- BBClist - maillist.psb.ugent.be

PostDoc positions available
by Claesson, Marcus 01 Jul '18

01 Jul '18

Two postdoc positions are now available in my lab: https://www.ucc.ie/en/hr/vacancies/research/full-details-888782-en.html https://www.ucc.ie/en/hr/vacancies/research/full-details-888796-en.html Please circulate to anyone who might be interested. Marcus -- Marcus J. Claesson, PhD Lecturer at School of Microbiology & Principal Investigator at APC Microbiome Ireland University College Cork Western Road, Cork, Ireland Tel: +353-(0)21-4901390 Email: m.claesson(a)ucc.ie<mailto:m.claesson@ucc.ie> http://orcid.org/0000-0002-5712-0623

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OLA'2019 @Thailand
by El-ghazali Talbi 28 Jun '18

28 Jun '18

Apologies for cross-posting. Appreciate if you can distribute this CFP to your network. **************************************************************************************** OLA'2019 International Conference on Optimization and Learning: Challenges and Applications 29-31 Jan 2019 Bangkok Thailand http://ola2019.sciencesconf.org/ **************************************************************************************** OLA is a conference focusing on the future challenges of optimization and learning methods and their applications. The conference OLA'2019 will provide an opportunity to the international research community in optimization and learning to discuss recent research results and to develop new ideas and collaborations in a friendly and relaxed atmosphere. OLA'2019 welcomes presentations that cover any aspects of optimization and learning research such as optimization for learning, learning for optimization, optimization and learning under uncertainty, new high-impact applications, parameter tuning, 4th industrial revolution, hybridization issues, optimization-simulation, meta-modeling, high-performance computing, parallel and distributed optimization and learning, surrogate modeling, multi-objective optimization ... Submission papers: We will accept submissions in two different formats: - S1: Extended abstracts of work-in-progress and position papers of a maximum of 3 pages - S2: Original research contributions of a maximum of 10 pages Important dates: =============== Submission deadline Oct 19 2018 Notification of acceptance Nov 9, 2018 Proceedings: Accepted papers in categories S1 and S2 will be published in the proceedings that will be available at the conference. In addition, a post-conference indexed Springer book and special issue of Journal (ITOR International Transaction on Operational Research) is planned to be published. Participants will be invited to submit extended versions of their work for consideration. -- ******************************************** OLA'2019 Int. Conference on Optimization and Learning 29-31 Jan 2019, Bangkok, Thailand http://ola2019.sciencesconf.org ******************************************** Prof. El-ghazali TALBI Polytech'Lille, University Lille - INRIA - CNRS

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PhD and Postdoc positions
by Patrick Deelen 26 Jun '18

26 Jun '18

Application Deadline: Open Until Filled Job Description The *Radboud Institute of Molecular Life Sciences – department of Internal Medicine* – (https://www.radboudumc.nl) investigates the molecular mechanisms of human immune and infectious diseases. By integrating fundamental and clinical research, we obtain multifaceted knowledge of (patho) physiological processes. The Research Group of Vinod Kumar ( https://www.radboudumc.nl/en/people/vinod-kumar-magadi-gopalaiah) invites talented and highly motivated candidates to apply for a *PhD and Post-Doctoral Researchers (m/f) (Immuno-genetics, bioinformatics, Systems Biology)* starting on 1st of September 2018. The postdoctoral position will be for two years initially with a possibility of extension. The successful candidates will work in the domain of bioinformatics related to infectious diseases. Our group uses a multidisciplinary approach, including genetic/immunologic/transcriptomic/proteomic data integration and network biology, and GWAS to develop novel therapeutic treatments for infectious diseases. The successful postdoc candidate is expected to lead bioinformatics projects related mainly to human genetic and omic data analysis and develop bioinformatics pipelines for predicting genetic risk as well as to understand infectious processes. The successful candidate is expected to interact closely with clinicians and wet-lab scientists for discovering new genetic mechanisms using big data from both patient and population-based cohorts, followed by data analysis and data integration to determine correlations between molecular layers and genetics, and ends with the formulation of hypotheses that will be verified in functional experiments. *Your profile: *A strong interest in conducting collaborative research on the topic outlined above is paramount. Candidates are expected to be interested in working at the boundaries of several research domains. • PhD degree in Systems Biology, Computational Biology, Bioinformatics, Biophysics, Computer Science or a related discipline • Documented knowledge and experience in the analysis of biological high-throughput data is a requirement • Knowledge in statistical methods in the context of biological systems • Strong experience with programming (Python, Perl, C++, R) • Well-developed collaborative skills *For further information:* Please contact Dr. Vinod Kumar Email: v.kumar(a)umcg.nl *Applications:* Complete applications in English should include a CV, certificates, transcripts, a brief statement of research experiences and interests and the contact details of at least two possible referees.

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CALL FOR ABSTRACTS: Summer School on Machine Learning in Drug Design, August 20-22, 2018, Leuven, Belgium - DEADLINE: JULY 15, 2018
by Yves Moreau 25 Jun '18

25 Jun '18

Dear Colleague, The Summer School on Machine Learning in Drug Design will take place on August 20-22, 2018 in Leuven, Belgium. This Summer School will bring together the machine learning, chemoinformatics, and bioinformatics communities from academia and industry to tackle the challenges of complex data integration in drug design and discovery. The format of the event will combine multiple keynote presentations, oral contributions selected from submitted abstracts, and extensive poster sessions with ample time for discussion. We invite you to submit your abstract for oral presentation or poster by July 15, 2018 at http://mldd.esat.kuleuven.be. More information is available below and at http://mldd.esat.kuleuven.be, or by email at mldd(a)esat.kuleuven.be. Registration will open shortly. Best regards, Prof. Yves Moreau, University of Leuven Prof. Sepp Hochreiter, Johannes Kepler University of Linz Prof. Samuel Kaski, Aalto University SCOPE The data sets amenable to mining for drug design are rapidly expanding. This holds not only for the volume of conventional annotation of chemicals (i.e., representations of their chemical structure and their activities in a growing set of validated assays). It also goes for less conventional data sources, such as cellular microscopy or gene expression profiles of chemicals acquired at high throughput. Powerful novel machine learning methods unleashed on these massive volumes of heterogeneous and rich, but noisy and biased data, hold the promise of better and safer drugs to address unmet medical needs. To deliver on that promise, the Summer School calls on the machine learning, big data analytics, cheminformatics and bioinformatics communities to join forces and strengthen collaborative work at the interface of their disciplines. The Summer School will bring together contributors from both academia and industry to foster interdisciplinary exchange in this area where the need for expertise is growing rapidly. Contributions will cover recent advances in chemogenomics, strategies for data fusion, and machine learning. INVITED SPEAKERS Djork-Arné Clevert (Bayer) Daniel Reker (MIT) Gerard van Westen (Leiden University) Florian Nigsch (Novartis) Thomas Blaschke (AstraZeneca) Tim Becker (Harvard University) Gilles Marcou (University of Strasbourg) Val Gillet (University of Sheffield, TBC) INTENDED AUDIENCE AND FORMAT The summer school is intended for academic and industry researchers in machine learning, chemoinformatics, or bioinformatics who are either currently working at the interface between these fields or want to expand their skills to link these three areas. The summer school is also intended as a bridge between academia and industry. The format of the event will combine comprehensive invited presentations, oral contributions selected from submitted abstracts, and extensive poster sessions with ample time for discussion. ABSTRACT SUBMISSION Participants are invited to submit abstracts for oral contributions and posters by July 15, 2018. Abstracts can submitted for consideration for oral presentation (up to 1,000 words) or for consideration as poster only (up to 250 words). Abstracts selected for oral presentation will be notified by July 22, 2018. Abstracts will be available as a book of abstracts and online, but there will be no full proceedings. REGISTRATION AND FEE Early registration fee (before July 20, 2018): €150 (+ 21% VAT) = €181.5 Late registration fee (before August 13, 2018): €250 (+ 21% VAT) = €302.5 The fee covers participation to the meeting and includes coffee breaks and lunch (sandwich lunch). Registration will open shortly. VENUE The Summer School will be held at the Irish College, a beautifully restored historical building in the center of Leuven, Belgium.

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++ Submission deadline extension - ESCS 2018, Athens +++
by Daniele Parisi 25 Jun '18

25 Jun '18

Dear all, In case you hadn't submit your project yet, the executive team of the European Society of Computational Biology and Bioinformatics is glad to announce the extension of the submission to deadline to FRIDAY 13TH JULY 2018 (see flyer attached). Do not miss the chance to apply for a place at the poster session, at the student talk session or to request a travel fellowship. Among the other initiatives, we are also organizing a round table on ethics and bioinformatics, with speakers like prof. Yves Moreau and Dr. Masha Shabani, a unique opportunity for professional and personal growth. Register, submit and read more on our website http://escs2018.iscbsc.org/ -- DANIELE PARISI PhD student at ESAT - STADIUS, Yves Moreau's group President of RSG Belgium Chair of ESCS 2018 Kasteelpark Arenberg 10 - box 01.34 3001 Leuven, Belgium Tel: +32488794394

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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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