From nicosia at dmi.unict.it Sat Apr 2 12:22:09 2016 From: nicosia at dmi.unict.it (Giuseppe Nicosia) Date: Sat, 2 Apr 2016 12:22:09 +0200 Subject: [SocBiN] SSBSS 2016 - Application Deadline is Approaching - Call for Oral Presentations/Posters: 8-14 July 2016, Volterra (Pisa) Tuscany, Italy - 3rd Int. Synthetic & Systems Biology Summer School - Early Application: April 26, 2016 Message-ID: <8AE8EF20-7558-47E8-AAEA-600E1110ECE5@dmi.unict.it> ______________________________________________________ Call for Participation (apologies for multiple copies) ______________________________________________________ 3rd International Synthetic and Systems Biology Summer School - SSBSS 2016, 8-14 July 2016, Volterra (Pisa) - Tuscany, Italy *** New Speaker: Edoardo Boncinelli, Universita' Vita-Salute San Raffaele, Milano, Italy *** ssbss.school at gmail.com http://www.taosciences.it/ssbss/ https://www.facebook.com/ssbss.school/ https://twitter.com/SchoolSsbss EARLY APPLICATION DEADLINE: April 26, 2016 http://www.taosciences.it/ssbss/#application-form The Synthetic and Systems Biology Summer School (SSBSS) is a full-immersion five-day residential summer school at the Volterra Learning Center (Pisa - Tuscany, Italy) on cutting-edge advances in systems and synthetic biology with lectures delivered by world-renowned experts. The school provides a stimulating environment for students (from Master students to PhD students), Post-Docs, early career researches, academics and industry leaders. Participants will also have the chance to present their results (with Oral Talks and Posters), and to interact with their peers, in a friendly and constructive environment. SSBSS 2016 DEADLINES: Early Application: April 26, 2016 Notification Acceptance: from 2 to 28 April 2016 Late Application: from May 1st, to July 4th 2016 Notification Acceptance: from May 6th 2016 according to registration time Early Short Talk/Poster Submission: April 26, 2016 Notification Acceptance: from 2 to 28 April 2016 Late Short Talk/Poster Submission: from May 1st, to July 4th 2016 Notification of Decision for Oral/Poster Presentation: from May 6, 2016 according to submission time http://www.taosciences.it/ssbss/#application-form FINAL LIST OF SPEAKERS * Yaakov (Kobi) Benenson, Synthetic Biology Group at Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland Lecture 1: The practice of mammalian synthetic biology Lecture 2: Mammalian cell classifiers * Leonidas Bleris, Bioengineering Department, The University of Texas at Dallas, USA Lecture 1: Genome Editing Technologies and Therapeutic Modalities Lecture 2: Benchmark Circuits and Topological Properties * Edoardo Boncinelli, Universita’ Vita-Salute San Raffaele, Milano, Italy Lecture: TBA * Domitilla Del Vecchio, Department of Mechanical Engineering, MIT, USA Lecture 1: Modularity in genetic circuits: Dream versus Reality Lecture 2: Engineering Modularity in Genetic Circuits * Diego Di Bernardo, Dept of Chemical Materials and Industrial Production Engineering University of Naples "Federico II", Naples, Italy Lecture 1: "Engineering and Control of Biological Circuits in Yeast" Lecture 2: "Engineering and Control of Biological Circuits in Mammalian Cells * Barbara Di Ventura, Synthetic Biology Group, BioQuant/DKFZ, Heidelberg, Germany Lecture 1: Using blue light to control protein localization in living mammalian cells Lecture 2: Using split inteins for protein engineering in living cells * Jonathan S. Gootenberg, Feng Zhang and Aviv Regev Groups, Department of Systems Biology, Harvard Medical School, Harvard University, USA Lecture 1: "Discovering and Characterizing CRISPR effectors" Lecture 2: "Probing Biology with CRISPR Screening" * Markus Herrgard, Technical University of Denmark - Biosustain, Novo Nordisk Foundation Center for Biosustainability, Denmark Lecture 1: "Developing an Integrated Cell Factory Design Tool" Lecture 2: "Using Automated Laboratory Evolution to Optimize Cell Factories” * Shalev Itzkovitz, Department of Molecular Cell Biology, Weizmann Institute of Science, Israel Lecture 1: "Single Molecule Approaches for Studying Gene Expression in Intact Mammalian Tissues" Lecture 2: "Systems Biology of Stem Cell-Maintained Tissues” * Francesco Ricci, Dipartimento di Scienze e Tecnologie Chimiche, University of Rome Tor Vergata, Rome, Italy Lecture 1: "DNA Nanotechnology Tools and Reactions for Synthetic Biology" Lecture 2: "Nature-inspired DNA-based Nanodevices Next Generation Sequencing Workshop – Afternoon July 12th, 2016 * “How fast can we align sequences?” Mario Guarracino, CNR, Italy * “Advanced Bioinformatics tools for NGS” – TBC Luca Zammataro, Yale University, USA Tutorials: * “Detection and analysis of contaminating sequences in NGS sequencing data” Ilaria Granata, CNR, Italy * “Detection and interpretation of circular RNAs in RNA-seq experiments” Parijat Tripathi, CNR, Italy SSBSS 2016 DIRECTORS Diego Di Bernardo, TeleThon Institute of Genetics & Medicine - TIGEM and University of Napoli "Federico II", Italy Giuseppe Nicosia, University of Catania, Italy Luca Zammataro, Yale University, USA MORE INFORMATION ssbss.school at gmail.com http://www.taosciences.it/ssbss/ https://www.facebook.com/ssbss.school/ https://twitter.com/SchoolSsbss Social event(s): social tour and dinner in Florence. Please help us distributing in your circles (emails, blogs, and social networks) the call for participation and call for oral talks/posters for SSBSS 2016. Together we will make SSBSS a great event! See you in Tuscany in July! Ludovico Montalcini - SSBSS 2016 Organizing Committee Chair -- Giuseppe Nicosia, Ph.D. Associate Professor of Computer Engineering Dept of Mathematics & Computer Science University of Catania Viale A. Doria, 6 - 95125 Catania, Italy P +39 095 7383048 nicosia at dmi.unict.it http://www.dmi.unict.it/nicosia ================================================================== 3rd International Synthetic & Systems Biology Summer School - SSBSS 2016 * Biology meets Computer Science & Engineering * July 8-14, 2016 - Volterra (Pisa), Tuscany, Italy http://www.taosciences.it/ssbss/ ================================================================== 2nd International Workshop on Machine learning, Optimization & big Data - MOD 2016 August 26-29, 2016 - Volterra (Pisa), Tuscany, Italy http://www.taosciences.it/mod/ ================================================================== -------------- next part -------------- An HTML attachment was scrubbed... URL: From Tanja.Slotte at scilifelab.se Thu Apr 7 14:16:40 2016 From: Tanja.Slotte at scilifelab.se (Tanja Slotte) Date: Thu, 7 Apr 2016 14:16:40 +0200 Subject: [SocBiN] Jobs: Bioinformatics - Evolutionary Genomics, SciLifeLab & Stockholm University Message-ID: Position in Bioinformatics / Evolutionary Genomics at Science for Life Laboratory and Stockholm University * A 2-year position in bioinformatics/evolutionary genomics, with possibility for extension, is available in the research group of Dr. Tanja Slotte, a SciLifeLab Fellow in Ecological Genomics (https://tanjaslottelab.se). * We address fundamental biological and evolutionary questions using advanced combinations of laboratory work and computational analyses - for recent examples of our work, see e.g. Slotte et al. 2013 Nature Genetics, Douglas et al 2015 PNAS, Steige et al 2015 MBE. The position * For us, bioinformatics is central to staying at the forefront at our field, and you will have a key position in our team, working closely together with group members all the way from planning experiments to final analyses and visualizations of results. * You will be part of a tight interdisciplinary team working with large-scale data analyses based on NGS sequencing and omics data from multiple technology platforms. * You will be part of the vibrant and growing bioinformatics community at SciLifeLab, and for knowledge transfer within SciLifeLab, you will also be affiliated with the National Bioinformatics Infrastructure Sweden (NBIS; www.bils.se, www.nbis.se). Qualifications * We seek a candidate with a PhD in bioinformatics or a related field who has strong competence in analyses of next-generation sequencing (NGS) data, and who has the ability to drive projects and collaborate productively with team members. * You need to be proficient in one or more scripting languages (e.g. Perl, Python, Ruby) and familiar with Unix environments. * Basic understanding of statistics and probability, or a background in population genomics/comparative genomics is beneficial, as this is a strong component of our work. * Experience of working with PacBio data is a merit. * Excellent organizational skills and communication skills in both written and spoken English are required. The environment * We are located at Science for Life Laboratories in Stockholm (http://www.scilifelab.se), which harbors world-leading expertise in high-throughput sequencing technology and bioinformatics. * The working atmosphere is international with English as the working language. The city of Stockholm is known for its beauty, its buildings and architecture and its abundant clean and open water. Application * Please apply online through the Stockholm University application system no later than April 30th: http://www.su.se/english/about/vacancies/vacancies-new-list?rmpage=job&rmjob=1389 * For questions about the position, please contact Dr. Tanja Slotte (tanja.slotte at su.se) Tanja Slotte, SciLifeLab Fellow in Ecological Genomics Department of Ecology, Environment and Plant Sciences Stockholm University Email: Tanja.Slotte at su.se; Tanja.Slotte at scilifelab.se Visiting Address: SciLifeLab Stockholm Tomtebodav. 23 a 171 65 Solna SWEDEN From sofiak at kapsi.fi Mon Apr 11 07:46:07 2016 From: sofiak at kapsi.fi (sofiak at kapsi.fi) Date: Mon, 11 Apr 2016 08:46:07 +0300 Subject: [SocBiN] A master's thesis/internship project on NGS data handling, Helsinki Message-ID: Dear all, We are offering a master's thesis/internship project for one student in our lab located in Helsinki, Finland. The research group on hereditary breast cancer susceptibility is investigating the genetic background of breast cancer as well as breast and ovarian cancer by identifying genes and genetic variation for cancer development and progression. We have used exome sequencing to identify breast or ovarian cancer predisposing variants. Please see Kiiski JI et al. Exome sequencing identifies FANCM as a susceptibility gene for triple-negative breast cancer. Proc Natl Acad Sci U S A. 2014. Further information about the group: http://www.kll.helsinki.fi/groups/nevanlinna/ The aim of this project is to combine different whole exome sequencing batches (sequenced at different times) and one whole genome sequencing data set (extracting the exomes) to produce one combined data set that all the subsequent analyses will be based on. This would require performing the whole work-flow from raw data to variant calling and variant annotation. The successful candidate is a motivated student at more advanced stage of his/her studies in the field of bioinformatics or related field. The project also enables integrating Master's Thesis as a part of the work. Some knowledge of the basics of molecular biology would be desirable. Knowledge of bioinformatics tools for analysis of next-generation sequencing data would be a major plus. The position is initially for 3 to 4 months during the summer 2016. The starting date is negotiable. For further information about the project, please contact Sofia Khan (sofia.khan(at)helsinki.fi). Please send applications including cover letter, CV, and two references to sofia.khan(at)helsinki.fi by 17.4.2016. Best wishes, Sofia Khan Dept. of Obstetrics and Gynecology Helsinki University Central Hospital Biomedicum Helsinki P.O. BOX 700 00029 HUS Finland From albin at binf.ku.dk Mon Apr 11 11:33:50 2016 From: albin at binf.ku.dk (Albin Sandelin) Date: Mon, 11 Apr 2016 11:33:50 +0200 Subject: [SocBiN] Computational postdoc in transcriptomics Message-ID: Dear all. I am hiring a 2-3 computational postdoc to work on lncRNA analysis, including analysing FANTOM6 data. I would appreciate if you could share the link to promising candidates in your networks! http://jobportal.ku.dk/videnskabelige-stillinger/?show=818716 Best regards, 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 alexander.junge at gmail.com Tue Apr 12 13:09:07 2016 From: alexander.junge at gmail.com (Alexander Junge) Date: Tue, 12 Apr 2016 13:09:07 +0200 Subject: [SocBiN] Announcing CBioVikings Symposium on Tools for Reproducibility in Bioinformatics Message-ID: CBioVikings - ISCB Regional Student Group Denmark View this email in your browser Announcing CBioVikings Symposium on Tools for Reproducibility in Bioinformatics *Date:* April 21st 2016, 15:00-18:00 *Location:* Room A2-81.01 (3-01), Thorvaldsensvej 40, Frederiksberg, University of Copenhagen, Denmark *Sign up (by April 19th 2016):* http://goo.gl/forms/Pq5c0ES2NG *Synopsis: *This afternoon symposium will gather together researchers who are building and using open source tools to conduct reproducible science. We will discuss the advantages and difficulties with this approach, and will explore the best ways to implement it in practice. Refreshments will be served. This event is co-organized by IDA Biotechnology, the Danish Biotechnological Society (DBS) and CBioVikings - ISCB Regional Student Group Denmark. Event sponsors are intomics and Palantir. *Confirmed speakers Kai Blin* (Postdoc, Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark) Kai is an active contributor to many open source projects including Biopython and Samba, and is an advocate for open science approaches. His talk will discuss his personal approach to reproducible research. *Geoff Macintyre* (Research Associate, Cambridge Cancer Center, University of Cambridge, UK) Geoff is a computational biologist who models tumor evolution. His talk will focus on concrete ways in which reproducible science benefits the careers of the researchers who implement it. Full program will soon be available at: http://cbiovikings.org/events/upcoming/reproducibility.html *Why is reproducible research important to bioinformaticians?* It was reported last year that 50% of biomedical studies are not reproducible, and it may be the case that the percentage is even higher. The causes for not being able to reproduce research studies are numerous, but generally relate to a lack of documentation of materials, protocols, or study design. Regardless of the cause, the impacts of studies that cannot be verified are similar: they represent wasted funds and effort, and delay translation of research to the clinic. Reproducible analyses help to avoid these problems, since they can be easily rerun and verified by reviewers or third parties, and shared between research groups. Further, conducting research with a focus on reproducibility also gives direct benefits to the researchers themselves. For example, results can be brought more quickly up to date with less chance of human errors, which enables continuity on long term projects. Ultimately this means that higher quality science can be done faster. Since most bioinformatics analysis is done with computers, reproducibility initially seems like an easy goal to reach. However, in practice bioinformaticians face many barriers that prevent true reproducibility, such as versioning, data management, and documentation challenges. This symposium will focus on the tools that help overcome these challenges: languages like R and Python are used to script analyses, version control systems track changes between collaborators, documentation systems like knitR and Jupyter notebooks document analyses, and container systems like Docker deploy finished projects. Young researchers will learn how to implement these tools in their own research to the benefit of their own scientific development. References: http://whyopenresearch.org/ http://genomebiology.biomedcentral.com/articles/10.1186/s13059-015-0850-7 http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003285 *Sponsors* *intomics *- Visit their website at: https://www.intomics.com/ *Palantir *- Visit their website at: https://www.palantir.com/ Co-organizers: -------------- next part -------------- An HTML attachment was scrubbed... URL: From ari.loytynoja at helsinki.fi Wed Apr 13 10:17:50 2016 From: ari.loytynoja at helsinki.fi (=?UTF-8?Q?Ari_L=c3=b6ytynoja?=) Date: Wed, 13 Apr 2016 11:17:50 +0300 Subject: [SocBiN] POSTDOCTORAL POSITION (Helsinki) in Evolutionary Genomics In-Reply-To: <23C44FA0-049C-4D5A-A7A3-86AAE7DE634F@helsinki.fi> References: <23C44FA0-049C-4D5A-A7A3-86AAE7DE634F@helsinki.fi> Message-ID: <570E00AE.2060906@helsinki.fi> POSTDOCTORAL POSITION (Helsinki) in Evolutionary Genomics The postdoctoral researcher will be a part of the Ecological Genetics Research Unit (EGRU; http://www.helsinki.fi/biosci/egru/index.html) lead by Prof. Juha Merilä. The assignment can start in June 2016 (start date is flexible – early start preferred) and continue until end of December 2017. The post-doctoral fellow to be employed is expected to work with projects addressing broad and generally interesting problems relating to processes of population differentiation and genetics of adaptation as inferred from already available whole genome sequence datasets. The model system in these studies is the nine-spined stickleback (Pungitius pungitius) and its relatives, and their computational genome analysis is a collaboration with the bioinformatics group of Dr. Ari Löytynoja (http://www.biocenter.helsinki.fi/bi/loytynoja). An ideal candidate for this position would have a broad interest in evolutionary biology and a background in one or several of the following fields: bioinformatics, evolutionary genomics, statistical or population genetics/genomics, animal or plant breeding sciences. We are looking for an individual who is highly motivated and can work both independently and in a team. Capacity to face intellectual challenges, willingness to learn new skills, and to explore new intellectual territories are qualities expected from a strong candidate. A demonstrated track-record in research, and experience in bioinformatics analysis of next-generation sequencing data are required. An appointee to the position of post-doctoral researcher shall hold a doctoral degree, have the ability to conduct independent scholarly work. The working language will be English. An overview of our past and current research can be found at http://www.helsinki.fi/biosci/egru/index.html. The salary will be based on level 5 of the demands level chart for teaching and research personnel in the salary system of Finnish Universities. In addition, the appointee will bepaid a salary component based on personal work performance (total salary will be approximately 3050–3400 EUR per month). The application should include (i) CV, (ii) Publication list, (iii) statement of research interests and motivation for applying this position not exceeding two pages and (iv) contact information of two reference persons who have agreed to provide a written statement on behalf of the applicant. Applications should be addressed to the Department of Biological Sciences, P. O. Box 65 (Viikinkaari 1), FIN-00014 University of Helsinki, and sent to juha.merila at helsinki.fi. The deadline for applications is May 15 2016. More information on this position is available from Prof. Juha Merilä (e-mail: juha.merila at helsinki.fi). ............................................................. Juha Merilä Ecological Genetics Research Unit Department of Biosciences PO Box 65 (Biocenter 3, Viikinkaari 1) FIN-00014 University of Helsinki Finland E-mail: juha.merila at helsinki.fi Gsm: +358-(0)50-416 0561 Fax: +358-9-19157694 www: http://www.helsinki.fi/biosci/egru/ ResearchGate: https://www.researchgate.net/profile/Juha_Merilae?ev=hdr_xprf Publons: https://publons.com/author/341551/juha-merila#profile .............................................................. From juho.rousu at aalto.fi Thu Apr 14 12:35:22 2016 From: juho.rousu at aalto.fi (Rousu Juho) Date: Thu, 14 Apr 2016 10:35:22 +0000 Subject: [SocBiN] CFP: Machine Learning in Systems Biology, 10th international Workshop Message-ID: <7A08D77F-7777-4EB5-B6FC-9D6EF0B9D209@aalto.fi> Call for Papers & Highlight track abstracts: 10th International Workshop Machine Learning in Systems Biology (MLSB-2016) Organized as a ECCB pre-conference workshop, September 3-4, 2016, World Forum, The Hague, Netherlands SUMMARY Biology is rapidly turning into an information science, thanks to enormous advances in the ability to observe the molecular properties of cells, organs and individuals. This wealth of data allows us to model molecular systems at an unprecedented level of detail and to start to understand the underlying biological mechanisms. This field of systems biology creates a huge need for methods from machine learning, which find statistical dependencies and patterns in these large-scale datasets and that use them to establish models of complex molecular systems. MLSB is a scientific forum for the exchange between researchers from Systems Biology and Machine Learning, to promote the exchange of ideas, interactions and collaborations between these communities. TARGET AUDIENCE The aim of this workshop is to contribute to the cross­-fertilization between the research in machine learning methods and their applications to systems biology (i.e., complex biological and medical questions) by bringing together method developers and experimentalists. WORKSHOP TOPICS (NON EXHAUSTIVE) Methods: Active learning/Experimental design, Bayesian Methods, Clustering/Biclustering, Data integration/fusion/multi­-view learning, Feature/subspace selection, Graph inference/completion, Kernel Methods, Machine Learning Algorithms, Multi­task/Structured output prediction, Probabilistic inference, Semi­-supervised learning, Systems identification, Time­-series analysis Applications: Biomarker identification, Epigenetics, Genome­-wide association studies, Metabolic modeling and reconstruction, Metabolomics, Protein function and structure prediction, Protein­-protein interaction networks, Rational drug design methods, Regulatory genomics, Sequence Annotation, Signaling networks, Synthetic biology IMPORTANT DATES May 30, 2016: Full length manuscript submission May 30, 2016: Highlight track abstract submission June 30, 2016: Decision notifications for manuscripts and abstracts July 20, 2016: Final camera-ready manuscript submission August 19, 2016: Registration deadline September 3-4, 2016: Workshop INVITED SPEAKERS Prof. Ziv Bar­-Joseph, School of Computer Science Carnegie­-Mellon University, USA Prof. Jukka Corander, Department of Mathematics and Statistics, University of Helsinki, Finland Prof. Lodewyk Wessels, The Delft Bioinformatics Lab, Delft University of Technology, The Netherlands Prof. Yvan Saeys, VIB Inflammation Research Center, Ghent University, Belgium SUBMISSIONS We encourage submissions bringing forward methods for discovering complex structures (e.g. interaction networks, molecule structures), statistical machine learning methods for analysis of various high-throughput ­omics data, and methods supporting systems­-level data analysis. The submissions are organized into the following two tracks: 1. Manuscripts (preferentially up to 5000 words) describing original work on machine learning in systems biology. These should describe method development and applications broadly in the topics listed above (see Workshop topics). Accepted proceedings track papers will be published in BMC Bioinformatics. The publications need to match the standards of the journal; please prepare your submissions using the BMC instructions (http://www.bioinformatics.nl/MLSB2016/BMC_guidelines.pdf). The publication is subject to open access fee (special reduced price negotiated by MLSB). 2. Highlights Track abstracts (1­-2 pages) describing computational aspects of work that has been recently published in a journal (or are “in press”) as well as unpublished/on-going work. Submissions will be evaluated by at least three reviewers from an international programme committee of experts in the field. The most relevant and most original submissions will be accepted as full oral presentations and/or as poster presentations at the workshop. Submission is through the Easychair system: https://easychair.org/conferences/?conf=mlsb2016 REGISTRATION Registration via the general ECCB2016 registration system http://www.eccb2016.org/registration/ PROGRAMME COMMITTEE Antti Airola Chloé-Agathe Azencott Alexis Battle Michael A. Beer Andreas Beyer Karsten Borgwardt Céline Brouard Gal Chechik Chao Cheng Manfred Claassen Florence D’Alché-buc Dick de Ridder Saso Dzeroski Pierre Geurts Markus Heinonen James Hensman Lars Kaderali David Knowles Stefan Kramer Anshul Kundaje Harri Lähdesmäki François Laviolette Christina Leslie Hiroshi Mamitsuka Martin Renqiang Min Yves Moreau Alan Moses Sara Mostafavi Bernard Ng Mahesan Niranjan William Noble Uwe Ohler Tapio Pahikkala Nico Pfeifer Gerald Quon Magnus Rattray Juho Rousu Yvan Saeys Guido Sanguinetti Li Shen Motoki Shiga Oliver Stegle Koji Tsuda Giorgio Valentini Aalt-Jan van Dijk Jinbo Xu From daginge.vage at nmbu.no Mon Apr 25 12:31:40 2016 From: daginge.vage at nmbu.no (=?iso-8859-1?Q?Dag_Inge_V=E5ge?=) Date: Mon, 25 Apr 2016 10:31:40 +0000 Subject: [SocBiN] Vacant position - Systems engineer/developer, biology knowledge databases. Ref.no 16/01768 Message-ID: <83361f1c01c4474db1d2e09d816f7a8f@EXCH-MBX04.NMBU.NO> Hi, We would like to announce a one-year positon as Systems engineer/developer, biology knowledge databases. For more information: https://www.jobbnorge.no/en/available-jobs/job/125041/systems-engineer-developer-biology-knowledge-databases-refno-16-01768 Closing date: May 11, 2016 Regards Dag Inge Våge Department of Animal and Aquacultural Sciences/CIGENE Norwegian University of Life Sciences P.O. Box 5003 NO-1432 Ås Norway Phone: +47 6723 2703 -------------- next part -------------- An HTML attachment was scrubbed... URL: From iamb at genesilico.pl Mon Apr 25 14:31:59 2016 From: iamb at genesilico.pl (Janusz Bujnicki) Date: Mon, 25 Apr 2016 14:31:59 +0200 Subject: [SocBiN] Positions in RNA bioinformatics, Bujnicki lab in IIMCB, Warsaw In-Reply-To: <83361f1c01c4474db1d2e09d816f7a8f@EXCH-MBX04.NMBU.NO> References: <83361f1c01c4474db1d2e09d816f7a8f@EXCH-MBX04.NMBU.NO> Message-ID: <571E0E3F.1050103@genesilico.pl> Dear All, Two PhD student positions in RNA bioinformatics (one focused on 3D structure modeling, and one focused on data mining and evolutionary analyses) are available in my group in IIMCB, Warsaw, Poland Please distribute to anyone you think might be interested. Feel free to contact me for more information. Thank you and best regards, Janusz Bujnicki -------------------------------------------------- Two PhD student positions in RNA bioinformatics are available in the Bujnicki group in IIMCB, Warsaw, Poland We are looking for junior scientists with energy and passion, interested in bioinformatics, software development and biological data analysis, and motivated to develop a successful career in an interdisciplinary and international team. 1) PhD-soft: You will develop computer software for RNA 3D structure prediction and modeling, building on our successful tools, including ModeRNA and SimRNA. Our big goal is to model RNA-ligand interactions towards the development of new drugs, and to design new RNA molecules that bind to selected ligands. You must have skills in programming: C/C++ or Python (you will need to learn and use both). Experience in bioinformatics or any type of molecular modeling will be an advantage, but is not essential. 2) PhD-data: You will analyze RNA sequences and structures, and develop online databases. Our big goal is to solve the mysteries of evolution of all RNA molecules, develop new ways to classify RNA sequences and structures, and present our results online via databases and servers. You must have skills in analyzing biological sequences or in database/website development (you will need to learn and use both). Experience in molecular phylogenetics analyses will be an advantage, but is not essential. About us: • We are an interdisciplinary team that combines basic science (to solve the mysteries of nature) and applied science (to make the discoveries practically useful). In our laboratory, software developers meet with experimental biologists, and high-throughput data analysis combines with sophisticated studies of individual biomacromolecules. We have a wild ambition: to understand the structure of all RNA molecules that exist, and design molecules that do not exist yet. We develop new computational methods, new tools for biotechnology, and molecules that will hopefully become drugs against diseases! • We are driven towards publication and application of our results. Our recent focus and biggest successes are in computational and experimental analyses of RNA and protein-RNA complexes. For examples, see: Smietanski et al. Nature Commun 2014, Boniecki et al. Nucleic Acids Res 2015, Matelska et al. Genome Biol Evol 2016. We also develop databases that are widely used, such as the MODOMICS database of RNA modification pathways. Check out http://genesilico.pl for details. • We are hosted by IIMCB (http://iimcb.gov.pl), the top-ranked (A+) Polish research institute in biology. The institute provides cutting-edge equipment and facilities, in particular for bioinformatics (e.g. a computing cluster with >2000 cores), experimental molecular biology, and structural biology. We offer: • Focused scientific projects with well-defined goals that balance safety (high chance to generate publishable results quickly) and big challenges (high risk and high gain). • Flexible PhD studies with 100% focus on research (no teaching obligations). • Unique environment for junior scientists to work in a top research center, develop skills in bioinformatics, and gain experience in analyzing real biological data. • A chance to collaborate with and learn from extraordinary, exceptional, and eccentric ;-) experts. • Participation in courses, scientific training, support from peers, and academic mentoring • Individual thesis advisory committee, with top international experts. • Basic funding (3000 PLN/month, PhD fellowship or contract for specific work) to start full time work between June and October 2016, guaranteed for 4 years • Opportunity and support to compete for additional funding from grants. How to apply: • We will collect applications until May 15th. • Apply now to employment at genesilico.pl • Best candidates will be given additional questions and tasks before the final interview. • Please include "PhD-soft" or "PhD-data" and your first and last name in the email subject. • Your application must be in English and should contain a CV, a motivation letter (Why do you want to work with us? What are your key strengths? How can you contribute?), and contacts to at least two potential referees, including at least one former or current direct supervisor. • The application must contain the following statement to allow us to process your data: "I hereby give consent for my personal data included in the job offer to be processed for the purposed of recruitment under the Data Protection Act 1997 (Dz. U. 2002 no. 101, item 926 with subs. changes)." / "Wyrażam zgodę na przetwarzanie danych osobowych w celach rekrutacji zgodnie z ustawą z dnia 29 sierpnia 1997 r. o ochronie danych osobowych (tekst jedn.: Dz U. z 2002 r. Nr 101, poz 926 z późn. zm.)." • If need be, we may continue recruitment until suitable candidates are found. From sdh at genesilico.pl Wed Apr 27 22:47:03 2016 From: sdh at genesilico.pl (Stanislaw Dunin-Horkawicz) Date: Wed, 27 Apr 2016 22:47:03 +0200 Subject: [SocBiN] PhD student and postdoc positions available Message-ID: <665EB7BD-F719-41E6-9E4E-2184DC78544C@genesilico.pl> Hello, two positions in structural bioinformatics (protein design) are available. Localization: University of Warsaw (http://cent.uw.edu.pl/en), Poland Details: http://cent.uw.edu.pl/en/node/3285 http://cent.uw.edu.pl/en/node/3281 Best wishes, Staszek Dr. Stanislaw Dunin-Horkawicz University of Warsaw (Centre of New Technologies) S. Banacha 2c 02-097 Warsaw From nicosia at dmi.unict.it Fri Apr 29 09:24:11 2016 From: nicosia at dmi.unict.it (Giuseppe Nicosia) Date: Fri, 29 Apr 2016 09:24:11 +0200 Subject: [SocBiN] SSBSS 2016: Call for Oral Presentations/Posters: 9-13 July 2016, Volterra (Pisa) Tuscany, Italy - 3rd Int. Synthetic & Systems Biology Summer School - Early Application: May 26, 2016 Message-ID: <4DFEA7D9-540C-46C3-AAA3-272F61D6BD84@dmi.unict.it> _________________________________________________________________________ Call for Participation (apologies for multiple copies) Please help forward it to other potentially interested attendees, thanks! _________________________________________________________________________ 3rd International Synthetic and Systems Biology Summer School - SSBSS 2016, 9-13 July 2016, Volterra (Pisa) - Tuscany, Italy ssbss.school at gmail.com http://www.taosciences.it/ssbss/ https://www.facebook.com/ssbss.school/ https://twitter.com/SchoolSsbss EARLY APPLICATION DEADLINE: May 26, 2016 http://www.taosciences.it/ssbss/#application-form The Synthetic and Systems Biology Summer School (SSBSS) is a full-immersion five-day residential summer school at the Volterra Learning Center (Pisa - Tuscany, Italy) on cutting-edge advances in systems and synthetic biology with lectures delivered by world-renowned experts. The school provides a stimulating environment for students (from Master students to PhD students), Post-Docs, early career researches, academics and industry leaders. Participants will also have the chance to present their results (with Oral Talks and Posters), and to interact with their peers, in a friendly and constructive environment. SSBSS 2016 DEADLINES: Early Application: May 26, 2016 Notification Acceptance: from April 2 to 28 May 2016 Late Application: from May 27, to July 4th 2016 Notification Acceptance: from May 28th 2016 according to registration time Early Short Talk/Poster Submission: May 26, 2016 Notification Acceptance: from 2 April to 28 May 2016 Late Short Talk/Poster Submission: from May 27, to July 4th 2016 Notification of Decision for Oral/Poster Presentation: from May 28, 2016 according to submission time http://www.taosciences.it/ssbss/#application-form FINAL LIST OF SPEAKERS * Yaakov (Kobi) Benenson, Synthetic Biology Group at Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland Lecture 1: The practice of mammalian synthetic biology Lecture 2: Mammalian cell classifiers * Leonidas Bleris, Bioengineering Department, The University of Texas at Dallas, USA Lecture 1: Genome Editing Technologies and Therapeutic Modalities Lecture 2: Benchmark Circuits and Topological Properties * Edoardo Boncinelli, Universita’ Vita-Salute San Raffaele, Milano, Italy Lecture: TBA * John Cumbers, Founder SynBioBeta, Mountain View, CA, USA Lecture: Synthetic Biology: new tools for an industry at an inflection point. * Domitilla Del Vecchio, Department of Mechanical Engineering, MIT, USA Lecture 1: Modularity in genetic circuits: Dream versus Reality Lecture 2: Engineering Modularity in Genetic Circuits * Diego Di Bernardo, Dept of Chemical Materials and Industrial Production Engineering University of Naples "Federico II", Naples, Italy Lecture 1: "Engineering and Control of Biological Circuits in Yeast" Lecture 2: "Engineering and Control of Biological Circuits in Mammalian Cells * Barbara Di Ventura, Synthetic Biology Group, BioQuant/DKFZ, Heidelberg, Germany Lecture 1: Using blue light to control protein localization in living mammalian cells Lecture 2: Using split inteins for protein engineering in living cells * Jonathan S. Gootenberg, Feng Zhang and Aviv Regev Groups, Department of Systems Biology, Harvard Medical School, Harvard University, USA Lecture 1: "Discovering and Characterizing CRISPR effectors" Lecture 2: "Probing Biology with CRISPR Screening" * Markus Herrgard, Technical University of Denmark - Biosustain, Novo Nordisk Foundation Center for Biosustainability, Denmark Lecture 1: "Developing an Integrated Cell Factory Design Tool" Lecture 2: "Using Automated Laboratory Evolution to Optimize Cell Factories” * Shalev Itzkovitz, Department of Molecular Cell Biology, Weizmann Institute of Science, Israel Lecture 1: "Single Molecule Approaches for Studying Gene Expression in Intact Mammalian Tissues" Lecture 2: "Systems Biology of Stem Cell-Maintained Tissues” * Francesco Ricci, Dipartimento di Scienze e Tecnologie Chimiche, University of Rome Tor Vergata, Rome, Italy Lecture 1: "DNA Nanotechnology Tools and Reactions for Synthetic Biology" Lecture 2: "Nature-inspired DNA-based Nanodevices Next Generation Sequencing Workshop – Afternoon July 12th, 2016 * “How fast can we align sequences?” Mario Guarracino, CNR, Italy * “Advanced Bioinformatics tools for NGS” – TBC Luca Zammataro, Yale University, USA Tutorials: * “Detection and analysis of contaminating sequences in NGS sequencing data” Ilaria Granata, CNR, Italy * “Detection and interpretation of circular RNAs in RNA-seq experiments” Parijat Tripathi, CNR, Italy SSBSS 2016 DIRECTORS Diego Di Bernardo, TeleThon Institute of Genetics & Medicine - TIGEM and University of Napoli "Federico II", Italy Giuseppe Nicosia, University of Catania, Italy Luca Zammataro, Yale University, USA MORE INFORMATION ssbss.school at gmail.com http://www.taosciences.it/ssbss/ https://www.facebook.com/ssbss.school/ https://twitter.com/SchoolSsbss Social event(s): social tour and dinner in Florence. Please help us distributing in your circles (emails, blogs, and social networks) the call for participation and call for oral talks/posters for SSBSS 2016. Together we will make SSBSS a great event! See you in Tuscany in July! More Info: ssbss.school at gmail.com http://www.taosciences.it/ssbss/ -- Giuseppe Nicosia, Ph.D. Associate Professor of Computer Engineering Dept of Mathematics & Computer Science University of Catania Viale A. Doria, 6 - 95125 Catania, Italy P +39 095 7383048 nicosia at dmi.unict.it http://www.dmi.unict.it/nicosia ================================================================== 3rd International Synthetic & Systems Biology Summer School - SSBSS 2016 * Biology meets Computer Science & Engineering * July 8-14, 2016 - Volterra (Pisa), Tuscany, Italy http://www.taosciences.it/ssbss/ ================================================================== 2nd International Workshop on Machine learning, Optimization & big Data - MOD 2016 August 26-29, 2016 - Volterra (Pisa), Tuscany, Italy http://www.taosciences.it/mod/ ================================================================== -------------- next part -------------- An HTML attachment was scrubbed... URL: From lro at cbs.dtu.dk Fri Apr 29 18:54:18 2016 From: lro at cbs.dtu.dk (=?utf-8?Q?Lars_R=C3=B8nn_Olsen?=) Date: Fri, 29 Apr 2016 18:54:18 +0200 Subject: [SocBiN] Three fellow positions at University of Oxford References: Message-ID: Three 5 year MRC bioinformatics fellowships are offered at the Weatherall Institute for Molecular Medicine in Oxford. The fellowships are suitable for postdocs looking to establish independent research groups in genomics and proteomics - single cell analysis is of particular interest. Deadline: noon, May 18. https://www.recruit.ox.ac.uk/pls/hrisliverecruit/erq_jobspec_version_4.jobspec?p_id=122980 Lars Rønn Olsen, PhD Assistant Professor, Center for Biological Sequence Analysis, Technical University of Denmark Visiting researcher, MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford M: (+45) 28734892 E: lro at cbs.dtu.dk | lars.olsen at rdm.ox.ac.uk W: www.young-alliance.org L: www.linkedin.com/in/larsronnolsen -------------- next part -------------- An HTML attachment was scrubbed... URL: From andreas.lennartsson at ki.se Sat Apr 30 11:53:59 2016 From: andreas.lennartsson at ki.se (Andreas Lennartsson) Date: Sat, 30 Apr 2016 09:53:59 +0000 Subject: [SocBiN] fellow position at Karolinska Institute Message-ID: <2162B7E9E131804BA3A00D2D1110A1E5FF35AD70@KIMSX01.user.ki.se> Dear all, I am recruiting a postdoc for analysis of epigenomics and transcriptomics in acute myeloid leukemia (AML), see link. https://ki.mynetworkglobal.com/en/what:job/jobID:98037/where:4/ I would be grateful, if you can share the add with potential candidates. best regards /Andreas Andreas Lennartsson, PhD Research Associate Karolinska Institutet Department of Biosciences and Nutrition Hälsovägen 7 SE-14183 Huddinge, Sweden -------------- next part -------------- An HTML attachment was scrubbed... URL: