February 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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Registration open for: BioSB RNA-seq data analysis course - 9-13 May 2022 in Breda, The Netherlands
by Femke Francissen 29 Mar '22

29 Mar '22

*BioSB RNA-seq data analysis course* Date: 9-13 May 2022 Location: Breda, The Netherlands Organizers: BioSB research school, Erasmus Medical Center and Avans Hogeschool Website: https://www.dtls.nl/courses/rna-seq-data-analysis-2022/ --> *registration is open!* *Course coordinators* Andrew Stubbs, Erasmus MC Miaomiao Zhou, Avans University of Applied Sciences *Course credits* 1.5 ECTS *Course overview* This course covers the basic concepts and methods required for RNA-seq analysis. Particular attention is given to the data analysis pipelines for differential transcript expression and variant calling. Presentations are followed by hands-on computer sessions using Linux command line tools, Galaxy and R to directly apply and get more insight in the analysis methods. One afternoon is dedicated to the analysis of a new data set, allowing the students to refresh and extend their analysis skills. Students can also bring their own RNA-seq data for practicing. We will also explore the potential of long-read based RNA-seq in a Friday afternoon literature club. After the course, the presentations, practicals and test data will remain available for future reference. Software packages used are freeware. *Target audience* Participants for the RNA-seq course should preferably have participated in a general next-generation sequencing (NGS) course or otherwise have some hands-on experience with NGS data analysis. The course is aimed at PhD students and post-docs, but scientific programmers and data analysts with a background in biology and bioinformatics may also attend. *Learning outcomes* After having followed this course: - The participant has insight into the issues involved in good experimental design of RNA-seq experiments. - The participant knows and can perform analysis steps in reference-based and de novo RNA-seq data analysis, and visually present and judge the results for: - quality control and preprocessing, - finding differentially expressed genes, - variant calling, - cluster analysis, - classification analysis, - pathway testing. - The participant has insight in various RNA-seq platforms, their specificity in solving certain biological questions, and the bottlenecks in these applications. - The participant has insight into the different algorithms and options available to perform an analysis, and can make an informed choice. - The participant knows the pitfalls of existing analyses and is able to critically judge the statistical analysis of RNA-seq data performed by others. Read more and register now via: https://www.dtls.nl/courses/rna-seq-data-analysis-2022/ BioSB research school www.dtls.nl/biosb education(a)biosb.nl [image: signature_1684185780] <https://www.dtls.nl/biosb/>

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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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Open roles at AstraZeneca
by Sergio Martinez Cuesta 28 Feb '22

28 Feb '22

Dear all, For those of you reaching your end of contract, the following open positions at AstraZeneca may be of interest: *Senior Bioinformatician for Oligonucleotide Therapeutics* Gothenburg (Sweden) Deadline for applications: February 28th https://careers.astrazeneca.com/job/gothenburg/senior-bioinformatician-for-… *Senior Bioinformatics Scientist – Knowledge Graph and Networks* Cambridge (UK) Deadline for applications: March 12th https://careers.astrazeneca.com/job/cambridge/senior-bioinformatics-scienti… *Senior Bioinformatician for Therapeutic Gene Editing* Gothenburg (Sweden) Deadline for applications: March 12th https://careers.astrazeneca.com/job/gothenburg/senior-bioinformatician-for-… *Bioinformatician - Proteomics* Cambridge (UK) Deadline for applications: - https://careers.astrazeneca.com/job/cambridge/bioinformatician-proteomics-u… Best wishes, Sergio

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Reminder Research Software Engineers Survey - still one week for submission
by Alexander Botzki 28 Feb '22

28 Feb '22

Dear all, I'd like to send you the link for a survey which a number of international supporters for Research Software Engineering have put together recently. Our effort has been lead by Simon Hettrick from the Software Sustainability Institute. A blog about the results from 2018 is here: https://www.software.ac.uk/blog/2019-02-15-rse-survey-2018-results We would be delighted to have as many as possible answers from persons who write software used in research. So, please have a look at this link for more information and the questions: https://softwaresaved.limequery.com/386272?lang=en The survey will stay open for one more week. Thanks a lot for your consideration. Best regards, Alex Alexander Botzki - Head of VIB Bioinformatics Core, ELIXIR Belgium Training Coordinator VIB Bioinformatics Core Technologiepark-Zwijnaarde 75 9052 Zwijnaarde Belgium tel +32 9 224 9870 https://vib.be/labs/vib-bioinformatics-core/research | https://www.bits.vib.be | @vibbioinfocore Alexander Botzki – Head of VIB Bioinformatics Core, ELIXIR Belgium Training Coordinator VIB Bioinformatics Core Technologiepark-Zwijnaarde 75 9052 Zwijnaarde Belgium tel +32 9 224 9870 https://vib.be/labs/vib-bioinformatics-core/research | https://www.bits.vib.be | @vibbioinfocore [signature_351744268]

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[Could not verify sender] Position for: Postdoctoral researcher in Medical Genetics/Bioinformatics
by Berry Kriesels 24 Feb '22

24 Feb '22

Dear all, We want to draw your attention to our vacancy for a postdoctoral researcher position in Medical Genetics/Bioinformatics. See attached. With kind regards. *Berry Kriesels* - Founder / General director *Omnigen* Bioinformatics research, services and consultancy. Papsouwselaan 119-A 2624AK Delft, 3rd floor b.kriesels(a)omnigen.nl | +31616750561 | www.omnigen.nl

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PhD position in bioinformatics: mechanisms of genetic interactions in pediatric cancer
by Kemmeren-2, P.P.C. (Patrick) 24 Feb '22

24 Feb '22

Dear all, Happy to share that we have an opening for a PhD student in bioinformatics working on understanding mechanisms of genetic interactions in pediatric cancer! Interested in working on this topic and be part of a unique pediatric oncology center with multidisciplinary and dynamic environment, then please apply through the link below: https://werkenbijprinsesmaximacentrum.nl/vacature/phd-student-bioinformatic… Regards, Patrick -- Patrick Kemmeren, PhD Principal Investigator & head Big Data Core Princess Máxima Center Associate Professor UMC Utrecht T +31 (0)88 972 90 00 | M +31 (0)6 53 11 25 53 [signature_1113111550] [signature_1581634270] Princess Máxima Center for Pediatric Oncology Heidelberglaan 25 | 3584 CS Utrecht | T +31 (0)88 972 90 00 | > Website<https://research.prinsesmaximacentrum.nl/en/research-groups/kemmeren-group>

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Software engineer - multi-omics data management
by Laurent Gatto 22 Feb '22

22 Feb '22

Dear all, There's a software engineer position open in my group to develop a multi-omics data management platform. The project is in collaboration with Sébastien Jodogne from the EPL (Engineering school at UCLouvain) and a large multi-disciplinary team (including clinicians from the university hospital) at in Brussels. Details and application: https://jobs.uclouvain.be/PersonnelAdministratif/job/Ing%C3%A9nieur%C2%B7e-… Do not hesitate to get in touch if you have any questions. Best wishes, Laurent --- Prof Laurent Gatto Computational Biology Unit (CBIO) de Duve Institute - UCLouvain Avenue Hippocrate, 75 - bte B1.74.10 1200 Brussels, Belgium Tel: +32 (0)2 764 74 15 http://lgatto.github.io/about

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Open position: Data Governance Bioinformatics (m/f/d)
by Erick Antezana 22 Feb '22

22 Feb '22

*apologies for cross-posting* Become part of our team of highly motivated data science experts (m/f/d) to solve major challenges in modern crop protection by molecular and chemical genetics approaches. In this role you´ll be involved in developing a master data strategy for OMICs data and drive data curation and integration. Join us at Bayer to work on purposeful projects to bring our mission to life: “Health for all and Hunger for none”. YOUR TASKS AND RESPONSIBILITIES - You will develop and implement a data governance strategy for OMICs technologies in coordination with IT and semantics technology experts (m/f/d) - You will manage data maintenance, identify relevant data sources, and ensure data quality in terms of completeness, format, and consistency - You will contribute to product and platform teams in demand planning, prioritization and monitoring the use of services within project requests towards our partner - You will build cross-functional relationships to partner with the business stakeholders (m/f/d) and collaborate with Bayer’s Data Science community to co-develop innovative solutions - You will present your results in compelling stories to various stakeholders (m/f/d) to create both strategic and operational changes in business WHO YOU ARE - You have a PhD or MSc with first experience in bioinformatics, computational biology, computer science, physics or related fields - You are experienced in OMICS data and Meta-data management and able to support innovation and future-oriented data concepts - Molecular and/ or Cellular Biology experience is a plus (preferably in insects, plants and fungi) - You are experienced with relational and/or Graph Databases and proficient in using querying languages such as SQL & SPARQL - You have excellent scripting and programming skills in common Data Science languages such as R, Perl, Python (Django framework) - You have a strategic mindset and a result-oriented, motivated, and proactive personality with proven ability to efficiently work in cross-functional teams reaching joint goals You have good communication skills in English, both written and spoken; a good working knowledge of the German or French language can be beneficial This position is initially limited to two years. https://karriere.bayer.de/en/job/data-governance-bioinformatics-m-f-d--SF55… You can contact me in case of questions.

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Job opportunity at NIZO | Sr. Data Scientist Management and Bioinformatics
by MA groupbox 22 Feb '22

22 Feb '22

Dear all, We would like to inform you about a new job opportunity offered by NIZO food research. Link here https://www.nizo.com/careers/senior-scientist-data-management-and-bioinform… We would appreciate that you share this information with your contacts. Sincerely, HR Department NIZO | T +31 318 659 511 A Kernhemseweg 2, 6718 ZB Ede, NL | P.O. Box 20, 6710 BA Ede, NL | [cid:image001.jpg@01D827F5.78A32C20] <https://www.linkedin.com/company/nizo-food-research/>

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