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    BACKGROUND

    We are seeking to augment our award-winning biomedical analytics team. This opportunity is immediate, and we are looking for a contractor that is able to contribute immediately to ongoing projects.

    RESPONSIBILITIES

    Contribute to cutting edge NIH-funded research.

    REQUIREMENTS

    M.S. degree or 3 years bioinformatics experience, Python skills, and familiarity with GenBank, UniProt required. Reactome, GO, and HPO familiarity a plus.

    TERMS

    This is a Contractor/Consultant position.

    LOCALE

    Cambridge, MA

    COMPENSATION

    Good rates, flexible schedule.

    HOW TO APPLY

    Email resume to careers[at]iomics.us

    DEADLINE

    Seeking to fill immediately.

    DESCRIPTION

    Project title: Single-cell analysis of viral infection

    In the laboratory of Dr. Andreas Bergthaler at the CeMM Research Center for Molecular Medicine in Vienna, Austria, we study pertinent pathophysiological questions linked to viral infections, inflammation and immunity. A major aspect of our research is the integration of data-driven approaches to our biological research at the host-pathogen interface and pathology. We have acquired extensive, in-depth knowledge of host responses to viral infection emphasizing complex interactions between different organs and the immune system (e.g. Lercher A et al. Immunity 2019 DOI: doi.org/10.1[...]0.014; Baazim H et al. Nature Immunology 2019 DOI: doi.org/10.1[...]397-y; Bhattacharya A et al. Immunity 2015 DOI: doi.org/10.1[...]0.013). In this context, we look for an ambitious Master student with Bioinformatics background to model the dynamics of viral infection at the single-cell level.

    As a Master student in the Bergthaler lab, you will be co-supervised by the Senior Data Analyst Dr. Alexandra Popa. You will analyze single-cell data from virus infected organs, build robust machine learning models to label cells as well as their dynamics across infection timelines and perform analyses on interaction and biological pathways of the observed changes.

    As a member of the Bergthaler team, you will be part of cutting-edge research projects and will have the opportunity to model and integrate multiple types of data, from single-cell transcriptomics to proteomics and metabolomics. As a member of the host institution CeMM, you will be integrated in a highly collaborative environment and benefit from in-house generated large datasets of next-generation sequencing, proteomics and metabolomics. You will also be part of the vibrant community of bioinformaticians and attend bi-weekly bioinformatics meetings at CeMM.

    The Lab: The principal investigator Dr. Bergthaler received training in premier laboratories at the University and ETH Zurich, University of Tokyo and at the Institute for Systems Biology in Seattle. His team consists of ten members representing seven nationalities and different scientific backgrounds, who closely collaborate across projects. The Bergthaler lab is supported by competitive funding from the European Research Council (ERC), the Austrian Science Fund (FWF) and the Austrian Academy of Sciences.

    Lab Twitter account: twitter.com/Bergthalerlab Lab website: www.bergthaler1.at

    The Institute: CeMM is a biomedical research institute of the Austrian Academy of Sciences and provides a collaborative and dynamic environment for its employees from more than 45 nationalities. CeMM aims to promote equality of opportunity for all with the right mix of talent, competences, and potential and thus we welcome applications from candidates with diverse backgrounds. More information: cemm.at

    The Location: Austria's capital Vienna is located in the heart of Europe and ranks as one of the most attractive cities worldwide. Vienna hosts one of the headquarters of the United Nations, which together with many academic institutions and companies results in a vibrant melting pot of expat communities who may enjoy, for example, numerous cultural and culinary occasions or the nearby outdoors of the Vienna Woods.

    HOW TO APPLY

    Please submit your application at cemm.jobbase.io/job/hkqgru9i and include a cover letter, CV, academic transcripts and contact details of three referees. Deadline for application is 15.3.2020. Applications will be reviewed on a rolling basis. Starting dates are flexible.

    Submitter

    BACKGROUND

    Genomics England have a very interesting and challenging role available for a Senior Rare Disease Analyst, skilled in statistical and human genetics to join their world-leading team.

    To build on the success of the 100,000 Genomes Project, Genomics England are launching a new NHS Genomic Medicine Service. Through 7 Genomic Laboratory Hubs this offers equitable access to the 55 million people in England to the latest genomic medicine and research. This will lead to faster diagnosis and personalised medicine.

    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 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 analyst role is part of a highly motivated Bioinformatics team, working as part of a small team responsible for rare disease analysis.

    RESPONSIBILITIES

    Key accountabilities include:
    • Benchmarking tools for quality control, processing and analysis of whole genome sequence data, e.g., alignment, variant callers for variants of different size ranges
    • Performing custom computational analysis for a range of projects in rare disease/germline samples
    • Developing and prototyping new features for rare disease/germline genome analysis in collaboration with internal and potentially external stakeholders
    • Collaborating with software developers responsible for converting prototypes to production pipelines
    • Establishing general bioinformatics resources for day-to-day use by colleagues

    REQUIREMENTS

    Skills required:
    • MSc or PhD with experience of working within Rare Diseases or Bioinformatics/Computational Biology and Systems Biology or equivalent work experience
    • Good knowledge in one or more areas of human DNA analysis, such as rare disease genomics, family based analysis, genetic association testing, risk score prediction, structural variation, pharmacogenomics, typing of complex genomic regions such as HLA/KIR
    • Good knowledge of statistics and/or machine learning, and ideally some quantitative background (e.g. physics, computer science, or maths). These skills could also have been developed, for example, through a PhD in computational biology, statistical genomics, or statistical genetics.
    • Practical knowledge of high throughput sequencing algorithms and available resources. Experience with full cycle of analysing NGS data from sequencing QC to annotation and prioritization of variants.
    • Strong programming skills (Python, R); ability to develop codes as a part of team
    • Excellent technical writing skills
    • A demonstrable ability to cope under pressure and deliver to deadlines
    • Ability to communicate effectively within a multidisciplinary team
    • Flexible and co-operative approach to colleagues
    • Ability to work independently and to show initiative within a team
    • Ability to prioritise and balance competing demands

    COMPENSATION

    There are some great benefits on offer with this role 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: Rare, Disease, Analyst, Cancer, WGS, WES, Genomics, Bioinformatics, Python, Pipelines, Statistics, Testing, Writing, Variants, Alignment, Statistical, Genetics, NGS, London

    Submitter

    BACKGROUND

    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 senior level analyst role is part of a highly motivated Bioinformatics team, working as part of a small team responsible for cancer analysis.

    RESPONSIBILITIES

    Your responsibilities will include:
    • Monitoring quality of WGS data
    • Benchmarking tools for cancer WGS analysis
    • Performing computational analyses for a range of projects
    • Developing and implementing new features for cancer sequencing data analysis
    • Establishing general bioinformatics resources for day-to-day use by colleagues

    REQUIREMENTS

    You will need to meet the following requirements:
    • MSc or PhD (or equivalent experience) in Bioinformatics or Cancer Molecular Biology or equivalent work experience
    • Good knowledge of cancer genomics
    • Solid skillset in Bioinformatics and experience of working as a computational biologist
    • Practical knowledge of NGS algorithms and available resources for cancer bioinformatics
    • Experience with full cycle of analysing NGS data from sequencing QC to annotation and prioritization of variants
    • Experience with handling large data sets and setting pipelines
    • Strong programming skills (Python, R); ability to develop codes as a part of team
    • Practical knowledge and understanding of statistics
    • Excellent technical writing skills
    • A demonstrable ability to cope under pressure and deliver to deadlines
    • Ability to communicate effectively within a multidisciplinary team
    • Flexible and co-operative approach to colleagues
    • Ability to work independently and to show initiative within a team
    • Ability to prioritise and balance competing demands

    COMPENSATION

    There are some great benefits on offer with this role 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: Bioinformatics, Genomics, London, WGS, WES, Cancer, NGS, Molecular, Biology, Computational, QA, QC, Analyst, Python, R, Statistics, Somatic, Pipelines
    Opportunity: Software Engineer @ EMBL -- Hamburg, Germany
    Submitted by EMBL Recruitment; posted on Tuesday, February 11, 2020

    BACKGROUND

    We are seeking to recruit an enthusiastic software engineer who wishes to develop and maintain the software controlling high-end instruments and the associated large-volume flows of data, a crucial element for enabling Structural Biology. At EMBL Hamburg an exciting opportunity has arisen for a Software Engineer to work in the field of "Big Data" management affiliated to the beamline instrumentation team. EMBL is operating an Integrated Facility for Structural Biology at the PETRA III synchrotron radiation source at DESY, Hamburg. The core of the facility is formed by three X-ray beamlines providing state-of-the-art conditions for X-ray crystallography and small-angle X-ray scattering experiments and a protein crystallisation facility. The facilities are open to the international scientific community and hundreds of users visit them every year.

    RESPONSIBILITIES

    You will participate in the design, implementation, documentation, maintenance, and continuous improvement of the data acquisition systems and the integrated beamline control. Tasks will range from cutting edge data management of large data volumes created by high frame rate area detectors, integration of real-time data analysis and visualization, instrument server programming, scripting of experimental flows to further development and operation of the beamline high-performance computing and storage infrastructure. You will work in an international team of technicians, engineers and scientists and will support user operation at the beamlines which can include also off-hours work on short notice.

    REQUIREMENTS

    Applicants should:
    • Have a master or an equivalent degree in software engineering, computer science or a related discipline
    • Have a minimum of 2 years experience in control software and/or application programming of scientific instruments
    • Be acquainted with multithreaded programming and client-server applications in a distributed, primarily LINUX based control environment
    • Have proven skills in C/C++, Python and expertise in software development tools
    • Have excellent communication skills to collaborate in an international and multidisciplinary team of scientists and engineers. The working language is English.

    PREFERENCES

    We are Europe's flagship research laboratory for the life sciences – an intergovernmental organisation performing scientific research in disciplines including molecular biology, physics, chemistry and computer science. We are an international, innovative and interdisciplinary laboratory with more than 1600 employees from many nations, operating across six sites, in Heidelberg (HQ), Barcelona, Hinxton near Cambridge, Hamburg, Grenoble and Rome. Our mission is to offer vital services in training scientists, students and visitors at all levels; to develop new instruments and methods in the life sciences and actively engage in technology transfer activities, and to integrate European life science research. Please note that appointments on fixed term contracts can be renewed, depending on circumstances at the time of the review.

    LOCALE

    Hamburg, Germany

    HOW TO APPLY

    Please apply via: www.embl.de/jobs[...]c[]=0

    DEADLINE

    11/03/2020

    BACKGROUND

    John A. Burns School of Medicine (JABSOM) at the University of Hawaiʻi is seeking a Bioinformatics Specialist in support of the Bioinformatics Core at the Department of Quantitative Health Sciences.

    JABSOM is ranked at No. 56 in research, and in #55 in Primary Care in 2020 Best Medical School Rankings. Our Bioinformatics core also supports the University of Hawaiʻi Cancer Center which is the only National Cancer Institute-designated cancer center in Hawaiʻi and the Pacific.

    Regular, Full-Time, RCUH Non-Civil Service position with the John A. Burns School of Medicine (JABSOM), Office of Bioinformatics Core, Department of Quantitative Health Sciences, located at the University of Hawaiʻi (UH) at Manoa, Kaka'ako Campus on Honolulu, Hawaiʻi.

    RESPONSIBILITIES

    Analyzes high-throughput, microarray, next- and third-generation sequencing "omics" data, including data from genomics, transcriptomics, proteomics, epigenomics, metabolomics, and metagenomics experiments. Interacts closely with physician scientists and bioscience researchers to facilitate precision medicine development by analyzing and interpreting vast amounts of "omics" and clinical data. Assists in the preparation of grant applications. Writes peer-reviewed abstracts, publications, and manuscripts. Contributes to data management and research methods development. Oversees graduate students and undergraduate assistants. Conducts training workshops and courses on Bioinformatics with the PI and other bioinformaticians. Focuses on NIH (R-01) funded translational medicine study and identifying biomarkers for early detection of cancer and prediction of clinical outcomes of cancer treated with different strategies. The projects are highly valuable for clinical use with potential industrial application as well as with great basic scientific knowledge.

    REQUIREMENTS

    Education/Training: Master or Doctor Degree from an accredited college or university in Bioinformatics, Computational Biology, Molecular Biology, Biochemistry, Computer Science, Statistics, Engineering or a related field.

    Experience: Experience using statistics and bioinformatics software. Experience in UNIX operating systems, or equivalent. Experience working in bioinformatics projects. Experience with high-performance computing environments and computer programming. Experience writing peer-reviewed abstracts and publications.

    Ability /Knowledge/Skills: Knowledge of advanced bioinformatics techniques applicable to clinical research. General knowledge of medical terminology. Knowledge of human genetics and the next generation sequencing data analysis. Working knowledge of at least one (1) programming language (such as R or Python). Ability to be flexible, work on multiple tasks and meet deadlines. Ability to communicate effectively both orally and in writing. Ability to teach bioinformatics concepts to students and non-experts. Ability to implement components of a bioinformatics software pipeline to analyze next generation sequencing and microarray data. Ability to handle multiple tasks and demands. Strong analytical skills.

    Post Offer/Employment Condition: Must be able to pass a post offer criminal background check.

    PREFERENCES

    Experience with biomarker and machine learning, running programs in HPC and integrative "omics" data analysis.

    TERMS

    Continuation of employment is dependent upon program/operational needs, satisfactory work performance, availability of funds, and compliance with applicable Federal/State laws. However, this is a core staff scientist position, the position is relatively stable.

    LOCALE

    Honolulu, HI, USA

    COMPENSATION

    Salary is competitive and commensurate with qualifications.

    HOW TO APPLY

    Please go to www.rcuh.com and click on "Job Postings.". The position ID# is 220060. You may also submit your application including cover letter, resume and supervisory references to dengy[at]hawaii.edu

    DEADLINE
    March 06, 2020

    Submitter

    BACKGROUND

    This is a very interesting role with a fast-moving global pharma company focused on the discovery and development of innovative medicines and solutions to transform the lives of people living with severe diseases.

    The genetics group within this company work globally across both the Drug Discovery and Clinical Development functions, with a focus on leveraging genetics to support target identification and validation as well as clinical development projects i.e. pharmacogenetics.

    RESPONSIBILITIES

    The role will be responsible for forming the bridge between the Genetics group and the local Discovery and Clinical Development groups in Braine-l'Alleud, Belgium, leading efforts to ensure interpretation and extraction of maximal value from results. The ability to run analyses, such as PheWAS, on specific platforms will be required.

    The successful candidate will support the development and implementation of the Genetics strategy, with a focus on the pharmacogenetic component. By working with the Therapeutic Areas and Biomarker Leaders, the incumbent will provide expert leadership and support in ensuring that genetics is being systematically, but optimally applied across the drug development portfolio. The successful candidate will also lead efforts to ensure integration of genetics data with other data sets, using machine learning approaches, to ensure a holistic approach is used to extract maximal value from the data.

    This post holder will be a key member of a highly motivated and dynamic multidisciplinary project team consisting of geneticists and computational biologists. As part of the Data and Translational Sciences, and the Translational Medicine groups, the candidate will have access to, and work with, the required complementary functions including bioinformaticians, data scientists, biomarker experts and clinical development teams.

    Key accountabilities include:
    • To develop cross-functional relationships, ensuring all projects are informed and supported by genetic data
    • To lead and deliver projects for Therapeutic Areas and Early Clinical Development
    • To support development, implementation and integration of pharmacogenetics across the company, and work with Early Development teams and Biomarker Leaders
    • To generate, interpret and follow up on data
    • To work with the Genetics team to generate data to support projects, including running in silico analyses and coordinating wet lab work as required

    REQUIREMENTS

    Key competencies include:
    • Direct experience of the application of genetics and genetic approaches to drug discovery and development
    • Direct experience of working within multidisciplinary projects teams within the Pharmaceutical sector
    • Direct experience of devising, implementing and leading genetics strategies to support clinical development programs i.e. pharmacogenetics. Experience with protocol/ICF development is a plus.
    • Direct experience of generating, analysing and using genetic data generated through multiple platforms, including next generation sequencing (NGS) and genome-wide association studies (GWAS). Direct experience of interpreting and contextualizing genetic data for non-geneticists.
    • Problem solving skills
    • Experience/understanding of approaches and methods in functional genomics
    • Experience/understanding of ML/AI approaches

    COMPENSATION

    There are some great benefits on offer with this role including a competitive salary, strong 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: Genetics, Lead, Pharmacogenetics, Pharma, Drug, Discovery, Clinical, Proteomic, Belgium, Transcriptomic, Statistics, Machine, Learning, AI, Biomarkers, Bioinformatics, GWAS, PheWAS, NGS

    BACKGROUND

    The International Agency for Research on Cancer (IARC) is the specialized cancer agency of the World Health Organization (www.iarc.fr). The objective of the IARC is to promote international collaboration in cancer research. The Agency is inter-disciplinary, bringing together skills in epidemiology, laboratory sciences, and biostatistics to identify the causes of cancer so that preventive measures may be adopted and the burden of disease and associated suffering reduced. The research aim of the Biomarkers Group is to develop new approaches to identify, validate and implement biomarkers, to better understand the relationship of nutrition, environmental, and lifestyle factors (the exposome) with carcinogenesis. This position involves applying computational and high-resolution mass spectrometry for the analysis of biofluid samples to identify new biomarkers of exposure, food intake and of gut microbiota functions and to explore mechanisms linking them with cancer.

    RESPONSIBILITIES

    This postdoctoral scientist opportunity is immediately available within the Group, under the supervision of Dr Reza Salek, to develop informatics solutions. Familiarity with metabolomic data analysis approaches is essential and knowledge of omics data integration (implementing existing methods/solutions) and the willingness to tackle complex biological questions would be advantageous. The main objective is to develop a novel computational framework to integrate different knowledge-based metabolic computational networks (genome-scale metabolic networks, MS/MS similarity network, chemical similarity). This is an ANR-DFG funded project, across four different closely collaborating groups (IARC- France, IPB-Halle-Germany- France, INRA and Helmholtz Zentrum München -Germany). We have also obtained a plethora of cancer biofluid metabolomics data using high-resolution mass spectrometry (LC-MS) from large cohort studies, and we aim to validate the tools and to help interpret and publish the findings.

    REQUIREMENTS

    Candidates should hold a recent doctoral degree in a relevant field, be ambitious, self-motivated, very independent, with excellent English skills, and have a track record of productivity. The Biomarkers Group is composed of 18 persons highly skilled in the application of metabolomics to cohort studies and clinical trials. The Biomarkers Group laboratory is equipped with state-of-the-art high and low-resolution mass spectrometers.

    Skills required:
    • Candidates should have, ideally, a background in MS-based metabolomics data analysis.
    • Priority will be given to candidates with computational biology, bioinformatics or biostatistics degree or skills.
    • Candidates with a background in Life sciences who have a strong working informatic knowledge on R or Python with a keen interest in pursuing computational projects are welcome.
    • Candidates highly motivated to be in an English-speaking multinational team and environment are strongly encouraged to apply.

    PREFERENCES

    • Interest in complex problem solving such analyzing and integrating multi-omics data using computational and statistical approaches (mainly implementation of existing methods)
    • Understanding of genome-scale metabolic models
    • Experience in setting up workflow and data analysis pipelines within HPC environment and familiar with Nextflow, Galaxy or common workflow environments and Docker technologies

    TERMS

    This postdoctoral opportunity is initially for one year (project funding for 3 years and up to a maximum of 5 years) with the possibility of renewal, and is suitable for candidates who have completed a Ph.D., or who have acquired equivalent training. The IARC stipend is currently €2,820 per month (Net/month). The cost of travel for the Postdoctoral Scientist, and in certain circumstances for dependents, will be met, a dependent's allowance paid, and health insurance covered. IARC welcomes around 40 postdoctoral scientists, at any one time, distributed across its sixteen research groups. Postdoctoral scientists at IARC have access to a wide spectrum of scientific disciplines and to a unique network of collaborators across the world.

    LOCALE

    Lyon, France

    COMPENSATION

    The cost of travel for the Postdoctoral Scientist, and in certain circumstances for dependents, will be met, a dependent's allowance paid, and health insurance covered.

    HOW TO APPLY

    Applicants should send a CV, including a list of publications and a description of previous research experience, as well as the names and addresses of two academic referees, to:

    Dr. Reza Salek
    Biomarkers Group, Section of Nutrition and Metabolism
    International Agency for Research on Cancer
    150 Cours Albert-Thomas, 69008 Lyon, France
    email: Salekr[at]iarc.fr

    DEADLINE

    Until position is filled

    POLICY

    Applications from women and from nationals from low and middle-income countries are particularly encouraged. Compared with traditional postdoctoral fellowships, IARC Postdoctoral Fellows have many opportunities to establish an international network, become involved in multinational studies and consortia, and meet renowned researchers who are collaborating with or working at IARC. The programme is designed to provide young researchers with a strong foundation for a career in cancer research.

    DESCRIPTION

    The Institute for Biostatistics and Informatics in Medicine and Ageing Research at the Rostock University Medical Center (Germany) seeks a highly qualified candidate for a PhD scholarship with a focus on bioinformatics (NGS/omics) analyses.

    Your tasks:
    • Intervention effect analyses using omics data, specifically in a study of the effect of food on cellular senescence and health
    • Biomarker analyses using omics data, specifically in a study investigating cellular senescence and disease
    • Machine learning and network‐biology based analyses and data integration
    • Writing of scientific reports and papers
    What we offer:
    • Investigating the exciting biological mechanisms behind cellular senescence, ageing, microbiome changes and fibrosis
    • A stimulating diverse and international research environment, where your contribution can have a real impact
    • Funding for travelling, equipment, books, etc.
    What you need to bring to the table:
    • A master degree in bioinformatics or computer science or a related field in the medical/life/natural sciences
    • Programming/ scripting skills, e.g. in Java/ R
    • Experience in bioinformatics data analysis
    • High motivation to work in an interdisciplinary team spanning cancer, neuro, and ageing research
    • Strong communication skills (oral presentations and in writing)

    LOCALE

    For most of the year, Rostock (at the Baltic Coast) is a number one vacation area in Germany, with a very pleasant climate and nice beaches nearby.

    HOW TO APPLY

    If this describes you and your intentions then please send your application until 22.02.2020 in a single PDF document, consisting of:
    • Cover letter explaining relevant experiences, a brief statement of research interests, and qualifications
    • CV
    • Contact details of 2‐4 scientists who may write a letter of recommendation
    Please send your application to us, c/o Prof. Fuellen, bioinfo-jobs[at]med.uni-rostock.de. Please indicate "Rostock_PhD_Application" in the title of the e‐mail.

    BACKGROUND

    One programmer/systems admin position is available in the areas of bioinformatics and big data analytics.

    RESPONSIBILITIES

    Mandatory:
    • System administration (Linux) and operations / monitoring
    • Daily maintenance of servers and databases
    • Comfortable with programming in bash, Java and Python
    • Web technologies (Galaxy, J2EE/JSF, HTML5, Jquery)
    • Relational databases (RDBMS), such as MySQL and Postgres
    • NOSQL databases, such as MongoDB
    • Attention to detail, good communication and organizational skills and ability to work in a highly interactive group
    • Capable of getting multiple tasks assigned at once and making them all progress steadily
    Strong Assets:
    • Experience with cloud computing
    • Git version control system (e.g., BitBucket)
    • Applications containerization (e.g., Docker)
    • Basic knowledge of the various layers involved in web application development (full-stack)
    • Experience with computer hardware and file servers
    • Interest in the field of bioinformatics

    REQUIREMENTS

    The candidate is expected to have a BSc or MSc degree in Computer Science or Engineering with training and experience in the relevant areas.

    TERMS

    Full-time or part-time

    LOCALE

    McGill University, Montreal, QC Canada

    COMPENSATION

    40-50K (depending on experience)

    HOW TO APPLY

    To apply, submit a cover letter (1-2 pages, demonstrating fit with the position) and curriculum vitae (max 5 pages, outlining experience) to Dr. Soufan (othman.soufan[at]mcgill.ca). Please highlight in the cover letter how you meet the requirements and provide details about the related projects in the resume.

    DEADLINE

    March 31, 2020

    DESCRIPTION

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

    ELBE postdoctoral fellows

    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 (TUD), 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.

    Since 2012, the TU Dresden is one of eleven Excellence Universities in Germany.

    What we seek:
    The ELBE program seeks outstanding external candidates who bring new ideas, concepts, or systems to the Center. ELBE postdoctoral fellows pursue an interdisciplinary research project in collaboration with members of the CSBD. They develop and use theoretical or computational approaches to study biological systems in close collaboration with experimental groups at the MPI-CBG and the TUD. The CSBD is an office environment, but fellows can perform experiments in the labs of an experimental collaborator when a project requires it. Ideal candidates have backgrounds in physics, computer science, mathematics or a related discipline, with a strong interest in working in a cross-disciplinary life-science environment. In some exceptional cases, ELBE fellows are analytically-minded experimentalists in the field of cell or developmental biology, who work between a lab and a CSBD research group.

    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 28 May, 2020, with travel costs covered by the CSBD.

    DEADLINE

    Deadline for applications is 17 March, 2020.

    POLICY

    The Max Planck Society is an equal opportunity 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[...]ities.

    Submitter

    BACKGROUND

    This position is a great opportunity for a strong Bioinformatician to join a world-leading institute in their cancer therapeutics unit. The role focuses on the development and provision of broad, state-of-the art bioinformatics analysis to support drug discovery and will involve both applying bioinformatics and the development of pipelines to support these. The successful applicant will be exposed to, and contribute to, all aspects of drug discovery and will be responsible for supporting specific drug discovery projects, interacting with biologists, software developers and bioinformaticians.

    RESPONSIBILITIES

    • Evaluate and apply broad bioinformatics analysis expertise to support drug discovery in the CTU.
    • Contribute to drug discovery projects by analysing genomic, transcriptomic or proteomic data using established and state-of-the-art approaches.
    • Evaluate and tailor such approaches and create bioinformatics pipelines for specific drug discovery project requirements.
    • Deploy bioinformatics pipelines using scripting languages such as Perl/Python and statistical packages such as R.
    • Perform GSEA and other suitable downstream analyses required to help the biological interpretation of complex data with view to aid decision making in drug discovery projects.

    REQUIREMENTS

    • Proven work experience of applying bioinformatics analyses (2 years minimum)
    • Proven experience in analysing large scale genomic, transcriptomic or proteomic data
    • Proven experience in interpretation of large scale data including the application of Gene Set Enrichment Analysis (GSEA)
    • Proven experience of developing scripts to enable bioinformatics workflows
    • Proven experience in cancer informatics
    • Established skills in the application of broad bioinformatics analysis tools and databases including gene and protein sequence analysis and annotation tools
    • Skilled in using statistical analysis packages such as R or Matlab
    • Good working knowledge of Unix and shell/bash
    • Proven scripting skills using a scripting language such as Python and/or Perl
    • Good applied knowledge of complex bioinformatics pipeline suites including NGS analysis pipelines such as Broad Best Practice pipeline or good applied knowledge of proteomic analysis tools such as MASCOT, OpenMS or equivalent
    • Establishment and execution of bioinformatics pipeline on High-Throughput Computing infrastructure

    COMPENSATION

    There are some great benefits on offer with this role including a competitive salary, strong 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: Cancer, Genomics, Bioinformatics, NGS, Proteomics, Drug, Discovery, Transcriptomics, Pipelines, Perl, Python, Data, Science, Analysis, Workflows, Shell, Bash, HPC, Sutton, Surrey

    BACKGROUND

    This is a long-term contract position which offers:
    • Competitive salary with comprehensive benefit package
    • Opportunity to work at NIH, the world's foremost medical research center
    Learn more about what Kelly can do for you at www.kellygovernmentsolutions.com.

    Kelly Government is a strategic supplier and business partner to the federal government and its key suppliers. Through our partnership with the National Institutes of Health, Kelly Government offers administrative, IT, engineering, scientific, and healthcare professionals the opportunity to work with one of the most prestigious research organizations in the world. We are currently seeking a PhD level Bioinformatics Programmer to support the National Human Genome Research Institute in Bethesda, MD.

    RESPONSIBILITIES

    • Develop and maintain whole-genome and exome variant calling methodologies in support of multiple laboratories pursuing gene discovery, gene therapy, and related clinical research projects within NHGRI/DIR.
    • Serve as the lead scientific programmer for The Genome Ascertainment Consortium, a flagship effort aimed at improving our understanding of the phenotypic consequences of genetic variation and predicting genotypes from phenotypes. This effort involves numerous intramural research groups at NHGRI and other NIH ICs, as well as high-profile external clinical research partners.
    • Optimize variant calling pipelines to take advantage of the NIH Biowulf high-performance supercomputing environment, parallelizing per-sample processing steps and designing methodologies to increase processing speeds and reduce network overhead. This includes working directly with NIH high-performance computing team leadership at the NIH Center for Information Technology (CIT) to enable and ensure that any and all required infrastructure needs are in place for the successful execution of projects.
    • Develop, implement, and maintain new web-based genome browsers for visualizing aggregate genome and exome data, providing new functionality to NHGRI/DIR investigators and allowing for faster identification of mutations that may be involved in disease causation.
    • Work directly with the NIH Intramural Sequencing Center (NISC) to capitalize on the analysis and visualization of data derived from emerging sequencing methodologies. This includes new efforts pertaining to the detection and evaluation of copy number variants, genome structural variants, and chromosomal rearrangements that play a role in human disease but are difficult to analyze.
    • Actively interact with scientists in NHGRI/DIR laboratories to assess their needs with respect to massive (terabyte-sized) data sets, then develop concrete and tractable project plans for completing these projects.
    • Provide broad-based programming and analytic support for a wide variety of bioinformatics and genomic research projects. including the development of software pipelines for the processing and high-level analysis of next-generation sequence data, including chromatin immunoprecipitation (ChIP-seq) and RNA-seq data.
    • Share scientific information by writing portions of scientific manuscripts and presenting data in seminars and poster sessions.
    • Collaborate with staff on teaching activities, in both small- and large-group fora.
    • Provide one-on-one training to NHGRI/DIR bioinformatics trainees with regards to all aspects of developing new pipelines for the analysis of high-throughput data and the optimization of code for use in supercomputing environments.
    • Provide detailed project documentation so that all methodologies can be reproduced and applied to similar studies in the future.

    REQUIREMENTS

    • Ph.D. in genomics, bioinformatics, or a related discipline. Three (3) years of specialized experience plus a Master's degree considered to be equivalent to a Ph.D.
    • A minimum of (2) years of post-degree relevant bioinformatics experience, including demonstrated experience in running the GATK pipeline to call sequence variants and building warehouses to store, query, and display the resulting genotypes
    • Two (2) years professional experience programming in Perl, Python or an equivalent scripting language
    • Demonstrated experience in developing and deploying applications on UNIX or Linux platforms in a high-performance computing (HPC) environment
    • Strongly qualified applicants will also have:
      • Knowledge and experience with full-stack web application development, particularly using MongoDB, Python (Flask framework), and javascript (React, jquery)
      • Knowledge and demonstrated experience analyzing other types of next-generation sequencing data, (e.g., RNA-seq, ChIP-seq, or related data)
      • Demonstrated success in sharing scientific information, through the writing of scientific manuscripts and the oral presentation of data in seminars and poster sessions
      • Strong communications skills, both oral and written
      • Fluency in both written and spoken English
      • Excellent analytical, interpersonal, organizational and time management skills
      • Proven critical-thinking skills and demonstrated ability to manage and interpret large biological data sets

    LOCALE

    Bethesda, MD

    HOW TO APPLY

    Interested candidates should submit resumes to Ryan O'Toole, Scientific Recruiter, at ryao149[at]kellyservices.com.

    DEADLINE

    Open until filled

    BACKGROUND

    This is a long-term contract position which offers:
    • Competitive salary with comprehensive benefit package
    • Opportunity to work at NIH, world's foremost medical research center
    Learn more about what Kelly can do for you at www.kellygovernmentsolutions.com.

    Kelly Government is a strategic supplier and business partner to the federal government and its key suppliers. Through our partnership with the National Institutes of Health, Kelly Government offers administrative, IT, engineering, scientific, and healthcare professionals the opportunity to work with one of the most prestigious research organizations in the world. We are currently seeking a M.S or PhD level Database Manager with Bioinformatics experience to support the National Human Genome Research Institute in Bethesda, MD.

    RESPONSIBILITIES

    • Optimize and maintain best practice pipelines to call whole genome SNPs/indels/SVs. Impute genome wide genotypes using large scale reference genome panels where necessary.
    • Implement quality control measures to curate RNA-seq and ATAC-seq data (single cell and bulk), chip-seq, and develop pipeline to analyze the data.
    • Develop and maintain databases and datasets to track inventories of DNAs, RNAs, or tissue samples in the laboratory.
    • Prepare and submit various genomics data, including genotypes, next generation sequence reads of samples to NCBI databases, including dbGaP, SRA or GEO.
    • Provide broad-based programming and analytic support for a wide variety of bioinformatic and genomic research projects. Write custom scripts to analyze public or data generated in the lab to answer immediate questions.
    • Provide detailed documentation of custom scripts to allow efficient sharing.
    • Assist researchers with running third-party software, interpret results, and summarize findings.
    • Work on multiple projects concurrently with other laboratory members as needed.

    REQUIREMENTS

    • Two (2) years of experience in data management. Familiarity with computer platforms and statistical packages. Experience in creating data management tracking systems, error-checking procedures and back-up procedures to prevent loss of data. The ability to write programs in MATLAB and other languages to extract, analyze, and format data. Knowledge of Federal information technology policies and regulations.
    • Efficiency in working with Unix/Linux, ability to install software, and bash scripting
    • Fluency in writing scripts in Perl and/or Python, and R
    • Ability to use version control systems, including GitHub and the Subversion control system
    • Ability to visualize and generate figures to graphically represent complex data
    • Good collaborative work ethics in a group environment
    • Ability to quickly convert analysis ideas to implementation, and to multi-task on different projects
    • Excellent ability to document work being completed and to reproduce analysis results
    • Good communication and writing skills

    PREFERENCES

    Preferred skills and experience:
    • Ability to work with relational databases, including MySQL and Oracle
    • Knowledge of packaging software Snakemake and containers like Singularity, Docker
    • Interest or experience in bioinformatics or a degree in bioinformatics is preferred.
    • Experience in handling various types of sequence data, including SNP array, exome, ChIP-seq, RNA-seq, and whole genome data, single cell RNA-seq, ATAC-seq data
    • Familiarity with genomic public databases such as UCSC, dbGaP, Ensembl, and the SRA

    HOW TO APPLY

    Interested candidates should submit resumes to Ryan O'Toole, Scientific Recruiter, at ryao149[at]kellyservices.com.

    DEADLINE

    Open until filled.

    BACKGROUND

    The research group of Wolfgang Huber (www.huber.embl.de) at EMBL works on biological data science and mathematical / computational method development. The interdisciplinary and international team uses statistical data analysis and modelling to discover and understand biological principles and biomedical applications and has strong collaborations with researchers in basic biology and cancer research.

    About the project SMART-CARE:
    The SMART-CARE consortium is a collaboration between EMBL, the German Cancer Research Centre, the University Hospital Heidelberg, Heidelberg University and Mannheim University of Applied Sciences, that aims to develop new systems medicine approaches to battle cancer recurrence, using the integration of proteome and metabolome mass spectrometry approaches with other 'omics and clinical data. The consortium brings together clinical, mass spectrometry and computational expertise.

    Cancer recurrence is the main determinant of cancer related death and therefore a major global health problem. The surge of genomic technologies in clinical practice has brought great benefit in disease stratification, however genomic information alone is often insufficient to accurately predict or identify the dynamic process of disease progression. Systematic analyses of proteins and metabolites using mass spectrometry in combination with statistical data analysis and mathematical modelling promise a new generation of biomarkers that could be used to tailor personalized cancer therapy. There is a need to develop and establish powerful and standardizable pipelines for proteome and metabolome analysis in the clinical setting. The aim of the SMART-CARE project is to firmly establish mass spectrometry-based systems medicine technologies and data analysis methods and apply these to predict cancer recurrence across paradigmatic tumor entities and thus improve patient stratification.

    RESPONSIBILITIES

    You will be part of the Huber group at EMBL's Heidelberg site, participate in the SMART-CARE project and shape your own research profile by pursuing research in method development and collaborative analysis of novel datasets. Your activities will comprise the following:
    • Advanced statistical inference and biological model building: Compare the information content of the different data types, in terms of their ability to map patient and disease heterogeneity, and predict tumor recurrence and treatment response. Use and adapt methods for data integration developed within the group, e.g. the Multi Omics Factor Analysis (MOFA) or further develop state of the art methods from statistical learning.
    • Data-type specific "preprocessing" and feature engineering.
    • Automated data quality assessment / control (QA/QC) and visualization.
    • Publish computational methods and biological discoveries in scientific articles, and publish scientific software as, e.g., R/Bioconductor packages.

    REQUIREMENTS

    A PhD or equivalent qualification in a quantitative science (mathematics, statistics, physics, computer science, computational biology). We are looking for a range of talents, which should include some of the following: solid training in mathematical statistics, understanding of high-dimensional statistics, machine learning and Bayesian approaches; experience in biological data science and data-driven discovery; scientific programming, and good software engineering skills. Applications from "newcomers" into biology are welcome.

    PREFERENCES

    You are excited by making or contributing to biological discoveries, you are interested in interdisciplinary science, enjoy collaborative work and like to communicate concepts and results to other scientists in different fields of research. You are interested in understanding and comparing methods in computational biology and in pushing them forward with your own ideas.

    LOCALE

    Heidelberg, Germany

    COMPENSATION

    Stipend

    EMBL is an inclusive, equal opportunity employer offering attractive conditions and benefits appropriate to an international research organisation with a very collegial and family friendly working environment. The remuneration package comprises a competitive salary, a comprehensive pension scheme, medical, educational and other social benefits. You will be included in the EMBL Postdoctoral Programme. A child care facility is available on campus.

    HOW TO APPLY

    Please apply online through our website: www.embl.de/jobs[...]en_GB

    DEADLINE

    28 February 2020
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