March 2015 - BBClist - maillist.psb.ugent.be

[Gtpb] GTPB Bioinformatics Training Course Announcement/Reminder
by Pedro Fernandes 09 Mar '15

09 Mar '15

Dear all, The Applications for the PHSMCP15 course, "Promoter hunting and systems modelling of cellular pathways", are now OPEN. IMPORTANT DATES for this Course Deadline for applications: April 2nd 2015 Latest notification of acceptance: April 3rd 2015 Course date: April 22nd - April 24th 2015 With Alexander Kel Details are available here: http://gtpb.igc.gulbenkian.pt/bicourses/PHSMCP15/ In short: Learn how to find promoters in NGS data an how to use genes and promoters to produce inferences at the pathway and system levels. Full description: Overview This course starts by reviewing basic principles of gene regulation and how information is encoded in the huge part of genome - it's so called "non-coding" part. Bioinformatics plays a huge role in exploring how gene regulation works. We will introduce mathematical modelling of cellular pathways and address the interplay between feedback and feed-forward loops of regulation. We will see how a range of modelling techniques can help us to: - find master regulators - understand disease mechanisms - build models for use in precision medicine - design novel systems for biotechnology Starting from techniques for the computational prediction of promoters and distant enhancers, we will deal with the analysis of the structure of regulatory regions by identifying binding sites for transcription factors. A complete annotation of a newly sequenced genome has to address the identification of these regions in addition to the classical task of finding genes in terms of coding regions. Regulatory regions determine where, under which conditions and when genes become active. Thus, they are a fundamental part of the definition of the function of a gene. We will have a chance to introduce and acquire *hands-on* practice in next generation sequencing (NGS) techniques for genome-wide epigenetic analyses such as ChIP-seq. Then we will approach the analysis and modelling of biological systems from several practical angles. Systems biology and modelling are approched here from the interaction and network-based perspectives. We will introduce several pathway databases, such as Reactome, KEGG, TRANSPATH, TRANSFAC, ConsensusPathDB and use these information resources to perform pathway analysis. Next, we will use modelling of biological systems to look at different mathematical modelling strategies, such as Boolean networks and ordinary differential equation systems (ODEs). We will describe computational tools, like Cytoscape and CellDesigner, for the set-up and development of model prototypes and show further tools, such as Copasi, BioUML and PyBioS that can be used for parameter-fitting and sensitivity analysis. We will follow-on by looking at methods for reconstructing gene regulatory networks from gene expression data. The application of such methods can reveal key nodes in networks as potential biomarkers or drug targets. Dynamic systems modelling will be used to check the consistency of target and biomarker predictions. We will show real examples of application of these methods for identification of disease related biomarkers, drug discovery and personalized medicine. Special attention will be given to the application of the above mentioned methods in designing novel biological systems, in the growing field of Synthetic Biology. Methods Participants will learn about several techniques of finding promoters and enhancers and the principles on which these methods are based on. In the hands-on exercises, several analytical tools will be introduced and the results critically evaluated to assess their reliability. The course sessions will consist of lectures that lay out the conceptual framework as needed, and hands-on exercises, which will provide the practical insight on the use of the methods, gradually, in order to produce skills that can be used with a relatively high degree of independence. Participants will learn how to set-up some of the programs, and use publicly available servers for more complex analytical jobs, in an informed fashion, so that they fully understand the output generated and how their quality can be assessed. Participants will also learn the novel principles of organization of gene regulatory regions, which will help them to interpret their results of genomic and transcriptomic studies. The course will provide sufficient skills for the participants to address problems using open source software and freely accessible data resources. It will also be a chance to use commercially licensed resources such as TRANSFAC or the geneXplain integrated analytic platform for specific purposes. Target Audience The course was designed for researchers in biology, bioinformatics, biochemistry and medicine that have an interest in gene regulation and related topics. Course Pre-requisites Basic biochemistry. Elementary computing skills. Background knowledge in bioinformatics is not absolutely necessary, but may be instrumentally useful. Best wishes Pedro Fernandes GTPB Coordinator -- Pedro Fernandes 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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VIB11 is looking for a Bioinformatics Specialist for Single-cell Genomics and Transcriptomics
by Mark Fiers 06 Mar '15

06 Mar '15

Dear all, The VIB Center for the Biology of disease is looking to recruit a bioinformatics specialist on Single-cell Genomics and Transcriptomics. More information can be found here: http://www.vib.be/en/jobs/Pages/Bioinformatics-Specialist-for-Single-cell-G… with best regards Mark Fiers

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Internship position Schneider group, LCSB, Luxembourg
by ISCBSC announcement 03 Mar '15

03 Mar '15

Dear all, The ISCB Student Council is pleased to announce a 6-month internship position with the Schneider group at Bioinformatics Core, Luxembourg Centre For Systems Biomedicine (LCSB), University of Luxembourg. The internship is expected to start in June 2015 and it is available to Masters and PhD students in computational biology or related areas from developing nations. We welcome you to apply for this internship if you meet the eligibility criteria. Further, we would like to seek your help in spreading the word to your friends and colleagues! Many thanks for your assistance. More information is available here: http://www.iscbsc.org/internships/Schneider-lab-032015 Best regards, ISCB Student Council

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BioSB 2015 - Call for abstracts & nominations BioSB Young Investigator Award 2015
by Femke Francissen 03 Mar '15

03 Mar '15

*BioSB 2015 - Call for abstracts & nominations BioSB Young Investigator Award 2015* Netherlands Bioinformatics & Systems Biology Conference 2015 - BioSB 2015 Date: 20-21 May 2015 Venue: De Werelt, Lunteren, the Netherlands Website: http://www.aanmelder.nl/biosb2015 Registration: https://www.aanmelder.nl/biosb2015/subscribe *Abstract submission* You can now submit an abstract for the BioSB 2015 conference programme. Abstracts can be submitted for the following topics / topical tracks: - Metabolism - Gene regulation - Networks & Data integration - Next Generation Sequencing - Bioinf & SysBio in practice: industrial and medical applications (industry track) - Statistics & modeling - Genotype/phenotype & disease - Proteomics - Whole-cell modeling / multi-scale modeling / genome-scale modeling - Metagenomics topical track - NSBM Spring meeting 2015 (biomolecular modelling track) You can submit an abstract for a lecture in one of the parallel sessions, a poster presentation or for a demo in the application showcase. Read more about the abstract submission here: https://www.aanmelder.nl/biosb2015/wiki/93751/abstracts. *Abstract submission deadline: March 19, 2015* *Nominations for BioSB Young Investigator Award 2015* Young researchers can now be nominated for the BioSB Young Investigator Award 2015. The winner will present an honorary lecture at the conference (May 20) and will receive an award provided by the BioSB research school <http://www.biosb.nl>. You can now submit your nominations via: https://www.aanmelder.nl/biosb2015/wiki/93721/biosb%20young%20investigator%…. *Nomination deadline: April 10, 2015*. *BioSB 2015: Merging two research fields* BioSB 2015 will be the first in a series of yearly organised Dutch Bioinformatics & Systems Biology (BioSB) conferences focusing on both bioinformatics and systems biology research. The BioSB 2015 combines the annual Netherlands Bioinformatics Conference (NBIC) and the annual Systems Biology Symposium (SB@NL). Because of the success of the NBIC conference format in the past, the BioSB conference will be organised in the familiar style: a 2-day conference at Congrescentrum De Werelt in Lunteren. The BioSB 2015 will be co-organised by the BioSB research school <http://www.biosb.nl> and the Utrecht Bioinformatics Center <http://ubc.uu.nl/>.

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Update: ICBO 2015, Call for Submissions, *Deadline extended*
by Francisco Couto 02 Mar '15

02 Mar '15

ICBO2015 Call for submissions *Deadline extended* *** Relevant dates *** Conference paper submission: Mar 9, 2015 (11:59pm PST) <-- *Deadline extended* Conference paper notification: Apr 6, 2015 Camera-ready conference papers: Apr 20, 2015 Workshop paper, software demonstration and early career submission: Apr 13, 2015 Workshop paper, software demonstration and early career notification: May 11, 2015 Camera-ready workshop papers, software demonstration papers/abstracts and early career abstracts: May 25, 2015 Demos and Poster abstract submissions: May 18, 2015 Demos and Poster abstract notifications: June 8th, 2015 Camera-ready poster abstracts: June 15th, 2015 *** Topics *** Ontologies are knowledge representation tools widely used in the semantic description of biological and medical data from creation to publication and consumption for research and software applications including expert systems. To be maximally effective for a wide range of diverse purposes, such ontologies must be of good quality and work well together. Therefore, issues like good ontology design, ontology coordination, methods for harnessing ontologies for research and applications, and ontology maintenance need to be addressed. The International Conference on Biomedical Ontology (ICBO) series is designed to meet this need. ICBO 2015, the sixth event in the highly successful series, will bring together representatives of all major communities involved in ontology use and development in biomedical research, health care, and related areas. *** Call for Papers *** ICBO 2015 is soliciting submissions of novel (not previously published nor concurrently submitted) research papers in the areas of the application of ontologies to biomedical problems, ontology design and ontology interoperability, at any stage in the process from data creation to use in applications or scientific analyses. Submissions will be welcome from a broad range of approaches to ontology building and use. In addition, we would like to invite contributions showcasing methods for ontology-based research, including statistical methods, and contributions addressing the challenges associated with working with multiple ontologies at the same time, including ontology development, visualization, annotation of data, analysis, and applications. We will accept full-length research and application papers (5 pages), poster submissions (2 page abstracts), software demonstrations (2 page abstracts), and early career researcher symposium submissions (2 page abstracts). A selection of successful poster abstracts will be invited to give flash presentations during the conference. We are also looking for submissions of half-day or full-day workshops and tutorials. Workshops should be working sessions with a specific outcome that can be subsequently presented at the main conference. Tutorials are educational events and may involve hands-on practicals. Submission of papers is via EasyChair ( https://www.easychair.org/conferences/?conf=icbo2015) according to the templates provided on the conference web site. A Best Paper Award, Best Poster Award, Best Demonstration Award, and a Best Early Career Paper Award will be conferred to the author(s) at the conference, selected by the Organizing Committee. All accepted papers and abstracts will be published in an issue of CEUR-WS ( http://ceur-ws.org/) In addition, authors of selected papers will be invited to submit an extended version for publication in a special issue of the Journal of Biomedical Semantics (JBMS), an open-access journal published by BioMed Central (BMC). Note that publication in the JBMS special issue will incur article processing charges. *** Contact *** For more information please email icbo2015(a)googlegroups.com *** Organizing Committee *** Scientific Chairs: Francisco Couto (Lisboa, Portugal) and Janna Hastings (Cambridge, UK) Local Chair: Catia Pesquita (Lisboa, Portugal) Program Chair: Stefan Schulz (Graz, Austria) Workshop and Tutorial Chairs: Melanie Courtot (Vancouver, Canada) and João Ferreira (Lisboa, Portugal) Proceedings and Special Issue Chair: Dietrich Rebholz-Schuhmann (Zurich, Switzerland) Early Career Chair: Pierre Grenon (London, UK) Poster and Demonstrations Chair: Matthew Horridge (Stanford, USA) Sponsorship and Publicity: Emanuel Santos (Lisboa, Portugal) and Pedro Fernandes (Oeiras, Portugal) *** Program Committee *** Alan Ruttenberg (University at Buffalo, USA) Alexander D. Diehl (The Jacobs Neurological Institute, University at Buffalo, USA) Amanda Hicks (University of Arkansas for Medical Sciences, USA) Anika Oellrich (Sanger Institute, UK) Barry Smith (SUNY Buffalo, USA) Bill Hogan (University of Florida) Christophe Lambert (Montana State University, USA) Christopher Baker (UNB Saint John, Canada) Colin Batchelor (Royal Society of Chemistry, UK) Cristian Cocos (Mayo Clinic, USA) Cui Tao (SBMI, University of Texas Health Science Center at Houston, USA) Dagobert Soergel (Department of Library and Information Studies, University at Buffalo, USA) Daniel Schober (Leibniz Institute of Plant Biochemistry, Germany) Despoina Magka (Oxford University Computing Laboratory, UK) Frank Loebe (University of Leipzig, Germany) Fred Freitas (CIn-UFPE, Brazil) Georgios Gkoutos (University of Cambridge, UK) Gwen Frishkoff (Georgia State University, USA) Harold Solbrig (Mayo Clinic, USA) Heinrich Herre (Institute of Medical Informatics, Statistics and Epidemiology, University of Leipzig, Germany) Helen Parkinson (European Bioinformatics Institute, UK) James Malone (The European Bioinformatics Institute, Cambridge, UK) James J Cimino (National Institutes of Health, USA) James P. McCusker, 5AM Solutions Jesualdo Tomás Fernández-Breis (Departamento de Informatica y Sistemas, Universidad de Murcia, Spain) Jim Mccusker (5AM solutions, USA) Jin-Dong Kim (Database Center for Life Science, Japan) John Gennari (University of Washington, USA) José Luís Oliveira (Universidade de Aveiro, Portugal) Judy Blake (JAX, USA) Laura Slaughter (Oslo University Hospital, Norway) Lindsay Cowell (University of Texas Southwestern Medical Center at Dallas, USA) Ludger Jansen (University of Rostock, Germany) Mário J. Silva (Universidade de Lisboa, Portugal) Mark Musen (Stanford University, USA) Martin Boeker (University Medical Center Freiburg, Germany) Mathias Brochhausen (University of Arkansas for Medical Sciences, USA) Melissa Haendel (Oregon Health & Science University) Michael Schroeder (TU Dresden, Germany) Michel Dumontier (Stanford University, USA) Nigam Shah (Stanford University, USA) Olivier Bodenreider (US National Library of Medicine, USA) Onard Mejino (University of Washington, USA) Paolo Ciccarese (Harvard Medical School & Massachusetts General Hospital, USA) Pascale Gaudet (Swiss Institute of Bioinformatics, Switzerland) Paul Schofield (University of Cambridge, UK) Peter Robinson (Charite Universittsmedizin Berlin, Germany) Phillip Lord (School of Computing Science, Newcastle University, UK) Robert Stevens (University of Manchester, UK) Samuel Croset (European Bioinformatics Institute, UK) Simon Jupp (European Bioinformatics Institute, UK) Sivaram Arabandi (ONTOPRO, USA) Suzanne E. Lewis (Lawrence Berkeley National Lab) Werner Ceusters (SUNY at Buffalo, USA) Yongqun He (University of Michigan, USA)

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FW: Favour: urgently seeking a PhD student
by Judith Risse 01 Mar '15

01 Mar '15

From: Karim Gharbi [mailto:Karim.Gharbi@ed.ac.uk] Sent: 01 March 2015 16:28 To: ashworthsocial(a)lists.ed.ac.uk Subject: Fwd: Favour: urgently seeking a PhD student Dear all: Joe Hofman at the University of Bielefeld is urgently looking for a student to fill a funded PhD position in marine population genomics to join our Marie Curie International Training Network (ITN). Please feel free to forward to anyone who might be interested (or know someone who might). Cheers, Karim -------- Forwarded Message -------- Subject: Favour: urgently seeking a PhD student Date: Sun, 1 Mar 2015 10:30:12 +0000 From: Joe Hoffman <mailto:j_i_hoffman@hotmail.com> <j_i_hoffman(a)hotmail.com> To: karim gharbi <mailto:karim.gharbi@ed.ac.uk> <karim.gharbi(a)ed.ac.uk> Hi Karim Could you post this in Edinburgh for me? Many thanks Joe Joe Hoffman Department of Animal Behaviour University of Bielefeld Postfach 100131 33501 Bielefeld Germany +49 (0)521 1062711 http://www. <http://www.uni-bielefeld.de/biologie/animalbehaviour/hoffman/publications.h tml> thehoffmanlab.com <http://thehoffmanlab.com/> -- Dr Karim Gharbi Head of Genomics Edinburgh Genomics Ashworth Laboratories The University of Edinburgh Edinburgh, EH9 3FL, UK Phone: +44 (0)131 650 7489 Fax: +44 (0)131 651 3629 http://genomics.ed.ac.uk https://twitter.com/GenePoolNews The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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Bioinformatician position at AstraZeneca
by Magali Michaut 01 Mar '15

01 Mar '15

We are seeking a talented scientist to lead pre-clinical biomarker discovery efforts for the Oncology Bioinformatics team at AstraZeneca. The career level will be relevant to individuals with a number of years of experience applying bioinformatics/computational-biology to deliver impactful scientific discovery, supported by a relevant PhD and post-doc or equivalent. The role is particularly suited to an individual with strengths applying network biology, mathematical and/or machine learning approaches to find mechanistic patterns in pan-omic data. Closing date for applications is 23rd March 2015. http://jobs.astrazeneca.com/jobs/details/l1rRD1289-associate-principal-bioi… Jonathan Dry Principal Scientist II at AstraZeneca

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