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    Latest announcements
    Events: Definiens International Symposium on Tissue Phenomics
    Submitted by Colleen Craig; posted on Thursday, February 22, 2018

    April 24-25, 2018
    Hotel Marlowe, Cambridge, MA, USA
    www.tissuephenomics.com

    You're Invited: Please join us for the Definiens International Symposium for Tissue Phenomics.

    This Symposium advances innovation in translational immuno-oncology, and features diverse perspectives from visionaries who drive the field in the early stages of discovery to transform healthcare through the integration of digital science and medical Big Data.

    Topics discussed will include:
    • 20 years of Artificial Intelligence
    • Immuno-Profiling and Biomarkers
    • Generating Biological Insights
    • Big Data Integration
    • Translating Science into Development
    • Digital Pathology for Patient Care
    Join the conversation with these thought leaders:
    • Simone Bianco, PhD, Research Staff Member, IBM Almaden Research Center
    • Bernie Fox, Ph.D. Chief, Laboratory of Molecular and Tumor Immunology, EACRI, Associate Professor, MMI and Env and Biomolec systems; Leader, Tumor Immunology Focus Group, OHSU Cancer Inst., Oregon Health Science University
    • Pam Ohashi, Ph.D. Director, Tumor Immunotherapy Program, Princess Margaret Cancer Centre
    • Elfriede Noessner, Research Scientist, Institute of Molecular Immunology, Helmholtz Institute, Munich
    • Julien Adam, IGR Paris
    • James Gulley, MD, PhD, Director of the Medical Oncology Service, Office of the Clinical Director, National Cancer Institute
    • Famke Aeffner, Principal Pathologist; Comparative Biology and Safety Sciences; Amgen Inc
    • Robert Kinders, Head of the Pharmacodynamics assay development (PADIS) laboratory, Frederick National Laboratory, National Institute of Health
    • Holger Moch, MD, Professor, Institut für Pathologie und Molekularpathologie, University of Zurich
    • Chris Heery, MD, Chief Medical Officer, Bavarian Nordic
    • Kenneth Lacovara, Explorer / Paleontologist / Author
    • Chandra Saravanan, Senior Veterinary Pathologist, Novartis Institutes for BioMedical Research, Novartis
    • David Rimm, MD, Professor in the Departments of Pathology and Medicine (Oncology); Director of Yale Pathology Tissue Service, Yale University School of Medicine
    • Dirk Jaeger, MD, Professor, University of Heidelberg
    • David Harrison, John Reid Chair of Pathology, Director of Research & Director of Laboratory Medicine, University of St. Andrew
    • Ralf Huss, Chief Medical Officer, Definiens
    • Thomas Heydler, Chief Executive Officer, Definiens
    And many more.

    May 23-25, 2018
    Bologna, Italy
    genomeanalysis2018.febsevents.org

    The workshop intends to present the state-of-the-art of the computational tools for interpreting at the molecular level the effects that genome variations induce in the cell system, contributing to fill the knowledge gap between genotype and phenotype.

    NGS techniques allow detection of the differences in genetic sequences and in gene expression that can be associated to different phenotypes, and statistical methods can estimate a significance level for each association. However, the exploitation of genetic association data requires elucidation of how variations affect the structure of macromolecules and their interaction patterns and how biological processes and pathways are hampered. Proteins, their stability and their relationships in interactomes will be the central topic. Furthermore, a particular regard will be given to the regulation at the transcriptional and translational levels, as derived from epigenomic and ribosome profiling data.

    Computational tools are absolutely necessary to perform the analysis of massive amounts of biomedical data and modern techniques for database integration, non parametric statistics, machine-learning and in particular deep-learning approaches, can have a huge impact in the field. The exploitation of data in the applicative domains, and in particular in translational and stratified medicine, strongly rely on the availability of computational methods able to extract, elaborate and generalise biologically relevant information

    The workshop aims at presenting the state-of-the-art of computational methods for genome interpretation and collects expert scientists from both experimental biomedicine and computational biology. The mixing of competences is fundamental for generating significant advancements, and the proposed workshop .

    The format of the workshop allows extensive interaction among students and lecturers, and offers to young researchers the possibility of presenting their work at poster sessions and with short selected talks.

    IMPORTANT DATES

    Application deadline: April 15, 2018
    Deadline for applying to FEBS Youth Travel Funds (YTF): February 28, 2018

    Two microbiome challenges launched this week with a common goal: evaluate and advance the ability of computational methods to accurately detect known microbial strains in metagenomic samples.

    Both Challenges are great opportunities for the community to come together to advance research and for members in this group to test out their microbiome tools.

    The CFSAN Pathogen Detection Challenge, hosted by precisionFDA, asks participants to develop and use bioinformatics pipelines to identify the types and distribution of Salmonella strains in each of several metagenomics samples. This type of technology will expedite determining the source of foodborne illness. As the food safety community moves to metagenomic sequencing, bioinformatics algorithms must be developed to detect pathogens amongst a mix of organisms sequenced directly from a sample. This Challenge was designed as the first step towards this goal.

    The Mosaic Community Challenge: Strains #2, hosted by Janssen Research & Development, LLC, aims to speed the translation of microbiome science into novel products by tracking the presence of certain known strains in a sample. It is critical to accurately determine the type and quantity of microbes in a sample at the strain-level in order to bring safe and effective products to market, and to precisely monitor their status within the human body. Insights from the Challenge will provide an objective comparison of the performance of different tools. Participants can submit multiple entries and see immediate results of their performance throughout the Challenge using the Mosaic Platform.

    Join us today to get started! Access both Challenges at www.dnanexus.com/microbiome.

    RESPONSIBILITIES

    The Faculty of Health Sciences (healthsci.queensu.ca) and the Department of Pathology and Molecular Medicine at Queen's University are seeking an international leader and innovator in the areas of bioinformatics and health analytics. Applicants should have an established research program focused on precision medicine, particularly in relation to the identification of cancer diagnostic and prognostic markers and potential therapeutic targets. The successful candidate will become the designated nominee for an approved Tier I Canada Research Chair (www.chairs-chaires.gc.ca/prog[...].aspx). This is a tenured appointment at the level of Professor.

    REQUIREMENTS

    Candidates must hold a PhD or MD/PhD (or equivalent). The main criteria for selection are an established record of global leadership and innovation in bioinformatics, and a track record of mentorship and training of high-quality personnel in various emerging areas in the field. Queen's University is committed to establishing an international reputation in health related informatics, building on existing assets that include: the Centre for Advanced Computing (CAC, cac.queensu.ca ), a cluster of computer systems and storage resources shared by five universities and three colleges; the biobank resources and ongoing capabilities of the Canadian Cancer Trials Group (CCTG, www.ctg.queensu.ca ), which is a major national and international cooperative oncology clinical trials organization, and the national database of chronic disease management developed by the Canadian Primary Care Sentinel Surveillance Network (cpcssn.ca ) , a trans-Canadian network of 11 primary care networks. In addition, robust linkages exist between CAC and the CCTG with the informatics programs of the Ontario Brain Institute (braininstitute.ca ) and the Ontario Institute for Cancer Research (oicr.on.ca ), respectively.

    The successful candidate will be expected to play a leadership role in: i) developing and applying modern data analytics concepts, methods and techniques to utilize an ever-growing wealth of biomedical data generated by existing and emerging world-class research programs at Queen's University (www.queensu.ca/research/centres ), ii) fostering collaborative links between existing researchers involved in health related analytics and informatics across the University, and iii) the recruitment and mentorship of new faculty in the informatics/analytics areas. Salary is commensurate with qualifications and experience.

    LOCALE

    Department of Pathology and Molecular Medicine, Queen's University, Kingston, Ontario, Canada

    HOW TO APPLY

    The University invites applications from all qualified individuals. Queen's is committed to diversity and inclusion and has an employment equity program that meets the goals of the CRC program and the requirements of our collective agreement with the Faculty Association. Until such time as we have met our equity targets (queensu.ca/vpr/[...]-crcp), preference will be given to members of the Four Designated Groups under the Canada Research Chairs program: "women, Indigenous/Aboriginal peoples, persons with disabilities and racialized persons/visible minorities." All applicants will be invited to self-identify once they have applied; those who wish to be considered under our employment equity provisions are required to self-identify. Self-identification information will be held in confidence by the Equity Office and one member of the selection committee. All qualified candidates are encouraged to apply; however, in accordance with Canadian Immigration requirements, Canadian citizens and Permanent Residents of Canada will be given priority.

    To comply with Federal laws, the University is obliged to gather statistical information about how many applicants for each job vacancy are Canadian citizens / permanent residents of Canada. Applicants need not identify their country of origin or citizenship, however, all applications must include one of the following statements: "I am a Canadian citizen / permanent resident of Canada"; OR, "I am not a Canadian citizen / permanent resident of Canada". Applications that do not include this information will be deemed incomplete.

    A complete application consists of: (i) a cover letter (including one of the two statements regarding Canadian citizenship / permanent resident status specified in the previous paragraph), (ii) a full curriculum vitae (including a list of publications, awards and grants received), and (iii) a summary of the proposed plan of research. Please send your application electronically to Dr. Roger Deeley, Chair of the search committee (c/o Ms. Barbara Latimer bal[at]queensu.ca).

    The University will provide support in its recruitment processes to applicants with disabilities, including accommodation that takes into account an applicant's accessibility needs. If you require accommodation during the interview process, please contact: Ms. Barbara Latimer (bal[at]queensu.ca).

    Academic staff at Queen's University are governed by a Collective Agreement between the University and the Queen's University Faculty Association (QUFA), which is posted at queensu.ca/facu[...]ement and at www.qufa.ca.

    Appointments are subject to review and final approval by the Principal. Only nominees external to Queen's University will be considered. (Please note that, for the purposes of this competition, Queen's Term Adjuncts and Adjunct-1s will be considered as external nominees.) Review of applications will commence on 22 March 2018 and remain open until a suitable candidate is recruited.

    March 13-16, 2018
    National Institutes of Health
    9000 Rockville Pike
    Building 60, Room 162
    Bethesda, MD 20892, USA
    events.r20.constantcontact.com/regi[...]c3073

    BACKGROUND

    Predicting the effect of a mutation on the structure and function of a protein is not just for researchers with super-computer facilities. Thanks to public cloud computing options, anyone with basic molecular biology background can setup and run compute intensive computational modeling and dynamics experiments.

    OBJECTIVES

    Participants will use popular open source tools and techniques necessary for conducting successful molecular modeling and dynamics experiments in the cloud.

    Hands-on Skills/Tools Taught:
    • Ab initio protein structure modeling: QUARK / Rosetta
    • Remote homology detection: HHpred
    • Fragment-based protein structure modeling: Phyre2
    • Homology-based protein structure modeling: I-TASSER, MODELLER
    • Protein structure quality analysis: PROCHECK, WHAT_IF, Verify3D, PDB-REDO
    • Protein structure refinement: ModRefiner, ModLoop, Ramachandran plot
    • Macromolecular visualization: VMD, USCF Chimera
    • Molecular dynamics: NAMD

     

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