June 2022 - 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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ELIXIR Train the Trainer course at EMBL Heidelberg - 19-22nd of July
by Alexander Botzki 30 Jun '22

30 Jun '22

Hi all, -- FYI - on behalve of the organizers -- The Bio-IT<https://bio-it.embl.de/> project at EMBL<https://www.embl.org/>, in collaboration with de.NBI<https://www.denbi.de/>, is going to host an ELIXIR Train the Trainer in July. 📅 Course dates: 19th - 22nd July 🕛 Time: from 13:30 to 17:00 CEST ❓ ELIXIR Train the Trainer<https://elixir-europe.org/platforms/training/train-the-trainer> 🎫 Registration and more info: bio-it.embl.de/events/elixir-train-the-trainer<https://bio-it.embl.de/events/elixir-train-the-trainer/> Feel free to forward this information to your networks via email or retweet our event announcement: twitter.com/EMBL_BioIT/status/1541747996404097025<https://twitter.com/EMBL_BioIT/status/1541747996404097025>. Thank you! Best, Lisanna -- ___________________________________________________ Lisanna Paladin, PhD - Bio-IT<https://bio-it.embl.de/> member Bioinformatics Community Project Manager, EMBL Heidelberg<https://www.embl.org/sites/heidelberg/> email: lisanna.paladin(a)gmail.com<mailto:lisannapaladin@gmail.com>, lisanna.paladin(a)embl.de<mailto:lisanna.paladin@embl.de> ___________________________________________________

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Diatom research PhD position available in Ghent University
by Michiel Van Bel 27 Jun '22

27 Jun '22

Dear all, we would like to advertise the following PhD position: [ https://www.ugent.be/en/work/scientific/phd-student-27 | https://www.ugent.be/en/work/scientific/phd-student-27 ] Michiel Van Bel - Senior bioinformatician Applied Bioinformatics And Biostatistics VIB-UGent Center for Plant Systems Biology Ghent University Technologiepark-Zwijnaarde 71 - 9052 Ghent - Belgium Tel. +32(0)9 331 36 95 [ http://www.psb.ugent.be/ | www.psb.ugent.be ] Genome editing, cutting-edge technology for a sustainable agriculture

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Wanted: Bioinformatics Lab Manager (MSc or PhD)
by Bas E. Dutilh 22 Jun '22

22 Jun '22

Dear colleagues, I recently moved to the Cluster of Excellence “Balance of the Microverse” at the Friedrich Schiller University in Jena where I founded the Viral Ecology and Omics group (VEO). We focus on metagenomics and microbiome modelling with a particular focus on the role of viruses and bacteriophages. *We are now looking for a Bioinformatics Lab Manager to support the dry lab activities of the VEO group.* For more details, please email me. Check the link for further details including an application link: https://jobs.uni-jena.de/jobposting/ad8e538b469960841c8634247e83601c9546766… Best regards, Bas Your responsibilities: Install, update, and maintain the group’s software, create patches, raise issues if needed. Maintain databases on our system, manage/update database download scripts (see for example https://github.com/MGXlab/cirtap) Advise and help group members, including those with little experience. Create and maintain pipelines for often-used computational tasks. Establish and maintain best practices and dry lab rules, provide documentation, instruct students who use our computers in these best practices. Contribute to course development (see for example https://github.com/MGXlab/Viromics-Workshop-MGX) Collaborate productively with experimental and computational researchers. Your profile: - A MSc or PhD degree in bioinformatics with a focus on (meta-) genomics. Experience with bacteriophages is beneficial. - Experience with Linux, Bash, Python, R, Git, Snakemake, Conda, Slurm. - Experience with database maintenance and/or data stewardship is beneficial. - Experience with hardware (computers, HPC) is beneficial. - Enthusiasm and talent for working on interdisciplinary projects. - Excellent communication skills, ability to work in a team and to interact with people from diverse nationalities and scientific backgrounds. - You have a sense of responsibility, organisational skills, and ability to contribute to a friendly and collaborative academic working environment. - Languages: English and German. We offer: - Embedding in the VEO/MGX groups, a highly collaborative and energetic team of international scientists in viral ecology and metagenomics. - A comprehensive continuing education programme for personal development, individual qualification and development measures. - Jena – City of Science is a lovely and lively town with a vibrant local cultural agenda. Jena is among the most liveable cities in Germany. Situated on the Saale River and surrounded by the famous Thuringian Forest, this city is ideal for lovers of nature and hiking. - A family-friendly working environment with a variety of offers for families: University Family Office ‘JUniFamilie’ and flexible childcare options (‘JUniKinder’ program). - FSU’s occupational health promotion scheme ( https://www.uni-jena.de/en/Gesundheit) and a wide range of university sports activities. - Attractive fringe benefits, e.g. capital formation benefits (VL), Job Ticket (benefits for public transport), and an occupational pension (VBL). - Remuneration based on the provisions of the Collective Agreement for the Public Sector of the Federal States (TV-L) up to salary scale E 13 (depending on the candidate’s personal qualifications) including a special annual payment in accordance with the collective agreement. -- Prof. Dr. Bas E. Dutilh <http://tbb.bio.uu.nl/dutilh> Viral Ecology and Omics Group | Metagenomics Group Microverse Cluster <https://microverse-cluster.de/en/> | Theoretical Biology and Bioinformatics <https://tbb.bio.uu.nl/> European Virus Bioinformatics Centre <http://evbc.uni-jena.de/> | Utrecht Bioinformatics Center <https://ubc.uu.nl/> Friedrich Schiller University Jena <https://www.uni-jena.de/en/> | Utrecht University <https://www.uu.nl/>

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MSCA INSPIRE Fellowship
by Claesson, Marcus 18 Jun '22

18 Jun '22

Hi all, Are you interested in a prestigious INSPIRE <https://www.ucc.ie/en/inspire/apply/> Fellowship, which is a Horizon 2020 Marie Sklodowska-Curie cofunded postdoctoral fellowship programme? The first call will open on the 30th of June and the project will be based in APC Microbiome Ireland, Cork, one of the world's leading microbiome institutes. The successful applicant would carry out bioinformatics-based research on the role of the microbiome in paediatric Crohn's disease under my supervision and in collaboration with Queen Mary University London. Please contact me for details at your earliest convenience. Feel free to circulate this to anyone you might be interested. Regards, Marcus J. Claesson, PhD Associate Professor of Bioinformatics School of Microbiology & APC Microbiome Ireland University College Cork Western Road, Cork, Ireland Tel: +353-(0)21-4901390 Email: m.claesson(a)ucc.ie<mailto:m.claesson@ucc.ie> http://orcid.org/0000-0002-5712-0623

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Open position for BioIT post-doc on ERC-project
by Katleen De Preter 17 Jun '22

17 Jun '22

Dear all, We are hiring 2 post-docs (focus on bio-informatics<https://career012.successfactors.eu/career?company=C0000956575P&career_job_…> and focus on wet lab<https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fcareer012…> work, respectively) on a recently granted ERC-CoG-project at Ghent University in the lab for Translational Onco-genomics and Bio-Informatics (TOBI). Also welcome to share this with your network via Twitter<https://twitter.com/kdpreter/status/1535146945609617408?s=20&t=6eBDI6L42vfK…> or LinkedIn<https://www.linkedin.com/posts/katleend_tobi-lab-activity-69409125986325463…>. Kind regards Katleen De Preter prof. dr. ir. Katleen De Preter Principal Investigator of Translational Onco-Genomics and Bioinformatics Team (TOBI), Department of Biomolecular Medicine & Cancer Research Institute Ghent (CRIG), UGent Corneel Heymanslaan 10, 9000 Gent, Belgium Ghent University Hospital, Medical Research Building (MRB), 2nd floor, room 120.055 Tel: +32 (0) 9 332 45 39 https://www.crig.ugent.be/en/prof-katleen-de-preter-phd https://www.ugent.be/ge/biomolecular-medicine/en/research/research-labs/tra… https://tobi.ugent.be/ [signature_2113051554]

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posting bioinformatician position on BBC list
by Puck Knipscheer 16 Jun '22

16 Jun '22

Hi, I am a group leader at the Hubrecht institute in Utrecht, the Netherlands. We are looking for a bioinformatician to work with us on MNase sequencing and mutational analysis. Specifically we are seeking a (junior) bioinformatician who has programming experience (python and R), affinity with life science, and is looking for a position to learn and gain experience. For more information, see attached advertisement. Could you post this position on the BBC list? Thanks you! Puck

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CMSB 2022: call for posters and for highlight talks
by Ion Petre 14 Jun '22

14 Jun '22

CMSB 2022: call for posters and highlight talks ====================================== September 14-16, 2022 at the University of Bucharest, Romania CMSB 2022 website: https://fmi.unibuc.ro/en/cmsb-2022/ Accepted papers: https://fmi.unibuc.ro/en/cmsb-2022/cmsb-2022-program/ CMSB series website: https://cmsb.sciencesconf.org/ CMSB, the conference on Computational Methods in Systems Biology, aims to bring together researchers from across the biological, mathematical, computational, and physical sciences, interested in the modelling, simulation, analysis, inference, design, and control of biological systems. IMPORTANT NOTE CONCERNING THE COVID-19 PANDEMIC CMSB 2022 is planned as a physical, in-person event, with certain support for remote presence, both for speakers and for other participants who are unable or unwilling to come. INVITED SPEAKERS Alessandra Carbone (Sorbonne Université, France) Gabriela Chiosis (Memorial Sloan Kettering Cancer Center, USA) Loïc Paulevé (Laboratoire Bordelais de Recherche en Informatique, France) Alfonso Rodríguez-Patón (Universidad Politécnica de Madrid, Spain) Erik Sonnhammer (Stockholm University, Sweden) IMPORTANT DATES (all dates are AoE) Poster/highlight talk: July 14, 2022 Conference: September 14-16, 2022 PAPER SUBMISSION CMSB 2022 solicits high quality papers reporting research results and/or tools related to the topics mentioned below. In this call we solicit two types of papers: posters and highlight talks: POSTERS: Extended abstracts should be submitted to propose poster presentation of original unpublished work, or of major results published or accepted in the last year in a high-quality journal or conference. The abstracts should be submitted in Springer LNCS style and should not exceed 4 pages all included. Authors of accepted abstracts will be invited for presentation in poster sessions and for flash presentations in plenary conference sessions. Note: poster submissions will not be included in the Springer LNBI proceedings. HIGHLIGHT TALKS: Highlight talk proposals should be submitted in the form of an extended abstract, for possible oral presentation in a plenary conference session, without publication of related material in the conference proceedings. We particularly welcome submission of work recently published in high quality forums. Submitted abstracts summarizing the results and their relevance should not exceed 2 pages including references. Note: extended abstracts will not be included in the Springer LNBI proceedings. The poster and highlight talks submissions will undergo a review process with a quick turnover. Papers must be submitted electronically as PDF files via EasyChair: https://easychair.org/conferences/?conf=cmsb2022 TOPICS * formalisms for modelling biological processes; * methods and tools for biological system analysis, modelling and simulation; * frameworks for model verification, validation, analysis, and simulation of biological systems; * high-performance methods for computational systems biology; * identification of biological systems; * applications of machine learning and data analytics in biology; * network modelling, analysis, inference; * automated parameter and model synthesis; * model integration and biological databases; * multi-scale modelling and analysis methods; * design, analysis, and verification methods for synthetic biology; * methods for biomolecular computing and engineered molecular devices; * data-based approaches for systems and synthetic biology; * optimality and control of biological systems; * modelling, analysis and control of microbial communities. ORGANIZATION COMMITTEE David Pacioianu, University of Bucharest, Romania Andrei Paun, University of Bucharest, Romania (co-chair) Ion Petre, University of Turku, Finland (co-chair) Nicoleta Siminea, University of Bucharest Joel Sjöberg, University of Turku, Finland PROGRAM COMMITTEE Alessandro Abate – University of Oxford (UK) Paolo Ballarini – Centrale Supélec (France) Daniela Besozzi – University of Milan Bicocca (Italy) Luca Cardelli – University of Oxford (UK) Milan Češka – Brno University of Technology (Czech Republic) Eugenio Cinquemani – Inria Grenoble-Rhône-Alpes (France) Eugen Czeizler – University of Helsinki (Finland) Franck Delaplace – Université Paris-Saclay (France) François Fages – INRIA (France) Jerome Feret – Inria Paris (France) Clémence Frioux – Inria Bordeaux (France) Ashutosh Gupta – IIT Bombay (India) Monika Heiner – Brandenburg Technical University Cottbus-Senftenberg (Germany) Jane Hillston – University of Edinburgh (UK) Tommaso Mazza – CSS Mendel (Italy) Andrzej Mizera – University of Luxembourg (Luxembourg) Jun Pang – University of Luxembourg (Luxembourg) Nicola Paoletti – University of London (UK) Loïc Paulevé – CNRS, LaBRI (France) Andrei Paun – University of Bucharest, Romania, co-chair Ion Petre – University of Turku, Finland, co-chair Tatjana Petrov – University of Konstanz (Germany) Ovidiu Radulescu – University of Montpellier France) Andre Ribeiro – University of Tampere (Finland) Maria Rodriguez Martinez – IBM Zürich Research Laboratory (Switzerland) Olivier Roux – École Centrale de Nantes (France) David Šafránek – Masaryk University (Czech Republic) Carolyn Talcott – SRI International (USA) Jing Tang – University of Helsinki (Finland) Adelinde Uhrmacher – University of Rostock (Germany) Andrea Vandin – Technical University of Denmark (Denmark) Verena Wolf – Saarland University (Germany) Christoph Zechner – Max Planck Institute of Molecular Cell Biology and Genetics (Germany) TOOL EVALUATION COMMITTEE Georgios Argyris – Technical University of Denmark, Copenhagen (Denmark) Candan Çelik – Comenius University, Bratislava (Slovakia) Anastasis Georgoulas – University College London (UK) Lukrécia Mertová – Heidelberg Institute for Theoretical Studies (Germany) Samuel Pastva – IST Austria (Austria) Misbah Razzaq – INRAe, Tours (France) David Šafránek – Masaryk University (Czech Republic), chair Jakub Šalagovič – KU Leuven (Belgium) Matej Trojak – Masaryk University (Czech Republic) STEERING COMMITTEE Luca Cardelli – University of Oxford (UK) François Fages – INRIA (France) Monika Heiner – Brandenburg Technical University Cottbus-Senftenberg (Germany) Tomasso Mazza – CSS Mendel (Italy) Satoru Miyano – University of Tokyo (Japan) Ion Petre – University of Turku, Finland Gordon Plotkin – University of Edinburgh (UK) Corrado Priami – University of Pisa (Italy) Carolyn Talcott – SRI International (USA) Adelinde Uhrmacher – University of Rostock (Germany) Alessandro Abate – University of Oxford (UK) Eugenio Cinquemani – Inria Grenoble-Rhône-Alpes (France) Jun Pang – University of Luxembourg (Luxembourg) Loïc Paulevé – CNRS, LaBRI (France) Andrei Paun – University of Bucharest, Romania Tatjana Petrov – University of Konstanz (Germany) Verena Wolf – Saarland University (Germany) CONTACT All questions about the conference should be emailed to the organizers Ion Petre (ion.petre(a)utu.fi) and Andrei Paun (apaun(a)fmi.unibuc.ro)

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Two open positions bioinformatics @Sciensano
by Kevin Vanneste 14 Jun '22

14 Jun '22

Dear all, The Bioinformatics Platform at the Belgian Institute of Health (www.sciensano.be<http://www.sciensano.be>) currently has two open vacancies for bioinformaticians to work in the field of microbial genomics. More info and applications are available on our job site: https://jobs.sciensano.be/content/jobpage.asp?a=DETAIL&jdkid=921&l=DUTCH https://jobs.sciensano.be/content/jobpage.asp?a=DETAIL&jdkid=950&l=DUTCH Sincerely, K Kevin Vanneste, PhD Senior scientist - Responsible Bioinformatics Platform Transversal activities in Applied Genomics (TAG) T + 32 2 642 50 65 [cid:image001.jpg@01D4595B.6D6E05D0] Rue Juliette Wytsmanstraat 14 * 1050 Brussels www.sciensano.be<http://www.sciensano.be/> P Please consider the environment before printing this e-mail

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Open postdoc and staff scientist positions - Human Genetics department, Wellcome Sanger Institute
by Hilary Martin 10 Jun '22

10 Jun '22

I am seeking a highly motivated computational postdoc and staff scientist to join my group <https://www.sanger.ac.uk/group/martin-group/> at the Wellcome Sanger Institute. The group investigates the genetic basis of rare and common diseases and complex traits, primarily in populations with European and South Asian ancestry. We currently have projects in the following areas: * The role of both rare and common variants in rare developmental disorders, using data from the Deciphering Developmental Disorders<https://www.sanger.ac.uk/collaboration/deciphering-developmental-disorders-…> study (N=13,000 exome-sequenced patients) and the Genomics England 100,000 Genomes project<https://www.genomicsengland.co.uk/about-genomics-england/the-100000-genomes…> (N~33,000 whole-genome sequenced rare disease patients), in collaboration with GeneDx (>60,000 exome sequenced patients) and with Matt Hurles’ group<https://www.sanger.ac.uk/group/hurles-group/>. We have a particular focus on the contribution of recessive variants across diverse populations (building on previous work<https://www.science.org/doi/10.1126/science.aar6731>), and on the interplay of rare and common variants. We are also beginning new projects investigating the genetic contribution to sex differences in autism and autistic traits, and on the impact of endogamy versus consanguinity on rare disease risk. * The genetics of cognitive and behavioral traits, using sequence and genotype data from UK Biobank and from two large UK birth cohorts, the Avon Longitudinal Study of Parents and Children<http://www.bristol.ac.uk/alspac/> and the Millenium Cohort Study<https://cls.ucl.ac.uk/cls-studies/millennium-cohort-study/> (N~20,000), in collaboration with with Matt Hurles’ group<https://www.sanger.ac.uk/group/hurles-group/>. This work is building on recent findings about the genetic overlap between rare neurodevelopmental disorders and cognitive/mental health traits in the general population (e.g. Niemi et al., Nature, 2018<https://www.nature.com/articles/s41586-018-0566-4>; Gardner et al., Nature, 2022<https://www.nature.com/articles/s41586-022-04549-9>). * The genetic basis of complex diseases and traits in British South Asian populations, using data from the Genes & Health project<https://www.genesandhealth.org/> (N~50,000 British Pakistani and Bangladeshi individuals with linked electronic health records). An industry consortium has recently funded exome-sequencing of the cohort to complement the existing genotype chip data. We are investigating the contribution of rare and common variants to complex disease risk, as well as the role of autozygosity. Both are three-year posts. Please get in touch if either sounds of interest. Applications will be considered on an ongoing basis and the role will close when a successful appointment has been made. https://jobs.sanger.ac.uk/vacancy/computational-postdoctoral-fellow-in-medi… https://jobs.sanger.ac.uk/vacancy/computational-senior-staff-scientist-medi… Best wishes, Hilary Martin -- The Wellcome Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.

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