August 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 PostDoc and PhD position (apply by Sep 15)
by Kircher, Martin 30 Aug '21

30 Aug '21

Dear colleagues, My lab in Germany is currently looking for a PostDoc (https://www.biostars.org/p/9486861/, an appointment for up to 5 years) and a PhD student (https://www.biostars.org/p/9486464/, fully-funded 3 year appointment) in Bioinformatics/Computational Biology. Both positions are generally on the topic of non-coding DNA variant effects and include machine/deep learning as well as sequence analysis aspects. The application deadline is Sep 15. I hope you can help me distributing these job posts to everyone who might be interested. Please do not hesitate to contact me with questions. Best regards, Martin ___________________________ Dr. Martin Kircher Group Leader JRG Computational Genome Biology Berlin Institute of Health @ Charité Charitéplatz 1, 10117 Berlin www.bihealth.org

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BSC: Life Sciences vacancy
by BSC Human Resources 30 Aug '21

30 Aug '21

Dear all, We would like to inform you about a new job opportunitiy offered by Barcelona Supercomputing Center: - Junior Research Engineer - development of data science web apps for epidemiology (RE1). Deadline: 30 September, 2021 Link here <https://www.bsc.es/join-us/job-opportunities/33021lscbre1> 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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PhD position in plant virus bioinformatics
by Kupczok, Anne 26 Aug '21

26 Aug '21

Dear colleagues, The Evolutionary (Meta-)genomics group in the Bioinformatics Group at Wageningen University invites applications for a bioinformatics PhD student in ‘Virus diversity and evolution in natural plant ecosystems’. You might share our view that wild plant communities might act as viral reservoirs that are also connected to agricultural plants. Since viruses can spill over from natural to agricultural systems, it is highly relevant to characterize virus diversity in wild plants. Plant virus genomes are highly diverse and evolve rapidly. To know which role plant viruses play in shaping natural plant communities, we must characterize their biodiversity and evolution. You might be familiar with the phenomenon that plant virus infections are often asymptomatic, i.e., they do not cause overt disease, and can even be beneficial for the host. Recently, plant virus research expanded from the study of individual virus-host systems into characterizing global diversity using metagenomics, i.e., sequencing the genetic content of environmental samples without the need for prior virus isolation. Metagenomics led to the surprising observation that virus infections are ubiquitous, that there is a high incidence of mixed infection, and that most plant viruses identified in crops also occur in wild plants. There is growing evidence that viruses can impact plant ecosystems, which calls for a reappraisal of the role of viruses in natural ecosystems and accentuates the need to understand virus genomes and their function and evolution. The aim of this project is to develop bioinformatics methods to analyze plant virus metagenome data that has been sampled from wild plants in the Netherlands. This (and potentially your) project will contribute to understanding plant virus diversity and evolution in natural Dutch ecosystems. You will contribute to developing bioinformatics methods to discover and reconstruct virus genomes from high-throughput plant virus sequencing data and to analyze ecological and evolutionary properties of these viruses. To this end, we aim to analyze the effect of host range and mixed infections on intra-host diversity and estimate how recombination and selection impact virus genome evolution. Beyond the scientific and potentially application merits, you will build a wide network for your future career both within and outside Wageningen University. The research is embedded within the chair group of Bioinformatics at Wageningen University which is led by Prof. Dick de Ridder (https://www.bioinformatics.nl/) You will be supervised by Dr. Anne Kupczok (https://annecmg.github.io/) The research will be carried out in close collaboration with Dr. Mark Zwart at the Netherlands Institute of Ecology (NIOO-KNAW) (https://nioo.knaw.nl/nl/employees/mark-zwart) The position is for four years and funded by the graduate school Experimental Plant Sciences (https://www.graduateschool-eps.info/) We ask • a successfully completed MSc degree in bioinformatics or a related field; • excellent background in high-throughput sequencing analysis and comparative genomics; • affinity with ecology, evolution, and population genomics; • interest in close collaborations with experimental biologists and ability to work effectively as a team member and to carry out individual research; • very good level of oral and written English. Please find all details and instructions how to apply here: https://www.wur.nl/en/vacancy/PhD-position-Virus-diversity-and-evolution-in… For enquiries regarding the position and research topic, please contact Anne Kupczok: anne.kupczok(a)wur.nl<mailto:anne.kupczok@wur.nl> -- Dr. Anne Kupczok Assistant Professor Bioinformatics, Department of Plant Sciences, Wageningen University

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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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