Category: Uncategorized

The Biodiversity Genomics Initiative, Smithsonian Institution (SI) is seeking skilled professionals with bioinformatics and computational expertise in genomics. Successful applicants will be part of a bioinformatics group working as an integrated team with Smithsonian scientists and computer support professionals. Incumbents will interact with scientists in all participating SI units including the National Museum of Natural History, National Zoological Park, Smithsonian Tropical Research Institute and Smithsonian Environmental Research Center, and may have his/her duty station located within any one of these units.

Responsibilities of these positions include:

1) Developing or implementing data analysis pipelines for Next Generation DNA Sequence (NGS) or other genome scale datasets

2) Working closely with SI scientists on the experimental design of NGS and other genome scale projects

3) Making high performance computational resources accessible to SI researchers involved in genome scale research via consultation, training, and web site development

4) Developing new experimental protocols for NGS data production in the laboratory and new procedures for computational analysis of the data produced

5) Consulting and collaborating with Biodiversity Genomics scientists, postdocs and students on research grant proposals and publication of results

6) Coordinating bioinformatics activities of the Biodiversity Genomics Initiative

7) Keeping abreast of new developments and related research conducted elsewhere in order to improve genome scale research at SI.

Knowledge, skills and experience desirable for these positions include: Relevant scripting and/or programming skills and experience, Expertise with NGS workbench environments (e.g., Galaxy, Biolinux, Genious, Qiime), Experience with NGS data analysis from multiple platforms (e.g., Illumina and 454), Expertise in computational aspects of one or more of the following research areas: phylogenetics, population genetics, metagenomics, gene expression, evolutionary genomics.

These positions will begin as two-year contracts, with the possibility of extension. Salaries will be commensurate with experience. To apply, submit resume, statement of relevant experience, and names and contact information of 3 references via e-mail to Michael Braun, Chair, Biodiversity Genomics Steering Committee (braunm@si.edu).

Review of applications will begin on April 1 and continue until the positions are filled.

We are seeking a bioinformatician to join our team to conduct computational biology work on high throughput sequencing data. The successful applicant will contribute computational and bioinformatics expertise to an ANR and EU-funded project devoted to characterise the genomics of speciation in the house mouse. Work will include the development of bioinformatics pipelines in Perl and/or Python to automate the analysis of NGS data sets (assembly of genome resequencing and RNAseq data, SNP and structural variant detection, epigenomics and transcriptomics analysis). The successful applicant will be expected to work as part of a team and to train biologist colleagues to NGS data analysis.  Candidates will hold a Master or PhD degree in any relevant area of expertise (bioinformatics, computer sciences, genomics) with some working experience in bioinformatics or life science research IT.  Extensive knowledge of  bioinformatics tools and NGS applications as well as a proven background in analysing Next Generation Sequencing data is required.  Strong programming skills in Perl/Python is expected, and knowledge in R and C ++ programming would be a plus.

This post will be based in Montpellier (South of France), European centre of excellence in biodiversity research and known for its quality of life in the Mediterranean region. The Institute for Evolutionary Biology has a long lasting history of research excellence in genetics and evolution and the successful applicant will directly benefit from  this outstanding scientific environment while building a strong and valuable experience in biodiversity informatics. Candidates will not need to speak French and the working language will be English.

This post is fixed term for 2 years and net monthly salary will be 2100-2500 Euros depending on experience.

Applications should be sent to carole.smadja@univ-montp2.fr AND Pierre.boursot@univ-montp2.fr by ***10 April 2012*** and should include a detailed CV, names and contact details of 3 referees and a 1-page statement which will detail your bioinformatics experience (programming languages, research projects, training workshops, development of software, pipelines or tutorials).

Dr. Carole Smadja

CNRS research scientist

Chargée de recherches CNRS

http://www.carole-smadja.staff.shef.ac.uk/

Institut des Sciences de l¹Evolution

cc065, Université Montpellier 2

34095 Montpellier, France

Phone: +33 (0)4 67 14 92 70

There are several openings for Bioinformaticians and Software Developers at the University of Glasgow (UK). The successful candidates will join a new facility – jointly funded by the Wellcome Trust and the University of Glasgow – that will develop and extend data analysis tools for integrated genomics, transcriptomics, proteomics and metabolomics studies. This is a great opportunity to interact closely with biologists, clinicians and ecologists, and to establish varied collaborations within and outside the University.

Closing date is 2 March 2012.

For more information see the Naturejobs ads: http://bit.ly/xeaq3H (Bioinformaticians, 4 jobs), http://bit.ly/zh09py (Software developer, 1 job) and http://bit.ly/xEyO27 (Software development manager, 1 job). And the ad on the University website: http://bit.ly/ykeLSc

To learn more about research in the College of Medical, Veterinary and Life Sciences at the University of Glasgow, visit:
http://www.gla.ac.uk/colleges/mvls/.  The University of Glasgow, charity number SC004401

A position is available in Nick Goldman’s group at the EMBL-European Bioinformatics Institute (near Cambridge, UK) for a Research Associate (post-doctoral level).

The position is available from 1 April 2012 or later by mutual agreement, and is expected to be for 3 years in the first instance.  Full details are viewable at http://ig14.i-grasp.com//fe/tpl_embl01.asp?newms=jj&id=47907&aid=15470 and http://www.nature.com/naturejobs/science/jobs/245341-Research-Associate -in Molecular-Evolution and the job description is included below.

Nick Goldman, EMBL – European Bioinformatics Institute

tel: +44-(0)1223-492530

fax: +44-(0)1223-494468

Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK

A Research Associate (Officer) position exists in Nick Goldman’s research group (http://www.ebi.ac.uk/goldman) at the European Bioinformatics Institute (EBI) which is located on the Wellcome Trust Genome Campus near Cambridge in the UK.

The group studies the evolutionary analysis of DNA and protein sequences, computational data analysis methods, probabilistic modelling of molecular evolutionary processes and statistical inference based on these models. We are particularly interested in applications of existing and novel sequence analyses in large-scale comparative genomics and Next (2nd- and 3rd-) Generation Sequencing, and benefit from  association with other groups at the EBI (http://www.ebi.ac.uk/Groups) and elsewhere.

The Research Associate will work with Nick Goldman and other members of the group on issues relating to evolutionary sequence or NGS analysis. It is expected that these would include phylogenetic methodology and biological applications. The position permits freedom for the postholder to be involved in research projects already under way in the group (for example, detection of adaptive evolution, analysis of patterns of DNA mutations and amino acid replacements, sequence alignment, comparative analysis of genome-scale sequences, methods to exploit NGS data) and to develop his/her own interests in related areas; the Research Associate will be expected to do both of these things.

In addition to pursuing their research projects, a suitably experienced Research Associate will take responsibility for various tasks maintaining and developing the efficient operation of the group. These may include management and/or leadership of research projects of their own and the group leader’s devising; preparation of grant applications, liaison with colleagues and collaborators both within and outside of EMBL; promotion of the group’s work at EBI and elsewhere (including abroad); teaching at training events (including abroad); compilation of materials for reports and presentations; scientific supervision of other staff (including post-graduate students and junior visitors).

The EBI is part of the European Molecular Biology Laboratory (EMBL) and is Europe’s leading provider of information services to biological researchers in academia and industry.  For further information please visit www.ebi.ac.uk

Qualifications and Experience

The post holder will have a PhD, and further research experience in related fields will be advantageous. Necessary qualifications include: understanding of and enthusiasm for the questions molecular biologists need to ask of sequence data, experience of mathematical modelling and statistical data analysis, and scientific computer programming. A background in biology, mathematics/statistics, computer science or other technical disciplines, combined with subsequent cross-disciplinary experience, is the likely career path. Demonstrated previous success in the additional responsibilities described above, and aptitude for all of them, will be preferred.

The successful candidate will have a good research record with previous publications in a related area of research.  Excellent communication and interpersonal skills are required.

Application Instructions

Please apply online through www.embl.org/jobs

Additional Information

EMBL is an inclusive, equal opportunity employer offering attractive conditions and benefits appropriate to an international research organisation.

Please note that appointments on fixed term contracts can be renewed, depending on circumstances at the time of the review.  Note that special visa requirements apply to employees from non EU countries working at EMBL-EBI in the UK. The period of work does not qualify them for the Highly Skilled Migrants Programme.

Ranked the number one agricultural institute in Europe and number two in the world, INRA (National Institute for Agricultural Research)

carries out mission-oriented research for high-quality and healthy foods, competitive and sustainable agriculture and a preserved and valorised environment.

Every year, INRA seeks researchers from all disciplines to reinforce laboratory and fieldwork teams. Researchers will be heavily involved in scientific networks and tackle environmental, economic and social issues. They are expected to strive for excellence and come up with useful, concrete applications for the real world. Individual research projects will go hand in hand with group efforts in a bid to further knowledge and innovation, in order to produce sustainably, preserve the environment, and improve human nutrition.

INRA is recruiting 51 scientists through open competition and offering permanent positions.

Positions are opened to PhD (or equivalent) in a wide range of scientific disciplines such as biochemistry, biology, genetics, ecology, genomics, mathematics, physiology, microbiology, economics, forest sciences, environmental sciences, sociology, animal production sciences, computer science, chemistry, neurosciences, entomology, statistics, virology and many more.

There are 10 permanent positions in genomics and genetics:

– Computational biology and bovine sequence data

– Statistical genomics for genetic analysis of polygenic traits and genomic selection of crops

– Methods of genomic selection and optimisation of genetic management  for animal production systems based on crossbreeding

– Genomic selection of cattle and sustainability of livestock production

– Mining genetic diversity and wheat genomic selection

– Quantitative genetics and breeding methods for forest trees

– Durability of wheat resistance to fungal diseases

– Evolution of populations of plant viruses in an agricultural landscape: consequences for epidemiology

– Functional genomics of fish pathogenic bacteria

– Genomics of beef cattle breeds

Applications are available of January 26 to February 28, 2012.  All useful information to apply are available on:

www.international.inra.fr (see “Join us”) For further details:  concours_chercheurs@paris.inra.fr

Fabienne Giroux

Assistante RH en charge

de la communication sur le recrutement

fabienne.giroux@paris.inra.fr

Dr. Toomajian’s Molecular Population Genetics Lab investigates genetic variation in natural populations of plants and fungi with an aim of  understanding the genetics of adaptation. The lab spans the intersection of computational biology, evolution, and functional   genomics. We are recruiting a highly motivated postdoc to help analyze Arabidopsis next-generation transcriptome sequence to characterize gene expression variation. This project is laying the groundwork for studies of the genetic control and evolution of gene expression and the integration with population genomics data. The candidate will also participate in the lab’s fungal population genomics projects, and training on techniques related to all projects is available.

Toomajian lab website https://sites.google.com/site/toomajianlab/

NSF Arabidopsis 2010 project website http://seqr-1.biology.utah.edu/NSF2010/index.html

Department website www.plantpath.ksu.edu

The lab interacts with K-State’s Ecological Genomics Institute http://ecogen.ksu.edu/

The area of emphasis for this position will be bioinformatics and genomics. The successful candidate may develop independent projects related to the main goals of the lab. This position requires excellent independent discretion and judgment and may involve some supervision of graduate and/or undergraduate students.

Qualifications include:  PhD in a Biosciences field, Computer programming skills (i.e., C/C++, Python, PERL, Ruby, or R), Familiarity with the UNIX/LINUX computer-operating environment and with databases, Experience in and/or knowledge of bioinformatics and  statistical analysis

Other preferred qualifications include:  Previous experience with molecular biology laboratory techniques, Experience working with next-generation sequencing datasets and analysis tools, Experience analyzing RNA-Seq data, Knowledge of population genetics and/or molecular evolution.

Application procedure:  See full ad with complete instructions at: http://www.plantpath.ksu.edu/doc1303.ashx

A complete application must include: 1) a cover letter that includes timing of availability for this position and lists your research  interests in working in the lab of Dr. Toomajian; 2) a curriculum vitae; 3) a statement describing your relevant educational and  research experiences and how they relate to the qualifications (necessary and preferred) of the position (2 pages maximum); 4) up to 3 reprints; and 5) arrange to have 3 professional letters of recommendation sent.

All application materials may be sent as hard copies or PDF documents electronically.

E-mailed applications should be sent to plantpath@ksu.edu Use “Genome bioinformatics position” in subject line of email to ensure your application materials are received.

Deadline for applications: 02/20/2012.

Kansas State University is an equal opportunity, affirmative action employer and actively seeks diversity among its employees. Background checks required.

Christopher Toomajian
Assistant Professor
Kansas State University
Department of Plant Pathology
4024 Throckmorton Plant Sciences Center
Manhattan, KS 66506
office: (785) 532-0879
fax: (785) 532-5692
toomajia@ksu.edu
http://sites.google.com/site/toomajianlab/

The Faculty of Agricultural Sciences at Georg-August-Universitaet Goettingen, Germany, invites applications for a Junior Professorship (W1) for a Population Genomics of Host-Pathogen-Systems in  Livestockâ.  The position is to be filled at the earliest possible date and is a fixed-term professorship for the duration of three years.  Pending a positive evaluation, the position may be extended by another period of three years.

The successful candidate shall represent the subject in research and teaching.  The approaches in research will aim at a better understanding of adaptation mechanisms and interactions between host and pathogens on the genomic level.  Research activities will be concentrated on selected host-pathogen-systems in livestock (including aquaculture) and may have either an experimental or a more theoretical focus.  The candidate will hold an excellent PhD in a relevant discipline (e.g., agricultural science, biology, statistics).  Experience in population genomics research and interest in interdisciplinary collaboration as well as in the participation in existing collaborative projects are supposed.  Please visit www.nutztierwissenschaften.uni-goettingen.de for additional information on this position (in German).  Further requirements for employment are stated in the Niedersachsisches Hochschulgesetz (NHO) from February 26th, 2007.  If the applicant was employed as a research assistant either before or after obtaining the doctoral degree, the entire duration of the period of employment and of the doctoral degree should not exceed six years. The Georg-August-University Goettingen Public Law Foundation owns the right of appointment.  Further details can be given upon request.  Applications of candidates from abroad are explicitly welcome.  The University of Goettingen places particular emphasis on fostering career opportunities for female scientists and scholars and therefore strongly encourage qualified women to apply.  Disabled persons with equivalent qualification will be given preference.  Applications should include a full CV, a list of publications, a statement of academic achievements including teaching, as well as an own representative research paper.  Please submit your electronic application until Jan. 10, 2012,  to Prof. Dr. Achim Spiller, Dean of the Faculty of Agricultural Sciences, Buesgenweg 5, D-37077 Goettingen, Germany, E-Mail: dekagrar@uni-goettingen.de

Bioinformatics students, Wen-Chi Chou and Juber Patel, present their research at the Cold Spring Harbor Genome Informatics Meeting, November 2-5, 2011. Wen-Chi Chou presented a poster entitled: Bacterial Genome Sequence Finishing with Functional Genome Structure. Juber Patel presented a poster entitled: DAWGPACK: Ultra-fast NGS Alignment and Analysis in the Cloud.

The Department of Computing is one of the leading departments of Computer Science in the world. In the UK, it has consistently been awarded the highest research rating (5*) in Research Assessment Exercises (RAE), coming 2nd in the UK 2008 RAE, and was rated as “Excellent” in the previous national assessment of teaching quality. In the 2010 Times Higher Education, it is ranked as the
9th best in the world.

An exciting opportunity has arisen for a Research Associate (post-doctoral) for the prestigious European Research Council Starting Grant funded project on analysis of biological  networks. The purpose of the project is to develop and apply sophisticated  graph theoretic algorithms and models carefully tuned to extract biological knowledge from topologies of real-world biological networks, including protein-protein interaction, metabolic, transcriptional regulation, and disease association networks. The aim is to mine biological network data for new biological insight that would complement the knowledge that can be obtained from mining genetic sequence data. The developed graph theoretic tools will further be applied to other network domains including economic, social, and computer networks.

The successful applicant will be responsible for developing new graph theoretic models and algorithms for some of the foremost problems in computational systems biology, including network alignment and network integration of various types of data.  You will design and implement the models and algorithms, apply them to real-world biological network (and other domain) data from public and private sources, statistically analyze the results, write research papers, present the work at international conferences, and contribute to updating our open source software package, GraphCrunch, with the new methods.

To apply you will have a PhD (or equivalent) in Computer Science, Engineering, Mathematics, Physics, Bioinformatics, or a related discipline. You should have a proven knowledge and track record in several of the following areas: graph and complexity theory, algorithms, bioinformatics, programming in C, C++, a scripting language and Matlab, using a parallel computing environment, scientific computing, data analysis, statistics and machine learning.

How to apply:

Our preferred method of application is online via our website at: http://www3.imperial.ac.uk/employment (please select  $B!H (Bjob search $B!I (B then enter the job title or vacancy reference number *EN2011XXXBD* into $B!H (Bkeywords $B!I (B).Please complete and upload an application form as directed.

Applications must include the following:

* A college application form – quoting reference number *NP 10 11* on the form * A full CV including: University degrees and dates, past and present posts and list of publications.

* A 2-page statement indicating what you see are interesting research issues relating to the above post and why your expertise is relevant.

For queries regarding the application process contact Joanne Day by email to: research.officer@doc.ic.ac.uk

*Closing date for applications: November 7, 2011*