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

Bioinformatics position available at the Erasmus MC Cancer Computational Biology Center
by Harmen van de Werken 04 Oct '19

04 Oct '19

A bioinformatics position is currently available at the Erasmus MC Cancer Computational Biology Center. http://www.erasmusmc.nl/vacature/?num=21578 Please apply, if you are enthusiastic and eager to improve our knowledge on cancer biology. Harmen van de Werken

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COMPUTATIONAL BIOLOGIST - TUMOR IMMUNOLOGY
by Lodewyk Wessels 25 Jul '19

25 Jul '19

VACANCY COMPUTATIONAL BIOLOGIST - TUMOR IMMUNOLOGY YOUR ROLE WITHIN THE INSTITUTE The research groups of Dr Karin de Visser, dr Marleen Kok and Prof dr Lodewyk Wessels, are looking for a motivated and talented Computational Biologist to join their teams at the Netherlands Cancer Institute (NKI). The Inflammation and Cancer group of dr. Karin de Visser is studying the impact of the immune system on metastatic breast cancer utilizing sophisticated mouse tumor models and state-of-the art ex vivo and in vitro immunological and molecular assays. The lab of de Visser closely collaborates with the translational research group of medical oncologist dr Marleen Kok. The mission of this team is to discover novel mechanisms underlying the crosstalk between breast cancer and the immune system, to optimize immunotherapy for breast cancer patients using novel combination treatments in clinical trials and the discovery of predictive biomarkers. The Computational cancer biology group of Prof dr Lodewyk Wessels is focused on quantifying and understanding treatment response in model systems and patients. To this end we develop bespoke and novel computational methods focusing on data integration and tailored to new technologies. We actively collaborate with many research groups in the NKI and strongly believe in the power of 'team science'. PROJECTS You will be involved in the following projects: 1. MOUSE MODELS FOR METASTATIC ESCAPE FROM IMMUNE CONTROL. To study the causal relationship between immune cells and metastatic breast cancer, we utilize state-of-the art genetically engineered mouse tumor models. We have extensive RNA-sequencing datasets of isolated immune cell populations, as well as RNA-sequencing and exome sequencing data of primary breast tumors and organ-specific metastases from these mouse models. You will be responsible for the computational analyses of the data, and to extract candidate pathways/genes from these datasets that can subsequently be tested in follow up experiments in the lab. Moreover, you will link these pre-clinical data to human datasets. 2. SYSTEMIC AND INTRA-TUMORAL IMMUNOMONITORING FOR PRECISION IMMUNE-MODULATION. We are performing extensive immunomonitoring studies in human breast cancer patients treated with immune checkpoint blockade, with the ultimate aim to validate hypotheses derived from our preclinical research in human cancer patients, and to stratify breast cancer patients for immunomodulatory therapies. We are setting-up multiplex immunohistochemistry with antibody panels that audit intratumoral lymphoid and myeloid cell populations and their functional state. In parallel, we have established an extensive multiplex flow cytometry pipeline to monitor the systemic immune landscape of breast cancer patients and healthy controls. These analyses generate a substantial amount of data which require thorough computational analyses. 3. MAPPING IMMUNO-GENOMIC INTERACTIONS. We are interested in dissecting the impact of the genetic make-up of breast tumors on the intra-tumoral and systemic immune landscape. You will be responsible for the identification and validation of genotype-immunophenotype associations by connecting DNA exome sequencing data, RNA sequencing data and immune profiles derived from our mouse tumor models and cancer patients. You will use both publicly available datasets and newly generated datasets. You will be embedded in the collaborative and enthusiastic international research groups of dr. Karin de Visser, dr Marleen Kok and Prof. dr. Lodewyk Wessels, providing a unique environment that combines computational cancer biology with pre-clinical and translational research into immune-oncology. YOUR PROFILE We seek to recruit an ambitious postdoc, capable of independent thinking, with a strong commitment to translational research. Candidates should hold a degree in bioinformatics, computer science or a related discipline, have experience in statistics and/or machine learning and be proficient in bioinformatics programming languages (e.g. R, Python). We expect candidates to be highly self-motivated, creative, and a team-player with strong communication skills. General background knowledge in biology and immunology is essential, and experience with projects involving the use of genomics and immune profiling data to identifying candidate targets and biomarkers is a plus. WANT MORE INFORMATION? Please visit our home pages https://www.nki.nl/divisions/tumor-biology-immunology/de-visser-k-group/ https://ccb.nki.nl or contact Karin de Visser: k.d.visser(a)nki.nl Marleen Kok: m.kok(a)nki.nl Lodewyk Wessels: l.wessels(a)nki.nl

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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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