- BBClist - maillist.psb.ugent.be

Registration open for EBI Roadshow Amsterdam 9-10 April 2013
by Celia van Gelder 12 Mar '13

12 Mar '13

Dear colleague, On 9-10 April 2013, NBIC and AMC will organize an EBI Roadshow at AMC Amsterdam. Topics are _April 9, 2013:_ Introduction to the databases at the EBI Sequence Searching and Alignment _April 10, 2013_ ArrayExpress: Public database for transcriptomics data & Gene Expression Atlas Ensembl for new Ensembl users This course is aimed at researchers across the Netherlands who wish to develop their understanding of the data resources and tools available from EMBL-EBI. The programme provides an overview of commonly-used EBI public resources for the analysis of nucleotide, protein and microarray data. Delegates will learn about these data resources in short lectures and then gain hands-on experience in using them to analyse data. The practical exercises use web-browser-based tools and assume no previous training in bioinformatics programming. Registration is now open. See: http://www.nbic.nl/education/course-overview/pages3/1/coursedetails/ebi-roa… a page including programme and link to registration form. Furthermore, you can find a flyer in the attachment. I want to ask you if you can spread this information in your organisation. Thank you, Best regards, Celia van Gelder NBIC Education Dr. Celia W.G. van Gelder Coordinator Education CMBI Projectleader Education NBIC tel. +31-(0)24-3666120 e-mail:C.vanGelder@cmbi.ru.nl websites:www.cmbi.ru.nl,www.nbic.nl Postal address: CMBI 260 Radboud University Nijmegen-Medical Centre /NCMLS PO Box 9101, 6500 HB Nijmegen The Netherlands

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ISCB Student Council Symposium 2013 - Call for abstracts
by ISCB Student Council Symposium 11 Mar '13

11 Mar '13

_ISCB Student Council Symposium 2013_ *The ISCB Student Council Symposium will be held on July 19th (directly preceding ISMB/ECCB 2013) in Berlin, Germany.* The Student Council Symposium is a forum for students, post docs, and young researchers in the fields of Computational Biology and Bioinformatics. Participants have the opportunity to present their work to an international audience, build a network within the computational biology community and develop important soft skills in an environment that fosters exchange of ideas and knowledge. We encourage you to submit an abstract and to bring a poster for showcasing your work at the Symposium's poster session. As a central part of the Symposium, ten abstracts will be selected for an oral presentation. We accept abstracts covering both scientific studies as well as novel tools and applications in the field of computational biology and bioinformatics. Travel fellowships will be available for accepted abstracts, and awards will be given to best posters and presentations. *LINKS* _Symposium website_: http://symposium.iscbsc.org/ _Submission link_: http://www.iscb.org/submissions/index.php?id=156 _Travel Fellowships information_: http://symposium.iscbsc.org/content/travel-fellowships *IMPORTANT DATES* April 16: Abstract submission deadline April 26: Travel Fellowship submission deadline April 30: Abstract acceptance notifications May 14: Travel fellowship acceptance notifications July 19th: Student Council Symposium 2013 We look forward to receiving your abstract! Tomás Di Domenico, Chair Tomasz Stokowy, Co-chair

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Fwd: Postdoctoral Researcher Post - VACANCY
by Sanne Abeln 10 Mar '13

10 Mar '13

Postdoctoral Researcher in Computational Structural Biology and Associate Director of the Doctoral Training Centre We invite applications for a postdoctoral position, jointly funded by UCB and the University of Oxford Doctoral Training Centres, focussing on the development of methods for membrane protein structure prediction. The research will be carried out under the supervision of Prof Charlotte Deane and based within the Department of Statistics. The post-holder will also act as an Associate Director of the Doctoral Training Centre, being involved in the teaching and administration of the DTC training programme. The appointment will be for up to 18 months in the first instance with the possibility of an 18 month extension, is available with immediate effect and offers a salary of £29,541 - £36,298 per annum (Grade 7). The successful candidate will have a doctorate degree in a relevant discipline and experience in scientific computing, software development and structural biology. Excellent programming skills are essential as well as a strong understanding of biology. Experience of scientific teaching or training would also be desirable. Applications must be made online through the main University website: http://www.ox.ac.uk/about_the_university/jobs/research/ Applicants are required to upload a full CV and supporting statement as part of the online application for this post and must ask two referees to submit recommendations directly to: Samantha.miles(a)dtc.ox.ac.uk by the deadline, quoting reference DTC/UCB 106979. For research related queries regarding this post, please contact Prof Charlotte Deane charlotte.deane(a)dtc.ox.ac.uk. All other queries should be directed to the DTC Administrator, Samantha Miles in the first instance (e-mail as above or telephone 01865 610660). Only applications made online before midday on Wednesday 3rd April 2013 will be considered. Please do pass this message on to anyone you think may be suitable or interested (and preferably both) -- Sanne Abeln Assistant Professor Bioinformatics - VU University Amsterdam s.abeln(a)vu.nl +31 20 59 87816 www.few.vu.nl/~abeln

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CAPRI2013 meeting Utrecht
by Barbara van Kampen 07 Mar '13

07 Mar '13

Dear all, The full programme for the CAPRI2013 meeting organized in Utrecht in April is now available online, including the selected short talks. www.capri2013.nl <http://www.capri2013.nl/> -> timetable Or direct link: http://tintin.science.uu.nl/CAPRI2013/program/timetable The registration is still open but a late registration fee of 50 euros will be charged after March 11th. Looking forward to see you in Utrecht. Best regards Alexandre Bonvin & the CAPRI committee -- Barbara van Kampen CMBI 260 Radboud University Nijmegen-Medical Centre / NCMLS CMBI Office / Room 0.02 PO Box 9101 Geert-Grooteplein 26-28 6500 HB Nijmegen 6525 GA Nijmegen Phone: +31(0)24 36 19390 Fax: +31 (0)24 36 19395 www.cmbi.ru.nl

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PhD position at Lille University: Statistical learning to improve gene knockout predictions for metabolic networks
by Celine Kuttler 06 Mar '13

06 Mar '13

PhD: Statistical learning to improve gene knockout predictions for metabolic networks Lille University, France (BioComputing team) http://www.lifl.fr/BioComputing/data/learningPhD2013.html 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 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 developing prediction algorithms that benefit from the additional quantitative information, based on techniques from the area of formal program analysis. The supervisory team: J. Niehren (INRIA) and C. Kuttler (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 Engi- neering 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. ----------------------------------------------------------------------------------------- Celine Kuttler, PhD Lille 1 University, LIFL http://www.lifl.fr/~kuttler phone: +33 3 20 33 59 55

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Job announcement: GIGA PhD and Postdoctoral Opportunities in Genomics
by marilou.ramospamplona＠ulg.ac.be 06 Mar '13

06 Mar '13

GIGA PhD and Postdoctoral Opportunities in Genomics The GIGA-Genetics unit from the University of Liege (Belgium) seeks applicants for PhD and postdoctoral positions to join research projects in the areas of medical (CAUSIBD) and fundamental genomics (DAMONA). The successful applicants will have the motivation to make a strong contribution in the area of bioinformatics and statistical genetics, and will have a strong training in either biological, computer, engineering, physical or mathematical sciences. Information about the GIGA institute and the Unit of Animal Genetics can be obtained from: http://www.giga.ulg.ac.be/jcms/c_5015/en/home and http://www.giga.ulg.ac.be/jcms/prod_205624/unit-of-animal-genomics. The fulltime positions are immediately available and will be for an initial period of two years with a possibility of renewal. Applications or requests for further information should be sent to michel.georges(a)ulg.ac.be. The advertisement will remain open until suitable candidates are selected, with a first round of selection to be done by 30 April 2013. Description of projects CAUSIBD Inflammatory Bowel Disease (IBD), which includes Crohn’s disease (CD) and ulcerative colitis (UC), afflicts ~1/300 inhabitants of developed countries at one point during their lifetime. CD and UC are characterized by chronic and relapsing inflammation of the gastrointestinal tract associated with debilitating symptoms and tissue damage leading to complications and surgical resections of bowel segments. IBD strongly compromises life quality of the patients, and is a major burden to society due to the costs of treatment but also of unemployment and disability allowance. The incidence of IBD, as of other inflammatory pathologies, has increased dramatically during the 20-ies centuries in Western societies (particularly and worryingly in the young), pointing towards a major - as of yet unidentified - environmental or behavioral trigger. However, all individuals are not equally susceptible to the effects of these environmental risk factors. Twin and familial studies indicate that the heritability of inherited predisposition to IBD (assuming a threshold model with underlying liability) is higher than 50%. Genome wide association studies have uncovered more than 100 “common” risk loci for IBD, including CD specific, UC-specific and CD/UC-shared risk loci, which jointly explain ~25% of inherited risk. Analysis of a subset of GWAS hits has revealed the importance of perturbed autophagy, innate immunity and IL23 signaling in determining inherited predisposition. Drug development targeting these pathways is ongoing. However, for the vast majority of risk loci (which typically encompass ~200 Kb, 500 DNA sequence variants and 5 genes) causative genes and variants remain unidentified. Moreover, the fact that identified loci only explain 25% of the heritability raises the question about the molecular nature of the 75% missing heritability. The Belgian IBD consortium (BIBDC), comprising gastro-enterologists and geneticists from the ULg (E. Louis & M. Georges), ULB (D. Franchimont), KUL (S. Vermeire), and RUG (M. De Vos), has assembled one of the largest IBD case-control cohorts in the world. This has allowed BIBDC to make important contributions to recent studies into the genetics of IBD (f.i. Libioulle et al., PLoS Genetics 3:e58 (2007); Barrett et al., Nature Genetics 40:955-962 (2008); Imielinski et al. Nature Genetics 41:1335-1340 (2009); Franke et al., Nature Genetics 42:1118-1125 (2010); Momozawa et al., Nature Genetics 43:43-47 (2011); Anderson et al., Nature Genetics 43: 246-252 (2011)), and to be a major partner in the International IBD Genetics Consortium (IIBDGC), providing the Belgian IBD community with privileged access to meta-data. The objectives of the CAUSIBD project are: 1. To identify causative genes and variants in known IBD risk loci using an integrated genomic, epigenomic, transcriptomic and endo-phenotypic approach. 2. To study the effect of host genotype on gut microbiome composition in relation to inherited predisposition to IBD. 3. To analyze the contribution of rare and low frequency risk variants, quasi-infinitesimal architecture, and epistatic interactions to the missing heritability for IBD predisposition. 4. To study the potential diagnostic utility of quasi-infinitesimal modeling of IBD predisposition, disease-progression, co-morbidity and differential diagnosis. DAMONA Mutation and recombination are fundamental biological processes that determine the adaptability of populations in changing environments. The mutation rate that prevails in a population reflects the equilibrium between the need to be adaptable, the burden of the mutation load, the resources invested in reducing the error rate (cost of fidelity), and random drift that determines a lower limit in achievable fidelity. Recombination fulfills an essential mechanistic role during meiosis and is exquisitely regulated to ensure proper chromosomal segregation. Recombination affects the rate of creation and loss of haplotypes with cis configured favorable alleles, imposing second order selection pressure on local and global modifiers of recombination. It is becoming increasingly apparent that recombination and mutation rates vary between individuals, and that these differences are in part inherited. Both processes are therefore evolvable themselves, and hence amenable to genomic analysis. Identifying genetic determinants underlying these differences would provide novel insights in the molecular mechanisms regulating mutation and recombination. The mutational load, and in particular the number of lethal equivalents per average individual, remains poorly defined as epidemiological and molecular data yield estimates that differ by one order of magnitude. A relationship between recombination and fertility has been reported in Icelandic women but awaits confirmation. Population structure (small effective population size; large harems), phenotypic data collection (systematic recording of > 50 traits on millions of cows), and large-scale SNP genotyping (for genomic selection), make cattle populations uniquely suited for genetic analyses. Damona proposes to exploit these unique resources, combined with recent advances in next generation sequencing and genotyping, to: 1. Quantify and characterize inter-individual variation in male and female mutation and recombination rates, 2. Map, fine-map and identify causative genes and variants underlying QTL influencing these four phenotypes, 3. Test the effect of loss-of-function variants in protein-coding genes on >50 phenotypes including fertility, and study the effect of variation in recombination on fertility.

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Call for Papers IFAC CAB 2013
by Eric Bullinger 05 Mar '13

05 Mar '13

*CALL FOR PAPERS* *IFAC CAB 2013* 12^th International Symposium on *C*omputer *A*pplications in *B*iotechnology 16-18 December 2013, Mumbai, India http://www.cab2013.org/ Dear colleague, It is our pleasure to announce the 12^th International Symposium on *C*omputer *A*pplications in *B*iotechnology, IFAC CAB 2013, which will be held in Mumbai, India from 16^th to 18^th December, 2013. Organized under the auspices of the International Federation of Automatic Control (IFAC), the CAB 2013 Symposium aims to stimulate contacts between specialists active in academic research and industrial development in all major areas of biotechnology, where computers are used to aid bioprocess design, supervision, diagnosis, operation, optimization and control. Please note the following important dates related to CAB 2013: * Deadline for receipt of draft papers: March 31, 2013 * Author Notification: June 30, 2013 * Final paper submission deadline: July 31, 2013 * Final programme will be available by: September 30, 2013 We cordially invite you to consider submitting one or more original papers in the areas listed below: 1. Systems Biology, Metabolic Engineering 2. Disease modelling, Synthetic networks 3. Modelling and Identification, Parameter and State Estimation, Dynamics and Control 4. Fault Diagnosis and Monitoring, Data Mining Tools 5. Bioinformatics, Downstream Processing 6. Integrated Bioprocessing, Scheduling, Coordination, Optimization 7. Life Cycle Analysis 8. Applications: Microbial technology, mammalian insect and plant cell technology, gene therapy, pharmaceutical processes, food engineering, bulk chemicals production, environmental (wastewater, bioremediation), biofuels. For the third time, CAB is organized in coordination with DYCOPS (International Symposium on DYnamics and COntrol of Process Systems). DYCOPS2013 and CAB2013 conferences will be held contiguously at the same venue with an overlap of one day during the week of December 16-20, 2013. Please visit the conference site (http://www.cab2013.org/) for more information. We will be updating the site periodically as more details are firmed up. We look forward to seeing you in Mumbai. With Best Regards, Eric Bullinger (IPC Chair), Liège, Belgium S. Lakshminarayanan (IPC Co-chair), NUS, Singapore Jayant Modak (NOC Chair), IISc Bangalore K.V. Venkatesh (NOC Co-chair), IIT Bombay and Members of the IPC and NOC, CAB 2013 *********************************************************************** IFAC Copyright Conditions "The material submitted for presentation at an IFAC meeting (Congress, Symposium, Conference, Workshop) must be original, not published or being considered elsewhere. All papers included in the program will be distributed to the participants. Proceedings of the IFAC Congress, Symposia, Conferences and Workshops will be hosted on-line on the IFAC-PapersOnLine.net website. The presented papers will be further screened for possible publication in the IFAC Journals (Automatica, Control Engineering Practice, Annual Reviews in Control, Journal of Process Control, Engineering Applications of Artificial Intelligence, and Mechatronics), or in IFAC affiliated journals. All papers presented will be recorded as an IFAC Publication. Copyright of material presented at an IFAC meeting is held by IFAC. Authors will be required to transfer copyrights electronically or by hard copy. The IFAC Journals and, after these, IFAC affiliated journals have priority access to all contributions presented. However, if the author is not contacted by an editor of these journals, within three months after the meeting, he/she is free to submit an expanded version of the presented material for journal publication elsewhere. In this case, the paper must carry a reference to the IFAC meeting where it was originally presented and, if the paper has appeared on the website www.IFAC-PapersOnLine.net, also a reference to this publication".

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PhD or Postdoc position in Delft Bioinformatics Lab @ the Delft University of Technology
by Jeroen de Ridder - EWI 04 Mar '13

04 Mar '13

We have an open position for a PhD or PostDoc on the topic of Computational Cancer Biology / Bioinformatics! http://recruitment2.tudelft.nl/vacatures/index.php?type=a&lang=en&id=526490 Postdoc or PhD in Bioinformatics Department/faculty: Electrical Engineering, Mathematics and Computer Science Level: Master degree Working hours: 38 hours per week Contract: 3 years (4 for PhD) Salary: €2042 to €3755 per month gross Job description Cancer is a complex disease caused by a myriad of changes in the DNA sequence. We are currently entering an era in which it is possible to determine the complete sequence of a cancer genome and capture a nearcomplete DNA mutation profile. As a result, it is becoming clear that each individual tumour is unique. A key question in cancer research is thus: how can we resolve the molecular mechanisms of cancer if the mutation profile is different for each tumour? In this project, we address this challenge with scalespace theory, allowing us to redefine a common mutation without making prior assumptions on the scale at which these mutations are apparent. This is important because a cancer gene can be disrupted by a single base pair change or a largescale deletion of a chromosome arm, two completely different (spatial) scales along the genome axis. By combining data across all possible scales, and by defining structure in these data at the appropriate scale, statistical power to detect a common ‘mutation’, and thus cancer genes, is maximised. Scalespace theory can also be used when scale is defined in terms of a functional distance, such as in gene interaction networks, rather than a base pair distance. This allows us to define common mutation of function, such as signaling cascades (smallscale) or whole genetic pathways (largescale). In addition to revealing novel biomarkers for cancer, we envision this will provide invaluable insight into the context in which cancer genes deregulate important cellular processes, thus revealing new avenues for personalised treatment strategies. Requirements We are looking for candidates who have demonstrated excellence in one of the following (or related) fields: bioinformatics, (bio)statistics, machine vision, pattern recognition or computer science. Candidates should possess an MSc degree (PhD for a postdoc appointment) and are expected to be fluent in written and spoken English. Knowledge of molecular biology is an advantage. Candidates are expected to be interested in working at the boundaries of several research domains (computer science, bioinformatics, molecular biology), and with people from several international institutes (e.g. Kluyver, NKI). Conditions of employment The successful PhD candidate will be employed fulltime by TU Delft for a fixed period of 4 years within which he or she is expected to write a dissertation leading to a doctoral degree (PhD thesis). The starting salary for a PhD is €2062 gross per month increasing to a maximum of €2638 gross per month in the fourth year. The starting salary for a Postdoc is €3007. TU Delft offers an attractive benefits package, including a flexible work week, free highspeed Internet access from home (with a contract of two years or longer), and the option of assembling a customised compensation and benefits package (the 'IKA'). Salary and benefits are in accordance with the Collective Labour Agreement for Dutch Universities. Information and application For more information about this position, please contact Dr. Jeroen de Ridder, phone: +31 (0)152783418, email: j.deridder(a)tudelft.nl<mailto:j.deridder@tudelft.nl>. To apply, please email a detailed CV including contact details of references, a course list with grades and a letter of application in which you explain both your interest and the relevance of your skills and experience in the context of this research project. Please email your application by 15 april 2013 to Mrs. W. M. Dicke, Hreemcs(a)tudelft.nl<http://tudelft.nl/>. When applying for this position, please refer to vacancy number EWI201307.

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Pathogen Bioinformatics Post-doc advert
by Smit, Sandra 02 Mar '13

02 Mar '13

Available: Postdoc position in Pathogen Bioinformatics University of Pretoria http://fabiserv.up.ac.za/fabinet/research/mppi/postdocbif2013 ~~~~~~~~~~~ Dave Berger, PhD Professor, Plant Science Department Room 4-18, Plant Sciences Complex, University of Pretoria Hatfield 0028, South Africa Phone: +27-12-420 4634 / 4239 Fax: +27-12-420 6668 http://fabinet.up.ac.za/research/mppi Postal address: Private Bag X20, Hatfield, 0028, South Africa

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Research Associate – Computational Expert in Structural Biology or Deep Sequencing – Influenza Research
by Judy Fonville 01 Mar '13

01 Mar '13

Dear BBC list, Our group is currently advertising a position for a Computational Expert in Structural Biology or Deep Sequencing (Centre for Pathogen Evolution, Department of Zoology, University of Cambridge). Information on the post is attached to this email. If you know anybody who might be interested, please feel free to forward this information to them. http://www.zoo.cam.ac.uk/zooone/administration/vacancy.html http://www.zoo.cam.ac.uk/zooone/administration/FI_PF00982.pdf Best wishes, Judy Fonville

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