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    Events: Rocky Mountain Bioinformatics Conference (Rocky 2018)
    Submitted by Suzi Smith; posted on Wednesday, April 25, 2018

    December 6-8, 2018
    The Viceroy Hotel
    130 Wood Road
    Snowmass Village, CO
    www.iscb.org/rocky2018

    The Rocky series began sixteen years ago as a regional conference, and has grown into an international program with a spotlight on regional development in the computational biosciences. The presenters of the Rocky conference are scientists representing a broad spectrum of universities, industrial enterprises, government laboratories, and medical libraries from around the world. The meeting is a chance to get to know your colleagues near and far, seek collaborative opportunities, and find synergies that can drive our field forward.

    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

    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

    Submitter

    We are pleased to announce a new resource from our group for predicting cell penetration peptides containing modified residues, which may serve as drug delivery vehicles.

    AVAILABILITY

    Web server link: webs.iiitd.edu.in/raghava/cellppdmod/

    ARTICLE

    Paper link: www.frontiersin.org/arti[...]/full

    May 8-11, 2018
    National Institutes of Health
    9000 Rockville Pike
    Building 60, Room 162
    Bethesda, MD 20892, USA
    events.r20.constantcontact.com/regi[...]0f112

    BACKGROUND

    This course will introduce students to bioinformatic analysis of next generation sequencing data, particularly for DNA-seq, RNA-seq, CHIP-seq, and epigenomics. The course will be comprised of lectures and hand-on sessions. Lectures will cover background knowledge and survey various software programs.

    Hands-on Skills/Tools Taught:
    • Command line tools will be presented
    • Galaxy web based platform will be used to analyze primary data
    • Cloud computing
    • Genomic databases
    • De novo assembly will be surveyed

    April 24-27, 2018
    National Institutes of Health
    9000 Rockville Pike
    Building 60, Room 162
    Bethesda, MD 20892, USA
    events.r20.constantcontact.com/regi[...]16440

    BACKGROUND

    Computer programs are meant to perform repeated, monotonous, fast, reproducible tasks, handling any amount of data. Researchers often come across situations where existing programs don't suit their needs. In the era of BigData, without the ability to quickly put together a program that would solve their problem, researchers face a road block that is not efficiently solvable by a human.This training will walk through participants in writing programs that would help them solve their own problems.

    OBJECTIVES

    Participants will get a brief introduction to the programming concepts, followed by hands-on walkthrough for writing scripts using the Unix Shell Programming Language, R, Perl and Python. We will start from reading the data, processing it and all the way until saving the processed data.

    HIGHLIGHTS

    • Participants will work in a Unix environment.
    • Participants will get a copy of all the scripts used in the class.
    • Participants will also receive a cookbook style manual for all the hands-on exercises.
    • After training support is also provided through exclusive members only forum.

    Submitter

    June 10-12, 2018
    Los Angeles, CA, USA
    icibm2018.zhaobioinfo.org

    The purpose of the 2018 International Conference on Intelligent Biology and Medicine (ICIBM 2018) is to bring together eminent scholars with expertise in various fields of computational biology, systems biology, computational medicine, as well as experimentalists interested in application of computational methods in biomedical studies.

    You are invited to submit abstracts with unpublished original work describing recent advances on all aspects of bioinformatics, Systems Biology and intelligent Computing, including but not restricted to the following topics:

    Systems Biology:
    • Mathematical and quantitative models of cellular and multi-cellular systems
    • Modeling and simulation of biological processes, pathways and networks
    • Multi-dimensional omics data integration
    • Metabolomics
    • Synthetic biological systems
    • Applications of systems biology approaches to biomedical studies
    • Self-organization in living systems (cells, organisms, swarms, ecosystems, etc.)
    Bioinformatics:
    • Next generation sequencing data analysis, applications, software and tools
    • Genomics and genetics, including integrative and functional genomics and genome evolution
    • Personalized medicine and translational bioinformatics
    • Big data science including storage, analysis, modeling and visualization
    • Proteomics, protein structure prediction, molecular simulation and evolution
    • Drug discovery, design and repurposing
    • Image analysis and processing
    • Intelligent Computing:
    • Evolutionary computing, swarm intelligence/optimization, ensemble methods
    • Machine learning, data mining, pattern recognition and knowledge and discovery
    • Natural langue processing, literature mining, semantic ontology and date privacy
    • Neural computing, kernel, methods, feature selection/extraction
    • Manifold learning theory, artificial life and artificial immune systems

    PAPER SUBMISSION

    All submitted papers will be peer-reviewed. Selected papers of the registered authors will be published in special issues of several journals, including BMC Genomics, BMC Systems Biology, BMC Bioinformatics, BMC Medical Genomics, BMC Medical Informatics and Decision Making, International Journal of Computational Biology and Drug Design (IJCBDD), Human Heredity, and Quantitative Biology. Authors need to prepare manuscripts in the format of the corresponding journal that they prefer.

    TRAVEL AWARDS

    Up to 20 travel awards for students and postdocs are open for applications: See here for details: icibm2018.zhaobioinfo.org/Travel.htm#award

    REGISTRATION

    Registration site: icibm2018.zhaobioinfo.org/Registration.htm

    IMPORTANT DATES

    Conference early registration opens: April 1, 2018
    Conference early registration deadline: May 10, 2018
    Deadline for travel award application: May 1, 2018
    Conference regular registration: May 11 - June 10, 2018
    ICIBM 2018 conference: June 10-12, 2018
    Education: Epigenomics Workshop in Berlin
    Submitted by Carlo Pecoraro; posted on Thursday, March 29, 2018

    May 28 - June 1, 2018
    Berlin, Germany
    www.physalia-courses.org/cour[...]se31/

    OVERVIEW

    This course will introduce researchers and technical workers to the bioinformatic analysis of large epigenomic data sets obtained using Next-Generation Sequencing (NGS) technologies, with a focus on ChIP-seq, RNA-seq and DNase-seq / ATAC-seq. The course will cover the theoretical foundations of the most widely adopted algorithms and analysis pipelines, a targeted introduction to scripting in bash and R/BioConductor, and extensive hands-on tutorials using publicly available NGS data sets. At the end of this course, the students should be able to efficiently analyze their own data and identify common pitfalls of genomics data analyses.

    INSTRUCTORS

    Dr. Federico Comoglio ( Division of Gene Regulation, Netherlands Cancer Institute)
    Dr. Iros Barozzi (Imperial College London (UK))

    For more information about the Workshop, please visit our website.
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