April 2020 - 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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ESCS 2020 | Abstract submission is open
by ESCS 11 Jun '20

11 Jun '20

[image: ESCS2020_banner-notPaint.png] Dear all, The abstract submission process for the *European Student Council Symposium 2020 (ESCS 2020)* is open! The ESCS 2020 will take place on *6th September 2020 in Sitges, Spain* directly preceding the opening of the European Conference on Computational Biology (ECCB 2020). The ESCS provides a forum for students and young researchers in the fields of Bioinformatics and Computational Biology to meet, present their work in front of an international audience, build a network within the computational biology community and obtain opportunities that can contribute to the development of their scientific career. In this scope, we invite all participants to submit *an abstract for an oral or poster presentation*. The submission deadline for abstracts is: *11th June 2020*. You can find all relevant information about ESCS 2020 here: *https://www.escs2020.iscbsc.org/ <https://www.escs2020.iscbsc.org/>*. For any further inquiries don't hesitate to contact us at *escs(a)iscbsc.org <escs(a)iscbsc.org>*. Best regards, Gabriel Olguín Orellana, chair ESCS 2020 Sofia Papadimitriou, co-chair ESCS 2020

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BSC: Life Sciences offer
by BSC Human Resources 29 Apr '20

29 Apr '20

Dear all, We would like to inform you about a new job opportunitiy offered by BSC: - Bioinformatics Data Analyst (RE2). Deadline: 31 May, 2020 Link here <https://www.bsc.es/join-us/job-opportunities/10420lscbre2> 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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BSC STARS postdoctoral programme call until 14th July
by Alba Jene 28 Apr '20

28 Apr '20

Dear, At the Barcelona Supercomputing Center we are looking for 6 outstanding postdoctoral researchers within the STARS COFUND call of the Marie Sklodowska Curie Actions within the Horizon 2020 Programme: https://www.bsc.es/join-us/excellence-career-opportunities/stars. Deadline 14th July 2020. Four of these positions are available at the Life Sciences Department; if you are interested to know more please visit the website, and do not hesitate to contact me if you have any questions/want to know more about the groups offering a position. Best, -- Alba Jené Sanz, PhD Bioinformatics Unit Coordinator Barcelona Supercomputing Center (BSC) <https://maps.google.com/?q=C/+Jordi+Girona+29,+08034-Barcelona,+Spain&entry…> C/ Jordi Girona 29, 08034-Barcelona, Spain http://life.bsc.es/compbio <https://www.bsc.es/sites/default/files/public/newsletter/other/imatge-rrhh.…> Third Call for STARS PROGRAMME APPLICATIONS ! Dear all, We have officially open the Third Call for Applications to our SupercompuTing And Related applicationS Fellows Programme ! See the BSC News: HERE <https://www.bsc.es/news/bsc-news/bsc-will-incorporate-6-outstanding-post-do…> Don´t hesitate to share the information in your network and to apply if you are interested. Deadline for applications: 14th of July 2020 at 11PM CET. You can find more information about the requirements and conditions here: https://www.bsc.es/join-us/excellence-career-opportunities/stars Have a good day, Regards, The HR Team <https://www.bsc.es/> BSC is a public consortium made up of <http://empresa.gencat.cat/> <http://www.ciencia.gob.es/portal/site/MICINN/> <https://www.upc.edu/> <https://ec.europa.eu/regional_policy/en/funding/erdf/> http://bsc.es/disclaimer

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BSC: Life Sciences vacancy
by BSC Human Resources 28 Apr '20

28 Apr '20

Dear all, We would like to inform you about a new job opportunitiy offered by BSC: - Research Engineer (RE2). DeadlMayine: 31 , 2020 Link here <https://www.bsc.es/join-us/job-opportunities/10020lsinbre2> 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 Community Conference: Abstract submission and registration are open
by Dave Clements 27 Apr '20

27 Apr '20

2020 Bioinformatics Community Conference (BCC2020) Online, July 17-26 https://bcc2020.github.io/ The 2020 Bioinformatics Community Conference (BCC2020) <https://bcc2020.github.io/> will be online, global, affordable, and accessible. Key Dates: May 8: Deadline for submitting talk/poster/demo abstracts <https://bcc2020.github.io/submit/> (this will not be extended) June 6: Authors notified about talk/poster/demo acceptance July 10: Early registration <https://bcc2020.github.io/Registration/> ends July 17-19: BCC2020 Training sessions <https://bcc2020.github.io/training/> July 19-22: BCC2020 Main meeting <https://bcc2020.github.io/schedule/> July 22-24, 24-26: CollaborationFest Core and Encore <https://bcc2020.github.io/cofest/> BCC2020 BCC2020 <https://bcc2020.github.io/> is a joint event bringing together the Bioinformatics Open Source Conference (BOSC) <https://www.open-bio.org/events/bosc/> and Galaxy <https://galaxyproject.org/> Communities. If you are working in data intensive life science research then there is no better event for sharing your work, and learning from other researchers addressing the challenges of modern data driven biology. BCC2020 will be held July 17-26 <https://bcc2020.sched.com/>, and offer 2 days of training <https://bcc2020.sched.com/overview/type/Training>, a 3 day meeting <https://bcc2020.sched.com/overview/type/Meeting>, and a 4 day CollaborationFest <https://bcc2020.sched.com/overview/type/CoFest>. BOSC is organized by the Open Bioinformatics Foundation (OBF) <https://www.open-bio.org/>, a non-profit group dedicated to promoting the practice and philosophy of open source software development and open science within the biological research community. Galaxy <https://galaxyproject.org/> is an open source data integration and analysis platform for the life sciences that is used, deployed, maintained and extended by a worldwide community of researchers, students, software engineers, and infrastructure providers. BCC2020 is Online All BCC2020 events will be held online <https://bcc2020.github.io/blog/going-virtual>. Training will be live and interactive. The meeting will feature keynotes, accepted talks, lightning talks, posters, demos, and birds-of-a-feather and other networking opportunities. Talks (with the possible exception of keynotes) will be pre-recorded. Posters, demos, and BoFs will be live and interactive. The CoFest will also be live and interactive. BCC2020 is Global BCC2020 events will be held twice <https://bcc2020.github.io/blog/going-global>: once in the originally scheduled Toronto time zone (BCC West) <https://bcc2020.sched.com/venue/West>, and then again 12 hours later in the Eastern hemisphere (BCC East) <https://bcc2020.sched.com/venue/East>. Training will differ between East and West, with enrollment open to all, regardless of where you are. The main conference content will be presented in both East and West. We are striving to have the CoFest run continuously <https://bcc2020.sched.com/overview/type/CoFest>, with participants from every part of the world. BCC2020 is Affordable We have slashed registration rates for BCC2020 <https://bcc2020.github.io/Registration/>, and are offering even larger discounts to participants based in low and lower-middle income countries. Pricing starts at US$3 per training session, and $12 for the 3 day meeting. The CoFest <https://bcc2020.github.io/cofest/> is free. BCC2020 is Accessible Going online and global, combined with the low registration rates this enables, makes this the most accessible Galaxy or BOSC conference ever. If you work in open source bioinformatics then this is 2020’s best opportunity to share your work and learn from others. Abstracts Due May 8 BCC2020 is seeking oral presentations, lightning talks, posters, and demos, from researchers working in bioinformatics, and all over the world. Abstracts are due May 8 (and that deadline will not be extended). Please submit your work <https://bcc2020.github.io/submit/> today. Register Now BCC2020 registration is now open <https://bcc2020.github.io/Registration/>. Registering early saves 50% off of the full rates. We hope to see you in July at BCC2020, BCC2020 Organizers -- https://galaxyproject.org/

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Postdoc in Multi-omics data integration for systems vaccinology
by Yvan Saeys 23 Apr '20

23 Apr '20

A joint postdoctoral research position in the area of multi-omics data integration is available between the Saeys lab atVIB <http://www.vib.be/en/Pages/default.aspx>and GSK. The successful candidate will apply state-of-the-art machine learning and statistical tools for integrating several types of omics and classical immune data in the area of vaccine research. About the lab TheSaeys lab <http://www.vib.be/en/research/scientists/Pages/Yvan-Saeys-Lab.aspx>at theVIB-UGent Center for Inflammation Research <http://www.vib.be/en/research/departments/Pages/VIB-UGent-Center-for-Inflam…>studies the design and application of data mining and machine learning techniques for biomedical applications. The lab is renowned for its research on single-cell technologies, including flow and mass cytometry, single-cell RNA sequencing, and is currently pioneering novel single-cell technologies including spatial transcriptomics and single-cell multi-omics (e.g. CITE-seq). GSK is a science-led global healthcare company with a mission: to help people to do more, feel better, live longer. Belgium is the heart of GSK Vaccines, with three major vaccine sites, in Wavre, Rixensart and Gembloux, including the global headquarters from the vaccines division of the group. That also means we represent the largest industrial network of vaccines worldwide. The translational research team in the R&D department focuses on complex immunological questions in order to improve vaccines and vaccine strategies. Your project GSK conducted a clinical research study for exploring in depth the mechanisms of action of adjuvant systems. Adjuvant systems are used to improve vaccine immunogenicity and efficacy by enhancing antigen presentation to antigen-specific immune cells with the aim to confer long-term protection against targeted pathogens. We are interested in applying integrative data analysis approaches to characterize the antibody quality profile measured after vaccination. In this research project the main objectives are two-fold: in a first step we want to perform an exploratory study that integrates different data types to paint a better picture of the antibody quality profile for the different adjuvanted vaccines. In a subsequent analysis we want to link these antibody quality profiles to specific responses in the innate and adaptive immune system using a complementary set of read-outs. Profile * PhD in bioinformatics, computational biology, computer science, bioengineering or similar * Background in data mining, machine learning and statistics * Working proficiency in appropriate programming languages and software (eg. R, Python) * High intrinsic motivation and a strong scientific curiosity. * Willingness to work across academy (VIB-Ghent University) and industry (GSK) * Willingness to work at different locations (Ghent, Rixensart) * Team player that can work independently in a multidisciplinary (international) team. * Excellent oral and written English communication skills. * Proactive, flexible, and problem-solving attitude. We offer * A full-time contract for two years at the interface of a state-of-the-art research institute and a top pharmaceutical company * A stimulating (international, multidisciplinary) research environment where quality, professionalism and team spirit are encouraged. * The ability to work on unique data in the area of systems vaccinology *The position is immediately available.* How to apply? Please apply online via https://vibvzw.jobsoid.com/j/26795/gsk-postdoc-in-multi-omics-data-integrat… Please complete the online application procedure and include a detailed CV incl. list of publications, a motivation letter and the contact information of three referees. For more information contact Yvan Saeys <mailto:yvan.saeys@ugent.be>. For more information: * Website: http://www.vib.be/en/research/scientists/Pages/Yvan-Saeys-Lab.aspx -- =============================================================================== Prof. dr. Yvan Saeys VIB Group Leader Data mining and modeling for biomedicine UGent Department of Applied Mathematics, Computer Science and Statistics Krijgslaan 281, S9, B-9000 Gent Inflammation Research Center, a VIB-UGent Department Technologiepark-Zwijnaarde 71 , B-9052 Zwijnaarde , Belgium Tel : +32(0)9 331 37 40 Fax : +32(0)9 221 76 73 Mailto: yvan.saeys(a)ugent.be http://www.dambi.ugent.be ===============================================================================

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vacancy for an assistent professor bioinformatics @ Utrecht
by Berend Snel 21 Apr '20

21 Apr '20

Dear computational biologists, To strengthen our team and our educational mission, we are seeking a driven and enthusiastic colleague. Are you an ambitious and inspirational educator with a background in bioinformatics, demonstrated teaching experience, and a clear vision on academic education in an international classroom? Do you want to contribute to, and develop new bioinformatics courses, mentor and coach students at levels ranging from BSc to PhD? Besides education you will have the opportunity to be involved in research, either ongoing projects or personal interest. You will be embedded within a diverse and collaborative community of Bioinformatics Teachers and Researchers across the Utrecht Science Campus. For more information and to apply please see: https://www.uu.nl/organisatie/werken-bij-de-universiteit-utrecht/vacatures/… best wishes, Berend Snel, PhD Professor Bioinformatics Theoretical Biology and Bioinformatics Department of Biology Science Faculty Utrecht University Email: b.snel(a)uu.nl

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Closing soon: PhD positions in Bioinformatics and Biophysics and Junior Teacher Bioinformatics
by Sanne Abeln 20 Apr '20

20 Apr '20

Dear All, Please find information below about two PhD position and one junior teaching position in our group the VU Amsterdam: 1) in Bioinformatics and Neurochemistry and 2) in Biophysics and Molecular Modelling and 3) a junior teacher in Bioinformatics. The PhD positions are part of a large european collaborative project, MIRIADE <https://miriade.eu/>, aiming for novel approaches in biomarker discovery for dementias. More information on the position in Bioinformatics and Neurochemistry can be found here: https://workingat.vu.nl/ad/miriade-esr2-phd-position-in-bioinformatics-and-… *closing date: 30-04-2020* More information on the position in biophysics and molecular modelling can be found here: https://workingat.vu.nl/ad/miriade-esr3-phd-position-in-biophysics-and-mole… *closing date: 30-04-2020* More information on the *Junior Teacher in Bioinformatics* position can be found here, it is a position that is suitable if you have just finished an MSc in Bioinformatics: https://workingat.vu.nl/ad/junior-teacher-bioinformatics/q8x4y5 *closing date*: *30-04-2020* Candidates for the PhD positions: - Must not already hold a PhD; - Must be within the first four years (full-time equivalent) of their research career; - Must not have resided or carried out their main activity (work, studies, etc.) within the Netherlands for more than 12 months in the three years immediately prior to their recruitment. Best wishes, Sanne -- Sanne Abeln Associate Professor Bioinformatics - VU University Amsterdam s.abeln(a)vu.nl +31 20 59 87816 www.few.vu.nl/~abeln

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