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Author Details

Jan Baumbach
University of Hamburg
2006
196
35
Trey Ideker (CM4AI)
PMIDPaper TitleJournal TitlePublished Year
36879901<i>De-novo</i> reconstruction and identification of transcriptional gene regulatory network modules differentiating single-cell clusters.NAR Genom Bioinform2023
37485422circRNA-sponging: a pipeline for extensive analysis of circRNA expression and their role in miRNA sponging.Bioinform Adv2023
37705830Alternative splicing impacts microRNA regulation within coding regions.NAR Genom Bioinform2023
37084275spongEffects: ceRNA modules offer patient-specific insights into the miRNA regulatory landscape.Bioinformatics2023
37443829A YAP/TAZ-ARHGAP29-RhoA Signaling Axis Regulates Podocyte Protrusions and Integrin Adhesions.Cells2023
37408191CTCF and Its Multi-Partner Network for Chromatin Regulation.Cells2023
37106565Multi-scale systems genomics analysis predicts pathways, cell types, and drug targets involved in normative variation in peri-adolescent human cognition.Cereb Cortex2023
37436815The FeatureCloud Platform for Federated Learning in Biomedicine: Unified Approach.J Med Internet Res2023
37233198Online bias-aware disease module mining with ROBUST-Web.Bioinformatics2023
36966134Lacking mechanistic disease definitions and corresponding association data hamper progress in network medicine and beyond.Nat Commun2023
37228113Hierarchical association of COPD to principal genetic components of biological systems.PLoS One2023
36995759Federated Machine Learning, Privacy-Enhancing Technologies, and Data Protection Laws in Medical Research: Scoping Review.J Med Internet Res2023
37260511Alternative splicing analysis benchmark with DICAST.NAR Genom Bioinform2023
36789427circRNA-sponging: a pipeline for extensive analysis of circRNA expression and their role in miRNA sponging.bioRxiv2023
34388849Platelet Surface Protein Expression and Reactivity upon TRAP Stimulation after BNT162b2 Vaccination.Thromb Haemost2022
35580047Cancer driver drug interaction explorer.Nucleic Acids Res2022
35796460Consensus draft of the native mouse podocyte-ome.Am J Physiol Renal Physiol2022
35853974Un-biased housekeeping gene panel selection for high-validity gene expression analysis.Sci Rep2022
35567921Tumour cell budding and spread through air spaces in squamous cell carcinoma of the lung - Determination and validation of optimal prognostic cut-offs.Lung Cancer2022
35753693Online in silico validation of disease and gene sets, clusterings or subnetworks with DIGEST.Brief Bioinform2022
35412913MoSBi: Automated signature mining for molecular stratification and subtyping.Proc Natl Acad Sci U S A2022
37132521TF-Prioritizer: a Java pipeline to prioritize condition-specific transcription factors.Gigascience2022
36812603Privacy-aware multi-institutional time-to-event studies.PLOS Digit Health2022
36532064Hypothesis of a potential BrainBiota and its relation to CNS autoimmune inflammation.Front Immunol2022
36698974Network-based approaches for modeling disease regulation and progression.Comput Struct Biotechnol J2022
36073911dsMTL: a computational framework for privacy-preserving, distributed multi-task machine learning.Bioinformatics2022
36267208The limits of molecular signatures for pancreatic ductal adenocarcinoma subtyping.NAR Cancer2022
36054833Federated machine learning for a facilitated implementation of Artificial Intelligence in healthcare - a proof of concept study for the prediction of coronary artery calcification scores.J Integr Bioinform2022
35917163Namco: a microbiome explorer.Microb Genom2022
35132075CTCFL regulates the PI3K-Akt pathway and it is a target for personalized ovarian cancer therapy.NPJ Syst Biol Appl2022
34984440Robust disease module mining via enumeration of diverse prize-collecting Steiner trees.Bioinformatics2022
35073941sPLINK: a hybrid federated tool as a robust alternative to meta-analysis in genome-wide association studies.Genome Biol2022
34850807A systematic comparison of novel and existing differential analysis methods for CyTOF data.Brief Bioinform2022
35309325A Systematic Review of Tissue and Single Cell Transcriptome/Proteome Studies of the Brain in Multiple Sclerosis.Front Immunol2022
35173764KeyPathwayMineR: <i>De Novo</i> Pathway Enrichment in the R Ecosystem.Front Genet2022
35139148Federated Random Forests can improve local performance of predictive models for various healthcare applications.Bioinformatics2022
34957922Mass cytometry of platelet-rich plasma: a new approach to analyze platelet surface expression and reactivity.Platelets2022
32780286Network Medicine-Based Unbiased Disease Modules for Drug and Diagnostic Target Identification in ROSopathies.Handb Exp Pharmacol2021
33796877On the Consistency between Gene Expression and the Gene Regulatory Network of <i>Corynebacterium glutamicum</i>.Netw Syst Med2021
33603109CSF proteome in multiple sclerosis subtypes related to brain lesion transcriptomes.Sci Rep2021
33627512Primer, Pipelines, Parameters: Issues in 16S rRNA Gene Sequencing.mSphere2021
33647976ASimulatoR: splice-aware RNA-Seq data simulation.Bioinformatics2021
33671149The Transcriptional Regulatory Network of <i>Corynebacterium pseudotuberculosis</i>.Microorganisms2021
33782690On the limits of active module identification.Brief Bioinform2021
33528912Novel DNA methylation marker discovery by assumption-free genome-wide association analysis of cognitive function in twins.Aging Cell2021
34857024Functional enrichment of alternative splicing events with NEASE reveals insights into tissue identity and diseases.Genome Biol2021
34906207Flimma: a federated and privacy-aware tool for differential gene expression analysis.Genome Biol2021
34824199Network medicine for disease module identification and drug repurposing with the NeDRex platform.Nat Commun2021
34713083Success Factors of Artificial Intelligence Implementation in Healthcare.Front Digit Health2021
34220744An Integrated Database of Small RNAs and Their Interplay With Transcriptional Gene Regulatory Networks in Corynebacteria.Front Microbiol2021
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Collaborators

Simon J Larsen
University of Southern Denmark
Co-authored papers 9
Richard Reynolds
Co-authored papers 6
Fabio Vandin
University of Padova
Co-authored papers 5
Amjad Ali
Research Institute for Medical and Health Sciences, University of Sharjah
Co-authored papers 5
Riccardo E Marioni
Institute of Genetics and Cancer, University of Edinburgh
Co-authored papers 4
Uwe V??lker
University Medicine
Co-authored papers 4
Mario Albrecht
Institute for Knowledge Discovery, Graz University of Technology
Co-authored papers 4
Martin R Larsen
University of Southern Denmark
Co-authored papers 4
Dorothea Emig
Departments of Bioinformatics and Clinical Genomics, Illumina Inc.
Co-authored papers 3
Alexander Goesmann
Co-authored papers 3
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Brigham and Women's Hospital
Co-authored papers 3
John A McCulloch
Center for Cancer Research, National Cancer Institute
Co-authored papers 3
Finn Sellebjerg
Co-authored papers 2
Gary D Bader
University of Toronto
Co-authored papers 2
Rehan Zafar Paracha
National University of Sciences and Technology (NUST)
Co-authored papers 2
Leonard Apeltsin
Department of Pharmaceutical Chemistry, University of California san francisco
Co-authored papers 2
Anam Naz
Institute of Molecular Biology and Biotechnology, University of Lahore Pakistan.
Co-authored papers 2
John H Morris
University of California san francisco
Co-authored papers 2
Jan Taubert
Rothamsted Research
Co-authored papers 2
Andre Franke
Institute of Clinical Molecular Biology, Kiel University
Co-authored papers 2
Amy G Robertson
Present address: Dxige Research Inc.
Co-authored papers 1
Cecilia N Arighi
University of Delaware
Co-authored papers 1
Viviane Labrie
Center for Neurodegenerative Science, Van Andel Research Institute
Co-authored papers 1
Knut Reinert
Institut fur Informatik, Freie Universitat Berlin
Co-authored papers 1
Sona Vasudevan
Co-authored papers 1
Vikram Sirupurapu
University of California San Diego
Co-authored papers 1
Matthias Nauck
University Medicine Greifswald
Co-authored papers 1
Harald Grallert
Co-authored papers 1
Jan O Korbel
European Bioinformatics Institute (EMBL-EBI)
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