February 2014 - BBClist - maillist.psb.ugent.be

Postdoc in Computational Cancer Biology
by l.wessels＠nki.nl 07 Jul '14

07 Jul '14

POSTDOC IN COMPUTATIONAL CANCER BIOLOGY PROJECT OUTLINE At the Netherlands Cancer Institute (NKI) several high throughput screens are performed, such as imaging-based high-content screens that aim to capture genotype-phenotype relations, and transposon reporter screens that are used to study the effect of chromatin organization on gene expression. Moreover, the size and number of publicly available datasets, such as ENCODE, TCGA and the drug screening datasets is increasing. In the Delft Bioinformatics Lab (bioinformatics.tudelft.nl) and the Computational Cancer Biology group at the NKI (ccb.nki.nl) we develop machine learning algorithms to extract biologically relevant structure from these data. However, integrally analyzing these heterogeneous data, while ensuring that the derived models remain amenable to biological interpretation is a major challenge. In this project we aim to develop machine learning based data integration algorithms that can deal with heterogeneous, partially unlabeled data. A special emphasis is placed on deriving models that are interpretable, thus maximizing the biological utility of such models. The successful candidate will - Be responsible for performing and supervising the research project; - Act as a liaison between the TUDelft and the NKI with the aim of identifying synergies between these institutions and developing these projects further; - Contribute to education at the BSc, MSc and PhD levels, as well as assist in the supervision of MSc and PhD students. REQUIREMENTS The candidates should have a strong computational background in bioinformatics or machine learning with a track-record in (cancer) genomics. The candidate must be able to work effectively in a multidisciplinary team environment and be able to partner with leading, worldwide institutions (university, government agencies, national labs, and professional organizations). The candidate must have exceptional communication skills, capable of interacting with peers and students and technical staff. EMPLOYER PROFILES The Delft Bioinformatics Lab at the TUDelft develops computer algorithms to further fundamental biological knowledge, apply these to advance the state-of-the-art in health care and industry. To this end, we closely collaborate with researchers in molecular and cell biology, medicine and biotechnology. The Computational Cancer Biology group at the NKI, focuses on developing novel computational approaches which exploit a wide variety of (high-throughput) data sources to further our basic understanding of cancer and to translate these findings to the clinic. 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 to obtain further information. Also see ccb.nki.nl for further information. CLOSING DATE: 1 MAY 2014

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BBC 2013 abstract submission through EasyChair
by BBC2013 01 Apr '14

01 Apr '14

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 1, 2013 Dear Colleagues, The 8th edition of the BeNeLux Bioinformatics Conference will take place in Brussels on the 9th and 10th of December 2013. 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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NRNB Google Summer of Code 2014
by Egon Willighagen 27 Feb '14

27 Feb '14

Hi all, as you may know the BiGCaT group in Maastricht collaborates with others in the USA NRNB consortium on WikiPathways, PathVisio, and BridgeDb. This National Resource for Network Biology (NRNB) was accepted into our 8th year of Google Summer of Code! It will be mentoring Cytoscape, WikiPathways, PathVisio, MedSavant, Virtual Cell, and other network-related projects. The GSoC funds students to work on Open Source bioinformatics tools (in fact, NRNB is just one of the bioinformatics mentoring organizations) during the summer holidays. The next week or two is the time for students to show there interest and hook up with the developers to work out a project plan they will submit and hope to get accepted (e.g. mashups to other BeNeLux bioinformatics tools with Cytoscape, PathVisio, etc!). http://nrnb.org/gsoc/ On this page is also provided a long list of project ideas, though students can come up with new ideas too: http://nrnb.org/gsoc/ideas2.html Students should keep in mind that this is a particularly active time for our developer communities, so please be patient with the uptick in GSoC-related questions and newbie introductions on these mailing lists over the next few weeks, though. Potential Students: 1. Now is your time to shine. Get on over to our program page (see link above), browse the resource links, read the FAQ, and dive into the Project Ideas tab. 2. Research a few project ideas that catch your attention. 3. Formulate specific questions and original thoughts related to the ideas (or your own idea). 4. THEN contact your potential mentors via the provided contact information associated with each idea. Serious students should have 2-3 projects well-researched and be in touch with mentors BEFORE March 10. We will work with you to make the best possible application and give you specific feedback during the application period from March 10-21. Pro-tip: do not submit your first draft on the last day. Please feel free to forward this to bachelor, master, *and* PhD students whom may be interested. With kind regards, Egon Willighagen -- E.L. Willighagen Department of Bioinformatics - BiGCaT Maastricht University (http://www.bigcat.unimaas.nl/) Homepage: http://egonw.github.com/ LinkedIn: http://se.linkedin.com/in/egonw Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers ORCID: 0000-0001-7542-0286

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ISCB Student Council Symposium 2014, Boston, USA.
by ISCBSC announcement 26 Feb '14

26 Feb '14

*ISCB Student Council Symposium 2014, Boston, USA.* *Call for Abstract open from February 10th, 2014* Dear Colleagues, We are pleased to announce that the call is now open for the submission of abstracts to the 10th ISCB Student Council Symposium, to be held on the 11 of July 2014 in Boston, USA, as a satellite meeting of the International Conference on Intelligent Systems for Molecular Biology (ISMB). The Student Council Symposium is a forum for students, post docs, and young researchers in the fields of Computational Biology and Bioinformatics. Participants will have the opportunity to present their work to an international audience of young scientists, 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 to showcase your work at the Symposium's poster session. As the central part of our symposium, 10 abstracts will be selected for an oral presentation. Awards will be given to outstanding posters and presentations. Travel fellowships will be available and candidates with accepted abstracts will be invited to apply. *Important Dates:* April 18, 2014: Submission closes April 25, 2014: Acceptance notifications May 2, 2014: Travel fellowship deadline July 11, 2014: Student Council Symposium Submit your work at http://scs2014.iscbsc.org/scs14-call . For updates and news, keep an eye on symposium website http://scs2014.iscbsc.org/ . We look forward to receiving your abstract. On behalf of the SCS organizers, Farzana Rahman (Chair) Tomás Di Domenico (Co-Chair)

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Post-doctoral position in perinatal and maternal epidemiology at McMaster University Health Sciences
by Olivier Sand 26 Feb '14

26 Feb '14

Post-doctoral position in perinatal and maternal epidemiology at McMaster University Health Sciences A post-doctoral position is available immediately in the Department of Obstetrics and Gynecology at McMaster University Health Sciences/Department of Clinical Epidemiology and Biostatistics, to work on analytic methodology and advanced issues in systematic review/meta-analytic methodology in the field of perinatal and maternal epidemiology to improve the health of women and infants. The successful candidate will be co-supervised by Dr. Sarah McDonald, a perinatal clinical epidemiologist and high risk obstetrician and Dr Joseph Beyene, an academic biostatistician and methodologist. Work will involve development and application of advanced analytic techniques using large perinatal data sets, examining both maternal and infant outcomes. Opportunities include collaborations with teams in other departments, centres and provinces. Applicants should have a Ph.D. in Clinical Epidemiology, (Bio)Statistics, Bioinformatics, Psychology, or a related field. Excellent programming (SAS/R) and communication skills are required. The applicant should be enthusiastic and comfortable working with real as well as simulated data and must be able to work independently. Experience in clinical epidemiology or perinatology would be an asset. The appointment will be for two years, with possible extension. Salary is commensurate with qualifications. McMaster University is recognized and internationally ranked research and educational institution, and the Dept of Clinical Epidemiology & Biostatistics is particularly renowned with a vibrant series of rounds and other educational opportunities. Interested applicants should send their curriculum vitae, along with a letter expressing why they are interested in this position, copies of all their transcripts (notarized translated if necessary) and copies of all publications on which they have been an author (first or co-author), as well the names and contact information for three references by email to: Dr. Sarah McDonald Departments of Obstetrics & Gynecology, Radiology, and Clinical Epidemiology & Biostatistics McMaster University 1280 Main Street West, room 3N52B Hamilton, Ontario, Canada, L8S 4K1 Email: mcdonals(a)mcmaster.ca Applications will continue to be processed until the position is filled. We thank all applicants, but only those selected for an interview will be contacted.

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Open position: bioinformatician/data analylist
by Verweij, N (thorax) 25 Feb '14

25 Feb '14

Dear all, We are looking for a highly motivated and enthusiastic (bio) informatician with interest in human genetics, epigenetics including microRNA biology to further strengthen and expand the research of the translational unit in the Department of Cardiology. The post-holder will be working closely with scientific staff to evaluate, develop, test and validate new algorithms and bioinformatics tools to assist in the interpretation of microRNAs and DNA variants and the provision of bioinformatics training for staff within the department. You will be involved in a large collaborative project within the Netherlands (CVON) and in the development and implementation of efficient analysis pipelines of high-throughput data analyses and epigenetic data. There are close local collaborations with the Department of Genetics and Epidemiology and active international collaborations in Europe, the United States and Japan. http://www.umcg.nl/NL/UMCG/Werken_in_het_UMCG/Vacatures/Externe_vacatures/M… Best regards, Niek Verweij ________________________________ De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht. The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message.

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NBIC2014 - Extended submission deadline for oral presentation - March 2
by Femke Francissen 24 Feb '14

24 Feb '14

***Netherlands Bioinformatics Conference 2014*** April 8 & 9, 2014, Conference Center De Werelt, Lunteren Conference website: http://www.aanmelder.nl/nbic2014 **Extended deadline abstract submission for oral presentation** Due to numerous requests, we have decided to extend the submission deadline for oral presentation at the NBIC2014 with one week. The new deadline is: March 2, 2014 Read more about abstract submission: https://www.aanmelder.nl/nbic2014/wiki/abstract%20submission **Call for nominations NBIC Young Investigator Award 2013** On April 8, during the conference programme, we will announce the winner of the NBIC Young Investigator Award 2014. This year the winner will receive a prize of 250 euros sponsored by BioSB and will present an honorary lecture. The call for nominations is open! Group leaders can now nominate researchers who recently finished their PhD for the award. The criteria and submission form can be found here: https://www.aanmelder.nl/nbic2014/wiki/nbic%20young%20investigator%20award **Birds of a Feather sessions** This year we are organising Birds of a Feather (BOF) sessions on April 9 in the afternoon. The aim of a BOF session is to discuss a topic of your choice in an informal setting. The BOF topics will be announced via the conference website so participants will be able to join the session that interests them most. If you would like to submit a topic for a BOF session, please send us an e-mail! **Key dates** Abstract submission deadline for oral presentations: March 2, 2014 Notification date: March 16, 2014 Abstract submission deadline for posters and demos: April 4, 2014 Contact: Femke Francissen, femke.francissen(a)nbic.nl<mailto:femke.francissen@nbic.nl>

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postdoc position in comparative genomics CMBI
by Martijn.Huijnen＠radboudumc.nl 24 Feb '14

24 Feb '14

The Comparative Genomics group of Martijn Huynen (CMBI, Radboud University Medical Centre, Nijmegen) has a position for a talented and motivated scientist to do bioinformatics research into unraveling the patterns behind intellectual disability. We have compiled a catalogue of more than 600 genes, mutations in which give rise to intellectual disability. Several of these genes have already been demonstrated to act together in molecular pathways. However, a global overview of the biological coherence underlying intellectual disability genes is missing and the link between molecular pathways and the various intellectual disability phenotypes has not been established. The challenge is to address this, e.g. via analyzing protein-protein interactions, tissues specific gene expression, shared phenotypes in human and model organisms, shared evolutionary origin and sharing of transcription factor binding sites. Your work will shed light onto genetic design principles that underlie human brain function and will identify new candidate genes for intellectual disability by Bayesian integration of genomics data. The project combines the expertise of the Huynen group in the analysis of genomics data to predict protein function with the expertise in studying genetic disease of the group of Annette Schenck (Genetics Department Radboud University Medical Centre). This collaboration ensures direct experimental testing of interesting newly predicted candidate proteins and pathways. The position is initially for 1.3 years with possibilities for extension. Starting date: as soon as possible. Requirements: You have a PhD in Bioinformatics or in Natural Sciences with a published affinity for large-scale comparative analyses of genomics data coupled to in depth study of biological systems. Salary: starting at 40.458 – 46.695 Euro, depending on experience. For more information please contact Martijn Huynen (huynen(a)cmbi.ru.nl, www.cmbi.ru.nl) To apply, please e-mail a letter describing research interests and past research activities, a CV, and the names of two referees before March 7th , 2013. Het Radboudumc staat geregistreerd bij de Kamer van Koophandel in het handelsregister onder nummer 41055629. The Radboud university medical center is listed in the Commercial Register of the Chamber of Commerce under file number 41055629.

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international shortcourse on next generation sequencing
by Marja Peters 20 Feb '14

20 Feb '14

Dear reader, We, Avans University of Applied Sciences, Research Group Analysis Techniques in Life Science, organize an international shortcourse on next generation sequencing in Breda from 1 until 4 April 2014. Aim of the course: DNA sequencing technologies are currently developing at an incredible speed and new applications are presented monthly, incl. DNA/RNA profiling, ChIP-seq, re-sequencing, de novo genome sequencing and metagenomics. The aim of this course is to introduce next generation sequencing technologies, highlight different applications of these new technologies, and show ways to analyse data. Please visit the course website for detailed information: http://www.alsavans.nl/avans-training-2542.htm Looking forward to meeting you in Breda Best regards, Marja peters Avans university of applied science p.o. box 90116 Disclaimer ( http://www.avans.nl/over-avans/e-mail-disclaimer )

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Deadline Abstract submission February 23: NSBM Spring meeting 2014 April 8th - NBIC Conference
by Barbara.vanKampen＠radboudumc.nl 20 Feb '14

20 Feb '14

Abstract submission deadline for oral presentations: February 23, 2014 [logo.png]NSBM Spring meeting April 8th 2014 In conjunction with the Netherlands Bioinformatics Conference 2014 Venue: Congrescentrum De Werelt, Lunteren The Netherlands Society on Biomolecular Modelling (NSBM) cordially invites you to visit its spring meeting, a topical track of the Netherlands Bioinformatics Conference 2014 (NBIC2014) on April 8th 2014. During several parallel sessions, the floor will be given to PhD students and postdocs who study protein structure and/or structural bioinformatics or related topics (see a list below). Speakers and attendees will have the opportunity to join the NBIC2014 activities and visit keynote lectures. Programme April 8th Invited speaker: Christian Ottmann<https://www.aanmelder.nl/nbic2014/wiki/christian%20ottmann>, Eindhoven University of Technology, the Netherlands Abstract submission All abstracts should be submitted via the NBIC2014 abstract submission system<https://www.aanmelder.nl/nbic2014/wiki/abstract%20submission>. Please indicate in the form that you are submitting for the NSBM Spring meeting. Starting PhD students are particularly encouraged to present their research! For questions regarding the abstract or meeting please contact Gert Vriend, gerrit.vriend(a)radboudumc.nl<mailto:gerrit.vriend@radboudumc.nl> Topics for presentations may include, but are not limited to: * Computational Biology and Bioinformatics * Computer-aided drug design * Drug design and drug discovery * Grid computing * Homology modelling * Molecular and supramolecular dynamics * Molecular modeling and simulation * Mutational analysis * Protein crystallography * Protein NMR * Protein structure analysis * Protein structure prediction * Protein-protein interactions * Protein-small molecules interaction * Protein software design * Proteomics * Structural bioinformatics * Structure-function analysis * Text mining & information extraction * Virtual screening Registration Registration should be done via the NBIC2014 registration form<https://www.aanmelder.nl/nbic2014/wiki/registration>. Registration for the conference (for one day/April 8th) includes: participation to conference and evening poster session on April 8th, lunch, coffee/tea during breaks, internet access and conference dinner. Should a lack of funding be a hurdle for visiting the NSBM Spring meeting, please contact prof. Gert Vriend at gerrit.vriend(a)radboudumc.nl<mailto:gerrit.vriend@radboudumc.nl> so that an arrangement can be made. Key dates * Abstract submission deadline for oral presentations: February 23, 2014 * Notification date selection oral presentations: March 4, 2014 * Abstact submission deadline for posters & demos: April 4, 2014 Sponsored by: [DSM]<http://www.dsm.com/> [Genalice] <http://www.genalice.com/> [Keygene NV]<http://www.keygene.com/> [Bio-prodict] <http://www.bio-prodict.nl/> NSBM Mailing list --- NEW EMAIL: barbara.vankampen(a)radboudumc.nl<mailto:barbara.vankampen@radboudumc.nl> Barbara van Kampen [Radboudumckleine.png] CMBI 260 Radboud University Medical Centre / RIMLS 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<http://www.cmbi.ru.nl/> Het Radboudumc staat geregistreerd bij de Kamer van Koophandel in het handelsregister onder nummer 41055629. The Radboud university medical center is listed in the Commercial Register of the Chamber of Commerce under file number 41055629.

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