June 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.

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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

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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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Barcelona Supercomputing Center: Post-doc Researchers in Computer Science and Bioinformatics (R2)
by BSC RRHH 28 Jun '19

28 Jun '19

Post-doc Researchers in Computer Science and Bioinformatics (R2) *Reference:*180_19_LS_ICB_R2 *Job title:*Post-doc Researchers in Computer Science and Bioinformatics (R2) *About BSC* The Barcelona Supercomputing Center - Centro Nacional de Supercomputación (BSC-CNS) is the leading supercomputing center in Spain. It houses MareNostrum, one of the most powerful supercomputers in Europe, and is a hosting member of the PRACE European distributed supercomputing infrastructure. The mission of BSC is to research, develop and manage information technologies in order to facilitate scientific progress. BSC combines HPC service provision and R&D into both computer and computational science (life, earth and engineering sciences) under one roof, and currently has over 600 staff from 49 countries. Look at the BSC experience: BSC-CNS YouTube Channel <https://www.youtube.com/channel/UC-jQw5yIjnUTRAg4DwOY4aA> Let's stay connected with BSC Folks! <https://www.youtube.com/watch?v=VRkEii7OzRE> *Context And Mission* Professor Nataša Pržulj is looking for several post-docs to work in machine learning and network science. They will be developing new algorithms for computationally hard problems and applying them to analyzing large-scale molecular and patient data to aid drug discovery and personalizing treatment. The successful candidates will work on the prestigious ERC Consolidator grant of Prof. Pržulj. The successful candidates will address developing and applying sophisticated machine learning and network science models and algorithms. The algorithms will be carefully tuned to extract relevant biological and medical knowledge from systems-level real-world molecular and medical data. The aim is to utilize them to understand the structure of the data that would enable mining the data for new biological and medical insight that would further lead to improving diagnostics, discovering new biomarkers, improving patient stratification and treatment, personalizing treatment and facilitate rational drug development. The successful candidates will join a dynamic research group of Prof. Przulj within BSC. The students will work in a highly sophisticated HPC environment, will have access to systems and computational infrastructures, and will establish collaborations with experts in different areas. *Key Duties* * Conduct high-quality research * Publish in high impact journals and conferences * Present research at national and international conferences and meetings * Collaborate with various research groups across Europe and elsewhere * Help supervise PhD and MSc students * Participate in grant writing and organizational activities * Participate in educational and outreach activities MORE INFO & APPLY HERE: https://www.bsc.es/join-us/job-opportunities/18019lsicbr2 http://bsc.es/disclaimer

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Assistant/associate professor position at Wageningen University
by Ridder, Dick de 28 Jun '19

28 Jun '19

Position: assistant/associate professor in bioinformatics or computational biology The Wageningen Bioinformatics Group has a vacancy for an assistant / associate professor in bioinformatics or computational biology. As a candidate, you have a good scientific track record and a drive to develop your own research line. You can attract funding to build and support a group and you are able to set up a strong academic and industrial network. Your research should connect method development to application, be relevant for plant, animal or microbial biotechnology, and complement the current expertise in the group. Relevant areas include (but are not limited to) metagenomics, metabolomics, proteomics and phenomics. You strive to become an enthusiastic and knowledgeable teacher and supervisor in bioinformatics. Finally, you are a collaborative team member, contributing to the organization of the group, the university and the scientific community at large. Wageningen University & Research focuses on food, health and the living environment and is one of the leading organisations in this domain worldwide. The Bioinformatics Group provides a collaborative working environment with young, dedicated staff with expertise in a number of areas, particularly in genomics. Our group is strongly embedded in the Plant Sciences Group and collaborates intensively with Wageningen Research. We maintain extensive computational resources and have the opportunity to teach (advanced) MSc courses and supervise thesis projects in the Master’s Programme in Bioinformatics. We offer a meaningful job with a competitive salary (depending on your experience) and good benefits. The Wageningen tenure-track system provides an excellent opportunity and support for academic development. For more information and an online application form (deadline September 8, 2019), please see https://tinyurl.com/y3ucfwys or contact Dick de Ridder (dick.deridder(a)wur.nl)

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Barcelona Supercomputing Center: Technician at Text Mining Unit (RE2)
by BSC RRHH 28 Jun '19

28 Jun '19

Technician at Text Mining Unit (RE2) Reference: 179_19_LS_TM_RE2 *Context And Mission* The Text Mining Unit of the BSC-CNS (TeMU-BSC) is funded through the Plan de Impulso de las Tecnologías del Lenguaje de la Agenda Digital, by the Secretary of State of Telecommunications and the Information. It is the first publicly funded text mining unit in Spain and has the aim to promote the development of natural language processing and machine translation resources for Spanish and other co-official languages in the area of biomedicine. We search for a technician who will be responsible of the integration of data, applications and search tools, and the maintenance of the servers and other infrastructure of the unit. *Key Duties* * Administration task on servers, operating systems and applications. * Installation of new releases of software/server patches. * Integration of NLP components using IUMA, GATE, OpenNLP, etc. * Development of mechanisms for the integration of resources and a data warehouse. MORE INFO & APPLY VIA: https://www.bsc.es/join-us/job-opportunities/17919lstmre2 http://bsc.es/disclaimer

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Tenure Track Assistant Professor Artificial Intelligence for Systems Medicine @TUEindhoven
by Riel, N.A.W. van 27 Jun '19

27 Jun '19

We are hiring: Tenure Track Assistant Professor Artificial Intelligence for Systems Medicine @TUEindhoven: https://jobs.tue.nl/en/vacancy/assistant-professor-artificial-intelligence-… . We seek to appoint a scientist/engineer who is passionate about research as well as teaching. We are looking for a creative and pro-active team player to establish a complementary research line. We work on biomedical systems biology, which ranges from fundamental science to clinical applications. Existing research lines focus on oncology and metabolic disease. We search for candidates with a PhD degree in computational biology, biomedical signal processing, or other relevant discipline to develop a research line on 'Artificial Intelligence for Systems Medicine'. In this Tenure Track position model-based data analysis and signal processing will be developed, combining computer simulation models of the human physiological system, stochastic models of uncertainties and variation in the process, and (biosensor) data, for application in systems medicine. Artificial Intelligence (AI) technology is applied for real-time learning and adaptation of the models, to accurately estimate the current state of the system and to predict its future trajectory. In addition to execution of research and education the candidate is expected to actively setup collaborations and secure research funding. The candidate will play an active role in the new TU/e Artificial Intelligence institute. Kind regards, Prof. dr. ir. Natal van Riel

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job opening Genomics Bioinformatician at BRIGHTcore (the VUB-ULB genomics platform) in Brussels
by Catharina Olsen 27 Jun '19

27 Jun '19

Dear all, We are looking for a Genomics Bioinformatician at BRIGHTcore. Details about the position: https://www.uzbrusselwerkt.be/en/vacatures/viewjob/174860 Best regards, Catharina

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JOB: PhD position in the Thomas More University of Applied Sciences and Hasselt University
by Ziv SHKEDY 27 Jun '19

27 Jun '19

Dear All, As a part of a H2020 European project “NanoInformaTIX” ( http://www.nanoinformatix.eu/) we open a PhD position in Biostatistics/Data science in the Thomas More University of Applied Sciences - Radius group (http://radius.thomasmore.be) and the center of statistics (CenStat), Hasselt University (https://www.uhasselt.be/censtat) The 4 years research project will be focused on nanoparticle toxicity modelling. The PhD candidate will be located in the Thomas More Radius group (3-4 days per week) and UHasselt (1-2 days per week). Strating date of the PhD project: *01/10/2019*. Specific research lines of the PhD project include: · Dose-response modelling of nanoparticle toxicity. · Extrapolation of the (in vitro based) dose-response models to an in vivo setting. · Integrated data analysis of several nanoparticle toxicity databases. Your Profile: · Master in biostatistics/statistics/bioinformatics. · Knowledge of R and SAS (knowledge of Winbugs/JAGS would be an asset). · Good written and excellent communication skills. · Ability to work independently and as a part of multidisciplinary team. · Problem solving skills and team player This PhD position offers a unique opportunity to conduct research as a part of multidisciplinary team in collaboration with several European institutes. If you are interested in the position, please contact by email Geert Verheyen (geert.verheyen(a)thomasmore.be) or Ziv Shkedy ( ziv.shkedy(a)uhasselt.be) Closing date to send an email is 07*/07/2019*

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