Expertises of e:Med consortia and alliances
To add/change information, please fill in this form
Systems medicine research consortia
CancerTelSys
Keywords
Cancer, pediatric, brain, glioblastoma, medulloblastoma, MM, lymphoma
histone, telomere maintenance mechanism, ALT pathway, alternative lengthening of telomeres, systems medicine, systems biology, epigenomics
functional genome analysis, computer-based image analysis, cytological features, 3D multi-channel microscopy images, tissue microarrays, 3D colocalization, Gene regulatory network, machine learning, High-throughput screening, High-content-screening, siRNA
Technologies
network modeling, high-throughput fluorescence microscopy, Linear Models, mixed-integer optimization, PathWave, confocal microscopy, RNA interference, Whole-genome sequencing, DNA methylation analysis, RNA sequencing, fluorescence in-situ hybridisation (FISH), in vitro assays, 3D image analysis
CAPSyS
Keywords
systemic inflammation, pneumonia, CAP, community acquired pneumonia, infection, sepsis
host defence, immune defence, innate immunity, barrier failure, lung failure, multi organ failure, systems medicine, precision medicine, systems biology,
signalling pathways, macrophage signalling, epithelial cell signaling, cell-cell interaction, cellular crosstalk, pathomechanisms, pathogen recognition, pathogen clearance, pathogen persistence, biostatistic analysis, modeling, intermediate phenotype, cohort studies, transcriptom, proteom, metabolom, microbiom, kinetic modeling, multi-level modelling, genotype-phenotype mapping, in vivo experiments, in vitro experiments, ex vivo experiments, data integration, data sharing, visual data analysis, cluster analysis
Technologies
flow cytometry, multiplex protein analysis, mouse models, infection models, cell culture, bacterial culture, mathematical modelling, model calibration, sensitivity analysis, Biostatistics
Disciplines
biochemistry, bioinformatics, cell biology, clinical chemistry, clinics, epidemiology, immunology, infection biology, informatics, intensive care medicine, internal medicine, mathematics, microbiology, modeling, molecular biology, physics, pulmonology, statistics, veterinary medicine
Further information on CAPSyS
CLIOMMICS
Keywords
Cancer, Multiple Myeloma
response to treatment, side effects, risk, associations, prognosis, systems medicine, support of an individualized therapy
gene expression, HM-metascore, integrative analysis, prediction of course of disease, patient report, multi level data management, IT architecture
Technologies
RNA Sequencing, Genome wide association studies (GWAS), Service-oriented architectures, Data harmonization processes, Data warehouse, Data mining algorithms, Stochastic models, Case-based reasoning
eAtheroSysMed
Keywords
Cardiovascular diseases, atherosclerosis, coronary artery disease (CAD), ischemic stroke, myocardial infarction
systems medicine, enhancers, regulatory SNPs
bioinformatics, epidemiology, molecular biology, statistics, omics, Genome wide association studies (GWAS), computational biology, network analysis, regulatory networks, single nucleotide polymorphism (SNP), microRNA, eQTL, Bayesian statistical modeling, data integration
Technologies
Computational biology, Bioinformatics, statistical modeling, graphical models, data integration, Baysian statistics, eQTLs, WCNA network analysis, expression profiling, proteomis, GWAS, PWAS, Reporter Assay, Doube fluorescence microscopy
Disciplines
bioinformatics, informatics, mathematics, molecular biology, statistics
e:Kid
Keywords
renal transplantation, Kidney rejection
Systems medicine, Immunosuppression, biomarker, tolerance, mRNA Expression, B cells, regulatory T cells, epigenetic markers
Technologies
Single cell PCR, Real-time PCR, Quantitative DNA-Methylation (activated genes), RNA Isolation, cDNA-Synthesis, RNA/cDNA Biobank, Next-Generation-Sequencing (T-Zell Receptor), NMR Spectroscopy, ELISA , Protein-Microrarray Surface-Plasmon ResonanceTechnology (BiaCore®), flow-cytometry-based cytokine quantification (regulatoric T-cells, Allo-specific effector T -cells), Array Technology (Luminex©, ONE Lamda, anti-HLA and anti-donor specific HLA Antibodies), Single HLA Antigen Beads-Assay, Multidimensional System-biological analysis, Microfluidic cards, Biacore, Peptid Microarrays, in vitro Diagnostics, bisulfite conversion
Disciplines
biochemistry, bioinformatics, cell biology, clinics, epigenetics, exploitation, immunology, informatics, internal medicine, mathematics, modeling, molecular biology, nephrology, physics, proteomics, regenerative medicine, statistics, transplant medicine
IntegraMent
Keywords
psychiatric diseases, schizophrenia, depression, bipolar disorder, affectice disorder
neuroimaging, imaging genetics, transdiagnostic biomarkers, vulnerability, Risk score, genetic risk, risk mechanisms, environmental risk, gene-environment interaction, epigenetics, non-coding RNA, disease modeling, genetic mouse models, omics
Technologies
genetic mouse models, mouse genetics, behavioral studies, omics, functional and structural magnet resonance tomography, psychological and neuropsychological assessments, genetic analyses, iPS cell technology, next-generation sequencing (NGS), bioinformatics, ZFN- and TALE-nuclease techology
Disciplines
cell biology, modeling
Multiscale HCC
Keywords
Cancer, Hepatocellular carcinoma (HCC)
classification, regression, diagnosis, therapy prediction
Volume perfusion CT (VPCT), transarterial Chemoembolisation (TACE), Bioinformatics, data integration, image processing, image registration, statistical models, classification, data mining
Technologies
Volume perfusion CT (VPCT), Positron emission tomography (PET), Magnetic resonance imaging (MRI), Computer modelling, NMR metabolomics, proteomics, transcriptomics, genomics, multiparametric imaging, angiography, Contrast enhanced ultrasound (CEUS)
PANC-STRAT
Keywords
Cancer, pancreatic cancer, pancreatic ductal adenocarcinoma, PDAC
Technologies
generation of patient specific xenograft models, whole genome sequencing, clinical validation
SMOOSE
Keywords
Cancer, lung cancer, neuroblastoma
cancer research, cancer genome, tumor evolution, resistance mechanism, egigenetic modifications
genome sequencing, statistical analysis, data handling, optimization of analysis workflows and applications, targeted therapy options
Technologies
Next Generation Sequencing (NGS), genome sequencing, mathematical modelling, statistical inference, clustering, Supercomputer, GPGPUs, Intel Xeon Phis, FPGAs, cancer genome assay, tissue culture, mouse modeling, ChIP, clinical trials
SYSIMIT
Keywords
Transplantation, hereditary breast cancer
image, analysis, tissue diagnostics, image mining, multiscale modeling, systems biology, biomathematics
Technologies
Definiens Cognition Network Technology, tissue phenomics, agent-based models, mathematical analysis, data mining, machine learning,
sysINFLAME
Keywords
Inflammation, chronic inflammatory diseases, chronic inflammation, inflammatory bowel disease, rheumatoid arthritis, ankylosing spondylitis, immune-mediated disease
monogenic, oligogenic, complex traits, genotype, phenotype, cross-phenotype studies, individual disease course, epigenome, transcriptome, microbiome, immune monitoring, mass cytometry, systems biology, statistics, data-mining, data management, i2b2, tranSMART, privacy, analysis, data sources, ETL, ontology, semantics, research database, research data warehouse, next generation sequencing (NGS)
Technologies
genotyping, epigenetics, 16S rRNA Gen Sequenzierung (MiSeq), next generation sequencing(NGS), (re-) sequencing, shotgun sequening (HiSeq), microbiome analysis, transcriptome analysis, weighted genetic risk scores, autozygosity mapping, multi-layer omics-data analysis, pathway analyses, in vitro assays, animal models, meta genome, exome array, Calprotectin, bisulfite conversion, multiparametric flow cytometry, mass cytometry (CyTOF-technology), gene expression profiling, i2b2, tranSMART, privacy, analysis, data sources, ETL
SysMedAlcoholism
Keywords
Neuropsychiatric Disoders, alcoholism, alcohol addiction, alcohol use disorder, substance use disorder
psychiatry, neuroscience, genetics, endophenotyping, MRT, imaging genetics, brain imaging, imaging x genetics, computational neuroscience, computational modeling, animal models, validation of candidate genes, cellular stress response, inducible pluripotent stem cells, prefrontal cortex, neurotransmitter, pharmacological treatment, clinical trials
Technologies
imaging, imaging genetics, (functional) magnetic resonance imaging, drosophila genetics, mouse genetics, neuroanatomy, neuropsycology, psychometric methods, behavioral studies, multielectrode array, electrophysiology in vivo, single unit activity, microdialysis in vivo, local field potential, mathematical modelling, computational modeling, advanced machine learning techniques,network dynamics, multimodal imaging, biomarkers, relapse prediction
Disciplines
brain imaging, clinics, modeling, neurobiology, neuroscience, psychiatry, statistic, mathematics
SYSMED-NB
Keywords
Cancer research, neuroblastoma
primary sugar metabolism, systems biology, epigenetics, bromodomains, Histondeacetylase
Technologies
enzymatic activity tests, Molecular cloning, Mathematical modelling of metabolic pathways, miRNA expression profiles, RNA-sequencing, bioinformatic network calculation
Sys-Stomach
Keywords
Cancer, Stomach cancer, Gastric carcinoma
targeted tumor therapy, response and resistance factors, biomarker, trastuzumab, cetuximab, systems medicine, cell migration, metastasis, cell interaction, motility coefficient
computational model, statistical models, mechanistical models, machine learning, knowledge management, semantic mapping, network analysis
Technologies
2D analysis of cell motility by time-lapse microscopy, cell invasion assay, mRNA, miRNA (MACE, miRNAseq), epigenetic (MSDK) and proteome profiling, sequencing, RPPA, 3D spheroid formation, siRNA silcening, MALDI Imaging Mass Spectrometry, knowledge management, network analysis, machine learning, computational modelling, mathematical modelling, federated data warehouse, self organising maps, shortest path search, network blast, ontologies, semantic mapping, graph representation, agent-based computer simulation
Demonstrators for an individualized medicine
HaematOPT
Keywords
Cancer, Leukeamia
haematopoiesis, CML, AML, chemotherapy, growth factors, clinical descison making
mathematical modelling, mechanistic model, computer simulation,
Technologies
Differential equations, Agent-based models
Disciplines
cell biology, clinics, bioinformatics, informatics, mathematics, modeling, statistics
HER2Low
Keywords
Cancer, breast cancer
HER, ERBB, therapy, antibody, dynamic modeling, pathway activation, biomarker, signaling protein
Technologies
RPPanalyzer Toolbox (R Package for analyzing reverse phase protein array data), R2LC (calculating risk classification scores), RBiopaxParser (processing Pathway information in R)
Leukeamia, haematopoiesis, growth factors, chemotherapy, mathematical model, computer simulation, clinical descison making
MAPTor-NET
Keywords
Cancer, pancreatic neuroendocrine Tumors (pNET)
clinical data, clinical study, biomaterial, patient-derived pNET xenografts, PI3K, mTOR, signaling
primary cultures, next-generation sequencing (NGS), proteomics data, model parameterization, mathematical MAPK/PI3K/mTOR modeling, signal transduction networks, modular-response analysis, differential-equation models, statistical analysis, scientific data management platform, European Neuroendicrine Tumor Society (ENETS)
Technologies
proteomics, modeling, shRNA screen, patient-derived cell lines, 2D / 3D cell culture, genome-editing CRISPR/CAS genomic editing, proteom analyses, SILAC, mass spectrometry, BioPlex, ODE, Modular Response Analyse (MRA), next generation sequencing (NGS), RNA Sequenzierung, drug response experiments, clinical data, database, parameterization
Melanoma sensitivity
Keywords
Cancer, melanoma
apoptosis, signal transduction, systems biology, SYSACT
statistical and network modeling, 3D organotypic screening models, Probabilistic Boolean Network
individualized medicine, alternative treatment options
Technologies
mathematical modeling, Probabilistic Boolean Networks, 3D cellular tumor models, antibody engineering
Disciplines
biochemistry, bioinformatics, cell biology, clinics, modeling, molecular biology
MitoPD
Keywords
Neuropsychiatric Disoders, Parkinson's disease
pathogenesis, mitochondria, treatment, systems biology
bioinformatics, data management, omic, disease modeling
Technologies
genetics, cell biology, biochemistry, proteomics, proteome analyses, transcriptomics, transcriptome analyses, epigenomics, cellomics, metabolome analyses, behaviour analyses, pathological analyses, imaging, data integration, automated data processing pipeline, animal models
Disciplines
bioinformatics, molecular biology
MMML- Demonstrators
Keywords
Cancer, malignant lymphoma, Burkitt lymphoma, diffuse large B-cell lymphoma
metabolomics biomarker discovery, mathematical models, computational, experimental, gene expression signatures
Technologies
toponomic modeling, mathematical modeling, Algorithms for cross platform signatures, NanoString based diagnostics, SWATH based diagnostics, diagnostic platform nCounter® Analysis System, Toponomic Concepts, Luminex Assays & Modelling, BiopaxParser, web-portal LYMMML (interactive access to the MMML data repositories)
SMART
Keywords
Cardiovascular diseases, heart failure, aortic valve stenosis
angiotensin II, in memory technology, real-time data analytics, genome data, cloud platform, RNA-seq, next generation sequencing, bioinformatics, PBPK, cardiovascular modeling, PK-Sim
Technologies
Cardiac Magnetic Resonance Imaging, image based modelling, cell physiology, genetics and epigenetics, proteomics, next generation sequencing (NGS), bioinformatics, heart failure management, in memory technology, HTML5, CSS, JavaScript, R, L, C++, Python, Ruby on Rails, Clustering, Ranking, Filtering, PBPK, MCMC
SYS-GLIO
Keywords
Cancer, glioblastoma
biomarkers, molecular signatures, regulatory interaction, genome, exome, transcriptome and methylome, data integration, statistical methods, machine learning, mechanistic modeling
Technologies
machine learning, statistics, bioinformatics, modeling, mouse models
Junior research groups
ComorbSysMed
Keywords
chronic inflammatory skin diseases
comorbidity
machine learning, omics technologies, methods evaluation, simulation
Technologies
machine learning, simulation framework, quality control and analysis of omics data (genetic, gene expression, methylaton, metabolomics), R, Bioconductor, statistics
Disciplines
bioinformatics, chemistry, mathematics, statistics
DiNGS
Keywords
Neuropsychiatric Disoders, schizophrenia
pluripotent stem cells, gene regulatory elements (GREs), gene regulatory network analyses
Technologies
epigenomic profiling, reporter assays, CRISPR genome engineering, human pluripotent stem cell differentiation
MultiPath
Keywords
Network Medicine, Network Biology
Technologies
Pathway Databases, Cytoscape, R, Bioconductor
NeuroCon
Keywords
Neuropsychiatric Disoders, depression, schizophrenia, addiction
brain network activity, neurochemistry disease models, biomarker, neuroimaging
Technologies
mathematical modeling and simulation, functional differential equation, machine learning, functional imaging, functional magnetic resonance imaging (fMRI), phMRI, in vivo micro dialysis
PreNeSt
Keywords
Neuropsychiatric Disoders, affective disorders, depression, mania, manic, depressive, psychiatry
brain networks, transcranial magnetic stimulation (TMS), therapy, functional magnetic resonance imaging (fMRI), mapping
Technologies
functional magnetic resonance imaging (fMRI), network-based transcranial magnetic stimulation
Quan-T-cell
Keywords
chronical infections, cancer, melanoma
T cell avidity, T-cell differentiation, adoptive T-cell-therapy (ACT), immunotherapy, biomarker, vaccination, preclinical mouse models, mathematical models, differentiation models
Technologies
mathematical modeling combined with single-T-cell fate-mapping, mouse models of chronic viral infection and melanoma, differentiation pathways
SYMPATHY
Keywords
Cancer, lymphoma and leukemia
biomarkers, drug response, pathway activity mapping
Technologies
systematic functional assays, multi-omic profiling, bioinformatic analysis, mathematical modeling
SysMedOS
Keywords
Obesity, obesity related complications
oxidative stress, oxidized lipids and lipid-modified proteins, multi-omics datasets, mathematical modeling, oxlipidomics, proteomics, LPP-modified proteins (lipox-proteomics), biomarker
Technologies
clinical characterization, statistics, mathematical modeling, genome-scale metabolic modeling , regulatory protein networks analysis
Junior research alliances
DeCaRe
Keywords
Cardiovascular diseases, acute myocardial infarction (MI), myocardial injury, myocardial necrosis, replacement fibrosis, post-ischemic heart failure
zebrafish models, cardiac regeneration, inflammation, miRNA-controlled signalling
Technologies
miRNA, Cytosinmethylation, ChIP-seq, modeling
GlioPATH
Keywords
Cancer, malignant gliomas
signaling, metabolic pathways, transcriptomics, proteomics, epigenetics, clinical data, metabolomics, kinetic biochemical analyses, Trp and NAD metabolism, Mammalian target of rapamycin (mTOR) network
Technologies
network modeling
MILES
Keywords
Cancer
signaling, transcription, cloud computing, medical clouds, medical data, information security, information privacy
Technologies
computational biology, network
Disciplines
bioinformatics, informatics, modeling, statistics
mitOmics
Keywords
mitochondrial defects genetics, functional genomics, statistics
Technologies
exome sequencing, whole-genome sequencing, transcriptome profiling, genome-wide functional genomics screens, statistics, modeling
PsychoSys
Keywords
Neuropsychiatric Disoders, schizophrenia, delusion
dopamine, perceptual inference
Technologies
behaviour experiments, functional magnet resonance tomography, placebo controled pharmacological intervention, bayesian modeling, electrophysiological measurements of single neurons, statistics of point processes, change point analysis, stochastic models for neurophysiological data, especially spike trains, statistical analysis of spike patterns and neuronal coordination
Disciplines
mathematics, modeling, statistics
SUPR-G
Keywords
Cancer, brain tumors, glioblastoma, diffuse glioma
neural stem and progenitor cells, unfolded protein response (UPR), translational reprogramming, translational regulation, proteomics, lipidomics, bioinformatics, network, integration, protein interaction, NSC, NPC, , IDH1 mutation, TP53 mutation, PTEN mutation, ribosomal profiling, migration, NIH3T3 cells, endoplasmatic, endoplasmic reticulum (ER) stress
Technologies
ribosomal profiling, targeted proteomics, glioma animal models, SPIM, SRM, MRM, primary cultures, migration assays, RNA profile, GPCR signaling, in vitro and in vivo analyses of invasion
symAtrial
Keywords
Cardiovascular diseases, atrial fibrillation
systems medicine, systems biology, UHZ, genetic epidemiology, risk stratification, omics
Technologies
epidemiology, molecular biology, cell biology, bioinformatics, statistics, cohort studies, genom wide assotiation studies (GWAS), sequencing, data mining
SYMBOL-HF
Keywords
Cardiovascular diseases, heart failure (HF)
cardiomyocyte systems (primary and iPS), animal models (zebrafish, mouse), bioinformatics, transcriptome datasets, transcriptome networks
Technologies
heart failure models in zebrafish, mice, and humans, bioinformatics
TIL-REP
Keywords
Cancer, pancreatic cancer, melanoma
tumor-infiltrating lymphocytes, immunotherapy, T-cell receptor repertoire, next-generation sequencing, vaccination, immuno-stimulatory antibodies, TIL, immune checkpoint blocker, ipilimumab, PD-1 antibody
Technologies
in vivo experiments, vaccination, mathematical modeling, statistics, T-cell isolation from human cancer patients, T-cell receptor analysis by next-generation sequencing(NGS), flow cytometry, computer assisted immunohistochemistry, survival analysis, TIL expansion