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

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

04 Jun '24

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

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NERC Bursaries for Edinburgh Genomics Courses
by TRAIN edgenomics-training 02 Mar '22

02 Mar '22

Dear All We are pleased to announce we have a number of bursaries available to cover up-to the full fees of any of our upcoming bioinformatics courses. These bursaries are available to UK based students or researchers funded by the NERC or working on research that falls under the remit of the NERC (https://nerc.ukri.org/research/portfolio/remit/) Bursaries are available for any of our courses (see below) but are available for a LIMITED TIME ONLY: They are available for any course booked BEFORE 27th MARCH. So please don't wait to sign up! Our upcoming courses: Linux for Genomics, 13th March - An introduction to working on the command line, running commands and handling data relevant to bioinformatics. https://genomics.ed.ac.uk/services/linux-genomics R for Genomics, 14-15th March - An introduction to the statistical environment R, taking you from the very basics to writing basic functions and creating beautiful figures with ggplot2 https://genomics.ed.ac.uk/services/r-genomics Introduction to Python for Biologists, 18-22 March - This introductory course gives an overview of the language with an emphasis on practical problem-solving, using examples and exercises drawn from various aspects of bioinformatics work. https://genomics.ed.ac.uk/services/introduction-python-biologists-0 Data Manipulation and Visualisation with Python, 08 - 12 April - Python has a many high-quality libraries for working with scientific data. In this workshop we will see how to leverage these libraries to efficiently work with and visualise large volumes of data. https://genomics.ed.ac.uk/services/data-manipulation-and-visualisation-pyth… Introduction to RNA-seq Data Analysis, 9-10th May - This two-day course takes you through a tried-and-tested workflow for analysing RNA-seq data, from read mapping and QC to differential expression and result visualisation. https://genomics.ed.ac.uk/services/introduction-rna-seq-data-analysis If you think you are provably eligible for one of these bursaries, sign up to your desired course through the link provided and we will be in contact regarding fees. Kind Regards Nathan Medd Training and Outreach Manager - Edinburgh Genomics G.06, Ashworth Laboratories, Charlotte Auerbach Road, The King's Buildings, The University of Edinburgh, EH9 3FL, Edinburgh, Scotland Edinburgh Genomics' Privacy Notice can be viewed at: http://genomics.ed.ac.uk/about-us/privacy-notice This email and any attachments are confidential and intended solely for the use of the recipient(s) to whom they are addressed. If you have received it in error, please destroy all copies and inform the sender. The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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ISMB/ECCB 2021 CompMS – Save the date & call for proposals
by Wout Bittremieux 30 Mar '21

30 Mar '21

— ISMB/ECCB 2021 CompMS – Save the date & call for proposals — Dear colleagues, Please join us during the virtual ISMB/ECCB 2021 conference for the Computational Mass Spectrometry (CompMS)COSI session on July 25–27, 2021. Combining the annual Intelligent Systems for Molecular Biology (ISMB)and the European Conference on Computational Biology (ECCB), this is the world's largest bioinformatics/computational biology conference. Every year it brings together scientists from computer science, molecular biology, mathematics, statistics, and related fields and provides an intense multidisciplinary forum for disseminating the latest developments in bioinformatics/computational biology. The conference fosters fresh dialogues, collaboration and learning opportunities, and is a gathering which shapes the future of the field. With a focus on everyone’s safety, the ISMB/ECCB 2021 conference will be a virtual event. Moving the conference to a state of the art virtual interface will not change what attendees have come to expect from this conference. The virtual interface will only enhance the attendee experience and ensure that more people can enjoy it. At the heart of the scientific program are ISCB’s Communities of Special Interest (COSIs), enabling community involvement and bolstering ISMB/ECCB’s reputation as the leading conference in the field. The CompMS COSIpromotes the efficient, high quality analysis of mass spectrometrydata through dissemination and training in existing approaches and discussion of new, innovative approaches. The CompMS initiative aims to exploit synergies between different mass spectrometry-based application domains, in particular proteomics, metabolomics, and lipidomics. A strong scientific and technical program showcases the best international developments in bioinformatics and computational biology, making ISMB/ECCB 2021 a must attend event. Date: July 25–27, 2021 (CompMS COSI) / July 25–30, 2020 (ISMB/ECCB) Website: https://www.iscb.org/ismbeccb2021 <https://www.iscb.org/ismbeccb2021> Key dates May 6, 2021: Abstract submission deadline May 27, 2021: Talk/poster acceptance notifications June 3, 2021: Late poster submission deadline June 10, 2021: Late poster acceptance notifications July 25–30, 2020: ISMB/ECCB conference Call for proposals Abstract submission for ISMB/ECCB 2021 is now open! Submit your abstract to ISMB/ECCB to present your work at the leading bioinformatics/computational biology conference. Attend the CompMS session to learn about the latest algorithmic advances in computational mass spectrometry. Please remember to select the CompMS COSI as your session of interest upon submitting your abstract. Call for abstracts: https://www.iscb.org/ismbeccb2021-submit/ismbeccb2021-submit-abstracts <https://www.iscb.org/ismbeccb2021-submit/ismbeccb2021-submit-abstracts> We look forward to seeing you at ISMB/ECCB! The CompMS organizing committee. Wout Bittremieux Isabell Bludau Lindsay Pino Timo Sachsenberg

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BioSB 2021 conference - Call for abstracts!
by Femke Francissen 30 Mar '21

30 Mar '21

*Call for abstracts BioSB 2021 conference* You can now submit an abstract for a presentation at the BioSB 2021 conference <https://www.aanmelder.nl/biosb2021/abstract-submission>. The main programme of the conference will feature several parallel sessions that will be set up via abstract selection. - Virtual conference - Date: 15-16 June 2021 - Website: www.aanmelder.nl/biosb2021 - Register here <https://www.aanmelder.nl/biosb2021/registration> *Submission deadlines* - Oral & highlight presentations: *3 May 2021 *- 23h59 (will not be extended!) - Notification date: 17 May 2021 - Posters & demos: 23 May 2021 *Submission topics* - Single cell technologies and applications - Single cell computational biology - Epidemiology - COVID-19 - Omics/Multi-omics - Precision Oncology - Kinetic models - New therapeutics discovery - Clinical genomics - Modeling cell behavior - Evolution & comparative genomics - Immunology - Classical bioinformatics - Imaging - Bioinformatics and systems biology in industry - Metabolomics and metabolic modelling - Metagenomics - Machine learning & AI - Ageing bioinformatics - Biophysics - ELIXIR-NL ELIXIR Netherlands <https://www.dtls.nl/elixir-nl/> will organise a parallel track in the conference programme. Submissions about other services and infrastructure for researchers in the life sciences are also welcome! *Latest news* Confirmed *keynote speakers*: - *Sarah Teichmann*, Head of Cellular Genetics and Senior Group Leader, Sanger Institute - *Edda Klipp*, Professor for Theoretical Biophysics, Humboldt-Universität zu Berlin (HUB) - *Kathleen Marchal*, associated professor dept. of Plant Biotechnology and Bioinformatics, dept. of Information Technology, IMinds, Ghent University *About* The 7th Dutch Bioinformatics and Systems biology conference discusses the latest developments in bioinformatics, systems and computational biology and interrelated disciplines, and their wide-ranging applications in life sciences & health, agriculture, food & nutrition. The conference is organised by the BioSB research school <http://www.biosb.nl> together with the Eindhoven University of Technology <https://www.tue.nl/en/> and the Princess Máxima Center <https://www.prinsesmaximacentrum.nl/en> for paediatric oncology. The conference will be organized as a virtual conference, featuring: - keynote lectures - parallel sessions featuring selected, highlight and invited talks - poster & demo sessions - network breaks *Stay up to date* You can follow us on Facebook or via Twitter: #BioSB2021 or you can subscribe to the BioSB newsletter <https://biosb.nl/newsletter/> to stay up to date about the conference. *Any questions?* Contact Femke Francissen: femke.francissen(a)biosb.nl (event manager)

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Workshop: Plant Transcriptomics using Galaxy
by Kim DE RUYCK 30 Mar '21

30 Mar '21

Dear All, The Galaxy community is organizing a one-week free workshop on Plant Transcriptomics from the 19th to the 23rd of April , with a focus on bulk and single-cell RNA-Seq data analysis in Arabidopsis thaliana . Although it is designed to deal with plant transcriptome data analysis, most of the analysis can be adapted to other organisms too. The workshop will have recorded sessions with live support in chat and is aimed at biologists, researchers or scholars that are interested to know what RNA-Seq analysis is and how Galaxy can be used for that kind of data analysis. For more information and registration , please visit: [ https://docs.google.com/document/d/1Y5MqYmMxFCy7PDImYYuHLhgCKVV7MjoGMr22G2U… | https://docs.google.com/document/d/1Y5MqYmMxFCy7PDImYYuHLhgCKVV7MjoGMr22G2U… ] Please feel free to forward this information to anyone that could find this workshop interesting. Kind regards, Kim De Ruyck Kim De Ruyck PhD Coordinator ELIXIR Belgium VIB-UGent Center for Plant Systems Biology Technologiepark 71, 9052 Ghent, Belgium [ http://www.elixir-belgium.org/ | www.elixir-belgium.org ] [ https://twitter.com/ELIXIRnodeBE | @ELIXIRnodeBE ] [ http://eepurl.com/cl-xOX | Subscribe to our mailing list ]

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BSC: Life Sciences vacancy
by BSC Human Resources 25 Mar '21

25 Mar '21

Dear all, We would like to inform you about a new job opportunitiy offered by Barcelona Supercomputing Center: - Bioinformatics Data Analyst (RE1). Deadline: 30 April, 2021 Link here <https://www.bsc.es/join-us/job-opportunities/1921lsinbre1> 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/> http://bsc.es/disclaimer

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Bioinformatics Vacancy
by John Baker 25 Mar '21

25 Mar '21

Hello, I'm reaching out in regards to the current job vacancy at the NIOO for a bioinformatician. Please feel free to contact Mattias Hollander, < M.deHollander(a)nioo.knaw.nl>. The ad is here: https://www.academictransfer.com/en/298896/bioinformatician-nioo-knaw-wagen… Best, John

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Bioinformatics position at NIOO-KNAW (Wageningen, The Netherlands)
by Hollander, Mattias de 22 Mar '21

22 Mar '21

Research at the Netherlands Institute of Ecology (NIOO-KNAW) is making increased use of high-throughput sequencing methods, including metagenomics, comparative genomics, and transcriptomic research. Also other data-rich research is performed such as metabolomics and R-based simulation modeling. We are looking for a bioinformatician. In this role you will give support to researchers in each of the four NIOO-KNAW research departments. Projects are very diverse, ranging from bacteria and fungi to plants, insects, birds and genetic material recovered directly from soil or other environmental samples. Your task is to interact with researchers, ICT staff and data stewards to facilitate researchers in performing their bioinformatics analyses, both for sequencing-based and other data-rich research. This includes tutoring, helping with data management, building pipelines, providing training, and advising researchers. You will not do research yourself. You will be part of a team with another bioinformatician to give support and advice to researchers during the complete research cycle, develop and give (carpentry) workshops, teaching coding and data science skills to researchers, develop and contribute to existing open-source workflows and learn others how to use them, develop infrastructure consisting of several Linux servers available to researchers, and act as a knowledge hub within the institute by providing documentation and training material. More info, contact & application details: https://www.academictransfer.com/en/298896/bioinformatician-nioo-knaw-wagen… Application deadline: 11 April

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Global Survey for Instructors Who Deliver Training For Life Scientists - Life Science Trainers
by Melquiond, A.S.J. (Adrien) 15 Mar '21

15 Mar '21

Dear colleagues, You still have a few days to fill in the survey over short courses/training in the life sciences. Thank you so much for your participation! Workshops, bootcamps, and short courses are important ways professionals in the life sciences (research, medicine, pharma, etc.) update their skills. If you have instructed life scientists using these types of training, please take this first-ever global survey. We want to highlight the important role of trainers and understand how supporting them can accelerate progress in the scientific field. This 20-minute survey by the lifescitrainers.org<http://lifescitrainers.org> community is available in several languages and will be open until March 20, 2021. Thank you and please share! Survey Links: • English: https://www.surveymonkey.com/r/lifescitraining-en • Arabic: https://www.surveymonkey.com/r/lifescitraining-ar • French: https://fr.surveymonkey.com/r/lifescitraining-fr • Portuguese: https://pt.surveymonkey.com/r/lifescitraining-pt • Spanish: https://es.surveymonkey.com/r/lifescitraining-es Learn more about LifeSciTrainers and join our community: https://lifescitrainers.org/ ------------------------------------------------------------------------ Adrien Melquiond<https://www.uu.nl/staff/ASJMelquiond>, PhD * Coordinator of the Utrecht Bioinformatics Center (UBC) | Hans Freudenthal 0.07 | Budapestlaan 6, 3584CD Utrecht | https://ubc.uu.nl<https://ubc.uu.nl/> | +31.(0)30.2536617 | ubc_AT_uu.nl<mailto:ubc@uu.nl> * Asst. Prof. in Bioinformatics at the Center for Molecular Medicine (CMM), UMC Utrecht | Stratenum 1.304 | Universiteitsweg 100, 3584CG Utrecht | +31.(0)88.75.68790 | a.s.j.melquiond_AT_umcutrecht.nl<mailto:a.s.j.melquiond@umcutrecht.nl> Contact hours: UBC: Tue-Thu | CMM: Mon-Wed-Fri ------------------------------------------------------------------------ Who are we and what do we do? Watch our movie<https://goo.gl/mx1mPN> ------------------------------------------------------------------------------ De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender direct te informeren door het bericht te retourneren. Het Universitair Medisch Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin van de W.H.W. (Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat geregistreerd bij de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197. Denk s.v.p aan het milieu voor u deze e-mail afdrukt. ------------------------------------------------------------------------------ This message may contain confidential information and is intended exclusively for the addressee. If you receive this message unintentionally, please do not use the contents but notify the sender immediately by return e-mail. University Medical Center Utrecht is a legal person by public law and is registered at the Chamber of Commerce for Midden-Nederland under no. 30244197. Please consider the environment before printing this e-mail.

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Opening Conference | March 16th, 18h CET | SEX AND GENDER BIASES IN AI AND HEALTH
by Eva Alloza 15 Mar '21

15 Mar '21

Dear colleagues, Please find below information about the series *"Sex and Gender Biases in AI and Health"* <http://bioinfo4women.bsc.es/sex-and-gender-bias-in-artificial-intelligence-…>organised by the bioinfo4women <http://bioinfo4women.bsc.es> programme (BSC) which will kick-off with the opening conference taking place tomorrow including talks by Alfonso Valencia (BSC, ICREA, INB/ELIXIR-ES) and Maria Teresa Ferretti (Women's Brain Project - WBP). ------------------------------------------------------------------------ *T*he series in *"Sex and Gender Bias in Artificial Intelligence and Health: Building the future for Equality"*, organised by the Bioinfo4women programme of the Barcelona Supercomputing Center and the La Caixa Foundation, kicks off tomorrow, March 16th, and will continue until June 16th, 2021. The program will tackle the problem of sex and gender bias in health and the impact of new technologies, such as personalized medicine and artificial intelligence (AI), from different perspectives. We will discuss and analyze the opportunities these technologies may offer to health, but also the risks that they pose if misused. We invite you to join this challenge, follow the lectures and participate in the debate. It is a unique opportunity to understand and to talk to national and international experts in this field. The opening conference will take place tomorrow, Tuesday *March 16, from 6:00 p.m. to 8:00 p.m. (CET)*. Below you will find all the information about the programme and the links to attend in person or online via streaming. We would appreciate if you could help us spread the word and *disseminate this event among your contacts*. We look forward to your participation for a better future! Series Website: http://bioinfo4women.bsc.es/sex-and-gender-bias-in-artificial-intelligence-… Opening conference: * Streaming in English: https://www.youtube.com/watch?v=tEWtnldJln4 * Streaming in Spanish: https://www.youtube.com/watch?v=mp2JGJaT8fQ * Book your seat to attend the opening conference in person in the Palau Macaya: https://proticketing.com/palaumacaya/es_ES/entradas/evento/19721/session/11… Warm regards, -- -- Eva Alloza Training and Support Officer Spanish National Bioinformatics Institute (INB/ELIXIR-ES) mail: eva.alloza(a)bsc.es web: http://inb-elixir.es Barcelona Supercomputing Center (BSC-CNS) c/Jordi Girona, 31 - Torre Girona Building 08034 Barcelona (Spain) http://bsc.es/disclaimer

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