March 2023 - 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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Upcoming BioSB courses!
by BeNeLux bioinformaticians forum 04 Apr '23

04 Apr '23

Dear colleagues, A number of interesting courses from the BioSB Research school are scheduled in the coming months. Please note that two courses still have an early bird rate, so register in time! Knowledge Graphs in the Life Sciences 13 - 17 March, Wageningen NOTE: there are only a few spots still available The first part of the course introduces you to the knowledge, theory, and skills needed to work with Linked Data. We will then focus on research and industrial data applications and needs that are increasingly in demand. The course is aimed at PhD students with a background in biology, computer science or a related field, and life sciences. Participants from the private sector are also welcome. Preparation material will be distributed dug the course. **************************************************** More information about the course can be found here<https://eur04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.dtls.…> Registration can be done here<https://eur04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.aanme…> **************************************************** Molecular Epidemiology of Complex Diseases 12 - 16 June, Maastricht NOTE: deadline early bird rate = 16 April 2023 This course aims to facilitate the acquisition of the essentials of molecular epidemiology: combining information from molecular biomarkers as obtained through omics technologies, with lifestyle and environmental factors, to understand disease occurrence and prognosis in population-based studies. The audience targeted is two-fold, firstly PhD students, postdoctoral fellows, PIs, and all other researchers/R&D staff working in bioinformatics and systems biology, who want to extend, update or refresh their knowledge on this dynamic domain. Secondly, we also invite participants with a(n original) background in epidemiology, biology, biomedical sciences, medicine, statistics, and related fields, who want to become acquainted with this expanding research area. **************************************************** More information about the course can be found here<https://eur04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.dtls.…> Registration can be done here<https://eur04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.aanme…> **************************************************** Algorithms for Biomolecular Networks 26 - 30 June, Wageningen NOTE: deadline early bird rate = 30 April 2023 In this course, we will first give a brief overview of molecular biology, the advent of high-throughput measurement techniques and large databases containing biological knowledge, and the importance of networks to model all this. Next, we will discuss variing network models Building on the network inference methods, a number of ways of integrating various data sources and databases to refine biological networks will be discussed. The course is aimed at PhD students with a background in bioinformatics, computer science or a related field; a working knowledge of basic statistics and linear algebra is assumed. **************************************************** More information about the course can be found here<https://eur04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.dtls.…> Registration can be done here<https://eur04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.aanme…> **************************************************** We hope to welcome you to one of our courses! Kind regards, Petra Aarnoutse Community manager BioSB research school

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4 vacancies INB/ELIXIR-ES at the BSC
by BeNeLux bioinformaticians forum 27 Mar '23

27 Mar '23

Dear BBC list, The INB/ELIXIR-ES <https://inb-elixir.es> coordination node, hosted at the Barcelona Supercomputing Center (BSC <https://www.bsc.es>), is hiring! * *Senior Research Engineer (RE3):* https://www.bsc.es/join-us/job-opportunities/17323lsinbre3 * *Web Front-end Developer (RE2):* https://www.bsc.es/join-us/job-opportunities/17523lsinbre2 * *Bioinformatics Technical Community Engagement Officer (RE2):* https://www.bsc.es/join-us/job-opportunities/17423lsinbre2 * *Junior Research Engineer (RE1):* https://www.bsc.es/join-us/job-opportunities/17223lsinbre1 Applications will be regularly reviewed and potential candidates will be contacted. We are particularly interested for this role in the strengths and lived experiences of women and underrepresented groups to help us avoid perpetuating biases and oversights in science and IT research. Please share as you see fit. Best regards, -- -- Eva Alloza Training coordinator and support officer Spanish National Bioinformatics Institute (INB/ELIXIR-ES) 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

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Call for papers - CIBB 2023: Special session on Distributed computing in bioinformatics and computational biology
by BeNeLux bioinformaticians forum 21 Mar '23

21 Mar '23

CIBB 2023: Special session on Distributed computing in bioinformatics and computational biology Call for papers September 6-7, 2023, Padua, Italy Website: https://cibb2023.dei.unipd.it/call-for-special.html Distributed computing systems have become pivotal in the analysis of bioinformatics data, especially for the investigation of complex biological problems that require intense computational workloads. The usage of distributed computing systems like Apache Spark, in fact, might allow scientific discoveries on bioinformatics data that otherwise would be impossible if the analyses were performed on personal computers. Our special session on "Distributed computing in bioinformatics and computational biology" aims at calling for researchers able to show the potential and the advance of distributed computing resources to make accurate computational analyses in biological datasets. With this special session, we would like to gather scientific contributions aimed at optimizing the usage of distributed computing systems and resources in any bioinformatics, genomics, and proteomics context. The results presented in these studies would be useful and helpful both for the distributed computing experts and for inexperienced users approaching this subject for the first time. *Topics of interest include:* - - Distributed computing systems in genomics and proteomics - - Bioinformatics projects enhanced by distributed computing platforms - - Optimisation of distributed computing systems - - Application of machine learning methods to bioinformatics datasets enhanced through distributed computing - - Protocols for efficient usage of distributed computing systems *Special session organizers:* - Davide Chicco <https://sites.google.com/view/davidechicco> , University of Toronto, Canada - Umberto Ferraro Petrillo <https://sites.google.com/site/umbfer/home> , Sapienza Università di Roma, Italy - Giuseppe Cattaneo <https://docenti.unisa.it/000763/en/curriculum> , Università di Salerno, Italy - Raffaele Giancarlo <https://pure.unipa.it/en/persons/raffaele-giancarlo-4> , Università di Palermo, Italy - Lorenzo Di Rocco <https://phd.uniroma1.it/web/LORENZO-DI-ROCCO_nP1581944_IT.aspx> , Sapienza Università di Roma, Italy - Giorgio Grani <https://research.uniroma1.it/researcher/cf18984a5eefd5ae99d20c71f239ff7d28a…> , Sapienza Università di Roma, Italy *Important Dates* - Short paper submission: April 30, 2023 - - Acceptance/rejection notification: June 9, 2023 - - Camera-ready short paper submission: June 23, 2023 - - Conference: September 6-8, 2023 *Proceedings* The proceedings will not be indexed on Scopus, but, after the conference, the authors of all the accepted short papers presented at the conference will be invited to submit an extended version of their manuscripts to the conference proceedings book in Springer Lecture Notes in Bioinformatics (LNBI) <https://www.springer.com/series/5381>, or to a supplement in a journal such as BMC Bioinformatics <https://bmcbioinformatics.biomedcentral.com/> or BMC Medical Informatics and Decision Making <https://bmcmedinformdecismak.biomedcentral.com/>. -- Lorenzo Di Rocco PhD Student Department of Statistical Sciences La Sapienza - University of Rome P.le Aldo Moro, 5 00185 - Rome, Italy e-mail: lorenzo.dirocco(a)uniroma1.it

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FW: ISMB/ECCB 2023: Call for Submissions!
by BeNeLux bioinformaticians forum 21 Mar '23

21 Mar '23

Hi all, FYI – a message from Patricia Palagi (SIB) regarding abstracts for the ISMB/ECCB in Lyon, France. Best regards, Alex Dear Education COSI colleagues, don't forget to submit your abstracts<https://www.iscb.org/ismbeccb2023-submissions/proceedings> for a talk or poster for the Education COSI track at ISMB/ECCB in Lyon, France! Deadline closing on April 20. Please also mark in your diary several activities related to Training at ISMB/ECCB this year: * on Monday 17 and Tuesday 18 July: six computational biology tutorials <https://www.iscb.org/ismbeccb2023-programme/tutorials> online * on Sunday 23 July: eight computational biology tutorials<https://www.iscb.org/ismbeccb2023-programme/tutorials> in person * on Tuesday 25 July: WEB - Workshop on Education for Bioinformatics around the theme of "IDEAs in Bioinformatics training" (IDEA standing for Inclusivity, diversity etc) * on Wednesday 26 July: Education COSI track with talks and posters (submit your abstract until April 20) I’m looking forward to seeing you in Lyon or online at the conference. Kind regards Patricia Ps: please share this message with your friends and colleagues. -- Patricia Palagi, PhD SIB Training SIB | Swiss Institute of Bioinformatics Quartier Sorge, Bâtiment Amphipôle - 1015 Lausanne - Switzerland patricia.palagi(a)sib.swiss<mailto:patricia.palagi@sib.swiss> - www.sib.swiss<http://www.sib.swiss>

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open positions AZ Delta Roeselare bioinformatics - Molecular Diagnostics CGP WGS Microbial sequencing
by BeNeLux bioinformaticians forum 20 Mar '23

20 Mar '23

Beste, In AZ Delta ziekenhuis, Roeselare, hebben we open posities voor biomedical data crunchers – bioinformatici, zowel op pre-doc als post-doc niveau. Je ontwikkelt, binnen de Dienst Laboratoriumgeneeskunde, pipelines voor genomische analyse van solide tumoren, NIPT en microbiële sequencing. Daarnaast werk je deeltijds op big data modeling binnen het innovatiecentrum RADar van AZ Delta. De resultaten van je werk hebben directe impact op patiëntenzorg, en je krijgt de kans om de lead te nemen in diverse translationele onderzoeksprojecten. Rock and roll en innovatie-gerichte werkomgeving! Dear, At AZ Delta hospital, Roeselare, we are looking for data crunchers/bio-informatics fluent in common languages such as Python/Bash. You will work on genomic data of patients (oncology, microbiology) and develop advanced pipelines for clinical use. You will also work part time on translational research projects and big data modeling in the AZ Delta innovation center, RADar (Google Cloud Customer Award 2022). Dutch language skills required. The lab has extensive sequencing capabilities (MiSeq, NextSeq, NovSeq, ONT) for targeted/CGP and whole genome sequencing. Your job will have a real impact on cutting-edge patient care. - Bio-informaticus (pre-doc): https://bit.ly/3Lmt6rx - Bio-informaticus (post-doc): https://bit.ly/3Fn8eN0 “ Prof. Dr. Geert Martens Met vriendelijke groeten [cid:image71706c.PNG@53e3da57.4b83e58f] Prof. Dr. Geert Martens Laboratoriumgeneeskunde Moleculaire diagnostiek t e geert.martens(a)azdelta.be<mailto:geert.martens@azdelta.be> ◦ w www.azdelta.be<http://www.azdelta.be> Brugsesteenweg 90 ◦ 8800 Roeselare AZ Delta: Campus Rumbeke, campus Brugsesteenweg Roeselare, campus Menen en campus Torhout. Deze e-mail en alle bijlagen bevatten vertrouwelijke informatie die wordt beschermd door het beroepsgeheim en de discretieplicht. Deze informatie is strikt persoonlijk en moet confidentieel behandeld worden. Als deze e-mail niet voor u bedoeld is, mag u de inhoud van deze e-mail niet lezen, kopiëren of doorgeven aan anderen.

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PhD candidate vacancy data science
by BeNeLux bioinformaticians forum 15 Mar '23

15 Mar '23

Dear maillist, At RIVM are recruiting a PhD candidate with a background in data science and interest to work in the domain of healthy and sustainable foods. The project is call See 'werkenvoornederland.nl': https://www.werkenvoornederland.nl/vacatures/phd-student-data-science-artif… Or academictransfer.nl PhD student data science/artificial intelligence for protein transition | RIVM - AcademicTransfer<https://www.academictransfer.com/en/324529/phd-student-data-scienceartifici…> Would it be possible to promote the vacancy through your network? KR Marga Ocke ----------------------------------------------------------------- Marga C Ocké, PhD Centre for Nutrition, Prevention and Health Services National Institute for Public Health and the Environment (RIVM) Postal address: PO Box 1, 3720 BA Bilthoven, the Netherlands Visiting address: Antonie van Leeuwenhoeklaan 9, 3721 MA Bilthoven, the Netherlands T: +31 88 6893814; M: +31 6 52096988 ----------------------------------------------------------------- See http://www.wateetnederland.nl for information on the Dutch food consumption surveys Dit bericht kan informatie bevatten die niet voor u is bestemd. Indien u niet de geadresseerde bent of dit bericht abusievelijk aan u is verzonden, wordt u verzocht dat aan de afzender te melden en het bericht te verwijderen. Het RIVM aanvaardt geen aansprakelijkheid voor schade, van welke aard ook, die verband houdt met risico's verbonden aan het elektronisch verzenden van berichten. www.rivm.nl<http://www.rivm.nl/> De zorg voor morgen begint vandaag This message may contain information that is not intended for you. If you are not the addressee or if this message was sent to you by mistake, you are requested to inform the sender and delete the message. RIVM accepts no liability for damage of any kind resulting from the risks inherent in the electronic transmission of messages. www.rivm.nl/en<http://www.rivm.nl/en> Committed to health and sustainability

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Postdoc position computational epigenomics available within Epi-Guide-Edit NWO Key Technology consortium
by BeNeLux bioinformaticians forum 15 Mar '23

15 Mar '23

Dear all, The NWO Key Technology funded Epi-Guide-Edit consortium is dedicated to developing tools for durable epigenetic editing across different applications including health and agriculture. Within the consortium we have a postdoc position (1 fte for 3 years or 0.8 fte for 4 years) available focused on single-cell resolution pooled epigenetic CRISPR/dCas screens to study epigenetic reprogramming in (breast cancer) cell lines. The position offers ample possibilities for the development and application of state-of-the art bioinformatics methods. The position is embedded in the group of the program coordinator, Prof. dr. Pernette Verschure, Swammerdam Institute for Life Sciences and the Dept. of Medical Biochemistry, Amsterdam University Medical Centers (AUMC), University of Amsterdam (UvA), NL. For computational analyses you will work closely together with Dr. Perry Moerland, Bioinformatics Lab, Dept. of Epidemiology and Data Science, AUMC, UvA, NL and Dr. Remco Loos, Informatics & Predictive Sciences, Bristol Myers Squibb, Spain. Further details on the position can be found in the attachment. Feel free to contact me (p.d.moerland at amsterdamumc.nl) if you have any questions. Best wishes, Perry --- Dr. ir. P.D. Moerland Bioinformatics Laboratory | Epidemiology and Data Science (EDS) Amsterdam UMC | Location AMC | J1B-225 | Meibergdreef 9 | 1105 AZ AMSTERDAM E: p.d.moerland(a)amsterdamumc.nl<mailto:p.d.moerland@amsterdamumc.nl> W: https://bioinformaticslaboratory.eu/ ______________________________________________________ AmsterdamUMC disclaimer : www.amsterdamumc.org/disclaimers

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Open position in the CBIO lab: single-cell proteomics
by BeNeLux bioinformaticians forum 14 Mar '23

14 Mar '23

A fully-funded position for a PhD student (4 years) or a post-doctoral researcher (2 - 3 years, depending on experience) is open in the Computational Biology and Bioinformatics lab (CBIO) at the de Duve Institute, UCLouvain in Brussels, Belgium. The CBIO lab (https://lgatto.github.io/cbio-lab) has developed a leading expertise in mass spectrometry-based single-cell proteomics data processing, analysis and interpretation (https://paperpile.com/shared/paTK2y) and is looking for a researcher to contribute to this research theme. The position will focus on computational and statistical approaches, including research software development, integration with other omics modalities, and could, depending on the candidate interests and experience, also include a small wet lab component. The successful candidate will have a degree in bioinformatics, statistics, computer sciences, biomedical sciences, bio-engineering, or equivalent and be able to demonstrate experience and/or keen interest in one or several of the following: - experience in one or multiple omics experimental technologies, data processing, analysis and/or interpretation - experience in mass spectrometry and proteomics is an advantage; - a keen interest in understanding and tackling biomedically relevant questions; - interest in robust method development; - background/expertise in statistics, machine learning and/or artificial intelligence; - open and reproducible research (e.g. Rmarkdown, Jupyter notebooks, Github, version control, ...); - research software development (e.g. unit testing, version control, continuous integration, ...); - experience in R/Bioconductor data structures, in particular those used for omics data analysis (e.g. SummarizedExperiment, SingleCellExeriment, QFeatures, ...); - contribution to an open and inclusive research environment; - good written and oral communication skills. The project is funded by the Fonds National de la Recherche Scientifique (FNRS). The position is open immediately until filled. To apply for the position, please send the following documents to Laurent Gatto: - A cover letter describing why you would like to join the lab and how you match the requirement; - A detailed CV including, depending on seniority, some or all of the following: a list of publications, pre-prints, posters and/or software contributions; a link to publicly available code/data analysis you have contributed to; education and professional experience; current and past positions; awards; obtained funding; teaching experience; any additional information you deem relevant. - If no code is publicly available, please include code chunks that illustrate best your programming experience and interests. - Among your publications/software/projects, select up to 3 and provide a short narrative describing why these are important in your career, your specific contributions and/or the unique skills you have gained through these. - A list of at least 2 (for a PhD application) or 3 (for a post-doctoral researcher application) academic references. Expectations are different for PhD or PDRA application and will be assessed accordingly. More information is available here: https://lgatto.github.io/scp-job-2023/

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VACANCY: PhD position in computational cancer biology (@NKI and VU Amsterdam)
by BeNeLux bioinformaticians forum 10 Mar '23

10 Mar '23

Dear all, For an exciting project using state-of-the-art single cell measurements to elucidate the mechanisms behind multi-drug combinations we are looking for an enthusiastic PhD candidate with a strong quantitative background. The position is shared between the groups of Lodewyk Wessels (NKI) and Evert Bosdriesz (VU). More information in the link. <https://www.nki.nl/careers-study/vacancies/phd-position-in-computational-si…> PhD position in computational single-cell cancer biology | Netherlands Cancer Institute<https://www.nki.nl/careers-study/vacancies/phd-position-in-computational-si…> nki.nl<https://www.nki.nl/careers-study/vacancies/phd-position-in-computational-si…> [apple-touch-icon-180x180.png]<https://www.nki.nl/careers-study/vacancies/phd-position-in-computational-si…> Kind regards, Evert Bosdriesz ---- Assistant Professor Bioinformatics - VU Amsterdam www.evertbosdriesz.org | e.bosdriesz(a)vu.nl

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