From Tatiana.Starikovskaya at ens.fr Thu Dec 3 14:28:51 2020 From: Tatiana.Starikovskaya at ens.fr (Tatiana Starikovskaya) Date: Thu, 3 Dec 2020 14:28:51 +0100 Subject: [SocBiN] =?utf-8?q?CFP=3A_32nd_Annual_Symposium_on_Combinatorial_?= =?utf-8?q?Pattern_Matching_=28CPM=29=2C_Wroc=C5=82aw=2C_Poland=2C_July_5-?= =?utf-8?q?7=2C_2021?= Message-ID: <0B466253-409B-44C2-A034-B8A7B4E8D1E1@di.ens.fr> (Apologies for multiple copies) ================================ The Annual Symposium on Combinatorial Pattern Matching (CPM) has by now over 30 years of tradition and is considered to be the leading conference for the community working on Stringology. The objective of the annual CPM meetings is to provide an international forum for research in combinatorial pattern matching and related applications such as computational biology, data compression and data mining, coding, information retrieval, natural language processing, and pattern recognition. The 32nd Annual Symposium on Combinatorial Pattern Matching (CPM 2021) will be held in Wroclaw, Poland, July 5-7, 2021. WEBSITE OF THE CONFERENCE: http://cpm2021.ii.uni.wroc.pl/ ================================ CALL FOR PAPERS Papers on original research unpublished elsewhere in all areas related to combinatorial pattern matching and its applications are welcome. The proceedings will be published by LIPIcs (of Dagstuhl). TOPICS OF INTEREST Papers are solicited on, but not limited to, the following topics: Bioinformatics and computational biology Coding and data compression Combinatorics on words Data mining Information retrieval Natural language processing Pattern discovery String algorithms String processing in databases Symbolic computing Text searching and indexing KEYNOTE SPEAKERS Hideo Bannai (Tokyo Medical and Dental University, Japan) Michal Koucký (Charles University, Czech Republic) Nadia Pisanti (University of Pisa, Italy & Erable Team INRIA, France) DEADLINE Friday, January 29, 2021, anywhere on Earth SUBMISSION Submission is through the EasyChair conference system: https://easychair.org/conferences/?conf=cpm2021 SUBMISSION FORMAT The authors should submit an extended abstract not exceeding 15 pages, including figures, title, authors, affiliations, e-mail addresses, and a short abstract. The authors are required to use the LaTeX style file supplied by Dagstuhl (LIPIcs) with the original settings (including the font size and the margins). References will not be counted in the page limit. At least one author of an accepted paper is expected to present the paper at the conference as a registered participant. Papers must be submitted as a single file in PDF format. Additional material intended for the referee but not for publication in the final version—for example details of proofs—may be placed in a clearly marked appendix that is not included in the page limit. Papers submitted for review should represent original, previously unpublished work. At the time the extended abstract is submitted to CPM, and for the entire review period, the paper (or essentially the same paper) should not be under review by any other conference with published proceedings or by a scientific journal. COVID-19 We are carefully watching the situation with the Covid-19 pandemic. We hope to conduct a physical event, but we will certainly offer the possibility of remote participation (with a significantly lower registration fee) for those who are unable to come due to travel restrictions or other circumstances. In the worst case, we will move the event online but are not planning to postpone it. PROGRAM COMMITTEE MEMBERS Golnaz Badkobeh (Goldsmiths University of London, UK) Frédérique Bassino (University Paris 13, France) Christina Boucher (University of Florida, USA) Laurent Bulteau (CNRS and Université Paris-Est Marne-la-Vallée, France) Raphaël Clifford (University of Bristol, UK) Fabio Cunial (MPI-CBG, Germany) Funda Ergun (Indiana University, USA) Paweł Gawrychowski (University of Wrocław, Poland), Co-Chair Inge Li Gørtz (Technical University of Denmark) Stepan Holub (Charles University in Prague, Czech Republic) Tomohiro I (Kyushu Institute of Technology, Japan) Shunsuke Inenaga (Kyushu University, Japan) Tomasz Kociumaka (University of California, Berkeley, USA) Christian Komusiewicz (Philipps-Universität Marburg, Germany) Dmitry Kosolobov (Ural Federal University, Russia) Gad M. Landau (University of Haifa, Israel) Florin Manea (University of Göttingen, Germany) Pierre Peterlongo (INRIA, France) Cinzia Pizzi (University of Padova, Italy) Leena Salmela (University of Helsinki, Finland) Srinivasa Rao Satti (Seoul National University, South Korea) Marinella Sciortino (University of Palermo, Italy) Braha-Riva Shalom (Shenkar College of Engineering and Design, Israel) Tatiana Starikovskaya (École normale supérieure, France), Co-Chair Yasuo Tabei (RIKEN, Japan) Tomasz Waleń (University of Warsaw, Poland) -------------- next part -------------- An HTML attachment was scrubbed... URL: From paul.bourgine at med.lu.se Fri Dec 4 17:52:53 2020 From: paul.bourgine at med.lu.se (Paul Bourgine) Date: Fri, 4 Dec 2020 16:52:53 +0000 Subject: [SocBiN] ERC-funded Bioinformatician position Message-ID: Dear colleagues, Please find attached a job description regarding our available bioinformatician position at Lund University, Sweden. The project is funded through an ERC starting grant, and consist in deciphering the cellular heterogeneity in engineered human stem cell-derived tissues. We are primarily looking for a postdoc applicant, but would be willing to consider PhD with relevant background. Wishing you all a very nice weekend! Best regards, Paul Paul Bourgine, Assistant Prof. Cell, Tissue & Organ engineering Laboratory Wallenberg Center for Molecular Medicine Stem Cell Centre - Lund University +46 46 222 0771 www.bourginelab.com Twitter: @CTO_Bourgine -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Postdoc Bioinformatician.pdf Type: application/pdf Size: 238662 bytes Desc: Postdoc Bioinformatician.pdf URL: From jenni.e.hamalainen at helsinki.fi Mon Dec 7 09:32:55 2020 From: jenni.e.hamalainen at helsinki.fi (=?utf-8?B?SMOkbcOkbMOkaW5lbiwgSmVubmkgRQ==?=) Date: Mon, 7 Dec 2020 08:32:55 +0000 Subject: [SocBiN] Postdoc/Bioinformatician in computational cancer and autoimmunity research, University of Helsinki Message-ID: <58707FB7-7EBC-4115-B1D0-332896098FF7@helsinki.fi> Dear all, Professor Satu Mustjoki’s lab Hematology Research Unit at the University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center has an opening for a POSTDOCTORAL RESEARCHER / BIOINFORMATICIAN in computational cancer and autoimmunity research. Description The new researcher / bioinformatician will play a critical role in the computational analysis and statistical modelling of large-size WES, WGS, lncRNA-seq, and scRNA-seq datasets and integration of these data with clinical information. The aim of the research is to further advance our understanding on the pathogenesis of cancer and autoimmunity diseases and builds upon the group’s previous successful work on the topic (please see our webpage and the latest publication list at https://pubmed.ncbi.nlm.nih.gov/?term=mustjoki+s%5Bau%5D&) The contract will be for two years starting at your earliest convenience. Trial period of 6 months will be applied. Salary will depend upon the applicant's level of skills, knowledge, and abilities and is based on the university salary system Requirements We require fluency with Python, Perl, R or equivalent in a UNIX environment. Experience in biostatistics and machine-learning as well as understanding on and/or demonstrated ability to process genomics data and especially scRNA-seq data is desired. Strong publication record is an advantage. How to apply: Please submit your application via the University of Helsinki recruitment system here: https://www.helsinki.fi/en/open-positions/postdoctoral-researcher-bioinformatician-in-computational-cancer-and-autoimmunity-research Applications should include a resume and a cover letter as a single PDF file. The deadline for the applications is 17.12.2020. For further information Please contact Satu Mustjoki: satu.mustjoki (at) helsinki.fi or Matti Kankainen: matti.kankainen (at) helsinki.fi. If you need support with the recruitment system, please contact recruitment (at) helsinki.fi. University of Helsinki The University of Helsinki (UH), founded in 1640, is a vibrant scientific community of 40,000 students and researchers. It is one of the leading multidisciplinary research universities and ranks among the top 100 international universities in the world. It is currently investing heavily in life sciences research. UH offers comprehensive services to its employees, including occupational health care and health insurance, sports facilities, and opportunities for professional development. Together with the Helsinki University Hospital (HUS) and the Helsinki Institute of Life Sciences (HiLIFE), the Faculty of Medicine, University of Helsinki, constitutes the Academic Medical Center Helsinki (AMCH). This medical center has been very successful in international comparisons, ranking among the top 10 medical campuses in Europe and among the top 50 globally. Please see the University of Helsinki Careers page to see what UH offers its employees: https://www.helsinki.fi/en/university/careers-at-the-university-of-helsinki -------------- next part -------------- An HTML attachment was scrubbed... URL: From doncheva at rth.dk Wed Dec 9 12:33:27 2020 From: doncheva at rth.dk (Nadezhda Doncheva) Date: Wed, 9 Dec 2020 12:33:27 +0100 Subject: [SocBiN] Associate computational biologist in MICROBIAL GENOMICS Message-ID: Dear all, The following position is available at New York University Langone Health: We are seeking a talented and highly motivated Associate Computational Biologist to join us in the analysis of large-scale microbial genomics data, including whole-genome sequences, metagenomes, and RNA-Seq. For more information see https://urlproxy.sunet.se/canit/urlproxy.php?_q=aHR0cHM6Ly93d3cucGlyb250aWxhYi5vcmcvYXNzb2NpYXRlLWNvbXB1dGF0aW9uYWwtYmlvbG9naXN0&_s=ZGVmYXVsdA%3D%3D&_c=5df263e0&_r=c3Utc2U%3D Best wishes, Nadezhda Nadezhda T. Doncheva Novo Nordisk Foundation Center for Protein Research University of Copenhagen -------------- next part -------------- An HTML attachment was scrubbed... URL: From ehovig at ifi.uio.no Sun Dec 13 23:08:21 2020 From: ehovig at ifi.uio.no (Eivind Hovig) Date: Sun, 13 Dec 2020 23:08:21 +0100 Subject: [SocBiN] Postdoc position available in Oslo Message-ID: <8FE0E42C-1C1C-46C5-B755-B008C5D2AE60@ifi.uio.no> Applications are invited for a 3-year postdoctoral position in statistics and/or bioinformatics at the Oslo Centre for Biostatistics and Epidemiology (OCBE), Institute of Basic Medical Sciences, University of Oslo. See https://www.jobbnorge.no/en/available-jobs/job/196534/3-year-postdoctoral-position-in-statistics-and-or-bioinformatics -------------- next part -------------- An HTML attachment was scrubbed... URL: From marcela.davila at gu.se Mon Dec 14 16:02:35 2020 From: marcela.davila at gu.se (Marcela Davila) Date: Mon, 14 Dec 2020 15:02:35 +0000 Subject: [SocBiN] Fw: PEST-BIN PhD position In-Reply-To: References: <0a0ae907068944058f4d0d4944f85d68@biosustain.dtu.dk>, <99D29035-9208-4B3E-A5E5-006A35244164@altrabio.com>, Message-ID: <6439f3dca9c64f5ea9595badc797ccb5@gu.se> Hi everyone, 3 years PhD opportunity: https://www.altrabio.com/phd-position-pest-bin-project Feel free to forward within your networks best, /Marcela Davila University of Gothenburg -------------- next part -------------- An HTML attachment was scrubbed... URL: From vang at clin.au.dk Tue Dec 15 21:22:14 2020 From: vang at clin.au.dk (=?utf-8?B?U8O4cmVuIFZhbmc=?=) Date: Tue, 15 Dec 2020 20:22:14 +0000 Subject: [SocBiN] Post doc position in Aarhus Message-ID: <6820512B-7B5D-49CD-95C8-923650EB0CD7@clin.au.dk> Dear all, If anyone is looking for a post doc position (or know someone who is), we have an open position at MOMA, on a very interesting project where we are going to investigate the clonal dynamics of tumour-specific T-cells, at diagnosis, through treatment, and over time. We are basically going to deep sequence the T-cell receptor, and integrate with tumour and normal exome data, and with ctDNA data. The project is in collaboration with a pharmaceutical company. Heavy use of NGS, lots of bioinformatics analysis, some pipeline design, and potential for methods development. You can apply here: https://www.au.dk/om/stillinger/job/re-advertisement-post-doc-position-in-bioinformatics-liquid-biopsies-and-cancer-genomics And feel free to get back to me with any questions!! Merry Christmas & happy New Year! Best, -Nicolai ——— Nicolai Birkbak, PhD Associate Professor Department of Molecular Medicine (MOMA) Aarhus University Hospital Science Center Skejby Brendstrupgårdsvej 21A, 2nd floor 8200 Aarhus N Denmark Phone: (+45) 7845 5347 Mobile: (+45) 2539 4779 From skanduri at ifi.uio.no Thu Dec 17 14:21:23 2020 From: skanduri at ifi.uio.no (Chakravarthi Kanduri) Date: Thu, 17 Dec 2020 13:21:23 +0000 Subject: [SocBiN] A permanent position as an Associate Professor in Bioinformatics available in Oslo Message-ID: Applications are invited for a permanent position as an Associate Professor in Bioinformatics at the Centre for Bioinformatics, University of Oslo, together with the Departments of Pharmacy and Chemistry. Please circulate to relevant candidates who might be interested. https://www.jobbnorge.no/en/available-jobs/job/197931/associate-professor-in-bioinformatics Closing date for applications: 14 Jan 2021 -------------- next part -------------- An HTML attachment was scrubbed... URL: From arne at bioinfo.se Thu Dec 17 15:59:06 2020 From: arne at bioinfo.se (Arne Elofsson) Date: Thu, 17 Dec 2020 15:59:06 +0100 Subject: [SocBiN] Fwd: Postdoctoral Researcher Vacancy - OPIG, University of Oxford In-Reply-To: References: Message-ID: *Sent on behalf of Prof. Charlotte Deane* The Oxford Protein Informatics Group is currently recruiting for a Postdoctoral Researcher in collaboration with Boehringer Ingelheim. I would be grateful if you could share with your network the opportunity detailed below. *Postdoctoral Researcher * *Statistics, 24-29 St Giles’, Oxford, OX1 3LB * *Grade 8: £41,526- £49,553 p.a. * There is an exciting new opportunity in the Oxford Protein Informatics group for a postdoctoral researcher to work in collaboration with Boehringer Ingelheim. We are recruiting to the vacancy now, for someone to start as soon as possible. You will carry out research in the area of immunoinformatics, in a dynamic and collaborative group and department, where our research is world-leading. We need you to hold a relevant PhD/DPhil and to have programming experience. Your track record will include working with protein data in particular knowledge of antibody and/or general protein engineering. Interested in working in immunoinformatics, you will be an excellent communicator with an appreciation of the different working environments on offer in industry and academia. *Queries about this post should be addressed to Professor Charlotte Deane (deane at stats.ox.ac.uk ) or Dr Dan Nissley (daniel.nissley at stats.ox.ac.uk ). * *This post is fixed-term for three years, in the first instance.* *Only applications received before 12.00 midday on 8 January 2021 will be considered. * *Interviews will be held on 26 January 2021.* *Contact Person : Shabana Akthar * *Vacancy ID : 148667 * *Closing Date & Time : 08-Jan-2021 12:00 * *Contact Email : HR at stats.ox.ac.uk
* *Click here to apply * Kind regards *Professor Charlotte Deane* ------------------------------------------------------------------------------------------------------------------------------ Professor of Structural Bioinformatics, Department of Statistics, University of Oxford, 24 – 29 St Giles', Oxford, OX1 3LB Head of the Oxford Protein Informatics Group Website: http://opig.stats.ox.ac.uk/ PA: lauren.haynes at stats.ox.ac.uk | 01865 281252 ------------------------------------------------------------------------------------------------------------------------------ -------------- next part -------------- An HTML attachment was scrubbed... URL: From dirk.repsilber at oru.se Tue Dec 22 11:10:06 2020 From: dirk.repsilber at oru.se (Dirk Repsilber) Date: Tue, 22 Dec 2020 11:10:06 +0100 Subject: [SocBiN] PostDoc position (2-3 years) in Biostatistics and Statistical Bioinformatics in Biomedical Research Message-ID: At the School of Medical Sciences, Örebro University, we are looking for a Postdoctoral researcher in Biostatistics and Statistical Bioinformatics in Biomedical Research https://www.oru.se/english/working-at-orebro-university/jobs-and-vacancies/job/?jid=20200477 fixed-term 2-3 years position, 100% The candidate will build and investigate statistical as well as mathematical/mechanistic models of biomedical/molecular processes on various scales, with machine learning methodology, based on dynamical data and connected to large-scale clinical data, molecular data, questionnaire data, and national registry data on chronic pain both from clinical collaboration partners in Örebro, and multimodal pain services in Sweden. The project is transdisciplinary and includes business partners from the Life Science sector. As a postdoctoral researcher, you would join an interdisciplinary research environment comprised of biomedical researchers, statisticians, bioinformaticians, psychologists and physicians connected to several projects. The position is hosted by the Functional Bioinformatics group at the School of Medical Sciences and is affiliated to the School of Criminology, Law, Psychology and Social Work at Örebro University. THANKS FOR SPREADING THIS TO ELIGIBLE CANDIDATES! With best wishes for a merry Christmas and happy new year! Sincerely yours Dirk -- ______________________________________________________ Dirk Repsilber Professor Functional Bioinformatics School of Medical Sciences (MV) University of Örebro S - 701 82 Örebro Sweden mobile: +46 73 270 7633 personal:www.oru.se/personal/dirk_repsilber group:www.oru.se/forskning/forskargrupper/fg/?rdb=g206 ______________________________________________________ -------------- next part -------------- An HTML attachment was scrubbed... URL: From arne at bioinfo.se Wed Dec 30 17:13:02 2020 From: arne at bioinfo.se (Arne Elofsson) Date: Wed, 30 Dec 2020 17:13:02 +0100 Subject: [SocBiN] Fwd: Post-doc position on Inference of RNA structure and function from sequence data at ENS In-Reply-To: References: Message-ID: Yours Arne ----------------------------------------- Arne Elofsson Science for Life Laboratory Tel:+46-(0)70 695 1045 Stockholm University http://bioinfo.se/ Box 1031, Email: arne at bioinfo.se 17121 Solna, Sweden Twitter: https://twitter.com/arneelof Scholar: http://scholar.google.se/citations?user=s3OCM3AAAAAJ ORCID: 0000-0002-7115-9751 ---------- Forwarded message --------- From: Simona Cocco Date: Tue, Dec 29, 2020 at 5:13 PM Subject: Post-doc position on Inference of RNA structure and function from sequence data at ENS To: Remi Monasson Dear colleagues, I am writing to advertise a post-doctoral opening on statistical physics and inference for biological data. Please forward this announcement to potential candidates. Best wishes, Simona Cocco *Postdoc position on * *Inference of RNA structure and function from sequence data * Laboratory of Physics of the Ecole Normale Supérieure, under the supervision of Simona Cocco and Rémi Monasson *Context and project:* RNA, long recognized as a crucial intermediate in the fundamental biological process of production of proteins from genetic material (DNA) is also involved in many catalytic and enzymatic processes. In this context, a fundamental question is to relate the sequence of RNA molecule to its structural and functional properties. The sequence content must encode the 3D conformation of RNA (and alternative conformations e.g. resulting from binding to a ligand), In addition, the sequence is subject to functional constraints due to the need to achieve catalytic activity and specific interactions with other molecules or chemical species (RNA, proteins, DNA, ions..). RNAs designed by nature and obtained by sequencing many evolutionary distinct organisms can be used to unveil the constraints acting on RNA. Combining this sequence data available in databases such as RFAM with statistical physics and computational methods will allow us to reconstruct the landscape associated to a given function and structure. Our approach will also be tested on well-controlled RNA sequence data obtained from in vitro selection (selex). In turn, we will exploit the reconstructed landscapes to design new RNA sequences, whose structural and functional properties will be experimentally tested. The latter scope is part of the currently very active field of design in material sciences, chemistry and biomedicine. *Practical information:* This post-doc is funded by the ANR Decrypted for 18 months and should start in Spring 2021. The recruited postdoc will work in collaboration with Simona Cocco and Rémi Monasson, in the Statistical Physics and Inference for Biology group in the Laboratory of Physics of the Ecole Normale Supérieure. She/he will also benefit from the collaboration with Bruno Sargueil (CiTCoM, Paris Descartes University ) and Yann Ponty (LIX, Ecole Polytechnique ). *How to apply:* The candidate should have a PhD (or have it completed before the start of the position) in a relevant field, and a strong experience in theoretical physics, statistical physics or bioinformatic and machine learning. To apply, please send a CV and a cover letter describing your interests and previous work to simona.cocco at phys.ens.fr and remi.monasson at phys.ens.fr *Bibliography:* [1]Inverse Statistical Physics of Protein Sequences: A Key Issues Review. S. Cocco, C. Feinauer, M. Figliuzzi, R. Monasson, M. Weigt. Reports on Progress in Physics 81, 032601 (2018). [2] Direct-Coupling Analysis of nucleotide coevolution facilitates RNA secondary and tertiary structure prediction E. De Leonardis, S. Lutz, S. Ratz, S. Cocco, R. Monasson, A. Schug, M. Weigt Nucleic Acid Research, doi: 10.1093/nar/gkv932 (2015) (supplemental text and supplemental figures ) [3] 3D RNA and Functional Interactions from Evolutionary Couplings. Weinreb, C., Riesselman, A.J., Ingraham, J.B., Gross, T., Sander, C. and Marks, D.S. Cell 165(4), pp. 963–975 (2016). [4] An evolution-based model for designing chorismate mutase enzymes W.P. Russ, M. Figliuzzi, C. Stocker, P. Barrat-Charlaix, M. Socolich, P. Kast, D. Hilvert, R. Monasson, S. Cocco, M. Weigt, R. Ranganathan Science 369, 6502 (2020) -------------- next part -------------- An HTML attachment was scrubbed... URL: