June 2018 - BBClist - maillist.psb.ugent.be

REMINDER: Exciting postdoc opportunity in Copenhagen
by Magali Michaut 18 Jun '18

18 Jun '18

One more week to apply to this computational postdoc position in cancer stem cell research with exciting single cell data and more ! Check it out and/or spread the word: http://jobportal.ku.dk/alle-opslag/?show=147220 If you have questions about our group, please contact me. Looking forward to hearing from you, Magali ======= An exciting position in cancer bioinformatics with focus on normal and malignant hematopoiesis as well as cancer stem cell models is available in the Porse Group, at the Biotech Research and Innovation Centre (BRIC)/DanStem in Copenhagen. We are seeking a PhD level computational biologist with an expertise in analysis and interpretation of complex biological data. In our group, we generate omics data using the latest technologies (RNA-seq, single cell RNA-seq, ChIP-seq, proteomics) and have expertise in integrated analysis of gene expression and epigenetic data using cutting edge machine learning approaches. The Research Centre The Biotech Research and Innovation Centre (BRIC) is a research centre of excellence for biomedical research, focusing on disease-oriented basic research, at the Faculty of Health and Medical Sciences, University of Copenhagen. BRIC hosts 24 independent research groups that perform basic and translational research aimed to understand diseases like cancer, neurological and metabolic disorders. For further information about the Porse group and BRIC: http://www.bric.ku.dk/ Our research Several cancers, including acute myeloid leukemias (AML), are maintained by Cancer Stem Cells (CSCs). Similar to normal stem cells, CSCs are able to self-renew and are thus the cells that need to be targeted in order to efficiently eradicate the disease. The focus of the Porse group is therefore to study cancer from a stem-cell centric viewpoint. Specifically, we address the gene regulatory mechanisms governing both normal and malignant hematopoiesis with the aim to identify novel targets for future therapeutic intervention in patients suffering from AML. Additionally, we use single-cell technologies to unravel cellular heterogeneity in normal and malignant stem cells. Key publications relevant for computational biologists: Paul F et al., Cell 2015, 163, 1663-77 Pundhir S, Nucleic Acids Research 2016, 44, 4037-51 Bagger FO et al., Nucleic Acids Research (2016), 44, D917-24 Rapin N. et al., Blood 2014, 123, 894-904 Vitting-Seerup K et al., BMC Bioinformatics 2014, 15, 81 Jakobsen JS et al., Genome Research 2013, 23, 592-603 Weischenfeldt J. et al, Genome Biology 2012, 13, R35 Your job The successful candidate will join our bioinformatics team, currently consisting of two people. Your time will be shared between involvement/support in projects originating from our wet lab, and your own projects, on which you can dedicate 20-30% of your time. You will have the opportunity to develop your own research ideas, which can potentially be supported by experiments from our wet lab. Profile We are looking for a highly motivated and enthusiastic scientist with the following competences and experience: 〈 Essential: PhD in Computer Science, Bioinformatics, or Computational Biology 〈 Strong experience in Python or R and in Linux/UNIX computing environment. 〈 Documented experience with NGS data analysis (ChIP-seq, ATAC-seq, or RNA-seq) 〈 Experience in integrated analysis of large-scale biological data sets 〈 Strong communication and collaboration skills, including the ability to work well in a diverse academic setting, and to balance scientific and day-to-day needs 〈 Ability to work in a team of multidisciplinary scientists, and independently with minimal direction 〈 Excellent written and oral communication skills in English Desirable but not required: 〈 Experience with analysis of single cell RNA-seq data 〈 Experience with applying supervised and unsupervised statistical learning and mathematical methods to biological problems 〈 Experience with system administration 〈 Interest in modern visualisation tools (e.g. plotly, dash, tableau, shiny) 〈 Background in molecular biology and genetics, especially related to disease and drug development will be considered an advantage. We offer - A two-year (possibly extendable) with a competitive salary and social benefits (e.g. social security, health coverage, parental leave) - Access to state-of-the art tools and infrastructure - Tailored support in raising competitive funds and communicate your research - A stimulating and supportive international research environment We have weekly internal seminars with PhD students and postdocs presenting their work as well as external seminars with international speakers. BRIC also hosts several research clubs; hematology club, Chromosome Biology club, Stem cell club and single cell transcriptomics seminar series. The institute has an association for students and postdocs (ASAP), a PhD programme (MoMeD) and a Postdoc Career Programme (PCP). BRIC has extensive international collaborations and actively participates in the European alliance, EU-LIFE consisting of 13 excellent life science research institutions and is part of the EU-funded LIBRA initiative to obtain gender balance in life science research. BRIC has a highly international profile (>60% international researchers) and English as working language. An International Staff Mobility Office at UCPH supports and guides international researchers through your initial steps in Denmark (e.g. residence and work permits, tax and pension, banking, medical care, childcare). They also offer a dual career network open for spouses of our researchers. Start date: preferably Sep 1 or after agreement For further information regarding the position, please contact Bo Porse on e-mail: bo.porse(a)bric.ku.dk Terms of salary and employment Salary, pension and terms of employment will be in accordance with the agreement between the Ministry of Finance and The Academics Central organization. Currently, the monthly salary starts at 33,224.48 DKK / 4.456 Euro. An additional 17.1 % monthly contribution to pension will be paid by the employer. Depending on qualifications, a higher salary may be negotiated. Non-Danish and Danish applicants may be eligible for tax reductions, if they hold a PhD degree and have not lived in Denmark the last 10 years. The position is covered by the “Memorandum on Job Structure for Academic Staff at the Universities” of June 28, 2013. Application Your application must be submitted electronically by clicking ‘Apply now’ below or via BRIC’s website on http://www.bric.ku.dk/jobs/. The application must include the following documents/attachments – all in PDF format: 1. Motivated letter of application (max. one page). 2. CV incl. education, work/research experience, language skills and other skills relevant for the position. 3. A certified/signed copy of a) PhD certificate and b) Master of Science certificate. If the PhD is not completed, a written statement from the supervisor will do. 4. List of publications. Letters of recommendation Furthermore, the shortlisted applicant should provide two letters of recommendation. To be taken into consideration, the letter must be signed by the supporting person on paper with institutional letter head and in PDF-format and send to bo.porse(a)bric.ku.dk with subject “name candidate-postdoc-year”; preferably by the supporting person. The letters should be received 1 week after being notified about shortlisting. Please make sure that an easy match between the recommendation letter and the individual applicant is possible. Application deadline: July 1, 2018 We reserve the right not to consider material received after the deadline, and not to consider applications or letters of recommendation that do not live up to the abovementioned requirements. Application procedure After the expiry of the deadline for applications, the authorized recruitment manager selects applicants for assessment on the advice of the Appointments Committee. All applicants are then immediately notified whether their application has been passed for assessment by an expert assessment committee. Selected applicants are notified of the composition of the committee and each applicant has the opportunity to comment on the part of the assessment that relates to the applicant him/herself. You can read about the recruitment process at http://employment.ku.dk/faculty/ BRIC and University of Copenhagen wish to reflect the diversity of society and welcome applications from all qualified candidates regardless of age, disability, gender, nationality, race, religion or sexual orientation. Appointment will be based on merit alone.

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FW: 2 positions for Computational Systems Biology Postdoc at Institut Curie
by Alexander Botzki 15 Jun '18

15 Jun '18

On behalf of Emmanuel Barillot, Institut Curie: Dear colleagues, We are looking for brilliant postdocs to join our Cancer Computational Systems Biology group. Could you please spread the word about this opportunity and forward the attached announcements to whoever might be interested? Many thanks in advance. Best wishes Emmanuel

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course on computational systems biology of cancer in Institut Curie in September 2018
by Alexander Botzki 14 Jun '18

14 Jun '18

On behalf of Emmanuel: Dear colleagues, We are organizing a course on computational systems biology of cancer in institut Curie in September 2018, with outstnading speakers. Could you please spread the word about this opportunity and forward the attached announcements to whoever might be interested? Many thanks in advance. Best wishes Emmanuel ========================================================================= The international multidisciplinary course entitled '1ST COURSE ON COMPUTATIONAL SYSTEMS BIOLOGY OF CANCER’ will take place on September 24-29, 2018 in Institut Curie, Paris, France The application/registration is in progress. Register now! https://enseignement.curie.fr/en/course/sysbiocancer2018 In order to apply, click on ‘CREATE AN ACCOUNT TO REGISTER’ and follow the stepwise instructions. Application deadline: 25 July 2018 Results of selection: August 5, 2018 Registration fees: No fees are requested (the free-of-charge registration is compulsory) Course objective To promote better integration of computational approaches into biological and clinical labs. We aim to help participants to improve interpretation and use of omics data that nowadays are accumulated in any biological or medical lab. We invited leading international speakers from different fields in cancer systems biology that will expose an umbrella of systems biology methods from data analysis to modelling and integration of rationalized treatment schemes into the clinical trials. Course program https://enseignement.curie.fr/sites/default/files/programme_10.pdf The course will contain the following sessions: Session 1: Pathway databases and networks resources in cancer Session 2: Visualisation and interpretation of cancer data Session 3: Cancer genomics Session 4: Multi-level omics data analysis and tumour heterogeneity Session 5: Mathematical modelling of signalling networks in cancer Session 6: integration of multi-level data into models of cancer signalling Session 7: Treatment response prediction and patient stratification Session 8: Single cell data analysis in cancer Session 9: Bioimage informatics for cancer research Session 10: Cancer evolution studies In addition the attendees of the course will take part in: -Presentation of their own scientific project with a flash presentation and a poster (for PhD Students and Post-docs). -Journal Club to present and discuss milestone papers in the cancer systems biology field. Scientific papers within the main topics covered by the course will be sent to the accepted applicants for presentations during the journal club (for Master 2 students). -Career development workshop during the Saturday morning session (all participants). CRC Taylor&Francis Publishing Group sponsored student’s prizes for best presentations and posters. Audience Master 1, 2 and PhD students, postdoctorants from French and international universities/teams. In addition, we expect attendees among researchers and medical doctors that interested to learn about systems biology impact into cancer research and treatment. !! Note that the registration is mandatory for all-levels participants Contact c.sysbiocancer2018(a)curie.fr Organizers Emmauel BARILLOT Institut Curie - INSERM U900, Paris, France Gregory BATT Inria - Saclay - Institut Pasteur, Paris, France Inna KUPERSTEIN Institut Curie - INSERM U900, Paris, France Vassili SOUMELIS Institut Curie - INSERM U932, Paris, France Denis THIEFFRY Institut de Biologie de l'École Normale Supérieure, Paris, France Jean-Philippe VERT Centre of Computational Biology, MINES - ParisTech, Paris, France Thomas‎ WALTER Centre of Computational Biology, MINES - ParisTech, Paris, France Scientific committee Laurence CALZONE Institut Curie – INSERM U900, Paris, France Tatiana POPOVA Institut Curie – INSERM U830, Paris, France Andrei ZINOVYEV Institut Curie – INSERM U900, Paris, France

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Job vacancy Software Developer/Data Analyst Radboud University Medical Centre Nijmegen
by Celia van Gelder 14 Jun '18

14 Jun '18

Dear all, For your information please find below an interesting job vacancy in Nijmegen, group of Peter Bram ‘t Hoen. https://www.radboudumc.nl/en/vacancies/57401-software-developer-data-analyst Please spread in your organization as you see fit. Best regards, Celia, on behalf of Peter-Bram Dr. Celia W.G. van Gelder Programme Manager DTL Learning Training Coordinator ELIXIR-NL ELIXIR Training Platform Leader tel. +31613375327 e-mail: celia.van.gelder(a)dtls.nl websites: www.dtls.nl, www.biosb.nl skype: celia.van.gelder Office: DTL | Jaarbeurs Innovation Mile (JIM) | 6th floor Beatrixgebouw | Jaarbeursplein 6 | 3521 AL Utrecht Postal address: Postbus 8500 | 3503 RM Utrecht

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post doc position in molecular dynamics
by l.lins＠uliege.be 12 Jun '18

12 Jun '18

The Laboratory of Molecular Biophysics at the Interfaces (LBMI) from Uliège (GBX ABT) is looking for a post doc in the field of molecular dynamics. Candidate profile : The candidate should have a PhD in biophysics (science) and expert skills in molecular dynamics (MD) simulations are mandatory. Skills in experimental biophysics (langmuir trough, ITC, …) and knowledge in the field of surfactant molecules and lipopeptides are an advantage. Being fluent in english (written and spoken) is mandatory. He (she) will not have been working in Belgium for the two last years. The project : In the context of an ERA-COBIOTECH european project, BestBioSurf is dedicated to design new dispersant molecules, based on the properties of lipopeptides, especially the surfactin family. The task for LBMI is to define parameters for the molecules in relation with their dispersant properties and, based on those parameters, to predict a good candidate molecule with adequate dispersing properties using molecular modelling approaches and more specifically MD approaches. The molecule will then be producted and tested by the other partners. We propose a one year contract as post doc, with a possible extension of few months. Contact : Pr Magali Deleu : magali.deleu(a)uliege.be Pr Laurence Lins : l.lins(a)uliege.be Dr Laurence Lins FNRS Senior Research Associate Head of Molecular Biophysics at Interface Lab (LBMI) University of Liège-Gembloux Agro Bio Tech Passage des Déportés,2-5030 Gembloux-Belgium http://www.gembloux.ulg.ac.be/biophysique-moleculaire-aux-interfaces/ Tél : (00-32) (0)-81-622644 Partner of VALBRAN Interreg project (Interreg FVW - V): www.valbran.eu

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BIOINFORMATICS POSITION IN MOLECULAR GENETICS AND PLANT PATHOLOGY IN BIG COLLABORATIVE PROJECT WITH INDUSTRY
by Peter van Esse (TSL) 11 Jun '18

11 Jun '18

http://2blades.tsl.ac.uk/vacancies.html A position is available in the 2Blades group of Peter van Esse at the Sainsbury Laboratory. The appointee will deploy state-of-the-art bioinformatic approaches to identify novel resistance genes effective against Asian soybean rust, and will have significant responsibility for addressing the bioinformatic challenges in the project. https://www.businesswire.com/news/home/20180522005405/en/ The main activity will be to develop methods that accelerate resistance gene discovery. In addition, the successful candidate will be involved in genomic studies of rust fungi. We seek an individual with outstanding talent and abilities in Bioinformatics. The successful candidate will have a demonstrated record of achievement in academia or industry, and an eagerness to work as part of a collaborative, multi-disciplinary, international team in collaboration with industry. Candidates would be advantaged by an understanding of high-throughput genomic analysis and familiarity with widely used genomic databases and methods. Competence with bioinformatic scripting languages, particularly Python and/or Perl, is essential, as is experience handling data from the Illumina platform or other high throughput sequence systems. A PhD in bioinformatics or biology is required. The successful candidate has excellent writing skills and a talent for communication. In addition, the successful candidate has an interest to see research outcomes reach practical application. We offer a salary within the UEA Research and Analogous staff Grade scale 7 between £32,548 and £38,833; however, the appointment level will reflect qualifications, skills, knowledge and achievements. The position will initially be a three-year appointment with possibility for a two-year extension. The Sainsbury Laboratory (TSL) is a world leader in plant and microbial science that is dedicated to making fundamental discoveries in the science of plant-microbe interactions. For more information please visit www.tsl.ac.uk. The 2Blades Foundation is a U.S. nonprofit organization that discovers and advances technologies that significantly reduce, or entirely prevent, crop disease in order to improve agricultural output and the lives of people around the world. For more information please visit www.2blades.org. The position is open until filled. Applicants should provide a CV, including the names and contact details of two or more referees, and a cover letter of no more than one A4 addressing the selection criteria. Please send formal applications, quoting the reference number below, either by e-mail to HR(a)TSL.ac.uk or by post to Lynda Barnes, HR Administrator, The Sainsbury Laboratory, Norwich Research Park, Colney, Norwich, NR4 7UH, UK Ref: PvE02/2017

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Looking for Post-doc scientist to apply for MSCA IF fellowship at VIB
by Alexander Botzki 11 Jun '18

11 Jun '18

Dear All, The Vandenbroucke lab<http://www.vib.be/en/research/scientists/Pages/Roos-Vandenbroucke-Lab.aspx> (Barriers in Inflammation) in collaboration with the VIB Bioinformatics Core is looking for an energetic and motivated post-doctoral scientist to work on '-omics' data integration at VIB & Ghent University and who is willing to apply for a MSCA IF fellowship. VIB greatly values diverse standpoints and promotes an inclusive environment in which everyone is respected. More info at: https://vibvzw.jobsoid.com/j/13426/post-doctoral-scientist Thank you very much for your consideration. Best regards, Alex Alexander Botzki - Head of VIB Bioinformatics Core | Training Coordinator ELIXIR-BE VIB Bioinformatics Core Rijvisschestraat 126, 9052 GENT, Belgium | +32 9 248 16 00 www.bits.vib.be<http://www.bits.vib.be/> | @vibbioinfocore | https://corefacilities.vib.be<https://corefacilities.vib.be/> [MAIL SIGNATURE - CTLS2018] [signatureFooter (002)]

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Bioinformatics Engineer and Genetics data analysis in Lille (France)
by SAND Olivier 11 Jun '18

11 Jun '18

Bioinformatics Engineer and Genetics data analysis (12 months renewable) CNRS unit UMR 8199 (http://www.good.cnrs.fr) based in Lille (France), is a research lab of 50 people led by Pr Philippe Froguel. It is part of the European Genomics Institute of Diabetes (http://www.egid.fr) Research activities are mainly focused on characterization of genetic variants associated to metabolic diseases like diabetes and obesity, and use modern approaches of genomics, bioinformatics, biostatistics, molecular biology and animal models. As a member of the bioinformatics team, the engineer will participate in Next Generation Sequencing data analysis. He/She will develop and install data analysis techniques for research projects and services. She/He will also take care of maintenance and follow up of the evolution in that area. Main activities: - collect, manage and analyse data from NGS sequencers (Illumina) - develop variant annotation and selection tools - develop bioinformatics tools and deploy them on our intranet - develop, manage and maintain databases - organise data storage Profile and skills: - Master degree or higher in bioinformatics, preferably with experience, but beginners can apply - practice knowledge of scripting languages (Python, Perl, shell, R…) - knowledge of variant annotation and selection procedures - knowledge in genetics would be an asset - knowledge of SQL and - oral and written English - organisation skills (autonomy, deadlines, anticipate delay sources…) If interested, please contact: Amelie Bonnefond (amelie.bonnefond(a)cnrs.fr) or Stefan Gaget (stefan.gaget(a)cnrs.fr)

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Bioinformatics PhD position at the NIOZ
by Julia Engelmann 11 Jun '18

11 Jun '18

Dear all, I am looking for a PhD student in bioinformatics, modeling marine microbial interactions at the NIOZ on Texel. *What is it about?* The project is concerned with elucidating marine microbial inter-species interactions based on high-throughput genomic data by applying network modeling. Microbes in the oceans, sediment and in microbiomes of higher organisms, form communities which keep the element and nutrient cycles in the seas and on land running. Different microorganisms have different metabolic capabilities. The product of one species can be the substrate for another. Besides dependencies based on individual nutrients, more complex interactions, such as symbiosis, predator-prey and competition for limited resources among marine microbes, will be elucidated in this project. Moreover, the impact of changing environmental conditions due to climate change on microbial communities will be assessed. To do so, causal network modelling will be applied to microbial abundance data and measurements of environmental parameters such as temperature and salinity to predict causal effects of species and environmental parameters on other species. The PhD student will then perform follow-up experiments in the lab to validate predicted interactions. *Who are we looking for? * We like to get into contact with a PhD student holding an MSc degree in Bioinformatics, Computational Biology, Computer Science, Mathematics, (Bio-)Statistics, Physics, Microbiology, Molecular Biology, Microbial Ecology or related fields. You are highly organized, motivated, and fluent in oral and written English. Experience with Unix is mandatory. Candidates need to have a proven record of their bioinformatics and programming skills. Candidates with good command of R, Bash and Python are preferred. If your background is in Biology-related fields, you will need to catch up with some mathematics and statistics. The ideal candidate also has experience in the analysis of high-throughput genomic data, including metagenomic data. *For more information and to apply, see:* https://www.workingatnioz.com/our-jobs/phd-student-%E2%80%9Cmodelling-causa… Please apply before July 15, 2018. Thanks and kind regards, Julia -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Julia C. Engelmann Tenure-track scientist Department of Marine Microbiology and Biogeochemistry NIOZ Royal Netherlands Institute for Sea Research and Utrecht University Landsdiep 4, 1797 SZ ‘t Horntje Texel, The Netherlands Phone: +31 (0) 222 369 388 Email: julia.engelmann(a)nioz.nl

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Post-doc in applied mathematics at CEA (Paris)
by SAND Olivier 08 Jun '18

08 Jun '18

Post-doc in applied mathematics: Innovative mathematical methods for the integration of proteomics and metabolomics data Context Proteomics and metabolomics provide unique and complementary information to decipher gene function and pathways, elucidate phenotypes, and robustly discover new biomarkers for disease treatments. Integration of both approaches is a mathematical challenge because of the heterogeneity and the complexity of the proteomics and metabolomics data, and the partial annotation (i.e. metabolite identification) provided by the metabolomics mass spectrometry technologies. The national infrastructures in bioinformatics (IFB), metabolomics (MetaboHUB), proteomics (ProFI), genomics (France Génomique), and mouse phenogenomics (PHENOMIN) have decided to join forces and develop new biostatistics and bioinformatics methods and tools for high-throughput and combined proteomics and metabolomics data analysis. Project First, statistical modeling will be used to explore the specific and common information from each type of omics data, and to determine how their combination as molecular signatures can optimally be used to interpret and predict the phenotypes. Such approaches will include linear and nonlinear methods for multivariate analysis. Second, network integration will be used to facilitate interpretation and annotation of the data. Proteins and metabolites will be mapped on the metabolic networks to facilitate chemical annotation and biological interpretation, and to suggest new biomarkers and metabolic functions. The mathematical approaches and tools will be validated on two use cases: 1) the high-throughput molecular phenotyping of comprehensive collections of mouse models and 2) the discovery of new gene functions in a bacterial model of interest for environmental and biotechnological applications. Profile Interested applicants should have a PhD in applied statistics (data analysis, network analysis), and be motivated by multidisciplinary applications (chemistry, biology). Contact Etienne Thévenot (CEA Saclay, Laboratory for Data Analysis and Systems’ Intelligence) Email: etienne.thevenot(a)cea.fr<mailto:etienne.thevenot@cea.fr> Web: http://etiennethevenot.pagesperso-orange.fr/index.html David Vallenet (CEA Evry, Laboratory of Bioinformatics Analyses for Genomics and Metabolism) Email: vallenet(a)genoscope.cns.fr<mailto:vallenet@genoscope.cns.fr> Web: http://orcid.org/0000-0001-6648-0332

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