From etienne.ruppe at genomic.ch Thu Sep 1 15:25:25 2016 From: etienne.ruppe at genomic.ch (Etienne =?UTF-8?B?UnVwcMOp?=) Date: Thu, 01 Sep 2016 15:25:25 +0200 Subject: [SocBiN] 7 good reasons to attend ICCMg (Geneva, October 13-14) Message-ID: <1472736325-dc476b1b2fcf2e9f55df6b4117aae8f0@genomic.ch> Dear colleagues, We are pleased to inform you that inscriptions to the first International Conference on Clinical Metagenomics (ICCMg, Campus Biotech, Geneva, October 13-14 2016) are still available from the [conference website](http://www.clinicalmetagenomics.org/). **Here are at least 7 reasons to attend ICCMg:** 1.The conference welcomes **prestigious speakers** (see the program below) 2.**Clinical metagenomics is one the most exciting,** emerging fields in medicine 3.Geneva is an **easily accessible city**, and so is Campus Biotech where ICCMg will be held 4.Conference schedule fits with an **early arrival on the 13th**, and an **early departure** on the 14h (but you can also choose to stay and enjoy Geneva) 5.**The conference fee is low** (100CHF for students, 250CHF for others, with 1CHF=1USD) 6.For 50CHF more, you�ll get a **wonderful dinner at the Vieux Bois**, close to the **Geneva Lake** 7.And before that, we will hold a **convivial poster session with open bar** **FINAL PROGRAM** **NGS and bio-informatics** **Patrick Wincker** *(Genoscope, Evry, France)*: Next-generation sequencing. **Nick Loman** *(University of Birmingham, UK)*: What's next in NGS? The Nanopore technology. **Aitana Lebrand** *(Swiss Institute of Bio-informatics, Geneva, Switzerland)*: Management of metagenomic data. **Clinical Metagenomics****** **Georges Weinstock** *(Jackson Laboratory, Farmington, US)*: Probing the Medical Microbiome. **Marc Eloit** *(Institut Pasteur, Paris, France)*: Clinical metagenomics in immunocompromized patients. **Jerôme Bouquet** *(University of San Francisco, US)*: Clinical metagenomics for diagnosis of acute Infectious diseases. **Gilbert Greub** *(Institute of Microbiology, Lausanne, Switzerland)*: Clinical metagenomics for the discovery of new pathogens. **Derrick Crook** *(University of Oxford, UK)*: Inferring the antibiogram from genomes. **Etienne Ruppé** *(Geneva University Hospitals, Switzerland)*: Clinical metagenomics in bone and joint infections. **Frank Aarestrup** *(Danish Technical institute, Lyngby, Denmark)*: Clinical metagenomics in urinary-tract infection. **Judith Breuer** *(Faculty of Medical Sciences, London, UK)*: Detection of Mycobacterium tuberculosis directly from samples. **Intestinal Microbiota** **Dusko Ehrlich** *(Metagenopolis, Jouy-en-Josas, France)*: The intestinal microbiota and the link with diseases. **Eric Pamer** *(Memorial Sloan-Kettering Cancer Center, New York, US)*: Microbiota-mediated defense against intestinal infections. **Christopher Ford** *(Seres Therapeutics, Cambridge, US)*: Microbiome therapeutics. ** Oncology** **Stylianos Antonarakis** *(Geneva University Hospitals, Switzerland)*: Metagenomics and tumor profiling **Peer Bork** *(EMBL, Heidelberg, Germany)*: Diagnostic of colon cancer using metagenomics. **Cynthia Sears** *(John Hopkins University, Baltimore, US)*: Using Biofilms and Metagenomics to Diagnose Colon Cancer. ICCMg will start on Thursday October 13 at 1:45pm and will end on Friday October 14 at 3:40pm. ICCMg will take place at **Campus Biotech**, which is nicely located close to the **Geneva Lake**and **easily accessible by public transportation** from the train station or airport. **Late-breaker abstracts** are still welcomed for **poster presentations** (). The posters will be presented at the specific poster exhibition and open bar on Thursday evening, followed by the **conference dinner** (optional). We hope to welcome you in Geneva and are looking forward to receiving your registration. With best regards Etienne Ruppé, Enrico Zuffi and Jacques Schrenzel      ____________________________________ *ICCMg 2016 Campus Biotech, Geneva October 13-14, 2016 Organised by the International Society for Clinical Metagenomics More information at [www.clinicalmetagenomics.org](http://www.clinicalmetagenomics.org/) * -------------- next part -------------- An HTML attachment was scrubbed... URL: From asta.laiho at btk.fi Fri Sep 2 11:43:54 2016 From: asta.laiho at btk.fi (Asta Laiho) Date: Fri, 02 Sep 2016 12:43:54 +0300 Subject: [SocBiN] Postdoc position in computational biomedicine group, University of Turku, Finland Message-ID: Dear all, A grant for a postdoctoral researcher is open for applications in the project directed by Dr. Laura Elo, Research Director in Bioinformatics at Turku Centre for Biotechnology, University of Turku, Finland. The project of this postdoctoral researcher involves setting up analysis workflows and analyzing genomic data. The specific focus is on variant annotation and prioritization in the context of complex diseases in close collaboration with clinical teams. The grant is initially for one year, starting from October 1, 2016, with a possibility for extension. We are looking for a highly motivated scientist with previous experience in genomic research and related analysis platforms and tools. General knowledge in bioinformatics, statistics and R, Matlab or other mathematical/statistical software is required. Good communication skills in English, both oral and written, are essential. Independency and self-driven attitude are highly appreciated, but the candidate should be able to do research as part of a team as well. The candidate should hold a PhD degree or complete one within next months. For further information, please contact Jenni Vaarno, jenni.vaarno(at)utu.fi or +358 (0)2 333 8313. https://www.btk.fi/research/research-groups/elo/ Best regards, Asta Laiho ‹ Bioinformatics Unit Turku Centre for Biotechnology University of Turku and Åbo Akademi University http://www.btk.fi/bioinformatics -------------- next part -------------- An HTML attachment was scrubbed... URL: From arne at bioinfo.se Fri Sep 2 15:37:55 2016 From: arne at bioinfo.se (Arne Elofsson) Date: Fri, 2 Sep 2016 15:37:55 +0200 Subject: [SocBiN] Wallenberg Academy Fellows Message-ID: Wallenberg Academy Fellows This autumn, DBB, Stockholm University can again nominate candidates for the Wallenberg Academy Fellows (WAF) program ( http://www.wallenbergacademyfellows.se/en/theprogramme/). The program provides significant support to young researchers aiming at establishing independence, and it is both prestigious and competitive. Candidates *must have obtained their PhD after 1 January 2009 *(if the WAF guidelines stays the same as previous years). If anybody knows of a senior postdoc/young PI that *has a strong CV *and that would like to *establish a research group at DBB- *Note that preference will be given to candidates whose research is synergistic with existing activities at DBB, and to those candidates that are currently external to DBB (on account of the WAF guidelines, i.e. *not worked in Sweden during the last five years*). Also note that at this stage there are no guarantees that DBB will nominate any candidate (most likely only one or a few will be nominated). If you know any very strong candidates (including yourself) please contact me arne at bioinfo.se Yours Arne ----------------------------------------- Arne Elofsson Science for Life Laboratory Tel:+46-(0)852481531 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 mika.hilvo at zora.fi Mon Sep 5 09:10:34 2016 From: mika.hilvo at zora.fi (Mika Hilvo) Date: Mon, 5 Sep 2016 07:10:34 +0000 Subject: [SocBiN] Zora Biosciences is looking for a Bioinformatician Message-ID: Hi, We are looking for a Bioinformatician to join our team. The job consists of statistical and bioinformatics work for both customer as well as R&D projects. Please see additional details about the position in the attached PDF file. Best regards, - Mika Mika Hilvo Head of Bioinformatics, PhD Zora Biosciences Oy e-mail: mika.hilvo at zora.fi tel. +358-50-5347782 -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: ZoraBioinformatician16.pdf Type: application/pdf Size: 107195 bytes Desc: ZoraBioinformatician16.pdf URL: From dnnm at novonordisk.com Mon Sep 5 13:36:26 2016 From: dnnm at novonordisk.com (DNNM (Dennis Madsen)) Date: Mon, 5 Sep 2016 11:36:26 +0000 Subject: [SocBiN] Jobs: Post Doc at Novo Nordisk in Denmark Message-ID: <201609051136.u85BaSiE017979@e-mailfilter03.sunet.se> We have an exciting post doc position in the Bioinformatics department at Novo Nordisk in Denmark: http://www.novonordisk.com/careers/see-list-of-all-available-jobs.41451BR.Internal.5013.html Best regards, _____________________ Dennis Madsen, PhD Principal Scientist Bioinformatics Novo Nordisk A/S Novo Nordisk Park G8.2.32 DK-2760 Måløv Denmark +45 4444 8888 (phone) +45 3075 6959 (mobile) dnnm at novonordisk.com Facebook | Twitter | LinkedIn | Youtube | Pinterest A life-changing career at Novo Nordisk How could your talent benefit you and millions of others? Find out more here This e-mail (including any attachments) is intended for the addressee(s) stated above only and may contain confidential information protected by law. You are hereby notified that any unauthorized reading, disclosure, copying or distribution of this e-mail or use of information contained herein is strictly prohibited and may violate rights to proprietary information. If you are not an intended recipient, please return this e-mail to the sender and delete it immediately hereafter. Thank you. -------------- next part -------------- An HTML attachment was scrubbed... URL: From arne at bioinfo.se Wed Sep 7 09:55:41 2016 From: arne at bioinfo.se (Arne Elofsson) Date: Wed, 7 Sep 2016 09:55:41 +0200 Subject: [SocBiN] PhD position in ITN network (short deadline) Message-ID: Dear colleagues If you have some excellent students looking for PhD positions and fulfills the rules (not lived more than 12 month in Sweden), please have them to apply for the following position. It is a part of a very nice ITN network. *Ref No SU FV-2476-1* *Deadline Sept 15 2016* http://www.su.se/english/about/vacancies/vacancies-new-list *Project title: Prediction and studies of membrane protein interactions *(Please note that thet project title and description on the application page is different, but this is a sudden opening) Project leader: Arne Elofsson, arne at bioinfo.se, Homepage: http://bioinfo.se/ Membrane proteins are the gateways to the cells and as such they are of great importance for the development of drugs. In addition membrane proteins are quite difficult to handle experimentally, therefore prediction methods are important to gain information about these protein. We have developed many of the leading methods for prediction of membrane protein structures. For a full list of publication see http://bioinfo.se/papers/ . The primarily aim of this project is to obtain detailed structural information about large biological complexes and networks, such as membrane protein translocases, by integrating different types of genomic sequence data. The information from a sufficient number of homologous sequences is often sufficient to predict the fold of soluble globular proteins or membrane proteins. Two types of information will primarily be used. First, the identification of co-evolving residues can be used to predict interacting residue pairs. Secondly the use of structural homology combined with analysis of interaction surfaces can be used to identify potentially interacting proteins. These purely computational methods will then, if needed, be combined with experimental data from Cryo-EM and other techniques. A general interest in protein, programming and machine learning methods and a solid background in bioinformatics, physics or computer science is suitable for this position. This position is a part of a European Union Marie Skłodowska Curie Initial Training Network named “protein factory”. The overall aim of this network is to develop new protein production systems that can deliver secreted enzymes and membrane proteins in greater yields, with higher quality and at lower costs. The network consists of 11 partners from 7 different European countries and in total 15 PhD students will be recruited. All these students will participate in several workshops, meetings and courses. This provides a unique possibility to form a network of fewllow scientists with a common research interest. The position is funded by a European Union Marie Skłodowska Curie Initial Training Network. Therefore, *potential candidates must not have resided or carried out their main activity (work, studies, etc.) in Sweden for more than 12 months in the 3 years immediately prior to the recruitment, and have no more than 4 years of research experience. * Include a short motivation, a CV (plus diplomas and certificates/date when you expect to finish your studies), an example of computer code you have written and the contact details of at least 2 references in your application. References: 1) Bernsel, A., Viklund, H., Falk, J., Lindahl, E., von Heijne, G. and Elofsson, A. (2008) Prediction of membrane-protein topology from first principles. Proc Natl Acad Sci U S A 105 (20) : 7177-718 2) Bendz, M., Skwark, M., Nilsson, D., Granholm, V., Cristobal, S., Kall, L. and Elofsson, A. (2013) Membrane protein shaving with thermolysin can be used to evaluate topology predictors. Proteomics 13 (9) : 1467-1480. 3) Peters, C. and Elofsson, A. (2014) Why is the biological hydrophobicity scale more accurate than earlier experimental hydrophobicity scales? Proteins 82 (9) : 2190-2198. 4) Skwark, M.J., Raimondi, D., Michel, M. and Elofsson, A. (2014) Improved contact predictions using the recognition of protein like contact patterns. PLoS Comput Biol 10 (11) : e1003889. *http://web103.reachmee.com/ext/I007/927/job?site=8&lang=UK&validator=d3e6a58db9058c5eab7ea3e324f063f6&ref=http%3A%2F%2Fwww.su.se%2Fenglish%2Fstaff-info%2Frelocation&ihelper=http%3A%2F%2Fwww.su.se%2Fenglish%2Fabout%2Fvacancies%2Fvacancies-new-list&job_id=1810 * -------------- next part -------------- An HTML attachment was scrubbed... URL: From dnnm at novonordisk.com Wed Sep 7 09:58:49 2016 From: dnnm at novonordisk.com (DNNM (Dennis Madsen)) Date: Wed, 7 Sep 2016 07:58:49 +0000 Subject: [SocBiN] Jobs: Post Doc at Novo Nordisk in Denmark In-Reply-To: <201609051136.u85BaSiE017979@e-mailfilter03.sunet.se> References: <201609051136.u85BaSiE017979@e-mailfilter03.sunet.se> Message-ID: <201609070758.u877wqpp013506@e-mailfilter03.sunet.se> Sorry - wrong link - this is the correct link: http://www.novonordisk.com/careers/see-list-of-all-available-jobs.41451BR.External.5027.html Best regards, Dennis Madsen From: SocBiN [mailto:socbin-at-sbc.su.se-bounces at lists.su.se] On Behalf Of DNNM (Dennis Madsen) Sent: 5. september 2016 13:36 To: socbin-at-sbc.su.se at lists.su.se Subject: [SocBiN] Jobs: Post Doc at Novo Nordisk in Denmark We have an exciting post doc position in the Bioinformatics department at Novo Nordisk in Denmark: http://www.novonordisk.com/careers/see-list-of-all-available-jobs.41451BR.Internal.5013.html Best regards, _____________________ Dennis Madsen, PhD Principal Scientist Bioinformatics Novo Nordisk A/S Novo Nordisk Park G8.2.32 DK-2760 Måløv Denmark +45 4444 8888 (phone) +45 3075 6959 (mobile) dnnm at novonordisk.com Facebook | Twitter | LinkedIn | Youtube | Pinterest A life-changing career at Novo Nordisk How could your talent benefit you and millions of others? Find out more here This e-mail (including any attachments) is intended for the addressee(s) stated above only and may contain confidential information protected by law. You are hereby notified that any unauthorized reading, disclosure, copying or distribution of this e-mail or use of information contained herein is strictly prohibited and may violate rights to proprietary information. If you are not an intended recipient, please return this e-mail to the sender and delete it immediately hereafter. Thank you. -------------- next part -------------- An HTML attachment was scrubbed... URL: From samuel.kaski at aalto.fi Wed Sep 7 20:42:13 2016 From: samuel.kaski at aalto.fi (Kaski Samuel) Date: Wed, 7 Sep 2016 18:42:13 +0000 Subject: [SocBiN] Several Postdoc and Research Fellow Positions in computational biology and medicine Message-ID: Aalto University and University of Helsinki, the two leading universities in Finland within computer science and information technology, are looking for 20 excellent researchers in various areas of ICT. Many of the positions (e.g. those by Samuel Kaski, Juho Rousu and Harri Lähdesmäki) are on computational biology and medicine, and many others are related. The full list of open positions is as follows: - HIIT Research Programme on Computational Inference, Professors Samuel Kaski, Jukka Corander, Petri Myllymäki, Antti Oulasvirta, Matti Pirinen, Aki Vehtari - HIIT Research Programme on Foundations of Computational Health, Professors Juho Rousu, Veli Mäkinen, Tero Aittokallio, Aristides Gionis, Keijo Heljanko, Jari Saramäki - HIIT Research Brogramme on Building Trust in Secure Computing Systems,Professors Tuomas Aura, N. Asokan, Valtteri Niemi, Stavros Tripakis, Sasu Tarkoma - HIIT Research Programme on Augmented Research, Professors Giulio Jacucci, Samuel Kaski, Petri Myllymäki, Aristides Gionis, Sasu Tarkoma, Niklas Ravaja - Information Retrieval, Human-Computer Interaction HCI, Machine Learning, Professor Giulio Jacucci - Adaptive and immersive environments for augmented social interaction, Professor Giulio Jacucci - Complex Systems Computation, Professor Petri Myllymäki - Internet of Things, Professor Mario Di Francesco - Creative software: automated text generation, adaptive software architectures, Professor Hannu Toivonen - Machine Learning and Adaptive User Interfaces, Professors Antti Oulasvirta, Jukka Corander, Samuel Kaski - Probabilistic Machine Learning, Professor Samuel Kaski - Probabilistic machine learning for precision medicine and data-driven healthcare, Professor Samuel Kaski - Machine learning for high-dimensional and structured data, Professors Hiroshi Mamitsuka, Samuel Kaski - Solver technology for answer-set programming, Professor Ilkka Niemelä, Dr. Tomi Janhunen - High-throughput bioinformatics and regulatory genomics, Professor Harri Lähdesmäki - Probabilistic modeling for biomedicine and personalised medicine, Professor Harri Lähdesmäki For the full call text and information about the application process, please visit https://www.hiit.fi/openpositions/Fall2016. The deadline for sending the application is September 30, 2016, at 2pm Finnish time. From Carsten.Daub at ki.se Thu Sep 8 15:07:05 2016 From: Carsten.Daub at ki.se (Carsten Daub) Date: Thu, 8 Sep 2016 13:07:05 +0000 Subject: [SocBiN] Laboratory technician in Bioinformatics at Karolinska Institutet, Carsten Daub research group Message-ID: <24D8D3D8-DD95-465D-A2C6-939593AB2255@ki.se> Open call: Laboratory technician in Bioinformatics at Karolinska Institutet, Carsten Daub research group https://ki.mynetworkglobal.com/en/what:job/jobID:112137/where:4/ Duties The laboratory technician will work with the collection and annotation of ZENCODE-ITN genomics and transcriptomics datasets as well as their storage in databases. These datasets will be quality controlled, structured, annotated and shared in the consortium and ultimately opened to the public. The laboratory technician will be working in a team and be involved in the development and maintenance of the database and the web interface. Furthermore he/she will perform meta-analysis of the collected data. A research stay in London at the Imperial College of up to 8 months is planned for the laboratory technician. Qualifications We are seeking one highly motivated and talented laboratory technician, who plans and executes data collection and data annotation of various types of next-gen sequencing data. As successful candidate you have a masters degree in Bioinformatics, computational biology or a related field. Thorough understanding of the concepts of molecular biology is essential. Experience with analysis of high-throughput data in UNIX environment or bioinformatic database and web application development is a strong plus. Your interest in medical and clinical questions together with the willingness to improve your knowledge in this field is important. Excellent communication skills, ability to work in a team, a proactive and constructive personality as well as fluent English speaking and writing abilities are expected. This position is funded by a European Union Marie Sklodowska Curie Initial Training Network (ITN). To be eligible, potential candidates must not have resided or carried out their main activity (work, studies, etc.) in Sweden for more than 12 months in the 3 years immediately prior to the recruitment, and have no more than 4 years of research experience. From arne at bioinfo.se Mon Sep 12 22:31:41 2016 From: arne at bioinfo.se (Arne Elofsson) Date: Mon, 12 Sep 2016 22:31:41 +0200 Subject: [SocBiN] Faculty opening in Computational Biology Message-ID: Dear Colleagues, We would highly appreciate if you attract attention of qualified individuals to a tenure-track faculty opening in Computational Biology at The University of Kansas - see the ad attached. Thank you very much! Ilya ------ Ilya Vakser Professor and Director Computational Biology Program and Center for Computational Biology Professor Department of Molecular Biosciences The University of Kansas 2030 Becker Dr. Lawrence, KS 66045 vakser at ku.edu, +1-785-864-1057 www.compbio.ku.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: CB faculty position.pdf Type: application/pdf Size: 69439 bytes Desc: not available URL: From erik.sonnhammer at scilifelab.se Tue Sep 13 17:02:44 2016 From: erik.sonnhammer at scilifelab.se (Erik Sonnhammer) Date: Tue, 13 Sep 2016 17:02:44 +0200 Subject: [SocBiN] PhD position in Network Inference and Systems Biology (deadline Sept 15) Message-ID: Dear colleagues, Please forward this announcement to bioinformatics students that might be looking for a PhD positionin Network Inference and Systems Biology. See http://sonnhammer.org/download/ads/Utlys_phd_160915.pdf Many thanks ___________________________________ Erik Sonnhammer, Ph.D. Professor of Bioinformatics DBB, Stockholm University Science for Life Laboratory Box 1031, SE-17121 Solna, Sweden Tel: +46-(0)70-5586395 Email: Erik.Sonnhammer at scilifelab.se Web: http://sonnhammer.org ___________________________________ -------------- next part -------------- An HTML attachment was scrubbed... URL: From jonovik at gmail.com Mon Sep 19 07:27:27 2016 From: jonovik at gmail.com (Jon Olav Vik) Date: Mon, 19 Sep 2016 07:27:27 +0200 Subject: [SocBiN] =?utf-8?q?JOB=3A_Two_researcher_positions_-_systems_biol?= =?utf-8?q?ogy_modelling_of_salmon_metabolism_=E2=80=93_ref=2Eno=2E?= =?utf-8?q?_16/04447?= Message-ID: Dear list, Two researcher positions in systems biology modelling of salmon metabolism are available at the Norwegian University of Life Sciences, Centre for Integrative Genetics, as described below. Email enquiries welcome: Jon Olav Vik (jon.vik at nmbu.no) or Simen Sandve (simen.sandve at nmbu.no). Best regards, Jon Olav Vik *Two researcher positions - systems biology modelling of salmon metabolism – ref.no . 16/04447* Two researcher positions (2-3 years with possibility of extension) in systems biology of Atlantic salmon metabolism are available at the Department of Animal and Aquacultural Sciences, NMBU, Norway. The successful candidate will work within the Centre for Integrative Genetics ( CIGENE ), which includes comprehensive molecular lab facilities and a strong environment dedicated to genomics, bioinformatics, and mathematical modeling. The researchers will work on two interlinked systems biology projects, DigiSal and GenoSysFat , promoting sustainable growth of salmon farming by building model-based knowledge about salmon metabolism. The projects are highly interdisciplinary and combine expertise in physiology and nutrition, cutting-edge high-throughput omics technologies and model-based analysis of omics data. We will encourage visits to international collaborators such as the Systems and Synthetic Biology unit in Wageningen, the Netherlands. Main tasks: Analyze how salmon metabolism depends on variation in diet and genotype, based on omics and microscopy data and using a variety of modelling frameworks, both top-down multivariate analysis and bottom-up metabolic network modelling. There will also be opportunities to link modelling work to ongoing evolutionary genomics projects to address questions regarding consequences of genome duplication on the function of metabolic systems. *Qualifications* *Required* - PhD in systems biology, computational biology, bioinformatics, physics or mathematics *Preferred* - Experience with analyzing and visualizing multivariate data - Experience with constraint-based modelling - Experience with integrating -omics data and biological knowledge - Proficiency in R, Python or similar for simulations and data analysis Full advertisement: https://www.jobbnorge.no/en/av ailable-jobs/job/129214/two-researcher-positions-systems-bio logy-modelling-of-salmon-metabolism-refno-16-04447 *Application deadline: Wednesday, October 5, 2016* Please forward this announcement to anyone you think might be interested! -- Jon Olav Vik jonovik at gmail.com http://www.nmbu.no/ans/jon.vik -------------- next part -------------- An HTML attachment was scrubbed... URL: From Carsten.Daub at ki.se Mon Sep 19 15:40:37 2016 From: Carsten.Daub at ki.se (Carsten Daub) Date: Mon, 19 Sep 2016 13:40:37 +0000 Subject: [SocBiN] Fwd: post doc in high-res. in vivo microscopy / gene regulation References: <62E9BB65-4641-48FD-A86C-0444FAEDDD70@bham.ac.uk> Message-ID: <3905D321-7963-462B-A9D6-B343C5741C4D@ki.se> Research Fellow in Gene regulation / Molecular-resolution in vivo microscopy University of Birmingham, UK College of Medical and Dental Sciences Institute of Cancer and Genomic Sciences Applications are invited from outstanding individuals with ambition to develop their independent research to work under the supervision of Professor Ferenc Mueller, Professor of Developmental Genetics, on a H2020 funded research project to work in an international consortium for the study of nuclear functions in embryos and by super resolution imaging / molecular resolution microscopies in real time. The Mueller laboratory studies gene regulation in vertebrate development from different angles and using interdisciplinary approaches. For recent publications and topics of research see: www.birmingham.ac.uk/Ferenc-Mueller. Their research is integrated in the Birmingham Centre for Genome Biology www.birmingham.ac.uk/genome-biology. In this project the fellow will study transcription in the living vertebrate embryo by using zebrafish as model. The successful candidate will combine programmable genome editing in zebrafish with temporal in vivo, in situ transcription analyses by cutting edge high-resolution microscopy technologies. The successful applicant will have a first degree and a PhD in an area of specialism relevant to the project. They will also have strong background in molecular biology and high-resolution microscopy, and previous experience with model organism and/or in vivo imaging. The post is available from 1st October for a period of 3 years. Informal enquiries should be directed to Prof. Ferenc Mueller tel: +44 (0)12142895; email f.mueller at bham.ac.uk Salary will be in on Grade 7 according to experience. Closing date: 28 September 2016, Ref: 55966 (Naturejobs) http://www.jobs.ac.uk/job/AOP603/research-fellow-in-gene-regulation-molecular-resolution-in-vivo-microscopy/ Details from 0121 415 9000 or www.hr.bham.ac.uk/jobs HR, University of Birmingham, Edgbaston, Birmingham B15 2TT A University of Fairness and Diversity -------------- next part -------------- An HTML attachment was scrubbed... URL: From erik.larsson at gu.se Wed Sep 21 12:54:02 2016 From: erik.larsson at gu.se (Erik Larsson Lekholm) Date: Wed, 21 Sep 2016 10:54:02 +0000 Subject: [SocBiN] Postdoc in computational cancer genomics, Gothenburg, Sweden Message-ID: <69CFF8D3-3BF1-46BC-BBD8-9FEAF0F498FD@gu.se> Dear everyone, We have an opening for a postdoctoral researcher in computational cancer genomics to join my group at the Sahlgrenska Academy, University of Gothenburg, Sweden. The applicant should be a "biologically minded" bioinformatician who wishes to take on the challenge of studying somatic genomics alterations in non-coding regions of tumor genomes. This needs to be a highly motivated and skilled person with a practical and self-driven mindset. Further information is available here: http://www.gu.se/english/about_the_university/announcements-in-the-job-application-portal/?languageId=0&disableRedirect=true&id=19144&Dnr=783841&Type=E Deadline in 4 weeks! Erik -------------- next part -------------- An HTML attachment was scrubbed... URL: From henrik.lantz at bils.se Thu Sep 22 09:13:47 2016 From: henrik.lantz at bils.se (Henrik Lantz) Date: Thu, 22 Sep 2016 09:13:47 +0200 Subject: [SocBiN] Post doc position in Bioinformatics/Software engineering in Uppsala Sweden Message-ID: <2651B00E-A706-403A-AA9A-11FBAD4D5412@bils.se> Dear all, please see the link below for a post doc position in tools/algorithm development (C++) in Manfred Grabherr’s group in Uppsala Sweden. Application deadline is Oct 3. http://www.uu.se/en/about-uu/join-us/details/?positionId=112634 Best regards, Henrik Henrik Lantz NGS-coordinator, NBIS Uppsala, Sweden From andersson.robin at gmail.com Tue Sep 27 11:33:33 2016 From: andersson.robin at gmail.com (Robin Andersson) Date: Tue, 27 Sep 2016 11:33:33 +0200 Subject: [SocBiN] Open PhD student position in computational genomics and transcriptional regulatory variation in Copenhagen, Denmark Message-ID: Dear all, Please see link below for an open PhD student position in my group at University of Copenhagen, Denmark. Application deadline: October 31, 2016. http://employment.ku.dk/phd/?show=857805 Context The lab of Robin Andersson focuses on genomics and computational/statistical modeling of transcriptional regulation based on large-scale sequencing data, including experimental data generated from within the lab. We aim to characterize and better understand the architectures and complexities of transcriptional regulation (see e.g. Andersson et al. 2014, Nature, http://dx.doi.org/10.1038/nature12787) and gain insights into the mechanisms of regulation. We further focus on the fundamental properties of enhancers and promoters (see e.g. Andersson et al. 2015, Trends Genet, http://dx.doi.org/10.1016/j.tig.2015.05.007) as well as the biogenesis and characteristics of enhancer RNAs (see e.g. Andersson et al. 2014, Nat Comms, http://dx.doi.org/10.1038/ncomms6336). The group is also active in the international FANTOM consortium and is part of the FANTOM6 project http://fantom.gsc.riken.jp/6/. For more information, see http://anderssonlab.org. Project The correct function of regulatory elements and their interplay are essential for the precisely coordinated transcriptional activities within a cell. Disrupted regulatory activities may therefore have detrimental effects leading to disease. However, most variants have no or an only weakly associated trait and, in general, the impact of genetic variants on regulation is not well understood. Therefore, using our established accurate transcription-based method to assess activities of regulatory elements and the associations between them, we aim to systematically characterize human regulatory variation and its consequences. We further aim to infer models describing the function of a regulatory element and its importance, and thus the impact on regulation upon disruption. The successful candidate is expected to work on projects related, but not limited, to 1) computational modeling of enhancer regulation and genome-wide mapping of enhancer architectures; and 2) assessment of the extent and impact of individual variation and genetic variants in regulatory architectures in order to understand their importance, stochasticity and robustness. 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 edsgard at gmail.com Fri Sep 30 00:07:27 2016 From: edsgard at gmail.com (=?UTF-8?Q?Daniel_Edsg=C3=A4rd?=) Date: Fri, 30 Sep 2016 00:07:27 +0200 Subject: [SocBiN] Postdoc positions in New York (Bioinformatics/Cancer Genomics/Data analysis) Message-ID: Dear all, Please see two exciting postdoc positions below, provided by Nils Weinhold at MSKCC, New York. Best, Daniel Edsgärd Sandberg lab, Karolinska Institutet ------------------------------------------------------- Hi Daniel, How are things in Stockholm - hope everything is well! I'm currently looking for postdocs and I was wondering if you happen to know anyone who might be interested to spend some time in New York to work on cancer genomics projects? Would be awesome if you could forward the job description if someone comes to mind. Postdoctoral Positions in New York (Bioinformatics/Cancer Genomics/Data analysis) We are seeking two motivated postdoctoral researchers to join our lab at Memorial Sloan Kettering Cancer Center in New York City. Our lab specializes in large-scale analysis of complex genomics data, and we are particularly interested in understanding the principles of tumor evolution and tumor immunogenicity, i.e. how tumors evolve genomically over time and how the immune system responds to the subclonal composition of a tumor. We also have extensive expertise in analyzing non-coding variation from whole genome sequencing data. Our lab maintains close collaborations with clinical investigators at the institute, providing us with rich genomic data sets and offering unique opportunities for computational biologists to have immediate impact on how cancer patients are being treated today. For further information visit weinholdlab.org. Relevant Qualifications PhD in Computational Biology, Bioinformatics, or related field Interest in cancer biology and genomics Experience analyzing NGS data Proficiency in R, MATLAB, or other programming languages (e.g. Python, Java, etc.) Solid understanding of molecular biology Experience with cloud computing/compute cluster environments is a plus Experience with TCGA/1000 Genomes/ENCODE or other genomics data is a plus Responsibilities Develop computational methods to analyze and integrate various genomics data types Use existing tools and pipelines to analyze large-scale cancer genomics data (whole genome/exome, RNA-Seq, CHiP-Seq, etc.) Communicate research findings to collaborators and the scientific community at large Successful candidates will pursue their research projects in a highly collaborative environment. Memorial Sloan Kettering Cancer Center is consistently ranked as one of the leading cancer center in the world. Our main campus occupies three city blocks in the heart of New York City, next to The Rockefeller University and Weill Cornell Medicine. Within this tri-institutional research and education community, postdocs can cultivate rewarding collaborations and participate in a rich agenda of academic, professional, and social events. Compensation is highly competitive and includes health insurance and other benefits. Informal inquiries and applications should be addressed to Nils Weinhold (weinholn at mskcc.org)