- BBClist - maillist.psb.ugent.be

Free f-TALES conference on Big Data in Biomedicine - Ghent - 26-27 september 2018
by Laukens Kris 06 Sep '18

06 Sep '18

Dear Colleagues, On 26 and 27 September, we organize a free f-TALES conference on Big Data in Biomedicine in Ghent. Needless to say, this is a big and important topic that is relevant to all of us, and should therefore interest many of you. This conference (did I mention that it was free?) is specifically geared towards PhD students and postdocs, and covers a variety of interesting topics, through inspiring top speakers from all over the world. Moreover, there are 12 slots for selected flash talks by participants, as well as ample poster presentation opportunities. Prizes will be awarded for both top posters as well as top flash talks, so there could easily be something in it for you! Attached you can find the programme, and the link to the conference website and registration, which is also provided below. https://ftales.be/gent-2018/homebigdatabiomedice Importantly, the abstract submission deadline has been extended, so there's still time to submit your abstract! PS: feel free to forward this email to any (or any group of) interested people! PPS: But don't forget to register yourself first; when it's full, it's full :D. Very much looking forward to seeing you at this conference! Kris -- Kris Laukens, PhD Associate professor bioinformatics - biodata mining Advanced Database Research and Modelling (ADReM) Biomedical Informatics Network Antwerpen (biomina) Department of Mathematics and Computer Science University of Antwerp Middelheimlaan 1, G.111 B-2020 Antwerpen, Belgium T +32 (0)3 265 33 10 E kris.laukens(a)uantwerpen.be<mailto:kris.laukens@uantwerpen.be> W www.uantwerpen.be/en/staff/kris-laukens/<http://www.uantwerpen.be/en/staff/kris-laukens/>

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Fwd: Extended Deadline Abstract - Sept 7-, UBC symposium
by Patrick Kemmeren 04 Sep '18

04 Sep '18

For those of you who are interested, we are organizing our fifth Utrecht Bioinformatics Symposium the first of October. There are still places available! Regards, Patrick -------- Forwarded Message -------- Subject: Extended Deadline Abstract - Sept 7-, UBC symposium Date: Tue, 4 Sep 2018 08:59:08 +0000 From: Utrecht Bioinformatics Center <b.vanbreukelen(a)uu.nl> Reply-To: Utrecht Bioinformatics Center <b.vanbreukelen(a)uu.nl> To: p.kemmeren(a)umcutrecht.nl Extended Deadline Abstract - Sept 7-, UBC symposium UBC Announcements View this email in your browser <https://mailchi.mp/328d12ea00bb/extended-deadline-abstract-sept-7-ubc-sympo…> *EXTENDED ABSTRACT DEADLINE* *SEPTEMBER 7th* Send in your poster abstract and and get a chance to win the poster prize Save the date * Sept 13th, SnakeMake workshop: sign up here <https://ubc.us12.list-manage.com/track/click?u=02d188b181bc253cd9b1e5c1b&id…> * Oct 1st, UBC symposium: register here <https://ubc.us12.list-manage.com/track/click?u=02d188b181bc253cd9b1e5c1b&id…> * Nov 5th, UBC seminar Dear all, Please make sure you *send in your abstract* for a poster before september 7th. Based on the submitted abstracts, three abstracts will be selected to give an oral presentation, so this provides you with a great opportunity to highlight what you are working on! We expect an exciting full day program on October 1st, *_with two international keynotes speakers_*, principal investigators from our local community, selected talks from abstracts, posters and of course ample time to mingle with your fellow bioinformaticians! More information and registration: https://ubc.uu.nl/symposium-big-data-in-life-sciences/ <https://ubc.us12.list-manage.com/track/click?u=02d188b181bc253cd9b1e5c1b&id…> Registration is open for everyone, poster abstracts can be submitted by master students (doing a bioinformatics internship), PhDs or Postdocs. So make sure you register and submit your abstract before September 1st, we will also award 150 euro for the best poster! *Two International Keynote Speakers* * *Debora Marks: *Harvard Medical School, well known for her work on predicting 3D protein structures * *Paul Tompson: *University of Southern California, who will talk about the work done within the ENIGMA consortium combining brain imaging with genetics for over 70,000 individuals. *And also...* * *Frank Holstege, *principal investigator*, *coordinating single cell genomics activities within the Princess Maxima Center for pediatric oncology * *Wouter van Solinge**, *involved in ADAM, an applied data analytics for medicine program within the University Medical Center Utrecht. * *Geert Kops, *Hubrecht Insitute/UMCU, group studies the processes involved in chromosome segregation during cell division, with a focus on molecular mechanisms, evolution and chromosomal instability *Registration is free* Read more and Register <https://ubc.us12.list-manage.com/track/click?u=02d188b181bc253cd9b1e5c1b&id…> *Submit your abstract for a poster* Have a chance at winning the poster prize. Submit your poster abstract_ before September 1st_ /Copyright © *|2016|* *|Utrecht Bioinformatics Center|*, All rights reserved./ You are receiving this e-mail because you are a member of the Utrecht Bioinformatics Center. https://ubc.uu.nl Want to change how you receive these emails? You can update your preferences <https://ubc.us12.list-manage.com/profile?u=02d188b181bc253cd9b1e5c1b&id=cc6…> or unsubscribe from this list <https://ubc.us12.list-manage.com/unsubscribe?u=02d188b181bc253cd9b1e5c1b&id…> This email was sent to p.kemmeren(a)umcutrecht.nl <mailto:p.kemmeren@umcutrecht.nl> /why did I get this?/ <https://ubc.us12.list-manage.com/about?u=02d188b181bc253cd9b1e5c1b&id=cc682…> unsubscribe from this list <https://ubc.us12.list-manage.com/unsubscribe?u=02d188b181bc253cd9b1e5c1b&id…> update subscription preferences <https://ubc.us12.list-manage.com/profile?u=02d188b181bc253cd9b1e5c1b&id=cc6…> Utrecht Bioinformatics Center · Padualaan 8 · Utrecht, NH 3584 CH · Netherlands Email Marketing Powered by MailChimp <http://www.mailchimp.com/monkey-rewards/?utm_source=freemium_newsletter&utm…>

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Vacancy Bioinformatician Genome Diagnostics Amsterdam UMC
by Sie, D.L.S. (Daud) 03 Sep '18

03 Sep '18

Dear all, We are recruiting for a bioinformatician in the Genome Diagnostics section of the Clinical Genetics department Amsterdam UMC. Do you want to be part of bringing Next Generation Sequencing to patient care? https://www.werkenbijvumc.nl/vacatures/bioinformaticus-genoomdiagnostiek/ English summary: Our lab focusses on processing and analyzing Next Generation Sequencing data. A fully automated laboratory street, an array of Illumina NGS sequencers and high performance computing infrastructure allows us to efficiently process a large number of samples for patient care. Applications include non invasive prenatal testing (NIPT), deep whole genome sequencing, whole exome sequencing, targeted sequencing and amplicon sequencing. We collaborate intensively with research groups to develop CRIPSR/CAS assays, Liquid Biopsy techniques and RNA-seq applications where bioinformatics support is indispensable. We are recruiting an additional member for our bioinformatics team, currently consisting of 5 people. Your responsibilities include: - Tending to routine diagnostics workflows - Validation and implementation of novel data analysis pipelines and algorithms - Development and maintenance of data analysis pipelines - Development and maintenance of HPC compute and storage infrastructure - Development and maintenance of lab information systems - Development and maintenance of lab robotics systems - Bioinformatics support for clinicians and researchers Your profile includes: - HBO/WO degree in bioinformatics, preferably with relevant work experience - Experience with development and maintenance of analysis pipelines - Experience with scripting languages Python, Bash or PERL - Experience with Unix / Linux - Experience with R / Bioconductor / R Studio - Experience with High Performance Computing (SLURM / SGE) - Excellent communication skills For more information you can contact: Dr. Daoud Sie E: d.sie(a)vumc.nl<mailto:d.sie@vumc.nl> T: +31204442428 Or Dr. Janneke Weiss E: j.weiss(a)vumc.nl<mailto:j.weiss@vumc.nl> T: +31204448355 Kind regards, Daoud Sie, PhD [cid:image001.png@01D3FE70.9A3875A0] Dr. Daoud Sie | Coordinator Bioinformatics | Co-chair HPC Center of Expertise Genome Diagnostics - Department of Clinical Genetics Locatie VUmc | MF-J391 | Van Der Boechorststraat 7, 1081 BT Amsterdam Locatie AMC | K-211 | Meibergdreef 9, 1105 AZ Amsterdam T: (+31)20-4442428 | E: d.sie(a)vumc.nl www.amsterdamumc.nl<http://www.amsterdamumc.nl/> | www.vumc.nl<http://www.vumc.nl/> / www.amc.nl<http://www.amc.nl/> ______________________________________________________ VUmc disclaimer: www.vumc.nl/disclaimer<http://www.vumc.nl/disclaimer> AMC disclaimer: www.amc.nl/disclaimer<http://www.amc.nl/disclaimer>

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POSTDOC: ANT ADAPTATION TO HOT AND ARID AREAS – TRANSCRIPTOMICS DATA ANALYSIS, BRUSSELS
by Matthieu Defrance 30 Aug '18

30 Aug '18

POSTDOC: ANT ADAPTATION TO HOT AND ARID AREAS – TRANSCRIPTOMICS DATA ANALYSIS, BRUSSELS The Evolutionary Biology & Ecology lab (ULB Belgium) and the Interuniversity Institute of Bioinformatics in Brussels (ULB and VUB Belgium) are recruiting a 2-year postdoc researcher to study how desert ants have evolved their extreme degree of thermophily. The project is based on a comparative approach to examine how similar desert conditions have led either to the evolution of convergent traits in different lineages or to the adoption of alternative strategies. The postdoc will use a variety of molecular methods (including but not limited to RNA-seq) to explore the heat-shock responses (HSRs) in ants and will focus on the computational analysis of sequencing data (e.g. RNA-seq de novo assembly, differential expression analysis, clustering). Candidates should have a strong experience with RNA-seq (including library preparation and computational analysis of sequencing data) and must have effective written and oral communication skills, with a demonstrated ability to publish peer-reviewed papers. He/She must have a PhD pending or obtained within the last 3 years in computer science, biology or bioinformatics. The applicant may not have resided or pursued his/her main activity (studies, employment, etc.) in Belgium for more than 24 months during the last 3 years immediately preceding the first period of postdoctoral residence. The post-doc will be based in the the Interuniversity Institute of Bioinformatics in Brussels under direct supervision of Matthieu Defrance (Associate Professor) and Serge Aron (Research Director of the Belgian NSF/ FNRS). He/She will work closely with a PhD student, who will focus on empirical data collection. The position is funded for 2 years. Start date is early 2019. The candidate's salary for the first year will be ~2 450 euros, net of tax; it will increase the second year in accordance with the legal rules in force in Belgium. To apply, please send a cover letter, CV, and names and contact information for three references to Serge Aron (saron(a)ulb.ac.be) and Matthieu Defrance (matthieu.dc.defrance(a)ulb.ac.be) The application deadline is December 1st, 2018. ULB is an Equal Opportunity Employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, age, disability, protected veteran status, or any other characteristic protected by law. For more information, please visit the Evolutionary Biology & Ecology lab website (http://ebe.ulb.ac.be) and the Interuniversity Institute of Bioinformatics in Brussels website (ibsquare.be) or contact Serge Aron (saron(a)ulb.ac.be) or Matthieu Defrance (matthieu.dc.defrance(a)ulb.ac.be)

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Fwd: [rsg-belgium] [ELIXIR Belgium workshop] Shell-Git-Python
by Daniele Parisi 24 Aug '18

24 Aug '18

Dear all, We would hereby like to announce an upcoming training in GENT on OCTOBER 24TH AND 25TH, organised by ELIXIR BELGIUM. This two day workshop will aim to teach basic programming skills to PhD researchers in life sciences, who need them to do their research more effectively. The workshop will cover multiple tools, such as SHELL, GIT, and PYTHON. The workshop is FREE OF CHARGE, and sponsored by the ELIXIR-EXCELERATE program. More information is available at the following link: https://orchid00.github.io/2018-10-24-ugent/ Please forward this information to anyone who you think might be interested. With best regards, Daniele Parisi on behalf of Paula Martinez, ELIXIR Belgium trainer -- DANIELE PARISI PhD student at ESAT - STADIUS, Yves Moreau's group President of RSG Belgium Chair of ESCS 2018 Kasteelpark Arenberg 10 - box 01.34 3001 Leuven, Belgium Tel: +32488794394

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Bioinformatician application
by Harmen van de Werken 16 Aug '18

16 Aug '18

The Erasmus MC Cancer Computational Biology Center(CCBC <https://ccbc.erasmusmc.nl/>) is seeking a highly motivated bioinformatician to join our team. If you are eager to combine cancer biology with computational biology please apply. https://www.academictransfer.com/en/49444/bioinformatician/#.W3VWAoiRB_s.li… Kind regards, Harmen van de Werken

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Transcriptomics data analysis expert vacancy
by Jo Vandesompele 13 Aug '18

13 Aug '18

'Transcriptomics data analysis expert' vacancy at UGent spin-off Biogazelle. More information via flanders.bio at https://www.flanders.bio/en/jobs/?jbtClsJobId=1303488 -- prof. dr. ir. Jo Vandesompele Ghent University Center for Medical Genetics Ghent (CMGG) Cancer Research Institute Ghent (CRIG) Bioinformatics Institute Ghent N2N (BIG N2N)

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Bioinfomatician/biostatistician position at LBMCC
by Anthoula Gaigneaux 10 Aug '18

10 Aug '18

Dear all, LBMCC is a research lab located in Luxembourg, dedicated to basic and applied research in the field of cancer and inflammation. We have one job opening for a post-doc scientist with experience in biostatistics and -omics data analysis. Detailed description and contact information can be found in the attached document. Kind regards, Anthoula Gaigneaux, PhD Laboratoire de Biologie Moléculaire et Cellulaire du Cancer (LBMCC) Hôpital Kirchberg 9, rue Edward Steichen L-2540 Luxembourg tel: +352 2468 4046 anthoula.gaigneaux(a)lbmcc.lu <mailto:anthoula.gaigneaux@lbmcc.lu>

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Fwd: postdoc position in my lab
by Lieven Sterck 03 Aug '18

03 Aug '18

> From: "Olivier De Clerck" <Olivier.DeClerck(a)UGent.be> > Dear all, > Assaf Vardi is looking for a bioinformatics postdoc to work Ehux host pathogen > interactions. > See attached. > Please distribute to potential candidates. > Olivier > From: Assaf Vardi [mailto:assaf.vardi@weizmann.ac.il] > Sent: vrijdag 3 augustus 2018 14:07 > To: Olivier De Clerck <Olivier.DeClerck(a)UGent.be> > Subject: postdoc position in my lab > Hi again > If you happen to know a potential candidate for bioinformatics position in my > lab, im looking for a good one please see the attached ad. > Many thanks and enjoy your vacation. > Cheers > Assaf

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FINAL CALL FOR ABSTRACTS: Summer School on Machine Learning in Drug Design, August 20-22, 2018, Leuven, Belgium - ABSTRACT DEADLINE: JULY 22, 2018
by Yves Moreau 01 Aug '18

01 Aug '18

Dear colleague, The Summer School on Machine Learning in Drug Design will take place on August 20-22, 2018 in Leuven, Belgium. This Summer School will bring together the machine learning, chemoinformatics, and bioinformatics communities from academia and industry to tackle the challenges of complex data integration in drug design and discovery. The format of the event will combine multiple keynote presentations, oral contributions selected from submitted abstracts, and extensive poster sessions with ample time for discussion. As this is an emerging area, the event will aim at giving good exposure to promising junior researchers. We invite you to submit your short abstract for oral presentation or poster by July 22, 2018 (extended deadline) at http://mldd.esat.kuleuven.be <http://mldd.esat.kuleuven.be/>. Please forward this announcement to members of your team and to interested colleagues. More information is available below and at http://mldd.esat.kuleuven.be <http://mldd.esat.kuleuven.be/>, or by email at mldd(a)esat.kuleuven.be <mailto:mldd@esat.kuleuven.be>. Apologies for multiple postings. Best regards, Prof. Yves Moreau, University of Leuven Prof. Sepp Hochreiter, Johannes Kepler University of Linz Prof. Samuel Kaski, Aalto University SCOPE The data sets amenable to mining for drug design are rapidly expanding. This holds not only for the volume of conventional annotation of chemicals (i.e., representations of their chemical structure and their activities in a growing set of validated assays). It also goes for less conventional data sources, such as cellular microscopy or gene expression profiles of chemicals acquired at high throughput. Powerful novel machine learning methods unleashed on these massive volumes of heterogeneous and rich, but noisy and biased data, hold the promise of better and safer drugs to address unmet medical needs. To deliver on that promise, the Summer School calls on the machine learning, big data analytics, cheminformatics and bioinformatics communities to join forces and strengthen collaborative work at the interface of their disciplines. The Summer School will bring together contributors from both academia and industry to foster interdisciplinary exchange in this area where the need for expertise is growing rapidly. Contributions will cover recent advances in chemogenomics, strategies for data fusion, and machine learning. PRELIMINARY INVITED SPEAKER PROGRAM * Djork-Arné Clevert (Bayer): Deep learning for proteochemometric modeling * Gerard van Westen (Leiden University): Combining cheminformatics and bioinformatics through deep learning * Gilles Marcou (University of Strasbourg): Chemical space modeling and visualization with Generative Topographic Maps * Günter Klambauer (JKU Linz): Boosting drug discovery with deep learning * Florian Nigsch (Novartis): From heterogeneous data to highly predictive models and their applications in early drug discovery * Daniel Reker (MIT): Machine learning for natural product target prediction and chemogenomic data compression * Tim Becker (Harvard University): Machine learning and deep learning to predict drug-target activity from high-content imaging * Thomas Blaschke (AstraZeneca): The rise of deep learning in drug discovery * Val Gillet (University of Sheffield): TBA INTENDED AUDIENCE AND FORMAT The summer school is intended for academic and industry researchers in machine learning, chemoinformatics, or bioinformatics who are either currently working at the interface between these fields or want to expand their skills to link these three areas. The summer school is also intended as a bridge between academia and industry. The format of the event will combine comprehensive invited presentations, oral contributions selected from submitted abstracts, and extensive poster sessions with ample time for discussion. ABSTRACT SUBMISSION Participants are invited to submit abstracts for oral contributions and posters by July 22, 2018 (extended deadline). Abstracts can submitted for consideration for oral presentation (up to 1,000 words) or for consideration as poster only (up to 250 words). Abstracts selected for oral presentation will be notified by July 25, 2018. Abstracts will be available as a book of abstracts and online, but there will be no full proceedings. REGISTRATION AND FEE Early registration fee (before July 20, 2018): €180 (including VAT) Late registration fee (before August 13, 2018): €300 (including VAT) The fee covers participation to the meeting and includes coffee breaks and lunch (sandwich lunch). VENUE The Summer School will be held at the Irish College, a beautifully restored historical building in the center of Leuven, Belgium.

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