- BBClist - maillist.psb.ugent.be

Postdoc & PhD positions available in single-cell regulatory genomics
by Stein Aerts 02 Feb '22

02 Feb '22

Dear Bioinformatics community, We have two fully funded positions (PhD or postdoc) available in the Laboratory of Computational Biology (http://www.aertslab.org) in Leuven. You can join us in our quest to decipher the genomic regulatory code, using a combination of single-cell ATAC-seq, single-cell RNA-seq, and spatial transcriptomics. Central to this work will be the use of computational and machine-learning methods. Depending on your interest, you can also be involved in the wet-lab experiments, to perform single-cell sequencing experiments, technology development, and single-cell CRISPR screens. In both projects you will also have opportunities to explore connections with industry, particularly related to gene therapy. Project 1: the human brain In this project you will develop new computational strategies to identify human genetic variation linked to cell state changes in the human brain, with a particular focus on brain regions affected by Parkinson’s disease. You will use and combine large in-house atlases of single-cell multi-ome data (scATAC-seq + scRNA-seq) with spatial gene expression, Fiber-seq, and whole-genome sequencing (with long read) data. You will also get the opportunity to explore new analysis methods using deep learning. Check out our recent work on decoding gene regulation in the fly brain (Janssens, Aibar & Taskiran, Nature 2022). This project is funded by Aligning Science Against Parkinson’s Disease (ASAP) and brings you in contact with a vibrant international community of neuroscientists. Vacancy: https://jobs.vib.be/j/39320/computational-postdoc-single-cell-regulatory-ge… Project 2: tumor heterogeneity You will study enhancers and dynamic regulatory programs underlying cancer cell plasticity, and investigate how cancer cell states are affected by cell-cell communication within the tumor microenvironment. Check out our recent work on cancer regulatory genomics: a melanoma single-cell atlas of phenotype switching, by Wouters et al., (Nat Cell Biol 2020), and the deep learning models DeepMEL and DeepMEL2 (Minnoye & Taskiran, Genome Research 2020; Kalender Atak & Taskiran, Genome Research 2021). This project is part of our newly funded EOS consortium with the Blanpain, Marine, Lagae, and Saeys labs, so plenty of collaboration opportunities. Vacancy: https://www.kuleuven.be/personeel/jobsite/jobs/60089060 More info? Check out our website (https://aertslab.org) and our publications https://aertslab.org/#publications. Interested? Apply through the vacancies above, or drop me an email if you want to discuss further. Cheers, Stein Stein Aerts, PhD KU Leuven Professor & VIB Group Leader Laboratory of Computational Biology Herestraat 49, P.O. Box 602 3000 Leuven, Belgium Office +32 16 330710 Lab + 32 16 330142 Mobile +32 486 659003 http://www.aertslab.org

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vacancy bioinformatics scientist @ new spin-off company ImmuneWatch
by Kris Laukens 02 Feb '22

02 Feb '22

Dear colleagues, ImmuneWatch is a new bioinformatics spin-off company from the University of Antwerp and Antwerp University Hospital (Belgium). At ImmuneWatch we aim to accelerate the development of T-cell based diagnostic tools and therapies. Our mission is to make immune repertoire sequencing data interpretable and actionable by annotating T cell receptors in a clinically meaningful way. To achieve this goal, we are looking for a bioinformatics scientist who will help build and improve the products that will serve our first customers, in close collaboration with the rest of our team. See the complete job add in attachment or visit our website<https://www.immunewatch.com/careers/bioinformatics-scientist/>. Thanks for distributing the vacancy to possible candidates. Kind regards, Kris Laukens

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Presentation of Dr. Marek Ostaszewski on "COVID-19 Disease Map" at TransMed webinar series for the ISCB academy, February 1st, 11:00 AM EST
by Irina-Afrodita BALAUR 01 Feb '22

01 Feb '22

Dear all, We are very happy to let you know that we will start our TransMed webinar series for the ISCB academy today with Dr. Marek Ostaszewski from Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, who will present the “COVID-19 Disease Map: building a computational repository of SARS-CoV-2 virus-host interaction mechanisms”! Details on the registration at: https://www.iscb.org/iscbacademy-upcoming#ostaszewski. We are looking forward to meeting you today 11:00 AM EST. Abstract: Disease Maps are computational and visual knowledge repositories constructed to catalogue, standardise, and model disease-related mechanisms. They allow to bridge the knowledge gap between biomedical experts and the computational biologists towards contextualised data analysis and modelling of a given pathophysiology. Disease Maps are built using graphical and computational Systems Biology standards and can be used as interactive knowledge repositories, platforms for visual analytics of omics datasets, or integrated into large-scale computational workflows. With the global impact of COVID-19, we organised a community effort to develop a COVID-19 Disease Map to help researchers worldwide to study the mechanisms of the SARS-CoV-2 – host interactions. Our effort engaged over 250 members, contributing as domain experts, diagram curators, analysts, and modellers. This talk will discuss the challenges of community biocuration and integration of a plethora of resources, from Systems Biology diagrams, through interaction databases and text mining results to modelling pipelines of varying granularity. Best regards, The TransMed COSI organizers — Irina Balaur PhD. Postdoctoral Researcher Bioinformatics Core Luxembourg Centre For Systems Biomedicine (LCSB) UNIVERSITÉ DU LUXEMBOURG Campus Belval, House of Biomedicine II 6, avenue du Swing L-4367 Belvaux irina.balaur(a)uni.lu http://lcsb.uni.lu ----- This message is confidential and may contain privileged information. It is intended for the named recipient only. If you receive it in error please notify me and permanently delete the original message and any copies. -----

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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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