From arne at bioinfo.se Thu Aug 6 16:52:55 2015 From: arne at bioinfo.se (Arne Elofsson) Date: Thu, 6 Aug 2015 07:52:55 -0700 Subject: [SocBiN] Fwd: Principal & research scientist positions at genomics core lab in Saudi Arabia In-Reply-To: <5D1F334B-0BDC-480B-8C9A-D83D1B37D3E3@scilifelab.se> References: <5D1F334B-0BDC-480B-8C9A-D83D1B37D3E3@scilifelab.se> Message-ID: From: Mikael Huss The Genomics Core Laboratory (NGS/qPCR) at King Abdullah University of Science and Technology are recruiting for several positions, including a principal scientist (group head) and a research scientist (see attachments for descriptions of the positions). The web page of the university is http://www.kaust.edu.sa/ -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 20150726_Principal Scientist at Genomic Core Facility.odt Type: application/vnd.oasis.opendocument.text Size: 9813 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 20150726_Research_Scientist_at_Genomic_Core_Lab.odt Type: application/vnd.oasis.opendocument.text Size: 10664 bytes Desc: not available URL: From paolo.romano at hsanmartino.it Mon Aug 10 08:59:08 2015 From: paolo.romano at hsanmartino.it (Paolo Romano) Date: Mon, 10 Aug 2015 08:59:08 +0200 Subject: [SocBiN] NETTAB IB 2015: Selected oral communications list available Message-ID: Dear all, the list of selected oral communications for next NETTAB and Integrative Bioinformatics 2015 joint meeting (October 14-16, 2015, Bari, Italy) is now available. Date and time of presentations will be communicated early in September. A quick remind for next deadlines: - Submission of abstracts for posters and software demos: September 7, 2015 - Early registration: September 17, 2015 All updated information at http://www.igst.it/nettab/2015/ . I'm looking forward to meeting you in Bari on October 14-16, 2015. Best regards. Paolo Romano (==) Oral Communications * Taxonomic and functional metagenomic analysis of anodic communities in two pilot-scale microbial fuel cells treating different industrial wastewaters Larisa Kiseleva, Sofya K. Garushyants, Hongwu Ma, David J. W. Simpson, Viatcheslav Fedorovich, Michael F. Cohen and Igor Goryanin * Machine Learning approach to discriminate Saccharomyces cerevisiae yeast cells using sophisticated image features Mohamed Tleis and Fons Verbeek * RetroMine, or how to provide in-depth retrospective studies from Medline in a glance: The hepcidin use-case Bertrand Ameline de Cadeville, Olivier Loréal and Fouzia Moussouni-Marzolf * OpenLabNotes – An Eletronic Laboratory Notebook Extension for OpenLabFramework Markus List, Michael Franz, Qihua Tan, Jan Mollenhauer and Jan Baumbach * Managing and Documenting Legacy Scientific Workflows Ruben Acuna, Jacques Chomilier and Zoe Lacroix * A semantic-based metadata validation for an automated High-Throughput Screening workflow: Case study in CytomicsDB Enrique Larios Vargas, Zhihan Xia, Joris Slob and Fons Verbeek * Clustering, Querying, and Updating Biological Sequences with CLAST Vicente Molieri, Lina Karam and Zoe Lacroix * The LAILAPS plant science search engine: Explore plant genome databases Jinbo Chen, Christian Colmsee, Uwe Scholz and Matthias Lange * WISE: Workflow Instrumentation for Structure Extraction and Semantic Mapping Ruben Acuna and Zoe Lacroix * Differential analysis of gene networks in chemical perturbations Francesca Mulas and Stefano Monti * Bioinformatic and Genomic technologies to uncover inter-varietal structural variation in grape genome Maria Francesca Cardone, Pietro D’Addabbo, Can Alkan, Carlo Bergamini, Claudia Rita Catacchio, Fabio Anaclerio, Giorgia Chiatante, Annamaria Marra, Rocco Perniola, Giuliana Giannuzzi, Mario Ventura and Donato Antonacci * Prediction and simulation of multi-target therapies for triple negative breast cancer through a network-based data integration approach Francesca Vitali, Angela Amato, Alberto Zambelli and Riccardo Bellazzi * Integrating Gene Regulatory Networks to identify cancer-specific genes Valeria Bo, Dimple Chudasama, Emmanouil Karteris and Allan Tucker * MSA-PAD: Novel DNA Multiple Sequence Alignment Guided by PFAM Conserved Domains Bachir Balech, Saverio Vicario, Giacinto Donvito, Alfonso Monaco, Pasquale Notarangelo and Graziano Pesole * Improving the Prediction of miRNA:mRNA Interactions by Exploiting Co-Clustering Methods Gianvito Pio, Michelangelo Ceci, Domenica D’Elia and Donato Malerba * MetaShot: a complete workflow for the characterization of human microbiome from shotgun metagenomic data Bruno Fosso, Monica Santamaria, Domenica Lovero, Giacomo Corrado, Enrico Vizza, N Passaro, Marco Crescenzi and Graziano Pesole * Phenomics validation of the Escherichia coli underground metabolic reconstruction Claudio Angione * Identification of functional interaction between Transcription Factors and their targets: a computational approach focused on lncRNA Marika Catapano, Elena Grassi, Ivan Molineris and Paolo Provero * In silico prediction of lncRNA function Umberto Perron, Paolo Provero and Ivan Molineris * Comparison between heuristic and statistical analysis on protein structural properties Eugenio Del Prete, Serena Dotolo, Anna Marabotti and Angelo Facchiano -- Paolo Romano (paolo.romano at hsanmartino.it) Bioinformatics IRCCS AOU San Martino - IST National Cancer Research Institute Largo Rosanna Benzi, 10, I-16132, Genova, Italy Tel: +39-010-555-8288 -------------- next part -------------- An HTML attachment was scrubbed... URL: From rune.linding at gmail.com Sun Aug 16 18:58:30 2015 From: rune.linding at gmail.com (Rune Linding) Date: Sun, 16 Aug 2015 18:58:30 +0200 Subject: [SocBiN] Fwd: 3 year postdoc fellowship in cancer genomics (UK) In-Reply-To: References: Message-ID: ---------- Forwarded message ---------- From: Pedro Beltrao Date: Thu, Aug 13, 2015 at 5:11 PM Subject: 3 year postdoc fellowship in cancer genomics (UK) To: Cc: Martin Miller Dear colleague, My group, along with the groups of Martin Miller and Pippa Corrie are looking for applicants for a 3 year postdoctoral fellowship. The general theme of the project is to study the mutational properties that associate with anti-tumour immune response. We are looking for applicants with past experience in bioinformatics and genomics and an interest in cancer and evolution. We would appreciate if you could forward this to members of your group that might be interested. The deadline for this call is already on the 3rd of September. Details can be found here: http://www.evocellnet.com/2015/08/ebpod-postdoctoral-fellowship-to-study.html and here: http://www.ebi.ac.uk/research/postdocs/ebpods Thank you in advance of your help best regards Pedro & Martin -------------- next part -------------- An HTML attachment was scrubbed... URL: From erik.sonnhammer at scilifelab.se Tue Aug 25 13:19:25 2015 From: erik.sonnhammer at scilifelab.se (Erik Sonnhammer) Date: Tue, 25 Aug 2015 13:19:25 +0200 Subject: [SocBiN] Fwd: Call for Abstracts for 1:st International Conference on Pharmaceutical Bioinformatics, Pattaya, Thailand, January 24-26, 2016 In-Reply-To: <8c53f5d1d9b2443aafdb5bb13943f94d@ebox-prod-srv12.win.su.se> References: <8c53f5d1d9b2443aafdb5bb13943f94d@ebox-prod-srv12.win.su.se> Message-ID: <55DC4F3D.5070906@scilifelab.se> -------- Forwarded Message -------- Subject: Call for Abstracts for 1:st International Conference on Pharmaceutical Bioinformatics, Pattaya, Thailand, January 24-26, 2016 Resent-Date: Mon, 24 Aug 2015 08:35:47 +0200 Resent-From: erik.sonnhammer at dbb.su.se Date: Sat, 22 Aug 2015 04:12:51 +0000 From: Jarl Wikberg Reply-To: Jarl Wikberg To: farmbio-bioinformatics at lists.uu.se Dear Colleague, On behalf of the ICPB2016 organizing committee we would like to invite you to submit an Abstract for Oral or Poster Presentation at the 1:st International Conference on Pharmaceutical Bioinformatics to be held in Pattaya, Thailand, during January 24-26, 2016. Pharmaceutical Bioinformatics is an area dedicated to the development of informatics and computational methods that can drive drug discovery and development effectively forward. As you know genomics and high throughput methods has given great promises to the accelerated discovery and development of new drugs. Unfortunately, it has turned out very difficult to translate the wealth of information into practical results. Contrary to what one could have expected, less drugs are now discovered at ever increasing costs, in spite of these advances having made the opportunities almost limitless. The way to remedy this is the development of informatics and computational methods that really translates the wealth of biomedical knowledge into clinically useful drugs. Pharmaceutical Bioinformatics collects this into an umbrella, merging fields such as predictive sciences, cheminformatics, bioinformatics, mathematical statistics, molecular modeling and clinical modeling, and is thus truly multidisciplinary attracting scientists from virtually all areas including biomedicine, chemistry, pharmacy and informatics. For abstract submission and participation in the conference please visit: http://icpb.net. We welcome you to be a part of this exciting event ICPB2016 as a Delegate/Speaker. Kindly contact us for any sort of further assistance. Sincerely, Jarl Wikberg, MD, PhD Professor of Pharmaceutical Pharmacology Head of Pharmaceutical Bioinformatics at Uppsala University Department of Pharmaceutical Biosciences Uppsala University Sweden email: Jarl.Wikberg at farmbio.uu.se Chanin Nantasenamat, PhD Associate Professor Head of Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology, Mahidol University Thailand email: chanin.nan at mahidol.edu Conference site and contact: Web: www.icpb.net Mail: admin at icpb.net -------------- next part -------------- An HTML attachment was scrubbed... URL: From Inge.Jonassen at ii.uib.no Tue Aug 25 14:07:41 2015 From: Inge.Jonassen at ii.uib.no (Inge Jonassen) Date: Tue, 25 Aug 2015 14:07:41 +0200 Subject: [SocBiN] PhD position in bioinformatics and systems biology Message-ID: <38957398-6CDC-4D4B-9A43-399BFF145307@ii.uib.no> We have an open PhD student position in bioinformatics and systems biology. For more information and for submitting your application, see http://www.jobbnorge.no/en/available-jobs/job/116582/phd-position-in-bioinformatics-and-systems-biology or contact me :-) Please also pass on to potential applicants. Inge --- Inge Jonassen, Prof PhD Head of Node, Elixir Norway Computational Biology Unit Department of Informatics University of Bergen HiB N5020 Bergen Norway inge at ii.uib.no -------------- next part -------------- An HTML attachment was scrubbed... URL: From matti.kankainen at helsinki.fi Wed Aug 26 16:24:36 2015 From: matti.kankainen at helsinki.fi (Matti Kankainen) Date: Wed, 26 Aug 2015 17:24:36 +0300 Subject: [SocBiN] Postdoctoral research fellow position at the Institute of Biotechnology, University of Helsinki Message-ID: <366AD016-FB99-4401-A894-ADA5EC5E31E2@helsinki.fi> Postdoctoral research fellow position at the forefront of digital health revolution at the Institute of Biotechnology, University of Helsinki A postdoctoral research fellow position is available from September 2015 in the laboratory of prof. Liisa Holm at the University of Helsinki to develop algorithms for sequence analysis and their application to microbial community transcriptomic data from clinical samples. The position is suitable for an experienced and highly motivated computational research scientist and provides an opportunity to work as part of a collaborative team of top Finnish clinicians, geneticists, translational medicine experts, next-generation sequencing specialists, and microbiologists aiming to revolutionize infection control and develop a clinically relevant next-generation sequencing-based solution for the early recognition and personalized treatment of hospital acquired infections. Our preferred candidate has a strong background in computer science, systems biology, or bioinformatics. Strong programming skills and experience with Linux, statistical analysis, and software development are essential. The candidate must be fluent in written and spoken English, be able to communicate efficiently in an interdisciplinary team, and have excellent communication and presentation skills. A background in microbiology or experience in sequence analysis is an advantage. The research takes place at the Institute of Biotechnology (BI), an independent research institute of University of Helsinki located at the Viikki campus 10 km east from the center of Helsinki, and involves frequent visits to the University of Helsinki Meilahti campus in western Helsinki. The position is funded by a grant from the Academy of Finland and initially for 2 years with an option for continuation, depending on performance. The salary for this post is based on level 5 of the job requirement level chart for research staff in the University Salary System. In addition to the requirement level component, the successful applicant will be paid a personal work performance component. The post will have a trial period of three months. For more information, please contact prof. Holm (liisa.holm at helsinki.fi) or Dr. Kankainen (matti.kankainen at helsinki.fi). To apply for the position, please send your motivation letter and CV, including list of publications and contact information for two references, to prof. Holm. Apply at the latest 25.9.2015. Matti Kankainen, Ph.D NGS bioinformatics team leader FIMM - Institute for Molecular Medicine Finland P.O. BOX 20, FI-00014 University of Helsinki, Finland +358 50 5636960, matti.kankainen at helsinki.fi www.fimm.fi -------------- next part -------------- An HTML attachment was scrubbed... URL: From coordinator at rth.dk Fri Aug 28 09:48:54 2015 From: coordinator at rth.dk (Betina Wingreen Jensen) Date: Fri, 28 Aug 2015 09:48:54 +0200 Subject: [SocBiN] 2nd Announcement: Danish National workshop on non-coding RNA, Oct 7, 2015 Message-ID: <002d01d0e165$fd095c60$f71c1520$@rth.dk> Dear All, We are delighted to announce the Danish National Workshop on non-coding RNA, which will take place on Oct 7, 2015, 10.00-14:35 at University of Copenhagen, The Ceremonial Hall, Frue Plads 4, 1168 Copenhagen. Keynote Speakers: Ronald Breaker, Yale University & Bruce Sullenger, Duke University Medical Center. Other speakers include: Morten Sommer, Torben Heick Jensen and Anders Lund. Provisional Programme: 10:00:10.05 Welcome Carsten Hjort, Novozymes / Jan Gorodkin, University of Copenhagen 10:05-10:20 Introduction to non-coding RNAs Jørgen Kjems, Aarhus University 10:20-10:35 RNA bioinformatics: an overview Jan Gorodkin, University of Copenhagen 10:35-11:20 KEYNOTE: TBA Ron Breaker, Yale University 11:20-11:35 TBA Torben Heick Jensen, Aarhus University 11:35-11:50 TBA Anders Lund, University of Copenhagen 11:50-13:00 Lunch and coffee Break 13:00-13:45 KEYNOTE: TBA Bruce Sullenger, Duke University Medical Center 13:45-14:30 TBA Morten Sommer, The Technical University of Denmark 14:30-14:35 Closing Remarks Carsten Hjort, Novozymes / Jan Gorodkin, University of Copenhagen To register go to: http://rth.dk/trysingnup/ For further information please go to http://rth.dk/posts/national-workshop-on-non-coding-rna-174.php Kind regards, Betina -- Betina Wingreen Jensen Scientific and Administrative Coordinator Center for non-coding RNA in Technology and Health Department of Veterinary Clinical and Medical Sciences University of Copenhagen Groennegaardsvej 3 1870 Frederiksberg C Denmark Phone: +4535334704 Mob: +4521510932 -------------- next part -------------- An HTML attachment was scrubbed... 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