October 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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Vacancies
by BeNeLux bioinformaticians forum 25 Oct '23

25 Oct '23

Hi all, We’re Hartwig Medical Foundation, a non-profit organization that wants to make sure every cancer patient gets the best treatment available. To reach this goal, we offer a ‘complete DNA-test’ to hospitals to treat the patients of today. To help the patient of tomorrow, we collect the genomic data of the patients and together with treatment outcomes, make the data available to researchers. To make our ambitions a reality in the next couple of years, we’re looking to hire: * Software Developer ACTIN<https://www.linkedin.com/feed/update/urn:li:activity:7122119163413712896/?a…> * Software Developer IT Infrastructure Team<https://www.linkedin.com/feed/update/urn:li:activity:7122820576531869696/?a…> * Data Steward<https://www.linkedin.com/feed/update/urn:li:activity:7119921473523195904/?a…> * Moleculair Analist / Lab Technician<https://www.linkedin.com/feed/update/urn:li:activity:7109867983312670720/?a…> You can also find all our open positions at https://www.hartwigmedicalfoundation.nl/vacancies/. With kind regards, Daphne van Beek Innovation Specialist Absent on Monday [Hartwig Medical Foundation]<https://www.hartwigmedicalfoundation.nl/en/> A Science Park 408, 1098 XH Amsterdam T +31 (0)20 226 9712 W hartwigmedicalfoundation.nl<https://www.hartwigmedicalfoundation.nl/en/> | oncoact.nl<https://oncoact.nl/?lang=en> N Subscribe to our newsletter<https://mailchi.mp/475bfde5c6f3/nieuwsbrieven-hartwig-medical-foundation> [Facebook]<https://www.facebook.com/HartwigMedicalFoundation> [LinkedIn] <https://www.linkedin.com/company/hartwig-medical-foundation> [Twitter] <https://twitter.com/hartwigmedical> [Instagram] <https://www.instagram.com/hartwigmedicalfoundation/?hl=en> [YouTube] <https://www.youtube.com/channel/UCK8juCiUGC1OsEXPtdEEwPA> It is our mission to realize that every cancer patient receives a personalized treatment using a complete DNA test<https://oncoact.nl/?lang=en>.

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Request to post: Computational biologist / AI method development - job opening @ BASF Ghent
by BeNeLux bioinformaticians forum 25 Oct '23

25 Oct '23

Dear Sir / Miss, Can you consider posting the following job opening in computational protein engineering / AI methods development in the BBC mailing list? The job opening is in Ghent. Since I did not see it posted (see previous request below) ... I was wondering whether I missed the post, or missed your feedback? With best regards, Koen From: Koen Bruynseels Sent: Monday, October 9, 2023 5:12 PM To: bbclist(a)psb.vib-ugent.be; bbclist(a)psb.ugent.be Subject: Computational biologist / AI method development - job opening @ BASF Ghent Dear, Can you share the following job opening in my team in Ghent with the mailing list? Best regards, Koen Computational Protein Engineer (basf.jobs)<https://basf.jobs/dark_blue_EMEA/job/Gent-Computational-Protein-Engineer/99…> Computational Protein engineer We are seeking an entrepreneurial and highly skilled Computational Protein Engineer with Expertise in AI methods and Molecular Biology to join our innovative team. The ideal candidate will possess a profound understanding of machine learning models in the field of protein engineering, a deep interest in plant molecular biology, and solid communication skills. As a crucial member of our research and development team, you will identify opportunities to leverage advanced AI models for protein design and optimization, and you will apply them to enhance crop traits for increased resilience and yield. Task package: * You will develop and utilize AI-driven and modeling approaches to analyze and predict protein structures, interactions, and functions, with a focus on optimizing traits related to pest control, disease resistance and yield enhancement. * You collaborate closely with cross-functional teams, including molecular biologists, agronomists, and bioinformaticians to integrate advanced methodologies into broader crop improvement programs. * You will identify creative opportunities for developing desired agronomic traits, by leveraging on your expertise in molecular biology and machine learning methods. * Furthermore, you will contribute to the development and execution of research plans, experimental designs, and data analysis pipelines. * You will stay abreast of the latest advancements in protein engineering, AI methodologies, and plant molecular biology, and apply this knowledge to drive innovation within the company. Expertise: * You have a Ph.D. or equivalent in Protein Engineering, Bioinformatics, Molecular Biology, or a related field. * You are known for your entrepreneurial attitude, with the ability to identify innovation opportunities that leverage on knowledge in molecular biology and machine learning methods. * Additionally, you have excellent verbal and written communication skills, with experience in conveying complex scientific concepts to both technical and non-technical audiences. * You have proven expertise in the development and application of machine learning models, including large language models (e.g., AlphaFold, ESMfold), for protein engineering and structure prediction. * Proficiency in molecular biology, including a deep understanding of genomics, gene expression, signaling pathways, and metabolic processes is a must. * Programming skills (Python, R, etc.) for data analysis and computational modeling are a plus. * You have demonstrated ability to work collaboratively in a fast-paced, interdisciplinary research environment. Benefits: * Responsibility from day one in a challenging but dynamic work environment and "on-the-job" training as part of a committed team. * Competitive compensation including attracting benefits as well as excellent career opportunities in an international company. BASF is a multinational company dedicated to revolutionizing agricultural science. We are committed to developing innovative solutions that address global challenges in food security and sustainability. Our diverse team combines expertise in computational protein engineering, artificial intelligence, and plant molecular biology to create cutting-edge technologies that redefine the agricultural industry. Do you have any questions about the application process or the job? Please contact Nele (Talent acquisition) Phone: +49 30 2005-58363. Dr. Koen Bruynseels Phone: +32 474 296 225, Email: koen.bruynseels(a)basf.com<mailto:koen.bruynseels@basf.com> Postal Address: BASF Belgium Coordination Center CommV, Technologiepark 101, 9052 Gent Zwijnaarde, Belgium [cid:image001.png@01DA0732.D91A4E30] BASF Business Services NV, Registered Office: Scheldelaan 600, 2040 Antwerp 4, Belgium Companies' Register: Handelsregister Antwerpen, 0463.642.875 Companies' Register: Rechtspersonenregister Antwerpen, 0463.642.875 Managing Director: Stefan Beck Information on data protection can be found here: https://www.basf.com/global/en/legal/data-protection-at-basf.html

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Invitation CompMS webinar Dr. Andy Lin – Challenges and applications of small databases in mass spectrometry-based proteomics data analysis
by BeNeLux bioinformaticians forum 19 Oct '23

19 Oct '23

Dear colleagues, We would like to invite you to an ISCBacademy<https://www.iscb.org/iscbacademy> webinar hosted by CompMS<https://compms.org/> and presented by Dr. Andy Lin (PNNL) on Monday, October 23 at 11:00 EDT / 17:00 CET. Challenges and applications of small databases in mass spectrometry-based proteomics data analysis The most common statistic for assigning statistical significance to peptide detections that result from a proteomics experiment is the false discovery rate (FDR). The FDR of a set of peptide-spectrum matches (PSMs) is typically estimated through a process called target-decoy competition, where spectra generated from a proteomics experiment are searched against a database of target and decoy sequences. This methodology is well adapted to most proteomics experiments, where the database is large or many proteins in the database are present in the sample. However, this methodology is challenged by small databases or when few peptides in the database are present in the sample. Recent advances, such as subset-neighbor search, aim to address to this challenge. Unfortunately, we show this approach fails for cases when the database is extremely small. In addition to discussing the unclear future of how to approach this scenario, we give several example applications that could utilize future solutions. You can join the webinar through the ISCB Nucleus<https://iscb.junolive.co/> platform. Feel free to share this information with any interested colleagues. Best, On behalf of CompMS, Wout, Timo, Lindsay, Isabell

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Empirical evaluations of large language models for bioinformatics education and research - ISCBacademy webinar, Thursday, November 9 at 11 am EDT
by BeNeLux bioinformaticians forum 17 Oct '23

17 Oct '23

Subject: Empirical evaluations of large language models for bioinformatics education and research - ISCBacademy webinar, Thursday, November 9 at 11 am EDT Dear all, The ISCBacademy webinar on Thursday, November 9 at 11 am EDT will be hosted by the ISCB Education COSI. Stephen Piccolo, from the Brigham Young University, will talk about “Empirical evaluations of large language models for bioinformatics education and research” (see the abstract below). You will find the information on how to connect at https://www.iscb.org/iscbacademy. You are most welcome to join us and spread the news among your colleagues. Kind regards, Patricia, Russell, and Wai Keat (ISCB Education COSI chairs) -- Abstract: Large language models (LLMs) have ignited great interest in the bioinformatics community. Many of us are interested in their potential uses (and misuses?) in research and education. The Piccolo Lab is undertaking empirical research to answer three such questions. 1) How well can LLMs translate human-language prompts into functional computer code? 2) How well can LLMs translate code snippets from one programming language to another? 3) How effectively can LLMs act as virtual assistants to students who are learning to write code? We have addressed each of these questions in the context of introductory bioinformatics and biostatistics education at the undergraduate level. In this seminar, I will describe our findings and discuss potential practical implications for education and research. -- [SIB logo] Patricia Palagi Head of Training SIB | Swiss Institute of Bioinformatics Quartier Sorge - Bâtiment Amphipôle - CH 1015 Lausanne - Switzerland t +41 21 692 40 78 Patricia.Palagi(a)sib.swiss<mailto:Patricia.Palagi@sib.swiss> - www.sib.swiss<http://www.sib.swiss> The information in this e-mail, and those ensuing, is confidential and may be legally privileged. It is intended solely for the addressee. If you are not the intended recipient, please destroy this message and notify the sender immediately.

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Join Our New Slack Community on Computational Mass Spectrometry
by BeNeLux bioinformaticians forum 11 Oct '23

11 Oct '23

Dear colleagues and fellow enthusiasts of computational mass spectrometry, As part of the CompMS<https://compms.org/> initiative, we are happy to share that we have launched an open Slack community dedicated to computational mass spectrometry, encompassing proteomics, metabolomics, and other fascinating applications. Our community will provide a space for: 1. Knowledge Sharing: Share your latest research findings, techniques, and insights in the field of computational mass spectrometry. Engage in discussions and exchange ideas with peers who share your enthusiasm. 2. Collaboration Opportunities: Discover potential collaboration partners, whether you are working on repository-scale analyses or other exciting projects. Forge connections that can drive your research forward. 3. Problem-Solving: Have a challenging problem or a question in your research? Our community is here to help. Tap into the collective wisdom of experts in the field. 4. Resource Exchange: Share valuable resources, tools, and software that can aid fellow members in their research endeavors. To join our Slack community, please use this invitation link<https://join.slack.com/t/compms/shared_invite/zt-24neur6wz-gu2KmKAnWcDAWspC…>, and feel free to share this further. We look forward to seeing you on Slack. If you have any questions or suggestions, please feel free to reach out to me directly or through Slack. Thank you for being a part of this exciting venture, and let's work together to push the boundaries of computational mass spectrometry! Best, On behalf of CompMS, Wout

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LAST CHANCE for early birds: BioSB course "Integrated Modeling and Optimization"
by BeNeLux bioinformaticians forum 11 Oct '23

11 Oct '23

Dear Colleagues, Please note, there are still four days to register at an early-bird reduced rate for the BioSB course: Integrated Modeling and Optimization<https://www.dtls.nl/courses/integrated-modeling-and-optimization-fundamenta…> Wageningen, 11 - 15 December 2023 (early bird fee until October 16) What it's about? In validating models one always meet with the need to fit models to data. So, the parameters that are present in any realistic model have to be chosen based on comparison of model predictions with data. In this matching process optimization techniques are indispensable. That’s why a considerable part of this course is spent on getting you acquainted with the optimization techniques that are nowadays available and widely used. Numerical optimization also is the basis for so-called flux balance analysis (FBA), commonly used to study large metabolic networks. This type of models and their analysis and simulation is also introduced in the course. More information and registration: click here<https://www.dtls.nl/courses/integrated-modeling-and-optimization-fundamenta…>. We look forward to welcoming you. Kind regards, Petra Aarnoutse Community manager BioSB [cid:part1.c5aevw0a.AiUrJ7j9@health-RI.nl]

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Junior Lecturer Bioinformatics and Systems Biology VU/UvA master’s programme
by BeNeLux bioinformaticians forum 10 Oct '23

10 Oct '23

Dear all, We have are again hiring junior lecturer to strengthen the bioinformatics teaching team within the VU/UvA joint degree master programme Bioinformatics & Systems Biology in Amsterdam. For details and application procedure, please see https://werkenbij.vu.nl/ad/junior-lecturer-juniordocent-masters-programme-b… -- Groetjes, Anton _____________ _______________________________________________________ | | | | _ _ ___,| K. Anton Feenstra | | / \ / \'| | | IBIVU/Bioinformatics - Vrije Universiteit Amsterdam | |( | )| | | De Boelelaan 1111 - 1081 HV Amsterdam - Netherlands | | \_/ \_/ | | | Tel: +312059 87783 - skype: kafeenstra - room NU 12A31| | | Feenstra(a)few.vu.nl - www.few.vu.nl/~feenstra/ | | | "If we knew what it was we were doing, it would not | | | be called research, would it?" (Albert Einstein) | |_____________|_______________________________________________________| _______________________________________________ BBClist mailing list BBClist(a)psb.ugent.be https://maillist.psb.ugent.be/mailman/listinfo/bbclist

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job vacancy Project Lead Artificial Intelligence
by BeNeLux bioinformaticians forum 09 Oct '23

09 Oct '23

Dear Sirs, Could you please share the vacancy below with the mailing list? *Project Lead Artificial Intelligence* *Job objective * Our organization keeps moving. This results in a fast-changing and, therefore, challenging environment. As a Project Lead Artificial Intelligence and Data Science you strengthen the R&D Trait Genetics group. With your solid background in bioinformatics you lead projects, work packages and activities on the design of algorithms and pipelines using high throughput phenotyping methods like imaging data. You translate these pipelines into solutions for our global breeding and research programs. In addition, you are responsible for setting up, developing and maintaining the IT solutions for our Trait Genetics team. Collaboration is key for this job position. You will work closely with breeders and scientists from different backgrounds (including bioinformatics, biology, genetics, phytopathology and trait discovery) to develop tailored solutions that meet their needs. You will report to the Technology Lead Trait Genetics in the Breeding Technology Centre in De Lier. *Your tasks and responsibilities* · Design, improve and maintain innovative software solutions for large data challenges within the global Dümmen Orange R&D portfolio. · Initiate and lead work packages and projects on developing pipelines for computer vision (preprocessing, segmentation, machine learning, deep learning, etc), which feed into genomic analyses and molecular breeding applications. · Deploy software tools and pipelines for routine breeding application through automation or for end-users through web-apps or Notebooks. · Perform scouting activities for novel tools and technologies. · Design, improve and maintain IT infrastructure and solutions for our Trait Genetics team. · Build and maintain an internal and external network of collaborations. · Provide functional and organizational leadership. *Your profile* · PhD in a relevant field in computer science or biology with a strong computational focus (for example bioinformatics, data science) and preferably >2 years experience in industry. · You have a thorough understanding of the Linux operating system and are proficient in coding in Python and R (other programming languages are nice to have). - Proven experience in advanced computer vision applications preferably using various deep learning approaches (for example for object detection and segmentation). - Proven experience in analyzing large datasets and data visualization. · Experience with DevOps (Kubernetes, Docker), databases (SQL), workflow management (Airflow) and cloud computing (Azure) is desirable. · Experience with front-end development (Dash, Pyscript, Rshiny) is desirable. - Prior knowledge of biology is not essential, but affinity with plant breeding and quantitative genetics is desirable. · Ability to work independently as well as in fast-paced multidisciplinary teams. · Inquisitive, innovative and critical mind-set and a creative and pro-active attitude. · Ability to communicate across disciplines and functions. · Excellent command of English and willingness to learn Dutch. Vancy can be found online on : https://emea.dummenorange.com/site/nl/vacatures/detail?job=project-lead-art… *Camillo Berenos*

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[bioinfo] CMSB 2022: call for participation
by BeNeLux bioinformaticians forum 09 Oct '23

09 Oct '23

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