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    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

    Submitter

    DESCRIPTION

    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.

    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.

    DESCRIPTION

    Two postdoctoral positions are available immediately in the laboratory of Dr. LuZhe Sun, Dielmann Endowed Chair in Oncology and Professor in the Department of Cell Systems & Anatomy, Long School of Medicine, UT Health San Antonio.

    Applicants should have demonstrated experience in applying bioinformatics tools for cancer and stem cell research.

    The successful applicants will investigate the molecular mechanisms of hepatocellular carcinogenesis in Latinos or aberrant aging mammary stem cells.

    The positions are jointly funded by grants from NIH and Clayton Foundation for Research. Persons with newly granted doctoral degrees are encouraged to apply.

    COMPENSATION

    Attractive stipend and fringe benefits will be offered.

    ABOUT US

    The UT Health San Antonio is a Tier One research institution and the department enjoys a dynamic research program that offers opportunities for multidisciplinary collaborative investigation. San Antonio is a dynamic and multicultural city with a relatively low cost-of-living and an outstanding cultural and educational environment.

    HOW TO APPLY

    Please email your CV to SUNL[at]UTHSCSA.EDU.

    POLICY

    All postdoctoral appointments are designated as security sensitive positions. UT Health San Antonio is an Equal Employment Opportunity/Affirmative Action Employer.

    Submitter

    BACKGROUND

    An exciting opportunity has arisen for a strong Bioinformatician to join a renowned institute in the field of Genomics and Bioinformatics. The organisation has an outstanding history of applying cutting-edge genomics technologies to the discovery of novel disease genes as well as successfully translating genomics into the clinic to inform diagnosis and treatment of patients.

    The ideal candidate will be familiar with a variety of methods for generating and analysing human genome sequence data. Experience using a range of genomic bioinformatics pipelines to provide comprehensive annotation and interpretation of variants, including single nucleotide, copy number and structural variants, is required. Knowledge of publicly accessible databases and resources is expected, as is the programming expertise to develop and troubleshoot new pipeline elements to improve speed and accuracy of annotation. In addition, familiarity with use of other 'omics data sets to provide a detailed catalogue of information supporting candidate disease variants would be desirable.

    RESPONSIBILITIES

    • Develop and apply bioinformatics pipelines for analysis of human genome sequencing data including alignment, calling, annotation and interpretation of single nucleotide, copy number, non-coding and structural variants. Develop novel algorithms to improve the performance of the pipeline and address annotation of variants in regulatory and non-coding regions.
    • Conduct analysis of genome sequencing data from rare diseases and cancer patient samples leading to identification of disease causing variants.
    • Contribute to maintenance of the pipeline and data management ensuring quality and version control and integrity and security of genome sequencing datasets.
    • Contribute to Genomics England (GEL) national 100,000 Genomes programme through analysis and interpretation of GEL data, liaising with GEL bioinformaticians and Oxford PIs. Provide bioinformatics expertise on Genomics England Clinical Interpretation Partnerships (GeCIPs) as required and appropriate. Conduct special data analyses in close collaboration with GEL and bioinformaticians from other GeCIP-associated research groups.
    • Incorporate protein informatics and pathway analyses to support a comprehensive assessment of variants and integrate data from other `omics as required.
    • Conduct own research projects in development of novel bioinformatics tools and algorithms and/or contribute to disease specific research projects within the group. Write up results for publication in high quality journals and present research results at international meetings. Contribute to grant applications, taking the initiative to identify sources for funding research projects.
    • Keep abreast of methodology developments relevant to the field, including evaluation of commercial or other software packages for analysis, annotation and interpretation of sequencing data, and integrate with existing data analysis pipelines.
    • As appropriate for the projects, assist with translation of sequencing technology / pipelines into clinical use. Contribute ideas and communicate effectively with other bioinformaticians, geneticists, clinical researchers, statisticians and clinical informatics staff.
    • Provide written reports on activity for internal use and for funding agencies.
    • Communicate frequently and effectively with the BRC project teams, including laboratory scientists, clinicians and PIs, to discuss the bioinformatics requirements of projects, report data, review results and ensure that the tasks are completed satisfactorily. Participate in lab group meetings and contribute to discussions at these.

    REQUIREMENTS

    • A PhD in Bioinformatics or Statistical Genetics
    • Strong postdoctoral experience in analysis and interpretation of genome sequencing data to include full spectrum of single nucleotide and structural variants, copy number abnormalities as well as assessment of variants in regulatory or non-coding regions
    • Excellent programming skills in languages such as Perl, C/C++, R, Python, Java, SQL or similar
    • Experience of improving and maintaining bioinformatics pipelines and demonstrable commitment to quality and version control and secure data management
    • Knowledge of genetic variant databases such as Decipher, ClinVar, Clingen and disease-specific databases to inform variant annotation
    • Familiarity with protein informatics to inform assessment of impact of variants on proteins' secondary and tertiary structures, protein-protein interactions and protein expression
    • Demonstrable experience in conducting independent research delivering high quality scientific outputs and with proven ability to write up scientific findings in peer-reviewed journals
    • Ability and willingness to assess relevant new bioinformatics developments relevant to genomic and protein bioinformatics, including commercial software packages, and apply them efficiently, as appropriate to improve data analysis
    • Willingness to contribute to collaborative programmes including Genomics England and DDD and analyse data within the environments and according to the regulations of these programmes
    • A high degree of self-motivation and initiative and ability to both work independently and collaborate within teams to meet project deadlines
    • High level of attention to detail, self-organisation and timeliness
    • Excellent communication skills (both written and oral) with the ability to communicate effectively at all levels (of technical knowledge)
    • Enjoy working in a fast moving and motivated scientific environment

    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: Bioinformatics, Statistical, Genetics, Genomics, Rare Diseases, Cancer, Omics, NGS, WGS, WES, Germline, Somatic, RNA, Machine Learning, Clinical, Variants, Python, Perl, R, Senior, Oxford

    Submitter

    BACKGROUND

    An exciting opportunity has arisen for a Lead Bioinformatician to join a renowned institute in the field of Genomics and Bioinformatics. The organisation has an outstanding history of applying cutting-edge genomics technologies to the discovery of novel disease genes as well as successfully translating genomics into the clinic to inform diagnosis and treatment of patients.

    You will be a senior bioinformatician, familiar with a range of sequencing methods and data (including Illumina, Oxford Nanopore) and be an expert in developing and applying custom bioinformatic tools and pipelines for annotation and interpretation of human genomes. Development of novel methods to interrogate non-coding and regulatory regions and integrate `omics data sets will be an important focus. An interest in machine learning methods to explore patterns in the complex genome sequencing datasets would be highly relevant. The postholder will be responsible for collaborating with scientists across a range of disciplines as well as supervising research scientists and bioinformaticians to achieve this.

    RESPONSIBILITIES

    • Lead development of innovative approaches to genome sequence analysis to provide a bespoke bioinformatics pipeline for alignment, calling, annotation and interpretation of single nucleotide, copy number, non-coding and structural variants from human genome sequence data.
    • Conduct analysis of genome sequencing data from rare disease and cancer patients incorporating other `omics data sets (eg transcriptomics, metabolomics) as required, to support a comprehensive assessment of variants.
    • Explore opportunities to develop and apply machine learning approaches to explore complex patterns in the genome sequencing datasets available to the group.
    • Conduct independent research projects in development of novel bioinformatics tools and algorithms and/or contribute to disease specific research projects within the group, identifying emerging areas of research.
    • Play a leading role in the contribution to the UK's national Genomics England (GEL) 100,000 Genomes programme, through analysis and interpretation of GEL data. Collaborate with GEL bioinformaticians and Oxford PIs and provide bioinformatics expertise on Genomics England Clinical Interpretation Partnerships (GeCIPs)
    • Supervise a growing team of bioinformaticians and research scientists undertaking WGS data analysis. Co-ordinate activities and meet with members on a regular basis to ensure familiarity and consistency of methods and utilisation of pipelines. Provide motivation and supportive leadership in a team working environment.
    • Take responsibility for maintaining the bioinformatics pipeline and ensuring standards of quality and version control are attained.
    • Write up research results for publication in high quality journals and present these at national/international meetings. Lead applications for grant funding in own research area.
    • Identify and evaluate methodology developments relevant to the field, including evaluation of commercial or other software packages for analysis, annotation and interpretation of sequencing data, and integrate with existing data analysis pipelines.
    • As appropriate for the projects, lead the translation of bioinformatics pipelines into clinical use, liaising with clinical teams to achieve this.
    • Communicate frequently and effectively with project teams, including laboratory scientists, clinicians and PIs, to discuss the bioinformatics requirements of projects, report data, review results and ensure that the tasks are completed satisfactorily.
    • Participate in lab group meetings and contribute to discussions at these.

    REQUIREMENTS

    • A PhD in Bioinformatics or Statistical Genetics
    • Strong postdoctoral experience in analysis, annotation and interpretation of genome sequencing data to include single nucleotide and structural variants, copy number abnormalities as well as assessment of variants in regulatory or non-coding regions. Experience of a wide range of publicly accessible resources and databases to support this
    • Excellent programming skills in languages such as Perl, Python, Java, C/C++, R or similar
    • Experience of supervising bioinformaticians and/or lab scientists and clear evidence of developing and managing collaborative teams
    • Proven ability to develop novel bioinformatics tools and algorithms for analysis of genetic data
    • Experience of implementing, improving and maintaining bioinformatics pipelines and troubleshooting problems. Demonstrating experience of developing quality and version control standards and secure data management
    • Familiarity with protein informatics to inform assessment of impact of variants on proteins' secondary and tertiary structures, protein-protein interactions and protein expression
    • Track record of independent research with proven ability to write up scientific findings in peer-reviewed journals and in contributing to grant applications
    • Demonstrable experience of assessing new developments in the field, including commercial software packages and applying them efficiently
    • Willingness to provide bioinformatics leadership for the Theme's contributions to national collaborative programmes including Genomics England and DDD and analyse data within the environments and according to the regulations of these programmes
    • Excellent communication skills (both written and oral) with the ability to communicate effectively at all levels (of technical knowledge)
    • A high degree of self-motivation and initiative and ability to both work independently and as a team member to meet project deadlines
    • Familiarity with expression and pathway analyses
    • Experience with analysis and integration of multi-omics datasets including RNASeq and metabolomics
    • Success in being awarded grant applications to support research projects

    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: Bioinformatics, Statistical, Genetics, Genomics, Rare Diseases, Cancer, Omics, NGS, WGS, WES, Germline, Somatic, RNA, Machine Learning, Clinical, Variants, Python, Perl, R, Lead, Senior, Oxford

    Submitter

    BACKGROUND

    Paramount Recruitment are currently representing a biotechnology company in the Paris area who are looking to hire a talented new Senior Biostatistician / Statistician on a permanent contract.

    This company specialises in the development of innovative drugs to support personalised therapies in metabolic diseases and other related disorders. With new global partnerships, advanced clinical programs and research projects, the business is thriving and continues to grow their team in Paris.

    RESPONSIBILITIES

    In this position you will be working within a small team of Analysts, Biostatisticians and Bioinformaticians who are responsible for the development and maintenance of a bioinformatics pipeline for metagenomics research. As a Senior Biostatistician you will be in charge of biostatistical analyses for metagenomic research projects on the drug discovery and biomarkers programs.

    Additional responsibilities:
    • Supervise and perform biostatistical analysis across different projects.
    • Develop new statistical methods for metagenomic data analysis and discovery.
    • Define and compile statistical analysis plans according to studies protocols and main objectives.
    • Write statistical reports and documentation.
    • Present and discuss statistical analysis plans and results both internally and with external partners or CROs.

    REQUIREMENTS

    We are keen to hear from candidates who have strong quantitative skills, knowledge and understanding of biomarker discovery and good multi-omics analysis experience. This company have doubled in size since 2016, and have been established for almost 10 years. You will experience the best of both worlds here, working in an exciting start up environment, but with the added security of global partnerships and venture capital and strategic investors.

    Experience required:
    • Experience with quantitative metagenomic data analysis and/or multi-omics analysis
    • Experience with biomarkers discovery and development from -omics data, and with validation analysis from e.g. qPCR assays data
    • Good knowledge of Python programming
    • Proficient in R, with a solid expertise using the major statistical methods and packages, including advanced data visualisations and automated documentation generation with Markdown.
    • Fluent in English and professional level of French
    • Excellent communication and presentation skills in English
    • Biological background with a good understanding of functional genomics

    HOW TO APPLY

    Please apply to this advert or send your CV to jpage[at]pararecruit.com if you are interested in this position! All applicants must be eligible to work in France.

    Keywords: Senior Biostatistician, Drug Discovery, Metagenomics, Personalized Medicine, Biomarker Discovery, Statistics, Biostatistics, Omics Data, Biotechnology

    DESCRIPTION

    The Center for Systems Biology Dresden (CSBD) calls for applications for

    ELBE postdoctoral fellowships

    The ELBE postdoctoral fellows program fosters theoretical and computational approaches to biological systems and provides an ideal springboard to an independent research career.

    What we provide:
    The CSBD provides 2-3 year fully funded positions in an international and cross-disciplinary research environment. ELBE postdoctoral fellows benefit from close collaborations with scientists at the Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), the Max Planck Institute for the Physics of Complex Systems (MPI-PKS), and the Technische Universität Dresden (TU Dresden), and a stimulating and inspiring atmosphere, see www.csbdresden.de

    They will have full access to state-of-the-art research facilities and infrastructure on the campus. Dresden is a vivid and international scientific center, with a large number of research institutions that are collaborating under the DRESDEN-concept umbrella. Its position as an outstanding location for research and science is recognized world-wide, and since 2012, the Technische Universität Dresden is one of eleven Excellence Universities in Germany.

    What we seek:
    We seek outstanding young researchers with a strong interest and background in using theoretical and computational approaches to study biological systems and processes. Ideal candidates have a doctoral degree in physics, computer science, mathematics or a related discipline. A strong commitment to work in a multi-disciplinary environment between biologists and theoreticians is expected. ELBE postdoctoral fellows are encouraged to collaborate with more than one research group and are given the opportunity to include experimental work in their projects.

    HOW TO APPLY

    For details about the application procedure, please visit our website www.csbdresden.de/join[...]tdoc/

    Selection of ELBE Fellows is based on scientific merit with two application cycles per year. Short-listed candidates should be prepared to join a selection symposium held in Dresden on May 15, 2019, with travel costs covered by the CSBD. Deadline for applications is March 10, 2019.

    POLICY

    The Max Planck Society is an equal opportunities employer. Disabled individuals are strongly encouraged to apply. The Center for Systems Biology, the MPI-CBG and the MPI-PKS aim to increase the number of women in scientific positions, therefore female applicants are particularly welcome. For more information on our efforts to balance family and career please see www.csbdresden.de/abou[...]ties/
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