January 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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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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BSC: Life Sciences vacancy
by BSC Human Resources 28 Jan '22

28 Jan '22

Dear all, We would like to inform you about a new job opportunitiy offered by Barcelona Supercomputing Center: - Research Engineer (RE2). Deadline: 16 March, 2022 Link here <https://www.bsc.es/join-us/job-opportunities/3822lstmre2> 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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Postdoc position in computational biophysics applied to nanomedicine and antibody design - IIT, Genoa, Italy
by Walter Rocchia 26 Jan '22

26 Jan '22

Dear all, the Computational mOdelling of NanosCalE and bioPhysical sysTems – (CONCEPT) lab at the Italian Institute of Technology (Genova, Italy), Italy, invites applications for a Postdoc position in computational biophysics applied to nanomedicine: https://iit.taleo.net/careersection/ex/jobdetail.ftl?lang=en&job=2200000F The project is specifically about developing and applying computational techniques, especially classical molecular dynamics and enhanced sampling, for the in silico design of high affinity and selectivity protein binders. The project will primarily involve the use and development of Molecular Dynamics and Monte Carlo based methods coupled with scoring functions to introduce and develop novel strategies for the design and optimisation of antibody fragments. The ideal candidate is expected to have a strong motivation in applying those computational techniques to problems of medical interest, while their prior knowledge is preferable but not mandatory. A PhD in Chemistry, Physics, or Engineering are required, as well as the knowledge of a programming and/or scripting language. The CONCEPT lab is part of a multidisciplinary collaborative network composed by biologists, chemists, physicists, and engineers working towards speeding up the development of novel clinical protocols and new diagnostic devices by integrating computational and experimental techniques for the design of new nanotechnology solutions of problems of medical interest. We offer a competitive salary and a range of benefits. The application deadline is very close: 2 February 2022, while it is possible that it is extended, we invite interested candidates to register online apply directly to the institute portal here: https://iit.taleo.net/careersection/application.jss?lang=en&type=1&csNo=2&p… For further information and application inquiries feel free write to: Dr. Walter Rocchia Walter.Rocchia(a)iit.it<mailto:walter.Rocchia@iit.it> or visit: https://www.iit.it/it/web/computational-modelling-of-nanoscale-and-biophysi… ********************************************************************* Walter Rocchia, PhD, Head Computational mOdelling of NanosCalE and bioPhysical sysTems - CONCEPT Lab<https://concept.iit.it> ISTITUTO ITALIANO DI TECNOLOGIA Via Melen – 83, B Block, 16152 - Genova, Italy Phone: +39 010 2897418

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ECCB2022 - Call for Tutorials - Call for Workshops/SIGs - Save the dates!
by Eva Alloza 25 Jan '22

25 Jan '22

Dear colleagues, On behalf of the ECCB2022 organising committee, I would to invite you to the *21st European Conference on Computational Biology (ECCB2022)* <https://eccb2022.org>. The calls for Tutorials and Workshops/SIGs proposals are now open until 17th of February. * *Call for Tutorials: **https://eccb2022.org/tutorials/** * * *Call for Workshops/SIGs: **https://eccb2022.org/workshops/* We encourage you to consider submitting your proposals and help us disseminate the open calls among your contacts. Warm regards, Eva Alloza Training and Support Officer Spanish National Bioinformatics Institute (INB) coordination node mail:eva.alloza@bsc.es web:http://inb-elixir.es Barcelona Supercomputing Center (BSC-CNS) Pl. Eusebi Güell, 1-3. E-08034 Barcelona, Spain. ------------------------------------------------------------------------ 21st European Conference on Computational Biology 21st European Conference on Computational Biology <http://mail.eventsairmail.com/ls/click?upn=EU9ggqWL9UGtw-2FWRLoBKrtd8JsjWfs…> Save the dates We are pleased to announce the *21st European Conference on Computational Biology*, which will be held in Sitges (Barcelona, Spain) in hybrid format from the *12th to the 21st of September 2022* Keep me updated <http://mail.eventsairmail.com/ls/click?upn=vTVo9WAROVynOTbDemV86EYQq5tjWxdx…> News trends *Call for Workshops/SIGs & Tutorials is now open!* New Trends in Bioinformatics will take place virtually from the *12th to the 16th of September 2022* and face-to-face on the *18th of September 2022*, immediately preceding the *ECCB2022* main conference. Send your proposals and do not miss the opportunity to be an active part of the conference. *SUBMISSION DEADLINE* *Thu, 17 Feb 2022* I'm an image *Workshops/SIGs* Read the call <http://mail.eventsairmail.com/ls/click?upn=vTVo9WAROVynOTbDemV86JcXNlWtAtMr…> Submit your proposal <http://mail.eventsairmail.com/ls/click?upn=vTVo9WAROVynOTbDemV86GyIs3RJaME8…> I'm an image *Tutorials* Read the call <http://mail.eventsairmail.com/ls/click?upn=vTVo9WAROVynOTbDemV86MM2gSpKarbt…> Submit your proposal <http://mail.eventsairmail.com/ls/click?upn=vTVo9WAROVynOTbDemV86GyIs3RJaME8…> Visit our website for more information *ECCB2022.org <http://mail.eventsairmail.com/ls/click?upn=EU9ggqWL9UGtw-2FWRLoBKrtd8JsjWfs…>* #ECCB2022 <http://mail.eventsairmail.com/ls/click?upn=vTVo9WAROVynOTbDemV86I9M5CnW9VF-…> #ECCB2022 <http://mail.eventsairmail.com/ls/click?upn=vTVo9WAROVynOTbDemV86IIhk8LA29p1…> *Organised by:* BSC <http://mail.eventsairmail.com/ls/click?upn=vTVo9WAROVynOTbDemV86NN8S7iAhePN…> INB <http://mail.eventsairmail.com/ls/click?upn=vTVo9WAROVynOTbDemV86ITKzm0FTLx7…> ELIXIR Spain <http://mail.eventsairmail.com/ls/click?upn=vTVo9WAROVynOTbDemV86ITKzm0FTLx7…> Bco Congresos <http://mail.eventsairmail.com/ls/click?upn=vTVo9WAROVynOTbDemV86IZ8Vkhn8oIW…> Facebook <http://mail.eventsairmail.com/ls/click?upn=vTVo9WAROVynOTbDemV86JXpdeYbu-2F…> Twitter <http://mail.eventsairmail.com/ls/click?upn=vTVo9WAROVynOTbDemV86EaVGS8wj4kB…> LinkedIn <http://mail.eventsairmail.com/ls/click?upn=vTVo9WAROVynOTbDemV86LjbR4s-2BPd…> Instagram <http://mail.eventsairmail.com/ls/click?upn=vTVo9WAROVynOTbDemV86FV50uhrxSD-…> Web Site <http://mail.eventsairmail.com/ls/click?upn=vTVo9WAROVynOTbDemV86IZ8Vkhn8oIW…> E-Mail <mailto:congresos@bcocongresos.com> *TECHNICAL SECRETARIAT* Plaza Europa 17-19, 1st floor 08908 L'Hospitalet del Llobregat, Barcelona (Spain) +34 93 882 38 78 eccb2022(a)bcocongresos.com Policy Privacy <http://mail.eventsairmail.com/ls/click?upn=vTVo9WAROVynOTbDemV86IZ8Vkhn8oIW…> | View Browser <http://mail.eventsairmail.com/ls/click?upn=vTVo9WAROVynOTbDemV86F-2F6kFiVgu…>

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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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