July 2021 - 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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NERC Bursaries for Edinburgh Genomics Courses
by TRAIN edgenomics-training 02 Mar '22

02 Mar '22

Dear All We are pleased to announce we have a number of bursaries available to cover up-to the full fees of any of our upcoming bioinformatics courses. These bursaries are available to UK based students or researchers funded by the NERC or working on research that falls under the remit of the NERC (https://nerc.ukri.org/research/portfolio/remit/) Bursaries are available for any of our courses (see below) but are available for a LIMITED TIME ONLY: They are available for any course booked BEFORE 27th MARCH. So please don't wait to sign up! Our upcoming courses: Linux for Genomics, 13th March - An introduction to working on the command line, running commands and handling data relevant to bioinformatics. https://genomics.ed.ac.uk/services/linux-genomics R for Genomics, 14-15th March - An introduction to the statistical environment R, taking you from the very basics to writing basic functions and creating beautiful figures with ggplot2 https://genomics.ed.ac.uk/services/r-genomics Introduction to Python for Biologists, 18-22 March - This introductory course gives an overview of the language with an emphasis on practical problem-solving, using examples and exercises drawn from various aspects of bioinformatics work. https://genomics.ed.ac.uk/services/introduction-python-biologists-0 Data Manipulation and Visualisation with Python, 08 - 12 April - Python has a many high-quality libraries for working with scientific data. In this workshop we will see how to leverage these libraries to efficiently work with and visualise large volumes of data. https://genomics.ed.ac.uk/services/data-manipulation-and-visualisation-pyth… Introduction to RNA-seq Data Analysis, 9-10th May - This two-day course takes you through a tried-and-tested workflow for analysing RNA-seq data, from read mapping and QC to differential expression and result visualisation. https://genomics.ed.ac.uk/services/introduction-rna-seq-data-analysis If you think you are provably eligible for one of these bursaries, sign up to your desired course through the link provided and we will be in contact regarding fees. Kind Regards Nathan Medd Training and Outreach Manager - Edinburgh Genomics G.06, Ashworth Laboratories, Charlotte Auerbach Road, The King's Buildings, The University of Edinburgh, EH9 3FL, Edinburgh, Scotland Edinburgh Genomics' Privacy Notice can be viewed at: http://genomics.ed.ac.uk/about-us/privacy-notice This email and any attachments are confidential and intended solely for the use of the recipient(s) to whom they are addressed. If you have received it in error, please destroy all copies and inform the sender. The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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Open Position in Marseille Medical Genetics - Computational Biology for Rare Diseases
by Anaïs BAUDOT 24 Jul '21

24 Jul '21

We have an open position for a research engineer in bioinformatics/computational biology. The successful applicant will be involved in the development of bioinformatics tools and software based on graph theory, dimensionality reduction and machine learning. The applications will focus specifically on rare diseases and involve the analysis of a wide range of -omics data. Offer Fully-funded position for 1 year in Marseille, with the possibility to be renewed. The starting date is expected in 2021. The salary will be based on experience. The MMG Unit is located in the La Timone faculty of Medicine campus and is a leader in the field of rare genetic diseases. Qualifications - PhD in Bioinformatics, Computational Biology, Computer Sciences or related fields. - Solid knowledge in manipulation and analysis of a wide variety of biological -omics data - Proficiency in programming (R, Python, bash...), solid knowledge in the Linux environment and experience in algorithm implementation - Experience in the development of bioinformatics workflows or packages - Flexibility and adaptability to work in a multidisciplinary environment on multiple projects and in collaboration - Good communication and reporting skills More information https://www.marseille-medical-genetics.org/a-baudot/ I wish you all a very good summer! Anaïs --------------------------------------------------------- Anaïs BAUDOT MMG, Marseille Medical Genetics U 1251, Faculté de Médecine de La Timone, 27 Bd Jean Moulin 13385 Marseille Cedex 5 0491324948 France anais.baudot(a)univ-amu.fr

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Open position at the European Institute for Systems Biology and Medicine
by Bertrand 22 Jul '21

22 Jul '21

The EISBM is hiring a developer for AI based on multiple oncology data modalities. Key words: Computational systems biology, machine learning/AI, web platform, clinical users’ acceptance. We are looking for a dynamic and self-driven candidate thrilled to join an international cross-disciplinary team of biologists, clinicians, epidemiologists and computer scientists from academy and industry in their effort to better understand and treat solid tumour cancers. Scientific project: This job offer is in relation with an Innovative Medicines Initiative (IMI) Research and Innovation Actions project. We aim at revolutionise oncology care in Europe by designing, developing, and delivering the first interoperable and GDPR-compliant European real-world oncology data and evidence generation platform, along with decision support toolsets for prostate, lung and breast cancer. By designing this platform from the onset based on the needs of the clinicians and patients in an inclusive and sustainable way, the project aims to strengthen shared decision-making based on innovative data and AI-driven technology and tools. To achieve our vision, we have united the key partners from other data-driven European wide oncology initiatives (PIONEER, EHDEN, HARMONY) in our project along with Europe’s leading clinicians in the fields of breast, prostate and lung cancer. At the core of the project are the major guideline offices of the three indications, whilst the project is further strengthened by patient advocacy groups, professional societies and 6 SMEs as partners. The platform will build on existing open source solutions such as the OMOP-CDM , tranSMART and OHDSI ATLAS whilst developing novel AI models based on federated learning to facilitate knowledge discovery. At the start of the project, we will already have access to datasets covering over 120M people in Europe, along with high quality data patient cohorts for AI model building. Moreover, the platform will be hosted in-kind on existing infrastructure. Finally, we envision sustainability of the platform through a value-based approach with various business models for commercial users. Job context: She/he will be part of the association EISBM led by Charles Auffray and based in the Lyon suburban area. EISBM is an equal opportunity employer offering attractive compensation packages and flexible working conditions. Scope: -Participation in the development of AI models based on multiple data modalities (clinical, omics, imaging…) to answer several clinical research questions selected within the project. -Integration of those models with the project’s web platform and with clinical guidelines-based models developed in the project. -Gathering and prioritization of the user’s feedback (clinicians, researchers) using the AI models. -Participation in the performance evaluation of the models and the web platform, including the level of use/acceptance by the users. Skills: Engineer degree with 3+ years of experience, master’s degree in computer science with 3+ years of experience or PhD in sciences with the relevant expertise in the following: -Machine learning (R, python…) -AI (deep learning, convolutional neural network, natural language processing) -Knowledge of the OMOP common data model -Federated learning (e.g. NVIDIA Clara framework) -Communication skills within an inter-disciplinary team of clinicians, patients, epidemiologists -Fluent in English Contract details: This contract will be for up to 48 months, starting in Q4 2021. The salary will be depending on qualifications and experience, based on the pharmaceutical industry salary grid. The applicants should send their CV, cover letter and two references to: jobs(a)eisbm.org <mailto:jobs@eisbm.org>, with the reference 'EISBM-07-21-AI-BBC' Shortlisted candidates will be invited for an interview. With my best regards, Bertrand De Meulder, Senior Researcher, association EISBM -- L'absence de virus dans ce courrier électronique a été vérifiée par le logiciel antivirus Avast. https://www.avast.com/antivirus

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Open position at European Institute for Systems Biology and Medicine
by Bertrand 22 Jul '21

22 Jul '21

The EISBM is hiring an oncology guidelines-based clinical decision support systems developer. Key words: Computational systems biology, clinical guidelines modelling, integration, web platform, acceptance. We are looking for a dynamic and self-driven candidate thrilled to join an international cross-disciplinary team of biologists, clinicians, epidemiologists and computer scientists from academy and industry in their effort to better understand and treat solid tumour cancers. Scientific project: This job offer is in relation with an Innovative Medicines Initiative (IMI) Research and Innovation Actions project. We aim at revolutionise oncology care in Europe by designing, developing, and delivering the first interoperable and GDPR-compliant European real-world oncology data and evidence generation platform, along with decision support toolsets for prostate, lung and breast cancer. By designing this platform from the onset based on the needs of the clinicians and patients in an inclusive and sustainable way, the project aims to strengthen shared decision-making based on innovative data and AI-driven technology and tools. To achieve our vision, we have united the key partners from other data-driven European wide oncology initiatives (PIONEER, EHDEN, HARMONY) in our project along with Europe’s leading clinicians in the fields of breast, prostate and lung cancer. At the core of the project are the major guideline offices of the three indications, whilst the project is further strengthened by patient advocacy groups, professional societies and 6 SMEs as partners. The platform will build on existing open source solutions such as the OMOP-CDM , tranSMART and OHDSI ATLAS whilst developing novel AI models based on federated learning to facilitate knowledge discovery. At the start of the project, we will already have access to datasets covering over 120M people in Europe, along with high quality data patient cohorts for AI model building. Moreover, the platform will be hosted in-kind on existing infrastructure. Finally, we envision sustainability of the platform through a value-based approach with various business models for commercial users. Job context: She/he will be part of the association EISBM led by Charles Auffray and based in the Lyon suburban area. EISBM is an equal opportunity employer offering attractive compensation packages and flexible working conditions. Scope -Participation in the development of clinical guidelines modelling. -Participation to the integration of those models in a clinical decision support tool compatible with several data models in place in hospitals (HL7-FHIR) -Integration of the clinical decision support tool in the project’s web platform -Gathering and prioritization of users’ feedback using the clinical decision support tool and the web platform -Participation to the evaluation of the tool’s performances and the clinicians use and acceptance of the tool and web platform. Skills Engineer degree with 3+ years of experience, master’s degree in computer science with 3+ years of experience or PhD in sciences with relevant experience in the following: -Modelling -Software development in a collaborative environment -Clinical data standards and models (HL7-FHIR, OMOP) -Communication skills with interdisciplinary team (clinicians, patients, epidemiologists…) -Fluent in English Contract details: This contract will be for up to 60 months, starting in Q4 2021. The salary will be depending on qualifications and experience, based on the pharmaceutical industry salary grid. The applicants should send their CV, cover letter and two references to: jobs(a)eisbm.org <mailto:jobs@eisbm.org>, with the reference 'EISBM-07-21-Guidelines-BBC' Shortlisted candidates will be invited for an interview. With my best regards, Bertrand De Meulder, Senior researcher, association EISBM -- L'absence de virus dans ce courrier électronique a été vérifiée par le logiciel antivirus Avast. https://www.avast.com/antivirus

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Open position at European Institute ofr Systems Biology and Medicine
by Bertrand 22 Jul '21

22 Jul '21

The EISBM is hiring two research question leads for PIONEER prostate cancer project. Key words: Computational systems biology, data integration and modelling, data standards We are looking for a dynamic and self-driven candidate thrilled to join an international cross-disciplinary team of biologists, clinicians, epidemiologists and computer scientists from academy and industry in their effort to better understand and treat prostate cancer. Scientific project: The PIONEER consortium (https://prostate-pioneer.eu/ <https://prostate-pioneer.eu/>) is part of the Innovative Medicine Initiative (IMI)’s “Big Data for Better Outcomes” umbrella programme. The BD4BO mission is to improve health outcomes and healthcare systems in Europe by maximising the potential of Big Data. PIONEER aims to transform the field of prostate cancer care with particular focus on improving prostate-cancer related outcomes, health system efficiency and the quality of health and social care across Europe. It involves scientists from universities, research institutes, hospitals, members of the pharmaceutical industry and small companies across Europe. Job context: She/he will be part of the association EISBM led by Charles Auffray and based in the Lyon suburban area. EISBM is an equal opportunity employer offering attractive compensation packages and flexible working conditions. Scope: Development and running of statistical and bioinformatics analyses to answer a clinically relevant research question selected by a multi-disciplinary team of researchers. Leadership of at least one research question (from team building across partners of the project until results dissemination). Skills: The candidate has an engineer’s degree, a master’s degree in computer science or a PhD in science with relevant experience in the following: -Programming (R, python) -Application development (R shiny) -Biostatistics and/or bioinformatics analysis for clinical, omics, imaging data -Modelling -Machine learning and/or AI -OMOP common data model and OHDSI ATLAS software -Fluent in English Contract details: This contract will run for the remainder of the PIONEER project (18 months), starting in Q4 2021. The salary will be depending on qualifications and experience, based on the pharmaceutical industry salary grid. The applicants should send their CV, cover letter and two references to: jobs(a)eisbm.org <mailto:jobs@eisbm.org> Shortlisted candidates will be invited for an interview. With my best regards, Bertrand De Meulder, Senior Researcher, association EISBM -- L'absence de virus dans ce courrier électronique a été vérifiée par le logiciel antivirus Avast. https://www.avast.com/antivirus

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FW: sincellTE 2022
by Alexander Botzki 13 Jul '21

13 Jul '21

Dear all, I would like to share with you a single-cell training we are organizing in Roscoff (France) in early 2022 with different partners (including institut Pasteur / Curie) This training is dedicated to bioinformaticians/scientists with a first experience in single data analysis (and familiar with unix/R). This year, we will try to focus on multi-omics and spatial transcriptomics analysis. Feel free to share this training in your different network ! All the best Nicolas Training : Single-Cell : Transcriptomics, Spatial and Multi-Omics (sincellTE) Date : 9 January 2022 - 14 January 2022 Place : Roscoff, France Deadline pre-registration: 15th September 2021 This one-week class focuses on the large-scale study of heterogeneity across individual cells from the genomic, transcriptomic and epigenomic points of view. New technological developments enable the characterization of molecular information at a single cell resolution for large numbers of cells. The high dimensional omics data that these technologies produce comes with novel methodological challenges for the analysis. In this regard, specific bioinformatics and statistical methods have been developed in order to extract robust information. This course is directed towards engineers and researchers who regularly need to undertake single-cell data analysis as well as PhD Student and Post Doc in computational biology or bioinformatics that are interested in the development of methods and pipelines for highly dimensional single-cell data analysis. A wide range of single cell topics will be covered in lectures, demonstrations and practical classes. Among others, the areas and issues to be addressed will include the choice of the most appropriate single-cell sequencing technology, the experimental design and the bioinformatics and statistical methods and pipelines. For this edition, new courses/practicals will focus on spatial transcriptomics, cell phenotyping and additional multi-omics. Requirements : Participants must have prior experience on NGS data analysis with everyday use of R and good knowledge of Unix command line. Before the training, participants will be asked to familiarize themselves with the processing and primary analyses steps of scRNA-seq datasets with provided pedagogic material. It is not necessary to have personal single-cell data to analyse. All information and pre-registration: https://www.france-bioinformatique.fr/formation/single-cell-2022/ -- Nicolas Servant, PhD co-Director of the Bioinformatics core facility Bioinformatics & Biostatistics Analysis Team Institut Curie INSERM U900 - Institut Curie - Mines ParisTech 26, rue d'Ulm - 75248 Paris Cedex 05 - FRANCE Nicolas.Servant(a)curie.fr<mailto:Nicolas.Servant@curie.fr> +331 56 24 69 85

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BSC: Life Sciences vacancy
by BSC Human Resources 13 Jul '21

13 Jul '21

Dear all, We would like to inform you about a new job opportunitiy offered by Barcelona Supercomputing Center: - PhD student in Computer Science and Bioinformatics (R1). Deadline: 31 August, 2021 Link here <https://www.bsc.es/join-us/fellowships/25121lsiconbir1> We would appreciate that you share the information with your contacts. Sincerely, /Human Resources/* Barcelona Supercomputing Center – Centro Nacional de Supercomputación* Tel. +34- 934137745 <mailto:anais.delastre@bsc.es>www.bsc.es <http://www.bsc.es/>

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Erasmus Summer Programme 2021 - Advanced Course on Genome-Wide Association Studies
by Vid Prijatelj 08 Jul '21

08 Jul '21

To all interested, This year's revamped edition is offered completely online, under the organizational arm of the programme director of Genomic & Molecular Epidemiology programme at NIHES - prof. dr. Fernando Rivadeneira. View this email in your browser <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmailchi.m…> Genome-wide association studies [ESP74] *Do you have a study that has been or will soon be profiled for GWAS? This course is perfect if you want to receive state-of-the-art training in how to perform the statistical analysis of a GWAS yourself.* The course Genome-wide association studies (GWAS) constitute a powerful approach to investigate the genetic basis of complex traits and disorders. The course consists of virtual lectures providing a conceptual framework on crucial aspects of quality control, genotype imputation, methods to detect and correct for stratification, meta-analysis and genomic annotation of GWAS signals. *Register here* <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fnihes.us2…> [image: Twitter] <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fnihes.us2…> [image: Facebook] <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fnihes.us2…> [image: LinkedIn] <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fnihes.us2…> [image: YouTube] <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fnihes.us2…> [image: Website] <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fnihes.us2…> *Copyright © 2021 NIHES, All rights reserved.* test *Our mailing address is:* NIHES Postbus 2040 ROTTERDAM, Zuid-Holland 3000 CA Netherlands Add us to your address book <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fnihes.us2…>

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Bioinformatician MSc/PhD
by Hanneke van Deutekom 06 Jul '21

06 Jul '21

Hi all, I have a vacancy in my team; https://www.werkenbijumcutrecht.nl/international/vacancies/Pages/bioinforma… The Genetics department is in search of an enthusiastic, creative bioinformatician to strengthen their bioinformatics team. Patient care is central to the Genetics department. Therefore, we constantly innovate. Bioinformatics has a crucial role in this innovation. Within the Genetics department, the bioinformatic challenges range from the detection of genetic variants using different techniques (e.g. WGS, RNAseq, and long-read sequencing) to advanced data analysis and interpretation. We offer an innovative, multidisciplinary environment in which you will work as an independent professional on the development of a new standard in genetic care. We are in need of a talent who can develop software that integrates WGS data and RNA sequencing data to interpret genetic variants. You will contribute to shape the genetic care of the future! Best wishes Hanneke van Deutekom Head of Bioinformatics, Genome Diagnostics, Genetics, UMC Utrecht

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