Post-doctoral position in Computational Biology of Terrestrial Deep Biosphere
- Last Updated on Thursday, 07 March 2013 15:19
(DL. September 30, 2012)
The Department of Information and Computer Science at Aalto University (http://ics.aalto.fi) and VTT Technical Research Centre of Finland (http://www.vtt.fi) in Espoo, Finland are looking for a motivated, self-driven computational biologist, or bioinformatics specialist to join our multidisciplinary research team deciphering the metagenomics and metatranscriptomics of deep earth crust microbial communities. Research is connected to ICDP (International Continental Scientific Drilling Program) and global network of Deep carbon observatory (https://dco.gl.ciw.edu/) as well as the National Centre of Excellence on Algorithmic Data Analysis.
We expect the applicants to have a PhD (or to have submitted a dissertation for evaluation) in Computer Science, Statistics, Computational Biology, Bioinformatics or a related field, with excellent publication record and expertise in one or more of the following fields:
- Next generation sequencing
- Algorithm design
- Machine learning and data mining
- Systems biology
Excellent programming (Python, MATLAB, R, C++) and technical skills, as well as excellent written and oral communication skills are required. Previous expertise in metagenomics data analysis or metabolic modelling is considered an advantage.
The successful candidate will join a team of researches led by Docent Merja Itävaara (VTT Technical Research Centre of Finland) and Professor Juho Rousu (Aalto University and Helsinki Institute for Information Technology). The post doc position is for two years and is jointly affiliated with both VTT and Aalto University.
- Expression of interest that includes contact information of the applicant, and names and contact information of two senior academics available for reference per e-mail.
- A complete curriculum vitae describing education and employment history
- List of publications, with pointers to openly available online versions of at most three of the most relevant publications
Please use “DeepBiosphere” as a reference in the application. Applications received by September 30, 2012 will receive full consideration.
The salary level for a starting postdoctoral researcher is between 3200 and 3600 euros per month, depending on experience and qualifications. The contract includes occupational health services and Finland has a comprehensive social security system. In addition to research work, a postdoctoral researcher is expected to participate in the supervision of students and teaching related to their research topic. Candidates may be invited for an interview on the Otaniemi campus of Aalto University in Espoo/Helsinki. Good command of English is a necessary prerequisite.
For further information, please contact:
Professor Juho Rousu
Department of Information and Computer Science, Aalto University
PO Box 15400 (Konemiehentie 2, Espoo), 00076 Aalto, Finland
Docent Merja Itävaara
VTT Technical Research Center of Finland
Tietotie 2, 02044 VTT, Finland
About the Department of Information and Computer Science, Aalto University
Aalto University is a new university created in 2010 from the merger of the Helsinki University of Technology TKK, the Helsinki School of Economics, and the University of Art and Design Helsinki. The University’s cornerstones are its strengths in education and research, with 20,000 basic degree and graduate students, and a staff of 4,500 of whom 300 are professors. For further information, see http://www.aalto.fi/en
The Department of Information and Computer Science at Aalto University in Espoo/Helsinki, Finland, pursues research on advanced computational methods for modelling, analysing, and solving complex tasks in technology and science. The research aims at the development of fundamental computer science methods for the analysis of large and high-dimensional data sets, and for the modelling and design of complex software, networking and other computational systems. In the recent Research Assessment Exercise covering all the 46 units of Aalto University, the Department of Information and Computer Science was one of two units achieving an almost perfect score of 24 out of 25, from review panels assessing the units on a scale of 1 to 5 in the five subareas of scientific quality, scientific impact, societal impact, research environment, and future potential. The Department has a web site at http://ics.aalto.fi/
VTT Technical Research Centre of Finland is an impartial expert organisation. Its objective is to develop new technologies, create new innovations and value added thus increasing customer's competitiveness. With its know how VTT produces research, development, testing and information services to public sector and companies as well as international organisations. Through its international scientific and technology network, VTT can produce information, upgrade technology knowledge, create business intelligence and value added to its stakeholders. VTT is a non-profit-making research organisation.
The geobiology research consortium at Biotechnology cluster of VTT (www.vtt.fi) in Espoo/Helsinki Finland is studying terrestrial deep biosphere. The research is connected to biogeochemistry and microbial ecology of deep earth crust ecosystems. Metadata and metapathway analysis of multispecies microbial communities will be studied in collaboration with multidiscicplinary research team of Aalto University and VTT.
PhD Position: Engineering Executable Models of Biological Networks
- Last Updated on Thursday, 07 March 2013 15:19
At the Department of Computer Science at the Vrije Universiteit (VU) in Amsterdam, one PhD position for four years is available on a research project devoted to
Engineering Executable Models of Biological Networks
Starting date of the PhD position: as soon as possible.
The goal of the project is to describe gene regulatory networks by formal interaction patterns/models. Using these formal models, we aim to derive new insights in the behaviour of gene networks. These models, ultimately, describe cells' behaviour, and cell components, as independent, communicating entities. Simulating cell behaviour this way at the same time promises new insights and poses new challenges on the execution and verification environment due to the complexity, heterogeneity and variability of the modeled entities.
The work will start with the application of our formal framework using Petri nets to model gene network behaviour. Additionally, extensions of the framework and new methods and tools for analysis of the behaviour patterns will be developed.
For more detailed information on the project, see
This project is a collaboration between two research groups at the VU: Bioinformatics (Anton Feenstra and Jaap Heringa), and Theoretical Computer Science (Wan Fokkink). For experimental validation of predictions, we collaborate with two experimental groups; the group Receptor Systems Biology at the VU (Martine Smit), and Bertie Göttgens at the Cambridge Institute for Medical Research.
Candidates should have completed their studies in computer science, bioinformatics or a closely related area. Experience with biological systems, a good theoretical background, and an open attitude to applications are considered advantages. You should enjoy working in an internationally oriented and interdisciplinary research environment. Communicative skills and the ability to work in a team are important.
Information and application
For further information about these positions please contact either:
You are invited to send an application by email to the above email addresses no later than September 1, 2012. Your application should consist of a cover letter, a curriculum vitae (including detailed information regarding your academic degree), and the names and addresses of two references.
Head of a bioinformatics/biostatistics platform (ICM, Paris, France)
- Last Updated on Thursday, 07 March 2013 15:19
INRIA and the IHU of Translational Neurosciences hire Scientific coordinator of a bioinformatics/biostatistics platform
Starting date: as soon as possible
The ICM (Brain and Spine Institute) is located in the heart of the Pitié-Salpêtrière hospital in Paris, France. The institute is dedicated to fundamental and clinical research on the central nervous system. The institute hosts in a single building about 500 clinicians and scientists, who work altogether to make new discoveries about the human brain function, to develop new treatments for neurologic diseases and to deliver them to the patients. The institute covers a large clinical scope with a particular emphasis on Alzheimer’s disease, Parkinson’s disease, multiple sclerosis, epilepsy, depression and paraplegia.
The ICM is a founder member of the university hospital institute (IHU-A-ICM) for translational neurosciences. In the framework of this program, the ICM and the IHU-A-ICM want to collaborate with INRIA to set up a mutual biostatistics and bioinformatics platform (WP7 project). They are looking for the scientific coordinator of the platform.
The platform coordinator will set up, develop and maintain the platform that is dedicated to bioinformatics and biostatistics. He/She will be responsible of a staff of about 7 people composed of data manager, statisticians, computer scientists, etc.. Staff will be recruited using the funds available trough the IHU grant. These funds will also cover the costs of the computing facilities.
The platform aims to gather and analyze all kinds of data acquired within the IHU. The final goal will be to integrate multi-modal databases and to use them to model multi-scale physiological and pathological processes. At first, the platform will focus on genetic, genomic and transcriptomic (DNA-Array and RNAseq) data, and then on epigenetic, proteomic and metabolomic data, aiming to identify and/or use biomarkers of neurologic diseases. These databases will be integrated with the available clinical data. Moreover, these data will be used in conjunction with neuroimaging data such as MRI, PET images and MEG/EEG signals. This later aspect will be done in close collaboration with the neuroimaging platform (CENIR), the research team Cogimage and the platform for image and signal analysis (CATI). The candidate does not need to have a particular expertise in neuro-imaging, since he/she could rely on the current expertise within the IHU on this topic. More precisely, the scientific coordinator will supervise the:
- development and maintenance of the databases,
- integration and utilization of these databases for statistical studies,
- data modeling and validation of the models,
- dissemination of results and methods.
In terms of research, the platform will be developing its own methodological research in biostatistics/bioinformatics in relation to the acquired data (in priority the “omics” and
clinical data). In biostatistics, one could develop original methods for multivariate data analysis, regression or model selection within massive amount of data, for instance. The platform could rely at first on the research team Cogimage and CATI, before developing its own research activity with the support of INRIA.
The position requires a strong expertise in the field of biostatistics and/or bioinformatics.The candidate should hold a PhD in these fields and have a postdoctoral experience of at least 5 years.The candidate should have strong relational and managerial skills with a great interest for multi-disciplinary work, and in particular for interactions with neuroscientists and clinicians. The salary will be determined according to the candidate’s experience at the best international standards.
Please send resume and cover letter (mail or electronic format) to:
Cecile Proust :
Institut du Cerveau et de la Moelle epiniere (ICM)
Groupe Hospitalier de la Pitie Salpetrier
47 boulevard de l’hopital
Position Available: Bioinformatics & Integrative Genomics Specialist, VIB & KU Leuven
- Last Updated on Thursday, 07 March 2013 15:19
The VIB Center for the Biology of Disease at the University of Leuven is a vibrant and international research centre where key issues relevant to major human health challenges are tackled. Within this Center, we are seeking a highly motivated and experienced Bioinformatics & Integrative Genomics Specialist. You will collaborate with the 14 research groups within the Center and provide essential input on computational biology aspects of their research projects. In this job you will be confronted with exciting research questions in cancer and neurodegeneration; and with a broad spectrum of computational challenges and omics data sets. You will be embedded in the Laboratory of Computational Biology at the University of Leuven (Stein Aerts Lab: http://med.kuleuven.be/bioinformatics), and you will be part of an active bioinformatics community in Leuven, allowing daily interactions with colleague bioinformaticians.
Your main activity will be to provide support for large-scale data analysis, and to setup and manage a Bioinformatics consulting core within the Center through which:
- you will collaborate with wet-lab scientists on a variety of research problems. You will deal with the data analysis part of the research project. The focus of the service will be mainly on genome bioinformatics: microarrays, RNA-Seq, ChIP-Seq, exome/genome re-sequencing, gene regulation, network biology, pathway analysis, gene prioritization, data integration, text-mining, etc.
- you will gradually manage a team of 1-3 Bioinformatics experts
- you will interact with the core facility of the VIB-BITS (http://www.bits.vib.be/), with the Genomics Core facility at the University Hospital (allowing close interaction with the next-generation sequencing instruments Illumina HiSEQ2000, Illumina MiSEQ, Roche 454, PacBio), and with other consulting units and research groups, for example for advanced biostatistics or proteomics data analysis.
- you will make hardware (e.g., local linux servers, high performance computing, cloud), software (e.g., a local Galaxy instance), and analysis pipelines (e.g., scripts, workflows) available to scientists; train and guide scientists to analyze their own datasets; and organize training courses and seminars.
- you will take your own initiatives to continuously optimize the bioinformatics flux through the Center, through the VIB and through the Group of Biomedical Sciences, for example to organize a weekly "data clinic" where small user problems can be solved.
- Master's degree in Life sciences or computational field
- PhD degree is strongly preferred
- At least five years bioinformatics experience
- Proven track record of high-impact publications in the field of computational biology, analysis of high-throughput data sets, data integration
- Solid experience with Linux, programming (e.g. Java), and database management (sql and no-sql).
- Solid experience with bioinformatics programming and statistics for bioinformatics, including scripting (e.g., Python), R (incl. Bioconductor), Galaxy, UCSC Genome Browser, Ensembl API, etc.
- Thorough understanding of molecular and developmental biology, and of disease biology (preferably cancer and/or neurological disorders).
- Experience with the analysis of next-generation sequence data is a plus: whole exome re-sequencing, whole-genome re-sequencing, SNP/indel calling, CNV, Structural variation; RNA-Seq, ChIP-Seq
- Experience with pathway analysis and cis-regulatory sequence analysis is a plus.
- Knowledge of machine learning and data mining is a plus.
- The Center for the Biology of Disease
- The Laboratory of Computational Biology
- Center for Human Genetics
- University of Leuven
Postdoc Position in systems biology with applications in prostate cancer
- Last Updated on Thursday, 07 March 2013 15:19
Karolinska Institutet, Inst. för medicinsk epidemiologi och biostatistik
About the Department and the biostatistics group
The Department of Medical Epidemiology and Biostatistics presently employ approximately 250 staff with 15 full professors and over 40 graduate students. The department is one of the largest departments of epidemiology in Europe. Unique data resources – such as the Swedish Twin Registry, several large prospective studies, ongoing nation-wide case-control studies, access to clinical data, biological material and high-throughput genotype, expression, proteins/metabolites and sequence data – are effectively explored at the department. Further information can be found at: www.ki.se/meb
The prostate cancer research group currently comprises 4 senior and 2 junior researcher as well as 8 PhD students. Several large case-control and cohort prostate cancer populations are available with collected biological samples (blood, urine, tumor) and complete information about clinical characteristics and disease progression. The research is performed in an interdisciplinary setting with strong collaboration with clinical departments and other national and international research groups. The position will be part of WP4 of the e-Science for Cancer Prevention and Control project (http://e-science.se/community/eCPC), a flagship project at the Swedish e-Science Research Centre (SeRC, http://www.e-science.se); a strategic research area funded by Vetenskapsrådet. The position also holds a tight connection to the studies in the Cancer Risk Prediction Center (CRisP, www.crispcenter.org).
Area of responsibilities/description of the work
Applications are invited for a two-years postdoctoral research position to characterize prostate cancer progression, aggressiveness and prognosis by integrating genetic and transcriptomics deep sequencing data with clinical information using a large population based prostate cancer cohort. The applicant is expected to work with high-level data analysis and modeling in the field of medical systems biology using high quality in-house produced data. The results from computational analyses will be validated with independent experiments.
The applicant should have a PhD degree in computer science, applied mathematics, bioinformatics, systems biology, or related discipline. Ideally, applicant has strong methodological expertise (e.g., graph theory, probability theory, machine learning), good programming and communication skills, and is interested in developing and applying novel computational methods in cancer research.
An employment application must contain the following documents in English or Swedish:
- A complete curriculum vitae, including date of the thesis defence, title of the thesis, previous academic positions, academic title, current position, academic distinctions, and committee work
- A complete list of publications
- A brief statement of research interest
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