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

Post-doc position in Structural Bioinformatics in Brussels
by Wim Vranken 06 Dec '15

06 Dec '15

Dear all, Please find attached a PDF detailing a job opening for a structural bioinformatics post-doc at the (IB)2 Interuniversity Institute of Bioinformatics in Brussels via the Vrije Universiteit Brussel, in collaboration with the Universiteit Gent. Best regards, Wim

1 0

AlCoB 2016: 2nd call for papers
by GRLMC 04 Dec '15

04 Dec '15

*To be removed from our mailing list, please respond to this message with UNSUBSCRIBE in the subject line* ************************************************************************************ 3RD INTERNATIONAL CONFERENCE ON ALGORITHMS FOR COMPUTATIONAL BIOLOGY ALCOB 2016 TRUJILLO, SPAIN JUNE 21-23, 2016 Organized by: Computer Architecture and Logic Design Group (ARCO) University of Extremadura Extremadura Centre for Advanced Technologies (CETA-Ciemat) Research Group on Mathematical Linguistics (GRLMC) Rovira i Virgili University http://grammars.grlmc.com/alcob2016/ ************************************************************************************ 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. Previous events were held in Tarragona (2014) and Mexico City (2015). 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 2016 will take place in Trujillo, homeland of the so-called "conquistadores" who arrived in Peru in the XVI century. The venue will be the Extremadura Centre for Advanced Technologies. 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 2016 will consist of: invited lectures invited tutorials peer-reviewed contributions INVITED SPEAKERS (to be completed): S. Cenk Sahinalp (SimonFraserUniversity), Big Data Algorithmics for Cancer Genomics David Sankoff (University of Ottawa), The Evolution of Gene Order in the Flowering Plants PROGRAMME COMMITTEE: Can Alkan (Bilkent University, Ankara, Turkey) Timothy L. Bailey (University of Queensland, Brisbane, Australia) Vladimir Bajic (King Abdullah University of Science and Technology, Thuwal, Saudi Arabia) Geoff Barton (University of Dundee, UK) Inanc Birol (University of British Columbia, Vancouver, Canada) Jacek Błażewicz (PoznańUniversity of Technology, Poland) Alan P. Boyle (University of Michigan, Ann Arbor, USA) Vladimir Brusic (NazarbayevUniversity, Astana, Kazakhstan) Liming Cai (University of Georgia, Athens, USA) Rita Casadio (University of Bologna, Italy) Ken Chen (University of Texas MD AndersonCancerCenter, Houston, USA) Jason Ernst (University of California, Los Angeles, USA) Laurent Gautier (Novartis Institutes for BioMedical Research, Cambridge, USA) Manolo Gouy (ClaudeBernardUniversity Lyon 1, France) Michael Gribskov (PurdueUniversity, West Lafayette, USA) Iman Hajirasouliha (Stanford University, USA) John Hancock (Genome Analysis Centre, Norwich, UK) Artemis Hatzigeorgiou (University of Thessaly, Volos, Greece) Fereydoun Hormozdiari (University of California, Davis, USA) Kazutaka Katoh (Osaka University, Japan) Evangelos Kranakis (Carleton University, Ottawa, Canada) Lukasz Kurgan (University of Alberta, Edmonton, Canada) Bill Majoros (DukeUniversity, Durham, USA) Lennart Martens (Ghent University, Belgium) Maria-Jesus Martin (European Bioinformatics Institute, Hinxton, UK) Carlos Martín-Vide (Rovira i VirgiliUniversity, Tarragona, Spain, chair) Folker Meyer (Argonne National Laboratory, USA) Kenta Nakai (University of Tokyo, Japan) Matteo Pellegrini (University of California, Los Angeles, USA) Mihaela Pertea (JohnsHopkinsUniversity, Baltimore, USA) Ben Raphael (BrownUniversity, Providence, USA) Paolo Ribeca (Pirbright Institute, Woking, UK) Denis Shields (UniversityCollegeDublin, Ireland) Fredj Tekaia (Pasteur Institute, Paris, France) Alessandro Verri (University of Genova, Italy) Fuli Yu (BaylorCollege of Medicine, Houston, USA) Daniel Zerbino (European Bioinformatics Institute, Hinxton, UK) Kaizhong Zhang (University of WesternOntario, London, Canada) Weixiong Zhang (WashingtonUniversity in St. Louis, USA) Zhongming Zhao (VanderbiltUniversity, Nashville, USA) Yaoqi Zhou (GriffithUniversity, Brisbane, Australia) ORGANIZING COMMITTEE: María Botón-Fernández (Trujillo, co-chair) Carlos Martín-Vide (Tarragona, co-chair) Miguel A. Vega-Rodríguez (Cáceres, co-chair) Florentina Lilica Voicu (Tarragona) LOCAL COMMITTEE: Leslye Alarcón (Cáceres) María Botón-Fernández (Trujillo, co-chair) José M. Granado-Criado (Cáceres) Sergio Santander-Jiménez (Cáceres) Miguel A. Vega-Rodríguez (Cáceres, co-chair) 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, references, proofs, etc.) and should be prepared 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=alcob2016 PUBLICATIONS: A volume of proceedings published by Springer in the LNCS/LNBI series will be available by the time of the conference. A special issue of the journal IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB, 2014 JCR impact factor: 1.438, quartile Q1) will be later published containing peer-reviewed substantially 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 October 30, 2015 to June 21, 2016. The registration form can be found at: http://grammars.grlmc.com/alcob2016/Registration.php DEADLINES: Paper submission: January 26, 2016 (23:59 CET) Notification of paper acceptance or rejection: March 1, 2016 Final version of the paper for the LNCS/LNBI proceedings: March 15, 2016 Early registration: March 15, 2016 Late registration: June 7, 2016 Submission to the journal special issue: September 23, 2016 QUESTIONS AND FURTHER INFORMATION: florentinalilica.voicu (at) urv.cat POSTAL ADDRESS: AlCoB 2016 Research Group on Mathematical Linguistics (GRLMC) Rovira i Virgili University Av. Catalunya, 35 43002 Tarragona, Spain Phone: +34 977 559 543 Fax: +34 977 558 386 ACKNOWLEDGEMENTS: Centro Extremeño de Tecnologías Avanzadas (CETA-CIEMAT) Universidad de Extremadura Universitat Rovira i Virgili

1 0

Post-doc Position in Epigenetic Bioinformatics at the German Cancer Research Center (Heidelberg, Germany)
by Pavlo Lutsik 04 Dec '15

04 Dec '15

Dear all, See below a job opening for a bioinformatics post-doc in the department of Prof. Christoph Plass at DKFZ. Best regards, Pavlo ================================= The German Cancer Research Center (DKFZ) offers a Postdoc position in the department of Epigenomics and Cancer Risk Factors headed by Prof. Dr. Christoph Plass. Our Research To gain a comprehensive understanding of individual and general epigenetic defects in cancer diseases (leukemias, prostate cancer, breast cancer and others) we combine various modern genome-wide technologies, including sequencing, bisulfite sequencing, ChIP-seq and others. The intgration of these heterogeneous data sources enables the identification of risk factors, cause and the prediction of progression (prognosis) and therapy suitability. Appropriate evaluation of the different data types requires an in-depth knowledge of modern bioinformatic computing tools and at least basic education in molecular genetics. Supported by statisticians and bioinformaticians (Profs. B. Brors and R. Eils, Universität Heidelberg and DKFZ), we are developing an integrated bioinformatics environment for cancer epigenomics. Your profile We are searching for a bioinformatician to perform integration of multiple epigenomic and genomic datasets, exploratory analysis of novel cohorts, comparative analysis of sample groups, candidate biomarker prioritization, as well as power analysis. Highly motivated bioinformatician or computer scientists with strong biological, biochemical or medical background or biologists, biochemists, physicians with strong informatic background are welcome to apply. Advanced programming skills (R, Perl, Python, and/or Java), experience with NGS tools and the application of unsupervised and supervised learning methods are required. Knowledge in epigenetics is an advantage. The position is initially limited until 09.2017 with a possibility of extension. How to apply Please send a cover letter, CV, full publication list and at least two references (contact persons) using the online job application portal at the following link: http://www.dkfz.de/en/stellenangebote/index.php?id=254/2015 =================================

1 0

BioSB 2016: 2nd Dutch Bioinfrmatics & Systems Biology Conference - Save the date!
by Femke Francissen 04 Dec '15

04 Dec '15

*** Save the date!* *Dutch Bioinformatics & Systems Biology Conference 2016* Date: April 19 / 20, 2016 Venue: Congrescentrum De Werelt, Lunteren, NL Website: http://www.aanmelder.nl/biosb2016 *** Conference* ------------------------------------------------------------ BioSB 2016 is the second edition of the Dutch Bioinformatics & Systems Biology conference. BioSB 2016 discusses the latest developments in bioinformatics, systems and computational biology and interrelated disciplines, and their wide-ranging applications in life sciences & health, agriculture, food & nutrition. This year's conference will be co-organised by the BioSB research school <http://www.biosb.nl> and the Wageningen UR <http://www.wageningenur.nl>. *** Programme* ------------------------------------------------------------ BioSB 2016 will be a 2-day scientific conference (April 19-20, 2016) with keynote speakers, parallel sessions based on abstract submission, an evening poster session and a nice evening programme. The conference will offer lots of opportunities to meet with fellow Bioinformatics and Systems Biology colleagues from academia and industry as well as master students. On April 18, the day preceeding the conference, the YoungCB retreat will be organised. As this is the annual conference of BioSB <http://www.biosb.nl>, the national Bioinformatics & Systems Biology research school, BioSB 2016 will offer a programme with a mix of state-of-the-art work in both areas. Looking back at BioSB 2015 conference <http://biosb.nl/conferences/biosb2015/> *** Keynote speakers* ------------------------------------------------------------ First confirmed keynote speaker: * *Mick Watson*, Director of ARK-Genomics, The Roslin Institute, R(D)SVS, University of Edinburgh. *** Sponsors* *-----------------------------------------------------------* * Utrecht Bioinformatics Center <http://ubc.uu.nl/> Read about our sponsor opportunities <https://www.aanmelder.nl/biosb2016/wiki/154969/sponsorship%20opportunities> *** Save the date!* ------------------------------------------------------------ More information about the conference programme will follow soon! You can find the latest conference updates at the conference website <http://www.aanmelder.nl/biosb2016>. Regular updates will also be sent via the BioSB mailing list <http://biosb.nl/newsletter/>. *** Social media* *-----------------------------------------------------------* * On Twitter we will use the hashtag: #biosb2016 * Like us on Facebook <(https://www.facebook.com/BIOSB-122337454509903/?ref=hl> * Follow us on LinkedIn <https://www.linkedin.com/company/biosb-research-school>

1 0

CFP META'2016 - save the date
by El-ghazali Talbi 03 Dec '15

03 Dec '15

Apologies for cross-posting. Appreciate if you can distribute this CFP to your network. ********************************************************************** META'2016 International Conference on Metaheuristics and Nature Inspired Computing 27-31 Oct 2016 Marrakech, Morocco http://meta2016.sciencesconf.org/ ********************************************************************** META is one of the main event focusing on the progress of the area of metaheuristics and their applications. As in previous editions, META’2016 will provide an opportunity to the international research community in metaheuristics to discuss recent research results, to develop new ideas and collaborations, and to meet old friends and make new ones in a friendly and relaxed atmosphere. META'2016 welcomes presentations that cover any aspects of metaheuristic research such as new algorithmic developments, high-impact applications, new research challenges, theoretical developments, implementation issues, and in-depth experimental studies. META'2016 strives for a high-quality program that will be completed by a number of invited talks, tutorials, workshops and special sessions. The scope of the META’2016 conference includes, but is not limited to: * Local search, tabu search, simulated annealing, VNS, ILS, … * Evolutionary algorithms, swarm optimization, scatter search, … * Emergent nature inspired algorithms: quantum computing, artificial immune systems, bee colony, DNA computing, … * Parallel algorithms * Hybrid methods with machine learning, game theory, mathematical programming, constraint programming, co-evolutionary, … * Application to: logistics and transportation, networks, scheduling, data mining, engineering design, energy, cloud, bio-medical, … * Theory of metaheuristics, landscape analysis, convergence, problem difficulty, very large neighbourhoods, … * Multi-objective optimization, bi-level optimization * Dynamic optimization, problems with uncertainty, … * Parameter tuning (static, dynamic, adaptive, self-adaptive) * Hyper-heuristics, cross-domain metaheuristics * Software frameworks for metaheuristics and nature inspired computing Submission of papers: ____________________ - Submission of papers via the website S1) Short papers: Extended abstracts of work-in-progress and position papers of a maximum of 3 pages. S2) Long papers: Original research contributions of a maximum of 10 pages. S3) Journal papers: High-quality manuscripts that have recently, within the last year, been submitted or accepted for journal publication. For this special case, the submission should have the same title that the accepted work, the abstract AND the complete reference of the work. - Proceedings of the conference will be provided. Selected papers of type S1 and S2 will be published in a Springer book and international journals (ISI journals). - Predefined styles are available on the website http://meta2016.sciencesconf.org/ - Proposals for invited sessions, workshops and tutorials: Deadline 15th April 2016. contact el-ghazali.talbi(a)univ-lille1.fr Important dates _______________ - Submission deadline: May 6, 2015 - Notification of acceptance: June 3, 2015 E-G. Talbi (Conference Chair) -- ********************************** META'2016 Marrakech, 27-31 Oct 2016 http://meta2016.sciencesconf.org ********************************** Prof. E-G. Talbi Univ. Lille, CNRS, INRIA

1 0

VIB - Upcoming Bioinformatics Training Sessions in January 2016
by Alexander Botzki | VIB | 01 Dec '15

01 Dec '15

VIB Bioinformatics Training January sessions IN THIS ISSUE * Hands-on introduction to Python programming * Introduction to gene regulation Hands-on introduction to Python programming With the help of plenty of hands-on exercises, you will get introduced in Python, the peculiarities of Python and good programming habits. You will learn: * the basics of Python: different variables, reading files, writing files, conditional statements * to write a basic Python script from scratch Requirements: if you want to follow the Biopython<http://bits.cmail19.com/t/r-l-zudirdt-shyuuqkd-d/> training and you have little/no experience with Python, please register for this training Date: 11 and 18 January Location: Bioaccelerator, Gent Trainer: Wim Vranken (VIB Structural Biology Research Center) More information and registration: VIB website<http://bits.cmail19.com/t/r-l-zudirdt-shyuuqkd-h/> Introduction to gene regulation This training will give researchers insight and hands-on experience in the analysis of the regulation of eukaryotic gene expression at the transcriptional and post-transcriptional level. Date: 25 January Location: Bioaccelerator, Gent Trainer: Pieter De Bleser (IRC, VIB-Ugent) More information and registration: VIB website<http://bits.cmail19.com/t/r-l-zudirdt-shyuuqkd-o/>

1 0

Vacancy: PhD position in bioinformatics/biostatistics at the Netherlands Cancer Institute
by Sander Canisius 01 Dec '15

01 Dec '15

PhD position in bioinformatics/biostatistics at the Netherlands Cancer Institute http://www.nki.nl/working-at-the-nki/vacature-biostatisticianbioinformatici… Your function within the department The Netherlands Cancer Institute (NKI) in Amsterdam is a Comprehensive Cancer Centre combining a hospital and research laboratories in a single independent organization. The group of Marjanka Schmidt works in Molecular Pathology, and Epidemiology and Biostatistics, focussing on molecular and genetic breast cancer epidemiology. We are looking for a PhD student to work on a project funded by the Dutch Cancer Society. The main objective of the project is to identify novel germline genetic variants associated with breast cancer survival in specific tumour and treatment subgroups. We make use of the large breast cancer series collated in the Breast Cancer Association Consortium (BCAC) of >60 studies with >80,000 breast cancer patients. These patients have been richly characterised with data including genome-wide genetic, clinical and epidemiological data. Analyses will involve statistical and computational methods to combine these data with knowledge on biological pathways, with the aim of identifying and interpreting the genetic contribution to breast cancer survival. You are expected to provide state-of-the-art statistical and/or bioinformatic expertise as an active and assertive collaborator. This involves developing and implementing diverse statistical and bioinformatic approaches to cover survival and (biological) pathway analyses of large datasets, the identification of prognostic and predictive biomarkers, and prognostication. You have access to complementary expertise and tools from the Computational Cancer Biology group led by Lodewyk Wessels and the Biostatistics group led by Michael Hauptmann at the Netherlands Cancer Institute, Amsterdam. Your profile We are looking for an enthusiastic, skilled, and proactive statistician/bioinformatician who has the ability to facilitate high quality science. Other requirements are: * A MSc degree in (bio)statistics, bioinformatics, computer science, mathematics, or physics, or equivalent qualifications; * Knowledge of statistical theory and methods; * Experience with statistical software (STATA or SAS); * Experience with programming and scripting languages (e.g. R, Python); * Fluent in spoken and written English. Your career opportunities and terms of employment Approximately 550 people work in the research laboratories. Research discussions, lectures and seminars in English and a large number of Dutch and non-Dutch postdocs, students and staff members contribute to the stimulating and international atmosphere of the Institute. We offer an inspiring and interactive research environment, state-of-the-art facilities, training, a competitive salary (including possibilities for tax-reduction) and housing facilities in the vicinity of the Institute. The Institute is located close to the city centre of Amsterdam and the international Schiphol airport. The appointment will initially be for 4 years. The gross salary per month is € 2.529,- to € 3.115,- according to the PhD (OIO) scales and depends on previous experience. The terms of employment will be in accordance with the CAO Ziekenhuizen (Collective Labour Agreement for Hospitals). Interested? For further information please consult our website: www.nki.nl or contact Marjanka Schmidt and/or Sander Canisius at mk.schmidt(a)nki.nl /s.canisius(a)nki.nl or +31 20 512 2767. The application deadline is *13 December 2015*.

1 0