Markus List

42 papers Journal 40
YearRankTypeTitle / Venue / Authors
2025 J jnl
Conversational no-code and multi-agentic disease module identification and drug repurposing prediction with ChatDRex.
CoRR
Simon Süwer, Kester Bagemihl, Sylvie Baier, Lucia Dicunta, Markus List, Jan Baumbach, Andreas Maier, Fernando M. Delgado-Chaves
2025 J jnl
Deep learning models for unbiased sequence-based PPI prediction plateau at an accuracy of 0.65.
Bioinform.
Timo Reim, Anne Hartebrodt, David B. Blumenthal, Judith Bernett, Markus List
2025 J jnl
NApy: Efficient Statistics in Python for Large-Scale Heterogeneous Data with Enhanced Support for Missing Data.
CoRR
Fabian Woller, Lis Arend, Christian Fuchsberger, Markus List, David B. Blumenthal
2025 J jnl
Refinement strategies for Tangram for reliable single-cell to spatial mapping.
Bioinform.
Merle Stahl, Lena J. Straßer, Chit Tong Lio, Judith Bernett, Richard Röttger, Markus List
2025 J jnl
Single-cell differential expression analysis between conditions within nested settings.
Briefings Bioinform.
Leon Hafner, Gregor Sturm, Sarah Lumpp, Mathias Drton, Markus List
2025 J jnl
Systematic evaluation of normalization approaches in tandem mass tag and label-free protein quantification data using PRONE.
Briefings Bioinform.
Lis Arend, Klaudia Adamowicz, Johannes R. Schmidt, Yuliya Burankova, Olga I. Zolotareva, Olga Tsoy, Josch Konstantin Pauling, Stefan Kalkhof, Jan Baumbach, Markus List, Tanja Laske
2024 J jnl
Cracking the black box of deep sequence-based protein-protein interaction prediction.
Briefings Bioinform.
Judith Bernett, David B. Blumenthal, Markus List
2023 J jnl
Multi-omics regulatory network inference in the presence of missing data.
Briefings Bioinform.
Juan D. Henao, Michael Lauber, Manuel Azevedo, Anastasiia Grekova, Fabian J. Theis, Markus List, Christoph Ogris, Benjamin Schubert
2023 J jnl
Online bias-aware disease module mining with ROBUST-Web.
Bioinform.
Suryadipto Sarkar, Marta Lucchetta, Andreas Maier, Mohamed M. Abdrabbou, Jan Baumbach, Markus List, Martin H. Schaefer, David B. Blumenthal
2023 J jnl
Systematic analysis of alternative splicing in time course data using Spycone.
Bioinform.
Chit Tong Lio, Gordon Grabert, Zakaria Louadi, Amit Fenn, Jan Baumbach, Tim Kacprowski, Markus List, Olga Tsoy
2023 J jnl
spongEffects: ceRNA modules offer patient-specific insights into the miRNA regulatory landscape.
Bioinform.
Fabio Boniolo, Markus Hoffmann, Norman Roggendorf, Bahar Tercan, Jan Baumbach, Mauro A. A. Castro, A. Gordon Robertson, Dieter Saur, Markus List
2022 J jnl
A systematic comparison of novel and existing differential analysis methods for CyTOF data.
Briefings Bioinform.
Lis Arend, Judith Bernett, Quirin Manz, Melissa Klug, Olga Lazareva, Jan Baumbach, Dario Bongiovanni, Markus List
2022 J jnl
Cancer driver drug interaction explorer.
Nucleic Acids Res.
Michael Hartung, Elisa Anastasi, Zeinab M. Mamdouh, Cristian Nogales, Harald H. H. W. Schmidt, Jan Baumbach, Olga I. Zolotareva, Markus List
2022 J jnl
Robust disease module mining via enumeration of diverse prize-collecting Steiner trees.
Bioinform.
Judith Bernett, Dominik Krupke, Sepideh Sadegh, Jan Baumbach, Sándor P. Fekete, Tim Kacprowski, Markus List, David B. Blumenthal
2021 J jnl
A framework for modeling epistatic interaction.
Bioinform.
David B. Blumenthal, Jan Baumbach, Markus Hoffmann, Tim Kacprowski, Markus List
2021 J jnl
ASimulatoR: splice-aware RNA-Seq data simulation.
Bioinform.
Quirin Manz, Olga Tsoy, Amit Fenn, Jan Baumbach, Uwe Völker, Markus List, Tim Kacprowski
2021 J jnl
BiCoN: network-constrained biclustering of patients and omics data.
Bioinform.
Olga Lazareva, Stefan Canzar, Kevin Yuan, Jan Baumbach, David B. Blumenthal, Paolo Tieri, Tim Kacprowski, Markus List
2021 J jnl
Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research.
Briefings Bioinform.
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
2021 J jnl
DIGGER: exploring the functional role of alternative splicing in protein interactions.
Nucleic Acids Res.
Zakaria Louadi, Kevin Yuan, Alexander Greß, Olga Tsoy, Olga V. Kalinina, Jan Baumbach, Tim Kacprowski, Markus List
2021 J jnl
Machine learning for deciphering cell heterogeneity and gene regulation.
Nat. Comput. Sci.
Michael Scherer, Florian Schmidt, Olga Lazareva, Jörn Walter, Jan Baumbach, Marcel H. Schulz, Markus List
2021 J jnl
On the limits of active module identification.
Briefings Bioinform.
Olga Lazareva, Jan Baumbach, Markus List, David B. Blumenthal
2021 J jnl
The FeatureCloud AI Store for Federated Learning in Biomedicine and Beyond.
CoRR
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
2020 — ch.
De Novo Pathway Enrichment with KeyPathwayMiner.
Protein-Protein Interaction Networks
Nicolas Alcaraz, Anne Hartebrodt, Markus List
2020 — ch.
De Novo Pathway-Based Classification of Breast Cancer Subtypes.
Protein-Protein Interaction Networks
Markus List, Nicolas Alcaraz, Richa Batra
2020 J jnl
EpiGEN: an epistasis simulation pipeline.
Bioinform.
David B. Blumenthal, Lorenzo Viola, Markus List, Jan Baumbach, Paolo Tieri, Tim Kacprowski
2020 J jnl
EpiRegio: analysis and retrieval of regulatory elements linked to genes.
Nucleic Acids Res.
Nina Baumgarten, Dennis Hecker, Sivarajan Karunanithi, Florian Schmidt, Markus List, Marcel H. Schulz
2020 J jnl
Federated Multi-Mini-Batch: An Efficient Training Approach to Federated Learning in Non-IID Environments.
CoRR
Mohammad Bakhtiari, Reza Nasirigerdeh, Reihaneh Torkzadehmahani, Amirhossein Bayat, David B. Blumenthal, Markus List, Jan Baumbach
2020 J jnl
Privacy-preserving Artificial Intelligence Techniques in Biomedicine.
CoRR
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
2019 J jnl
Comprehensive evaluation of transcriptome-based cell-type quantification methods for immuno-oncology.
Bioinform.
Gregor Sturm, Francesca Finotello, Florent Petitprez, Jitao David Zhang, Jan Baumbach, Wolf-Herman Fridman, Markus List, Tatsiana Aneichyk
2019 J jnl
Large-scale inference of competing endogenous RNA networks with sparse partial correlation.
Bioinform.
Markus List, Azim Dehghani Amirabad, Dennis Kostka, Marcel H. Schulz
2018 J jnl
An ontology-based method for assessing batch effect adjustment approaches in heterogeneous datasets.
Bioinform.
Florian Schmidt, Markus List, Engin Cukuroglu, Sebastian Köhler, Jonathan Göke, Marcel H. Schulz
2018 J jnl
JAMI: fast computation of conditional mutual information for ceRNA network analysis.
Bioinform.
Andrea Hornáková, Markus List, Jilles Vreeken, Marcel H. Schulz
2017 J jnl
DeepBlueR: large-scale epigenomic analysis in R.
Bioinform.
Felipe Albrecht, Markus List, Christoph Bock, Thomas Lengauer
2017 J jnl
Interactive microbial distribution analysis using BioAtlas.
Nucleic Acids Res.
Jesper Lund, Markus List, Jan Baumbach
2017 J jnl
Ten Simple Rules for Developing Usable Software in Computational Biology.
PLoS Comput. Biol.
Markus List, Peter Ebert, Felipe Albrecht
2017 J jnl
Using Docker Compose for the Simple Deployment of an Integrated Drug Target Screening Platform.
J. Integr. Bioinform.
Markus List
2016 J jnl
DeepBlue epigenomic data server: programmatic data retrieval and analysis of epigenome region sets.
Nucleic Acids Res.
Felipe Albrecht, Markus List, Christoph Bock, Thomas Lengauer
2016 J jnl
KeyPathwayMinerWeb: online multi-omics network enrichment.
Nucleic Acids Res.
Markus List, Nicolas Alcaraz, Martin Dissing-Hansen, Henrik J. Ditzel, Jan Mollenhauer, Jan Baumbach
2016 J jnl
Robust
F1000Research
Nicolas Alcaraz, Markus List, Martin Dissing-Hansen, Marc Rehmsmeier, Qihua Tan, Jan Mollenhauer, Henrik J. Ditzel, Jan Baumbach
2015 J jnl
OpenLabNotes - An Electronic Laboratory Notebook Extension for OpenLabFramework.
J. Integr. Bioinform.
Markus List, Michael Franz, Qihua Tan, Jan Mollenhauer, Jan Baumbach
2014 J jnl
Classification of Breast Cancer Subtypes by combining Gene Expression and DNA Methylation Data.
J. Integr. Bioinform.
Markus List, Anne-Christin Hauschild, Qihua Tan, Torben Arvid Kruse, Jan Mollenhauer, Jan Baumbach, Richa Batra
2014 J jnl
Microarray R-based analysis of complex lysate experiments with MIRACLE.
Bioinform.
Markus List, Ines Block, Marlene Lemvig Pedersen, Helle Christiansen, Steffen Schmidt, Mads Thomassen, Qihua Tan, Jan Baumbach, Jan Mollenhauer