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

NERC Bursaries for Edinburgh Genomics Courses
by TRAIN edgenomics-training 02 Mar '22

02 Mar '22

Dear All We are pleased to announce we have a number of bursaries available to cover up-to the full fees of any of our upcoming bioinformatics courses. These bursaries are available to UK based students or researchers funded by the NERC or working on research that falls under the remit of the NERC (https://nerc.ukri.org/research/portfolio/remit/) Bursaries are available for any of our courses (see below) but are available for a LIMITED TIME ONLY: They are available for any course booked BEFORE 27th MARCH. So please don't wait to sign up! Our upcoming courses: Linux for Genomics, 13th March - An introduction to working on the command line, running commands and handling data relevant to bioinformatics. https://genomics.ed.ac.uk/services/linux-genomics R for Genomics, 14-15th March - An introduction to the statistical environment R, taking you from the very basics to writing basic functions and creating beautiful figures with ggplot2 https://genomics.ed.ac.uk/services/r-genomics Introduction to Python for Biologists, 18-22 March - This introductory course gives an overview of the language with an emphasis on practical problem-solving, using examples and exercises drawn from various aspects of bioinformatics work. https://genomics.ed.ac.uk/services/introduction-python-biologists-0 Data Manipulation and Visualisation with Python, 08 - 12 April - Python has a many high-quality libraries for working with scientific data. In this workshop we will see how to leverage these libraries to efficiently work with and visualise large volumes of data. https://genomics.ed.ac.uk/services/data-manipulation-and-visualisation-pyth… Introduction to RNA-seq Data Analysis, 9-10th May - This two-day course takes you through a tried-and-tested workflow for analysing RNA-seq data, from read mapping and QC to differential expression and result visualisation. https://genomics.ed.ac.uk/services/introduction-rna-seq-data-analysis If you think you are provably eligible for one of these bursaries, sign up to your desired course through the link provided and we will be in contact regarding fees. 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 24

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

Positions available: 2 Research Engineers in Network Biology and Network Bioinformatics (TAGC; Marseille)
by Christine Brun 29 Apr '19

29 Apr '19

Dear all We have been funded for 2 Research Engineer positions in our labs (2 years each), working on systems genetics and network biology of cardiac aging in flies. Details are in the adds bellow. Please spread the information around you, Best Regards, Christine Brun, PhD, DR CNRS TAGC Deputy Director TAGC Inserm U1090, Aix-Marseille Université, Parc Scientifique et Technologique de Luminy, Case 928, 13288 Marseille cedex 9, France +33 4 91 82 87 12 christine-g.brun(a)inserm.fr <mailto:christine-g.brun@inserm.fr> https://tagc.univ-amu.fr/en/users/brun-christine <https://tagc.univ-amu.fr/en/users/brun-christine> and Laurent Perrin, CNRS Theories and Approaches of Genomic Complexity (TAGC) INSERM/AMU UMR_1090 Parc Scientifique de Luminy case 928 163, avenue de Luminy 13288 Marseille France Phone: 33491828727 laurent.perrin(a)univ-amu.fr <mailto:laurent.perrin@univ-amu.fr> Websites: https://tagc.univ-amu.fr/ <https://tagc.univ-amu.fr/> https://tagc.univ-amu.fr/en/users/perrin-laurent

1 0

Postdoc positions in London
by Peter Van Loo 28 Apr '19

28 Apr '19

Hi all, For those interested in cancer genomics, we’ve got two postdoc positions in sarcoma genomics in London (one at Crick, one at UCL, in collaboration with Adrienne Flanagan): https://www.crick.ac.uk/research/labs/peter-van-loo/vacancies Best wishes, Peter -- Peter Van Loo, PhD Winton Group Leader – Cancer Genomics The Francis Crick Institute 1 Midland Road London NW1 1AT http://www.crick.ac.uk/peter-van-loo The Francis Crick Institute Limited is a registered charity in England and Wales no. 1140062 and a company registered in England and Wales no. 06885462, with its registered office at 1 Midland Road London NW1 1AT

1 0

Register now for our BioSB course Algorithms for Genomics - 1-5 July 2019 in Delft
by Femke Francissen 23 Apr '19

23 Apr '19

BioSB course: Algorithms for Genomics (1st edition) Date: 1-5 July 2019 Location: Delft, the Netherlands Course information: website Registration: link Comparative genomics aims to compare large sets of genomes in order to understand and explain differences in traits of an organism. Contemporary methods are powered by fundamental algorithms and data structures, which are efficient and scale to large data sets. A thorough understanding of these algorithms and data structures is necessary for advanced users and developers in this area. In addition, understanding how comparative genomics is developing is important to shape your own research. In this course, we will cover genome analysis, variant analysis, and pangenomics. Core concepts, applications, and future trends will be discussed, with a focus on the algorithms and data structures underlying state-of-the-art methods. The course offers an engaging mix of lectures, paper discussions, hands-on tutorials, and a do-it-yourself project. Target audience The course is aimed at PhD students with a background in bioinformatics, computer science or a related field. Participants are expected to have experience in command-line usage (Unix shell) and programming (Python), and have basic knowledge of genomics. Learning outcomes After having followed this course, the student has a good understanding of algorithms and data structures in comparative genomics, is able to read and understand method papers in bioinformatics in detail, and is able to work with state-of-the-art command-line tools for genomics. Course coordinators: • dr. Thomas Abeel (TU Delft), • prof. dr. Alexander Schönhuth (CWI) • dr. Sandra Smit (Wageningen University) Registration for the course is open! Find out more information at the course website. BioSB Education Programme This course is part of the BioSB Education programme, the Netherlands Bioinformatics and Systems Biology research school, which offers training and education in bioinformatics and systems biology. More information about BioSB can be found at www.biosb.nl.

1 0

PhD position in Bioinformatics with joint doctoral degree from universities of Mainz and Maastricht
by Lenz, Michael 23 Apr '19

23 Apr '19

Dear colleagues, We are looking for a Bioinformatics PhD candidate for a project entitled "Multifaceted data analysis of coagulant activity in arterial/venous thrombo-inflammation", which is part of the TICARDIO innovative training network. Please see the attached pdf file as well as the TICARDIO homepage (www.ticardio.eu<http://www.ticardio.eu>) for more detailed information. Thanks in advance for forwarding this e-mail to any potentially interested candidates! Best wishes, Michael Lenz ----------------------- Dr. Michael Lenz Postdoctoral researcher University Medical Center of the Johannes Gutenberg University Mainz, and Computational Biology and Data Mining group, Johannes Gutenberg University Mainz, Mainz, Germany -----------------------

1 0

Bioinformatics job opportunity in Cambridge
by Adrian Liston 18 Apr '19

18 Apr '19

May you please add this job opportunity to the Benelux bioinformatics mailing list? https://babrahaminstitute.livevacancies.co.uk/#/job/details/77 We have a post-doc opportunity for a data scientist to join an immunology lab. No immunology experience needed - you bring the data skills and we'll teach you the immunology! Regards, Adrian Adrian Liston Senior Group Leader, Lymphocyte Signalling Babraham Institute, Cambridge The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT Registered Charity No. 1053902. The information transmitted in this email is directed only to the addressee. If you received this in error, please contact the sender and delete this email from your system. The contents of this e-mail are the views of the sender and do not necessarily represent the views of the Babraham Institute. Full conditions at: www.babraham.ac.uk<http://www.babraham.ac.uk/terms>

1 0

Fwd: Tenure Track Bioinformatics Innsbruck
by Lieven Sterck 15 Apr '19

15 Apr '19

> From: "Sigrid Neuhauser" <Sigrid.Neuhauser(a)uibk.ac.at> > To: "Sigrid Neuhauser" <Sigrid.Neuhauser(a)uibk.ac.at> > Sent: Monday, 15 April, 2019 11:35:58 > Subject: Tenure Track Bioinformatics Innsbruck > Dear all, > the Institute of Microbiology in Innsbruck ist hiring – we are looking for a > tenure track fellow in bioinformatics – see the attached job description. > The positon scope is very broad and open to attract as many bright minds as > possible. The person we are looking for should have experience in working with > bioinformatics data of microorganisms (including bacteria, archea, fungi, > protists) in the widest sense. So a good track record either in > genomics/transcriptomics or biodiversity or network analyses or metabolomics > will make you a promising canditate. > More info can be found here: > https://lfuonline.uibk.ac.at/public/karriereportal.details?asg_id_in=10452 > If you have any questions, please do not hesitate to get in touch! > Please forward to any prospecitve PostDocs or anybody who you think might fit > for this positon! > Best regards > Sigrid > PS: apologies for cross posting! > ------------------------------------------- > Dr. Sigrid Neuhauser > Institute of Microbiology > University of Innsbruck > Technikerstraße 25 > 6020 Innsbruck > e-mail: [ https://zmail.psb.ugent.be/Sigrid.Neuhauser@uibk.ac.at | > Sigrid.Neuhauser(a)uibk.ac.at ] > tel: +43 (0)512 507 51259

1 0