June 2014 - BBClist - maillist.psb.ugent.be

PhD position Bioinformatics/NGS/MS/sORF detection @ BioBix
by Gerben Menschaert 18 Jun '14

18 Jun '14

Dear colleagues, We have a vacancy for a PhD position in our lab for someone with a background in bioinformatics and data analysis and a keen interest in sequencing and mass spectrometry, for a project exploring small ORFs and micropeptide translation products. (see description in attachment)! I would very much appreciate it if you could circulate the attached advertisement to any relevant candidates or advertise the position within your institute. Kind regards, Gerben dr. ir. Gerben Menschaert Post-doctoral fellow FWO Lab of Bioinformatics and Computational Genomics FBE - Ghent University Coupure Links 653 9000 Ghent, Belgium MAIL Gerben.Menschaert(a)ugent.be PHONE +32 9 264 99 22 SKYPE gerben.menschaert WEB www.biobix.be/gerben-menschaert/

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Fwd: Postdoc position working on sRNAs - please circulate
by Yao-Cheng Lin 13 Jun '14

13 Jun '14

---------- Forwarded message ---------- From: Nathaniel Street <nathaniel.street(a)umu.se> Date: Fri, Jun 13, 2014 at 4:20 PM Subject: Postdoc position working on sRNAs - please circulate Hi I have an open postdoc position for a project exploring the relationship between sRNA, methylation and repeats in Norway spruce. I would very much appreciate it if you could circulate the attached advertisement to any relevant candidates or advertise the position within your institute. Kind regards Nat -- Yao-Cheng Lin Bioinformatics and Systems Biology VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, B-9052 Ghent, Belgium TEL: +32 (0)9 33 13 821 GSM: +32 (0)472 480 968 http://bioinformatics.psb.ugent.be

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NBIC/BioSB Course Algorithms for Biological Networks (3th edition) - still some seats open!!
by Celia.vanGelder＠radboudumc.nl 13 Jun '14

13 Jun '14

NBIC/BioSB Course Algorithms for Biological Networks (3rd edition) - still some seats open! Date: 30 June - 4 July, 2014 Course coordinators: Dick de Ridder (WUR), Jeroen de Ridder (TUD), Celia van Gelder (NBIC/BioSB) Location: Delft University of Technology (TUD), Delft, the Netherlands Website: http://biosb.nl/education/course-portfolio/bioinformatics-portfolio/course-… Registration: http://biosb.nl/education/enrollment-algorithms-for-biological-networks-cou… More information: education(a)biosb.nl<mailto:education@biosb.nl> Target audience PhD students with a background in bioinformatics, computer science or a related field; a working knowledge of basic statistics and linear algebra is assumed. Course Description In the third edition of this course, we will first give a brief overview of molecular biology, the advent of high-throughput measurement techniques and large databases containing biological knowledge, and the importance of networks to model all this. We will highlight a number of peculiar features of biological networks. Next, a number of basic network models (linear, Boolean, Bayesian) will be discussed, as well as methods of inferring networks from observed measurement data and of integrating various data sources and databases to refine networks. Once networks are derived they often serve as the cornerstone in the visualization, analysis and interpretation of high-throughput data; we will discuss a number of methods in this area. As an alternative to static networks, a number of alternative dynamic network models more suited for high-level simulation of cellular behaviour for will be introduced. Finally, we will give some examples of algorithms exploiting the networks found to learn about biology, specifically for inspecting protein interaction networks and for finding active sub networks. Course programme The course website, including full course programme, can be found at http://helix.ewi.tudelft.nl/nbic/abn/. BioSB Course Programme The course portfolios of NBIC (bioinformatics) and NCSB (systems biology) will be integrated and continued in the Netherlands Bioinformatics and Systems Biology Research School (BioSB). The Education Portfolio of BioSB can be found at http://biosb.nl/education/course-portfolio/. More information For more information about the course you can contact Celia van Gelder at education(a)biosb.nl<mailto:education@biosb.nl>. Dr. Celia W.G. van Gelder Coordinator Education CMBI Projectleader Education NBIC/BioSB tel. +31-(0)24-3666120 e-mail: Celia.vanGelder(a)radboudumc.nl<mailto:C.vanGelder@umcn.nl> websites: www.cmbi.ru.nl<http://www.cmbi.ru.nl/>, www.nbic.nl<http://www.nbic.nl/>, www.biosb.nl<http://www.biosb.nl> Postal address: CMBI 260 Radboud University Nijmegen-Medical Centre /NCMLS PO Box 9101, 6500 HB Nijmegen The Netherlands Het Radboudumc staat geregistreerd bij de Kamer van Koophandel in het handelsregister onder nummer 41055629. The Radboud university medical center is listed in the Commercial Register of the Chamber of Commerce under file number 41055629.

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9th Benelux Bioinformatics Conference (BBC 2014) - call for papers
by Joanna SMULA-OSTASZEWSKA 13 Jun '14

13 Jun '14

Dear Colleagues, Luxembourg Centre for System Biomedicine of University of Luxembourg (LCSB) and Centre de Recherché Public de la Santé (CRP-Santé) organize the 9th edition of the Benelux Bioinformatics Conference (BBC 2014). The conference is affiliated by International Society for Computational Biology (ISCB)<http://www.iscb.org/>. The event entitled Bioinformatics: Integrating data, teams and disciplines will take place in Novotel-Kirchberg in Luxembourg, on December 8th-9th. Conference coordinators invite you to submit your abstracts through the registration/submission system<http://lcsb.ldorganisation.lu/v2/produits.php?langue=english&cle_menus=1240…>. Conference topics cover all fields of bioinformatics, including: · Biotechnologies · Computational biology · Research on biological networks · Structural bioinformatics · The analysis of the high-throughput sequencing data · Micro-array expression data, etc. Detailed information may be found on the conference website http://www.bbc2014.lu/ We anticipate that the BBC 2014 will once again greatly foster the collaboration and research activities between scientists in the Benelux area. Please feel free to distribute this announcement to your interested colleagues and do not hesitate to contact us in case of further questions. We look forward to meeting you in Luxembourg. Yours sincerely, Joanna Smula-Ostaszewska [cid:image003.jpg@01CF86FB.7FADE5D0] Dr.Eng. Joanna Smula-Ostaszewska Scientific assistant Université du Luxembourg Luxembourg Centre for Systems Biomedicine (LCSB) Campus Belval; 7, Avenue des Hauts-Fourneaux; L-4362 Esch-Belval; Luxembourg T: +352 46 66 44 6373 http://lcsb.uni.lu<http://lcsb.uni.lu/> --- This message is confidential and may contain privileged information. It is intended for the named recipient only. If you receive it in error please notify me and permanently delete the original message and any copies.

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MLSB 2014: deadline extension and call for posters
by Pierre Geurts 13 Jun '14

13 Jun '14

[Apologies for cross-posting] UPDATES: - Deadline for submission has been extented to ** JUNE 22 ** - Abstracts for poster presentations can be submitted until ** JULY 13 ** Last Call for Contributions MLSB14, the eighth International Workshop on Machine Learning in Systems Biology http://www.mlsb.cc Organized in conjunction with ECCB 2014 Strasbourg, France, September 6-7, 2014. Submission deadlines: Extended abstracts: June 22 Posters: July 13 WORKSHOP DESCRIPTION MLSB14, the Eighth International Workshop on Machine Learning in Systems Biology, is a workshop of the ECCB 2014 conference. It aims to contribute to the cross-fertilization between the research in machine learning methods and their applications to systems biology by bringing together method developers and experimentalists. We are soliciting submissions bringing forward methods for discovering complex structures (e.g. interaction networks, molecule structures) and methods supporting genome-wide data analysis Please see the workshop website http://www.mlsb.cc for more details. SUBMISSIONS OF EXTENDED ABSTRACTS We invite you to submit an extended abstract of up to 4 pages in PDF format describing new or very recently published results. Each extended abstract must be submitted by *June 22 2014* (extended) electronically via the Easychair submission system: https://www.easychair.org/conferences/?conf=mlsb2014 Submissions will be reviewed by the scientific programme committee. They will be selected for oral or poster presentation according to their originality and relevance to the workshop topics. SUBMISSIONS OF POSTER PRESENTATIONS We invite you also to apply for poster presentations on topics of relevance to the workshop. Each poster presentation should be described in a 1 page summary and should be submitted by July 13, 2014 via the Easychair submission system: https://www.easychair.org/conferences/?conf=mlsb2014 KEY DATES - Deadline for submission of extended abstracts: ** June 22, 2014 ** - Deadline for submission of poster presentations: July 13, 2014 - Author notification: July 15, 2014 - Early registration deadline ECCB14: August 2, 2014 - Workshop: September 6-7, 2014 CONFIRMED INVITED SPEAKERS Pierre Baldi, UCI University, California, USA Karsten Borgwardt, Max Planck Institute, Tubingen, Germany CONTACT For further information, please contact chairsmlsb2014(a)gmail.com CHAIRS Florence d'Alché-Buc (University of Evry, France) Pierre Geurts (University of Liege, Belgium) ORGANIZING COMMITTEE Florence d'Alché-Buc (University of Evry, France) Markus Heinonen (University of Evry, France) Pierre Geurts (University of Liege, Belgium) Vân Anh Huynh-Thu (University of Edinburgh, UK) Nizar Touleimat (Centre National de génotypage, CEA, Evry, France) PROGRAM COMMITTEE Florence d'Alché-Buc (University of Evry, France) Chloé-Agathe Azencott (CBIO, Mines ParisTech, Institut Curie, INSERM, France) Karsten Borgwardt (MPI Tubingen, Germany) Sašo Džeroski (Jožef Stefan Institute, Slovenia) Mohamed Elati (Universite d'Evry, France) Pierre Geurts (University of Liège, Belgium) Markus Heinonen (University of Evry, France) Van Anh Huynh-Thu (University of Edinburgh, UK) Ross King (Aberystwyth University, UK) Stefan Kramer (University of Mainz, Germany) Yves Moreau (Katholieke Universiteit Leuven, Belgium) Sach Mukherjee (Netherlands Cancer Institute, Netherlands) Mahesan Niranjan (University of Southampton, UK) Uwe Ohler (Duke University, USA) John Pinney (Imperial College London, UK) Simon Rogers (University of Glasgow, UK) Juho Rousu (University of Helsinki, Finland) Yvan Saeys (University of Ghent, Belgium) Peter Sykacek (BOKU University, Austria) Nizar Touleimat (Centre National de Genotypage, CEA, France) Koji Tsuda (National Institute of Advanced Industrial Science and Technology, Japan) Jean-Philippe Vert (Ecole des Mines de Paris, France) Filip Zelezny (Czech Technical University in Prague, Czech Republic)

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Missed the submission for ECCB 2014? Submit your abstract for the 3rd European Student Council Symposium, directly preceding ECCB 2014!
by ISCBSC announcement 12 Jun '14

12 Jun '14

Dear Colleagues, If you missed the submission for the ECCB2014, take this second change to present your work to the European Computational Biology network! Submit your abstract now for the 3rd European Symposium of the International Society for Computational Biology Student Council, to be held on September 6th 2014 in Strasbourg, France, as a satellite meeting of the European Conference on Computational Biology (ECCB)! ESCS2014 will bring together young computational biologists from several research areas and regions of the world. As the central part of our symposium, 10 students will be selected for an oral presentation from the submitted abstracts. This is your chance to present your work to an international audience of young scientists! In addition, we are proud to host several keynotes from distinguished scientists, such as Dr. Lennart Martens from the University of Ghent and Dr. Jeroen de Ridder from the Delft University of Technology. We welcome abstracts covering both scientific studies as well as novel tools and applications in the field of computational biology and bioinformatics. As in previous editions, awards will be given to outstanding posters and presentations. All abstracts accepted for oral presentation will be published in a special issue of the BMC Bioinformatics journal. Submission information: http://escs2014.iscbsc.org/escs-submission General information: http://escs.iscbsc.org/ Important dates April 24, 2014: Abstract submission opens June 23, 2014: Abstract submission closes July 15, 2014: Abstract acceptance notifications We look forward to receiving your abstract! On behalf of the ESCS organizers, Pieter Meysman Chair, 3rd European Student Council Symposium 2014 Margherita Francescatto Co-Chair, 3rd European Student Council Symposium 2014

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WCB '14: final call for papers
by Nicos Angelopoulos 12 Jun '14

12 Jun '14

------------------------------------------------------------ CALL FOR PAPERS ------------------------------------------------------------ WCB 2014 10th Workshop on Constraint-Based Methods for Bioinformatics http://cp2014.a4cp.org/workshops/bioinfo14 Co-located with 20th International Conference on Principles and Practice of Constraint Programming September 8, Lyon, France Submissions deadline: June 30 ------------------------------------------------------------ Technical Description --------------------- During the last years, Biology has become a source of challenging problems for the entire field of Computer Science in general, and for the areas of computational logic and constraint programming in particular. Successful approaches to these problems are likely to have significant applications in several fields of research, such as medicine, agriculture, industry, etc. Several successful applications of the Logic and Constraint Programming paradigms in Bioinformatics have been carried out in the last years, in the area of phylogenetic tree reconstruction, in haplotype inference, in proteins structure prediction, in RNA secondary structure prediction, and in system biology, just to cite a few. The workshop aims at exchanging ideas between researchers and collecting, if possible, new problems to be faced in the next future by our community. Workshop Format --------------- WCB'14 is the 10-th of a series of consecutive Workshops on Constraint-Based Methods for Bioinformatics. Previous editions of WCB were co-located with various important international conferences, as reported below: - WCB'05: co-located with ICLP-CP 2005 in Sitges - WCB'06: co-located with CP 2006 in Nantes - WCB'07: co-located with ICLP 2007 in Porto - WCB'08: co-located with CPAIOR 2008 in Paris - WCB'09: co-located with CP 2009 in Lisbon - WCB'10: co-located with FLOC 2010 in Edinburgh - WCB'11: co-located with CP 2011 in Perugia - WCB'12: co-located with ICLP 2012 in Budapest - WCB'13: co-located with CP 2013 in Uppsala Details about last-year WCB'13 can be found at http://cp2013.a4cp.org/workshops/wcb Paper Submission ---------------- The topic of interest are all those concerning bioinformatics and constraints and related (SAT/ASP/Logic Programming/ILP) techniques, such as: - RNA prediction and motif search - protein structure and functional prediction - genetic linkage analysis and haplotype inference - pedigree reconstruction and diagnosis - genomic selection design - gene regulatory network inference and analysis - biochemical network simulation and visualization - solvers for problems in biology - metabolic pathway analysis - DNA sequence assembly - contig scaffolding - multiple sequence alignment - machine learning and big data - ontologies - constraint databases - logical interfaces to relational databases - web services - databases integration and federation - RDF graphs and tools Submitted papers can be: - Full papers describing new research results - Extended Abstracts concerning original (unpublished) results. - Abstracts describing ongoing work. - System descriptions (with demos at the workshop). - Summaries of already accepted or recently published papers/results. - Well-motivated proposals of bioinformatics problems for constraint based methods. Submitted papers should be 3-15 pages long in the LNCS format. Submissions are managed through EasyChair https://www.easychair.org/conferences/?conf=wcb14 Important dates --------------- - Paper Submission Dealine June 30 - Notification to Authors July 28 - Final Version August 18 - Workshop Date September 8 Invited Speaker --------------- - Graham Kemp, Chalmers University, Sweden Workshop Organizers ------------------- - Nicos Angelopoulos, Imperial College, London, UK - Simon de Givry, MIAT INRA, Toulouse, France Program Committee ----------------- - Pedro Barahona, Universidade Nova de Lisboa, Portugal - Alexander Bockmayr, Freie Universitat Berlin, Germany - Mats Carlsson, SICS AB, Uppsala, Sweden - Agostino Dovier, Universita degli Studi di Udine, Italy - Francois Fages, INRIA Paris-Rocquencourt, France - Arun Konagurthu, Monash University, Australia - David Lesaint, University of Angers, France - Ines Lynce, INESC-ID, Lisbon, Portugal - Nigel Martin, Birkbeck College, UK - Chris Mungall, Lawrence Berkeley National Laboratory, CA, USA - Alessandro Dal Palu, Universita degli Studi di Parma, Italy - Enrico Pontelli, New Mexico State University, USA - Sylvain Soliman, INRIA France - Sebastian Will, University Leipzig, Germany - Matthias Zytnicki, MIAT INRA, Toulouse, France

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4 PhD opportunities at Wageningen Univeristy
by Besten, Heidy den 06 Jun '14

06 Jun '14

Dear sir/madam, Please find attached 4 vacancies for PhD students in the Food Domain of Wageningen University. I would be grateful if you can please pass this information on to relevant contacts/people that may be interested in applying. Thanks in advance Heidy den Besten dr. ir. H. M. W. den Besten (Heidy) Assistant Professor in Food Microbiology Wageningen University Laboratory of Food Microbiology Postal address: PO Box 17, 6700 AA Wageningen, The Netherlands Visiting address: Building 118 (Axis-X office 3.10B), Bornse Weilanden 9, 6708 WG Wageningen, The Netherlands T: +31-317-483213 E-mail: heidy.denbesten(a)wur.nl<mailto:heidy.denbesten@wur.nl> I: www.fhm.wur.nl<http://www.fhm.wur.nl/> **************************** Food System Dynamics Press release The Food Science cluster of Wageningen University decided to integrate their expertise and to further consolidate their leading position by setting up a System Dynamics program. Cluster Food Sciences: * Laboratory of Food Chemistry<http://www.wageningenur.nl/en/Expertise-Services/Chair-groups/Agrotechnolog…> * Laboratory of Food Microbiology<http://www.wageningenur.nl/en/Expertise-Services/Chair-groups/Agrotechnolog…> * Food Process Engineering Group<http://www.wageningenur.nl/en/Expertise-Services/Chair-groups/Agrotechnolog…> * Food Quality and Design<http://www.wageningenur.nl/en/Expertise-Services/Chair-groups/Agrotechnolog…> * Physics and Physical Chemistry of Foods<http://www.wageningenur.nl/en/Expertise-Services/Chair-groups/Agrotechnolog…> The Food Sciences cluster has allocated funds for five PhDs projects (one is already assigned) * PhD Food Microstructure System Dynamics May 22, 2014<http://www.wageningenur.nl/en/Jobs/Vacancies/Show/PhD-Food-Microstructure-S…> * PhD Food Design System Dynamics May 22, 2014<http://www.wageningenur.nl/en/Jobs/Vacancies/Show/PhD-Food-Design-System-Dy…> * PhD Food Safety System Dynamics May 22, 2014<http://www.wageningenur.nl/en/Jobs/Vacancies/Show/PhD-Food-Safety-System-Dy…> * PhD Food Digestion Dynamics - Molecular Aspects May 22, 2014<http://www.wageningenur.nl/en/Jobs/Vacancies/Show/PhD-Food-Digestion-Dynami…> The projects are organized along two main trajectories * Food production Dynamics - on the transition from food supply chains that are now effective, but not efficient in the use of resources generating a lot of waste. * Food digestion dynamics - on the bridging between food sciences and nutrition sciences, which will focus on understanding how the composition and structure of food products determines the release and uptake of nutrients. The goal is to construct a comprehensive Systems Dynamics approach providing suitable tools to manage complex systems and to deliver sound scientific bases allowing the creation of new products and sustainable and safe processes. The ultimate mission is to supply people suitable foods for their specific needs promoting at the same time the development of zero-waste sustainable circular food chains.

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CSCDA 2014
by CSCDA2014＠montefiore.ulg.ac.be 06 Jun '14

06 Jun '14

--- APOLOGIES FOR CROSS-POSTING--- Dear Friends and Colleagues, On behalf of the entire organizing committee, we are glad to announce the third edition of CAPITA SELECTA IN COMPLEX DISEASE ANALYSIS (CSCDA2014). This year’s meeting aims to create a broad platform to discuss issues in complex disease analysis, in particular in uncovering population and patient heterogeneity, as well as in data fusion and integration to improve mechanistic insights in rare diseases. Our targeted audience has a background in life sciences, biomedical sciences, statistics, bioinformatics, statistical genetics and medicine, or related disciplines. The mini-conference will exist of two parts: tutorial sessions in the forenoon of November 24, and keynote speaker sessions, followed by contributed oral and poster presentations on November 24 – November 26. The ABSTRACT SUBMISSION DEADLINE IS JULY 15, 2014. More information about abstract submission and registration details are available on the conference website. MARK YOUR AGENDA: Date: 24 November – 26 November 2014 Place: Liège, GIGA, Belgium URL: http://www.statgen.ulg.ac.be/CSCDA2014/cscda2014.html We already have an impressive list of confirmed speakers for this edition, and hope to see you in Liège during the fall! Please do feel free to forward this e-mail correspondence to others who you might think would be interested in the event. With best regards, on behalf of the CSCDA2014 Organizing committee, Kristel Van Steen and Kristel Sleegers

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Academic research position in Systems biology in Leuven (BOFZAP)
by Stein Aerts 04 Jun '14

04 Jun '14

FYI: a full time academic research position in Systems Biology in Leuven: see https://icts.kuleuven.be/apps/jobsite/vacatures/52952761?lang=en Best, Stein Aerts Stein Aerts, PhD Assistant Professor Laboratory of Computational Biology Center for Human Genetics University of Leuven Herestraat 49, P.O. Box 602 3000 Leuven, Belgium Office +32 16 330710 Lab + 32 16 330142 Mobile +32 486 659003 http://med.kuleuven.be/lcb/

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