- BBClist - maillist.psb.ugent.be

Bioinformatics position @ Bayer, NL
by Joan Wong 15 Feb '16

15 Feb '16

Dear all, We are looking for a motivated and enthusiastic bioinformatician to join our growing team at Bayer based in Nunhem, the Netherlands. The posting can be viewed here: http://career.bayer.nl/nl/job/Bioinformatics-Researcher--0000156142.html. Best regards, Joan Wong Bioinformatics Scientist [cid:C15DEDD5-288E-4312-857A-B6E1A5E2692F] Nunhems Netherlands B.V. Vegetable Seeds Napoleonsweg 152 6083 AB Nunhem, the Netherlands Tel: +31 475 599 545 Mobile: +31 634 959 061 E-mail: joan.wong(a)bayer.com<mailto:joan.wong@bayer.com> Web: http://www.bayer.com<http://www.bayer.com/> ________________________________________________________________________ The information contained in this e-mail is for the exclusive use of the intended recipient(s) and may be confidential, proprietary, and/or legally privileged. Inadvertent disclosure of this message does not constitute a waiver of any privilege. If you receive this message in error, please do not directly or indirectly use, print, copy, forward, or disclose any part of this message. Please also delete this e-mail and all copies and notify the sender. Thank you. For alternate languages please go to http://bayerdisclaimer.bayerweb.com ________________________________________________________________________

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PhD Candidate - Single Cell Transcriptomics of the Early Stages of Alzheimer’s Disease
by Mark Fiers 12 Feb '16

12 Feb '16

Dear all, We are looking for a PhD candidate to explore single-cell transcriptome data of the early stages of Alzheimer's Disease. The early stages of Alzheimer's disease are still poorly understood. It is unknown how the different cell types react to early amyloid stress and how these changes propagate through the different brain regions (in particular the hippocampus). In this project we will apply single cell transcriptomics to an Alzheimer's mouse model. Combining this data with a number of different technologies, such as in-situ hybridization and electrophysiology, will allow us to build a detailed spatio-temporal model, distinguishing different cell types, of the earliest steps in the progression of Alzheimer's disease. The candidate will work on the analysis of transcriptomics data and integrate this data with data from other sources, both locally generated, as well as public data. The ultimate goal is to generate a spatial and temporal model of the transcriptional changes at the onset of AD. More information: http://www.vib.be/en/jobs/Pages/PhD-Candidate---Single-Cell-Transcriptomics… With best regards Mark Fiers

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Postdoc position in the Archie lab
by Karoline Faust 11 Feb '16

11 Feb '16

POSTDOC POSITION Post-doctoral position in the ecology and evolution of baboon gut microbiomes A postdoctoral position applying ecological and evolutionary frameworks to understand the causes and consequences of gut microbial dynamics is available in the lab of Elizabeth Archie (University of Notre Dame, Department of Biological Sciences; http://blogs.nd.edu/archielab/) The postdoc will have access to an unprecedented data set of 20,000 microbiome samples, collected from 600+ individual baboons and spanning over 15 years. These samples are currently being sequenced at the 16S rRNA v4 region in collaboration with the Earth Microbiome Project (http://www.earthmicrobiome.org/) data will be available in the spring of 2016. Samples were collected from the well-studied Amboseli baboon population in Kenya (http://amboselibaboons.nd.edu/) which has long-term data on the baboons ecology, social interactions, health, and fitness. Some relevant recent publications include: Tung et al. (2015) eLife and Archie & Tung (2015) Curr Opin Behav Sci. Postdoctoral applicants should have a strong background two or more of the following areas: microbial ecology, community ecology, evolution, behavior, bioinformatics, and genomics. Strong data analysis skills, including programming and statistical modeling experience, are preferred. Familiarity or experience with primates is a plus, but is not essential. Several projects are available; applicants will have the freedom to choose their own projects as long as they fit within the general interests of the collaborative research. The Archie lab offers congenial research environments that foster strong interdisciplinary training and collaborative exchange. Collaborators on this project include Jenny Tung (http://www.tung-lab.org/) Ran Blekhman (http://blekhmanlab.org/) Luis Barreiro (http://luis-barreirolab.org/) Stuart Jones (http://www3.nd.edu/~sjones20/) and David Boone (IU School of Medicine), all of whom are available for advice and interaction. The postdoc is funded by the Eck Institute for Global Health, and the Environmental Change Initiative at Notre Dame. To apply for the position please send an email to Elizabeth Archie (earchie(a)nd.edu) including a cover letter, current CV, and contact information for at least two references. The anticipated start date is in late spring or summer 2016. Applicants should submit their materials by March 1 to ensure full consideration.

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GATK Best Practices for Variant Discovery workshop 14-15 April 2016 (second announcement)
by Bert Overduin 10 Feb '16

10 Feb '16

Dear all, I am very happy to announce that, after the success of the GATK workshop last year, Edinburgh Genomics again has been able to get a 3-person-strong team from the Broad Institute in Boston over to Edinburgh to deliver a two-day workshop on 14 and 15 April 2016. This workshop will focus on the core steps involved in calling variants with the Broad’s Genome Analysis Toolkit ( https://www.broadinstitute.org/gatk/) using the “Best Practices” developed by the GATK team. The workshop is composed of one day of lectures (including many opportunities for Q&A) and one optional day of hands-on training. For more information and to register, please visit https://genomics.ed.ac.uk/gatk-best-practices-variant- <https://genomics.ed.ac.uk/gatk-best-practices-variant-discovery>discovery <https://genomics.ed.ac.uk/gatk-best-practices-variant-discovery>. Note that for the hands-on part places are limited and allocated on a first come, first served basis. Also note that a similar workshop will be given on Monday 18 and Tuesday 19 April 2016 at the University of Oxford. For more information about this, please contact David Sims (david.sims(a)dpag.ox.ac.uk) Please feel free to forward this mail to anyone else potentially interested and/or to print out the attached flyer for further distribution. Hope to see many of you in April! With kind regards, Bert -- Bert Overduin, PhD TRAINING AND OUTREACH BIOINFORMATICIAN Bert.Overduin(a)ed.ac.uk EDINBURGH GENOMICS The University of Edinburgh Ashworth Laboratories The King's Buildings Charlotte Auerbach Road Edinburgh EH9 3FL Scotland, United Kingdom tel. +44(0)1316507403 http://genomics.ed.ac.uk The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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FW: Bioinformatician job offer
by Alexander Botzki 09 Feb '16

09 Feb '16

From: Bioinformatics Interest Group (BIG) [mailto:BIG@LS.KULEUVEN.BE] On Behalf Of Vimac Nolla Ardevol Sent: 09 February 2016 18:40 To: BIG(a)LS.KULEUVEN.BE Subject: Bioinformatician job offer Dear all, A colleague of mine has just forwarded me this opening for a bioinformatician in Mind the byte, a start-up bioinformatics company specializing in computational drug discovery using a pay-peruse SaaS platform (software as a service) located in Barcelona. Feel free to distribute the offer. Cheers, Vimac --------------------------------- Dr Vímac Nolla Ardèvol Division of Soil and Water Management KU Leuven Kasteelpark Arenberg 20 - box 2459 3001 Leuven room: 02.214 tel. +32 16 37 47 47<tel:+32+16+37+47+47> fax +32 16 3 21997<tel:+32+16+3+21997> e-mail: vimac.nollaardevol(a)ees.kuleuven.be<mailto:vimac.nollaardevol@ees.kuleuven.be> vimacnolla(a)gmail.com<mailto:vimacnolla@gmail.com>

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Job opening - PhD Candidate 'Metabolomics data evaluation for Systems Biology'
by Egon Willighagen 06 Feb '16

06 Feb '16

Dear colleagues, our group at Maastricht University is looking for a PhD candidate to work on metabolomics data analysis. Full information can be found at: https://www.academictransfer.com/employer/UM/vacancy/31818/lang/en/ Please forward this information to anyone who might be interested. Best regards, -- 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 ImpactStory: https://impactstory.org/EgonWillighagen

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Position at Unit of Animal Genomics (Liège, Belgium)
by Tom Druet 05 Feb '16

05 Feb '16

The Unit of Animal Genomics (Liège, Belgium) and the Walloon Breeders Association invite applications for a position to implement genomic selection in Belgian Blue Beef cattle. The Unit of Animal Genomics (http://www.giga.ulg.ac.be/cms/c_20639/fr/unit-of-animal-genomics-home) under the supervision of Prof Michel Georges, focuses on the forward genetic dissection of Mendelian and complex traits in domestic animals and humans. One of the key projects of the group is the development of approaches for the utilization of molecular information in livestock breeding, including genomic selection and transgenics. The lab is based in the Interdisciplinary Cluster of Applied Genoproteomics (GIGA-Research) at the University of Liège in Belgium (http://www.giga.ulg.ac.be <http://www.giga.ulg.ac.be/>). The researcher will join our team to implement a genomic selection program in the Belgian Blue Beef cattle breed, whose animals are famous for their exceptional muscular development referred to as « double-muscling ». The main responsibility will be the development of a new evaluation model for all traits recorded on farm. In addition, he will explore solutions to improve the accuracy of genome-enabled predictions through the development of statistical models or through integration of information obtained through whole-genome sequencing (causative or functional variants). The successful candidate will have access to high-density genotyping and whole-genome sequencing data in addition to phenotypes for a large serie of traits. The candidates should have good skills and strong interest in statistical modeling and programming. A background in quantitative genetics is an asset. Experience in genetic and genomic evaluation and in animal breeding would be desirable. The work will be performed in an international environment with communication in English. Applications, including a C.V., a letter of interest in the position and a list of three referees (with contact information) should be adressed per e-mail to : tom.druet(a)ulg.ac.be Dr Tom Druet Unit of Animal Genomics GIGA-Research and Faculty of Veterinary Medicine University of Liège Belgium The position remains open until a good candidate is identified.

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INSTRUCT practical course on advanced methods for the integration of diverse structural data with NMR data
by Alexandre Bonvin 04 Feb '16

04 Feb '16

INSTRUCT practical course Advanced methods for the integration of diverse structural data with NMR data – 2nd Edition See the online course page at: http://www.bonvinlab.org/education/INSTRUCT-practical-course/ Aims of the course The course aims at training young researchers in the combined use of NMR data with other structural biology techniques, such as SAXS, X-ray diffraction or Cryo-EM in order to understand and rationalize the structural and dynamical properties of macromolecular systems. In addition, this course will introduce and make extensive use of user-friendly e-science portals to facilitate the adoption of the methods and techniques by the students in their everyday work. This INSTRUCT <http://www.structuralbiology.eu/> course will provide lectures describing the basics of the methods applied and hands-on training with the intuitive, web-based services of the WeNMR <http://www.wenmr.eu/> infrastructure, in collaboration with the MoBrain <http://mobrain.egi.eu/> Competence Center, the West-Life <http://www.west-life.eu/> VRE and the BioExcel <http://www.bioexcel.eu/> center of excellence H2020 EU projects, with the support of SURFSara <https://www.surf.nl/en/about-surf/subsidiaries/surfsara/>, which is part of the MoBrain CC and is supporting us in the organisation of this course. The hands-on sessions will allow the students to try the methods on either pre-packaged or their own research data. The course will address state-of-the-art tools and facilities. Participants will be selected among all applicants taking into account the following criteria: previous experience in the field of biomolecular NMR and structure biology; experience in computational aspects of structural biology; gender balance; relevance of current research to the course contents. Location and dates Event Date: 11th Apr 2016 to 15th Apr 2016 Location: SURF Offices Hoog Overborch (Hoog Catharijne), Moreelsepark 48, 3511 EP Utrecht, The NetherlandsPadualaan 8 Directions <https://www.google.nl/maps/place/SURF/@52.0891266,5.1113904,17z/data=!3m1!4…> Plan you travel within NL <http://9292.nl/en> The course will start on Monday afternoon April 11th and run until lunch time on Friday April 15th, allowing for arrival and departure in the morning/afternoon of the first and last days. Utrecht can easily be reached from various airports: Several low-cost companies fly into Amsterdam Schiphol <http://www.schiphol.nl/>, Rotterdam <http://www.rotterdamthehagueairport.nl/en/> or Eindhoven <http://www.eindhovenairport.com/en/> airports, which are all connected by direct and fast trains <http://www.ns.nl/en> to Utrecht (between half an hour to one hour travel time). The SURF location <https://www.google.nl/maps/place/SURF/@52.0891266,5.1113904,17z/data=!3m1!4…> is very close to Utrecht central station. Application procedure: Applicants should send to the lead contact (see below) by email a short CV and letter of motivation explaining how they will benefit from attending this course. The deadline for applying is set to February 15th, 2016. Accepted applicants will be notified by March 1st, 2016. Lead contact Prof. Dr. Alexandre M.J.J. Bonvin – a.m.j.j.bonvin(a)uu.nl Number of participants: 20 Course programme The course will start in the afternoon of April 11th at 13:00 and end at 12:00 on April 15th. Lunch will be provided for all days except the Monday. A detailed programme will be provided at a later stage. April 11 (room 3.1): MS and solution NMR Morning: arrival 13:00-13:10 Welcome + intro (Bonvin) 13:10-13:30 Short intro to HPC/HTC infrastructure and services (SURFSara) 13:30-15:00 Heck: Characterization of large assemblies by mass spectrometry 15:00-15:30 coffee break 15:30-17:00 Boelens: Characterization of macromolecular assemblies by solution NMR April 12 (room 3.3): NMR-based protein structure refinement + integration with SAXS 9:00-10:45: Parigi: Paramagnetic NMR data and integration of SAXS and NMR data for the analysis of protein structure/dynamics 10:45-11:15: coffee break 11:15:13:00: Rosato: Molecular dynamics for NMR-based protein structure refinement 13:00:13:45: Lunch 13:45-17:00: AMPS-NMR + FANTEN + MAXOCC computer practicals (Rosato / Parigi) April 13 (room 3.3): Cryo-EM / Xray 9:00-10:45: Gros: Characterization of macromolecular complexes by X-Ray crystallography and cryo-EM 10:45-11:15: coffee break 11:15-13:00: Carazo: Cryo-EM analysis of biomolecular assemblies 13:00:13:45: Lunch 13:45:17:00: Cyro-EM computer practical (Jose Miguel de la Rosa) Evening: workshop dinner April 14 (room 4.1): Integrative modelling 9:00-10:45: Bonvin: Integrative modelling of biomolecular complexes by docking 10:45-11:15: coffee break 11:15-13:00: Bonvin: Integrative modelling of biomolecular complexes by docking 13:00:13:45: Lunch 13:45:17:00: HADDOCK computer practical (Bonvin + local assistant) April 15 (room 3.3): Solid state NMR lecture + open discussion / question and answers 9:00-10:45: Baldus: Characterization of macromolecular assemblies by solid-state NM 10:45-11:15: coffee break 11:15-12:15: Open discussion / question and answers 12:15:13:00: Lunch Departure Note that participants are required to bring their own laptop for the practicals, ideally with applications allowing remote ssh access and also VirtualBox installed to allow for running Virtual Machines that will be provided to the participants so that the students can take them back with them for further analysis/use back home. We will also make use of SURFSara cloud resources for the practicals. Case studies will be provided via the web for re-examination also at the home lab. Lecturers: Alexandre Bonvin <http://www.uu.nl/staff/amjjbonvin> (Bijvoet/Instruct-NL) Albert Heck <http://www.uu.nl/staff/AJRHeck> (Bijvoet/Instruct-NL) Piet Gros <http://www.uu.nl/staff/PGros> (Bijvoet/Instruct-NL) Rolf Boelens <http://www.uu.nl/staff/RBoelens> (Bijvoet/Instruct-NL) Marc Baldus <http://www.uu.nl/staff/MBaldus> (Bijvoet/Instruct-NL) Antonio Rosato <http://www.cerm.unifi.it/people/antonio-rosato> (CERM/INSTRUCT-IT) Giacomo Parigi <http://www.cerm.unifi.it/people/giacomo-parigi> (CERM/INSTRUCT-IT) José Maria Carazo <http://biocomp.cnb.csic.es/carazo> (I2PC) Costs: 100 euros for participants from Instruct countries (check here <https://www.structuralbiology.eu/resources/countries>), 300 euros for others. The registration fee covers lunches and coffee breaks and the course dinner. Travel and lodging are not included. Housing information: A list of hotels, hostels and bed and breakfast possibilities in Utrecht can be downloaded here <http://www.bonvinlab.org/docs/Hotels-Utrecht-Nov2015.pdf>. Participants are responsible for arranging their own housing. --------------------------------------------------------------------------------------------------------------------------- Dr. Alexandre M.J.J Bonvin | Professor of Computational Structural Biology Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands Phone: +31-30-2533859 / 2652 | Fax: +31-30-2537623 Email: a.m.j.j.bonvin(a)uu.nl http://www.uu.nl/staff/AMJJBonvin | http://www.bonvinlab.org ---------------------------------------------------------------------------------------------------------------------------

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BioSB 2016 - Call for abstracts & registration open!
by Femke Francissen 04 Feb '16

04 Feb '16

*Dutch Bioinformatics & Systems Biology Conference 2016 (BioSB 2016)* Date: April 19 / 20, 2016 Venue: Congrescentrum De Werelt, Lunteren, NL Conference website: http://www.aanmelder.nl/biosb2016 *Call for abstracts* Abstract submission for the BioSB 2016 conference is now open. You can submit an abstract for the following topics/sessions: - Gene regulation - Genotype/phenotype & disease - Industrial applications & synthetic biology - Metabolomics - Modeling - Networks & data integration - NGS data analysis - Proteomics - Statistics - Systems medicine - Infrastructure (ELIXIR-ISBE track) - Metagenomics - Structural bioinformatics (NSBM) You can submit an abstract for a lecture in one of the sessions, a poster presentation or a poster/demo. Find out here how to submit your abstract <https://www.aanmelder.nl/biosb2016/wiki/154972/abstract%20submission>. *Keydates* - Abstract submission deadline for oral presentations: March 1, 2016 - Notification date oral presentations: March 22, 2016 - Abstract submission deadline for posters: April 14, 2016 *Our keynote speakers* Our confirmed keynote speakers for the conference are: - *Mick Watson*, Director of ARK-Genomics, The Roslin Institute, R(D)SVS, University of Edinburgh. - *Jasmin Fisher*, Senior Researcher in the Programming Principles and Tools group at Microsoft Research Cambridge - *Jonathan Karr*, Fellow, Institute and Department for Genetics and Genomic Sciences Icahn School of Medicine at Mount Sinai, New York - *Sander Tans*, Groupleader, FOM-Institute for Atomic and Molecular Physics (AMOLF), Amsterdam - *Adriano Henney *(After Dinner Keynote Speaker), Executive director of the VHP Institute (Virtual Physiological Human Institute for Integrative Biomedical Research), Leuven, Belgium *Call for nominations: BioSB Young Investigator Award 2016 * During the BioSB 2016 on April 19, we will present the BioSB Young Investigator Award 2016. The winner will receive a prize of 500 Euros sponsored by the BioSB research school and will present an honorary lecture. Read more about the criteria and how to nominate a candidate <https://www.aanmelder.nl/biosb2016/wiki/164489/biosb%20young%20investigator…>. Submission deadline: March 15, 2016. *BioSB PhD retreat* The Young Computational Biologists are pleased to invite you to the BioSB PhD retreat 2016 on April 18. Like previous years the retreat will be hosted in Lunteren, directly preceding the BioSB conference. The retreat provides you with the opportunity to present your research to fellow students and young professionals. In the evening there will be a dinner in Lunteren, followed by a social activity, which allows you to network with fellow young systems biologists and bioinformaticians. Read more <https://www.aanmelder.nl/biosb2016/wiki/154925/biosb%20phd%20retreat> *Our sponsors* - DSM - Utrecht Bioinformatics Center (UBC) - Keygene NV - Wageningen UR *Conference updates* More information about the conference programme will follow soon! You can find the latest conference updates at the conference website. Regular updates will also be sent via the BioSB mailing list. Contact: Femke Francissen, community manager BioSB, email: femke.francissen(a)biosb.nl ** **

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Job opening - Bioinformatician at CHU Liège
by Stephane Wenric 01 Feb '16

01 Feb '16

Dear colleagues, The genetics department at the university hospital of Liège is looking for a full-time bioinformatician. More details can be found in the attached document. Please forward this information to anyone who might be interested. Best regards, Stephane Wenric -- Stephane Wenric, Ir PhD candidate Human Genetics GIGA +2, CHU, Sart Tilman Liège Belgium 04 366 47 20

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