July 2020 - BBClist - maillist.psb.ugent.be

Research Associate in Bioinformatics (Cambridge, UK)
by Sergio Martinez Cuesta 09 Jul '20

09 Jul '20

Dear BBC list, We have a research associate position in bioinformatics available in our group in Cambridge, UK. It would be great if you could please share it with whoever may be interested. We seek a highly motivated computational researcher for a key role within Professor Sir Shankar Balasubramanian's pioneering research programme at the Cancer Research UK Cambridge Institute (CI). Our research focuses on the chemical biology of the genome and epigenome ( https://www.balasubramanian.co.uk/publications) Our lab invents and applies new computational methods for the analysis of sequence, structure and chemical modifications in DNA and RNA. This position provides opportunities to develop computational tools at the interface between chemistry, biology and bioinformatics from experimental design to the analysis of novel types of data in collaboration with talented experimental scientists. http://www.jobs.cam.ac.uk/job/24439/ Deadline for applications *20th July 2020* Thanks in advance Sergio

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PhD TU Delft: An optimal soft-fruit chain starts at the harvest
by Thomas Abeel 08 Jul '20

08 Jul '20

Dear colleagues, We are recruiting for a four year fully-paid PhD position in Computer Science and Artificial Intelligence at Delft University of Technology “An optimal soft-fruit chain starts at the harvest”: Are you interested in learning about and developing new decision support algorithms, extending state-of-the-art computer vision and machine learning techniques? Are you prepared to take on real-life challenges related to harvesting strawberries? Join us as a PhD student in a project where we aim to advise growers of strawberries on when to harvest, based on weather predictions and time-series of images of these strawberries during their growth. The main tasks for the PhD student will be: 1) to combine algorithms for computer vision and methods for learning from time series data with algorithms on decision support from the fields of constraint programming, mathematical optimisation, and/or reinforcement learning to solve this harvesting problem, and 2) to deepen our understanding of these techniques and how they can be successfully combined. This position is jointly between Mathijs de Weerdt from the Algorithmics research group and Thomas Abeel from the Delft Bioinformatics Lab, both at the Delft University of Technology. We are looking for excellent candidates who meet the following requirements: - a MSc degree in Computer Science, Artificial Intelligence, Mathematics, or a closely related field; - affinity with interdisciplinary work; - good programming skills; - good English speaking and writing skills. If you’re interested, please send your CV (including a transcript of the grades for relevant courses), a motivation letter and (a link to) your master thesis to Sophie den Hartog <S.C.denHartog(a)tudelft.nl> before August 31, 2020. kind regards, Thomas

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Postdoc TU Delft: modelling single-cell heterogeneity in response to proton therapy
by Joana Gonçalves -EWI 08 Jul '20

08 Jul '20

Dear all, We are looking for a 2-year computational postdoc in a flagship collaboration between the TU Delft, the Erasmus MC, and the Holland Proton Therapy Center under the Convergence for Health and Technology initiative. The project aims to model single-cell heterogeneity in response to proton therapy in head and neck cancer patient biopsies. The computational postdoc at the TU Delft will work alongside a fellow experimental postdoc at Erasmus MC to: (1) characterize (un)treated tumor samples at the single-cell level using optogenetic imaging, photoselection, and single-cell RNA sequencing; (2) model single-cell and subclonal response to treatment based on transcriptomic profiles and functional imaging features, including cell dynamics and morphology; (3) identify and interpret biomarker signatures associated with resistance to proton therapy. The successful candidate should have a background in computer science or related, and experience in bioinformatics. There is ample opportunity for innovation and development of new ideas on fundamental algorithmic and statistical learning topics, in connection with this and other projects ongoing in the lab. The postdoc will be primarily affiliated with the Gonçalves lab in the Department of Intelligent Systems at the TU Delft, with a secondary appointment in the Chien lab at Erasmus MC, and will be embedded in a larger network of 24 postdocs funded by the Convergence initiative. The successful candidate will work in a highly multidisciplinary environment, and interact with a diverse group of faculty in computer science, pattern recognition and machine learning, bioinformatics, biomedical science, and molecular biology. This project will also enable access to and collaboration with other leading research scientists and laboratories in the Netherlands, including the Oncode Institute. See some of what we are currently working on at http://joanagoncalves.org/people.html. If you believe that you are a great fit, we would like to hear from you! For more information please contact me (joana.goncalves(a)tudelft.nl<mailto:joana.goncalves@tudelft.nl>), or apply directly at https://convergence.healthandtechnology.nl/square/position/37. Applications sent before July 18, 2020 will be given priority. Please, share this information with potential candidates. Kind regards, Joana -- Joana Gonçalves Assistant Professor TU Delft Faculty EEMCS, Dept. Intelligent Systems Van Mourik Broekmanweg 6, 2628 XE Delft Building 28, Office E05.060 http://joanagoncalves.org

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BioSB course: Machine Learning for bioinformatics and systems biology - 5-9 October 2020
by Femke Francissen 08 Jul '20

08 Jul '20

*Machine Learning for bioinformatics and systems biologyDate: 5-9 October 2020, online course* Modern biology is a data-rich science, driven by our ability to measure the detailed molecular characteristics of cells, organs, and individuals at many different levels. Interpretation of these large-scale biological data requires the detection of statistical dependencies and patterns in order to establish useful models of complex biological systems. Techniques from machine learning are key in this endeavour. Typical examples are the visualization of single-cell RNA-seq data using dimensionality reduction methods, base calling for nanopore sequencing data using hidden Markov models and (recurrent) neural networks, and classification of high-throughput microscopy image data using convolutional neural networks. In this one-week course, the foundations of machine learning will be laid out and commonly used methods for unsupervised (clustering, dimensionality reduction, visualization) and supervised (mainly classification) learning will be explained in detail. Methods will be illustrated using recent examples from the fields of systems biology and bioinformatics. Methods discussed in the morning lectures will be put into practice during the afternoon computer lab sessions. Topics include: - Density estimation, including histograms, nearest neighbour, Parzen - Evaluation, including ROC, cross-validation - Parametric and non-parametric classifiers, including linear discriminant analysis, k-nearest neighbours, logistic regression, decision trees and random forests - Feature selection, including search algorithms (forward, backward, branch & bound) and sparse classifiers (ridge, lasso, elastic net) - Dimensionality reduction, including principal component analysis, multidimensional scaling, t-SNE. - Clustering, including hierarchical clustering, k-means, Gaussian mixture models - Hidden Markov models - (Deep) neural networks - Kernel-based methods, including support vector machines After having followed this course, the student has a good understanding of a wide range of machine learning techniques and is able to recognize what method is most applicable to data analysis problems (s)he encounters in bioinformatics and systems biology applications. *Target audience* This course is aimed at PhD students with a background in bioinformatics, systems biology, computer science or a related field, and life sciences. Participants from the private sector are also welcome. A working knowledge of basic statistics and linear algebra is assumed. Preparation material on statistics and linear algebra will be distributed before the course, to be studied by students missing the required background. *More information and registration* via: https://www.biosb.nl/archive-courses/machine-learning-for-bioinformatics-an… *About BioSB* The Netherlands Bioinformatics and Systems Biology research school (BioSB) is the national platform in which the Dutch community of researchers in bioinformatics and systems biology is organized. BioSB also organizes fundamental and advanced post-graduate courses, the yearly BioSB conference and hot topics meetings. The aim of the BioSB research school is to offer PhD students, postdocs and senior researchers a vibrant environment for their scientific development as well as education in bioinformatics and systems biology. BioSB research school E-mail: education(a)biosb.nl Website: w <http://goog_1921660760>ww.biosb.nl [image: BioSB_logo_full_250x226.png]

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Training on (automated) Machine Learning 16 July, 2020
by Dupuis, Lauren (BIGCAT) 08 Jul '20

08 Jul '20

Dear colleague, On the 16th of July 2020, Helis Academy and TU/e will organize an online course on Machine Learning. This online program provides the opportunity to get insights on theory, current practice in industry and expected possible future practice in industry within just one day, right from behind your own PC. At the end of the training, you should be able to identify and explain the key concepts of (automated) machine learning, to outline its use in practice, to use one or more relevant techniques and tools in LSH context using minimal guidance, to apply these to your own work with limited guidance, identify and assess the benefits of (automated) machine learning for a sustained career in the LSH sector, and to identify and describe gaps in your competence profile. More information and registration is available here: https://www.eventbrite.com/e/training-on-automated-machine-learning-for-lif… Please see the attached flyers for more information. We hope to see you there! Best regards, Helis Academy Data Analysis and Data Stewardship Team

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ECCB2020 | Registration is now open!
by Eva Alloza 07 Jul '20

07 Jul '20

/- Apologies for multiple posting -/ Dear colleagues, The ECCB2020 Organising Committee is excited to share that the *virtual ECCB2020 registration is now open* <https://eccb2020.info/registration/> and that we have make public the first three confirmed speakers. We offer individual and group registrations that can fit your needs, and we will publish shortly information about registration fellowships offer by ISCB. Don't miss the opportunity to join the community during the main conference and the 19 workshops and tutorials listed in the New Trends in Bioinformatics. Besides, students are still on time to submit their abstracts to the ESCS 2020 that it is included in the registration. Please help us sharing this newsletter among your contacts. Warm regards, - Coordination team Spanish National Bioinformatics Institute (INB) mail: inb.hub(a)bsc.es web: http://inb-elixir.es Barcelona Supercomputing Center (BSC-CNS) c/Jordi Girona, 31 - Torre Girona Building 08034 Barcelona (Spain) Merge Doc View this email in your browser <http://mail.eventsairmail.com/ls/click?upn=vTVo9WAROVynOTbDemV86EYQq5tjWxdx…> Go to the ECCB2020 website! <http://mail.eventsairmail.com/ls/click?upn=vTVo9WAROVynOTbDemV86LwaCU7QCPYc…> ECCB2020 WEBSITE <http://mail.eventsairmail.com/ls/click?upn=vTVo9WAROVynOTbDemV86LwaCU7QCPYc…> REGISTRATION <http://mail.eventsairmail.com/ls/click?upn=vTVo9WAROVynOTbDemV86BNqr2wI24G8…> PRELIMINARY PROGRAMME <http://mail.eventsairmail.com/ls/click?upn=vTVo9WAROVynOTbDemV86Ftxl3wNR9BT…> NEW TRENDS IN BIOINFORMATICS <http://mail.eventsairmail.com/ls/click?upn=vTVo9WAROVynOTbDemV86Eu0P6vPbxWw…> *First keynote speakers confirmed!* Fabian Theis <http://mail.eventsairmail.com/ls/click?upn=vTVo9WAROVynOTbDemV86CfpzWqO6nT8…> *Fabian Theis* Institute of Computational Biology, Helmholtz Zentrum München, Germany Debora Marks <http://mail.eventsairmail.com/ls/click?upn=vTVo9WAROVynOTbDemV86Jqd-2BurAqh…> *Debora Marks* Department of Systems Biology, Harvard Medical School, Boston, United States Modesto Orozco <http://mail.eventsairmail.com/ls/click?upn=vTVo9WAROVynOTbDemV86PgngxFLGWhC…> *Modesto Orozco* Institute for Research in Biomedicine Barcelona (IRB Barcelona), Spain KNOW MORE <http://mail.eventsairmail.com/ls/click?upn=vTVo9WAROVynOTbDemV86KUl1JVmdICc…> *Register for the virtual ECCB2020!* ECCB2020 offers *high-quality, attractive and diverse scientific contents* through a virtual platform. The entire conference will be *streamed online* with the possibility for questioning and answering in real time. This online event will be a great opportunity *to connect attendees from all around the globe* and facilitate their interactions while keeping the spirit of the ECCB series. *You'll love it!* REGISTRATION <http://mail.eventsairmail.com/ls/click?upn=vTVo9WAROVynOTbDemV86BNqr2wI24G8…> New Trends in Bioinformatics by ECCB <http://mail.eventsairmail.com/ls/click?upn=vTVo9WAROVynOTbDemV86Eu0P6vPbxWw…> *Don't miss the workshops and tutorials before they fill up!* New Trends in Bioinformatics by ECCB is a newly designed format to virtually host a *selection of ECCB2020 workshops and tutorials.* They will run the week before the main conference during the afternoon to promote broad participation at both European and International level. *Limited places for some sessions*! Sign up now and guarantee your seat to develop your skills and deepen your knowledge in cutting edge bioinformatics and computational biology research topics with leading experts. READ MORE <http://mail.eventsairmail.com/ls/click?upn=vTVo9WAROVynOTbDemV86Eu0P6vPbxWw…> #ECCB2020 <http://mail.eventsairmail.com/ls/click?upn=vTVo9WAROVynOTbDemV86N7WOuYfIwMj…> *#ECCB2020 <http://mail.eventsairmail.com/ls/click?upn=vTVo9WAROVynOTbDemV86IIhk8LA29p1…>* <http://mail.eventsairmail.com/ls/click?upn=vTVo9WAROVynOTbDemV86IZ8Vkhn8oIW…> TECHNICAL SECRETARIAT Ph. + 34 93 882 38 78 eccb2020(a)bcocongresos.com <mailto:eccb2020@bcocongresos.com> www.bcocongresos.com <http://mail.eventsairmail.com/ls/click?upn=uJGsKvA4CvNznJb2JMu3nBHwHcOYy8PE…> http://bsc.es/disclaimer

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Fwd: Post-doc position
by mbizet 07 Jul '20

07 Jul '20

Dear BBC members, we have a position at the "Laboratory of Cancer Epigenetics", ULB, Brusels, Belgium, for a highly motivated post-doc bioinformatician. Please find the annoucement in attachment and also hereafter. Best regards, OPEN BIOINFORMATICS POSTDOC POSITION FOR EPIGENOMICS Job description: A postdoctoral position is available for a highly motivated researcher that wishes to join the Laboratory of Cancer Epigenetics headed by Prof. François Fuks (ULB-Cancer Research Center, Brussels). The research goal will be the analysis of transcriptomic and epigenomic changes (e.g. DNA methylation) that arise in cancers. Our major focus is particularly on the analysis of next generation sequencing data concerning a novel RNA epigenetic modification, which our lab recently investigated, will be one of the main challenging tasks of the candidate (Delatte et al., Science 2016). He/she will participate in several projects with high impact publication potentials. Working environment: The candidate will have the possibility to analyse many types of sequencing methods (RNA-seq, ChIP-seq, RIP-seq, CLIP-seq, Oxford Nanopore, …), while having a direct interaction with the wet lab biologists generating the data. The host lab is part of the ULB-Cancer Research Center (U-CRC) (http://ucrc.ulb.be/) providing opportunity to interact with high profile scientific community. The candidate will join other experienced bioinformaticians working on transcriptomics and epigenomics. The lab has collaborations in Belgium and abroad, while being international, the working language is English. Profile: The candidate should hold a PhD (or submitted) in bioinformatics, computational biology, bioengineering or computer sciences. He/She should demonstrate proficiency in statistics and programming with R, Python, and/or Bash. Pipeline development and automation will be a plus. Experience with next-generation sequencing (esp. RNA-seq, ChIP-seq) and clinical data will be assets. The applicant should have good organizational skills, a taste for interdisciplinary research, excellent scientific writing and presenting skills and abilty to work independently and with team. The interaction with the biologists in the lab will be key and genuine interest for biology and clinical researches is required. This position is funded for 2 years, with the possibility of further renewal. Screening of applications begins immediately and continues until an outstanding candidate is selected (flexible starting date). How to apply? Informal enquiries, a motivation letter, a CV and names of two referees should be sent to: Martin BIZET (mbizet(a)ulb.ac.be) Lab website: http://fukslab.ulb.be/ Selected publications: - Bonvin et al., Cancer Res. 2019 - Collignon et al., Science Adv. 2018 - Jeschke*, Bizet* et al., J. Clin. Invest. 2017 - Van Grembergen et al., Science Adv. 2016 - Delatte et al. Science 2016 - Boumahdi et al. Nature 2014 - Deplus et al. Cell Rep. 2014 - Dedeurwaerder*, Defrance* et al. Briefings in Bioinformatics 2014 - Delatte et al. EMBO J. 2014 - Deplus et al. EMBO J. 2013 - Volkmar et al. EMBO J. 2012 - Dedeurwaerder et al. EMBO Mol Med.2011 - Dedeurwaerder*, Defrance* et al. Epigenomics 2011 - Fuks F. Nature 2010 - Villa et al. Cancer Cell 2007 - Viré et al. Nature 2006 On 23/12/19 07:19, Matthieu Defrance wrote: > Bonjour Martin, > > J’espère également que tout se passe bien de ton côté. Concernant > l’annonce, c’est une bonne idée d’utiliser la liste (IB)2. Je n’ai par > contre personne pour cela. Nous avons également des difficultés à > trouver de bonnes recrues, particulièrement pour les postdocs. Pour > les collaborations, cela me semble difficile pour le moment. Je suis > déjà impliqué dans de nombreux projets qui me laissent peu de champ libre. > > Bonne fin d’année, > > Matthieu > >> On 20 Dec 2019, at 09:45, mbizet<mbizet(a)ulb.ac.be> wrote: >> >> Bonjour Matthieu ! >> >> >> J'espère que tout va bien pour toi ! >> >> >> 1) Nous cherchons désespérement un nouveau bioinformaticien (post-doc >> ou technicien), est-ce que tu aurais quelqu'un d'intéressé ? Rebekah >> t'en a peut-être parlé je lui ai demandé si elle pouvait poster une >> annonce sur l'(IB)² mailing-list. J'espère que cela ne te dérange pas >> (dis-moi si ce n'est pas autorisé...). >> >> 2) On se demandait si tu serais intéressé de collaborer avec nous... >> On fait tellement de sorte d'analyses: Motif, MeRIP, splicing, >> RNA-Bisulphite, PAR-CLIP, ... Il y a surement quelque chose qui >> pourrait t'intéresser !? >> >> >> Merci de me tenir au courant... >> >> >> Joyeuses fêtes !!! >> >> >> --- >> >> Martin >>

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Job opening Postdoctoral Scientist Single-Cell Bioinformatics in Multiple Sclerosis
by Matthieu Moisse 02 Jul '20

02 Jul '20

Dear All, The Laboratory for Neuroimmunology at the KU Leuven (Belgium), is seeking a highly motivated individuals with a strong background and track record in single-cell analysis and bioinformatics and a strong interest in the application of these technologies to the immunogenetics in health and disease. The Laboratory for Neuroimmunology focusses on translational research on multiple sclerosis (MS). This means that we start from important clinical questions, and investigate these in the laboratory. The aim is to translate the results back to improved health care for MS patients. To reach this goal, the Laboratory for Neuroimmunology has a translational structure with a clear research and clinical pillar. These two pillars build on the complementary expertise of Prof. An Goris and Prof. Bénédicte Dubois. Our research lines include identification of genetic risk factors for susceptibility of MS, genetic risk factors for heterogeneity in MS and functional follow-up of genetic risk factors. More information and examples of recent work can be found on our website: http://gbiomed.kuleuven.be/lni. Our research group also contributes to leading large-scale international communities, such as the International Multiple Sclerosis Genetic Consortium (www.imsgc.net) and the MultipleMS project (www.multiplems.eu) Website unit <http://gbiomed.kuleuven.be/lni> Responsibilities You will play a key role in local projects (Research Foundation Flanders, Queen Elisabeth Medical Foundation, …) as well as in international collaborative projects. In particular, you will analyze multi-omics (DNA, RNA, T- and B-cell receptor, …) single-cell data from blood and cerebrospinal fluid of patients with multiple sclerosis and combine these with other types of data on the same patients (clinical, immunological, imaging, …). You will be co-responsible for management and successful completion of these projects and play a key role in the publication of the results. You will train multidisciplinary team members in the usage of computational analysis methods, and you will co-supervise PhD and Master thesis students. Profile We are seeking highly motivated individuals with a strong background and track record in single-cell analysis and bioinformatics and a strong interest in the application of these technologies to the immunogenetics in health and disease. Essential knowledge, skills, and experience required: •MSc in a relevant field such as Biomedical Sciences, Bio-engineering, Bioinformatics or Life Sciences with a PhD in a relevant topic •A computational mindset and a strong interest in computational biology •Expertise and proven track record in large-scale biological data analysis in health sciences, preferably single-cell analysis •Proficiency in UNIX/Linux and in R programming language •Experience with large-scale computational analysis; running software on a high-performance computing cluster •High sense of accuracy •Excellent critical thinking and problem-solving skills •Able to work independently but also as a team member and in collaboration with international colleagues •Fluency in written and spoken English Additional desirable skills and experience: •Knowledge of human genetics and/or immunology •Programming skills in other languages than R Offer We offer a full-time postdoctoral scientist position for one year, renewable for up to three years, in an intellectually challenging environment with state-of-the-art infrastructure and extensive international contacts. We offer a competitive salary or fellowship, with extra benefits (e.g. health insurance, ecocheques, holiday package, reimbursement of train/bus, children day care, access to facilities such as student restaurant, sport infrastructure etc.). KU Leuven is a research-intensive, internationally oriented university that carries out both fundamental and applied scientific research. It is highly inter- and multidisciplinary focused and strives for international excellence. In this regard, it actively works together with research partners in Belgium and abroad. You will work in Leuven, a historic, dynamic and lively city located in the heart of Belgium, within 20 minutes from Brussels, the capital of the European Union, and less than two hours from Paris, London and Amsterdam. Interested? For more information please contact Prof. dr. An Goris, tel.: +32 16 33 07 72, mail: an.goris(a)kuleuven.be. To apply, please complete the online application procedure and include a detailed CV including a list of publications, a motivation letter, and the contact information of three references. You can apply for this job no later than July 08, 2020 via the online application tool <http://www.kuleuven.be/eapplyingforjobs/light/55719980> KU Leuven seeks to foster an environment where all talents can flourish, regardless of gender, age, cultural background, nationality or impairments. If you have any questions relating to accessibility or support, please contact us at diversiteit.HR(a)kuleuven.be.

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Research Software Developers Day - 3 Dec 2020
by Tuur Muyldermans 01 Jul '20

01 Jul '20

Dear, The VIB Bioinformatics Core and ELIXIR Belgium jointly started the Belgium Research Software Engineers community. The aim is to foster a community of research software developers and to collectively improve the standard of software used for scientific research. We're happy to welcome everyone interested via chat or Twitter (link on our website<https://www.be-rse.org/>). On 3 December 2020 we're organizing our very first conference, the Research Software Developers Day 2020. Two parallel tracks with presentations and workshops on topics like software quality, (cloud) infrastructure, reproducibility and devops. The event will be hosted online and tickets are free of charge! Visit https://www.be-rse.org/rsdd2020 to discover our program, register for the event or submit a proposal for a talk or workshop! Please find attached our e-flyer. Kind regards, The organizing committee Tuur Muyldermans - ELIXIR Bioinformatics Trainer ELIXIR Belgium | VIB Bioinformatics Core Lo²cus Gent Researchbuilding FSVM 2 Technologiepark 75, 9052 Zwijnaarde www.elixir-belgium.org<https://www.elixir-belgium.org/> | https://corefacilities.vib.be<https://corefacilities.vib.be/> Subscribe to our mailing list<http://eepurl.com/cl-xOX> [ELIXIR logo]

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