From awe at signatur.dk Mon Oct 9 14:54:37 2017 From: awe at signatur.dk (Alan Wervick) Date: Mon, 9 Oct 2017 14:54:37 +0200 Subject: [SocBiN] PhD in computational disease systems biology at The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen Message-ID: PhD in computational disease systems biology PhD in computational disease systems biology A number of PhD positions are available in the Translational Disease Systems Biology group at The Novo Nordisk Foundation Center for Protein Research (CPR – www.cpr.ku.dk). The Center was established at the Faculty of Health and Medical Sciences, University of Copenhagen, to promote basic and applied discovery research on human proteins of medical relevance. The Center comprises a wide range of expertise and resources including proteomics, protein production, bioinformatics and general characterization of disease mechanisms. The Programme for Disease Systems Biology (DSB) consists of two research groups covering many systems level aspects of biology and medicine, including the integration of molecular-level data and healthcare data, for example laboratory test data and biomedical texts. The Translational Disease Systems Biology group ( www.cpr.ku.dk/research/disease-systems-biology/brunak/) part of DSB and led by Søren Brunak, focuses on establishing early competitive advantages in disease-relevant computational analyses across the general areas of bioinformatics, chemoinformatics, systems biology and medical informatics. *Job description* The PhDs will work in a multidisciplinary project team. One candidate will work in the EU-ToxRisk consortium, a H2020-funded pan-European research consortium, aiming at delivering strategies to enable reliable animal-free hazard and risk assessment of chemicals. One goal of the EU-ToxRisk consortium is to integrate advancements in system biology and computational modeling to define the complex chains of events that link chemical exposure to toxic outcome. Another candidate will work on data-driven models of temporal disease development using a combination of molecular data and data from the healthcare sector, where the latter has the form of clinical, registry data or complete electronic patient records. These models will in part be descriptive and show how different diseases and diagnosis follow each other over long periods and in part predictive in the sense that longitudinal patterns of illnesses, medication and procedures will indicate future events. The models may be augmented by molecular level biomarker data from genomics or proteomics further increasing the predictive power. Prior knowledge of disease classification schemes and standard vocabularies is an advantage. The candidates will focus on data analysis using computational systems biology methods. The candidates will utilize data integration, statistical genetics and pathway-based methods to identify novel biomarkers associated to toxicology. *Qualifications * The candidates hold a master degree or equivalent in biology, genetics, statistics, computational biology, bioinformatics or a related discipline of biomedical research. Preferably, the candidates have experience in statistical genetics, genomics, computational chemistry and knowledge of R. Programming experience is an advantage as is having worked with big data. Research experience in chemical toxicology is a plus. Furthermore, the successful candidates have experience within some of the following areas: - Bioinformatics and systems biology at the molecular level - Experience with toxicology - Medicine, pharmacology or genomics - Project management of interdisciplinary research projects within translational bioinformatics - Experience with data structures, databases, and data architectures - Knowledge of biomedical resources and infrastructures - Competences within statistics and/or machine learning techniques - Broad understanding of Healthcare data from national registries and electronic patient records from hospitals - Prior research experience with healthcare terminologies, schemes and ontologies, e.g. ICD9, ICD10, ATC, and SNOMED CT - Experience with CDISC The translational disease systems biology group is highly multidisciplinary and collaborates with many other research groups nationally and internationally. Strong networking and team player skills are therefore preferred. *Place of employment and work * The employment is at CPR (www.cpr.ku.dk), University of Copenhagen, located in central Copenhagen. The research environment at CPR is ambitious and international, with approx. 30 different nationalities currently represented. The Center comprises modern laboratories, supercomputer resources and state-of-the-art facilities within protein science. The Center organizes seminars with high-profile international speakers and regular internal research seminars. The selected candidate should expect some travel activity. For more information on working and living in Denmark, visit www.ism.ku.dk (International staff mobility) and www.workingconditions.ku.dk. *Salary and terms of employment * The duration of the positions is three years. It is conditioned upon the candidates´ successful enrollment in the PhD programme. This requires submission and acceptance of an application for the specific project formulated by the candidate. The PhD study must be completed in accordance with The Ministerial Order on the PhD programme (2013) and the University’s rules on achieving the degree. Salary, pension and terms of employment are in accordance with the agree­ment between the Ministry of Finance and The Danish Confederation of Professional Associations on Academics in the State. Depending on seniority, the monthly salary begins around 26,000 DKK (ca. 3.450 EUR) plus 17% pension. The Danish Ministry of Finance and the Danish Confederation of Professional Associations (AC) have agreed on a protocol that makes it possible for all international researchers employed by the University to achieve a pension exemption, where the pension will be paid as salary. For more information about the different pension schemes: http://ism.ku.dk/onarrival/pension/ *Further information * For further information, please contact Nanna Birch, nanna.birch at cpr.ku.dk. *Application procedure* Your application must be submitted electronically by clicking ‘Apply now’ below or via http://employment.ku.dk/faculty/ Your application should include the following documents: 1. Motivated letter of application 2. Curriculum vitae, incl. education and experience, publications (if any), language skills and other skills relevant for the position 3. A certified/signed copy of Master of Science certificate. If not completed, a certified/signed copy of a recent transcript of records or a written statement from the institution or supervisor will do 4. Names and contact details for two referees *Deadline for application: October 31th 2017 * After the expiry of the deadline for applications, the authorized recruitment manager selects applicants for assessment on the advice of the Appointments Committee. All applicants are then immediately notified whether their application has been passed for assessment by an expert assessment committee. Selected applicants are notified of the composition of the committee and each applicant has the opportunity to comment on the part of the assessment that relates to the applicant him/herself. Assessment: The selected applications will be assessed according to the Ministry Order on the Appointment of Academic Staff at Universities 2012 and the University of Copenhagen’s guidelines 2013. The Assessment Committee makes a non-prioritized assessment of the academic qualifications and experience with respect to the above mentioned area of research, techniques, skills and other requirements listed in the advertisement. You can read about the recruitment process at www.employment.ku.dk CPR and the University of Copenhagen wish to reflect the diversity of society and welcome applications from all qualified candidates regardless of personal background. *APPLY NOW * https://candidate.hr-manager.net/ApplicationInit.aspx?cid=1307&ProjectId=145955&DepartmentId=18997&MediaId=4636&SkipAdvertisement=true Part of the International Alliance of Research Universities (IARU), and among Europe’s top-ranking universities, the University of Copenhagen promotes research and teaching of the highest international standard. Rich in tradition and modern in outlook, the University gives students and staff the opportunity to cultivate their talent in an ambitious and informal environment. An effective organisation – with good working conditions and a collaborative work culture – creates the ideal framework for a successful academic career. -------------- next part -------------- An HTML attachment was scrubbed... URL: From torognes at ifi.uio.no Thu Oct 12 10:41:07 2017 From: torognes at ifi.uio.no (=?utf-8?Q?Torbj=C3=B8rn_Rognes?=) Date: Thu, 12 Oct 2017 10:41:07 +0200 Subject: [SocBiN] Call for NCMM Group Leader Positions in Precision Medicine and Systems Medicine - PLS DISTRIBUTE Message-ID: Call for NCMM Group Leader Positions in Precision Medicine and Systems Medicine - PLS DISTRIBUTE Dear Friends and Colleagues. I am contacting you as the Director of NCMM. NCMM is part of the Nordic EMBL Partnership and has a model such as the EMBL with recruitment of young group leaders in the area of molecular and translational medicine internationally for 5+4 years non-tenured positions with a generous start-up package and the possibility of starting new groups. In Oslo this serves as a green house for bringing forward young new faculty after international recruitment. We now have an open group leader call this fall for two positions with attractive start-up packages in the areas of Precision Medicine and Systems Medicine. I enclose the full announcement texts below. The key part of the text that defines the profile of candidates for each position is: Precision Medicine: “...candidates with experience in and a research programme focusing on precision medicine and individualized diagnostics and therapy in areas such as genetic and rare diseases (including pediatric diseases and in-born errors of metabolism, immunology and infection, neurology a.o.), and/or individualized cancer therapy.” Systems Medicine: “...candidates with experience in and a research programme on medical bioinformatics, computational biology and modelling or systems biology focussed on human organ system physiology and pathophysiology.” We are looking for outstanding young candidates with good upward trajectory and a clear vision for where they want to go with their ambitious research programmes. PLEASE FORWARD to relevant candidates and CIRCULATE in relevant fora and mailing lists. Best regards, Kjetil CALLS: HOW TO APPLY: https://www.jobbnorge.no/en/available-jobs/job/141940/group-leader-position-with-start-up-package-in-precision-medicine https://www.jobbnorge.no/en/available-jobs/job/142442/group-leader-position-with-start-up-package-in-systems-medicine Kjetil Taskén, Professor of Medicine, M.D., Ph.D.; Director, Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo and Oslo University Hospital; Director, The Biotechnology Centre of Oslo, University of Oslo; P.O. Box 1125, Blindern N-0317 Oslo NORWAY email: kjetil.tasken at ncmm.uio.no Web: www.ncmm.uio.no -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: CALL-NCMM-Grl-Systems-Medicine.pdf Type: application/pdf Size: 111774 bytes Desc: not available URL: -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: CALL-NCMM-Grl-Precision-Medicine.pdf Type: application/pdf Size: 111658 bytes Desc: not available URL: -------------- next part -------------- An HTML attachment was scrubbed... URL: From arne at bioinfo.se Thu Oct 12 17:42:36 2017 From: arne at bioinfo.se (Arne Elofsson) Date: Thu, 12 Oct 2017 17:42:36 +0200 Subject: [SocBiN] Fwd: News and postdoc positions In-Reply-To: References: <4C37A363-F96D-4ACA-B16B-E73CA6435D0D@epfl.ch> Message-ID: Patrick Barth wriites: I moved to EPFL a few weeks ago and I just wanted to give you my new contact info. Things are exciting here with great support, scientific interactions all within a wonderful environment! We have affiliation with the Ludwig Institute for Cancer Research in Lausanne and we are also in close contact with the Brain Mind Institute at EPFL. This proximity enables us to link our research on signaling receptors to important neurobiological and cancer immunotherapeutic applications and we are already setting up a few collaborations. I am in the process of building my lab here and I will be posting a few ads for postdoc positions (computational and experimental, see attached). I am looking for motivated and talented people and I would be grateful to you if you could pass along the info to suitable candidates in the bioinformatics and membrane protein structure/function communities. EPFL provides a truly international environment, start of the art facilities and very generous postdoc salaries. The area of Lausanne has become one of the major European hubs for biomedical start-ups and there are many job opportunities in industries around here. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: UPBarth_post-doc_compbiology.pdf Type: application/pdf Size: 22373 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: UPBarth_post-doc_proteindesign.pdf Type: application/pdf Size: 22011 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: UPBarth_post-doc_compbiophys.pdf Type: application/pdf Size: 21869 bytes Desc: not available URL: From kjetil.tasken at ncmm.uio.no Thu Oct 12 02:40:15 2017 From: kjetil.tasken at ncmm.uio.no (Kjetil Tasken) Date: Thu, 12 Oct 2017 00:40:15 +0000 Subject: [SocBiN] Call for NCMM Group Leader Positions in Precision Medicine and Systems Medicine - PLS DISTRIBUTE Message-ID: <18FCA999-1BD3-422C-BFB7-F3372F7EFFF5@ncmm.uio.no> Call for NCMM Group Leader Positions in Precision Medicine and Systems Medicine - PLS DISTRIBUTE Dear Friends and Colleagues. I am contacting you as the Director of NCMM. NCMM is part of the Nordic EMBL Partnership and has a model such as the EMBL with recruitment of young group leaders in the area of molecular and translational medicine internationally for 5+4 years non-tenured positions with a generous start-up package and the possibility of starting new groups. In Oslo this serves as a green house for bringing forward young new faculty after international recruitment. We now have an open group leader call this fall for two positions with attractive start-up packages in the areas of Precision Medicine and Systems Medicine. I enclose the full announcement texts below. The key part of the text that defines the profile of candidates for each position is: Precision Medicine: “...candidates with experience in and a research programme focusing on precision medicine and individualized diagnostics and therapy in areas such as genetic and rare diseases (including pediatric diseases and in-born errors of metabolism, immunology and infection, neurology a.o.), and/or individualized cancer therapy.” Systems Medicine: “...candidates with experience in and a research programme on medical bioinformatics, computational biology and modelling or systems biology focussed on human organ system physiology and pathophysiology.” We are looking for outstanding young candidates with good upward trajectory and a clear vision for where they want to go with their ambitious research programmes. PLEASE FORWARD to relevant candidates and CIRCULATE in relevant fora and mailing lists. Best regards, Kjetil CALLS: HOW TO APPLY: https://www.jobbnorge.no/en/available-jobs/job/141940/group-leader-position-with-start-up-package-in-precision-medicine https://www.jobbnorge.no/en/available-jobs/job/142442/group-leader-position-with-start-up-package-in-systems-medicine Kjetil Taskén, Professor of Medicine, M.D., Ph.D.; Director, Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo and Oslo University Hospital; Director, The Biotechnology Centre of Oslo, University of Oslo; P.O. Box 1125, Blindern N-0317 Oslo NORWAY email: kjetil.tasken at ncmm.uio.no Web: www.ncmm.uio.no -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: CALL-NCMM-Grl-Systems-Medicine.pdf Type: application/pdf Size: 111774 bytes Desc: not available URL: -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: CALL-NCMM-Grl-Precision-Medicine.pdf Type: application/pdf Size: 111658 bytes Desc: not available URL: -------------- next part -------------- An HTML attachment was scrubbed... URL: From krogh at binf.ku.dk Tue Oct 17 11:27:08 2017 From: krogh at binf.ku.dk (Anders Krogh) Date: Tue, 17 Oct 2017 11:27:08 +0200 Subject: [SocBiN] Postdoc position in Bioinformatics of Bacterial Resistance, deadline Oct 30 Message-ID: Hi, I have a postdoc position. http://employment.ku.dk/faculty/?show=145895 Please help me spread the word. Best wishes, - Anders -- Anders Krogh Professor krogh at binf.ku.dk - The Bioinformatics Centre Dept of Biology, University of Copenhagen Ole Maaloes Vej 5, 2200 Copenhagen, Denmark Ph. +45 3532 1329 Dept +45 3532 3710 www.binf.ku.dk From olofem at kth.se Thu Oct 19 10:57:16 2017 From: olofem at kth.se (Olof Emanuelsson) Date: Thu, 19 Oct 2017 10:57:16 +0200 Subject: [SocBiN] Course announcement - Analysis of data from high-throughput molecular biology experiments (fall 2017) NB! short notice! In-Reply-To: <5693B8A8.3090504@kth.se> References: <5693B8A8.3090504@kth.se> Message-ID: Dear SocBiN, Dear SciLifeLab, We, Lars Arvestad (SU), Lukas Käll (KTH), and Olof Emanuelsson (KTH), will give a course named "Analysis of data from high-throughput molecular biology experiments" 7.5hp, course code BB2490, starting 30 October 2017 and finishing 15 January 2018. The course starts really soon, but we have some seats for PhD students left! The course will cover how to analyze (i) massively parallel sequencing data (e.g., assembly, RNA-seq, ChIP-seq) and (ii) mass spectrometry data (e.g., peptide identification and quantification, post-translational modifications). There are 12 lectures, 4 computer exercises, 3 seminars, and one project. The project is done in groups of 3 students, with real data and the results will be presented in poster format at a "poster session" towards the end of the course. We require student presence and active participation at most events. This is also a master level course offered at the School of Biotechnology master programs. Hence, most of the activities will take place at the KTH-AlbaNova campus. The official course plan is available here: http://www.kth.se/student/kurser/kurs/BB2490?l=en_UK If you're a PhD student interested in taking this course, first talk to your supervisor to find out if it fits into your course package. This year we also ask you to suggest a project, based on your (or your PI's) own data. Note, however, that the project will be done in groups (see above), so it must be a project where your PI approves of other (most likely master level) students get access to the data and involved in the analysis. Note also that the project will have to be approved by the course leaders, this will be decided before the project start 24 November. Email a short motivation (absolutely max 1/2 A4 page) of why you would like to participate, and a short description (absolutely max 1/2 A4 page) of the project that you suggest. Please note that the number of participants is limited. Please email your application to olofem at kth.se as soon as possible (and at the very latest by noon Wednesday 25 October), by replying to this email and keeping the Subject line intact. This is the 8:th time this course is given, and you may very well have a course alumnus in your vicinity. The course is given by the School of Biotechnology at KTH in collaboration with Science for Life Laboratory and NGI, National Genomics Infrastructure. Welcome with your application! Lars Arvestad (lars.arvestad at scilifelab.se), Olof Emanuelsson (olofem at kth.se), Lukas Käll (lukas.kall at scilifelab.se) From jing.tang at helsinki.fi Thu Oct 19 17:40:39 2017 From: jing.tang at helsinki.fi (Tang, Jing) Date: Thu, 19 Oct 2017 15:40:39 +0000 Subject: [SocBiN] Postdoc and PhD positions at Institute for Molecular Medicine Finland, University of Helsinki Message-ID: <8e6b8c9f14a24425b883f3103da65058@helsinki.fi> Dear all, I have one Postdoc and one PhD student openings to develop computational and statistical methods for predicting and testing drug combinations in cancer. More details and application links can be found at: https://www.fimm.fi/en/research/groups/tang Please help spread the word to those potentially interested. Best, Jing Jing Tang, PhD, Group leader, Docent in Biometry Quantitative Systems Pharmacology Institute for Molecular Medicine Finland, University of Helsinki, Finland Department of Mathematics and Statistics, University of Turku https://www.fimm.fi/en/research/groups/tang -------------- next part -------------- An HTML attachment was scrubbed... URL: From anders at thep.lu.se Fri Oct 20 14:50:13 2017 From: anders at thep.lu.se (=?UTF-8?Q?Anders_Irb=c3=a4ck?=) Date: Fri, 20 Oct 2017 14:50:13 +0200 Subject: [SocBiN] Job opening in systems biology Message-ID: <1470ceff-e01f-6a6c-9a67-1129cc4a2e83@thep.lu.se> Dear all, We are looking to fill an opening for a tenure track position at Computational Biology and Biological Physics, Lund in systems biology. For more information, see: https://lu.mynetworkglobal.com/en/what:job/jobID:156447/type:job/where:4/apply:1 Best regards, Anders Irbäck (anders at thep.lu.se) Mattias Ohlsson (mattias at thep.lu.se) From vidya.velagapudi at helsinki.fi Fri Oct 27 11:01:16 2017 From: vidya.velagapudi at helsinki.fi (Velagapudi, Vidya) Date: Fri, 27 Oct 2017 09:01:16 +0000 Subject: [SocBiN] (Bio)-informatician/statistician position Message-ID: <5348FF41-1182-4789-9377-591A624C7F3F@helsinki.fi> Dear all, (Bio)-informatician/statistician position is available in our Metabolomics Unit. For more details, please see here https://www.helsinki.fi/en/open-positions/post-doctoral-researcher-in-bio-informaticsstatistics Kindly share within your networks. Thank you. BR Vidya ----------------------------------------------------------------------------------------------------- A/Prof. Vidya Velagapudi, Ph.D, Docent, Principal Investigator, Faculty of Medicine, University of Helsinki, Head of Metabolomics Unit, Institute for Molecular Medicine FIMM, Chair of Metabolomics Platforms, Biocenter Finland and HiLIFE, P.O Box-20, Helsinki-00014, Finland. Phone: 00358503175087, Website: https://www.fimm.fi/en/services/technology-centre/metabolomics ----------------------------------------------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: From Carsten.Daub at ki.se Thu Oct 26 09:28:28 2017 From: Carsten.Daub at ki.se (Carsten Daub) Date: Thu, 26 Oct 2017 07:28:28 +0000 Subject: [SocBiN] Call for applications to the Swedish National Graduate School in Medical Bioinformatics References: <8406adcc-120f-4a57-b55a-2b6e23c3a738@Spark> Message-ID: Call for applications to the Swedish National Graduate School in Medical Bioinformatics Begin forwarded message: From: Samuel Flores > Subject: Please forward widely: Call for applications to the Swedish National Graduate School in Medical Bioinformatics Date: 18 October 2017 at 13:54:42 CEST Dear Colleagues, The Swedish National Graduate School in Medical Bioinformatics (MedBioInfo) provides courses, soft-skills workshops, and networking in Medical Bioinformatics for PhD students enrolled or soon to enroll in a relevant program at any Swedish University. MedBioInfo has 36 affiliated faculty from 12 universities -- nearly all of the leading Bioinformatics teachers in Sweden. We limit enrollment to 20 incoming students per year, in order to maintain a low student/faculty ratio. By pooling resources and students, we are able to offer more courses at a higher level of specialization than any one university can provide. Students are assigned a faculty mentor to provide career and scientific advice supplementary to that of their advisor. I am pleased to announce that MedBioInfo is now accepting applications for our 2018 incoming class. The deadline for application is Feb 28 2018. You can read more about MedBioInfo here, and apply here. There is a preference for students beginning the PhD between January 2017 and April 2018, and an effort to maintain the geographical and improve the gender balance. For aspiring students who do not yet have a PhD position, there are two MedBioInfo-affiliated openings in the Arne Elofsson Lab. The project uses deep learning for various aspects of protein structure prediction. These two students will be automatically admitted to MedBioInfo. For details on those positions, contact arne at bioinfo.se . I very much appreciate your consideration in forwarding this announcement and attached flyer for posting on all relevant email lists, or to potentially interested individuals. Current MedBioInfo faculty and students, please forward to your departmental email lists. 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 26a 171 65 Solna SWEDEN Mobil: +46.706000464 skype: samuelfloresc QQ: 3236579471 -------------- next part -------------- An HTML attachment was scrubbed... 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