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    Submitter

    EXCERPT

    Man is not the measure of all things, at least not all thing genomic. Otherwise, we could have sequenced the human genome and called it a day. No, we're widening our genomic vision so far that we just sequence the DNA of every eukaryotic organism on the planet. It would be a huge undertaking, but well worth the effort, insist the advocates of the Earth BioGenome Project (EBP), a moonshot for biology that would complete its task in 10 years.

    To date, the genomes of less than 0.2% of eukaryotic species---that is, all nonbacterial and nonarchaeal species---have been sequenced. That leaves a lot of work for the EBP, an international initiative that proposes to sequence and functionally annotate the genomes of 1.5 million known species of eukaryotes, a massive group that includes plants, animals, fungi, and other organisms whose cells have a nucleus that houses their chromosomal DNA. The EBP also seeks to reveal some of the estimated 10 to 15 million unknown species of eukaryotes, most of which are single-cell organisms, insects, and small animals in the oceans.
    Source: www.genengnews.com/gen-[...]55744

    ARTICLE

    Harris A. Lewin et al. 2018. Earth BioGenome Project: Sequencing life for the future of life. PNAS 115 (17): 4325-4333. doi.org/10.1[...]15115

    May 15-18, 2018
    National Institutes of Health
    9000 Rockville Pike
    Building 60, Room 162
    Bethesda, MD 20892, USA
    events.r20.constantcontact.com/regi[...]05c1c

    OBJECTIVES

    Apart from performing the routine differential expression analysis using two different suite of tools, this hands-on training will help participants learn advanced RNA-Seq analysis techniques and tools for detecting snps, fusion genes, allele specific expressions, circular RNAs, viral/bacterial sequence identification, alternative polyadenylation and transcriptional regulatory network analysis.

    Hands-on Skills/Tools Taught:
    • Differential expression analysis: Tuxedo tools
    • Differential expression analysis: Trinity tools
    • Fusion gene analysis : Tophat-Fusion SNP detection: GATK
    • Allele specific expression : WASP
    • Circular RNA identification : circexplorer
    • Alternative polyadenylation : DaPars
    • Viral integration : VirusFinder
    • Network analysis : Cytoscape

    BACKGROUND

    About the role:
    Dr Claus Jorgensen, Group Leader of the Systems Oncology Group, is looking for a computational Postdoctoral Scientist to join his group. This is a great opportunity for a self-motivated, innovative, meticulous and organised candidate with excellent communication skills to work in a dynamic laboratory undertaking cutting edge research.

    The goal of the Systems Oncology Group is to understand how aberrations in cellular signalling affect tumour progression. In particular, we are interested in understanding how signalling between cancer cells and cells in the tumour microenvironment promote tumour progression and drug resistance. Using global approaches such as proteomics, mass cytometry, CRISPR and RNA sequencing we aim to identify and understand the mechanisms of cell-cell communication (Tape et al Cell 2016, Jorgensen et al Science 2009, Tape et al Mol Cell Proteomics 2014, Tape et al Anal Chem 2014, Worboys et al Nature Methods 2014). This role is an exciting opportunity to join a multidisciplinary team to study these problems.

    RESPONSIBILITIES

    This position is part of an ERC consolidator award to understand the evolutionary constraints of the tumour microenvironment on pancreatic cancer progression. Specifically, you will develop an independent research project to interrogate cellular interactions in the tumour microenvironment and help identify key regulatory events that drive clonal selection. Using computational analysis of available and newly generated data (proteomics, single cell analysis) you will develop a framework to associate changes in tumour and stromal departments and to develop experimental testable hypotheses. You will be experienced in computational biology/bioinformatics, analysis of quantitative signalling data and expression data.

    REQUIREMENTS

    About you:
    You should have a PhD in systems biology, engineering, computational biology or a relevant field. Experience in computational modelling, data integration and analysis is essential to the success of the project. Key qualities should include independent thinking, ability to work in a team and good communication skills, all of which are needed to efficiently work in a multidisciplinary team.

    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.

    TERMS

    Duration: Fixed term for 3 years

    COMPENSATION

    Salary starting: £31,604 – £41,929 per annum (depending on qualifications and experience)

    HOW TO APPLY

    To apply for this position please visit our website: www.cruk.manchester.ac.uk/Oppo[...]-Home

    Informal enquiries can be directed to Dr Claus Jorgensen via email: claus.jorgensen[at]cruk.manchester.ac.uk

    Job Ref: MI/18/25

    DEADLINE

    Closing date: 20 May 2018.

    Submitter

    EXCERPT

    There's never been data available on as many people's genes as there is today. And that wealth of information is allowing researchers to guess at any person's chance of getting common diseases like diabetes, arthritis, clogged arteries, and depression.

    Doctors already test for rare, deadly mutations in individual genes. Think of the BRCA breast cancer gene. Or the one-letter mutation that causes sickle-cell anemia. But such one-to-one connections between a mutation and a disease – "the gene for X" – aren't seen in most common ailments. Instead, these have complex causes, which until recently have remained elusive.
    Source: www.technologyreview.com/s/61[...]rate/

    October 9-12, 2018
    Sherbrooke, Quebec, Canada
    recombcg2018.usherbrooke.ca

    SCOPE

    The annual RECOMB Comparative Genomics Satellite Conference (RECOMB-CG) brings together leading researchers in the mathematical, computational and life sciences to discuss cutting edge research in comparative genomics,with an emphasis on computational approaches and the analysis of novel experimental results. The program will include keynote talks, contributed talks, and a poster session.

    The 16th RECOMB-CG conference will be held at the Manoir des Sables, in beautiful Magog-Orford, near Sherbrooke, Québec, Canada on October 9-12 2018. With this Call for Papers we invite high-quality original full papers on topics related to the conference theme. The conference will also have a poster session. A detailed call for posters will be published later on the conference web page.

    TOPICS

    Papers are solicited on, but not limited to, the following topics:
    • Genome evolution
    • Population genomics
    • Genome rearrangements
    • Genome variation, diversity and dynamics
    • Phylogenomics
    • Comparative tools for genome assembly
    • Comparison of functional networks
    • Gene identification and/or annotation
    • Cancer evolutionary genomics
    • Comparative epigenomics
    • Paleogenomics
    • Epidemiology

    CONFIRMED KEYNOTE SPEAKERS

    • Belinda Chang (Department of Ecology and Evolutionary Biology, University of Toronto, Canada)
    • Dannie Durand (Department of Biological Sciences, Carnegie Mellon University, USA)
    • Daniel Durocher (The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, University of Toronto, Canada)
    • Christian Landry (Institute for Integrative Systems Biology, Laval University, Canada)
    • Gwenaël Piganeau (Banyuls Oceanographic Observatory and National Centre for Scientific Research, France)
    • Xavier Roucou (Department of Biochemistry, University of Sherbrooke, Canada)

    DETAILS ON SUBMITTING MANUSCRIPTS

    Submitted papers must have not been published or be currently under consideration for publication in any other journal or conference with formal proceedings. Each accepted paper has to be presented by one of the authors at the conference.

    Accepted papers will be published in the conference proceedings, a volume in the Lecture Notes in Bioinformatics (LNBI) series. In addition, authors of selected papers will be invited, but not required, to submit a significantly extended version of their papers to Algorithms for Molecular Biology. Extended papers submitted will be handled by the Program Committee co-chairs. Authors who choose to publish their extended manuscripts will have to pay the journal's publication fees.

    Authors are encouraged to submit their manuscripts in PDF format according to the LNBI series guidelines: www.springer.com/us/c[...]lines

    Submitted papers must be within 15 pages (in the LNBI format), with optionally a clearly marked appendix containing supplementary material made available to the reviewers.

    All submissions must be made online, through the EasyChair submission system, at the following address: easychair.org/conf[...]g2018

    Authors need to register on that web site before submitting. A standard PDF file must be received by midnight on June 18, 2018 (any time zone) in order for a submission to be considered. Re-submission of already submitted papers will be possible until midnight June 18, 2018 (any time zone).

    IMPORTANT DATES

    Paper Submission Deadline: June 18, 2018
    Author Notification: July 20, 2018
    Final Version Due: August 3, 2018
    Conference: October 9-12, 2018

    CONTACT

    blanchem[at]cs.mcgill.ca
    aida.ouangraoua[at]usherbrooke.ca

     

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