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    BACKGROUND

    Position:
    The Computational Plant Genomics Lab invites applications for a Postdoctoral position in the Department of Ecology and Evolutionary Biology at the University of Connecticut. We focus on developing computational approaches that integrate next generation sequence data to address questions in non-model plants, particularly forest trees. The lab has the following ongoing projects: 1) Understanding the evolution of alternative translation initiation using RNA-seq data 2) Integrating new and existing approaches to gene prediction to improve the annotation of complex genomes 3) Analysis of gene family evolution and related comparative genomics questions 4) Detecting variation in populations from GBS and related sequence data.

    REQUIREMENTS

    • Ph.D in Genetics, Plant Genetics, Evolutionary Biology, Bioinformatics, Computational Biology, or other related field
    • Track record of publications in comparative genomics
    • Programming skills in Python, Perl, Java, C++, R or other language
    • Experience with Linux and high performance computing environments
    • Demonstrated ability in developing/applying statistical or machine learning methods in computational biology
    • Experience in genome scale data analysis including RNA-Seq data, genome annotation, biological sequence analysis or other relevant computational genomics experience
    • Highly motivated for interdisciplinary research, excellent communication skills, and the ability to work independently as well as within a research group

    TERMS

    Initial appointment is one year, with possible extension.

    LOCALE

    UCONN, Storrs, CT

    HOW TO APPLY

    Interested applicants should send their C.V., 2-3 page research statement, available start date, and contact information for three references to: jill.wegrzyn[at]uconn.edu. Applications that do not contain all materials will not be considered.

    BACKGROUND

    Within the office of the Chief Health Information Officer, the Director of Bioinformatics will serve Dana-Farber Cancer Institute and its patients by building and leading a small, central team of bioinformaticists and computational biologists, developing methods, analysis tools, and pipelines as needed to support Clinical and Research communities, and by helping coordinate, harmonize, and ensure the excellence of bioinformatics-related support activities across the Institute. The role requires a strong background in bioinformatics and genomics and their applications in biomedical research and oncology clinical care, as well as a high level of communication, interpersonal, and team-building skills.

    RESPONSIBILITIES

    Primary Duties and Responsibilities:
    • Manage a small, versatile team of bioinformaticists, computational biologists, and other informatics professionals to tackle high-priority and cross-functional DFCI institutional needs.
    • Collaborate with research information services, scientific computing, data science and engineering teams to create and manage multidisciplinary project teams.
    • Collaborate with strategic Centers and functions, such as the Knowledge Systems group to design and build translational/genomic research systems and decision-support models that integrate research and clinical data, and support precision cancer medicine efforts.
    • Help develop a standardized data management, access, integration, and analysis strategy and approach for translational / 'omic data for Dana-Farber and our strategic partner institutions.
    • Support and participate in methods development and data analysis strategy for the PROFILE precision medicine program, CCGD (Center for Cancer Genome Discovery), Center for Cancer Precision Medicine (CCPM), and other strategic centers at Dana-Farber.
    • Support PROFILE/CCGD project bioinformatics research and development: Provide expertise and foster collaborative decision-making and research efforts around new methods, tools, and data. Collaborative work may include integration of somatic and Germline DNA, copy number, RNAseq, immune profiling, etc. to support both clinical decision-making and research needs. Help maintain DFCI's leading position in cancer molecular profiling and use of genomic data in clinical practice. Provide scientific informatics mentorship to PROFILE/CCGD bioinformatics team.
    • Collaborate with Pathology leadership and informatics personnel from BW and DFCI to continue advancing and help systematize scientific, pipeline, and process improvements, including support for scientific and clinical interpretation of genomic assay results.
    • Collaborate with Radiation Oncology leadership and informatics personnel from BWH and DFCI to continue advancing scientific and process improvements and to support development of research databases, informatics workflow software, and analytics/reporting tools.
    • Assemble appropriate governance bodies to support prioritization or work, strategic directions, and tactical decisions.
    • Help cultivate and support a DFCI network of bioinformaticists and computational biologists. Establish and maintain community of practice for best-practice and expertise-sharing, collaborations, mentorship, and career development for staff bioinformatics personnel of all levels across the institute.
    • Supply scientific expertise for internal software development projects.
    • Interact with senior executives, management, and all levels of faculty and staff on current and future initiatives to ensure high-quality, high-impact decisions on technical/scientific solutions and innovative projects in the biological and translational research areas.
    • Ensure all employees are treated with dignity and respect, have appropriate performance feedback and career development conversations and support, and have the tools they need to do their jobs.

    REQUIREMENTS

    Minimum Job Qualifications:
    1. Ten years of bioinformatics and genomics-related professional experience, including at least 5 years of people management in a biomedical research setting. Industry experience preferred.
    2. Strong technical and scientific background with hands-on experience and proficiency
    3. Doctorate in Bioinformatics or Computational Biology, or equivalent experience, including a strong scientific publication record
    4. At least three years of relevant experience in the oncology domain
    Knowledge, Skills, and Abilities Required:
    • Proven leadership, strategic, and execution abilities
    • Excellent verbal and written communications skills, with ability to deliver compelling, persuasive presentations to technical, scientific, and administrative audiences
    • Exceptional interpersonal and collaboration skills, demonstrated ability to be effective within a complex organizational structure
    • Ability to set and manage annual budget and goals, and to manage a portfolio of multiple simultaneous projects with defined deadlines, using a combination of matrix and direct resources
    • Keen attention to detail
    • Superior analytical, evaluative, and problem-solving abilities
    • Exceptional service orientation
    • Ability to motivate and inspire others in a team-oriented, collaborative environment
    • Ability to work under minimal supervision in complex environments
    • Ability to effectively manage client and partner expectations
    • Ability to interact professionally with senior executives
    • Ability to establish immediate credibility among peers – a professional who is respected for intelligence and technical expertise

    HOW TO APPLY

    Apply Here: www.Click2apply.net/v56n98mrp2

    BACKGROUND

    The World's Brightest Never Stop Innovating

    At St. Jude Children's Research Hospital, we know what can be achieved when the brightest scientific minds face the fewest barriers. That's why we provide world-class facilities, state-of-the-art technologies, and extraordinary support for your research to ensure scientific progress is never halted from a lack of resources.

    RESPONSIBILITIES

    The position is responsible for basic and advanced analysis on data produced from next generation sequencing systems (DNA-seq, RNA-seq, metagenomics, ChIP-seq, etc.) as well as gene expression microarrays. Develop, improve, modify, and operate data analysis pipelines. Develop software or use extant software in conducting data analysis for NGS and microarray datasets at basic and advanced levels. Work closely with experimental researchers to generate/provide analysis reports, project reports and perform requested custom analyses. Post-processing statistical analysis of results and biological interpretation of data may also be required. Will be involved in the evaluation and recommendation of new software tools to meet the growing needs of the department. Will be involved in training members of the department on software usage and data analysis techniques.

    REQUIREMENTS

    Minimum Education:
    • Requires a Master's Degree in Computer Science or Bioinformatics, with a background in the biological sciences, PhD preferred
    • In lieu of a Master's degree, a Bachelor's in Computer Science or Bioinformatics and five (5) years of related experience is required
    Minimum Experience:
    • Experience in desktop computing hardware, software, operating systems and desktop applications
    • Prefer end user support and training experience
    • Familiarity with object oriented analysis, design, and programming
    • Prefer cross training in a biological science

    LOCALE

    Memphis, TN

    COMPENSATION

    Competitive

    HOW TO APPLY

    Please visit research-stjude.icims.com/jobs[...]ub=15

    BACKGROUND

    Position Context:
    The Canadian Center for Computational Genomics (C3G) at McGill University provides bioinformatics analysis and high performance computing services for the life science research community. C3G develops customized and case-by-case bioinformatics solutions as well as an extensive suite of open-source software. We are seeking a Bioinformatics Specialist to perform advanced analysis and to contribute to the development of analysis pipelines associated with Next-Generation Sequencing (NGS) instruments. Under the direction of the Bioinformatics Manager, the Bioinformatics Specialist will contribute to the research and development activities and perform advanced statistical analyses to facilitate genomics data interpretation. The selected candidate will work closely with the C3G team, and scientists at the center. He will be exposed to a wide variety of novel sequencing technologies, bioinformatics approaches, and state of the art computing resources in a dedicated facility for high-throughput sequencing and large-scale genomic studies.

    RESPONSIBILITIES

    Primary:
    • Actively participate to the Technical Development group and provide Standard Operation Procedure and analysis.
    • Provide, support and guide Bioinformatics Consultants in the unit on tools and what analyses to do. Monitor progress of assignments and results.
    • Use and develop analysis pipelines using in-house and 3rd party tools or algorithms, and incorporate them into specialized analysis workflows.
    • Develop bioinformatics solutions for the analysis of complex genomic datasets.
    • Update and extend bioinformatics tools and software methods used or developed at the C3G.
    • Provide detailed reports with analysis results and descriptions of methods used.
    • Contribute to problem-solving discussions.
    • Provide regular internal reports regarding the progress of projects (oral presentations).
    • Keep online documentation up-to-date, explaining the services offered and the analysis methods used.
    • Stay informed on the most relevant bioinformatics practices in genomics.
    • Lecture in bioinformatics training workshop organized by the center.
    • Manage several analysis projects at the same time.

    REQUIREMENTS

    Education/Experience:
    • Undergraduate degree (related field)
    • Three (3) years' related experience
    Other Qualifying Skills and/or Abilities:
    MSc in Bioinformatics, Statistics, Computer Science or related field preferred. Three (3) years of experience in bioinformatics or genomics research. Excellent understanding of statistics is a must. Experience with Python is a requirement. Experience with cancer data analysis is a plus. Good knowledge of R, git, and bash is needed. Additional programming experience (Perl and Java) is an asset. Experience in using HPC environment. Experience lecturing in training workshops is desirable. Very good communication and writing skills in French and English is also required.

    HOW TO APPLY

    Please submit your application online at www.mcgill.ca/medh[...]y-now. Click on "APPLY NOW" and clearly indicate the reference number.

    DEADLINE

    Applications must be received no later than October 6, 2016 at 5:00 PM.

    We thank all applicants for their interest, however, only those applicants selected for an interview will be contacted.

    POLICY

    McGill University is committed to equity in employment and diversity. It welcomes applications from indigenous peoples, visible minorities, ethnic minorities, persons with disabilities, women, persons of minority sexual orientations and gender identities, and others who may contribute to further diversification.

    BACKGROUND

    A position is available at the La Jolla Institute for Allergy and Immunology in the research group of Dr. Catherine Hedrick to perform bioinformatics research in immunology in the fields of cancer and atherosclerosis. The project will include analysis of RNA sequencing and ChIP-sequencing experiments in immune cells, as well as high-dimensional analysis and clustering of mass cytometry data.

    LJI is an independent, non-profit research institute, and is a great place for postdoctoral fellows to work. It was recently ranked in the world's top 5 immunology research institutes and was ranked #1 in a survey of postdocs as 'best places to work' worldwide by The Scientist magazine.

    REQUIREMENTS

    The successful candidate should have a PhD or MD. Knowledge of Matlab and R is required. Knowledge of bioinformatics, immunology, atherosclerosis, or cancer biology is a plus.

    COMPENSATION

    Full-time employment at LJI includes a competitive salary, medical/dental/vision benefits and contributions to a retirement plan (403B).

    Salary: La Jolla Institute postdoctoral payscale based on NIH recommendations, commensurate with experience.

    ABOUT US

    In 2016, LJI was ranked as one of the best places to work in San Diego by the San Diego Business Journal. The Institute hosts 24 world-renowned faculty and over 70 postdoctoral researchers hailing from 21 different countries. LJI is located in the Science Research Park on the campus of UC San Diego, with easy access to the San Diego life sciences community and all that the area has to offer.

    HOW TO APPLY

    Please send CV, brief description of current research activities, and contact information of 3 references. Attach all documents within a single file attachment.

    Please apply here: www.lji.org/care[...]tion/

    POLICY

    LJI provides Equal Employment Opportunity (EEO) to all employees and applicants regardless of race, national origin, religion, sex, marital status, age, mental or physical disability, medical condition, veteran status, sexual orientation, or pregnancy. This applies to all personnel practices, including recruitment, hiring, training, promotion, compensation, benefits, transfers, educational assistance, and social and recreational programs.

    RESPONSIBILITIES

    The Great Lakes Bioenergy Research Center (GLBRC) is one of three Department of Energy centers established to conduct fundamental, genomics-based research on microbial and plant systems required to realize the national need for low-cost biofuels. The GLBRC is housed at the University of Wisconsin with collaborators at Michigan State University and other universities and national labs.

    As a member of a research team of faculty, staff, post docs, and graduate students, the Web Developer - Software Engineer will be part of an Informatics team supporting the research objectives of the GLBRC in scientific computing and computational infrastructure. The position requires a highly motivated team player who will participate in the design and implementation of custom web-based and desktop applications and databases for use by GLBRC scientists. Specific duties may include database design and implementation; requirements gathering; and software analysis, design, implementation, documentation, testing, deployment, and support. This will require effective communication and collaboration with end users (including researchers and bench scientists), bioinformaticians, software developers, and operational IT personnel.

    The candidate will design, develop, maintain, and operate scientific and analytical software, databases, and knowledgebases required by GLBRC. The well-qualified candidate will have knowledge of, and experience in developing and maintaining, medium-to-large scale strategic web-based software solutions in a research environment, using best practices with minimal supervision. The candidate may also help in developing and delivering user training and should be comfortable communicating in a variety of formats to scientists, management, and staff at all levels of a research institution.

    This position requires the ability to work both in a team and independently and the ability to communicate and collaborate with members of an inter-disciplinary team. Willingness and ability to rapidly learn new skills, concepts, and technologies is essential.
    This position offers an opportunity to play an important role in creating a keystone research center for the first great national challenge of the 21st century, sustainable energy independence. For additional information regarding the GLBRC, visit our website: www.glbrc.org.

    REQUIREMENTS

    B.S. or M.S. in Computer Science or related field.

    Experience with web-application development and database design and implementation, ideally with Ruby on Rails. Experience with designing and implementing large-scale relational databases with Oracle or MySQL. Programming experience in Ruby on Rails, JavaScript, R, Java, C++, C#, Perl, PHP, and/or Python. Experience with version control (e.g., SVN or git) and configuration management.

    Experience with jQuery, automated testing, Bioconductor, BioPerl, BioRuby, Apache, and bioinformatics tools and applications is desirable. Experience with code reviews and modern software quality assurance practice is a definite plus. Some knowledge of molecular biology and/or statistics would also be welcome.

    LOCALE

    University of Wisconsin-Madison
    Wisconsin Energy Institute
    1552 University Avenue
    Madison, WI 53726

    COMPENSATION

    $50,000 - $80,000, Depending on Qualifications

    HOW TO APPLY

    In order to apply, applications must be submitted online at uwjobapply.wisc.edu/Appl[...]86880

    In order to be considered for this position, please upload your resume and cover letter by the deadline.

    Questions may be directed to Emily Hickey, 608-890-2286, hr[at]energy.wisc.edu.

    Relay Access (WTRS): 7-1-1 (out-of-state: TTY: 800.947.3529, STS: 800.833.7637) and above Phone number (See RELAY_SERVICE for further information.)

    If you need to request an accommodation because of a disability you can find information about how to make a request at the following website: www.oed.wisc.edu/478.htm

    DEADLINE

    October 15, 2016

    POLICY

    A criminal background check will be conducted prior to hiring.

    A period of evaluation will be required.

    NOTE: Please indicate in writing if you request that your identity be kept confidential. If you do not indicate your preference to remain confidential, the University may be required to disclose your identify and/or application materials. The identity of finalists and successful candidates will be revealed upon request. See Wis. Stat. sec. 19.36(7).

    UW-Madison is an equal opportunity/affirmative action employer.

    We promote excellence through diversity and encourage all qualified individuals to apply.

    BACKGROUND

    An exciting Software Development opportunity has become available working with Dr Serena Nik-Zainal on several projects, including the clinical study INSIGNIA, which forms part of the research initiative COMSIG. The COMSIG consortium, funded by a Wellcome Trust Strategic Award, is focused on exploring the mutational signatures of DNA damage and repair processes. This includes work performed across a range of model organisms (yeast, worm), as well human studies such as INSIGNIA, which are a key focus for Dr Nik-Zainal's team. As part of this we are generating human iPSC lines from patients with germline mutations in DNA repair/replication pathways and generating parallel CRISPr/CAS-9 edited iPSC lines of the same genes. The over-arching objective is to explore mutational signatures in the context of the biological mechanisms associated with DNA repair, by integrating cellular/molecular approaches with genome-wide assays including genomic sequencing, RNA-seq and ChIP-seq.

    The successful candidate will be embedded in a multidisciplinary team and will be tasked with further contributing towards developing the analysis pipelines for this project and towards developing the public-facing website/database for the mutational signatures projects. The role involves working at the interface between scientific and IT staff on these projects to ensure efficient analysis of the DNA sequencing data sets. This website/database in envisaged as a reference resource for mutational signatures in the future. The position would suit a Bioinformatician/Software Developer who enjoys developing or enhancing software tools for analysis of complex NGS biological data sets and to make these efficient, visually appealing and interpretable by the scientific/clinical community. We are looking for an individual who enjoys working in a multi-disciplinary team environment to help solve complex IT issues which will ultimately aid our understanding of mutational processes in human cells.

    REQUIREMENTS

    Essential Skills:
    • Good degree in Bioinformatics or Computer Science with a scientific background
    • Software development skills (using Perl and/or Python)
    • ORACLE/MySQL databases
    • Experience of handling Next Generation sequencing data
    • LSF or Open Grid scheduling software
    • Experience working, developing and compiling software tools in a UNIX/LINUX environment
    • Enjoy working as part of a team

    PREFERENCES

    Ideal Skills:
    • Software development using a compiled language (C,C++,Java)
    • Experience of statistical analysis in a bioinformatics (in R)
    • Experience of workflow management IT systems
    • Experience of VMware, OpenStack or Amazon Web Services (AWS)
    • Experience of working in an Agile Software Development Group
    • Web development using Perl, Java, HTML(5), CSS, JavaScript
    • Background in cancer genetics

    COMPENSATION

    Salary range: £31,033 to £39,142 pa depending on experience.

    Our Benefits include: Defined Contribution Pension Scheme, Group Income Protection, Healthcare scheme, Childcare Vouchers, Workplace Nursery and 25 days Annual Leave, increasing by one day per year up to a maximum of 30, plus Bank Holidays. We also have a gym, two cafes, dining facilities, and a free campus bus service. Our thriving Sports and Social Club provides many opportunities to meet with people working across the campus.

    ABOUT US

    The Sanger Institute is a charitably funded research centre focused on understanding the role of genetics in health and disease. We use state of the art large-scale genomic approaches to drive world-leading projects to uncover the basis of genetic and infectious disease. Our goal is to provide results that can be translated into diagnostics, treatments or therapies that reduce global health burdens. The Institute is located near Cambridge, UK on the stunning Wellcome Genome Campus. This growing and dynamic site is the British hub of genomic science. It hosts the European Bioinformatics Institute (EBI), Open Targets, a Biodata Innovation Centre and will soon host Genomics England Limited's 100,000 Genomes Sequencing Centre.

    The Campus is also home to the Wellcome Genome Campus Courses, Conferences and Public Engagement (CCPE) programme. The CCPE programme delivers training and engagement focussed around genomics, its applications, and implications. Its vision is to inspire a range of audiences both on the Campus and beyond it, and make the world of genomics open and accessible to all. To help researchers to develop their skills and networks, the Institute hosts a range of scientific seminars with internal and invited speakers, scientific group meetings and skills development workshops. In addition the Campus is home to the Wellcome Trust Advanced Course and Scientific Conferences programme and the Wellcome Trust Conference Centre.

    HOW TO APPLY

    Please include a covering letter and CV with your application via: jobs.sanger.ac.uk/wd/p[...]79950

    DEADLINE

    Closing date for applications: 19th October 2016, however applications will be considered and reviewed on an on-going basis and therefore the post may be filled before the deadline.

    POLICY

    Wellcome Trust Sanger Institute welcomes applications from all candidates irrespective of age, disability, gender, gender identity, sexual orientation, race, religion or belief, or marital or civil partnership status.

    BACKGROUND

    NIH funded postdoctoral scholar position is available in the laboratory of Dr. Igor B. Zhulin at the Oak Ridge National Laboratory and the University of Tennessee (genomics.utk.edu). We study signal transduction in systems ranging from bacteria to humans using evolutionary genomics and protein sequence and structure analysis. Practical implications of this work are ranging from fundamental discoveries [Science Signaling 3: ra50 (2010), PLoS Genetics 7: e1002430 (2011), Nature Communications 4: 2881 (2013), PLoS Computational Biology 12: e1004862 (2016)] to medical applications [Nature Communications 7: 10464 (2016), Genetics in Medicine, Epub ahead of print doi: 10.1038/gim.2015.208 (2016)].

    RESPONSIBILITIES

    Your primary responsibility will be carrying out one or more research projects within a broadly defined research theme. In addition, you will help maintaining and improving our bioinformatics infrastructure (hardware and software).

    REQUIREMENTS

    Ideal candidate will have a Ph.D. in bioinformatics, computational biology, or computer science. Strong computer skills (Linux, Python, HTML, Javascript) and working knowledge of basic bioinformatics tools are required. Excellent oral and written communication skills and the ability to work in a team environment are also required.

    PREFERENCES

    Experience with databases (PostgreSQL, MongoDB) and numerical or statistical analysis is a plus.

    TERMS

    Position is guaranteed for 2 years with a possible extension for another 1-2 years.

    LOCALE

    Oak Ridge and Knoxville, Tennessee, USA

    COMPENSATION

    Salary according to NIH postdoctoral scale.

    HOW TO APPLY

    Please visit ut.taleo.net/care[...]001AH
    and/or send a message to Igor B. Zhulin: ijouline[at]utk.edu

    DEADLINE

    November 1, 2016

    BACKGROUND

    The Department of Biostatistics & Medical Informatics (BMI) at the University of Wisconsin School of Medicine & Public Health (SMPH) is seeking tenure track assistant, associate, and full professors starting around July 2017.

    A key consideration is the ability and interest to work in a collaborative, interdisciplinary environment.

    RESPONSIBILITIES

    Successful candidates will maintain superb research programs that ideally involve applications to high throughput biological experiments, genetics and genomics, precision medicine, clinical trials, population health research or health services research, and/or the improvement of clinical care. It is expected that the candidate will attract and maintain external funding to support his/her program, and will collaborate with scientists at UW-Madison, either in the SMPH and/or across campus, and/or its partner institutions. Additional responsibilities will include training graduate students, teaching, and participating in professional, university, and community service appropriate to rank.

    REQUIREMENTS

    Candidates should have a doctoral degree (PhD, ScD, or equivalent) in Biostatistics, Statistics, or a closely related quantitative area. Key areas of interest include clinical and population health biostatistics, and statistical genetics and genomics.

    ABOUT US

    The University of Wisconsin-Madison is a world-class academic institution with an international reputation for basic, applied, and interdisciplinary research. UW-Madison regularly ranks in the top 10 or 12 among U.S. public universities, and regularly surpasses $1 billion in annual research expenditures. Madison provides a vibrant, culturally rich environment highly ranked in national surveys for quality of life. The BMI department also provides an exceptional environment for academic activity and interdisciplinary collaboration. BMI faculty collaborate with scientists across UW and the state, including the Institute for Clinical and Translational Research, the UW Carbone Cancer Center, the Marshfield Clinic Research Foundation, the Wisconsin Institute for Discovery, and the Morgridge Institute for Research. BMI maintains strong ties to the world-class Departments of Computer Sciences and of Statistics, through which many of its graduate students are trained. BMI is home to a Center for Predictive Computational Phenotyping, funded under the NIH "Big Data to Knowledge" initiative.

    HOW TO APPLY

    To ensure full consideration, applications must be received by November 15, 2016, although late applications may be accepted. Candidates should submit their applications through the UW employment website: www.ohr.wisc.edu/Webl[...]87874. To aid in applicant screening, please indicate primary area of interest as either "clinical and population health biostatistics", or "statistical genetics and genomics" in cover letter.

    POLICY

    AA/EOE. Women and minorities are encouraged to apply. Unless confidentiality is requested in writing, information regarding the applicants must be released upon request. Finalists cannot be guaranteed confidentiality. A criminal background check will be required prior to employment.

    Submitter

    BACKGROUND

    We're looking for a problem solver with a background working in data integrity and testing to ensure high quality data and metadata is distributed to the cancer research community. Elevate your career with this opportunity to work with one of the world's largest collections of harmonized cancer genomic data. This role focuses on the Genomic Data Commons, which is at the forefront of both cutting edge research and production systems supporting cancer research. You will join a team of engineers developing innovative technologies who will keep you challenged in our dynamic environment as we work together to pursue discovery through data-driven cancer research.

    You will join the team as the lead engineer for data quality and integrity. You will focus on leading data quality efforts related to data integration, higher level data products, and distribution to the cancer research community. To accomplish this, you will work across multiple teams to build and automate frameworks such as anomaly detection, reporting, and alerting to ensure data quality. You shall gain expertise not only in the data itself, but the systems as well in order to interrogate the data and understand gaps in data quality. Data and metadata quality has a broad scope therefore you are expected work collaboratively across teams to determine priorities and best methods for achieving objectives.

    RESPONSIBILITIES

    Data Quality and Integrity – Drive the design of the data QA infrastructure and execution of testing protocols to validate pipelines, integrated datasets, and data products. Use a combination of exploratory, regression and automated testing to ensure data quality standards. Assess appropriate inclusion/exclusion of data based on defined data dictionary; assist in evaluation of data dictionaries and utilize data specification and code to validate data as it relates to quality.

    Data Quality Improvement – Proactively identify potential data issues and downstream impact. Identify existing data issues and perform research and root cause analyses to determine resolution. Work collaboratively with software engineers and bioinformaticians to achieve and verify resolution. Establish processes and standards to improve data quality assurance and implement efficiencies in data management. Define measurements and metrics to conduct and present routine data reports to the project team and stakeholders.

    Data Management – Participate in data acquisition and integration planning efforts including data modeling, data dictionary definitions, and data harmonization pipeline development. Develop a deep understanding of multiple genomic datasets and the technical data management software and processes of the underlying system. Define data quality and integrity criteria and develop a comprehensive data quality management plan to lead key data QC efforts through team collaboration for all phases of the data management life cycle.

    Technical Writing – Contribute written knowledge and expertise to system documentation, user documentation, scientific manuscripts, reporting, grant proposals and reports, and presentation materials. Stay abreast of broad knowledge of existing and emerging technologies and QC tools in the cancer genomics space.

    REQUIREMENTS

    • Bachelor's degree in Computer Science, Bioinformatics, or relevant engineering or scientific field such as Physics or Genomics required.
    • 5+ years of experience in progressive technical business analysis role required.
    • Experience with Agile methodology required.
    • Experience with writing technical specifications required, with a focus on full stack architecture, including REST APIs, SQL and noSQL data solutions and distributed infrastructure required.
    • Experience with business analysis and quality assurance professional standards, business processes, workflows, methodologies and leading practices required.
    • Experience leading business analysis activities while ensuring the traceability and optimum coverage of business requirements defined required.
    • Experience working in a Linux command line environment required.

    PREFERENCES

    • PhD in an relevant engineering or scientific field highly preferred.
    • Experience in Change Management, Release Management, Incident, Problem Management and working on Business Intelligence preferred.
    • Experience with HIPAA and/or FISMA security regulations preferred.
    • Experience with cancer or human genomics preferred.
    • Experience with bioinformatics preferred.
    • Experience managing a backlog of requirements in an Agile workflow preferred.
    • Experience creating user stories from requirements preferred.
    • Experience with JIRA project tracking software preferred.

    TERMS

    Full-time

    LOCALE

    Chicago, IL

    ABOUT US

    About the Genomic Data Commons:
    The Genomic Data Commons (GDC) is a comprehensive computational facility to centralize and harmonize cancer genomic data generated from NCI-funded programs. The GDC is the foundation for a genomic precision medicine platform and will enable the development of a knowledge system for cancer. The GDC will provide an open-source, scalable, modern informatics framework that uses community standards to make raw and processed genomic data broadly accessible. This will enable previously infeasible collaborative efforts between scientists.

    gdc.cancer.gov

    About the Center for Data Intensive Science:
    The Center for Data Intensive Science at the University of Chicago is developing the emerging field of data science with a focus on applications to problems in biology, medicine, and health care. Our vision is a world in which researchers have ready access to the data and tools required to make discoveries that lead to deeper understanding and improved quality of life. We democratize access, speed discovery, create new knowledge and foster innovation through implementation using data at scale. Our scientific data clouds and commons include the Genomic Data Commons, Bionimbus Protected Data Cloud, and Open Science Data Cloud.

    cdis.uchicago.edu

    HOW TO APPLY

    Apply under Requisition #101319 at jobopportunities.uchicago.edu/appl[...]32808

    POLICY

    The University of Chicago is an Affirmative Action / Equal Opportunity / Disabled / Veterans Employer.

    Submitter

    BACKGROUND

    The Center for Precision Health (CPH) at the School of Biomedical Informatics (SBMI), the University of Texas Health Science Center at Houston (UTHealth) has a non-tenure track position at the assistant professor level in the areas of precision medicine and bioinformatics.

    UTHealth is in the world-renowned Texas Medical Center (TMC) located in cosmopolitan Houston, Texas, the fourth largest city in the United States. SBMI currently offers Master's and Ph.D. Degrees, along with a certificate program in biomedical and health informatics.

    RESPONSIBILITIES

    The successful candidate will be expected to plan, supervise, and direct research in bioinformatics, genomic medicine, and the related in CPH's director, Dr. Zhongming Zhao's lab. The candidate will provide technical expertise to facilitate the study design, sample or data collection, pipeline development, data analysis, results implementation, manuscript writing, and grant proposal preparation. Collaborative research with other faculty in the CPH, school and across UTHealth and TMC (e.g., MD Anderson Cancer Center and Baylor College of Medicine) is also encouraged.

    REQUIREMENTS

    The individual should possess a doctoral degree in one of the following areas: bioinformatics, genomics, genetics, computational biology, biomedical informatics, computer science, medicine, biostatistics, or related disciplines. A record of verifiable and published research in bioinformatics and genomics and potential for obtaining extramural funding are preferred. Excellent teamwork and communication skills are required. Please provide a CV and a research statement.

    PREFERENCES

    Some grant writing experience.

    LOCALE

    Houston, Texas, USA

    COMPENSATION

    By experience.

    HOW TO APPLY

    Apply at jobs.uth.tmc.edu (search Requisition # 160942 for RAP position).

    Please send an email to zhongming.zhao[at]uth.tmc.edu to inquire any information.

    DEADLINE

    Open until the position is filled.

    Submitter

    BACKGROUND

    Postdoctoral positions are available in Dr. Zhongming Zhao's Bioinformatics and Systems Medicine Laboratory (BSML, www.uth.edu/bioinfo/), now moved to School of Biomedical Informatics, University of Texas Health Science at Houston (UTHealth) from Vanderbilt University Medical Center. The successful candidate is expected to join an established bioinformatics team. The ongoing projects in BSML focus on precision medicine, functional roles of genetic variants in complex disease, next-generation sequencing data analyses, and regulatory networks. Integrative genomics and systems biology approaches are often applied. Funding is available to support this position for up to three years and future promotion is possible. The candidate will have the opportunity to access many high throughput datasets and interact with investigators across UTHealth and Texas Medical Center. The lab has an excellent post-doctoral training track record (e.g. 13 former postdocs are currently faculty members, two received Young Investigator Awards from national foundations, and three were finalists for the Vanderbilt Postdoc of the Year Award). Recent publications:

    Jia P, Jin H, Meador CB, Xia J, Ohashi K, Liu L, Pirazzoli V, Dahlman KB, Politi K, Michor F, Zhao Z, Pao W (2013) Next-generation sequencing of paired tyrosine kinase inhibitor-sensitive and -resistant EGFR mutant lung cancer cell lines identifies spectrum of DNA changes associated with drug resistance. Genome Research 23:1434-1445

    Cheng F, Jia P, Wang Q, Lin CC, Li WH, Zhao Z (2014) Studying tumorigenesis through network evolution and somatic mutational perturbations in the cancer interactome. Molecular Biology and Evolution, 31(8):2156-2169

    Jia P, Wang Q, Chen Q, Hutchinson K, Pao W, Zhao Z (2014) MSEA: detection and quantification of mutation hotspots through mutation set enrichment analysis. Genome Biology 15:489

    Zhao Z, Xu J, Chen J, Kim S, Reimers M, Bacanu SA, Yu H, Liu C, Sun J, Wang Q, Jia P, Xu F, Zhang Y, Kendler KS, Peng Z, Chen X (2015) Transcriptome sequencing and genome-wide association analyses reveal lysosomal function and actin cytoskeleton remodeling in schizophrenia and bipolar disorder. Molecular Psychiatry, 20(5):563-72

    The BSML lab is part of the new Center for Precision Health (CPH), a joint enterprise by the School of Biomedical Informatics and School of Public Health, The University of Texas Health Science at Houston. The center is established in UTHealth in response to the emerging need of precision health and President Obama's Precision Medicine Initiative. The center focuses on precision cancer medicine, systems medicine, pharmacogenomics, and translational bioinformatics. Ten tenure-tracked faculty and a few non-tenure track faculty will be recruited to form this center. UTHealth is in the world-renowned Texas Medical Center (TMC) located in cosmopolitan Houston, Texas, the fourth largest city in the United States. SBMI currently offers Master's and Ph.D. Degrees, along with a certificate program in biomedical and health informatics.

    REQUIREMENTS

    The qualified candidates should be highly motivated in research and have a Ph.D. in bioinformatics, quantitative science, computational biology, molecular biology, or related field upon the job start date. The successful candidate should have some experience in analyzing high-throughput genomic data and proven skills in at least one programming language (Perl, Java, or C/C++). Good understanding of genetics or molecular biology and familiarity with biostatistics are plus. For more information about our research, please visit the web site www.uth.edu/bioinfo/.

    PREFERENCES

    NGS data analysis experience.

    TERMS

    Up to three years, and with potential to get promotion to upper level positions.

    LOCALE

    Houston, Texas, USA

    COMPENSATION

    NIH standard or by experience.

    HOW TO APPLY

    Email: zhongming.zhao[at]uth.tmc.edu

    DEADLINE

    Available until being filled.

    BACKGROUND

    We seek a postdoctoral fellow for a project that aims at quantitatively extracting features from imaging data sets (MRI, PET-CT, CT scans) to assess the correspondence with molecular profiles and clinical parameters and outcome of patients. A combination of automated and manual image characterization methods will be used to characterize these quantitative imaging biomarkers, using a so-called "radiomics" approach+++. The goal is to develop and evaluate novel computational imaging processing methods applied to existing and future datasets from throughout North America and Europe. This position will allow for close collaboration with world leading experts in the fields of imaging, image analysis, bioinformatics, computational biology, machine learning, and artificial intelligence. The candidate will be directly supervised by Dr. Benjamin Haibe-Kains and co-supervised by Drs. Fei-Fei Liu (University Health Network, Canada) and Hugo Aerts (Dana-Farber Cancer Institute, USA).

    +++ Decoding tumour phenotype by noninvasive imaging using a quantitative radiomics approach. Aerts HJ, Velazquez ER, Leijenaar RT, Parmar C, Grossmann P, Carvalho S, Bussink J, Monshouwer R, Haibe-Kains B, Rietveld D, Hoebers F, Rietbergen MM, Leemans CR, Dekker A, Quackenbush J, Gillies RJ, Lambin P. Nat Commun. 2014 Jun 3;5:4006. PMID: 24892406

    REQUIREMENTS

    Doctorate in Engineering, Physics, Bioinformatics, Computer Science, or related subject, with an interest in advanced image analysis, artificial intelligence, and machine learning. Expertise in R, C/C++ and Unix programming environments.

    PREFERENCES

    Hands-on experience in high performance computing, especially for parallelizing code in C/C++ (openMP) and/or R in a cluster environment (Sun Grid Engine/Torque). An understanding of image acquisition and reconstruction protocols and standardization would be helpful.

    ABOUT US

    Labs:
    Research in the Haibe-Kains lab is focused on the development of novel computational approaches to best characterize carcinogenesis, drugs' mechanisms of action and their therapeutic effects from high-throughput genomic data. We have strong expertise in machine learning applied to biomedical problems, including the development of robust prognostic and predictive biomarkers in cancer. We are collaborating with the Aerts lab to apply machine learning approaches in the context of Radiomics. Our large network of national and international collaborators, including clinicians, molecular biologists, engineers, statisticians and bioinformaticians uniquely positions us to perform cutting-edge translational research to bring discoveries from bench to bedside. See the lab website for further information: www.pmgenomics.ca/bhklab/

    Research in the Liu lab is focused on translational molecular oncology, including the development of biomarkers for head & neck cancers, high-throughput screens to identify novel anti-cancer therapeutics, and stem cell regenerative therapy. Using DNA, RNA, and protein extracted from diagnostic human cancer samples, we are in the process of conducting multi-omic global expression analyses. See the lab website for further information: www.uhnresearch.ca/labs/liu/

    Research in the Aerts lab is focused on the integration and analysis of various types of data for personalized medicine, specifically from imaging and genomic data. See the lab website for further information: www.cibl-harvard.org

    Lab Directors:
    Dr. Benjamin Haibe-Kains has over 10 years of experience in computational analysis of genomic data, including genomic and transcriptomic data. He is the (co-)author of more than 100 peer-reviewed articles in top bioinformatics and clinical journals. For an exhaustive list of publications, go to Dr. Haibe-Kains' Google Scholar Profile.

    Dr. Fei-Fei Liu is Chief and Chair, and Professor in the Departments of Radiation Oncology, Medical Biophysics and Otolaryngology at the University of Toronto. She holds the Dr. Mariano Elia Chair in Head and Neck Oncology. For an exhaustive list of publications, go to Dr. Liu's Google Scholar profile.

    Dr. Hugo Aerts has a broad background in engineering, with specific expertise in the extraction and analysis of medical imaging data, in bioinformatics and in genomic data analysis. For an exhaustive list of publications, go to Dr. Aerts' Google Scholar Profile.

    Princess Margaret Cancer Centre:
    The Princess Margaret Cancer Centre (PM) is one of the top 5 cancer centres in the world. PM is a teaching hospital within the University Health Network and affiliated with the University of Toronto, with the largest cancer research program in Canada. This rich working environment provides ample opportunities for collaboration and scientific exchange with a large community of clinical, genomics, computational biology, and machine learning groups at the University of Toronto and associated institutions, such as the Ontario Institute of Cancer Research, Hospital for Sick Children and Donnelly Centre.

    HOW TO APPLY

    Submit a CV, a copy of your most relevant paper, and the names, email addresses, and phone numbers of three references to benjamin.haibe.kains[at]utoronto.ca. The subject line of your email should start with "POSTDOC RADIOMICS – BHKLAB". All documents should be provided in PDF.

    BACKGROUND

    The laboratories of Drs. Joerg Gsponer and Thibault Mayor are looking for an outstanding candidate for a postdoc position. The position is funded by both the CIHR and NSERC and is integrated in the Michael Smith Laboratories of the University of British Columbia (UBC), a well-equipped research facility providing stimulating grounds for scientific progress in an international, multidisciplinary research environment. Dr. Mayor's laboratory develops and applies cutting-edge proteomics approaches, in order to probe changes in proteostasis and get new insights into protein quality control. Dr Gsponer's interest are complementary in that his laboratory develops computational tools that, guided by fundamental principals of biochemistry and biophysics, exploit genomic, transcriptomic and proteomic data to understand deficits in proteostasis and how they link to neurodegenerative diseases like Alzheimer's.

    RESPONSIBILITIES

    • Develop new pipelines for the analysis of proteomics data
    • Integrate and mine data from the public domain
    • Analyze data with appropriate statistical methods
    • Use supervised learning methods for predictive modeling
    • Collaborate closely with experimentally working group members to optimize experiments and analysis pipelines.
    • Participate in regular group meetings and contribute as first author to scientific publication output

    REQUIREMENTS

    We are looking for a highly motivated person with excellent academic record, including first author publications in peer-reviewed journals. The candidate is expected to be a motivated team player who fits into a multidisciplinary research environment. Interested individuals must have or be close to obtaining a Ph.D. in bioinformatics, computational biology, computer or information sciences, mathematical modeling or a related field. The ideal candidate should have proficiency in programming and machine learning. Applicants are expected to have excellent oral and written communication skills.

    LOCALE

    UBC Vancouver, Canada

    HOW TO APPLY

    Please submit your application to Joerg Gsponer (gsponer[at]chibi.ubc.ca) with a curriculum vitae (including scientific publications, posters and talks) and brief research statement interest with a summary of PhD work.

    DEADLINE

    We will start interviewing candidates on October 15, but the position is open until filled.

    DESCRIPTION

    The laboratory of Dr. Shaun Mahony in the Biochemistry and Molecular Biology Department at Penn State University (mahonylab.org) is seeking an outstanding computational biologist to fill a postdoctoral research position. The primary focus of this postdoctoral position is to develop machine-learning approaches for characterizing protein-DNA interactions from ChIP-exo and other high-resolution protein-DNA binding assays. Prior experience developing machine-learning applications and/or regulatory genomics analysis methods is strongly preferred. A Ph.D. in a relevant field is required.

    HOW TO APPLY

    Interested individuals should upload their curriculum vitae, letters from three references, and a personal statement of background and interests at psu.jobs/job/62985. Review of applications will begin immediately and continue until the position is filled.

    POLICIES

    Campus Crime Statistics: For more about safety at Penn State, and to review the Annual Security Report which contains information about crime statistics and other safety and security matters, please go to www.police.psu.edu/clery/, which will also provide you with detail on how to request a hard copy of the Annual Security Report.

    Penn State is an equal opportunity, affirmative action employer, and is committed to providing employment opportunities to all qualified applicants without regard to race, color, religion, age, sex, sexual orientation, gender identity, national origin, disability or protected veteran status.
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