Jan Baumbach

113 papers A* 1A 3B 4C 4Misc 2Journal 87Unranked 10
YearRankTypeTitle / Venue / Authors
2026 J jnl
A systematic analysis of the impact of data variation on AI-based histopathological grading of prostate cancer.
Medical Image Anal.
Patrick Fuhlert, Fabian Westhaeusser, Esther Dietrich, Maximilian Lennartz, Robin Khatri, Nico Kaiser, Pontus Röbeck, Roman David Bülow, Saskia Von Stillfried, Anja Witte, Sam Ladjevardi, Anders Drotte, Peter Severgårdh, Jan Baumbach, Victor G. Puelles, Michael Häggman, Michael Brehler, Peter Boor, Peter Walhagen, Anca Dragomir, Christer Busch, Markus Graefen, Ewert Bengtsson, Guido Sauter, Marina Zimmermann, Stefan Bonn
2026 J jnl
Detection of alternative splicing: deep sequencing or deep learning?
Briefings Bioinform.
Lena Maria Hackl, Fabian Neuhaus, Sabine Ameling, Uwe Völker, Jan Baumbach, Olga Tsoy
2026 J jnl
Farthest better or nearest worse optimizer: a novel metaheuristic algorithm.
Artif. Intell. Rev.
Ahmad Taheri, Keyvan RahimiZadeh, Jan Baumbach, Amin Beheshti, Olga I. Zolotareva, Mohammed Azmi Al-Betar, Seyedali Mirjalili, Amir H. Gandomi
2026 J jnl
On the power and limits of foundation model image embeddings for privacy-preserving federated learning.
Array
Jens Johann Georg Lohmann, Anja Witte, Andreas Maier, Christina Caroline Saak, Guido Sauter, Marina Zimmermann, Stefan Bonn, Jan Baumbach
2026 J jnl
ViMOP: a user-friendly and field-applicable pipeline for untargeted viral genome nanopore sequencing.
Bioinform.
Nils Peter Petersen, Mia Le, Annick Renevey, Ehizojie Emua, Sarah Ryter, Giuditta Annibaldis, Jacob Camara, Sanaba Boumbaly, Cyril Erameh, Tanja Laske, Jan Baumbach, Philippe Lemey, Stephan Günther, Sophie Duraffour, Liana Eleni Kafetzopoulou
2025 J jnl
A Privacy-Preserving Ecosystem for Developing Machine Learning Algorithms Using Patient Data: Insights from the TUM.ai Makeathon.
CoRR
Simon Süwer, Mai Khanh Mai, Christoph Klein, Nicola Götzenberger, Denis Dalic, Andreas Maier, Jan Baumbach
2025 J jnl
Conversational no-code and multi-agentic disease module identification and drug repurposing prediction with ChatDRex.
CoRR
Simon Süwer, Kester Bagemihl, Sylvie Baier, Lucia Dicunta, Markus List, Jan Baumbach, Andreas Maier, Fernando M. Delgado-Chaves
2025 J jnl
DRaCOon: a novel algorithm for pathway-level differential co-expression analysis in transcriptomics.
BMC Bioinform.
Fernando M. Delgado-Chaves, Ferdinand Spurny, Tanja Laske, Mhaned Oubounyt, Jan Baumbach
2025 J jnl
FTA-FTL: A Fine-Tuned Aggregation Federated Transfer Learning Scheme for Lithology Microscopic Image Classification.
CoRR
Keyvan RahimiZadeh, Ahmad Taheri, Jan Baumbach, Esmael Makarian, Abbas Dehghani, Bahman Ravaei, Bahman Javadi, Amin Beheshti
2025 J jnl
Potentials and limitations in the application of Convolutional Neural Networks for mosquito species identification using wing images.
PLoS Comput. Biol.
Kristopher Nolte, Jan Baumbach, Christian Lins, Jens Johann Georg Lohmann, Philip Kollmannsberger, Felix Gregor Sauer, Renke Lühken
2025 J jnl
Privacy-preserving multicenter differential protein abundance analysis with FedProt.
Nat. Comput. Sci.
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 F. Lichtenthaler, Axel Imhof, Matthias Mann, Christina Ludwig, Bernhard Küster, Jan Baumbach, Olga I. Zolotareva
2025 J jnl
Systematic evaluation of normalization approaches in tandem mass tag and label-free protein quantification data using PRONE.
Briefings Bioinform.
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
2025 J jnl
Transcription factor prediction using protein 3D secondary structures.
Bioinform.
Jeanine Liebold, Fabian Neuhaus, Janina Geiser, Stefan Kurtz, Jan Baumbach, Khalique Newaz
2024 J jnl
FedRBE - a decentralized privacy-preserving federated batch effect correction tool for omics data based on limma.
CoRR
Yuliya Burankova, Julian Klemm, Jens Johann Georg Lohmann, Ahmad Taheri, Niklas Probul, Jan Baumbach, Olga I. Zolotareva
2024 — conf
NeDRex-Web: An Interactive Web Tool for Drug Repurposing by Exploring Heterogeneous Molecular Networks.
BIBM
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
2024 J jnl
Partial reinforcement optimizer: An evolutionary optimization algorithm.
Expert Syst. Appl.
Ahmad Taheri, Keyvan RahimiZadeh, Amin Beheshti, Jan Baumbach, Ravipudi Venkata Rao, Seyedali Mirjalili, Amir H. Gandomi
2024 J jnl
Personalized Prediction Models for Changes in Knee Pain among Patients with Osteoarthritis Participating in Supervised Exercise and Education.
CoRR
Mahdie Rafiei, Supratim Das, Mohammad Bakhtiari, Ewa M. Roos, Søren T. Skou, Dorte T. Grønne, Jan Baumbach, Linda Baumbach
2024 J jnl
Privacy-Preserving Multi-Center Differential Protein Abundance Analysis with FedProt.
CoRR
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 F. Lichtenthaler, Axel Imhof, Matthias Mann, Christina Ludwig, Bernhard Küster, Jan Baumbach, Olga I. Zolotareva
2024 J jnl
Privacy-preserving federated prediction of pain intensity change based on multi-center survey data.
CoRR
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
2024 J jnl
UnPaSt: unsupervised patient stratification by differentially expressed biclusters in omics data.
CoRR
Michael Hartung, Andreas Maier, Fernando M. Delgado-Chaves, Yuliya Burankova, Olga I. Isaeva, Fábio Malta de Sá Patroni, Daniel He, Casey Shannon, Katharina Kaufmann, Jens Johann Georg 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
2023 B conf
Analysing Utility Loss in Federated Learning with Differential Privacy.
TrustCom
Anastasia Pustozerova, Jan Baumbach, Rudolf Mayer
2023 B conf
Differentially Private Federated Learning: Privacy and Utility Analysis of Output Perturbation and DP-SGD.
IEEE Big Data
Anastasia Pustozerova, Jan Baumbach, Rudolf Mayer
2023 J jnl
Federated machine learning in data-protection-compliant research.
Nat. Mac. Intell.
Alissa Brauneck, Louisa Schmalhorst, Mohammad Mahdi Kazemi Majdabadi, Mohammad Bakhtiari, Uwe Völker, Christina Caroline Saak, Jan Baumbach, Linda Baumbach, Gabriele Buchholtz
2023 C conf
Human-in-the-Loop Integration with Domain-Knowledge Graphs for Explainable Federated Deep Learning.
CD-MAKE
Andreas Holzinger, Anna Saranti, Anne-Christin Hauschild, Jacqueline Michelle Beinecke, Dominik Heider, Richard Röttger, Heimo Müller, Jan Baumbach, Bastian Pfeifer
2023 J jnl
Inference of differential key regulatory networks and mechanistic drug repurposing candidates from scRNA-seq data with SCANet.
Bioinform.
Mhaned Oubounyt, Lorenz Adlung, Fábio Malta de Sá Patroni, Nina Kerstin Wenke, Andreas Maier, Michael Hartung, Jan Baumbach, Maria L. Elkjaer
2023 J jnl
Online bias-aware disease module mining with ROBUST-Web.
Bioinform.
Suryadipto Sarkar, Marta Lucchetta, Andreas Maier, Mohamed M. Abdrabbou, Jan Baumbach, Markus List, Martin H. Schaefer, David B. Blumenthal
2023 J jnl
Systematic analysis of alternative splicing in time course data using Spycone.
Bioinform.
Chit Tong Lio, Gordon Grabert, Zakaria Louadi, Amit Fenn, Jan Baumbach, Tim Kacprowski, Markus List, Olga Tsoy
2023 J jnl
spongEffects: ceRNA modules offer patient-specific insights into the miRNA regulatory landscape.
Bioinform.
Fabio Boniolo, Markus Hoffmann, Norman Roggendorf, Bahar Tercan, Jan Baumbach, Mauro A. A. Castro, A. Gordon Robertson, Dieter Saur, Markus List
2022 J jnl
A systematic comparison of novel and existing differential analysis methods for CyTOF data.
Briefings Bioinform.
Lis Arend, Judith Bernett, Quirin Manz, Melissa Klug, Olga Lazareva, Jan Baumbach, Dario Bongiovanni, Markus List
2022 J jnl
Cancer driver drug interaction explorer.
Nucleic Acids Res.
Michael Hartung, Elisa Anastasi, Zeinab M. Mamdouh, Cristian Nogales, Harald H. H. W. Schmidt, Jan Baumbach, Olga I. Zolotareva, Markus List
2022 J jnl
Federated Random Forests can improve local performance of predictive models for various healthcare applications.
Bioinform.
Anne-Christin Hauschild, Marta Lemanczyk, Julian O. Matschinske, Tobias Frisch, Olga I. Zolotareva, Andreas Holzinger, Jan Baumbach, Dominik Heider
2022 J jnl
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.
Justus Wolff, Julian O. Matschinske, Dietrich Baumgart, Anne Pytlik, Andreas Keck, Arunakiry Natarajan, Claudio E. von Schacky, Josch Pauling, Jan Baumbach
2022 J jnl
Online
Briefings Bioinform.
Klaudia Adamowicz, Andreas Maier, Jan Baumbach, David B. Blumenthal
2022 J jnl
Robust disease module mining via enumeration of diverse prize-collecting Steiner trees.
Bioinform.
Judith Bernett, Dominik Krupke, Sepideh Sadegh, Jan Baumbach, Sándor P. Fekete, Tim Kacprowski, Markus List, David B. Blumenthal
2022 J jnl
dsMTL: a computational framework for privacy-preserving, distributed multi-task machine learning.
Bioinform.
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
2021 J jnl
A framework for modeling epistatic interaction.
Bioinform.
David B. Blumenthal, Jan Baumbach, Markus Hoffmann, Tim Kacprowski, Markus List
2021 J jnl
ASimulatoR: splice-aware RNA-Seq data simulation.
Bioinform.
Quirin Manz, Olga Tsoy, Amit Fenn, Jan Baumbach, Uwe Völker, Markus List, Tim Kacprowski
2021 J jnl
BiCoN: network-constrained biclustering of patients and omics data.
Bioinform.
Olga Lazareva, Stefan Canzar, Kevin Yuan, Jan Baumbach, David B. Blumenthal, Paolo Tieri, Tim Kacprowski, Markus List
2021 J jnl
Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research.
Briefings Bioinform.
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
2021 J jnl
DIGGER: exploring the functional role of alternative splicing in protein interactions.
Nucleic Acids Res.
Zakaria Louadi, Kevin Yuan, Alexander Greß, Olga Tsoy, Olga V. Kalinina, Jan Baumbach, Tim Kacprowski, Markus List
2021 J jnl
EWASex: an efficient R-package to predict sex in epigenome-wide association studies.
Bioinform.
Jesper Lund, Weilong Li, Afsaneh Mohammadnejad, Shuxia Li, Jan Baumbach, Qihua Tan
2021 J jnl
Enabling single-cell trajectory network enrichment.
Nat. Comput. Sci.
Alexander G. B. Grønning, Mhaned Oubounyt, Kristiyan Kanev, Jesper Lund, Tim Kacprowski, Dietmar Zehn, Richard Röttger, Jan Baumbach
2021 J jnl
HyFed: A Hybrid Federated Framework for Privacy-preserving Machine Learning.
CoRR
Reza Nasirigerdeh, Reihaneh Torkzadehmahani, Julian O. Matschinske, Jan Baumbach, Daniel Rueckert, Georgios Kaissis
2021 J jnl
Lessons from the COVID-19 pandemic for advancing computational drug repurposing strategies.
Nat. Comput. Sci.
Gihanna Galindez, Julian O. Matschinske, Tim D. Rose, Sepideh Sadegh, Marisol Salgado-Albarrán, Julian Späth, Jan Baumbach, Josch Konstantin Pauling
2021 J jnl
Machine learning for deciphering cell heterogeneity and gene regulation.
Nat. Comput. Sci.
Michael Scherer, Florian Schmidt, Olga Lazareva, Jörn Walter, Jan Baumbach, Marcel H. Schulz, Markus List
2021 A* conf
On the Privacy of Federated Pipelines.
SIGIR
Reza Nasirigerdeh, Reihaneh Torkzadehmahani, Jan Baumbach, David B. Blumenthal
2021 J jnl
On the limits of active module identification.
Briefings Bioinform.
Olga Lazareva, Jan Baumbach, Markus List, David B. Blumenthal
2021 J jnl
Success Factors of Artificial Intelligence Implementation in Healthcare.
Frontiers Digit. Health
Justus Wolff, Josch Pauling, Andreas Keck, Jan Baumbach
2021 J jnl
The FeatureCloud AI Store for Federated Learning in Biomedicine and Beyond.
CoRR
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
2020 J jnl
EpiGEN: an epistasis simulation pipeline.
Bioinform.
David B. Blumenthal, Lorenzo Viola, Markus List, Jan Baumbach, Paolo Tieri, Tim Kacprowski
2020 J jnl
Federated Multi-Mini-Batch: An Efficient Training Approach to Federated Learning in Non-IID Environments.
CoRR
Mohammad Bakhtiari, Reza Nasirigerdeh, Reihaneh Torkzadehmahani, Amirhossein Bayat, David B. Blumenthal, Markus List, Jan Baumbach
2020 — conf
GANNSTER: Graph-Augmented Neural Network Spatio-Temporal Reasoner for Traffic Forecasting.
AALTD@PKDD/ECML
Carlos Salort Sánchez, Alexander Wieder, Paolo Sottovia, Stefano Bortoli, Jan Baumbach, Cristian Axenie
2020 J jnl
Privacy-preserving Artificial Intelligence Techniques in Biomedicine.
CoRR
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
2020 J jnl
netDx: Software for building interpretable patient classifiers by multi-'omic data integration using patient similarity networks.
F1000Research
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
2019 C conf
An Online Incremental Clustering Framework for Real-Time Stream Analytics.
ICMLA
Carlos Salort Sánchez, Radu Tudoran, Mohamad Al Hajj Hassan, Stefano Bortoli, Goetz Brasche, Jan Baumbach, Cristian Axenie
2019 J jnl
Community effort endorsing multiscale modelling, multiscale data science and multiscale computing for systems medicine.
Briefings Bioinform.
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
2019 J jnl
Comprehensive evaluation of transcriptome-based cell-type quantification methods for immuno-oncology.
Bioinform.
Gregor Sturm, Francesca Finotello, Florent Petitprez, Jitao David Zhang, Jan Baumbach, Wolf-Herman Fridman, Markus List, Tatsiana Aneichyk
2019 C conf
Fuzzy Inference System for Risk Evaluation in Gestational Diabetes Mellitus.
BIBE
Carlos Salort Sánchez, Suzanne Smyth, Elizabeth Tully, Joanna Griffin, Luke Heaphy, Niamh Redmond, Fionnuala Breathnach, Jan Baumbach, Cristian Axenie
2019 J jnl
PanRV: Pangenome-reverse vaccinology approach for identifications of potential vaccine candidates in microbial pangenome.
BMC Bioinform.
Kanwal Naz, Anam Naz, Shifa Tariq Ashraf, Muhammad Rizwan, Jamil Ahmad, Jan Baumbach, Amjad Ali
2018 — conf
From gene panels to systems medicine.
BIBM
Jan Baumbach
2018 — ed.
IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018, Madrid, Spain, December 3-6, 2018
BIBM
Huiru Jane Zheng, Zoraida Callejas, David Griol, Haiying Wang, Xiaohua Hu, Harald H. H. W. Schmidt, Jan Baumbach, Julie Dickerson, Le Zhang
2018 J jnl
On the power of epigenome-wide association studies using a disease-discordant twin design.
Bioinform.
Weilong Li, Lene Christiansen, Jacob v. B. Hjelmborg, Jan Baumbach, Qihua Tan
2018 J jnl
Parameter estimation of qualitative biological regulatory networks on high performance computing hardware.
BMC Syst. Biol.
Muhammad Tariq Saeed, Jamil Ahmad, Jan Baumbach, Josch Pauling, Aamir Shafi, Rehan Zafar Paracha, Asad Hayat, Amjad Ali
2018 — conf
Systems Medicine - The Next Generation of Computer-assisted Precision Medicine.
Bildverarbeitung für die Medizin
Jan Baumbach
2018 — conf
Weighted gene co-expression network analysis of microarray mRNA expression profiling in response to electroacupuncture.
BIBM
Afsaneh Mohammadnejad, Shuxia Li, Hongmei Duan, Jesper Lund, Weilong Li, Jan Baumbach, Qihua Tan
2017 J jnl
CytoMCS: A Multiple Maximum Common Subgraph Detection Tool for Cytoscape.
J. Integr. Bioinform.
Simon J. Larsen, Jan Baumbach
2017 J jnl
Efficient detection of differentially methylated regions using DiMmeR.
Bioinform.
Diogo Almeida, Ida Skov, Artur Silva, Fabio Vandin, Qihua Tan, Richard Röttger, Jan Baumbach
2017 J jnl
Interactive microbial distribution analysis using BioAtlas.
Nucleic Acids Res.
Jesper Lund, Markus List, Jan Baumbach
2017 J jnl
LifeStyle-Specific-Islands (LiSSI): Integrated Bioinformatics Platform for Genomic Island Analysis.
J. Integr. Bioinform.
Eudes Barbosa, Richard Röttger, Anne-Christin Hauschild, Siomar de Castro Soares, Sebastian Böcker, Vasco Ariston de Carvalho Azevedo, Jan Baumbach
2016 A conf
A Simulated Annealing Algorithm for Maximum Common Edge Subgraph Detection in Biological Networks.
GECCO
Simon J. Larsen, Frederik G. Alkærsig, Henrik J. Ditzel, Igor Jurisica, Nicolas Alcaraz, Jan Baumbach
2016 J jnl
CytoGEDEVO - global alignment of biological networks with Cytoscape.
Bioinform.
Maximilian Malek, Rashid Ibragimov, Mario Albrecht, Jan Baumbach
2016 J jnl
Jllumina - A comprehensive Java-based API for statistical Illumina Infinium HumanMethylation450 and MethylationEPIC data processing.
J. Integr. Bioinform.
Diogo Almeida, Ida Skov, Jesper Lund, Afsaneh Mohammadnejad, Artur Silva, Fabio Vandin, Qihua Tan, Jan Baumbach, Richard Röttger
2016 J jnl
KeyPathwayMinerWeb: online multi-omics network enrichment.
Nucleic Acids Res.
Markus List, Nicolas Alcaraz, Martin Dissing-Hansen, Henrik J. Ditzel, Jan Mollenhauer, Jan Baumbach
2016 J jnl
PetriScape - A plugin for discrete Petri net simulations in Cytoscape.
J. Integr. Bioinform.
Diogo Almeida, Vasco Ariston de Carvalho Azevedo, Artur Silva, Jan Baumbach
2016 J jnl
Robust
F1000Research
Nicolas Alcaraz, Markus List, Martin Dissing-Hansen, Marc Rehmsmeier, Qihua Tan, Jan Mollenhauer, Henrik J. Ditzel, Jan Baumbach
2015 J jnl
Covering tree with stars.
J. Comb. Optim.
Jan Baumbach, Jiong Guo, Rashid Ibragimov
2015 J jnl
OpenLabNotes - An Electronic Laboratory Notebook Extension for OpenLabFramework.
J. Integr. Bioinform.
Markus List, Michael Franz, Qihua Tan, Jan Mollenhauer, Jan Baumbach
2014 J jnl
BacillusRegNet: A transcriptional regulation database and analysis platform for Bacillus species.
J. Integr. Bioinform.
Goksel Misirli, Jennifer Hallinan, Richard Röttger, Jan Baumbach, Anil Wipat
2014 J jnl
Classification of Breast Cancer Subtypes by combining Gene Expression and DNA Methylation Data.
J. Integr. Bioinform.
Markus List, Anne-Christin Hauschild, Qihua Tan, Torben Arvid Kruse, Jan Mollenhauer, Jan Baumbach, Richa Batra
2014 B conf
Compactness-Preserving Mapping on Trees.
CPM
Jan Baumbach, Jiong Guo, Rashid Ibragimov
2014 Misc conf
Complexity of Dense Bicluster Editing Problems.
COCOON
Peng Sun, Jiong Guo, Jan Baumbach
2014 — conf
Efficient Large-scale bicluster editing.
GCB
Peng Sun, Jiong Guo, Jan Baumbach
2014 J jnl
KeyPathwayMiner 4.0: condition-specific pathway analysis by combining multiple omics studies and networks with Cytoscape.
BMC Syst. Biol.
Nicolas Alcaraz, Josch Pauling, Richa Batra, Eudes Barbosa, Alexander Junge, Anne Christensen, Vasco Ariston de Carvalho Azevedo, Henrik J. Ditzel, Jan Baumbach
2014 J jnl
Microarray R-based analysis of complex lysate experiments with MIRACLE.
Bioinform.
Markus List, Ines Block, Marlene Lemvig Pedersen, Helle Christiansen, Steffen Schmidt, Mads Thomassen, Qihua Tan, Jan Baumbach, Jan Mollenhauer
2014 A conf
Multiple graph edit distance: simultaneous topological alignment of multiple protein-protein interaction networks with an evolutionary algorithm.
GECCO
Rashid Ibragimov, Maximilian Malek, Jan Baumbach, Jiong Guo
2014 — conf
On the limits of computational functional genomics for bacterial lifestyle prediction.
GCB
Eudes Barbosa, Richard Röttger, Anne-Christin Hauschild, Vasco Ariston de Carvalho Azevedo, Jan Baumbach
2013 J jnl
An Integrative Clinical Database and Diagnostics Platform for Biomarker Identification and Analysis in Ion Mobility Spectra of Human Exhaled Air.
J. Integr. Bioinform.
Till Schneider, Anne-Christin Hauschild, Jörg Ingo Baumbach, Jan Baumbach
2013 C conf
Cluster Editing.
CiE
Sebastian Böcker, Jan Baumbach
2013 Misc conf
Covering Tree with Stars.
COCOON
Jan Baumbach, Jiong Guo, Rashid Ibragimov
2013 J jnl
Density parameter estimation for finding clusters of homologous proteins - tracing actinobacterial pathogenicity lifestyles.
Bioinform.
Richard Röttger, Prabhav Kalaghatgi, Peng Sun, Siomar de Castro Soares, Vasco Ariston de Carvalho Azevedo, Tobias Wittkop, Jan Baumbach
2013 — conf
GEDEVO: An Evolutionary Graph Edit Distance Algorithm for Biological Network Alignment.
GCB
Rashid Ibragimov, Maximilian Malek, Jiong Guo, Jan Baumbach
2013 — conf
NABEECO: biological network alignment with bee colony optimization algorithm.
GECCO (Companion)
Rashid Ibragimov, Jan Martens, Jiong Guo, Jan Baumbach
2013 B conf
Neighborhood-Preserving Mapping between Trees.
WADS
Jan Baumbach, Jiong Guo, Rashid Ibragimov
2012 J jnl
CoryneRegNet 6.0 - Updated database content, new analysis methods and novel features focusing on community demands.
Nucleic Acids Res.
Josch Pauling, Richard Röttger, Andreas Tauch, Vasco Ariston de Carvalho Azevedo, Jan Baumbach
2012 A conf
Efficient algorithms for extracting biological key pathways with global constraints.
GECCO
Jan Baumbach, Tobias Friedrich, Timo Kötzing, Anton Krohmer, Joachim Müller, Josch Pauling
2012 J jnl
How Little Do We Actually Know? On the Size of Gene Regulatory Networks.
IEEE ACM Trans. Comput. Biol. Bioinform.
Richard Röttger, Ulrich Rückert, Jan Taubert, Jan Baumbach
2012 J jnl
Integrated simultaneous analysis of different biomedical data types with exact weighted bi-cluster editing.
J. Integr. Bioinform.
Peng Sun, Jiong Guo, Jan Baumbach
2012 — conf
Online Transitivity Clustering of Biological Data with Missing Values.
GCB
Richard Röttger, Christoph Kreutzer, Thuy Duong Vu, Tobias Wittkop, Jan Baumbach
2011 J jnl
Extension and Robustness of Transitivity Clustering for Protein-Protein Interaction Network Analysis.
Internet Math.
Tobias Wittkop, Sven Rahmann, Richard Röttger, Sebastian Böcker, Jan Baumbach
2011 J jnl
KeyPathwayMiner: Detecting Case-Specific Biological Pathways Using Expression Data.
Internet Math.
Nicolas Alcaraz, Hande Kücük, Jochen Weile, Anil Wipat, Jan Baumbach
2011 J jnl
clusterMaker: a multi-algorithm clustering plugin for Cytoscape.
BMC Bioinform.
John H. Morris, Leonard Apeltsin, Aaron M. Newman, Jan Baumbach, Tobias Wittkop, Gang Su, Gary D. Bader, Thomas E. Ferrin
2010 J jnl
AltAnalyze and DomainGraph: analyzing and visualizing exon expression data.
Nucleic Acids Res.
Dorothea Emig, Nathan Salomonis, Jan Baumbach, Thomas Lengauer, Bruce R. Conklin, Mario Albrecht
2010 J jnl
Efficient Online Transcription Factor Binding Site Adjustment by Integrating Transitive Graph Projection with MoRAine 2.0.
J. Integr. Bioinform.
Tobias Wittkop, Sven Rahmann, Jan Baumbach
2009 J jnl
Reliable transfer of transcriptional gene regulatory networks between taxonomically related organisms.
BMC Syst. Biol.
Jan Baumbach, Sven Rahmann, Andreas Tauch
2009 J jnl
Towards the integrated analysis, visualization and reconstruction of microbial gene regulatory networks.
Briefings Bioinform.
Jan Baumbach, Andreas Tauch, Sven Rahmann
2008 — —
CoryneRegNet: a reference database and analysis platform for corynebacterial gene regulatory networks
Jan Baumbach
2008 J jnl
MoRAine - A web server for fast computational transcription factor binding motif re-annotation.
J. Integr. Bioinform.
Jan Baumbach, Tobias Wittkop, Jochen Weile, Thomas Kohl, Sven Rahmann
2007 J jnl
CoryneCenter - An online resource for the integrated analysis of corynebacterial genome and transcriptome data.
BMC Syst. Biol.
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
2007 J jnl
CoryneRegNet 4.0 - A reference database for corynebacterial gene regulatory networks.
BMC Bioinform.
Jan Baumbach
2007 J jnl
IMS2 - An integrated medical software system for early lung cancer detection using ion mobility spectrometry data of human breath.
J. Integr. Bioinform.
Jan Baumbach, Alexander Bunkowski, Sita Lange, Timm Oberwahrenbrock, Nils Kleinbölting, Sven Rahmann, Jörg Ingo Baumbach
2007 J jnl
Large scale clustering of protein sequences with FORCE -A layout based heuristic for weighted cluster editing.
BMC Bioinform.
Tobias Wittkop, Jan Baumbach, Francisco Pereira Lobo, Sven Rahmann
2006 J jnl
CoryneRegNet 2: An Integrative Bioinformatics Approach for Reconstruction and Comparison of Transcriptional Regulatory Networks in Prokaryotes.
J. Integr. Bioinform.
Jan Baumbach, Karina Brinkrolf, Tobias Wittkop, Andreas Tauch, Sven Rahmann
2006 J jnl
Graph-based analysis and visualization of experimental results with ONDEX.
Bioinform.
Jacob Köhler, Jan Baumbach, Jan Taubert, Michael Specht, Andre Skusa, Alexander Rüegg, Christopher J. Rawlings, Paul Verrier, Stephan Philippi