August 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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We are looking for a Senior Scientist, Bioinformatics
by Breukelen, B. van (Bas) 18 Aug '22

18 Aug '22

Senior Scientist, Bioinformatics Research (San Carlos, CA) | Hybrid in Eindhoven, Noord-Brabant, Netherlands | Full Time JOB DESCRIPTION Ambagon Therapeutics is an early-stage biotechnology company dedicated to the discovery and development of small molecule molecular glues stabilizing the interaction between the 14-3-3 adaptor proteins and their disease-promoting client proteins. Our academic founders are the world leaders in this novel approach and launched Ambagon with a mission to provide new therapies for unmet needs in oncology. Learn more at our website: www.ambagontx.com<http://www.ambagontx.com/> Ambagon has an immediate opening for a Senior Scientist, Bioinformatics. The successful candidate will be based near Ambagon’s research sites in the San Francisco Bay Area or in Eindhoven, the Netherlands and will report to the Executive Director, Structural Biology & Informatics. This role is an opportunity to join Ambagon as an early employee, bringing your scientific talent and passion to build the company. Key responsibilities include, but are not limited to: * Conduct multi-omic bioinformatics research (RNA-seq, DNA-seq, Chip-seq, Single-cell, CRISPR, RNAi, etc.), and integrate with other preclinical and clinical data sources for exploratory analysis and reporting * Contribute to the strategic planning and design of functional genomic experiments that are critical for the evaluation and understanding of Ambagon’s novel therapeutic agents * Query public data sources and perform necessary computational analysis to answer specific questions regarding target/disease biology and potential biomarker selection * Develop bioinformatics and research application tools for data query, analysis, and visualization to enhance end-to-end scientific processes and enable real time collaboration * Maintain a current understanding of bioinformatics literature and methodology, as well as other scientific literature related to drug discovery projects * Collaborate closely and effectively with researchers across disciplines and serve as a resource for colleagues in a team environment * Prepare and deliver scientific presentations and reports to communicate key findings to the R&D group * Influence discovery decisions and contribute significantly to corporate goals and project milestones * Follow the best practices for ensuring analytical reproducibility The position requires the following experience and qualifications: * PhD degree in Bioinformatics, System Biology, Computational Biology, Biostatistics, Data Science or a related discipline requiring strong computational and statistical skills with ideally at least 2 years of relevant industry experience * Extensive hands-on experience with the wide range of bioinformatics methods for NGS sequence and expression analysis * Strong proficiency in functional genomic data analysis, with solid understanding on the appropriate statistical and bioinformatics methodologies * Experience in analyzing high dimensional genomics and biomarker data from studies in oncology, neurological disorder, and other indications * Proficient in R coding; experience in applying machine learning algorisms to bioinformatic research would be a plus, but not required * Practical knowledge of the latest sequencing technologies, library prep methods, etc. * Good understanding of molecular and cell biology relevant to cancer genomics * Highly motivated and able to work in a fast-paced environment with a desire to learn and tackle new challenges * Proven track record of scientific publications in bioinformatics and genomics * Demonstrated technical proficiency, scientific creativity, problem solving ability, and capable of independently planning and executing functional genomic data analysis * Excellent interpersonal, verbal, and written communication skills are essential in this collaborative and multi-disciplinary team environment * Candidates must be authorized to work in the Netherlands We offer a chance to work with talented people in a collaborative environment and offer a competitive package including, benefits, generous time off, stock options and much more. Ambagon Therapeutics is an equal opportunity employer. We are committed to creating an inclusive environment for all employees. In accordance with applicable law, Ambagon does not discriminate in hiring or otherwise in employment on the basis of race, color, religion, sex, national origin, age, marital or veteran status, disability, sexual orientation, or any other legally protected status. Visit: https://careers.jobscore.com/careers/ambagon/jobs/senior-scientist-bioinfor… For more information you can also send an email to: m.altelaar(a)uu.nl<mailto:m.altelaar@uu.nl>

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Research Assistant/Postdoc position in scRNAseq analysis
by Giorgia Tosoni 17 Aug '22

17 Aug '22

The Neurogenesis & Neurodegeneration lab at the Netherlands Institute for Neuroscience (Amsterdam, NL) has a position open for Post-doc / Research Assistant in Computational Biology. The Neurogenesis & Neurodegeneration laboratory led by Dr. Evgenia Salta employs transcriptomics and other molecular and imaging approaches to map the cellular and molecular complexity of the adult hippocampal neurogenic niche and dissect the biological pathways that are deregulated in Alzheimer’s disease. Check out the vacancies: -Research Assistant: https://nin.nl/about-us/vacancies/research- assistant-in-computational-biology/ -Post-doc: https://nin.nl/about-us/vacancies/postdoc-in- computational-biology/

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Introduction to Linux for Genomics, Online course @ Edinburgh Genomics on the 27-28 September 2022
by Chieko Kontani 15 Aug '22

15 Aug '22

Please forward to new students who might benefit. Hi All, We have online training courses coming up @ Edinburgh Genomics including our Introduction to Linux for Genomics<https://genomics.ed.ac.uk/services/introduction-linux-genomics>, Online course @ Edinburgh Genomics on the 27-28 September 2022 The linux workshop consists of guided tutorials and hands-on exercises. Roughly 3/4 of the workshop will be spent on Linux and 1/4 on command-line tools for genomics and file formats. For more information or to sign up the registration form for the Linux course can be found here<https://forms.office.com/Pages/ResponsePage.aspx?id=sAafLmkWiUWHiRCgaTTcYQO…>. 12 - 15 September (9:00 - 3:30) Variant-Analysis https://genomics.ed.ac.uk/services/variant-analysis Course aims to provide an introduction to the principles of short variant discovery (both germline and somatic) from short read data. We will look at a complete workflow, from data QC to functional interpretation of variant calls. There are many others including an online RNA Seq analysis course<https://genomics.ed.ac.uk/services/rna-seq-data-analysis>! Do join us online! Thank you, Chieko Kontani Project Training and Support Officer Edinburgh Genomics The University of Edinburgh EH9 3FL Scotland, UK genomics.ed.ac.uk Please look at our other training course options here: Training | Edinburgh Genomics<https://genomics.ed.ac.uk/services/training> The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. Is e buidheann carthannais a th' ann an Oilthigh Dh?n ?ideann, cl?raichte an Alba, ?ireamh cl?raidh SC005336.

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Research Assistant/Postdoc position in scRNAseq analysis
by Giorgia Tosoni 15 Aug '22

15 Aug '22

The Neurogenesis & Neurodegeneration lab at the Netherlands Institute for Neuroscience (Amsterdam, NL) has a position open for Post-doc / Research Assistant in Computational Biology. The Neurogenesis & Neurodegeneration laboratory led by Dr. Evgenia Salta employs transcriptomics and other molecular and imaging approaches to map the cellular and molecular complexity of the adult hippocampal neurogenic niche and dissect the biological pathways that are deregulated in Alzheimer’s disease. Check out the vacancies: -Research Assistant: https://nin.nl/about-us/vacancies/research-assistant-in-computational-biolo… -Post-doc: https://nin.nl/about-us/vacancies/postdoc-in-computational-biology/

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BioSB course Integrated Modeling and Optimization (preliminary announcement)
by Bosnacki, Dragan 15 Aug '22

15 Aug '22

Dear colleagues, Also in the new academic year the BioSB research school, Wageningen University & Reserach and Eindhoven University of Technology will organize the course: *Integrated Modeling and Optimization* 12-16 December 2022, Wageningen University Computational modelling is an absolute requisite to gain understanding of the biological mechanisms underlying patterns observed in experimental data. However, one could say that modelling is a craftsmanship, that can only be learned via intense exercising and ‘learning by doing’. In this course we offer the participants the possibility to learn and exercise the modeling process and the optimization techniques needed to fit models to data. In the course the students will learn: - to understand the common ground and the differences for applications of dynamic modeling in metabolic, regulatory, signaling, and multi-scale biological processes - how to set-up a dynamic model to represent biological networks using different interaction mechanisms - to implement, simulate and analyze dynamic network models - to understand the wide variety of problems in modelling that can be solved with optimization · - to apply different types of numerical optimization methods: global and local search methods: steepest descent, Levenberg-Marquardt, genetic algorithms, linear programming. - the combination of dynamic modeling and optimization to integrate experimental data in modelling, estimate model parameters and design experiments. - to understand how numerical optimization (linear programming) works in flux balance analysis to simulate metabolic network models. Lecturers: · Prof. Natal van Riel, Eindhoven University of Technology (course coordinator) · Dr. Aalt-Jan van Dijk, Wageningen University & Research · Prof. Jaap Molenaar, Wageningen University & Research · Dr. Hans Stigter, Wageningen University & Research · Dr. Robert Smith, Wageningen University & Research · Dr. Dragan Bosnacki, Eindhoven University of Technology Target audience: The course is aimed at PhD students with a background in bioinformatics, systems biology, computer science or a related field, and life sciences. Participants from the private sector are also welcome. A working knowledge of mathematics, especially differential equations, is recommendable, but we will distribute preparation material to be studied by students missing the required background. Furthermore, at the start we offer a math refresher to help those participants who are not (yet) involved in modelling on a daily basis. More about the last year's edition: https://www.dtls.nl/courses/integrated-modeling-and-optimization/<https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.dtls.…>  <image001.jpg><https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.dtls.…> Integrated modeling and optimization - Dutch Techcentre for Life Sciences<https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.dtls.…> Course date 13-17 December 2021, Wageningen Location: The course will be held at: Forum Building (building nr 102), with number B0409. A Biocafe (on Thursday) will be held in “The Spot” in Building Orion (gebouw nummer 103) in the Wageningen… www.dtls.nl<https://eur02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.dtls.n…>  More details about the programme and the registration will follow soon. Please feel free to contact Dragan Bosnacki (D.Bosnacki(a)tue.nl) for more information. --------------------- *About BioSB* The Netherlands Bioinformatics and Systems Biology research school (BioSB) is the national platform in which the Dutch community of researchers in bioinformatics and systems biology is organized. BioSB also organizes: 1. fundamental and advanced post-graduate courses <https://eur04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.biosb…<https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.biosb…>> 2. the yearly BioSB conference <https://eur04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.biosb…<https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.biosb…>> 3. hot topics meetings <https://eur04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.biosb…<https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.biosb…>> The aim of the BioSB research school is to offer PhD students, postdocs and senior researchers a vibrant environment for their scientific development as well as education in bioinformatics and systems biology. In addition, BioSB acts as a parent organization for YoungCB <https://eur04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.youngc…<https://eur02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.youngc…>>, the official Regional Student Group (RSG) of the International Society of Computational Biology (ISCB).

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Colloquium on Bioinformatics Learning, Education and Training (CoBLET) and GOBLET AGM, 11-14 October 2022, Istanbul, Turkey (Hybrid event)
by Celia van Gelder 14 Aug '22

14 Aug '22

Dear all, We are delighted to invite you to the 1st Colloquium on Bioinformatics Learning, Education and Training (CoBLET), which will be held hybridly from 11-14th October 2022. CoBLET2022 will be in conjunction with the 11th annual general meeting (AGM) of the Global Organisation for Bioinformatics Learning, Education and Training (GOBLET). CoBLET2022 will be a hybrid event and will be held for the first time in Turkey, hosted by Bezmialem Vakıf University, Istanbul. We have a great organizing team in place from Bezmialem Vakif University, and under the lead of Asif Khan, GOBLET Executive Board Member, an award was obtained from Code for Science & Society, made possible by a grant from The Chan Zuckerberg Initiative. COBLET2022 will focus on thematic discussions targeting education and training in bioinformatics. A mix of keynotes, short talks, poster sessions and an Eduthon shall foster an interactive environment for integrated bioinformatics education and training. We invite you to look at the programme and submit your abstracts for oral presentations and/or workshops at https://coblet2022.bezmialem.edu.tr/ ! The deadline for the abstract submission is 30 August 2022. Registration is free of charge and you can register at https://coblet2022.bezmialem.edu.tr/registration . We are looking forward to seeing you at CoBLET2022, whether it will be in person or virtually! Best regards Celia van Gelder, Chair of GOBLET Ayesha Fatima, Chair of the COBLET 2022 Organizing Committee -- Dr. Celia W.G. van Gelder Training Programme Manager DTL/ELIXIR-NL/Health-RI tel. +31613375327 e-mail: celia.van.gelder(a)dtls.nl websites: https://www.dtls.nl/, https://www.health-ri.nl/, https://www.elixir-europe.org/platforms/training twitter: celia_vgelder Office: DTL | Jaarbeurs Innovation Mile (JIM) | 6th floor Beatrixgebouw | Jaarbeursplein 6 | 3521 AL Utrecht While I may be sending this email outside my normal office hours, I have no expectation to receive a reply outside yours. -- Dr. Celia W.G. van Gelder Training Programme Manager DTL/ELIXIR-NL/Health-RI tel. +31613375327 e-mail: celia.van.gelder(a)dtls.nl websites: https://www.dtls.nl/, https://www.health-ri.nl/, https://www.elixir-europe.org/platforms/training twitter: celia_vgelder Office: DTL | Jaarbeurs Innovation Mile (JIM) | 6th floor Beatrixgebouw | Jaarbeursplein 6 | 3521 AL Utrecht While I may be sending this email outside my normal office hours, I have no expectation to receive a reply outside yours.

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Job opening for a clinical bioinformatician
by Kemmeren-2, P.P.C.W. (Patrick) 11 Aug '22

11 Aug '22

Dear all, Within the Princess Maxima Center for Pediatric Oncology we currently have an opening for a clinical bioinformatician to develop and operate our whole-exome and RNA-sequencing based diagnostic pipelines. Interested in working in a stimulating, cross-disciplinary research hospital dedicated to curing children with cancer, then please apply using the link below! https://werkenbijprinsesmaximacentrum.nl/en/vacancy/clinical-bioinformatici… Also on behalf of Dr. Jayne Hehir-Kwa. 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_3129348511] [signature_1704258484] 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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Permanent position of Scientist in Modelling and Systems biology at Gencovery
by Karoline Faust 10 Aug '22

10 Aug '22

Permanent position of Scientist in Modelling and Systems biology * Company: Gencovery SAS * Website: https://gencovery.com * Starting date: Sept 2022 * Contact: D. A. Ouattara, douattara(a)gencovery.com<mailto:douattara@gencovery.com> Description of the company GENCOVERY is a software company based in Lyon (France) which develops a collaborative AI software to accelerate bioengineering and bioproduction processes of biotechnology and pharmaceutical companies. The developments of the company are focused on two axes: * - a collection of algorithms for the construction and simulation of cell metabolic models, and * - a collaborative software suite, ConstellabTM, designed to handle complex omics data and analytical pipelines. Generated in silico models, called digital twins of cell metabolism, can be used to simulate experiments, and assess biological hypothesis, thereby significantly shortening time and cost of in vivo and in vitro experiments. The company is looking today for a talented scientist in systems biology and cell metabolism modelling to develop and manage its modeling pipelines. Required qualifications * You have a PhD in systems biology and/or bioinformatics * You have a strong expertise in the modelling of cell metabolism, modelling of the metabolism of microbial communities (e.g. whole-genome metabolic modelling, metabolic network reconstruction, flux balance/variability analysis, cell metabolic interactions, keystone species analysis, etc.). Gencovery, SAS – 47 Boulevard du 11 Novembre 1918, 69100 Villeurbanne, https://gencovery.com Connecting people through innovation [page2image38214352] * You have a good experience in the analysis of omics data (e.g. genomics, transcriptomics, proteomics, metabolomics data). * You have a good experience on standard bioinformatics tools and databases: o Python, R, Jupyter lab, o Biopython, Scikit-learn, Pandas, o Reference Fluxomics / FBA toolboxes (e.g. OpenCobra) o NCBI databases, EMBL-EBI databases, Kegg, BioCyc, etc. o BioModels, BiGG, Agora databases, etc. Missions * You will be in charge of developing the in-house bioinformatics and modeling pipelines that will feed our portfolio of analytics methods. * You will be accountable of the execution and delivery of the bioinformatics analyses to our clients (data integration and curation, modelling and simulation, reporting). * Your will be in charge of the supervision of bioinformaticians and students. Working place Gencovery technologies are designed for collaborative remote work. This is important for next-generation research and development with the COVID-19 pandemic. Gencovery has therefore decided to encourage and develop remote work for its own employees. The recruited candidate must be autonomous and committed to quality reporting. She/He will have the opportunity to be based outside Lyon during the first 3 months but is expected to move to Lyon after. Closing application date: 31 Aug. 2022 Position type: Permanent position Salary: Attractive with career evolution opportunities To apply for this position, please send a resume and cover letter to: douattara(a)gencovery.com<mailto:douattara@gencovery.com>

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Student positions - Computational Cancer Research
by Vosberg, Sebastian 10 Aug '22

10 Aug '22

Dear list members, for my research group (Computational Cancer Research) at Medical University of Graz, I am seeking for a PhD candidate with a high interest in implementing bioinformatics approaches to cancer research questions. Candidates may have any background such as bioinformatics/biology/genetics/biotechnology/medicine/etc. Here a quick overview of our work: We are aiming at developing novel computational approaches for cancer research with a major focus on characterizing the molecular background of tumors across different omics levels and its evolution under therapy. We want to learn about mechanisms of treatment resistance and/or cancer recurrence and to stratify personalized treatment options. Our projects are motivated by actual clinical research questions and we work in a highly interactive environment with very close contact to clinicians and wet-lab researchers. In particular, I am currently seeking for a PhD student for a computational cancer research project focusing on epigenetic signatures in lung and breast cancer, starting as soon as possible. More details can be found at https://www.medunigraz.at/doktoratsstudien/phd-program/phd, interested candidates may apply via the online form until September 20. Thank you very much and best wishes, Sebastian Vosberg

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