From arne at bioinfo.se Thu Sep 1 13:27:02 2022 From: arne at bioinfo.se (Arne Elofsson) Date: Thu, 1 Sep 2022 13:27:02 +0200 Subject: [SocBiN] PhD position in deep learning on protein-protein interactions Message-ID: Dear all I am happy to announce 1-2 PhD positions in deep learning on protein-protein interactions, in Stockholm in a great scientific environment. Please forward to suitable candidates *Project description* Protein structure is essential for understanding their function as well as for developing drugs targeting proteins. Recently, a deep learning method that can predict the structure of most proteins was made freely available, and a database with predicted structure was released. However, proteins do not act alone - they act together with other proteins. Therefore, the next major challenge is to use these types of methods for predicting protein-protein interactions. Initial studies from us have shown that it is possible to predict accurate structures of a large part of dimeric proteins using either a modified version of AlphaFold2 or AlphaFold-multimer. However, there are still many proteins that cannot be built accurately, nor are we able always to distinguish interacting from non-interacting protein pairs and to build larger complexes accurately is still an unsolved problem. In this project, we are recruiting 1-2 PhD students which will work together with two recently recruited postdocs to leverage recent advances in the field of machine learning to build better deep-learning models for predicting protein-protein interactions and to apply these methods to biologically relevant problems. More information on how to apply etc https://www.su.se/english/about-the-university/work-at-su/available-jobs/phd-student-positions-1.507588?rmpage=job&rmjob=18555&rmlang=UK Feel free to contact me 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 Zoom: https://stockholmuniversity.zoom.us/my/arneelof/ Scholar: http://scholar.google.se/citations?user=s3OCM3AAAAAJ ORCID: 0000-0002-7115-9751 -------------- next part -------------- An HTML attachment was scrubbed... URL: From nordic.compbio at gmail.com Tue Sep 13 18:21:09 2022 From: nordic.compbio at gmail.com (Nordic Computational Biology) Date: Tue, 13 Sep 2022 18:21:09 +0200 Subject: [SocBiN] Nordic Computational Biology Message-ID: Dear all, We are pleased to introduce Nordic Computational Biology (Nordic CompBio, NCB); a platform that aims to amplify ongoing efforts within the fields of computational biology and computer science across the Nordic region. NCB was launched in 2020 with a goal to become a resource platform and a community space for cross-border collaborations across the Nordics. With this email, we invite you to be part of the NCB, so you can contribute to some of the future initiatives listed below: - Nordic CompBio Conference: We are looking to put together an organising team from each Nordic region including Estonia and other underrepresented Nordic regions. The idea is to have a geographically-distributed hybrid conference i.e. 1-2 days of conference taking place in one Nordic region, and the next 1-2 days taking place in another region while talks and workshops are live-streamed. Our aim is to increase the visibility of ongoing research, as well as highlight industrial organisations (including startups) in the Nordics. We would like to start off with planning soon and brainstorm ideas - *to express your interest and share your suggestions, visit: https://forms.gle/w3UVq18MDM9PF3eWA * - Nordic CompBio Web Resources: If you have experience or interest in database and/or web development, join our team to help develop new resources such as creating a job portal. In addition, we welcome contributions to our website content e.g. to build ‘Computational Biology in Nordics’ page ( https://nordic-compbio.iscbsc.org/computational-biology-in-nordics/) We are currently a team of industrial scientists, researchers, and bioinformaticians. To join us, follow this link https://nordic-compbio.iscbsc.org/get-involved/. We welcome people from all academic levels. If you are a PI or associate professor, we encourage you to become a part of our advisory group - we aim for at least 4-5 board members from each Nordic region. The purpose of our advisory board is to guide and help our core team when need be, and there is no requirement to attend our core team meetings. There is much more we are planning to announce and share! For any queries, visit nordic-compbio.iscbsc.org/help/ or send us an email. We look forward to hearing from you! *Nordic Computational Biology Team* *---* Website | LinkedIn | YouTube | Twitter Subscribe to NCB Newsletter -------------- next part -------------- An HTML attachment was scrubbed... URL: From mauno.vihinen at med.lu.se Fri Sep 16 16:22:30 2022 From: mauno.vihinen at med.lu.se (Mauno Vihinen) Date: Fri, 16 Sep 2022 16:22:30 +0200 Subject: [SocBiN] Bioinformatics postdoc position in variation analysis and interpretation Message-ID: We are looking for a candidate to work on analysis and method development for variation (mutation) interpretation in our group at Lund University. Our group has released several of the best performing prediction methods for variation interpretation. For details and application instructions see https://lu.varbi.com/en/what:job/jobID:542421/ The position is initially open for two years, with a possibility for one year extension. Note that according to Swedish regulations, no more than three years are allowed from the date of PhD. There are some exceptions, as well. -- Mauno Vihinen Professor of Medical Structural Biology Department of Experimental Medical Science Lund University BMC B13 SE-22184 Lund Sweden http://structure.bmc.lu.se tel +46 72 526 0022 ORCID iD 0000-0002-9614-7976 From arne at bioinfo.se Tue Sep 20 09:32:31 2022 From: arne at bioinfo.se (Arne Elofsson) Date: Tue, 20 Sep 2022 09:32:31 +0200 Subject: [SocBiN] Assistant Professor in Data-Driven Cell and Molecular Biology Message-ID: https://www.su.se/english/about-the-university/work-at-su/available-jobs?rmpage=job&rmjob=18793&rmlang=UK Assistant Professor in Data-Driven Cell and Molecular Biology Stockholm Ref. No. SU FV-3250-22 *at Stockholm University . Closing date: 9 November 2022.* The SciLifeLab and Wallenberg National Program for Data-Driven Life Science (DDLS) is a 12-year initiative funded with a total of 3,1 billion SEK from the Knut and Alice Wallenberg Foundation. The purpose of the program is to recruit and train the next-generation of data-driven life scientists and to create globally leading computational and data science capabilities in life science in Sweden. The program will recruit 39 eminent junior group leaders as DDLS Fellows, launch over 210 postdoctoral positions and establish a research school for 260 PhDs, within both academia and industry. The program is coordinated by SciLifeLab , a nationwide research infrastructure and a hub for cross-disciplinary life sciences. The Fellows will be recruited to the 11 participating host universities/organizations, enabling them to link up with strong local research environments as well as with the national DDLS program. The DDLS program promotes collaborative interdisciplinary work and engagement with industry, healthcare and other national and international partners, such as WASP , with the aim of bridging the life science and data science communities. The DDLS program will focus on four strategic areas of data-driven research: cell and molecular biology, evolution and biodiversity, precision medicine and diagnostics, epidemiology and infection biology. The first 20 junior group leaders to join the DDLS Fellows program are now recruited to different Swedish universities. Each DDLS Fellow will receive a recruitment package of 17 MSEK, which is meant to cover 5 years of his/her own salary, two PhD students and two postdoc positions, as well as running costs. The Fellow positions are tenure-track, and the universities/organizations will assume the long-term responsibility of their support as tenured faculty. The subject area cell and molecular biology concerns research that fundamentally transforms our knowledge about how cells function by peering into their molecular components in time and space, from single molecules to native tissue environments. This research subject area aims to lead the development or application of novel data-driven methods relying on machine learning, artificial intelligence, or other computational techniques to analyze, integrate and make sense of cell and molecular data. At Stockholm University the Department of Molecular Biosciences, The Wenner-Gren Institute is looking to fill a position as DDLS fellow in data driven cell and molecular biology. *Subject*Datadriven Cell and Molecular Biology *Subject description, Stockholm University*The subject area concerns research that fundamentally transforms our knowledge about how cells function by peering into their molecular components in time and space, from single molecules to native tissue environments. The successful candidate is expected to lead the development or application of novel data-driven methods relying on machine learning, artificial intelligence, or other computational techniques to analyze and/or integrate and make sense of cellular and molecular data. *Main responsibilities* Research and in addition some teaching and supervision. *Qualification requirements* In order to qualify for the position as assistant professor, the applicant must have completed a doctoral degree in Sweden or an equivalent degree from another country. In the first instance, an applicant should be considered who has received such a degree no more than five years before the deadline for applications. However, an applicant who has received such a degree earlier may be considered under special circumstances. All teaching positions at Stockholm University require the ability to collaborate and the general ability and suitability to perform one’s duties. *Assessment criteria* In the appointment process, special attention will be given to research skills. Teaching skills will also be considered. The assessment of research skills will focus primarily on merits within the subject area of the position. *Terms of employment*For this position, the assistant professor is employed until further notice, but no longer than six years. The contract may be extended to a maximum of eight years under special circumstances, such as due to sick leave or parental leave. An assistant professor may, on application, be promoted to a permanent position as associate professor. Specific criteria for promotion from assistant professor to associate professor have been established by the Faculty of Science. An application for promotion to associate professor should be submitted to the faculty at least nine months before the appointment as assistant professor expires. This position (in Swedish, “biträdande lektor”) is a tenure track position, and the qualification requirements and terms of employment are regulated by the Higher Education Ordinance (SFS 2017:844). During the first six years, the main workplace for this position will be at the Science for Life Laboratory. The formal employment will be at the Department of Molecular Biosciences, The Wenner-Gren Institute (MBW), Stockholm University. Assuming a successful promotion to Associate Professor, the main workplace will thereafter be at this department, located at Stockholm University main campus. *Additional information*During the first five years, the position is funded by a grant from Knut and Alice Wallenberg Foundation to Stockholm University. Thereafter the position will be funded by the host department. *Contact* Further information about the position can be obtained from the Deputy Dean of the Faculty of Science, Professor Lena Mäler, telephone: +46 8 16 24 48, lena.maler at dbb.su.se. and Head of Department, Professor Neus Visa, +46 8 16 41 11, neus.visa at su.se. For questions regarding the application process, please contact administrator Rahwa Ghebresellase, telephone: +46 8 16 21 27, rahwa.ghebresellase at su.se. *Union representatives* Ingrid Lander (Saco-S), telephone: +46 708 16 26 64, saco at saco.su.se, Alejandra Pizarro Carrasco (Fackförbundet ST/Lärarförbundet), telephone: +46 8 16 34 89, alejandra at st.su.se, and seko at seko.su.se (SEKO). *Application* Apply for the position at Stockholm University's recruitment system. It is the responsibility of the applicant to ensure that the application is complete in accordance with the instructions in the job advertisement, and that it is submitted before the deadline. We would appreciate it if your application is written in English. Since it will be examined by international experts, English is the working language. The University’s rules of employment and instructions for applicants are available at: How to apply for a position . The criteria for promotion within the Faculty of Science are available at: Guidelines – Employment *You are welcome to apply! * Stockholm University contributes to the development of sustainable democratic society through knowledge, enlightenment and the pursuit of truth. *Closing date:* 09/11/2022 URL to this page https://www.su.se/english/about-the-university/work-at-su/available-jobs?rmpage=job&rmjob=18793&rmlang=UK 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 Zoom: https://stockholmuniversity.zoom.us/my/arneelof/ Scholar: http://scholar.google.se/citations?user=s3OCM3AAAAAJ ORCID: 0000-0002-7115-9751 -------------- next part -------------- An HTML attachment was scrubbed... URL: From veli.makinen at helsinki.fi Wed Sep 28 17:18:50 2022 From: veli.makinen at helsinki.fi (=?iso-8859-1?Q?M=E4kinen=2C_Veli_A_T?=) Date: Wed, 28 Sep 2022 15:18:50 +0000 Subject: [SocBiN] Swedish-speaking professor of computer science at the University of Helsinki Message-ID: Forwarding the following announcement of an open professor position at the Department of Computer Science of the University of Helsinki: *** Dear colleagues, Apologies in case you get this message multiple times. At the Department of Computer Science at University of Helsinki we have opened a position for a Swedish-speaking professor of computer science. The position is open at all levels (assistant, associate, full). The announcement is available at https://jobs.helsinki.fi/job/Svenskspråkig-professor-eller-biträdande-professor-i-datavetenskap/753813502/ and the application deadline is October 31. One of the main tasks of this position is to expand our Swedish-language computer science teaching at the BSc level and also participate in teacher education, by teaching basics of computer science and artificial intelligence to those studying to be teachers of natural sciences in schools. This is why the position requires fluent Swedish skills. We are trying to reach potential candidates in all Nordic countries. Research area of the position is around AI and its societal implications, but qualified candidates in other areas of CS can also apply as long as there is some link to AI in their work. The language requirement is more important than the research area. Please feel free to spread the announcement to any qualified and interested candidates you know. If you have any questions, please feel free to contact me. Best regards, Jussi -- Jussi Kangasharju Professor, Department of Computer Science, University of Helsinki Head of Department https://www.helsinki.fi/collaborative-networking/ Tel: +358 50 415 1708 Twitter: @kangasharju From Tatiana.Starikovskaya at ens.fr Thu Sep 29 15:56:28 2022 From: Tatiana.Starikovskaya at ens.fr (Tatiana Starikovskaya) Date: Thu, 29 Sep 2022 15:56:28 +0200 Subject: [SocBiN] =?utf-8?q?Postdoctoral_position_at_=C3=89cole_Normale_Su?= =?utf-8?q?p=C3=A9rieure_Paris_on_Approximation_and_Randomised_String_Proc?= =?utf-8?q?essing?= Message-ID: <9D241360-D8EF-462A-8738-9C0BE8FDA313@di.ens.fr> The PARSe project funded by ANR (France) opens one postdoc position at École Normale Supérieure Paris, hosted by Tatiana Starikovskaya. The position comes with a highly competitive salary, a travel allowance, and carries no teaching responsibilities. The postdoc researcher will contribute efficient tools for processing large-scale, noisy string data. One of the main goals of this postdoc is to understand the limit of computations, and to provide new ultra-efficient algorithms and data structures for processing such data, inspired by approaches in hashing and high-dimensional geometry. For more information about the project, please see https://starikovskaya.github.io/homepage/parse/. The post will require a high level of expertise in areas which may include but not be limited to string algorithms and streaming / property testing algorithms; a background in bioinformatics will be considered as a plus, but is not mandatory. A PhD in mathematics, computer science, or bioinformatics is required. Applications will be processed starting on October 31 and reviewing will continue until the positions are filled. Start date negotiable but ideally by January 2023. To apply, please send your CV and research statement to starikovskaya at di.ens.fr, and arrange for two reference letters to be sent to the same address. For informal discussion about the post you are welcome to contact: Tatiana Starikovskaya (Assistant Professor at École Normale Supérieure Paris, principal investigator of the ANR PARSe project, starikovskaya at di.ens.fr) Duration: 12 months with a possibility for extension for up to 24 months Location: 45 rue d'Ulm, Paris, France