Bioinformatics.org
[NEU MS in Bioinformatics]
Not logged in

Bioinformatics.org
Membership (37278+) Group hosting [?]

Careers
About bioinformatics
Bioinformatics training
Bioinformatics jobs

Research
All information groups
Online databases Online analysis tools Online education tools More tools

Development
All software groups
FTP repository
SVN & CVS repositories [?]
Mailing lists

Forums
News & Commentary
Jobs Forum
(Career Center)

Career Center - News

Latest announcements
Submit Archive Subscribe
BACKGROUND:
DuPont has a rich history of scientific discovery that has enabled countless innovations and today, we're looking for more people, in more places, to collaborate with us to make life the best that it can be. Pioneer Hi-Bred International, Inc. is the world leader in plant biotechnology, including the discovery, development and delivery of elite crop genetics. We are currently seeking a Senior Software Developer in Hayward, CA or Johnston, IA for our cross-functional agile software development teams within our Computation Genomics and Bioinformatics Systems group. The Senior Software Developer will work within agile software development teams to create and enhance software based on business-driven requirements. The successful candidate will work closely with software architects, test engineers and product owners to: implement rich multi-tier web solutions that are aligned with and extend shared platforms and solutions; review user stories to determine technical dependencies, estimate relative effort required, and ensure consistency across applications. The candidate will also research and identify patterns, tool kits and services that support well designed service oriented architecture on all of Pioneer's internal software as well as work with various software teams to support adoption of these tools and services. Communication and team work are key elements of this role; excellent verbal and written communication skills are required.

RESPONSIBILITIES:
* Enable a robust and scalable end-to-end working scientific pipeline, and work with customers and other bioinformatics teams to provide custom analytical solutions.
* Provide and promote software engineering best practices and standards.
* Work closely with R&D to understand process workflows, bioinformatics pipeline, and integrations in order to deliver production grade informatics solutions.
* Build beautiful applications and interfaces for biologists to explore high dimensional data
* Deploy and support applications on high performance computing clusters
* Integrate front-end GUIs with back-end databases, APIs, and other computational frameworks
* Provide accurate scoping and estimation of scientific development efforts for projects based on product requirements and a solid grasp of the relevant informatics tools
* Ability to properly allocate development resources to staff projects
* Collaborate with Core Team Leaders, Software Engineers, Bioinformaticians, Project Managers, and other group members to fully define and implement innovative new products and services.
* Ensure that projects are developed in accordance to regulatory standards and departmental SOPs.
* Experience using established engineering methodologies through all stages of the software development lifecycle (SDLC)
* Bioinformatics design, implementation, and support for sequence analysis pipelines.
* Develop new tools to aid in the analysis of genomics annotation and interpretation.
* Build and maintain a knowledge base for the discovery of novel variations and association with phenotypes.
* Provide rapid and responsive bioinformatics support to genome sequencing analysis pipelines.
* Familiar with Biostatistics and hypothesis testing problems.
* International travel required.

REQUIREMENTS:
Education & Experience:
* The position requires a Bachelor's degree or equivalent in Computer Science or related field, and 5-10 years experience in bioinformatics software integration, computational genomics, scientific computing algorithms and tools, preferably in agile projects.
* Proven experience developing multi-tier web/web service based applications is required, and experience with Python, Flask, AngularJS, and ASP.NET is preferred.
* Experience working with agile development methodology is a strong plus. Also, candidate should have an interest in biology, genetics, or science in general and the ability to understand complex problems
* Minimum of 5 years of experience in bioinformatics software development and custom analysis, with demonstrated ability to deliver high quality products on time
* Experience developing and optimizing tools and workflows around sequence data
* Expertise in object-oriented languages (i.e. Python, Perl, C#), and mathematics software (i.e. R, Matlab, Mathematica, etc.)
* Experience with Python required, Django/Flask is a plus.
* Experiences with AngularJS, TypeScript, and visualization libraries like d3.js
* Data management and data extraction skills; familiarity with data science toolkits such as Spark, Hadoop
* Experience with a Linux/Unix development environment
* Object-orient programming with Java/C is a plus.

Required Competencies:
* Proven skill in an object-oriented language, C#, Python, preferred or Java, C
* Familiarity with high performance computing and computing clusters
* Proven experience working with relational databases and experience in data modeling and ORM
* Proven experience working on teams using agile software development methodologies and processes
* Understanding of Service Oriented Architecture (SOA)
* Ability to demonstrate solid analytical skills and exceptional attention to detail
* Proven ability to lead software development projects in an agile team framework
* Track record of delivering software results for time-sensitive projects

PREFERENCES:
Desired Competencies:
* Familiarity with bioinformatics workflows and online databases and web servers such as the UCSC genome browser, and Jbrowse
* Familiarity with build tools (grunt/gulp/npm, team city, Visual Studio preferred)
* Ability to interpret biological data using visualization tools, such as genome browsers.
* Track record of delivering bioinformatics analytical results for time-sensitive projects

TERMS:
Permanent

LOCALE:
Hayward, CA

COMPENSATION:
Unspecified

HOW TO APPLY:
Apply online at: [link]

DEADLINE:
7/1/2016

BACKGROUND:
The Plant Computational Genomics laboratory at University of Connecticut (Storrs, CT) has an opening for a database and software developer position as part of a collaborative project involving researchers from all of the world. This person will take a lead role in the continued development of the TreeGenes database and the CartograTree application (treegenesdb.org and cartogratree.org). These resources serve vast amounts of genomic, phenotypic, and environmental data to the user community. In addition, we are committed to providing greater collaboration and data sharing among partner databases through Galaxy modules, and new analysis/visualization platforms.

URL: http://compgenomics.lab.uconn.edu/

RESPONSIBILITIES:
The successful candidate will work as part of a small interdisciplinary team of bioinformaticians and data curators. Tasks will include maintenance of the existing database, developing connections to collaborating databases, improving the user experience (interface development) and the implementation of novel analysis and visualization tools. The Postdoctoral Scholar will be provided with training opportunities and will attend conferences to present/train users on these new tools. In addition, publications on specific software products will result.

REQUIREMENTS:
The qualified applicant will have a PhD degree in Bioinformatics, Information Systems, Computer Science, or a related field. Biology/Bioinformatics experience is essential as well as previous experience with web/database development. The applicant should have strong knowledge of Java (Struts/JSP) and JavaScript (jQuery). Experience with Linux/Unix, scripting languages (Python), and relational databases (PostgreSQL).

TERMS:
Full-time

Start Date: ASAP

LOCALE:
University of Connecticut, Storrs, CT, USA

HOW TO APPLY:
Please send the following THREE documents: cover letter, research statement, and CV to: jill.wegrzyn[at]uconn.edu

DEADLINE:
Applications will be accepted until May 30th or until the position is filled.

Submitter BACKGROUND:
A postdoc position in Bioinformatics and/or Computational Biology is available at the Center for Precision Health, a newly established joint center of School of Biomedical Informatics and School of Public Health in The University of Texas Health Science Center at Houston.

RESPONSIBILITIES:
Using integrative computational approaches, we focus on the understanding of genotype-phenotype relationships underlying complex diseases. We seek for highly motivated postdoctoral candidates who are interested in the following research areas.
1. Methodology development on integrative analysis of multidimensional data. Representative methods developed by our group include dmGWAS (Bioinformatics, 27:95-102), EW_dmGWAS (Bioinformatics, 31:2591-2594), gamGWAS (J Med Genet, 49:96-103), VarWalker (PLoS Computational Biology, 10(2):e1003460), and MSEA (Genome Biology, 15:489). Success candidates will continue the work in developing computational methods on genomic data.
2. Computational genetic and genomic investigation of complex diseases, in particular psychiatric diseases. We have years of scientific record on bioinformatics and systems biology analysis of schizophrenia, bipolar, and major depressive disorder, published in top journals of psychiatry (e.g., Molecular Psychiatry). Candidates with experience in genetics are preferred.
3. Bioinformatics and systems biology research on cancer. Our lab has a long standing interest in developing methods in translational bioinformatics to aid precision medicine in cancer (Genome Research, 23:1434-1445; Cancer Discovery, 2:791--797).

REQUIREMENTS:
* PhD in Bioinformatics, Genetics, Biostatistics, or Computational Biology
* Strong programming skills (R, Python, Java, C or C++)
* Experience in next-generation sequencing analysis
* Strong mathematical and statistical background (machine learning)
* Solid skills in spoken and writing English
* Experience in analyzing biological and genomic databases

TERMS:
3 years

LOCALE:
Houston, TX

HOW TO APPLY:
Interested applicants should send a cover letter describing your past research experience/skills and future research interests/plans, a curriculum vitae, and the contact information of three references to peilin.jia[at]uth.tmc.edu.



BACKGROUND:
Project Description:
The team works on advanced bioinformatics technology programs that focused in support of precision-based medical trials for the National Cancer Institute in Rockville, Maryland. The project is organized into cross-functional teams that work closely with stakeholders, developers, QA Engineers, Product Managers, and designers to build state-of-the-art portfolio of exploratory projects that are inherently multidisciplinary that impact cancer research and treatment.

Position Description:
The full-time Senior Bioinformatics Software Engineer will be an integral key member of the team that brings their premium user interfaces experience and expertise to create cutting-edge software solutions. The position is ideal for a talented Senior Software Engineer who is interested in working in an exciting growth environment among people passionate about advanced technologies in the fight against cancer.

RESPONSIBILITIES:
* Analyze and interpret complex requirements from scientists and doctors, and write and test software implementations within an established and distributed software development architecture that leverages modern technologies, methodologies and principles Analyze and interpret complex requirements from scientists and doctors
* Implement solutions with software architects and technical leads
* Work with software QA team and system administrators to test and deploy code
* Interface with stakeholders, management for status reports, presentations, and software demonstrations
* Be a part of development team to create practical solutions in Agile/DevOps environment
* Be an expert to research and identify technical solution and be a mentor to our junior staff

REQUIREMENTS:
Required Qualifications:
* Excited about creating amazing application in cutting-edge environment
* Minimum of six (6) years of experience with one or a combination of the following technology: Ruby, Python , C++, R, Java, Rails, MongoDB, or AngularJS
* Proficiency in client side JavaScript and modern JavaScript frameworks
* Passionate to object-oriented programming; strong design skills
* Excellent problem solving skills
* Take ownership and work independently on large portions of a project with minimal supervision
* Ability to work effectively with a team on complex projects with strict requirements
* Strong communication (written and verbal) and organizational skills
* Bachelor's degree in Bioinformatics or a Bachelor's degree, Computer Science, Information Systems, Engineering and a Master's degree in Bioinformatics
* Must be able to obtain Public Trust security clearance

PREFERENCES:
Preferred Qualifications:
* Master's degree in Bioinformatics
* Background in bioinformatics or healthcare IT
* Comfortable with GIT and bug tracking systems such as JIRA
* Ability in formulating and implementing IT solutions to meet business requirements

TERMS:
The full-time Senior Bioinformatics Software Engineer

COMPENSATION:
Benefits Summary:
* Competitive base salary plus bonus
* Paid time off
* Ten paid holidays
* Medical Insurance
* Health Savings Account
* Retirement benefits with employer contributions
* Dependent Care Flexible Spending Account
* Life Insurance, Short and Long Term disability

HOW TO APPLY:
Send resumes to careers[at]lucidus.com to apply.



BACKGROUND:
DuPont has a rich history of scientific discovery that has enabled countless innovations and today, we're looking for more people, in more places, to collaborate with us to make life the best that it can be.

DuPont Pioneer is seeking a Post Doctoral Fellow to join the Trait Informatics group to conduct research into the area of computational biology, genomics and transcriptomics. The Trait Informatics groups is responsible for bioinformatics systems and analyses across the Agricultural Biotechnology Research and Development organization. The advertised post-doctoral position will work together with Trait Informatics scientists and developers, as well as scientists from across research departments. The position will be based at the DuPont Pioneer world-wide headquarters in Johnston, Iowa (USA). Duration of employment will be 12 months with a possibility of renewal for an additional 12 months depending on evaluated performance and business need.

RESPONSIBILITIES:
Utilize existing data to develop and implement computational strategies to develop transcriptional networks. Collaborate across research departments to conduct experiments to plan and execute experiments to test hypotheses around transcriptional regulatory control and functional output. Prepare internal scientific reports as well as scientific manuscripts for external publication to document the findings of the methodology development and evaluation steps.

Problem Solving:
Assist in the development and evaluation of novel computational and/or statistical genetics techniques targeted towards improved regulatory network determination. Interact with scientific teams of researchers to manipulate and summarize large amounts of data, interpret scientific results and communicate scientific findings in a clear and concise manner.

Decision Making:
Make scientific evaluations, recommendations and routine communications to scientists regarding the performance and utility of advanced computational and/or statistical genetics techniques that integrate biological, physiological, environment, phenotypic and genomic/genetic data. Identify, design, develop and help implement data analysis tools to meet project goals and timelines, communicate key issues and discoveries appropriately.

REQUIREMENTS:
* PhD in Computational biology, Molecular biology, Statistics or a related field
* Demonstrated ability to quantitatively evaluate and analyze complex scientific problems, interpret scientific results, and work easily with large volumes of data
* Good understanding of RNA expression analyses, as evidenced by strong publication record
* Demonstrated competency in statistical programming languages such as R and scripting languages such as Perl/Python is Required; Proficiency in scientific programming languages such as C is a plus.
* Demonstrated ability to work in dynamic scientific teams, and demonstrated ability to contribute to complex research projects performed under tight deadlines
* Strong communication skills; ability to speak, read, and write in English

TERMS:
Permanent

LOCALE:
Johnston, IA

COMPENSATION:
Unspecified

HOW TO APPLY:
Apply online at: [link]

DEADLINE:
6/28/16

BACKGROUND:
Zymeworks is a fast-growing biotechnology company dedicated to the research, development and commercialization of best-in-class therapeutic bispecific antibodies and antibody drug conjugates for treatment of cancer and autoimmune diseases. Zymeworks is proud to have active collaborations with Merck & Co., Inc., Eli Lilly and Co., GSK and Celgene Corporation, and is committed to making a meaningful difference in the lives of patients.

RESPONSIBILITIES:
Zymeworks is seeking a Scientist, who will be responsible for developing statistical and bioinformatics tools for advancing our in-house technology platform for antibody engineering and therapeutic development. The position reports to the Technology Integration Team Lead.

Roles and Responsibilities:
* Develop and implement bioinformatics methods for application in protein engineering, optimization and antibody discovery.
* Develop and implement robust statistical and data mining techniques for the analysis of experimental and in silico data.
* Work with the Protein engineering and Therapeutics R&D teams to gather requirements and specifications for bioinformatics developments.
* Assist in data driven statistical analysis and validation of Protein Engineering and Preclinical experiments.
* Collaborate with the software development group for the implementation of user-friendly bioinformatics tools.
* Conduct analysis of genomic data from external data sources and literature supporting the discovery and characterization of targets and biomarkers.
* Assist with special projects and other duties as assigned.
* Participate in the development of rigorous documentation and standard operating procedures.

REQUIREMENTS:
Required Qualifications and Experience:
* MSc or PhD in Bioinformatics, Mathematics, Computer Science or related field
* Strong skills in protein informatics and protein science, including protein sequence analysis and genomic analysis
* Strong background in statistical analysis with experience in R, SPSS or other statistical packages
* Experienced in implementing and validating protein informatics methods
* Experienced in manipulation and analysis of high-throughput sequencing data
* Experienced in analyzing biological and genomic databases such as TCGA, ICGC etc.
* Experienced in the application of machine learning algorithms for data analysis
* Proficient in Python or any other programming language
* Demonstrated ability to effectively communicate in spoken and written English

Additional Qualifications and Experience:
* Knowledge of molecular simulations
* Experienced in biostatistics and clinical data analysis

ABOUT US:
Why Work for Us?

Zymeworks' employees are passionate, engaged and extremely motivated to succeed. Our environment is progressive, collaborative, focused and pragmatic.

Compensation is on par with industry standards and commensurate with experience and includes an extended benefits plan and participation in the employee stock-option plan.

To learn more about Zymeworks Inc. and our current openings, please visit our website at http://www.zymeworks.com

HOW TO APPLY:
If you are interested in applying for this position, please do so through our online jobs board at [link]. Although we appreciate all applications, due to the high volume of responses only those selected for interviews will be contacted.

RESPONSIBILITIES:
Seeking a talented and highly motivated Computational Biologist to pursue research projects in collaboration with bench biologists. The candidate will work with an interdisciplinary team, will carry out high throughput data analysis and data integration across various domains and will develop novel methods for genomic data analysis.

The duties include, but are not limited to: perform quality bioinformatics analysis of high throughput genomic data and assist others in the interpretation of analyzed data; conceive and develop algorithms and analytic approaches for genomic data analysis and integration; solve challenges in genomic data analysis, and implement solutions in usable software tools ; establish procedures and work-flow for routine data analysis; independently and proficiently utilize web resources (such as Entrez, RefSeq, GEO, BLAST), visualization tools , genome assemblies, and available analysis software; provide clear and concise professional reports on data analysis and results; and other related duties as assigned.

REQUIREMENTS:
Minimum Requirement:
MS/PhD degree from an accredited college or university in Bioinformatics , Bio-statistics, Computational Biology, Genomic Medicine or similar field, with a strong publication record and a minimum Of one year of relevant experience

Knowledge, Abilities, Skills:
Excellent verbal and written communication, interpersonal, and observational skills. Experience in Microsoft Word, Excel, and other computer software/databases. Theoretical knowledge of genetics , epigenetics, statistics, and molecular biology. .. Extensive experience with gene-expresslon micro array and proteomics data. Must be detail--oriented with strong logic, problem solving, and organizational skills. Proficiency in a high-level statistical language such as R, or SAS. Fluency with "Bio-conductor" packages for micro array data analysis. Experience in computer programming and use of biological software applications; database structure and management. Ability to work independently; make responsible decisions; lift/carry up to 40 pounds; maintain confidentiality.

PEFERENCES:
Experience in database management, server management, and web-based programming is highly desirable

LOCALE:
Augusta, Georgia

COMPENSATION:
Salary: $48,341.00/Annually

HOW TO APPLY:
Visit http://www.augusta.edu/jobs Click University Careers Search for job opening id 11147

DEADLINE:
Open until filled

POLICY:
Augusta University and AU Health is an equal opportunity employer including individuals with disabilities and veterans.

BACKGROUND:
We seek a postdoctoral fellow for a project that aims at finding solutions to the high fatality rate of pancreatic cancer by analyzing genomic and biologic subsets of disease, mechanisms of tumorigenesis, and tailored treatment options. The position involves integrative data analysis of PanCuRx, the largest genomic profiling project for pancreatic cancer, as part of the International Cancer Genome Consortium. Molecular profiles include whole-genome sequencing and RNA-seq for a large cohort of micro-dissected patient tumors and patient-derived xenografts. The project includes high-throughput discovery of prognostic and predictive biomarkers, molecular subtyping and drug repurposing.

For representative projects please consider the following references:

Genomic analyses identify molecular subtypes of pancreatic cancer
Bailey P, Chang DK, Nones K, ..., Waddell N, Biankin AV, Grimmond SM.
Nature. 2016 Mar 3;531(7592):47-52. PMID: 26909576

Pancreatic cancer genomes reveal aberrations in axon guidance pathway genes
Biankin AV, Waddell N, ... , Pearson JV, McPherson JD, Gibbs RA, Grimmond SM.
Nature. 2012 Nov 15;491(7424):399-405. PMID: 23103869

Subtypes of pancreatic ductal adenocarcinoma and their differing responses to therapy
Collisson EA, Sadanandam A, Olson P, Gibb WJ, Truitt M, Gu S, Cooc J, Weinkle J, Kim GE, Jakkula L, Feiler HS, Ko AH, Olshen AB, Danenberg KL, Tempero MA, Spellman PT, Hanahan D, Gray JW.
Nat Med. 2011 Apr;17(4):500-3. PMID: 21460848

REQUIREMENTS:
Doctorate in computational biology, computer science, engineering, statistics, or physics. Published/submitted papers in genomics and/or machine learning research. Experience with analysis of high-throughput omics data, such as next-generation sequencing and gene expression microarrays, in cancer research. 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).

ABOUT US:
Lab:
Our research focuses on the development of novel computational approaches to best characterize carcinogenesis, drugs' mechanisms of action and their therapeutic potential, 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. 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 our lab website for further information: http://www.pmgenomics.ca/bhklab/

Lab director:
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 95 peer-reviewed articles in top bioinformatics and clinical journals. For an exhaustive list of publications, go to Dr. Haibe-Kains' 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 PANCURX -- BHKLAB". All documents should be provided in PDF. Deadline for submission: July 1, 2016

BACKGROUND:
We seek a postdoctoral fellow to develop novel integrative approaches to develop molecular predictors of response to approved and novel drugs for breast cancer. We have generated high-dimensional molecular (mutations, copy number variations, transcriptomics, epigenomics) and pharmacological (drug sensitivity) profiles of a large panel of breast cancer cell lines. We are profiling patient-derived xenografts as well, therefore providing a unique opportunity to explore the biology underlying drug response, and develop predictors that can be validated in vivo before their use in clinical trials.

REQUIREMENTS:
Doctorate in computational biology, computer science, engineering, statistics, or physics. Published/submitted papers in cancer genomics and/or machine learning research. Experience with analysis of high-throughput omics data, such as next-generation sequencing and gene expression microarrays, in cancer research. Very strong expertise in programming and machine learning (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).

ABOUT US:
Lab:
Our research focuses on the development of novel computational approaches to best characterize carcinogenesis, drugs' mechanisms of action and their therapeutic potential, 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. 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 our lab website for further information: http://www.pmgenomics.ca/bhklab/

Lab director:
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.

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 BCPRED -- BHKLAB". All documents should be provided in PDF.

DEADLINE:
Applications must be submitted before July 1st 2016.
RESPONSIBILITIES:
Description of the content of the position in relation to:
* The candidate is expected to oversee and run the computational parts of a whole genome sequencing pipeline for nationwide screening of childhood oncology patients in a diagnostic setting. He/she will also be driving data analyses in the underlying research group working with germline predispositions towards childhood leukaemia aetiology, biology, and drug disposition and response.
* The role will involve data integration and machine learning across genomic, transcriptomic, clinical, epidemiological data and prior biological knowledge. It is expected in the future to also include metagenomic and metabolomic data.
* The candidate will supervise, coordinate, and train junior researchers within the field. The coordination role will also include our emerging industrial collaborations.

The position will be based at the Technical University of Denmark in the Functional Human Variation group headed by Associate Professor Ramneek Gupta, in close collaboration with Professor MD Kjeld Schmiegelow at the Department of Paediatrics and Adolescent Medicine, Rigshospitalet.

Other content of the position:
* It is expected that the candidate will use his experience for actively contributing to research based teaching programmes, as well as participating in grant writing for growing activities in the area.
* As WGS becomes mainstream in the clinic, the candidate will participate in ethical/social discussions and technical coordination of large data pipelines across multiple geographical sites.

REQUIREMENTS:
* Hold a PhD degree or equivalent as well as academic qualifications equivalent to those obtained by holding a position as Researcher or Postdoc.

Further qualifications:
Applicants should hold a PhD in bioinformatics, biology, engineering, computer science or similar, with 2-5 years of postdoctoral experience. The candidate must have strong computational skills and prior experience with large data sets, Unix command line environments, as well as either Perl, Python or a comparable scripting language. R and relational database skills are considered a strength, as is experience with application of statistics, systems biology, machine learning and multi-omics data integration methods. A strong background in biology is a prerequisite, preferably with experience in oncology.

Strong communication skills, participating in academic assessment work and the ability to interface across multiple disciplines are required, as well as the ability to work through several priorities. The applicant must be a team player and strong in written as well as spoken English.

It is expected that the candidate is experienced with genome wide association studies, targeted and whole genome sequencing.

PREFERENCES:
* Hold a PhD degree or equivalent as well as academic qualifications equivalent to those obtained by holding a position as Researcher or Postdoc.

TERMS:
The period of employment is for 2 years with possibility of extension.

HOW TO APPLY:
Please visit http://www.career.dtu.dk

Further information may be obtained from Associate Professor Ramneek Gupta ramneek[at]cbs.dtu.dk or Professor MD Kjeld Schmiegelow kjeld.Schmiegelow[at]regionh.dk

You can read more about the department and research groups on http://www.cbs.dtu.dk [link], http://www.rh.dk and http://goo.gl/Qxsutl.

DEADLINE:
9 May 2016

BACKGROUND:
The Molecular Profiling group is looking for a Scientist to analyze immuno-oncology (I/O) clinical, preclinical, and public profiling data to support I/O target mechanism studies, biomarker and target discovery & development, as well as implement and develop I/O data analysis pipeline using cutting-edge algorithms and statistically sound methodologies.

RESPONSIBILITIES:
* Collaborate with immuno-Oncology (I/O) scientists in preclinical and clinical departments to design profiling experiments and draft data analysis plan
* Communicate results with I/O scientists, refine analysis based on feedback, and plan/prioritize follow-up experiments
* Prepare clear, concise and easy-to-understand presentations and documentations for collaborators, senior management and government agencies
* Analyze proprietary and public profiling data to support I/O targets and biomarker discovery
* Analyze proprietary tox profiling data to support Tox studies
* Analyze proprietary clinical profiling data to support Clinical studies
* Contribute to team effort of developing I/O data analysis strategies and establishing I/O data analysis best practices
* Participate in team effort of organizing and integrating proprietary and public molecular profiling data to enable data sharing and visualization for bench scientists

REQUIREMENTS:
This position requires a minimum of a PhD in a related field, and preferably 2+ years postdoctoral experience. Additional requirements include, but are not limited to:
* Expertise in immuno-oncology
* Expertise in NGS data analysis to detect gene expression, variants, copy number variation, fusion and alternative splicing
* Strong preference for R power users, especially DeSeq 6+
* Strong preference for experience in Single Cell Sequencing
* Experience with analyzing cancer profiling data in the public domain such as TCGA
* Experience with a variety of molecular profiling platforms such as microarray and NGS, and their data analysis best practices
* Familiarity with TCR repertoire sequence analysis, antigen prediction, modeling (e.g., machine learning) and network building (e.g. gene regulation networks): Keen interest and determination to be at the cutting-edge of algorithms and model building
* Familiarity with bioinformatics tools and software such as R/Matlab, Linux, Perl, Python, Ruby, Java, Ruby on Rails, SQL, web programming

PREFERENCES:
PhD with 2+ years postdoctoral experience analyzing TCR repertoire.

TERMS:
Regular, full Time position eligible for employee benefits.

LOCALE:
Tarrytown, New York.

COMPENSATION:
Commensurate to experience.

HOW TO APPLY:
Please visit [link]

DEADLINE:
No deadline.

POLICY:
EEO

BACKGROUND:
The Regeneron Genetics Center is a wholly-owned subsidiary of Regeneron Pharmaceuticals organized to collaborate with health systems and research groups to elucidate, on a large scale, genetic factors that cause or influence a range of human diseases. The Analytical/Statistical Genetics team in the Genetics Center is responsible for the design, statistical analysis, and interpretation of all genetic studies conducted by the center.

RESPONSIBILITIES:
* Perform quality control checks and data management of large genomic sequencing and phenotypic datasets derived from electronic health records, display and report summary statistics for these data, creating analysis-ready datasets by implementing study designs developed for population and family-based projects, implementing inclusions / exclusions, and carrying out phenotype adjustments and transformations
* Carry out statistical genetic analyses to determine genotype-phenotype relationships including regression, logistic regression, rare variant aggregation tests, family-based tests in pedigrees and trios for quantitative biomarkers and disease traits
* Work with computational biologists and others to develop and provide programming support for the creation of algorithms and automated pipelines for analysis of NGS and array data
* Support the creation of queryable databases summarizing results across multiple projects

REQUIREMENTS:
This position requires a minimum of an MS, or BS with 3 years relevant experience in Bioinformatics, Biostatistics, Genetic Epidemiology, Genetics, Genomics or related field. Additional requirements include:
* Experience with handling & managing large datasets/software associated with high-throughput instruments for genetics/genomics
* Excellent oral and written communication skills as well as documented skills in communicating scientific findings
* Strong work ethic and enthusiasm for collaborative science
* Experience working independently and in a team environment
* Statistical knowledge and experience as well as strong background in computer programming
* Strong knowledge in use of statistical software (e.g. R, Perl/Python, etc.), with ability to perform statistical analysis, interpretation, and effective communication results

PREFERENCES:
Strong Statistical knowledge with direct experience analyzing NGS data (i.e. Illumina HiSeq, PacBio).

TERMS:
Regular, full Time position eligible for employee benefits.

LOCALE:
Tarrytown, New York

COMPENSATION:
Commensurate to experience.

HOW TO APPLY:
Please visit [link]

DEADLINE:
No deadline.

POLICY:
EEO

BACKGROUND:
We are seeking a creative, self-motivated scientist to join VelocImmune -- the Antibody Generation Technology and Discovery Centers of Regeneron Pharmaceutical Inc. in Tarrytown, NY.

RESPONSIBILITIES:
The successful candidate will support on-going, and initiate new, research projects towards generating, identifying, characterizing, and modifying novel antigen receptor molecules based on analyses of Next Generation Sequencing (NGS) data. The ideal candidate should have a strong combined background in computer science, immunology and molecular biology, as well as experience in bioinformatic analyses of NGS data from different sequencing platforms.

REQUIREMENTS:
This position requires a minimum of a Ph.D degree in Bioinformatics, Computational Biology, Computer Science, Biomedical Engineering or related fields, with 1-3 years research experience analysis of NGS data. The candidate needs to be familiar with most up-to-date sequencing platforms (e.g. Iliumina Mi-seq, Hi-seq, Pac Bio, Ion torrent, etc). Solid knowledge of scripting languages (Perl, Python, R or Ruby), SQL and Unix OS are strictly required. The candidate should also understand basic lab technologies in molecular biology, especially for NGS sample preparation. Experience in computational structural biology is strongly preferred. Candidate should have good oral and written communication skills and a clear sense of organization, purpose, and accountability.

PREFERENCES:
Direct experience with immunogenomics or antibody repertoire.

TERMS:
Regular, full Time position eligible for employee benefits.

LOCALE:
Tarrytown, New York

COMPENSATION:
Commensurate to experience

HOW TO APPLY:
Please visit [link]

DEADLINE:
No deadline

POLICY:
EEO

BACKGROUND:
The Rady Children's Institute for Genomic Medicine brings together world-class scientists and clinicians into a shared research infrastructure, one that will enable them to accelerate the translation and implementation of research discoveries for prevention, diagnosis, treatment, and ultimately cures for childhood diseases. Under the direction of world-renowned researcher Stephen Kingsmore, M.D., D.Sc., the Institute seeks to translate research findings into new clinical tests and treatments to improve patient outcomes, enhance the knowledge in this field among current and future healthcare providers and generate and share data and discoveries with other researchers.

We have an immediate opening a Bioinformaticist.

RESPONSIBILITIES:
We are looking for superstar computational-biologists/bioinformaticists who have a demonstrated experience in a large-scale production setting to deploy, maintain and evolve the bioinformatics framework for a high-throughput; ultra-rapid turnaround time whole-genome sequencing based clinical setting. You will have the opportunity to be a part of a team that'll build the infrastructure ground up using the latest and greatest of the technologies in infrastructure, data storage and analytics, with a strong focus on automation and integration. The environment is highly cross-functional, with a rich medical research heritage and multitude of collaborations with the biotech industry, academic institutions and federal programs. The end deliverable from your work will tangibly influence the quality of life of the children being seen at the hospital making your work experience exciting, challenging, rewarding and meaningful. And to top it all, you'll be located in one the finest cities in the country, with a wonderful year-round weather and a multitude of outdoor activity options.

Depending on the level of relevant experience, your candidature will be considered for the (junior/senior) bioinformaticist positions.

REQUIREMENTS:
Minimum Qualifications:
Bachelor's degree in Computer Science, Information Systems, Bioinformatics or Life Sciences, including fields, i.e., Biology, Molecular Biology, Genetics.
Two to five years' experience analyzing next-gen sequencing data (Illumina whole genomes or exomes): BCL to annotated variants
Two to five years' experience developing and maintaining pipelines for 24x7 automated bioinformatics analyses
Two to five years' experience integrating pipeline with the LIMS
Two to five years' experience working with and understanding of open source NGS tools like bwa, samtools, vcftools, picard, GATK, Freebayes, ANNOVAR, VEP, etc.
Two to five years' experience incorporating dbGaP, 1000 genomes, ExAC, Clinvar, OMIM, etc
Two to five years' experience with unix/linux operating system
Two to five years' experience software development using any of Ruby, Python, Perl, Bash
Two to five years' experience working with SVN, git
Two to five years' experience working with HPC scheduling systems such as Moab, TORQUE, LSF, OpenGrid Engine, etc.

PREFERENCES:
Preferred Qualifications:
Demonstrated experience working in CNV and SV calling
Demonstrated experience in phenotype-genotype integration frameworks
Demonstrated experience working with cloud-based development or analysis
Demonstrated experience working in a CAP/CLIA environment
Demonstrated experience performing benchmarking of bioinformatics tools
Demonstrated experience developing and working with Docker and AWS images
Demonstrated experience in database development using MySQL, or any NoSQL flavors
Demonstrated experience in setting up and computing on a hadoop cluster
Demonstrated experience programming using C or Java

HOW TO APPLY:
For more information and to apply: [link]

POLICY:
EEO/AA/Minorities/Females/Disabled/Veterans

BACKGROUND:
A 3 year postdoctoral position is available within Professor Caroline Dive's Clinical and Experimental Pharmacology Group to conduct cutting edge translational research on Small Cell Lung Cancer (SCLC). The focus of our research is translational medicine with an emphasis on next-generation sequencing in the characterisation of tumour heterogeneity, as well as prognostic or predictive biomarker discovery to aid novel therapeutics and clinical efficacy.

RESPONSIBILITIES:
The successful candidate will focus on unique lung cancer circulating tumour cell (CTC) derived explant tumour models (CDX) and analysis of CTCs isolated from lung cancer patients (see Hodgkinson et al., Nature Medicine, 2014). We have developed a library of CDX representing the full spectrum of chemosensitivity found in SCLC patients. These CDX have been used to generate an integrated oncogenomic datatset with the intent of developing novel platforms to investigate tumour response to both standard-of-care and novel targeted agents. This post, core funded by the CRUK Manchester Institute, sits within the CRUK Lung Cancer Centre of Excellence, a partnership between Manchester and University College London with associated opportunities for collaboration.

REQUIREMENTS:
The successful applicant should have a PhD in computational biology, mathematics, computer science or a related discipline. A background in cancer biology is desirable but not required.

TERMS:
Duration of post: 3 years

LOCALE:
We are situated in Manchester, England, a vibrant and dynamic city that is surrounded by beautiful countryside and has excellent transport links both nationally and internationally.

COMPENSATION:
Salary in the range of GBP 30,000 - GBP 39,800 (dependent upon qualifications and experience)

ABOUT US:
The Cancer Research UK Manchester Institute (http://www.cruk.manchester.ac.uk), an Institute of The University of Manchester (http://www.manchester.ac.uk), is a world-leading centre for excellence in cancer research. The Institute is core funded by Cancer Research UK (http://www.cancerresearchuk.org), the largest independent cancer research organisation in the world. We are adjacent to The Christie NHS Foundation Trust (http://www.christie.nhs.uk), one of the largest cancer treatment centres in Europe. These factors combine to provide an exceptional environment in which to pursue basic, translational and clinical research programmes.

Our aim is to understand the fundamental basis of cancer and apply that knowledge to developing new treatment strategies for cancer patients. Our advanced research programmes span a spectrum of cancer research, from the molecular and cellular basis of cancer through to drug discovery, translational research and clinical trials.

The Institute has outstanding laboratory facilities and exceptional core services, including next generation sequencing, microarrays, confocal microscopy, bioinformatics, histology and mass-spectrometry.

HOW TO APPLY:
Informal enquiries should be directed to Professor Caroline Dive, email: caroline.dive[at]cruk.manchester.ac.uk or her Preclinical Pharmacology Team lead Dr Kris Frese, email: kris.frese[at]cruk.manchester.ac.uk.

To apply for this position please visit our website: http://www.cruk.manchester.ac.uk

For applicants who are unable to download this information from our website, please contact HR department on 0161 446 3231, email: jobs[at]cruk.manchester.ac.uk to have this information sent by post.

Job Ref: MI/15/80-2

DEADLINE:
Closing date: 18th May 2016.

Submit Archive Subscribe

 

Copyright © 2016 · Scilico, LLC