Projects: Not specified
Institutions: Not specifiedorcid.org/0000-0002-8363-0678
Institutions: National Institute of Biologyorcid.org/0000-0003-4776-7164
Projects: HYp - Spatiotemporal analysis of hypersensitive response to Potato virus Y in potato, pISA-tree, TID - Dynamics of tolerant potato-potato virus Y interaction, SUSPHIRE - Sustainable Bioproduction of Pheromones for Insect Pest Control in Agriculture, INDIE - Biotechnological production of sustainable indole, FAIRDOM user meeting
Institutions: National Institute of Biologyorcid.org/0000-0001-5906-8569
Institutions: National Institute of Biologyorcid.org/0000-0003-3644-7827
Ph.D. in Biotechnology
Research associate at Department of Biotechnology and Systems Biology, National Institute of Biology
Projects: Millar group, TiMet, PHYTOCAL: Phytochrome Control of Resource Allocation and Growth in Arabidopsis and in Brassicaceae crops, POP - the Parameter Optimisation Problem, Regulation of flowering time pathways in Arabidopsis on the summer Solstice., PlaSMo model repository
Institutions: University of Edinburghorcid.org/0000-0003-1756-3654
Institutions: University of Edinburghorcid.org/0000-0003-0737-2408
Institutions: National Institute of Biologyorcid.org/0000-0003-0913-2715
Institutions: Wageningen University & Researchorcid.org/0000-0001-5845-146X
Assistant professor at Wageningen University & Research
Projects: Systems toxicology of Atlantic cod
Institutions: University of Bergenorcid.org/0000-0002-2484-9047
Professor, Centre of Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne
My research interests focus on understanding metabolic homeostasis. We are mainly using genetically modified mouse models and systems approaches. I am also very keen in exploring how Omics approaches is changing, or not changing, key biological concepts.
Link to complete publication list : http://orcid.org/0000-0001-5483-288X
Projects: HUMET Startup
Institutions: Leiden University Medical Centerorcid.org/0000-0002-2172-7394
Professor in genetics and systems biology of the metabolic syndrome
Professor of Systems Medicine/Biology at the Academic Medical Center, Amsterdam and University Medical Center Groningen, Groningen, The Netherlands
My major projects focus on understanding the etiology of metabolic syndrome and its comorbidities type2 diabetes and cardiovascular disease. To get grip on the sequence of events in disease progression we make use of longitidunal models and apply multiscal systems biology approaches.
My published work can be found at:
Projects: HUMET Startup
Institutions: Centro de Investigación Príncipe Felipeorcid.org/0000-0003-3318-120X
Tools: Bioinformatics, Computational and theoretical biology, Computational Systems Biology, Data Management, Databases, Dynamic modelling, Genetics, Genomics, R, Systems Biology, Transcriptomics, Java
My scientific interests revolve around functional genomics, systems biology and the development of algorithms and software for the analysis of high-throughput data (mainly, but not restricted to, Next Generation Sequencing) and its application to the relationship between genotype and phenotype, mainly oriented to personalized and precision medicine. I am especially interested in the study of disease mechanisms and drug action mechanisms, drug repositioning and the definition of mechanism-based
Projects: Not specified
Institutions: Not specifiedorcid.org/0000-0003-2727-9518
I am had of the Research Group PiDOMICS which aims at the identification of human biomarkers for fungal infection using omics-data. Moreover, I am PI Infrastructure project of the Collaborative Research Center / Transregio 124 Pathogenic fungi and their human host: Networks of Interaction - FungiNet. Thereby my expertise is the implementation and usage of pipeline for OMICS (genome, transcriptome, protoem) data analysis, as well as data-warehouses for visualizing these data.
Professor in Jinan University, Guangzhou, China.
My research interest is in the modeling of translation. Connecting various processes in translation, we can investigate the impact of different factors on protein biosynthesis and biogenesis in genome-wide scale. This may reveal various general mechanisms on control level of gene expression and folding efficiency regulation in different growth conditions.
Institutions: University of Milano-Bicocca
I am a PostDoc working on yeast metabolomics. During my PhD I studied the interplay between metabolism, cell cycle and signalling, mainly focusing on the Snf1/AMPK pathway. I am currently interested in studying metabolic rewiring caused by different nutrients, generating high-throughput data suitable for modelling.
Geneticist and Microbiologist with research focus on Archaea. Professor of Genetics in Ecology (Faculty of Life Sciences/University of Vienna, Austria) and associate professor of the Center of Geobiology (University of Bergen/Norway).
Roles: Project Coordinator
Expertise: genetic engineering, Streptomyces, Protein-DNA-interaction, Microarray experiments with prokaryotes, Molecular microbiology, bacterial gene regulation, regulation of gene expression, Transcriptomics, Microbiology
Tools: transcription analysis, analysis of functional genomics data, microbiology techniques, reporter gene analyses, site-directed and random mutagenesis, Mutant and Strain Construction, Molecular biology techniques (RNA/DNA/Protein), Bioconductor Packages in R, Northern analyses), Chip-chip, PCR, Microarray analysis, Transcriptomics, Genetic modification, Microbiology
Research fellow in Bioinformatics at the Warwick Systems Biology Centre, University of Warwick.
Working on high throughput data analysis (microarray data, next generation sequencing) and data integration (database management, text-mining, gene annotation via public databases)...
I am currently Professor of Systems Biology at the University of Manchester. My research interests focus on the development of innovative computational approaches for post-genomic systems biology, statistical methods for high-throughput biological experimentation and the dynamic modelling of cellular systems. This work is highly interdisciplinary and usually involves close collaboration with experimental biologists and clinicians. A recurrently theme is the study of complex cellular networks at
Post doc. in the SysMO-LAB2 project from August 2010. I work at Nofima and the Norwegian University of Life Sciences (UMB) at Ås, Norway. My focus in SysMO-LAB2 will be on four Lactobacillus plantarum strains, diversity analysis, omics-technologies, genome scale modelling.
Background: Ph.D. in Molecular Microbiology June 2010, where I worked with Lactobacillus sakei, metabolism and diversity studies.
Roles: Project Coordinator
The Veening lab is interested in phenotypic bi-stability in Streptococcus pneumoniae and its importance in virulence of this human pathogen.
University of Rostock, Germany
Institute of Biological Sciences
Division of Microbiology
Expertise: microscopy, fluorescence protein fusions (transcriptional and translational), localisation studies, protein secretion, functional protein expression, gene regulation, stress responses, phenotypic heterogeneity, Bacillus subtilis, Microarray analysis, Molecular Biology, Genetics
Tools: DNA affinity chromatography, EMSA, Molecular biology techniques (RNA/DNA/Protein), transposon mutagenesis, Fluorescence microscopy, Flow cytometry, Immunofluorescence, Site-directed mutagenesis, Fluorecence based reporter gene analyses/single cell analyses, Microarray analysis, Transcriptomics, Genetic modification
PhD student. Analyzing CcpA affinity to cre boxes (catabolite responsive elements) and response of B. subtilis to membrane protein overproduction stress.
Institutions: University of Leidenorcid.org/0000-0002-1279-5133
I am an Assistant Professor at Leiden University in the Leiden Institute of Advanced Computer Science. I am a bioinformatician and my research interests are in data integration. I use scientific workflows and semantic web technologies to integrate and analyse data in systems biology and functional genomics.
I started to work with B. subtilis during my diploma thesis in Marburg, analyzing the gene expression pattern during sporulation and their control by the four sporulation sigma factors. This work was continued during my PhD thesis in Greifswald. In collaboration with Prof. Bremer and Prof. Marahiel in Marburg we also studied additional adaptation processes of B. subtilis, like the adaptation to low temperatur and high osmolarity.
I am now working as a staff scientist in Prof. Völkers lab in
Expertise: Mathematical and statistical modeling, bioreactor models, dynamics of biological networks, dynamics and control of biological networks, parameter estimation, Reactor models, Mathematical modelling, Bioinformatics, Molecular Biology
Tools: evaluation of process dynamics, continuous cultivation, DIVA, differential algebraic equations, linux, Material balance based modeling, stimulus response experiments, Microarray analysis, Matlab, Linear equations, ODE, Model organisms, Single Cell analysis, SBML, Transcriptomics, Computational and theoretical biology, Bioinformatics
I'm an engineer at the MPI Magdeburg and I'm working in the field of mathematical modeling, model verification, parameter identification, model analysis and experimental design. I'm involved in two projects, KOsmoBac and PSYSMO.
Projects: SysMO DB, FAIRDOM, ICYSB 2015 - International Practical Course in Systems Biology, ZucAt, SysMO-LAB, Kinetics on the move - Workshop 2016, Example use cases, FAIRDOM user meeting, ErasysApp Funders, EraCoBiotech 2 nd call proposal preparation, Service to URV Tarragona, Spain with respect to their Safety Assessment of Endocrine Disrupting Chemicals model (Active NOW), FAIRDOM & LiSyM & de.NBI Data Structuring Training, MESI-STRAT, INCOME, Multiscale modelling of state transitions in the host-microbiome-brain network, BESTER, TRALAMINOL, Sustainable co-production, INDIE - Biotechnological production of sustainable indole, Project/Kublanov, PoLiMeR - Polymers in the Liver: Metabolism and Regulationorcid.org/0000-0003-3540-0402
I am a researcher at the Scientific Databases and Visualization Group at Heidelberg Institute for Theoretical Studies (HITS) , one of the developers of SabioRK - System for the Analysis of Biochemical Pathways - Reaction Kinetics (http://sabiork.h-its.org/) . I am working on design and maintenance of the information systems to store, query and analyse systems biology data; definition and implementation of methods for the integration of data from multiple sources. In SySMO-DB project
I am assistant professor at the Laboratory of Microbiology and my interest is in the area of molecular microbiology. Research focuses on the analysis of the metabolism of anaerobic fermentative bacteria and archaea, especially with respect to biofuel production (hydrogen, butanol). Within SysMo our tasks concern the effect of butanol stress, using metabolomics and transcriptomics.
Expertise: protein secretion, C- and N- metabolism, gene regulation, stress responses, pathogens, virulence factors, metal ion homeostasis, Gram positive bacteria (Bacillus, Lactococcus, Streptococcus), competence, sporulation, germination, antimicrobial peptides, phenotypic heterogeneity, bistability
Group leader Molecular Genetics
A molecular microbiologist with a passion for Clostridia! Interested in the development of more effective countermeasures (diagnosis, prevention & treatment) against pathogens, specifically Clostridium difficile and Clostridium botulinum as well as the exploitation of the medical and industrial properties of beneficial strains, specifically in cancer therapy and biofuel production
From 2005 to 2008 I was group leader at the Institute for System Dynamics at the University of Stuttgart. Since 2008 I am now Professor of Systems Biology at the University of Luxembourg.
The research of the Systems Biology Group at the University of Luxembourg is focussed in the area of experimental and theoretical systems biology. We are applying different modelling techniques (mainly ODE and logical) to biological systems to develop suitable computational models. The analysis of these models
Tools: molecular biological techniques (RNA/DNA techniques), protein interaction studies, DNA technology RNA technology Protein analysis Fermentation Mutagenesis, gene regulation, Proteomics (2D-PAGE), Model organisms, Proteomics, Transcriptomics, Genetic analysis, Genomics, Cell biology, Biochemistry and protein analysis, Molecular Biology, Microbiology
Optimisation of Bacillus subtilis for the secretion of heterologous proteins Therapeutic proteins (including those required for experimental purposes and clinical trials) are major products of biomanufacturing processes and considerable time and expense are expended to maximise the yield and quality of proteins produced in heterologous hosts. The production host of choice is the Gram-negative bacterium Escherichia coli for which many strains and expression systems have been developed. However,
I am PhD student at Prof.Uwe Voelker lab in Department of Functional Genomics. My area of research is microbial functional genomics in particular analysing the whole transcriptome(by microarray and other molecular biolology methods) of B.subtilis under various stress conditions.
I use QconCAT strategy for absolute quantification of carbon metabolic enzymes via MRM(multiple reaction monitoring) by LC-MS/MS.
I also perofrm experiments for understanding of dynamics of SigmaB network for modelling.
I am a post-doctoral research associate working in Sheffield in the SUMO consortium. My research focuses on transcriptional regulation in E. coli, with particular emaphasis on the transcriptomic analysis of steady-state chemostat cultures using both microarray and qRT-PCR approaches.
Previous experience, especially that gained during my PhD, involved work on Salmonella physiology and lag phase growth, focusing particularly on gene-expression and transcriptional regulation. Other techniques used
Work in my laboratory is focussed on microbial physiology - the study of how bacteria and other microorganisms work. Although rooted in the tradition of bacterial growth and intermediary metabolism, microbial physiology now embraces molecular biology, genetics, biochemistry, and indeed any discipline that can shed light on bacterial function. Much of our experimental work is conducted with Escherichia coli, the pre-eminent ‘model’ organism with unrivalled ease of genetic and physiological
Roles: Project Coordinator
By training I am a molecular microbiologist with a particular interest in bacterial stress adaptation reactions. Since the early 90ies we have used functional genomics technologies, particularly proteomics, to investigate the response of Bacillus subtilis to environmental challenges.
I am currently Head of the Functional Genomics Department of the Interfaculty Institute of Genetics and Functional Genomics at the Ernst-Moritz-Arndt-University Greifswald. Within the Department we are applying
Senior Research Scientist at SINTEF, Dept. of Biotechnology and Nanomedicine, Research Group Mass Spectrometry
Contributor: Sebastian Curth
Assay type: Transcriptional Profiling
Technology type: Microarray
Snapshots: No snapshots
Investigation: Investigation on the effect of pulsed metabolit...
SOPs: No SOPs
Data files: No Data files
RNAseq analysis of S. solfataricus grown on either L-fucose or D-glucose
Contributor: Jacqueline Wolf
Investigations: L-fucose degradation in Sulfolobus solfataricus P2
Assays: RNA sequencing:l-fuc/d-glu
Recent studies revealed the unsuspected complexity of the bacterial transcriptome but its systematic analysis across many diverse conditions remains a challenge. Here we report the condition-dependent transcriptome of the prototype strain B. subtilis 168 across 104 conditions reflecting the bacterium's life-styles. This data set composed of 269 tiling array hybridizations allowed to observe ~85% of the annotated CDSs expressed in the higher 30% in at least one hybridization and thus provide an
Contributor: Leif Steil
Investigations: Redefining the Complete Transcriptome of Bacill...
Transcriptional profiles of steady-state chemostat cultures were measured at a range of oxygen levels using microarrays. Oxygen levels were defined by the aerobiosis scale of Alexeeva et al. (2002).
This Excel template is for use with affy transcriptomics data in Matrix table format. It was created from a template on the GEO web site (http://www.ncbi.nlm.nih.gov/geo/info/geo_affy.html) and modified to conform to the SysMO JERM for transcriptomics.
Date Published: 27th Sep 2011
Journal: PLoS ONE
PubMed ID: 21980479
Date Published: 8th Aug 2012
Journal: Open Biol
PubMed ID: 22870390