January 2019 - BBClist - maillist.psb.ugent.be

Open PostDoc Position in Computational Biology - Marseille, France
by BAUDOT Anaïs 16 Nov '19

16 Nov '19

Dear colleagues, We have an opening position for a postdoctoral fellow in the network and systems biology group, in the Marseille Medical Genetics Unit. The project is dedicated to network modeling for rare genetic diseases. Please see attachement for more details, and feel free to forward this message to potential candidates. Best regards, Anaïs --------------------------------------------------------- Anaïs BAUDOT MMG, Marseille Medical Genetics U 1251, Faculté de Médecine de La Timone, 27 Bd Jean Moulin 13385 Marseille Cedex 5 0491324948 France anais.baudot(a)univ-amu.fr

2 1

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

Open vacancy professor KU Leuven Applied Bioinformatics in Microbial Ecology and related fields
by Hans Rediers 31 Jan '19

31 Jan '19

Dear, At KU Leuven's Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM), there is an open position for a professor (Junior/Senior) in the field of 'Applied Bioinformatics in Microbial Ecology and related fields'. I dare to bring this vacancy to your attention. More information on the PME&BIM lab can be found on: https://iiw.kuleuven.be/onderzoek/pme-bim For all information regarding the job profile, consult: https://www.kuleuven.be/personeel/jobsite/jobs/54649637?hl=en&lang=en We are offering full-time employment in an intellectually challenging environment. KU Leuven is a research-intensive, internationally oriented university that carries out both fundamental and applied scientific research. You will work at Campus Group T in Leuven, a historic, dynamic and lively city located in the heart of Belgium, within 20 minutes from Brussels, the capital of the European Union, and less than two hours from Paris, London and Amsterdam. Feel free to pass on this announcement to all possibly interested researchers (including former PhD students, post-docs, colleagues etc). The deadline is February 28, 2019. A concise research plan defining main lines of research is requested as an annex to the application tool. For all your questions, please feel free to contact me Yours sincerely, Hans Rediers ------------- Prof. dr. ir. Hans Rediers Programme coordinator Master IW: Biotechnology Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM) Cluster for Bioengineering Technology (CBeT) Department of Microbial and Molecular Systems (M2S) Faculty of Engineering Technology KU Leuven - Campus De Nayer Fortsesteenweg 30A | BE-2860 Sint-Katelijne-Waver | Belgium Tel. +32 (0)15 30 55 90 Fax. +32 (0)15 30 55 99 Website: www.kuleuven.be/pme-bim<http://www.kuleuven.be/pme-bim> E-mail: hans.rediers(a)kuleuven.be<mailto:hans.rediers@kuleuven.be>

1 0

Vacancy for Software Developer Bioinformatics
by Hanneke van Deutekom 31 Jan '19

31 Jan '19

Dear bbclist(a)psb.ugent.be, GenDx is looking for a driven, creative *Software Developer (MSc)* or *Bioinformatics PhD* to innovate the algorithms behind our software. GenDx software is used worldwide as a diagnostic tool for transplantation purposes. For more information: *http://www.GenDx.com/company/careers <http://www.gendx.com/company/careers>.* To draw attention to this position to a wide audience, we would like to ask you to put this message to the e-mailing list of all your members. Thanks in advance. I’m looking forward to hearing from you. Roelien Brommersma Chief HR Officer at GenDx.

1 0

Available position in computational proteomics and applied machine learning in Amsterdam
by Kers, J. (Jesper) 30 Jan '19

30 Jan '19

Dear colleagues, via dr. Perry Moerland at the AMC in Amsterdam, I came in contact with your mailing list. Together with prof. Garry Corthals at the University of Amsterdam (Van ’t Hoff Institute for Molecular Sciences; HIMS, faculty of science), I have an interesting PhD position available and we are searching for computational/system biologists with experience in mass spectrometry (proteomics) that are interested in a PhD project related to the field of kidney transplantation. The position can be found at the link below. If there are specific questions related to the project or when you’d want to check if your background is suitable, do not hesitate to email me at j.kers(a)amc.uva.nl<mailto:j.kers@amc.uva.nl> http://www.uva.nl/en/content/vacancies/2019/01/19-042-phd-candidate-in-comp…<http://www.uva.nl/en/content/vacancies/2019/01/19-042-phd-candidate-in-comp…> kind regards, Jesper Kers ——————————— J. Kers, MD, PhD, Immunopathologist j.kers(a)amc.uva.nl<mailto:j.kers@amc.uva.nl> jkers(a)mgh.harvard.edu<mailto:jkers@mgh.harvard.edu> Amsterdam UMC, Dept. of Pathology, University of Amsterdam, Amsterdam, The Netherlands Biomolecular Systems Analytics, HIMS, University of Amsterdam, Amsterdam, The Netherlands Ragon Institute of MGH, MIT & Harvard, Cambridge, MA, USA ________________________________ AMC Disclaimer : https://www.amc.nl/disclaimer ________________________________

1 0

Two bioinformatics vacancies at Rijk Zwaan
by Michiel Wels 30 Jan '19

30 Jan '19

At Rijk Zwaan we have two vacancies in our bioinformatics team; one for a technician and one for a scientific programmer. Please visit the appropriate web pages on our website for more information on the positions, as well as for applying: https://www.rijkzwaancareers.com/careers/technician-bioinformatics https://www.rijkzwaancareers.com/careers/scientific-programmer Michiel Wels, PhD Teamleader Bioinformatics Rijk Zwaan <i><font size="3" color="grey"> You can find the disclaimer that applies to emails of Rijk Zwaan at: http://www.rijkzwaan.com/edisclaimer The registration number of Rijk Zwaan companies can be found at: http://www.rijkzwaan.com/registrationnumbers </font>

1 0

Registration open for "Boost Your Visibility - Improving F of FAIR for your Training and Data Resources through Bioschemas", 7-8 February 2019, Utrecht, the Netherlands
by Celia van Gelder 29 Jan '19

29 Jan '19

Dear colleagues, I am writing you to announce an ELIXIR-NL/DTL event& hackathon that we are hosting in Utrecht early February that might be interesting for you or members of your organisation. Registration is free of charge. Please spread this further to people who are working with resources in Training, Biobanks, Samples, Beacons, Tools and would benefit of making their resources better annotated and better visible and findable. Thank you! Best Celia - apologies for cross posting -- Dear colleague, Are you a training provider/organizer with a catalogue of training events and/or training materials or a data provider, curator or manager of Life Science resources such as Biobanks, Proteins, Samples, Beacons, Tools? Then this hackathon may be very relevant for you! DTL and ELIXIR-NL are organising a workshop/hackathon for content providers of Life Science resources such as Proteins, Samples, Beacons, Tools, and Training events and materials. Join this event to learn how to make your resources rank higher on (Google, Bing, Yahoo and other) search result pages or include your resource in relevant registries (like TeSS, the ELIXIR Training Portal) and receive more web traffic can raise the exposure of your work to be found by larger audiences. The event will start at lunch time on Thursday February 7 and will finish on Friday February 8 at 4pm. Participants can register either for the first day (Feb 7) or for both days (Feb 7 + Feb 8). In the first half day of this 1.5 day event participants will learn about <http://schema.org/> schema.org and bioschemas from experts working on Bioschemas definitions and implementations for ELIXIR resources and they will get some examples of successful Bioschemas implementations in Life Science resources, both from within and outside the Netherlands. This day is suitable for anyone wanting to learn more about <http://schema.org/> schema.org, bioschemas annotations and how they can help increase the visibility of Life Science web resources. The second day will have the form of a hackathon during which participants will work on adding Bioschemas metadata to their resources with the help of the experts. To make it possible participants will need the skills to modify the source code behind the web pages of the resource as well as have the access and permission to do it. For training materials and events we will also add them to the ELIXIR's Training Portal TeSS. You can find the agenda of the meeting on the <https://www.dtls.nl/events/boost-your-visibility-improving-f-of-fair-for-du tch-training-and-data-resources-through-bioschemas/> DTL website and register <https://goo.gl/forms/QzOn6E7bBhQGpDKf1> here (free of charge). We are looking forward to seeing you at the event! On behalf of DTL/ELIXIR-NL, Celia van Gelder and Mateusz Kuzak Dr. Celia W.G. van Gelder Programme Manager DTL Learning Training Coordinator ELIXIR-NL ELIXIR Training Platform Leader tel. +31613375327 e-mail: <mailto:celia.van.gelder@dtls.nl> celia.van.gelder(a)dtls.nl websites: <http://www.dtls.nl/> www.dtls.nl, <http://www.biosb.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.

1 0

Two Introductory Bioinformatics Courses
by TRAIN edgenomics-training 28 Jan '19

28 Jan '19

New to Bioinformatics? Need a comprehensive introduction to the languages and environments needed to start analysing your genomic data? Edinburgh Genomics is pleased to announce we will be running two of our ever-popular introductory bioinformatics courses this March: Linux for Genomics - 13 March 2019 "Genomic studies produce vast amounts of data, usually in the form of very large text files. Linux is particularly suited to working with such files, and is therefore arguably one of the most important tools in a bioinformatician's toolkit. The Linux command-line enables one to view, filter and manipulate large text files that are difficult or impossible to handle with applications like Word or Excel, write pipelines to perform certain tasks, and run bioinformatics software for which no web interface is available. In this workshop we will first cover the most used Linux commands, followed by a short introduction to several popular command-line tools that were especially developed for genomics as well as file formats commonly used in genomics (BED, FASTA, FASTQ, GFF/GTF, SAM/BAM, VCF)." Duration: 1 day (9am - 5pm) Location: Ashworth Laboratories, Kings Buildings Edinburgh, EH9 3FL Spaces: 12 Cost: £225 More information: https://genomics.ed.ac.uk/services/linux-genomics Register: https://www.surveymonkey.co.uk/r/WNC23SS And R for Genomics 14-15th March 2019 "The aim of this course is to introduce participants to the statistical computing language 'R' using examples and skills relevant to genomic data science. This two day workshop is taught by experienced Edinburgh Genomics' bioinformaticians and trainers. By the end of the workshop, you will be comfortable with the basics of the R and R studio environments, learning about the rules of the language and how R works with different data types. We then move on to using functions, including those specific to genomic science. We look at how to handle various genomic data files and where to find relevant tools via online resources. Finally we use mock RNA-seq data to learn how to visualize your data to generate publication ready plots using the package ggplot2." Duration: 2 days (9am - 5pm) Location: Ashworth Laboratories, Kings Buildings Edinburgh, EH9 3FL Spaces: 12 Cost: £400 More information: https://genomics.ed.ac.uk/services/r-genomics Register: https://www.surveymonkey.co.uk/r/WJMTXNJ If you have any specific questions about these, or any other, courses at Edinburgh Genomics please contact our Training team at edge-training(a)ed.ac.uk Not the courses you were looking for? Let us know what courses you would like to see us run in the future by filling out this quick training needs survey: https://www.surveymonkey.co.uk/r/7M6QB2D Kind Regards Nathan Medd Training and Outreach Manager - Edinburgh Genomics G.06, Ashworth Laboratories, Charlotte Auerbach Road, The King's Buildings, The University of Edinburgh, EH9 3FL, Edinburgh, Scotland 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 1

BioSB 2019 conference - 3 open calls!
by Femke Francissen 28 Jan '19

28 Jan '19

*3 open calls for the BioSB 2019 conference!* *5th Netherlands Bioinformatics and Systems Biology Conference (BioSB 2019)* *2-3 April 2019* *Congrescentrum De Werelt, Lunteren, the Netherlands* We have 3 open calls: - Call for Breakout sessions - *deadline January 14* - Call for Abstracts - *deadline January 25 *(for oral presentations) - Call for nominations for the BioSB Young Investigator Award 2019 - *deadline February 22* Find more information at the conference website <http://www.aanmelder.nl/biosb2019>! *About BioSB 2019* The BioSB 2019 conference discusses the latest developments in bioinformatics, systems and computational biology and interrelated disciplines, including their wide ranging applications in life science and health, agriculture, food and nutrition. The conference will feature keynote lectures, parallel sessions featuring selected and invited talks, breakout sessions, a Hot topic session, poster & demo sessions, network breaks, a conference dinner and a social event. Join us in April! Best regards, on behalf of the programme committee Femke Francissen *Femke Francissen* Community manager BioSB Research School

1 2