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Latest announcements
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BACKGROUND:
The laboratories of Profs Jun S. Liu and X. Shirley Liu invite applications for a joint postdoctoral position. Jun Liu ([link]) is at the Statistics Department at Harvard University and his research focuses on Bayesian modeling and computation methodology, statistical genetics, and Monte Carlo methods, with applications to large-scale computation and optimization. Shirley Liu (http://liulab.dfci.harvard.edu/) is at the Department of Biostatistics and Computational Biology at Dana-Farber Cancer Institute and Harvard School of Public Health, and her research focuses on genomics and bioinformatics of transcription and epigenetic gene regulation, with applications to cancer biology. The postdoctoral fellow will be jointly supervised by both laboratories to work on statistical and computational methodologies for gene regulation problems.
REQUIREMENTS:
Ideal applicant should have:
* PhD degree in physical sciences or related fields
* Strong programming skills: ((Python | Perl) & (C | C++ | Java) & R)
* Strong quantitative background (machine learning, Bayesian inference, etc.) or computational genomics experiences (DNA sequence analysis, microarray analysis, etc.)
* Good knowledge of molecular biology and genomics
* At least two (four if co-first author) first author papers written in English in previous area of research (not necessarily computational biology) with submitted, accepted or published status in journals or conference proceedings
* Good spoken and written communication skills, mature and motivated.
* In addition, applicant must be able to visit Boston for potential interviews without visa application.
HOW TO APPLY:
Interested applicants should submit a letter of interest with a research proposal for a project (~2 pages) to be conducted during postdoctoral training, CV, and three references (including name and contact information) to jliu (At) stat (Dot) harvard (Dot) edu and xsliu (At) jimmy (Dot) harvard (Dot) edu and with subject line "Joint postdoc application".
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BACKGROUND:
The laboratory of X. Shirley Liu (http://liulab.dfci.harvard.edu/) invites applications for a postdoctoral position at the Department of Biostatistics and Computational Biology at Dana-Farber Cancer Institute and Harvard School of Public Health. Research in the Liu Lab focuses on genomics and bioinformatics of transcription and epigenetic gene regulation, with applications to cancer biology. Her laboratory developed a number of widely used algorithms for transcription factor motif finding (cited over 1500 times), ChIP-chip/seq and DNase-seq data analysis (over 6000 users). Shirley Liu published 92 papers, with 27 in Nature, Science or Cell series. She has good track record for mentoring, with one PhD student and five postdocs graduated from her lab taking on tenure track faculty positions (since she became a faculty in 2003).
REQUIREMENTS:
Ideal applicant should have:
* PhD degree in physical sciences or related fields
* Strong programming skills: ((Python | Perl) & (C | C++ | Java) & R)
* Strong quantitative background (machine learning, Bayesian inference, etc.) or computational genomics experiences (DNA sequence analysis, microarray analysis, etc.)
* Good knowledge of molecular biology and genomics
* At least two (four if co-first author) first author papers written in English in previous area of research with submitted, accepted or published status in journals or conference proceedings
* Good spoken and written communication skills, mature and motivated.
* In addition, applicant must be able to visit Boston for potential interviews without visa application.
HOW TO APPLY:
Interested applicants should submit a letter of interest with a research proposal for a project (~2 pages) to be conducted during the postdoctoral training, CV, and three references (including name and contact information) to xsliu (At) jimmy (Dot) harvard (Dot) edu and with subject line "Postdoc application".
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BACKGROUND:
Computercraft seeks a highly motivated individual who will use his or her biological expertise to define RefSeq sequence standards and to contribute functional annotation of both the sequence record and the companion resource, NCBI's Gene database. The NCBI Reference Sequence (RefSeq) project provides reference sequence standards that are used internationally for genome annotation. RefSeqs provide a stable reference for gene characterization, mutation analysis, expression studies, and polymorphism discovery.
This is an exciting opportunity to contribute to the RefSeq project while using state-of-the art computational tools and databases. You will work on-site at the National Institutes of Health, National Center for Biotechnology Information (NCBI) in Bethesda, Maryland.
RESPONSIBILITIES:
* Evaluate and analyze sequence data to provide the most complete and accurate reference sequence to define coding and non-coding transcripts, protein products, and genomic regions
* Review literature and database resources and resolve database conflicts to provide gene-specific information for display in Gene
* Communicate with other scientists to ensure the highest quality data content for RefSeq records and the Gene database
* Contribute toward an international collaborative effort to define genes for human and other organisms
* Coordinate with model organism databases and other organism-specific interest groups to ensure timely processing of genomic sequence data and accurate display of annotation in NCBI resources
REQUIREMENTS:
* Ph.D. in biology, molecular biology, or related field
* Extensive experience with sequence analysis
* Strong logic, problem-solving, and organizational skills
* Excellent verbal and written communication skills and full fluency in the English language
* Ability to work as part of a team and to collaborate with other scientists
* Ability to adhere to established procedures and review work for completeness and accuracy
* A detail-oriented perspective
* Postdoctoral experience on a genomics project, while not required, is advantageous
* Genuine interest in contributing to the support of public database resources such as RefSeq and Gene
This is an intellectually challenging, detail-oriented position which will provide an excellent opportunity to use your biology expertise in a non-laboratory position. For more information about the RefSeq project and Gene, please see:
RefSeq: [link]
Gene: http://www.ncbi.nlm.nih.gov/gene/
COMPENSATION:
Computercraft offers a competitive salary and an excellent benefits package including PPO health insurance with 100% company paid premiums, 401K program with matching, paid time off and holiday pay, life insurance, flexible spending and disability coverage. We offer an excellent work life balance with a standard 40 hour work week and the chance to work alongside accomplished scientists at NIH/NCBI.
HOW TO APPLY:
To apply for this position or learn about other Computercraft job opportunities, please visit the Careers section of our website: http://www.computercraft-usa.com/
POLICY:
Computercraft is an equal opportunity employer.
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BACKGROUND:
It's 2 am. You type the name of your favorite gene into Genbank and are rewarded with information---sequence, references, related genes. You are intrigued by the countless possibilities for new experiments, but part of you longs for a different career away from the bench and 2 am dates with your computer.
If you see yourself in this scenario, consider experiencing life on the other side of a Genbank query. Computercraft is seeking new additions to its team of creative and dedicated scientists who have supported GenBank since 1991. Molecular biologists just completing a post-doc are especially encouraged to apply.
As a Genbank biologist you would work together with professionals at the National Center for Biotechnology Information (NCBI), part of the National Institutes of Health (NIH) in Bethesda, MD.
RESPONSIBILITIES:
Your responsibilities would include: creating complete and accurate Genbank records from the sequence data and annotation submitted by individual investigators and large-scale sequencing projects and helping to administer and maintain GenBank.
REQUIREMENTS:
* A Ph.D. in molecular biology or a related field
* Extensive laboratory experience in molecular biology
* Excellent verbal and written communication skills
* An aptitude for DNA sequence analysis (experience with DNA sequence analysis software is a plus)
* The ability to work as part of a team
* A strong desire to support public scientific databases such as Genbank
* A detail-oriented outlook coupled with a love for puzzle and problem solving
All applicants must complete the GenBank questionnaire as part of the application process. For more Information about GenBank visit:
http://www.ncbi.nlm.nih.gov/Genbank/
COMPENSATION:
Computercraft offers a competitive salary and an excellent benefits package including PPO health insurance with 100% company paid premiums, 401K program with matching, paid time off and holiday pay, life insurance, flexible spending and disability coverage. We offer an excellent work life balance with a standard 40 hour work week and the chance to work alongside accomplished scientists at NIH/NCBI.
HOW TO APPLY:
To apply for this position or learn about other Computercraft job opportunities, please visit the Careers section of our website: http://www.computercraft-usa.com/
POLICY:
Computercraft is an equal opportunity employer.
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BACKGROUND:
Computercraft seeks a Genome Assembly Data Management Specialist. The National Center for Biotechnology Information (NCBI) recently established a database of genome assemblies that provides the scientific community with information about the structure and sequence content of each version of an assembled genome. We are seeking a biologist experienced in working with Linux/UNIX and SQL to help maintain the highest quality data content, along with comprehensive representation, in NCBI's Assembly resource.
The successful candidate will investigate errors, inconsistencies and deficiencies in the data stored in NCBI's Assembly resource and then use web-based interfaces, command-line tools and specialized databases to correct the genome assembly data. The successful candidate will work onsite at the National Institutes of Health, National Center for Biotechnology Information (NCBI) in Bethesda MD.
RESPONSIBILITIES:
* Monitor and respond to reports of data issues in the Assembly database
* Investigate and correct data errors using both GUI and command-line tools
* Load missing assembly data
* Design checks for data consistency in the Assembly database and between the Assembly database and related NCBI resources
* Collaborate with other scientists and programmers to ensure the highest quality data content for NCBI's Assembly resource
* Provide help documentation and FAQs for the Assembly resource
* Write protocols and SOPs for assembly data curation
REQUIREMENTS:
* Biology knowledge (minimum: Masters of Science in a Biological field, or equivalent)
* Experience with genomics desirable
* Linux/UNIX experience
* Experience with SQL
* Scripting experience in Perl
or Awk desirable
* Strong organizational skills
* Strong verbal and written communication skills
* Detail-oriented perspective
* Interest in contributing to public database resources
COMPENSATION:
Computercraft offers a competitive salary and an excellent benefits package including PPO health insurance with 100% company paid premiums, 401K program with matching, paid time off and holiday pay, life insurance, flexible spending and disability coverage. We offer an excellent work life balance with a standard 40 hour work week and the chance to work alongside accomplished scientists at NIH/NCBI.
HOW TO APPLY:
To apply for this position or learn about other Computercraft job opportunities, please visit the Careers section of our website: http://www.computercraft-usa.com/
POLICY:
Computercraft is an equal opportunity employer.
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BACKGROUND:
The Wellcome Trust Sanger Institute is a world leader in genomic research, with an expanding scientific programme dedicated to understanding gene function in health & disease.
The Sanger Institute is Europe's leading genome research institute. Funded primarily by the Wellcome Trust, we use high-throughout genomics-based techniques to investigate host and pathogen genetics. The pathogen group is applying large-scale next-generation sequencing technologies to pathogen populations to track transmission pathways and identify determinants of drug resistance and virulence.
Within the Pathogen Genomics group, the role of the Pathogen Informatics team is to support the researchers by providing data processing pipelines, analysis pipelines, visualisation software and annotation databases and tools. We have developed some of the most popular tools in bioinformatics such as Artemis ([link]) and ACT. However, the continued scale up of next-generation sequencing to hundreds and thousands of pathogen samples for analysis provides us with many new challenges.
RESPONSIBILITIES:
We currently have two open positions in the group for two experienced bioinformaticians with good knowledge and experience of bioinformatics tools who can interact with the researchers in the group to elicit requirements and develop new analysis tools and pipelines that are required to produce high quality scientific results.
REQUIREMENTS:
Essential Skills:
* Significant programming experience in one or more modern programming languages (e.g. Perl, Python, C++ etc.)
* Significant demonstrable experience in bioinformatics
* Knowledge and experience of UNIX / LINUX on an advanced level
* Strong interpersonal and communication skills
* Ability to understand and apply new concepts quickly
* Highly developed problem solving skills with proven ability to think beyond immediate scope of a problem
PREFERENCES:
Ideal Skills:
* Knowledge and experience of Modern Perl and Moose
* Experience with managing large volumes of data
* Experience with running software on a compute farm or cluster
* Experience with processing next-generation sequencing data
* Knowledge of relational database systems
COMPENSATION:
Salary range GBP 27589 to GBP 38067 dependent on experience
The Institute has excellent purpose built facilities on the Genome Campus, Hinxton on the outskirts of Cambridge. We offer a comprehensive range of benefits including a final salary pension scheme and excellent on-site facilities. Further details can be found on our website https://jobs.sanger.ac.uk/.
HOW TO APPLY:
To submit your CV and apply for this job please go to https://jobs.sanger.ac.uk/ to register and apply on line.
http://twitter.com/sangerinstjobs/
For further information about this post please contact Jacqui McQuillan (jm15[at]sanger.ac.uk).
DEADLINE:
Closing Date: 18th June 2012
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BACKGROUND:
Our group is driving a research program showing that, besides SNPs and InDels, variable repeats are an overlooked source of genetic variability. Using a combination of experiments and bio-informatics, we have already demonstrated that repeats are present in 20% of all ORFs and 20% of all promoters of most organisms, including humans (see our publications in Cell, Science, Nature Genetics, Genome Research...). Now, in a joint effort with the human genetics department, we are sequencing thousands of repeats in different humans and will try to link variation in these with phenotypes and diseases. Moreover, we are also interested in in-silico analyses and comparative genomics of repeats in the tree of life, and/or as functional studies with specific repeats. For details, see lab website: http://www.kuleuven.be/verstrepen
RESPONSIBILITIES:
Head a research project aimed at unraveling the biological role of tandem repeats.
REQUIREMENTS:
* PhD in bio-informatics, bio-engineering, genetics, biology, systems biology
VIB International Postdoc program "OMICS@vib" is open to applicants from all nationalities. Applicants should not have been carrying out research in Belgium for more than 12 months during the last 3 years before the deadline of the program on 15/09/2012.
Postdocs selected for this program should be able to start their postdoc project before 1/6/2013.
For more information, see:
[link]
LOCALE:
Laboratory of Kevin J. Verstrepen, Leuven, Belgium http://www.kuleuven.be/verstrepen
COMPENSATION:
Attractive salary and benefits (including full health insurance for family members)
HOW TO APPLY:
Applicants must apply through the following website: http://www.vib.be/omics and select project hosted by prof. Kevin Verstrepen.
Applicants are expected to write s brief research proposal on the topic of "Hunting for unstable tandem repeats in the human genome: an overlooked source of missing heritability and cryptic diseases".
Applicants do NOT have to directly contact the PI for this program, online submission using the website http://www.vib.be/omics (select research proposal on tandem repeats hosted by prof. Kevin Verstrepen) is the only way to apply!
DEADLINE:
September 14th 2012
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OVERVIEW:
Oregon State University is conducting three open rank searches for collaboratively-minded faculty who demonstrate enthusiasm for research and teaching at the interface of the quantitative and life sciences, to join our strong growing genomics and systems biology community.
Nucleic Acid Sequence Bioinformatics:
The appointee will execute a strong research and teaching program at the interface of computer and life sciences that advances the use of nucleic acid sequence data to understand the functions of biological systems at any scale. This is a tenure-track, 9-month, full-time faculty position at any rank that will reside jointly in the School of Electrical Engineering and Computer Science, and in a life science unit depending on the appointee's expertise and interest.
Systems Biology of Host-Microbe Interactions:
The appointee will conduct research addressing host-microbe interactions through integrating experimental life science and quantitative methods. The context of the research may be infectious disease, allergic or chronic disease in humans, animals or plants, or mutualistic interactions at the level of individuals or communities. This is a tenure-track, 9-month, full-time faculty position at any rank that will reside jointly in a life science department and in a quantitative science department depending on the appointee's expertise and interest.
Applied Discrete Mathematics in Systems Biology:
The appointee will execute a strong research and teaching program at the interface of applied discrete mathematics and molecular, cellular or organismal systems biology. The context of research may include, but is not limited to, areas of discrete mathematics centered around data integration, network inference, or modeling in systems biology. This is a tenure-track, 9-month, full-time faculty position (Associate or Full Professor) that will reside jointly in the Department of Mathematics, and in a life science unit depending on the appointee's expertise and interest.
HOW TO APPLY:
More information and application procedures can be found at [link]
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BACKGROUND:
Fluidigm Corporation, based in South San Francisco, CA, is a cutting-edge biotechnology company that develops and manufactures complete systems based on its patented microfluidic valve technology.
Fluidigm Corporation seeks an outstanding individual to join a vibrant interdisciplinary group of scientists and engineers to develop single cell analysis, sequencing, genotyping, and gene expression products.
RESPONSIBILITIES:
Essential duties include but are not limited to:
* Provide NGS analysis and develop analysis tools for targeted re-sequencing, methylation, whole genome amplification, and whole transcriptome amplification
* Design and analyze panels of NGS assays for targeted disease genes.
* Participate in the assay design pipeline development.
REQUIREMENTS:
Education/Experience/Skills:
* Ph.D. in Bioinformatics or a related field, including biological sciences, statistics, computer science, or mathematics and two years working experience in Bioinformatics
Knowledge/Skills/Abilities:
* Extensive experience with NGS technologies and sequence analysis tools.
* Understanding and hand-on experience in biostatistics and bioinformatic algorithms.
* Hand-on experience in PCR assay design.
* Good understanding biochemistry, genetics and epi-genetics.
* Proficiency in Unix/Linux, Perl, Python, R and/or MySQL.
* Highly self-motivated and enjoy working as part of a multi-disciplinary team.
* Strong analytical and problem-solving skills.
* Outstanding oral and written communication skills.
* Excellent organizational and documentation skills, thorough and detail-orientated.
HOW TO APPLY:
Apply Here: http://www.Click2Apply.net/7bwrjnw
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BACKGROUND:
The Alkek Center for Metagenomics and Microbiome Research (CMMR) is coordinating and leading research and development efforts in this area across the Texas Medical Center, with collaborators from around the US, and with those abroad. CMMR researchers are developing molecular and informatic tools and resources to advance diverse clinical and basic research projects pertaining to the organisms that comprise the microbiome, the genetic makeup of these bacteria, viruses and fungi, and how these commensal microorganisms interact with human cells and tissues during the course of life. The intent is for these projects to lead to the development of new treatments and diagnostics for a variety of heritable and infectious diseases as well as the development of additional reagents having other biotech applications. We continuously seek individuals who are looking to work in a diverse research environment that supports ongoing genomics research and improvements in metagenomic sequencing technology and analyses.
RESPONSIBILITIES:
We are looking to fill the position of Bioinformatician within the CMMR. The Bioinformatician will be expected to lead metagenomic and statistical analyses of microbial community data sets derived from Next Generation Sequencing (NGS) data.
Duties:
* Initiation/implementation, troubleshooting, and maintenance of analysis software in support of microbial ecology studies
* Proactively providing data analysis support to multiple metagenomic sequencing projects
* Coordination of data flow with a wide variety of external scientific collaborators
* Tracking project data and reporting analysis results
* Collaboration with the software engineering groups to define software requirements
* Ability to plan and organize detailed projects with multiple tasks and deadline
* Proven ability to work effectively in a collaborative team environment
REQUIREMENTS:
He/she is expected to have experience in scientific programming with applications to biological research, plus experience with Perl, HTML, CGI, relation databases and SQL. Experience with C++ and programming using UNIX/LINUX clusters are desirable. Experience with NexGen data and metagenomic analyses are strongly desired. May be at the B.S., M.S., or Ph.D. level.
Skills:
* A degree in quantitative science (bioinformatics, molecular biology, physics, etc)
* Broad knowledge of biology, especially microbial ecology and/or genetics
* Experience with large genomic data sets (Next-generation sequence, genotyping, or expression data), data mining, and data analysis
* Experience with UNIX and cluster computing preferred
* Perl, Ruby, or other scripting development experience
* Experience with machine learning and/or artificial intelligence programming a plus
* Demonstrated independent thinking and problem solving ability
* Strong oral and written communication skills
HOW TO APPLY:
Our positions are processed through the Baylor College of Medicine Human Resources Department. For information about how to apply for this opening please visit the BCM employment website: https://www.medschooljobs.org/.
Qualified candidates may also submit resumes via mail, e-mail or fax to:
Alkek Center for Metagenomics and Microbiome Research
Attn: Megan Coombs
One Baylor Plaza -- 700B, BCM MS385
Houston, Texas 77030
Email: winwood[at]bcm.edu
Fax: 713-798-1418
POLICY:
Baylor College of Medicine is an Equal Opportunity, Affirmative Action, and Equal Access Employer.
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Organization: GN-Genomics
RESPONSIBILITIES:
The DOE Joint Genome Institute (JGI) in Walnut Creek, CA (a division of the Lawrence Berkeley National Lab) has an exciting research opportunity available for an experienced Plant Scientist. This position will be responsible for leading a plant genome annotation and research group, focused on comparative genomics of plants relevant to energy and the environment. Will take responsibility for the timely and accurate annotation of JGI plant genomes, and for developing manuscripts describing JGI plant genomes, as well as serve as the lead scientist for Phytozome, the JGI's comparative plant genome analysis portal. Position reports to the Computational Genomics Program lead.
Duties/Responsibilities:
* Supervise a small team of plant genome annotators, guiding timely completion of annotation projects and genome analyses.
* Collaborate with JGI users to write manuscripts describing JGI plant genomes.
* Collaborate with the Phytozome technical lead to develop Phytozome as a web portal for JGI and other plant genomes.
* Interact with JGI users and other plant biologists to identify community informatics needs.
* Participate in JGI computational genome and JGI plant genomics programs.
* Present scientific results at seminars, conferences, and internal groups.
REQUIREMENTS:
Qualifications:
* PhD in Plant Science or other related discipline
* Familiarity with computational methods for genome analysis and significant expertise in genome annotation and/or analysis
* Demonstrated ability to conduct and perform collaborative research and effectively interact with a broad range of colleagues with tact and diplomacy
* Strong publication record with extensive experience in the preparation and handling of scientific manuscripts and reports
* Effective problem-solving and decision-making skills
* Strong analytical, organizational, and record-keeping skills
* Excellent verbal and written communication skills, including public-speaking and presentation skills
* Ability to work independently as well as part of a diverse team
* Demonstrated ability to accurately and eloquently represent and promote scientific projects to audiences of diverse technical backgrounds
* Demonstrated scientific leadership experience to coach, guide, and effectively manage a small team of scientific researchers
HOW TO APPLY:
Apply directly online at http://bit.ly/lbl73541Bioinformatics and follow the instructions to complete the application process.
POLICY:
Berkeley Lab is an Affirmative Action/Equal Employment Opportunity employer committed to the development of a diverse workforce.
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Organization: GN-Genomics
RESPONSIBILITIES:
The DOE Joint Genome Institute (JGI) in Walnut Creek, CA (a division of the Lawrence Berkeley National Lab) has an exciting opportunity available for an experienced Software Developer / Engineer to support the Phytozome group. The Phytozome group in the JGI Plant Genomics Program is responsible for the annotation and analysis of plant genomes, and for providing both internal and external users with visualization, querying and data access capabilities to facilitate progress in fundamental, biofuel and climate-related Plant science. The Phytozome website and associated databases and analysis tools provide JGI's collaborators and the broader plant biology community with intuitive and powerful interfaces to access and explore plant genomic data. As the JGI anticipates a massive increase in RNA-Seq and resequencing output, we have an opportunity for an experienced developer to help us enhance and expand Phytozome to host even more plant genomes and their annotations, and to develop new databases and interfaces to support users' exploration of plant genomic diversity and gene expression data.
Under broad supervision, the ideal candidate will develop, implement, test, integrate and deploy new and/or existing software components of the Phytozome system for the visualization and querying of plant genomic and related data. They should demonstrate detailed knowledge and strong technical ability in web user interface design concepts and implementation, data modeling, and database schema design, as well as extensive familiarity with standard genomic sequence data types and analysis methods.
The selected candidate will be hired at the Software Developer 3 or 4 classification level depending upon the candidate's level of experience and qualifications. Position reports to the Phytozome Group Lead.
Specific Job Duties:
Essential-
* Work as a member of the Phytozome development team to create, maintain and extend the suite of visualization, backend, and data management tools that support the public interface to the JGI's Plant Genomics program.
* Create and maintain database-backed web applications for the display and querying of genomic data.
* Evaluate the suitability of third party open source tools (e.g. GMOD) versus in-house development to provide desired functionality to Phytozome.
* Optimize the Phytozome user experience by constantly monitoring and improving backend data retrieval performance (as determined by benchmarking) and front-end usability (as determined by user surveys and best practices).
* Follow best practices for software version control, documentation, testing and release engineering.
Marginal-
* Work with Phytozome/Metazome internal and external user community and Scientific Advisory Board to prioritize new feature requests, and provide accurate estimates of implementation timelines.
* Assist in the preparation of manuscripts, tutorials and conference presentations based on Phytozome.
* Work with JGI's Systems group to anticipate hardware needs for increasing data set sizes and expanded functionality.
Essential duties for the Software Developer 4-
In addition to the job duties described above, the Software Developer 4 will:
* Operate at a higher level of independence and responsibility when carrying out assignments.
* Will serve as a technical lead and key contributor called upon to solve highly technical, complex problems.
REQUIREMENTS:
Key Success Factors:
Essential -
* B.S. in technical or scientific field (or equivalent experience) and a minimum of five years programming experience
* Minimum five years experience and demonstrated success designing and implementing bioinformatics analysis systems and software in a scientific or technical environment, e.g., University, National Laboratory, corporate R&D
* Familiarity with standard genomic sequence data repositories (e.g, GenBank, SwissProt) and functional classification databases and ontologies (e.g., KEGG, Panther, Metacyc, GO)
* Solid experience programming with object-oriented Perl and Java
* Advanced knowledge of SQL and relational database design
* High degree of comfort developing on, and for, linux systems
* Demonstrated experience developing database-backed applications and experience with web technologies including: Apache, Tomcat, CGI programming, JDBC, JAXB, GWT, AJAX
* Ability to effectively learn and apply new technical concepts to troubleshoot and solve problems and challenges of a diverse scope
* Effective interpersonal communication and presentation skills
* Effective time management, organization, and planning skills
* Ability to work effectively in a diverse team environment
Desirable-
* M.S./Ph.D. in Molecular Biology, Genetics or related field
* Mathematical sophistication to understand algorithmic concepts behind sequence alignment, gene family clustering, and phylogenetic tree building
* Experience with the management and visualization of gene expression and genomic diversity data
* Solid understanding of statistics
* Experience developing software that includes or interacts with GMOD and bioperl components
* Working knowledge of Python and PHP
Essential Qualifications for the Software Developer 4 -
In addition to the qualifications listed above, the Software Developer 4 requires:
* A minimum of eight years related experience
* Demonstrated ability to solve highly complex problems and work independently on end-to-end implementation and maintenance of software projects through multiple releases
HOW TO APPLY:
Apply directly online at http://bit.ly/lbl74226Bioinformatic and follow the instructions to complete the application process.
POLICY:
Berkeley Lab is an Affirmative Action/Equal Employment Opportunity employer committed to the development of a diverse workforce.
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Organization: GN-Genomics
RESPONSIBILITIES:
The Plant Genomics Program at the DOE Joint Genome Institute (JGI), in Walnut Creek, CA, has two openings for Bioinformatics Analysts to contribute to our Plant Genome Annotation efforts. Under broad supervision, will work within the Phytozome group to generate new as well as refined plant genome annotations and facilitate the acquisition, incorporation and display of functional, genetic and other genome-anchored data in Phytozome. Responsibilities include: collecting data for genome-specific tuning of the plant annotation pipeline, assessing the quality of input data, incorporating the data into the Phytozome visualization environment, running and troubleshooting the annotation pipeline, analyzing predicted genes and functional assignments. Will interact with internal and external collaborators and the JGI Project Management group at all stages of annotation projects to ensure accurate and timely completion of projects. Position will report to the Plant Annotation Group Lead.
The selected candidate will be hired at the Analyst 2 or 3 classification depending upon the candidate's level of experience and qualifications.
Specific Job Duties:
Genome Annotation-
* Responsible for annotation and analysis of plant genomes.
* Collect data for genome annotation (from internal or public databases, collaborators, etc).
* Configure, run and troubleshoot genome annotation tools.
* Assess quality of input data and produced predictions.
* Apply and refine methods for mapping annotations between assembly versions, for identifying gene splits and merges, and assigning gene family names and functions.
* Apply analytical skills and creativity to troubleshoot and solve problems of a moderate scope.
* Provide feedback to improve protocols, methods and tools for genome annotation.
* Develop and present reports for annotated genomes, and participate in writing of scientific articles describing the genome annotation and related analyses.
Data Management-
* Ensure integrity and up-to-date status of internal (results of pipeline analyses) and external (e.g., GO, PFAM, SuperFAM. UniProt databases, externally-generated genomic assemblies and annotations) data required for the genome annotation system.
* Work with internal and external collaborators to make genome-anchored data available via the Phytozome system.
* Troubleshoot data parsers.
Essential Duties for the Analyst 3 - In addition to the required duties for a level 2, the Analyst 3 will:
* Work at a higher level of independence and responsibilities in carrying out assignments.
* Develop and implement substantial, known or novel, computational methods to improve the analysis capabilities and output of the group.
* Troubleshoot more complex systems and data analysis problems.
REQUIREMENTS:
Key Success Factors:
Essential-
* Typically requires a Bachelor's degree in Biology, Life Sciences, Bioinformatics, Computer Science or related field with a minimum of two years of work experience, or an equivalent combination of education and experience.
* Demonstrable understanding of genomics and molecular biology
* Knowledge of standard bioinformatics methods and tools for gene and protein sequence analysis
* Demonstrated experience with biological databases
* Experience in annotation and analysis of genomes, pathways and families of genes and proteins
* Experience with databases and running programs in a UNIX environment
* Working knowledge of SQL and Perl
* Strong problem-solving, decision-making, and analytical skills to independently make sound judgments and recommend creative solutions to complex problems
* Strong interpersonal, communication, and presentation skills to effectively work with large user communities
* Detail-oriented with strong organizational skills to address user needs in an effective and timely manner
* Ability to work in a diverse team environment
Preferred-
* Master's degree or higher in Biology, Bioinformatics, Life Sciences, Computer Sciences, or related field preferred
* Experience configuring and troubleshooting Gbrowse/GMOD components
* Knowledge of Plant Genetics
* Knowledge of Python
Essential Qualifications for the Systems Analyst 3 - In addition to the required qualifications for a level 2, the Analyst 3 will have:
* Bachelor's degree in Biology, Life Sciences, Bioinformatics, Computer Science or related field with a minimum of five years of work experience, or an equivalent combination of education and experience
* Advanced SQL, Perl or Java software skills
* Experience deploying, configuring and debugging GMOD components such as Jalview, BioMart, GBrowse
* Ability to troubleshoot complex systems and data analysis problems
HOW TO APPLY:
Apply directly online at http://bit.ly/lbl73542Bioinformatics and follow the instructions to complete the application process.
POLICY:
Berkeley Lab is an Affirmative Action/Equal Employment Opportunity employer committed to the development of a diverse workforce.
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BACKGROUND:
Waksman Genomics Core Facility is seeking a highly motivated and talented Bioinformatics scientist to our group at the Waksman Institute of Microbiology, Rutgers University, New Jersey, USA. Initial appointment will be for one year with an opportunity to extend further based on the performance. Reporting to the Genomics Laboratory Supervisor, this position is responsible for managing data analysis pipeline from the high-throughput sequencer SOLiD 5500xl. The analysis entails assessing the quality of the data, processing of the data through appropriate analysis pipelines, determining the quality of the analysis and whether further analysis should be done, and assembling results for researchers. Consults with researchers on experimental design related to data analysis, develops new pipeline analysis techniques and communicates project updates and results to researchers.
RESPONSIBILITIES:
Main Responsibilities:
* The successful candidate will develop and implement computational algorithms and statistical analysis pipelines using next-generation sequencing data.
* Evaluate published bioinformatics tools and resources for analysis and interpretation of genomic data.
* Present results through clear and concise representation of ideas and concepts to other team members and the management.
* Manage multiple independent projects under tight deadlines.
REQUIREMENTS:
Essential Requirements:
* Ph.D. in Bioinformatics, Computational Biology, or related discipline
* Strong programming and scripting skills (eg; Perl, Python, Ruby, Java, C++, XML, using MySQL Server; and efficiency in Linux/Unix operating systems)
* Knowledge in one statistical language (S/R/SPSS/MATLAB/Octav) and some machine learning concepts
* Have good communication skills, strong team-work spirit with self-learning abilities
* 2+ years of experience in Bioinformatics data analysis tools and databases
PREFERENCES:
Desirable:
* Knowledge about gene regulatory networks and graphical models
* Experience in analysis of genome, transcriptome, epigenome and other genomic datasets
LOCALE:
Piscataway, NJ
COMPENSATION:
Competitive
HOW TO APPLY:
hr[at]waksman.rutgers.edu or dk[at]waksman.rutgers.edu
DEADLINE:
June 30, 2012
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BACKGROUND:
Scionics Computer Innovation GmbH provides IT products, consulting, and support to enhance the efficiency of scientific research in the life sciences and other knowledge based industries. We are located in Dresden, Germany, and work in close contact with the local research community.
Scionics Computer Innovation seeks to recruit a Web Interface Developer to work in a service team in an academic research environment. The service team provides IT support, services, and consulting directly to the scientists. The environment is an exciting combination of corporate and academic culture and provides a wide range of interesting daily tasks, access to high-end hardware and equipment, and flexible hours.
The Web Interface Developer will be part of a team that will support scientists on a project-by-project basis with algorithm development, data presentation, web database design and implementation, data handling / analysis, and the usage of HPC resources.
RESPONSIBILITIES:
* Create, in collaboration with scientists, web based applications for the display, management, and analysis of scientific data
* Design rich, dynamic, and attractive interfaces for displaying large data sets with their corresponding analysis and metadata
* Design systems and interfaces for the presentation of genomic and proteomic data
* Design systems and interfaces for the presentation, handling, and rapid display of large microscopy image data sets
* Work on and maintain existing systems and web interfaces
REQUIREMENTS:
* A university or equivalent degree in an IT related or scientific discipline - or a good explanation why the career path you've chosen gives you equivalent skills.
* JavaScript skills using AJAX, JSON, CSS, and HTML
* Knowledge of JavaScript frameworks such as jQuery, GWT, Dojo
* Knowledge of industry standards for XHTML, CSS, and common web technologies
* Proven experience (3+ years) developing web applications or interfaces
* Must be living in or willing to relocate to Germany. Open-mindedness and a desire to experience other cultures is a definite bonus as our environment is heavily international.
* Must be fluent in English and have excellent communication skills both verbal and written. Knowledge of German is welcome but not required.
* Ability to work in a team
PREFERENCES:
* Experience in Java, Python, or similar development language
* Experience in a research environment is a strong plus
* Statistics experience
LOCALE:
Dresden, Germany, Europe
HOW TO APPLY:
If you are interested in this position, please send your CV and any relevant documents to: interfacejob[at]scionics.com with the subject "Web Interface Developer".
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