http://nbic.roquin.net/about-nbic/jobspositions/ The 20 most recent positions available at NBIC en http://nbic.roquin.net/about-nbic/jobspositions/detail/jobdetails/hbo-bsc-bioinformatician-1/ http://nbic.roquin.net/about-nbic/jobspositions/detail/jobdetails/hbo-bsc-bioinformatician-1/ Wed, 03 Mar 2010 17:40:30 +0100
Within the department of human genetics of the RUNMC we are currently working with a new technology for the analysis of the complete human DNA. For the analysis of these huge amounts of sequencing and microarray data as well as the data management and automation we are currently looking for assistance within the current group of enthusiastic bioinformaticians.]]> http://nbic.roquin.net/about-nbic/jobspositions/detail/jobdetails/phd-researcher-on-concept-recognition-and-disambiguation-in-biomedical-literature-and-clinical-recor/ http://nbic.roquin.net/about-nbic/jobspositions/detail/jobdetails/phd-researcher-on-concept-recognition-and-disambiguation-in-biomedical-literature-and-clinical-recor/ Wed, 24 Feb 2010 11:09:11 +0100
Project description
A lot of scientific knowledge is contained in unstructured text, such as the scientific literature. The first step in extracting this knowledge is identifying the relevant concepts mentioned in the text. Concept recognition in the biomedical domain is extremely difficult due to a wide use of synonyms (several names for the same entity) and homonyms (several entities with the same name). In this project, the PhD student will investigate ways to improve the recognition of concepts by using a wide range of information sources, such as the text around the ambiguous terms, background knowledge about concepts, and background knowledge about the text (e.g. the journal or the author). A key element will be user feedback: users will be able to correct the system, and the system should learn from this feedback. ]]> http://nbic.roquin.net/about-nbic/jobspositions/detail/jobdetails/bioinformatician/ http://nbic.roquin.net/about-nbic/jobspositions/detail/jobdetails/bioinformatician/ Fri, 19 Feb 2010 16:18:07 +0100
Within the department of human genetics of the RUNMC we are currently working with a new technology for the analysis of the complete human DNA. For the analysis of these huge amounts of sequencing and microarray data as well as the data management and automation we are currently looking for assistance within the current group of enthusiastic bioinformaticians.
]]> http://nbic.roquin.net/about-nbic/jobspositions/detail/jobdetails/open-positions-for-computer-scientists-or-bioinformaticians/ http://nbic.roquin.net/about-nbic/jobspositions/detail/jobdetails/open-positions-for-computer-scientists-or-bioinformaticians/ Fri, 19 Feb 2010 11:53:26 +0100 www.microbial-genomics.de. The Ph.D. fellowships are part of a multi-national research projects MAMBA (Marine Metagenomics for new Biotechnological Applications) and MIMAS (Microbial Interactions in MArine Systems) funded by the European Union (http://mamba.bangor.ac.uk/) and the Federal Ministry of Education and Research (www.mimas-projekt.de), respectively. The task will be to participate in mining large amounts of next-generation sequencing data from marine habitats, with a focus on ecological functioning as well as enzyme candidates with potential biotechnological applicability.]]> http://nbic.roquin.net/about-nbic/jobspositions/detail/jobdetails/phd-student-and-post-doc-position/ http://nbic.roquin.net/about-nbic/jobspositions/detail/jobdetails/phd-student-and-post-doc-position/ Fri, 19 Feb 2010 11:22:09 +0100 The departments of psychiatry and biological psychology of the VU University Medical Center and VU University collaborate in a large-scale study into the genetics of major depressive disorder. For this study, genome-wide data (SNP and CNV) are available. Recently, further funding was obtained from the National Institutes of Health in America and the Dutch interuniversity ‘Center for Medical Systems Biology (CMSB)’, which will be used to generate gene-expression profiles of normal twins and depressed persons. This will enable us to examine the gene-environment interaction in predicting major depressive disorder. To achieve this, we will use both existing statistical models, but also further develop those to better answer the study’s research questions. For that, we will collaborate with Dr. de Menezes from the Biostatistics group at the VU University Medical Center.]]> http://nbic.roquin.net/about-nbic/jobspositions/detail/jobdetails/postdoc-bioinformatics-integration-of-different-types-of-biological-information-in-genomics-anal/ http://nbic.roquin.net/about-nbic/jobspositions/detail/jobdetails/postdoc-bioinformatics-integration-of-different-types-of-biological-information-in-genomics-anal/ Tue, 02 Feb 2010 16:19:46 +0100 Postdoc Bioinformatics – Integration of different types of biological information in genomics analysis: from pathway back to sequence
Biological effects are generally the result from interactions between a magnitude of related gene products and metabolites. Studying these cellular components on a high-throughput scale is a main focus of current research in genomics. As such, analysis on the level of biological pathways is very important for the understanding of the outcome of these studies. Recently, the departmentof Bioinformatics has introduced Wikipathways, in collaboration with the University of California, San Francisco. This community based pathway platform supports development and curation of pathways (www.wikipathways.org) and has already been used by international domain experts to contribute content. Directly connected to this effort, our department has developed a novel pathway analysis tool, PathVisio (www.pathvisio.org). PathVisio is a Java-based, open-source tool. The focus of the postdoc position is on the integration of various types of available biological information by making use of network analysis. A commonly used tool for visualizing, modeling and analyzing molecular and genetic interaction networks is the free software package Cytoscape. Cytoscape is very flexible and allows users to extend its functionality by creating or downloading additional software models called “plugins”. The networks can be analyzed by identifying putative functional and structural modules. A connection between Wikipathways and Cytoscape is already realized, enabling the exchange of information. First, all the interactions between gene products and metabolites present in Wikipathways and information available in genomics repositories should be integrated. By integrating these information repositories a complete overview of interactions can be generated. Adding more data does not automatically lead to a better understanding of the mechanism, it can also make the interpration more complex. Therefore, it is necessary to select the most important information. This filtering can be done in several ways. Second, additional information on more recently discovered gene and protein regulation mechanisms should be added to the pathways in WikiPathways. Regulation of gene expression and proteins occurs at several levels by for example transcription factors and microRNAs. Various databases describe target sites for these gene regulators. By coupling the information on target sites to the genes present in the pathways, regulation can be incorporated, taking the visualization and analysis of pathways to the next level. Third, a single nucleotide polymorphism (SNP), which is a variation of a single nucleotide in a DNA sequence on population level, can be related to a certain disease state or susceptibility to pathogens. Genes within the pathways should be linked to important SNPs. This will enable the analysis of SNP arrays and in the near future sequencing studies. The postdoc will collaborate with excellent researchers in nutrigenomics and nutrigenetics to use the data integration approaches developed in real life studies and will visit some of the research groups involved. Bioinformatics is evolving rapidly. One should keep up with novel techniques and methods. This makes Bioinformatics a challenging research field with new and exciting opportunities. ]]> http://nbic.roquin.net/about-nbic/jobspositions/detail/jobdetails/senior-software-engineer-for-e-laboratories/ http://nbic.roquin.net/about-nbic/jobspositions/detail/jobdetails/senior-software-engineer-for-e-laboratories/ Fri, 22 Jan 2010 12:12:23 +0100 http://nbic.roquin.net/about-nbic/jobspositions/detail/jobdetails/postdoctoral-position-at-laboratory-of-cancer-epigenetics/ http://nbic.roquin.net/about-nbic/jobspositions/detail/jobdetails/postdoctoral-position-at-laboratory-of-cancer-epigenetics/ Fri, 15 Jan 2010 10:05:40 +0100
The candidate will tackle integrative analysis of higth-throughput transcriptomics, genomics and epigenomics data sets generated using cutting edge genome-wide technologies. Both clinical and fundamental aspects of cancerogenesis will be addressed. The position is funded for 2 years, with possible extension. Screening of applications begins immediately and continues until an outstanding candidate is selected.]]> http://nbic.roquin.net/about-nbic/jobspositions/detail/jobdetails/post-doc-in-computational-and-systems-biology/ http://nbic.roquin.net/about-nbic/jobspositions/detail/jobdetails/post-doc-in-computational-and-systems-biology/ Tue, 12 Jan 2010 17:13:34 +0100 “A Systems Approach to the Yeast Transcriptional Regulatory Network”. The DynamiX project is a collaborative project that involving the Maerkl (EPFL), Shore (U Geneva), Unser (EPFL) and Naef (EPFL) labs.

The specific project involves studying the transcriptional regulation of ribosome biogenesis in the yeast Saccharomyces cerevisiae and the role of chromatin structure in this process. The Shore and Maerkl labs have generated a large body of data, e.g. ChIP-seq and in vitro binding energy measurements for the major transcription factors involved in ribosome biogenesis, which will be analyzed and modeled in combination with publicly available data such as nucleosome position maps. Specifically, the candidate will apply computational tools to combine these data and construct a computational model of the gene regulation network based on biophysical principles. Computational prediction should suggest new experiments, such as the design of synthetic promoter constructs to be tested directly in fluorescent reporter assays.  The successful candidate will develop research activities pertaining to:

• Analysis of chromatin immunoprecipitation data from ultra high-throughput sequencing
• Integration of public datasets and designing relevant comparative studies
• Biophysical modelling of transcription regulatory networks
• Quantification of time-lapse imaging data
  

]]> http://nbic.roquin.net/about-nbic/jobspositions/detail/jobdetails/bioinformatician-oncogenomics-in-a-biotech-company/ http://nbic.roquin.net/about-nbic/jobspositions/detail/jobdetails/bioinformatician-oncogenomics-in-a-biotech-company/ Tue, 12 Jan 2010 17:05:01 +0100 The Bioinformatician shall collaborate with academic parties to evaluate and ensure the implementation of their discoveries in the medical diagnostic market. Key domains for this Bioinformatician are in product feasibility investigations, research and product development. The candidate will closely collaborate internally with another bioinformatician, a bio-statistician, technicians, the quality assurance and regulatory group and consultants dedicated to various topics and externally with Affymetrix Bioinformatics and Chip design.]]> http://nbic.roquin.net/about-nbic/jobspositions/detail/jobdetails/phd-fellowships-in-computational-biology-and-scientific-computing/ http://nbic.roquin.net/about-nbic/jobspositions/detail/jobdetails/phd-fellowships-in-computational-biology-and-scientific-computing/ Fri, 11 Dec 2009 17:19:01 +0100 Computational Biology: biological sequence analysis · sequence comparison ·  phylogeny reconstruction genome analysis · gene expression and proteomics data analysis · transcriptional regulation · modeling and simulation of biological processes · data integration techniques · mathematical modeling of biochemical reaction networks · systems biology · algorithms and statistical methods for molecular biology. Scientific Computing: scientific engineering and industrial modeling · inverse problems · optimization and visualization · algorithm oriented numerical analysis · nonlinear systems · ordinary differential equations partial differential equations · Markov chains · adaptive finite element methods · free boundary problems applications in phase transitions · porous media flow · continuum mechanics · long-term behaviour of nonlinear highly oscillatory dynamical systems · statistical modeling and efficient simulation algorithms modeling and efficient algorithms for fast time scales.]]> http://nbic.roquin.net/about-nbic/jobspositions/detail/jobdetails/postdoc-bio-informatics/ http://nbic.roquin.net/about-nbic/jobspositions/detail/jobdetails/postdoc-bio-informatics/ Fri, 11 Dec 2009 17:00:13 +0100 We are looking for a postdoctoral fellow bioinformatics/-statistics who will help us to analyze complex metagenomic data in relation to epidemiological parameters. Besides the complex problem of interpreting phylogenetic data of microbiota, we find there are currently no generally accepted statistical methods available to analyze complex communities in relation to epidemiological determinants, especially not in multivariate ways. Our final goal is to model complex microbiota with the help of environmental and individual characteristics, with the ultimate goal to predict when disease will develop and to design preventive strategies.]]> http://nbic.roquin.net/about-nbic/jobspositions/detail/jobdetails/postdoctoral-positions-available-in-mit-computational-biology-group/ http://nbic.roquin.net/about-nbic/jobspositions/detail/jobdetails/postdoctoral-positions-available-in-mit-computational-biology-group/ Fri, 11 Dec 2009 16:41:27 +0100 http://nbic.roquin.net/about-nbic/jobspositions/detail/jobdetails/bio-informatician/ http://nbic.roquin.net/about-nbic/jobspositions/detail/jobdetails/bio-informatician/ Thu, 26 Nov 2009 09:36:12 +0100 www.nbic.nl) and in close collaboration with the Bioinformatics Department.]]> http://nbic.roquin.net/about-nbic/jobspositions/detail/jobdetails/2-pfh-students/ http://nbic.roquin.net/about-nbic/jobspositions/detail/jobdetails/2-pfh-students/ Mon, 26 Oct 2009 15:09:43 +0100 Arabidopsis root system is in many ways an ideal model system to study developmental processes in plants. Roots have a simple morphology and a relatively small number of cell types, and they exhibit all developmental stages simultaneously. They can be efficiently transformed and chemically perturbed and dure to their near transparency, they offer unmatched opportunities to observe the molecular phenotypes of such treatments. The development of lateral root organs is one of the research foci at the Plant Systems Biology department. We are looking for a PhD student to reverse engineer the lateral root initiation (LRI) process and its interface with hormone signaling and cell cycle processes from molecular and morphological data. We are also looking for a PhD student to study the impact of duplication of functional divergence of developmental regulators on the evolution of LRI and other developmental processes. The project will initially be focused on Aux/IAAs and ARFs, two classes of transcriptional regulators that play important roles in auxin responses and plant development. ]]> http://nbic.roquin.net/about-nbic/jobspositions/detail/jobdetails/bioinformatics-scientist-sequence-applications/ http://nbic.roquin.net/about-nbic/jobspositions/detail/jobdetails/bioinformatics-scientist-sequence-applications/ Tue, 13 Oct 2009 14:36:41 +0200 http://nbic.roquin.net/about-nbic/jobspositions/detail/jobdetails/bioinformatics-expert/ http://nbic.roquin.net/about-nbic/jobspositions/detail/jobdetails/bioinformatics-expert/ Mon, 12 Oct 2009 16:36:13 +0200 http://www.bits.vib.be), with a bioinformatics expert. Your goal will be to support cutting-edge projects involving high throughput genomics datasets generated by whole-genome sequencing projects using multiple platforms (Illumina, SOLiD, 454, Complete Genomics, others). You will play a key role in setting up a Bioinformatics-infrastructure to enable processing, analysis, visualization and dissemination of genomics datasets, unprecedented in scale. In this position, you will also broker between VIB scientists and leading genomics and bioinformatics companies to discuss study design, sequence analysis strategies and data processing as well as IT-infrastructure. You will assist in the analysis of the generated data and disseminate information through comprehensive research reports and presentations. Additionally, you will evaluate new and existing algorithms, software (commercial and open source) and computer infrastructure requirements. This is a once-in-a-lifetime opportunity to pioneer a bioinformatics platform to enable translational genomics at VIB.]]> http://nbic.roquin.net/about-nbic/jobspositions/detail/jobdetails/postdoc-or-phd-student-computational-biology-visual-analysis-of-computer-tomography-scans/ http://nbic.roquin.net/about-nbic/jobspositions/detail/jobdetails/postdoc-or-phd-student-computational-biology-visual-analysis-of-computer-tomography-scans/ Mon, 12 Oct 2009 16:27:50 +0200 research program Visual Interactive Effective Worlds (VIEW). The project is a collaboration with the research group from Dr. J.A. Kaandorp (Section Computational Science, University of Amsterdam). In this project we propose to develop visualization techniques for quantitative research on complex shaped and variable biological and simulated objects and techniques for the visualization of abstract n-dimensional parameter spaces in models of gene regulatory networks. The project aims to develop methods and tools to extract and present geometrical information from spatial measurements and simulation, to develop visualization methods to compare simulation models and measured data, and techniques for the navigation of morphometric parameter spaces (morphospaces) and model parameter spaces. In this part of
the project we will focus on the analysis of calcification in  3D images (Computer Tomography Scans) of scleractinian corals. A better understanding of calcification in corals is of fundamental importance in research on the potentially detrimental impact of increasing atmospheric carbon dioxide concentrations, reducing ocean pH and carbonate ion concentrations on the calcification process in corals.  The candidate is expected to collaborate extensively with  biologists.]]> http://nbic.roquin.net/about-nbic/jobspositions/detail/jobdetails/phd-student-in-computational-biology-for-the-projectgenetic-and-cellular-mechanisms-for-controlled/ http://nbic.roquin.net/about-nbic/jobspositions/detail/jobdetails/phd-student-in-computational-biology-for-the-projectgenetic-and-cellular-mechanisms-for-controlled/ Mon, 12 Oct 2009 15:57:20 +0200 http://nbic.roquin.net/about-nbic/jobspositions/detail/jobdetails/postdoc-or-phd-student-in-computational-biology/ http://nbic.roquin.net/about-nbic/jobspositions/detail/jobdetails/postdoc-or-phd-student-in-computational-biology/ Mon, 12 Oct 2009 15:42:11 +0200