JB
Jan Baumbach
SoftwarebioinformaticsGene Regulatory NetworksAlgorithmsCluster Analysiscs.LGPrivacyAlternative SplicingDNA MethylationComputational Biology
On Valency
published · living versionsW_hk8japdy·v1 · currentpublished
Quantum Optimisation for Protein-Protein Interaction Network Alignment
with Merle Stahl, Robert J. Banks, Matthias Traube, Josua Unger +2
1 version
Preprints & journals
390 papers in the corpus · 1994–2026Integrating network medicine and foundation models reveals cell-type-specific regulatory alterations in Alzheimer's disease.42840584 · Álvarez-Pérez, Andrea, Rodríguez-González, Alejandro, Baumbach, Jan et al.2026 · 0 citationsNAR genomics and bioinformatics. 2026;8(4):lqag116
Quantum Optimisation for Protein-Protein Interaction Network Alignment2609.05238v1 · Merle Stahl, Robert J. Banks, Matthias Traube et al.2026 · 0 citationsarXivon Valency
Fedflow: cloud orchestration for federated learning with the FeatureCloud platform.42725323 · Weilguny, Lukas, Probul, Niklas, Ren, Yani et al.2026 · 0 citationsBioinformatics advances. 2026;6(1):vbag255
Corrigendum to "Unveiling the interplay between soluble guanylate cyclase activation and redox signalling in stroke pathophysiology and treatment" [Biomed. Pharmacother. 183 (2025) 117829].42686442 · Grønning, Alexander G, Vonhof, Sebastian E, Elbatreek, Mahmoud et al.2026 · 0 citationsBiomedicine & pharmacotherapy = Biomedecine & pharmacotherapie. 2026;203:119881
EXPOSE: Explainable and Domain-Robust Embeddings from Pathology Vision Foundation Models using Sparse Autoencoders2608.28191v1 · Anja Witte, Maximilian Lennartz, Jan Baumbach et al.2026 · 0 citationsarXiv
Clifti-GPT: privacy-preserving federated fine-tuning and transferable inference of foundation models on clinical single-cell data.42557585 · Bakhtiari, Mohammad, Elkjaer, Maria Louise, Can, Ali Oğuz et al.2026 · 0 citationsBioData mining. 2026;19(1)
Transcriptome signatures for the identification of bevacizumab responders in ovarian cancer.42576234 · Zolotareva, Olga, Legler, Karen, Tsoy, Olga et al.2026 · 1 citationGenome medicine. 2026;18(1)
Prediction of single cell expression from low-plex immunofluorescence images for guiding precision oncology.42502133 · Heidrich, Markus, Nilsson, Daniel, Frank, Asger Meldgaard et al.2026 · 0 citationsNPJ precision oncology. 2026;10(1)
Exploring the Comedone Switch through Single-Cell Resolution of Human Acne Lesions10.64898/2026.07.09.737640v2 · Duez, T., Rolka, T., Torocsik, D. et al.2026 · 0 citationsbioRxiv
Aberrant splicing in human cancer shows possible functional impact on transcription factors.42399676 · Newaz, Khalique, Tsoy, Olga, Baumbach, Jan2026 · 0 citationsOncogene. 2026;45(32):3287-3298
An integrated skin cell atlas decodes the pilosebaceous unit.42392254 · Düz, Tolga, Torocsik, Daniel, Momnougui, Sonia M E et al.2026 · 0 citationsThe Journal of investigative dermatology. 2026
Inferring and evaluating network medicine-based disease modules with nextflow.42412786 · Kersting, Johannes, Bucheron, Chloé, Spindler, Lisa M et al.2026 · 2 citationsBioinformatics (Oxford, England). 2026;42(1)
ChronoMedKG: A Temporally-Grounded Biomedical Knowledge Graph and Benchmark for Clinical Reasoning2605.22734v1 · Md Shamim Ahmed, Farzaneh Firoozbakht, Lukas Galke Poech et al.2026 · 0 citationsarXiv
Drugst.One DREAM-Drug repurposing through expert annotation and modification.42108670 · Spindler, Lisa M, Kersting, Johannes, Manz, Quirin et al.2026 · 2 citationsBritish journal of pharmacology. 2026;183(13):3503-3516
Automated landmark and semilandmark annotation for wing geometric morphometrics in Diptera using deep learning10.64898/2026.04.17.719146v1 · Nolte, K., Baumbach, J., Kollmannsberger, P. et al.2026 · 1 citationbioRxiv
Biomedical systems biology workflow orchestration and execution with PoSyMed2604.20906v1 · Simon Suwer, Zoe Chervontseva, Kester Bagemihl et al.2026 · 0 citationsarXiv
Estimating motion artifacts of HR-pQCT scans using automatically derived standard parameters of bone structure- and density-quantification.41932417 · Albrecht, Elias, Bartosik, Mikolaj, Simon, Alexander et al.2026 · 0 citationsBone. 2026;208:117878
Older adults with osteoarthritis show lower functional performance compared to those with diabetes or hypertension: Evidence from the SHARE dataset.41969620 · Rafiei, Mahdie, Probul, Niklas, Baumbach, Jan et al.2026 · 0 citationsOsteoarthritis and cartilage open. 2026;8(2):100781
Astrocyte-specific FoxF2 modulates immune and myelin repair: Evidence from multiple sclerosis lesions and an animal model.41785663 · Damsbo, Karina, Reyahi, Azadeh, Nik, Ali M et al.2026 · 0 citationsJournal of neuroimmunology. 2026;415:578896
Privacy-preserving federated prediction of health outcomes using multi-center survey data.41639794 · Das, Supratim, Rafiei, Mahdie, Kammer, Paula T et al.2026 · 1 citationBMC medical research methodology. 2026;26(1)
A microenvironment-determined risk continuum refines subtyping in meningioma and reveals determinants of machine learning-based tumor classification.41663806 · Maas, Sybren L N, Tang, Yiheng, Stutheit-Zhao, Eric et al.2026 · 11 citationsNature genetics. 2026;58(2):341-354
The power and limits of predicting inter-protein exon-exon interactions using protein 3D structures.41816009 · Liebold, Jeanine, Del Moral-Morales, Aylin, Manalastas-Cantos, Karen et al.2026 · 0 citationsBioinformatics advances. 2026;6(1):vbag032
Long-term outcome and predictors for recurrence after medical and interventional treatment of arrhythmias at the UniverSity Heart CenTer Hamburg (TRUST): design and patient profile snapshot of a prospective clinical cohort study.41743284 · Obergassel, Julius, Rieß, Jan Leon, Jaeckle, Sandro et al.2026 · 2 citationsEuropean heart journal open. 2026;6(1):oeag002
Detection of alternative splicing: deep sequencing or deep learning?41520225 · Hackl, Lena Maria, Neuhaus, Fabian, Ameling, Sabine et al.2026 · 3 citationsBriefings in bioinformatics. 2026;27(1)
Cracks in the Foundation: How Data-Hungry and Sensitive to Domain Shift are Vision Foundation Models for Computational Pathology?10.64898/2026.01.06.25342815v1 · Bonn, S., Zimmermann, M., Sauter, G. et al.2026 · 0 citationsmedRxiv
NetMedGPT - A network medicine foundation model for extensive disease mechanism mining and drug repurposing10.64898/2026.01.04.697552v1 · Firoozbakht, F., Suwer, S., Elkjaer, M. L. et al.2026 · 2 citationsbioRxiv
ViMOP: a user-friendly and field-applicable pipeline for untargeted viral genome nanopore sequencing.41460182 · Petersen, Nils Peter, Le, Mia, Renevey, Annick et al.2026 · 2 citationsBioinformatics (Oxford, England). 2026;42(1)
Corticosterone regulates the balance between freezing and rearing in defensive responses to predator threat.41371387 · Baumbach, J L, Mui, C Y Y, Leonetti, A M et al.2026 · 2 citationsProgress in neuro-psychopharmacology & biological psychiatry. 2026;144:111579
Reticulated platelets in coronary artery disease: a multidimensional approach unveils prothrombotic signalling and novel therapeutic targets.40886063 · Kirmes, Kilian, Han, Jiaying, Klug, Melissa et al.2025 · 11 citationsEuropean heart journal. 2025;46(45):4901-4917
Conversational No-code, Multi-agentic Disease Module Identification and Drug Repurposing Prediction with ChatDRex2511.21438v2 · Simon Suwer, Kester Bagemihl, Sylvie Baier et al.2025 · 0 citationsarXiv
A systematic analysis of the impact of data variation on AI-based histopathological grading of prostate cancer.41308537 · Fuhlert, Patrick, Westhaeusser, Fabian, Dietrich, Esther et al.2025 · 3 citationsMedical image analysis. 2026;108:103884
Deletion of cardiac fibroblast growth factor-23 beneficially impacts myocardial energy metabolism in left ventricular hypertrophy.41152461 · Latic, Nejla, Lari, Arezou, Sun, Na et al.2025 · 5 citationsnpj metabolic health and disease. 2025;3(1):42
Aberrant splicing in human cancer has a large-scale functional impact on transcription factors10.1101/2025.10.16.682783v1 · Newaz, K., Tsoy, O., Baumbach, J.2025 · 0 citationsbioRxiv
Development of an Integrated Single-Cell and Spatial Transcriptomics Atlas of Healthy Human Skin Focusing on the Pilosebaceous Unit10.1101/2025.09.09.675235v1 · Duz, T., Torocsik, D., Momnougui, S. M. E. et al.2025 · 0 citationsbioRxiv
Potentials and limitations in the application of Convolutional Neural Networks for mosquito species identification using wing images.40911551 · Nolte, Kristopher, Baumbach, Jan, Lins, Christian et al.2025 · 6 citationsPLoS computational biology. 2025;21(9):e1013435
Phenotypic Changes in a Monocyte Cluster with High Interleukin-1 Beta Expression during Long-Term Anti-CD20 Therapy.40879186 · Waede, Mie, Kingo, Christina, Damsbo, Karina et al.2025 · 1 citationAnnals of neurology. 2025;98(6):1283-1298
Artificial Intelligence and Network Medicine: Path to Precision Medicine.40918693 · Altucci, Lucia, Badimon, Lina, Balligand, Jean-Luc et al.2025 · 14 citationsNEJM AI. 2025;2(9)
Systematic Comparison of Bone Proteome Extraction Methods to Allow for Integrated Proteomics-Metabolomics Correlation.40796122 · Wiltzsch, Vivien, Schmidt, Johannes R, Adamowicz, Klaudia et al.2025 · 4 citationsJournal of proteome research. 2025;24(9):4362-4376
Drug Repurposing for Kala-Azar.40871042 · Arsić, Biljana, Ilić, Budimir S, Maier, Andreas et al.2025 · 4 citationsPharmaceutics. 2025;17(8)
Phenotypic similarity of adverse drug reactions and disease phenotypes is a bridge to mechanistic discovery.42380258 · Firoozbakht, Farzaneh, Wenke, Nina, Tsoy, Olga et al.2026 · 1 citationnpj drug discovery. 2025;2(1)
FedscGen: privacy-preserving federated batch effect correction of single-cell RNA sequencing data.40696440 · Bakhtiari, Mohammad, Bonn, Stefan, Theis, Fabian et al.2025 · 6 citationsGenome biology. 2025;26(1):216
Pathology-oriented multiplexing enables integrative disease mapping.40681898 · Kuehl, Malte, Okabayashi, Yusuke, Wong, Milagros N et al.2025 · 28 citationsNature. 2025;644(8076):516-526
Regulation of the transcriptome, miRNAs, and alternative splicing in a FSGS zebrafish injury model10.1101/2025.07.09.663814v1 · Mattias, F., Tsoy, O., Iervolino, A. et al.2025 · 1 citationbioRxiv
Privacy-preserving multicenter differential protein abundance analysis with FedProt.40646319 · Burankova, Yuliya, Abele, Miriam, Bakhtiari, Mohammad et al.2025 · 5 citationsNature computational science. 2025;5(8):675-688
DIGGER 2.0: digging into the functional impact of differential splicing on human and mouse disorders.40337913 · Albrecht, Elias, Pelz, Konstantin, Gress, Alexander et al.2025 · 4 citationsNucleic acids research. 2025;53(W1):W245-W252
High-Resolution Spatial Map of the Human Facial Sebaceous Gland Reveals Marker Genes and Decodes Sebocyte Differentiation.40449655 · Düz, Tolga, Torocsik, Daniel, Simmering, Annika et al.2025 · 16 citationsThe Journal of investigative dermatology. 2026;146(1):40-54.e14
Alternative Splicing in Mechanically Stretched Podocytes as a Model of Glomerular Hypertension.40418580 · Mattias, Francescapaola, Tsoy, Olga, Hammer, Elke et al.2026 · 6 citationsJournal of the American Society of Nephrology : JASN. 2025;36(9):1702-1715
DRaCOon: a novel algorithm for pathway-level differential co-expression analysis in transcriptomics.40419963 · Delgado-Chaves, Fernando M, Spurny, Ferdinand, Laske, Tanja et al.2025 · 0 citationsBMC bioinformatics. 2025;26(1):137
To Implement or Not to Implement? A Commentary on the Pitfalls of Judging the Value and Risks of Personalized Prognostic Statistical Models.40387583 · Baumbach, Linda, Hötzendorfer, Walter, Baumbach, Jan2025 · 0 citationsJournal of medical Internet research. 2025;27:e69341
Synergistic Network Pharmacology: Preclinical Validation and Clinical Safety in Acute Ischemic Stroke.40371623 · Casas, Ana I, Nogales, Cristian, Szepanowski, Rebecca D et al.2025 · 6 citationsJournal of the American Heart Association. 2025;14(10):e039098
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