From paolo.romano at hsanmartino.it Tue Jul 2 12:07:29 2019 From: paolo.romano at hsanmartino.it (Romano Paolo) Date: Tue, 2 Jul 2019 10:07:29 +0000 Subject: [SocBiN] NETTAB/BBCC 2019: CALL FOR ABSTRACTS FOR ORAL COMMUNICATIONS - DEADLINE EXTENDED UNTIL JULY 15, 2019 Message-ID: Dear list members, I'm glad to inform you that the NETTAB/BBCC 2019 joint meeting has recently been recognized as ISCB Affiliated Conference. Moreover, we have just established a collaboration with the ELIXIR Proteomics Community that will support participation of ELIXIR members to the meeting. As a consequence, the deadline for submitting four-page abstracts for oral presentations has been postponed to Monday July 15, 2019. I apologize for possible duplications of this message. Paolo Romano [X] JOINT NETTAB/BBCC 2019 MEETING November 11-13, 2019 Fisciano Campus, University of Salerno, Italy http://www.nettab.org/2019 https://www.bbcc-meetings.it/ CALL FOR ABSTRACTS FOR ORAL COMMUNICATIONS New deadline: MONDAY JULY 15, 2019 (four-page abstracts) TOPICS A Special session of the meeting will be devoted to Computational Proteomics, but contributions on usual NETTAB and BBCC topics are also welcome. Computational Proteomics topics include bioinformatics methods, tools and platforms for: * Standardization of data and methods * Annotation, visualization, integrated discovery * Protein identification and validation * Biomarker discovery * Quantitative proteomics * Single cell proteomics * Targeted proteomics * Molecular imaging by mass spectrometry * Microbial proteomics See the full list of topics at http://www.nettab.org/2019/submissions/topics . AUTHORS' INSTRUCTIONS Abstracts must be submitted through EasyChair at https://easychair.org/?conferences/conf=nettabbcc2019 . New submission deadline: Monday JULY 15, 2019. Notification to authors: Monday September 2, 2019 Abstracts' length: MAX FOUR A4 PAGES. Templates are available for MS Word and LaTeX. See detailed instructions at http://www.nettab.org/2019/submissions/instructions-for-authors . CONFIRMED SPEAKERS * Davide CACCHIARELLI, Telethon Institute of Genetics and Medicine, Naples, Italy. * Martin EISENACHER, Medizinisches Proteom-Center (MPC), Ruhr-Universität Bochum, Germany. * Lennart MARTENS, VIB, University of Gent, Belgium. * Juan Antonio VIZCAÍNO, EMBL-European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, United Kingdom. CONFIRMED TUTORIALS Tutorial 1, Monday November 11, 2019 (09:00 - 11:00) Analysis of scRNA-seq using R Annamaria Carissimo, Monika Krzak, Dario Righelli and Claudia Angelini Institute for Applied Mathematics "Mauro Picone" (IAC), National Research Council, Naples, Italy. Tutorial 2, Thursday November 14, 09:00 - 17:00 Label-free quantification with OpenMS Oliver Kohlbacher, Julianus Pfeuffer and Timo Sachsenberg University of Tuebingen, Germany Tutorial supported by the GERMAN NETWORK FOR BIOINFORMATICS INFRASTRUCTURE (DE.NBI). IMPORTANT DATES Abstract submission deadlines * Abstracts for oral communications: Monday July 15, 2019 * Abstracts for posters: Friday September 20, 2019 Registration deadlines * Early registration: October 10, 2019 Meeting * Tutorials: November 11, 2019 and November 14, 2019 * Workshop: November 11-13, 2019 CONTACT INFORMATION For further information, please email to nettab.workshops at gmail.com or bbcc.meetings at gmail.com . Paolo Romano Ospedale Policlinico San Martino Genova, Italy Disclosure: despite any misleading formatting of my Institutional email address, please note that my name is Paolo, So, please, call me Paolo. Skype: p.romano Email: paolo.romano at hsanmartino.it - paolo.dm.romano at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From Ola.Spjuth at farmbio.uu.se Thu Jul 4 21:55:08 2019 From: Ola.Spjuth at farmbio.uu.se (Ola Spjuth) Date: Thu, 4 Jul 2019 19:55:08 +0000 Subject: [SocBiN] 2 open positions AI/ML in Bioinformatics, Uppsala University Message-ID: <99ECE6FE-E56D-4B00-9862-1D5632193C81@farmbio.uu.se> Dear all, I have two open positions in my lab at Department of Pharmaceutical Biosciences, Uppsala University: one PhD student position with focus on AI/Machine Learning on large-scale microscopy image data within the SSF-funded project HASTE (http://haste.research.it.uu.se/), and a 1-year Lecturer position with focus on Bioinformatics and Big Data analytics. Please see more information about the positions on my research group website: https://pharmb.io/blog/recruitment-phd-lecturer-2019/ Thanks, Ola -- Ola Spjuth, PhD, Docent Associate Professor, Department of Pharmaceutical Biosciences Director of Studies, Pharmaceutical Bioinformatics Box 591, Uppsala University, Uppsala, Sweden Email: ola.spjuth at farmbio.uu.se Ph: +46 (0)70 425 06 28 Web: https://pharmb.io N?r du har kontakt med oss p? Uppsala universitet med e-post s? inneb?r det att vi behandlar dina personuppgifter. F?r att l?sa mer om hur vi g?r det kan du l?sa h?r: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy -------------- next part -------------- An HTML attachment was scrubbed... URL: From bpn at icm.uu.se Mon Jul 15 14:47:05 2019 From: bpn at icm.uu.se (Bengt Persson) Date: Mon, 15 Jul 2019 14:47:05 +0200 Subject: [SocBiN] The Swedish Elixir node is looking for a Data Steward Message-ID: Dear all, The Swedish Elixir node is looking for a Data Steward. Deadline is 10 September. More details are available at: https://www.uu.se/en/about-uu/join-us/details/?positionId=277048 All the best, Yours, Bengt Persson Head of Node Elixir-SE -- Bengt Persson, M.D., Ph.D. Professor of Bioinformatics Director of NBIS (National Bioinformatics Infrastructure Sweden) Science for Life Laboratory Uppsala University & Karolinska Institutet Telephone: +46 18 471 4422 Mobile phone: +46 70 425 0230 Facsimile: +46 18 530 396 E-mail: bpn at icm.uu.se, bpn at nbis.se, bengt.persson at ki.se Addresses: Uppsala University | Karolinska Institutet SciLifeLab | SciLifeLab ICM -- Department of | MBB -- Department of Medical Cell and Molecular Biology | Biochemistry and Biophysics BMC, room C10:308c | House Gamma, level 6, G6613 Box 596 | Box 1031 S-751 24 Uppsala, SWEDEN | S-171 21 Stockholm, SWEDEN När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy From luca.bortolussi at gmail.com Mon Jul 15 13:58:19 2019 From: luca.bortolussi at gmail.com (Luca Bortolussi) Date: Mon, 15 Jul 2019 13:58:19 +0200 Subject: [SocBiN] Tenure track position (RTDb) in computer science (INF/01) at the university of Trieste - call opened Message-ID: <83BA5E74-2D5F-4D82-9D45-B68823D5649D@units.it> [please forward to potentially interested candidates] The University of Trieste is offering a tenure track position in computer science (Ricercatore tipo b, RTDb in INF/01), at the Department of Mathematics and Geosciences (DMG). The official call is out, with deadline for application on July 25. You can find the call and the instructions to apply here: http://web.units.it/node/37361/ricerca/pub We are looking for national or international strong and motivated candidates, which have the qualification for associate professor or are likely to get it in the next three years (this is a necessary condition to get a tenured associate professor position).* The RTDb position corresponds to an assistant professor or lecturer, and lasts for 3 years, at the end of which qualified candidates can get the tenure and become associate professors (a permanent position). The gross salary for RTDb positions is about 35k euros, rising to 50k once tenured. In the context of computer science, DMG is the leading department of a novel master program in Data Science and Scientific Computing, jointly organised with the university of Udine, SISSA and ICTP. Hence, the RTDb will be interacting and collaborating in the broader context of the Trieste and FVG system of scientific institutions. The scientific profile of the candidate has to be preferably focussed on the areas of Data Science and Scientific Computing. We look for expertise in one or more of the following areas of computer science: modelling and simulation of complex systems, statistical predictive modelling, quantitative formal methods, machine learning, data management, information retrieval, data mining, artificial intelligence, bioinformatics, cyber-physical systems We prefer scientific profiles with experience in more than one of these areas, and with a background certifying the ability and attitude to interact in multi-disciplinary research groups. Teaching: the candidate is expected to teach approximatively two courses, to be identified according to her/his scientific profile and competences. The candidate is also expected to teach in english in the international master program in Data Science and Scientific Computing (http://dssc.units.it) and in the ESFM phd program of the department (http://web.units.it/dottorato/esfm/). The candidate may also teach foundational courses in computer science (in Italian, once proficient in it). Interested candidates can also contact prof. Luca Bortolussi (lbortolussi at units.it). * for information about italian qualification please visit http://abilitazione.miur.it. A necessary condition for qualification is to have a value >= in at least two of these three indicators in scopus: >= 4 journal papers in the last 5 years, >= 157 citations in the last 10 years, h-index for the last 10 years >= 7. More info on the italian academic system here:https://www.eui.eu/ProgrammesAndFellowships/AcademicCareersObservatory/AcademicCareersbyCountry/Italy. -------------- next part -------------- An HTML attachment was scrubbed... URL: From arian.lundberg at stanford.edu Thu Jul 25 23:39:42 2019 From: arian.lundberg at stanford.edu (Arian Lundberg) Date: Thu, 25 Jul 2019 21:39:42 +0000 Subject: [SocBiN] Postdoctoral Scholar in Translational Bioinformatics at Stanford University Message-ID: <1CD0408B-D521-4892-B593-ECDDF7185D8D@stanford.edu> Dear all, Please help us spread the word about available positions in our team (http://med.stanford.edu/lilab) at Stanford University. Thank you! Kind regards, Arian Lundberg JOB DESCRIPTION: Postdoctoral Scholar in Translational Bioinformatics for Precision Cancer Medicine at Stanford University We are looking for a highly motivated postdoctoral scholar at Stanford University School of Medicine. The major focus of the NIH-funded lab is to develop, validate, and clinically translate diagnostic, prognostic, predictive biomarkers for precision cancer medicine. We integrate datasets of large patient populations and develop novel statistical and machine learning methods. Through close collaboration with clinicians at Stanford and beyond, we have access to unique, high-quality, well-annotated clinical specimens to support our biomarker research. Our lab is generously funded by 3 active NIH R01 grants. Our work has been published in top clinical journals such as JAMA Oncology, Clinical Cancer Research, Radiology, etc. Please visit http://med.stanford.edu/lilab Candidates from a diverse background are encouraged to apply. The applicant may hold a PhD either in physical sciences or engineering with a strong motivation to solve biomedical problems, or in biomedical sciences with a strong interest to apply computational approaches. The project involves the integration of diverse types of high-throughput molecular data for developing diagnostic, prognostic, and/or predictive biomarkers for precision oncology. The ideal candidates will have strong analytic and programming skills, as well as prior research experience in cancer genomics, epigenomics, or transcriptomics. Knowledge in molecular biology and tumor immunology, or experience with single-cell gene expression analysis, multi-omic data integration and/or network analysis is strongly preferred. I am dedicated to cultivating and mentoring the next generation scientists in biomedical research. Postdocs and students in the lab have gone on to establish their own independent labs in academia or secure jobs in technology industry. Major awards to my postdoc trainees include ASTRO Resident Clinical/Basic Science Research Award, ASTRO Basic/Translational Science Award, and RSNA Introduction to Academic Radiology for Scientists. ASTRO and RSNA are the world’s largest professional society for radiation oncologists and radiologists, respectively. One of my postdocs received the prestigious NIH K99/R00 Pathway to Independence Award from the NCI, which provides $1,000,000 over 5 years to establish an independent research program. He has recently secured a tenure-track faculty position at MD Anderson Cancer Center. Stanford University is located at the heart of Silicon Valley, epicenter of the technology revolution in biomedicine. This is an excellent opportunity not only for those motivated to pursue an academic career, but also for those interested in entrepreneurship with the goal of commercialization and translation of new technology into clinical practice. Interested applicants should send a research statement, CV, and names of three references to: Ruijiang Li, PhD Email: rli2 at stanford.edu ---- Arian Lundberg, Ph.D. Post-doctoral scholar office (650) 724-9383 mobile (650) 407-7891 email arlundbg at stanford.edu [signature_1739951372] -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 14994 bytes Desc: image001.png URL: From kimleeng at gmail.com Mon Jul 29 13:19:20 2019 From: kimleeng at gmail.com (Kim Ng) Date: Mon, 29 Jul 2019 13:19:20 +0200 Subject: [SocBiN] Bioinformatics/Programmer position at SSI (Copenhagen), deadline 15-08-2019 Message-ID: Dear all, I'd like to inform about a available position here at Statens Serum Institut for a bioinformatician/programmer (web developer). It'll be within the Foodbourne Infecation team but work will be related to a cross group project in which I'm involved in. Ideally the candidate will have experience in web development and we're using a technology stack utilizing dash/plotly, mongoDB, snakemake, python in order to develop front end components for mixing epi and genetic data we have here into a platform for outbreak detection and investigation to be used within a consortium of partner countries. Taking this project forward can impact how Danish outbreak detection and investigation is performed in a meaningful manner. I hope you can recommend good candidates for this position. If you have any questions outside of what's listed you can contact the people listed in the posting or myself. https://candidate.hr-manager.net/ApplicationInit.aspx?cid=5001&ProjectId=124300&DepartmentId=9178&MediaId=5&SkipAdvertisement=False&uiculture=en Kind regards, -Kim Ng -------------- next part -------------- An HTML attachment was scrubbed... URL: From ari.loytynoja at helsinki.fi Mon Jul 29 17:36:34 2019 From: ari.loytynoja at helsinki.fi (=?ISO-8859-15?Q?Ari_L=F6ytynoja?=) Date: Mon, 29 Jul 2019 18:36:34 +0300 (EEST) Subject: [SocBiN] Postdoc position in Evolutionary Sequence Analysis, University of Helsinki Message-ID: A postdoc position in evolutionary sequence analysis is available in the research group of Dr. Ari Loytynoja at the Institute of Biotechnology, University of Helsinki, Finland. The position is for three years and will start in October 2019, or later by agreement. Project: Template switching is a poorly known mutational mechanism that copies short stretches of sequence from the opposite strand and causes clusters of differences between homologous sequences. The mechanism has previously been studied in microbes and we recently showed (https://genome.cshlp.org/content/27/6/1039) that mutation patterns consistent with it are polymorphic also in humans. The role and significance of template switching in evolution of genes and organisms is not known. We are now looking for a dedicated and enthusiastic post-doctoral fellow to join in a project studying this mechanism in more detail. The applicant is required to hold PhD in evolutionary biology, bioinformatics, computer science, or a related field, as well as strong written and oral communication skills. The working language of the lab is English; knowledge of the Finnish language is not necessary. Strong experience in computer programming and Linux systems is required, prior experience in evolutionary sequence analysis is an advantage. See the links below for more information and instructions for applying the position: http://loytynojalab.biocenter.helsinki.fi https://www.helsinki.fi/en/open-positions/postdoctoral-researcher-in-evolutionary-sequence-analysis The deadline for submitting applications is August 31, 2019.