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List of works by Jan Baumbach

A case-only genome-wide association study on gene-sex interaction in allergic rhinitis

article

A framework for modeling epistatic interaction

scientific article published on 30 November 2020

A genome-wide cis-regulatory element discovery method based on promoter sequences and gene co-expression networks

scientific article

A global network for network medicine

scientific article published on 31 August 2020

A singular value decomposition approach for improved taxonomic classification of biological sequences

scientific article

A systematic review of breath analysis and detection of volatile organic compounds in COPD.

scientific article published on 31 August 2016

Age-dependent DNA methylation patterns on the Y chromosome in elderly males

scientific article published on 21 February 2019

AltAnalyze and DomainGraph: analyzing and visualizing exon expression data

scientific article

An Early Stage Researcher's Primer on Systems Medicine Terminology

publication published on 25 February 2021

An Integrative Clinical Database and Diagnostics Platform for Biomarker Identification and Analysis in Ion Mobility Spectra of Human Exhaled Air.

scientific article published in June 2013

An integrative clinical database and diagnostics platform for biomarker identification and analysis in ion mobility spectra of human exhaled air.

scientific article published on 2 April 2013

An integrative in-silico approach for therapeutic target identification in the human pathogen Corynebacterium diphtheriae

scientific article published on 19 October 2017

Analysis of quality raw data of second generation sequencers with Quality Assessment Software ⬇️

scientific article

Analysis of the airway microbiota of healthy individuals and patients with chronic obstructive pulmonary disease by T-RFLP and clone sequencing

scientific article

Arrhythmic Gut Microbiome Signatures Predict Risk of Type 2 Diabetes

scientific article published on 29 June 2020

Author Correction: Osteogenesis depends on commissioning of a network of stem cell transcription factors that act as repressors of adipogenesis

scientific article published on 01 April 2019

BALSAM-An Interactive Online Platform for Breath Analysis, Visualization and Classification

scientific article published on 02 October 2020

BacillusRegNet: A transcriptional regulation database and analysis platform for Bacillus species

scientific article published in June 2014

BacillusRegNet: a transcriptional regulation database and analysis platform for Bacillus species

scientific article published on 8 July 2014

Bi-Force: large-scale bicluster editing and its application to gene expression data biclustering

scientific article

BiCluE - Exact and heuristic algorithms for weighted bi-cluster editing of biomedical data.

scientific article

BiCoN: Network-constrained biclustering of patients and omics data

scientific article published on 26 December 2020

CMRegNet-An interspecies reference database for corynebacterial and mycobacterial regulatory networks

scientific article published on 11 June 2015

CSF proteome in multiple sclerosis subtypes related to brain lesion transcriptomes

scientific article published on 18 February 2021

CTCFL regulates the PI3K-Akt pathway and it is a target for personalized ovarian cancer therapy

scientific article published on 07 February 2022

Carotta: Revealing Hidden Confounder Markers in Metabolic Breath Profiles

scientific article published on 10 June 2015

Classification of Breast Cancer Subtypes by combining Gene Expression and DNA Methylation Data

scientific article published in June 2014

Classification of breast cancer subtypes by combining gene expression and DNA methylation data.

scientific article

Cluster Editing

CoNVaQ: a web tool for copy number variation-based association studies.

scientific article published on 18 May 2018

Community effort endorsing multiscale modelling, multiscale data science and multiscale computing for systems medicine.

scientific article published on 5 December 2017

Compactness-Preserving Mapping on Trees

Comparative transcriptome analysis reveals key epigenetic targets in SARS-CoV-2 infection

scientific article

Comparing the performance of biomedical clustering methods.

scientific article published on 21 September 2015

Complexity of Dense Bicluster Editing Problems

Comprehensive Analysis of DNA Methylation and Prediction of Response to NeoadjuvantTherapy in Locally Advanced Rectal Cancer

scientific article published on 22 October 2020

Comprehensive analysis of high-throughput screens with HiTSeekR

scientific article

Comprehensive cluster analysis with Transitivity Clustering

scientific article published on 10 February 2011

Comprehensive evaluation of computational cell-type quantification methods for immuno-oncology

Comprehensive evaluation of transcriptome-based cell-type quantification methods for immuno-oncology

scientific article published on 01 July 2019

Computational Integrative Biology--on the joint analysis of diverse biological data sets

scientific article

Computational Strategies to Combat COVID-19: Useful Tools to Accelerate SARS-CoV-2 and Coronavirus Research

scientific article published on 23 May 2020

Computational methods for metabolomic data analysis of ion mobility spectrometry data-reviewing the state of the art.

scientific article

Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research

scientific article published on 04 November 2020

Consensus draft of the native mouse podocyte-ome

scientific article published in 2022

Conserved host-pathogen PPIs. Globally conserved inter-species bacterial PPIs based conserved host-pathogen interactome derived novel target in C. pseudotuberculosis, C. diphtheriae, M. tuberculosis, C. ulcerans, Y. pestis, and E. coli targeted by P

scientific article published on March 2013

CoryneCenter - an online resource for the integrated analysis of corynebacterial genome and transcriptome data

scientific article

CoryneRegNet 3.0--an interactive systems biology platform for the analysis of gene regulatory networks in corynebacteria and Escherichia coli.

scientific article published on 20 December 2006

CoryneRegNet 4.0 - A reference database for corynebacterial gene regulatory networks

scientific article

CoryneRegNet 6.0--Updated database content, new analysis methods and novel features focusing on community demands.

scientific article

CoryneRegNet 7, the reference database and analysis platform for corynebacterial gene regulatory networks

scientific article published on 11 May 2020

CoryneRegNet: an ontology-based data warehouse of corynebacterial transcription factors and regulatory networks

scientific article

Covering Tree with Stars

Covering tree with stars

Current breathomics--a review on data pre-processing techniques and machine learning in metabolomics breath analysis

scientific article

CytoGEDEVO-global alignment of biological networks with Cytoscape.

scientific article published on 14 December 2015

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

scientific article

DIGGER: exploring the functional role of alternative splicing in protein interactions

scientific article published on 25 September 2020

DNA methylome profiling in identical twin pairs discordant for body mass index

scientific article published on 31 May 2019

DNA methylome profiling of all-cause mortality in comparison with age-associated methylation patterns

scientific article published on 08 February 2019

De novo pathway-based biomarker identification.

scientific article published in September 2017

DeepCLIP: predicting the effect of mutations on protein-RNA binding with deep learning

scientific article published on 19 June 2020

Democratising Knowledge Representation with BioCypher

scientific article published on 27 December 2022

Democratizing knowledge representation with BioCypher

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

scientific article published on 9 November 2012

DiMmer: Discovery of Differentially Methylated Regions in Epigenome-Wide Association Study (EWAS) Data

scientific article published on 01 January 2018

Differential long noncoding RNA profiling of BMI in twins

scientific article published on 09 September 2020

Differentially Methylated Genomic Regions in Birth-Weight Discordant Twin Pairs.

scientific article published on February 2016

Drug repurposing by integrated literature mining and drug-gene-disease triangulation

scientific article published on 22 October 2016

Drugst.One — a plug-and-play solution for online systems medicine and network-based drug repurposing

scientific article published in 2024

Dynamic biclustering of microarray data by multi-objective immune optimization

scientific article

E. coli gene regulatory networks are inconsistent with gene expression data

article

EWASex: an efficient R-package to predict sex in epigenome-wide association studies

scientific article published on 11 December 2020

EXACT AND HEURISTIC ALGORITHMS FOR WEIGHTED CLUSTER EDITING

scholarly article published September 2007

Efficient Management of High-Throughput Screening Libraries with SAVANAH

Efficient algorithms for extracting biological key pathways with global constraints

Efficient detection of differentially methylated regions using DiMmeR.

scientific article

Efficient key pathway mining: combining networks and OMICS data

scientific article

Efficient online transcription factor binding site adjustment by integrating transitive graph projection with MoRAine 2.0.

scientific article published on 25 March 2010

Efficient sample tracking with OpenLabFramework

scientific article

Elucidation of Altered Pathways in Tumor-Initiating Cells of Triple-Negative Breast Cancer: A Useful Cell Model System for Drug Screening

scientific article published on 10 June 2017

Elucidation of epithelial-mesenchymal transition-related pathways in a triple-negative breast cancer cell line model by multi-omics interactome analysis.

scientific article published on November 2014

Enriched power of disease-concordant twin-case-only design in detecting interactions in genome-wide association studies

scientific article published on 18 January 2019

EpiGEN: an epistasis simulation pipeline

scientific article published on 14 April 2020

Evidence for reductive genome evolution and lateral acquisition of virulence functions in two Corynebacterium pseudotuberculosis strains

scientific article

Exact and heuristic algorithms for weighted cluster editing

scientific article published in January 2007

Exploratory analysis of age and sex dependent DNA methylation patterns on the X-chromosome in whole blood samples

scientific article published on 28 April 2020

Exploring the SARS-CoV-2 virus-host-drug interactome for drug repurposing

scientific article published on 14 July 2020

Extension and Robustness of Transitivity Clustering for Protein–Protein Interaction Network Analysis

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

scientific article published in 2022

Flimma: a federated and privacy-aware tool for differential gene expression analysis

scientific article published on 14 December 2021

From Corynebacterium glutamicum to Mycobacterium tuberculosis--towards transfers of gene regulatory networks and integrated data analyses with MycoRegNet

scientific article

From single drug targets to synergistic network pharmacology in ischemic stroke

scientific article published on 20 March 2019

GIPSy: Genomic island prediction software.

scientific article published on 12 September 2015

Generalized correlation coefficient for genome-wide association analysis of cognitive ability in twins

scientific article published on 24 November 2020

Genomic profiling in ovarian cancer retreated with platinum based chemotherapy presented homologous recombination deficiency and copy number imbalances of CCNE1 and RB1 genes

article

Global Gene Expression Profiling and Transcription Factor Network Analysis of Cognitive Aging in Monozygotic Twins

scientific article published on 14 June 2021

Graph-based analysis and visualization of experimental results with ONDEX

scientific article

Guiding biomedical clustering with ClustEval

scientific article published on 24 May 2018

High-resolution detection of DNA binding sites of the global transcriptional regulator GlxR in Corynebacterium glutamicum

scientific article published on 25 October 2012

How little do we actually know? On the size of gene regulatory networks

scientific article published in September 2012

Identification of a global regulator and its involvement in the regulation network of rubber degradation in Gordonia polyisoprenivorans VH2

scientific article published on 22 May 2020

Increased Levels of Genomic Instability and Mutations in Homologous Recombination Genes in Locally Advanced Rectal Carcinomas.

scientific article

Individuating Possibly Repurposable Drugs and Drug Targets for COVID-19 Treatment through Hypothesis-Driven Systems Medicine Using CoVex

scientific article published on 06 November 2020

Inflammatory Breast Cancer: Clinical Implications of Genomic Alterations and Mutational Profiling

scientific article published on 30 September 2020

Integrated analysis and reconstruction of microbial transcriptional gene regulatory networks using CoryneRegNet

scientific article published in January 2009

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

scientific article

Integrative computational biology ⬇️

scientific article published on June 15, 2012

Interactive microbial distribution analysis using BioAtlas

scientific article published on 29 April 2017

Ion mobility spectrometry for microbial volatile organic compounds: a new identification tool for human pathogenic bacteria ⬇️

scientific article published on February 12, 2012

Jllumina - A comprehensive Java-based API for statistical Illumina Infinium HumanMethylation450 and Infinium MethylationEPIC BeadChip data processing

scientific article published in October 2016

Jllumina - A comprehensive Java-based API for statistical Illumina Infinium HumanMethylation450 and MethylationEPIC data processing

scientific article

Joining European Scientific Forces to Face Pandemics

scientific article published on 06 November 2020

KeyPathwayMiner 4.0: condition-specific pathway analysis by combining multiple omics studies and networks with Cytoscape.

scientific article

KeyPathwayMiner: Detecting Case-Specific Biological Pathways Using Expression Data

KeyPathwayMinerWeb: online multi-omics network enrichment.

scientific article published on 5 May 2016

Large scale clustering of protein sequences with FORCE -A layout based heuristic for weighted cluster editing

scientific article

LifeStyle-Specific-Islands (LiSSI): Integrated Bioinformatics Platform for Genomic Island Analysis.

scientific article published on 5 July 2017

Linking Cytoscape and the corynebacterial reference database CoryneRegNet

scientific article

Live sequence charts to model medical information.

scientific article published on 15 June 2012

Long-term instability of the intestinal microbiome is associated with metabolic liver disease, low microbiota diversity, diabetes mellitus and impaired exocrine pancreatic function

scientific article published on 09 November 2020

Mass-spectrometry-based draft of the Arabidopsis proteome

scientific article published on 11 March 2020

Massive fungal biodiversity data re-annotation with multi-level clustering

scientific article

Mature Epitope Density--a strategy for target selection based on immunoinformatics and exported prokaryotic proteins

scientific article

Metagenomic evidence for the presence of phototrophic Gemmatimonadetes bacteria in diverse environments.

scientific article published on 4 December 2015

Microarray R-based analysis of complex lysate experiments with MIRACLE.

scientific article published on September 2014

MoRAine--a web server for fast computational transcription factor binding motif re-annotation.

scientific article published on 25 August 2008

MoSBi: Automated signature mining for molecular stratification and subtyping

scientific article published on 11 April 2022

Modeling and analysis of innate immune responses induced by the host cells against hepatitis C virus infection

scientific article published on 7 April 2015

Molecular networks in Network Medicine: Development and applications

scientific article published on 19 April 2020

Molecular signature of different lesion types in the brain white matter of patients with progressive multiple sclerosis

scientific article published on 11 December 2019

MotifAdjuster: a tool for computational reassessment of transcription factor binding site annotations

scientific article published on May 2009

Multiple Sclerosis Atlas: A Molecular Map of Brain Lesion Stages in Progressive Multiple Sclerosis

scientific article published on 27 August 2020

Multiple graph edit distance

NABEECO

NOX5-induced uncoupling of endothelial NO synthase is a causal mechanism and theragnostic target of an age-related hypertension endotype

scientific article published on 10 November 2020

Neighborhood-Preserving Mapping between Trees

Network Medicine-Based Unbiased Disease Modules for Drug and Diagnostic Target Identification in ROSopathies

scientific article published on 12 August 2020

Network analysis methods for studying microbial communities: A mini review

publication published on 04 May 2021

Network and Systems Medicine: Position Paper of the European Collaboration on Science and Technology Action on Open Multiscale Systems Medicine

scientific article published on 06 July 2020

Network medicine for disease module identification and drug repurposing with the NeDRex platform

scientific article published on 25 November 2021

Novel DNA methylation marker discovery by assumption‐free genome‐wide association analysis of cognitive function in twins

scientific article published in 2021

On the Consistency between Gene Expression and the Gene Regulatory Network of <i>Corynebacterium glutamicum</i>

scientific article published on 08 March 2021

On the importance of statistics in breath analysis--hope or curse?

scientific article

On the limits of 16S rRNA gene-based metagenome prediction and functional profiling

scientific article published in 2024

On the limits of computational functional genomics for bacterial lifestyle prediction.

scientific article published on 22 May 2014

On the performance of de novo pathway enrichment.

scientific article

On the performance of pre-microRNA detection algorithms.

scientific article published on 24 August 2017

On the power and limits of evolutionary conservation--unraveling bacterial gene regulatory networks.

scientific article

On the power of epigenome-wide association studies using a disease-discordant twin design

scientific article published on 01 December 2018

On the trail of EHEC/EAEC--unraveling the gene regulatory networks of human pathogenic Escherichia coli bacteria

scientific article

Online Interactive Microbial Classification and Geospatial Distributional Analysis Using BioAtlas

scientific article published on 01 January 2018

OpenLabNotes - An Electronic Laboratory Notebook Extension for OpenLabFramework

scientific article published in September 2015

OpenLabNotes--An Electronic Laboratory Notebook Extension for OpenLabFramework

scientific article published on 6 October 2015

Orthologous proteins of experimental de- and remyelination are differentially regulated in the CSF proteome of multiple sclerosis subtypes

scientific article published in PLoS ONE

Osteogenesis depends on commissioning of a network of stem cell transcription factors that act as repressors of adipogenesis.

scientific article

PIPS: pathogenicity island prediction software.

scientific article

PTPN2 Deficiency Enhances Programmed T Cell Expansion and Survival Capacity of Activated T Cells

scientific article published on 01 July 2020

PanRV: Pangenome-reverse vaccinology approach for identifications of potential vaccine candidates in microbial pangenome

scientific article published on 12 March 2019

Parameter estimation of qualitative biological regulatory networks on high performance computing hardware

Partitioning biological data with transitivity clustering

scientific article

Peak detection method evaluation for ion mobility spectrometry by using machine learning approaches

scientific article published on 16 April 2013

PetriScape - A plugin for discrete Petri net simulations in Cytoscape

scientific article published in March 2016

PetriScape - A plugin for discrete Petri net simulations in Cytoscape.

scientific article published on 4 June 2016

Privacy-Preserving Artificial Intelligence Techniques in Biomedicine

scientific article published on 21 January 2022

Proteomic meta-study harmonization, mechanotyping and drug repurposing candidate prediction with ProHarMeD

scientific article published in 2023

Rapid hybrid de novo assembly of a microbial genome using only short reads: Corynebacterium pseudotuberculosis I19 as a case study

article

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

scientific article

Retraction Note: Unique RNA signature of different lesion types in the brain white matter in progressive multiple sclerosis

scientific article published on 21 August 2019

RhizoRegNet--a database of rhizobial transcription factors and regulatory networks

scientific article published on 16 November 2010

Robust de novo pathway enrichment with KeyPathwayMiner 5.

scientific article published on 28 June 2016

SARS-CoV-2 infection is associated with a pro-thrombotic platelet phenotype

scientific article published on 05 January 2021

The AIMe registry for artificial intelligence in biomedical research

scientific article published on 25 August 2021

The Druggable Pocketome of Corynebacterium diphtheriae: A New Approach for in silico Putative Druggable Targets

scientific article published on 13 February 2018

The Economic Impact of Artificial Intelligence in Health Care: Systematic Review

scientific article published on 20 February 2020

The End of Medicine as We Know It: Introduction to the New Journal, Systems Medicine

The GlxR regulon of the amino acid producer Corynebacterium glutamicum: in silico and in vitro detection of DNA binding sites of a global transcription regulator

scientific article published on 3 June 2008

The Selection of a Hepatocyte Cell Line Susceptible to Sporozoite Invasion That Is Associated With Expression of Glypican-3 ⬇️

scientific article published on 28 February 2019

The epigenetic factor BORIS (CTCFL) controls the androgen receptor regulatory network in ovarian cancer

scientific article published on 12 August 2019

Time-Resolved Systems Medicine Reveals Viral Infection-Modulating Host Targets

scientific article published on 28 March 2019

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

scientific article published on 12 December 2008

Unique RNA signature of different lesion types in the brain white matter in progressive multiple sclerosis

scientific article published on 25 April 2019

Value of a newly sequenced bacterial genome

scientific article

Weighted gene co-regulation network analysis (WGCNA) of promoter DNA methylation on all-cause mortality in old-aged birth cohorts finds modules of high-risk associated biomarkers

scientific article published on 10 March 2020

clusterMaker: a multi-algorithm clustering plugin for Cytoscape

scientific article

netDx: Software for building interpretable patient classifiers by multi-'omic data integration using patient similarity networks

scientific article published on 22 January 2021

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