Graph-based analysis and visualization of experimental results with ONDEX. - Jacob Köhler; Jan Baumbach; Jan Taubert; Michael Specht; Andre Skusa; Alexander Rüegg; Christopher J. Rawlings; Paul Verrier; Stephan Philippi (Bioinform., 2006)

CoryneRegNet 2: An Integrative Bioinformatics Approach for Reconstruction and Comparison of Transcriptional Regulatory Networks in Prokaryotes. - Jan Baumbach; Karina Brinkrolf; Tobias Wittkop; Andreas Tauch; Sven Rahmann (J. Integr. Bioinform., 2006)

CoryneRegNet 4.0 - A reference database for corynebacterial gene regulatory networks. - Jan Baumbach (BMC Bioinform., 2007)

Large scale clustering of protein sequences with FORCE -A layout based heuristic for weighted cluster editing. - Tobias Wittkop; Jan Baumbach; Francisco Pereira Lobo; Sven Rahmann (BMC Bioinform., 2007)

CoryneCenter - An online resource for the integrated analysis of corynebacterial genome and transcriptome data. - Heiko Neuweger; Jan Baumbach; Stefan P. Albaum; Thomas Bekel; Michael Dondrup; Andrea T. Hüser; Jörn Kalinowski; Sebastian Oehm; Alfred Pühler; Sven Rahmann; Jochen Weile; Alexander Goesmann (BMC Syst. Biol., 2007)

IMS2 - An integrated medical software system for early lung cancer detection using ion mobility spectrometry data of human breath. - Jan Baumbach; Alexander Bunkowski; Sita Lange; Timm Oberwahrenbrock; Nils Kleinbölting; Sven Rahmann; Jörg Ingo Baumbach (J. Integr. Bioinform., 2007)

MoRAine - A web server for fast computational transcription factor binding motif re-annotation. - Jan Baumbach; Tobias Wittkop; Jochen Weile; Thomas Kohl; Sven Rahmann (J. Integr. Bioinform., 2008)

CoryneRegNet: a reference database and analysis platform for corynebacterial gene regulatory networks - Jan Baumbach (2008)

Towards the integrated analysis, visualization and reconstruction of microbial gene regulatory networks. - Jan Baumbach; Andreas Tauch; Sven Rahmann (Briefings Bioinform., 2009)

Reliable transfer of transcriptional gene regulatory networks between taxonomically related organisms. - Jan Baumbach; Sven Rahmann; Andreas Tauch (BMC Syst. Biol., 2009)

Efficient Online Transcription Factor Binding Site Adjustment by Integrating Transitive Graph Projection with MoRAine 2.0. - Tobias Wittkop; Sven Rahmann; Jan Baumbach (J. Integr. Bioinform., 2010)

AltAnalyze and DomainGraph: analyzing and visualizing exon expression data. - Dorothea Emig; Nathan Salomonis; Jan Baumbach; Thomas Lengauer; Bruce R. Conklin; Mario Albrecht (Nucleic Acids Res., 2010)

clusterMaker: a multi-algorithm clustering plugin for Cytoscape. - John H. Morris; Leonard Apeltsin; Aaron M. Newman; Jan Baumbach; Tobias Wittkop; Gang Su; Gary D. Bader; Thomas E. Ferrin (BMC Bioinform., 2011)

KeyPathwayMiner: Detecting Case-Specific Biological Pathways Using Expression Data. - Nicolas Alcaraz; Hande Kücük; Jochen Weile; Anil Wipat; Jan Baumbach (Internet Math., 2011)

Extension and Robustness of Transitivity Clustering for Protein-Protein Interaction Network Analysis. - Tobias Wittkop; Sven Rahmann; Richard Röttger; Sebastian Böcker; Jan Baumbach (Internet Math., 2011)

Online Transitivity Clustering of Biological Data with Missing Values. - Richard Röttger; Christoph Kreutzer; Thuy Duong Vu; Tobias Wittkop; Jan Baumbach (GCB, 2012)

Efficient algorithms for extracting biological key pathways with global constraints. - Jan Baumbach; Tobias Friedrich 001; Timo Kötzing; Anton Krohmer; Joachim Müller; Josch Pauling (GECCO, 2012)

Integrated simultaneous analysis of different biomedical data types with exact weighted bi-cluster editing. - Peng Sun 008; Jiong Guo; Jan Baumbach (J. Integr. Bioinform., 2012)

CoryneRegNet 6.0 - Updated database content, new analysis methods and novel features focusing on community demands. - Josch Pauling; Richard Röttger; Andreas Tauch; Vasco Ariston de Carvalho Azevedo; Jan Baumbach (Nucleic Acids Res., 2012)

How Little Do We Actually Know? On the Size of Gene Regulatory Networks. - Richard Röttger; Ulrich Rückert 002; Jan Taubert; Jan Baumbach (IEEE ACM Trans. Comput. Biol. Bioinform., 2012)

Cluster Editing. - Sebastian Böcker; Jan Baumbach (CiE, 2013)

GEDEVO: An Evolutionary Graph Edit Distance Algorithm for Biological Network Alignment. - Rashid Ibragimov; Maximilian Malek; Jiong Guo; Jan Baumbach (GCB, 2013)

NABEECO: biological network alignment with bee colony optimization algorithm. - Rashid Ibragimov; Jan Martens 003; Jiong Guo; Jan Baumbach (GECCO (Companion), 2013)

Neighborhood-Preserving Mapping between Trees. - Jan Baumbach; Jiong Guo; Rashid Ibragimov (WADS, 2013)

Density parameter estimation for finding clusters of homologous proteins - tracing actinobacterial pathogenicity lifestyles. - Richard Röttger; Prabhav Kalaghatgi; Peng Sun 008; Siomar de Castro Soares; Vasco Ariston de Carvalho Azevedo; Tobias Wittkop; Jan Baumbach (Bioinform., 2013)

An Integrative Clinical Database and Diagnostics Platform for Biomarker Identification and Analysis in Ion Mobility Spectra of Human Exhaled Air. - Till Schneider; Anne-Christin Hauschild; Jörg Ingo Baumbach; Jan Baumbach (J. Integr. Bioinform., 2013)

Complexity of Dense Bicluster Editing Problems. - Peng Sun 008; Jiong Guo; Jan Baumbach (COCOON, 2014)

Compactness-Preserving Mapping on Trees. - Jan Baumbach; Jiong Guo; Rashid Ibragimov (CPM, 2014)

On the limits of computational functional genomics for bacterial lifestyle prediction. - Eudes Barbosa; Richard Röttger; Anne-Christin Hauschild; Vasco Ariston de Carvalho Azevedo; Jan Baumbach (GCB, 2014)

Efficient Large-scale bicluster editing. - Peng Sun 008; Jiong Guo; Jan Baumbach (GCB, 2014)

Multiple graph edit distance: simultaneous topological alignment of multiple protein-protein interaction networks with an evolutionary algorithm. - Rashid Ibragimov; Maximilian Malek; Jan Baumbach; Jiong Guo (GECCO, 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)

KeyPathwayMiner 4.0: condition-specific pathway analysis by combining multiple omics studies and networks with Cytoscape. - Nicolas Alcaraz; Josch Pauling; Richa Batra; Eudes Barbosa; Alexander Junge; Anne Christensen; Vasco Ariston de Carvalho Azevedo; Henrik J. Ditzel; Jan Baumbach (BMC Syst. Biol., 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)

BacillusRegNet: A transcriptional regulation database and analysis platform for Bacillus species. - Goksel Misirli; Jennifer Hallinan; Richard Röttger; Jan Baumbach; Anil Wipat (J. Integr. Bioinform., 2014)

Covering tree with stars. - Jan Baumbach; Jiong Guo; Rashid Ibragimov (J. Comb. Optim., 2015)

OpenLabNotes - An Electronic Laboratory Notebook Extension for OpenLabFramework. - Markus List; Michael Franz; Qihua Tan; Jan Mollenhauer; Jan Baumbach (J. Integr. Bioinform., 2015)

A Simulated Annealing Algorithm for Maximum Common Edge Subgraph Detection in Biological Networks. - Simon J. Larsen; Frederik G. Alkærsig; Henrik J. Ditzel; Igor Jurisica; Nicolas Alcaraz; Jan Baumbach (GECCO, 2016)

CytoGEDEVO - global alignment of biological networks with Cytoscape. - Maximilian Malek; Rashid Ibragimov; Mario Albrecht; Jan Baumbach (Bioinform., 2016)

Robust de novo pathway enrichment with KeyPathwayMiner 5. - Nicolas Alcaraz; Markus List; Martin Dissing-Hansen; Marc Rehmsmeier; Qihua Tan; Jan Mollenhauer; Henrik J. Ditzel; Jan Baumbach (F1000Research, 2016)

PetriScape - A plugin for discrete Petri net simulations in Cytoscape. - Diogo Almeida; Vasco Ariston de Carvalho Azevedo; Artur Silva; Jan Baumbach (J. Integr. Bioinform., 2016)

Jllumina - A comprehensive Java-based API for statistical Illumina Infinium HumanMethylation450 and MethylationEPIC data processing. - Diogo Almeida; Ida Skov; Jesper Lund; Afsaneh Mohammadnejad; Artur Silva; Fabio Vandin; Qihua Tan; Jan Baumbach; Richard Röttger (J. Integr. Bioinform., 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)

Efficient detection of differentially methylated regions using DiMmeR. - Diogo Almeida; Ida Skov; Artur Silva; Fabio Vandin; Qihua Tan; Richard Röttger; Jan Baumbach (Bioinform., 2017)

LifeStyle-Specific-Islands (LiSSI): Integrated Bioinformatics Platform for Genomic Island Analysis. - Eudes Barbosa; Richard Röttger; Anne-Christin Hauschild; Siomar de Castro Soares; Sebastian Böcker; Vasco Ariston de Carvalho Azevedo; Jan Baumbach (J. Integr. Bioinform., 2017)

CytoMCS: A Multiple Maximum Common Subgraph Detection Tool for Cytoscape. - Simon J. Larsen; Jan Baumbach (J. Integr. Bioinform., 2017)

Interactive microbial distribution analysis using BioAtlas. - Jesper Lund; Markus List; Jan Baumbach (Nucleic Acids Res., 2017)

From gene panels to systems medicine. - Jan Baumbach (BIBM, 2018)

Weighted gene co-expression network analysis of microarray mRNA expression profiling in response to electroacupuncture. - Afsaneh Mohammadnejad; Shuxia Li; Hongmei Duan; Jesper Lund; Weilong Li; Jan Baumbach; Qihua Tan (BIBM, 2018)

Systems Medicine - The Next Generation of Computer-assisted Precision Medicine. - Jan Baumbach (Bildverarbeitung für die Medizin, 2018)

On the power of epigenome-wide association studies using a disease-discordant twin design. - Weilong Li; Lene Christiansen; Jacob v. B. Hjelmborg; Jan Baumbach; Qihua Tan (Bioinform., 2018)

Parameter estimation of qualitative biological regulatory networks on high performance computing hardware. - Muhammad Tariq Saeed; Jamil Ahmad; Jan Baumbach; Josch Pauling; Aamir Shafi; Rehan Zafar Paracha; Asad Hayat; Amjad Ali 001 (BMC Syst. Biol., 2018)

Fuzzy Inference System for Risk Evaluation in Gestational Diabetes Mellitus. - Carlos Salort Sánchez; Suzanne Smyth; Elizabeth Tully; Joanna Griffin; Luke Heaphy; Niamh Redmond; Fionnuala Breathnach; Jan Baumbach; Cristian Axenie (BIBE, 2019)

An Online Incremental Clustering Framework for Real-Time Stream Analytics. - Carlos Salort Sánchez; Radu Tudoran; Mohamad Al Hajj Hassan; Stefano Bortoli; Goetz Brasche; Jan Baumbach; Cristian Axenie (ICMLA, 2019)

Community effort endorsing multiscale modelling, multiscale data science and multiscale computing for systems medicine. - Massimiliano Zanin; Ivan Chorbev; Blaz Stres; Egils Stalidzans; Julio Vera; Paolo Tieri; Filippo Castiglione; Derek Groen; Huiru Zheng; Jan Baumbach; Johannes A. Schmid; José Basilio; et al. (Briefings Bioinform., 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)

PanRV: Pangenome-reverse vaccinology approach for identifications of potential vaccine candidates in microbial pangenome. - Kanwal Naz; Anam Naz; Shifa Tariq Ashraf; Muhammad Rizwan; Jamil Ahmad; Jan Baumbach; Amjad Ali 001 (BMC Bioinform., 2019)

GANNSTER: Graph-Augmented Neural Network Spatio-Temporal Reasoner for Traffic Forecasting. - Carlos Salort Sánchez; Alexander Wieder; Paolo Sottovia; Stefano Bortoli; Jan Baumbach; Cristian Axenie (AALTD@PKDD/ECML, 2020)

EpiGEN: an epistasis simulation pipeline. - David B. Blumenthal; Lorenzo Viola; Markus List; Jan Baumbach; Paolo Tieri; Tim Kacprowski (Bioinform., 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; et al. (CoRR, 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)

netDx: Software for building interpretable patient classifiers by multi-'omic data integration using patient similarity networks. - Shraddha Pai; Philipp Weber; Ruth Isserlin; Hussam Kaka; Shirley Hui; Muhammad Ahmad Shah; Luca Giudice; Rosalba Giugno; Anne Krogh Nøhr; Jan Baumbach; Gary D. Bader (F1000Research, 2020)

On the Privacy of Federated Pipelines. - Reza Nasirigerdeh; Reihaneh Torkzadehmahani; Jan Baumbach; David B. Blumenthal (SIGIR, 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; et al. (Briefings Bioinform., 2021)

On the limits of active module identification. - Olga Lazareva; Jan Baumbach; Markus List; David B. Blumenthal (Briefings 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)

ASimulatoR: splice-aware RNA-Seq data simulation. - Quirin Manz; Olga Tsoy; Amit Fenn; Jan Baumbach; Uwe Völker; Markus List; Tim Kacprowski (Bioinform., 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; et al. (CoRR, 2021)

HyFed: A Hybrid Federated Framework for Privacy-preserving Machine Learning. - Reza Nasirigerdeh; Reihaneh Torkzadehmahani; Julian O. Matschinske; Jan Baumbach; Daniel Rueckert; Georgios Kaissis (CoRR, 2021)

Success Factors of Artificial Intelligence Implementation in Healthcare. - Justus Wolff; Josch Pauling; Andreas Keck; Jan Baumbach (Frontiers Digit. Health, 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)

Lessons from the COVID-19 pandemic for advancing computational drug repurposing strategies. - Gihanna Galindez; Julian O. Matschinske; Tim D. Rose; Sepideh Sadegh; Marisol Salgado-Albarrán; Julian Späth; Jan Baumbach; Josch Konstantin Pauling (Nat. Comput. Sci., 2021)

Enabling single-cell trajectory network enrichment. - Alexander G. B. Grønning; Mhaned Oubounyt; Kristiyan Kanev; Jesper Lund; Tim Kacprowski; Dietmar Zehn; Richard Röttger; Jan Baumbach (Nat. Comput. Sci., 2021)

Machine learning for deciphering cell heterogeneity and gene regulation. - Michael Scherer; Florian Schmidt 003; Olga Lazareva; Jörn Walter; Jan Baumbach; Marcel H. Schulz; Markus List (Nat. Comput. Sci., 2021)

Online in silico validation of disease and gene sets, clusterings or subnetworks with DIGEST. - Klaudia Adamowicz; Andreas Maier 009; Jan Baumbach; David B. Blumenthal (Briefings 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)

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)

Federated Random Forests can improve local performance of predictive models for various healthcare applications. - Anne-Christin Hauschild; Marta Lemanczyk; Julian O. Matschinske; Tobias Frisch; Olga I. Zolotareva; Andreas Holzinger; Jan Baumbach; Dominik Heider (Bioinform., 2022)

Federated machine learning for a facilitated implementation of Artificial Intelligence in healthcare - a proof of concept study for the prediction of coronary artery calcification scores. - Justus Wolff; Julian O. Matschinske; Dietrich Baumgart; Anne Pytlik; Andreas Keck; Arunakiry Natarajan; Claudio E. von Schacky; Josch Pauling; Jan Baumbach (J. Integr. Bioinform., 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)

dsMTL: a computational framework for privacy-preserving, distributed multi-task machine learning. - Han Cao 001; Youcheng Zhang; Jan Baumbach; Paul R. Burton; Dominic B. Dwyer; Nikolaos Koutsouleris; Julian O. Matschinske; Yannick Marcon; Sivanesan Rajan; Thilo Rieg; Patricia Ryser-Welch; Julian Späth; et al. (Bioinform., 2022)

Differentially Private Federated Learning: Privacy and Utility Analysis of Output Perturbation and DP-SGD. - Anastasia Pustozerova; Jan Baumbach; Rudolf Mayer (IEEE Big Data, 2023)

Human-in-the-Loop Integration with Domain-Knowledge Graphs for Explainable Federated Deep Learning. - Andreas Holzinger; Anna Saranti; Anne-Christin Hauschild; Jacqueline Michelle Beinecke; Dominik Heider; Richard Röttger; Heimo Müller; Jan Baumbach; Bastian Pfeifer (CD-MAKE, 2023)

Analysing Utility Loss in Federated Learning with Differential Privacy. - Anastasia Pustozerova; Jan Baumbach; Rudolf Mayer (TrustCom, 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., 2023)

Federated machine learning in data-protection-compliant research. - Alissa Brauneck; Louisa Schmalhorst; Mohammad Mahdi Kazemi Majdabadi; Mohammad Bakhtiari; Uwe Völker; Christina Caroline Saak; Jan Baumbach; Linda Baumbach; Gabriele Buchholtz (Nat. Mac. Intell., 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., 2023)

Inference of differential key regulatory networks and mechanistic drug repurposing candidates from scRNA-seq data with SCANet. - Mhaned Oubounyt; Lorenz Adlung; Fábio Malta de Sá Patroni; Nina Kerstin Wenke; Andreas Maier 009; Michael Hartung; Jan Baumbach; Maria L. Elkjaer (Bioinform., 2023)

NeDRex-Web: An Interactive Web Tool for Drug Repurposing by Exploring Heterogeneous Molecular Networks. - Andreas Maier 009; Mahdie Rafiei; Elisa Anastasi; Olga I. Zolotareva; James Skelton; Maria L. Elkjaer; Ana I. Casas; Cristian Nogales; Harald H. H. W. Schmidt; Tim Kacprowski; David B. Blumenthal; Anil Wipat; et al. (BIBM, 2024)

Privacy-Preserving Multi-Center Differential Protein Abundance Analysis with FedProt. - Yuliya Burankova; Miriam Abele; Mohammad Bakhtiari; Christine von Törne; Teresa Barth; Lisa Schweizer; Pieter Giesbertz; Johannes R. Schmidt; Stefan Kalkhof; Janina Müller-Deile; Peter A. van Veelen; Yassene Mohammed; et al. (CoRR, 2024)

UnPaSt: unsupervised patient stratification by differentially expressed biclusters in omics data. - Michael Hartung; Andreas Maier 009; Fernando M. Delgado-Chaves; Yuliya Burankova; Olga I. Isaeva; Fábio Malta de Sá Patroni; Daniel He; Casey Shannon; Katharina Kaufmann; Jens Lohmann; Alexey Savchik; Anne Hartebrodt; et al. (CoRR, 2024)

Privacy-preserving federated prediction of pain intensity change based on multi-center survey data. - Supratim Das; Mahdie Rafiei; Paula Kammer; Søren T. Skou; Dorte T. Grønne; Ewa M. Roos; André Hajek; Hans-Helmut König; Md Shihab Ullaha; Niklas Probul; Jan Baumbach; Linda Baumbach (CoRR, 2024)

Personalized Prediction Models for Changes in Knee Pain among Patients with Osteoarthritis Participating in Supervised Exercise and Education. - Mahdie Rafiei; Supratim Das; Mohammad Bakhtiari; Ewa M. Roos; Søren T. Skou; Dorte T. Grønne; Jan Baumbach; Linda Baumbach (CoRR, 2024)

FedRBE - a decentralized privacy-preserving federated batch effect correction tool for omics data based on limma. - Yuliya Burankova; Julian Klemm; Jens Lohmann; Ahmad Taheri; Niklas Probul; Jan Baumbach; Olga I. Zolotareva (CoRR, 2024)

Partial reinforcement optimizer: An evolutionary optimization algorithm. - Ahmad Taheri; Keyvan RahimiZadeh; Amin Beheshti; Jan Baumbach; Ravipudi Venkata Rao; Seyedali Mirjalili; Amir H. Gandomi (Expert Syst. Appl., 2024)

Systematic evaluation of normalization approaches in tandem mass tag and label-free protein quantification data using PRONE. - 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 (Briefings Bioinform., 2025)

FTA-FTL: A Fine-Tuned Aggregation Federated Transfer Learning Scheme for Lithology Microscopic Image Classification. - Keyvan RahimiZadeh; Ahmad Taheri; Jan Baumbach; Esmael Makarian; Abbas Dehghani 002; Bahman Ravaei; Bahman Javadi; Amin Beheshti (CoRR, 2025)

DRaCOon: a novel algorithm for pathway-level differential co-expression analysis in transcriptomics. - Fernando M. Delgado-Chaves; Ferdinand Spurny; Tanja Laske; Mhaned Oubounyt; Jan Baumbach (BMC Bioinform., 2025)