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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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Position for a Bioinformatician at University of Amsterdam
by Han Rauwerda 02 Jun '14

02 Jun '14

Dear collegues, At the University of Amsterdam, Swammerdam Institute of Life Science, MAD/RNA Biology & Applied Bioinformatics the following position is available: *Bioinformatician* *Faculty of Science - Swammerdam Institute for Life Sciences* Level of education Higher professional education / University Salary indication EUR2,542 to EUR3,831 gross per month, based on 38 hours per week Closing date 15 June 2014 Hours 32 to 38 hours per week Vacancy number 14-176 The _Swammerdam Institute for Life Sciences (SILS)_ <http://sils.uva.nl/>is one of the _Faculty of Science's_ <http://www.uva.nl/en/about-the-uva/organisation/faculties/faculties/faculti…>largest institutes. Its approximately 230 scientists and staff members work in 14 research groups that perform excellent research centered on four themes: 1) The Living Cell, 2) Plant Signaling, 3) Neuroscience, and 4) Life Science Technologies. The MAD: Dutch Genomics Service & Support Provider is the genomics technologies and applied bioinformatics expertise center of SILS. Since 2000 an enthusiastic team of over 15 diverse specialists focuses on the innovation, implementation and application of microarray technology, next-generation sequencing technology, and bioinformatics methods. This includes the use of these approaches in biological and biomedical research in collaboration with many other research groups. As such, the MAD operates as a genomics scientific collaborator in numerous research projects within SILS, other universities and academic hospitals, as well as various companies in the Netherlands. In the context of these collaborations, we are seeking a Bioinformatician. *Job description * The MAD has a long-standing expertise in advanced transcriptomics as well as genomics analysis using several well-established microarray technology and next-generation sequencing platforms. Also proficient bioinformatics expertise and an extensive ICT infrastructure, have been set-up. This offers a unique starting point for an exciting mixture of established and innovative genomics experimentation both for our own research and that of our collaborators. These experiments concern transcriptome research, cancer research, toxicogenomics, food safety, ageing, plant sciences, ecogenomics, neurosciences, etc. MAD is intertwined with the recently established research group 'RNA Biology and Applied Bioinformatics (RB&AB)'. The applied bioinformatician will play a key role in the bioinformatics analysis of transcriptomics and genomics experiments. He/she will employ all necessary bioinformatics methods, tools and infrastructure in close cooperation with MAD and RB&AB wet-lab scientists as well as scientists from collaborating institutes and companies. The bioinformatician will be embedded in and supported by the whole MAD/RB&AB dry-lab team. *Requirements * * Higher professional education (HBO) or MSc. in bioinformatics or expertise at a comparable professional level; * Experience with scripting in R, Python or Perl; * Affinity with life-science research; * Good communicative skills. *Further information * For more detailed information regarding this position you are invited to contact: * _Dr. Timo Breit_ <mailto:t.m.breit@uva.nl>, group leader MAD, RB&AB T: +31 (0)20 525 7058 * _Dr. Martijs Jonker_ <mailto:j.rauwerda@uva.nl>, MAD Dry-lab T: +31 (0)20525 7939 *Appointment * The appointment will be on a temporary basis for a period of two years. Based on a full-time appointment (38 hours per week), the salary will range from EUR2.542 to EUR 3,491 gross per month (salary scale 9). If your expertise and experience are such that you are able to function at a higher level, a salary according to scale 10 (to EUR3,831) may be negotiable. The Collective Employment Agreement of the Dutch Universities is applicable. *Job application * Applications should be submitted by sending your application to _application-science(a)uva.nl_ <mailto:application-science@uva.nl>. To process your application immediately, please quote the vacancy number 14-081 and the position you are applying for in the subject-line. Applications must include a curriculum vitae, a list of publications, a cover letter and the names and contact details of two referees. All these should be grouped in one PDF attachment. /No agencies please/ Kind regards, Han Rauwerda -- ================================================================ Han Rauwerda www.micro-array.nl +31 (0)20 525 7201 MAD - Dutch Genomics Service & Support Provider RB&AB - RNA Biology & Applied Bioinformatics Swammerdam Institute for Life Sciences University of Amsterdam room C2.201 Science Park 904 1098 XH Amsterdam The Netherlands ================================================================

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2nd CFP - MLSB14, the 8th Machine Learning in Systems Biology workshop
by Pierre Geurts 02 Jun '14

02 Jun '14

[Apologies for cross-posting] 2nd 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 deadline: *** June 11, 2014 *** 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 INSTRUCTIONS We invite you to submit an extended abstract of up to 4 pages in PDF format describing new or very recently published results. 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. KEY DATES Submission deadline: June 11, 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 Edimburgh, 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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Job: lecturer/researcher bioinformatics in Groningen
by Noback MA, Michiel 01 Jun '14

01 Jun '14

We have an opening for a lecturer/researcher bioinformatics. Please also forward to any potentially interested candidates you might know. https://www.hanze.nl/NL/over-de-hanzehogeschool/werken-bij/solliciteren/Pag… Additional information can be obtained through me. With kind regards, Michiel Noback Dr. M A. Noback | Bioinformatics senior lecturer & researcher | Institute for Life Science and Technology | Hanze University of Applied Sciences | Phone +50-5954691 | Postbus 3037 | 9701 DA Groningen | The Netherlands

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Job: lecturer bioinformatics at Hogeschool van Arnhem en Nijmegen (Dutch)
by Bruggen Martijn van der 28 May '14

28 May '14

We have an opening for a lecturer Bioinformatics/informatics. Please also forward to any potentially interested candidates you might know. http://ssl1.peoplexs.com/Peoplexs22/CandidatesPortalNoLogin/Vacancy.cfm?Por… (Dutch) Thanks, Martijn van der Bruggen Drs. M.H.H. van der Bruggen Lecturer bioinformatics / Programme director bioinformatics HAN University of Applied Sciences Institute of Applied Sciences (www.han.nl/appliedsciences) Postal address: P.O. Box 6960 | 6503 GL NIJMEGEN | The Netherlands | Martijn.vanderBruggen(a)han.nl<mailto:Martijn.vanderBruggen@han.nl> Visiting Address: Laan van Scheut 2 | Room 0.06 | 6525 EM NIJMEGEN | The Netherlands | +31-6-55206344 Present: Monday - Tuesday - Wednesday - Thursday - Friday [untitled]

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