From arne at bioinfo.se Fri Dec 6 09:12:26 2019 From: arne at bioinfo.se (Arne Elofsson) Date: Fri, 6 Dec 2019 09:12:26 +0100 Subject: [SocBiN] Fwd: CASP: Job opportunity at TTI-Chicago In-Reply-To: <20191206052632.887FB37C3617@predictioncenter5.genomecenter.ucdavis.edu> References: <20191206052632.887FB37C3617@predictioncenter5.genomecenter.ucdavis.edu> Message-ID: A communication from Prof. Jinbo Xu: Research and Tenure-Track Faculty Positions at TTI-Chicago TTI-Chicago invites applications for the following faculty positions in computer science: • endowed three-year research assistant professor • tenure-track assistant professor • full or associate (tenured) professor • visiting professor While we welcome applications from many areas of computer science, we will give preference to candidates working in the following areas: • machine learning • computer vision • natural language processing and speech • robotics • computational biology • algorithms and complexity theory About TTI-Chicago TTI-Chicago is a philanthropically endowed academic institute dedicated to fundamental research and graduate education in computer science. TTI-Chicago produces cutting-edge research (our faculty routinely publish their results at top conferences and are recognized with distinctions such as the Sloan Research Fellowships, NSF CAREER Awards, and Best Paper Awards) and offers world-class graduate education. At the same time, TTI-Chicago faculty members enjoy a uniquely light teaching load, which helps them focus on their research. TTI-Chicago research assistant professor alumni have an excellent employment track record ( https://www.ttic.edu/faculty-alumni/). Located on the University of Chicago campus, TTI-Chicago has strong ties to the University. In addition to having access to TTI-Chicago's excellent computing infrastructure, faculty members have access to many of the University of Chicago's state-of-the-art facilities. TTI-Chicago faculty members frequently collaborate with colleagues from leading academic institutions around the world. Moreover, TTI-Chicago supports travel and visitor hosting (through annual research funds for research and tenured faculty and start-up packages for tenure-track faculty). TTI-Chicago's faculty and students enjoy the close proximity of a vibrant urban environment with flourishing culture, business, and entertainment scenes. We invite candidates with an outstanding academic record and passion for computer science research to join our world-class team of 12 tenured/tenure-track faculty and 11 research faculty members. Teaching Requirements Tenure-track faculty teach one quarter per year. Research faculty have no teaching duties, but have the opportunity to teach and co-advise students. TTI-Chicago/Simons-Berkeley Joint Program Applicants for research assistant professor (RAP) positions in relevant areas are encouraged to simultaneously apply for the TTI-Chicago RAP program and the Simons-Berkeley Research Fellowship. In 2020-21, the Simons Institute is running four programs: “Probability, Geometry, and Computation in High Dimensions”, “Theory of Reinforcement Learning”, “Satisfiability: Theory, Practice, and Beyond”, and “Theoretical Foundations of Computer Systems” (see http://simons.berkeley.edu/programs/current for details). Applicants selected by TTI-Chicago will be offered an RAP position. Applicants selected by both institutions will be able to participate in a program at the Simons Institute before joining TTI-Chicago. Please note that applicants interested in the joint program must submit separate applications to TTI-Chicago and the Simons Institute. Timeline We will start reviewing applications on December 1, 2019, and will continue until the positions are filled. Application Requirements 1. cover letter 2. curriculum vitae 3. research statement 4. teaching statement (optional for RAP applicants) 5. names and contact information of at least three references If interested in the joint program, please check the Simons Fellowship requirements (https://simons.berkeley.edu/programs/fellows). Please note that the Simons Institute has a different deadline. Where to Apply https://ttic.edu/facultyapplication Instead of submitting an application online, senior applicants may directly contact the Chief Academic Officer (avrim at ttic.edu) or faculty members in their areas. Questions recruiting at ttic.edu TTI-Chicago is an equal opportunity employer. -------------- next part -------------- An HTML attachment was scrubbed... URL: From bartoszekkj at gmail.com Sun Dec 8 20:52:50 2019 From: bartoszekkj at gmail.com (Krzysztof Bartoszek) Date: Sun, 8 Dec 2019 20:52:50 +0100 Subject: [SocBiN] Stochastic differential equations with R school at Linkoping University Message-ID: Dear all, At the Division of Statistics and Machine Learning, Department of Computer and Information Science, Linköping University, Sweden, 14th-19th May 2020, we will be hosting a school concerning stochastic differential equations and the YUIMA R package (Simulation and Inference for SDEs and Other Stochastic Processes, https://cran.r-project.org/web/packages/yuima/index.html). The lectures will be given by members of the YUIMA team ( https://yuimaproject.com/ ). The nearly final program of the school is : Dates (fixed and final): May 14 (Thu), May 15 (Fri), May 18 (Mon), May 19 (Tue) in 2020 The 5th YUIMA Conference will be held in parallel. Program DAY 1 09:00-10:00 Introduction to R programming 10:15-11:00 Refresh on stochastic processes 11:30-12:30 Introduction to SDE I (Brownian motion and its properties) 14:30-15:30 Introduction to SDE II (stochastic integrals and Ito's formula with some applications) 16:00-17:00 Introduction to SDE III (SDE) DAY 2 09:00-09:45 Time series import and Date/timestamps manipulation in R 10:00-11:00 Overview of Yuima and Yuima GUI 11:30-12:30 Simulation of diffusion processes I (theoretical background and introduction to YUIMA) 14:30-15:30 Simulation of diffusion processes II (simulation of notable models for illustrations) 16:00-17:00 Supplements DAY 3 09:00-10:00 Inference for diffusion processes I (QMLE) 10:30-11:30 Inference for diffusion processes II (quasi Bayesian estimation) 13:30-14:30 Model selection (information criteria: CIC, BIC and QBIC) 15:00-16:00 Implementation via Yuima GUI DAY 4 (this day is for gentle introductions of topics with a more software oriented approach) 09:00-10:00 Compound Poisson process (basics, simulation and estimation) 10:30-11:30 Introduction to Levy processes 13:30-14:30 Point processes 15:00-16:00 Sparse estimation (Lasso and other regularizations) A similar event took place in summer 2019: https://yuimaproject.com/yss2019/ Please feel free to spread information about the school to anyone who could be interested. If there are any questions or somebody would like to attend, they should e-mail me directly. Best wishes Krzysztof Bartoszek, PhD Docent, Senior Lecturer in Statistics Division of Statistics and Machine Learning Department of Computer and Information Science Linköping University krzysztof[_dot_]bartoszek[_at_]liu[_dot_]se From Anita.Sveen at rr-research.no Mon Dec 9 12:56:15 2019 From: Anita.Sveen at rr-research.no (Anita Sveen) Date: Mon, 9 Dec 2019 11:56:15 +0000 Subject: [SocBiN] Bioinformatician in cancer genomics Message-ID: Dear all, We have an available position as engineer/senior engineer in bioinformatics in our research group at the Institute for Cancer Research, Oslo University Hospital. The candidate will be part of a large, multidisciplinary team and work with multi-level cancer genomics data to identify new treatment strategies for patients with colorectal cancer. We are offering a 2-year position with possibility for extension (application deadline Dec 24, 2019): https://www.finn.no/job/fulltime/ad.html?finnkode=164662786 Sincerely, Anita Sveen ------------------- Anita Sveen, PhD Lothe group, Dept Molecular Oncology Inst Cancer Research, Oslo University Hospital P.O.Box 4953 Nydalen, NO-0424 Oslo, Norway Associate Professor Inst Clinical Medicine, University of Oslo Phone: +47 22 78 17 19 E-mail: anita.sveen at rr-research.no -------------- next part -------------- An HTML attachment was scrubbed... URL: From kimleeng at gmail.com Mon Dec 9 14:13:31 2019 From: kimleeng at gmail.com (Kim Ng) Date: Mon, 9 Dec 2019 14:13:31 +0100 Subject: [SocBiN] Position: Viral bioinformatician (PostDoc) at Statens Serum Institut (Copenhagen, Denmark) 1.1.2020 Message-ID: Dear all, We have a PostDoc (3 years) position available as a Viral bioinformatician at Statens Serum Institute, (National Surveillance in Copenhagen, Denmark). The position will be located in the Department of Virus & Microbiological Special Diagnostics where you'll work within a team of virologists. Work will be related to Viral WGS data from both animal and humans with a primary project related to finding markers in influenza for that may have caused its jump from Pig to Human (using Danish Samples). Experience with viral bioinformatics tools and pipelines are a strong plus. Here is a link to the posting, the deadline is the start of next year currently (1.1.2020): https://candidate.hr-manager.net/ApplicationInit.aspx?cid=5001&ProjectId=127881&DepartmentId=9179&MediaId=5&SkipAdvertisement=False&uiculture=en You can also contact me if you have any questions, below is a copy of the description Do you want to have notable impact on how Statens Serum Institut works with viral Next Generation Sequencing (NGS) data for surveillance? *About Department of Virus & Microbiological Special Diagnostics* As our new colleague, you will be a part of the Department of Virus & Microbiological Special Diagnostics (VMS), where we perform diagnostics and provides clinical guidance for viral infections and serology. The department is the national central laboratory for human virology, including surveillance of viral infections and research and development within the field. The department comprises the national WHO Centre on influenza, polio and measles/rubella. The department is also a member of the European Network for Imported Viral Diseases (ENIVD), thus participating in the European collaboration on surveillance of viral infections. *About the position:* We are looking for a highly motivated and dynamic postdoc. You will be involved in research activities within the frame of the FluZooMark project. Your primary task will be to assist in the bioinformatics requirements for the FluZooMark project as well as assisting in implementing additional viral bioinformatic tools for viral surveillance. The research project involves bioinformatics, and you will be looking for viral molecular markers in the viral genome related to zoonotic transmission from NGS data of thousands of influenza virus samples from both human and swine origin. *Required qualifications:* Ideally, you are a bioinformatician with a PhD. You have experience working with viral data and you feel comfortable working with this data already. You will require the ability to install and run various viral bioinformatics pipelines on a Linux server and be able to, with the assistance of the Virologists, interpret the results. You speak English fluently though Danish fluency is also a benefit. Technical requirements: - Fluency within a Linux environment - Install, run, debug, and maintain bioinformatic pipelines Optional requirements: - Knowledge of virology (i.e. Influenza) - Programming/Statistical knowledge (i.e. Python, R) - Experience with bioinformatic tools/pipelines (i.e. V-pipe, NextStrain, PyMol, BEAST) - Experience with Sweep Dynamics plots *Terms of employment:* The employment as postdoc is a full time and fixed-term position for three years. The employment will be in accordance with the terms of the collective agreement between the Ministry of Finance and the Danish Federation of Professional Associations (AC-overenskomsten) and the Danish Ministry of Finance’s circular concerning the job structure for scientific staff working with research at sector research institutions (Stillingsstruktur for videnskabeligt personale med forskningsopgaver ved sektorforskningsinstitutioner). If you come from abroad, we will be happy to assist you in the transition process. *Further information.* For further details and informal enquiries please contact Senior Scientist Ramona Trebbien phone +45 32683591 or email ratr at ssi.dk *Application and recruitment process:* Click “apply” to send your job application with the following appendixes - curriculum vitae (CV) - copies of relevant academic diplomas (master and PhD) - list of scientific publications - 2-3 scientific publications. Your research qualifications will be assessed by a scientific assessment committee in accordance with the current Danish rules for employment of scientific staff working with research at sector research institutions in Denmark. Interviews is expected to be held between 6 January 2020 and 17 January 2020. Kind regards, -Kim Ng -------------- next part -------------- An HTML attachment was scrubbed... URL: From arne at bioinfo.se Mon Dec 9 09:28:22 2019 From: arne at bioinfo.se (Arne Elofsson) Date: Mon, 9 Dec 2019 08:28:22 +0000 Subject: [SocBiN] Fwd: Call for applications to the National Graduate School in Medical Bioinformatics, Deadline 28 February 2020 In-Reply-To: <75411f1226654050a11aace537d961f7@ebox-prod-srv13.win.su.se> References: <75411f1226654050a11aace537d961f7@ebox-prod-srv13.win.su.se> Message-ID: Dear Colleague, I would much appreciate it if you could forward the attached message to Departmental and other relevant email lists. Please print out the attached flyer and post on your physical bulletin board if applicable. To all current and prospective 1st year PhD students in Bioinformatics, You are invited to apply to MedBioInfo, the National Graduate School in Medical Bioinformatics, established to provide advanced training in bioinformatics to the next generation of world-class life-science researchers. Our 43 affiliated faculty members include most of the leading bioinformaticians in Sweden, and we also draw on the faculty of NORBIS, our Norwegian sister school. Alongside your peers, this will form a key part of your future scientific network. Our courses are short, worth 3 or 5 HP(ECTS). Each course typically requires a one-week at-home pre-assignment, one week in residence, and (often) a take-home one-week post-assignment. You would typically take two courses per year, for a total of 3 years. The courses are more specialised than can be provided by your home university. You will be matched with a faculty mentor, providing a perspective and advice complementary to that of your advisor. We also have an annual meeting where you will attend faculty talks and soft-skills workshops, present your research, network, and get feedback. You will be granted a yearly travel budget. Best of all, this should be fun. You are eligible to apply if you began or will begin your PhD between January 2019 and April 2020, though there is some flexibility in this. Target groups include PhD students in Life Science doing primarily computational research.Selection criteria include your CV, transcript, and the relevance of your research project. You will also need an endorsement letter from your advisor and a suitable laptop. We will strive to have a broad distribution of Swedish home universities as well as a good gender balance.. By applying, you agree to set aside three days in May to attend our Annual Meeting, 18-20 May near Göteborg, as well as a week (probably in June) to attend your first course, "Applied Bioinformatics," as will be announced on MedBioInfo.se . Several of our core courses require programming in Python. If your Python background is weak, you will need to start strengthening your skills soon after admissions. BILS sometimes offers python courses (https://www.scilifelab.se/education ), and we also recommend Shaw's "Python 3 the hard way." Due to the climate crisis we ask students (with the possible exception of those from Umeå) to avoid flying to MedBioInfo events. The deadline is February 28, 2020. Enrollment is limited to approximately 20 incoming students per year. You should sign upfollowing https://ec.europa.eu/eusurvey/runner/MedBioInfo-application-2020 , also linked to from medbioinfo.se. Feel free to email me with any questions. We look forward to reading your application. With kind regards, Sam Samuel Coulbourn Flores, Docent *Studierektor för den nationella forskarskolan inom medicinsk bioinformatik * Department of Biochemistry and Biophysics Stockholm University Visiting: SciLifeLab A6220 (Alpha Tr. 6) Deliveries: Samuel Flores Stockholms Universitet, Org # 202100-3062 Tomtebodavägen 23a 171 65 Solna SWEDEN Mobil: +46.706000464 Mexank: 0816-3949 skype: samuelfloresc facebook.com/MedBioInfo -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: poster-forskarskola.A4.2020-LIGHT.pdf Type: application/pdf Size: 5555391 bytes Desc: not available URL: From anders.andersson at scilifelab.se Tue Dec 17 10:00:30 2019 From: anders.andersson at scilifelab.se (Anders Andersson) Date: Tue, 17 Dec 2019 10:00:30 +0100 Subject: [SocBiN] Fwd: Postdoctoral position at the MEG Verbania In-Reply-To: <2ac75831-82ab-233c-56e2-f63c03092071@cnr.it> References: <2ac75831-82ab-233c-56e2-f63c03092071@cnr.it> Message-ID: ---------- Forwarded message --------- From: Gianluca Corno Date: Mon, Dec 16, 2019 at 4:13 PM Subject: Postdoctoral position at the MEG Verbania To: Dear friend, as many of you we are also surfing on the same wave, so we are looking for another bioinformatician. So if you already found one or more for you and you know somebody potentially interested in a superexciting 1+1 year position with us at the MEG on the shore of the most beautiful lake of the world, a few steps from Rome, Venice, Paris and whatever a person can find interesting to see, to eat, to drink and to whatever else... please forward this email :-) Thank you! Gluca *Postdoc Position in Bioinformatics, Metagenomics and the Environmental Antibiotic Resistome* The Molecular Ecology Group (MEG) of the Water Research Institute of the National Research Council of Italy (CNR-IRSA) in Verbania is looking for a postdoctoral researcher in the computational analysis of microbiome data ranging from water and wastewater microbial communities to host- and environment-associated microbial communities, to single strain genomic reconstruction and analysis, and metatranscriptomics. Specific tasks will focus on the development of specific pipelines for the analysis of the antibiotic resistome in microbial communities, gene phylogeny, phenotype evolution, and transcriptomics. Expected Profile: PhD or equivalent certified experience in bioinformatics, computational biology, statistical genetics, human microbiota, and microbial ecology. Good programming skills, proficiency in Unix/Linux and cluster experience. Strong independence and willingness in collaborating in researches covering multiple fields of microbial ecology The MEG is an exciting, interdisciplinary group with excellent facilities and a leading position in microbial ecology, biogeography and in the study of antibiotic resistance in the environment. The MEG is located in Verbania at the CNR-IRSA Institute, on the beautiful shore of Lake Maggiore in Italy at the border with Switzerland. The MEG is involved in several projects in partnership with more than 50 national or international leading research centres and universities. The selected candidate will have free access for 1 month to the Institute’s guest house. The contract is for 1+1 year, extendable for a maximum of additional 4 years. Net salary is about 1500 euros/month for the first year, the position is not imposing the continuative presence of the researcher in the Institute. Deadline for application: 17 of January 2017, expected starting date: March 2020. To apply: Please contact Dr. Gianluca Corno (gianluca.corno at cnr.it) to get more information on the procedures (a couple of forms in Italian to be filled, CV and publications list are required). -- *Gianluca Corno* MEG Microbial Ecology Group - Water Research Institute CNR - National Research Council of Italy Largo Tonolli 50, 28922 Verbania Phone (direct): +39 0323 518321 Fax: +39 0323 556513 Microbial Ecology Group Website: www.meg.ise.cnr.it GLuca on CNR WebTV: www.cnrweb.tv/gianluca-corno -- Associate Professor SciLifeLab School of Biotechnology KTH Royal Institute of Technology Stockholm, Sweden Webpage: https://urlproxy.sunet.se/canit/urlproxy.php?_q=aHR0cDovL2Vudmdlbi5naXRodWIuaW8v&_s=ZGVmYXVsdA%3D%3D&_c=0ce448ea&_r=c3Utc2U%3D Email: anders.andersson at scilifelab.se Phone: +46-8-5248-1414; +46-73-9838962 -------------- next part -------------- An HTML attachment was scrubbed... URL: From rbh at intomics.com Fri Dec 20 11:05:19 2019 From: rbh at intomics.com (Rasmus Borup Hansen) Date: Fri, 20 Dec 2019 11:05:19 +0100 Subject: [SocBiN] Position as System Administrator for bioinformatics systems at Intomics, Lyngby (Copenhagen) Message-ID: <94F28789-F2FF-48C3-95EB-C078C4EB2417@intomics.com> Linux System Administrator for Bioinformatics Systems Do you want to run Linux systems and IT infrastructure for bioinformatics and/or data science, supporting research that discovers the medicine of tomorrow? Responsibilities As Linux System Administrator you will be part of a small team that runs Intomics’ internal IT systems consisting of network equipment, Linux servers and macOS clients. To begin with, the focus will be on standard services, but depending on your skills and potential, you may later be involved in data management, or perhaps design, implementation and operations of specialized services for Intomics’ clients. You will be part of the Informatics department and work at our office in Lyngby. Requirements We are looking for someone with experience running Linux systems, preferably with first-hand knowledge on using Linux systems for bioinformatics or data science. As you will make systems for handling big data sets and complex databases, prior practical experience with this will be an advantage. We prefer candidates who have a background or an interest in engineering, computer science and/or natural sciences like biology, chemistry, physics, mathematics, or, of course, bioinformatics. Any knowledge on the entire IT stack, including hardware, networking, virtualization, cloud solutions, databases, web technologies, or programming in e.g. Python will be considered an advantage. You will also be tasked with writing structured and precise documentation and possibly reports or policies in English. You will have challenging tasks and get the opportunity to leverage your experience or to acquire new skills to find the best technical solutions to meet our needs. Your colleagues will be specialists highly skilled in IT. They will be available for sparring, and you will interact closely with them to build systems that support their work and get the most out of our IT investments without any nonsense. Intomics as your next career step At Intomics we work in close collaboration with our clients from the pharmaceutical industry to discover new drugs, improve research and find the most effective treatments for patients, and we are specialized in analysis and integration of biological big data. Our size allows us to operate in an agile and informal environment and we are characterized by having world-class expertise while maintaining an entrepreneurial spirit and a strong company culture. We offer a workplace with a friendly and informal atmosphere, where you will be collaborating with colleagues with strong scientific backgrounds and who are extremely passionate about finding innovative solutions together. We work with dedication and efficiency, while maintaining a high degree of flexibility to keep a healthy work-life balance, ensuring a high level of employee satisfaction. Please send your application, CV and references to applications-1907 at intomics.com in pdf no later than January 27th. Applications will be reviewed on a rolling basis. Any enquiries can be made to Head of Informatics, Rasmus Borup Hansen (+45 88807979). -------------- next part -------------- An HTML attachment was scrubbed... URL: From arne at bioinfo.se Sat Dec 21 20:43:58 2019 From: arne at bioinfo.se (Arne Elofsson) Date: Sat, 21 Dec 2019 20:43:58 +0100 Subject: [SocBiN] Fwd: interesting job in Paris at Martin Weigt's place (please forward to anyone potentially interested) In-Reply-To: References: Message-ID: ---------- Forwarded message --------- From: Erik Aurell Date: Sat, 21 Dec 2019, 20:42 Subject: interesting job in Paris at Martin Weigt's place (please forward to anyone potentially interested) To: Carsten Daub , Andreas Lennartsson < andreas.lennartsson at ki.se>, Ozan Öktem , Antti Niemi < antti.niemi at me.com>, Arne Elofsson , Erik Arner < erik.arner at riken.jp>, Ralf Eichhorn , Stefano Bo < stefabo at pks.mpg.de>, Andrea De Martino , gino.delferraro at gmail.com And Merry Christmas and Happy New Year everyone! Erik ________________________________________ Från: Martin Weigt [martin.weigt at upmc.fr] Skickat: den 21 december 2019 19:59 Ämne: please forward to potentially interested candidates Dear friends and colleagues, Please send this message to anybody potentially interested: A professorship in Computer Science will be opened at the beginning of the academic year 2020 at Sorbonne University to join the Unit Computational and Quantitative Biology (http://www.lcqb.upmc.fr/) in the heart of Paris. Please see the description in attachement. Best regards, Martin Weigt -- Martin Weigt UMR 7238 - Computational and Quantitative Biology Sorbonne Université (former Université Pierre et Marie Curie) 4 place Jussieu 75005 Paris, FRANCE Tel: +33 (0)1.44.27.73.68 Fax: +33 (0)1.44.27.73.36 Email: martin.weigt at upmc.fr -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: announcement-LCQB.pdf Type: application/pdf Size: 170536 bytes Desc: not available URL: From ingemar.andre at biochemistry.lu.se Sun Dec 29 12:50:00 2019 From: ingemar.andre at biochemistry.lu.se (=?utf-8?B?SW5nZW1hciBBbmRyw6k=?=) Date: Sun, 29 Dec 2019 11:50:00 +0000 Subject: [SocBiN] Postdoctoral fellow in computational protein design Message-ID: <59C6E204-359C-4A19-8539-291A7D348DBF@biochemistry.lu.se> Dear all, We are looking to recruit a postdoc in computational protein design to the André research group (andrelab.biochemistry.lu.se) at Lund University. The researcher will be tasked in computational method development for structure-based computational protein design. Custom-made programs will be developed for adapting geometric shape matching approaches to protein design and design algorithms will be developed in the Rosetta macromolecular modeling suite. The position has a application deadline of January 23rd. More information about the position, requirements and how to apply can be found at https://lu.varbi.com/en/what:job/jobID:304539/type:job/where:4/apply:1 Ingemar André Biochemistry & Structural Biology Lund University PO Box 124 221 00 Lund tel: +46 46 222 4470 email: ingemar.andre at biochemistry.lu.se -------------- next part -------------- An HTML attachment was scrubbed... URL: