- BBClist - maillist.psb.ugent.be

BSC: Life Sciences vacancy
by BSC Human Resources 25 Jan '22

25 Jan '22

Dear all, We would like to inform you about a new job opportunitiy offered by Barcelona Supercomputing Center: - ASHo Text Mining (RE2). Deadline: 28 February, 2022 Link here <https://www.bsc.es/join-us/job-opportunities/1622lstmre2> 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/>

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Fwd: postdoc position : computational analysis of microbiome data
by Stephane Rombauts 24 Jan '22

24 Jan '22

> Begin forwarded message: > > From: Jeroen Raes <jeroen.raes(a)kuleuven.be> > Subject: postdoc position > Date: 24 January 2022 > > Postdoc in Bioinformatics of the Human Gut Microbiome > > Description > The lab of Jeroen Raes (VIB, KU Leuven - Leuven, Belgium) is looking for a postdoctoral researcher in the computational analysis of microbiome data, with a particular emphasis on human-associated microbial communities in health and disease. > > Projects will focus on: > > (i) bioinformatics/statistics method development for joint host and microbiota data analysis and ecology, multi-omics, diagnostic model development and clinical data integration, and/or > (ii) their application to large scale datasets generated within the Flemish Gut Flora project cohort (n>5000), in a wide range of disease cohorts as well as in international projects and/or > (iii) time series analysis of longitudinal and intervention cohorts > > We look for an excellent track record in (meta-)omics data analysis and strong scientific drive. We provide a stimulating and fun environment to pursue your scientific dreams. Further info on http://www.raeslab.org > > Profile > PhD in bioinformatics, computational biology, datamining, biostatistics, population and/or statistical genetics, human microbiota, numerical/microbial ecology or equivalent > Good programming skills (perl/python/ruby/java/C++ etc, SQL, R), proficiency in Unix/Linux and cluster experience > A strong track record in omics data analysis (e.g. (meta)genomics, transcriptomics, proteomics, metabolomics, epigenomics, genotyping data) is a plus > Experience in clinical datamining/machine learning, biomarker detection is a plus > > We offer > VIB-KULeuven is an exciting, interdisciplinary research institute with excellent facilities and leading research groups in e.g. gastroenterology, oncology, immunology, microbiology & virology, clinical genetics/-omics, molecular biology and translational research. The Raes lab is located on the Gasthuisberg campus of the KU Leuven (Fac. of Medicine) and has on-site robotic sample processing, high-throughput computing resources, next-gen sequencing facilities (mi/next/hi/novaSeq. PacBio, oxford nano pore) as wel as wet-lab microbiology for validation of leads. > > Interested? Check out some of our recent work!: > > Falony G*, Joossens M*, Vieira-Silva S*, Wang J* et al (2016) Population-level analysis of gut microbiome variation. Science 352:560-4 > > Vieira-Silva S*, Falony G* et al (2016) Species-function relationships shape ecological properties of the human gut microbiome. Nature Microbiology doi:10.1038/nmicrobiol.2016.88 > > Vieira-Silva S, Sabino J, Valles-Colomer M, Falony G, Kathagen G, Caenepeel C, Cleynen I, van der Merwe S, Vermeire S, Raes J. (2019) Quantitative microbiome profiling disentangles inflammation- and bile duct obstruction-associated microbiota alterations across PSC/IBD diagnoses. Nat Microbiol. doi: 10.1038/s41564-019-0483-9. > > Hughes DA*, Bacigalupe R*, Wang J, Ruehlemann MC, Tito RY, Falony G, Joossens M, Vieira-Silva S, Henckaerts L, Rymenans L, Verspecht C, Ring S, Franke A, Wade KH, Timpson NJ*, Raes J*. (2020). Genome-wide associations of human gut microbiome variation and implications for causal inference analyses. Nat Microbiol. doi: 10.1038/s41564-020-0743-8 > > Vieira-Silva S*, Falony G*, Belda E*, Nielsen T, [41 authors], Bäckhed F, Clement K* & Raes J*. (2020) Statin therapy is associated with lower prevalence of gut microbiota dysbiosis, Nature. DOI: 10.1038/s41586-020-2269-x > > Vandeputte D, De Commer L, Tito RY, Kathagen G, Sabino J, Vermeire S, Faust K, Raes J. (2021) Temporal variability in quantitative human gut microbiome profiles and implications for clinical research. Nat. Commun. 12(1):6740 > > > How to apply? > Interested candidates are encouraged to apply online at https://jobso.id/dsyz <https://jobso.id/dsyz> > > Our institute greatly values diverse standpoints and promotes an inclusive environment in which everyone is respected. > > >

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Vacancy tenure track professorship at Ghent University
by Tim De Meyer 24 Jan '22

24 Jan '22

Dear Madam, Sir, Please find below a vacancy for a tenure track professorship at Ghent University, Belgium. Given that it’s also relevant for bioinformaticians, I hope it can be forwarded through the Benelux Bioinformatics Conference mailing list. Best regards, Tim De Meyer Tenure track position on “Computational design of biosystems” available at the Department of Data Analysis and Mathematical Modelling of the Faculty of Bioscience Engineering, Ghent University, Belgium. The Faculty of Bioscience Engineering at the Ghent University is looking for a Professor in a tenure track system, in the discipline of Computational design of biosystems. On the one hand, the candidate is expected to lecture various courses, supervise bachelor and master thesis students and contribute to post-academic programs. On the other hand, the candidate conducts research in the modelling, algorithmic design and optimization of biosystems. Part of this academic research also consists of publishing in international scientific peer-reviewed journals and attracting funding and PhD students. The candidate’s position will be funded for an initial period of 5 years and will be converted into a permanent appointment as an associate professor after a positive evaluation by the University Board. A € 210.000 package will also be provided as a starting grant. The complete vacancy<https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fcareer012…> can be found on the job page of Ghent University. Interested candidates are expected to submit their application before the 23rd of February 2022 through the e-recruitment system on this page. [cid:image001.jpg@01D8113E.05CE2470]<https://www.ugent.be/bw/nl/faculteit/100> Prof. dr. ir. Tim De Meyer Associate professor T +32 9 264 59 87 Department Data Analysis and Mathematical Modelling Research Unit BIOBIX: Bioinformatics and Computational Genomics Campus Coupure, Block A 1st floor 110.058, Coupure links 653, B-9000 Ghent, Belgium directions<https://www.google.com/maps/dir/Coupure+Links+653,+9000+Gent/@51.0527795,3.…> T administration office +32 9 264 59 32 www.ugent.be<https://www.ugent.be/bw/en> www.biobix.be e-maildisclaimer<https://helpdesk.ugent.be/e-maildisclaimer.php>

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Free, Global Galaxy Training: Learn about RNA-Seq, Single Cell, SARS-CoV-2, and more!
by Celia van Gelder 21 Jan '22

21 Jan '22

Dear colleagues , On behalf of Helena Rasche I am sending you information about upcoming Galaxy related events that might be of interest for you. Please spread this in your organisation as you see fit. Please contact Helena (e.rasche(a)erasmusmc.nl) if you have any questions! Best Celia van Gelder --- The Galaxy Training Network is hosting two large, online, asynchronous events this March in collaboration with the Gallantries and the entire Galaxy Community. These events are beginner-friendly, open to everyone, and will be supported by a global community of instructors during the week. All of the content will remain online afterwards, in case you miss it! Check below to find out more. *GTN Smörgåsbord 2022: Tapas* >From March 14-18, Galaxy is hosting a global 5-day Galaxy Training event showcasing a wide variety of Galaxy Training Network tutorials. This will be an online event, spanning all time zones. All training sessions are pre-recorded, so you can work through them at your own pace, and manage your own time. A large community of GTN trainers will be available via online support to answer all your questions. We'll be covering a wide array of topics, - Intro to Galaxy - NGS - RNA-Seq - Single Cell - Proteomics - *New*: SARS-CoV-2 Analysis - *New*: Machine Learning - *New*: Climate & Ecology - *New*: Galaxy Admin Training *When *March 14-18, 2022 (all time zones). *Who* Open for everybody *Cost* Free *Format* Virtual and asynchronous. All training session are pre-recorded and captioned, you can work through these at your own pace, with instructors available online for support *Accessibility*: The event is asynchronous video tutorials with captioned english speech, all materials are also available in plain-text versions, and discussion / Q & A occurs over slack. Register now! https://bit.ly/smorgasbord2 *Galaxy Admin Training* This workshop will cover introductory and advanced topics you need to know to set up your own production, high-performance and multi-user Galaxy instance. Sessions will be intensive and hands-on, and taught by experienced instructors from the Galaxy Community. Participants will learn how to install, configure, customize, and extend their own Galaxy servers. Find out more and register here: https://galaxyproject.org/events/2022-03-admin-training/ -- Dr. Celia W.G. van Gelder Programme Manager DTL Learning Training Coordinator ELIXIR-NL ELIXIR Training Platform Leader tel. +31613375327 e-mail: celia.van.gelder(a)dtls.nl websites: https://www.dtls.nl/, https://www.elixir-europe.org/platforms/training skype: celia.van.gelder Office: DTL | Jaarbeurs Innovation Mile (JIM) | 6th floor Beatrixgebouw | Jaarbeursplein 6 | 3521 AL Utrecht Postal address: Postbus 8500 | 3503 RM Utrecht While I may be sending this email outside my normal office hours, I have no expectation to receive a reply outside yours. -- Dr. Celia W.G. van Gelder Programme Manager DTL Learning Training Coordinator ELIXIR-NL ELIXIR Training Platform Leader tel. +31613375327 e-mail: celia.van.gelder(a)dtls.nl websites: https://www.dtls.nl/, https://www.elixir-europe.org/platforms/training skype: celia.van.gelder Office: DTL | Jaarbeurs Innovation Mile (JIM) | 6th floor Beatrixgebouw | Jaarbeursplein 6 | 3521 AL Utrecht Postal address: Postbus 8500 | 3503 RM Utrecht While I may be sending this email outside my normal office hours, I have no expectation to receive a reply outside yours.

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Postdoc position on genotyping complex genomes at the Schneeberger Lab
by Raúl Wijfjes 20 Jan '22

20 Jan '22

Dear all, We are looking for an open-minded and enthusiastic bioinformatics postdoc candidate for a three year project on developing computational methods for the analysis of complex genomes. The project will follow up on a recently developed method of the group that assembles individual haplotypes of tetraploid genomes using a combination of bulk long-read and single gamete genome sequencing (Sun /et al., /2021, bioRxiv, https://doi.org/10.1101/2021.05.15.444292) The candidate will develop computational methods to genotype samples based on individual haplotypes of any genome and apply these methods to analyze the inheritance of such haplotypes in recombinant pollen genomes of potato cultivars. It is expected that the haplotype-based genotyping methods developed in this project will be applicable beyond the field of plant genomics (e.g. human genomics). Applicants should hold a PhD degree in bioinformatics or a similar field in computational biology. We are specifically searching for a candidate with strong programming skills (Java, C++, Python), experience in the analysis of high-throughput sequencing data, and the ability to make use of high-performance computational clusters. Good oral and writing skills in English are a must. The Schneeberger group is located at the Faculty of Biology of the Ludwig-Maximilians University in Munich, with a part of the group working at the Max Planck Institute (MPI) for Plant Breeding Research in Cologne, Germany. The candidate for this project will be based at the MPI in Cologne. Please find the attached PDF for additional details about the position and how to apply. Kind regards, Raúl Wijfjes Schneeberger Group, Ludwig-Maximilians University Munich, Germany

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1st CfP: CMSB 2022, Sep 14-16, Bucharest, Romania
by Ion Petre 18 Jan '22

18 Jan '22

CMSB2022: the 20th International Conference on Computational Methods in Systems Biology University of Bucharest Bucharest, Romania, September 14-16, 2022 Conference website https://fmi.unibuc.ro/en/cmsb-2022/ Submission link https://easychair.org/conferences/?conf=cmsb2022 Abstract registration deadline April 27, 2022 Submission deadline May 4, 2022 CMSB 2022 - First Call for Papers The 20th conference on Computational Methods in Systems Biology (CMSB 2022, https://fmi.unibuc.ro/en/cmsb-2022/) will take place on September 14-16, in Bucharest (Romania), on-site, hybrid, or online, depending on the evolution of the Covid-19 pandemic. CMSB is a well established conference series, whose aim is 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. List of 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. Committees Program Committee (preliminary, to be completed) * Alessandro Abate<https://www.cs.ox.ac.uk/people/alessandro.abate/> – University of Oxford (UK) * Paolo Ballarini<https://sites.google.com/site/pballarini/> – Centrale Supélec (France) * Daniela Besozzi<https://www.linkedin.com/in/daniela-besozzi-3370868/> – University of Milan Bicocca (Italy) * Luca Cardelli<http://www.lucacardelli.name/> – University of Oxford (UK) * Milan Češka<https://www.fit.vut.cz/person/ceskam/.cs> – Brno University of Technology (Czech Republic) * Eugenio Cinquemani<https://team.inria.fr/ibis/eugenio-cinquemani/> – Inria Grenoble-Rhône-Alpes (France) * Eugen Czeizler<https://www.linkedin.com/in/eugenczeizler/?originalSubdomain=fi> – University of Helsinki (Finland) * Jerome Feret<http://www.di.ens.fr/~feret> – Inria Paris (France) * Clémence Frioux<https://cfrioux.github.io/> – Inria Bordeaux (France) * Ashutosh Gupta<https://www.linkedin.com/in/ashutosh-gupta-3b7a63141/> – IIT Bombay (India) * Monika Heiner<https://www-dssz.informatik.tu-cottbus.de/DSSZ/Main/MonikaHeiner> – Brandenburg Technical University Cottbus-Senftenberg (Germany) * Jane Hillston<http://homepages.inf.ed.ac.uk/jeh> – University of Edinburgh (UK) * Tommaso Mazza<http://bioinformatics.css-mendel.it/> – CSS Mendel (Italy) * Jun Pang<https://satoss.uni.lu/members/jun/> – University of Luxembourg (Luxembourg) * Loïc Paulevé<https://loicpauleve.name/> – CNRS, LaBRI (France) * Andrei Paun<https://www.researchgate.net/profile/Andrei-Paun> – University of Bucharest, Romania, co-chair * Ion Petre<https://users.utu.fi/ionpet/> – University of Turku, Finland, co-chair * Tatjana Petrov<https://www.tatjanapetrov.info/> – University of Konstanz (Germany) * Maria Rodriguez Martinez<https://researcher.watson.ibm.com/researcher/view.php?person=zurich-MRM> – IBM Zürich Research Laboratory (Switzerland) * David Šafránek<https://www.fi.muni.cz/~xsafran1/> – Masaryk University (Czech Republic) * Carolyn Talcott<https://www.sri.com/bios/carolyn-talcott/> – SRI International (USA) * Jing Tang<https://researchportal.helsinki.fi/en/persons/jing-tang> – University of Helsinki (Finland) * Adelinde Uhrmacher<https://mosi.informatik.uni-rostock.de/team/staff/prof-dr-rer-nat-adelinde-…> – University of Rostock (Germany) * Andrea Vandin<http://people.compute.dtu.dk/anvan/> – Technical University of Denmark (Denmark) * Verena Wolf<http://mosi.cs.uni-sb.de/verena.html> – Saarland University (Germany) * Christoph Zechner<https://zechnerlab.wordpress.com/> – Max Planck Institute of Molecular Cell Biology and Genetics (Germany) Organizing committee * David Pacioianu, University of Bucharest, Romania * Andrei Paun<https://www.researchgate.net/profile/Andrei-Paun>, University of Bucharest, Romania (co-chair) * Ion Petre<https://users.utu.fi/ionpet/>, University of Turku, Romania (co-chair) * Nicoleta Siminea, University of Bucharest * Joel Sjöberg, University of Turku, Finland Publication The submissions to CMSB 2022 will be fully peer-reviewed. The accepted articles will be published in the conference proceedings, expected to be in the Springer LNCS/LNBI series and to be indexed by ISI Web of Science, Scopus, ACM Digital Library, DBLP, and Google Scholar. A special issue of a widely recognized international journal is expected to be organized after the conference. A selection of the best papers will be invited to be extended and submitted to this special issue. Important dates * May 4, 2022: regular and tool paper submission * June 10, 2022: acceptance notifications * June 17, 2021: poster abstract submission * September 14-16, 2021: conference Venue The conference will be held in Bucharest (Romania), on-site, hybrid, or online, depending on the evolution of the Covid-19 pandemic. Contact All questions about submissions should be emailed to the conference organizers Ion Petre (ion.petre(a)utu.fi) and Andrei Paun (apaun(a)fmi.unibuc.ro)

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Pathomation is hiring
by Yves Sucaet 18 Jan '22

18 Jan '22

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OLA'2022 deadline approaching
by El-ghazali Talbi 11 Jan '22

11 Jan '22

Apologies for cross-posting. Appreciate if you can distribute this CFP to your network. **************************************************************************************** OLA'2022 International Conference on Optimization and Learning 18-20 July 2022 Syracuse (Sicilia), Italy http://ola2022.sciencesconf.org/ SCOPUS Springer Proceedings **************************************************************************************** OLA is a conference focusing on the future challenges of optimization and learning methods and their applications. The conference OLA'2022 will provide an opportunity to the international research community in optimization and learning to discuss recent research results and to develop new ideas and collaborations in a friendly and relaxed atmosphere. OLA'2022 welcomes presentations that cover any aspects of optimization and learning research such as big optimization and learning, optimization for learning, learning for optimization, optimization and learning under uncertainty, deep learning, new high-impact applications, parameter tuning, 4th industrial revolution, computer vision, hybridization issues, optimization-simulation, meta-modeling, high-performance computing, parallel and distributed optimization and learning, surrogate modeling, multi-objective optimization ... Submission papers: We will accept two different types of submissions: - S1: Extended abstracts of work-in-progress and position papers of a maximum of 3 pages - S2: Original research contributions of a maximum of 10 pages Important dates: =============== Invited session organization Dec 20, 2021 Paper submission deadline Jan 28, 2022 Notification of acceptance March 25, 2022 Proceedings: Accepted papers in categories S1 and S2 will be published in the proceedings. A SCOPUS and DBLP indexed Springer book will be published for accepted long papers. Proceedings will be available at the conference. -- ********************************************************************** OLA'2022 International Conference on Optimization and Learning (SCOPUS, Springer) 18-20 July 2022, Syracuse, Sicilia, Italy http://ola2022.sciencesconf.org *********************************************************************** Prof. El-ghazali TALBI Polytech'Lille, University Lille - INRIA CRISTAL - CNRS

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Lab technician position in SeqBiome
by Claesson, Marcus 10 Jan '22

10 Jan '22

Do you want to work in a dynamic and growing microbiome spin-out company? Do you have experience of DNA extraction, amplification and NGS library preparation and/or equivalent molecular microbiology experience (ideally to at least MSc level)? We are now hiring a Lab Technician, either on a full-time or part-time basis. Please send you CV and a cover letter with references to info(a)seqbiome.com<mailto:info@seqbiome.com> before the 24th Jan. -- Marcus Claesson Chief Executive Officer +353 (0)87 7592733 [cid:image001.jpg@01D7EDB0.A27591C0]<http://www.seqbiome.com/>

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Full tenured Prof in Cancer Bioinformatics (deadline next Monday 10 Jan!)
by Laurent Gatto 07 Jan '22

07 Jan '22

Professor in Cancer Bioinformatics Job ID: 047988. Deadline: 12 noon GMT/7am EST/11am CEST on Monday Jan 10th next The official job description, details and application form are at http://ul.ie/hrvacancies/ I recently moved to UL, and we launched the Limerick Digital Cancer Research Center, which brings together oncology, digital pathology, data science, AI/ML and technological research and the University Hospital. We have a bold vision to develop clinically impactful digital cancer research and broad areas of interest include 3D digital pathology, cancer organoids, tumor-immune, tumor microenvironment, viral cancer biology, integrative analysis of single cell ‘omics data, proteomics, transcriptomics, MS/MS metabolomics, wearable technology data with clinical and other data. It is leveraging UL’s research leadership in software engineering, math, data science, AI/ML, industry 4.0/digital twin technology, real-time in vivo monitoring, biomaterials, nanotechnology, drug-delivery and materials science. UL runs several undergrad, masters and professional degrees in R programming/data science and other software languages, providing students skilled to engage in biostatisticial, computational and bioinformatics research. Candidate should be willing to engage in innovative cutting-edge science across disciplines. Candidates from academic, industry or non-traditional career paths are encouraged. Happy to talk to anyone about the position. Best Aedin -- Aedín C. Culhane, Ph.D. Professor of Cancer Genomics School of Medicine, GEMS3-007 University of Limerick Limerick, V94 T9PX Ireland aedin.culhane(a)ul.ie (she/her/hers) [I work flexible hours across several time zones. I don't expect you to read or respond to my emails outside of your normal working hours]

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