M. List

Marcel H. Schulz, K. Jang, A. Kiemer, 2019, Cellular physiology and biochemistry : international journal of experimental cellular physiology, biochemistry, and pharmacology.

BALSAM—An Interactive Online Platform for Breath Analysis, Visualization and Classification

Jan Baumbach, Markus List, Philipp Weber, 2020, Metabolites.

In Silico Cell-Type Deconvolution Methods in Cancer Immunotherapy.

F. Finotello, M. List, G. Sturm, 2020, Methods in molecular biology.

University of Southern Denmark Robust de novo pathway enrichment with KeyPathwayMiner

H. Ditzel, M. Rehmsmeier, J. Baumbach, 2016 .

Inference of differential gene regulatory networks from gene expression data using boosted differential trees

David B. Blumenthal, J. Baumbach, T. Kacprowski, 2022, bioRxiv.

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

Robert D. Finn, Alex Bateman, Niko Beerenwinkel, 2020, Briefings Bioinform..

Targeting infectious diseases: The CoVex example

David B. Blumenthal, Julian O. Matschinske, A. Stukalov, 2022, Targeting infectious diseases: The CoVex example.

On the limits of graph neural networks for the early diagnosis of Alzheimer’s disease

M. List, J. Matias‐Guiu, Laura Hernández-Lorenzo, 2022, Scientific Reports.

Gut Microbial Disruption in Critically Ill Patients with COVID-19-Associated Pulmonary Aspergillosis

D. Haller, K. Janssen, K. Neuhaus, 2022, bioRxiv.

Multi-Omics Regulatory Network Inference in the Presence of Missing Data

B. Schubert, M. List, Christoph Ogris, 2022, bioRxiv.

Network-based approaches for modeling disease regulation and progression

J. Baumbach, T. Kacprowski, M. List, 2022, Computational and structural biotechnology journal.

Network pharmacology: curing causal mechanisms instead of treating symptoms.

Harald H. H. W. Schmidt, C. Kiel, M. List, 2021, Trends in pharmacological sciences.

circRNA-sponging: a pipeline for extensive analysis of circRNA expression and their role in miRNA sponging

J. Baumbach, L. Hennighausen, P. Furth, 2023, bioRxiv.

Network analysis methods for studying microbial communities: A mini review

J. Baumbach, T. Kacprowski, D. Haller, 2021, Computational and structural biotechnology journal.

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

Tim Kacprowski, Jan Baumbach, Zakaria Louadi, 2020, Nucleic Acids Res..

Exploring the SARS-CoV-2 virus-host-drug interactome for drug repurposing

David B. Blumenthal, Reza Nasirigerdeh, Julian Matschinske, 2020, Nature Communications.

TF-Prioritizer: a java pipeline to prioritize condition-specific transcription factors

Marcel H. Schulz, David B. Blumenthal, J. Baumbach, 2022, bioRxiv.

Mechanistic Modeling and Multiscale Applications for Precision Medicine: Theory and Practice

Stefan Scheiner, Jan Baumbach, Massimiliano Zanin, 2020, Network and Systems Medicine.

Functional enrichment of alternative splicing events with NEASE reveals insights into tissue identity and diseases

J. Baumbach, T. Kacprowski, Z. Illés, 2021, Genome Biology.

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

Jan Baumbach, Jitao David Zhang, Markus List, 2019, Bioinform..

Multi-Omics Analysis in a Network Context

Jan Baumbach, Markus List, Tim Kacprowski, 2021 .

Machine learning for deciphering cell heterogeneity and gene regulation

Florian Schmidt, Marcel H. Schulz, Jan Baumbach, 2021, Nature Computational Science.

Immunedeconv: An R Package for Unified Access to Computational Methods for Estimating Immune Cell Fractions from Bulk RNA-Sequencing Data.

Markus List, Francesca Finotello, Gregor Sturm, 2020, Methods in molecular biology.

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

Reza Nasirigerdeh, Reihaneh Torkzadehmahani, Tobias Frisch, 2021, ArXiv.

On the limits of active module identification

David B. Blumenthal, Jan Baumbach, Markus List, 2021, Briefings Bioinform..

sPLINK: a hybrid federated tool as a robust alternative to meta-analysis in genome-wide association studies

Julian O. Matschinske, D. Rueckert, E. Pitkänen, 2022, Genome biology.

sPLINK: A Federated, Privacy-Preserving Tool as a Robust Alternative to Meta-Analysis in Genome-Wide Association Studies

Reza Nasirigerdeh, Reihaneh Torkzadehmahani, Julian Matschinske, 2020, bioRxiv.

Arrhythmic Gut Microbiome Signatures Predict Risk of Type 2 Diabetes.

J. Linseisen, W. Rathmann, T. Spector, 2020, Cell host & microbe.

TF-Prioritizer: a java pipeline to prioritize condition-specific transcription factors

Marcel H. Schulz, David B. Blumenthal, J. Baumbach, 2023, bioRxiv.

Comprehensive evaluation of cell-type quantification methods for immuno-oncology

Jan Baumbach, Jitao David Zhang, Markus List, 2018 .

Privacy-Preserving Artificial Intelligence Techniques in Biomedicine pdf

Andreas Holzinger, Jan Baumbach, David B. Blumenthal, 2020, Methods of information in medicine.

miRNA-26a expression influences the therapy response to carmustine wafer implantation in patients with glioblastoma multiforme

J. Oertel, Yoo-Jin Kim, M. List, 2019, Acta Neurochirurgica.

Clinical epigenetics settings for cancer and cardiovascular diseases: real-life applications of network medicine at the bedside

E. Silverman, A. Barabási, J. Loscalzo, 2021, Clinical epigenetics.

CYANUS - a web platform for analyzing drug response markers in cytometry data

J. Baumbach, M. List, D. Bongiovanni, 2022, CYANUS - a web platform for analyzing drug response markers in cytometry data.

Primer, Pipelines, Parameters: Issues in 16S rRNA Gene Sequencing

J. Baumbach, K. Neuhaus, M. List, 2021, mSphere.

De Novo Pathway-Based Classification of Breast Cancer Subtypes

Markus List, Richa Batra, Nicolas Alcaraz, 2020, Protein-Protein Interaction Networks.

On the Consistency between Gene Expression and the Gene Regulatory Network of Corynebacterium glutamicum

J. Baumbach, A. Tauch, V. Azevedo, 2021, Network and systems medicine.

Syddansk Universitet De novo pathway-based biomarker identification

Jan Baumbach, Fabio Vandin, Henrik J. Ditzel, 2017 .

SPONGEdb: a pan-cancer resource for competing endogenous RNA interactions

Marcel H Schulz, Marcel H. Schulz, Jan Baumbach, 2021, NAR cancer.

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

Mauro A. A. Castro, A. G. Robertson, J. Baumbach, 2023, bioRxiv.

Namco: a microbiome explorer

J. Baumbach, D. Haller, T. Skurk, 2021, bioRxiv.

MiRNA-181d Expression Significantly Affects Treatment Responses to Carmustine Wafer Implantation.

J. Oertel, Yoo-Jin Kim, M. List, 2019, Neurosurgery.

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

David B. Blumenthal, Tim Kacprowski, Jan Baumbach, 2020, Bioinformatics.

BiCoN: Network-constrained biclustering of patients and omics data

David B. Blumenthal, Markus List, Tim Kacprowski, 2020, bioRxiv.

The AIMe registry for artificial intelligence in biomedical research

David B. Blumenthal, Julian O. Matschinske, T. Kacprowski, 2021, Nature Methods.

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

Markus List, M. List, 2017, J. Integr. Bioinform..

Mass cytometry of platelet-rich plasma: a new approach to analyze platelet surface expression and reactivity

G. Condorelli, J. Baumbach, J. Ruland, 2021, Platelets.

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

Marcel H. Schulz, Sebastian Köhler, Markus List, 2018, Bioinform..

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

Thomas Lengauer, Christoph Bock, Markus List, 2016, Nucleic Acids Res..

Alternative splicing analysis benchmark with DICAST

J. Baumbach, T. Kacprowski, M. List, 2022, bioRxiv.

ASimulatoR: splice-aware RNA-Seq data simulation

Uwe Völker, Tim Kacprowski, Jan Baumbach, 2021, Bioinform..

Platelet Surface Protein Expression and Reactivity upon TRAP Stimulation after BNT162b2 Vaccination

G. Condorelli, J. Baumbach, J. Ruland, 2021, Thrombosis and Haemostasis.

Platelet expression and reactivity after BNT162b2 vaccine administration

G. Condorelli, J. Ruland, J. Baumbach, 2021, medRxiv.

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

Marcel H. Schulz, Jilles Vreeken, Markus List, 2018, Bioinform..

Microarray R-based analysis of complex lysate experiments with MIRACLE

Mads Thomassen, Qihua Tan, Jan Mollenhauer, 2014, Bioinform..

Flimma: a federated and privacy-aware tool for differential gene expression analysis

David B. Blumenthal, Julian O. Matschinske, J. Baumbach, 2021, Genome Biology.

Un-biased housekeeping gene panel selection for high-validity gene expression analysis

Harald H. H. W. Schmidt, J. Baumbach, Ahmed A Hassan, 2022, Scientific Reports.

De novo pathway-based biomarker identification

Jan Baumbach, Fabio Vandin, Henrik J. Ditzel, 2017, Nucleic acids research.

Emergence of power-law distributions in protein-protein interaction networks through study bias

Martin H. Schaefer, David B. Blumenthal, M. List, 2024, bioRxiv.

Cracking the black box of deep sequence-based protein-protein interaction prediction

David B. Blumenthal, M. List, J. Bernett, 2023, bioRxiv.

TF-Prioritizer: a Java pipeline to prioritize condition-specific transcription factors

Marcel H. Schulz, David B. Blumenthal, J. Baumbach, 2022, bioRxiv.

Protein-based nanotoxicology assessment strategy.

Jan Mollenhauer, Ines Block, Markus List, 2017, Nanomedicine : nanotechnology, biology, and medicine.

A framework for modeling epistatic interaction.

David B. Blumenthal, Tim Kacprowski, Jan Baumbach, 2020, Bioinformatics.

Functional enrichment of alternative splicing events with NEASE reveals insights into tissue identity and diseases

J. Baumbach, T. Kacprowski, Z. Illés, 2021, Genome Biology.

KeyPathwayMinerWeb: online multi-omics network enrichment

Markus List, Jan Baumbach, Jan Mollenhauer, 2016, Nucleic Acids Res..

Flimma: a federated and privacy-aware tool for differential gene expression analysis

David B. Blumenthal, Julian O. Matschinske, J. Baumbach, 2021, Genome Biology.

Flimma: a federated and privacy-preserving tool for differential gene expression analysis.

David B. Blumenthal, Reza Nasirigerdeh, Reihaneh Torkzadehmahani, 2020, 2010.16403.

On the performance of de novo pathway enrichment

H. Ditzel, J. Baumbach, R. Batra, 2017, npj Systems Biology and Applications.

KeyPathwayMineR: De Novo Pathway Enrichment in the R Ecosystem

J. Baumbach, M. List, Michael C. Lauber, 2022, Frontiers in Genetics.

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

David B. Blumenthal, S. Fekete, J. Baumbach, 2022, Bioinform..

circRNA-sponging: a pipeline for extensive analysis of circRNA expression and their role in miRNA sponging

J. Baumbach, L. Hennighausen, P. Furth, 2023, bioRxiv.

Online bias-aware disease module mining with ROBUST-Web

David B. Blumenthal, J. Baumbach, M. List, 2023, Bioinformatics.

Ten Simple Rules for Developing Usable Software in Computational Biology

Peter Ebert, Markus List, Felipe Albrecht, 2017, PLoS Comput. Biol..

BioAtlas: Interactive web service for microbial distribution analysis

Jan Baumbach, Markus List, Jesper Lund, 2017 .

OpenLabNotes - An Electronic Laboratory Notebook Extension for OpenLabFramework

Michael Franz, Qihua Tan, Jan Mollenhauer, 2015, J. Integr. Bioinform..

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

David B. Blumenthal, J. Baumbach, M. List, 2020, ArXiv.

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

B. Schubert, F. Theis, M. List, 2023, bioRxiv.

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

Marcel H. Schulz, Dennis Kostka, Azim Dehghani Amirabad, 2019, Bioinform..

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

Qihua Tan, Jan Mollenhauer, Anne-Christin Hauschild, 2014, J. Integr. Bioinform..

Drugst.One - A plug-and-play solution for online systems medicine and network-based drug repurposing

Gary D Bader, David B. Blumenthal, Julian O. Matschinske, 2023, ArXiv.

Interactive microbial distribution analysis using BioAtlas

Jan Baumbach, Markus List, Jesper Beltoft Lund, 2017, Nucleic Acids Res..

A Systematic Comparison of Differential Analysis Methods for CyTOF Data

J. Baumbach, M. List, D. Bongiovanni, 2021, bioRxiv.

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

Marcel H. Schulz, Dennis Kostka, M. List, 2019, Bioinform..

The FeatureCloud Platform for Federated Learning in Biomedicine: Unified Approach

Julian O. Matschinske, Marcus D. Bloice, Nina C. Donner, 2023, Journal of medical Internet research.

Alternative splicing impacts microRNA regulation within coding regions

J. Baumbach, T. Kacprowski, M. List, 2023, bioRxiv.

De novo pathway-based biomarker identification

H. Ditzel, Fabio Vandin, J. Baumbach, 2017, Nucleic Acids Research.

De novo pathway-based biomarker identification

H. Ditzel, Fabio Vandin, J. Baumbach, 2017, Nucleic Acids Research.

Cracking the black box of deep sequence-based protein-protein interaction prediction

David B. Blumenthal, M. List, J. Bernett, 2023, bioRxiv.

Development of Bioinformatics Tools for Biomedical High-Throughput Analyses

Markus List, M. List, 2015 .

De Novo Pathway Enrichment with KeyPathwayMiner

Markus List, Nicolas Alcaraz, Anne Hartebrodt, 2020, Protein-Protein Interaction Networks.

Hepatocellular Carcinoma and Nuclear Paraspeckles: Induction in Chemoresistance and Prediction for Poor Survival.

Marcel H. Schulz, K. Jang, A. Kiemer, 2019, Cellular physiology and biochemistry : international journal of experimental cellular physiology, biochemistry, and pharmacology.

Cracking the black box of deep sequence-based protein–protein interaction prediction

David B. Blumenthal, M. List, J. Bernett, 2023, bioRxiv.

Inference of differential gene regulatory networks using boosted differential trees

M. List, Gihanna Galindez, Uwe Völker, 2024, Bioinformatics advances.

Privacy-Preserving Artificial Intelligence Techniques in Biomedicine

Andreas Holzinger, David B. Blumenthal, Reza Nasirigerdeh, 2020, Methods of information in medicine.

Exploring the SARS-CoV-2 virus-host-drug interactome for drug repurposing

David B. Blumenthal, Julian O. Matschinske, J. Baumbach, 2020, Nature Communications.

Computational tools for inferring transcription factor activity

Fatemeh Behjati Ardakani, Dennis Hecker, M. List, 2023, Proteomics.

On the performance of de novo pathway enrichment

Jan Baumbach, Marc Hellmuth, Markus List, 2017, npj Systems Biology and Applications.

Network medicine-based epistasis detection in complex diseases: ready for quantum computing

K. Bønnelykke, D. Ellinghaus, Héctor Climente-González, 2023, medRxiv.

Blood transcriptomics analysis offers insights into variant-specific immune response to SARS-CoV-2

M. List, H. Lee, Markus Hoffmann, 2023, bioRxiv.

EpiGEN: an epistasis simulation pipeline

Jan Baumbach, David B. Blumenthal, Tim Kacprowski, 2020, Bioinform..

Drugst.One — a plug-and-play solution for online systems medicine and network-based drug repurposing

Gary D Bader, Alexander R. Pico, David B. Blumenthal, 2024, Nucleic acids research.