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2020 – today
- 2023
[j28]Juan D. Henao
, Michael Lauber, Manuel Azevedo, Anastasiia Grekova, Fabian J. Theis, Markus List, Christoph Ogris, Benjamin Schubert:
Multi-omics regulatory network inference in the presence of missing data. Briefings Bioinform. 24(5) (2023)- [j27]Chit Tong Lio, Gordon Grabert, Zakaria Louadi, Amit Fenn, Jan Baumbach, Tim Kacprowski, Markus List, Olga Tsoy:
Systematic analysis of alternative splicing in time course data using Spycone. Bioinform. 39(1) (2023) - [j26]Fabio Boniolo, Markus Hoffmann, Norman Roggendorf, Bahar Tercan, Jan Baumbach, Mauro A. A. Castro, A. Gordon Robertson, Dieter Saur, Markus List:
spongEffects: ceRNA modules offer patient-specific insights into the miRNA regulatory landscape. Bioinform. 39(5) (2023) - 2022
- [j25]Lis Arend, Judith Bernett, Quirin Manz, Melissa Klug, Olga Lazareva, Jan Baumbach, Dario Bongiovanni, Markus List:
A systematic comparison of novel and existing differential analysis methods for CyTOF data. Briefings Bioinform. 23(1) (2022) - [j24]Judith Bernett, Dominik Krupke, Sepideh Sadegh, Jan Baumbach, Sándor P. Fekete, Tim Kacprowski, Markus List, David B. Blumenthal:
Robust disease module mining via enumeration of diverse prize-collecting Steiner trees. Bioinform. 38(6): 1600-1606 (2022) - [j23]Alexander Dietrich, Gregor Sturm, Lorenzo Merotto, Federico Marini, Francesca Finotello, Markus List:
SimBu: bias-aware simulation of bulk RNA-seq data with variable cell-type composition. Bioinform. 38(Supplement_2): ii141-ii147 (2022) - [j22]Michael Hartung, Elisa Anastasi, Zeinab M. Mamdouh, Cristian Nogales, Harald H. H. W. Schmidt, Jan Baumbach, Olga I. Zolotareva, Markus List:
Cancer driver drug interaction explorer. Nucleic Acids Res. 50(W1): 138-144 (2022) - 2021
- [j21]Franziska Hufsky, Kevin Lamkiewicz, Alexandre Almeida, Abdel Aouacheria, Cecilia N. Arighi, Alex Bateman, Jan Baumbach, Niko Beerenwinkel, Christian Brandt, Marco Cacciabue, Sara Chuguransky, Oliver Drechsel, Robert D. Finn, Adrian Fritz, Stephan Fuchs, Georges Hattab, Anne-Christin Hauschild, Dominik Heider, Marie Hoffmann, Martin Hölzer, Stefan Hoops, Lars Kaderali, Ioanna Kalvari, Max von Kleist, Renó Kmiecinski, Denise Kühnert, Gorka Lasso, Pieter Libin, Markus List, Hannah F. Löchel, Maria Jesus Martin, Roman Martin, Julian O. Matschinske, Alice C. McHardy, Pedro Mendes, Jaina Mistry, Vincent Navratil, Eric P. Nawrocki, Áine Niamh O'toole, Nancy Ontiveros-Palacios, Anton I. Petrov, Guillermo Rangel-Pineros, Nicole Redaschi, Susanne Reimering, Knut Reinert, Alejandro Reyes, Lorna J. Richardson, David L. Robertson, Sepideh Sadegh, Joshua B. Singer, Kristof Theys, Chris Upton, Marius Welzel, Lowri Williams, Manja Marz:
Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research. Briefings Bioinform. 22(2): 642-663 (2021) - [j20]Olga Lazareva, Jan Baumbach, Markus List, David B. Blumenthal:
On the limits of active module identification. Briefings Bioinform. 22(5) (2021) - [j19]Olga Lazareva, Stefan Canzar, Kevin Yuan, Jan Baumbach, David B. Blumenthal, Paolo Tieri, Tim Kacprowski, Markus List:
BiCoN: network-constrained biclustering of patients and omics data. Bioinform. 37(16): 2398-2404 (2021) - [j18]Quirin Manz, Olga Tsoy, Amit Fenn, Jan Baumbach, Uwe Völker, Markus List, Tim Kacprowski:
ASimulatoR: splice-aware RNA-Seq data simulation. Bioinform. 37(18): 3008-3010 (2021) - [j17]Zakaria Louadi, Kevin Yuan, Alexander Greß, Olga Tsoy, Olga V. Kalinina, Jan Baumbach, Tim Kacprowski, Markus List:
DIGGER: exploring the functional role of alternative splicing in protein interactions. Nucleic Acids Res. 49(Database-Issue): D309-D318 (2021) - [j16]Michael Scherer, Florian Schmidt, Olga Lazareva, Jörn Walter, Jan Baumbach, Marcel H. Schulz, Markus List:
Machine learning for deciphering cell heterogeneity and gene regulation. Nat. Comput. Sci. 1(3): 183-191 (2021) - [i4]Julian O. Matschinske, Julian Späth, Reza Nasirigerdeh, Reihaneh Torkzadehmahani, Anne Hartebrodt, Balázs Orbán, Sándor Fejér, Olga I. Zolotareva, Mohammad Bakhtiari, Béla Bihari, Marcus D. 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 Kerstin Wenke, Jan Baumbach:
The FeatureCloud AI Store for Federated Learning in Biomedicine and Beyond. CoRR abs/2105.05734 (2021) - 2020
- [j15]David B. Blumenthal, Lorenzo Viola, Markus List, Jan Baumbach, Paolo Tieri, Tim Kacprowski:
EpiGEN: an epistasis simulation pipeline. Bioinform. 36(19): 4957-4959 (2020) - [j14]Nina Baumgarten, Dennis Hecker, Sivarajan Karunanithi, Florian Schmidt, Markus List, Marcel H. Schulz:
EpiRegio: analysis and retrieval of regulatory elements linked to genes. Nucleic Acids Res. 48(Webserver-Issue): W193-W199 (2020) - [p2]Nicolas Alcaraz, Anne Hartebrodt, Markus List:
De Novo Pathway Enrichment with KeyPathwayMiner. Protein-Protein Interaction Networks 2020: 181-199 - [p1]Markus List, Nicolas Alcaraz, Richa Batra:
De Novo Pathway-Based Classification of Breast Cancer Subtypes. Protein-Protein Interaction Networks 2020: 201-213 - [i3]Reihaneh Torkzadehmahani, Reza Nasirigerdeh, David B. Blumenthal, Tim Kacprowski, Markus List, Julian O. Matschinske, Julian Späth, Nina Kerstin Wenke, Béla Bihari, Tobias Frisch, Anne Hartebrodt, Anne-Christin Hauschild, Dominik Heider, Andreas Holzinger, Walter Hötzendorfer, Markus Kastelitz, Rudolf Mayer, Cristian Nogales, Anastasia Pustozerova, Richard Röttger, Harald H. H. W. Schmidt, Ameli Schwalber, Christof Tschohl, Andrea Wohner, Jan Baumbach:
Privacy-preserving Artificial Intelligence Techniques in Biomedicine. CoRR abs/2007.11621 (2020) - [i2]Mohammad Bakhtiari, Reza Nasirigerdeh, Reihaneh Torkzadehmahani, Amirhossein Bayat, David B. Blumenthal, Markus List, Jan Baumbach:
Federated Multi-Mini-Batch: An Efficient Training Approach to Federated Learning in Non-IID Environments. CoRR abs/2011.07006 (2020)
2010 – 2019
- 2019
- [j13]Gregor Sturm, Francesca Finotello, Florent Petitprez, Jitao David Zhang, Jan Baumbach, Wolf-Herman Fridman, Markus List, Tatsiana Aneichyk:
Comprehensive evaluation of transcriptome-based cell-type quantification methods for immuno-oncology. Bioinform. 35(14): i436-i445 (2019) - [j12]Markus List, Azim Dehghani Amirabad, Dennis Kostka, Marcel H. Schulz:
Large-scale inference of competing endogenous RNA networks with sparse partial correlation. Bioinform. 35(14): i596-i604 (2019) - 2018
- [j11]Andrea Hornáková, Markus List, Jilles Vreeken, Marcel H. Schulz:
JAMI: fast computation of conditional mutual information for ceRNA network analysis. Bioinform. 34(17): 3050-3051 (2018) - [j10]Florian Schmidt, Markus List, Engin Cukuroglu, Sebastian Köhler, Jonathan Göke, Marcel H. Schulz:
An ontology-based method for assessing batch effect adjustment approaches in heterogeneous datasets. Bioinform. 34(17): i908-i916 (2018) - 2017
- [j9]Felipe Albrecht, Markus List, Christoph Bock, Thomas Lengauer:
DeepBlueR: large-scale epigenomic analysis in R. Bioinform. 33(13): 2063-2064 (2017) - [j8]Markus List:
Using Docker Compose for the Simple Deployment of an Integrated Drug Target Screening Platform. J. Integr. Bioinform. 14(2) (2017) - [j7]Jesper Lund, Markus List, Jan Baumbach:
Interactive microbial distribution analysis using BioAtlas. Nucleic Acids Res. 45(Webserver-Issue): W509-W513 (2017) - [j6]Markus List, Peter Ebert, Felipe Albrecht:
Ten Simple Rules for Developing Usable Software in Computational Biology. PLoS Comput. Biol. 13(1) (2017) - 2016
- [j5]Felipe Albrecht, Markus List, Christoph Bock, Thomas Lengauer:
DeepBlue epigenomic data server: programmatic data retrieval and analysis of epigenome region sets. Nucleic Acids Res. 44(Webserver-Issue): W581-W586 (2016) - [j4]Markus List, Nicolas Alcaraz, Martin Dissing-Hansen, Henrik J. Ditzel, Jan Mollenhauer, Jan Baumbach:
KeyPathwayMinerWeb: online multi-omics network enrichment. Nucleic Acids Res. 44(Webserver-Issue): W98-W104 (2016) - [i1]Nicolas Alcaraz, Markus List, Martin Dissing-Hansen, Marc Rehmsmeier, Qihua Tan, Jan Mollenhauer, Henrik J. Ditzel, Jan Baumbach:
Robust de novo pathway enrichment with KeyPathwayMiner 5. F1000Research 5: 1531 (2016) - 2015
- [j3]Markus List, Michael Franz, Qihua Tan, Jan Mollenhauer, Jan Baumbach:
OpenLabNotes - An Electronic Laboratory Notebook Extension for OpenLabFramework. J. Integr. Bioinform. 12(3) (2015) - 2014
- [j2]Markus List, Ines Block, Marlene Lemvig Pedersen, Helle Christiansen, Steffen Schmidt, Mads Thomassen, Qihua Tan, Jan Baumbach, Jan Mollenhauer:
Microarray R-based analysis of complex lysate experiments with MIRACLE. Bioinform. 30(17): 631-638 (2014) - [j1]Markus List, Anne-Christin Hauschild, Qihua Tan, Torben Arvid Kruse, Jan Mollenhauer, Jan Baumbach, Richa Batra:
Classification of Breast Cancer Subtypes by combining Gene Expression and DNA Methylation Data. J. Integr. Bioinform. 11(2) (2014)
Coauthor Index
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