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BACKGROUND:
Organization: NE-NERSC
NERSC and the Joint Genome Institute (JGI) are searching for an individual who can help biologists exploit advanced computing platforms. JGI provides production sequencing and genomics for the Department of Energy. These activities are critical to the DOE missions in areas related to clean energy generation and environmental characterization and cleanup. JGI has recently partnered with NERSC, the DOE Office of Science's flagship computing center, a world leader in providing high-performance computing tools and expertise that enable computational science of scale. This partnership gives JGI staff access to supercomputer class systems, advanced architectures, and large-scale storage systems enabling JGI to address the most demanding genomic problems. This position will help bridge the gap from biology to computational science. The position will support the JGI mission by directly engaging with biologists to assist them with effectively using the range of computational resources at their disposal.
RESPONSIBILITIES:
Computer Systems Engineer 2:
The individual is expected to provide assistance on how to architect and implement genomic applications that would include porting or modifying existing pipelines to run on new architectures and platforms including HPC systems and Cloud computing systems. This includes investigating and developing new more efficient and scalable algorithms that can handle the growing volume of genomic data. In addition, the individual will have the opportunity to explore new computing models such as Hadoop, HBase, and accelerators to understand how they can be used to address challenges for the JGI. The individual will serve as the main point of contact between JGI and NERSC, assessing user requirements and communicating user scientific and computing needs to both organizations. The successful candidate will help educate and train users by creating content for the NERSC website with online tutorials and documentation, giving presentations, and attending conferences and will communicate with users about new opportunities and capabilities in software and systems and advise them in effectively transitioning to new technologies.
Computer Systems Engineer 3:
In addition to the duties of the CSE 2, the CSE 3 will take a lead role in at least one of the activities described above, take responsibility for managing and solving complex problems, have frequent interactions with users to provide technical guidance, participate in setting direction for future user activities and participate in collaborations with research scientists.
REQUIREMENTS:
Computer Systems Engineer 2:
* Bachelor's degree in a science or a computer science discipline or equivalent experience and a minimum of 4 years related experience
* Demonstrated ability to work independently, work collaboratively in an interdisciplinary team, and contribute to an active intellectual environment
* Experience with a variety of bioinformatics tools (assemblers, comparative analysis tools, phylo-genetic, etc.)
* Broad computational background including knowledge of Linux, C, C++, Perl, and Python
* Ability to work effectively with scientists understanding user needs, showing initiative, tact and judgment developing solutions
* Excellent written and oral communication skills
Computer Systems Engineer 3:
In addition to the above requirements for a CSE 2, the CSE 3 must have a minimum of 8 years related experience. The CSE 3 must have a demonstrated ability to assume a leadership role, ability to grasp complex problems and develop solutions, and possess in-depth background in bioinformatics tools.
PREFERENCES:
* An advanced degree in computational science, computer science, or bioinformatics
* Familiarity with high-performance computing (including MPI , novel architectures (accelerator, FPGA, etc) or cloud computing
* Familiarity with emerging distributed computing models such as Hadoop
* Experience supporting and deploying bioinformatics pipelines
TERMS:
Note: This is a one year term, renewable each year, with the possibility for conversion to an indefinite (career) appointment based on satisfactory job performance, availability of funds and ongoing operational needs.
HOW TO APPLY:
Apply directly online at http://bit.ly/lbl73194Bioinformatics and follow the instructions to complete the application process.
POLICY:
Berkeley Lab is an affirmative action/equal opportunity employer committed to the development of a diverse workforce.
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BACKGROUND:
Social & Scientific Systems (SSS) is an employee-owned company dedicated to improving public health around the world. SSS offers an excellent total compensation package, including medical, life, and disability insurance, annual leave, stock ownership, 401(k) plan, education assistance, casual work environment, commuter benefits, flexible hours, and more.
RESPONSIBILITIES:
We are seeking a Programmer II that under general supervision will manage databases and write, test, debug and run complex computer programs.
* Writes programs from routine or moderately complex program specifications.
* May be given responsibility to administer a database and respond to requests.
* Develops estimates of time and computer resources for assigned activities.
* Runs production programs and reviews for accuracy.
* Maintains programs, project files, audit trails, and data libraries. Creates and maintains associated documentation, including data flow diagrams and flow charts.
* Performs routine data management activities, including data transfers, backups, etc.
* May interact with clients to resolve work issues, as agreed upon with the supervisor.
* Keeps supervisor informed of progress.
* Performs additional duties as required.
REQUIREMENTS:
Bachelor's degree or equivalent experience, plus 2-3 years of related experience as an applications programmer is required. All candidates must have significant experience in the use of the SAS Data Step in manipulating data and transposing/transforming data. Experience in working with longitudinal datasets as they relate to survey/epidemiology/public health research is essential. Proficiency in specified editors and programming languages such as SAS, SQL, Stata, MS Access and Visual Studio .Net using C# is preferred. All candidates must have excellent organizational skills as well as the ability to be flexible to shifting priorities. A 'Team Player' personality is essential.
LOCALE:
Durham, NC
HOW TO APPLY:
Review full requirements/description and apply online at http://www.s-3.com - see Req. #915.
POLICY:
EOE M/F/D/V
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RESPONSIBILITIES:
Organization: GN - Genomics Division
The DOE Joint Genome Institute (JGI) in Walnut Creek, CA (a division of the Lawrence Berkeley National Lab) has opportunities available for experienced software developers. In cooperation with other units of JGI, the selected candidates will be responsible for designing, developing and implementing software solutions to manage and process data from new sequencing technologies. Will work on problems of a diverse scope, exercise independent judgment and select appropriate methods and techniques for solving and recommending solutions. Assignments will span the full software development lifecycle, including participation in requirements gathering, implementation, testing, and deployment. Positions report to the Genomic Technologies Informatics Group Lead.
Specific Job Duties:
Essential-
* Design, implement, test and deploy software for the handling of new sequencing technologies and techniques, and corresponding data with the eventual goal of integrating these systems with the institution's existing informatics infrastructure.
* Gather feedback and requirements to develop software using a mix of the following: Java, Perl, Perl/CGI, Javascript, CVS, PL/SQL.
* Interact with peers to ensure efficient communication and completion of projects.
* Apply analytical skills and creativity to solve diverse and challenging problems.
Marginal-
* Stay current with new sequencing technologies.
* Develop and present updates and reports at group meetings.
REQUIREMENTS:
* B.S. in Computer Engineering, Bioinformatics or a related field with a minimum of five years related experience, or an equivalent combination of education and experience. MS degree is preferred
* Demonstrated experience with the following: Java and/or Perl, UNIX and SQL
* Demonstrated experience with database programming and interfaces
* Full life-cycle software development experience with the ability to work with scientific and administrative peers to define needs and priorities
* Ability to effectively learn and apply new technology concepts to troubleshoot and solve problems and challenges of a diverse scope
* Effective time management, organization, and planning skills
* Talent for working well under short deadlines and handling multiple tasks simultaneously
* Ability to work effectively in a diverse team environment
PREFERENCES:
* Demonstrated experience with the following: Spring/JEE or similar programming frameworks, Tomcat, Apache, Subversion or other version control software
* Demonstrated experience in providing support for software solutions
* Experience developing web-based GUIs
* Experience working with scientific users
* Experience working with bioinformatics tools and/or analysis techniques, ideally involving next-generation sequencing platforms
HOW TO APPLY:
For a detailed job description and instructions regarding how to apply, please visit: [link]
POLICY:
Berkeley Lab is an affirmative action/equal opportunity employer committed to the development of a diverse workforce.
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BACKGROUND:
Fred Hutchinson Cancer Research Center, home of three Nobel laureates, is an independent, nonprofit research institution dedicated to the development and advancement of biomedical research to eliminate cancer and other potentially fatal diseases. Recognized internationally for its pioneering work in bone-marrow transplantation, the Center's five scientific divisions collaborate to form a unique environment for conducting basic and applied science. The Hutchinson Center, in collaboration with its clinical and research partners, the University of Washington and Seattle Children's, is the only National Cancer Institute-designated comprehensive cancer center in the Pacific Northwest. Join us and make a difference!
RESPONSIBILITIES:
A Postdoctoral Research Fellow position is available immediately in the Vaccine and Infectious Disease Division (VIDD) of the Fred Hutchinson Cancer Research Center (FHCRC), Seattle, W A. The successful applicant will work with Dr. Raphael Gottardo to develop statistical and computational methods for analyzing and integrating high throughput data from immunological assays such as flow cytometry, antigen microarrays, next generation sequencing, etc. He/She will also work with scientists from VIDD to apply the tools in the field of computational immunology and vaccine development. The successful applicant will interact with both scientists in VIDD and in the program in Computational Biology. The FHCRC provides a highly interactive and supportive environment for junior investigators to grow and develop their future career; it consistently ranks in the top 20 best places to work for postdocs, as surveyed by The Scientist.
REQUIREMENTS:
Suitable applicants should have a PhD degree in statistics/biostatistics, computer science, applied mathematics, electrical/biomedical engineering, physics, computational biology or other fields with strong quantitative training. Strong programming skills in C/C++, R or similar languages are required. Previous experience with genomics or biological data analyses is a plus.
LOCALE:
Seattle, Washington
COMPENSATION:
Full time position, salary based on the NIH scale + excellent benefits
HOW TO APPLY:
Please also apply for this position [link] and reference job ID "24327".
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BACKGROUND:
Columbia University Medical Center is one of the world's foremost centers for patient care and health science education. It is also one of the world's leading biomedical research organizations, and provides a unique environment to support breakthrough discoveries in this fundamental area of biology.
The Haghighi laboratory is studying the epigenetic profiles of human brain development and its emerging role in gene regulation, as well as its fundamental importance for our understanding of normal and pathological neuronal function. Epigenetic patterns in the genome vary among tissues and cell types in normal and pathological states. A major unanswered question is how epigenetics plays a role in neuronal development and how alterations in normal epigenetic processes during development lead to neurodevelopmental diseases, such as autism and schizophrenia. Next-gen sequencing technologies now allow a global view of whole genome epigenetic profiles.
RESPONSIBILITIES:
Studies involve development and application of epigenomic techniques including library construction for next-gen sequencing of DNA methylation and histone modifications (BS-seq and ChIP-Seq).
REQUIREMENTS:
Experience in bisulfite sequencing, real-time PCR, chromatin IP, and neuronal nuclei isolation is highly desirable. Candidates with a PhD in the biological sciences with a strong background in molecular biology are encouraged to apply.
The successful candidate will be a highly motivated individual capable of working independently, with excellent written and verbal communication skills. All applicants must currently be eligible to work in the U.S.
COMPENSATION:
Commensurate with experience
HOW TO APPLY:
[link]
DEADLINE:
6/31/2012
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BACKGROUND:
The Lawrence Berkeley National Laboratory (Berkeley Lab) is seeking a dynamic leader with demonstrated technical excellence and an international reputation in high performance networking to lead and direct the newly established Scientific Networking Division. This position is critical in defining the role of networking in the growing area of data driven science. The core of this division is made up of the Energy Sciences Network (ESnet - http://www.es.net/), the international high-performance networking facility of the Department of Energy (DOE) Office of Science managed by Berkeley Lab. ESnet provides innovative, high-performance network services linking scientists at national laboratories, universities and other research institutions, enabling them to collaborate on some of the world's most important scientific challenges including energy, climate science, and the origins of the universe. ESnet offers resources and services for the scientific community, and will play a key role as scientific exploration continues to be more data intensive.
RESPONSIBILITIES:
The Scientific Networking Division Director:
* Serves as an intellectual leader of the Scientific Networking Division at Berkeley Lab and provide substantial contributions to the formulation and direction of Laboratory programs and projects that enhance Berkeley Lab's preeminence as a national laboratory
* Provides vision and leadership to establish, maintain, and extend ESnet's leading-edge network capabilities
* Provides planning, organization, monitoring, and control functions for a group of over 40 staff members with an annual budget of approximately $30M
* Participates as a senior member of the Berkeley Lab Computing Sciences Area, and as a division director in the creation and implementation of the LBNL vision for computational science at the lab
* Collaborates with other scientific research projects at Berkeley Lab in the identification and resolution of cross-cutting problems that have Lab-wide impact
* Develops, directs, and evaluates technological and architectural strategies to introduce new networking capabilities that improve usability for the division's user community
* Establishes and communicates division policy, mission, goals, and accomplishments; develop initiatives and budgets and obtain funding (specific areas of current interest are technology scaling to the Tb/s level, and new technologies for increasing the energy efficiency of high performance networking platforms)
* Works directly with the user community and user advisory groups to ensure that the division's services, resources, and policies are responsive to their needs
* Represents the division internally and to external organizations and funding agencies; maintains a work environment that embraces diversity and fosters creativity and innovation; ensures that DOE and Laboratory rules and policies are observed
REQUIREMENTS:
Key Qualifications:
* Recognized national and international reputation as an authority on high performance networking and its role in scientific applications
* Demonstrated expertise in the architecture and implementation of a scientific high-performance network and/or demonstrated experience in operations and support of a continuous production high-performance networking facility
* Significant experience and demonstrated competence in the management of large-scale scientific projects and collaborative science
* Experience employing advanced network technology to serve hundreds to thousands of remote scientific users
* Demonstrated leadership ability applicable to running a large, diverse, and team-oriented organization
* Excellent oral and written communication skills
* Ability to interact at the highest level of management, both internally and externally
* Ph.D. or equivalent experience in an area of computational science or computer science, preferably in the area of advanced networking, and a record of significant impact in the research community
LOCALE:
Lawrence Berkeley National Laboratory (Berkeley Lab) is located in the San Francisco Bay Area on a 200-acre site in the hills above the University of California's Berkeley campus and is managed by the University of California for the U.S. Department of Energy. A leader in science and engineering research for 75 years, Berkeley Lab is the oldest of the U.S. Department of Energy's national laboratories.
COMPENSATION:
In addition to the intellectual and cultural advantages of being a member of the LBNL community, we offer employees in career and term appointments excellent terms and conditions of employment, outstanding health and welfare benefits, and programs for a secure retirement that are considered to be among the finest. More information about benefits can be found at: [link]
NOTE:
Effective January 1, 2011, all National Laboratory employees will be subject to a two year pay freeze. This position falls under this provision for Lawrence Berkeley National Lab's fiscal years: 2012-2013 (October 1, 2011 - September 30, 2013).
HOW TO APPLY:
For a detailed job description and instructions regarding how to apply, please visit: http://bit.ly/lbl74060Bioinformatics
Berkeley Lab is an affirmative action/equal opportunity employer committed to the development of a diverse workforce.
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RESPONSIBILITIES:
The Center for Biomolecular Science & Engineering (CBSE) at UC Santa Cruz invites applications from outstanding scientists for the position of Assistant Research Scientist in Comparative Genomics. We seek a self-motivated, creative scientist experienced in biological data analysis and having extensive programming knowledge to maintain an independent research program serving as principal investigator on federal grant awards and contracts and on privately-funded projects in the areas of molecular evolution, human variation, cancer genomics, and immunogenomics.
The incumbent will be expected to publish in top-tier scientific journals and present findings in scientific meetings. In the course of research, the incumbent will create algorithms, applications programming interfaces, and software systems used for comparative genomics by both the UCSC group and external groups. It is expected that the incumbent, as part of the UCSC comparative genomics group, will work with research groups at other institutions to set standards in the field. Our exceptional collegiality and interdisciplinary collaborations make UCSC an excellent environment for an innovative scientist who can benefit from and contribute to the rapid growth in the sciences and engineering at UCSC.
Specific projects in which the candidate may play a significant role include the following, all of which have a substantial comparative genomics component: the Genome 10K project, an effort to sequence a reference genome for each of 10,000 vertebrate species to understand how complex animal life evolved through changes in DNA and use this knowledge to become better stewards of the planet; the UCSC reference human genome project, associated with the UCSC Genome Browser, to map the world's biomedical data to a common reference human genome, unleashing the power of the Internet for biomedical research; the UCSC cancer genomics project, a collaborative effort with The Cancer Genome Atlas (TCGA), which is the National Cancer Institute's flagship cancer genomics project, a Stand Up to Cancer Dream Team involved in finding targeted therapies for breast cancer subtypes, the International Cancer Genome Consortium, and other groups to completely map the genetic changes that occur in different cancers; and the UCSC immunogenomics project, a new effort to map human genetic variation in the MHC region and other regions of the human genome that are important in immunology, including T-cell receptor sequences and B-cell antibody sequences associated with immune response.
The ideal candidate would lead a team building fundamental comparative genomics infrastructure that is applied in all four areas and have experience collaborating with national and international scientific research consortia. In addition, candidates with current knowledge of the fields of cancer genomics, epigenomics, and immunogenomics; experience developing efficient methods for multiple-genome alignment; experience mapping, assembling, aligning, and analyzing large-scale next-generation sequencing data are highly desired.
REQUIREMENTS:
Ph.D. in bioinformatics, computational biology, genomics, or a related discipline with at least 2 years relevant postdoctoral research experience; experience designing algorithms and developing software tools or computational resources for genomics research; experience working in and coding for a UNIX or Linux environment with large clusters, large databases, and large code bases; record of scientific publication in the area of comparative genomics in peer-reviewed research journals and at major scientific meetings; fluency with mathematical theories in genetics and comparative genomics and with current bioinformatic methods and research. The successful candidate will be highly articulate and have demonstrated ability to lead software engineers and students in developing novel computational tools or resources.
TERMS:
Initial appointment is for 2 years. Should the hiring unit propose reappointment, a review to assess performance will be conducted. In addition, reappointment is contingent upon availability of funding.
LOCALE:
University of California, Santa Cruz
COMPENSATION:
$84,700-98,500 annually, commensurate with qualifications and experience
HOW TO APPLY:
Get full information and apply for position #T12-32 at [link] (PDF)
DEADLINE:
March 1, 2012
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BACKGROUND:
We are a federally-funded, Boston-based, biomedical research organization. Our Biomedical Informatics Team develops next generation software applications, Data Warehouses, and analytical tools to enable translational research and improve clinical care. Current initiatives include building an informatics platform that will support integration and analysis of clinical, biospecimen and genomic data. We have a multi-disciplinary team consisting of highly skilled biomedical researchers, clinicians, systems analysts, project managers, and software developers. Resources include electronic medical record system, a new 160 node high performance computing cluster, and access to incredibly challenging projects with the potential to change the way health care is delivered.
This position will be funded through the Boston VA Research Institute (BVARI) who's mission is to promote and to support the medical research and education activities of the VA Boston Healthcare System and to advance the well being of veterans and the general public by these endeavors. BVARI is a non-profit, tax-exempt institute. We are an equal opportunity employer.
RESPONSIBILITIES:
* Interacts extensively with scientific users under the guidance of the Scientific Director to define the requirements for software development and defining use cases for genomic data analysis pipelines.
* Designs and develops cutting edge software solutions and implements Commercial off the shelf (COTS) applications for high throughput genomic studies.
* Implements 'omics data analysis pipelines and tools for use in High performance cluster computing environment.
* Develops and implements innovative data visualization capabilities by aggregating data from multiple applications and functional domains.
* Designs and develops bioinformatics tools for data-mining, analysis, integration and interpretation of large genomic data sets.
* Connects genes, pathway and protein information in different data repositories for analysis.
* Applies ontology and semantic web development skills and concepts in developing scientific data collection and management systems that support biomedical researchers.
REQUIREMENTS:
* Masters in Computer science/Mathematics/life sciences or related field
* Experience with experimental design and statistical methods and tools required to analyze DNA sequence data
* Knowledge about ontology, controlled vocabularies and their practical application in biomedical research
* Expertise in Data modeling and knowledge representation techniques, including Entity Relationship Diagrams
* Excellent communication skills
PREFERENCES:
* Ability to collaborate in a new and evolving technical and development environment, and to participate in the decisions that will define new processes and standards.
* Ability to work effectively with researchers, and technology staff.
* Self-starter, able to organize and lead complex efforts with minimal supervision
* Ability to work in a fast paced environment, working on multiple concurrent sub-projects.
COMPENSATION:
OPEN FOR DISCUSSION
Benefits:
* Health and Dental Insurance
* Life Insurance
* MBTA T-pass program
* Long term/short term disability Insurance
* 403(b) plan
HOW TO APPLY:
Applications from recruiters will not be accepted for this position. Interested candidates should send a cover letter and resume to: Victor Tam at: MIGCandidates[at]gmail.com Please specify the job title in your email.
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BACKGROUND:
The Center for Biomolecular Science & Engineering (CBSE, http://www.cbse.ucsc.edu/) at UC Santa Cruz seeks a customer-oriented individual with strong analytical skills and a commitment to quality to test biological software and data and to research and answer user questions. The successful candidate must be analytical, articulate, organized, detail-oriented, and adaptable. The position requires independence and self-motivation in a team environment.
The UCSC Center for Genomic Sciences, part of the CBSE, operates an important scientific web site for use by researchers worldwide, http://genome.ucsc.edu. Thousands of scientists use the site every day to access the fruits of the human genome project. The site combines cutting-edge research in genomics with solid software engineering and maintains a simple but flexible user interface.
RESPONSIBILITIES:
Under close supervision of the quality assurance manager, the selected candidate will systematically test software, data, and databases before public release and research answers to user questions regarding underlying biological assumptions and computational methods in the genome software and databases. This position works as part of a team of people performing similar work alongside a group of software developers. It interacts extensively with the manager, software developers, other team members, and genome researchers from throughout the world. The work is fast-paced and varied and requires both great attention to detail and a broad understanding of the entire genome browser.
REQUIREMENTS:
Qualifications include a BA or BS in either a biological science or computer science plus coursework or experience in the other or an equivalent combination of education and experience; general knowledge of UNIX; broad knowledge in biology; working knowledge of genomic sequence organization, genome maintenance, and gene expression and regulation in eukaryotes; ability to search the Internet to find answers to scientific questions.
TERMS:
Full time/ career
LOCALE:
Center for Biomolecular Science & Engineering/ Baskin School of Engineering/ University of California, Santa Cruz
COMPENSATION:
Starting salary range: $37,200 to $58,000/year, $3100-$4833/month. Salary commensurate with qualifications and experience.
HOW TO APPLY:
Apply for this job online at http://jobs.ucsc.edu; search for job #1103480.
DEADLINE:
Initial review of applications, 2/9/2012
POLICY:
UCSC is an affirmative action/equal opportunity employer. UCSC strives to embrace diversity in all its forms; it strives to be an inclusive community that fosters an open, enlightened & productive environment.
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BACKGROUND:
Outstanding and motivated candidates are sought for a postdoctoral position at The Hamner Institutes for Health Sciences in Research Triangle Park, NC. The successful applicant will be part of an interdisciplinary team of cell biologists, toxicologists, bioinformaticians and computational modelers, examining cellular signaling pathways affected by estrogenic xenobiotics. The project, supported by a diverse group of sponsors, seeks to map the detailed circuitry controlling dynamic responses to estrogenic compounds in uterus and uterine cells and to create computational dose-response models based on the detailed circuit structure at various dose levels.
This project and several others at The Hamner are directed at speeding implementation of key recommendations from a 2007 NAS report "Toxicity Testing in the 21st Century: A Vision and A Strategy" by developing improved in vitro test assays and interpretive pathway analysis tools that will suffice for human health risk assessment without recourse to animal experiments. This specific project focuses on estrogenic signaling and endocrine disruptor risk assessment.
RESPONSIBILITIES:
Responsibilities will include design and implementation of in vitro cell-based studies of estrogen signaling in uterine cells, and coordinating in vivo studies in rodents. Data sets on estrogen signaling through multiple receptors (ER-ƒÑ; ER-ƒÒ; GPER-1) will be collected using several uterine cell lines in monoculture and co-culture systems, and in vivo uterotrophic assays in rats. Data collection will utilize high throughput technologies for gene and protein response to estrogen signaling to assist in the development of computational pathway models for risk assessment. The position will require occasional travel to professional society meetings to present research findings and to visit sponsoring organizations to describe progress and conclusions. A major goal of the project will be publication of important findings in peer-reviewed journals.
REQUIREMENTS:
Candidate will have a Ph.D., DVM, and /or MD plus 2-3 years of postdoctorate study is required in biology or toxicology with experience in molecular biology and cell culture. Experience with the collection and analysis of gene array data is preferred. Prior experience with bioinformatics, or biological modeling and mechanistic considerations in risk assessment is desirable but not essential.
TERMS:
The initial appointment will be for one year, with the possibility of extension. The funding period for the project is 3 years.
COMPENSATION:
The Hamner Institutes is an independent, non-profit research institute and offers competitive salaries, medical & dental insurance, 401K savings and flex reimbursement plans, paid vacation and holidays, educational reimbursement, and a stimulating work environment.
HOW TO APPLY:
Qualified candidates need to submit their resume and Postdoctoral Fellowship application, which can be found at [link], to koverman[at]thehamner.org or fax to 919-558-1430. Please refer to the "Postdoctoral Fellow - Estrogen Pathway Biology" position. "Equal Opportunity / Affirmative Action Employer - m/f/d/v"
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BACKGROUND:
Outstanding, motivated candidates are sought for a postdoctoral position in a newly formed, trans-disciplinary program in network biology and its application for dose-response modeling in chemical risk assessment at The Hamner Institutes for Health Sciences in Research Triangle Park, NC. The successful applicant will be part of team, including bioinformaticians, computational modelers, cell biologists, and toxicologists, examining cellular signaling pathways affected by estrogenic xenobiotics.
The project, supported by a diverse group of sponsors, seeks to map the detailed circuitry controlling dynamic responses to estrogenic compounds in uterine and mammary tissue and cells and to create computational dose-response models based on the detailed circuit structure at various doses. This project and several others at The Hamner are directed at speeding implementation of key recommendations from the National Academy of Sciences report, "Toxicity Testing in the 21st Century: A Vision and A Strategy", by developing in vitro test assays and interpretive pathway analysis tools that will suffice for human health risk assessment without recourse to animal experiments
RESPONSIBILITIES:
Responsibilities will include integrating genomic, CHIP-seq, metabolomics, limited proteomic and other data streams to develop pathway models and applying the validated dynamic circuit structure as a basis for informed dose response modeling. Data sets on estrogen signaling through multiple receptors (ER-ƒÑ; ER-ƒÒ; GPER-1) will be from the published literature initially, but will be quickly augmented by broad, ongoing Hamner studies. The position will require occasional travel to professional society meetings to present research findings or to visit sponsoring organizations to describe progress and conclusions. A major goal of the project will be publication of important findings in peer-reviewed journals.
REQUIREMENTS:
Candidate will have a Ph.D., DVM, and /or MD plus 2-3 years of postdoctorate study is required in biology or toxicology with experience in genomics, bioinformatics, computational modeling, and complex network applications. Ph.D.s in engineering disciplines or other natural sciences with a strong computational background and experience or interest in quantitative biology/bioinformatics are also encouraged to apply. Prior experience with biological modeling is desirable but not essential.
TERMS:
The initial appointment will be for one year, with the possibility of extension. The funding period for the project is 3 years.
COMPENSATION:
The Hamner Institutes is an independent, non-profit research institute and offers competitive salaries, medical & dental insurance, 401K savings and flex reimbursement plans, paid vacation and holidays, and a stimulating work environment.
HOW TO APPLY:
Qualified candidates need to submit their resume and Postdoctoral Fellowship application, which can be found at [link], to koverman[at]thehamner.org or fax to 919-558-1430. Please refer to the "Postdoctoral Fellow - Network Biology and Dose-Response Modeling" position. "Equal Opportunity / Affirmative Action Employer - m/f/d/v"
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BACKGROUND:
A postdoctoral position in computational biology is available in the Betel lab at Weill Cornell Medical College in New York City. Our group is engaged in a number of collaborative projects with clinicians and experimentalists from several institutes. This work is related to areas of cancer genomics, neurobiology and stem cells. Specific projects include studying the role of microRNAs during development, in cancer, and in stem cells; investigating the molecular biology of memory process; and understanding human microbiome and its implication on cancer.
RESPONSIBILITIES:
Postdocs in the group will have the opportunity to take a leadership role in one or more of these projects, initiate new projects and foster new collaborations. The position entails development and application of novel computational tools for the analysis and interpretation of high-throughput genomic data often from novel assays. The work is based on techniques that include statistical learning, data integration, and visualization guided by specific biological questions.
REQUIREMENTS:
An ideal candidate should have Ph.D (or equivalent) training in statistics, machine learning, algorithmic development and computational biology as well as a detailed understanding of molecular biology and genetics. Prior experience in processing and managing high-throughput sequencing data is desired.
LOCALE:
"The Big Apple"
HOW TO APPLY:
Applications will be accepted until the position is filled. Please submit a CV, a brief research statement, bibliography (or preprints), and names of at least three references to Doron Betel (dob2014[at]med.cornell.edu).
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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 Wellcome Trust Sanger Institute, based south of Cambridge, is one of the world's leading genomic research centres funded primarily by the Wellcome Trust. Our mission is to use genome sequences to advance understanding of the biology of humans and pathogens in order to improve human health.
RESPONSIBILITIES:
We are looking for a talented and motivated Bioinformatician to work with Biologists in the laboratory. Our laboratory is working on characterising adult tissue stem cells and embryonic stem cells. The scientific work is novel and often complex in nature with the success of projects often dependent on an IT component. The candidates are expected to have an M.Sc in Bioinformatics and to have experience of performing Bioinformatics study in a wet lab including microarray gene expression, next generation sequencing, ChIP-Seq, RNA-Seq.
REQUIREMENTS:
* MSc in Bioinformatics or Compuational Biology
* Wet lab research experience
* Experience of performing bioinformatics analysis of next generation sequencing data including ChIP-seq, RNA-seq and exome sequencing
* Skills in analysing microarray gene expression data
* Excellent communication skills to allow efficient interactions with lab members
* High level of trouble shooting skills
* Ability to work within a team
* Ability to work independently and organise own workload
PREFERENCES:
* Experience of developing software systems
* Biomedical research education background or with relevant experience
* Experience of analysing gene expression or epigenetic changes in stem cells
* Experience presenting to outside groups
COMPENSATION:
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/.
Salary: Salary GBP 21,485 to GBP 28,489 per annum dependent on experience
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/
DEADLINE:
Closing Date: 17th February 2012
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RESPONSIBILITIES:
Organization: GN-Genomics Division
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 Bioinformatics Systems Analyst. Under general supervision, will serve as a Systems Analyst (level 2 or 3) to develop computational tools for the assembly of microbial genomes using 2nd-generation (Illumina HiSeq) and 3rd-generation (Pacific Biosciences and others) sequence data. Will play a central role in developing a high-throughput sequencing and analysis pipeline that is capable of producing 1000's of high quality `finished' microbial genome sequences per year. Will work closely with experimental biologists and other bioinformaticians to achieve these goals. Position will report to the head of the Genome Assembly Group.
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:
Essential-
* Perform primary analysis of sequence data including quality control and handling of multiplexed samples, and provide feedback to experimental biologists.
* Use publicly available and in-house developed software to develop high-throughput computational strategies for assembly of `draft' quality microbial genome sequences using second generation (illumina HiSeq) data.
* Develop computational strategies for improving and `finishing' microbial genome assemblies using 3rd generation sequencing technologies (e.g. Pacific biosciences)
* Develop computational tools to evaluate the accuracy and completeness of microbial genome assemblies, and to compare different assembly strategies.
* Evaluate the cost and computational resource demands of different assembly strategies to ensure suitability for the analysis of 1000's of genomes per year.
* Work closely with bioinformaticians in the production informatics department to develop the most promising assembly strategies into production-scale computational pipelines.
* Perform frequent improvement of assembly strategies by evaluating novel genome assembly algorithms, and sequence data types. Provide feedback to experimental biologists on the suitability of new sequence data types for genome assembly.
* Investigate alternative genome assembly strategies as new and improved sequencing technologies and assembly algorithms become available (e.g. assembly using only 3rd generation sequence data).
* Troubleshoot systems and data problems and exercise independent judgment to select appropriate solutions.
* Present progress at internal group meetings.
Marginal-
* Apply the tools and insights gained from microbial genome assembly to more complex sequence datasets (e.g. eukaryotic genome and metagenome assembly).
* Assist with the assembly of whole genome amplified DNA from single cells.
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:
Essential-
* Bachelor's degree in Biology, Bioinformatics, Computer Science or related field with a minimum of two years of work experience, or an equivalent combination of education and experience. Advanced degree preferred.
* Knowledge of standard bioinformatics methods preferably including tools for genome assembly.
* Experience in computational analysis of large next-generation sequence datasets.
* Experience programming with Perl / Python or similar language in a UNIX environment.
* Strong problem-solving, decision-making, and analytical skills to independently make sound judgments and recommend creative solutions to moderately complex problems.
* Strong interpersonal, communication, and presentation skills.
* Detail-oriented with strong organizational skills to address user needs in an effective and timely manner.
Marginal-
* Experience programming in a parallel environment strongly preferred
Essential requirements for the Systems Analyst 3 - In addition to the required duties for a level 2, the Analyst 3 will have:
* Bachelor's degree in Biology, Bioinformatics, Computer Science or related field with a minimum of five years of work experience, or an equivalent combination of education and experience.
* Demonstrated expertise processing large volumes of data, whole-genome data analysis, phylogenetics, and comparative genomics.
* Ability to troubleshoot complex systems and data analysis problems.
HOW TO APPLY:
Apply directly online at:
http://bit.ly/lbl73419Bioinformatics and follow the on-line instructions to complete the application process.
POLICY:
Berkeley Lab is an affirmative action/equal opportunity employer committed to the development of a diverse workforce.
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RESPONSIBILITIES:
Social & Scientific Systems, Inc. (SSS), a company dedicated to improving public health around the world, is looking for a Senior Database Administrator I to support our IT department to administer, maintain, develop and implement policies and procedures for ensuring the security and integrity of the company database. The Senior Database Administrator would also implement data models and database designs, data access and table maintenance codes; resolves database performance issues, database capacity issues, replication, and other distributed data issues.
Duties and Responsibilities:
* Implements and maintains smooth operation and physical design of databases.
* Conducts performance tuning of indexes and databases in general.
* Reviews database design and integration of systems, provides backup recovery and makes recommendations regarding enhancements and/or improvements.
* Analyzes and troubleshoots database interface problems and implements solutions.
* Confers with other SSS support staff and programmers to identify sources of information and assist with collecting and maintaining information.
* Performs assigned support tasks to meet client requirements with off-the-shelf application packages and database packages. Meets with other support technicians, user support specialists and/or clients to determine requirements and provides follow through support to assist clients in using database applications and systems.
* Maintains security, relational and textual database management system applications and integrity controls.
* Monitors support requests for trends and makes suggestions on improving the quality of support. Researches new technology for potential application to SSS and/or clients. Keeps abreast of current trends in the technology industry.
* Assists in the development of user guides and reference materials for specific applications or tasks. Assists in developing training approaches and helping users become familiar with new database packages. Provides one-on-one training as needed. Conducts workshops and seminars for end-user community on database-related topics.
* Formulates policies, procedures, and standards relating to database management, and monitors transaction activity and utilization.
* Participates in planning sessions to establish a common understanding of the requirements.
* Leads and or manages projects as assigned.
* Participates in the change management process by analyzing change dependencies and impacts on database interfaces, and by maintaining implementation schedules. May develop stored procedures and/or triggers.
REQUIREMENTS:
Bachelor's degree and four years of related database administration experience and six plus years of related database support experience; vendor certification for the current operating system; vendor certification for systems with direct responsibility; Microsoft Certified Database Administration (or equivalent) certification on the current database software; familiarity with current version of MS Office applications; familiarity with specified IT hardware, applications and environments. Must be capable of lifting items (boxes, computer equipment, etc.) weighing up to 30 pounds. Excellent verbal and written communication skills.
LOCALE:
This position is based in our Silver Spring, MD office.
COMPENSATION:
SSS offers an excellent total compensation package, including medical, life, and disability insurance, annual leave, stock ownership, 401(k) plan, education assistance, casual work environment, commuter benefits, flexible hours, and more.
HOW TO APPLY:
Review full requirements/description and apply online at http://www.s-3.com - see Req. #908.
POLICY:
EOE M/F/D/V
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