From alexandru.tomescu at helsinki.fi Wed Oct 7 08:47:18 2020 From: alexandru.tomescu at helsinki.fi (Tomescu, Alexandru) Date: Wed, 7 Oct 2020 06:47:18 +0000 Subject: [SocBiN] PhD student & Postdoc (Algorithmic Bioinformatics) @ U. Helsinki Message-ID: <32047230-4A4C-4BD4-B2A2-B0A8BC55BA0E@helsinki.fi> Dear colleagues, I am looking for a PhD student and a Postdoc in Algorithmic Bioinformatics, to join my team at the University of Helsinki. I am leading the Graph Algorithms team, of the wider Algorithmic Bioinformatics research group. These positions are partially funded by an ERC Starting Grant on Safe and Complete Algorithms for Bioinformatics. Current research topics include: string algorithms for pangenome graphs; safe string alignment solutions (i.e. base pairs appearing in all optimal and suboptimal alignments) and their correlation with protein function over the tree of life; graph algorithms for genome, RNA and viral assembly from genomic sequencing data. University of Helsinki hosts an active and wonderful Algorithmic Bioinformatics community, with interests ranging from theoretical computer science, to algorithm engineering and practical bioinformatics methods, and from graph algorithms to string algorithms. Application deadline December 7, 2020. Interested persons are welcome to ask for more information via e-mail to alexandru.tomescu at helsinki.fi. More details in the following calls: https://www.cs.helsinki.fi/u/tomescu/phd-student.pdf https://www.cs.helsinki.fi/u/tomescu/postdoc.pdf Please distribute this to all persons interested. Best regards, Alexandru Tomescu https://www.cs.helsinki.fi/u/tomescu/ alexandru.tomescu at helsinki.fi -------------- next part -------------- An HTML attachment was scrubbed... URL: From alexandru.tomescu at helsinki.fi Wed Oct 7 08:47:18 2020 From: alexandru.tomescu at helsinki.fi (Tomescu, Alexandru) Date: Wed, 7 Oct 2020 06:47:18 +0000 Subject: [SocBiN] PhD student & Postdoc (Algorithmic Bioinformatics) @ U. Helsinki Message-ID: <32047230-4A4C-4BD4-B2A2-B0A8BC55BA0E@helsinki.fi> Dear colleagues, I am looking for a PhD student and a Postdoc in Algorithmic Bioinformatics, to join my team at the University of Helsinki. I am leading the Graph Algorithms team, of the wider Algorithmic Bioinformatics research group. These positions are partially funded by an ERC Starting Grant on Safe and Complete Algorithms for Bioinformatics. Current research topics include: string algorithms for pangenome graphs; safe string alignment solutions (i.e. base pairs appearing in all optimal and suboptimal alignments) and their correlation with protein function over the tree of life; graph algorithms for genome, RNA and viral assembly from genomic sequencing data. University of Helsinki hosts an active and wonderful Algorithmic Bioinformatics community, with interests ranging from theoretical computer science, to algorithm engineering and practical bioinformatics methods, and from graph algorithms to string algorithms. Application deadline December 7, 2020. Interested persons are welcome to ask for more information via e-mail to alexandru.tomescu at helsinki.fi. More details in the following calls: https://www.cs.helsinki.fi/u/tomescu/phd-student.pdf https://www.cs.helsinki.fi/u/tomescu/postdoc.pdf Please distribute this to all persons interested. Best regards, Alexandru Tomescu https://www.cs.helsinki.fi/u/tomescu/ alexandru.tomescu at helsinki.fi -------------- next part -------------- An HTML attachment was scrubbed... URL: From arne at bioinfo.se Mon Oct 12 14:17:20 2020 From: arne at bioinfo.se (Arne Elofsson) Date: Mon, 12 Oct 2020 14:17:20 +0200 Subject: [SocBiN] =?utf-8?q?Fwd=3A_everyone=40dbb=2Esu=2Ese_Fwd=3A_Bitr?= =?utf-8?q?=C3=A4dande_lektorat_i_Ume=C3=A5?= In-Reply-To: <061677783bdd40a791758fb104a17089@ebox-prod-srv13.win.su.se> References: <08d856e6416a4667a9e1e39d945153e5@umu.se> <061677783bdd40a791758fb104a17089@ebox-prod-srv13.win.su.se> Message-ID: Hejsan kollegor!!! Vi har biträdande lektorat att söka i Umeå! *“Up to five tenure-track positions as Assistant professor*” https://www.umu.se/en/work-with-us/open-positions/up-to-five-tenure-track-positions-as-assistant-professor_339630/ Söker man via kemiska institutionen är paketen: *1.1 Mkr i drift samt 100% lön till en doktorand.* *Deadline: 2020-10-19* Om ni vet någon vass kandidat i erat nätverk som ni vill stödja får ni gärna vidarebefordra denna info. Mvh, magnus --------------------------------------------------------------------------------------------------------------------------- Dr. Magnus Wolf-Watz Professor Umeå University Chemistry Department Integrated Structural Biology (ISB), Twitter @ISB_UmU Phone:+46 90 786 76 90 Lab Home Page: www.biostruct.umu.se/principal-investigators/magnus-wolf-watz/ Twitter: @watz_wolf -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ everybody-at-dbb.su.se mailing list everybody-at-dbb.su.se at lists.su.se https://lists.su.se/mailman/listinfo/everybody-at-dbb.su.se From santhilalsubhash at hotmail.com Mon Oct 12 00:07:32 2020 From: santhilalsubhash at hotmail.com (Santhilal Subhash) Date: Sun, 11 Oct 2020 22:07:32 +0000 Subject: [SocBiN] Postdoctoral scholarship in bioinformatics (University of Gothenburg) Message-ID: Dear all, I am posting this on behalf of Tanmoy Mondal. Kindly please spread this information among bioinformatics communities and colleagues. For further queries please contact Tanmoy Mondal. https://www.nature.com/naturecareers/job/postdoctoral-scholarship-in-bioinformatics-university-of-gothenburg-gu-730729 A postdoctoral scholarship is available to study gene regulation by MYCN oncogene in Tanmoy Mondal lab (https://www.gu.se/en/research/tanmoy-mondal) at the Clinical Chemistry, Institute of Biomedicine at the University of Gothenburg, Sweden where project will require extensive bioinformatics expertise. The bioinformatics part of the project will be performed in close collaboration with Erik Larsson Lekholm lab (http://larssonlab.org) at Institute of Biomedicine, Gothenburg University. Project Description The researcher will work on a project aimed at better understanding the role of MYCN oncogene in Neuroblastoma and also in Neural crest cells development using high throughput sequencing data generated by various chromatin and RNA biology techniques. Qualifications We are looking for a recent PhD with expertise in bioinformatics or equivalent field. The candidate should be familiar with analysis of NGS data, and have experience with RNA-seq and ChIP-seq data or related methodologies. The successful candidate expected to have good programming/scripting skills and to actively contribute scientifically to the group. The candidate will have the opportunity to collaborate with Erik Larsson Lekholm lab´s bioinformatics team to improve on bioinformatics skill and to apply on the described project. Fluency in spoken and written English is essential. The scholarship: Funding is in the form of a tax-exempt scholarship. The funding is provided by Svenska Läkaresällskapet (SLS) for a maximum of two years. How to apply The position is available immediately, or according to agreement. Please send your application, containing the following documents in English, to tmondal.lab at gmail.com • A cover letter in which you describe your qualifications and motivation. • CV and publication list • Copies of relevant degree certificate(s) • Names and contact information of at least two reference persons For further information about the project and the stipend, please contact Tanmoy Mondal at tmondal.lab at gmail.com You are welcome with your application. Thanks and regards, ------------------------------------------------ Santhilal Subhash Department of Medical Biochemistry & Cell Biology Institute of Biomedicine Sahlgrenska Academy at University of Gothenburg Medicinaregatan 9A SE-413 90 Gothenburg, Sweden -------------- next part -------------- An HTML attachment was scrubbed... URL: From rbh at intomics.com Wed Oct 14 15:57:46 2020 From: rbh at intomics.com (Rasmus Borup Hansen) Date: Wed, 14 Oct 2020 15:57:46 +0200 Subject: [SocBiN] Scientific Developer at Intomics, Lyngby (Copenhagen) Message-ID: Scientific Developer Would you like to build bioinformatics systems that make a difference? As Scientific Developer you will use your scientific background as well as your Python and web programming skills and knowledge of Linux systems to build IT systems for various bioinformatics projects. At Intomics we collaborate closely with our clients from the pharmaceutical industry on building systems to support research and analysis of biomedical data, on discovering new drugs and biomarkers, and on finding the most effective treatments for patients. We are specialized in the analysis and integration of genomic and biomedical big data. Typical projects include data management of large amounts of data, implementing specialized processing pipelines, or designing, developing and maintaining bioinformatics tools for analysis or data presentation. We are looking for a bioinformatician with focus on 'informatics', and the ideal candidate has the following key qualifications: Strong programming skills in Python and possibly other languages A good understanding of working in a Linux environment Experience with web programming Good communication, collaboration and documentation skills A commercial mindset The ambition to become a project manager Knowledge of relational, graph or NoSQL databases Your workday at Intomics will be both fun and challenging. You will get the opportunity to use your experience to find the best technical solutions to meet the needs of our clients in close collaboration with your experienced and dedicated colleagues. Intomics as your next career step? We are a small company allowing us to operate in an agile and informal environment. 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 who hold a strong scientific background and are passionate about finding innovative solutions together. We are a value driven organization who 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. You will be part of the Informatics department and work out of our office in Lyngby, Denmark. Please send your motivated application, CV and references to applications-2001 at intomics.com in pdf, no later than 6th of November 2020. -------------- next part -------------- An HTML attachment was scrubbed... URL: From j.a.dahl at medisin.uio.no Wed Oct 14 23:50:41 2020 From: j.a.dahl at medisin.uio.no (John Arne Dahl) Date: Wed, 14 Oct 2020 21:50:41 +0000 Subject: [SocBiN] Exciting postdoc opportunities in epigenomics, Oslo University Hospital Message-ID: <1602712242613.51272@medisin.uio.no> >From the Dahl Lab, Oslo University Hosptial: We are looking for two postdocs to study the epigenetic reprogramming of early embryo development and its significance for mammalian and human reproduction. An overarching theme is the understanding of mechanisms and epigenetic information in the passing of life from one generation to the next, building on our recent discoveries (Dahl et al., Nature 2016; Sankar et al., Nat. Cell Biol. 2020). Postdoc 1: Bioinformatics Postdoc 2: Molecular biology Our team is located at the Oslo University Hospital, the Dahl Laboratory Applications must be submitted through the official recruitment website WebCruiter: https://candidate.webcruiter.com/nb-no/Home/companyadverts?&link_source_ID=0&companylock=241110#search Postdoc 1: Bioinformatics Enter Webcruiter ID in the search field: 4298348821 Postdoc 2: Molecular biology Enter Webcruiter ID in the search field: 4298260856 Application deadline October 23de The location We are located at the Oslo University Hospital, campus Rikshospitalet adjacent to an idyllic forest. Oslo is ranked as one of the best cities in the world to live in. We can offer * An ambitious and stimulating scientific environment with excellent opportunities for academic development * Full-time three-year position * Top modern and excellent lab facilities with a wide range of core facilities * Attractive salary according to the guidelines from the Oslo University Hospital * Favorable pension arrangements * Attractive welfare arrangements, with affordable high-quality childcare available Any questions regarding the position can be directed to: Principal Investigator Dr. John Arne Dahl. Email: j.a.dahl at medisin.uio.no More information can be found on the official recruitment website following the link and Webcruiter IDs presented above. Feel free to share :) Best regards, John Arne Dahl -------------- next part -------------- An HTML attachment was scrubbed... URL: From arne at bioinfo.se Mon Oct 19 13:06:15 2020 From: arne at bioinfo.se (Arne Elofsson) Date: Mon, 19 Oct 2020 13:06:15 +0200 Subject: [SocBiN] Fwd: leaflet with registration link In-Reply-To: References: Message-ID: https://www.eventbrite.co.uk/e/3d-bioinformatics-2020-annual-workshop-tickets-115706060943 Hi Everyone I've attached a revised version of the 3D-BioInfo AGM flyer which has a more obvious link for registration. Registration at: https://www.eventbrite.co.uk/e/3d-bioinformatics-2020-annual-workshop-tickets-115706060943 *3D-Bioinformatics 2020 Annual Workshop * *ELIXIR Community in Structural Bioinformatics – 3DBioInfo* ELIXIR Communities enable the participation of communities of practice in different areas of the life sciences in the activities of ELIXIR, which underpin the evolution of a data, tools, interoperability, compute and training infrastructure for European life science informatics (see www.elixir-europe.org/use-cases ). Structural bioinformatics has a broad impact across the life sciences and provides tools to archive, visualise, analyse, annotate, and predict molecular structures. Structural bioinformatics is traditionally very strong in Europe offering many software tools, methodologies, and databases, as well as community-wide prediction challenges. Its applications cover research activities from structural biology to drug discovery and personalised medicine that are all well represented within the national ELIXIR nodes. The meeting will be virtual this year due to the COVID-19 pandemic. Submission of abstracts for posters is encouraged, as researchers with accepted posters will be offered the opportunity to pre-record short talks for their poster. Authors of selected poster talks will be invited to give longer talks during the main meeting sessions. To find out more about the 3D-BioInfo Community, please go to the website: www.elixir-europe.org/communities/3d-bioinfo *Overview of Programme* The meeting will start with a brief overview of the aims of the 3DBioInfo Community. This will be followed by Breakout sessions for each of the major 3D-BioInfo Activities described below. These breakout sessions will be held sequentially, allowing participants to attend any number of sessions they want. Next will come a Plenary session, at which coordinators of the different Activities will present their reports. All the sessions and talks will be recorded, with the recordings made available at later dates. *Start date: * Tuesday 24 November 2020 *End date: *Thursday 26 November 2020 *Start time:* 09:00 CET time *End time: *17:00 CET time -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 3D BioInfo Annual Meeting 2020 vX.pdf Type: application/pdf Size: 1063573 bytes Desc: not available URL: From Karin.Lagesen at vetinst.no Mon Oct 19 16:40:13 2020 From: Karin.Lagesen at vetinst.no (Lagesen, Karin) Date: Mon, 19 Oct 2020 14:40:13 +0000 Subject: [SocBiN] Permanent position: Bioinformatics/sysadmin position at the Veterinary Institute Message-ID: <08976f127232427bbbafa2d3e38647b5@vetinst.no> The Norwegian Veterinary Institute has a permanent position available for a bioinformatics/unix sysadmin/database person. Feel free to contact me if you have questions, or if you know someone who might fit. https://vetinst.easycruit.com/vacancy/2577451/41906?iso=gb Karin -- Karin Lagesen, PhD Bioinformatician, Section for Epidemiology Norwegian Veterinary Institute From carsten.daub at ki.se Tue Oct 20 15:05:13 2020 From: carsten.daub at ki.se (Carsten Daub) Date: Tue, 20 Oct 2020 13:05:13 +0000 Subject: [SocBiN] The 7th RIKEN-KI-SciLifeLab Symposium: Biomedical Data for Artificial Intelligence Message-ID: <225F30E5-D130-473E-9039-AEA0B86F9A74@ki.se> Dear colleagues, We are happy to announce that The 7th RIKEN-KI-SciLifeLab Symposium: Biomedical Data for Artificial Intelligence will be held online on November 2, 2020, 9-11 Stockholm time (17-19 JST). The overall goals of this symposium series is to identify common scientific interests and to promote exchange and collaboration between RIKEN, SciLifeLab and KI. We kindly encourage everyone interested to register to the event. For details please refer to information below: Title: The 7th RIKEN-KI-SciLifeLab Symposium: Biomedical Data for Artificial Intelligence ~ The role of AI in the future direction of Life Science research~ Date: Monday, November 2, 2020, 9-11 Stockholm time (17-19 JST) Place: Online Zoom Web SciLifeLab: https://www.scilifelab.se/event/the-7th-riken-ki-scilifelab-symposium-biomedical-data-for-artificial-intelligence Web RIKEN: https://www.ims.riken.jp/events/RIKEN-KI-SciLifeLab_Sympo/ Registration: https://www.lyyti.in/RIKEN_KI_SciLifeLab_Symposium Organizers: Erik Arner (RIKEN IMS) Magnus Boman (KTH Royal Institute of Technology, Sweden) Carsten Daub (KI, SciLifeLab, RIKEN IMS) Agenda: • [5 min] Introduction to the topic and challenge addressed by this event • Erik Arner (RIKEN), Carsten Daub (KI and SciLifeLab) • [15 min] Welcome notes by Directors • Anders Gustafsson (Vice President of Karolinska Institutet) • Kazuhiko Yamamoto (Center Director of RIKEN IMS) • Olli Kallioniemi (Director of SciLifeLab) • [30 min] Keynote presentation: What renders AI specific in medicine and healthcare? • Sabine Koch (Professor of Health Informatics at Karolinska Institutet) • [15 min] Key conclusions from the 2019 Joint RIKEN-KI-SciLifeLab Symposium including White Paper • Magnus Boman (Professor in Intelligent Software Systems, KTH) • [20 min] Young researchers from RIKEN/ KI/ SciLifeLab present challenges and opportunities at the respective sites • Rebecka Skarstam (KI) • Masaru Koido (RIKEN) • [25 min] Ongoing AI initiatives at SciLifeLab, RIKEN, and KI • Kazuhiro Sakurada (RIKEN MIH) • Jun Seita (RIKEN MIH) • Sabine Koch (KI) • Carolina Wählby (Uppsala University) • Daniel Gillblad (Sweden.ai) • [10 min] Lessons learned from the Symposium, and ideas for the 2021 Symposium • Carl Johan Sundberg (KI) • Piero Carninci (RIKEN) We are looking forward to your participation! [cid:EAEA58FA-1DD2-4BB7-BD60-1E53EEE8297A at bionut.ki.se] När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI kommer att behandla dina personuppgifter. Här finns information om hur KI behandlar personuppgifter. Sending email to Karolinska Institutet (KI) will result in KI processing your personal data. You can read more about KI’s processing of personal data here. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: RIKEN-KI-SciLifeLab Symposium 2020 Poster.png Type: image/png Size: 148589 bytes Desc: RIKEN-KI-SciLifeLab Symposium 2020 Poster.png URL: From arne at bioinfo.se Thu Oct 22 03:03:00 2020 From: arne at bioinfo.se (Arne Elofsson) Date: Thu, 22 Oct 2020 03:03:00 +0200 Subject: [SocBiN] Talk by Nir Ben Tal today Message-ID: Dear All, Please remember our DBB seminar today (*Oct 22 at 4 pm*) that is given by Prof. Nir Ben Tal, Tel Aviv University, Israel. Who will talk about: *“Protein archeology: How proteins emerged and evolve?” * *Abstract: *Since their emergence about 3.7 billion years ago, proteins have been key to life as we know it. But how did they emerge and continue to evolve? The straightforward path, involving the addition of one amino acid after another—starting from scratch, is bound to fail, as the vast majority of such arbitrary strings can't even form stable structures, which are essential to function. Therefore, instead, evolution follows a cut-and-paste approach, where amino acid segments from existing proteins are grafted and stitched together to form new proteins. We know this, because the latter approach leaves traces, in the form of reused segments. By tracing these, we aim to decipher the origin of proteins, similarly to archeologists tracing human history. The talk will mainly cover the work published in Nepomnyachiy et al., PNAS 2014 (PMID: 25071170), and 2017 (PMID: 29078314)), Narunsky et al 2020 (PMID: 32079721), and current continuation (Kolodny et al, submitted*).* Please use the following zoom link: *https://stockholmuniversity.zoom.us/j/65497438579 * Kind regards, Arne 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From l.a.m.zepeda at ous-research.no Thu Oct 22 14:21:31 2020 From: l.a.m.zepeda at ous-research.no (Leonardo Andres Meza Zepeda) Date: Thu, 22 Oct 2020 12:21:31 +0000 Subject: [SocBiN] Bioinformatics postdoc position in Oslo Message-ID: <0958EBE8-5261-4227-867A-9DD4944AC253@uio.no> A two year position as Postdoctoral Fellow is available at the Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital. The candidate will be associated with the Translational Genomics project group and is financed by the Norwegian Cancer Society. The research will focus upon developing and utilizing computational approaches for the analysis of diverse genomic datasets to investigate the molecular evolution of gastrointestinal stromal tumours, as well as to study the novel mechanisms of resistance to targeted therapies. For full information about the position, and on how to apply follow the link bellow https://www.nature.com/naturecareers/job/postdoctoral-research-fellow-oslo-university-hospital-ous-730609 Application deadline November 1st, 2020. Best regards, Do to technical issues in our email system, I will be replying from this UiO account. Emails send to the RR-Research will be automatically forwarded to the UiO account. Leonardo A. Meza-Zepeda, Dr. philos. Department Head Department of Core Facilities Institute for Cancer Research Oslo University Hospital OSLO, Norway Mobile: +47-9903 5706 E-mail: Leonardm at uio.no Leonardo.Meza-Zepeda at rr-research.no www.ous-research.no/meza-zepeda Oslo.genomics.no Not sensitive, ikke sensitiv -------------- next part -------------- An HTML attachment was scrubbed... URL: From mahogny at areta.org Thu Oct 22 14:53:33 2020 From: mahogny at areta.org (mahogny at areta.org) Date: Thu, 22 Oct 2020 14:53:33 +0200 Subject: [SocBiN] =?utf-8?q?Senior_Lecturer_/_Professor_in_Molecular_Tumor?= =?utf-8?q?_Biology___--_ume=C3=A5=2C_sweden?= Message-ID: <5fe0a8d0f817dafd238c378e0fedfde0@areta.org> https://www.umu.se/en/department-of-molecular-biology/open-positions/senior-lecturer-professor-in-molecular-tumor-biology/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From bjorn.nystedt at scilifelab.se Tue Oct 27 12:49:56 2020 From: bjorn.nystedt at scilifelab.se (=?utf-8?Q?Bj=C3=B6rn_Nystedt?=) Date: Tue, 27 Oct 2020 12:49:56 +0100 Subject: [SocBiN] Permanent position: Data Manager/Bioinformatician, The Swedish Childhood Tumour Biobank Message-ID: <005DE6CF-9F03-4DBC-89CB-3716D854F947@scilifelab.se> Barntumörbanken (BTB), or in English: The Swedish Childhood Tumour Biobank, is a national infrastructure and sample collection for childhood tumors. BTB is currently also coordinating the national initiative Genomic Medicine Sweden (GMS) for paediatric cancer, with the purpose to implement whole genome sequencing in clinical practise for patients with childhood tumours. We are now looking for a motivated data manager/bioinformatician to contribute in developing sequencing data handling, and analysis, for the projects BTB manages and takes part in. This is an opportunity to work in a multi-disciplinary team in a continuously evolving research environment with the latest technologies in the field to support and enable high quality genomic research on childhood cancer. https://ki.varbi.com/en/what:job/jobID:359844/ On behalf of Johanna Sandgren, BTB johanna.sandgren at ki.se -------------- next part -------------- An HTML attachment was scrubbed... URL: