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Two job openings for computational biologists - Janssen R&D
by Joke Reumers 11 Aug '21

11 Aug '21

Dear all, We have two new comp bio positions in the Beerse based Discovery Omics team, one focused on computational immunology, one more aimed at using high throughput omics technologies for drug discovery applications. We will consider people at different levels of expertise for this position (fresh out of PhD versus several years on the job), so do not hesitate to apply if you think you could be a suited candidate! The links to the job postings: https://jobs.jnj.com/jobs/2105959410W?lang=en-us&previousLocale=en-US <https://jobs.jnj.com/jobs/2105959410W?lang=en-us&previousLocale=en-US> https://jobs.jnj.com/jobs/2105959323W?lang=en-us&previousLocale=en-US <https://jobs.jnj.com/jobs/2105959323W?lang=en-us&previousLocale=en-US> Feel free to distribute further in your network. Kind regards, Joke Reumers Head of Discovery Omics Discovery Sciences, Janssen R&D Belgium jreumers(a)its.jnj.com <mailto:jreumers@its.jnj.com>

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Open position Bioinformatics team leader and senior scientist at Galapagos (Mechelen)
by Tim Van den Bulcke 06 Aug '21

06 Aug '21

Team Leader Disease Bioinformatics - BE, Mechelen - Galapagos (glpg.com) <https://careers.glpg.com/o/team-leader-disease-bioinformatics-be-mechelen> Dear, we have two open positions for a *Bioinformatic team leader *and a *Senior Scientist*. Please find more information below and apply for the jobs using these respective links: Team Leader Disease Bioinformatics - BE, Mechelen - Galapagos (glpg.com) <https://careers.glpg.com/o/team-leader-disease-bioinformatics-be-mechelen> Senior Scientist Disease Bioinformatics - Galapagos (glpg.com) <https://careers.glpg.com/o/senior-scientist-disease-bioinformatics-mechelen> Kind regards, dr. ir. Tim Van den Bulcke Head Bioinformatics Galapagos (www.glpg.com) --------- Team Leader Disease Bioinformatics <https://careers.glpg.com/o/team-leader-disease-bioinformatics-be-mechelen> *Scope of the job* We are seeking an innovative, collaborative and accomplished Disease Bioinformatics Team Leader to manage an existing team of senior computational biologists. The Disease Bioinformatics Team works on various Multi-Omics driven projects in the fields of Inflammation, Fibrosis, Kidney and Autoimmune diseases. You will work as part of a larger dynamic bioinformatics team with two additional bioinformatics core teams on network/pathway modelling and on data sciences to contribute to Galapagos’ drug discovery pipeline. You collaborate with different stakeholders across Research as well as vendors and academic researchers to ensure successful planning, managing and execution of integrative bioinformatics projects. You lead your team by motivating and empowering each team member and organize the team’s resources. More specifically, you will: - Lead a team of computational biologists focused on Disease Area projects in the bioinformatics group. - Act as the lead for communicating key achievements and requirements for the Disease Bioinformatics team with Discovery, Translational and Biomarker development leaders - Act as an influencer and thought leader by staying up to date with relevant scientific developments and providing scientific recommendation within and across teams. - Act as a role model for your own team by offering guidance and support, and mentoring their professional development - Organize the workload and resources of the team - Is accountable for the correct implementation of GLPG values, behaviour, process and way of working in its own team. #LI-LB1 Job requirements *Who are you?* - A Ph.D. in Bioinformatics, Computer Science, Biology, Genetics or equivalent scientific discipline - 10 years of experience in computational biology is required with proven high levels of performance and publication record. A background in systems immunology, systems biology and/or single cell genomics and/or proteomics is a plus - A minimum of 5 years’ experience in pharmaceutical industry and drug development - Outstanding communication, organizational and leadership skills, with a successful track record of collaborating with cross-functional scientific teams and delivering on objectives in defined timelines - Strong experience with project conceptualization including refining objectives, experimental design, technology assessments and reporting strategies - Ability to identify new tools for the integrative analysis and visualization of integrative multi-omics datasets, assess requirements and strategic fit - Proficiency with R, Python or other scripting languages. Experience with data visualization platforms, data curation/organization and cloud computing is a plus - As a team player, you promote an open and supportive climate and a collaborative organization. - Your [basic / good / excellent] presentation skills guarantee a proper communication during meetings or amongst team. - Well organized, you are able to handle multiple tasks and project. *What’s in it for you?* You will be part of a fast growing and amazing company. As ‘make-it-happener’ you will get all the support you need to make your job successful. At Galapagos we aim to recruit the best people, who stand out among their peers, with integrity and excellent interpersonal and organizational skills. Our employees are the strength behind Galapagos, a highly motivated team, eager to maintain Galapagos’ leading position and achieve breakthroughs in pharmaceutical research. Galapagos offers a competitive remuneration package and a dynamic work environment. *We are Galapagos: together we can make it happen…!* *-----------------------------------------* Senior Scientist Disease BioinformaticsJob description Pleased to meet you, we are Galapagos, a dynamic fast growing Biotech company with offices in Europe in *Belgium *(Mechelen), *France *(Romainville & Paris), *the **Netherlands *(Leiden), *Switzerland *(Basel), *Italy * (Milano), *Spain *(Madrid), the *UK *(London), *Germany *(München), and in the *US *(Boston). We’re in the business of changing lives. In our quest to discover and develop life-improving medicines we go where no one has ever gone before. In every challenge we face, we see new opportunities. We want to challenge the impossible. We need thought leaders and rapid thinkers, entrepreneurs in spirit and status quo-fighters. Collaborative innovators and perseverant idealists. We need the best-in-class. In other words, we need you: The ‘make-it-happeners’. We are looking for a *Senior Scientist Bioinformatics – Chronic Kidney Disease - BE/Mechelen* *Scope of the job* We have an opportunity for a senior bioinformatics scientist with a profound interest in unravelling complex diseases from a holistic systems biology perspective to join our recently expanded Bioinformatics team. Your challenge is to contribute to and apply cutting-edge computational biology approaches to target discovery and characterization for our rapidly expanding research area. You will be part of a multi-disciplinary group of bioinformaticians who closely collaborate with Disease Area Scientists and Translational Research teams to directly impact our drug discovery pipeline. More specifically, you will: - Act as the lead bioinformatics scientist for our rapidly developing Chronic Kidney Disease area, spanning both Research and Translational efforts, and contribute to Immune Inflammation and/or Fibrosis related projects - Actively participate in the conceptualization and design of multi-omics experiments as well as their analysis, interpretation and integration with key datasets in support of collaborative projects that fuel our drug development pipeline. - Contribute to our mission to develop first in class therapeutics by bringing expert knowledge in the computational systems biology area - Share our relentless drive to innovate Job requirements - You have a Master’s degree or PhD in bioinformatics or Life Sciences. - You are a true computational system biologist, highly skilled in the analysis of complex biological datasets. - You have a solid understanding of disease driving processes such as dysregulation of immune/inflammation pathways preferably in the context of chronic kidney diseases - You have at least 5 years of combined academic/industry working experience (post PhD, or equivalent) with a proven track record of research achievements - You have ample experience working with a number of common –omics data types including bulk and single-cell RNA sequencing. Experience with computational analysis of proteomics, metabolomics or lipidomics data would be a considered a plus - You have hands-on experience running and developing, computational pipelines, preferably using R or Python. - You have successfully applied machine learning and data visualization strategies to prioritize functional leads and identify predictive biomarkers from complex biological datasets - You are a team player with excellent communication and organization skills. You are capable of assuming a leading role in high-profile projects with a variety of stakeholders under tight deadlines *What’s in it for you?* You will be part of a fast growing and amazing company. As ‘make-it-happener’ you will get all the support you need to make your job successful. At Galapagos we aim to recruit the best people, who stand out among their peers, with integrity and excellent interpersonal and organizational skills. Our employees are the strength behind Galapagos, a highly motivated team, eager to maintain Galapagos’ leading position and achieve breakthroughs in pharmaceutical research. Galapagos offers a competitive remuneration package and a dynamic work environment. *We are Galapagos: together we can make it happen…!*

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BaseClear looking for a new bioinformatician
by Mark Bessem 06 Aug '21

06 Aug '21

BaseClear is expanding their bioinformatics team! We're a Leiden based company offering a wide range of microbial genomics services to our clients. As a bioinformatician, you'd be working on our in-house pipelines, performing data analysis for tailor-made client requests and develop new products together with our product development team. If you're interested in working in the microbial genomics field in a team of dedicated bioinformaticians, please check out the vacancy at https://www.baseclear.com/career-jobs/bioinformatician/ or contact me directly. Met vriendelijke groet, Kind regards, Mark Bessem Manager Bioinformatics [BaseClear]<https://www.baseclear.com/> Direct: +31 (0)712 04 53 05 General: +31 (0)715 23 39 17 www.baseclear.com<https://www.baseclear.com> [BaseClear - The Microbial Genomics Experts]<https://www.youtube.com/watch?v=it2PVdfTqak> Please consider the environment before printing this email. Disclaimer<https://www.baseclear.com/disclaimer>

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Position available: Computational Biology for Infection Research at HZI Germany
by Loh-Bode, Yen Lee 05 Aug '21

05 Aug '21

Dear person-in-charge, Attached herewith is an open position for our department, Computational Biology for Infection Research. We ask kindly that you forward it to relevant departments, or publish it on your various mediums. Please do not hesitate to contact me for further assistance, and we thank you for your cooperation. Keep well! Kind regards / Beste Grüße, Annie Loh-Bode Assistant to the Head of Department (Prof. Alice McHardy) Computational Biology for Infection Research (BIFO) Email: yenlee.loh-bode(a)helmholtz-hzi.de Tel.: +49 (0)531 391-55270 Braunschweig Integrated Centre of Systems Biology (BRICS) Rebenring 56, 38106 Braunschweig Helmholtz Centre for Infection Research GmbH (HZI) Inhoffenstrasse 7, 38124 Braunschweig ________________________________ Helmholtz-Zentrum für Infektionsforschung GmbH | Inhoffenstraße 7 | 38124 Braunschweig | www.helmholtz-hzi.de Vorsitzende des Aufsichtsrates: Frau MinDir'in Prof. Dr. Veronika von Messling Stellvertreter: MinDirig Rüdiger Eichel, Niedersächsisches Ministerium für Wissenschaft und Kultur Geschäftsführung: Prof. Dr. Dirk Heinz; Silke Tannapfel Gesellschaft mit beschränkter Haftung (GmbH) Sitz der Gesellschaft: Braunschweig Handelsregister: Amtsgericht Braunschweig, HRB 477

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New bioinformatics journal: ISCB/OUP Bioinformatics Advances
by Yves Moreau 03 Aug '21

03 Aug '21

Dear colleague, I wanted to let you know about the new journal Bioinformatics Advances. Bioinformatics Advances is a fully open access, peer-reviewed journal published jointly by Oxford University Press and by the International Society for Computational Biology. The editors-in-chief are Alex Bateman and Thomas Lengauer. Best regards, Yves Moreau Bioinformatics Advances is an interdisciplinary journal on bioinformatics and computational biology. The journal covers bioinformatics methods, such as algorithms, statistics, databases and software as well as biological contributions for which the application of advanced computational methods is an essential factor. The major focus of the journal is on the molecular and cellular levels of biology. The journal covers bioinformatics both for established experimental approaches and for emerging technologies that require innovative computational support. Problems in basic research as well as applications and translational research are covered. The journal also will publish papers that will be of wide interest to the computational community in areas such as education and career development.Bioinformatics Advances is an interdisciplinary journal on bioinformatics and computational biology. The journal covers bioinformatics methods, such as algorithms, statistics, databases and software as well as biological contributions for which the application of advanced computational methods is an essential factor. The major focus of the journal is on the molecular and cellular levels of biology. The journal covers bioinformatics both for established experimental approaches and for emerging technologies that require innovative computational support. Problems in basic research as well as applications and translational research are covered. The journal also will publish papers that will be of wide interest to the computational community in areas such as education and career development. Journal website - https://academic.oup.com/bioinformaticsadvances Instructions to Authors - https://academic.oup.com/bioinformaticsadvances/pages/instructions-to-autho…

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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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