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    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.

    BACKGROUND

    A position as associate professor in the field of bioinformatics is available at the newly formed Department of Bio and Health Informatics (DTU Bioinformatics) at the Technical University of Denmark within one of the areas of Health Informatics, Biotechnology and Meta-Genomic Informatics and Artificial Intelligence in Life Science.

    DTU Bioinformatics:
    The research and teaching at DTU Bioinformatics is focused on benefitting from the wealth of new data and data types being generated within Life Science to improve human and animal health and develop solutions to problems of biotechnological and industrial interest. A cornerstone in achieving this is the dedicated effort within DTU Bioinformatics to develop artificial intelligence and machine learning solutions to the challenge of handling and interpreting large scale and heterogeneous data. The work is centered on the following themes:

    Machine learning in Life Science:
    Machine learning is a specialized field within artificial intelligence covering algorithms with the ability to learn (from data) without being explicitly programmed. In contrast to conventional top down hypothesis driven research, with machine learning techniques, biological mechanisms are identified directly from data most often without any prior hypotheses. Within biology this approach has proven very powerful. A focus of the department is thus to design and develop new algorithms and tools to meet the challenges of the amount and the complexity of big data within the health sector, and the upcoming data avalanche from the biotech industry.

    Health Informatics:
    Within the theme Health Informatics DTU Bioinformatics is engaged both in a) human genetics based health informatics, examples being the hologenetic view on childhood leukaemia and patient stratifications with traditional medicine approaches b) infectious diseases informatics, examples being the preparing for the next generation of global disease surveillance and building local outbreak predictors.

    Biotechnology and MetaGenomic Informatics:
    Within the theme Biotechnology and MetaGenomic Informatics DTU Bioinformatics has strong interaction with the Danish Biotech industry in the discovery and refining of industrially important processes, examples being using large scale omics together with machine learning concepts to improve food related processes like wine fermentation and milk production.

    RESPONSIBILITIES

    Responsibilities and tasks:
    The candidate must actively take part in the promotion, development and improvement of research and education in bioinformatics within the areas described above. The department is especially looking for candidates with expertise in high performance computing in the life sciences.

    The applicant should be able to document a strong potential and profile for research and education. The candidate is expected to have solid teaching experience and to participate in planning and teaching at bachelor, master and PhD levels. The candidate will also take on the task as the head of studies for the bachelor program within Human Life Science Engineering. Furthermore supervision of assistant professors, postdocs and master students are expected as well as continuing education and dissemination of research results at all levels.

    Please note that the expected teaching on undergraduate level is primarily to be in Danish (or a Scandinavian language) and on postgraduate level (M.Sc. or PhD) it is required to be in English. Also, the work as head of studies requires good command of a Scandinavian language.

    The department has a strong history of collaboration with national and international groups. The candidate will run several projects and collaborations in parallel and the work involves participation in large-scale international projects, as well as interaction with peers from relevant departments and centers at DTU (e.g., in particular DTU Compute, DTU BioEngineering, DTU Food, DTU Veterinary, DTU Aqua, and DTU BioSustain) and from other national and international research groups.

    REQUIREMENTS

    Qualifications:
    Candidates must hold a PhD degree (or equivalent) as well as academic qualifications equivalent to those obtained by holding an Assistant Professorship, and documented didactic/pedagogic training.

    TERMS

    Assessment:
    In the assessment of the candidates consideration will be given to:
    • Experience in teaching and education
    • Scientific production and research potential at an international level
    • The ability to promote and utilize research results
    • An all-round experience basis, preferably including international experience
    • The ability to contribute to development of the department's internal and external cooperation

    COMPENSATION

    We offer:
    DTU offers an interesting and challenging job in an international environment focusing on education, research, scientific advice and innovation which contribute to enhancing the economy and improving social welfare. We strive for academic excellence, collegial respect and freedom tempered by responsibility. DTU is a leading technical university in northern Europe and benchmarks with the best universities in the world.

    Salary and terms of employment:
    The appointment will be based on the collective agreement with the Confederation of Professional Associations. The allowance will be agreed with the relevant union.

    Further information:
    Further information may be obtained from Professor Ole Lund, mail olund[at]dtu.dk

    You can read more about the Department of Bio and Health Informatics on www.cbs.dtu.dk

    ABOUT US

    DTU Bioinformatics is a new department at DTU formed by the bioinformatic part of the former Department of Systems Biology. DTU Bioinformatics is operating at the highest level of research, teaching, innovation, and consultancy services within the areas biotechnological informatics and health informatics. The department's activities in the fields of research, teaching, scientific advice, and innovation are centered on the following research areas: health and cancer, immunology, infectious diseases, proteins, molecular biology, and molecular mechanisms, plants and biotechnology and big data infrastructure.

    DTU is a technical university providing internationally leading research, education, innovation and scientific advice. Our staff of 5,800 advance science and technology to create innovative solutions that meet the demands of society; and our 10,300 students are being educated to address the technological challenges of the future. DTU is an independent academic university collaborating globally with business, industry, government, and public agencies.

    HOW TO APPLY

    Applications must be submitted as one PDF file containing all materials to be given consideration. To apply, please open the link "Apply online," fill in the online application form, and attach all your materials in English in one PDF file. The file must include:
    • Application (cover letter)
    • CV
    • Diploma (MSc/PhD)
    • List of publications indicating scientific highlights
    • H-index, and ORCID (see e.g. orcid.org)
    • Documentation of teaching experience (e.g. in the form of a teaching portfolio)

    DEADLINE

    Please submit your online application no later than 11 October 2016.

    Applications and enclosures received after the deadline will not be considered.

    POLICY

    All qualified candidates irrespective of age, gender, race, disability, religion or ethnic background are encouraged to apply.

    RESPONSIBILITIES

    Position Summary:
    The Scripps Research Institute (TSRI) is currently seeking a Bioinformatics Analyst IV in computational genomics and systems biology in the Informatics – FL Department for its Florida facility. Our group provides scientific support to assist in the analysis and dissemination of data from the wide range of cutting edge research. Work will involve collaborating with bench scientists, understanding project objectives, evaluating, and providing informatics solutions. This position will be involved in gene expression and next-generation sequencing (NGS) data sets, and applying statistical methods to analyze and visualize scientific data. Responsibilities include, but are not limited to:
    • Direct, employ and guide a variety of complex, computational sequence analysis (mathematical and computing) tools to model and analyze molecular biological data.
    • Design, create, set up and manage large biological computer databases.
    • Guide the computational sequence analysis methods for database searches and analysis of resulting data, which may include utilizing existing or developing new algorithms, techniques, and computational statistical methodologies and theories to analyze datasets.
    • Work collaboratively with scientific project teams to successfully implement users' needs in database searching and integration, which includes interpretation of similarity of sequence searches, multiple sequence alignments and gene expression patterns, and the quality control of sequence data.
    • Maintain the computational infrastructure, as well as control the flow of samples and information for project studies.
    • Troubleshoot or modify procedures as required.
    • Provide web-based bioinformatics and access to public and proprietary relational databases.
    • Independently conduct a variety of standard and complex bioinformatics design and development of software systems.
    • May plan and conduct a project to complete a research plan.
    • Independently may determine methods and procedures on new assignment and provide guidance to lower level personnel.
    • Perform other related duties as required or assigned.

    REQUIREMENTS

    Basic Qualifications:
    • BS/BA degree, preferably in bioinformatics, computational biology or computer science or similar, or the equivalent combination of education, training and experience
    • Minimum 6 years bioinformatics or related experience, including experience with informatics data analysis from several of the "Omics" disciplines such as NGS, genomics, proteomics, structural biology, and metabolomics
    • Must possess extensive background in biostatistics, as well as experience setting up and analyzing large biological databases
    • In depth knowledge of and experience with data management and analysis theories and techniques
    • Expert in one, and strong knowledge of and experience in multiple high level programming languages, such as C/C++, Python, Java, R, PERL, PHP, Ruby, Visual Basic, csh/sh/tcsh/ksh, HTML, and associated tools
    • Ability to effectively prioritize workload and multi-task
    • Ability to communicate effectively in verbal and written form, as well as to clearly convey methods and results to provide information to scientific investigators from which researchers can draw conclusions

    PREFERENCES

    Preferred Qualifications:
    • MS/MA or Ph.D. in Bioinformatics, Biostatistics, Computer Science, Applied Mathematics, Bioengineering, Statistics, Physics, Computational Biology, or relevant field
    • Proficient in statistical data analysis of genomic data using R/BioConductor, Prism, SAS, MatLab, etc.
    • Experience with NGS pipelines (RNA-Seq and ChIP – Seq) and open source tools (Tophat, STAR, SAMTools)
    • Strong interpersonal and communication skills
    • Ability to be self-motivated and work independently, with minimal supervision
    • A solid knowledge of cancer biology, hands-on experience in large-scale cancer NGS data management and analysis
    • Experience with the design, implementation, modification, and enhancement of custom databases
    • Knowledge of database technologies such as MySQL, Oracle, or SQL Server with familiarity in source control practices and tools
    • Florida & Palm Beach County residents are preferred.

    COMPENSATION

    Commensurate with experience

    HOW TO APPLY

    In order to be considered for this position please apply directly at: careers.scripps.edu/postings/8935

    POLICY

    EEO Statement:
    The Scripps Research Institute is an Equal Opportunity Employer. All qualified applicants are encouraged to apply and will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, protected veteran status, or any other legally protected characteristic or status.

    BACKGROUND

    The University of Southern California (USC), founded in 1880, is located in the heart of downtown Los Angeles and is the largest private employer in the city. As an employee of USC, you will be part of a world-class research university and a member of the "Trojan Family," which is comprised of the faculty, students and staff that make the university what it is.

    The Center for Craniofacial Molecular Biology (CCMB) at the Herman Ostrow School of Dentistry of USC invites applications to fill a Senior Research Associate position to perform bioinformatic analyses, visualize and disseminate scientific data, and prepare manuscripts and grant applications for submission.

    RESPONSIBILITIES

    Job accountabilities:
    Serves as a senior researcher with expertise in field. Plans, designs, and conducts highly technical and complex research projects which require the regular use of ingenuity and innovation, independently and in consultation with supervisor. May contribute to the development of new concepts, techniques, and standards. Analyzes research data and provides interpretations. Contributes to the development of research documentation for publication and prepares technical reports, papers, and/or records. Develops solutions to complex research programs. Computer programming skills are also required.

    REQUIREMENTS

    The successful candidate will have the following qualities:
    • Training and experience in bioinformatics and the visualization of genomic data obtained through microarray analyses, RNASeq and enhancer analyses
    • Outstanding abilities in written and oral communication, including a record of successful publication in academic publications, are essential to this position
    • Experience in website design/maintenance and using content management systems (WordPress, Drupal, or similar)
    • Willingness to integrate administrative work, such as coordinating grant submissions, into daily duties. Must have the ability to maintain confidentiality
    • Serves as a liaison between CCMB faculty/staff and collaborators at other academic units within USC and elsewhere
    • Attends meetings, seminars, symposia and other events related to project efforts. Stays informed of developments in field
    • Experience in grant writing, particularly in response to NIH calls for proposals, is strongly preferred
    • Experience in biostatistics, statistically informed experimental design and analysis is preferred
    • Experience in academic illustration/graphic design using Adobe Illustrator, Photoshop, or similar is preferred
    • Performs other related duties as assigned or requested. The University reserves the right to add or change duties at any time
    • This position is supported for one year and may be renewable at the end of the first year
    For a detailed list of CCMB operations, please see the CCMB website: ccmb.usc.edu

    Qualifications:
    • Minimum: PhD or equivalent doctorate degree in bioinformatics, biology or a related field
    • Preferred: Doctoral degree in bioinformatics, biology or a related field

    HOW TO APPLY

    Applicants should send a cover letter, CV, and sample of academic writing and arrange to have three letters of reference sent to:

    Professor: Yang Chai
    Director
    c/o Ms. Patricia Thompson
    Center for Craniofacial Molecular Biology
    Ostrow School of Dentistry
    University of Southern California
    2250 Alcazar Street, CSA 103
    Los Angeles, CA 90033
    pathomps[at]usc.edu
    Fax (323)442-2981

    POLICY

    The University of Southern California values diversity and is committed to equal opportunity in employment.

    BACKGROUND

    This position is for a customer and field facing Bioinformatics Applications support person who will be based in our Menlo Park, CA headquarters with occasional travel to assist field applications scientists or to perform trainings.

    Pacific Biosciences is seeking a Bioinformatics Scientist with a strong customer focus to support analysis for collaborators and customers using SMRT® sequencing data. The candidate will employ expertise in bioinformatics, data analysis, biological insight, software engineering, and systems administration. The ability to communicate with customers and internal engineers, to interact with marketing, and to communicate results to diverse audiences, are important aspects of this role.

    We are building a multi-disciplinary team to establish a world-class Technical Support organization in support of our field-based teams and customers. Our ideal candidate is a well-rounded top performer who can be a key contributor in a high-energy growth environment.

    RESPONSIBILITIES

    • Participate as a key member of a diverse group of Technical Support Scientists and Engineers.
    • Assist customers with Experimental Design, Software installation/upgrade, and Data Analysis questions or complaints in a timely manner. Issues can be received via phone, email, and the Web.
    • Problem-solve to overcome technical challenges during installation or use of Pacific Biosciences analysis tools.
    • Triage and dispatch issues requiring field support to Field Applications Scientists and Engineers.
    • Log and manage case details using Salesforce CRM.
    • Contribute to the ongoing development of a troubleshooting guide to capture lessons learned and solutions to cases.
    • Represent our Customers, the Field and Technical Support Teams on Core teams in the development and delivery of new systems, software, and consumables.
    • Utilize Pacific Biosciences analysis tools and also open source academic tools to support customer projects for target applications.

    REQUIREMENTS

    Education:
    • B.S. or higher (Ph.D. preferred) in Bioinformatics, Computer Science, Genetics or related disciplines, along with 3+ years of relevant industry or academic experience
    • Preferred 2+ years of customer support, field service, or technical training
    Interpersonal Skills:
    • Customer-focused individual with the empathy and skills to understand and address customer concerns
    • Must have a "can do" attitude and be comfortable in a fast-paced start-up environment
    • Must have strong written and verbal communication skills
    • Self-starter who is able to work with minimal supervision
    • Must have excellent troubleshooting abilities
    • Outstanding interpersonal skills
    • Ability to balance several projects and customers concurrently
    Technical Expertise:
    • Hands-on experience in analysis of next-generation DNA sequencing data for various applications including variant calling, RNA-seq, ChIP-seq, 5mA detection, etc.
    • Hands-on experience with common DNA sequence analysis tools and workflows such as sequence alignment, genome visualization, comparative genomics, sequence/structural variation discovery, and epigenetics
    • Hands-on experience in scripting languages (python) and software development practices
    • Hands-on experience in distributed computing (SGE, PBS, LSF)
    • Some experience with Linux administration, permissions, network configuration
    • Knowledgeable in molecular biology, and biochemistry laboratory techniques

    LOCALE

    Menlo Park, CA

    HOW TO APPLY

    Please visit chm.tbe.taleo.net/chm0[...]=1599

    POLICY

    All qualified applicants will receive consideration for employment without regard to race, sex, color, religion, national origin, protected veteran status, or on the basis of disability, gender identity, and sexual orientation.

    BACKGROUND

    The Computational Breast Imaging Group (CBIG) of the Radiology Department at the University of Pennsylvania has open postdoctoral positions. CBIG is a group within the Center for Biomedical Image Computing and Analytics (CBICA) with a mission to act as a translational catalyst between computational imaging science and breast cancer research.

    RESPONSIBILITIES

    Work in our group focuses on developing innovative methodology for multimodality image analysis and also on incorporating such methods into clinically relevant applications. Specifically, radiomics related research focuses developign statistical methodology for cancer phenotyping via imaging using bioinformatics approaches, and relating such phenotypes to genomic/molecular sub-typing, treatment response, and long-term outcomes.

    REQUIREMENTS

    We are seeking highly motivated individuals with excellent academic track-record, including first-author publications in peer-reviewed journals. Successful candidates should have, or be in the process of completing, a PhD (or equivalent) in Biomedical, Electrical or Computer Engineering, Computer and Information Science, or related field. Ideal applicants should have a background on biomedical image analysis, computer vision, pattern recognition and/or machine learning. Proficiency in quantitative analytical methods and computer programming (e.g., Python, C/C++, ITK) is essential. Experience with medical image analysis (e.g., MRI, CT, X-ray, Ultrasound) and statistical methods and software packages (e.g., R/SPSS) is preferable. Applicants should demonstrate excellent oral and written communication skills, and the ability to work effectively independently and as part of a multidisciplinary team. Successful applicants will join a vibrant collaborative research environment, will work closely with clinical investigators, and will gain a first-hand experience of our breast imaging program. Collaborators include faculty in our Radiology department, the Abramson Cancer Center, the Institute for the Translational Medicine and Therapeutics, and the Center for Clinical Epidemiology and Biostatistics.

    PREFERENCES

    Additional experience on bioinformatics methods for unsupervised clustering of high-dimensional datasets (both imaging and/or non-imaging data) is a plus.

    TERMS

    Per University policy, all postdoctoral appointments are annual with possibility of renewal based on funding availability and research progress performance. Applications should include a letter of motivation, a curriculum vitae, and names and addresses of three references.

    LOCALE

    Philadelphia, PA

    COMPENSATION

    NIH Scale +

    ABOUT US

    For more information, please visit:

    Computational Breast Imaging Group (CBIG)
    www.uphs.upenn.edu/radi[...]cbig/

    Center for Biomedical Image Computing and Analytics (CBICA)
    www.cbica.upenn.edu

    Center for Clinical Epidemiology and Biostatistics (CCEB)
    www.cceb.upenn.edu

    Penn Biomedical Postdoctoral Programs:
    www.med.upenn.edu/postdoc/

    HOW TO APPLY

    For more details and to apply contact:

    Despina Kontos, Ph.D.
    Assistant Professor
    Computational Breast Imaging Group (CBIG)
    Center for Biomedical Image Computing and Analytics (CBICA)
    University of Pennsylvania, Department of Radiology
    Joint Affiliations: Bioengineering, Biostatistics and Epidemiology Graduate Groups
    Rm D702 Richards Bldg., 3700 Hamilton Walk, Philadelphia PA 19104
    ph: 215-746-4064 // em: Despina.Kontos[at]uphs.upenn.edu

    DEADLINE

    Position Open until Filled.

    POLICY

    The University of Pennsylvania is an equal opportunity employer.
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