June 2020 - BBClist - maillist.psb.ugent.be

Bioinformatician/Research Software Engineer position at de Duve Institute, UCLouvain
by Laurent Gatto 11 Jun '20

11 Jun '20

The Computational Biology (CBIO) unit at the de Duve Institute in Brussels, Belgium, seeks to appoint a full time research software engineer. The successful candidate will join the research group of Professor Laurent Gatto and will have the opportunity to work on projects across a broad range of biomedically relevant topics in collaboration with researchers of the biomedical campus of UCLouvain. The focus of the position is on rigorous research software engineering, analysis pipeline development and high-throughput biology data analysis, with the possibility of engaging in teaching activities. If you recognise yourself in any of the following profiles, please consider applying. - You have created/maintained/used software to address research problems in high throughput biology (such as, for example genomics, transcriptomics, epigenetics, proteomics and/or metabolomics). - You can rapidly assimilate understanding of new biomedical questions, and quickly connect research needs to software requirements. - You are committed to open source software development best practices and know how to adapt these to biomedical research contexts. Duties and activities The research software engineer will be expected to contribute to various activities, including : - Research projects: support and advise collaborators with their data analyses and contributed to scientific reports and publications. - Maintain and develop research software and repositories linked to the ongoing research in the group and collaborative projects. - Participate in the administration of the computing and data storage infrastructure. - Attend scientific conferences to present their research and development and workshops to improve and learn new sets of skills. - Contribute to bioinformatics teaching, both within the institute and the School of Biomedical Sciences. Required skills The ideal candidate would be either a researcher with a focus on research software and data analysis, or a software developer with an interest in research and biomedical sciences. We are looking for a motivated candidate with a PhD or a Master's degree in bioinformatics or equivalent, possessing computational and quantitative skills such as: - Good knowledge of the R programming language and the Bioconductor infrastructure (important). - Experience with the processing and analysis of omics data (important). - Experience in open and reproducible research, open source software and open data (desirable). - Experience in C/C++ (desirable). - Experience in JavaScript, specifically the development of online visualisation applications (optional). - Experience in teaching, ideally the Data and Software Carpentry curricula or interest in training to become an instructor (desirable). - Experience in high performance computing (desirable). - Experience with code versioning and collaborative tools such as, for example, git, and GitHub/GitLab (desirable). - Experience with other languages commonly used in computational biology and bioinformatics like Python or Julia (optional). - Knowledge of French and English is desirable. Contract on external resources, full time, with initial duration of 2 years (1 year renewable once). Position available mid August. We value equality, diversity and an open, collaborative and welcoming work environment. Please send your application by email to Laurent Gatto (laurent.gatto(a)uclouvain.be) referencing this position, including a CV, motivation letter and two references.

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ESCS 2020 | Abstract submission is open
by ESCS 11 Jun '20

11 Jun '20

[image: ESCS2020_banner-notPaint.png] Dear all, The abstract submission process for the *European Student Council Symposium 2020 (ESCS 2020)* is open! The ESCS 2020 will take place on *6th September 2020 in Sitges, Spain* directly preceding the opening of the European Conference on Computational Biology (ECCB 2020). The ESCS provides a forum for students and young researchers in the fields of Bioinformatics and Computational Biology to meet, present their work in front of an international audience, build a network within the computational biology community and obtain opportunities that can contribute to the development of their scientific career. In this scope, we invite all participants to submit *an abstract for an oral or poster presentation*. The submission deadline for abstracts is: *11th June 2020*. You can find all relevant information about ESCS 2020 here: *https://www.escs2020.iscbsc.org/ <https://www.escs2020.iscbsc.org/>*. For any further inquiries don't hesitate to contact us at *escs(a)iscbsc.org <escs(a)iscbsc.org>*. Best regards, Gabriel Olguín Orellana, chair ESCS 2020 Sofia Papadimitriou, co-chair ESCS 2020

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postdoc available in cancer pharmacogenomics modelling
by Pedro BALLESTER 10 Jun '20

10 Jun '20

Dear colleagues, A postdoc position in cancer pharmacogenomics modelling is available in my group. Further information, including how to apply, can be found at https://academicpositions.com/ad/aix-marseille-universite/2020/postdoc-in-p… Best wishes, Pedro -- (c)¤(c)¤(c)¤(c)¤(c)¤(c)¤(c)¤(c)¤(c)¤(c)¤(c)¤(c)¤(c)¤(c)¤(c)¤(c)¤(c)¤(c)¤(c)¤(c)¤(c) Dr. Pedro J. Ballester Group Leader at the Cancer Research Centre of Marseille Research scientist at INSERM http://crcm.marseille.inserm.fr/en/researchteams/pedro-ballester/ [1] https://publons.com/researcher/975063/pedro-j-ballester/ (c)¤(c)¤(c)¤(c)¤(c)¤(c)¤(c)¤(c)¤(c)¤(c)¤(c)¤(c)¤(c)¤(c)¤(c)¤(c)¤(c)¤(c)¤(c)¤(c)¤(c) Links: ------ [1] http://crcm.marseille.inserm.fr/en/researchTEAMs/pedro-ballester/

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PhD position: Computational Early Cancer Diagnostics
by Lodewyk Wessels 09 Jun '20

09 Jun '20

PhD Position OVI-DETECT: ACCURATE IDENTIFICATION OF OVARIAN CANCER FROM LIQUID BIOPSIES COLLABORATING INSTITUTES The Netherlands Cancer Institute (NKI), Amsterdam. Delft University of Technology (TUDelft), Delft VU University Medical Center (VUMC), Amsterdam The Johns Hopkins University School of Medicine, Baltimore, USA. PROJECT DESCRIPTION In the Netherlands, 7600 women are diagnosed yearly with an ovarian tumor. Only about 5% of these tumors are malignant. It is very important to accurately identify these malignant tumors prior to surgery to ensure proper treatment. Unfortunately, this can be very challenging. In this project, we aim to find specific molecular biomarkers in liquid biopsies that can efficiently discriminate between benign and malignant ovarian tumors with a sensitivity of at least 90% and a specificity of at least 80%. We will determine genetic abnormalities (mutations, copy number aberrations and chromosomal abnormalities) in circulating tumor DNA and RNA profiles of tumor educated platelets (TEPs). We will develop novel computational approaches to analyze these unique datasets separately and jointly, to arrive at accurate predictors to identify malignant tumors from liquid biopsies. INTERDISCIPLINARY COLLABORATION The groups of Lodewyk Wessels and Marcel Reinders and (NKI and TUDelft) will develop advanced machine learning approaches to construct (integrative) predictors from the different data streams. The supervisory team will be strengthened by the pathology expertise of Hugo Horlings (NKI) and collaborations with Victor Velculescu at Johns Hopkins (circulating copy number profiles from circulating DNA) and Tom Wurdinger at the VUMC (TEPs). The project is embedded within broad oncological collaborations within the VUMC, LUMC, Catharina Ziekenhuis in Eindhoven and the NKI. The successful candidate will be employed at the NKI and will spend at least two days per week at the TUDelft. Regular meetings between project partners will be held to generate sufficient cohesion and momentum. CANDIDATE PROFILE We are seeking a highly motivated PhD candidate with: • A degree in bioinformatics, computer science or a related discipline • Experience in statistics, machine learning and/or pattern recognition • Proficiency in bioinformatics programming languages (e.g. R, Python) • Good cross-disciplinary collaborative and communication skills • Experience in analysing high-throughput molecular data is a plus • Experience in cancer biology and clinical applications is a plus INTERESTED? Please send your CV and motivation letter to Lodewyk Wessels (l.wessels(a)nki.nl) Please include the contact information of at least two references. DEADLINE 01 September 2020

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Fwd: Reminder: Online UBC seminar on Monday at 16:00
by Sergio Martinez Cuesta 06 Jun '20

06 Jun '20

If interested to follow the online bioinformatics seminars organised by the Utrecht bioinformatics center, join on Monday 4pm using the zoom link below. All the best, Sergio ---------- Forwarded message --------- From: Utrecht Bioinformatics Center <a.s.j.melquiond(a)uu.nl> Date: Fri, 5 Jun 2020 at 09:59 Subject: Reminder: Online UBC seminar on Monday at 16:00 To: Sergio Martinez Cuesta <sermarcue(a)gmail.com> UBC Announcements View this email in your browser <https://mailchi.mp/b4cfb28a58fe/ubc-seminar-may-6th-stratenum-3108-2689425?…> *Reminder: Online UBC seminar Monday June 8 at 16:00 #ScienceMustGoOn* Mark your agenda - *Jul 6*: Online UBC seminar - *August*: *summer break* - *Sep 7*: (Hopefully) in-person UBC seminar *with drinks* - *Oct 27-28:* BioSB2020 in Lunteren - *Nov 2-6 2020*: 3rd edition of the EMBO course on "integrative modelling" <https://ubc.us12.list-manage.com/track/click?u=02d188b181bc253cd9b1e5c1b&id…> in Izmir (Turkey) - *Feb or Mar 2021?* UBC symposium Dear all, Just a friendly reminder that you are all invited to join our monthly online UBC seminar on Monday. Here is the link for the Zoom meeting: https://us02web.zoom.us/j/85046271916?pwd=Q2tPV0N6Mk9TS3pCaERkTVBVUGhjdz09 <https://ubc.us12.list-manage.com/track/click?u=02d188b181bc253cd9b1e5c1b&id…> Our speaker is Sergio Martinez Cuesta, research associate in bioinformatics at the Cancer Research UK (Balasubramanian lab @University of Cambridge) and he will present his work on *Developing new genomics methods to explore DNA epigenetics modifications in humans, parasites and disease.* Best regards, Adrien *PS: please correct the date in your agenda, the kick-off UBC seminar in September will be held on Monday Sept 7 (initially announced on Sept 6).* online UBC seminar: *@home* *Copyright © 2020 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 sermarcue(a)gmail.com *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 [image: Email Marketing Powered by Mailchimp] <http://www.mailchimp.com/email-referral/?utm_source=freemium_newsletter&utm…>

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Bioinformnatics/biostatistics position at LBMCC Luxembourg
by Marc Diederich LBMCC 06 Jun '20

06 Jun '20

Hello, LBMCC is a private cancer research lab in Luxembourg with a team of 12-15 researchers dedicated to basic and translational cancer research. We have a job opening for a postdoc with experience in biostatistics and omics data analysis. Please consider the attached job description. Yours sincerely, Prof. Marc Diederich

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Submit a Session Proposal for CarpentryCon @ Home
by Mateusz Kuzak 05 Jun '20

05 Jun '20

Hello, I hope you are all well and healthy despite the challenging circumstances we are all in. The Carpentries<https://carpentries.org/> is a volunteer-driven organisation that teaches programming and technical teaching skills to their global community of learners and educators. They are hosting the "CarpentryCon @ Home" online event series in July and August 2020, and invite you to present talks, lead breakout discussion sessions, share skills through short workshops or host social events in your time zone. Find more details in this blog post<https://carpentries.org/blog/2020/05/2020-carpentrycon-at-home-proposals/>. stay safe and healthy, Mateusz — Mateusz Kuzak (he, him, his) Community Manager, the Netherlands eScience Center e-mail: m.kuzak(a)esciencecenter.nl<mailto:m.kuzak@esciencecenter.nl> | Tel. +31 643707254 twitter: @matkuzak<http://twitter.com/matkuzak> | GitHub: mkuzak<https://github.com/mkuzak> | skype: mkuzak orcid: orcid.org/0000-0003-0087-6021<https://orcid.org/0000-0003-0087-6021> Science Park 140 (Matrix I) 1098 XG Amsterdam, The Netherlands The Netherlands eScience Center is a joint initiative by SURF and NWO www.esciencecenter.nl<https://www.esciencecenter.nl/> | Twitter<https://twitter.com/eScienceCenter> | LinkedIn<https://www.linkedin.com/company/netherlands-escience-center> | Facebook<https://www.facebook.com/NLeScienceCenter/> | YouTube<https://www.youtube.com/channel/UCYLAIMi62d8tx3Ru6DOSPeg> | Newsletter<https://esciencecenter.us8.list-manage.com/subscribe/post?u=a0a563ca342f194…>

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BSC: Life Sciences vacancies
by BSC Human Resources 05 Jun '20

05 Jun '20

Dear all, We would like to inform you about a new job opportunitiy offered by BSC: - Junior Research Engineer for simulations in biomedicine (RE1). Deadline: 31 July, 2020 Link here <https://www.bsc.es/join-us/job-opportunities/13420lscbre1> - Postdoctoral researcher in Machine Learning applied to simulations in biomedicine (R2). Deadline: 31 July, 2020 Link here <https://www.bsc.es/join-us/job-opportunities/13520lscbr2> We would appreciate that you share the information with your contacts. Sincerely, -- /Human Resources/* Barcelona Supercomputing Center – Centro Nacional de Supercomputación* Tel. +34- 934137745 <mailto:anais.delastre@bsc.es>www.bsc.es <http://www.bsc.es/> http://bsc.es/disclaimer

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BSC: Life Sciences vacancy
by BSC Human Resources 04 Jun '20

04 Jun '20

Dear all, We would like to inform you about a new job opportunitiy offered by BSC: - Junior research engineer for Social Link Analytics (RE1). Deadline: 31 July, 2020 Link here <https://www.bsc.es/join-us/job-opportunities/10120lscbre1#> We would appreciate that you share the information with your contacts. Sincerely, -- /Human Resources/* Barcelona Supercomputing Center – Centro Nacional de Supercomputación* Tel. +34- 934137745 <mailto:anais.delastre@bsc.es>www.bsc.es <http://www.bsc.es/> http://bsc.es/disclaimer

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job opening PhD fellowship in microbial systems genetics (Ugent/KU Leuven)
by Kathleen Marchal 02 Jun '20

02 Jun '20

*PhD fellowship in microbial systems genetics* IDLab/IMEC Ghent University (Belgium) has an open PhD position in the domain of microbial systems genetics. This PhD envisages a dual degree between the KU Leuven and UGent. The goal of the PhD research is to develop and apply graph-based methods to study adaptive evolution of microbial communities. Hereto innovative methods need to be developed that integrate genomic information with molecular profiling (metatransciptomics) data. The research will be performed in close collaboration with microbial ecologists and microbial molecular biologists at the KU Leuven. Applications involve studying the role of microbial communities in acquiring microbial antibiotic resistance or pesticide degradation. *Requirements* •You hold a Master degree in Bioinformatics, Engineering, Bioscience engineering, Informatics, Mathematics, or an equivalent degree. Last year students can also apply •A strong interest in interdisciplinary research •Interest/knowledge of computer science and/or machine learning •Interest in biology or molecular biology •Proficiency in programming languages such as Python, R and/or C++ as well as Linux systems. •Fluency in spoken and written English *More information* The student will be located in the group headed by K. Marchal located at the engineering faculty of Ghent University (IDLab/IMEC). The group’s research focus is on bioinformatics method development. The group is specialized in combining computerscience with biological principles (http://bioinformatics.psb.ugent.be/DBN/, http://www.ugent.be/ea/idlab/en/members/kathleen-marchal.htm) This PhD research will involve a close collaboration with Prof. D. Springael and Prof. H. Steenackers at the KU Leuven (promoters) and envisages a dual PhD degree in Ghent University and KU Leuven. For more information, contact kathleen.marchal(a)ugent.be <mailto:kathleen.marchal@ugent.be>. *Interested?* To apply, forward a copy of your CV, a motivation letter and contact information for two references, to the following email address kathleen.marchal(a)ugent.be <mailto:kathleen.marchal@ugent.be> Application deadline: July 31, 2020 Tentative start date: October 2020 Duration: 4 years -- Prof. Kathleen Marchal Dept. of Plant Biotechnology and Bioinformatics, Ghent University Dept. of Information Technology, IDLab, imec, Dept. of Genetics, University of Pretoria, South Africa http://bioinformatics.psb.ugent.be/DBN iGent Toren, Technologiepark 126, 9052 Gent, Belgium

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