Markus List

According to our database, Markus List authored at least 33 papers between 2014 and 2023.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2023

Multi-omics regulatory network inference in the presence of missing data.

Juan D. Henao, Michael Lauber, Manuel Azevedo, Anastasiia Grekova, Fabian J. Theis, Markus List, Christoph Ogris, Benjamin Schubert

Briefings Bioinform., September, 2023

spongEffects: ceRNA modules offer patient-specific insights into the miRNA regulatory landscape.

Fabio Boniolo, Markus Hoffmann, Norman Roggendorf, Bahar Tercan, Jan Baumbach, Mauro A. A. Castro, A. Gordon Robertson, Dieter Saur, Markus List

Bioinform., May, 2023

Systematic analysis of alternative splicing in time course data using Spycone.

Chit Tong Lio, Gordon Grabert, Zakaria Louadi, Amit Fenn, Jan Baumbach, Tim Kacprowski, Markus List, Olga Tsoy

Bioinform., January, 2023

2022

Cancer driver drug interaction explorer.

Michael Hartung, Elisa Anastasi, Zeinab M. Mamdouh, Cristian Nogales, Harald H. H. W. Schmidt, Jan Baumbach, Olga I. Zolotareva, Markus List

Nucleic Acids Res., 2022

Robust disease module mining via enumeration of diverse prize-collecting Steiner trees.

Judith Bernett, Dominik Krupke, Sepideh Sadegh, Jan Baumbach, Sándor P. Fekete, Tim Kacprowski, Markus List, David B. Blumenthal

Bioinform., 2022

A systematic comparison of novel and existing differential analysis methods for CyTOF data.

Lis Arend, Judith Bernett, Quirin Manz, Melissa Klug, Olga Lazareva, Jan Baumbach, Dario Bongiovanni, Markus List

Briefings Bioinform., 2022

2021

Machine learning for deciphering cell heterogeneity and gene regulation.

Michael Scherer, Florian Schmidt, Olga Lazareva, Jörn Walter, Jan Baumbach, Marcel H. Schulz, Markus List

Nat. Comput. Sci., 2021

DIGGER: exploring the functional role of alternative splicing in protein interactions.

Zakaria Louadi, Kevin Yuan, Alexander Greß, Olga Tsoy, Olga V. Kalinina, Jan Baumbach, Tim Kacprowski, Markus List

Nucleic Acids Res., 2021

The FeatureCloud AI Store for Federated Learning in Biomedicine and Beyond.

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

CoRR, 2021

ASimulatoR: splice-aware RNA-Seq data simulation.

Quirin Manz, Olga Tsoy, Amit Fenn, Jan Baumbach, Uwe Völker, Markus List, Tim Kacprowski

Bioinform., 2021

BiCoN: network-constrained biclustering of patients and omics data.

Olga Lazareva, Stefan Canzar, Kevin Yuan, Jan Baumbach, David B. Blumenthal, Paolo Tieri, Tim Kacprowski, Markus List

Bioinform., 2021

On the limits of active module identification.

Olga Lazareva, Jan Baumbach, Markus List, David B. Blumenthal

Briefings Bioinform., 2021

Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research.

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

Briefings Bioinform., 2021

2020

De Novo Pathway-Based Classification of Breast Cancer Subtypes.

Markus List, Nicolas Alcaraz, Richa Batra

Proceedings of the Protein-Protein Interaction Networks, Methods and Protocols., 2020

De Novo Pathway Enrichment with KeyPathwayMiner.

Nicolas Alcaraz, Anne Hartebrodt, Markus List

Proceedings of the Protein-Protein Interaction Networks, Methods and Protocols., 2020

EpiRegio: analysis and retrieval of regulatory elements linked to genes.

Nina Baumgarten, Dennis Hecker, Sivarajan Karunanithi, Florian Schmidt, Markus List, Marcel H. Schulz

Nucleic Acids Res., 2020

Federated Multi-Mini-Batch: An Efficient Training Approach to Federated Learning in Non-IID Environments.

Mohammad Bakhtiari, Reza Nasirigerdeh, Reihaneh Torkzadehmahani, Amirhossein Bayat, David B. Blumenthal, Markus List, Jan Baumbach

CoRR, 2020

Privacy-preserving Artificial Intelligence Techniques in Biomedicine.

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

CoRR, 2020

EpiGEN: an epistasis simulation pipeline.

David B. Blumenthal, Lorenzo Viola, Markus List, Jan Baumbach, Paolo Tieri, Tim Kacprowski

Bioinform., 2020

2019

Comprehensive evaluation of transcriptome-based cell-type quantification methods for immuno-oncology.

Gregor Sturm, Francesca Finotello, Florent Petitprez, Jitao David Zhang, Jan Baumbach, Wolf-Herman Fridman, Markus List, Tatsiana Aneichyk

Bioinform., 2019

Large-scale inference of competing endogenous RNA networks with sparse partial correlation.

Markus List, Azim Dehghani Amirabad, Dennis Kostka, Marcel H. Schulz

Bioinform., 2019

2018

JAMI: fast computation of conditional mutual information for ceRNA network analysis.

Andrea Hornáková, Markus List, Jilles Vreeken, Marcel H. Schulz

Bioinform., 2018

An ontology-based method for assessing batch effect adjustment approaches in heterogeneous datasets.

Florian Schmidt, Markus List, Engin Cukuroglu, Sebastian Köhler, Jonathan Göke, Marcel H. Schulz

Bioinform., 2018

2017

Ten Simple Rules for Developing Usable Software in Computational Biology.

Markus List, Peter Ebert, Felipe Albrecht

PLoS Comput. Biol., 2017

Interactive microbial distribution analysis using BioAtlas.

Jesper Lund, Markus List, Jan Baumbach

Nucleic Acids Res., 2017

Using Docker Compose for the Simple Deployment of an Integrated Drug Target Screening Platform.

Markus List

J. Integr. Bioinform., 2017

DeepBlueR: large-scale epigenomic analysis in R.

Felipe Albrecht, Markus List, Christoph Bock, Thomas Lengauer

Bioinform., 2017

2016

KeyPathwayMinerWeb: online multi-omics network enrichment.

Markus List, Nicolas Alcaraz, Martin Dissing-Hansen, Henrik J. Ditzel, Jan Mollenhauer, Jan Baumbach

Nucleic Acids Res., 2016

DeepBlue epigenomic data server: programmatic data retrieval and analysis of epigenome region sets.

Felipe Albrecht, Markus List, Christoph Bock, Thomas Lengauer

Nucleic Acids Res., 2016

Robust<i> de novo</i> pathway enrichment with <i>KeyPathwayMiner 5</i>.

Nicolas Alcaraz, Markus List, Martin Dissing-Hansen, Marc Rehmsmeier, Qihua Tan, Jan Mollenhauer, Henrik J. Ditzel, Jan Baumbach

F1000Research, 2016

2015

OpenLabNotes - An Electronic Laboratory Notebook Extension for OpenLabFramework.

Markus List, Michael Franz, Qihua Tan, Jan Mollenhauer, Jan Baumbach

J. Integr. Bioinform., 2015

2014

Classification of Breast Cancer Subtypes by combining Gene Expression and DNA Methylation Data.

Markus List, Anne-Christin Hauschild, Qihua Tan, Torben Arvid Kruse, Jan Mollenhauer, Jan Baumbach, Richa Batra

J. Integr. Bioinform., 2014

Microarray R-based analysis of complex lysate experiments with MIRACLE.

Markus List, Ines Block, Marlene Lemvig Pedersen, Helle Christiansen, Steffen Schmidt, Mads Thomassen, Qihua Tan, Jan Baumbach, Jan Mollenhauer

Bioinform., 2014