Bioinformatician / Computational Biologist

PhD candidate working on the CoolWine project

Andreas Dräger is the assistant professor for Computational Systems Biology of Infection and Antimicrobial-Resistant Pathogens at the University of Tübingen in Germany. His group aims to combat the spreading antibiotics resistances by using mathematical modeling and computer simulation of bacterial systems up to entire microbiomes and host-pathogen interactions. In doing so, his group actively contributes to the advancement of various COMBINE standards.

I completed my BSc in Biology and MSc in Cell Biology by the University of Valencia. During my last undergrad year I participated in synthetic biology’s iGEM competition where I dove in the use of models in Biology, which pushed me to pursue a PhD in the Department of Applied Mathematics in the Technical University of Valencia.

My research on Metabolic Engineering of hydrogen in cyanobacteria led me to be visiting researcher at Uppsala University, Denmark Technical University and EMBL Heidelberg.
...

Professor- University Clermont Auyvergne (UCA) - Institute of Chemistry of Clermont-Ferrand (ICCF)

I work as a project manager for the Innovative Training Network PoLiMeR - Polymers in the LIver: Metabolism and Regulation funded by the EU. In addition I am a project manager for the UMCG Research BV where I support scientist in the pre-award phase with writing their proposals and in the post-award phase with managing their awarded projects.

Head of the group of Molecular Enzyme Technology and Biochemistry (Faculty of Chemistry) at the University of Duisburg-Essen. My research interest is on archaeal physiology with a special focuss on the central carbohydrate metabolism of (hyper)thermophilic Archaea and its regulation. The aim is to gain a systems level understanding by the combination of modern highthrouput analyses with classical biochemistry and molecular biology.
Archaea possess many novel enzymes and pathways and our aim is
...

Computational Biologist, Young Researcher at Department of Biotechnology and Systems Biology, National Institute of Biology NIB and PhD candidate in Statistics, Ljubljana, Slovenia

Ph.D. in Biotechnology
Research associate at Department of Biotechnology and Systems Biology, National Institute of Biology

Prof. Dr. Kathrin Thedieck
MESI-STRAT Coordinator
Leader WP8 – Project Coordination

I studied Engineering Cybernetics at the University of Stuttgart and the University of Wisconsin, Madison. After my graduation, I started my PhD studies in systems biology for which I received a Ph.D. degree in 2013. A few months later I became team leader at the Institute of Computational Biology at the Helmholtz Zentrum München. Since August 2015, I lead an independent junior research group at the Helmholtz Zentrum München.

My research focuses on the development of methods for the data-driven
...

Associate Professor at Wageningen University & Research

I'm currently a PhD student in Laboratory of Systems and Synthetic Biology in Wageningen University & Research. My project involves using genome scale metabolic modelling to understand and improve chemical production capacities of microorganism.

Computational Biologist and App Designer @LifeGlimmer

I am a researcher (PhD student) working at Wageningen University & Research as bioinformatician and modeller. I am working as part of the MycoSynVac (http://www.mycosynvac.eu/) project on dynamic modelling of central carbon metabolism in M. pneumoniae, to be extended to full dynamic modelling of metabolism to be implemented in a whole cell model.
I am also looking into possibilities to improve standards in model generation using semantic technologies, improving automatic generation, annotation
...

Associate Professor for Systems Biomedicine, Luxembourg Centre for Systems Biomedicine, University of Luxembourg

Alexander Kel received his Ph.D. in Bioinformatics, Molecular Biology and Genetics in 1990. He studied biology and mathematics at Novosibirsk State University and obtained his M.S. in biology with special focus on mathematical biology in 1985. He worked for 15 years at the Institute of Cytology and Genetics, Russia (ICG) holding positions as a programmer, scientist, senior scientist and Vice-Head of the Laboratory of Theoretical Molecular Genetics. In 1995, he won the Academician Belaev Award.
...

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
...

POSITION
I am an emeritus professor in Biochemistry at the University of Amsterdam (retired 2010).

RESEARCH
My research focussed on the human chromatin in its natural environment, i.e. the nucleus of cultured living human cells.
Aspects, such as the dynamic folding of the chromatin fiber inside the nucleus and local chemical modification of histones and DNA at genetic loci, are the physical and chemical basis for epigenetic regulation of gene expression. In my group we worked parallel on human
...

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.

PhD student @ "Quantitative Microbial Phenotyping"
Institute of Bio- and Geosciences, IBG-1: Biotechnology
Forschungszentrum Jülich GmbH
52425 Jülich, Germany

Team leader "Quantitative Microbial Phenotyping"
Institute of Bio- and Geosciences, IBG-1: Biotechnology
Forschungszentrum Jülich GmbH
52425 Jülich, Germany

POSITION
Prof. Dr. Natal van Riel is Professor in Computational Modelling at the Academic Medical Center - University of Amsterdam (AMC - UvA) and Associate Professor in Systems Biology and Metabolic Diseases at the Department of Biomedical Engineering of the Eindhoven University of Technology (TU/e).

RESEARCH
My research applies mathematical modelling and computation to study metabolic diseases, in particular Metabolic Syndrome and co-morbidities. Systems biology approaches are developed for
...

Scientific Project Manager at Luxembourg Centre for Systems Biomedicine, University of Luxembourg
http://lcsb.uni.lu

Systems biology for salmon farming is what I do. I lead the DigiSal project (http://tinyurl.com/digisal), whose full title is "Towards the Digital Salmon: From a reactive to a pre-emptive research strategy in aquaculture". DigiSal is part of Digital Life, the first call dedicated to systems biology by the Research Council of Norway. I'm also one of the lead modellers in GenoSysFat (http://tinyurl.com/genosysfat), working to improve the omega-3 content of salmon farmed on sustainable feeds by
...

Data management and standardization expert for systems biology and systems medicine, responsible for the data management user requirements and user contacts within the German LiSyM network (Liver Systems Medicine: http://lisym.org/) and associated to the FAIRDOM team.
Involved in different standardization initiatives and committees, i.e. COMBINE (http://co.mbine.org), ISO/TC 276 Biotechnology (https://www.iso.org/committee/4514241.html), European COST action CHARME (http://www.cost-charme.eu) and
...

I am staff scientist in the lab of molecular-genetic systems at the Department of Systems Biology, Institute of Cytology and Genetics SB RAS and Postdoc Research Fellow at San Diego State University.
My research focus is dynamical modeling of gene network functioining.

My research is intended to contribute to the elucidation of the physiological and molecular processes involved in the biofilm formation of acidophilic leaching bacteria with emphasis in their cell-cell communication mechanisms.
In SysMetEx, our role is to understand biofilm formation at a microscopical and OMICS levels, in order to optimize it.

Research scientist

My group investigates dynamic regulation and control mechanisms of cellular signal transduction networks by a combination of theoretical, experimental and computational methods. We seek to make sense of our biological data with the help of mathematical models, which ideally enable us to make valid predictions for new experiments, thereby generating novel biological insights.

I am a biomodeler, PhD student. Actually, I've graduated from Novosibirsk State University on two specialities: my bachelor diploma is done in computer science and the master thesis is defended in information biology. So, I'm kind of drifting towards biology. I am a part of the Haploid Evolutionary Constructor project. Our research group studies are dedicated to the simulation of prokaryotic communities. Personally, I am involved into the simulation of spatially distributed bacterial communities
...

I studied Life Science (which is similar to chemical biology) at the University of Konstanz and became interested in Bioinformatics, Systems Biology and quantitative analyses during my Master's. In my PhD project I combine experimental analyses with modeling and parameter estimation approaches to quantitatively analyse regulation of apoptosis at the level of the Bcl-2 protein family.

I am a first year graduate student in the lab of Prof. Wilhelm Huck at the Radboud University Nijmegen. I am working on a project to create an artificial cell. This involves implementing complex genetic networks in cell-free systems which are far from equilibrium. My project involves designing, quantifying, modeling such networks. I am a molecular biologist by training and have basic modeling skills. I am looking to expand my skill-set to include microscopy, microfluidics and a little bit of
...

I am a PhD student in the Theoretical Systems Biology group, based at Imperial College London.
The aim of my PhD is to understand how noise can be the driving force of decision-making processes (differentiation, self-renewal, apoptosis or tumorgenesis), and what are our chances to control them. So far I have been working on method development for stochastic models, a moment closure framework and a stochastic reachability method, to look into cell-to-cell-variability.

Interested in systems + synthetic biology, biotechnology, mountaineering, swimming, running, and the occasional cup of tea. Once diagnosed as an ENFP.

I'm an experimentalist 'Pre-doc' (I still have to finish my PhD thesis) and my work on the COSMIC project will focus on setting up a metabolomic analysis method for Clostridium acetobutylicum.
In the past I have worked on metabolic engineering of the same organism by disrupting genes to asses their impact on acid and solvent formation.
I'm looking forward to joining the COSMIC web-community. It hopefully will all us to stay in touch and update each other on advances in the (computer)lab.

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
...

I am a postdoctoral researcher in the group of Julio Banga. My research is focused on computational systems biology with particular attention to the mathematical modelling of biosystems and bioprocesses. Some of the topics we address are:
- Parameter estimation
- Model identifiability
- Global sensitivity analysis
- Optimal experimental design
- Dynamic optimization
- Robust control of diffusion-reaction systems

Modelling of the general stress response activation cascade of sigB in B. subtilis in response to starvation.

Systems Biologist specialising in data integration, high-throughput sequence analysis, and evolutionary and comparative analyses.

Former:
PhD student as research associate at the Institute for System Dynamics (ISYS), Universität Stuttgart, Germany. Engineering background→modelling, identification and analyses. Detailed kinetic modelling, identification and analysis of the TCA cycle (tricarboxylic acid cycle, citric acid cycle) and the ETC (electron transport chains, respiratory chains) of Escherichia coli. One of the SysMO-DB pals for SUMO.
Now:
Industrial affiliation

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
...

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,
...

Modelling of cellular signalling, Dynamic Motifs and Feedback, Quantitative Measures, Theoretical Aspects of Modelling Biological Systems

I am a biologist in the lab of Prof. Reuss at the University of Stuttgart and I am working in the field of biotechnology and mathematical modelling.

I am a first year PhD student, working with Professor Robert Poole (University of Sheffield), Professor Jeff Green (University of Sheffield) and Dr Jamie Wood (University of York) using a systems biology approach to study respiration in Escherichia coli.

Professor for Biochemcial Engineering, University Stuttgart

I'm an 'experimentalist' (molecular microbiologist) Postdoc working on regulation and peptide signaling in Clostridium acetobutylicum.
I'm also a SysMO-DB PAL (Product Application Liason) for COSMIC, working on data management including standards and integration with SysMO SEEK.

biomathematician, PhD student at the University of Rostock, Systems Biology Group Rostock

My research activities has been to use mathematical models and Computational Biology to answer biological questions, intertwining in silico and experimental methods at all stages. I have a strong interest in exploring the interfaces between Fundamental Biology and bona fide Engineering, specifically in the realm of environmental and industrial problems. The research goals of my group are to contribute to the elucidation of mechanisms underlying basic cellular processes, evolution and ecological
...

I've become a SysMO DB PAL for MOSES project in 2007 being a post-doc in lab of Prof. Matthias Reuss at University of Stuttgart. In the MOSES project, our major efforts were in the experimental data acquisition for dynamic model of primary carbon and anaerobic energy metabolism in yeast. The model implements prediction of perturbations of two types: glucose pulse and temperature jump. We implement “stimulus-response” methodology for the unraveling the dynamic structure of the network and to
...

I am a biotechnologist with main focus on theoretical studies. Currently, I am working on the implementation of a parameter estimation algorithm on GPUs to reduce the computational burden of huge ODE systems.
I am a PAL and I am looking forward to communication with other SYSMO members.