July 2018 - BBClist - maillist.psb.ugent.be

Bioinformatics position available at the Erasmus MC Cancer Computational Biology Center
by Harmen van de Werken 04 Oct '19

04 Oct '19

A bioinformatics position is currently available at the Erasmus MC Cancer Computational Biology Center. http://www.erasmusmc.nl/vacature/?num=21578 Please apply, if you are enthusiastic and eager to improve our knowledge on cancer biology. Harmen van de Werken

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COMPUTATIONAL BIOLOGIST - TUMOR IMMUNOLOGY
by Lodewyk Wessels 25 Jul '19

25 Jul '19

VACANCY COMPUTATIONAL BIOLOGIST - TUMOR IMMUNOLOGY YOUR ROLE WITHIN THE INSTITUTE The research groups of Dr Karin de Visser, dr Marleen Kok and Prof dr Lodewyk Wessels, are looking for a motivated and talented Computational Biologist to join their teams at the Netherlands Cancer Institute (NKI). The Inflammation and Cancer group of dr. Karin de Visser is studying the impact of the immune system on metastatic breast cancer utilizing sophisticated mouse tumor models and state-of-the art ex vivo and in vitro immunological and molecular assays. The lab of de Visser closely collaborates with the translational research group of medical oncologist dr Marleen Kok. The mission of this team is to discover novel mechanisms underlying the crosstalk between breast cancer and the immune system, to optimize immunotherapy for breast cancer patients using novel combination treatments in clinical trials and the discovery of predictive biomarkers. The Computational cancer biology group of Prof dr Lodewyk Wessels is focused on quantifying and understanding treatment response in model systems and patients. To this end we develop bespoke and novel computational methods focusing on data integration and tailored to new technologies. We actively collaborate with many research groups in the NKI and strongly believe in the power of 'team science'. PROJECTS You will be involved in the following projects: 1. MOUSE MODELS FOR METASTATIC ESCAPE FROM IMMUNE CONTROL. To study the causal relationship between immune cells and metastatic breast cancer, we utilize state-of-the art genetically engineered mouse tumor models. We have extensive RNA-sequencing datasets of isolated immune cell populations, as well as RNA-sequencing and exome sequencing data of primary breast tumors and organ-specific metastases from these mouse models. You will be responsible for the computational analyses of the data, and to extract candidate pathways/genes from these datasets that can subsequently be tested in follow up experiments in the lab. Moreover, you will link these pre-clinical data to human datasets. 2. SYSTEMIC AND INTRA-TUMORAL IMMUNOMONITORING FOR PRECISION IMMUNE-MODULATION. We are performing extensive immunomonitoring studies in human breast cancer patients treated with immune checkpoint blockade, with the ultimate aim to validate hypotheses derived from our preclinical research in human cancer patients, and to stratify breast cancer patients for immunomodulatory therapies. We are setting-up multiplex immunohistochemistry with antibody panels that audit intratumoral lymphoid and myeloid cell populations and their functional state. In parallel, we have established an extensive multiplex flow cytometry pipeline to monitor the systemic immune landscape of breast cancer patients and healthy controls. These analyses generate a substantial amount of data which require thorough computational analyses. 3. MAPPING IMMUNO-GENOMIC INTERACTIONS. We are interested in dissecting the impact of the genetic make-up of breast tumors on the intra-tumoral and systemic immune landscape. You will be responsible for the identification and validation of genotype-immunophenotype associations by connecting DNA exome sequencing data, RNA sequencing data and immune profiles derived from our mouse tumor models and cancer patients. You will use both publicly available datasets and newly generated datasets. You will be embedded in the collaborative and enthusiastic international research groups of dr. Karin de Visser, dr Marleen Kok and Prof. dr. Lodewyk Wessels, providing a unique environment that combines computational cancer biology with pre-clinical and translational research into immune-oncology. YOUR PROFILE We seek to recruit an ambitious postdoc, capable of independent thinking, with a strong commitment to translational research. Candidates should hold a degree in bioinformatics, computer science or a related discipline, have experience in statistics and/or machine learning and be proficient in bioinformatics programming languages (e.g. R, Python). We expect candidates to be highly self-motivated, creative, and a team-player with strong communication skills. General background knowledge in biology and immunology is essential, and experience with projects involving the use of genomics and immune profiling data to identifying candidate targets and biomarkers is a plus. WANT MORE INFORMATION? Please visit our home pages https://www.nki.nl/divisions/tumor-biology-immunology/de-visser-k-group/ https://ccb.nki.nl or contact Karin de Visser: k.d.visser(a)nki.nl Marleen Kok: m.kok(a)nki.nl Lodewyk Wessels: l.wessels(a)nki.nl

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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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Bioinformatician / Data Scientist position available at NIZO
by Wels, Michiel 30 Jul '18

30 Jul '18

Currently we are looking for a Bioinformatician / Data Scientist to strengthen our Microbiomics team at NIZO. Best Regards, Michiel Wels [cid:image001.png@01D427EA.96C2B400]<http://www.nizo.com/news/courses/> M.W.W. (Michiel) Wels PhD Expertise Group Leader Microbiomics T: +31 318 659 674 M: +31 6 445 727 51 F: +31 318 650 400 E: Michiel.Wels(a)nizo.com<mailto:Michiel.Wels@nizo.com> P.O. Box 20, 6710 BA EDE, The Netherlands Kernhemseweg 2, 6718 ZB EDE, The Netherlands Visit our website at www.nizo.com<http://www.nizo.com/>. Follow us: [cid:image003.jpg@01D427EA.4231AF90] <https://www.linkedin.com/company/nizo-food-research/> [cid:image004.jpg@01D427EA.4231AF90] <https://twitter.com/NIZOfoodnews/> This message may contain information that is not intended for you. If you are not the addressee, intended addressee or if this message was sent to you by mistake, you are hereby notified that any disclosure, copying, distribution or taking action in reliance on the content of this email message is prohibited. You are kindly asked to inform the sender and delete the message. NIZO food research B.V. accepts no liability for damage of any kind resulting from the risks inherent in the electronic transmission of messages.

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job offer down under
by Stephane Rombauts 24 Jul '18

24 Jul '18

Anna Koltunow (CSIRO) is looking for a bioinformatician on her Gates project. She needs someone with capacity to do support work but also open to new fundamental stuff. The position is on the Waite campus, Adelaide based, and full time. Some information about Anna’s research can be found here: [ https://people.csiro.au/K/A/Anna-Koltunow | https://people.csiro.au/K/A/Anna-Koltunow ] , [ https://www.science.org.au/fellowship/fellows/dr-anna-mg-koltunow | https://www.science.org.au/fellowship/fellows/dr-anna-mg-koltunow ] . Stephane Rombauts - Senior staff scientist Bioinformatics VIB-UGent Center for Plant Systems Biology Ghent University Technologiepark 927 - 9052 Ghent - Belgium Tel. +32(0)9 331 38 21 [ http://www.psb.ugent.be/ | www.psb.ugent.be ]

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Postdoc position in (plant) genome biology
by Yves Van de Peer 24 Jul '18

24 Jul '18

Bioinformatics Postdoc Position in Evolutionary and Comparative Genomics A three-year postdoctoral position is available in the Van de Peer lab (http://bioinformatics.psb.ugent.be/beg/) at VIB/Ghent University, Belgium, starting October 1st, 2018. The Van de Peer lab is considered a center of excellence in gene prediction and genome annotation, and comparative and evolutionary genomics. As we are involved in several international plant genome and evolution projects, we are currently looking for a bioinformatician to strengthen our genome annotation and analysis team. You will also be involved in the study of gene and genome duplications, another major interest of the research group. *Required Qualifications* The ideal candidate holds a PhD degree in bioinformatics or computational biology (or equivalent through experience), is highly interested, ambitious, curiosity-driven and likes interdisciplinary work. He/she will need to interact productively with evolutionary biologists, genome biologists and computer scientists. Programming/scripting experience (e.g., Perl, Python, R, …) and experience working in a Linux environment are essential. A background in genomic, transcriptomic and/or epigenetic research and experience in evolutionary and/or comparative genomics is expected. Since English is the working language of the laboratory, excellent English communication skills are imperative. The candidate should have a proven track record with at least two publications as first author in renowned peer reviewed journals. *Working environment* The successful candidate will work in the Department of Plant Biotechnology and Bioinformatics/VIB Center of Plant Systems Biology, Ghent University, Belgium. VIB and Ghent University offer a supportive and stimulating environment, with access to excellent computer and academic facilities. More information on our research and research topics can be found at http://bioinformatics.psb.ugent.be/beg/. *Contact details* To apply, please send a single document including a letter of motivation describing your research motivation and experience, a detailed CV with a list of publications, summary of past research, and contact details for at least two referees to yves.vandepeer(a)psb.ugent.be. Review of applications will continue until a suitable candidate is found. Yves Van de Peer VIB Center for Plant Systems Biology Department of Plant Biotechnology and Bioinformatics Ghent University Belgium

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FW: call for group leader position in computational biology at institut Curie - update
by Alexander Botzki 23 Jul '18

23 Jul '18

To: Emmanuel Barillot <Emmanuel.Barillot(a)curie.fr> Subject: call for group leader position in computational biology at institut Curie - update Dear colleagues, We are recruiting group leader in computational biology at institut Curie (see attachment). I also add an URL in case you want to tweet it or share it this way: http://sysbio.curie.fr/texts/Call4GroupLeaderCurieU900-2018.pdf Could you please spread the word as widely as possible? Many thanks for your help Best wishes Emmanuel - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Dr Emmanuel Barillot Director of U900 Institut Curie - INSERM - PSL Research University / Mines ParisTech: "Bioinformatics and Computational Systems Biology of Cancer" Institut Curie 26 rue d'Ulm 75248 PARIS cedex 05 FRANCE Mail: Emmanuel.Barillot(a)curie.fr

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Open positions computational biology and data analyst at VIB
by Alexander Botzki 19 Jul '18

19 Jul '18

Dear all, VIB has several data science and computational biology-related openings Data Analyst https://vibvzw.jobsoid.com/j/13817/business-intelligence-analyst-bianalyst-… Single Cell Technology Specialist https://vibvzw.jobsoid.com/jobs/35bba14f-79b7-4388-b015-a4fb9d97ee41/14088/… Single Cell Bioinformatics Specialist https://vibvzw.jobsoid.com/jobs/35bba14f-79b7-4388-b015-a4fb9d97ee41/11971/… For more information and other jobs please visit http://www.vib.be/jobs Best regards, Alex Alexander Botzki - Head of VIB Bioinformatics Core | Training Coordinator ELIXIR-BE VIB Bioinformatics Core Rijvisschestraat 126, 9052 GENT, Belgium | +32 9 248 16 00 www.bits.vib.be<http://www.bits.vib.be/> | @vibbioinfocore | https://corefacilities.vib.be<https://corefacilities.vib.be/> [signatureFooter (002)]

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Registration Open for ELIXIR-NL Course Bioinformatics for Translational Medicine using Galaxy: see it, do it, teach it! - 17- 19 October 2018, Amsterdam
by Celia van Gelder 13 Jul '18

13 Jul '18

*ELIXIR-NL Course: * Bioinformatics for Translational Medicine using Galaxy: see it, do it, teach it! Please circulate this email to those who might be interested. Date: 17-19 October, 2018 Location: VU Amsterdam (O|2 Lab Building <https://goo.gl/maps/CphwJEFDegt>, Gustav Mahlerlaan 665, 1082 MK, 1082 MK Amsterdam) Organizers: This course is an ELIXIR-EXCELERATE course and is organised by ELIXIR-NL by Chao (Cico) Zhang (VU), Sanne Abeln (VU), Anton Feenstra (VU), Saskia Hiltemann (ErasmusMC), Mateusz Kuzak (DTL) and Celia van Gelder (DTL). Course page (incl. Application Form): https://www.biosb.nl/education/course-portfolio/bioinformatics-for-translat… TARGET AUDIENCE 1) Biomedical & translational medicine researchers/students who are keen on bioinformatics and 2) educators in the “bio” domain who would like to start using Galaxy in their courses as an introduction to Bioinformatics. COURSE DESCRIPTION Analysing molecular data in translational medicine involves a multitude of computational steps. Here, we introduce the basics of how to design and run these steps within Galaxy, a free and easy-to-use web platform that enables users to connect bioinformatics tools into a workflow without any prior programming expertise. This course consists of two parts. Part 1 will let you get familiar with Galaxy; it will introduce some bioinformatics workflows used for RNAseq, variant detection and metagenomics; and how to easily connect different computational steps in Galaxy. Part 2 will focus on how to teach bioinformatics with Galaxy and to design bioinformatics courses using Galaxy. Participants can register for both parts separately. This course is also interspersed with a few keynotes, from recognised researchers in the fields of Biomedicine, Bioinformatics education and Galaxy workflows. The confirmed speakers include Jaap Heringa, who is the scientific director of the Netherlands Bioinformatics Centre; and Björn Grüning, who is the leader of Galaxy training network, also actively involved in Bioconda. PREREQUISITE KNOWLEDGE The attendees of Part I are assumed to have the basic knowledge of biomedicine (molecular biology and genomics) and be interested in analysing patient derived sequencing data. The attendees of Part II are assumed to have some teaching experience in the relevant field (e.g., bioinformatics, computational biology, systems biology, quantitative biology, etc.) COURSE SCHEDULE The course consists of six modules, as the table below shows, covering a list of topics as follows: - Introduction to Galaxy. Run bioinformatics tools and workflows in Galaxy without the need for any programming expertise. - Reference-based RNA-Seq data analysis - Module detection in differential gene expression in meta transcriptomics samples. - Microbiota Analysis: 16S rRNA sequencing analysis in Galaxy - How to teach bioinformatics workflows. - Galaxy setup for teaching and training material development. Day 1 - Wed Oct 17 Day 2 - Thur Oct 18 Day 3 - Frid Oct 19 Morning Galaxy 101 + Variant detection <http://galaxyproject.github.io/training-material/topics/introduction/> Network analysis with microbiota metatranscriptome <https://www.ncbi.nlm.nih.gov/pubmed/26342232> Teaching bioinformatics workflows Saskia Hiltemann <https://shiltemann.github.io/> Chao Zhang <https://hi-it.org/> Anton Feenstra <http://www.few.vu.nl/~feenstra/> Keynote Speech* I: About bioinformatics workflows II: About Galaxy and ELIXIR III: About bioinformatics teaching TBD Björn Grüning <https://galaxyproject.org/people/bjoern-gruening/> Jaap Heringa <https://www.cs.vu.nl/~heringa/> Afternoon BWA + RNAseq <http://galaxyproject.github.io/training-material/topics/transcriptomics/> 16S rRNA sequencing with mothur <http://galaxyproject.github.io/training-material/topics/metagenomics/> Galaxy training material development <http://galaxyproject.github.io/training-material/> Saskia Hiltemann <https://shiltemann.github.io/> Saskia Hiltemann <https://shiltemann.github.io/> Saskia Hiltemann <https://shiltemann.github.io/> Evening Social dinner About the instructors: Each session is led by one instructor listed in the table above but strongly supported by multiple co-instructors, including, but not limited to, Saskia Hiltemann (ErasmusMC), Chao Zhang (VU), Leon Mei (LUMC), Ruben Vorderman (LUMC) and Sanne Abeln (VU). Note: The course is held in a computer classroom, so you don’t need to bring your own laptop. COURSE FEE Course participation is free of charge. A workshop dinner will be organized on Thursday (at participants’ own expenses) Should you have any question about this course, please contact Celia van Gelder (celia.van.gelder(a)dtls.nl) Dr. Celia W.G. van Gelder Programme Manager DTL Learning Training Coordinator ELIXIR-NL ELIXIR Training Platform Leader tel. +31613375327 e-mail: celia.van.gelder(a)dtls.nl websites: www.dtls.nl, www.biosb.nl skype: celia.van.gelder Office: DTL | Jaarbeurs Innovation Mile (JIM) | 6th floor Beatrixgebouw | Jaarbeursplein 6 | 3521 AL Utrecht Postal address: Postbus 8500 | 3503 RM Utrecht While I may be sending this email outside my normal office hours, I have no expectation to receive a reply outside yours.

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Available (permanent) positions in Sweden
by Lieven Sterck 13 Jul '18

13 Jul '18

> From: "Henrik Lantz" <henrik.lantz(a)nbis.se> > To: "Lieven Sterck" <lieven.sterck(a)psb.vib-ugent.be> > Sent: Wednesday, 11 July, 2018 11:48:20 > Subject: Available positions in Sweden > Hi Lieven, > We have two new permanent positions available in Lund in the Southernmost part > of Sweden. The positions focus on support to Swedish researchers under a > fee-for-service model and will most likely involve working with RNA-seq data. > As the positions are permanent I was thinking that there might be an interest > also in other countries, and I would appreciate if you could spread the below > link to interested people in Belgium. > https://lu.mynetworkglobal.com/en/what:job/jobID:216986/ > Cheers, > Henrik

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