September 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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BioSB news - courses and events
by BeNeLux bioinformaticians forum 27 Sep '23

27 Sep '23

Dear all, The BioSB research school is happy to invite you to the HotTopic Symposium: Computational Methods for (single cell) Spatial Data Analysis<https://www.dtls.nl/events/biosb-hottopics-symposium-computational-methods-…> – LUMC Leiden, 17 November 2023 (Free entrance after registration) BioSB and ‘single cell network Netherlands’ (scNL) are co-organising this symposium. The goal of this informal meeting is to bring together people who are interested in this topic in order to learn about the latest development, and to build a community. For more information click here. <https://www.dtls.nl/events/biosb-hottopics-symposium-computational-methods-…> BioSB also announces that registration is open for BioSB course: Integrated Modeling and Optimization<https://www.dtls.nl/courses/integrated-modeling-and-optimization-fundamenta…> - Wageningen, 11 - 15 December 2023 (early bird fee till October 16) 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. For more information click here<https://www.dtls.nl/courses/integrated-modeling-and-optimization-fundamenta…>. Last but not least: please mark your calendars and SAFE THE DATE for The BioSB 2024 conference: 18 - 19 June 2024, Egmond aan Zee, NL. More information will follow soon! We hope to see many of you at one of the BioSB events and courses. Be welcome! Best regards, Petra Aarnoutse BioSB community manager [cid:part1.pLKCtXnZ.4aYrC2St@health-RI.nl]

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Open Positions - BioMed X, Germany
by BeNeLux bioinformaticians forum 25 Sep '23

25 Sep '23

Hello, My name is Bianca, and I am the Recruiting & Communications Manager at the BioMed X Institute<https://bio.mx/>, in Heidelberg, Germany. We have two open positions in one of our research teams - Team VPE<https://bio.mx/research-teams/artificial-intelligence/team-vpe/>, Virtual Patient Engine - to be filled out by researchers with expertise in machine learning/AI and bioinformatics. Would it be possible for you to advertise these two positions? We would be very grateful for your help. Here are the links, let me know if you require more information (or if the information needs to be in a different format): 1) Bioinformatician Position at BioMed X<https://atpscan.global.hornetsecurity.com/index.php?atp_str=kpHUHng3sjeHbfj…> 2) Algorithm Researcher Position at BioMed X<https://atpscan.global.hornetsecurity.com/index.php?atp_str=EspSwRYAmgFUwDv…> Thank you very much! Best wishes, Bianca --------------------------------------------------- Flavia-Bianca Cristian PhD Recruiting & Communications Manager [cid:image001.jpg@01D9EFBF.4A084BF0] BioMed X GmbH Im Neuenheimer Feld 515 69120 Heidelberg, Germany Tel.: +49 6221 426 11 706 Mobile: +49 172 7540707 E-Mail: fbc(a)bio.mx<mailto:fbc@bio.mx> ----------------------------------------------------------------------------------------- Principal Office: Heidelberg Commercial Register: Mannheim, HRB 716390 Managing Director: Dr. Christian Tidona Chairman of the Supervisory Board: Dr. Gerhard Ries -----------------------------------------------------------------------------------------

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PhD application: Integration of multi-omics data for the analysis of microbial community dynamics in plant health
by BeNeLux bioinformaticians forum 23 Sep '23

23 Sep '23

Hi, Please find hereafter an annoncement for a PhD position at INRAe and Inria in modelling and applied mathematics, for the integration of multi-omic data in microbial community models in plant health. https://doctorat.campusfrance.org/en/CF202333407 Sincerely, Valentina Baldazzi & Simon Labarthe

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Vacancy: PhD position in computational single-cell cancer biology
by BeNeLux bioinformaticians forum 21 Sep '23

21 Sep '23

Dear all, For an exciting project using state-of-the-art single cell measurements to elucidate the interplay between cell state and drug response in cancer we are looking for an enthusiastic PhD candidate with a strong quantitative background. The position is shared between the groups of Lodewyk Wessels (NKI) and Evert Bosdriesz (VU). More information in the link. https://werkenbij.vu.nl/ad/phd-kwf-cell-state-dependent-drug-response/mq7m4j Kind regards, Evert Bosdriesz ---- Assistant Professor Bioinformatics - VU Amsterdam www.evertbosdriesz.org | e.bosdriesz(a)vu.nl

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Conference ELIXIR Belgium: Your data, Our services, European success - Registration open
by BeNeLux bioinformaticians forum 21 Sep '23

21 Sep '23

Dear, We are pleased to invite you to the ELIXIR Belgium conference: Your data, Our services, European success which will take place on 23 & 24 October 2023 in Ghent. At this year's national meeting, we will showcase the variety of services in our portfolio with scientists illustrating how the services facilitate their research. The connection with existing European initiatives will also be demonstrated. For the first time, our national event will run for two days - starting on Monday 23 October in the afternoon. Also new are the poster sessions covering more services and providing space for engaging discussions and networking. <https://www.elixir-belgium.org/events/elixir-belgium-your-data-our-services…>Link to the programme and registration <https://www.elixir-belgium.org/events/elixir-belgium-your-data-our-services…>. The registration deadline is 10 October 2023. Please feel free to advertise this further in your network. On behalf of the organising committee, Kim De Ruyck Kim De Ruyck, PhD VIB Data Core ELIXIR Belgium Node Coordinator Technologiepark-Zwijnaarde 71 9052 Zwijnaarde, Belgium

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