June 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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Postdoc Opportunity in Marine Genomics, IFREMER, France
by BeNeLux bioinformaticians forum 21 Jun '23

21 Jun '23

Postdoctoral Opportunity in Genomics and Bioinformatics at IFREMER Brest (French Research Institute for the Exploration of the Sea) Marine organisms living on intertidal habitats are exposed to highly variable environments to which they must respond rapidly. Understanding the mechanisms that allow intertidal organisms to respond to environmental change is an important step to better understanding species responses to climate change. Protein kinases are a family of molecules that are involved in signal transduction and stress response, and that are often involved in detecting and modulating cellular responses to environmental change. Increasing genomic resources allow us to examine the full complement of protein kinases in organisms (the kinome), providing an unique opportunity to better understand the role of kinases in the adaptation of organisms to climate change. We are currently seeking a postdoctoral researcher to work on the kinome of the honeycomb worm (Sabellaria alveolata), a reef-building species which commonly builds bioconstructions across Europe, and has been estimated to be the largest temperate reef-builder on European shores. We have recently sequenced and annotated the S. alveolata genome, and we have further developed a bioinformatics pipeline which searches for conserved motifs in protein kinases, allowing us to retrieve the kinome for any organism (KiNext). In order to better understand local adaptation to temperature in the honeycomb worm, we have transplanted reef blocks from 5 locations in Europe (Scotland, English Channel, southern Bay of Biscay, Portugal and Morocco), exposed them to 5 temperature treatments, and sequenced transcriptomes to examine heat stress and local adaptation to heat. We are looking for a postdoc who will conduct the transcriptomic analyses, examining all genes that are differentially expressed, but with a particular focus on the protein kinases. The postdoc will use the KiNext pipeline to annotate protein kinases, and further examine kinase response to heat stress. Candidates should have experience with bioinformatics (preferably command-line). Experience with transcriptomics or ecotoxicology are desired but not mandatory. Our funding source has eligibility criteria which stipulates that the position be open to all nationalities except French (unless currently residing outside of France). Please send an email and CV to flavia.nunes(a)ifremer.fr by June 30, 2023. -- Flavia Nunes Laboratory of Coastal Benthic Ecology Ifremer Centre de Bretagne 1625 route de Sainte-Anne, CS 10070 29280 Plouzané, France phone: +33 2 98 22 49 27 wwz.ifremer.fr/dyneco/Lab.-Lebco

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Open position: BioData.pt Executive Director
by BeNeLux bioinformaticians forum 16 Jun '23

16 Jun '23

Dear all, FYI. Best regards, Alex ________________________________ From: "Nuno Luís Barbosa Morais" <nmorais(a)medicina.ulisboa.pt> Sent: Tuesday, June 13, 2023 12:27:17 PM Subject: Open position: BioData.pt Executive Director Dear All, BioData.pt<http://BioData.pt> is looking for a new Executive Director. Here is the advert for the call: https://biodata.pt/node/463 Please spread the word. Many thanks and best wishes, Nuno

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Train-the-Trainer | Integration of the sex and gender dimension in life sciences research
by BeNeLux bioinformaticians forum 13 Jun '23

13 Jun '23

Dear BBC list, On behalf of the Bioinfo4Women programme, we are delighted to share this train the trainer course to equip research infrastructures, research centers and training providers on how to introduce the sex and gender dimension in life sciences training portfolios. The inclusion of the sex and gender dimension in life sciences is increasingly promoted by the European Union to rethink standards and reference models for sex and gender representation in research projects. Thus, training biomedical researchers in this topic will increase their capacity to integrate the sex and gender dimension into their work, leading to more inclusive and impactful science. We invite you to this train-the-trainer course aimed at developing participants’ skills on how to introduce the sex and gender dimension into their training related to the life sciences. Learning objectives At the end of this course, participants are expected to: * LO1: Understand the appropriate applications of the terms “sex” and “gender” in biomedical research in training actions * LO2: Identify, understand, and think critically about different perspectives on the complexity of sex and gender dimension in biomedical research and how to communicate them in training activities. * LO3: Identify how the categories of sex and gender affect the life sciences and training in this domain, in particular regarding the generation, collection and utilisation of data in research. * LO4: Select, compile, and synthesise information on the inclusion of the sex and gender dimension in research and integrate it into their training portfolio. *Course details* * What? Train-the-Trainer | Integration of the sex and gender dimension in life sciences research * When?Wednesday, June 28, 2023 from 14h to 18h and Thursday, June 29, 2023 from 9h to 13h * Where?Face to face at the Barcelona Supercomputing Center (BSC) premises, Barcelona, Spain * Target audience:Training coordinators, training organisers and trainers willing to introduce the sex and gender dimension in their training portfolio, and researchers with an interest in the topic and prospects of organising training about the topic. * More details and registration:https://www.eosc-life.eu/news/how-to-integrate-the-sex-and-gender-dimension-in-life-sciences-research/ <https://www.eosc-life.eu/news/how-to-integrate-the-sex-and-gender-dimension…> This course is organised by the Bioinfo4Women programme of the Life Sciences Department at the Barcelona Supercomputing Center (BSC), BBMRI-ERIC, INB/ELIXIR-ES, EATRIS, and it has been funded by the 3rd EOSC-Life Training Open Call. Please share as you see fit in order to benefit as much RI and institutions as possible. Best regards, -- -- Eva Alloza Training coordinator, communication 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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Two Postdoc positions in Bioinformatics
by BeNeLux bioinformaticians forum 12 Jun '23

12 Jun '23

Dear all, We would like to inform you about two positions available in the Dessimoz lab based in Switzerland. - Postdoc position in comparative genomics and bioinformatics: Working on a project about synteny, orthology, evolution, gene loss and tomato. Details: http://tinyurl.com/4fenkydr - Postdoc position in evolutionary structural bioinformatics: Reconstructing the last common ancestor of all animal’s genome! This position will be based in both Lausanne and Zurich with Prof. Pedro Beltrao's lab. Details: https://tinyurl.com/v3eu4e23 Best regards, Sina Majidian Dessimoz lab, University of Lausanne Switzerland

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Elixir 3D-bioinfo webinar on June 20th (5pm)
by BeNeLux bioinformaticians forum 06 Jun '23

06 Jun '23

Dear all, --- on behalf of Anastassia --- Please consider to register for the Elixir 3D-bioinfo webinar on June 20th (5pm). There will be two excellent talks on epistasis in protein evolution and design (by Charlotte Mitton, University of British Columbia, Vancouver) and a talk on AI-driven design of epitope-targeted antibodies (by Possu Huang, University of Stanford, California). In particular, if you're interested in nanobodies engineering, don't miss Possu's presentation! https://elixir-europe.org/events/3d-bioinfo-webinar-protein-design-and-evol… Best wishes, Anastassia Vorobieva

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Vacancy pre-Announcement: Data Scientist/PhD Student (Applied Bioinformatics)
by BeNeLux bioinformaticians forum 05 Jun '23

05 Jun '23

We are pleased to announce an upcoming vacancy for a Data Scientist/PhD Student to join our team. Recently, a VLAIO project has been approved, and we are looking for a skilled individual who can contribute to the project as a doctoral student. PLEASE NOTE that the text below is not an official vacancy announcement but a means to assess the potential interest of qualified candidates for an upcoming official vacancy announcement. The purpose of this text is to gauge the level of interest and potential response from eligible candidates before the official vacancy announcement is released. We appreciate your understanding. Project Description: The project focuses on a study on Dengue, wherein various techniques such as AIRR-seq, single-cell-seq, and Olink-proteomics will be performed. As a data scientist, your primary responsibility will be to conduct applied bioinformatics, integrating and analyzing diverse datasets. Additionally, effective reporting and communication of findings will be crucial. Responsibilities: * Conduct applied bioinformatics analysis, utilizing techniques such as AIRR-seq, single-cell-seq, and Olink-proteomics. * Integrate and analyze diverse datasets to derive meaningful insights. * Develop and implement statistical models and algorithms to analyze the data. * Collaborate with interdisciplinary teams to ensure effective communication and coordination. * Prepare detailed reports, presentations, and scientific publications to disseminate research findings. * Stay up-to-date with the latest advancements in the field of bioinformatics and data science. Requirements: * Master's degree * Strong background / afinity in bioinformatics and molecular biology. * Proficiency in programming languages such as Python, and/or R * Experience / Familiarity with analyzing high-throughput sequencing data, including AIRR-seq, single-cell-seq, Olink-proteomics or related techniques is preferred. * Solid understanding of statistical methods and data analysis techniques. * Excellent written and verbal communication skills in English. * Ability to work independently as well as collaboratively in a team environment. * Strong problem-solving skills and attention to detail. We offer: * The opportunity to contribute to an exciting research project on Dengue. * Full-time employment as a doctoral student at Ghent University. * Access to state-of-the-art laboratory facilities and computational resources. * Guidance and supervision from experienced researchers in the field. To apply: Please submit your interest, including a cover letter, CV to [ mailto:Filip.VanNieuwerburgh@UGent.be | Filip.VanNieuwerburgh(a)UGent.be ] . Lieven Sterck - Senior bioinformatician Bioinformatics VIB-UGent Center for Plant Systems Biology Ghent University Technologiepark-Zwijnaarde 71 - 9052 Ghent - Belgium Tel. +32(0)9 331 38 21 [ http://www.psb.ugent.be/ | www.psb.ugent.be ] Genome editing, cutting-edge technology for a sustainable agriculture [ https://originofimpact.sites.vib.be/ ]

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Data Engineer / Bioinformatician- AZ-Crick-Imperial College: Molecular Glue Discovery Partnership
by BeNeLux bioinformaticians forum 05 Jun '23

05 Jun '23

Hi all, We seek a talented, highly motivated candidate with experience modelling and analysing complex data sets with a strong knowledge of programming language(s) for the newly funded Molecular Glue Discovery Partnership - an exciting new research partnership between the Francis Crick Institute and Imperial College working in close collaboration with AstraZeneca, to develop systematic approaches to exploit endogenous protein degradation pathways to target undruggable disease-relevant proteins or protein complexes. More info: https://www.crick.ac.uk/careers-study/vacancies/2023-05-31-data-engineer/bi… Application deadline *21st June*. Thanks, Sergio

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PhD and Postdoc Positions in Artificial Intelligence for Bioinformatics
by BeNeLux bioinformaticians forum 03 Jun '23

03 Jun '23

We have two fantastic opportunities in the field of Artificial Intelligence for Bioinformatics. 1. PhD in Artificial Intelligence for Molecular Discovery: We are currently accepting applications for a three-year Ph.D. position at the University of the Cote d'Azur, in collaboration with the University of Antwerp. This position offers an exciting opportunity to develop reinforcement learning tools for the analysis of small molecule mass spectrometry data. As a Ph.D. candidate, you will work closely with renowned experts in analytical chemistry, machine learning, and bioinformatics. To apply, send an email to Prof. Dr. Louis-Felix Nothias (louisfelix.nothias(a)gmail.com<mailto:louisfelix.nothias@gmail.com>) and Prof. Dr. Wout Bittremieux (wout.bittremieux(a)uantwerpen.be<mailto:wout.bittremieux@uantwerpen.be>) by June 8, 2023 including a motivation letter, outlining your passion for artificial intelligence and molecular discovery, along with your CV highlighting your academic achievements and relevant experiences. 2. Postdoc in Molecular Artificial Intelligence: We have an exciting postdoctoral opportunity at the University of Antwerp. You will collaborate with world-leading pharmaceutical companies to develop artificial intelligence solutions to analyze billion-scale mass spectrometry-based metabolomics data and study the role of small molecules as fundamental building blocks of life. The application deadline for this position is June 15, 2023. We especially encourage candidates with a PhD in quantitative sciences and a strong interest in applying their data science skills to relevant life science challenges to apply. For more detailed information and to apply, please visit our website at: https://www.uantwerpen.be/en/jobs/vacancies/academic-staff/?q=2878&descr=Po…. We strongly encourage passionate individuals with a keen interest in Artificial Intelligence and Bioinformatics to apply for these positions. The University of Antwerp and the University of the Cote d'Azur offer vibrant research environments, state-of-the-art facilities, and a supportive community of scholars dedicated to pushing the boundaries of knowledge. Please feel free to share this information with anyone who may be interested or qualified. We appreciate your assistance in helping us spread the word and attract exceptional candidates to join our teams. Sincerely, Wout Bittremieux Assistant Research Professor University of Antwerp

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Senior bioinformatician position at the Pirbright Institute - UK
by BeNeLux bioinformaticians forum 01 Jun '23

01 Jun '23

The bioinformatics core facility at the Pirbright Institute is advertising for a permanent senior bioinformatician position. The post is primarily for the analysis of sequencing data and has a balance of service (~50%), room to pursue open ended projects with the two computational groups in the Institute (25%) and participation to bought-in time research projects (25%). The Institute has exceptional containment facilities producing unique datasets. Further details at: https://www.jobs.ac.uk/job/DAC810/23p-53-bioinformatician-senior-bioinforma… Informal enquiries can be addressed to bioinformatics(a)pirbright.ac.uk

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