June 2021 - BBClist - maillist.psb.ugent.be

PhD position in Integrating of multiple -omics datasets
by Claesen Jürgen 04 Jun '24

04 Jun '24

Dear all, SCK CEN and UHasselt are looking for candidates for a PhD project with the title: "Integromics - Towards integration of big biomolecular data to enable systems biology" Description The last decades, development of high-throughput technologies such as next-generation sequencing, microarrays and mass spectrometry has led to a paradigm shift in biology and life sciences. Where previously one biomolecule (for example, a gene, or a protein) was studied as a single entity, these experimental techniques allow to study a set of biomolecules (for example, the genome or the proteome) in one go and in a limited amount of time. While, at first, experiments were analyzed independently from each other, combining information of several experimental techniques, and correlating them with environmental and/or clinical parameters, is, nowadays, of great interest. As a consequence, novel statistical and computational methodologies for the analysis of multi-omics datasets have to be developed, allowing a multi-dimensional view on complex biological processes. In this PhD project, we aim at the development of computational methods for the analysis of multi-omics datasets, that are commonly generated by the three biology units of SCK*CEN, which will improve the understanding and valorization of the data, and which will keep the biology units up to date with current developments in biology and bioinformatics. Profile and diploma As a doctorate researcher you will join the dynamic bioinformatics team at SCK CEN and CenStat (UHasselt). A successful candidate should have : * A master degree in biostatistics/applied statistics/bioinformatics/statistical bioinformatics. * You are acquainted with statistical methodologies and had exposure to computer programming in SAS/R/Winbugs/Python. * You can work independently and within a team. * You have excellent communication skills. * You are interested to develop new methodology from both theoretical and applied aspects. * You enjoy working in a multidisciplinary and multicultural environment. * You are willing to closely collaborate with biologists/biostatisticians. * You speak and write English fluently. * You have work experience with at least two different "omics" platforms. For more information contact: Dr. Claesen Jürgen (SCK-CEN), jclaesen(a)sckcen.be<https://academy.sckcen.be/en/Mailform?contactid=b22040b5-cf18-496f-a82a-3bc…> Prof. Shkedy Ziv (Hasselt University), ziv.shkedy(a)uhasselt.be<https://academy.sckcen.be/en/Mailform?contactid=51ae7733-8006-4347-b211-9a4…> Link to the project in SCK-CEN: https://academy.sckcen.be/en/Your_thesis_internship/AllTopics/Integromics--… Kind Regards, Jürgen

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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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FW: 2 PhD positions in Norwich, UK in metagenomics
by Falk Hildebrand (QIB) 30 Jun '21

30 Jun '21

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Vacancy for a PhD-student
by L.M. Zandwijk - Hollestein 30 Jun '21

30 Jun '21

Dear Sir/Madam, We have a vacancy for a PhD-student at the Dermatology and Pathology department of the Erasmus MC Cancer Institute in Rotterdam for a project about metastasis of melanoma. The project includes analyses of histopathological images and DNA sequencing data. Could you spread this vacancy through the bbc mailinglist? I also attached the English vacancy, as the link below is in Dutch. https://www.werkenbijerasmusmc.nl/vacature/53541/phd-student-voor-integrati…<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.werke…> Best regards, Dr. L.M. (Loes) Hollestein Epidemiologist Dermatology [Erasmus MC] P.O. Box 2040, 3000 CA Rotterdam, The Netherlands, internal postal address NA-501 Visiting address: office NA-501, Dr.Molewaterplein 40, 3015 GD Rotterdam, The Netherlands Email l.hollestein(a)erasmusmc.nl<mailto:l.hollestein@erasmusmc.nl> | Telephone +31 6 500 324 07 www.erasmusmc.nl<http://www.erasmusmc.nl> [Twitter]<https://twitter.com/erasmusmcintl> [YouTube] <http://www.erasmusmc.nl/youtube> Presence: Monday, Tuesday, Wednesday, Thursday

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Phd opprtunities @University of Lille and INRIA
by El-ghazali Talbi 29 Jun '21

29 Jun '21

*** Re-Posting - Please help distribute it to interested once **** 2 PhD Opportunity in optimization, metaheuristics and deep learning - Deadline July 30, 2021 1. "Multi-criteria design and optimization of deep learning models: Application to embedded systems". Collaboration with IRT-SystemX Paris Saclay. See the linkhttps://www.irt-systemx.fr/recrutement/multi-criteria-automated-design-and-optimization-of-deep-neural-networks/ for more details. 2. "Optimization of deep learning models for spacio-temporel prediction", Collaboration with EDF Paris Saclay. contact: Prof. El-Ghazali TALBI, e-mail:el-ghazali.talbi@univ-lille.fr -- ********************************************************************** META'2021 International Conference on Metaheuristics and Nature Inspired Computing 27-30 Oct 2021, Marrakech, Morocco http://meta2021.sciencesconf.org *********************************************************************** ********************************************************************** OLA'2022 International Conference on Optimization and Learning July 2022, Sicilia, Italy *********************************************************************** Prof. El-ghazali TALBI Polytech'Lille, University Lille - INRIA CRISTAL - CNRS guide2research.com

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PhD or junior post-doc position in the Laboratory of Evolutionary and Computational Virology (Rega Institute - KU Leuven)
by Guy Baele 28 Jun '21

28 Jun '21

The Laboratory of Evolutionary and Computational Virology is looking for a motivated PhD student or junior post-doctoral researcher to perform research on ‘Data analysis and visualisation design for emerging infectious diseases’. More information on how to apply can be found here: https://www.kuleuven.be/personeel/jobsite/jobs/60032532 The Evolutionary and Computational Virology Laboratory at the Division of Clinical and Epidemiological Virology (Rega Institute, KU Leuven) focuses on the evolutionary processes that shape viral genetic diversity. This encompasses large-scale epidemic processes, such as population growth and spatial dispersal (a popular topic in phylogeographic and phylodynamic research), as well as small-scale transmission histories and within-host evolutionary processes, including adaptation and recombination. It is our objective to gain better insights into these evolutionary and population genetic processes and to clarify how they relate to epidemic and disease dynamics. To this aim, we focus on statistical and computational developments to analyze the increasing amount of data brought about by massive sequencing studies, mainly in a framework of Bayesian phylogenetic inference, for which our research group holds a strong track record. We also aim to explore the applicability of novel visualization approaches, in order to facilitate interpretation and dissemination of our research. Website unit: https://rega.kuleuven.be/cev/ecv Project In a first part of the project, useful software applications that complement Bayesian phylogenetic and phylodynamic inference will need to be designed and implemented. In order to translate the phylodynamic output of our proposed models into tangible responses, the goal will be to develop a user-friendly, feature-rich, interactive and flexible web-based visualization platform that can easily be applied to different pathogens and enables sharing these visualisations as frictionlessly as possible. The web technology platforms to be used are not carved in stone and can be chosen provided they scale well with increasing amounts of data. Our research group has previous experience in this area, in the development of the SPREAD software package (https://doi.org/10.1093/bioinformatics/btr481) and its successor that makes use of Data-Driven Documents: SpreaD3 (https://doi.org/10.1093/molbev/msw082) Knowledge of recent web technologies (see the profile description) is hence considered a strong plus. The second part of the project will involve becoming familiar with Bayesian phylogeographic reconstructions on various pathogens, but with an initial focus on rabies virus. While a previously hired PhD student will focus on developing novel models for phylogeographic inference, applying these models and comparing their inference results to one another constitutes an important responsibility within the current job description. A collection of useful data sets from different geographic regions will have to be established, and this for different pathogens, and will need to be carefully analysed alongside available metadata and current hypotheses on viral spread within the field of research. However, these types of analyses constitute only a starting point, and we certainly welcome novel ideas for analyses, model and/or application developments or interesting pathogens to study. Profile The candidate for this position should have a background in computer science and/or web design, and preferably hold a master's degree (with distinction/cum laude) and/or PhD in computer science / (bio-)informatics (or equivalent through experience). Take note that the specifics of the funded project do not allow senior post-doctoral researchers to be hired on a full-time basis (i.e. only PhD students or researchers that have recently obtained their PhD can be hired). The candidate is preferably experienced in one or more recent web technologies such as JavaScript, HTML, CSS, Python, Data-Driven Documents (https://d3js.org/) React (http://facebook.github.io/react/) and Node.js (http://nodejs.org) application. The candidate should be sufficiently proficient in English, motivated to work in a team and publish his/her findings, and willing to travel (when conditions allow for it). Offer The candidate will be able to perform research in a dynamic and multidisciplinary team (computer scientists, data analysts and evolutionary biologists), housed in the brand-new facilities of the Rega institute at the Gasthuisberg University hospital campus, and guided by prolific supervisors. The candidate will be able to contribute to the continued development of the BEAST application suite - used by many researchers in the fields of phylogenetics, phylodynamics and molecular evolution, and consisting of a wide range of software tools - and collaborate with top researchers in the field. Additionally, at the Division of Clinical and Epidemiological Virology, the candidate will be able to interact with several top researchers in the field of epidemiology, virology and metagenomics, and work on important infectious disease problems from an evolutionary perspective. The targeted starting date will be October 1st 2021, although both earlier and later starting dates can be negotiated, and the candidate should obtain his/her master’s and/or PhD degree by that time. All applicants are expected to submit a motivation letter, overview of their study results and two references (with their contact details). Funding is available for 4 years to perform a PhD, and between 2-3 years in case a junior post-doctoral researcher is selected. The position will remain open until a suitable candidate has been selected. Interested? Please use the KU Leuven university job portal only when applying for this position. For more information, contact Prof. Dr. Guy Baele (guy.baele(a)kuleuven.be) and/or Dr. Simon Dellicour (simon.dellicour(a)ulb.be) You can apply for this job no later than November 30, 2021 via the online application tool KU Leuven seeks to foster an environment where all talents can flourish, regardless of gender, age, cultural background, nationality or impairments. If you have any questions relating to accessibility or support, please contact us at diversiteit.HR(a)kuleuven.be. -- Guy Baele, Assistant Professor Department of Microbiology, Immunology and Transplantation Evolutionary and Computational Virology Section Rega Institute - KU Leuven Herestraat 49, 3000 Leuven, BELGIUM

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Vacature in Groningen aan Hanzehogeschool
by Noback MA, Michiel 21 Jun '21

21 Jun '21

Bij de Hanzehogeschool Groningen, opleiding bio-informatica zoeken we een collega. Zie https://www.tangram-tis.nl/20022/Vacatures/20022-02S0001YWP/Vacature-Docent… of neem gerust contact met mij op als je vragen hebt over deze vacature. Met vriendelijke groeten, with kind regards, Michiel Noback Dr. M.A. Noback | Bioinformatics Senior Lecturer Institute for Life Science & Technology | Hanze University of Applied Sciences Phone +31-50-595 4691<mailto:+31-50-595%204691> | E-mail m.a.noback(a)pl.hanze.nl<mailto:m.a.noback@pl.hanze.nl> Room H1.90 (via H1.88) | Van Doorenveste

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Tenure track: ASSISTANT PROFESSOR BIOINFORMATICS + AI - VU Amsterdam
by Sanne Abeln 17 Jun '21

17 Jun '21

Dear colleagues, The Vrije Universiteit Amsterdam has an open tenure track position in Bioinformatics and Machine Learning. We seek a new colleague who will actively contribute to the research in the Bioinformatics research group and will be responsible for teaching various courses in Bioinformatics and Artificial Intelligence curricula. We look for an active researcher in the bioinformatics domain, using machine learning as underlying methodology, or a researcher with a focus on Artificial Intelligence with applications in the domain of bioinformatics. The successful applicant will receive a well-structured tenure track appointment. For more details, see: https://werkenbij.vu.nl/ad/assistant-professor-bioinformatics-and-machine-l… Applications need to be received by 27 June 2021. It would be nice if you could share this position with potential candidates, Many thanks, Sanne -- Sanne Abeln Associate Professor Bioinformatics - VU University Amsterdam s.abeln(a)vu.nl +31 20 59 87816 www.few.vu.nl/~abeln

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Assistant Professor (DDLS Fellow) in Data-driven Evolution and Biodiversity at Uppsala University, Sweden
by Bengt Persson 17 Jun '21

17 Jun '21

Dear all, Assistant Professor (DDLS Fellow) in Data-driven Evolution and Biodiversity Uppsala University is recruiting an associate senior lecturer (equivalent to assistant professor) with tenure track in data-driven evolution and biodiversity. The position comes with a very generous package of SEK 17 million, which is intended to cover five years of the fellow’s salary, two doctoral students, two post-doc positions and ongoing costs. This position is part of a large initiative funded by the Knut and Alice Wallenberg Foundation, to promote data-drive life sciences, in collaboration with SciLifeLab (see more here: https://www.scilifelab.se/data-driven/) See the full description and apply here: https://www.uu.se/en/about-uu/join-us/details/?positionId=409922 Deadline 6 September 2021. Sorry for cross-posting. All the best, Yours, Bengt Persson -- Bengt Persson, M.D., Ph.D., Professor of Bioinformatics Head of department Department of Cell and Molecular Biology (ICM) Uppsala University Telephone: +46 18 471 4422 Mobile phone: +46 70 425 0230 Facsimile: +46 18 530 396 E-mail: bengt.persson(a)icm.uu.se<mailto:bengt.persson@icm.uu.se> Address: Uppsala University ICM -- Department of Cell and Molecular Biology BMC, room C10:308c Box 596 S-751 24 Uppsala, SWEDEN När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy

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Vacature praktijkdocent bioinformatica (tijdelijk)
by Martijn van der Bruggen 16 Jun '21

16 Jun '21

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