From haja.kadarmideen at iscb.org Fri Jan 4 20:55:31 2019 From: haja.kadarmideen at iscb.org (Haja Kadarmideen) Date: Fri, 4 Jan 2019 20:55:31 +0100 Subject: [SocBiN] Postdoc position in Epigenetics and Systems Biology at DTU Denmark Message-ID: Dear all, An exciting postdoc position in Epigenetics, Bioinformatics, Computational Systems Biology within animal sciences is available in my group at the Technical University of Denmark (DTU). Postdoc will have an opportunity to work within the large project consortium called “EliteOva” and closely interact with University of Copenhagen amongst many other national and international partners. Deadline is 8 Feb 2019. The period of employment is for two years from April 1, 2019 (or as soon as possible there after). For full job description and application procedure, go to: https://www.dtu.dk/om-dtu/job-og-karriere/ledige-stillinger/job?id=2265141c-90b2-46ec-9001-b55a88e2f8eb Advert is also posted at Nature Careers: https://www.nature.com/naturecareers/job?id=670597 Regards Haja Kadarmideen Professor & Head of Group Quantitative Genomics, Bioinformatics and Computational Biology (QBC) Group DTU Compute -------------- next part -------------- An HTML attachment was scrubbed... URL: From coordinator at rth.dk Tue Jan 8 12:52:41 2019 From: coordinator at rth.dk (Betina Wingreen Jensen) Date: Tue, 8 Jan 2019 12:52:41 +0100 Subject: [SocBiN] Postdoc in Bioinformatics in the Gorodkin lab -start Mar 1, 2019 Message-ID: <002c01d4a748$a93df1c0$fbb9d540$@rth.dk> Dear All, We have a postdoc position in bioinformatics in the Gorodkin Lab available from Mar 1, 2019 or as soon as possible thereafter. The postdoc will be working at the Department of Veterinary and Animal Sciences, University of Copenhagen on the research project NeuroStem funded by Innovation Fund Denmark. Application deadline is: Feb 10, 2019” For more information about the position and details of how to apply, please go to the full advertisement: https://employment.ku.dk/faculty/?show=148717 Please help us spread the word by forwarding this email to possible candidates in your network. Thank you in advance Best wishes, Betina Betina Wingreen Jensen Scientific and administrative Coordinator Københavns Universitet Det Sundhedsvidenskabelige Fakultet Grønnegårdsvej 3 DIR +45 35334704 MOB +45 21510932 bwj at sund.ku.dk -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.gif Type: image/gif Size: 5975 bytes Desc: not available URL: From joakim.lundeberg at scilifelab.se Tue Jan 8 23:44:55 2019 From: joakim.lundeberg at scilifelab.se (Joakim Lundeberg) Date: Tue, 8 Jan 2019 14:44:55 -0800 Subject: [SocBiN] Postdoctor in Spatial and Single Cell Bioinformatics Message-ID: <11E035D7-B02C-4643-86B0-7328F2CC419C@scilifelab.se> Dear All Two post-doctoral positions are available at the Department of Gene Technology at Science for Life Laboratory (SciLifeLab) in Stockholm. SciLifeLab is a Swedish national resource center for life science research. We are looking for enthusiastic and talented postdoctoral researchers to join the lab of Professor Joakim Lundeberg, affiliated with the School of CBH at KTH Royal Institute of Technology in Stockholm. Job description The work will consist of bioinformatics/computational method development its applications for gene expression analysis in single cells and in tissue sections combined with imaging data. A particular focus is on Spatial Transcriptomics technology (Ståhl et al Science 2016; Salmen et al Nat Prot 2018), developed in a collaboration between KTH and KI, that provides spatially resolved transcriptomes in tissue sections (i.e. RNA seq and imaging data). The proposed project aims to be included as part of the Human Developmental Cell Atlas project hosted at SciLifeLab. In this project we are using a multiple of tools and competences such as single cell RNA, Spatial Transcriptomics, In situ Sequencing and CODEX protein analysis in order to describe and catalog the genes involved in human development of brain, heart and lungs. A key component of the position is to provide new biological knowledge into the studied systems requiring some understanding of the investigated tissues. This project will be in collaboration with internal and external experimental and computational researchers. Link: https://www.kth.se/en/om/work-at-kth/lediga-jobb/what:job/jobID:238485/type:job/where:4/apply:1 .............................................................................................................................................................................................. Joakim Lundeberg Prof Science for Life Laboratory KTH Royal Institute of Technology Karolinska Institute Science Park Tomtebodavägen 23 A S- 171 65 Solna, Sweden From arne at bioinfo.se Wed Jan 9 09:40:16 2019 From: arne at bioinfo.se (Arne Elofsson) Date: Wed, 9 Jan 2019 09:40:16 +0100 Subject: [SocBiN] Reminder: Well funded assistant professor in Computational Biology at Stockholm University Message-ID: Assistant Professor in Computational biology Ref. No. SU FV-1696-18 Share Share Tweet *at the Department of Mathematics . Closing date: 15 January 2019.* Stockholm University is a leading European university and one of the world’s top 100 institutes of higher education and research. Stockholm University has more than 60,000 students and 5,000 staff. The Science for Life Laboratory (SciLifeLab) is a national center for large-scale biosciences with a focus on health and environmental research and is a collaboration between Stockholm University, Karolinska Institutet, the Royal Institute of Technology, and Uppsala University. SciLifeLab-Stockholm is located in a new building on the Karolinska Institutet campus. The last century of research has led the Department of Mathematics at Stockholm University to acquire a prominent place in Scandinavian mathematics. The department consists of three divisions: Mathematics, Mathematical statistics, and the recently formed Computational mathematics. The research in the division of mathematics include algebra, geometry and combinatorics, analysis and logic. The research in mathematical statistics include probability theory and statistical inference theory, with applications in biostatistics, climatology, econometrics, finance and insurance. Computational mathematics is a new direction for the department, with activities in computational biology, stochastic modelling, scientific computing for climatology, and logic of programs. 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 Mathematics. https://www.su.se/english/about/working-at-su/jobs?rmpage=job&rmjob=6380&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 Scholar: http://scholar.google.se/citations?user=s3OCM3AAAAAJ ORCID: 0000-0002-7115-9751 -------------- next part -------------- An HTML attachment was scrubbed... URL: From Erik.Bongcam at slu.se Thu Jan 17 11:44:15 2019 From: Erik.Bongcam at slu.se (Erik Bongcam Rudloff) Date: Thu, 17 Jan 2019 10:44:15 +0000 Subject: [SocBiN] Big Data Standards for Life Sciences Training School in Athens Message-ID: Dear all, This is an email to announce the next Cost Charme school to be held between 4-8th of March in Athens, Greece this year! The School will take place at the Agricultural University of Athens (AUA) and it will be hosted by the local Genetics Lab. The School's primary focus is on several concepts: Machine Learning (Classification, Filtering, Mining & Fusion of Big Data) Deep Learning (Using Multiple Frameworks, Neural Networks & Algorithm Design) 3D Molecular Modelling (Fusing Genomics with Structure, MultiDimensional Analysis) Data analysis to discover patterns and cross associations (multilevel/multiscale analysis) Standardizing Methods & Teaching for Big Data The School's goals are to: Integrate the realm of Big Data analysis under the Systems Biology context Insights on synergies among fields such as -omics, 3D modelling & Bioinformatics Promotion of teamwork and future collaborations The School is aimed at students: - with interest in the field of bioinformatics and/or medical bioinformatics - that work with diverse datasets in Life Sciences and wish to learn how to fuse/combine knowledge - who use or intent to use Life Science Big Data in their studies and projects So, on behalf of the School ’s organizing committee we welcome you all (based on eligibility) to apply! 25 students will be selected to receive a stipend of 800€ to be able to participate. You will find the application form and all relevant info at the school website: charme.geneticslab.gr Erik ----------------------------------- Dr. Erik Bongcam-Rudloff Professor of Bioinformatics Head of SLU Bioinformatics Infrastructure (SLUBI) Head of SGBC SLU-Uppsala +46-(0)72-535 55 87 +46 (0)18-67 21 21 --- När du skickar e-post till SLU så innebär detta att SLU behandlar dina personuppgifter. För att läsa mer om hur detta går till, klicka här E-mailing SLU will result in SLU processing your personal data. For more information on how this is done, click here -------------- next part -------------- An HTML attachment was scrubbed... URL: From andersson.robin at gmail.com Mon Jan 21 09:34:56 2019 From: andersson.robin at gmail.com (Robin Andersson) Date: Mon, 21 Jan 2019 09:34:56 +0100 Subject: [SocBiN] Postdoc position in deep learning of regulatory genetic variants Message-ID: <64177DBD-0560-4B0C-B119-76ADE89D2875@gmail.com> Dear all, We are looking for a motivated and talented postdoctoral researcher to join our group working on computational biology with a strong focus on enhancers and transcriptional regulation. The project will focus on on deep learning for modeling of regulatory genetic variants and their impact on enhancer and promoter activities. The ideal candidate should be comfortable in machine learning techniques and analysis of large-scale sequencing data and have a strong interest in transcription and transcriptional regulation. Please see the full job description and apply online at https://employment.ku.dk/faculty/?show=148728 . Read more about the Andersson lab at https://anderssonlab.org . Any question regarding the position should be directed to me at robin at binf.ku.dk . Please forward to potentially interested candidates. Deadline for applications is February 24, 2019. Best regards, Robin Andersson -- Robin Andersson, PhD Assistant professor, group leader The Bioinformatics Centre Department of Biology University of Copenhagen Ole Maaloes Vej 5 DK-2200 Copenhagen N, Denmark http://anderssonlab.org Twitter: @robin_andersson Skype: andersson.robin -------------- next part -------------- An HTML attachment was scrubbed... URL: From andersson.robin at gmail.com Mon Jan 21 09:41:11 2019 From: andersson.robin at gmail.com (Robin Andersson) Date: Mon, 21 Jan 2019 09:41:11 +0100 Subject: [SocBiN] Postdoc position in deep learning of regulatory genetic variants References: <64177DBD-0560-4B0C-B119-76ADE89D2875@gmail.com> Message-ID: I am sorry, the correct link to the job description should be https://employment.ku.dk/faculty/?show=148728 Best regards, Robin Andersson > Begin forwarded message: > > From: Robin Andersson > Subject: Postdoc position in deep learning of regulatory genetic variants > Date: 21 January 2019 at 09.34.56 CET > To: socbin at socbin.org, cph-bioinformatics at lists.binf.ku.dk > > Dear all, > > We are looking for a motivated and talented postdoctoral researcher to join our group working on computational biology with a strong focus on enhancers and transcriptional regulation. The project will focus on on deep learning for modeling of regulatory genetic variants and their impact on enhancer and promoter activities. > > The ideal candidate should be comfortable in machine learning techniques and analysis of large-scale sequencing data and have a strong interest in transcription and transcriptional regulation. > > Please see the full job description and apply online at https://employment.ku.dk/faculty/?show=148728 . Read more about the Andersson lab at https://anderssonlab.org . Any question regarding the position should be directed to me at robin at binf.ku.dk . > > Please forward to potentially interested candidates. > > Deadline for applications is February 24, 2019. > > Best regards, > Robin Andersson > > -- > Robin Andersson, PhD > Assistant professor, group leader > > The Bioinformatics Centre > Department of Biology > University of Copenhagen > Ole Maaloes Vej 5 > DK-2200 Copenhagen N, Denmark > > http://anderssonlab.org > Twitter: @robin_andersson > Skype: andersson.robin > -------------- next part -------------- An HTML attachment was scrubbed... URL: From albin at binf.ku.dk Thu Jan 24 15:12:49 2019 From: albin at binf.ku.dk (Albin Sandelin) Date: Thu, 24 Jan 2019 15:12:49 +0100 Subject: [SocBiN] PhD(s) in pancreatic cancer Message-ID: Dear all: Our ITN network has 15 PhD positions around the themes of ion transport in pancreatic cancer - one computational Phd project with me here in Copenhagen focusing on genetics and RNA changes due to pH. Me and the consortum would greatly appreciate if you could forward to excellent candidates. Deadline 20 feb. https://www.medizin.uni-muenster.de/fileadmin/einrichtung/phionic/190109-recruitment-flyer.pdf Interested applicants are of course invited to contact me for details. I am primarily looking for candidates with strong bioinformatics skills. Best, Albin Many thanks, Albin Albin Sandelin Professor, PhD Section for Computational and RNA Biology, Department of Biology & Biotech Research and Innovation Centre, Copenhagen University Ole Maaloes Vej 5, DK2200, Copenhagen N, Denmark tel +45 224 56668 albin at binf.ku.dk skype: albinsan twitter: @albin_san -------------- next part -------------- An HTML attachment was scrubbed... URL: From arne at bioinfo.se Fri Jan 25 13:28:04 2019 From: arne at bioinfo.se (Arne Elofsson) Date: Fri, 25 Jan 2019 13:28:04 +0100 Subject: [SocBiN] Fwd: Reminder: Applications to the National Graduate School in Medical Bioinformatics due 28 February 2019 In-Reply-To: <4dc454c85ade4ed3b1c321ff63dd2e28@ebox-prod-srv13.win.su.se> References: <4dc454c85ade4ed3b1c321ff63dd2e28@ebox-prod-srv13.win.su.se> Message-ID: Dear Colleague -- Kindly forward this message to your relevant colleagues and departmental and other email lists. 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 41 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 (typically 1 week in residence, with substantive pre- and/or post-course assignments), and offered 2-3 times per year, totalling about 30 HP over the course of 3 years. The courses are more specialised and varied 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 2018 and April 2019, though there is some flexibility in this. Target groups include PhD students in Life Science doing primarily computational research. By applying, you agree to set aside 8-10 May to attend our Annual Meeting (at Varbergs Kusthotell near Göteborg). Your first course is scheduled for 10-14 June 2019. The deadline is *February 28*, 2019. Enrollment is limited to approximately 20 incoming students per year. You can apply on 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 *Dean of the Swedish National Graduate School in Medical Bioinformatics * *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 QQ: 3236579471 -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: poster-forskarskola.A3.2019.light.pdf Type: application/pdf Size: 17564231 bytes Desc: not available URL: From Inge.Jonassen at ii.uib.no Thu Jan 31 09:34:58 2019 From: Inge.Jonassen at ii.uib.no (Inge Jonassen) Date: Thu, 31 Jan 2019 09:34:58 +0100 Subject: [SocBiN] Post-doc in bioinformatics and machine learning in Bergen Message-ID: <8C398B34-1CBD-43DF-8571-4567EAE185E8@ii.uib.no> The position is linked with a new ERA-net project aimed to develop better understanding and treatment of leukemia through molecular characterization including single-cell measurements, systems biology modeling, and machine learning. Great opportunities for the right candidate! Please help to distribute information to potential applicants! For more information and to submit your application, see https://www.jobbnorge.no/en/available-jobs/job/164129/postdoctoral-position-in-bioinformatics-and-machine-learning Application deadline: March 1st, 2019 Inge Inge Jonassen, Prof PhD Head of Node, Elixir Norway Director, Computational Biology Unit Department of Informatics University of Bergen HiB N5020 Bergen Norway Inge.Jonassen at uib.no -------------- next part -------------- An HTML attachment was scrubbed... URL: From albin at binf.ku.dk Thu Jan 31 12:15:42 2019 From: albin at binf.ku.dk (Albin Sandelin) Date: Thu, 31 Jan 2019 12:15:42 +0100 Subject: [SocBiN] Postdoc in computational biology: Prenatal programming of disease and analysis of the effect of probiotics Message-ID: Dear all (apologies for multiple postings…) We have a postdoc in computational biology in my group working on prenatal programming of disease and also probiotics/gut interaction. Please share with great candidates! https://jobportal.ku.dk/alle-opslag/?show=148841 Best regards, Albin Postdoc in computational biology: Prenatal programming of disease and analysis of the effect of probiotics The Sandelin group is looking to recruit a talented postdoctoral researcher to our highly dynamic research group working in the interface of computational biology and genomics. The position is part of two larger projects on i) how stress transfers between mother and fetus during pregnancy and ii) analysis of the effect of probiotics in tissue and organoid gut models. The 2.5 year postdoc will start 1 April 2019 or as soon as possible thereafter. Description of the scientific environment The projects are collaborations between the Sandelin group at Bioinformatics Centre, Department of Biology and BRIC, the Sørig Hougaard group at the National Research Centre for the Working Environment (NRCWE), and the Kim Jensen group at BRIC and Chr. Hansen, a world leading company in production of live bacteria. The Sandelin group is a high-profile joint computational/experimental group focusing on gene regulation and transcriptomics. The Bioinformatics Centre employs around 50 researchers and has many international connections to high-profile groups. The groups are housed in the Biocenter in central Copenhagen, Denmark, at University of Copenhagen. The Sørig Hougaard group at NRCWE focuses on developmental toxicology, working environment and in particular effects of particles and stress on reproduction and pregnancy. NRCWE is located within biking distance of the Biocenter. The Kim Jensen group at BRIC focuses on unraveling the molecular mechanisms that control stem cell fate during development, tissue homeostasis and during disease using state of the art technologies including various sequencing and patient derived organoid models. Project description The postdoc will work on two projects: i) Characterization on how acute stress induced in pregnant mothers transfers from mother to fetus, and the molecular signaling molecules and regulators that underlie this process. This will be done through a time series analysis in pregnant mice on RNA and protein levels, coupled to state of the art computational analysis, and parallel investigations of signaling molecules in blood. Experiments will mostly be done by one PhD student and technicians at NRCWE, while the postdoc advertised here will be primarily responsible for data analysis; however, the postdoc, PhD student and technicians are expected to work as a team. ii) Analysis of massive RNA-seq data sets from tissue and gut organoids subjected to probiotics treatment. This is a collaboration between University of Copenhagen and Chr. Hansen A/S, the world’s largest producer of live bacteria. This project involves five other experimental postdocs. The successful candidate will work both at the Biocenter, University of Copenhagen and at NFA. The postdoc will have a joint affiliation with Department of Biology, BRIC, NFA and Chr Hansen. Job description The position is available for a 2.5-year period and your key tasks as a postdoc at SCIENCE are: To manage and carry through your research project Write scientific articles Formal requirements Applicants must hold a PhD or equivalent in bioinformatics or a mathematical discipline with a strong biological interest, and a substantial publication record in high-quality international journals focused on the analysis of genomics data. Candidates finishing their PhD before 1 March 2019 will also be considered. Although the focus will be on computational work, the candidate will be working closely together with experimental scientists, and will be expected to understand the experiments and underlying biology and fruitfully interact with other specialists. Therefore, we require: Strong experience in analyzing high-throughput sequencing data, in particular RNA-seq Documented experience in statistical analyses of such data, including expression analysis, as well as quality control and visualization Strong programming skills in Python and R, or equivalents, and experience using linux/unix platforms Excellent English skills One or more first authorships in well-respected bioinformatics or genomics journals Experience in multivariate statistics, mass-spec data analysis, model building, network, time course analysis and sequence analysis are strong advantages. Similarly, experience/knowledge in microbiology, toxicology and/or inflammatory response, reproduction and developmental programming of disease is an advantage. Terms of employment The position is covered by the Memorandum on Job Structure for Academic Staff. Terms of appointment and payment accord to the agreement between the Ministry of Finance and The Danish Confederation of Professional Associations on Academics in the State. The starting salary is currently up to DKK 426.625 including annual supplement (+ pension up to DKK 72.952). Negotiation for salary supplement is possible. Application Procedure Apply at https://jobportal.ku.dk/alle-opslag/?show=148841 Please include Cover Letter, detailing your motivation and background for applying for the position CV PhD and MSc Diplomas List of publications Full contact details (Name, address, telephone & email) of 1-3 professional referees Two letters of recommendation. The University wishes our staff to reflect the diversity of society and thus welcomes applications from all qualified candidates regardless of personal background. The deadline for applications is 1 March 2019. After the expiry of the deadline for applications, the authorized recruitment manager selects applicants for assessment on the advice of the Interview Committee. Afterwards an assessment committee will be appointed to evaluate the selected applications. The applicants will be notified of the composition of the committee and the final selection of a successful candidate will be made by the Head of Department, based on the recommendations of the assessment committee and the interview committee. The main criterion for selection will be the research potential of the applicant and the above mentioned skills. You can read more about the recruitment process at http://employment.ku.dk/faculty/recruitment-process/. Questions For specific information about the position, please contact the principal supervisor, Professor Albin Sandelin, Department of Biology and BRIC, albin at binf.ku.dk, Direct phone: +45 35 32 12 85 Albin Sandelin Professor, PhD Section for Computational and RNA Biology, Department of Biology & Biotech Research and Innovation Centre, Copenhagen University Ole Maaloes Vej 5, DK2200, Copenhagen N, Denmark tel +45 224 56668 albin at binf.ku.dk skype: albinsan twitter: @albin_san -------------- next part -------------- An HTML attachment was scrubbed... URL: