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ORCIDJan Baumbach
Person information
- affiliation: Universität Hamburg, Germany
- affiliation (former): Saarland University, Saarbrücken, Germany
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2020 – today
- 2024
[j60]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): 122070 (2024)- [c24]Andreas Maier, 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, Sepideh Sadegh, Jan Baumbach:
NeDRex-Web: An Interactive Web Tool for Drug Repurposing by Exploring Heterogeneous Molecular Networks. BIBM 2024: 429-434 - [i11]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 abs/2407.15220 (2024) - [i10]Michael Hartung, Andreas Maier, Fernando Delgado-Chaves, Yuliya Burankova, Olga I. Isaeva, Fábio Malta de Sá Patroni, Daniel He, Casey Shannon, Katharina Kaufmann, Jens Lohmann, Alexey Savchik, Anne Hartebrodt, Zoe Chervontseva, Farzaneh Firoozbakht, Niklas Probul, Evgenia Zotova, Olga Tsoy, David B. Blumenthal, Martin Ester, Tanja Laske, Jan Baumbach, Olga I. Zolotareva:
UnPaSt: unsupervised patient stratification by differentially expressed biclusters in omics data. CoRR abs/2408.00200 (2024) - [i9]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:
Privacy-preserving federated prediction of pain intensity change based on multi-center survey data. CoRR abs/2409.07997 (2024) - [i8]Mahdie Rafiei, Supratim Das, Mohammad Bakhtiari, Ewa M. Roos, Søren T. Skou, Dorte T. Grønne, Jan Baumbach, Linda Baumbach:
Personalized Prediction Models for Changes in Knee Pain among Patients with Osteoarthritis Participating in Supervised Exercise and Education. CoRR abs/2410.12597 (2024) - [i7]Yuliya Burankova, Julian Klemm, Jens Lohmann, Ahmad Taheri, Niklas Probul, Jan Baumbach, Olga I. Zolotareva:
FedRBE - a decentralized privacy-preserving federated batch effect correction tool for omics data based on limma. CoRR abs/2412.05894 (2024) - 2023
- [j59]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) - [j58]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) - [j57]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) - [j56]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): 2-4 (2023) - [c23]Anastasia Pustozerova, Jan Baumbach, Rudolf Mayer:
Differentially Private Federated Learning: Privacy and Utility Analysis of Output Perturbation and DP-SGD. IEEE Big Data 2023: 5549-5558 - [c22]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: 45-64 - [c21]Anastasia Pustozerova, Jan Baumbach, Rudolf Mayer:
Analysing Utility Loss in Federated Learning with Differential Privacy. TrustCom 2023: 1230-1235 - 2022
- [j55]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) - [j54]Klaudia Adamowicz, Andreas Maier, Jan Baumbach, David B. Blumenthal:
Online in silico validation of disease and gene sets, clusterings or subnetworks with DIGEST. Briefings Bioinform. 23(4) (2022) - [j53]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): 1600-1606 (2022) - [j52]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): 2278-2286 (2022) - [j51]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): 4919-4926 (2022) - [j50]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) - [j49]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): 138-144 (2022) - 2021
- [j48]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): 642-663 (2021) - [j47]Olga Lazareva, Jan Baumbach, Markus List, David B. Blumenthal:
On the limits of active module identification. Briefings Bioinform. 22(5) (2021) - [j46]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): 2398-2404 (2021) - [j45]Quirin Manz, Olga Tsoy, Amit Fenn, Jan Baumbach, Uwe Völker, Markus List, Tim Kacprowski:
ASimulatoR: splice-aware RNA-Seq data simulation. Bioinform. 37(18): 3008-3010 (2021) - [j44]Justus Wolff, Josch Pauling, Andreas Keck, Jan Baumbach:
Success Factors of Artificial Intelligence Implementation in Healthcare. Frontiers Digit. Health 3: 594971 (2021) - [j43]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): D309-D318 (2021) - [j42]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): 33-41 (2021) - [j41]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): 153-163 (2021) - [j40]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): 183-191 (2021) - [c20]Reza Nasirigerdeh, Reihaneh Torkzadehmahani, Jan Baumbach, David B. Blumenthal:
On the Privacy of Federated Pipelines. SIGIR 2021: 1975-1979 - [i6]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 abs/2105.05734 (2021) - [i5]Reza Nasirigerdeh, Reihaneh Torkzadehmahani, Julian O. Matschinske, Jan Baumbach, Daniel Rueckert, Georgios Kaissis:
HyFed: A Hybrid Federated Framework for Privacy-preserving Machine Learning. CoRR abs/2105.10545 (2021) - 2020
- [j39]David B. Blumenthal, Lorenzo Viola, Markus List, Jan Baumbach, Paolo Tieri, Tim Kacprowski:
EpiGEN: an epistasis simulation pipeline. Bioinform. 36(19): 4957-4959 (2020) - [c19]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: 63-76 - [i4]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 abs/2007.11621 (2020) - [i3]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 abs/2011.07006 (2020) - [i2]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: 1239 (2020)
2010 – 2019
- 2019
- [j38]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): 1057-1062 (2019) - [j37]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): i436-i445 (2019) - [j36]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): 123 (2019) - [c18]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: 947-952 - [c17]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: 1480-1485 - 2018
- [j35]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): 4073-4078 (2018) - [j34]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): 146:1-146:15 (2018) - [c16]Jan Baumbach:
From gene panels to systems medicine. BIBM 2018: 3 - [c15]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: 1876-1883 - [c14]Jan Baumbach:
Systems Medicine - The Next Generation of Computer-assisted Precision Medicine. Bildverarbeitung für die Medizin 2018: 1 - [e1]Huiru Jane Zheng, Zoraida Callejas, David Griol, Haiying Wang, Xiaohua Hu, Harald H. H. W. Schmidt, Jan Baumbach, Julie Dickerson, Le Zhang:
IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018, Madrid, Spain, December 3-6, 2018. IEEE Computer Society 2018, ISBN 978-1-5386-5488-0 [contents] - 2017
- [j33]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): 549-551 (2017) - [j32]Eudes Barbosa, Richard Röttger, Anne-Christin Hauschild, Siomar de Castro Soares, Sebastian Böcker, Vasco Ariston de Carvalho Azevedo, Jan Baumbach:
LifeStyle-Specific-Islands (LiSSI): Integrated Bioinformatics Platform for Genomic Island Analysis. J. Integr. Bioinform. 14(2) (2017) - [j31]Simon J. Larsen, Jan Baumbach:
CytoMCS: A Multiple Maximum Common Subgraph Detection Tool for Cytoscape. J. Integr. Bioinform. 14(2) (2017) - [j30]Jesper Lund, Markus List, Jan Baumbach:
Interactive microbial distribution analysis using BioAtlas. Nucleic Acids Res. 45(Webserver-Issue): W509-W513 (2017) - 2016
- [j29]Maximilian Malek, Rashid Ibragimov, Mario Albrecht, Jan Baumbach:
CytoGEDEVO - global alignment of biological networks with Cytoscape. Bioinform. 32(8): 1259-1261 (2016) - [j28]Diogo Almeida, Vasco Ariston de Carvalho Azevedo, Artur Silva, Jan Baumbach:
PetriScape - A plugin for discrete Petri net simulations in Cytoscape. J. Integr. Bioinform. 13(1) (2016) - [j27]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) - [j26]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): W98-W104 (2016) - [c13]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: 341-348 - [i1]Nicolas Alcaraz, Markus List, Martin Dissing-Hansen, Marc Rehmsmeier, Qihua Tan, Jan Mollenhauer, Henrik J. Ditzel, Jan Baumbach:
Robust de novo pathway enrichment with KeyPathwayMiner 5. F1000Research 5: 1531 (2016) - 2015
- [j25]Jan Baumbach, Jiong Guo, Rashid Ibragimov:
Covering tree with stars. J. Comb. Optim. 29(1): 141-152 (2015) - [j24]Markus List, Michael Franz, Qihua Tan, Jan Mollenhauer, Jan Baumbach:
OpenLabNotes - An Electronic Laboratory Notebook Extension for OpenLabFramework. J. Integr. Bioinform. 12(3) (2015) - 2014
- [j23]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): 631-638 (2014) - [j22]Nicolas Alcaraz, Josch Pauling, Richa Batra, Eudes Barbosa, Alexander Junge, Anne Christensen, Vasco Ariston de Carvalho 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: 99 (2014) - [j21]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) - [j20]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) - [c12]Peng Sun, Jiong Guo, Jan Baumbach:
Complexity of Dense Bicluster Editing Problems. COCOON 2014: 154-165 - [c11]Jan Baumbach, Jiong Guo, Rashid Ibragimov:
Compactness-Preserving Mapping on Trees. CPM 2014: 162-171 - [c10]Peng Sun, Jiong Guo, Jan Baumbach:
Efficient Large-scale bicluster editing. GCB 2014: 54-60 - [c9]Eudes Barbosa, Richard Röttger, Anne-Christin Hauschild, Vasco Ariston de Carvalho Azevedo, Jan Baumbach:
On the limits of computational functional genomics for bacterial lifestyle prediction. GCB 2014: 79-84 - [c8]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: 277-284 - 2013
- [j19]Richard Röttger, Prabhav Kalaghatgi, Peng Sun, Siomar de Castro Soares, Vasco Ariston de Carvalho Azevedo, Tobias Wittkop, Jan Baumbach:
Density parameter estimation for finding clusters of homologous proteins - tracing actinobacterial pathogenicity lifestyles. Bioinform. 29(2): 215-222 (2013) - [j18]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) - [c7]Sebastian Böcker, Jan Baumbach:
Cluster Editing. CiE 2013: 33-44 - [c6]Jan Baumbach, Jiong Guo, Rashid Ibragimov:
Covering Tree with Stars. COCOON 2013: 373-384 - [c5]Rashid Ibragimov, Maximilian Malek, Jiong Guo, Jan Baumbach:
GEDEVO: An Evolutionary Graph Edit Distance Algorithm for Biological Network Alignment. GCB 2013: 68-79 - [c4]Rashid Ibragimov, Jan Martens, Jiong Guo, Jan Baumbach:
NABEECO: biological network alignment with bee colony optimization algorithm. GECCO (Companion) 2013: 43-44 - [c3]Jan Baumbach, Jiong Guo, Rashid Ibragimov:
Neighborhood-Preserving Mapping between Trees. WADS 2013: 427-438 - 2012
- [j17]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) - [j16]Josch Pauling, Richard Röttger, Andreas Tauch, Vasco Ariston de Carvalho 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): 610-614 (2012) - [j15]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): 1293-1300 (2012) - [c2]Richard Röttger, Christoph Kreutzer, Thuy Duong Vu, Tobias Wittkop, Jan Baumbach:
Online Transitivity Clustering of Biological Data with Missing Values. GCB 2012: 57-68 - [c1]Jan Baumbach, Tobias Friedrich, Timo Kötzing, Anton Krohmer, Joachim Müller, Josch Pauling:
Efficient algorithms for extracting biological key pathways with global constraints. GECCO 2012: 169-176 - 2011
- [j14]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: 436 (2011) - [j13]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): 255-273 (2011) - [j12]Nicolas Alcaraz, Hande Kücük, Jochen Weile, Anil Wipat, Jan Baumbach:
KeyPathwayMiner: Detecting Case-Specific Biological Pathways Using Expression Data. Internet Math. 7(4): 299-313 (2011) - 2010
- [j11]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) - [j10]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): 755-762 (2010)
2000 – 2009
- 2009
- [j9]Jan Baumbach, Andreas Tauch, Sven Rahmann:
Towards the integrated analysis, visualization and reconstruction of microbial gene regulatory networks. Briefings Bioinform. 10(1): 75-83 (2009) - [j8]Jan Baumbach, Sven Rahmann, Andreas Tauch:
Reliable transfer of transcriptional gene regulatory networks between taxonomically related organisms. BMC Syst. Biol. 3: 8 (2009) - 2008
- [b1]Jan Baumbach:
CoryneRegNet: a reference database and analysis platform for corynebacterial gene regulatory networks. Bielefeld University, Germany, 2008 - [j7]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) - 2007
- [j6]Jan Baumbach:
CoryneRegNet 4.0 - A reference database for corynebacterial gene regulatory networks. BMC Bioinform. 8 (2007) - [j5]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) - [j4]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: 55 (2007) - [j3]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) - 2006
- [j2]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): 1383-1390 (2006) - [j1]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)
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Unpaywalled article links
Add open access links from 
to the list of external document links (if available).
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Archived links via Wayback Machine
For web page which are no longer available, try to retrieve content from the 
of the Internet Archive (if available).
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Reference lists
Add a list of references from 
, 
, and 
to record detail pages.
load references from crossref.org and opencitations.net
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Citation data
Add a list of citing articles from and to record detail pages.
load citations from opencitations.net
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OpenAlex data
Load additional information about publications from 
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last updated on 2025-02-04 21:01 CET by the dblp team
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