- BBClist - maillist.psb.ugent.be

Fwd: RCAM2015 - Announcement and call for abstracts
by Magali Michaut 28 Jun '15

28 Jun '15

> > > > > > ------------------------------------------------------------------ > 2nd Edition of the Workshop > > Recent computational advances in metagenomics (RCAM'15) > ------------------------------------------------------------------ > > 6th October, 2015 > Institut Pasteur, 28 rue du Dr, Roux, Paris, France > Satellite Workshop of GdR BiM 2015 > > IMPORTANT DATES > --------------- > Submission Deadline (abstract) 6th September, 2015 > Notification 14th September, 2015 > Registration Deadline: 1st Octobre, 2015 > Workshop Date 6th October, 2015 > > > OBJECTIVES > ---------- > > This workshop aims at promoting discussions and collaborations between > biologists (modelers), computer scientists and applied-mathematicians > involved in metagenomics and/or metatranscriptomics studies, either in > the bioinformatics or statistical aspects of such analysis. > > Metagenomics studies refer to analyses based on high-throughput > sequencing of environmental samples and microbial ecosystems. Both > marker-gene (16S, 18S, ITS, ...) and whole-genome strategies will be > adressed to cover a wide array of question ranging from quantifying > the microbial diversity in order to find structuring factors to > assessing the functional role of microbial communities. > > The workshop will provide an overview of the state-of-the-art methods > currently used in metaomics including comparative metagenomics and > metatranscriptomics. At the other end of the spectrum, case-studies > will illustrate how these methods produce insightful biological > knowledge. > > > SCOPE > ----- > > The program of this workshop will consist mainly of presentations of > refereed papers (30 minutes) and invited talks (50 minutes). Contributions are > welcomed on all aspects about bioinformatics and statistical analyses > of metaomics datasets, including, but not limited to: > * new methods, tools or pipelines involved in the characterisation of microbial diversity, > * original methods for taxonomical assignment, > * data reduction, > * comparative metaomics, > * models for community assembly, > * challenges for tackling the complexity of metaomics datasets. > > CONFIRMED SPEAKER > ----- > > Christopher Quince, University of Glasgow > > SUBMISSION > ---------- > > Please send the abstract to rcam(a)jouy.inra.fr > > All submitted abstracts will be peer-reviewed by the program committee. > Submitted abstracts should not exceed 2 pages including bibliography, > > Abstracts must be written and presented in English. They may describe > work that has already been published or that is simultaneously > submitted to a journal, conference, or workshop with refereed > proceedings. > > REGISTRATION > --------------- > The worskhop is free of registration fees but registration still mandatory > though the registration form (to come) available at > http://maiage.jouy.inra.fr/?q=fr/rcam2015 > Registration will close on October 1st. > > IMPORTANT DATES > ----------------------------- > Submission Deadline (abstract): September 6th 2015 > Notification: September 14th 2015 > Registration deadline : October 1st 2015 > Workshop Date: October 6th 2015 > > ORGANIZERS > ---------- > Anne-Laure Abraham, INRA/MICALIS, Jouy-en-Josas, France > Valentin Loux, INRA/MaIAGE, Jouy-en-Josas, France > Mahendra Mariadassou, INRA/MaIAGE, Jouy-en-Josas, France > Eduardo Rocha, Institut Pasteur, Paris, France > Sophie Schbath, INRA/MaIAGE, Jouy-en-Josas, France > > SPONSOR > ------------------ > The workshop is supported by the metaprogramme "Metaomics of Microbial Ecosystems (M2E)" from the French National Institute for Agricultural Research (INRA) and the Institut Pasteur. > > > >

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group leader Bioinformatics
by Vera van Noort 25 Jun '15

25 Jun '15

Please forward to possible candidates: Group Leader position with start-up package in Bioinformatics NCMM is seeking new outstanding international candidates for the position of group leader with a start-up package in bioinformatics. We expect to hire one new principal investigator through this call and particularly encourage international applicants. The successful candidate is expected to initiate a new independent research program integrating bioinformatics and experimental science with a clear relevance to molecular medicine and disease mechanisms. The bioinformatics research should be closely linked to biological research in the same disease areas. NCMM provides attractive sustainable support packages for new group leaders of more than 2.0 million EUR over the first five-year period. This includes salaries of the group leader, a postdoctoral fellow, a doctoral student as well as a programmer / technician, consumables and modern laboratory facilities.The candidate is expected to complement this budget through other national or international grants and/or through industrial collaborations. Application deadline: July 2, 2015 See: http://www.ncmm.uio.no/open-positions/group-leader-position-with-start-up-pa ckage-in-bio.html and link to full add and web-based application portal, here: http://uio.easycruit.com/vacancy/1388168/70932?iso=no Best regards, Kjetil Kjetil Taskén, Professor of Medicine, M.D., Ph.D.; Director, Centre for Molecular Medicine Norway, Nordic EMBL Partnership; Director, The Biotechnology Centre of Oslo; University of Oslo P.O. Box 1125, Blindern N-0317 Oslo NORWAY Phone: +47-22840505 Fax: +47-22840506 Cellular phone: +47-90860759 email: kjetil.tasken(a)ncmm.uio.no or kjetil.tasken(a)biotek.uio.no Web: www.ncmm.uio.no <http://www.ncmm.uio.no/> or www.biotek.uio.no <http://www.biotek.uio.no/> -- Vera van Noort Professor Computational Systems Biology KU Leuven - Faculty of Bioscience Engineering Kasteelpark Arenberg 22 box 2460 3001 Leuven Belgium URL: www.biw.kuleuven.be/m2s/cmpg/research/CSB

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[Gtpb] GTPB PGDH15 Training Course REMINDER deadline June 28th
by Pedro Fernandes 24 Jun '15

24 Jun '15

REMINDER Dear friend, Applications are still open for PGDH15 Population Genetics and Demographic History: model-based approaches with Mark Beaumont, Lounes Chikhi, Willy Rodriguez and Barbara Parreira IMPORTANT DATES for this Course Deadline for applications: June 28th 2015 Latest notification of acceptance: July 1st 2015 Course date: July 6th - July 9th 2015 Details are available at: http://gtpb.igc.gulbenkian.pt/bicourses/PGDH15/ Course description Genetic data are increasingly used by ecologists and evolutionary biologists in general. It has thus become important for many biologists with different levels of experience to produce and analyse genetic (and genomic) data. In this course we will take a practical approach to the analysis of genetic data, but we will also provide some of the theoretical background required to understand the outputs of the software used. This course will be organised so as to mix lectures where important notions are introduced with practicals where freely available software will be used. While this will not be the focus of the course, we will also introduce and discuss genealogical (coalescent-based) simulation methods and those based on forward-in-time simulations. Altogether this will allow to discuss the potentialities and limitations of the tools available to the community. In this four-day course we will introduce the main concepts that underlie many of the models that are frequently used in population genetics. We will focus on the importance of demographic history (e.g. effective sizes and migration patterns) in shaping genetic data. We will go through the basic notions that are central to population genetics, insisting particularly on the statistics used to measure genetic diversity and population differentiation. The course will also cover a short introduction to coalescent theory, Bayesian inference in population genetics and data simulation, as they are connected to what makes landscape genetics today on the basis of multilocus data. We will also introduce two methods that have been recently developed to analyse genomic data. The PSMC of Li and Durbin reconstructs the demographic history of a species or population with the genome of a single individual. The Rehh package is an R implementation of the Extended Haplotype Homozygosity (EHH) test for selective sweeps and looks for signals of selection based on the analysis of genomic regions. Most theory will be put into practice in practical sessions, analyzing real and/or simulated datasets. In these sessions, we will look at measures of genetic diversity and differentiation and use methods to detect population structure as implemented in the program STRUCTURE and discuss related programs such as FastSTRUCTURE. We will learn how to perform coalescent simulations of genetic data (using SPAms and ms). Some exercises will make use of R scripts (R being a freely available statistical program). Basic R knowledge is a pre-requisite but we will provide a short introduction to R. The R statistical package is a very powerful tool to analyse data outputs from many population genetics software, and can also be used to simulate genetic data under simple demographic scenarios. Thanks for your interest, Pedro -- Pedro Fernandes GTPB Coordinator Instituto Gulbenkian de Ciência Apartado 14 2781-901 OEIRAS PORTUGAL Tel +351 21 4407912 http://gtpb.igc.gulbenkian.pt _______________________________________________ Gtpb mailing list Gtpb(a)igc.gulbenkian.pt https://lists.igc.gulbenkian.pt/mailman/listinfo/gtpb

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Job announcement: Postdoc position in Cancer Bioinformatics
by Can Kesmir 24 Jun '15

24 Jun '15

Dear all We have an exciting postdoc position available in cancer bioinformatics, that should be filled in as soon as possible. *Job description* The postdoc will be part of a joint international effort to implement personalized immunotherapy, targeting unique tumor associated mutations in patients. This is an exciting position at the crossroad of the blooming field of cancer genomics, and immunological bioinformatics. The postdoc will be working on two main projects: 1) evaluation and further development of existing models to predict the likelihood that a presented tumor mutation (in the form of a peptide-MHC complex) is recognized by the patient’s immune system, and 2) based on the primary sequence information of T cell receptors, predict their most likely ligands (e.g., mutations found in the individual patients). These innovative and ambitious projects will be performed in close collaboration with Prof. Ton Schumacher from Dutch Cancer Institute (NKI). The position is part of the EU Horizon2020 project called "APERIM: Advanced bioinformatics platform for PERsonalised cancer Immunotherapy” (H2020-PHC-2014), consisting of eight academic partners and three companies. *Qualifications* We are looking for a bioinformatician at the postdoc level with a keen interest in immunology and/or cancer. The position can be converted into a PhD student in case we have an excellent candidate. Applications from cancer immunologists with some computational experience are highly welcome. * Offer* The candidate is offered a full-time position for three years.The salary is supplemented with a holiday bonus of 8% and an end-of-year bonus of 8,3% per year. In addition we offer: a pension scheme, a partially paid parental leave, flexible employment conditions <http://www.uu.nl/EN/informationfor/jobseekers/Working-for-Utrecht-Universit…>. Conditions are based on the Collective Labour Agreement Dutch Universities. The research group will provide the candidate with necessary support on all aspects of the project. *About the organisation* Utrecht University <http://www.uu.nl/en> has great ambitions for its teaching quality and study success rates. This also applies to its clear research profiles which are centred around four themes: Dynamics of Youth, Institutions, Life Sciences and Sustainability. Utrecht University plays a prominent role in our society and contributes to finding the answers to topical and future societal issues. The Faculty of Science <http://www.uu.nl/en/organisation/faculty-of-science> consists of six departments: Biology, Pharmaceutical Sciences, Information and Computing Sciences, Physics and Astronomy, Chemistry and Mathematics. The Faculty is home to 3500 students and nearly 2000 staff and is internationally renowned for the quality of its research. The Faculty's academic programmes reflect developments in today's society. The theoretical biology and bioinformatics <http://tbb.bio.uu.nl/> (TBB) group at the Biology department of Utrecht University employs computational and mathematical models and bioinformatics to perform fundamental biological research in a variety of biological disciplines, and part of the group is specialized in immunology (Prof. Rob de Boer and Dr. Can Kesmir). We have long a standing expertise in modeling the immune system and in applying bioinformatics (mainly data-driven methods) to predict the specificity of the immune responses. The group is part of the Institute of Biodynamics and Biocomplexity <http://www.ibb-uu.nl/> (IBB <http://www.ibb-uu.nl/>), embedded in one of the largest Biology departments in the Netherlands (>200 new students per year). We are part of the Utrecht Center for Quantitative Immunology <http://tbb.bio.uu.nl/ucqi>(UCQI <http://tbb.bio.uu.nl/ucqi>), which brings together an experienced collaborative team of immunologists, bioinformaticians, and mathematical modelers. This unique position allows daily collaboration with wet lab immunologists and biologists. The group teaches modeling and bioinformatics to biology students at the bachelor and master level. PhD students in the group have diverse backgrounds ranging from biology, physics to mathematics, and typically half of them are from abroad. The IBB focuses on molecular life sciences, and is collaborating with other departments of the Faculty of Science, the Faculty of Medicine, and the Hubrecht Institute in Utrecht. UCQI is a joint effort between Utrecht University and the Utrecht Medical Center. *How to apply?* Application deadline is 1st of July. Please use the following link to apply: https://lnkd.in/dPDXR_7

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FW: Course offering - 2 and 3 July 2015 Disease causing mutation filtering and human connectome
by Alexander Botzki | VIB | 24 Jun '15

24 Jun '15

Dear all, On behalf of Adrian Liston, VIB KU Leuven: We kindly invite you to the seminar of Yuval Itan on July 1 at 11am (KUL, O&N4 auditorium): Finding a needle in a haystack: new approaches to identify disease-causing mutations in patients’ high-throughput sequencing data This seminar provides an insight into a new state-of-the-art gene-level metrics, tackling a crucial question in medicine genomics: how to identify the relevance of a mutated gene to a disease? We identified for the first time the biological distance between all human genes, as well as the accumulated mutational damage and mutation significance cutoff for each human gene. These gene-level approaches were shown to be particularly powerful for the identification of novel disease-causing genes in patients’ high-throughput data. The seminar is followed on July 2nd and 3rd by a practical tutorial on PC. Training 1: Disease causing mutations: filtering out disease-causing mutations Training 2: The human connectome: picking candidate genes for disease from all-exome analysis Trainer: Yuval Itan, Rockefeller University Date : Training 1: 2th July, 9am, ends 1pm Training 2: 3th July, 9am, ends 1pm Place : PC-LOKAAL ANATOMIE 2, ON2, 02.215 (KU Leuven) Host : Adrian.Liston(a)vib.be<mailto:Adrian.Liston@vib.be> Registration is free of charge, but places are limited, so register fast! https://docs.google.com/forms/d/1mYXe5dwh5WMPQn-hj_RRDxc5oEffR6fdfD0Nn1ZY4-… Best regards Alex

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Post-doc and PhD student positions available in the Bonvin lab@Utrecht University
by Alexandre Bonvin 22 Jun '15

22 Jun '15

Dear all I have a number of positions available in my group (bonvinlab.org) for two PhD students (for a four years period starting late 2015 and in 2016) and one post-doc (for a two year period in first instance, with a possibility of extension)(starting date fall 2015). These positions are funded by a number of European and Dutch research projects, related to our information-driven integrative modelling platform HADDOCK and involving various e-Infrastructure components in grid and cloud computing. The ideal candidates should have a good knowledge of structural biology and biomolecular modelling and possess some programming skills. Details of those positions have not yet been published, but some information on the projects can be found at: · http://bonvinlab.org/news/TOP-PUNT-NWO-proposal-granted · http:// bonvinlab.org /news/Two-new-H2020-projects-funded I would be grateful if you could disseminate and share this information with any suitable candidate. Interested candidates can contact me directly. All the best Alexandre --------------------------------------------------------------------------------------------------------------------------- Dr. Alexandre M.J.J Bonvin | Professor of Computational Structural Biology Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands Phone: +31-30-2533859 / 2652 | Fax: +31-30-2537623 Email: a.m.j.j.bonvin(a)uu.nl http://www.uu.nl/staff/AMJJBonvin | http://www.bonvinlab.org --------------------------------------------------------------------------------------------------------------------------- EU e-Infrastructure WeNMR project coordinator | http://www.wenmr.eu --------------------------------------------------------------------------------------------------------------------------- Chair GRC on Computational Aspects of Biomolecular NMR - Il Ciocco - June 7-12 2015 http://www.grc.org/programs.aspx?id=14571 ---------------------------------------------------------------------------------------------------------------------------

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position for bioinformatics lecturer/researcher in Groningen
by Noback MA, Michiel 22 Jun '15

22 Jun '15

please follow this link (in Dutch) for details on the position at the Hanze University of Applied Science: http://noorderlink.nl/participanten/hanzehogeschool-groningen/20022-0000001… Only one day left - sorry about that. Dr. M A. Noback | Bioinformatics senior lecturer & researcher | Institute for Life Science and Technology | Hanze University of Applied Sciences | Phone +31 50 5954691 | Postbus 3037 | 9701 DA Groningen | The Netherlands

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[Gtpb] Hands.on Training Course on Advanced Bioistatistics for Biologists
by Pedro Fernandes 19 Jun '15

19 Jun '15

Course Announcement / Reminder Applications are OPEN for the hands-on training course ABSTATB15 Advanced Biostatistics for Biologists IMPORTANT DATES for this Course Deadline for applications: July 10th 2015 Course dates: July 13th - July 17th 2015 with Lisete Sousa, Carina Silva and Pedro Fernandes Candidates with adequate profile will be accepted in the next 72 hours after the application, until we reach 20 participants. gtpb.igc.gulbenkian.pt/bicourses/ABSTATB15/ Course description: This course is a standalone advanced Biostatistics course that can be taken as a continuation of the Introductory Biostatistics for Bioinformatics (IBSTAT) course, that precedes it in GTPB. It is targeted for Biostatistical techniques often employed in analytical tools for high throughput data and multivariate data. Participants can expect to attend a thorough set of lectures that will reveal the conceptual frameworks that are needed to understand the methods. Extensive hands-on practice will be the main vehicle for providing the skills and user independence. To keep things in context, the course is exclusively based on biological examples, worked with Bioinformatics tools. Care has been taken not to use any proprietary data or software, so that the hands-on experience can carry on after the course, providing maximum user independence. We will be using custom-built R scripts and packages that are available from the CRAN and Bioconductor repositories. Course duration: 5 days | Attendance fee: Euro 450.00 Thankyou for your interest, P. Fernandes -- Pedro Fernandes GTPB Coordinator Instituto Gulbenkian de Ciência Apartado 14 2781-901 OEIRAS PORTUGAL Tel +351 21 4407912 http://gtpb.igc.gulbenkian.pt _______________________________________________ Gtpb mailing list Gtpb(a)igc.gulbenkian.pt https://lists.igc.gulbenkian.pt/mailman/listinfo/gtpb

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PhD POSITION ON BIOINFORMATIC METHODS FOR EPIGENOMICS (ULB, Brussels)
by Matthieu Defrance 17 Jun '15

17 Jun '15

PhD POSITION ON BIOINFORMATIC METHODS FOR EPIGENOMICS (ULB, Brussels) Job description: One PhD position on bioinformatic methods for epigenomics is available in the Laboratory of Cancer Epigenetics (Université Libre de Bruxelles, Belgium). The research goal is to develop new bioinformatic methodologies in order to analyze epigenetic changes (e.g. DNA methylation, histone modifications) that arise in cancers. Both fundamental and clinical aspects of the modifications will be addressed by analyzing high-throughput data generated using cutting edge next-generation sequencing platforms (available in the lab). The position is funded for 2 years, with a 2 years renewal. Screening of applications begins immediately and continues until an outstanding candidate is selected. PhD is expected to start in October 2015. Profile: The candidate should hold a master degree in bioinformatics, bio-engineering, biomedical sciences or eventually in engineering or computer sciences and demonstrate proficiency in statistics, algorithmics, programming (e.g R, python) and in software development. Experience with sequence data, genome-wide data sets (e.g ChIP-Seq, RNA-Seq, ...) or massive datasets analysis will be assets. The applicant should have good organizational skills, a taste for interdisciplinary research, excellent scientific writing and presenting skills and be able to work independently. How to apply? Applications should include a detailed CV (including grades and class ranking), a motivation letter, and names of two referees and should be sent to: Dr. Matthieu Defrance (matthieu.dc.defrance(a)ulb.ac.be) and Pr. François Fuks (ffuks(a)ulb.ac.be) Laboratory of Cancer Epigenetics, Faculty of Medicine, Free University of Brussels, 808 route de Lennik, Brussels, Belgium. Tel.: 32-2-555 62 45. Fax: 32-2-555 62 57. Selected publications: Viré et al. Nature 2006; Villa et al. Cancer Cell 2007; Dedeurwaerder, Defrance et al. EMBO Molecular Medicine. 2011; Dedeurwaerder*, Defrance* et al. Epigenomics 2011; Deplus et al., Cell Reports 2014; Bouhmadi et al., Nature 2014; Dedeurwaerder*, Defrance* et al. Briefings in Bioinformatics 2014.

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[Gtpb] GTPB Bioinformatics Training Course Announcement - Programming in Python
by Pedro Fernandes 15 Jun '15

15 Jun '15

ANNOUNCEMENT / REMINDER Dear Research Applications are open for BPBR15 Bioinformatics using Python for Biomedical Researchers with Allegra Via and Kaja Milanowska IMPORTANT DATES for this Course Deadline for applications: July 7th 2015 Latest notification of acceptance: July 10th 2015 Course date: July 20th - July 24th 2015 Details are available at: http://gtpb.igc.gulbenkian.pt/bicourses/BPBR15/ Course Description Python is an object-oriented programming language that is ideal for biological data analysis. The course will start from zero knowledge, and will introduce the participants to all the basic concepts of Python such as calculating, organizing data, reading and writing files, program logic and writing larger programs. All the examples and practical sessions will focus on solving biological problems. In particular the sessions will cover: working with DNA and protein sequences data retrieval from files and their manipulation running applications, such as BLAST, locally and from a script finding motifs in sequence parsing common file formats (Uniprot, GenBank, PDB, BLAST) with Biopython ways to find and correct program errors The course will be highly interactive and the students will continuously put theory into practice while learning. By the end of the course, the participants will have a good understanding of Python basics and will have acquired the skills to manage any type of bioinformatics database record and to run applications from scripts. Basic Unix/Linux skills will be provided at the beginning of the course. Target Audience End-users of bioinformatics databases and tools that aim at developing hands-on capabilities for biological data analysis, ie writing their own or adapting somebody else's Python scripts in an autonomous way. Course Pre-requisites Basic familiarity with bioinformatics data resources such as Uniprot/Swiss-Prot, Blast, ENSEMBL, PDB, etc. The course is directed to biologists with little or no programming experience and aims at making them capable to use Python to autonomously manage and analyse biological data. Thanks for your interest, Pedro -- Pedro Fernandes GTPB Coordinator Instituto Gulbenkian de Ciência Apartado 14 2781-901 OEIRAS PORTUGAL Tel +351 21 4407912 http://gtpb.igc.gulbenkian.pt _______________________________________________ Research mailing list Research(a)igc.gulbenkian.pt https://lists.igc.gulbenkian.pt/mailman/listinfo/research ----- End forwarded message ----- _______________________________________________ Gtpb mailing list Gtpb(a)igc.gulbenkian.pt https://lists.igc.gulbenkian.pt/mailman/listinfo/gtpb

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