- BBClist - maillist.psb.ugent.be

job opening for post-doc bio-informatician at CMGG-UGent
by Katleen De Preter 07 Oct '13

07 Oct '13

Dear Colleagues, Enclosed you can find a job opening at the CMGG in Ghent. Feel free to forward this vacancy to other potential candidates. Kind regards, Katleen De Preter Frank Speleman

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Tenure Track Position Assistant Professor Bioinformatics
by berend snel 07 Oct '13

07 Oct '13

*Open position: Assistant Professor Bioinformatics* The Theoretical Biology & Bioinformatics (TBB) group at Utrecht is searching for an assistant professor in bioinformatics with a track record reflecting exciting biological research. You will be functioning at the PI level, develop your own research line and supervise your own PhD students. Your background could be in biology provided you have a solid expertise in bioinformatics, or your background could be in computer science or physics provided you have a genuine biological research line. You are expected to develop your own research line in the life sciences using bioinformatics approaches. This involves acquisition of grants to form your own group within the Bioinformatics group. Assistant professor positionsinvolve both research and teaching. You will be expected to participate in existing bioinformatics courses at the bachelor/master levels and to participate in the development of a new advanced bioinformatics course. The staff researchers of theoretical biology and bioinformatics at the biology department use mathematics, computer science and bioinformatics to perform fundamental biological research in a variety of biological disciplines. Currently it is seeking to strengthen its bioinformatics research. The bioinformatics group develops novel bioinformatics approaches in the areas of comparative genomics and data integration to pursue research into evolution, signalling networks and plant bioinformatics. The group is part of the Institute of Biodynamics and Biocomplexity (IBB), embedded in one of the largest Biology departments in the Netherlands (>200 new students per year). The group teaches bioinformatics to biology students at the bachelor and master level. PhD students in the group have diverse backgrounds ranging from biology, chemistry to computer science, 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. To apply, please find the position here <http://ssl1.peoplexs.com/Peoplexs22/CandidatesPortalNoLogin/Vacancy.cfm?Por…>and attach a letter of motivation, a concise (half page) research plan and curriculum vitae. As part of the selection procedure successful candidates are expected to give an outline of his/her research plans in a written report and an oral presentation. The application deadline is December**1^st , 2013.Additional information about the vacancy can be obtained from: dr. B. Snel (b.snel(a)uu.nl) Conditions of employment: The candidate is offered a full-time position on a tenure track basis at the assistant professor level. The tenure track period is for 5 years, and after a successful evaluation this will be continued on a permanent basis. 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. 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. The gross salary is in the range between 3227 and maximum 5979 Euro per month.

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TPNC 2013: 2nd call for posters
by GRLMC 04 Oct '13

04 Oct '13

*To be removed from our mailing list, please respond to this message with UNSUBSCRIBE in the subject line* ************************************************************************* The 2nd International Conference on the Theory and Practice of Natural Computing (TPNC 2013) invites authors to submit poster presentations. TPNC 2013 will be held in Cáceres (Spain) on 3-5 December, 2013. See http://grammars.grlmc.com/tpnc2013/ Poster presentations are intended to enhance informal interactions with the conference participants, at the same time permitting in-depth discussion. TOPICS Authors are encouraged to submit presentations that discuss novel work in progress on: - nature-inspired models of computation, - synthesis of nature by means of computation, - nature-inspired materials, - information processing in nature, - applications of natural computing. Posters do not need to present final research results. Work that may lead to new interesting developments is welcome. KEY DATES Submission deadline: October 20, 2013 Notification of poster acceptance or rejection: October 27, 2013 SUBMISSION Please submit a .pdf abstract through: https://www.easychair.org/conferences/?conf=tpnc2013 It should contain the title, author(s) and affiliation, and should not exceed 500 words. PRESENTATION Posters will be allocated 8 minutes each in the programme for oral presentation. Moreover, they will remain hanging during the whole conference for discussion. PUBLICATION Posters will not appear in the LNCS proceedings volume of TPNC 2013. However, they will be eligible for submission to the post-conference Soft Computing journal special issue. REGISTRATION Authors of accepted posters have to register to the conference. Their registration fare is reduced: 150 Euro (appr. one third of the fare for PhD students).

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[Gtpb] Bioinformatics Training Course Announcement
by Pedro Fernandes 01 Oct '13

01 Oct '13

Course Announcement NOTE: please apply as soon as possible, the period for applications is exceptionally short due to operational reasons *ARANGS13* Automated and reproducible analysis of NGS data IMPORTANT DATES for ARANGS13 Deadline for applications: October 8th 2013 Notification of acceptance dates: October 15th 2013 Course date: October 21st - October 24th 2013 Course Description: Next generation sequencing (NGS) technologies for DNA have resulted in a yet bigger deluge of data. Researchers are learning that analysing such data sets is becoming the bottleneck in their work. In many cases, several steps in these analyses are fairly generic (e.g. quality control filtering, alignment to reference sequences, typing) so that off-the-shelf pipelines can be applied. In other cases, novel research approaches require development of new analysis pipelines. Either way, all analysis steps should be repeatable and any changes made to the data (e.g. renaming, annotation, alignment) should be recorded so that the provenance of the results is clear and inferences are reproducible. In this brief workshop we will establish several best practices of reproducibility and provenance recording in the (comparative) analysis of data obtained by NGS. In doing so we will encounter the commonly used technologies that enable these best practices by working through use cases that illustrate the underlying principles. Building on the basis of workflow development, we will further illustrate how custom-built workflows can be manipulated using graphical platforms (e.g. Galaxy, Taverna, etc.). Best practices Standardized project organization Projects 'runnable' without user intervention No loss of data, metadata, parameters or source code through versioning Sharing of scripts and workflows Technologies Next generation sequencing platforms File formats (e.g. FASTQ, SAM/BAM, GFF3) Command-line executables, command line scripting and batching High-level programming with domain-specific toolkits Revision control systems Workflow environments (both visual and command line) Use cases Phylogenetic placement of metagenomic data Typing of pathogens Comparative analysis of multicellular genomic data Post-assembly: handling richly annotated genomes More information, including application instructions, available at http://gtpb.igc.gulbenkian.pt/bicourses/ARANGS13/ Thank you 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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[BCC] BBC 2013: abstract submission deadline extended
by BBC2013 01 Oct '13

01 Oct '13

BBC2013 – BeNeLux Bioinformatics Conference 2013 Date: December 9 & 10, 2013 Venue: Salle Dupréel (Université Libre de Bruxelles), Brussels, Belgium Website: http://bbc2013.ibsquare.be Abstract submission deadline: October 6, 2013 (extended) Early registration deadline: November 8, 2013 Dear Colleagues, Due to multiple requests, the deadline for submitting abstracts to the 8th edition of the BeNeLux Bioinformatics Conference has been extended to October 6, 2013! Note that we introduced the possibility to submit late abstracts within October 20, but that they will be considered only for poster presentation. The theme of this year's conference is: "Bioinformatics at all scales of life". Since 2005, the BeNeLux Bioinformatics Conference gives bioinformaticians, from the BeNeLux and beyond, the opportunity to discuss their results and build new collaborations, in a relaxed and friendly atmosphere. This year's edition will be enhanced by the presence of three distinguished keynote speakers: Alfonso Valencia (Spanish National Cancer Research Center, http://bit.ly/14SAITQ) Anna Tramontano (University of Rome "La Sapienza", http://www.biocomputing.it) and Jim Haseloff (Plant Synthetic Biology, University of Cambridge, http://www.haseloff-lab.org) Call for abstracts We invite you to submit an abstract for an oral presentation (20 available slots: 6 long, 14 short) and/or a poster presentation. Contributions from all fields of bioinformatics are welcome and encouraged. We have provided a template to use for submission through the EasyChair system: https://www.easychair.org/conferences/?conf=bbc2013 . Details on the submission procedure can be found at http://bbc2013.ibsquare.be/content/call-abstracts . We hope to see you all in Brussels! -- The BBC 2013 organising committee BeNeLux Bioinformatics Conference 2013 December 9-10, 2013 (Brussels)

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BBC 2013 abstract submission deadline is approaching
by BBC2013 24 Sep '13

24 Sep '13

BBC2013 – BeNeLux Bioinformatics Conference 2013 Date: December 9 & 10, 2013 Venue: Salle Dupréel (Université Libre de Bruxelles), Brussels, Belgium Website: http://bbc2013.ibsquare.be Abstract submission deadline: October 1, 2013 Early registration deadline: November 8, 2013 Dear Colleagues, The deadline for submitting your abstract to the 8th edition of the BeNeLux Bioinformatics Conference is approaching! The theme of this year's conference is: "Bioinformatics at all scales of life". Since 2005, the BeNeLux Bioinformatics Conference gives bioinformaticians, from the BeNeLux and beyond, the opportunity to discuss their results and build new collaborations, in a relaxed and friendly atmosphere. This year's edition will be enhanced by the presence of three distinguished keynote speakers: Alfonso Valencia (Spanish National Cancer Research Center, http://bit.ly/14SAITQ) Anna Tramontano (University of Rome "La Sapienza", http://www.biocomputing.it) and Jim Haseloff (Plant Synthetic Biology, University of Cambridge, http://www.haseloff-lab.org) Call for abstracts We invite you to submit an abstract for an oral presentation (20 available slots: 6 long, 14 short) and/or a poster presentation. Contributions from all fields of bioinformatics are welcome and encouraged. We have provided a template to use for submission through the EasyChair system: https://www.easychair.org/conferences/?conf=bbc2013 . Details on the submission procedure can be found at http://bbc2013.ibsquare.be/content/call-abstracts . We hope to see you all in Brussels! -- The BBC 2013 organising committee BeNeLux Bioinformatics Conference 2013 December 9-10, 2013 (Brussels)

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positions available to study genetic links between brain development and evolution
by pierre vanderhaeghen 23 Sep '13

23 Sep '13

Dear Colleagues, Thanks a lot for relaying the info for this job offer by transmitting to potentially interested colleagues and posting the flyer in your Dept. Best regards, Pierre Vanderhaeghen What Makes us Humans? Positions (Bioinformatics) Available to Study the Genetic Links between Brain Development and Evolution. Postdoctoral positions are available in our group (Pierre Vanderhaeghen Lab http://dev.ulb.ac.be/pvdhlab) to study the molecular mechanisms underlying the development and evolution of the human cerebral cortex. This novel and exciting project, which just received funding by the European Research Council (ERC), will use a unique integrated approach combining molecular/bioinformatic tools, human pluripotent stem cell technology, and mouse developmental neurobiology (Nature 455 (2008), 351-357; Nature Neurosci. (2012), 15, 1627-1635; Neuron (2013), 77, 440-456). We are seeking highly motivated individuals with strong experience in bioinformatics/computational biology, as well as interest in developmental neurobiology and/or evolution. Positions are available immediately, but may be filled later in 2014 if necessary. Our lab is part of the Institute of Interdisciplinary Research (IRIBHM) (http://www.ulb.ac.be/medecine/iribhm/) the largest biomedical Department of University of Brussels (ULB) Medical School, and the newly created ULB Neuroscience Institute (http://uni.ulb.ac.be/) We are located in Brussels, a cosmopolitan city in the heart of Europe. Applications: Please send a cover letter explaining your motivations and previous work, a CV with a list of publications, and the name and coordinates of three references to: Pierre Vanderhaeghen, pierre.vanderhaeghen(a)ulb.ac.be Institute of Interdisciplinary Research (IRIBHM) ULB Neuroscience Institute (UNI) Universite Libre de Bruxelles ULB, Campus Erasme CP 602 Bldg. C Room 6.113/6.111 808, Route de Lennik B-1070 Brussels Belgium Pho: 32-2-555-4186 // 32-2-555-4185 Fax: 32-2-5554655 email: pvdhaegh(a)ulb.ac.be http://dev.ulb.ac.be/pvdhlab http://uni.ulb.ac.be/

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AlCoB 2014: 1st call for papers
by GRLMC 22 Sep '13

22 Sep '13

*To be removed from our mailing list, please respond to this message with UNSUBSCRIBE in the subject line* ********************************************************************* 1st INTERNATIONAL CONFERENCE ON ALGORITHMS FOR COMPUTATIONAL BIOLOGY AlCoB 2014 Tarragona, Spain July 1-3, 2014 Organized by: Research Group on Mathematical Linguistics (GRLMC) Rovira i Virgili University http://grammars.grlmc.com/alcob2014/ ********************************************************************* AIMS: AlCoB aims at promoting and displaying excellent research using string and graph algorithms and combinatorial optimization to deal with problems in biological sequence analysis, genome rearrangement, evolutionary trees, and structure prediction. The conference will address several of the current challenges in computational biology by investigating algorithms aimed at: 1) assembling sequence reads into a complete genome, 2) identifying gene structures in the genome, 3) recognizing regulatory motifs, 4) aligning nucleotides and comparing genomes, 5) reconstructing regulatory networks of genes, and 6) inferring the evolutionary phylogeny of species. Particular focus will be put on methodology and significant room will be reserved to young scholars at the beginning of their career. VENUE: AlCoB 2014 will take place in Tarragona, located 90 kms. to the south of Barcelona. The venue will be the Catalunya Campus. SCOPE: Topics of either theoretical or applied interest include, but are not limited to: Exact sequence analysis Approximate sequence analysis Pairwise sequence alignment Multiple sequence alignment Sequence assembly Genome rearrangement Regulatory motif finding Phylogeny reconstruction Phylogeny comparison Structure prediction Compressive genomics Proteomics: molecular pathways, interaction networks ... Transcriptomics: splicing variants, isoform inference and quantification, differential analysis Next-generation sequencing: population genomics, metagenomics, metatranscriptomics ... Microbiome analysis Systems biology STRUCTURE: AlCoB 2014 will consist of: invited talks invited tutorials peer-reviewed contributions INVITED SPEAKERS: to be announced PROGRAMME COMMITTEE: Tatsuya Akutsu (Kyoto, JP) Amihood Amir (Ramat-Gan, IL) Alberto Apostolico (Atlanta, US) Joel Bader (Baltimore, US) Pierre Baldi (Irvine, US) Serafim Batzoglou (Stanford, US) Bonnie Berger (Cambridge, US) Francis Y.L. Chin (Hong Kong, HK) Benny Chor (Tel Aviv, IL) Keith A. Crandall (Washington, US) Bhaskar DasGupta (Chicago, US) Joaquín Dopazo (Valencia, ES) Liliana Florea (Baltimore, US) Olivier Gascuel (Montpellier, FR) David Gilbert (Uxbridge, UK) Gaston H. Gonnet (Zurich, CH) Roderic Guigó (Barcelona, ES) Dan Gusfield (Davis, US) Vasant Honavar (University College, US) Sorin Istrail (Providence, US) Tao Jiang (Riverside, US) Inge Jonassen (Bergen, NO) Anders Krogh (Copenhagen, DK) Giovanni Manzini (Alessandria, IT) Carlos Martín-Vide (Tarragona, ES, chair) Satoru Miyano (Tokyo, JP) Burkhard Morgenstern (Göttingen, DE) Shinichi Morishita (Tokyo, JP) Cédric Notredame (Barcelona, ES) Graziano Pesole (Bari, IT) Mark Ragan (Brisbane, AU) Timothy Ravasi (Thuwal, SA) Allen G. Rodrigo (Durham, US) Steven Salzberg (Baltimore, US) David Sankoff (Ottawa, CA) Thomas Schiex (Toulouse, FR) João C. Setubal (São Paulo, BR) Steven Skiena (Stony Brook, US) Peter F. Stadler (Leipzig, DE) Wing-Kin Sung (Singapore, SG) Alfonso Valencia (Madrid, ES) Jacques van Helden (Marseille, FR) Arndt von Haeseler (Vienna, AT) Lusheng Wang (Hong Kong, HK) Limsoon Wong (Singapore, SG) Xiaohui Xie (Irvine, US) Dong Xu (Columbia, US) Zohar Yakhini (Santa Clara, US) Alex Zelikovsky (Atlanta, US) Michael Q. Zhang (Dallas, US) ORGANIZING COMMITTEE: Adrian Horia Dediu (Tarragona) Carlos Martín-Vide (Tarragona, chair) Bianca Truthe (Magdeburg) Florentina Lilica Voicu (Tarragona) SUBMISSIONS: Authors are invited to submit non-anonymized papers in English presenting original and unpublished research. Papers should not exceed 12 single-spaced pages (including eventual appendices) and should be formatted according to the standard format for Springer Verlag's LNCS series (see http://www.springer.com/computer/lncs?SGWID=0-164-6-793341-0) Submissions have to be uploaded to: https://www.easychair.org/conferences/?conf=alcob2014 PUBLICATIONS: A volume of proceedings expectedly published by Springer in the LNBI series will be available by the time of the conference. A special issue of a major journal will be later published containing peer-reviewed extended versions of some of the papers contributed to the conference. Submissions to it will be by invitation. REGISTRATION: The period for registration is open from September 21, 2013 to July 1, 2014. The registration form can be found at: http://grammars.grlmc.com/alcob2014/Registration.php DEADLINES: Paper submission: February 4, 2014 (23:59 CET) Notification of paper acceptance or rejection: March 15, 2014 Final version of the paper for the proceedings: March 22, 2014 Early registration: March 29, 2014 Late registration: June 17, 2014 Starting of the conference: July 1, 2014 End of the conference: July 3, 2014 Submission to the post-conference journal special issue: October 3, 2014 QUESTIONS AND FURTHER INFORMATION: florentinalilica.voicu(a)urv.cat POSTAL ADDRESS: AlCoB 2014 Research Group on Mathematical Linguistics (GRLMC) Rovira i Virgili University Av. Catalunya, 35 43002 Tarragona, Spain Phone: +34 977 559543 Fax: +34 977 558386 ACKNOWLEDGEMENTS: Departament dEconomia i Coneixement, Generalitat de Catalunya Universitat Rovira i Virgili

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PhD: Statistical learning to improve gene knockout predictions for metabolic networks
by Cristian Versari 17 Sep '13

17 Sep '13

The following position is again available for a very *short* period. If you are interested, please answer as *soon* as possible at bio-computing-apply(a)lists.gforge.inria.fr PhD: Statistical learning to improve gene knockout predictions for metabolic networks based on abstract interpretation Lille University, France (BioComputing team) Prediction algorithms from computer science will become increasingly relevant to guide the engineering of synthetic biological systems. An important instance is the prediction of gene knockouts from metabolic gene networks [2,6]. This problem is starting to gain industrial relevance for the production of bio-active products by bacteria. An important limitation of existing approaches, which are based on abstract interpretation (a formal approach steming from program analysis) or constraint based optimization, is the absence of quantitative information on the strength of metabolic fluxes in such networks. We propose to remedy the situation by inferring such quantitative information from experimental data by applying statistical machine learning techniques [5,7], and improving the previous prediction algorithms based on abstract interpretation such that they can benefit from the additional quantitative information. The supervisory team: J. Niehren (INRIA) and C. Versari (Lille 1 University), both from the LIFL's BioComputing team. Local collaborators will be, for statistical learning, M. Tommasi (Lille 3 University), and for the biological aspects P. Jacques and F. Coutte (ProBioGem, Polytech Lille). BioComputing and ProBioGem have already cooperated on related topics for two years [1,3,4]. ProBioGem will recruit a PhD student in biology, who will be cooperating with BioComputing's PhD student, on the wet lab side. background : A Master's level with first-class academic credentials is required, preferably in Computer Science, with knowledge on formal methods. We might also consider candidates from biostatistics or maths. duration : 3 years, starting from Sept/Oct 2013. the project is fully funded, an open to students of any citizenship. mail contact bio-computing-apply(a)lists.gforge.inria.fr Please contact us AS SOON AS POSSIBLE ! Publications [1] F. Coutte, M. John, M. Bechet, M. Nebut, J. Niehren, V. Leclère, and P. Jacques. Synthetic Engineering of Bacillus subtilis to Overproduce Lipopeptide Biosurfactants. In 9th European Symposium on Biochemical Engineering Science, Istanbul, Turkey, 2012. [2] A. Goelzer, F. B. Brikci, I. M. Verstraete, P. Noirot, P. Bessieres, S. Aymerich, and V. Fromion. Re- construction and analysis of the genetic and metabolic regulatory networks of the central metabolism of Bacillus subtilis. BMC Systems Biology, 2(1):20+, 2008. [3] M. John, F. Coutte, M. Nebut, P. Jacques, and J. Niehren. Knockout Prediction for Reaction Networks with Partial Kinetic Information: Application to Surfactin Overproduction in Bacillus subtilis. In 3rd International Symposium on Antimicrobial Peptides, Lille, France, June 2012. [4] M. John, M. Nebut, and J. Niehren. Knockout Prediction for Reaction Networks with Partial Kinetic Information. In 14th International Conference on Verification, Model Checking, and Abstract Inter- pretation, volume 7737 of Lecture Notes in Computer Science, pages 355–374, Rome, Italy, Jan. 2013. Springer. [5] K. Murphy and S. Mian. Modelling gene expression data using dynamic Bayesian networks. Technical report, UC Berkeley, 1999. [6] N. D. Price, J. L. Reed, and B. Ø. Palsson. Genome-scale models of microbial cells: evaluating the consequences of constraints. Nature reviews. Microbiology, 2(11):886–897, Nov. 2004. [7] K. Y. Yeung, K. M. Dombek, K. Lo, J. E. Mittler, J. Zhu, E. E. Schadt, R. E. Bumgarner, and A. E. Raftery. Construction of regulatory networks using expression time-series data of a genotyped population. Proceedings of the National Academy of Sciences, 108(48):19436–19441, 2011.

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[Gtpb] GTPB Bioinformatics Training Course Announcement: PNaS13 - Pathways, Networks and Systems
by Pedro Fernandes 16 Sep '13

16 Sep '13

Dear All, We are pleased to announce that the Bioinformatics Training Course PNaS13 - Pathways, Networks and Systems is now OPEN for applications IMPORTANT DATES for this Course Deadline for applications: October 7th 2013 Notification of acceptance within 72 hours of application (working days count) Course date: October 15th to October 17th 2013 Duration: 3 days (21 hours) Registration Fee: Eur 240.00 Short description Recent technological advances in high-throughput methods (such as NGS) and quantitative proteomics, allow us to analyse each individual all the way down to his/her proteins and chemicals and his/her own DNA sequences in just a few hours. In near future we may expect that a specifically trained physician will be able to use this type of data and quickly find support for deciding on individualised therapy, on the basis of analyses made on these data: which drugs, what health risks, what consequences of lifestyle changes, which diets or rehabilitation measures are appropriate for a patient with such an individualised profile. More information, including instructions on how to apply at: http://gtpb.igc.gulbenkian.pt/bicourses/PNaS13/ Thank you for your Interest P. 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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