From coordinator at rth.dk Thu Apr 4 11:58:23 2024 From: coordinator at rth.dk (Betina Wingreen Jensen) Date: Thu, 4 Apr 2024 11:58:23 +0200 Subject: [SocBiN] 1st Announcement - Summer School, Applied Deep Learning in Bioinformatics (Aug 12-16, 2024) Message-ID: <002b01da8676$a16dc700$e4495500$@rth.dk> Dear All, We are delighted to announce that we on Aug 12-16, 2024, will be hosting the 2nd Summer School Applied Deep Learning in Bioinformatics. VENUE: University of Copenhagen, Thorvaldsensvej 40, Auditorium A2-70.01, Frederiksberg C (and the symposium day at Copenhagen Biocenter, The Lundbeckfond Auditorium, Ole Maaløes vej 5, 2200 Copenhagen N) LECTURES: Sampo Pyysalo (University of Turku), Arne Elofsson (Stockholm University), Simon Rasmussen, Stefano Roncelli, Christian Anthon, Lars Juhl Jensen & Jan Gorodkin (University of Copenhagen) TOPICS: The summer school will (amongst other) cover the following topics: * Text-mining & Transformers * Language models for biological sequences * Variational autoencoders * Graphs & networks * Practical Applications The format will consist of an approximately equal mix of lectures and hands-on exercises. PARTICIPANTS: Max. 30 talented MSc students, PhDs and postdocs who are already comfortable in programming. PRICE: O DKK. There is no course fee, but you must cover your own travel, accommodation, and meals (expect those meals included in the programme). The course is run and hosted by the CRISPRnet project granted by the Novo Nordisk Foundation. STIPENDS: A handful of travel and accommodation stipends are available for talented applicants, who could otherwise not afford to participate. SYMPOSIUM: On Friday, August 16, 2024. All summer school attendees will be attending the Symposium - on Applied Deep Learning in Bioinformatics that will be held at University of Copenhagen, Copenhagen Biocenter, Ole Maaløesvej 5, 2200 Copenhagen N. All summer school participants will automatically be signed up for free. Sign up and registration for this event will be announced separately. DEADLINES: REGISTRATION DEADLINE - JUNE 6, 2024 - You will receive an email confirming your application to the course - this is NOT a confirmation of participation. All registrations received by the deadline will be evaluated by the course organisers and max 30 people will be selected for participation in the summer school. NOTIFICATION OF SUCCESSFUL PARTICIPANTS - LATEST JUNE 25, 2024 - Everyone approved for participation in the summer school and recipients of stipends will receive a confirmation email. If you do not hear back from us on June 25, your application has, unfortunately, not been successful. For more information and registration go to: https://conferencemanager.events/2024-summerschoolonapplieddeeplearninginbio informatics Best, Betina -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Poster_SummerSchool2024_v03.pdf Type: application/pdf Size: 491550 bytes Desc: not available URL: From coordinator at rth.dk Fri Apr 5 08:21:26 2024 From: coordinator at rth.dk (Betina Wingreen Jensen) Date: Fri, 5 Apr 2024 08:21:26 +0200 Subject: [SocBiN] 1st Announcement - Summer School, Applied Deep Learning in Bioinformatics (Aug 12-16, 2024) Message-ID: <003a01da8721$7d4c8bd0$77e5a370$@rth.dk> Dear All, Please find attached the latest version of the poster, as there was a mistake in the one, I sent you yesterday. Best wishes, Betina From: Betina Wingreen Jensen Sent: 4. april 2024 11:58 To: 'socbin at sbc.su.se' Subject: 1st Announcement - Summer School, Applied Deep Learning in Bioinformatics (Aug 12-16, 2024) Dear All, We are delighted to announce that we on Aug 12-16, 2024, will be hosting the 2nd Summer School Applied Deep Learning in Bioinformatics. VENUE: University of Copenhagen, Thorvaldsensvej 40, Auditorium A2-70.01, Frederiksberg C (and the symposium day at Copenhagen Biocenter, The Lundbeckfond Auditorium, Ole Maaløes vej 5, 2200 Copenhagen N) LECTURES: Sampo Pyysalo (University of Turku), Arne Elofsson (Stockholm University), Simon Rasmussen, Stefano Roncelli, Christian Anthon, Lars Juhl Jensen & Jan Gorodkin (University of Copenhagen) TOPICS: The summer school will (amongst other) cover the following topics: * Text-mining & Transformers * Language models for biological sequences * Variational autoencoders * Graphs & networks * Practical Applications The format will consist of an approximately equal mix of lectures and hands-on exercises. PARTICIPANTS: Max. 30 talented MSc students, PhDs and postdocs who are already comfortable in programming. PRICE: O DKK. There is no course fee, but you must cover your own travel, accommodation, and meals (expect those meals included in the programme). The course is run and hosted by the CRISPRnet project granted by the Novo Nordisk Foundation. STIPENDS: A handful of travel and accommodation stipends are available for talented applicants, who could otherwise not afford to participate. SYMPOSIUM: On Friday, August 16, 2024. All summer school attendees will be attending the Symposium - on Applied Deep Learning in Bioinformatics that will be held at University of Copenhagen, Copenhagen Biocenter, Ole Maaløesvej 5, 2200 Copenhagen N. All summer school participants will automatically be signed up for free. Sign up and registration for this event will be announced separately. DEADLINES: REGISTRATION DEADLINE - JUNE 6, 2024 - You will receive an email confirming your application to the course - this is NOT a confirmation of participation. All registrations received by the deadline will be evaluated by the course organisers and max 30 people will be selected for participation in the summer school. NOTIFICATION OF SUCCESSFUL PARTICIPANTS - LATEST JUNE 25, 2024 - Everyone approved for participation in the summer school and recipients of stipends will receive a confirmation email. If you do not hear back from us on June 25, your application has, unfortunately, not been successful. For more information and registration go to: https://conferencemanager.events/2024-summerschoolonapplieddeeplearninginbio informatics Best, Betina -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Poster_SummerSchool2024_v04.pdf Type: application/pdf Size: 493742 bytes Desc: not available URL: From besenbacher at clin.au.dk Tue Apr 9 11:39:52 2024 From: besenbacher at clin.au.dk (=?utf-8?B?U8O4cmVuIEJlc2VuYmFjaGVy?=) Date: Tue, 9 Apr 2024 09:39:52 +0000 Subject: [SocBiN] Bioinformatics PhD position in Aarhus, Denmark Message-ID: <2A1516E5-698C-4065-9E5A-1C5E9683FB92@birc.au.dk> A fully-funded PhD position is available in my research group at Aarhus University. The project is about modeling mutational processes in cancers. More details and a link to submit an application can be found here: https://phd.health.au.dk/application/opencalls/phd-project-bioinformatics-phd-project Please contact me with any questions regarding the project or the application procedure. Best, Søren Besenbacher From patrick.bryant at live.com Wed Apr 10 16:22:54 2024 From: patrick.bryant at live.com (patrick bryant) Date: Wed, 10 Apr 2024 14:22:54 +0000 Subject: [SocBiN] PhD student in AI for drug development Message-ID: Hi! I am hiring a PhD student in AI for drug development: https://web103.reachmee.com/ext/I007/927/job?site=13&lang=UK&validator=da57c1f2e2ddea2946680e7e5adb241d&ref=Twitter&job_id=23190 PhD student in AI for Drug development at the Department of Molecular Biosciences, The Wenner-Gren Institute. Closing date: 23 April 2024. Research at web103.reachmee.com The position is fully funded for 5 years including social security etc. Read more here https://www.su.se/department-of-molecular-biosciences-the-wenner-gren-institute/about-the-department/internal/phd-studies-at-mbw-1.572029 You don't need to speak Swedish, English (and Python) is enough. Also, please don't email me your application - apply through the portal. Come join us in beautiful Stockholm! Best, Patrick Bryant More info about the group: https://www.scilifelab.se/researchers/patrick-bryant/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From torognes at ifi.uio.no Thu Apr 11 11:13:44 2024 From: torognes at ifi.uio.no (=?utf-8?B?VG9yYmrDuHJuIFJvZ25lcw==?=) Date: Thu, 11 Apr 2024 09:13:44 +0000 Subject: [SocBiN] PhD scholarship within bioinformatics (environmental microbiota) in Norway Message-ID: Dear all, There is a PhD scholarship within bioinformatics available at the Norwegian University of Life Sciences (NMBU) in Ås, Norway: The research group BIAS (Bioinformatics and Applied Statistics), Faculty of chemistry, biotechnology and food sciences (KBM) at the Norwegian University of Life Sciences (NMBU) has a vacant three-year PhD–position related to environmental microbial communities, with the possibility of extension for up to one year. Application deadline: 2 May 2024 Link: https://www.jobbnorge.no/en/available-jobs/job/261338/phd-scholarship-within-bioinformatics [458b4e10-6e5a-462f-a309-42b374b09b2c.jpg] PhD scholarship within bioinformatics (261338) | Norwegian University of Life Sciences (NMBU) jobbnorge.no -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 458b4e10-6e5a-462f-a309-42b374b09b2c.jpg Type: image/jpeg Size: 231571 bytes Desc: 458b4e10-6e5a-462f-a309-42b374b09b2c.jpg URL: From nicosia at dmi.unict.it Thu Apr 11 11:35:04 2024 From: nicosia at dmi.unict.it (Giuseppe Nicosia) Date: Thu, 11 Apr 2024 11:35:04 +0200 Subject: [SocBiN] Last seats left @ 7th Advanced Course on Data Science & Machine Learning - ACDL 2024 - From Deep Learning to Multimodal Foundation Models | June 10-14 | Riva del Sole Resort & SPA - Italy -> Early Registration: by 23 April Message-ID: * Apologies for multiple copies. Please forward to anybody who might be interested, thanks * * Last 60 seats left, hurry up and register! * #ACDL2024, An Interdisciplinary Course: From Deep Learning to Generative AI ACDL 2024 is a full-immersion 5-day course in Tuscany on cutting-edge advances in AI, Deep Learning, LLMs, Data Sc. & Generative AI with lectures delivered by world-renowned experts. If you want to learn NLP, Generative AI Transformers, Diffusion Models, Large language models, Vision - Large-scale vision models, Vision and language, Beyond vision and language, Multimodal Foundation Models and much more then take part in ACDL 2024! ;-) Riva del Sole Resort & SPA - Tuscany, Italy, June 10-14 https://acdl2024.icas.events acdl at icas.cc EARLY REGISTRATION: by April 23 (AoE) https://acdl2024.icas.events/registration/ Oral Presentation Submission Deadline: by April 23 (AoE) LECTURERS: Each Lecturer will hold up to four lectures on one or more research topics. https://acdl2024.icas.events/lecturers/ * Joseph Sifakis, Verimag Laboratory, Grenoble, France *Turing Award* Lectures “Artificial Intelligence: Where We Are, Where We Are Going?” * Gabriel Barth-Maron, DeepMind, London, UK 4 Lessons on "Multimodal Foundation Models" * Sergiy Butenko, Texas A&M University, USA “Cluster-detection Methods in Network-based Data Analysis” “Continuous Approaches to Cluster-Detection Problems in Networks ” * Sven Giesselbach, Fraunhofer Institute - IAIS, Germany 5 Lessons on "Introduction on Foundation Models" * Ramin Hasani, MIT, USA 4 Lessons on "Continuous Neural Networks / Liquid Neural Networks" * Nora Kassner, DeepMind, London, UK "Large Language Models: Life after Pre-training" "Large Language Models: Evaluation" "Large Language Models: Reasoning and Factuality" "Large Language Models: Retrieval augmentation and Tool-use" * Petros Koumoutsakos, Harvard University, USA “Machine Learning for Modeling and Control of Complex Systems” 1/2 “Machine Learning for Modeling and Control of Complex Systems” 2/2 “Solving forward and inverse problems with and without neural networks” “Bayesian Uncertainty Quantification” * Maria Liakata, The Alan Turing Institute, UK 4 Lessons on "Longitudinal Language Processing with User Generated Content" * Panos Pardalos, University of Florida, USA Lectures 1-2 TBA Topics: Data Science, Application to Neuroscience * Jakub M. Tomczak, Eindhoven University of Technology, The Netherlands 4 Lessons on “Deep Generative Modelling” * Rianne van den Berg, Microsoft Research Amsterdam, The Netherlands 3 Lessons on "Diffusion Models" * Pascal Van Hentenryck, Georgia Institute of Technology, USA 3 Lessons on "Fusing Machine Learning and Optimization for Engineering" * Max Welling, University of Amsterdam, The Netherlands 3 Lessons on "Generalized Belief Propagation Algorithms for Tensor Network Contractions" PAST LECTURERS: https://acdl2024.icas.events/past-lecturers/ ACDL 2024 VENUE: https://acdl2024.icas.events/venue/ Riva del Sole Resort & SPA Località Riva del Sole‚ Castiglione della Pescaia (Grosseto) CAP 58043‚ Tuscany‚ Italy p: +39-0564-928111 e: booking.events at rivadelsole.it w: https://www.rivadelsole.it/en/ PAST EDITIONS: https://acdl2024.icas.events/past-editions/ REGISTRATION: https://acdl2024.icas.events/registration/ CERTIFICATE & 8 ECTS: PhD students, Postdocs, Industry Practitioners, Junior and Senior Academics, and will be typical profiles of the ACDL attendants. The Course will involve a total of 36-40 hours of lectures, according to the academic system the final achievement will be equivalent to 8 ECTS points for the PhD Students (and some strongly motivated master student) attending the Course. At the end of the course, a formal certificate will be delivered indicating the 8 ECTS points. TO PARTICIPATE IN ACDL 2024, all attendants must (1/2) register for the course (by April 23, 2024) and (2/2) book accommodation at the course venue, Riva del Sole Resort & SPA‚ (by April 23, 2024); all attendants must stay at the Riva del Sole Resort & SPA. Once accommodation has been booked at Riva del Sole Resort & SPA‚ the participant must send this information (including the Booking Number) to the ACDL organizing committee (acdl at icas.cc). ACDL is a residential course, so all lecturers and participants must reside in the same Hotel (Riva del Sole Resort & SPA). No exceptions are made. For privacy reasons, the Hotel cannot match people. If you have someone to share the apartment with, please send to the Hotel ( booking.events at rivadelsole.it) the name, surname and email address. Otherwise the solution is to book an apartment in single use. Anyone interested in participating in ACDL 2024 should register as soon as possible. See you in Riva del Sole in June! Giuseppe Nicosia & Panos Pardalos - ACDL 2024 Directors. ACDL 2024 Scientific & Organizing Committees. https://acdl2024.icas.events acdl at icas.cc -------------- next part -------------- An HTML attachment was scrubbed... URL: From marc.friedlander at scilifelab.se Mon Apr 15 16:33:31 2024 From: marc.friedlander at scilifelab.se (=?UTF-8?Q?Marc_Friedl=C3=A4nder?=) Date: Mon, 15 Apr 2024 16:33:31 +0200 Subject: [SocBiN] PhD student in Quantitative RNA Biology Message-ID: Dear all, The Friedländer lab is looking for a talented computational PhD student to analyze exciting single-cell data from our new in-house agoTRIBE method. Deadline is April 23rd. For more information: https://www.scilifelab.se/career/phd-student-in-quantitative-rna-biology/ Best regards, Marc Marc Friedländer, Associate Professor Head of Quantitative RNA Biology Group MBW department, Stockholm University Webpage: www.friedlanderlab.org Science for Life Laboratory Sweden -------------- next part -------------- An HTML attachment was scrubbed... URL: From daginge.vage at nmbu.no Thu Apr 18 15:45:24 2024 From: daginge.vage at nmbu.no (=?iso-8859-1?Q?Dag_Inge_V=E5ge?=) Date: Thu, 18 Apr 2024 13:45:24 +0000 Subject: [SocBiN] =?iso-8859-1?q?PhD_position_at_the_Norwegian_University_?= =?iso-8859-1?q?of_Life_Sciences_=28NMBU=29=2C_=C5s?= Message-ID: Hi, The Faculty of Veterinary Medicine at the Norwegian University of Life Sciences (NMBU) is offering a three-year PhD-position in reindeer genomics focusing on Chronic Wasting Disease (CWD). PhD fellowship in reindeer genomics: the role of prion gene haplotypes on CWD resistance (261950) | Norwegian University of Life Sciences (NMBU) (jobbnorge.no) Best regards Dag Inge Våge Professor, Pro-Dean of Education Faculty of Biosciences Norwegian University of Life Sciences P.O. Box 5003 NMBU NO-1432 Ås Norway -------------- next part -------------- An HTML attachment was scrubbed... URL: From erik.sonnhammer at scilifelab.se Mon Apr 22 17:16:54 2024 From: erik.sonnhammer at scilifelab.se (Erik Sonnhammer) Date: Mon, 22 Apr 2024 17:16:54 +0200 Subject: [SocBiN] =?utf-8?q?Conference_=22Connecting_communities_in_the_qu?= =?utf-8?q?est_for_orthologs=22_=28QfO8=29_-_July_17-18=2C_2024_-_Montr?= =?utf-8?b?w6lhbCwgQ2FuYWRhLg==?= In-Reply-To: References: Message-ID: <9ac74b17-22e7-4823-bd14-5b37920e9159@scilifelab.se> -------- Forwarded Message -------- QfO8: "Connecting communities in the quest for orthologs" - July 17-18, 2024 - Montréal, Canada. CALL : abstract submissions for Talks and/or Posters. SUBMISSION DEADLINE : April 26, 2024 Webpage: https://event.fourwaves.com/qfo8 Talk and/or Poster Acceptance Notifications: May 17, 2024 Confirmed Invited Speakers : Fiona Brinkman (Simon Fraser University), Elena Kuzmin (Concordia University), Markus Hecker (University of Saskatchewan), Christine Orengo (University College London). Scope: The QfO Consortium addresses a key challenge in molecular evolutionary biology and strives to develop large-scale methods for inferring orthology among fully sequenced genomes, and to reconstruct the complement of protein-coding genes in common ancestral genomes across the tree of life. The QFO meetings aim to bring together disparate groups around the world that work in the field to accelerate progress through sharing of ideas, methods and research findings. The particular aim of this QfO8 meeting is to gather an even more diverse set of end-users and to connect different research communities that are rooted in orthology. Travel and Caregiver Fellowships: Authors of accepted talks/posters will be eligible for travel and caregiver fellowships to attend the conference. The procedure for application will be communicated to the relevant people in the talk/poster acceptance email. ISCB members can receive a 15% discount on registration rates. Further information on abstract submission deadline and guidelines can be found here: https://event.fourwaves.com/qfo8/submission PLEASE FORWARD THIS ANNOUNCEMENT! -------------- next part -------------- An HTML attachment was scrubbed... URL: From esa.pitkanen at helsinki.fi Wed Apr 24 13:48:58 2024 From: esa.pitkanen at helsinki.fi (=?iso-8859-1?Q?Pitk=E4nen=2C_Esa_A?=) Date: Wed, 24 Apr 2024 11:48:58 +0000 Subject: [SocBiN] Postdoctoral Researcher position in Computational Genomics and Machine Learning In-Reply-To: References: Message-ID: Dear colleagues, we are looking for a postdoctoral researcher to join our groups at FIMM and NCMM through the NORPOD program. The goal of this 2.5 year project is to investigate gene regulatory logic by modeling NaNOME long-read sequencing, ATAC-seq and RNA-seq data. More information at https://jobs.helsinki.fi/job/31_5_2024-Postdoctoral-Researcher-in-Computational-Genomics-and-Machine-Learning/793289202/ Please contact me and Biswajyoti (cc'd) if you have any questions. Kind regards, Esa -- Esa Pitkänen, PhD FIMM-EMBL Group Leader, Academy of Finland Research Fellow Institute for Molecular Medicine Finland (FIMM), Nordic EMBL Partnership for Molecular Medicine Applied Tumor Genomics Research Program, Faculty of Medicine iCAN Digital Precision Cancer Medicine Flagship Biomedicum Helsinki 2U P.O. Box 20 (Tukholmankatu 8) FI-00014 University of Helsinki Finland https://www.helsinki.fi/en/researchgroups/machine-learning-in-biomedicine -------------- next part -------------- An HTML attachment was scrubbed... URL: From michael.hiller at senckenberg.de Mon Apr 29 14:16:31 2024 From: michael.hiller at senckenberg.de (Michael Hiller) Date: Mon, 29 Apr 2024 14:16:31 +0200 Subject: [SocBiN] ERC-funded PhD and Postdoc Positions in Comparative Genomics on Bats Message-ID: <7BCADCBC-C7C6-495D-9EF0-F1F428B2EB86@senckenberg.de> Dear all, we are looking for PhD students and postdocs to join our ERC synergy grant project BatProtect that will use bats as natural models of healthy aging and disease tolerance to elucidate the molecular mechanisms behind bats’ exceptional longevity and resistance to viral and age-related diseases. The student or postdoc would work on diverse topics including phylogenomics, performing comparative screens to identify key adaptations in coding and non-coding (miRNA) genes as well as differences in gene expression patterns across the bat phylogeny, associating genomic changes with longevity and viral reservoir status traits, identifying novel bat genes, and investigating endogenized viral elements. The exact project will be defined based on the interests of the applicants. The application deadline is June 7. Thanks a lot for forwarding this to potential applicants. Best regards, - Michael -- Michael Hiller, PhD Professor of Comparative Genomics LOEWE Centre for Translational Biodiversity Genomics, Senckenberg Society for Nature Research & Goethe University, Frankfurt am Main, Germany -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... 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