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    Submitter

    BACKGROUND

    The role will focus on the development and application of state-of-the art bioinformatics, computational biology and/or biostatistics analyses for key projects to support cancer research. The post holders will work with multidisciplinary teams including drug discovery and/or clinical teams. The post holder will contribute to the formation of the scientific questions and defining the required experiments and approaches needed to address those questions. The post holders will be expected to implement and perform the relevant analyses, interpret them in the context of the project present the results to project teams as well as internal and external collaborators. The post-holder will be expected to demonstrate proactivity, take initiative and identify and use the most appropriate state-of-the- art computational tools to answer the specific scientific questions.

    There are two positions available within this team:
    1) Bioinformatics with focus on Next Generation Sequence analysis, primarily on somatic data. Analysis of Whole Genome, Whole Exome, RNAseq and other biological data
    2) Bioinformatics with focus on Proteomics analysis including SILAC and TMT data analysis using relevant software such as MaxQuant

    RESPONSIBILITIES

    • Provide bioinformatics analysis, support and interpretation for a variety of research and/or drug discovery projects.
    • Work closely with other members of the department and project teams to deliver the scientific outputs to the projects.
    • Stay abreast of the computational biology literature. Horizon scan for state-of-the-art tools and technologies that apply to the area of research.
    • Develop innovative pipelines for large-scale data analysis.
    • Report the results of bioinformatics analyses to research teams across the organisation.
    • Contribute to publications, project reports and patents.
    • Work and communicate with a diversity of scientific teams relating to individual projects.
    • Present work at internal and external meetings.
    • Deliver high quality work against clear deadlines.

    REQUIREMENTS

    • PhD in Cancer Biology, Genetics, Computer Science or associated subject
    • A minimum of two years postgraduate experience working in bioinformatics or computational biology in cancer genomics or an associated field
    • Proven experience of bioinformatics analyses and interpretation in one or more of the following key areas:
      • Transcriptomics, including next generation RNA-Seq pipelines for profiling transcriptional and splicing deregulation and RNA editing
      • Genomics, including mutation and copy number profiling of exome and whole genome NGS DNA-Seq data, using analysis pipelines such as the Broad Best Practice workflows
      • Quantitative Proteomics, including SILAC and TMT data analysis using relevant software such as MaxQuant
    • Proven experience in the development of software pipelines to implement analysis workflows
    • Proven experience in use of high performance computing platforms and Unix-like operating systems
    • Proven experience of writing and maintaining code using one or more of the following: Python, Perl, R, Matlab, Git
    • A good working knowledge of bioinformatics suites including NGS analysis pipelines such as Broad Best Practice workflows
    • Ability to implement analysis pipelines using appropriate and relevant scripting languages such as Python, Perl, R or Matlab
    • Ability to effectively work on HPC systems in a Unix environment
    • Ability to keep abreast of and rapidly become familiar with new bioinformatics tools and databases
    • Ability to write reports that clearly convey information to other scientists

    COMPENSATION

    There are some great benefits available with this position including a competitive salary and the chance to work with some of the brightest minds in the industry, looking to revolutionise the way healthcare is carried out in the UK.

    HOW TO APPLY

    Please do not hesitate to contact Harvey Uppal at huppal[at]pararecruit.com or call (+44) 121 616 3407 to discuss this opportunity further.

    Keywords: Computational, Biology, Genomics, Bioinformatics, NGS, Proteomics, WES, WGS, RNA, Analysis, Machine, Learning, Cancer, Python, Perl, Git, Pipelines, South, London, Sutton.
    Opportunity: Clinical Bioinformatician @ Genomics England -- London, UK
    Submitted by Eugene Mc Daid; posted on Wednesday, February 20, 2019

    Submitter

    BACKGROUND

    Paramount are working in partnership with Genomics England to expand their team in order to deliver success as they move beyond the 100,000 Genomes Project. Genomics England will work with NHSE to launch the world's first Genomic Medicine Service within a national healthcare system. In partnership with government, the NHS, academia, industry and the public, Genomics England aims to realise the potential of genomic medicine: to embed state-of-the-art care in the NHS; bring health benefits to UK citizens; and consolidate the UK's position as the 'go to' destination for international genomic research and investment.

    Genomics England applies state of the art approaches to whole genome sequences for processing, analysis, quality assurance and annotation. This includes integrating phenotypic and other clinical data with whole genome sequencing to create a world-leading, high fidelity data repository for the NHS and third party users.

    The Bioinformatics team develops and applies state of the art approaches to 100,000 whole genome sequences (WGS) in the areas of:
    • Analysis of WGS in cancer and rare diseases 

    • Sequence alignment and variant calling of up to 100 genomes per day 

    • Quality assurance and sample provenance monitoring
    This role contributes to the Genomic Interpretation Group's review and reporting of findings back to the NHS.

    RESPONSIBILITIES

    • Contribute to our in-house pipeline to analyse WGS data of patients and aid in the interpretation of findings using clinical bioinformatics capabilities.
    • Perform quality assurance of the analysis and interpretation made by third parties and by our in-house pipeline for both Rare Disease and Cancer.
    • Review variant calls in a timely manner that can be used to inform clinical decisions and for research purposes within the NHS GMCs and academic communities.
    • Perform user acceptance testing of third party decision support tools for interpretation.
    • Handling, troubleshooting and prioritising GMC issues from interpretation/system.
    • Support with writing SOPs and documentation about the system.

    REQUIREMENTS

    • Degree level qualification, or equivalent, in a medical science or relevant discipline
    • Demonstrated commitment to quality
    • Demonstrate understanding of quality management systems and implementing process improvements and supporting staff with process development and documentation.
    • Familiarity with clinical research and the NHS
    • Experience of writing and following Standard Operating Procedures
    • Proven scripting skills (e.g. in one or more of Python, Bash, R, SQL) (essential)
    • Proven knowledge/understanding in genetics/genomics and variant calling (essential)
    • Knowledge of bioinformatics best practice guidelines (e.g. ACGS)
    • Experience of delivering training to a varied audience (desirable)
    • Ability to work independently and to show initiative within a team
    • Ability to prioritise and balance competing demands
    • Ability to communicate effectively within a multidisciplinary team and external stakeholders
    • Flexible and co-operative approach to colleagues

    COMPENSATION

    There are some great benefits on offer with this opportunity including a competitive salary, pension, generous holidays and more.

    HOW TO APPLY

    Please do not hesitate to contact Harvey Uppal at huppal[at]pararecruit.com or call (+44) 121 616 3407 to discuss this opportunity further.

    Keywords: Clinical, Bioinformatician, Genomics, Bioinformatics, WGS, Pipelines, Patient, Data, SOP, Python, SQL, Bash, NHS, Variant, Calling, London.

    Submitter

    BACKGROUND

    An innovative Biotech internationally renowned for its pioneering research in personalised immune-based cancer therapies has a new opening for a junior Bioinformatician to join their thriving computational R&D team. This opportunity is suitable for applicants with a relevant PhD or MSc degree who are genuinely excited about working on ground breaking research projects for novel personalised cancer therapies.

    RESPONSIBILITIES

    Working in close collaboration with a leading team of Biologists and Clinicians, designing, implementing and applying statistical techniques to analyse and integrate large NGS datasets.

    REQUIREMENTS

    The ideal candidate will have:
    • A good PhD (or a Msc degree + 2 years' industry exp.) in Bioinformatics, Computational Biology, Data Science, Statistical Genetics or a related discipline
    • Experience working with NGS data
    • Strong statistical skills/understanding of machine learning concepts
    • Demonstrable programming ability using R and Python
    • Understanding of Immunology/Cancer-Immunology/Oncology is desirable, but not essential
    • A passion for contributing to the technical development of novel cancer therapies

    HOW TO APPLY

    This is an opportunity to work alongside some of the leading experts in the field, contributing to cutting edge research into immune-oncology therapies. To apply, send across a copy of your cv to efrancis[at]pararecruit.com, or call Emilie on 0121 616 3477 for an informal chat.

    Key words: Immunology, Immuno-Oncology, Bioinformatics, Computational Biology, Neo-Antigens, Biotech, Perl, Python, Bioconductor, Data Analysis, Bioinformatician, Statistical Genetics, Statistics, Cancer, Data Science, Machine Learning, Cancer Genomics

    Submitter

    BACKGROUND

    A thriving genomics company specialised in developing and delivering world class genomic research solutions to leading clinical and academic institutions across the globe has just released a brand new opening in their talented Bioinformatics team. This is a fantastic opportunity to work in a commercial environment, contribute to cutting edge genomics projects and develop expert analysis skills. The ideal candidate will be an experienced Bioinformatician with an excellent academic background, experience working with genomic/NGS data and strong analysis skills.

    RESPONSIBILITIES

    • Developing new methods for analysing NGS data
    • Working closely with the R&D teams to provide high quality NGS analysis
    • Exploring novel computational tools and approaches to support
    • Liaise with customers to provide expert support on any data analysis queries.

    REQUIREMENTS

    Essential experience:
    • A BSc/MSc or PhD in Bioinformatics, Computational Biology, Data Science or a related discipline
    • Strong understanding of molecular biology
    • Demonstrable technical skills, and proficient in one or more programming languages eg. Python, Java, R or Perl
    • Experience working with omics data, particularly NGS
    • Fantastic team player with excellent communication skills
    NB: Candidates with only a BSc will still be considered, but will ideally require 1-2 years industry experience as a Bioinformaticians/Computational Biologist

    ABOUT US

    This successful genomics company is the perfect place to develop new bioinformatics skills; the team are known for their fantastic dynamic, and friendly work environment. Success and training is well supported and there is plenty of opportunity to grow your career.

    HOW TO APPLY

    To find out more about this position, send a copy of your CV to efrancis[at]pararecruit.com or call Emilie on 0121 616 3477.

    Key words: Bioinformatics, Bioinformatician, Computational Biology, Genomics, NGS, Oxford, London, Data Science, Data Analysis

    BACKGROUND

    The Department of Energy Joint Genome Institute (DOE JGI, a division of Berkeley Lab) is looking for a Data Scientist with a strong background in data mining and software development, with a particular emphasis on the data and methods related to functional annotation and metabolic reconstruction. Of specific interest is familiarity with major annotation and pathway databases and ontologies, knowledge of major bioinformatics tools for pairwise and multiple sequence alignment, profile alignment, phylogenetic tree reconstruction, and prior experience with benchmarking of bioinformatics tools and software. The incumbent is expected to work both independently, and as part of a team of biologists, bioinformaticists and software engineers to develop software and data framework for accurate functional annotation of microbial genomes and metagenomes, reconstruction of reaction networks and microbial phenotype inference. This position will be filled at the Data Scientist (Level 1) or Data Scientist (Level 2), dependent on experience.

    RESPONSIBILITIES

    Data Scientist (Level 1) Specific Responsibilities:
    • Work on designing and implementing a framework for accurate functional annotation and pathway reconstruction by collating the data and metadata from various data sources, and supporting manual curation efforts.
    • Work with the Integrated Microbial Genomes & Microbiomes (IMG) data warehouse team to ensure accurate representation of functional annotation and pathway data in IMG and support for major annotation and pathway analysis needs by IMG users.
    • Work with the DOE Systems Biology Knowledgebase (Kbase) team to ensure data portability and support for functional annotation and pathway analysis needs by Kbase users.
    • Contribute to the development of IMG pipelines through the selection of appropriate software, benchmarking and testing of existing and newly developed software, and providing feedback to troubleshoot and recommend solutions.
    • Create documentation and training materials.
    In addition to the above, Data Scientist (Level 2) Specific Responsibilities:
    • Independently identify resources of functional annotation and pathway data and develop the software to mine them in an automated manner.
    • Work with the Integrated Microbial Genomes & Microbiomes (IMG) data warehouse team to implement a scalable and portable pipeline to update functional annotations and pathway reconstructions for thousands of genomes and metagenomes.
    • Facilitate the training and transfer of knowledge of technologies to other group members in the division.
    • Develop qualitative and predictive analytics to inform organizational policy.

    REQUIREMENTS

    Data Scientist (Level 1) Required Qualifications:
    • B.Sc. in bioinformatics, computational science or engineering, or a related discipline or equivalent experience and a minimum of 2 years related work experience or the equivalent combination of education and experience
    • Demonstrated experience designing, developing, and testing quality software – preferably using Python in a UNIX/Linux environment
    • Knowledge of software development practices – unit testing, self-documenting code, source code management (Git), bug tracking
    • Excellent written and oral communications skills and the ability to collaborate and work as part of a large multidisciplinary team
    • Ability to apply analytical skills and creativity to solve highly technical/complex problems
    • Effective time management, organization, and planning skills with the ability to allocate resources and assign work to meet goals and deadlines
    • Detail-oriented with the ability to work effectively in both team and solo environments
    In addition to the above, Data Scientist (Level 2) Required Qualifications:
    • A minimum of 5 years of related experience, or a Master's degree in Bioinformatics, Computer Science, Engineering, or closely related field and a minimum of 3 years related experience
    • Experience with modern cluster/cloud/distributed computational and storage systems
    • Demonstrated experience in bioinformatics and computational biology methods and tools for pairwise and multiple sequence alignment, profile search, protein clustering and phylogenetic analysis
    • Familiarity with major concepts in recording of biochemical reactions and pathways, biological ontologies

    TERMS

    • This is a full time, 1 year, term appointment with the possibility of extension or conversion to Career appointment based upon satisfactory job performance, continuing availability of funds and ongoing operational needs.
    • Classification will depend upon the applicant's level of skills, knowledge, and abilities.
    • Full-time, M-F, exempt (monthly paid) from overtime pay.
    • This position may be subject to a background check. Any convictions will be evaluated to determine if they directly relate to the responsibilities and requirements of the position. Having a conviction history will not automatically disqualify an applicant from being considered for employment.
    • Work will be primarily performed at DOE Joint Genome Institute (JGI) – 2800 Mitchell Dr., Walnut Creek, CA.

    COMPENSATION

    • Salary is commensurate with experience.

    ABOUT US

    Berkeley Lab (LBNL, www.lbl.gov) addresses the world's most urgent scientific challenges by advancing sustainable energy, protecting human health, creating new materials, and revealing the origin and fate of the universe. Founded in 1931, Berkeley Lab's scientific expertise has been recognized with 13 Nobel prizes. The University of California manages Berkeley Lab for the U.S. Department of Energy's Office of Science.

    HOW TO APPLY

    Apply directly online at 50.73.55.13/coun[...]54926 and follow the on-line instructions to complete the application process.

    Title: Associate Data Scientist
    Job ID: 86097
    Organization: JG-Joint Genome Institute

    DEADLINE

    The posting shall remain open until the position is filled.

    POLICY

    Equal Employment Opportunity: Berkeley Lab is an Equal Opportunity/Affirmative Action Employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, age, or protected veteran status. Berkeley Lab is in compliance with the Pay Transparency Nondiscrimination Provision under 41 CFR 60-1.4 (www.dol.gov/ofcc[...].html). Click here (www.dol.gov/ofcc[...]t.pdf) to view the poster: "Equal Employment Opportunity is the Law".

    Submitter

    BACKGROUND

    Long-read Sequencing, Genomics, Permanent!

    Paramount are working in partnership with Genomics England to help expand their team – after successfully completing the 100,000 Genomes Project recently they are working together with the NHS to launch the World's First Genomic Medicine Service. This will transform the way patients are cared for in the future.

    A fantastic position has become available in their Bioinformatics team (based in Hinxton, Cambridge) for a Bioinformatician to support the R&D activities of Genomics England by comprehensively analysing sequence data sets from a variety of platforms (in particular long read sequencing technologies).

    This role would be an ideal fit for a Bioinformatician with a solid skills set in Bioinformatics, handling large data sets in an industry or academic setting, with ideally some background in long read sequencing technologies (e.g. PacBio, Illumina, Nanopore sequencing)

    RESPONSIBILITIES

    As a Bioinformatician you will have the following responsibilities:
    • Performing computational analyses for a range of R&D projects
    • Comparing tools and pipelines for NGS analysis
    • Informing on the design and implementation of new features for sequencing data analysis
    • Analysing sequence data sets from a variety of platforms (long read sequencing technologies)

    REQUIREMENTS

    The ideal Bioinformatician will meet the following requirements:
    • MSc or PhD in Bioinformatics or related discipline
    • Solid skills set in Bioinformatics and experience of working as a Computational Biologist
    • Practical knowledge of NGS algorithms and available resources for long read sequencing technologies
    • Experience of comparing NGS data sets (WGS is important), handling large data sets and building pipelines
    • Strong programming skills in Python and R
    • Understanding of basic statistical tests

    COMPENSATION

    In return you will receive a competitive salary package with the opportunity to work in a fantastic location and make a real difference to patients' lives.

    HOW TO APPLY

    If you're interested and would like to apply, please send an up-to-date CV to alauterjung[at]pararecruit.com (+44 121 616 3469).

    POLICY

    Please note: Only candidates who are eligible to work in the UK will be considered. This means you must have either UK/EU citizenship of indefinite leave to remain.

    Keywords: Bioinformatician, Bioinformatics, Computational Biologist, Computational Biology, NGS, WGS, pipeline, data analysis, Genomics, Long Read Sequencing, PacBio, Nanopore Sequencing, Illumina Sequencing, Python, R, algorithm, statistical, PhD, Cambridge, UK

    RESPONSIBILITIES

    Applications are invited for a Senior Bioinformatician in the Genomics of Inflammation and Immunity Group at the Wellcome Sanger Institute, led by Dr. Carl Anderson (www.andersonlab.info).

    You will play a central role in a substantial research programme aiming to use high-throughput genetics and genomics to further our biological understanding of immune-mediated diseases and, ultimately, identify new drug targets. To help us achieve this mission, we are currently generating whole-genome/exome sequencing data on tens of thousands of patients from the UK with inflammatory bowel disease (IBD) or primary sclerosing cholangitis (PSC). We are coupling this effort with the generation of single-cell RNA/ATAC sequencing of disease relevant tissues from a subset of these patients and healthy controls. Finally, we are combining results from these experiments (and others) with our detailed clinical phenotype data to identify causal biology underpinning disease susceptibility and progression.

    You will be responsible for developing and maintaining many of the computational pipelines that underpin the team's research. These include, but are not limited to, pipelines for single-cell RNA/ATAC-seq analysis, molecular QTL mapping, whole-genome/exome based association studies and causal variant fine-mapping. In addition, you will be responsible for further developing PhenoDB, our in-house database of phenotypic data from more than 15,000 inflammatory bowel disease patients.

    You will join a multi-disciplinary team of statisticians, geneticists, immunologists, computer scientists and clinicians who work together to understand the genetics and genomics of immune-mediated disease. You will have a collaborative approach to research and take a full and active role in discussions, contributing both ideas and expertise as necessary.

    REQUIREMENTS

    Essential Skills:
    • Ability to work with others in a friendly and collegiate environment
    • A degree (PhD, MSc or BSc with equivalent experience) in a quantitative field (e.g. Bioinformatics, Computer Science, Computational biology or similar quantitative discipline)
    • Demonstrable shell scripting skills (e.g. bash, tcsh, awk, sed)
    • Proficient Python programmer, including experience of using web development frameworks (e.g. Django, Flask)
    • Demonstrable experience of the design and use of relational SQL databases
    • Demonstrable experience of developing practical computational tools for data parsing, quality control, modelling and analysis of large-scale genetic or genomics datasets (e.g. 1000s of individuals with sequencing/GWAS data)
    • A passion for problem solving and creative thinking
    • A self-motivated and independent working style with good organisational skills and an attention to detail
    • A good communicator with an interest in using your skills to help others

    PREFERENCES

    Ideal Skills:
    • Experience of javascript libraries (e.g. jQuery, D3)
    • Experience of Unix server configuration (e.g. Nginx)
    • Experience of OpenStack, AWS, Google Cloud, Azure or other cloud computing environments
    • An interest in using genetics and genomics to identify drug targets for immune-mediated diseases such as inflammatory bowel disease

    TERMS

    Permanent

    LOCALE

    Human Genetics Anderson Faculty

    COMPENSATION

    Salary range from: £36,737 to £44,451 pa dependent on experience

    Our Benefits: Our employees have access to a comprehensive range of benefits and facilities including:
    • Group Defined Contribution Pension Scheme and Life Assurance
    • Group Income Protection
    • Private Health Insurance
    • 25 days annual leave, increasing by one day a year to a maximum of 30
    • Family friendly environment including options for flexible and part-time working, a childcare voucher scheme, Campus Nursery and Summer holiday club
    • Two days paid Employee Volunteering Leave a year
    • Employee Discount Scheme
    • Campus Gym, tennis courts, cricket pitch and sports hall plus a range of dining facilities
    • Active Campus Sports and Social Club
    • Free Campus Bus Service

    ABOUT US

    The Wellcome Sanger Institute is a charitably funded research centre and committed to training the next generation of genome scientists. Focused on understanding the role of genetics in health and disease and a world leader in the genomic revolution, our mission is to use genome sequences to advance understanding of human and pathogen biology in order to improve human health. We aim to provide results that can be translated into diagnostics, treatments or therapies that reduce global health burdens. Our science is large-scale and organised into Programmes, led by our Faculty who conceive and deliver our science, and supported by our Scientific Operations teams responsible for all data production pipelines at the Institute. Our Campus: Set over 125 acres, the stunning and dynamic Wellcome Genome Campus is the biggest aggregate concentration of people in the world working on the common theme of Genomes and BioData. It brings together a diverse and exceptional scientific community, committed to delivering life-changing science with the reach, scale and imagination to pursue some of humanity's greatest challenges.

    HOW TO APPLY

    Please visit www.jobs.sanger.ac.uk.

    Please include a covering letter and CV with your application.

    DEADLINE

    Closing date: 15 March 2019 however the role will remain open until filled with applications considered on an on-going basis.

    POLICY

    Genome Research Limited is an Equal Opportunity employer. We will consider all applicants without discrimination and are committed to creating an inclusive environment for all employees.

    BACKGROUND

    Health Data Research UK Cambridge is looking to recruit a highly-motivated, strategically aware and skilled Director of Health Informatics to join our pioneering organisation. The role will be based at the Wellcome Sanger Institute on the Wellcome Genome Campus.

    Formed in April 2018, Health Data Research UK (HDR UK) has six UK sites, comprising 22 universities and research institutes, whom work collaboratively as foundation partners to make game-changing improvements in people's health by harnessing data science at scale across the UK. HDR UK Cambridge is based at the Wellcome Sanger Institute and its collaborative partners are:
    • Wellcome Sanger Institute
    • EMBL-European Bioinformatics Institute
    • Cambridge University Hospitals NHS Foundation Trust
    • University of Cambridge

    RESPONSIBILITIES

    In conjunction with the HDR-Cambridge Director, you will feed into the overall HDR national strategy for Informatics by leading the formulation and implementation of the health informatics strategy and integration of health data for the new HDR-Cambridge partnership site. This will include:
    • Build and manage the HDR-Cambridge health informatics team
    • Project conception, planning and implementation in health informatics
    • Overseeing the operation of HDR-Cambridge's core hardware, network, software and data infrastructure and working with the HDR Cambridge Programme Manager on operational matters.
    • Development and implementation of appropriate security and governance strategies, including ethics and data protection.

    REQUIREMENTS

    Key to this role will be the ability to foster new collaborations and identify future opportunities (with a focus on informatics-related dimensions) to continue the growth of the programme. A key member of the Senior Leadership Forum at the Wellcome Sanger Institute you will also hold honorary posts (when deemed necessary) at other partner organisations within HDR Cambridge (i.e. Cambridge University and its associated hospitals and EMBL-European Bioinformatics Institute.

    You will have substantial working experience at a senior level in a complex organisational structure with a strong track record in health/clinical informatics research including a broad and detailed understanding of ethical and regulatory issues related to clinical research.

    A strategic thinker, you will be able to demonstrate senior leadership in managing budgets, people and projects and establish and develop key networks and collaborators.

    We are looking for a motivated, creative and flexible individual with a personal ethos of continuous improvement. If you think you have the attributes, skills and experience that we are looking for, please go to our job description and recruitment pack to find out more.

    Essential Skills:

    Education and qualifications:
    • Honours degree in computer science or similar numerical discipline [or relevant practical experience working in the health informatics domain e.g. within the NHS]
    Specialist knowledge and skills:
    • Extensive experience of project conception, planning and implementation in health informatics
    • Substantial experience with understanding ethical and regulatory issues related to clinical research, and confidentiality / data protection
    • Excellent IT skills and knowledge, with the ability to keep up to date with developments in the field
    • Broad and detailed understanding of IT/informatics, including IT infrastructure strategy
    Interpersonal & communication skills:
    • High level of influencing and negotiating skills
    • Strategic thinking, ability to see the `bigger picture', ability to provide concise analyses of complex issues and options
    • Ability to focus and accurately complete tasks within given timeframes while dealing with unscheduled interruptions e.g. changing priorities
    • Skilled in establishing and developing key networks and collaborators
    • Highly developed communication skills with experience of dealing with people at all levels successfully
    Relevant experience:
    • Strong track record in health/clinical informatics research
    • Substantial working experience at a senior level in a complex organisational structure, preferably in a Higher Educational Institution or an NHS organisation with a strong research profile
    • Demonstrated senior leadership, including management of budgets, people, and projects
    • IT systems strategy and implementation
    • The ability to quickly assimilate relevant scientific and technical details
    • Demonstrates initiative, creativity, flexibility and a personal ethos of continuous improvement
    • Proven organisational skills with the ability to plan and schedule effectively

    TERMS

    Fixed-term: 31 March 2023

    COMPENSATION

    Salary range: £71,584 - £81,810 per annum depending on experience plus excellent benefits

    Our Benefits: Our employees have access to a comprehensive range of benefits and facilities including:
    • Group Defined Contribution Pension Scheme and Life Assurance
    • Group Income Protection
    • Private Health Insurance
    • 25 days annual leave, increasing by one day a year to a maximum of 30
    • Family friendly environment including options for flexible and part-time working, a childcare voucher scheme, Campus Nursery and Summer holiday club
    • Two days paid Employee Volunteering Leave a year
    • Employee Discount Scheme
    • Campus Gym, tennis courts, cricket pitch and sports hall plus a range of dining facilities
    • Active Campus Sports and Social Club
    • Free Campus Bus Service

    ABOUT US

    The Wellcome Sanger Institute is a charitably funded research centre and committed to training the next generation of genome scientists. Focused on understanding the role of genetics in health and disease and a world leader in the genomic revolution, our mission is to use genome sequences to advance understanding of human and pathogen biology in order to improve human health. We aim to provide results that can be translated into diagnostics, treatments or therapies that reduce global health burdens. Our science is large-scale and organised into Programmes, led by our Faculty who conceive and deliver our science, and supported by our Scientific Operations teams responsible for all data production pipelines at the Institute. Our Campus: Set over 125 acres, the stunning and dynamic Wellcome Genome Campus is the biggest aggregate concentration of people in the world working on the common theme of Genomes and BioData. It brings together a diverse and exceptional scientific community, committed to delivering life-changing science with the reach, scale and imagination to pursue some of humanity's greatest challenges.

    HOW TO APPLY

    Please visit www.jobs.sanger.ac.uk.

    Please include a covering letter and CV with your application.

    For an informal chat about the role, please contact John Danesh at: jd292[at]medschl.cam.ac.uk

    DEADLINE

    Closing date for applications: 10th March 2019

    POLICY

    Genome Research Limited hold an Athena SWAN Bronze Award and will consider all individuals without discrimination and are committed to creating an inclusive environment for all employees, where everyone can thrive.

    DESCRIPTION

    Computercraft is seeking a biologist with a background in human clinical or animal model phenotype data. The successful candidate will curate clinical phenotype data from the National Center for Biotechnology Information (NCBI) database on Genotypes and Phenotypes (dbGaP), accessible online at www.ncbi.nlm.nih.gov/gap. Our scientists work on site at the National Institutes of Health (NIH) in Bethesda, MD, in a production-oriented, rather than research-oriented, environment.

    dbGaP was developed to archive and distribute the data and results from studies investigating the interaction of genotype and phenotype in humans to assist scientists in discovering associations between genetic variants and risks for disease. Responsibilities of the Bioinformatics Scientist, Scientific Data Curator will include data quality control and curation, annotation and integration of study metadata (study protocols and data collection forms), and communication with external investigators. Candidates require the organizational and managerial skills to see a study through the process of original submission, internal processing, quality testing, and public deployment. This is an opportunity to be involved in the advancement of a high-profile resource that is working to revolutionize human genetic disease research.

    REQUIREMENTS

    • Ph.D. or M.S. in a biomedical field (i.e., epidemiology, genetics, public health, pathology)
    • Strong organizational skills
    • Excellent oral and written communication skills
    • Ability to work with a team in a production environment
    • Strong interest in contributing to the development of public database resources
    • Advanced general computing skills
    • Linux and Windows experience

    PREFERENCES

    • Knowledge of human genetics, clinical data, and epidemiology
    • Experience with NCBI resources
    • Experience with SQL
    • Familiarity with UNIX commands, open files, and directory trees
    • Experience evaluating incoming phenotype data for accuracy and consistency
    • Scripting experience in Perl or related scripting languages
    • Programming experience with Linux/UNIX

    LOCALE

    On site at the National Center for Biotechnology Information (NCBI), National Institutes of Health (NIH), Bethesda, MD

    BENEFITS/OTHER:
    Computercraft offers a competitive salary, an excellent benefits package, and the opportunity for a positive work-life balance with a standard 40-hour work week and the chance to work alongside a team of highly accomplished professionals.

    HOW TO APPLY

    To apply for this position or learn about other Computercraft job opportunities, please visit the Careers section of our website: computercraft-usa.com

    POLICY

    Computercraft is an equal opportunity employer.

    OVERVIEW

    Located in Boston and the surrounding communities, Dana-Farber Cancer Institute brings together world renowned clinicians, innovative researchers and dedicated professionals, allies in the common mission of conquering cancer, HIV/AIDS and related diseases. Combining extremely talented people with the best technologies in a genuinely positive environment, we provide compassionate and comprehensive care to patients of all ages; we conduct research that advances treatment; we educate tomorrow's physician/researchers; we reach out to underserved members of our community; and we work with amazing partners, including other Harvard Medical School-affiliated hospitals.

    The Department of Data Sciences within the Dana-Farber Cancer Institute seeks an Associate Director, Immuno-Oncology Computational Biology. This is an Associate Director Level, Research Staff Scientist position to lead a new bioinformatics team, focused on enabling the computational and bioinformatics needs of theDFCI Center for Immuno-Oncology (CIO). We are seeking an exceptional candidate who has deep experience in computational biology and immuno-oncology andexperience leading a small team of computational biologists.

    RESPONSIBILITIES

    • Interface with faculty in the Department of Data Sciences and the Center for Immuno-Oncology (CIO) to develop a prioritized road-map of current and future computational needs for immuno-oncology.
    • Recruit, manage and mentor a small team of computational biologists.
    • Oversee the continued development of computational methods and pipelines needed for current and future I/O assays, including Multiplex ImmunoFluorescence (MiF), WES/WGS, RNA-seq, TCR/BCR sequencing, neoantigen prediction, CyTOF, and Multiplexed ion beam imaging (MIBI).
    • Oversee the creation of a common informatics platform for processing all I/O assays, integrating with clinical data, and ensuring rapid computational analysis needed for publications.
    • Conduct meta-analyses across different profiling techniques and across different immuno-oncology trials.
    • Contribute to collaborative projects and co-author publications.
    • Communicate new findings in a translational research environment strongly focused on discovery and development of novel immunotherapies to improve patient care.

    REQUIREMENTS

    Required skills:
    • PhD (or equivalent) in computational biology, bioinformatics, or related fields
    • Publication record in immuno-oncology and/or cancer genomics
    • Proven experience in managing a team of computational biologists
    • 5+ years of research / working experience in bioinformatics and genomics
    • Strong quantitative (statistics, computer science) and programming (Python & R) skills
    • Good knowledge of molecular genomics and immunology
    • Working experience with high throughput sequencing data is required.
    • Experiences with CyTOF, IHC, or serum cytokine analyses would be a significant plus.
    • Able to work independently to resolve time-sensitive issues and balance multiple projects
    • Able to communicate with collaborators at all levels
    • Strong project management skills and detail oriented
    • Strong interest in contributing to translational cancer research
    The candidate must also demonstrate outstanding personal initiative, work effectively as part of a team, meet deadlines, and efficiently multitask.

    HOW TO APPLY

    Apply here: www.Click2apply.net/qsd6k9r9ntc87zyp

    POLICY

    Dana-Farber Cancer Institute is an equal opportunity employer and affirms the right of every qualified applicant to receive consideration for employment without regard to race, color, religion, sex, gender identity or expression, national origin, sexual orientation, genetic information, disability, age, ancestry, military service, protected veteran status, or other groups as protected by law.

    PI107545477

    OVERVIEW

    Located in Boston and the surrounding communities, Dana-Farber Cancer Institute brings together world renowned clinicians, innovative researchers and dedicated professionals, allies in the common mission of conquering cancer, HIV/AIDS and related diseases. Combining extremely talented people with the best technologies in a genuinely positive environment, we provide compassionate and comprehensive care to patients of all ages; we conduct research that advances treatment; we educate tomorrow's physician/researchers; we reach out to underserved members of our community; and we work with amazing partners, including other Harvard Medical School-affiliated hospitals.

    The Department of Data Sciences at Dana-Farber Cancer Institute seeks a Lead Computational Biologist, to develop and implement cutting-edge technologies for cancer genomics and coordinate scientific projects at the Center for Cancer Genome Discovery (CCGD) at the Dana-Farber Cancer Institute. The primary mission of the CCGD is to facilitate genomic discoveries in human cancer samples through basic and translational cancer research using cutting-edge technologies. The CCGD has established platform groups to assist researchers in both genome-wide and gene-focused efforts using Illumina next generation sequencing. We strive to be at the forefront of cancer characterization, development and utilization of novel technologies, and adapting existing technologies for the advancement of cancer research. Technologies are selected and developed with a view to research-oriented ventures, as well as translational medicine and clinical relevance.

    This exceptional opportunity offers the chance to work at the forefront of mutation discovery and translational cancer technologies and applications. The Lead Computational Biologist will oversee activities within CCGD informatics and manage technology development.

    RESPONSIBILITIES

    The primary responsibility of this role will be to lead the development and validation of multi-omic analytical methodologies for both cutting-edge research and clinical applications (such as development of analyses for liquid biopsies and structural variant detection). Working with scientific and clinical colleagues, the capabilities developed will be applied to precision cancer medicine efforts at our institutions. To make significant contributions to the research and clinical efforts described above, the candidate will have the ability to quickly arrive at innovative and effective solutions both as part of a team and independently.
    • Project planning and supervision of team members
    • Work closely with and understand various disciplines such as scientists, molecular biologists, clinicians, pathologists and oncologists to interpret requirements and needs for novel analyses.
    • Develop and test new computational and bioinformatic tools for genomic analysis on patient samples; monitor and evaluate emerging analytical tools, and improve and/or develop existing or new methodologies for analyses of cancer specimens.
    • Process, analyze, and interpret experimental and clinical datasets derived from research and validation studies.
    • Understand, document, and present scientific and technical validation data to colleagues including good coding practices (code review) and explicit documentation of developed software.
    • Work independently on multiple ongoing projects with the flexibility to rapidly adjust to new priorities.
    • Cross-training bioinformatic colleagues on newly developed tools

    REQUIREMENTS

    • PhD (or equivalent) in computational biology, bioinformatics, or related fields
    • 5+ years relevant experience in cancer genomics.
    • Strong project management and supervisory skills, with the demonstrated ability to develop and manage complex projects in a matrixed environment
    • Familiarity with principles of experimental design and modern data analysis paradigms
    • Deep understanding of genomics and molecular biology (cancer genomics and massively parallel sequencing a plus)
    • Strong communication skills and ability to effectively translate informatics concepts to multidisciplinary (non-informatics) personnel
    • Strong proficiency with programming languages such as Python or Java, C/C++, statistical programming using R or related tools and queries through SQL required. Experience with web-development desirable.
    • Demonstrated ability to develop algorithms for analysis of biological data derived from complex, large datasets (such as massively parallel sequencing); experience developing analysis schemes for RNA-Seq, circulating tumor DNA (cell-free DNA and circulating tumor cells) and/or long-read sequencing is desirable.
    • Strong interpersonal skills and ability to effectively interact with all levels of staff and external contacts

    HOW TO APPLY

    Apply Here:http://www.Click2apply.net/zp3tpvsd3xc4ytx3

    POLICY

    Dana-Farber Cancer Institute is an equal opportunity employer and affirms the right of every qualified applicant to receive consideration for employment without regard to race, color, religion, sex, gender identity or expression, national origin, sexual orientation, genetic information, disability, age, ancestry, military service, protected veteran status, or other groups as protected by law.

    PI107545443

    BACKGROUND

    The Unit of Clinical and Translational Neuroscience in the Intramural Program of the National Institute on Aging (NIA) is seeking applicants for a post-doctoral research fellowship. Our current work has a major emphasis on understanding the metabolic basis of Alzheimer's disease (AD) pathogenesis using quantitative metabolomics of brain and blood tissue samples. We employ several computational methodologies (i.e. biostatistical, epidemiologic, computer science) on large longitudinal clinical, neuroimaging, cognitive, and metabolomics/proteomics datasets. We are also exploring in-silico approaches to drug repurposing in AD combining analyses of Electronic Health Record (EHR) data with large publicly available gene expression datasets.

    The following link provides details on our work: www.irp.nia.nih.gov/bran[...]u.htm

    REQUIREMENTS

    We are seeking to recruit a talented post-doctoral fellow with expertise in analyses of longitudinal data/machine-learning methods who can contribute to a growing portfolio of high-impact publications from our group. Candidates with strong writing skills will be preferred.

    HOW TO APPLY

    Please contact the Lab Chief, Madhav Thambisetty MD, Ph.D at thambisettym[at]mail.nih.gov and 443-852-7607 (cell).

    In your letter, please include:
    1. A full CV with a statement of research interests and career goals.
    2. Contact details of three references who can comment on your analytical expertise and writing skill

    POLICY

    DHHS and NIH are Equal Opportunity Employers.

    The NIH is dedicated to building a diverse community in its training and employment programs.

    BACKGROUND

    We are looking for a highly motivated postdoctoral scholar at Stanford University School of Medicine. The major focus of the NIH-funded lab is to develop, validate, and clinically translate diagnostic, prognostic, predictive biomarkers for precision cancer medicine. We employ several approaches: (1) analyze genomic, epigenomic, transcriptomic data, and (2) develop novel statistical and machine learning methods. Through close collaboration with clinicians at Stanford and beyond, we have access to unique, high-quality, well annotated clinical specimens to support our biomarker research. We are generously funded by 3 active NIH R01 grants. Our work has been published in top clinical journals such as JAMA Oncology, Clinical Cancer Research, Radiology, etc. Please visit med.stanford.edu/lilab

    REQUIREMENTS

    Candidates from a diverse background are encouraged to apply. The applicant may hold a PhD either in physical sciences or engineering with a strong motivation to solve biomedical problems, or in biomedical sciences with a strong interest to apply computational approaches. The project involves discovery and development of novel DNA methylation-based biomarkers for cancer detection and prognostication. The ideal candidates will have strong analytic and programming skills, and prior research experience in epigenomics-based cancer biomarkers. Experience in cancer genomics or transcriptomics is also relevant.

    LOCALE

    Stanford, CA, USA

    ABOUT US

    I am dedicated to cultivating and mentoring the next generation scientists in biomedical research. Postdocs and students in the lab have gone on to establish their own independent labs in academia or secure jobs in healthcare or technology industry. Major awards to my postdoc trainees include ASTRO Resident Clinical/Basic Science Research Award, ASTRO Basic/Translational Science Award. ASTRO is the world's largest professional society for radiation oncologists. One of my trainees recently received the prestigious NIH K99/R00 Pathway to Independence Award from the NCI, which provides $1,000,000 over 5 years to establish an independent research program with a tenure-track faculty position in the US.

    HOW TO APPLY

    Interested applicants should send a research statement, CV, and names of three references to:
    Ruijiang Li, PhD DABR
    Email: rli2[at]stanford.edu

    BACKGROUND

    We seek a motivated bioinformatician to be involved in our studies of post-transcriptional regulatory networks. Our laboratory at Memorial Sloan-Kettering Cancer Center combines computational and experimental approaches to discover, annotate and functionally elucidate diverse post-transcriptional regulatory pathways and their biological impacts. Currently, we are particularly interested in non-canonical small RNA pathways, alternative mRNA processing strategies, and RNA methylation. Towards these ends, we produce RNA-seq, 3'-seq, CLIP-seq, small RNA, RNA modification and ChIP-seq data, and analyze these with respect to the rich comparative genomic data available for Drosophila and mammals.

    www.mskcc.org/rese[...]c-lai

    Recent Studies involving genomics/bioinformatics approaches:

    Kan, L., A. V. Grozhik, J. Vedanayagam, D. P. Patil, N. Pang, K.-S. Lim, Y.-C. Huang, B. Joseph, C.-J. Lin, V. Despic, J. Guo, D. Yan, S. Kondo, W.-M. Deng, P. C. Dedon, S. R. Jaffrey and E. C. Lai (2017). The m6A pathway facilitates sex determination in Drosophila. Nature Communications 8: 15737, 1-16.

    Kondo S., J. Vedanayagam, J. Mohammed, S. Eizadshenass, L. Kan, N. Pang, R. Aradhya, A. Siepel, J. Steinhauer and E. C. Lai (2017). New genes often acquire male-specific functions but rarely become essential in Drosophila. Genes and Development 31: 1841--1846. (Highlighted in Genes and Dev 31: 1825-1826.)

    Sanfilippo P., J. Wen and E. C. Lai (2017). Landscape and evolution of tissue-specific alternative polyadenylation across Drosophila species. Genome Biology 18: 229 doi: 10.1186/s13059-017-1358-0.

    Mohammed, J., A. S. Flynt, A. M. Panzarino, M. Mondal, M. DeCruz, A. Siepel and E. C. Lai (2018). Deep experimental profiling of microRNA diversity, deployment, and evolution across the Drosophila genus. Genome Research 28: 52-65.

    Jee, D., J.-S. Yang, S. M. Park, D.J. Farmer, J. Wen, T. Chou, A. Chow, M. T. McManus, M. G. Kharas and E. C. Lai (2018). Dual strategies for Argonaute2 Slicer-dependent miRNA biogenesis of erythroid miRNAs underlie conserved requirements for slicing in mammals. Molecular Cell 69: 265-278.

    Lin C.-J., F. Hu, R. Dubruille, J. Vedanayagam, J. Wen, P. Smibert, B. Loppin and E. C. Lai (2018). The hpRNA/RNAi pathway is essential to resolve intragenomic conflict to permit transmission of sons. Developmental Cell 46: 316-326. (Featured in Developmental Cell 46: 251-253).

    RESPONSIBILITIES

    The candidate will integrate into projects that seek the mechanistic bases and impact of (1) tissue-specific alternative polyadenylation, and (2) regulation and dysregulation of miRNA biogenesis. There is a close exchange of ideas between dry and wet lab members to generate and test biologically-based hypotheses.

    REQUIREMENTS

    Relevant candidates will have strong computational skills and have demonstrated extensive experienced with analyzing deep-sequencing data, comparative genomics and statistics. Fluency with at least one general purpose programming languate (e.g. Perl or Python), a language for statistical computing (e.g. R), proficiency with bash/shell scripting in LINUX/UNIX environments for using high performance clusters, and knowledge of HTML/JavaScript for building web-based data interfaces.

    Excellent problem solving, independent thinking, communication skills and scientific curiosity are critical. Working knowledge (and desire to learn) how experimental datasets are generated, appreciation for biological variability, technical artifacts, and, experimental validation of computational conclusions, and teamwork between dry/wet lab are fundamental to the projects.

    Minimum requirement of Master's degree with at least two years of relevant research genomics/NGS experience.

    PREFERENCES

    Postdoctoral fellows or BA/MS level candidates seeking experience before graduate school will be considered.

    LOCALE

    New York City

    COMPENSATION

    NIH grant funded position. Postdoctoral fellows are offered a generous salary and comprehensive benefits package including full medical for themselves and all dependents and subsidized housing nearby. www.mskcc.org/educ[...]urces

    HOW TO APPLY

    Please send motivation letter including details of prior research experience, CV, and contact information of three references to laie[at]mskcc.org.

    DEADLINE

    Position is available and applicants will be considered until filled.

    POLICY

    MSKCC is an Equal Employment Opportunity/Affirmative Action Employer.

    Submitter

    Applicants must be eligible to work in the us.

    BACKGROUND

    A world renowned institute in Boston are looking for a Senior Software Engineer to join an applied genomics software and data sciences group, focused on enabling cancer genomics research and precision cancer medicine. This role will help to build a new open-source software to enable precision cancer medicine.

    The Senior Software Engineer should have 3-5 years software experience and an interest in applying their skills to tackling problems in human health. This position will allow you to contribute to projects within cancer genomics, software, and medicine. This team are going through extensive growth and are looking for people to join them in the next 4-6 weeks.

    The current group of bioinformaticians, software engineers and leaders are focused on mining of cancer genomic datasets, matching patients to clinical trials, and building cloud-based infrastructure for sharing of immunologic data.

    RESPONSIBILITIES

    • Design and develop software, databases and interfaces for analyzing and manipulating genomic and immunologic data, and matching patients to clinical trials.
    • Work towards the paradigm of a microservices architecture where services communicate via APIs.
    • Orchestrate cloud-based services via modern devops frameworks.
    • Develop in Python while adhering to the best practices of automated testing at all steps and code reviews.
    • Build and maintain cloud based data processing workflows, incorporating open source tools for scheduling, monitoring and resource management.

    REQUIREMENTS

    • Bachelor's or Master's Degree in Computer Science or a related field
    • 3-5 years of software engineering experience
    • 3-5 years of Python coding experience
    • Working knowledge of relational and non-relational databases, especially MongoDB
    • Strong interest in contributing to biological research with clinical applications
    • Ability to meet deadlines and efficiently multitask is a must.
    • Experience with containerization of software (Docker, Kubernetes, etc.)
    • Experience in modern software development technologies, including distributed versioning systems, continuous integration, and Agile programming practices
    • Candidates must demonstrate excellent communication skills, outstanding personal initiative and the ability to work effectively as part of a team.

    HOW TO APPLY

    This position is available immediately and I would love to hear from you if you are interested. Please apply to this advert and attach your resume or send through your resume to jpage[at]pararecruit.com

    Keywords: Software Engineer, Precision Medicine, Cancer Genomics, Software Engineering, Bioinformatician, Python, Boston
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