- BBClist - maillist.psb.ugent.be

permanent position in bioinformatics
by Petr Nazarov 09 Sep '21

09 Sep '21

Dear Members Luxembourg Institute of Health (LIH) has opened a permanent position in bioinformatics. We are looking for a highly motivated candidate with strong expertise in bioinformatics, multi-omics data analysis and data integration. The focus will be to support current research demands of all LIH departments mostly in the field of immunology and immune-related diseases. The candidate should have a strong background in the analysis and interpretation of RNA/DNA next generation sequencing or/and methylation data. Overall, the candidate should be able to demonstrate knowledge of algorithmic and statistical concepts in Biology and Biomedicine, as well as scientifically validated data analysis software. More details: https://www.lih.lu/jobs/detail/researcher-research-engineer-in-bioinformati… KEY ACCOUNTABILITIES * Support research groups of LIH in planning "omics" experiments from a bioinformatics and biostatistics point of view. * Collaborate on research projects and contribute to them with analyzing data, visualizing results and writing methods/results part of papers. * Develop targeted pipelines for "omics" data analysis in application to immunology and immune-related diseases. * Foster the development and establishment of novel data analysis methods. * Preserve up-to-date knowledge in multi-omics data analysis and data science at LIH. * Develop computational tools aimed at user's requests. * Contribute to training of LIH staff and PhD students. KEY SKILLS, EXPERIENCE AND QUALIFICATIONS * Master or PhD degree in Bioinformatics, Computational Biology or similar area. * Strong background in computational biology with a focus on genome-wide transcriptomic analysis and immunology (mutation analysis, copy number aberrations, epigenetics, immuno-phenotyping, microbiome analysis). * Previous experience in at least two of the following areas is required: transcriptomic data including single cell RNA-seq, multi-omics data integration, epigenetics. * Experience in analyzing single-cell RNA-seq (including CITE-seq) and ATAC-seq is an asset. * Knowledge of modern concepts in immunology and immune-mediated diseases is an asset. * Strong knowledge of R or Python (or other programming languages such as Julia) is an asset. * Good communication skills and ability to work effectively in a team and in close interaction with biomedical scientists. * Self-motivated, team spirit and service-oriented mindset. * Languages skills: fluent command of English as a working language, knowledge of other languages of the European Union is an asset. Please apply online https://www.lih.lu/jobs/detail/researcher-research-engineer-in-bioinformati… If you have any questions, feel free contacting me: petr.nazarov [at] lih.lu Best regards Petr Nazarov Petr Nazarov, PhD Group Leader, Multiomics Data Science Luxembourg Institute of Health Department of Oncology 1A-B, rue Thomas Edison, L-1445 Strassen Luxembourg Tel: +352 26970-385 Fax: +352 26970-719 Email: Petr.Nazarov(a)lih.lu<mailto:Petr.Nazarov@lih.lu> [https://files.lih.lu/outlookSignature/lih.jpg] More about LIH : https://www.lih.lu/ [https://files.lih.lu/outlookSignature/AR2020_email_signature_300.jpg]<https://www.lih.lu/page/activity-reports?Track_EmailS> Join us on Facebook and follow our activities on Twitter: https://www.facebook.com/Luxembourg.Institute.of.Health http://twitter.com/LIH_Luxembourg Petr.Nazarov(a)lih.lu<mailto:Petr.Nazarov@lih.lu> This message (including any attachments) is intended for the addressee only and may contain confidential and/or privileged information and/or information protected by intellectual property rights. If you have received this message by mistake, please notify the sender by return e-mail and delete this message from your system. You should not use, alter, copy or distribute this message or disclose its contents to anyone. E-mail transmission can not be guaranteed to be secure or error free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. Luxembourg Institute of Health shall not be responsible nor liable for the proper and complete transmission of the information contained in this communication nor for any delay in its receipt or damage to your system.

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Assistant Professor Position in Scalable Computational Science
by Sanne Abeln 09 Sep '21

09 Sep '21

The application deadline for the position below has now been extended until 10 October: ---------- Forwarded message --------- From: Sanne Abeln <s.abeln(a)vu.nl> Date: Fri, 23 Jul 2021 at 14:43 Subject: Open Assistant Professor Position in Scalable Computational Science To: <soft-matter(a)lists.leeds.ac.uk> Dear All, We have an open tenure track position for an assistant professor in Scalable Computational Science at the Vrije Universiteit, Amsterdam. The application deadline is 15 August 2021. We look for an active researcher in the Computational Science domain who either works with very large experimental data sets, and/or with computationally intensive simulations, with experience in AI and/or Large-Scale Computing. She/he will be responsible for adapting courses in AI and/or Large-Scale Computing for Computational Science students. For more details, see: https://werkenbij.vu.nl/ad/assistant-professor-scalable-computational-scien… Kind regards, Sanne -- Sanne Abeln Associate Professor Bioinformatics - VU University Amsterdam s.abeln(a)vu.nl +31 20 59 87816 www.few.vu.nl/~abeln

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20 Fully funded PhD studentships in Quantitative Biology in Lausanne, Switzerland
by Christophe Dessimoz 08 Sep '21

08 Sep '21

20 Fully funded PhD studentships in Quantitative Biology =========================================== The advent of large-throughput data is transforming life sciences into an increasingly quantitative discipline. The University of Lausanne (Switzerland) is at the forefront of this revolution, with quantitative research ramping up throughout the Faculty of Biology and Medicine, a dedicated department of Computational Biology, and interdisciplinary units such as the Center for Integrative Genomics. UNIL also hosts the headquarters of the Swiss Institute of Bioinformatics, to which many quantitative research groups are affiliated, and closely collaborates with EPFL on the same campus. Ideally situated along the lake of Geneva, near Lausanne's city center, UNIL brings together over 120 nationalities. UNIL's Faculty of Biology and Medicine has recently launched a doctoral program entitled "Quantitative Biology". A wide range of research groups are recruiting PhD students, covering areas as diverse as Genetics, Cell biology, Metabolism, Computational biology, Oncology, Evolution, Microbiology, Imaging, Molecular biology, Neuroscience, Gene regulation, Radiobiology, Plant science, Ancient DNA, Population Genetics, Single-cell Genomics, Epi-lipidomics, Stem Cell Biology, Tissue Engineering and Biomaterials. In 2021, hiring principal investigators include Francesca Amati, Claudia Bagni, Sven Bergmann, Christophe Dessimoz, Oscar Esteban, David Gfeller, Raphael Gottardo, Jerome Goudet, Emmanuella Guenova, Shukry James Habib, Laurent Keller, Zoltan Kutalik, Anna-Sapfo Malaspinas, Sophie Martin, Micah Murray, Alexandre Reymond, Tanja Schwander, Alessandro Villa, Claus Wedekind, Christian Widmann. Job information -------------------- Expected start date: 01.03.2022 or to be agreed Successful candidates will be offered one of two kinds of PhD student work contract, depending on the funding available to the hiring supervisor by the start of the contract: (1) Doctoral assistant on UNIL funds, at an activity rate of 85%. The initial contract is of one year but will be renewed up to 5 years. (2) Doctoral assistant on external funds, at an activity rate of 100%. The initial contract is of one year but will be renewed up to 4 years. Please also note that in some cases, again depending on the hiring supervisor situation, contracts will be issued from the CHUV (University Hospital) or a different UNIL faculty. Workplace: University of Lausanne (Dorigny, Bugnon, or Epalinges--depending on the supervisor) Your qualifications ------------------------ We are accepting applications from talented and enthusiastic candidates who are interested in a dynamic, well-supported lab at a top research institution. Candidates need to finish a Master's degree in a relevant area before the start date of their doctoral studies. We are looking for three main types of PhD students: * Students with a life science degree, interested in working in an experimental lab, but with a high degree of motivation to learn the fundamentals of computational biology, and to develop quantitative skills to analyse data more effectively * Students with a life science degree interested in working in a dry computational lab, keen to deepen their quantitative skills and broaden their horizon in terms of experimental and computational techniques * Students with a non-biological background (e.g. computer science, maths, physics), who are highly motivated to transition to Life Sciences A high level of written and spoken English proficiency is required since most scientific activities are conducted in English. What the position offers you ------------------------------------- You will develop your research project while working in a world competitive, interdisciplinary and highly collaborative environment. The PhD program in Quantitative Biology provides opportunities for professional training and acquisition of highly transferable skills. This is complemented by a wide range of activities (retreats, symposia, student life). The positions are fully funded. Salary and benefits are internationally highly competitive. Additional funding for consumables, computing, and to attend international conferences is available. Your application --------------------- For your application to be considered, you need to fill in two forms: The first form, at https://career5.successfactors.eu/sfcareer/jobreqcareer?jobId=18082&company…, requires the following informations: * Personal details * A cover letter. This can be very brief, since you should provide your motivation in the 2nd form below. * A single PDF document containing: * Your curriculum vitae (with extracurricular activities, internships, publications, conferences, awards, software contributions, etc.) * Master's thesis summary * The names and contact details of 2-3 referees. The second form, https://forms.gle/hBX5rZVBqjyeni7t9, requires you to answer the following questions * What your most meaningful research experience to date and why? [up to 4000 characters, i.e. approximately 850 words] * What accomplishment--academic or not--to date are you proudest and why? [up to 1500 characters, i.e. approximately 320 words] * Why would you like to pursue a PhD, and why specifically at the UNIL Quantitative Biology Ph.D. program? [up to 1500 characters, i.e. approximately 320 words] * Which recruiting labs are you the most interested in and why [up to 1500 characters, i.e. approximately 320 words] Remote interviews will take place on 17 and 18 November 2021. Lab visits and interviews will take place on 8-9 December 2021 in Lausanne (pandemic allowing--else remote alternative will be organized). Informal inquiries ------------------------ Prof. Christophe Dessimoz, Director of the UNIL Doctoral Program in Quantitative Biology (christophe.dessimoz(a)unil.ch) For more information, please consult http://unil.ch/quantitative-biology __________________________________________________________________ Associate Professor, Dept. of Computational Biology, University of Lausanne Professor, UCL Genetics Evolution and Environment & UCL Computer Science Group Leader, Swiss Institute of Bioinformatics https://lab.dessimoz.org - Tel: +41 21 692 4155 - Twitter: @cdessimoz

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Job: Senior Bioinformatician position at AstraZeneca, Cambridge (UK)
by Laurent Gatto 08 Sep '21

08 Sep '21

Senior Bioinformatician at AstraZeneca - Biology/Chemistry Interface and Proteomics Research (Cambridge, UK) Are you a bioinformatician passionate about biomedical research looking for an exciting and impactful new challenge? Do you have experience analysing proteome wide omics data and high-throughput molecular or genetic screens for target identification and drug discovery? Is research and development at the interface between biology and chemistry exciting for you? Then why not join our Data Sciences & Quantitative Biology team at AstraZeneca in Cambridge, UK and apply bioinformatics and computational solutions to help us grow and extend our capabilities in our drive to find the medicines of the future. Application deadline 16th September. For more information, please check the following: https://careers.astrazeneca.com/job/cambridge/senior-bioinformatician-biolo…

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Student positions - Bioinformatics in Cancer
by Vosberg, Sebastian 06 Sep '21

06 Sep '21

Dear list members, for my recently established research group (Bioinformatics in Cancer Research) at Medical University of Graz, Austria, I am seeking for students (PhD/Master/interns) with an interest in computational cancer research. Candidates may have any background such as bioinformatics/biology/medicine/mathematics/computer science/etc. Here a quick overview of our work: We are aiming at developing novel computational approaches for cancer research with a major focus on characterizing the molecular background of tumors across different omics levels and its evolution under therapy. We want to learn about mechanisms of treatment resistance and/or cancer recurrence and to stratify personalized treatment options. Our projects are motivated by actual clinical research questions and we work in a highly interactive environment with very close contact to clinicians and wet-lab researchers. In particular, I am currently seeking for a PhD student for a computational breast cancer research project starting ASAP. It is about delineating the molecular mechanisms of treatment response in patients treated within in a global clinical trial, for which we have exclusive data access (with a focus on RNAseq). It would be great if you could spread the word to relevant people within your department and beyond! Interested candidates can directly contact me at sebastian.vosberg(a)medunigraz.at. Thank you very much and best regards, Sebastian Vosberg

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Vacancies junior and senior bioinformatician @Sciensano - infectious diseases preparedness
by Kevin Vanneste 03 Sep '21

03 Sep '21

Dear all, The Bioinformatics Platform at the Belgian Institute of Health (www.sciensano.be<http://www.sciensano.be>) has two open vacancies for a junior and senior bioinformatician to help build national infrastructure to enable preparedness and response capacity using whole genome sequencing for infectious diseases outbreaks such as SARS-CoV-2 but also other relevant pathogens. More details can be found in the job descriptions in attachment. Applications are possible using our job site: - Junior profile: https://wiv-isp.hr-technologies.com/content/jobpage.asp?a=DETAIL&jdkid=818&… - Senior profile: https://wiv-isp.hr-technologies.com/content/jobpage.asp?a=DETAIL&jdkid=819&… Sincerely, K Kevin Vanneste, PhD Senior scientist - Responsible Bioinformatics Platform Transversal activities in Applied Genomics (TAG) T + 32 2 642 50 65 [cid:image001.jpg@01D4595B.6D6E05D0] Rue Juliette Wytsmanstraat 14 * 1050 Brussels www.sciensano.be<http://www.sciensano.be/> P Please consider the environment before printing this e-mail

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Vacancy Software Engineer Genome Diagnostics
by Sie, D.L.S. (Daud) 01 Sep '21

01 Sep '21

Dear BBC list, We have a job opening for a software engineer lab automation in the Genome Diagnostics lab at Amsterdam UMC. https://werkenbij.amsterdamumc.org/nl/vacatures/ondersteunende-diensten/sof…"Software+Engineer+Labautomatisering" If you're interested, be quick to respond (before 9th of September). And if you have any questions, drop me an email or phone call. Regards, Daoud [cid:image002.png@01D40E30.3E299A80] Dr. Daoud Sie | Head Bioinformatics | Consultant Core Facility Genomics Department of Human Genetics Location VUmc | MF-G423 | Van der Boechosrtstraat 7, 1081 BT Amsterdam Location AMC | K2-211 | Meibergdreef 9, 1105 AZ Amsterdam T: (+31)20-4442428 | E: d.sie(a)amsterdamumc.nl www.amsterdamumc.nl<http://www.amsterdamumc.nl/> | www.vumc.nl<http://www.vumc.nl/> / www.amc.nl<http://www.amc.nl/> ______________________________________________________ VUmc disclaimer: www.vumc.nl/disclaimer<http://www.vumc.nl/disclaimer> ______________________________________________________ VUmc disclaimer : www.vumc.nl/disclaimer AMC disclaimer : www.amc.nl/disclaimer

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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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