October 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

2 1

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

1 2

vacancy: bioinformatics support coordinator @UAntwerpen
by Laukens Kris 31 Oct '18

31 Oct '18

Dear colleagues, at the University of Antwerp, we are looking for a bioinformatics support coordinator. Information below. Feel welcome to distribute the news to possible candidates. Thank you! warm regards, Kris Laukens https://www.uantwerpen.be/en/jobs/vacancies/ap/2018bapfwetef325/ Bioinformatics Support Coordinator Job description * You establish and manage a bioinformatics service model towards academic life science researchers as well as to external clients. * You work towards unification of bioinformatics platforms and infrastructure for genomics, proteomics and metabolomics. * You organize bioinformatics training, seminars and networking events for researchers in Antwerp. * You support the maintenance and usage of bioinformatics hardware and software. * You manage collaborations and contribute to the bioinformatics component in life science research projects. Profile and requirements * You have a degree in Bioinformatics, preferably a PhD, or you can demonstrate an equivalent experience. * You are experienced in data processing pipelines for at least one type of omics data. Familiarity with machine learning and pattern discovery techniques is a plus. * You have strong programming skills, preferably in Python and R. * You demonstrate a collaborative, service-oriented attitude. Proven experience in supporting life scientists with bioinformatics expertise is a plus. * Your academic qualities comply with the requirements stipulated in the university’s policy<https://www.uantwerp.be/en/about-uantwerp/mission-vision/three-core-tasks/r…>. * You are quality-oriented, conscientious, creative and cooperative. * You are a team player who can build bridges between disciplines, and you have strong interdisciplinary communication skills. * You are fluent in academic English (speaking and writing). We offer * a contract according to your qualifications for a period of one year, with a possibility of renewal, within the Adrem team and the biomina consortium; * the starting date of the appointment is January 1, 2019, but can be adapted to the candidate; * an exciting, dynamic and stimulating multi-disciplinary working environment in an enthusiastic, fast-growing team; * plenty of opportunities to improve and extend you skill set, in diverse areas, ranging from new omics data processing techniques to data science and AI. How to apply? * Interested candidates are invited to send a strong motivation letter highlighting relevant previous work, a detailed CV (including honours, grades, skills, publications, …) and contact info of two references to Kris Laukens (kris.laukens(a)uantwerpen.be<mailto:kris.laukens@uantwerpen.be>). Please mention ‘Coordinator_BIOMINA2019' in the subject of your mail. * A pre-selection will be made amongst the submitted applications. * More information about the application form can be obtained from prof. Kris Laukens (kris.laukens(a)uantwerpen.be<mailto:kris.laukens@uantwerpen.be>). -- 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/>

1 0

Antwerp TCR Meeting 12/12/2018
by Meysman Pieter 31 Oct '18

31 Oct '18

Dear all, on the 12th of December 2018 the first Antwerp T-cell Receptor (TCR) Meeting will be organised. This one-day international meeting aims to offer a venue for researchers working on TCR sequencing and applications to present their data and discuss their views on this quickly evolving field. We refer to the attachment for an overview of our program. Although no registration fee is requested (with thanks to Adaptive Biotechnologies, Takara Bio Europe, 10x genomics, Qiagen for supporting catering), registration is needed. For more information and registration: https://www.uantwerpen.be/en/projects/audacis/antwerp-tcr-meeting/ . Our beautiful venue is limited to 100 visitors, thus we advise you to register on time if you are planning to come. Please note that there will be the opportunity for researchers to present their latest TCR related work via an oral presentation. If you are interested, send your abstract (max 300 words) to audacis(a)uantwerp.be<mailto:audacis@uantwerp.be> before the 30th of November. Best wishes, Benson Ogunjimi & Pieter Meysman for the Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS) https://www.uantwerpen.be/en/projects/audacis/

1 0

+++RSG Belgium BioHackhaton - registration deadline extension+++
by Daniele Parisi 29 Oct '18

29 Oct '18

_Dear __COLLEAGUES/STUDENTS/RESEARCHERS__,_ _RSG Belgium is still accepting registrations for the first RSG Belgium Hackathon, which will take place in Brussels on 16th November._ _This event represents a good opportunity for MSc/PhD students from all scientific backgrounds to Improve problem solving, teamwork and coding skills by working together as a multidisciplinary team._ _You can read about the four different short projects selected by the RSG Belgium team on the registration form, and express your preference. The most highly voted ones will be selected depending on the number of participants. Currently, the leading two projects are creating an AI generated paper and mining citation networks._ _REGISTRATION: https://docs.google.com/forms/d/e/1FAIpQLSdmv3Jroj1m0e_Edk2oCgLktZttmIp686X… _DATE AND TIME: 16/11/2018, 09:00 until 18:30_ _PLACE: Université Libre de Bruxelles, La Plaine campus, Building NO, 9th floor, room: 2NO906 ("Salle des professeurs"), Brussels, Belgium_ _REGISTRATION DEADLINE: 9 November 2018_ _Hope to see you there!_ _The RSG Belgium_ -- 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

1 0

Galaxy Training for life science researchers announcement
by Daniele Parisi 29 Oct '18

29 Oct '18

Dear all, We would hereby like to announce an upcoming GALAXY TRAINING for life science researchers in GENT on NOVEMBER 6TH, organised by ELIXIR Belgium. Galaxy software framework is an open-source application that enables researchers without informatics expertise to perform computational biology analyses through the web (usegalaxy.eu [1]). The workshop will be hands-on and will introduce participants to #USEGALAXY [2] for analysis of NEXT-GENERATION SEQUENCING data (RNA-Seq or DNA-Seq). The workshop is FREE OF CHARGE. More information and registration are available at the following link: https://tinyurl.com/y8vtq6f8 [3] 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 Links: ------ [1] https://t.co/Xw3HOUZpHZ [2] https://twitter.com/hashtag/useGalaxy?src=hash [3] https://t.co/xIbYziemWT

1 0

job adverstisement Maastricht University
by Ehrhart, Friederike (BIGCAT) 26 Oct '18

26 Oct '18

Dear all, we are looking for someone with both, bioinformatics and teaching skills: https://www.academictransfer.com/nl/50441/postdocteachergraduate-at-nutrim-… Best regards, Freddie

1 0

SWAT4(HC)LS 2018: Semantic Web Applications and Tools for Healthcare and Life Sciences - 3-6 December 2018 Antwerp, Belgium
by Femke Francissen 25 Oct '18

25 Oct '18

SWAT4(HC)LS 2018 - Semantic Web Applications and Tools for Healthcare and Life Sciences Join us for the SWAT4(HC)LS workshop on 3-6 December 2018 in Antwerp, Belgium! ** Conference website <http://www.swat4ls.org/> / Registration <http://www.swat4ls.org/workshops/antwerp2018/registration/> ** SWAT4(HC)LS is a venue for presenting and discussing novel ideas, experiences and issues in the application of Semantic and Web technologies in the biomedical domain at large. 3 December: Tutorials <http://www.swat4ls.org/workshops/antwerp2018/programme/#December_3rd_Tutori…> - 4-5 December: Conference <http://www.swat4ls.org/workshops/antwerp2018/programme/#December_4th-5th_Co…> - 6 December: Hackathon <http://www.swat4ls.org/workshops/antwerp2018/programme/#December_6th_Hackat…> Conference themes: Agriculture and Nutrition, Secondary Reuse of Healthcare Data and Open Data Keynotes: <http://www.swat4ls.org/workshops/antwerp2018/keynotes/> - Philip Bourne: How Does Data Science Impact the Semantic Web? - Dean Allemang: Semantic Web and the New Industrial Revolution - Medha Devare: Spinning a Semantic Web for Agriculture Spotlight: We have built a consistent program around agrosemantics <http://www.swat4ls.org/workshops/antwerp2018/agrisemantics/>, sponsored by the Global Open Data for Agriculture and Nutrition ( <https://www.linkedin.com/in/ACoAABuFID8BW4GSWnZGoPC0Fr19Bo4jbNzkXJo/>GODAN <https://www.godan.info/>) <https://www.linkedin.com/in/ACoAABuFID8BW4GSWnZGoPC0Fr19Bo4jbNzkXJo/>. This includes dedicate tutorials, keynote and panel discussions. Tutorials: We have setup a program of tutorials that cover pharma and healthcare industry standards such as FHIR, schema.org, CDISC, OMOP and their relations to the semantic web. Find the list of the tutorials here <http://www.swat4ls.org/workshops/antwerp2018/programme/tutorials/>. Hackathon: We are working on an hackathon <http://www.swat4ls.org/workshops/antwerp2018/programme/#December_6th_Hackat…> bringing together many of the above. Starting in 2008, SWAT4(HC)LS has been held continuously for more than 10 years, expanding from a one day workshop to a four day event composed of tutorials, conference and hackathon. SWAT4LS intends to provide an open and vibrant discussion space cross cutting across academia, industry and institutional participants. SWAT4(HC)LS is sponsored by GODAN <https://www.godan.info/> and Figshare <https://figshare.com/>. on behalf of the organizers, Femke Francissen DTL/ELIXIR-NL

1 0

Genomics Workshop spaces @ Edinburgh Genomics: Last few spaces!
by TRAIN edgenomics-training 24 Oct '18

24 Oct '18

Dear Budding Bioinformaticians We have a very limited number of spaces remaining on two introductory level bioinformatic workshops here at Edinburgh Genomics this November: Bioinformatics for Genomics 19-23 November: This weeklong workshop, taught by our experienced team of bioinformaticians, covers everything you need to know to get a footing with genome informatics. Starting with an introduction to Linux and then an introduction to R on days one and two, we will get you up to speed with the languages of bioinformatics. Day three covers some more involved genome analysis in the form of genome annotation in R along with a foray into data visualisation with R, then day four and five are focused on RNA-seq data analysis. This broad introduction is perfect for those new to genome analysis that want to be able to analyse their own data or contribute to collaborations using genomic data. For more info see: https://genomics.ed.ac.uk/services/bioinformatics-genomics To sign up: https://www.surveymonkey.co.uk/r/B4G_191118 R for Genomics 26-28 November: R for Genomics gives a comprehensive introduction to the R programming environment using genomic data examples. By the end of this two day course you will be familiar with Rstudio, loops, functions, genomic annotation data and be able to make beautiful graphs using ggplot2 ready for your next publication. No prior experience necessary for this beginner friendly course. For more info see: https://genomics.ed.ac.uk/services/r-genomics To sign up: https://www.surveymonkey.co.uk/r/R4G_261118 There are only a few places left on these courses so if you're interested act quickly, they are first come first served! Not the courses you're looking for? Tell us what courses you would like to see in the future by completing our training needs survey: https://www.surveymonkey.co.uk/r/7M6QB2D Kind Regards Nathan Medd Training and Outreach Manager - Edinburgh Genomics Edinburgh Genomics' Privacy Notice can be viewed at: http://genomics.ed.ac.uk/about-us/privacy-notice This email and any attachments are confidential and intended solely for the use of the recipient(s) to whom they are addressed. If you have received it in error, please destroy all copies and inform the sender. The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

1 0

CENTURI postdoctoral call now open - Marseille, France
by BAUDOT Anaïs 24 Oct '18

24 Oct '18

Dear Colleagues, CENTURI is recruiting up to 10 highly motivated postdoctoral fellows to work in an interdisciplinary life science environment. The available postdoctoral projects will be displayed on the "Recruitment" part of our website, with more projects being added to our website up until November 15. Candidates can either apply to one of the advertised CENTURI projects or submit their own project, providing that they meet the application criteria and that their application is supported by the host lab(s). These projects should be submitted to: postdocproject(a)centuri-livingsystems.org Deadline for application and project submission for postdoc candidates: November 30, 2018 More information about the projects and application: http://centuri-livingsystems.org/recruitment/ <http://centuri-livingsystems.org/recruitment/> We invite you to share this call with your professional network. Best regards, CENTURI management team

1 0