Expertises of e:Med consortia and alliances

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Technologien

Technologien
Interdisciplinarity

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

Further information on CancerTelSys

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

Further information on CLIOMMICS

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

Further information on eAtheroSysMed

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

Further information on e:Kid

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

Further information on IntegraMent

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)

Further information on Multiscale HCC

PANC-STRAT

Keywords

Cancer, pancreatic cancer, pancreatic ductal adenocarcinoma, PDAC

Technologies

generation of patient specific xenograft models, whole genome sequencing, clinical validation

Further information on PANC-STRAT

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

Further information on SMOOSE

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,

Further information on SYSIMIT

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

Further information on sysINFLAME

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 

Further information on SysMedAlcoholism

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

Further information on SYSMED-NB

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

Further information on Sys-Stomach

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

Further information on HaematoOPT

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

Further information on HER2Low

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

Further information on MAPTor-NET

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

Further information on Melanoma sensitivity

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

Further information on MitoPD

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)

Further information on MMML- Demonstrators

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

Further information on SMART

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

Further information on SYS-GLIO

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

Further information on ComorbSysMed

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

Further information on MultiPath

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

Further information on NeuroCon

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

Further information on PreNeSt

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

Further information on Quan-T-cell

SYMPATHY

Keywords

Cancer, lymphoma and leukemia
biomarkers, drug response, pathway activity mapping

Technologies

systematic functional assays, multi-omic profiling, bioinformatic analysis, mathematical modeling

Further information on SYMPATHY

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

Further information on SysMedOS

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

Further information on DeCaRe

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

Further information on GlioPATH

MILES

Keywords

Cancer
signaling, transcription, cloud computing, medical clouds, medical data, information security, information privacy

Technologies

computational biology, network

Disciplines

bioinformatics, informatics,  modeling, statistics

Further information on MILES

mitOmics

Keywords

mitochondrial defects genetics, functional genomics, statistics

Technologies

exome sequencing, whole-genome sequencing, transcriptome profiling, genome-wide functional genomics screens, statistics, modeling

Further information on mitOmics

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

Further information on PsychoSys

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

Further information on SUPR-G

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

Further information on symAtrial

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

Further information on SYMBOL-HF

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

Further information on TIL-REP