August 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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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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Amazing opportunities to learn Git and GitHub!
by BeNeLux bioinformaticians forum 23 Aug '23

23 Aug '23

[cid:image001.png@01D91546.6FFD3720] [signature_2008044598] Git and GitHub at VIB/ELIXIR-BE, check NOW! Dear colleagues, Join us for some amazing training sessions! Don’t forget to subscribe! Introduction to Git & GitHub ____________________________________________________________________________________ 11th and 12th Sep 2023 – Leuven Face to Face training This workshop will take you through the basic use of Git and GitHub. Git is a free and open source distributed version-control system designed to maintain code, track changes, recover old versions and collaborate with other developers The course will happen in the Park inn by Radisson in Leuven, next to the trains station (only 3 min walk). Easy to find! 2 days you can use Git on your own projects and for collaborations! Come join us! If you want to know of more about VIB<https://training.vib.be/all-trainings?date=Upcoming%20trainings> and ELIXR-BE<https://www.elixir-belgium.org/training> trainings, check our website. VIB Technology Training & ELIXIR Belgium Training teams Technologiepark-Zwijnaarde 75 9052 Zwijnaarde, Belgium [signature_2008044598] [cid:image001.png@01D91546.6FFD3720] [cid:image003.png@01D966EB.C9291200]

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Autumn courses at VIB/ELIXIR-BE, check NOW!
by BeNeLux bioinformaticians forum 18 Aug '23

18 Aug '23

[cid:image001.png@01D91546.6FFD3720] [signature_2008044598] [Pumpkin with solid fill] Autumn courses at VIB/ELIXIR-BE, check NOW! Dear colleagues, Join us for some amazing training sessions! Don’t forget to subscribe! Introduction to Git & GitHub ____________________________________________________________________________________ 11th and 12th Sep 2023 – Leuven Face to Face training This workshop will take you through the basic use of Git and GitHub. Git is a free and open source distributed version-control system designed to maintain code, track changes, recover old versions and collaborate with other developers Registration and info: Link for Git & GitHub<https://training.vib.be/all-trainings/introduction-git-github-7> Docker and Singularity for reproducible and automated data analysis ____________________________________________________________________________________ 12th and 13st Oct 2023 – Brussels Face to Face training The course will give an introduction to containers (Docker & Singularity) which are great components to achieve portability and reproducibility of your analysis. You will learn how to use containers and how to build a container from scratch, share it with others and how to re-use and modify existing containers. After an extensive explanation on Docker containers, Singularity will be highlighted as well. Registration and info: Docker and Singularity <https://training.vib.be/all-trainings/docker-and-singularity-apptainer-repr…> Nextflow for reproducible and automated data analysis ____________________________________________________________________________________ 16th and 17st Nov 2023 – Ghent Face to Face training You will learn how to use Nextflow for building scalable and reproducible bioinformatics pipelines and running them on a personal computer, cluster and cloud. Starting from the basic concepts we will build our own simple pipeline and add new features with every step, all in the new DSL2 language. Registration and info: NextFlow<https://training.vib.be/all-trainings/nextflow-reproducible-and-automated-d…> Research Data Management: your ally on the way to your publication ____________________________________________________________________________________ 13th and 14st Nov 2023 – Leuven Face to Face training It is better to start with the publication in mind! In this course you will learn how to use Research Data Management (RDM) in order to improve the writing of your publications and potentially increase its impact. Starting from basic concepts together with hands-on activities and discussions, during two days you will learn how to standardize, document and submit your data in a repository and how all of this will help you to underpin your publication! Registration and info: RDM is your ally<https://training.vib.be/all-trainings/research-data-management-your-ally-wa…> If you want to know of more about VIB<https://training.vib.be/all-trainings?date=Upcoming%20trainings> and ELIXR-BE<https://www.elixir-belgium.org/training> trainings, check our website. VIB Technology Training & ELIXIR Belgium Training teams Technologiepark-Zwijnaarde 75 9052 Zwijnaarde, Belgium [signature_2008044598] [cid:image001.png@01D91546.6FFD3720] [cid:image003.png@01D966EB.C9291200]

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PhD position in Bioinformatics: Investigating protein evolution using machine learning
by BeNeLux bioinformaticians forum 18 Aug '23

18 Aug '23

The Bioinformatics group at Wageningen University is seeking a PhD student - do you want to apply state-of-the-art machine learning methods on gene sequences and protein structures to analyze evolutionary patterns? Then this vacancy may be of interest to you! Orphan genes are genes that can only be found in one species. Even though more and more sequencing data is available, we cannot find homologs of these genes outside of that single species. The evolution of such genes is particularly intriguing, since they might arise from very fast divergence beyond recognition or entirely novel “from scratch” from a region that did not code for a protein before. Alternatively, some might simply be artefacts of the automatic annotation. Orphan genes have been mainly studied in eukaryotes, where they are associated with organismal novelties and species-specific traits, and are generally thought to be important for adaptation. Much less is known about prokaryotic orphans. However, prokaryotes evolve rapidly and are exposed to changing environments, in which orphan genes might provide novel adaptations. In this project, we will investigate orphans in human gut microbiome species. We will use state-of-the art machine learning approaches to study the properties of orphans and to learn about their evolutionary origin and potential function. In particular, we plan to use predicted protein structures to detect remote homology and to investigate the properties of proteins with potentially novel functions. This work will contribute to a fundamental understanding of how proteins evolve. The research is embedded within the Bioinformatics Group at Wageningen University, the Netherlands. Your daily supervisors will be dr. Anne Kupczok and dr. Aalt-Jan van Dijk, with complementary expertise: molecular evolution of microbes (Anne Kupczok) and machine learning and protein structures (Aalt-Jan van Dijk). Your qualities The ideal candidate must have the following qualities: * A successfully completed MSc degree in bioinformatics, biology, data science or a related discipline; * Proficiency in programming (e.g. in Python); * Experience in applying machine learning to biological data; * Strong affinity with molecular evolution and/or prokaryote genomics; * Good statistical and mathematical skills; * Perseverance in problem solving; * Excellent writing and oral communication skills in English. You can find more information and the application link here: https://www.wur.nl/en/vacancy/phd-researcher-in-bioinformatics-investigatin… -- Dr. Anne Kupczok Assistant Professor Bioinformatics, Department of Plant Sciences, Wageningen University http://www.wur.nl/en/Expertise-Services/Chair-groups/Plant-Sciences/Bioinfo…

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Two bioinformatics positions at the Erasmus MC
by BeNeLux bioinformaticians forum 17 Aug '23

17 Aug '23

Dear all, We have two bioinformatics positions available at the Department of Hematology, Erasmus MC. Both with an application deadline set at 30 August 2023 (ongoing selection): Bioinformatician Hematology: The department of Hematology seeks to recruit a highly motivated bioinformatician to join the multiple myeloma research group at the Erasmus MC. Multiple myeloma remains an incurable hematological cancer. At the department of hematology, scientists and clinicians collaborate to study myeloma development, progression and therapy response. Our research depends on molecular techniques, including single-cell RNA and ATAC sequencing, spatial transcriptomics and proteomics, and multi-parameter flow cytometry. You will join a research team operating at the interphase of wet-lab and in-silico analysis, and will work in close collaboration with PhD students and postdocs. Together with other bioinformaticians in the department, you will work on the development and implementation of novel and existing bioinformatical analysis pipelines. https://www.werkenbijerasmusmc.nl/en/vacancy/93828/bioinformatician-hematol… Senior Bioinformatician Hematology: We seek to recruit a highly motivated and skilled senior bioinformatician. With the advent of high-throughput methodologies and the increased sequencing pace, the need for proficient data analysis and interpretation is ever-growing. To cope with this increased demand of expert-level data analysis, we are now expanding our bioinformatics team. In this position, you will be involved in the support and development of new computational tools in concert with the research programs active within our department, are responsible for managing the bioinformatics team, keep the bioinformatics and research teams updated on the latest technological developments and independently initiate new collaborations to further our departmental research aims. Our current primary focus is on single-cell technologies, including single cell transcriptomics and spatial multiomics, and the development of new computational tools supporting our high-throughput-dependent research goals. You will be tasked with supporting and developing these technologies to make a lasting impact on our research. https://www.werkenbijerasmusmc.nl/en/vacancy/93827/senior-bioinformatician-… Do not hesitate to get in touch in case you would like to receive more information! ---- Mathijs Sanders Assistant Professor

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Phd in computational oncology at Institut Curie, Paris - machine learning for fighting cancer
by BeNeLux bioinformaticians forum 16 Aug '23

16 Aug '23

To anyone who may be interested: There is a position open for a talented PhD student in computational oncology. See details below: https://sysbio.curie.fr/texts/PhdComputationalOncologyInstitutCurieParis.pdf https://twitter.com/SysBioCurie/status/1678314494856970241?s=20 Best --- Marek Ostaszewski University of Luxembourg Luxembourg Centre for Systems Biomedicine (LCSB) Campus Belval | House of Biomedicine 6, avenue du Swing, L-4367 Belvaux, Luxembourg Tel: +352 46 66 44 5604 http://lcsb.uni.lu

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PhD position in integrative analysis of multi-omics spatial data
by BeNeLux bioinformaticians forum 08 Aug '23

08 Aug '23

Hi all, We have an opening for a PhD position in our group at the Leiden University Medical Center (Netherlands) to develop computational methods to analyze multi-omics spatial data to decipher biological processes involved in kidney development and regeneration. This is a collaboration with the lab of Prof. Ton Rabelink (Nephrology). Please don't hesitate to contact me for more details. *Deadline: 13 August 2023* Cheers, Ahmed *Ahmed Mahfouz, PhD **| Associate **Professor, Department of Human Genetics* Leiden University Medical Center | Dept. of Human Genetics | P.O. Box 9600, 2300 RC Leiden | Postal zone S4-P Room R-04-022 | Phone +31 71 52 69513 https://www.mahfouzlab.org/

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PhD student in computational analysis of health trajectories (R1)
by BeNeLux bioinformaticians forum 07 Aug '23

07 Aug '23

Hello, I hope this email finds you well. I am contacting you because we have opened a new PhD Student vacancy in the Life Sciences department, and we would be grateful if you could share them it with your contacts and post them in your website: * *PhD student in computational analysis of health trajectories (R1): *https://www.bsc.es/join-us/fellowships/38623lscbr1 o Deadline 16th of Septemnber If you need further information regarding any of our vacancies, or you need any additional steps from my side in order to disseminate it, please let me know. Thank you! Best regards, -- Laura Delshams /Human Resources - Talent & Development Officer/ *Barcelona Supercomputing Center – Centro Nacional de Supercomputación* <mailto:anais.delastre@bsc.es>Tel. +34- 93 413 40 72 <http://www.bsc.es/>laura.delshams(a)bsc.es www.bsc.es <http://www.bsc.es/>

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Open slots for BePA!VIB International Summer School from 28/08
by BeNeLux bioinformaticians forum 04 Aug '23

04 Aug '23

Dear all, Due to several cancellation, I'd like to warmly invite you to fill the open slots for the up-coming BePA@VIB International Proteomics Summer School. Don't hesitate to register at https://training.vib.be/all-trainings/bepavib-international-proteomics-summ… Best regards, Alex Alexander Botzki VIB Technology Training, ELIXIR Belgium Training Coordinator Technologiepark-Zwijnaarde 75 9052 Zwijnaarde Belgium tel +32 9 224 9870 https://technologytraining.sites.vib.be | https://elixir-belgium.org/training [signature_490181756]

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