene expression studies. NAR Genomics and Bioinformatics 3 (3), 2021 mehr… BibTeX Volltext ( DOI )
Zolotareva, Olga; Nasirigerdeh, Reza; Matschinske, Julian; Torkzadehmahani, Reihaneh; Bakhtiari, Mohammad; Frisch, Tobias; Späth, Julian; Blumenthal, David B.; Abbasinejad, Amir; Tieri, Paolo; Kaissis, Georgios; Rückert, Daniel; Wenke, Nina K.; List, Markus; Baumbach, Jan: Flimma: a federated and privacy-aware tool for differential gene expression analysis. Genome Biology 22 (1), 2021 mehr… BibTeX Volltext ( DOI )

2020

Baumbach, L.; List, M.; Grønne, D.T.; Skou, S.T.; Roos, E.M.: Individualized predictions of changes in knee pain, quality of life and walking speed following patient education and exercise therapy in patients with knee osteoarthritis – a prognostic model study. Osteoarthritis and Cartilage 28 (9), 2020, 1191-1201 mehr… BibTeX Volltext ( DOI )
Baumgarten, Nina; Hecker, Dennis; Karunanithi, Sivarajan; Schmidt, Florian; List, Markus; Schulz, Marcel H: EpiRegio: analysis and retrieval of regulatory elements linked to genes. Nucleic Acids Research 48 (W1), 2020, W193-W199 mehr… BibTeX Volltext ( DOI )
Blumenthal, David B; Baumbach, Jan; Hoffmann, Markus; Kacprowski, Tim; List, Markus: A framework for modeling epistatic interaction. Bioinformatics 37 (12), 2020, 1708-1716 mehr… BibTeX Volltext ( DOI )
Blumenthal, David B; Viola, Lorenzo; List, Markus; Baumbach, Jan; Tieri, Paolo; Kacprowski, Tim: EpiGEN: an epistasis simulation pipeline. Bioinformatics 36 (19), 2020, 4957-4959 mehr… BibTeX Volltext ( DOI )
Flosbach, Markus; Oberle, Susanne G.; Scherer, Stefanie; Zecha, Jana; von Hoesslin, Madlaina; Wiede, Florian; Chennupati, Vijaykumar; Cullen, Jolie G.; List, Markus; Pauling, Josch K.; Baumbach, Jan; Kuster, Bernhard; Tiganis, Tony; Zehn, Dietmar: PTPN2 Deficiency Enhances Programmed T Cell Expansion and Survival Capacity of Activated T Cells. Cell Reports 32 (4), 2020, 107957 mehr… BibTeX Volltext ( DOI )
Hufsky, Franziska; Lamkiewicz, Kevin; Almeida, Alexandre; Aouacheria, Abdel; Arighi, Cecilia; Bateman, Alex; Baumbach, Jan; Beerenwinkel, Niko; Brandt, Christian; Cacciabue, Marco; Chuguransky, Sara; Drechsel, Oliver; Finn, Robert D; Fritz, Adrian; Fuchs, Stephan; Hattab, Georges; Hauschild, Anne-Christin; Heider, Dominik; Hoffmann, Marie; Hölzer, Martin; Hoops, Stefan; Kaderali, Lars; Kalvari, Ioanna; von Kleist, Max; Kmiecinski, Renó; Kühnert, Denise; Lasso, Gorka; Libin, Pieter; List, Markus; Löchel, Hannah F; Martin, Maria J; Martin, Roman; Matschinske, Julian; McHardy, Alice C; Mendes, Pedro; Mistry, Jaina; Navratil, Vincent; Nawrocki, Eric P; O’Toole, Áine Niamh; Ontiveros-Palacios, Nancy; Petrov, Anton I; Rangel-Pineros, Guillermo; Redaschi, Nicole; Reimering, Susanne; Reinert, Knut; Reyes, Alejandro; Richardson, Lorna; Robertson, David L; Sadegh, Sepideh; Singer, Joshua B et al.: Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research. Briefings in Bioinformatics 22 (2), 2020, 642-663 mehr… BibTeX Volltext ( DOI )
Lazareva, Olga; Canzar, Stefan; Yuan, Kevin; Baumbach, Jan; Blumenthal, David B; Tieri, Paolo; Kacprowski, Tim; List, Markus: BiCoN: network-constrained biclustering of patients and omics data. Bioinformatics 37 (16), 2020, 2398-2404 mehr… BibTeX Volltext ( DOI )
Louadi, Zakaria; Yuan, Kevin; Gress, Alexander; Tsoy, Olga; Kalinina, Olga V; Baumbach, Jan; Kacprowski, Tim; List, Markus: DIGGER: exploring the functional role of alternative splicing in protein interactions. Nucleic Acids Research 49 (D1), 2020, D309-D318 mehr… BibTeX Volltext ( DOI )
Mergner, Julia; Frejno, Martin; List, Markus; Papacek, Michael; Chen, Xia; Chaudhary, Ajeet; Samaras, Patroklos; Richter, Sandra; Shikata, Hiromasa; Messerer, Maxim; Lang, Daniel; Altmann, Stefan; Cyprys, Philipp; Zolg, Daniel P.; Mathieson, Toby; Bantscheff, Marcus; Hazarika, Rashmi R.; Schmidt, Tobias; Dawid, Corinna; Dunkel, Andreas; Hofmann, Thomas; Sprunck, Stefanie; Falter-Braun, Pascal; Johannes, Frank; Mayer, Klaus F. X.; Jürgens, Gerd; Wilhelm, Mathias; Baumbach, Jan; Grill, Erwin; Schneitz, Kay; Schwechheimer, Claus; Kuster, Bernhard: Mass-spectrometry-based draft of the Arabidopsis proteome. Nature 579 (7799), 2020, 409-414 mehr… BibTeX Volltext ( DOI )
Reitmeier, Sandra; Kiessling, Silke; Clavel, Thomas; List, Markus; Almeida, Eduardo L.; Ghosh, Tarini S.; Neuhaus, Klaus; Grallert, Harald; Linseisen, Jakob; Skurk, Thomas; Brandl, Beate; Breuninger, Taylor A.; Troll, Martina; Rathmann, Wolfgang; Linkohr, Birgit; Hauner, Hans; Laudes, Matthias; Franke, Andre; Le Roy, Caroline I.; Bell, Jordana T.; Spector, Tim; Baumbach, Jan; O’Toole, Paul W.; Peters, Annette; Haller, Dirk: Arrhythmic Gut Microbiome Signatures Predict Risk of Type 2 Diabetes. Cell Host & Microbe 28 (2), 2020, 258-272.e6 mehr… BibTeX Volltext ( DOI )
Sadegh, Sepideh; Matschinske, Julian; Blumenthal, David B.; Galindez, Gihanna; Kacprowski, Tim; List, Markus; Nasirigerdeh, Reza; Oubounyt, Mhaned; Pichlmair, Andreas; Rose, Tim Daniel; Salgado-Albarrán, Marisol; Späth, Julian; Stukalov, Alexey; Wenke, Nina K.; Yuan, Kevin; Pauling, Josch K.; Baumbach, Jan: Exploring the SARS-CoV-2 virus-host-drug interactome for drug repurposing. Nature Communications 11 (1), 2020 mehr… BibTeX Volltext ( DOI )
Scherer, Michael; Nebel, Almut; Franke, Andre; Walter, Jörn; Lengauer, Thomas; Bock, Christoph; Müller, Fabian; List, Markus: Quantitative comparison of within-sample heterogeneity scores for DNA methylation data. Nucleic Acids Research 48 (8), 2020, e46-e46 mehr… BibTeX Volltext ( DOI )
Stalidzans, Egils; Zanin, Massimiliano; Tieri, Paolo; Castiglione, Filippo; Polster, Annikka; Scheiner, Stefan; Pahle, Jürgen; Stres, Blaž; List, Markus; Baumbach, Jan; Lautizi, Manuela; Van Steen, Kristel; Schmidt, Harald H.H.W.: Mechanistic Modeling and Multiscale Applications for Precision Medicine: Theory and Practice. Network and Systems Medicine 3 (1), 2020, 36-56 mehr… BibTeX Volltext ( DOI )
Weber, Philipp; Pauling, Josch Konstantin; List, Markus; Baumbach, Jan: BALSAM—An Interactive Online Platform for Breath Analysis, Visualization and Classification. Metabolites 10 (10), 2020, 393 mehr… BibTeX Volltext ( DOI )

2019

List, Markus; Dehghani Amirabad, Azim; Kostka, Dennis; Schulz, Marcel H: Large-scale inference of competing endogenous RNA networks with sparse partial correlation. Bioinformatics 35 (14), 2019, i596-i604 mehr… BibTeX Volltext ( DOI )
Sonja M. Kessler, Kevan Hosseini, Usama Khamis Hussein, Kyoung Min Kim, Markus List, Christina S. Schultheiß, Marcel H. Schulz, Stephan Laggai, Kyu Yun Jang, Alexandra K. Kiemer: Hepatocellular Carcinoma and Nuclear Paraspeckles: Induction in Chemoresistance and Prediction for Poor Survival. Cellular Physiology and Biochemistry 52 (4), 2019, 787-801 mehr… BibTeX Volltext ( DOI )
Sturm, Gregor; Finotello, Francesca; Petitprez, Florent; Zhang, Jitao David; Baumbach, Jan; Fridman, Wolf H; List, Markus; Aneichyk, Tatsiana: Comprehensive evaluation of transcriptome-based cell-type quantification methods for immuno-oncology. Bioinformatics 35 (14), 2019, i436-i445 mehr… BibTeX Volltext ( DOI )

2018

Schmidt, Florian; List, Markus; Cukuroglu, Engin; Köhler, Sebastian; Göke, Jonathan; Schulz, Marcel H: An ontology-based method for assessing batch effect adjustment approaches in heterogeneous datasets. Bioinformatics 34 (17), 2018, i908-i916 mehr… BibTeX Volltext ( DOI )