From ari.loytynoja at helsinki.fi Mon Sep 2 13:36:45 2019 From: ari.loytynoja at helsinki.fi (=?ISO-8859-15?Q?Ari_L=F6ytynoja?=) Date: Mon, 2 Sep 2019 14:36:45 +0300 (EEST) Subject: [SocBiN] Postdoc position in Evolutionary Sequence Analysis, University of Helsinki (LAST CHANCE!) Message-ID: As many people have been on holidays/travelling in August, the application deadline has been extended by one week. Best regards, Ari Löytynoja ---------- A postdoc position in evolutionary sequence analysis is available in the research group of Dr. Ari Loytynoja at the Institute of Biotechnology, University of Helsinki, Finland. The position is for three years and will start in October 2019, or later by agreement. Project: Template switching is a poorly known mutational mechanism that copies short stretches of sequence from the opposite strand and causes clusters of differences between homologous sequences. The mechanism has previously been studied in microbes and we recently showed (https://genome.cshlp.org/content/27/6/1039) that mutation patterns consistent with it are polymorphic also in humans. The role and significance of template switching in evolution of genes and organisms is not known. We are now looking for a dedicated and enthusiastic post-doctoral fellow to join in a project studying this mechanism in more detail. The applicant is required to hold PhD in evolutionary biology, bioinformatics, computer science, or a related field, as well as strong written and oral communication skills. The working language of the lab is English; knowledge of the Finnish language is not necessary. Strong experience in computer programming and Linux systems is required, prior experience in evolutionary sequence analysis is an advantage. See the links below for more information and instructions for applying the position: http://loytynojalab.biocenter.helsinki.fi https://www.helsinki.fi/en/open-positions/postdoctoral-researcher-in-evolutionary-sequence-analysis The deadline for submitting applications is September 8, 2019. From per.stenberg at umu.se Mon Sep 2 14:15:10 2019 From: per.stenberg at umu.se (Per Stenberg) Date: Mon, 2 Sep 2019 12:15:10 +0000 Subject: [SocBiN] 2 PostDoc scolarships, metagenomics Message-ID: <90fffc53a5c14a18a5f3a5c79569d232@umu.se> Hi, Please spread to anyone who might be interested. Deadline for application is end of this week. The Department of Ecology and Environmental Science (Umeå University, Sweden) invites applicants for two postdoctoral fellowships to a project focused on analyzing time series of shotgun metagenomics data aiming at producing forecasts of fungal pathogens of conifer trees that will be used by the industry to reduce the impact of this emerging threat. Application deadline is September 8th, 2019. The fellowships are funded by a tax-free 2-year scholarship amounting to 294 000 SEK per year. For more information see: https://www.umu.se/en/work-with-us/fellowships-and-grants/6-1235-19/ and https://www.umu.se/en/research/projects/swedish-biodiversity-in-time-and-space/ Cheers, \Per ------------------------------------------------------------ Per Stenberg, PhD, Principal investigator Department of Ecology and Environmental Science (EMG) Computational Life Science Cluster (CLiC) Umeå University SE-901 87 Umeå Sweden -------------- next part -------------- An HTML attachment was scrubbed... URL: From paolo.romano at hsanmartino.it Fri Sep 20 15:18:58 2019 From: paolo.romano at hsanmartino.it (Romano Paolo) Date: Fri, 20 Sep 2019 13:18:58 +0000 Subject: [SocBiN] NETTAB / BBCC 2019: Full list of keynote speakers available and more Message-ID: Dear list members, this is quick update on the NETTAB / BBCC 2019 Joint Meeting, held on November 11-14, 2019, in Fisciano, near Salerno, Italy. Recent news include: • The list of keynote speakers is now confirmed, including Davide Cacchiarelli, Martin Eisenacher, Artemis Hatzigeorgiou, Oliver Kohlbacher, Lennart Martens, and Juan Antonio Vizcaino. See short CVs and talk information here. • The agenda has been defined and it is now available on-line. See it here. • The tutorial ‘Label-free quantification with OpenMS’ will be on Monday and the tutorial ‘Analysis of scRNA-seq using R’ will be on Thursday. • The provisional list of oral communications is now available. See this page. • The registration form is now available and registration has been opened. See instructions here. • The deadline for submission of poster abstracts has been extended until Friday September 27, 2019. See instructions here. • A Research Topic on “Computational Proteomics and Integration of Data Resources for Advanced Studies in Life Sciences” has been launched in collaboration with Frontiers in Genetics – Bioinformatics and Computational Biology. See the topic here. The scientific programme will be defined soon and published next week. See full details at http://www.igst.it/nettab/2019/ . I hope that many of you will find this meeting of his/her interest and will join us in Fisciano. All the best. Paolo Romano Paolo Romano Ospedale Policlinico San Martino, Genova, Italy Email: paolo.romano at hsanmartino.it - paolo.dm.romano at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From alexandru.tomescu at helsinki.fi Mon Sep 23 19:07:36 2019 From: alexandru.tomescu at helsinki.fi (Tomescu, Alexandru) Date: Mon, 23 Sep 2019 17:07:36 +0000 Subject: [SocBiN] 1 PhD student & 2 Postdoc positions (Algorithmic Bioinformatics) Message-ID: <3B62F894-3CBA-4AC8-96AD-061838F6F407@helsinki.fi> Dear colleagues, I have one PhD student position and two Postdoc positions available in Algorithmic Bioinformatics, here at the University of Helsinki. These are funded by an ERC Starting Grant on "Safe and Complete Algorithms for Bioinformatics", beginning in 2020. The salaries are competitive, and also include a component based on performance. More details and application links at: https://www.cs.helsinki.fi/u/tomescu/ The deadlines for applications are 15 October (PhD position) and 31 October (Postdoc positions). Applications will be given full consideration if received by the deadline. Applications received after that will still be considered, until the positions are filled. Our research is at the intersection of theoretical and practical computer science. Our new approach is, given a computational problem, to look at those parts of a solution that are common to all solutions. We call these "safe", because we can ultimately trust them to be part of the correct solution. We plan to develop efficient safe algorithms for a range of graph problems, and apply them to real bioinformatics problems, such as genome assembly, RNA transcript assembly, and sequence alignment in pan-genome graphs. This is a new perspective from which to address real-world problems in computer science / bioinformatics. For the PhD student position, the ideal candidate has a strong background in algorithms, with a focus on graph algorithms and data structures. The following constitute an advantage, but are not required: - Experience in implementing efficient code. - Experience with handling high-throughput DNA sequencing data. - Achievements at international programming contests such as IOI or ACM ICPC. - Previous research experience and publications. Excellent written and oral communication skills in English are needed. For the Postdoc positions, applicants must hold a PhD degree in computer science, bioinformatics, or a related field. The two positions have slightly different scopes, but the persons hired are required to work together: - Algorithmic background: A strong experience in algorithm development is needed, with a focus on graph or string algorithms and data structures. Experience in processing high-throughput sequencing data is an advantage, but not required. - Bioinformatics method development background: A strong experience in developing practical bioinformatics methods dealing with high-throughput sequencing data, preferably based on advanced algorithms or mathematical models. Experience with the genome assembly problem is an advantage, but not required. Feel free to contact me at alexandru.tomescu at helsinki.fi for further details. Alexandru -------------- next part -------------- An HTML attachment was scrubbed... URL: From mahogny at areta.org Mon Sep 23 21:27:50 2019 From: mahogny at areta.org (mahogny at areta.org) Date: Mon, 23 Sep 2019 21:27:50 +0200 Subject: [SocBiN] forwarded: Postdoc fellowship in Daylight research Message-ID: <95a315278def81e77b7820e0252a60a9@areta.org> I am forwarding this on behalf of katharina wulff "For the postdoc position, I am looking for a person, who likes to work interdisciplinary, likes gadgets and collecting their own data, which they then analyse. Daylight is a fascinating topic - so for building engineers, biomedical engineers and mathematicians, ecologists this would be a great project. My collaborators and I have all in-depth experience with several techniques and understand the biological meaning for the techniques applied, for example I do melatonin analysis, rhythm analysis, actigraphy and EEG, Mirjam does also EEG and pupilography, Manuel does radiospectrometry and has written the scripts, and Stafford is the endocrinologist. We collaborate also with a lab in Groningen, who will run the LCMS with our samples. So, there is a lot of supervision at hand and the candidate can learn a lot. For day-to-day support, we have an experienced nurse in Grano, who will do the insertion of the microdialysis. The project is fully funded for 3 years, including a full postdoc position for the 3rd year. The protocol is for three years and the start date is 1st November 2019. The advert and more information about the research can be downloaded from the website https://urlproxy.sunet.se/canit/urlproxy.php?_q=aHR0cDovL3d3dy5rYXRsYWIub3JnLw%3D%3D&_s=ZGVmYXVsdA%3D%3D&_c=159c8059&_r=c3Utc2U%3D There is no deadline - I recruit until the position is filled." -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: ADVERT POSTDOCTORAL FELLOWSHIP.pdf Type: application/pdf Size: 134513 bytes Desc: not available URL: From henrik.lantz at nbis.se Tue Sep 24 15:16:21 2019 From: henrik.lantz at nbis.se (Henrik Lantz) Date: Tue, 24 Sep 2019 15:16:21 +0200 Subject: [SocBiN] Permanent bioinformatics staff position in Uppsala, Sweden Message-ID: <1A8A96D5-0CE9-438C-9148-1FD1D6F6A1A6@nbis.se> Dear all, National Bioinformatics Infrastructure Sweden (NBIS) is looking for a new expert to join the organisation in Uppsala, Sweden. The position focuses on giving support to Swedish researchers in RNA-seq based expression analyses, but could also include other areas depending on the qualifications of the applicant. We are especially keen to find experts with experience in single cell transcriptomics, but most of all we want to find the right person for the organisation. NBIS is one of the larger bioinformatics infrastructures in Europe, with close to 100 experts employed. To be a support expert in NBIS means being involved in exiting research projects together with researchers from all over Sweden. The variety of projects encountered will give you ample opportunity to learn and grow as a bioinformatician, all with the support of your fellow experts. Deadline is Oct 14. Please see here for more information and how to register: https://www.uu.se/en/about-uu/join-us/details/?positionId=286958 You are very welcome to contact henrik.lantz at nbis.se if you have any questions! Best regards, Henrik ———————— Henrik Lantz Support manager, NBIS Uppsala, Sweden -------------- next part -------------- An HTML attachment was scrubbed... URL: From dirk.repsilber at oru.se Wed Sep 25 13:09:43 2019 From: dirk.repsilber at oru.se (Dirk Repsilber) Date: Wed, 25 Sep 2019 13:09:43 +0200 Subject: [SocBiN] Post-doc positions: Biomedical Machine Learning, AI for environmental toxicity and medicine Message-ID: <7cd983dc-a46c-24ff-3f57-6a63db19ae6d@oru.se> Dear Bioinformaticians, at the School of Medical Sciences, Örebro University, we have now*three positions* available regarding *machine learning applied in multiple biomedical/medical projects*, as well as implementation and further development of *AI approaches for environmental toxicity and medicine*. We are looking for motivated candidates on Post-Doc level, eager to work in the truly trans-disciplinary environment of our multiple ongoing cooperations with all strong biomedical research environments at the medical faculty (and their international collaborators): Nutrition-gut-brain interactions research centre, Cardiovascular research centre, and Inflammatory Response and Infection Susceptibility Centre. Interested candidates should contact Prof. Dirk Repsilber (Dirk.Repsilber at oru.se, +46 73 270 7633) for further information. www.oru.se/English/Employee/dirk_repsilber (see also listing of Research Projects in the bottom of this page) https://www.oru.se/english/research/research-teams/rt/?rdb=g206 Looking forward to receiving your mail/call. Sincerely Dirk -- _________________________________________________________ Dirk Repsilber Professor Functional Bioinformatics School of Medical Sciences (MV) University of Örebro S - 701 82 Örebro Sweden phone: +46 19 30 1256 mobil: +46 73 270 7633 web: http://www.oru.se/English/Employee/dirk_repsilber/ _________________________________________________________ -------------- next part -------------- An HTML attachment was scrubbed... URL: From erik.kristiansson at chalmers.se Wed Sep 25 13:31:05 2019 From: erik.kristiansson at chalmers.se (Erik Kristiansson) Date: Wed, 25 Sep 2019 13:31:05 +0200 Subject: [SocBiN] Post-doc position at Chalmers University of Technology In-Reply-To: <4DA6F19D.2040109@chalmers.se> References: <4DA6F19D.2040109@chalmers.se> Message-ID: <1eadf986-7d20-f5a1-ab5d-34b5cab998f5@chalmers.se> Everyone, We have a open post-doc position in bioinformatics focused on metagenomics with applications to infection diseases and antibiotic resistant bacteria. For more information see https://www.chalmers.se/en/about-chalmers/Working-at-Chalmers/Vacancies/Pages/default.aspx?rmpage=job&rmjob=p7848 Best, Erik Kristiansson -- -------------------------------------------------------------------------------- Erik Kristiansson, Professor in biostatistics and bioinformatics Applied Mathematics and Statistics Department of Mathematical Sciences Chalmers University of Technology/University of Gothenburg, Sweden Email: erik.kristiansson at chalmers.se, Phone: +46 (0)31 772 3521 -------------------------------------------------------------------------------- From arne at bioinfo.se Sat Sep 28 16:59:55 2019 From: arne at bioinfo.se (Arne Elofsson) Date: Sat, 28 Sep 2019 16:59:55 +0200 Subject: [SocBiN] Fwd: Florence Nightingale Bicentennial Research Fellowship In-Reply-To: References: Message-ID: Research Fellow position in UK Below is the advertising blurb Florence Nightingale Bicentenary Research Fellow and Tutor in Bioinformatics The Florence Nightingale Bicentennial Fellowship and Tutor in Bioinformatics is a new fellowship at Oxford and we are recruiting to it with effect from January 2020 or as soon as possible thereafter. This is a rare and exciting opportunity to establish and sustain your own independent research programme of the highest academic standards within the Oxford Protein Informatics Group. You will join a dynamic and collaborative group and department, where our research is world-leading. We need you to hold a relevant PhD/DPhil with post-qualification research experience and have a strong publication record. You must be able to demonstrate the ability to plan and manage research projects independently. You will be an effective teacher of a range of topics and will bring the excellent interpersonal skills necessary for undertaking teaching and pastoral duties. Queries about this post should be addressed to Professor Charlotte Deane: deane at stats.ox.ac.uk or Professor Garret Morris: garrett.morris at stats.ox.ac.uk. This post is fixed-term for 3 years, in the first instance. Only applications received before 12.00 midday on 7 November 2019 will be considered. Interviews will be held on 22 November 2019. More details can be found here https://my.corehr.com/pls/uoxrecruit/erq_jobspec_version_4.display_form Please share with anyone who may be interested. Should you have any questions please do not hesitate to contact me. Best wishes Charlotte Professor Charlotte Deane ------------------------------------------------------------------------------------------------------------------------------ Professor of Structural Bioinformatics Department of Statistics University of Oxford, 24-29 St Giles', Oxford, OX1 3LB Head of the Oxford Protein Informatics group Website: http://opig.stats.ox.ac.uk/ PA: hodpa at stats.ox.ac.uk | 01865 281252 ------------------------------------------------------------------------------------------------------------------------------ -------------- next part -------------- An HTML attachment was scrubbed... URL: