Jan Baumbach

Publication Activity (10 Years)

Years Active: 2006-2024
Publications (10 Years): 55

Top Topics

Comprehensive Evaluation

Machine Learning

Regulatory Networks

Top Venues

J. Integr. Bioinform.

Briefings Bioinform.

Publications

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, Elke Hammer, Lis Arend, Klaudia Adamowicz, Tanja Laske, Anne Hartebrodt, Tobias Frisch, Chen Meng, Julian O. Matschinske, Julian Späth, Richard Röttger, Veit Schwämmle, Stefanie M. Hauck, Stefan Lichtenthaler, Axel Imhof, Matthias Mann, Christina Ludwig, Bernhard Küster, Jan Baumbach, Olga I. Zolotareva
Privacy-Preserving Multi-Center Differential Protein Abundance Analysis with FedProt. CoRR (2024)
Ahmad Taheri, Keyvan RahimiZadeh, Amin Beheshti, Jan Baumbach, Ravipudi Venkata Rao, Seyedali Mirjalili, Amir H. Gandomi
Partial reinforcement optimizer: An evolutionary optimization algorithm. Expert Syst. Appl. 238 (Part F) (2024)
Mhaned Oubounyt, Lorenz Adlung, Fabio Patroni, Nina Kerstin Wenke, Andreas Maier, Michael Hartung, Jan Baumbach, Maria L. Elkjaer
Inference of differential key regulatory networks and mechanistic drug repurposing candidates from scRNA-seq data with SCANet. Bioinform. 39 (10) (2023)
Anastasia Pustozerova, Jan Baumbach, Rudolf Mayer
Analysing Utility Loss in Federated Learning with Differential Privacy. TrustCom (2023)
Chit Tong Lio, Gordon Grabert, Zakaria Louadi, Amit Fenn, Jan Baumbach, Tim Kacprowski, Markus List, Olga Tsoy
Systematic analysis of alternative splicing in time course data using Spycone. Bioinform. 39 (1) (2023)
Andreas Holzinger, Anna Saranti, Anne-Christin Hauschild, Jacqueline Michelle Beinecke, Dominik Heider, Richard Röttger, Heimo Müller, Jan Baumbach, Bastian Pfeifer
Human-in-the-Loop Integration with Domain-Knowledge Graphs for Explainable Federated Deep Learning. CD-MAKE (2023)
Fabio Boniolo, Markus Hoffmann, Norman Roggendorf, Bahar Tercan, Jan Baumbach, Mauro A. A. Castro, A. Gordon Robertson, Dieter Saur, Markus List
spongEffects: ceRNA modules offer patient-specific insights into the miRNA regulatory landscape. Bioinform. 39 (5) (2023)
Alissa Brauneck, Louisa Schmalhorst, Mohammad Mahdi Kazemi Majdabadi, Mohammad Bakhtiari, Uwe Völker, Christina Caroline Saak, Jan Baumbach, Linda Baumbach, Gabriele Buchholtz
Federated machine learning in data-protection-compliant research. Nat. Mac. Intell. 5 (1) (2023)
Anastasia Pustozerova, Jan Baumbach, Rudolf Mayer
Differentially Private Federated Learning: Privacy and Utility Analysis of Output Perturbation and DP-SGD. BigData (2023)
Michael Hartung, Elisa Anastasi, Zeinab M. Mamdouh, Cristian Nogales, Harald H. H. W. Schmidt, Jan Baumbach, Olga I. Zolotareva, Markus List
Cancer driver drug interaction explorer. Nucleic Acids Res. 50 (W1) (2022)
Han Cao, 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, Carl Herrmann, Emanuel Schwarz
dsMTL: a computational framework for privacy-preserving, distributed multi-task machine learning. Bioinform. 38 (21) (2022)
Judith Bernett, Dominik Krupke, Sepideh Sadegh, Jan Baumbach, Sándor P. Fekete, Tim Kacprowski, Markus List, David B. Blumenthal
Robust disease module mining via enumeration of diverse prize-collecting Steiner trees. Bioinform. 38 (6) (2022)
Justus Wolff, Julian O. Matschinske, Dietrich Baumgart, Anne Pytlik, Andreas Keck, Arunakiry Natarajan, Claudio E. von Schacky, Josch Pauling, Jan Baumbach
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. J. Integr. Bioinform. 19 (4) (2022)
Lis Arend, Judith Bernett, Quirin Manz, Melissa Klug, Olga Lazareva, Jan Baumbach, Dario Bongiovanni, Markus List
A systematic comparison of novel and existing differential analysis methods for CyTOF data. Briefings Bioinform. 23 (1) (2022)
Anne-Christin Hauschild, Marta Lemanczyk, Julian O. Matschinske, Tobias Frisch, Olga I. Zolotareva, Andreas Holzinger, Jan Baumbach, Dominik Heider
Federated Random Forests can improve local performance of predictive models for various healthcare applications. Bioinform. 38 (8) (2022)
Klaudia Adamowicz, Andreas Maier, Jan Baumbach, David B. Blumenthal
validation of disease and gene sets, clusterings or subnetworks with DIGEST. Briefings Bioinform. 23 (4) (2022)
Quirin Manz, Olga Tsoy, Amit Fenn, Jan Baumbach, Uwe Völker, Markus List, Tim Kacprowski
ASimulatoR: splice-aware RNA-Seq data simulation. Bioinform. 37 (18) (2021)
Alexander G. B. Grønning, Mhaned Oubounyt, Kristiyan Kanev, Jesper Lund, Tim Kacprowski, Dietmar Zehn, Richard Röttger, Jan Baumbach
Enabling single-cell trajectory network enrichment. Nat. Comput. Sci. 1 (2) (2021)
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
Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research. Briefings Bioinform. 22 (2) (2021)
Michael Scherer, Florian Schmidt, Olga Lazareva, Jörn Walter, Jan Baumbach, Marcel H. Schulz, Markus List
Machine learning for deciphering cell heterogeneity and gene regulation. Nat. Comput. Sci. 1 (3) (2021)
Zakaria Louadi, Kevin Yuan, Alexander Greß, Olga Tsoy, Olga V. Kalinina, Jan Baumbach, Tim Kacprowski, Markus List
DIGGER: exploring the functional role of alternative splicing in protein interactions. Nucleic Acids Res. 49 (Database-Issue) (2021)
Reza Nasirigerdeh, Reihaneh Torkzadehmahani, Julian O. Matschinske, Jan Baumbach, Daniel Rueckert, Georgios Kaissis
HyFed: A Hybrid Federated Framework for Privacy-preserving Machine Learning. CoRR (2021)
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
The FeatureCloud AI Store for Federated Learning in Biomedicine and Beyond. CoRR (2021)
Olga Lazareva, Jan Baumbach, Markus List, David B. Blumenthal
On the limits of active module identification. Briefings Bioinform. 22 (5) (2021)
Olga Lazareva, Stefan Canzar, Kevin Yuan, Jan Baumbach, David B. Blumenthal, Paolo Tieri, Tim Kacprowski, Markus List
BiCoN: network-constrained biclustering of patients and omics data. Bioinform. 37 (16) (2021)
Justus Wolff, Josch Pauling, Andreas Keck, Jan Baumbach
Success Factors of Artificial Intelligence Implementation in Healthcare. Frontiers Digit. Health 3 (2021)
Gihanna Galindez, Julian O. Matschinske, Tim D. Rose, Sepideh Sadegh, Marisol Salgado-Albarrán, Julian Späth, Jan Baumbach, Josch Konstantin Pauling
Lessons from the COVID-19 pandemic for advancing computational drug repurposing strategies. Nat. Comput. Sci. 1 (1) (2021)
Reza Nasirigerdeh, Reihaneh Torkzadehmahani, Jan Baumbach, David B. Blumenthal
On the Privacy of Federated Pipelines. SIGIR (2021)
Mohammad Bakhtiari, Reza Nasirigerdeh, Reihaneh Torkzadehmahani, Amirhossein Bayat, David B. Blumenthal, Markus List, Jan Baumbach
Federated Multi-Mini-Batch: An Efficient Training Approach to Federated Learning in Non-IID Environments. CoRR (2020)
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
netDx: Software for building interpretable patient classifiers by multi-'omic data integration using patient similarity networks. F1000Research 9 (2020)
David B. Blumenthal, Lorenzo Viola, Markus List, Jan Baumbach, Paolo Tieri, Tim Kacprowski
EpiGEN: an epistasis simulation pipeline. Bioinform. 36 (19) (2020)
Carlos Salort Sánchez, Alexander Wieder, Paolo Sottovia, Stefano Bortoli, Jan Baumbach, Cristian Axenie
GANNSTER: Graph-Augmented Neural Network Spatio-Temporal Reasoner for Traffic Forecasting. AALTD@PKDD/ECML (2020)
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
Privacy-preserving Artificial Intelligence Techniques in Biomedicine. CoRR (2020)
Kanwal Naz, Anam Naz, Shifa Tariq Ashraf, Muhammad Rizwan, Jamil Ahmad, Jan Baumbach, Amjad Ali
PanRV: Pangenome-reverse vaccinology approach for identifications of potential vaccine candidates in microbial pangenome. BMC Bioinform. 20 (1) (2019)
Carlos Salort Sánchez, Suzanne Smyth, Elizabeth Tully, Joanna Griffin, Luke Heaphy, Niamh Redmond, Fionnuala Breathnach, Jan Baumbach, Cristian Axenie
Fuzzy Inference System for Risk Evaluation in Gestational Diabetes Mellitus. BIBE (2019)
Gregor Sturm, Francesca Finotello, Florent Petitprez, Jitao David Zhang, Jan Baumbach, Wolf-Herman Fridman, Markus List, Tatsiana Aneichyk
Comprehensive evaluation of transcriptome-based cell-type quantification methods for immuno-oncology. Bioinform. 35 (14) (2019)
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, Peter Klimek, Natasa Debeljak, Damjana Rozman, Harald H. H. W. Schmidt
Community effort endorsing multiscale modelling, multiscale data science and multiscale computing for systems medicine. Briefings Bioinform. 20 (3) (2019)
Carlos Salort Sánchez, Radu Tudoran, Mohamad Al Hajj Hassan, Stefano Bortoli, Goetz Brasche, Jan Baumbach, Cristian Axenie
An Online Incremental Clustering Framework for Real-Time Stream Analytics. ICMLA (2019)
Jan Baumbach
From gene panels to systems medicine. BIBM (2018)
Afsaneh Mohammadnejad, Shuxia Li, Hongmei Duan, Jesper Lund, Weilong Li, Jan Baumbach, Qihua Tan
Weighted gene co-expression network analysis of microarray mRNA expression profiling in response to electroacupuncture. BIBM (2018)
Weilong Li, Lene Christiansen, Jacob v. B. Hjelmborg, Jan Baumbach, Qihua Tan
On the power of epigenome-wide association studies using a disease-discordant twin design. Bioinform. 34 (23) (2018)
Muhammad Tariq Saeed, Jamil Ahmad, Jan Baumbach, Josch Pauling, Aamir Shafi, Rehan Zafar Paracha, Asad Hayat, Amjad Ali
Parameter estimation of qualitative biological regulatory networks on high performance computing hardware. BMC Syst. Biol. 12 (1) (2018)
Jan Baumbach
Systems Medicine - The Next Generation of Computer-assisted Precision Medicine. Bildverarbeitung für die Medizin (2018)
Diogo Almeida, Ida Skov, Artur Silva, Fabio Vandin, Qihua Tan, Richard Röttger, Jan Baumbach
Efficient detection of differentially methylated regions using DiMmeR. Bioinform. 33 (4) (2017)
Eudes Barbosa, Richard Röttger, Anne-Christin Hauschild, Siomar de Castro Soares, Sebastian Böcker, Vasco Azevedo, Jan Baumbach
LifeStyle-Specific-Islands (LiSSI): Integrated Bioinformatics Platform for Genomic Island Analysis. J. Integr. Bioinform. 14 (2) (2017)
Jesper Lund, Markus List, Jan Baumbach
Interactive microbial distribution analysis using BioAtlas. Nucleic Acids Res. 45 (Webserver-Issue) (2017)
Simon J. Larsen, Jan Baumbach
CytoMCS: A Multiple Maximum Common Subgraph Detection Tool for Cytoscape. J. Integr. Bioinform. 14 (2) (2017)
Maximilian Malek, Rashid Ibragimov, Mario Albrecht, Jan Baumbach
CytoGEDEVO - global alignment of biological networks with Cytoscape. Bioinform. 32 (8) (2016)
Simon J. Larsen, Frederik G. Alkærsig, Henrik J. Ditzel, Igor Jurisica, Nicolas Alcaraz, Jan Baumbach
A Simulated Annealing Algorithm for Maximum Common Edge Subgraph Detection in Biological Networks. GECCO (2016)
Nicolas Alcaraz, Markus List, Martin Dissing-Hansen, Marc Rehmsmeier, Qihua Tan, Jan Mollenhauer, Henrik J. Ditzel, Jan Baumbach
. F1000Research 5 (2016)
Markus List, Nicolas Alcaraz, Martin Dissing-Hansen, Henrik J. Ditzel, Jan Mollenhauer, Jan Baumbach
KeyPathwayMinerWeb: online multi-omics network enrichment. Nucleic Acids Res. 44 (Webserver-Issue) (2016)
Diogo Almeida, Ida Skov, Jesper Lund, Afsaneh Mohammadnejad, Artur Silva, Fabio Vandin, Qihua Tan, Jan Baumbach, Richard Röttger
Jllumina - A comprehensive Java-based API for statistical Illumina Infinium HumanMethylation450 and MethylationEPIC data processing. J. Integr. Bioinform. 13 (4) (2016)
Diogo Almeida, Vasco Azevedo, Artur Silva, Jan Baumbach
PetriScape - A plugin for discrete Petri net simulations in Cytoscape. J. Integr. Bioinform. 13 (1) (2016)
Jan Baumbach, Jiong Guo, Rashid Ibragimov
Covering tree with stars. J. Comb. Optim. 29 (1) (2015)
Markus List, Michael Franz, Qihua Tan, Jan Mollenhauer, Jan Baumbach
OpenLabNotes - An Electronic Laboratory Notebook Extension for OpenLabFramework. J. Integr. Bioinform. 12 (3) (2015)
Peng Sun, Jiong Guo, Jan Baumbach
Complexity of Dense Bicluster Editing Problems. COCOON (2014)
Markus List, Anne-Christin Hauschild, Qihua Tan, Torben Arvid Kruse, Jan Mollenhauer, Jan Baumbach, Richa Batra
Classification of Breast Cancer Subtypes by combining Gene Expression and DNA Methylation Data. J. Integr. Bioinform. 11 (2) (2014)
Rashid Ibragimov, Maximilian Malek, Jan Baumbach, Jiong Guo
Multiple graph edit distance: simultaneous topological alignment of multiple protein-protein interaction networks with an evolutionary algorithm. GECCO (2014)
Eudes Barbosa, Richard Röttger, Anne-Christin Hauschild, Vasco Azevedo, Jan Baumbach
On the limits of computational functional genomics for bacterial lifestyle prediction. GCB (2014)
Goksel Misirli, Jennifer Hallinan, Richard Röttger, Jan Baumbach, Anil Wipat
BacillusRegNet: A transcriptional regulation database and analysis platform for Bacillus species. J. Integr. Bioinform. 11 (2) (2014)
Nicolas Alcaraz, Josch Pauling, Richa Batra, Eudes Barbosa, Alexander Junge, Anne Christensen, Vasco Azevedo, Henrik J. Ditzel, Jan Baumbach
KeyPathwayMiner 4.0: condition-specific pathway analysis by combining multiple omics studies and networks with Cytoscape. BMC Syst. Biol. 8 (2014)
Peng Sun, Jiong Guo, Jan Baumbach
Efficient Large-scale bicluster editing. GCB (2014)
Markus List, Ines Block, Marlene Lemvig Pedersen, Helle Christiansen, Steffen Schmidt, Mads Thomassen, Qihua Tan, Jan Baumbach, Jan Mollenhauer
Microarray R-based analysis of complex lysate experiments with MIRACLE. Bioinform. 30 (17) (2014)
Jan Baumbach, Jiong Guo, Rashid Ibragimov
Compactness-Preserving Mapping on Trees. CPM (2014)
Jan Baumbach, Jiong Guo, Rashid Ibragimov
Neighborhood-Preserving Mapping between Trees. WADS (2013)
Rashid Ibragimov, Jan Martens, Jiong Guo, Jan Baumbach
NABEECO: biological network alignment with bee colony optimization algorithm. GECCO (Companion) (2013)
Rashid Ibragimov, Maximilian Malek, Jiong Guo, Jan Baumbach
GEDEVO: An Evolutionary Graph Edit Distance Algorithm for Biological Network Alignment. GCB (2013)
Sebastian Böcker, Jan Baumbach
Cluster Editing. CiE (2013)
Till Schneider, Anne-Christin Hauschild, Jörg Ingo Baumbach, Jan Baumbach
An Integrative Clinical Database and Diagnostics Platform for Biomarker Identification and Analysis in Ion Mobility Spectra of Human Exhaled Air. J. Integr. Bioinform. 10 (2) (2013)
Jan Baumbach, Jiong Guo, Rashid Ibragimov
Covering Tree with Stars. COCOON (2013)
Richard Röttger, Prabhav Kalaghatgi, Peng Sun, Siomar de Castro Soares, Vasco Azevedo, Tobias Wittkop, Jan Baumbach
Density parameter estimation for finding clusters of homologous proteins - tracing actinobacterial pathogenicity lifestyles. Bioinform. 29 (2) (2013)
Peng Sun, Jiong Guo, Jan Baumbach
Integrated simultaneous analysis of different biomedical data types with exact weighted bi-cluster editing. J. Integr. Bioinform. 9 (2) (2012)
Jan Baumbach, Tobias Friedrich, Timo Kötzing, Anton Krohmer, Joachim Müller, Josch Pauling
Efficient algorithms for extracting biological key pathways with global constraints. GECCO (2012)
Richard Röttger, Ulrich Rückert, Jan Taubert, Jan Baumbach
How Little Do We Actually Know? On the Size of Gene Regulatory Networks. IEEE ACM Trans. Comput. Biol. Bioinform. 9 (5) (2012)
Richard Röttger, Christoph Kreutzer, Thuy Duong Vu, Tobias Wittkop, Jan Baumbach
Online Transitivity Clustering of Biological Data with Missing Values. GCB (2012)
Josch Pauling, Richard Röttger, Andreas Tauch, Vasco Azevedo, Jan Baumbach
CoryneRegNet 6.0 - Updated database content, new analysis methods and novel features focusing on community demands. Nucleic Acids Res. 40 (Database-Issue) (2012)
Tobias Wittkop, Sven Rahmann, Richard Röttger, Sebastian Böcker, Jan Baumbach
Extension and Robustness of Transitivity Clustering for Protein-Protein Interaction Network Analysis. Internet Math. 7 (4) (2011)
Nicolas Alcaraz, Hande Kücük, Jochen Weile, Anil Wipat, Jan Baumbach
KeyPathwayMiner: Detecting Case-Specific Biological Pathways Using Expression Data. Internet Math. 7 (4) (2011)
John H. Morris, Leonard Apeltsin, Aaron M. Newman, Jan Baumbach, Tobias Wittkop, Gang Su, Gary D. Bader, Thomas E. Ferrin
clusterMaker: a multi-algorithm clustering plugin for Cytoscape. BMC Bioinform. 12 (2011)
Tobias Wittkop, Sven Rahmann, Jan Baumbach
Efficient Online Transcription Factor Binding Site Adjustment by Integrating Transitive Graph Projection with MoRAine 2.0. J. Integr. Bioinform. 7 (3) (2010)
Dorothea Emig, Nathan Salomonis, Jan Baumbach, Thomas Lengauer, Bruce R. Conklin, Mario Albrecht
AltAnalyze and DomainGraph: analyzing and visualizing exon expression data. Nucleic Acids Res. 38 (Web-Server-Issue) (2010)
Jan Baumbach, Sven Rahmann, Andreas Tauch
Reliable transfer of transcriptional gene regulatory networks between taxonomically related organisms. BMC Syst. Biol. 3 (2009)
Jan Baumbach, Andreas Tauch, Sven Rahmann
Towards the integrated analysis, visualization and reconstruction of microbial gene regulatory networks. Briefings Bioinform. 10 (1) (2009)
Jan Baumbach, Tobias Wittkop, Jochen Weile, Thomas Kohl, Sven Rahmann
MoRAine - A web server for fast computational transcription factor binding motif re-annotation. J. Integr. Bioinform. 5 (2) (2008)
Jan Baumbach, Alexander Bunkowski, Sita Lange, Timm Oberwahrenbrock, Nils Kleinbölting, Sven Rahmann, Jörg Ingo Baumbach
IMS2 - An integrated medical software system for early lung cancer detection using ion mobility spectrometry data of human breath. J. Integr. Bioinform. 4 (3) (2007)
Tobias Wittkop, Jan Baumbach, Francisco Pereira Lobo, Sven Rahmann
Large scale clustering of protein sequences with FORCE -A layout based heuristic for weighted cluster editing. BMC Bioinform. 8 (2007)
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
CoryneCenter - An online resource for the integrated analysis of corynebacterial genome and transcriptome data. BMC Syst. Biol. 1 (2007)
Jan Baumbach
CoryneRegNet 4.0 - A reference database for corynebacterial gene regulatory networks. BMC Bioinform. 8 (2007)
Jacob Köhler, Jan Baumbach, Jan Taubert, Michael Specht, Andre Skusa, Alexander Rüegg, Christopher J. Rawlings, Paul Verrier, Stephan Philippi
Graph-based analysis and visualization of experimental results with ONDEX. Bioinform. 22 (11) (2006)
Jan Baumbach, Karina Brinkrolf, Tobias Wittkop, Andreas Tauch, Sven Rahmann
CoryneRegNet 2: An Integrative Bioinformatics Approach for Reconstruction and Comparison of Transcriptional Regulatory Networks in Prokaryotes. J. Integr. Bioinform. 3 (2) (2006)