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    Several PhD project opportunities starting immediately in bioinformatics, genomics, and statistical genetics.

    BACKGROUND

    We are seeking highly motivated students to fill three (3) PhD positions and join the landmark Aboriginal Heritage Project (www.adelaide.edu.au/acad/ahp/), which is reconstructing Indigenous Australian history from a remarkable collection of hair samples and ethnographic data. The project cuts across traditional research boundaries, incorporating cutting-edge statistical and population genetic analyses with anthropological, archaeological and archival research, whilst maintaining long-term engagement with Indigenous communities throughout Australia. The first results from the project revealed a remarkably deep and abiding population structure across Australia tracing back to the peopling of the continent 50kya (Tobler et al. Nature 2017;544:180 – 184).

    REQUIREMENTS

    The candidates must have, as a minimum, an excellent undergraduate academic record and meet the English Language Proficiency (ELP) requirement. The call is open to international and domestic students with backgrounds in bioinformatics, mathematics, statistics, computer science, population/quantitative genetics, or a related field. While a background in biology is desirable, it is not a prerequisite for success, as training opportunities in genetics, human evolution, molecular biology, or other related areas can be provided during the PhD. Successful candidates will be involved in the analysing genomic datasets from Indigenous populations across Australia, New Guinea and Indonesia, with special emphasis on adoption and expansion of statistical tools to reconstruct the genetic history of the original human migrants into Australia.

    PREFERENCES

    Good computational and analytical skills are of high importance and a successful candidate would be competent in one or more of the following:
    • Statistical analysis of large datasets and/or mathematical modelling
    • Fluency in using Linux systems, with a prior hands-on experience with Bash scripting
    • Programming in a scripting language such as Python and/or R

    LOCALE

    The PhD will be situated in the Australian Centre for Ancient DNA (ACAD; www.adelaide.edu.au/acad/), a highly dynamic group based at the University of Adelaide, with world leading researchers in ancient DNA, human evolution, epigenetics, microbiomics, and megafaunal extinction.

    HOW TO APPLY

    Interested applicants are encouraged to send a CV (including names and contact details of three references) and a cover letter to Dr Ray Tobler (raymond.tobler[at]adelaide.edu.au) or Dr Yassine Souilmi (yassine.souilmi[at]adelaide.edu.au).

    BACKGROUND

    We are currently seeking a highly motivated, independent but team-oriented postdoctoral fellow with strong bioinformatics background. Our group applies functional and comparative genomics techniques to investigate the molecular basis of symbiosis and adaptation in corals and related cnidarian model organisms. The respective projects are focused on NGS data analysis and include RNAseq, genome and transcriptome assembly as well as bisulfite and ChIP-Seq data.

    The successful candidate will join the Group of Prof. Manuel Aranda at the Red Sea Research Center of the King Abdullah University of Science and Technology (KAUST). Strong computational skills in the areas of Perl or Python programing as well as the proficient use of open source software for data processing and analysis of NGS data are required.

    RESPONSIBILITIES

    • Handle and analyze NGS data (Illumina, PacBio)
    • Develop, assess, and adapt new technologies, protocols, and software
    • Write proposals and manuscripts for publication
    • Manage data, such as distribution and backup
    • Assist and train students

    REQUIREMENTS

    • PhD with emphasis in bioinformatics, molecular biology, or genetics
    • Must have bioinformatics skills and strong understanding of basic biology, genomics, high-content data analysis, and genome databases
    • Experience in programming, databases and Unix/Linux (Python or Perl, R,)
    • Experience with bioinformatics software such as assemblers, mappers, and general tools
    • Next-gen sequencing pipeline experience

    LOCALE

    KAUST is a dynamic new university campus and campus community in Saudi Arabia that opened in September 2009. The campus is located directly at the Red Sea, near Jeddah. More information is available at www.kaust.edu.sa.

    COMPENSATION

    The position includes a highly competitive tax free salary, accommodation, annual leave, and health insurance.

    HOW TO APPLY

    Please send cover letter summarizing your qualifications and interests, a curriculum vitae, and the names and contact information for 2 references to manuel.aranda[at]kaust.edu.sa. Applications that do not fulfill requirements outlined above will not be considered.

    DEADLINE

    Open till filled

    Submitter

    BACKGROUND

    The Center for Pediatric Cancer Systems Biology at the University of Texas Southwestern Medical School (UTSW) will use a systems biology approach to address fundamental questions on the metastatic cascade in Ewing sarcoma, as paradigm for pediatric cancer.

    This center brings together experts in the fields of pediatric oncology and genetic model organisms (James Amatruda), pathology (Stephen Skapek), single-cell genomics (Gary Hon), quantitative live-cell imaging (Gaudenz Danuser) and systems biology (Yang Xie) to remove the technical barriers to understanding the metastatic cascade within pediatric cancers.

    RESPONSIBILITIES

    We are seeking applicants for an integrated and dynamic postdoctoral training program to develop new paradigms in single-cell cancer functional genomics.

    REQUIREMENTS

    Specifically, we are seeking individuals with significant experience in genomics and bioinformatics, particularly statistical modeling and machine learning. We especially value motivated, creative, adventurous, and collaborative individuals. We are firmly committed to training these scientists to succeed as future independent investigators.

    COMPENSATION

    Post-doctoral position at NIH payscale.

    HOW TO APPLY

    To apply, please submit a CV, a brief statement of interests / accomplishments, and a list of references to Gary.Hon[at]utsouthwestern.edu and Yang.Xie[at]UTSouthwestern.edu .

    BACKGROUND

    The Duke Human Vaccine Institute and the Duke Center for HIV/AIDS Vaccine Immunology & Immunogen Discovery (CHAVI-ID), providing national and international leadership in the fight against major infectious diseases such as HIV, influenza, and malaria, are currently recruiting for a highly motivated individual to join our team. The Duke Human Vaccine Institute (DHVI) is an interdisciplinary, interdepartmental institute dedicated to the study of basic and translational science required to understand host-pathogen interactions that can be translated to vaccines against human diseases. DHVI comprises a team of highly interactive investigators that have expertise in virology, immunology, computational biology, molecular biology, microbiology and animal models.

    RESPONSIBILITIES

    We are seeking a candidate for the position of bioinformatician with a background in computational structural biology or sequence analysis or both. The computational structural work performed will involve structural modeling and analysis of antibody-antigen interactions, molecular simulation, as well as the implementation of computational protein design algorithms for improving vaccine immunogen designs. The sequence analysis-based work performed by the bioinformatician will involve developing and implementing innovative computational approaches for the analysis of large sequence datasets generated by next generation sequencing platforms, assistance in the creation of a software pipeline and database system for analyzing and cataloging antibody sequences as well as designing and implementing a high-performance computing pipeline for analyzing large-scale transcriptomics.

    REQUIREMENTS

    The position requires a Master's degree in bioinformatics, computer science, computational biology, or a related field. A PhD is a plus. Highly proficient programming skills are required. A minimum of five years relevant experience is required including experience in a UNIX/Linux environment, the development of computational methods and programs for the analysis of genomic and/or structural data, web-based bioinformatics tools, public domain biological databases and software tools for sequence and structural analysis. Experience with Perl or Python, R or MATLAB, web design, database systems, high performance computing environments, and statistics is also desired. Proficiency in C++ programming is highly preferred.

    HOW TO APPLY

    Candidates should apply to requisition 401326486 on the Duke employment website and send a cover letter and current CV to:

    Duke Human Vaccine Institute
    Email: dhvicareers[at]dm.duke.edu
    (Please reference "BIO-KW" in subject line of email)

    POLICY

    Duke University is an Affirmative Action/Equal Opportunity Employer committed to providing employment opportunity without regard to an individual's age, color, disability, genetic information, gender, gender expression, gender identity, national origin, race, religion, sexual orientation, or veteran status.
    Opportunity: Cancer Analyst @ Company in London, UK
    Submitted by Eugene Mc Daid; posted on Thursday, September 21, 2017

    RESPONSIBILITIES

    This senior level analyst role is part of a highly motivated Bioinformatics team and is responsible for:
    • Cancer analysis
    • Exome Sequencing / WGS
    • Performing computational analyses for a range of projects
    • Implementing programs for high-throughput sequencing data analysis
    • Establishing general bioinformatics resources for day-to-day use by colleagues

    REQUIREMENTS

    Required skills, knowledge and experience:
    • Experience of working as a computational biologist, delivering bioinformatics database solutions
    • Solid skillset in Bioinformatics
    • Coding knowledge and some statistical experience (Python coding experience)
    • Good knowledge of cancer genomics
    • MSc or PhD (or equivalent experience) in Biology or related discipline
    • Several years' experience of developing algorithms and software to analyse large data sets
    • Post doctorate with at least 2-3 years' experience of working in this field
    • 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
    • Excellent technical writing skills
    You must be eligible to work in the UK to apply for this role.

    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, Cancer, Analyst, Genomics, Python, Algorithms, WGS, WES, High Throughput Sequencing, London

    BACKGROUND

    An exciting Software Analysis and Development opportunity has become available to further develop our bioinformatics software stack to help in our goal of understanding human cancer and ageing. The position will be based in the IT Team in the Cancer, Ageing and Somatic Mutation (CASM) Division at the Wellcome Trust Sanger Institute.

    The role involves working closely with scientific/IT staff within CASM to develop novel analysis strategies and software. The analysis software needs to be efficient, visually appealing and interpretable by the scientific/clinical community.

    This position would suit a Bioinformatician/Software Developer who enjoys developing software tools for the analysis of large genomic data sets. We are looking for an individual who enjoys working in a multi-disciplinary team environment to help solve complex IT issues which will ultimately aid our understanding of mutational processes in humans.

    REQUIREMENTS

    • Good degree in the areas of Bioinformatics, Mathematics, Physics or Computer Science with a scientific background
    • Software development skills (e.g. Perl and/or Python)
    • Experience of statistical analysis in bioinformatics (e.g. R and/or Julia)
    • Experience of handling Next Generation sequencing data
    • Enjoy working as part of a team

    PREFERENCES

    • Software development using a compiled language (e.g. C,C++,Java)
    • LSF or Open Grid scheduling software
    • Experience of OpenStack, VMware or Amazon Web Services (AWS)
    • Experience of working in an Agile Software Development Group
    • ORACLE/MySQL/NoSQL databases
    • Web development using Perl, Java, HTML(5), CSS, JavaScript
    • Background in cancer genetics
    • Ability to work independently, organise own workload and meet tight deadlines
    • Ability to communicate ideas and results effectively
    • Keen to learn and share ideas and knowledge
    Although experience of bioinformatics would be a distinct advantage, applications are welcome from enthusiastic and committed graduates or candidates from other fields who wish to pursue a career in bioinformatics whilst carrying out a challenging and rewarding role. The CASM Support IT team has developed a suite of algorithms to analyse genetic variation in cancer genome data. This includes software to detect tumour genetic variation (e.g. single-base substitutions, structural rearrangements, copy number changes) and the ability to annotate the resulting variants and mine the data for interesting patterns and signatures (github.com/cancerit).

    TERMS

    Permanent contract.

    COMPENSATION

    Salary Range: up to £38,000 - £39,729 plus excellent benefits.

    Our Benefits include: Defined Contribution Pension Scheme, Group Income Protection, Healthcare scheme, Childcare Vouchers, Workplace Nursery and 25 days Annual Leave, increasing by one day per year up to a maximum of 30, plus Bank Holidays. We also have a gym, two cafes, dining facilities, and a free campus bus service. Our thriving Sports and Social Club provides many opportunities to meet with people working across the campus. Wellcome Trust Sanger Institute welcomes applications from all candidates irrespective of age, disability, gender, gender identity, sexual orientation, race, religion or belief, or marital or civil partnership status. Please include a covering letter and CV with your application.

    ABOUT US

    The CASM Division has led the way in the systematic analysis of cancer genomes by using the human genome sequence and high throughput mutation detection techniques to identify somatically acquired sequence variants/mutations and hence identify genes critical in the development of human cancers (www.sanger.ac.uk/genetics/CGP/). The Sanger Institute is a charitably funded research centre focused on understanding the role of genetics in health and disease. We use state of the art large-scale genomic approaches to drive world-leading projects to uncover the basis of genetic and infectious disease. Our goal is to provide results that can be translated into diagnostics, treatments or therapies that reduce global health burdens. The Institute is located near Cambridge, UK on the stunning Wellcome Genome Campus. This growing and dynamic site is the British hub of genomic science. It hosts the European Bioinformatics Institute (EBI), Open Targets, a Biodata Innovation Centre and will soon host Genomics England Limited's 100,000 Genomes Sequencing Centre. The Campus is also home to Wellcome Genome Campus Connecting Science. Connecting Science inspires new thinking, sparks conversation and supports learning by drawing on the ground-breaking research taking place on the Campus. Its mission is to enable everyone to explore genomic science and its impact on research, health and society.

    HOW TO APPLY

    By clicking on the following link: jobs.sanger.ac.uk/wd/p[...]26492

    DEADLINE

    Closing date for applications:22nd October 2017, however applications will be considered and reviewed on an on-going basis and therefore the post may be filled before the deadline.

    BACKGROUND

    Why choose Cancer Research UK Manchester Institute?
    The Cancer Research UK Manchester Institute (www.cruk.manchester.ac.uk), an Institute of The University of Manchester (www.manchester.ac.uk), is a world-leading centre for excellence in cancer research. The Institute is core funded by Cancer Research UK (www.cancerresearchuk.org), the largest independent cancer research organisation in the world. We are currently situated at the internationally-renowned life sciences campus at Alderley Park in Cheshire England, 15 miles from Manchester, a vibrant and dynamic city surrounded by beautiful countryside.

    We are partnered with The Christie NHS Foundation Trust (adjacent to the CRUK Manchester Institute, Paterson Building) in South Manchester (www.christie.nhs.uk), one of the largest cancer treatment centres in Europe. These factors combine to provide an exceptional environment in which to pursue basic, translational and clinical research programmes.

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

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

    RESPONSIBILITIES

    About the role:
    We are currently looking for a computational biologist within the Clinical and Experimental Pharmacology Group (CEP) and the newly established Manchester Centre for Cancer Biomarker Sciences (MCCBS). The aim of this post is to contribute to the success of translational research aimed at next generation sequencing (NGS) of nucleic acids obtained from patient blood samples. The overall goal of this project is to identify information that can be used to optimise cancer patient treatment selection.

    REQUIREMENTS

    About you:
    The successful applicant should have a degree in computational biology, mathematics or related discipline or substantial relevant experience analysing genomics data. Effective communication skills and the ability to work effectively within a highly collaborative environment are also required.

    TERMS

    Duration: Until 31.03.2022

    COMPENSATION

    Salary in the range of £19,600 - £31,900 (dependent upon experience) per annum

    HOW TO APPLY

    For any informal enquires about this post, please contact Ged Brady via email: ged.brady[at]cruk.manchester.ac.uk

    To apply for this position please visit our website: www.cruk.manchester.ac.uk/Jobs?jobId=302

    For applicants who are unable to download this information from our website, please contact HR department on 0161 306 0840, email: jobs[at]cruk.manchester.ac.uk to have this information sent by post.

    Job Ref: MI/17/50

    DEADLINE

    Closing date: 18 October 2017.

    BACKGROUND

    The computational biologist position will be opened in March 2018 for three years (renewed each year) in the laboratory of research on molecular basis of Acute Myeloid Leukemia headed by anERC / ATIP-AVENIR team leader Dr. Alexandre PUISSANT ( thepuissantlab.jimdo.com ).The Puissant laboratory deciphers molecular mechanisms involved in leukemia development in pre-clinical mouse models of AML. Unbiased in vivo screening approaches are deployed in order to provide new therapeutic strategies to treatAML. Large-scale shRNA screening, genetic, biochemical, cell biological, as well as genome-wide approaches (WES, RNA-Seq, ChIP-Seq) are currently used in this lab.

    RESPONSIBILITIES

    We are looking for a highly motivated candidate with a strong background in data analysis, statistics and in programming in R and/or Python, and an extensive experience in NGS data analysis (RNA-seq, ChIP-seq,WES). In addition, the candidate should able to run comparative marker, GSEA, ssGSEA, EdgeR/RIGER, and ICA analyses, be familiar with the use of cBioPortal or MSigDB datasets, and be able to implement their data on GENE-E/Morpheus and IGV softwares.

    Applicants should hold a PhD degree in Computational Sciences or related disciplines (or have recently submitted their thesis with scheduled defense).

    LOCALE

    The Puissant laboratory is housed at the Jean Bernard Center (INSERM U944) which is located at the Saint-Louis Hospital campus in Paris, France . The research developed in this institute encompasses a broad spectrum of fields, including cancer genomics, cancer biology and leukemia research. Most studies carried out in the unit have implications in translational research, together with clinical groups of the Saint-Louis Hospital. Our laboratory benefits from a direct access to the core facilities including: a recently extended animal facility, a sequencing facility (Mi-seq, Hi-seq, and Next gen-seq technologies), and a flow core facility.

    HOW TO APPLY

    Thanks to send your application (in French or English) to alexandre.puissant[at]inserm.fr before February 1st 2018, by including in one single pdf file (applicantName_application2018.pdf):
    • Description of the main past achievements and skills of the candidate (max 2 pages)
    • Full Curriculum Vitae
    • Contact details of three individuals who can be contacted for recommendation letters

    DEADLINE

    01 February 2018

    DESCRIPTION

    We are recruiting an ambitious computational postdoc for a collaboration project that seeks to revolutionize cancer therapy by targeted, drug-induced degradation of important regulatory protein complexes. The project combines the expertise of two labs at the CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences in Vienna, integrating large-scale data generation using cutting-edge technologies (chemical biology, epigenome sequencing, single-cell screening, mass spectrometry, imaging, etc.) with a deep interest in bioinformatics methods development and computational approaches in systems medicine.

    The Project:
    We pursue a systems-level understanding of gene regulation in leukemia, combining novel chemical biology, functional genetic screens, and cutting-edge sequencing technology. Using a powerful method for degrading any protein of choice in a matter of minutes (Winter et al. 2015 Science; Erb et al. 2017 Nature; Winter et al. 2017 Mol Cell), we will induce specific perturbations of gene regulation in leukemia cells, and we will monitor the cellular responses using high-throughput assays such as PRO-seq, ATAC-seq, ChIPmen-tation, and single-cell sequencing. Based on these data, the successful candidate will establish regulatory network models using causal modeling techniques, which will provide the basis for functional validations and for the identification of potential drug targets. In summary, the project will develop and apply computational methods to establish a model of cell state deregulation in leukemia and to provide a rationale for pharmacologic degradation in cancer therapy.

    The Candidate:
    We are looking for highly motivated and academically outstanding candidates who want to pursue a scientific career in the fields of computational biology and/or functional (epi-)genomics. A strong candidate may have a background in the computational sciences (bioinformatics, statistics, physics, engineering, etc.) and some prior experience with collaborative research in high-throughput biology. In the same way, we are considering applicants with a background in medicine or in biology (e.g., functional genomics, chemical biology, human genetics, molecular medicine, etc.) who have strong quantitative skills and a keen interest in pursuing systems medicine projects.
    We offer a monthly gross salary of EUR 3.626 which will be paid out 14 times a year.

    Bock Lab (epigenomics.cemm.oeaw.ac.at):
    The Medical Epigenomics Lab at CeMM pursues an interdisciplinary and highly collaborative research program aimed at understanding the cancer epigenome and establishing its utility for precision medicine. Led by Christoph Bock – a computational biologist, ERC grantee, and recipient of the Overton Prize of the International Society of Computational Biology (2017) – the lab pursues several lines of research:
    • Epigenomics. Many diseases show widespread deregulation of epigenetic cell states. As members of the International Human Epigenome Consortium, we use epigenome sequencing to dissect the epigenetic basis of cancer and immune disorders.
    • Technology. Groundbreaking biomedical research is often driven by new technologies. Our lab is therefore heavily invested into technology development, including single-cell sequencing, CRISPR screens, and epigenome editing.
    • Bioinformatics. New algorithms and advanced computational methods allow us to infer epigenetic cell states from large datasets, in order to reconstruct the epigenetic landscape of cellular differentiation and complex diseases.
    • Diagnostics. New technologies (genome sequencing, mobile devices, etc.) provide important information for personalized medicine. We develop and validate assays and algorithms for translating the value of digital medicine into routine clinical practice.
    Winter Lab (cemm.at/rese[...]roup/):
    The mission of our new lab at CeMM (started 2016) is to devise pharmacologic strategies to understand oncogenic gene regulation and to innovate novel therapeutic approaches to modulate transcriptional dysregulation in cancer. In particular, we are developing targeted protein degradation as a new paradigm to therapeutically disrupt, probe, and understand molecular machines involved in oncogenic transcription (Winter et al. 2015 Science; Erb et al. 2017 Nature; Winter et al. 2017 Mol Cell). Targeted protein degradation allows elimination of proteins within minutes after ligand exposure, hence enabling us to derive mechanistic insights at an unprecedented kinetic resolution. We are combining such acute perturbations with genome-scale technologies that report on gene activity, genome structure and chromatin function in a quantitative fashion. We expect that our strategy uncovers a new level of a functional under-standing of oncogenic transcription. Integrative analysis will enable us to model disease-relevant transcriptional circuits and gene-regulatory networks. This will rationalize novel therapeutic targets that are based on an unprecedented understanding of the transcriptional wiring of cancer cells.

    The Institute (www.cemm.at):
    CeMM is an international research institute of the Austrian Academy of Sciences and a founding member of EU-LIFE. It has an outstanding track record of top-notch science (last five years: >10 papers in Nature/Cell/Science/NEJM, >25 papers in Nature/Cell sister journals) and medical translation. With just over a hundred researchers, CeMM provides a truly collaborative and personal environment, while maintaining critical mass and all relevant technologies. Research at CeMM focuses on cancer, inflammation, and immune disor-ders. CeMM is located at the center of one of the largest medical campuses in Europe, within walking distance of Vienna's historical city center. A study by "The Scientist" placed CeMM among the top-5 best places to work in academia world-wide (the-scientist.com/2012[...]-2012). Vienna is frequently ranked the world's best city to live. It is a United Nations city with a large English-speaking community. The official language at CeMM is English, and more than 40 different nation-alities are represented at the institute. CeMM aims to promote equality of opportunity for all with the right mix of talent, competences and potential. We welcome applications from candidates with diverse backgrounds.

    HOW TO APPLY

    Please apply online (cemm.jobbase.io/job/57p8zjud) with cover letter, CV, academic transcripts, and contact details of three referees. Applications will be reviewed on a rolling basis. Any application received by 15 October 2017 will be considered. Start dates are flexible.

    BACKGROUND

    Paramount are working in partnership with Genomics England to expand their team in order to deliver success with the 100,000 Genomes Project. This is a challenging and fast moving project with the aim to carry out whole genome sequencing on 100,000 participants. Genomics England works with key partners to collect, transport, store, quality check and sequence the samples from participants. The aim for this project is to create a new genomic medicine service for the NHS – transforming the way people are cared for. Patients may be offered a diagnosis where there wasn't one before. In time, there is the potential of new and more effective treatments.

    The Technical Project Manager will be part of the Platform Engineering team and accountable for the delivery of projects to achieve agreed outcomes within timescale, cost and quality constraints. This includes acquiring resources and coordinating the efforts of team members and third-party contractors or consultants in order to deliver projects according to plan. The Technical Project Manager will also define the project's objectives and oversee quality control throughout its life cycle.

    RESPONSIBILITIES

    Key Accountabilities:
    • Drive the end-to-end delivery of projects to time, cost and quality criteria
    • Manage Platform Engineering dependencies received from other project teams, including hardware and software solutions
    • Develop and own the plan for the project. Manage progress against plan, budget and resource requirements to achieve project objectives
    • Ensure effective collaboration between all teams and individuals involved in the project e.g. the business, all parts of Genomics England, external suppliers / partners as appropriate
    • Ensure all stakeholders/teams are aware of each other's priorities and activities
    • Proactively manage risks, assumptions, issues and dependencies, ensuring that these are identified, mitigated or escalated as necessary to achieve key milestones
    • Identify potential changes to project scope and manage via the change control process
    • Clarify roles and expectations for all project participants and hold partners, suppliers and colleagues to account
    • Provide reporting on project status at the agreed frequency. Produce materials for project governance groups
    • Develop and implement a communications plan to engage key stakeholders within and outside of Genomics England to drive their sustained and active commitment to success
    • Manage suppliers and lead tender and selection processes where required
    • Support the management of contracts with partners and suppliers to meet key performance indicators and agreed targets

    REQUIREMENTS

    • Experience of managing diverse projects and large initiatives
    • Strong record of leadership and successful delivery of complex projects across multiple stakeholder groups while under tight timelines
    • Commercial contract and partnership experience
    • Project management and report writing, analytical and reporting skills
    • Independent, highly organised and good with senior stakeholders
    • Must have demonstrated excellent ability to interface with customers and internal teams ideally in infrastructure and development environments
    • Be able to work cross-functionally through many teams to execute goals and set and meet milestones

    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: Technology, Project Manager, London, Genomics, Bioinformatics, Commercial, Leadership, Infrastructure.

    BACKGROUND

    The diagnostic of cancer in a patient begins with a clinical examination followed by a blood test, medical imaging and often ends with the histopathological analysis of a tumor biopsy in order to establish the cancer type and the therapeutic strategy. One of the objectives of the France Genomic Medicine 2025 plan is to improve diagnostic and treatment selection by also taking into account genomic profiling obtained from NGS sequencing. However, recent research from the NCI Clinical Proteomic Tumor Analysis Consortium (CPTAC) demonstrated that the integration of proteomic profiles with genomic information, now referred to as "proteogenomics," reveals subtypes of cancers that are inaccessible by NGS.

    Our project is a transverse initiative (proteogenomics.wordpress.com) between three CEA French research centers: CNRGH-LBI (National Human Genome Research Center – Bioinformatics lab), BIG-EDyP (Biosciences and Biotechnology Institute of Grenoble – Proteomics lab), LIST-LADIS (Laboratory of Embedded Systems and Technology – Big data analysis lab) and BIFI-COSNET lab (Institute for Biocomputation and Physics of Complex Systems – Complex systems and networks lab) from the University of Zaragoza to contribute to the emergence of proteogenomics in precision medicine. Our final goal is to implement a "patient-centered" software solution capable of structuring, integrating and interrogating genomic and proteomic profiles from the same tumor in order to improve diagnostic and therapy. We will develop methods that capture and model the deregulations of molecular networks at stake in cancer, to identify patient-specific network perturbations and exploit them to provide better diagnostic.

    We already achieved significant progress on two in silico developments (not yet published) which can be considered as building blocks to our project:
    • We designed and implemented a graph-based database to structure and interrogate multi-omic tumoral data. This database was constructed using the triple-store technology to allow writing complex queries and to facilitate aggregation of public biological data repositories.
    • We developed a proteogenomic workflow to analyse proteomic data using a priori information extracted from transcriptome profiling. This approach, evaluated on a cancer cell line, allowed us to identify genetic alterations translated at the proteome level.

    RESPONSIBILITIES

    The post-doctorate will develop a methodology to explore patient-specific perturbations on molecular networks and particularly on signaling pathways caused by genetic alterations (single nucleotide variants, aberrant transcript splicing) identified from proteogenomic profiling of tumor biopsies. He will leverage complexity of these multi-omic data to assess the impact of genetic variants on multiple regulatory dimensions, from transcriptional to post-translational levels.

    To reach this goal, the applicant will first infer tissue-specific multidimensional gene networks to model normal cell activity from public genomic and proteomic resources. Then, he/she will analyse onco-proteogenomic data to identify patient-specific genetic alterations affecting its genome, transcriptome, proteome or phosphoproteome. Then, he/she will integrate multi-omic perturbations caused by genetic alterations into tissue-specific multidimensional gene networks. He/she will finally interrogate these networks to reveal multidimensional perturbations, to extract biological subnetworks, to identify genes with maximum influence on the process of perturbation spreading and to classify patients into cancer subtypes. These investigations will be carried out using the multilayer network formalism and algorithms which were already successfully applied for integration of omics data.

    Resources:
    This methodology will be developed using large-scale omics data made publicly available by several international research consortia (GTEX, CPTAC, NIH Epigenomics Roadmap) and tested on proteogenomic profiles in-house produced from cancer cell lines. Moreover, data storage and computational needs required by this large-scale project will be available at the CEA HPC infrastructure.

    REQUIREMENTS

    The applicant should have a PhD in bioinformatics/computational biology or related fields. He/she should be experienced in omics fields with at least one of these fields of expertise: bioinformatics, data integration or network science, and strong interest for all of them. Moreover, programming experience is required.

    LOCALE

    The recruited young researcher will be hosted by the BIG-EDyP laboratory in Grenoble and will evolve within a multidisciplinary research team. He/she will also spend research periods in collaborating laboratories to optimize progression of the research project.

    COMPENSATION

    Funding for a one-year post-doctoral contract is already available with gross annual salary range from about €41,000 to €58,000 depending on experience. We are looking for a candidate motivated to apply for additional funding at the CEA Enhanced Eurotalents Programme (eurotalents.cea.fr).

    HOW TO APPLY

    If you are interested by this opportunity please send your CV, a motivation letter and names of referees to christophe.battail[at]cea.fr.

    Bioinformatics, Leadership, Competitive salary, Relocation package!

    A fantastic new Director level position has become available with a Top research-driven pharmaceutical company in South-West Germany. If you're looking for a professional challenge within the field of Genomics & Computational Biology with attractive prospects and feel you can add to the company's success through your leadership experience, then this job could be a good fit!

    The company is looking for a Director Computational Biology & Genomics to join their Research department located in an idyllic town in South-West Germany. This role would suit someone from either an academic or pharmaceutical/biotech background who has the relevant scientific knowledge as well as extensive leadership experience.

    RESPONSIBILITIES

    Your main tasks and responsibilities will involve:
    • Leading and managing the research group Computational Biology & Genomics (~20 reports) within the department Target Discovery Research
    • Holding the entire responsibility for generation of necessary RNA/DNA-sequencing data using NGS or single cell analysis (internal lab and CRO), statistical and biological analysis and interpretation of internally produced and externally available biomedical data
    • Contributing to the generation of New Therapeutic Concepts and discovery of novel biomarkers in collaboration with Therapeutic Areas Immunology & Respiratory, Cardio-Metabolic, CNS-diseases, Cancer Immunology and Research Beyond Borders
    • Setting up and managing a network of external collaborations with the focus on New Therapeutic Concept generation and biomarker discovery
    • Accountable for budget and headcount of the Group Computational Biology & Genomics
    • Contributing to the coordination of global Computational Biology data and expertise platforms in collaboration with other Boehringer Ingelheim research centers in Vienna (AUT) and Ridgefield (US)

    REQUIREMENTS

    The ideal Director should be/have:
    • Ph.D. in bioinformatics, biology or a closely related field and a strong background in target discovery based on omics data
    • At least 5 years of experience within the field of Computational Biology in a pharmaceutical industry or biotech background
    • Experience in one of the above mentioned Therapeutic Areas is highly advantageous.
    • Additionally, applicants show a proven track record of several years of successfully scientific working.
    • Very strong leadership skills and networking capabilities and enjoy working in interdisciplinary teams
    • Excellent communication and presentation skills in English language complete the profile.

    HOW TO APPLY

    Please get in touch if you'd like to apply and we can discuss your suitability and the role in more detail. My number is +44 (0) 121 616 3469 and my email address is alauterjung[at]pararecruit.com. Look forward to hearing from you!

    Keywords: Bioinformatic*, Biology, Computational Biolog*,Target Discover*, Drug Discovery, Biomarker, Translational, Research, Cardiometabolic Disease Research, Cardio*, Immunology, Respiratory, Cardio*, CNS, Cancer, Alzheimers, Genomics, Computational Biology, Bioinformatic*, Deutschland, Germany, NGS, Next Generation Sequenc*, Collaboration*

    BACKGROUND

    A great opportunity is available with a world-leading Pharma company based in South Germany for a Director of Genomics and Computational Biology within the research department.

    RESPONSIBILITIES

    • As a Director you are overall responsible for leading and managing the research group Computational Biology & Genomics (~20 reports) within the department Target Discovery Research.
    • You will hold the entire responsibility for generation of necessary RNA/DNA-sequencing data using NGS or single cell analysis (internal lab and CRO), statistical and biological analysis and interpretation of internally produced and externally available biomedical data.
    • In your role you will contribute to the generation of New Therapeutic Concepts and discovery of novel biomarkers in collaboration with Therapeutic Areas Immunology & Respiratory, Cardio-Metabolic, CNS-diseases, Cancer Immunology and Research Beyond Borders.
    • You are responsible for setting up and managing a network of external collaborations with the focus on New Therapeutic Concept generation and biomarker discovery.
    • As a Director you are accountable for budget and headcount of the Group Computational Biology & Genomics.

    REQUIREMENTS

    • Ph.D. in bioinformatics, biology or a closely related field and a strong background in target discovery based on omics data
    • At least 5 years of experience within the field of Computational Biology in a pharmaceutical industry or biotech background
    • Experience in one of the above mentioned Therapeutic Areas is highly advantageous.
    • Additionally, applicants show a proven track record of several years of successfully scientific working.
    • Very strong leadership skills and networking capabilities and enjoy working in interdisciplinary teams
    • Excellent communication and presentation skills in English language complete the profile.

    COMPENSATION

    There are some fantastic benefits available with this role including a very competitive salary, generous relocation package and the opportunity to work with some of the smartest minds in this field.

    HOW TO APPLY

    If you are interested in this position and wish to discuss things further, please call Harvey Uppal on +44 (0) 121 616 3407 or via email at huppal[at]pararecruit.com

    Keywords: Principal Scientist, Director, Genomics, Computational Biology, Pharma, Life Sciences, Bioinformatics, In Silico, Therapeutics, Drug Discovery, Biomarker, Cardiometabolic, Cancer, Immunology, Neuroscience, Germany

    BACKGROUND

    Competitive salary, generous relocation package, great work-life balance!

    A fantastic, challenging new opportunity has become available with a Top Pharmaceutical company in Germany. This research-driven company is looking for talented Bioinformaticians/Computational Biologists/Scientists with NGS experience and a particular focus on Human Genetics (GWAS) to join their Research Department in South-West Germany. This position would suit someone who is looking to expand their career in the field of Human Genetics and has some previous experience in this field.

    RESPONSIBILITIES

    Your main responsibilities as a Scientist will include:
    • Working as an CompBio Expert within the Computational Biology Group together with members of the Therapeutic Area Partner function and members of the Computational Biology Core function
    • Establishing and developing new analysis strategies for RNA-Seq, single cell RNA-Seq and other NGS approaches
    • Overseeing and contributing to the development of automated standard analysis pipelines, automation of interactions between infrastructure components, or requirements analyses for such systems. Contributing to BI's global computational biology infrastructure in collaborations with bioinformaticians and members of IT and external partners in international teams
    • Acting as the key interface to the NGS lab within the Computational Biology group and play a driving role in the definition of experimental design strategies and coordinate the implementation and development of the LIMS. Together with the NGS lab developing outsourcing strategies
    • Carrying out data analyses to generate and test hypotheses in the context of new therapeutic concepts in collaboration with other members of the Computational Biology group or scientists from BI's Therapeutic Areas for Drug Discovery (Cardiometabolic Research, Central Nervous System Research, Inflammation & Respiratory Research, Immune Modulation & Research Beyond Borders). Supporting others and driving projects as the responsible computational biologist
    • Contributing to projects during all phases from experimental design to downstream analysis as the computational biology specialist in interdisciplinary teams

    REQUIREMENTS

    The ideal Principal Scientist should meet the following criteria:
    • PhD degree or equivalent qualification in Computational Biology or related fields several years of post-PhD experience with a focus on GWAS
    • Excellent knowledge and a broad spectrum in bioinformatics and computational biology with a focus on topics related to RNA-Seq, single cell RNA-Seq and other NGS applications. (Ideally analyzed from initial QC to downstream a large number of different RNA-Seq projects, and hands-on experience with scRNA-Seq data from multiple platforms. In addition you have a good overview of recent developments in terms of NGS instruments and protocols. Ideally you have collaborated closely with genomics teams and dealt with LIMS as well).
    • Your solid background in statistics and experimental design allows you to define the way forward also for complex questions.
    • Several years of experience in R/Bioconductor or Python and at least one additional programming language. You have robust coding skills, experience with version control systems (e.g. git) and constantly strive for well documented and reproducible analyses. In addition you are familiar with Linux, local and cloud-based HPC environments and have experience with queuing systems and modern pipelining systems (e.g. CWL, bpipe etc).
    • Experience with other type of omics data, network biology or machine learning is an additional asset.
    • Previously demonstrated that you can apply your skills to turn large datasets into relevant insight in concrete biological and disease related topics in interdisciplinary collaborations.
    • Fluency in English both in writing and in speaking will enable you to act in an international working environment.
    • You are characterized by a focused working style, flexibility as well as innovative thinking, and problem solving and analytical skills.
    • You are a reliable team player with excellent organization and communication skills, and with a high degree of motivation.

    HOW TO APPLY

    If you're looking to advance your career with a company that offers competitive salary, very generous relocation packages and excellent benefits as well as the opportunity to become a valuable member of a leading pharmaceutical company that puts an emphasis on a great work-life balance, please get in touch with Anna on +44 (0) 121 616 3469 or alauterjung[at]pararecruit.com

    I'd be happy to discuss your situation and this position with you in more detail and look forward to hearing from you.

    Keywords: GWAS, Human Genetics, Humangenetik, genome wide association*, Scientist, Computational Biology, Bioinformatics, Genetics, Pharma, Pharmaceutical, RNA-seq, scRNA-seq, pipeline, version control, Germany, Deutschland, RNA, microarray, NGS, WGS, WES, Python, R, LIMS, version, git, github, pipelines, variant calling, Systems Biology

    BACKGROUND

    The Cancer Research UK Manchester Institute
    Clinical Informatician to the Clinical Trial Bioinformatics Group

    About the role:
    We are currently looking for a Clinical Informatician for the digital Experimental Cancer Medicine Team (dECMT) (www.digitalECMT.org) within the Centre for Cancer Biomarkers, CRUK MI.

    The aim of this post is to support and drive new methods and approaches with the Manchester Cancer Research Centre (MCRC) and the Clinical Trial unit of The Christie NHS Foundation Trust (The Christie) by exploiting data collected during experimental cancer medicine clinical trials and by developing informatics methods and solutions.

    RESPONSIBILITIES

    Key responsibilities include:
    • Providing computational, technological and scientific expertise to Clinical programmes
    • Translating the scientific requirements of Clinical teams into computational solutions that have tangible impact
    • Performing coding or analysis that directly benefits Clinical Trials
    • Supporting information exploitation activities including integration, innovative technology solutions and analytics, essential for Clinical decision-making
    • Engaging with patients and healthcare professionals to gather user requirements in context of the business and systems analysis needed in The Christie environment
    • Contributing to the development of new capabilities, algorithms, tools and services that support Clinical teams
    • Working closely with software developers (internal and external) in defining and translating functional specifications
    • Testing of systems prior to go-live
    • Providing scientific domain knowledge relevant to requirement definition, system design and platform exploitation
    • Earning the trust and respect of teams across The Christie NHS Foundation, The University of Manchester and CRUK Manchester Institute
    • Publications in high impact journals

    REQUIREMENTS

    About you:
    You will have a degree in biological science/medical or health related background including working with clinical data (or equivalent relevant experience). You should have significant experience of developing informatics methods in a clinical environment along with experience of working with stakeholders including patients, clinicians, research scientists and other relevant functions such as statistics and IT. Experience in analysing clinical data is essential, alongside managing expectations of stakeholders, reporting back progress and getting input as required.

    For any informal enquiries about this post, please contact Jason Swift via email: Jason.Swift[at]digitalecmt.org

    Why choose Cancer Research UK Manchester Institute?
    The Cancer Research UK Manchester Institute (www.cruk.manchester.ac.uk), an Institute of The University of Manchester (www.manchester.ac.uk), is a world-leading centre for excellence in cancer research. The Institute is core funded by Cancer Research UK (www.cancerresearchuk.org), the largest independent cancer research organisation in the world. We are currently situated at the internationally-renowned life sciences campus at Alderley Park in Cheshire England, 15 miles from Manchester, a vibrant and dynamic city surrounded by beautiful countryside.

    We are partnered with The Christie NHS Foundation Trust (adjacent to the CRUK MI Paterson Building) in South Manchester (www.christie.nhs.uk), one of the largest cancer treatment centres in Europe. These factors combine to provide an exceptional environment in which to pursue basic, translational and clinical research programmes.

    TERMS

    Duration: fixed term until 31 December 2020

    COMPENSATION

    Salary in the range of £23,800 - £39,900 per annum (dependent upon experience)

    HOW TO APPLY

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

    Job Ref: MI/17/51

    DEADLINE

    Closing date: 9 October 2017.
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