December 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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Vacancy PhD position visual analytics of multi-layer networks
by BeNeLux bioinformaticians forum 21 Dec '23

21 Dec '23

We have an exciting new PhD position in visual analytics of multi-layer networks The Visual Data Analysis research group at KU Leuven (University of Leuven) is part of the department of Biosystems at the Faculty of Bioscience Engineering. The group focusses on complex data exploration in the domain of biological and agricultural sciences, through the use of visual analytics and topological data analysis. The group is currently looking for a dynamic and highly motivated PhD student. Project Networks and graphs - both static and dynamic - play an important role in data science. Not only can they represent primary relational data (e.g. gene interactions) but many algorithms generate networks either as intermediate or final output (e.g. DBSCAN clustering and topological data analysis). In particular, these data structures are critical when investigating (biological and other) systems as a whole. We can quantitatively compare networks at different resolutions, and distinguish between changes in topology and changes in characteristics of the nodes and links themselves. Although many measures exist to do so (including degree, closeness, betweenness, etc), they mainly focus on the amount of difference but fall short in giving real insight in the quality of that difference. We want to focus on this qualitative understanding of networks rather than only a quantitative one. We want to develop a human-in-the-loop visual analytics toolkit to support the user in exploring differences between two or more networks in depth. Visual Analytics (VA) is often described as the science of analytical reasoning facilitated by the visual interface and combines interactive data visualisation and novel visual design on one hand with machine learning on the other. The methodology will involve - among other things - custom visual design, definition and implementation of interestingness features, as well as definition of novel distance metrics for topological data analysis. This will be applied to different types of multi-layer networks (e.g. with/without ordering in 2 or more dimensions). Keywords: graph, network, topological data analysis, visual analytics, data visualisation, multilayer networks Example papers on the topic of multi-layer networks and topological data analysis: * McGee et al. The State of the Art in Multilayer Network Visualization. Computer Graphics Forum 38, no. 6 (2019): 125–49. https://doi.org/10.1111/cgf.13610 * Lum et al. Extracting Insights from the Shape of Complex Data Using Topology. Scientific Reports 3 (2013): 1236. https://doi.org/10.1038/srep01236 Profile The Ideal Candidate * has a Master's degree in Computer Science, Bioscience Engineering or similar, with distinction (required) * has a solid understanding of network analysis / graph theory and a strong foundation in general data visualisation principles and techniques * has experience in topological data analysis (TDA) * has good programming and data analysis skills (incl using Python and if possible Javascript) * can work independently as well as part of a collaborative cross-domain research team * is proficient in oral and written English, possess excellent communication and multi-tasking skills, is team-oriented, proactive and result-driven. Interested Candidates Should Submit The Following * curriculum vitae * digital copy of the diplomas, including a list of courses followed and grades * contact information of 2 or 3 referees * motivation letter, which specifies why they apply to this position, and clearly illustrate possible past experience in the area. Offer * A fully funded, full-time PhD position for one year; after a positive evaluation, the contract can be extended to three additional years (four years in total) * A working climate where trust, (international) collaboration, and commitment are essential * An excellent young, stimulating and supportive international research environment * High level scientific training at a top-ranked university; training in academic, thematic and soft skills. How to apply For more information on this opportunity, please contact Prof Jan Aerts, tel.: +32 16 32 21 40, mail: jan.aerts(a)kuleuven.be You can apply via the KU Leuven jobsite at https://www.kuleuven.be/personeel/jobsite/jobs/60288125 Deadline for submitting: 11/1/2024 --- Prof Jan Aerts Visual Data Analysis Lab Department of Biosystems KU Leuven, Belgium jan.aerts(a)kuleuven.be https://www.biw.kuleuven.be/biosyst ; http://vda-lab.io

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ESSAI 2024 CALL FOR COURSE PROPOSALS
by BeNeLux bioinformaticians forum 21 Dec '23

21 Dec '23

(Apologies for multiple postings) The 2nd European Summer School in Artificial Intelligence - ESSAI 2024 July 15-26, 2024 Athens, Greece https://essai2024.di.uoa.gr/ IMPORTANT DATES 07 Feb 2024: Course Title submission deadline (mandatory) 14 Feb 2024: Final submission 06 Mar 2024: Notification ABOUT ESSAI 2024 is the second edition of the annual summer school on AI held under the auspices of the European Association for Artificial Intelligence (EurAI). ESSAI 2024 will provide an interdisciplinary setting in which courses are offered in all areas of Artificial Intelligence and also from wider scientific, historical, and philosophical perspectives. ESSAI is a central meeting place for students and young researchers in Artificial Intelligence to discuss current research and share knowledge. Courses will consist of five 90-minute sessions, offered daily (Monday-Friday) in a single week, to allow students to develop in-depth knowledge of a topic. The first edition of ESSAI was held in Ljubljana, Slovenia (https://essai.si/ ) between the 24th and 28th of July 2023 and was extremely successful, attracting over 500 participants. We look forward to a second edition of ESSAI that is at least as successful. TOPICS AND FORMAT ESSAI aims to cover all subdisciplines of AI and the interactions between them. Proposals for courses at ESSAI 2024 are invited in all areas of Artificial Intelligence, including but not limited to the following: * Autonomous Agents and Multi-agent Systems (MAS) * Causality and Causal Learning (CL) * Ethical, Legal and Social Aspects of AI (ELS) * Foundation Models (FM) * Knowledge Representation and Reasoning (KR) * Learning Theory (LT) * Natural Language Processing (NLP) * Neuro-Symbolic Learning and Reasoning (NSLR) * Planning and Strategic Reasoning (PLAN) * Reinforcement Learning (RL) * Robotics (ROB) * Safe, Explainable and Trustworthy AI (SET) * Search and Optimization (SO) * Supervised and Unsupervised Learning (ML) * Vision (VIS) Each course will consist of five 90-minute lectures, offered daily (Monday-Friday) in a single week. While introductory courses will typically focus on one subarea of AI, introductory and advanced courses are encouraged to present a broader perspective on AI and should be of interest beyond one specific area. CATEGORIES Each proposal should fall under one of the following categories. INTRODUCTORY COURSES Introductory courses are intended to introduce a research field to students, young researchers, and other non-specialists, and to foster a sound understanding of its basic methods and techniques. Such courses should enable researchers from related disciplines to develop some comfort and competence in the topic considered. Introductory courses in a cross-disciplinary area may presuppose general knowledge of the related disciplines. ADVANCED COURSES Advanced courses are targeted primarily to graduate students who wish to acquire a level of comfort and understanding in the current research of a field. PROPOSAL GUIDELINES To be considered, course proposals should closely adhere to the following guidelines: * Courses must be presented by lecturers who submitted the proposal. For courses with more than two lecturers, the role of each lecturer should be clearly explained and justified in the proposal. * Course proposals should explicitly state the intended course category. Proposals for introductory courses should indicate the intended level, for example, as it relates to standard textbooks and monographs in the area. Proposals for advanced courses should specify the prerequisites in detail. Proposals must be submitted in PDF format via: https://easychair.org/conferences/?conf=essai2024 and include all the following: 1. Personal information for each proposer: Name, affiliation, contact address, email, homepage (optional) 2. General proposal information: Title, category 3. Information about the course content: a. Abstract of up to 150 words b. Motivation and description (up to two pages) c. Tentative outline d. Expected level and prerequisites e. Appropriate references (e.g., textbooks, monographs, proceedings, surveys) f. Whether the course will appeal to students outside of the main discipline of the course 4. Information about the proposer(s): a. Short CVs of the proposer(s) b. Evidence that the proposer(s) are excellent lecturers with relevant teaching experience, in particular in delivering intensive courses in an interdisciplinary setting. To keep participation fees to a minimum, all the instructional and organizational work of ESSAI is performed on a completely voluntary basis. However, the registration fees of organizers and instructors will be waived. In addition, and where appropriate, ESSAI will seek to partially reimburse travel and accommodation expenses associated with delivering a course. If lecturers can cover their travel and accommodation expenses from other sources, this is greatly appreciated. SUBMISSION INFORMATION By February 7, 2024: Proposers must submit on EasyChair at least the name(s) of the lecturers(s), the ESSAI area and course level and a short abstract. By February 14, 2024: Submission must be completed by uploading a PDF with the actual proposal as detailed above. SUBMISSION PORTAL Please submit your proposals to https://easychair.org/conferences/?conf=essai2024 ORGANIZING COMMITTEE Chair: Brian Logan, Utrecht University Co-chair: Magdalena Ortiz, TU Wien Local Chair: Manolis Koubarakis, National and Kapodistrian University of Athens ESSAI Steering Committee Chair (EurAI Board representative): Giuseppe De Giacomo, Oxford University

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Vacancy PhD position in bioinformatics for computational mass spectrometry/food science
by BeNeLux bioinformaticians forum 20 Dec '23

20 Dec '23

We have an exciting new PhD position in bioinformatics for computational mass spectrometry/food science available at the University of Antwerp. The selected PhD student will develop novel bioinformatics tools to analyze the molecular composition of foods from untargeted metabolomics data. This project is at the forefront of computational biology and offers a unique opportunity to contribute to groundbreaking research in food science and nutrition. An exciting aspect of this position is our collaboration with multiple teams in South Africa, offering a global perspective and the chance to work with international partners. The application deadline for this position is January 14, 2024. For more detailed information and to apply, please visit our website at: https://www.uantwerpen.be/nl/jobs/vacatures/ap/?q=3225 Feel free to spread this opportunity within your network. Best, Wout Bittremieux Assistant Research Professor University of Antwerp

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Job Advertisement: Model system genome database manager (f/m/x)
by BeNeLux bioinformaticians forum 14 Dec '23

14 Dec '23

Dear Madams & Sirs, The Max Planck Institute for Multidisciplinary Sciences in Göttingen, Germany, is a leading international research institute of exceptional scientific breadth. With more than 40 research groups and some 1,000 employees from over 50 nations, it is the largest institute of the Max Planck Society. The department of Tissue Dynamics and Regeneration (Dr. Jochen Rink) invites applications for a position as Model system genome database manager (f/m/x) You will find the complete job description as attachment to this email with a request to publish it in your department/division. Should you have any questions or need further information, please do not hesitate to contact me. We thank you in advance for your support and wish you a happy holiday season. Best Regards Martina Lingl Assistant to Prof. Dr. Jochen Rink Department of Tissue Dynamics and Regeneration Dr. Sonja Lorenz Research Group Ubiquitin Signaling Specificity Max-Planck-Institute for Multidisciplinary Sciences Am Faßberg 11, 37077 Göttingen, Germany Phone: ++49 551 201 26100 Fax: ++49 551 201 2705 office.rink(a)mpinat.mpg.de<mailto:office.rink@mpinat.mpg.de> martina.lingl(a)mpinat.mpg.de<mailto:martina.lingl@mpinat.mpg.de>

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A Postdoc project in UHasselt
by BeNeLux bioinformaticians forum 07 Dec '23

07 Dec '23

Dear, Can you please forward and share the email below with your e-mail list ? It is about a new Postdoc project in DSI-UHasselt. Please CC me on the email. Thanks in advance and best regards, ziv shkedy *The data science institute in Hasselt University announces a position for a (m/f/x):* *Postdoc researcher in Bioinformatics/Biostatistics** (18-24 months): **High Dimensional Integrated Unsupervised and Supervised Analysis of Single Cell RNASeq Data* *General information about the project * The postdoc research project will be conducted in a close collaboration between the data science institute (DSI, https://www.uhasselt.be/en/instituten-en/dsi) in Hasselt University and a global pharmaceutical company. The main objective of the postdoc research project is to analyze single cell omics data for immune profiling purposes applied to vaccinology. The project is focused on algorithm/procedures/software testing and development using publicly and in house available dataset with application on real vaccine development . Both parts will be based on single cell omics data generated on *Chromium 10X Genomics platform*. Data analysis tools and software products that will be developed in this project would be available as R or Python packages with full documentation. *Project description* The research project consists of two main tasks: *Task 1 - Unsupervised analysis:* 1) To identify the best numerical embedding methods for TCR/BCR protein sequences in order to merge this feature with other OMICs layers. 2) To identify methods for single omics and multi-omics clustering (gene expression, individual TCR sequences, surface proteins) that can better approximate antigen-specificity. *Task 2 - Supervised analysis:* Based on the results obtained in part 1, we will define which of the identified features may be predictive of antigen specificity and cross-reactivity. *Data analysis methods*: cluster analysis for single cell RNAseq data (for both single and multi-omics setting) , biclustering, classification and prediction. *Profile and diploma* As a postdoc researcher you will join the dynamic functional genomics team in the data science institute (DSI) in UHasselt and will collaborate with scientists from both academia and industry. The research work related to both tasks will be conducted in a close collaboration between DSI and the pharmaceutical company and the postdoc researcher will work in both organizations. A successful candidate should have - PhD in bioinformatics/ statistical bioinformatics/biostatistics (with experience of high dimensional data). - A PhD whose research focuses on single cell analysis is an advantage but not a must. - A PhD whose research is on AI/ML methodologies for unsupervised and supervised HD data analysis is a plus. - You are acquainted with statistical methodologies and had exposure to computer programming in R/Python. - You published manuscripts in the area of bioinformatics/biostatistics. - You developed software package(s) as a part of your PhD research. - You are interested in developing new methodology from both theoretical and applied aspects. - You are interested in developing software to the pipeline for data analysis and implement this software within a company environment. - You are willing to closely collaborate with biologists/biostatistians/bioinformations from the pharmaceutical industry. - You have a strong interest in working on both vaccine and drug development problems. - You can work independently and within a team. - You have excellent communication skills. - You can lead a team of researchers within a project. - You enjoy working in a multidisciplinary and multicultural environment. - You speak and write English fluently. *Offer* The appointment takes effect from January 2024 and at the latest from March 2024 for a period of 18-24 months, depending on the candidate experience. *Further information* Prof. dr. Ziv Shkedy, +32 11-26 82 40, ziv.shkedy(a)uhasselt.be <christel.faes(a)uhasselt.be> *Application*Applicants must send their application to ziv.shkedy @uhasselt.be <christel.faes(a)uhasselt.be> *Please add a copy of your PhD diploma and CV (including publication list) to your application.* Deadline for the Application 15, January, 2024

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ABLS2024: Bioinformatics conference in Leuven 7-8 March 2024 - abstract deadline 9th of January
by BeNeLux bioinformaticians forum 07 Dec '23

07 Dec '23

Dear all, We are looking forward to inviting you to the 5th edition of our Applied Bioinformatics in Life Sciences conference ABLS24. 🤯 Topics will range from personalized medicine, structural bioinformatics and genome function. Join our invited scientists on stage for a selected talk, or present your research on a poster! More info here: https://www.vibconferences.be/events/applied-bioinformatics-in-life-science… 🗓 Abstract deadline: 9 January 2024 Best regards, Alex Alexander Botzki Team Lead Technology Training, ELIXIR Belgium Training Coordinator VIB Technology Training ELIXIR Belgium Technologiepark-Zwijnaarde 75, 9052 Ghent – Belgium https://technologytraining.sites.vib.be<https://technologytraining.sites.vib.be/> | https://www.elixir-belgium.org/training [Graphical user interface Description automatically generated] [Hx1KyM2Q09lnAAAAAElFTkSuQmCC]

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FW: Community event: A.I. in Structural Biology Symposium, 19th Jan 2024, Brussels
by BeNeLux bioinformaticians forum 07 Dec '23

07 Dec '23

From: Carl Mensch <Carl.Mensch(a)uantwerpen.be> Date: Thursday, 7 December 2023 at 00:02 To: Ertaylan Gökhan <gokhan.ertaylan(a)vito.be> Subject: Community event: A.I. in Structural Biology Symposium, 19th Jan 2024, Brussels Dear All, As a reminder, we are pleased to invite you to our one-day symposium on AI's impact in structural biology, scheduled for 19th January 2024 at Hoek 38 (FWO, Brussels). This event, following the success of last year's symposium on AlphaFold, promises to offer insightful discussions and lectures on the evolving role of AI in the field. We are honored to have Arne Elofsson from Stockholm University as our keynote speaker. He will open the morning session of our symposium with his talk on the impact and advancements of AI in structural biology. Casper Goverde from EPFL will present on the application of deep learning-based tools in advancing our understanding and design of complex proteins. To conclude our morning lectures, Maxim Tsenkov from EMBL-EBI will delve into the AlphaFold database and Foldseek, offering valuable insights into these groundbreaking resources. Please fill out the registration form here<https://forms.gle/28eWrt3aXrTxuRpx5> to confirm your attendance and provide your lunch requirements (if you haven’t done so already). The symposium is held live at Hoek38, Brussels for our community. Additionally, the morning lectures will be live-streamed on our channels<https://www.vscentrum.be/events/alphafold-event-3> for those outside of the community, making them accessible to a wider audience. Best, Carl Mensch and Gökhan Ertaylan Dr. Carl Mensch | HPC Consultant | Computational chemist Faculty of Science | Department of Mathematics Campus Middelheim– M.G.309 Middelheimlaan 1 – 2020 Antwerp carl.mensch(a)uantwerpen.be<mailto:carl.mensch@uantwerpen.be> P +32 3 265 89 80<tel:+3232658980> [cidimage002.jpg(a)01D62873.83C42BF0]<https://twitter.com/VSC_HPC>[cidimage005.jpg(a)01D62873.83C42BF0]<https://www.linkedin.com/company/vschpc/mycompany/> [signature_2675831904]<https://www.vscentrum.be/>

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PhD Candidate in Computational and Developmental Biology
by BeNeLux bioinformaticians forum 05 Dec '23

05 Dec '23

Are you an aspiring researcher with an interest in embryonic development? And are you eager to understand how individual cells in the early mammalian embryo decide their future fate using computational approaches? Then join the Radboud Institute for Molecular Life Sciences as a PhD candidate! https://www.ru.nl/en/working-at/job-opportunities/phd-candidate-in-computat… The early mammalian embryo, or epiblast, is composed of pluripotent cells that can generate all specialised cell types of the body. The epiblast cell population is heterogeneous, showing stochastic differences in transcriptome and epigenome between cells that affect their differentiation potential. In this project, you will address how a system composed of intrinsically stochastic epiblast cells can show robust and deterministic fate decisions, utilising single-cell genomic/epigenomic datasets from in vitro developing mouse gastruloids that will be generated within the consortium. You will apply state-of-the-art genetic/epigenetic computational approaches, integrative -omics, cellular trajectory analysis, agent-based modelling and other types of predictive modelling, supported by our in-house computational biology unit. Dr. Marten Postma Assistant Professor Chair Examinations Board BSc BMW/MSc BMS Member SILS Educational Committee (SEC) Programme Developer MSc BioSB JD Track coordinator Systems Biology MSc BioSB JD Member Admission Committee MSc BioSB JD zoom : https://uva-live.zoom.us/j/2612815610 Room C2.102 (SILS) Swammerdam Institute for Life Sciences (SILS) University of Amsterdam (uVA) Science Park 904 1098 XH Amsterdam The Netherlands tel : +31 20 525 6225 e-mail : M.Postma(a)uva.nl<mailto:M.Postma@uva.nl> website : http://www.martenpostma.nl/science/

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Assistant/associate professor position in machine learning in bioinformatics
by BeNeLux bioinformaticians forum 04 Dec '23

04 Dec '23

Position: assistant/associate professor machine learning in bioinformatics The Wageningen Bioinformatics Group has a vacancy for an assistant / associate professor (depending on experience). In this role, you will contribute to the group’s research and teaching; set up and maintain a research line on machine learning/deep learning based method development in bioinformatics, with applications in the green life sciences; and help organize and deliver education in bioinformatics and data science. You will work on the Wageningen Campus in a group highly engaged in bioinformatics education and research, with an open, relaxed and collaborative atmosphere. For more information and an online application form (deadline January 8, 2024), please see https://www.wur.nl/en/vacancy/assistantassociate-professor-machine-learning… or contact Dick de Ridder (dick.deridder at wur.nl).

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