Jan Baumbach

According to our database, Jan Baumbach authored at least 93 papers between 2006 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

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., March, 2024

Personalized Prediction Models for Changes in Knee Pain among Patients with Osteoarthritis Participating in Supervised Exercise and Education.

M. Rafiei, Supratim Das, Mohammad Bakhtiari, Ewa M. Roos, Søren T. Skou, Dorte T. Grønne, Jan Baumbach, Linda Baumbach

CoRR, 2024

Privacy-preserving federated prediction of pain intensity change based on multi-center survey data.

Supratim Das, Mahdie Rafie, 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

UnPaSt: unsupervised patient stratification by differentially expressed biclusters in omics data.

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

CoRR, 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, 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

CoRR, 2024

2023

Inference of differential key regulatory networks and mechanistic drug repurposing candidates from scRNA-seq data with SCANet.

Mhaned Oubounyt, Lorenz Adlung, Fabio Patroni, Nina Kerstin Wenke, Andreas Maier, Michael Hartung, Jan Baumbach, Maria L. Elkjaer

Bioinform., October, 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., May, 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., January, 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., January, 2023

Analysing Utility Loss in Federated Learning with Differential Privacy.

Anastasia Pustozerova, Jan Baumbach, Rudolf Mayer

Proceedings of the 22nd IEEE International Conference on Trust, 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

Proceedings of the Machine Learning and Knowledge Extraction, 2023

Differentially Private Federated Learning: Privacy and Utility Analysis of Output Perturbation and DP-SGD.

Anastasia Pustozerova, Jan Baumbach, Rudolf Mayer

Proceedings of the IEEE International Conference on Big Data, 2023

2022

dsMTL: a computational framework for privacy-preserving, distributed multi-task machine learning.

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

Bioinform., October, 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

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

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

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

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

Online <i>in silico</i> validation of disease and gene sets, clusterings or subnetworks with DIGEST.

Klaudia Adamowicz, Andreas Maier, Jan Baumbach, David B. Blumenthal

Briefings Bioinform., 2022

2021

Machine learning for deciphering cell heterogeneity and gene regulation.

Michael Scherer, Florian Schmidt, Olga Lazareva, Jörn Walter, Jan Baumbach, Marcel H. Schulz, Markus List

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

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

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

Success Factors of Artificial Intelligence Implementation in Healthcare.

Justus Wolff, Josch Pauling, Andreas Keck, Jan Baumbach

Frontiers Digit. Health, 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

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, 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

CoRR, 2021

ASimulatoR: splice-aware RNA-Seq data simulation.

Quirin Manz, Olga Tsoy, Amit Fenn, Jan Baumbach, Uwe Völker, Markus List, Tim Kacprowski

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

On the limits of active module identification.

Olga Lazareva, Jan Baumbach, Markus List, David B. Blumenthal

Briefings Bioinform., 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, 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

Briefings Bioinform., 2021

On the Privacy of Federated Pipelines.

Reza Nasirigerdeh, Reihaneh Torkzadehmahani, Jan Baumbach, David B. Blumenthal

Proceedings of the SIGIR '21: The 44th International ACM SIGIR Conference on Research and Development in Information Retrieval, 2021

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

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

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, 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

CoRR, 2020

EpiGEN: an epistasis simulation pipeline.

David B. Blumenthal, Lorenzo Viola, Markus List, Jan Baumbach, Paolo Tieri, Tim Kacprowski

Bioinform., 2020

GANNSTER: Graph-Augmented Neural Network Spatio-Temporal Reasoner for Traffic Forecasting.

Carlos Salort Sánchez, Alexander Wieder, Paolo Sottovia, Stefano Bortoli, Jan Baumbach, Cristian Axenie

Proceedings of the Advanced Analytics and Learning on Temporal Data, 2020

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

BMC Bioinform., December, 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

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, Peter Klimek, Natasa Debeljak, Damjana Rozman, Harald H. H. W. Schmidt

Briefings Bioinform., 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

Proceedings of the 18th IEEE International Conference On Machine Learning And Applications, 2019

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

Proceedings of the 19th IEEE International Conference on Bioinformatics and Bioengineering, 2019

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

BMC Syst. Biol., 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

Systems Medicine - The Next Generation of Computer-assisted Precision Medicine.

Jan Baumbach

Proceedings of the Bildverarbeitung für die Medizin 2018 - Algorithmen - Systeme, 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

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2018

From gene panels to systems medicine.

Jan Baumbach

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2018

2017

Interactive microbial distribution analysis using BioAtlas.

Jesper Lund, Markus List, Jan Baumbach

Nucleic Acids Res., 2017

CytoMCS: A Multiple Maximum Common Subgraph Detection Tool for Cytoscape.

Simon J. Larsen, Jan Baumbach

J. Integr. 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

Efficient detection of differentially methylated regions using DiMmeR.

Diogo Almeida, Ida Skov, Artur Silva, Fabio Vandin, Qihua Tan, Richard Röttger, Jan Baumbach

Bioinform., 2017

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

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

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

Robust<i> de novo</i> pathway enrichment with <i>KeyPathwayMiner 5</i>.

Nicolas Alcaraz, Markus List, Martin Dissing-Hansen, Marc Rehmsmeier, Qihua Tan, Jan Mollenhauer, Henrik J. Ditzel, Jan Baumbach

F1000Research, 2016

CytoGEDEVO - global alignment of biological networks with Cytoscape.

Maximilian Malek, Rashid Ibragimov, Mario Albrecht, Jan Baumbach

Bioinform., 2016

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

Proceedings of the 2016 on Genetic and Evolutionary Computation Conference, Denver, CO, USA, July 20, 2016

2015

OpenLabNotes - An Electronic Laboratory Notebook Extension for OpenLabFramework.

Markus List, Michael Franz, Qihua Tan, Jan Mollenhauer, Jan Baumbach

J. Integr. Bioinform., 2015

Covering tree with stars.

Jan Baumbach, Jiong Guo, Rashid Ibragimov

J. Comb. Optim., 2015

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

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

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

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

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

Proceedings of the Genetic and Evolutionary Computation Conference, 2014

Efficient Large-scale bicluster editing.

Peng Sun, Jiong Guo, Jan Baumbach

Proceedings of the German conference on bioinformatics 2014, September 28, 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

Proceedings of the German conference on bioinformatics 2014, September 28, 2014

Compactness-Preserving Mapping on Trees.

Jan Baumbach, Jiong Guo, Rashid Ibragimov

Proceedings of the Combinatorial Pattern Matching - 25th Annual Symposium, 2014

Complexity of Dense Bicluster Editing Problems.

Peng Sun, Jiong Guo, Jan Baumbach

Proceedings of the Computing and Combinatorics - 20th International Conference, 2014

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

Density parameter estimation for finding clusters of homologous proteins - tracing actinobacterial pathogenicity lifestyles.

Richard Röttger, Prabhav Kalaghatgi, Peng Sun, Siomar de Castro Soares, Vasco Ariston de Carvalho Azevedo, Tobias Wittkop, Jan Baumbach

Bioinform., 2013

Neighborhood-Preserving Mapping between Trees.

Jan Baumbach, Jiong Guo, Rashid Ibragimov

Proceedings of the Algorithms and Data Structures - 13th International Symposium, 2013

NABEECO: biological network alignment with bee colony optimization algorithm.

Rashid Ibragimov, Jan Martens, Jiong Guo, Jan Baumbach

Proceedings of the Genetic and Evolutionary Computation Conference, 2013

GEDEVO: An Evolutionary Graph Edit Distance Algorithm for Biological Network Alignment.

Rashid Ibragimov, Maximilian Malek, Jiong Guo, Jan Baumbach

Proceedings of the German Conference on Bioinformatics 2013, 2013

Cluster Editing.

Sebastian Böcker, Jan Baumbach

Proceedings of the Nature of Computation. Logic, Algorithms, Applications, 2013

2012

How Little Do We Actually Know? On the Size of Gene Regulatory Networks.

Richard Röttger, Ulrich Rückert, Jan Taubert, Jan Baumbach

IEEE ACM Trans. Comput. Biol. 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

Integrated simultaneous analysis of different biomedical data types with exact weighted bi-cluster editing.

Peng Sun, Jiong Guo, Jan Baumbach

J. Integr. Bioinform., 2012

Efficient algorithms for extracting biological key pathways with global constraints.

Jan Baumbach, Tobias Friedrich, Timo Kötzing, Anton Krohmer, Joachim Müller, Josch Pauling

Proceedings of the Genetic and Evolutionary Computation Conference, 2012

Online Transitivity Clustering of Biological Data with Missing Values.

Richard Röttger, Christoph Kreutzer, Thuy Duong Vu, Tobias Wittkop, Jan Baumbach

Proceedings of the German Conference on Bioinformatics 2012, 2012

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

KeyPathwayMiner: Detecting Case-Specific Biological Pathways Using Expression Data.

Nicolas Alcaraz, Hande Kücük, Jochen Weile, Anil Wipat, Jan Baumbach

Internet Math., 2011

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

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

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

2009

Reliable transfer of transcriptional gene regulatory networks between taxonomically related organisms.

Jan Baumbach, Sven Rahmann, Andreas Tauch

BMC Syst. Biol., 2009

Towards the integrated analysis, visualization and reconstruction of microbial gene regulatory networks.

Jan Baumbach, Andreas Tauch, Sven Rahmann

Briefings Bioinform., 2009

2008

CoryneRegNet: a reference database and analysis platform for corynebacterial gene regulatory networks

Jan Baumbach

PhD thesis, 2008

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

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

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

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

CoryneRegNet 4.0 - A reference database for corynebacterial gene regulatory networks.

Jan Baumbach

BMC Bioinform., 2007

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

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