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CORRECTION Announcing CPW2018 during ECCB - Second Bioinformatics and computational pathology summit
by Yves Sucaet 24 Jun '18

24 Jun '18

CALL FOR ABSTRACTS: CPW2018 - Bioinformatics and computational pathology summit (second edition) When? Sunday, September 9, 2018. Where? Athens, Greece (during ECCB2018) Website? http://cpw1018.org Digital pathology is increasingly used to study biological processes and diseases as novel molecular probing and imaging techniques allow the measurement of single molecules in whole tissue sections. Resulting multi-gigapixel images can be viewed on a computer screen via dedicated software. However, automated analysis of such large-scale datasets is challenging and their combination with omics data is not trivial. This workshop wants to facilitate bridging opportunities between the bioinformatics and tissue image analysis communities. This second edition is organised as a full-day workshop during ECCB 2018 (http://www.eccb18.org) KEYNOTE SPEAKERS: The following keynote speakers have already agreed to speak at the conference: Thomas Fuchs, Memorial Sloan Kettering Cancer Center Chakra Chennubhotla, University of Pittsburgh Derek Magee, University of Leeds SUBMISSIONS: The conference solicits oral talks, posters, and proceeding papers contributions of original work or work that was recently accepted or published in a peer-reviewed journal or at a high level international conference. In the latter case, the publication reference should be clearly mentioned, and the abstracts should be checked mainly for relevance, rather than receive a full review. Conference proceedings will be published by the Journal of Pathology Informatics. The program committee will decide which contributions are selected for an oral presentation, and which ones are presented during a poster session. For submission instructions, please refer to https://www.fourwav.es/cpw2018 SCOPE: Computational pathology exists at the interphase between bioinformatics, machine learning, and digital pathology (microscopy). Submissions from all topics of interest are welcome (non-exhaustive list): Machine learning and image analysis for quantification in digital pathology (in 2D & 3D), Novel approaches (e.g. spatial or graph-based methods) to extract high-level features (e.g. molecular networks or spatial expression patterns) from tissue images for systems pathology, Software development methodologies and tools to ease the exploitation of large tissue images and integration with omics data, Novel molecular imaging techniques on tissues (molecular pathology, next generation pathology) and their analysis challenges, e.g. in situ hybridization, mass spectrometry imaging of formalin-fixed paraffin-embedded tissues, mass cytometry, and other spectroscopy techniques (Raman,...)... Research applications on non-human model organisms KEY DATES: Submission deadline: June 15, 2018. Notification of acceptance: June 30, 2018. Conference: Sunday September 9, 2018. Organizing committee: Yves Sucaet, Vrije Universiteit Brussel, Belgium Jeroen Van der Laak, UMC Radboud, Netherlands Zev Leifer, New York College of Podiatric Medicine, USA Yukako Yagi, Memorial Sloan Kettering Cancer Center, USA Raphaël Marée, Universit? de Li?ge, Belgium David Ameisen, IRIF, CNRS and Universit? Paris Diderot, France Paul Van Diest, UMC Utrecht, Netherlands Jeffrey Fine, Magee-Womens Hospital of UPMC

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Opening: Jr Bioinformatician in one of the largest next-gen sequencing service providers in the EU
by Ali May 20 Jun '18

20 Jun '18

Hi, Do you have the BIOINF3 a.k.a. "the next-generation gene" significantly upregulated? BaseClear <http://baseclear.com/> is searching for a Jr. Bioinformatician with a potential to disrupt the way bioinformatics works for microbial genomics, both in industry and academia. We will give you terabytes of Illumina, PacBio and ONT data, an advanced computing infrastructure, opportunities to write scientific papers, and most importantly good questions that will keep you going. To apply: https://www.baseclear.com/career-jobs/junior-bioinformatician-m-f/ <https://lnkd.in/eBFaf-E> To see some of the bioinformatics we do at BaseClear: https://www.baseclear.com/services/bioinformatics/ Best wishes, Ali

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PhD position linking genes to plant traits
by Nijveen, Harm 19 Jun '18

19 Jun '18

Hi, we are looking for a PhD student to work on linking genes to plant traits by combining (e)QTL data with prior knowledge: https://www.wur.nl/en/Jobs/Vacancies/Show/PhD-position-Finding-genes-for-tr… <https://www.wur.nl/en/Jobs/Vacancies/Show/PhD-position-Finding-genes-for-tr…> Regards, Harm Nijveen, PhD BICT Bioinformatics Group, Wageningen University, The Netherlands.

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Scientific Programmer position at AMC Amsterdam
by J.J.B. Koster 18 Jun '18

18 Jun '18

Dear colleagues, We are looking for an enthousiastic scientific programmer to extend our R2 development team at the AMC, Amsterdam, the Netherlands. Could you please spread the word about this job opportunity and bring the hyperlink to the attention of whoever might be interested? https://amc.easycruit.com/intranet/intranet/vacancy/2093857/137941?iso=nl Thank you in advance, Best, Jan Koster Jan Koster Ph.D. Group leader Bioinformatics Department of Oncogenomics, M1-132 Academic Medical Center (AMC) University of Amsterdam Meibergdreef 9 1105 AZ Amsterdam the Netherlands Tel: +31 20 56 67536 Email: j<https://webmail.amc.nl/owa/r2-support@amc.uva.nl/redir.aspx?SURL=ilk7fUTz3G…>ankoster(a)amc.uva.nl ________________________________ AMC Disclaimer : https://www.amc.nl/disclaimer ________________________________

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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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