- BBClist - maillist.psb.ugent.be

DSM is hiring! (Associate) Scientist Bioinformatics / Metabolic Engineering
by Roubos, Hans 12 Jul '13

12 Jul '13

(Associate) Scientist Bioinformatics / Metabolic Engineering http://www.linkedin.com/jobs?viewJob=&jobId=6408186 Hans Roubos, PhD Principal Scientist Bioinformatics & Modeling DSM Biotechnology Center | Alexander Fleminglaan 1 | 2613 AX Delft | The Netherlands | T +31 15 2792147 | F +31 15 2793771 | hans.roubos(a)dsm.com | www.dsm.com | Trade Registration number 27235314 ________________________________ DISCLAIMER: This e-mail is for the intended recipient only. If you have received it by mistake please let us know by reply and then delete it from your system; access, disclosure, copying, distribution or reliance on any of it by anyone else is prohibited. If you as intended recipient have received this e-mail incorrectly, please notify the sender (via e-mail) immediately.

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DSM is hiring! (Associate) Scientist Biostatistics
by Roubos, Hans 12 Jul '13

12 Jul '13

(Associate) Scientist Biostatistics http://www.linkedin.com/jobs?viewJob=&jobId=6409105 Hans Roubos, PhD Principal Scientist Bioinformatics & Modeling DSM Biotechnology Center | Alexander Fleminglaan 1 | 2613 AX Delft | The Netherlands | T +31 15 2792147 | F +31 15 2793771 | hans.roubos(a)dsm.com | www.dsm.com | Trade Registration number 27235314 ________________________________ DISCLAIMER: This e-mail is for the intended recipient only. If you have received it by mistake please let us know by reply and then delete it from your system; access, disclosure, copying, distribution or reliance on any of it by anyone else is prohibited. If you as intended recipient have received this e-mail incorrectly, please notify the sender (via e-mail) immediately.

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Computational Cancer Biology Positions
by Lodewyk Wessels 12 Jul '13

12 Jul '13

COMPREHENSIVE COMPUTATIONAL MODELING FOR COMBINATION TREATMENT DESIGN PROJECT OUTLINE All cancers arise due to alterations in their genomes. Although insight into the genetic lesions in tumors by genome sequencing does already assist in selecting some drug regimens, it rarely results in disease eradication due to the emergence of drug-resistance. More sophisticated combination therapies in which several oncogenic pathways are targeted simultaneously could alleviate this problem. However, at present we are unable to extract and interpret the necessary information from tumors to predict which drug regimen will be most adequate. In this project we will collaborate with Welcome Trust Sanger Center and employ the 1000 cancer cell line data set to tackle this problem. This data set comprises large-scale molecular characterization and cancer drug screening of all cell lines for 400 anti-cancer drugs. The molecular data currently consists of gene expression, copy number (SNP-6), and whole exome sequencing data and is being expanded. The successful candidate will work closely with scientists at the Welcome Trust Sanger Center and the Netherlands Cancer Institute and employ computational approaches to mine this rich, valuable pre-clinical resource. Potential results include 1) new molecular biomarkers to identify sensitive populations 2) repositioning of existing drugs in other tumor types and 3) potential drug combinations aimed at overcoming resistance mechanisms. Hypotheses emerging from these analyses will be validated in model systems and where possible in clinical settings. CANDIDATE REQUIREMENTS – EDUCATION AND EXPERIENCE We are seeking highly motivated Postdoc or PhD candidates with a degree in bioinformatics, computer science, mathematics or physics and with a strong cancer biology interest. Preferably applicants should have a documented experience in analyzing high-throughput genomic data. The candidate needs to be proficient in common bioinformatics scripting and programming languages. Fluency in spoken and written English is a strong requirement. LOCATION The project involves groups at the Netherlands Cancer Institute, Amsterdam (Rene Bernards, Molecular Carcinogenesis, and Lodewyk Wessels, Computational Biology) and the Welcome Trust Sanger Institute (Mathew Garnet and Ultan McDermott, Cancer Genome Project). This position will be embedded in the Computational Biology Group lead by Lodewyk Wessels. CONTACT DETAILS Please contact Lodewyk Wessels, tel. +31 20 512 7987 or e-mail: l.wessels(a)nki.nl. When applying, please ensure you include a CV, list of publications and the names and addresses of at least two persons that can be approached as references. Also see bioinformatics.nki.nl for further information. CLOSING DATE 3 February 2013

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Bioinformatics PostDoc position at UMC St Radboud Nijmegen
by Sacha van Hijum 11 Jul '13

11 Jul '13

Bio-informatics post-doc position for the development of a bacterial comparative genomics analysis pipeline and database General: At the Centre for Molecular and Biomolecular Informatics, UMC St Radboud, Nijmegen, the Netherlands 36 hour per week temporary contract for two years Max EUR 55784 gross per year (schaal 10) at full employment (incl. vacation bonus and end of year payments) Published 14-06-2013 Closing date 31-07-2013 Job description: We offer a challenging position part of an EU project in which you will develop a new database and pipeline for the prediction of bacterial phenotypes. This pipeline will consist of the latest technologies and approaches. In addition you will interact with the companies that are part of the project team to ensure delivery of appropriate results and to transfer knowledge. The consortium consists of a number of academic, research institutes and industrial participants from different EU countries. A framework needs to be created that allows predicting bacterial phenotypic properties based on a variety of genomic or experimental properties. The successful candidate will be working at the CMBI Bacterial Genomics group and will visit project partners regularly. Profile: We are looking for an enthusiastic and communicable person that is always willing to increase her/his knowledge as well as develop personal skills. You will be working in an enthusiastic team where project results are discussed openly and critically to ensure quality criteria are met. Besides good primary and secondary labor conditions, we offer a salary 13th month of salary and access to courses to develop knowledge and skills. We seek a motivated experienced post-doc that is able to work independently, is result-oriented, and delivers results on-time. Furthermore, you are a social person that would like to be engaged in social activities involving the research group. Preferably you have experience in bacterial genomics, next generation sequencing, and (genome) databases. Female applicants are encouraged to apply for this position. Organization: The Bacterial Genomics group is part of the Center of Molecular and Bio-Molecular Informatics (CMBI) bio-informatics cluster (NCMLS research school of the UMC St Radboud, Nijmegen, the Netherlands). CMBI employs about 50 bio-informatics researchers part of four successful research groups as well as the Netherlands Bio-informatics Centre headquarters. The Bacterial Genomics group (CMBI) is headed by Dr. Van Hijum and focuses on the study of the interaction of micro-organisms within complex microbial communities that impact health. Comments and contact information: Please apply online via the following link: http://goo.gl/2KM6X <https://webmail.umcn.nl/owa/redir.aspx?C=A5tEFGD6qkWjPtDKODCbXX4TR8KoPdAILE…> For further inquiries Dr. Sacha van Hijum can be reached at +31-(0)24-3619389 or by email: S.vanHijum(a)umcn.nl. -- Dr. Sacha van Hijum Group leader CMBI Bacterial Genomics, UMC St Radboud Senior scientist bioinformatics NIZO food research B.V. Bioinformatics platform leader Top Institute Food and Nutrition T: +31(0)318 659 570 F: +31(0)318 650 400 M: +31(0)624782895 E: sacha.vanhijum(a)nizo.nl or svhijum(a)cmbi.ru.nl P.O. Box 20, 6710 BA EDE, The Netherlands Kernhemseweg 2, 6718 ZB EDE, The Netherlands

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EU-transPLANT Bioinformatics survey
by Jan van Oeveren 05 Jul '13

05 Jul '13

Welcome to the trans-National Infrastructure for Plant Genomic Science's User Needs survey ! Please take the time to take part in our transPLANT's survey to tell us about your needs and what you feel is missing or not completely covered by existing bioinformatics projects, concerning data access, data query and data analysis in terms of bioinformatics tools or computer power or storage capacity. Your answer will help us to have an overview of stakeholder needs from public or private companies in terms of bioinformatics applications, to identify what is covered or not yet covered by transplant's project scope and to better coordinate bioinformatics developments in the future, by facilitating collaborations between teams at European level and international level. This survey was asked by the European commission and the results will be included in a general report that will be given to the EU this autumn. This report will also be used to fund new initiatives in the future. This survey should take around 30 minutes to complete : http://www.transplantdb.eu/survey => Do not hesitate to forward this email to your colleagues and partners in your lab at national, European or at international level ! ************************************************************************************************* On behalf of the transPLANT consortium Jan van Oeveren [http://www.keygene.com/images/maillogo.jpg]<http://www.keygene.com/> Keygene N.V. P.O. Box 216 6700 AE Wageningen The Netherlands Tel. (+31) 317 46 68 66 Fax. (+31) 317 42 49 39 Web: http://www.keygene.com<http://www.keygene.com/> [http://www.keygene.com/images/phenodays20131.jpg]<http://www.phenodays.com/> The information contained in this message, and attachments if any, may be privileged and/or confidential and is intended to be received only by persons entitled to receive such information. Use of any part of this message and/or its attachments if any, in any other way than as explicitly stated by the sender is strictly prohibited. Should you receive this message unintentionally please notify the sender immediately, and delete it together with all attachments, if any. Thank you. The transmission of messages and/or information via the Internet is not secured and may be intercepted by third parties. KeyGene assumes no liability for any damage caused by any unintentional disclosure and/or use of the content of this message and attachments if any.

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PhD position: green algal evolution
by Klaas Vandepoele 03 Jul '13

03 Jul '13

Dear all, please find enclosed a PhD position to work on the evolution of green algal seaweeds, a collaborative project between The Phycology Research Group (O. De Clerck - UGent BE) and Comparative & Integrative Genomics lab (K. Vandepoele - UGent/VIB BE). Thanks to forward to other potentially interested candidates. best regards, Klaas -- Prof. Dr. Klaas Vandepoele Tel. 32 (0)9 33 13822 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, Belgium E-mail: Klaas.Vandepoele(a)psb.vib-ugent.be Website: http://bioinformatics.psb.ugent.be/cig/ Twitter: http://twitter.com/plaza_genomics ---------------------------------------------------------

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COMBINE 2013
by Eric Bonnet 03 Jul '13

03 Jul '13

The "Computational Modeling in Biology" Network (COMBINE) is an initiative to coordinate the development of the various community standards and formats in systems biology and related fields. The fourth annual COMBINE meeting is hosted by the U900 Sysbio group and will take place at the Institut Curie, from Monday September 16 through Friday Sep. 20, 2013. COMBINE is a workshop-style event with oral presentations, posters and breakout sessions. The first day of the meeting will be dedicated to presentations of modelling approaches in biology either not currently covered by our efforts, or using them in new or innovative ways. Oral presentations will be selected from the submitted abstracts. Please note that attending this day is free of charge (registration is mandatory, though). More info at: http://co.mbine.org/events/COMBINE_2013 Registration: http://binom.curie.fr/combine2013/

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Lorentz Training Workshop: Interdisciplinary Life Sciences
by Roeland Merks 02 Jul '13

02 Jul '13

Lorentz Training Workshop: Interdisciplinary Life Sciences Date: 2013 October 21-25 (Monday-Friday) Location: Snellius Buiding (2nd floor), Lorentz Center, Niels Bohrweg 1, 2333CA Leiden, The Netherlands Organisers: Roel van Driel (UvA), Roeland Merks (CWI), Jaap Molenaar (WUR) Contact: Jaap.Molenaar(a)wur.nl Webpage: www.ncsb.nl/workshop/InterdisciplinaryLS Registration: www.lorentzcenter.nl/lc/web/2013/598/application.php3?wsid=598&venue=Snelli… Deadline: 2013-08-23 The aim of this training workshop is to bring together 25 young researchers from the life sciences and to train them in modelling of biological systems based on ‘learning by doing'. We aim at about 25 student participants forming teams of 4 (or 5) members. Each team will work on one specific modelling challenge during the workshop. Possible topics might be: Sensitivity analysis of a synthetic mammalian oscillator, Modelling of networks regulating flowering time in plants, Modelling of blood vessel growth, and Modelling of cell division. For more information, read the workshop webpage: http://www.ncsb.nl/workshop/InterdisciplinaryLS

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SSTiC 2013: last call
by GRLMC 28 Jun '13

28 Jun '13

*To be removed from our mailing list, please respond to this message with UNSUBSCRIBE in the subject line* ********************************************************************* 2013 INTERNATIONAL SUMMER SCHOOL ON TRENDS IN COMPUTING SSTiC 2013 Tarragona, Spain July 22-26, 2013 Organized by Rovira i Virgili University http://grammars.grlmc.com/SSTiC2013/ ********************************************************************* AIM: SSTiC 2013 will be an open forum for the convergence of top class well recognized computer scientists and people at the beginning of their research career (typically PhD students) as well as consolidated researchers. SSTiC 2013 will cover the whole spectrum of computer science by means of 54 six-hour courses dealing with hot topics at the frontiers of the field. By actively participating, lecturers and attendees will share the idea of scientific excellence as the main motto of their research work. ADDRESSED TO: Graduate students from around the world. There are no pre-requisites in terms of the academic degree the attendee must hold. However, since there will be several levels among the courses, in the description of some of them reference may be made to specific knowledge background. SSTiC 2013 is appropriate also for people more advanced in their career who want to keep themselves updated on developments in the field. Finally, senior researchers will find it fruitful to listen and discuss with people who are main references of the diverse branches of computing nowadays. REGIME: 6 parallel sessions will be held during the whole event. Participants will be able to freely choose the courses they will be willing to attend as well as to move from one to another. VENUE: Campus Catalunya Universitat Rovira i Virgili Av. Catalunya, 35 43002 Tarragona COURSES AND PROFESSORS: Shun-ichi Amari (Riken) [introductory] Information Geometry and Its Applications James Anderson (Chapel Hill) [intermediate] Scheduling and Synchronization in Real-Time Multicore Systems Pierre Baldi (Irvine) [intermediate] Big Data Informatics Challenges and Opportunities in the Life Sciences Yoshua Bengio (Montréal) [introductory/intermediate] Deep Learning of Representations Stephen Brewster (Glasgow) [advanced] Multimodal Human-Computer Interaction Bruno Buchberger (Linz) [introductory] Groebner Bases: An Algorithmic Method for Multivariate Polynomial Systems. Foundations and Applications Rajkumar Buyya (Melbourne) [intermediate] Cloud Computing Jan Camenisch (IBM Zurich) [intermediate] Cryptography for Privacy Larry S. Davis (College Park) [intermediate] Video Analysis of Human Activities Paul De Bra (Eindhoven) [intermediate] Adaptive Systems Paul Dourish (Irvine) [introductory] Ubiquitous Computing in a Social Context Max J. Egenhofer (Maine) [introductory/intermediate] Qualitative Spatial Relations: Formalizations and Inferences Richard M. Fujimoto (Georgia Tech) [introductory] Parallel and Distributed Simulation David Garlan (Carnegie Mellon) [advanced] Software Architecture: Past, Present and Future Mario Gerla (Los Angeles) [intermediate] Vehicle Cloud Computing Ralph Grishman (New York) [intermediate] Information Extraction from Natural Language Francisco Herrera (Granada) [intermediate] Imbalanced Classification: Current Approaches and Open Problems Paul Hudak (Yale) [introductory] Euterpea: From Signals to Symphonies Using Haskell Niraj K. Jha (Princeton) [intermediate] FinFET Circuit Design George Karypis (Minnesota) [introductory] Introduction to Parallel Computing: Architectures, Algorithms, and Programming Aggelos K. Katsaggelos (Northwestern) [intermediate/advanced] Sparsity-based Advances in Image Processing Arie E. Kaufman (Stony Brook) [advanced] Advances in Visualization Hugo Krawczyk (IBM Research) [intermediate] An Introduction to the Design and Analysis of Authenticated Key Exchange Protocols Pierre L'Ecuyer (Montréal) [intermediate] Quasi-Monte Carlo Methods in Simulation: Theory and Practice Laks Lakshmanan (British Columbia) [intermediate/advanced] Information and Influence Spread in Social Networks Wenke Lee (Georgia Tech) [introductory] DNS-based Monitoring of Malware Activities Maurizio Lenzerini (Roma La Sapienza) [intermediate] Ontology-based Data Integration Ming C. Lin (Chapel Hill) [introductory/intermediate] Physically-based Modeling and Simulation Jane W.S. Liu (Academia Sinica) [intermediate] Critical Information and Communication Technologies for Disaster Preparedness and Response Satoru Miyano (Tokyo) [intermediate] How to Hack Cancer Systems with Computational Methods Aloysius K. Mok (Austin) [intermediate] From Real-time Systems to Cyber-physical Systems Hermann Ney (Aachen) [intermediate/advanced] Probabilistic Modelling for Natural Language Processing - with Applications to Speech Recognition, Handwriting Recognition and Machine Translation Cathleen A. Norris (North Texas) & Elliot Soloway (Ann Arbor) [introductory] Primary & Secondary Educational Computing in the Age of Mobilism Jeff Offutt (George Mason) [intermediate] Cutting Edge Research in Engineering of Web Applications Bijan Parsia (Manchester) [introductory] The Semantic Web: Conceptual and Technical Foundations Charles E. Perkins (FutureWei) [intermediate/advanced] Beyond 4G Prabhakar Raghavan (Google) [introductory/intermediate] Web Search and Advertising Phillip Rogaway (Davis) [introductory/intermediate] Provably Secure Symmetric Encryption Gustavo Rossi (La Plata) [intermediate] Topics in Model Driven Web Engineering Kaushik Roy (Purdue) [introductory/intermediate] Low-energy Computing Robert Sargent (Syracuse) [introductory] Validating Models Douglas C. Schmidt (Vanderbilt) [intermediate] Patterns and Frameworks for Concurrent and Networked Software Bart Selman (Cornell) [intermediate] Fast Large-scale Probabilistic and Logical Inference Methods Mubarak Shah (Central Florida) [intermediate/advanced] Visual Crowd Surveillance Ron Shamir (Tel Aviv) [introductory] Revealing Structure in Disease Regulation and Networks Dawn Xiaodong Song (Berkeley) [introductory] Selected Topics in Computer Security Mike Thelwall (Wolverhampton) [introductory] Sentiment Strength Detection for the Social Web Julita Vassileva (Saskatchewan) [introductory/intermediate] Engaging Users in Social Computing Systems Philip Wadler (Edinburgh) [introductory] Topics in Lambda Calculus and Life Yao Wang (Polytechnic New York) [introductory/advanced] Video Compression: Fundamentals and Recent Development Gio Wiederhold (Stanford) [introductory] Software Economics: How Do the Results of the Intellectual Efforts Enter the Global Market Place Limsoon Wong (National Singapore) [introductory/intermediate] The Use of Context in Gene Expression and Proteomic Profile Analysis Michael Wooldridge (Oxford) [introductory] Autonomous Agents and Multi-Agent Systems Ronald R. Yager (Iona) [introductory/intermediate] Fuzzy Sets and Soft Computing Philip S. Yu (Illinois Chicago) [advanced] Mining Big Data REGISTRATION: It has to be done at http://grammars.grlmc.com/SSTiC2013/Registration.php Since the capacity of the venue is limited, registration requests will be processed on a first come first served basis. The registration period will be closed when the capacity of the venue will be complete. It is highly convenient to register prior to the event. FEES: Fees may be for the whole week (full-time participant) or per blocks of days (part-time participant). They are a flat rate allowing one to attend all courses within the time window set: 5, 4, 3 or 2 days. Fees vary depending on the deadline. ACCOMMODATION: Information about accommodation is available on the website of the School. CERTIFICATE: Participants will be delivered a certificate of attendance. QUESTIONS AND FURTHER INFORMATION: Lilica Voicu: florentinalilica.voicu(a)urv.cat POSTAL ADDRESS: SSTiC 2013 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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2 PhD and 1 Postdoc position at Van de Peer Lab (VIB/UGent)
by Thomas Van Parys 27 Jun '13

27 Jun '13

The following positions are now open in the Van de Peer Lab at VIB/Ghent University, Belgium (http://bioinformatics.psb.ugent.be/) in relation to the ERC Advanced Grant Double-Up, on the importance of gene and genome duplications for natural and artificial organism populations. 2 PhD positions 1 Postdoc position The long-term establishment of ancient organisms that have undergone whole genome duplications has been exceedingly rare. On the other hand, tens of thousands of now-living species, both plants and animals, are polyploid, and contain multiple copies of their genome. The apparent paucity of ancient genome duplications and the existence of many species that are currently polyploid provide an interesting and fascinating enigma. A question that remains to be answered is whether these older genome duplications have survived by coincidence or whether they could survive only because they did occur, or were selected for, at very specific times, for instance during major ecological upheavals and periods of extinction. We hope to address these questions at different levels through 1) the analysis of whole plant genome sequence data and 2) the in silico modeling and evolution of artificial gene regulatory networks to mimic the genomic consequences of genome doubling and how this may affect network structure, redundancy, rewiring, and dosage balance. Furthermore, we aim at using simulated robotic models running on artificial gene regulatory networks in complex and challenging environments to evaluate how both natural and artificial organism populations can potentially benefit from gene and genome duplications for adaptation, survival, and evolution in general. DOUBLE-UP is a truly interdisciplinary proposal that will open up new horizons and perspectives for different fields of research, from bioinformatics and systems biology over comparative and evolutionary biology, to network modeling and evolutionary robotics. We are looking for 2 highly motivated PhD students and 1 highly motivated Postdoc to help us achieve these ambitious goals. A strong (bio)informatics background, good programming skills, and previous modeling/simulation experience are all required. A background in evolutionary biology and population biology is strongly preferred. Some interest in evolutionary robotics and artificial life is an advantage. Applicants should be proficient in English, both speaking and writing. The positions are available starting October 1st, 2013, with funding secured for at least four years. Contact Yves Van de Peer at yves.vandepeer(a)psb.ugent.be for more information and/or to apply. To apply, please send a detailed CV and motivation letter before August 15th. -- ================================================================== Thomas Van Parys Tel:+32 (0)9 331 36 95 fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM thomas.vanparys(a)psb.vib-ugent.be http://bioinformatics.psb.ugent.be ==================================================================

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