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    Archived pages: 51 . Archive date: 2014-11.

  • Title: neXtProt - exploring the universe of human proteins
    Descriptive info: .. Login.. or.. Sign up.. now!.. x.. loading.. close X.. Oooops, an error occured.. Home.. Recent activites.. My favorites.. My labels.. Downloads.. Or Sign up Now!.. Exploring the universe of human proteins.. Go.. everywhere.. name/identifier.. function.. localisation/interaction.. medical.. family.. domain.. sequence annotation.. publications.. has truc.. has function.. gold data only.. (.. e.. g.. look for insulin in all fields.. ,.. find all proteins located in the mitochondrion and expressed in liver.. ).. New to neXtProt?.. Brought to you by.. The Swiss Institute of  ...   Research.. A mutation in the UGT8 gene correlated with musical ability.. May 19, 2014.. Research news archives.. The SIB - Swiss Institute of Bioinformatics and GeneBio launch neXtProt knowledge platform on human proteins.. Apr 21, 2011.. Press news archives.. 14.. resources.. Selected and integrated.. UniProtKB/Swiss-Prot.. Bgee.. COSMIC.. Ensembl.. ENZYME.. GO.. HPA.. IntAct.. InterPro.. MeSH.. PeptideAtlas.. PROSITE.. PubMed.. SRMAtlas.. neXtProt release 2014-09-19.. 20,055.. Protein entries.. 141,546.. Controlled vocabularies.. 428,294.. Publications.. release details.. About neXtProt.. Contact us.. 2011 SIB & GeneBio.. Legal disclaimer.. All rights reserved..

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  • Title: neXtProt - exploring the universe of human proteins
    Descriptive info: Developed in collaboration between the.. SIB Swiss Institute of Bioinformatics.. and.. Geneva Bioinformatics (GeneBio) SA.. , neXtProt will be a comprehensive human-centric discovery platform, offering its users a seamless integration of and navigation through protein-related data.. Background.. In September 2008, the.. UniProt/Swiss-Prot.. group achieved the first complete manual annotation of what is believed to be the full set of human proteins (derived from about 20,000 genes).. This was a major milestone as this collection of data is already quite rich in information pertinent to modern biomolecular medical research.. But there remains a large gap in our knowledge of human proteins in terms of functional information as well as protein characterization (PTMs, protein/protein interactions, sub cellular locations, etc).. The SIB and GeneBio have joined their efforts and expertise to bring to you neXtProt that was designed to help researchers make sense of what all these human proteins do in our bodies.. At the SIB, neXtProt is developed in the.. CALIPHO.. (Computer Analysis and Laboratory Investigation of Proteins of Human Origin) group that was created jointly with the University of Geneva.. Headed by Amos Bairoch and Lydie Lane, CALIPHO is an interdisciplinary team which aims to use a variety of methodologies to help uncover the function of uncharacterized human proteins.. The development of neXtProt is carried out in close collaboration with the Swiss-Prot group, which was led by Professor Bairoch for 23 years, and with GeneBio.. The team is currently working on three different challenges:.. Adding more information to the corpus of data on human proteins that is already in Swiss-Prot.. In addition to all the data available in Swiss-Prot on human proteins, data originating from a variety of high-throughput approaches (such as micro-array, antibodies screens, proteomics, interactomics, structural genomics) are being added to neXtProt.. All of these data sets are carefully selected so as to only provide high-quality data.. More data will be integrated into neXtProt.. In the short and medium term this will include:.. High-quality proteomics experimental data.. siRNA experimental data.. 3D experimental data.. Pathway data.. Population-related variant information.. Protein-protein and protein-drug interaction data.. Organizing the data in such a way that it is possible to seamlessly build powerful queries in the most user-friendly way possible.. Developing software tools ranging from sequence analysis to text and data mining to be integrated in various research environments.. These tools will meet the specific needs of both academic and industrial users.. Our vision.. "A journey of a thousand miles begins with a single step.. ".. Lao-Tzu, Chinese philosopher (604 BC - 531 BC).. You are now using the public beta release of neXtProt.. This is the beginning of what we hope will be a long journey.. We invite you to join  ...   data.. This is why the neXtProt data integration philosophy is based on a three-tier system:.. Gold - included.. By default searches will only consider gold-level data.. Silver – included, but not shown in searches unless specified by user.. Bronze - excluded.. However, we cannot annotate all these high-throughput data sets alone.. We need to capitalize on the high-quality databases and bioinformatics resources maintained by dedicated groups worldwide.. These collaborations will be key to the success of neXtProt.. We already want to thank the groups of Mathias Uhlen (HPA from KTH-Stockholm) and Marc Robinson-Rechavi (Bgee from SIB Lausanne) who allowed us to make use of their excellent protein and mRNA expression resources.. We are in discussion with many other groups that have carried out such filtering and cleaning up tasks in fields such as interactomics, proteomics or phylogenomics, to name a few.. We are convinced that the comprehensive biocuration of human proteins is a participative endeavor.. It is with this goal in mind that we have built neXtProt as a web-based participative platform and we will need to ask for your contribution very soon.. We want to convince you that investing some of your time in an altruistic manner will be good for the community and therefore also good for you!.. Data is useful, but we want neXtProt to be much more than a well-organized comprehensive data repository.. In addition to enhanced search capabilities, we want to offer tools that will help to make sense of the contents.. Some of these tools will be sequence-based (we already offer Blast and will soon add a multiple alignment option), but we want to go beyond sequence into the realm of the semantic analysis of protein lists.. The big challenge is to be able to understand how a given set of proteins share or differ in their various features.. This is far from being trivial and here we also want to collaborate.. We will also offer APIs to allow our users to develop tools that will benefit from neXtProt’s clean and high-quality data.. Ultimately, our goal is to be able to offer the capability of modeling hypotheses within neXtProt.. This perhaps sounds a bit ambitious! Maybe it is, but we want you to take this first step and begin to take part in this collaborative journey.. Start by using this beta release of neXtProt and tell us what features you like or what you dislike about it.. Enjoy your journey!.. Amos Bairoch and the neXtProt team at the Swiss Institute of Bioinformatics and GeneBio.. Contact details.. CMU - Rue Michel-Servet 1.. 1211 Geneva.. Switzerland.. Tel : +41 22 379 5050.. 25 avenue de Champel.. 1206 Geneva.. Tel: +41 22 702 99 00..

    Original link path: /db/open/page/about-nextprot
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  • Title: The neXtProt HUPO2014 release | neXtProt
    Descriptive info: Skip to content.. Skip to footer.. Submitted on October 3, 2014.. For the.. 2014 HUPO international conference.. in Madrid (October 5-8, 2014) we deployed a new release of neXtProt with major data updates of interest to the proteomics community.. Noteworthy is:.. - The human complete proteome version of the.. is now public and we have integrated the mapping to the nearly 150'000 peptides that are available in this first public release.. We show these mapping in our proteomics view and we added a new "feature track" called "SRM Peptide" to display this information.. - Integration of the latest version of.. (from 2014-07-31), containing over 1 million peptides mapping  ...   new proteomics studies that have been re-analyzed and integrated in PeptideAtlas.. - neXtProt has nearly 34,000 post translational annotations obtained from the curation of research articles, and covering several different types of modifications: phosphorylation, N- and O-glycosylation, sumoylation, ubiquitylation, acetylation, and methylation.. neXtProt is being built as a participative platform and we look forward to receiving users' input for the future development of neXtProt.. Recent.. neXtProt and the human proteome project, news from HUPO 2013.. Release notes - neXtProt release Jan 2013.. New Publication: neXtProt: Organizing Protein Knowledge in the Context of Human Proteome Projects.. neXtProt version 3.. 0.. A new release of neXtProt.. neXtProt news archive.. Share..

    Original link path: /news/nextprot/2014-10-03/nextprot-hupo2014-release
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  • Title: neXtProt | neXtProt
    Descriptive info: Archive for neXtProt news.. Read more.. Submitted on September 24, 2013.. We are just back from the.. HUPO2013.. meeting, which took place in Yokohama from September 14th to 18th!.. Submitted on February 8, 2013.. New data.. - We have integrated data from two new resources: COSMIC (variants of somatic origin) and Peptide Atlas (peptide identifications of high quality);.. - Updated HPA to release 10;.. - Updated Bgee to release 12;.. -  ...   15, 2013.. neXtProt: Organizing Protein Knowledge in the Context of Human Proteome Projects.. Gaudet P, Argoud-Puy G, Cusin I, Duek P, Evalet O, Gateau A, Gleizes A, Pereira M, Zahn-Zabal M, Zwahlen C, Bairoch A, Lane L.. J Proteome Res.. 2013 Jan 4;12(1):293-8.. doi:10.. 1021/pr300830v.. Epub 2012 Dec 3.. PMID: 23205526.. Abstract.. Submitted on September 2, 2011.. Submitted on May 9, 2011.. A human-centric discovery platform.. Submitted on April 21, 2011..

    Original link path: /news/nextprot/archive
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  • Title: A mutation in the UGT8 gene correlated with musical ability | neXtProt
    Descriptive info: Submitted on May 19, 2014.. Music is universal.. It is an important communication tool in human populations, complementary to language.. Very young infants are able to process and respond to musical patterns before they can talk, suggesting that musical aptitude is an inborn property of human beings.. However, musical abilities such as recognizing music or singing in tune can substantially differ between individuals, from absolute pitch to amusia.. Whereas it is estimated that about 40 to 50% of our musical abilities are linked to genetics, the exact genes that may be responsible for musical talent remain to be discovered.. A.. genome-wide study.. conducted in a thousand of individuals from 73 families recruited in  ...   encodes an enzyme called UDP glycosyltransferase 8, which performs a key step in the production of galactosylceramides (or cerebrosides).. These complex lipids are particularly important for the development of central and peripheral nervous systems.. The variation that was found to be associated with musical abilities, the SNP.. rs4148254.. , changes amino acid 226 of the protein from proline to leucine and may affect its enzymatic function.. A mutation in the ABCC9 gene correlated with sleep duration.. Solving the mystery of missing fingerprints.. A single mutation in AKT1 responsible for Elephant Man s disfigurement.. Mutations in LAMC3 linked to occipital cortical development.. Mutations in SCN9A linked to both analgesia and anosmia.. Research news archive..

    Original link path: /news/research/2014-05-19/mutation-ugt8-gene-correlated-musical-ability
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  • Title: Research | neXtProt
    Descriptive info: Archive for research news.. Submitted on March 15, 2012.. Sleep is essential for surviving in all higher animals.. Humans sleep approximately a third of their lifetime, and too little or too much sleep was often found to be associated with metabolic or psychiatric disorders.. Sleep duration can be influenced by photoperiod and sleep time, and strongly depends on age and gender.. However, a genetic component is also strongly suspected since twin studies indicate as much as 40% heritability in  ...   ridges) are characteristic of the human skin.. They are widely used for identity check because their morphology remains permanent without any modification from their establishment at 24 weeks post-fertilization throughout lifespan.. Individuals completely missing fingerprints are extremely rare, but famous for encountering difficulties entering foreign countries.. That is why their condition, scientifically termed adermatoglyphia, was surnamed the "immigration delay disease".. Submitted on August 30, 2011.. Submitted on August 17, 2011.. Mutations in SYN1 linked to both epilepsy and autism..

    Original link path: /news/research/archive
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  • Title: The SIB - Swiss Institute of Bioinformatics and GeneBio launch neXtProt knowledge platform on human proteins | neXtProt
    Descriptive info: The SIB - Swiss Institute of Bioinformatics and GeneBio today announced the launch of neXtProt, an on-line knowledge platform centered on human proteins.. This exceptional resource provides life scientists with a broad spectrum of information on all human proteins via an intuitive interface.. With already over 25,000 unique visitors since its first Beta release in January of this year, neXtProt is expected to become the central resource for any life scientist who requires high-quality information on human proteins in the context of modern biomedical research.. The SIB and GeneBio’s scientists, developers and bio-curators, have been working closely together since 2009, under the leadership of Prof.. Amos Bairoch and Dr.. Lydie Lane, to address one of the major problems faced by life scientists today: making sense of the huge body of human protein-related data in order to facilitate knowledge creation and therefore scientific innovation.. High-quality content on human proteins.. At the content level, neXtProt aims to be a comprehensive resource on human proteins, including information such as proteins’ function, subcellular location, expression, interactions and role in diseases.. Rigorous standards are applied before any data is added to neXtProt, ensuring a commitment to the quality that the Swiss are renowned for.. Prof.. Bairoch says, “technological advances have allowed the life sciences to accumulate enormous amount of data.. It is therefore essential to provide researchers with the tools to fish out knowledge from such an ocean of data.. We are building neXtProt to answer such a challenge..  ...   favorites and tags.. More than a database, neXtProt is developed in the spirit of an open collaborative platform to foster collective intelligence.. GeneBio brings to this project the software development expertise and business acumen of its long-standing team.. Nasri Nahas, CEO of GeneBio, says, “neXtProt faces up to a major challenge our customers are experiencing by offering them the tools to turn large quantities of data into knowledge.. With second-to-none quality data and a set of intuitive features, we believe that this new product offering will enhance scientific discovery and innovation.. To achieve these ambitious goals, the neXtProt team is working closely with users in both academia and industry to develop features and include content the community requires.. In this context, the next major development goal is linked with our close collaboration with the Human Proteomics Organization (HUPO) in the support of the Human Proteomics Project (HPP).. HPP is a very important initiative whose goal is to produce a comprehensive catalog of all human proteins using various proteomics technologies.. The 10th Annual World Congress of HUPO will take place in Geneva on September 4 to 7, 2011.. During this conference, we will launch a new version of neXtProt that will address some of the needs of the proteomics community.. Collaborations are key to the success of neXtProt as only through data sharing and partnerships can researchers unlock the role of human proteins in health and disease.. Visit neXtProt at:.. www.. nextprot.. org.. Press news archive..

    Original link path: /news/press/2011-04-21/sib-swiss-institute-bioinformatics-and-genebio-launch-nextprot-knowledge-platf
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  • Title: Press | neXtProt
    Descriptive info: Press.. Archive for press releases..

    Original link path: /news/press/archive
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  • Title: Release contents
    Descriptive info: About.. Release contents.. Release statistics.. neXtProt release contents.. Database release.. :.. 2014-09-19.. Application release.. 3.. 24.. Data Release.. description.. UniProt knowledgebase Swiss-Prot section.. release.. 2014_09.. last import.. 2014-09-02.. BGee.. Database for gene expression evolution.. 12.. 2012-12-20.. Catalogue of somatic mutations in cancer.. v68.. 2014-05-18.. Ensembl human genome browser.. 75.. 2014-04-24.. Enzyme nomenclature database..  ...   interaction database.. 2014-07-18.. 2014-09-03.. Integrated resource of protein families, domains and functional sites.. 48.. Medical Subject Headings.. desc2014/2014-01-22.. 2014-01-22.. Peptides identified by mass spectrometry.. 201408.. 2014-08-20.. Protein domain and family database.. 20.. 107.. Citations for biomedical literature from MEDLINE, life science journals, and online books.. Targeted proteomics assays.. 2014-08-30.. UniProt-GOA.. Gene Ontology annotations.. 2014-07-08..

    Original link path: /db/statistics/release
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  • Title: neXtProt - exploring the universe of human proteins
    Descriptive info: Copyright notice for neXtProt.. neXtProt is developed in collaboration between the SIB Swiss Institute of Bioinformatics and Geneva Bioinformatics (GeneBio).. All intellectual property rights on neXtProt, belong to the SIB and GeneBio.. GeneBio owns the worldwide exclusive distribution rights on this intellectual property.. Copyright © 2010 SIB and GeneBio – All rights reserved.. Swiss Institute of Bioinformatics.. CMU, 1 Rue Michel-Servet, CH-1211 Geneva, Switzerland.. 25, Avenue de Champel.. CH-1206  ...   read carefully the copyright notices and legal disclaimer of the said resources.. neXtProt uses the following third parties software:.. Drupal: Copyright © Drupal is a registered trademark of Dries Buytaert.. Grails: Copyright © 2009 SpringSource.. jQuery: Copyright © 2010 The jQuery Project.. Postgres: Copyright © 1996 – 2010 PostgreSQL Global Development Group.. Spring: Copyright © 2010 (.. http://www.. springsource.. org/.. ).. Tomcat: Copyright © 1999-2010, The Apache Software Foundation..

    Original link path: /db/open/page/copyright
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  • Title: neXtProt search
    Descriptive info: Search in.. Proteins.. Terminology.. Filter..

    Original link path: /db/search
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    Archived pages: 51