Thu, 21 Aug 2008 15:27:36 BST CiteULike: asddd's library [42 articles] http://www.citeulike.org/user/asddd CiteULike.org en-gb Copyright © 2004-2008 citeulike.org http://www.citeulike.org/user/asddd/article/175024 <i>(07 July 1997)</i><br /><br />This magnificent tour de force presents a comprehensive overview of a wide variety of algorithms and the analysis of them. Now in its third edition, <I>The Art of Computer Programming, Volume I: Fundamental Algorithms</I> contains substantial revisions by the author and includes numerous new exercises.<P> Although this book was conceived several decades ago, it is still a timeless classic. One of the book's greatest strengths is the wonderful collection of problems that accompany each chapter. The author has chosen problems carefully and indexed them according to difficulty. Solving a substantial number of these problems will help you gain a solid understanding of the issues surrounding the given topic. Furthermore, the exercises feature a variety of classic problems.<P> <I>Fundamental Algorithms</I> begins with mathematical preliminaries. The first section offers a good grounding in a variety of useful mathematical tools: proof techniques, combinatorics, and elementary number theory. Knuth then details the MIX processor, a virtual machine architecture that serves as the programming target for subsequent discussions. This wonderful section comprehensively covers the principles of simple machine architecture, beginning with a register-level discussion of the instruction set. A later discussion of a simulator for this machine includes an excellent description of the principles underlying the implementation of subroutines and co-routines. Implementing such a simulator is an excellent introduction to computer design.<P> In the second section, Knuth covers data structures--stacks, queues, lists, arrays, and trees--and presents implementations (in MIX assembly) along with techniques for manipulating these structures. Knuth follows many of the algorithms with careful time and space analysis. In the section on tree structures, the discussion includes a series of interesting problems concerning the combinatorics of trees (counting distinct trees of a particular form, for example) and some particularly interesting applications. Also featured is a discussion of Huffmann encoding and, in the section on lists, an excellent introduction to garbage collection algorithms and the difficult challenges associated with such a task. The book closes with a discussion of dynamic allocation algorithms.<P> The clear writing in <I>Fundamental Algorithms</I> is enhanced by Knuth's dry humor and the historical discussions that accompany the technical matter. Overall, this text is one of the great classics of computer programming literature--it's not an easy book to grasp, but one that any true programmer will study with pleasure. Art of Computer Programming, Volume 1: Fundamental Algorithms (3rd Edition) Donald Knuth (07 July 1997) 2005-04-30T15:57:37-00:00 1997 Addison-Wesley Professional algorithms book-review computer computer-science programming http://www.citeulike.org/user/asddd/article/2448526 <i>Nat Biotech, Vol. 22, No. 8. (2004), pp. 969-976.</i> In vivo cancer targeting and imaging with semiconductor quantum dots Xiaohu Gao Yuanyuan Cui Richard Levenson Leland Chung Shuming Nie doi:10.1038/nbt994 Nat Biotech, Vol. 22, No. 8. (2004), pp. 969-976. 2008-02-29T17:58:25-00:00 2004 Nat Biotech 22 8 969 976 active-targeting fluorescence-imaging murine-model passive-targeting quantum-dots tumor http://www.citeulike.org/user/asddd/article/1859441 <i>(01 September 1999)</i><br /><br />This extensive rigorous texbook, developed through instruction at MIT, focuses on nonlinear and other types of optimization: iterative algorithms for constrained and unconstrained optimization, Lagrange multipliers and duality, large scale problems, and the interface between continuous and discrete optimization. Among its special features, the book: 1) provides extensive coverage of iterative optimization methods within a unifying framework 2) provides a detailed treatment of interior point methods for linear programming 3) covers in depth duality theory from both a variational and a geometrical/convex analysis point of view 4) includes much new material on a number of topics, such as neural network training, discrete-time optimal control, and large-scale optimization 5) includes a large number of examples and exercises detailed solutions of many of which are posted on the internet Much supplementary/support material can be found at the book's web page http://www.athenasc.com/nonlinbook.html Nonlinear Programming Dimitri Bertsekas (01 September 1999) 2007-11-03T08:48:14-00:00 1999 Athena Scientific nonlinear-programming optimization programming http://www.citeulike.org/user/asddd/article/2448813 <i>Nature, Vol. 409, No. 6818. (18 January 2001), pp. 409-411.</i> The relationship between matter and life Rodney Brooks doi:10.1038/35053196 Nature, Vol. 409, No. 6818. (18 January 2001), pp. 409-411. 2008-02-29T18:44:45-00:00 2001 Nature 409 6818 409 411 life http://www.citeulike.org/user/asddd/article/1039136 <i>ChemPhysChem, Vol. 7, No. 8. (2006), pp. 1641-1647.</i><br /><br />DNA tile based self-assembly provides an attractive route to create nanoarchitectures of programmable patterns. It also offers excellent scaffolds for directed self-assembly of nanometer-scale materials, ranging from nanoparticles to proteins, with potential applications in constructing nanoelectronic/nanophotonic devices and protein/ligand nanoarrays. This Review first summarizes the currently available DNA tile toolboxes and further emphasizes recent developments toward self-assembling DNA nanostructures with increasing complexity. Exciting progress using DNA tiles for directed self-assembly of other nanometer scale components is also discussed. DNA Tile Based Self-Assembly: Building Complex Nanoarchitectures Chenxiang Lin Yan Liu Sherri Rinker Hao Yan doi:10.1002/cphc.200600260 ChemPhysChem, Vol. 7, No. 8. (2006), pp. 1641-1647. 2007-01-12T22:07:46-00:00 2006 ChemPhysChem 7 8 1641 1647 dna nanoelectronics nanotechology nanotiles review self-assembly http://www.citeulike.org/user/asddd/article/2388780 <i>Proceedings of the National Academy of Sciences (15 February 2008), 0711983105.</i><br /><br />The generation of patient-specific pluripotent stem cells has the potential to accelerate the implementation of stem cells for clinical treatment of degenerative diseases. Technologies including somatic cell nuclear transfer and cell fusion might generate such cells but are hindered by issues that might prevent them from being used clinically. Here, we describe methods to use dermal fibroblasts easily obtained from an individual human to generate human induced pluripotent stem (iPS) cells by ectopic expression of the defined transcription factors KLF4, OCT4, SOX2, and C-MYC. The resultant cell lines are morphologically indistinguishable from human embryonic stem cells (HESC) generated from the inner cell mass of a human preimplantation embryo. Consistent with these observations, human iPS cells share a nearly identical gene-expression profile with two established HESC lines. Importantly, DNA fingerprinting indicates that the human iPS cells were derived from the donor material and are not a result of contamination. Karyotypic analyses demonstrate that reprogramming of human cells by defined factors does not induce, or require, chromosomal abnormalities. Finally, we provide evidence that human iPS cells can be induced to differentiate along lineages representative of the three embryonic germ layers indicating the pluripotency of these cells. Our findings are an important step toward manipulating somatic human cells to generate an unlimited supply of patient-specific pluripotent stem cells. In the future, the use of defined factors to change cell fate may be the key to routine nuclear reprogramming of human somatic cells. 10.1073/pnas.0711983105 Generation of human induced pluripotent stem cells from dermal fibroblasts WE Lowry L Richter R Yachechko AD Pyle J Tchieu R Sridharan AT Clark K Plath doi:10.1073/pnas.0711983105 Proceedings of the National Academy of Sciences (15 February 2008), 0711983105. 2008-02-16T17:42:12-00:00 2008 Proceedings of the National Academy of Sciences 0711983105 adult cell de-differentiation expression gene reprograming stem stemcells http://www.citeulike.org/user/asddd/article/1391693 <i>BMC Bioinformatics, Vol. 8 (14 June 2007), 204.</i> Genomorama: genome visualization and analysis Jason Gans Murray Wolinsky doi:10.1186/1471-2105-8-204 BMC Bioinformatics, Vol. 8 (14 June 2007), 204. 2007-06-15T09:52:24-00:00 2007 BMC Bioinformatics 1471-2105 8 204 bioinformatics bio-tools genome genomics http://www.citeulike.org/user/asddd/article/884146 <i>BMC Bioinformatics, Vol. 7 (03 October 2006), 427.</i> MICA: desktop software for comprehensive searching of DNA databases William Stokes Benjamin Glick doi:10.1186/1471-2105-7-427 BMC Bioinformatics, Vol. 7 (03 October 2006), 427. 2006-10-04T23:09:55-00:00 2006 BMC Bioinformatics 1471-2105 7 427 bioinformatics bio-tools databases data-mining search http://www.citeulike.org/user/asddd/article/1512565 <i>Brief Bioinform, Vol. 4, No. 3. (September 2003), pp. 292-296.</i><br /><br />Life scientists who work with the supermarket of genome data will find the EnsMart database and software package offers a valuable door to a wealth of genes and genome features. Not only available to lab biologists on the web, this popular multi-organism genome database can be installed and used on your own Unix computer with relative ease. It offers a flexible, fast and practical data-mining framework for computer-savvy biologists and bioinformaticians. Shopping in the genome market with EnsMart. D Gilbert Brief Bioinform, Vol. 4, No. 3. (September 2003), pp. 292-296. 2007-07-30T10:48:47-00:00 2003 Brief Bioinform 1467-5463 4 3 292 296 bioinformatics bio-tools data-mining ensembl genome genomics java perl software http://www.citeulike.org/user/asddd/article/825494 <i>BMC Bioinformatics, Vol. 7 (01 September 2006), 398.</i> PhyloPat: phylogenetic pattern analysis of eukaryotic genes Tim Hulsen Jacob de Vlieg Peter Groenen doi:10.1186/1471-2105-7-398 BMC Bioinformatics, Vol. 7 (01 September 2006), 398. 2006-09-01T20:01:53-00:00 2006 BMC Bioinformatics 1471-2105 7 398 bioinformatics bio-tools gene phylogenetic http://www.citeulike.org/user/asddd/article/1158654 <i>Genome Res., Vol. 14, No. 1. (1 January 2004), pp. 160-169.</i><br /><br />The EnsMart system (www.ensembl.org/EnsMart) provides a generic data warehousing solution for fast and flexible querying of large biological data sets and integration with third-party data and tools. The system consists of a query-optimized database and interactive, user-friendly interfaces. EnsMart has been applied to Ensembl, where it extends its genomic browser capabilities, facilitating rapid retrieval of customized data sets. A wide variety of complex queries, on various types of annotations, for numerous species are supported. These can be applied to many research problems, ranging from SNP selection for candidate gene screening, through cross-species evolutionary comparisons, to microarray annotation. Users can group and refine biological data according to many criteria, including cross-species analyses, disease links, sequence variations, and expression patterns. Both tabulated list data and biological sequence output can be generated dynamically, in HTML, text, Microsoft Excel, and compressed formats. A wide range of sequence types, such as cDNA, peptides, coding regions, UTRs, and exons, with additional upstream and downstream regions, can be retrieved. The EnsMart database can be accessed via a public Web site, or through a Java application suite. Both implementations and the database are freely available for local installation, and can be extended or adapted to `non-Ensembl' data sets. 10.1101/gr.1645104 EnsMart: A Generic System for Fast and Flexible Access to Biological Data Arek Kasprzyk Damian Keefe Damian Smedley Darin London William Spooner Craig Melsopp Martin Hammond Philippe Rocca-Serra Tony Cox Ewan Birney doi:10.1101/gr.1645104 Genome Res., Vol. 14, No. 1. (1 January 2004), pp. 160-169. 2007-03-13T22:40:25-00:00 2004 Genome Res. 14 1 160 169 bioinformatics bio-tools data-mining ensembl genome genomics java perl software http://www.citeulike.org/user/asddd/article/2445347 <i>Hum Genomics, Vol. 2, No. 3. (September 2005), pp. 187-190.</i><br /><br />The available web-based genome data and related resources provide great opportunities for biomedical scientists to identify functional elements in a particular genome region or to explore the evolutionary pattern of genome dynamics. Comparative genomics is an indispensable tool for achieving these goals. Because of the broad scope of comparative genomics, it is difficult to address all of its aspects in this short survey. A few currently 'hot' topics have therefore been selected and a brief review of the availability of web-based databases and software is given. Web-based resources for comparative genomics. X Gu Z Su Hum Genomics, Vol. 2, No. 3. (September 2005), pp. 187-190. 2008-02-28T22:17:14-00:00 2005 Hum Genomics 1479-7364 2 3 187 190 bioinformatics comparative genomics internet http://www.citeulike.org/user/asddd/article/2445345 <i>Mol Med, Vol. 9, No. 9-12. (c 2003), pp. 185-192.</i><br /><br />The inherent potential underlying the sequence data produced by the International Human Genome Sequencing Consortium and other systematic sequencing projects is, obviously, tremendous. As such, it becomes increasingly important that all biologists have the ability to navigate through and cull important information from key publicly available databases. The continued rapid rise in available sequence information, particularly as model organism data is generated at breakneck speed, also underscores the necessity for all biologists to learn how to effectively make their way through the expanding "sequence information space." This review discusses some of the more commonly used tools for sequence discovery; tools have been developed for the effective and efficient mining of sequence information. These include LocusLink, which provides a gene-centric view of sequence-based information, as well as the 3 major genome browsers: the National Center for Biotechnology Information Map Viewer, the University of California Santa Cruz Genome Browser, and the European Bioinformatics Institute's Ensembl system. An overview of the types of information available through each of these front-ends is given, as well as information on tutorials and other documentation intended to increase the reader's familiarity with these tools. Using genomic databases for sequence-based biological discovery. AD Baxevanis Mol Med, Vol. 9, No. 9-12. (c 2003), pp. 185-192. 2008-02-28T22:16:06-00:00 2003 Mol Med 1076-1551 9 9-12 185 192 bioinformatics databases genomics review sequences http://www.citeulike.org/user/asddd/article/1041436 <i>Nucleic Acids Res, Vol. 34, No. Web Server issue. (1 July 2006)</i><br /><br />Taverna is an application that eases the use and integration of the growing number of molecular biology tools and databases available on the web, especially web services. It allows bioinformaticians to construct workflows or pipelines of services to perform a range of different analyses, such as sequence analysis and genome annotation. These high-level workflows can integrate many different resources into a single analysis. Taverna is available freely under the terms of the GNU Lesser General Public License (LGPL) from http://taverna.sourceforge.net/. Taverna: a tool for building and running workflows of services. D Hull K Wolstencroft R Stevens C Goble MR Pocock P Li T Oinn Nucleic Acids Res, Vol. 34, No. Web Server issue. (1 July 2006) 2007-01-14T22:00:04-00:00 2006 Nucleic Acids Res 1362-4962 34 Web Server issue bioinformatics bio-tools http://www.citeulike.org/user/asddd/article/1260809 <i>Nucleic Acids Res, Vol. 35, No. Database issue. (January 2007)</i><br /><br />The Ensembl (http://www.ensembl.org/) project provides a comprehensive and integrated source of annotation of chordate genome sequences. Over the past year the number of genomes available from Ensembl has increased from 15 to 33, with the addition of sites for the mammalian genomes of elephant, rabbit, armadillo, tenrec, platypus, pig, cat, bush baby, common shrew, microbat and european hedgehog; the fish genomes of stickleback and medaka and the second example of the genomes of the sea squirt (Ciona savignyi) and the mosquito (Aedes aegypti). Some of the major features added during the year include the first complete gene sets for genomes with low-sequence coverage, the introduction of new strain variation data and the introduction of new orthology/paralog annotations based on gene trees. Ensembl 2007. TJ Hubbard BL Aken K Beal B Ballester M Caccamo Y Chen L Clarke G Coates F Cunningham T Cutts T Down SC Dyer S Fitzgerald J Fernandez-Banet S Graf S Haider M Hammond J Herrero R Holland K Howe K Howe N Johnson A Kahari D Keefe F Kokocinski E Kulesha D Lawson I Longden C Melsopp K Megy P Meidl B Ouverdin A Parker A Prlic S Rice D Rios M Schuster I Sealy J Severin G Slater D Smedley G Spudich S Trevanion A Vilella J Vogel S White M Wood T Cox V Curwen R Durbin XM Fernandez-Suarez P Flicek A Kasprzyk G Proctor S Searle J Smith A Ureta-Vidal E Birney Nucleic Acids Res, Vol. 35, No. Database issue. (January 2007) 2007-04-27T17:06:10-00:00 2007 Nucleic Acids Res 1362-4962 35 Database issue bioinformatics databases genome genomics viewer http://www.citeulike.org/user/asddd/article/1110346 <i>Nucleic Acids Res, Vol. 35, No. Database issue. (January 2007)</i><br /><br />The NAR online Molecular Biology Database Collection is a public resource that contains links to the databases described in this issue of Nucleic Acids Research, previous NAR database issues, as well as a selection of other molecular biology databases that are freely available on the web and might be useful to the molecular biologist. The 2007 update includes 968 databases, 110 more than the previous one. Many databases that have been described in earlier issues of NAR come with updated summaries, which reflect recent progress and, in some instances, an expanded scope of these databases. The complete database list and summaries are available online on the Nucleic Acids Research web site http://nar.oxfordjournals.org/. The Molecular Biology Database Collection: 2007 update. MY Galperin Nucleic Acids Res, Vol. 35, No. Database issue. (January 2007) 2007-02-17T07:54:16-00:00 2007 Nucleic Acids Res 1362-4962 35 Database issue directory links molecular-biology http://www.citeulike.org/user/asddd/article/1573343 <i>Nucleic Acids Res, Vol. 35, No. Web Server issue. (1 July 2007)</i><br /><br />The Bioinformatics Links Directory, http://bioinformatics.ca/links_directory, is an actively maintained compilation of servers published in this and previous issues of Nucleic Acids Research issues together with many other useful tools, databases and resources for life sciences research. The 2007 update includes the 130 websites highlighted in the July 2007 Web Server issue of Nucleic Acids Research and brings the total number of servers listed in the Bioinformatics Links Directory to just under 1200 links. In addition to the updated content, the 2007 update of the Bioinformatics Links Directory includes new features for improved navigation, accessibility and open data exchange. A complete listing of all links listed in this Nucleic Acids Research 2007 Web Server issue can be accessed online at, http://bioinformatics.ca/links_directory/narweb2007. The 2007 update of the Bioinformatics Links Directory, which includes the Web Server list and summaries is also available online, at the Nucleic Acids Research web site, http://nar.oupjournals.org. Conducting research on the web: 2007 update for the bioinformatics links directory. JA Fox S McMillan BF Ouellette Nucleic Acids Res, Vol. 35, No. Web Server issue. (1 July 2007) 2007-08-18T04:43:21-00:00 2007 Nucleic Acids Res 1362-4962 35 Web Server issue bioinformatics directory links http://www.citeulike.org/user/asddd/article/1573308 <i>Appl Bioinformatics, Vol. 5, No. 1. (2006), pp. 29-39.</i><br /><br />The Internet consists of a vast inhomogeneous reservoir of data. Developing software that can integrate a wide variety of different data sources is a major challenge that must be addressed for the realisation of the full potential of the Internet as a scientific research tool. This article presents a semi-automated object-oriented programming system for integrating web-based resources. We demonstrate that the current Internet standards (HTML, CGI [common gateway interface], Java, etc.) can be exploited to develop a data retrieval system that scans existing web interfaces and then uses a set of rules to generate new Java code that can automatically retrieve data from the Web. The validity of the software has been demonstrated by testing it on several biological databases. We also examine the current limitations of the Internet and discuss the need for the development of universal standards for web-based data. An object-oriented programming system for the integration of internet-based bioinformatics resources. A Beveridge Appl Bioinformatics, Vol. 5, No. 1. (2006), pp. 29-39. 2007-08-18T04:16:46-00:00 2006 Appl Bioinformatics 1175-5636 5 1 29 39 bioinformatics bio-tools data-mining gene genome interface internet oop progamming http://www.citeulike.org/user/asddd/article/2445316 <i>BMC Bioinformatics, Vol. 6 (2005)</i><br /><br />BACKGROUND: Collecting and managing information is a challenging task in a genome-wide profiling research project. Most databases and online computational tools require a direct human involvement. Information and computational results are presented in various multimedia formats (e.g., text, image, PDF, word files, etc.), many of which cannot be automatically processed by computers in biologically meaningful ways. In addition, the quality of computational results is far from perfect and requires nontrivial manual examination. The timely selection, integration and interpretation of heterogeneous biological information still heavily rely on the sensibility of biologists. Biologists often feel overwhelmed by the huge amount of and the great diversity of distributed heterogeneous biological information. DESCRIPTION: We developed an information management application called GeneNotes. GeneNotes is the first application that allows users to collect and manage multimedia biological information about genes/ESTs. GeneNotes provides an integrated environment for users to surf the Internet, collect notes for genes/ESTs, and retrieve notes. GeneNotes is supported by a server that integrates gene annotations from many major databases (e.g., HGNC, MGI, etc.). GeneNotes uses the integrated gene annotations to (a) identify genes given various types of gene IDs (e.g., RefSeq ID, GenBank ID, etc.), and (b) provide quick views of genes. GeneNotes is free for academic usage. The program and the tutorials are available at: http://bayes.fas.harvard.edu/genenotes/. CONCLUSIONS: GeneNotes provides a novel human-computer interface to assist researchers to collect and manage biological information. It also provides a platform for studying how users behave when they manipulate biological information. The results of such study can lead to innovation of more intelligent human-computer interfaces that greatly shorten the cycle of biology research. GeneNotes--a novel information management software for biologists. P Hong WH Wong doi:10.1186/1471-2105-6-20 BMC Bioinformatics, Vol. 6 (2005) 2008-02-28T21:59:37-00:00 2005 BMC Bioinformatics 1471-2105 6 bioinformatics bio-tools data-mining gene genome interface internet http://www.citeulike.org/user/asddd/article/1573309 <i>Appl Bioinformatics, Vol. 5, No. 1. (2006), pp. 63-66.</i><br /><br />Currently there are many bioinformatics applications being developed, but there is no easy way to publish them on the World Wide Web. We have developed a Perl script, called Biotool2Web, which makes the task of creating web interfaces for simple ('home-made') bioinformatics applications quick and easy. Biotool2Web uses an XML document containing the parameters to run the tool on the Web, and generates the corresponding HTML and common gateway interface (CGI) files ready to be published on a web server. AVAILABILITY: This tool is available for download at URL http://www.uni-muenster.de/Bioinformatics/services/biotool2web/ CONTACT: Georg Fuellen (fuellen@alum.mit.edu). Biotool2Web: creating simple Web interfaces for bioinformatics applications. M Shahid I Alam G Fuellen Appl Bioinformatics, Vol. 5, No. 1. (2006), pp. 63-66. 2007-08-18T04:17:56-00:00 2006 Appl Bioinformatics 1175-5636 5 1 63 66 bioinformatics bio-tools internet http://www.citeulike.org/user/asddd/article/1110339 <i>Nucleic Acids Res, Vol. 35, No. Database issue. (January 2007)</i><br /><br />To bridge the gap between the rising information needs of biological and medical researchers and the rapidly growing number of online bioinformatics resources, we have created the Online Bioinformatics Resources Collection (OBRC) at the Health Sciences Library System (HSLS) at the University of Pittsburgh. The OBRC, containing 1542 major online bioinformatics databases and software tools, was constructed using the HSLS content management system built on the Zope Web application server. To enhance the output of search results, we further implemented the Vivísimo Clustering Engine, which automatically organizes the search results into categories created dynamically based on the textual information of the retrieved records. As the largest online collection of its kind and the only one with advanced search results clustering, OBRC is aimed at becoming a one-stop guided information gateway to the major bioinformatics databases and software tools on the Web. OBRC is available at the University of Pittsburgh's HSLS Web site (http://www.hsls.pitt.edu/guides/genetics/obrc). The Online Bioinformatics Resources Collection at the University of Pittsburgh Health Sciences Library System--a one-stop gateway to online bioinformatics databases and software tools. YB Chen A Chattopadhyay P Bergen C Gadd N Tannery Nucleic Acids Res, Vol. 35, No. Database issue. (January 2007) 2007-02-17T07:31:44-00:00 2007 Nucleic Acids Res 1362-4962 35 Database issue bioinformatics databases list http://www.citeulike.org/user/asddd/article/299529 <i>Bioinformatics, Vol. 21, No. 16. (15 August 2005), pp. 3439-3440.</i> BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis Steffen Durinck Yves Moreau Arek Kasprzyk Sean Davis Bart De Moor Alvis Brazma Wolfgang Huber doi:10.1093/bioinformatics/bti525 Bioinformatics, Vol. 21, No. 16. (15 August 2005), pp. 3439-3440. 2005-08-20T13:51:36-00:00 2005 Bioinformatics 1367-4803 21 16 3439 3440 Oxford University Press bioinformatics bio-tools data-mining ensembl genome genomics java perl software http://www.citeulike.org/user/asddd/article/2393973 <i>Nature Reviews Genetics, Vol. 9, No. 3., pp. 165-178.</i> Toll-like receptors — taking an evolutionary approach François Leulier Bruno Lemaitre doi:10.1038/nrg2303 Nature Reviews Genetics, Vol. 9, No. 3., pp. 165-178. 2008-02-18T13:20:30-00:00 Nature Reviews Genetics 1471-0056 9 3 165 178 Nature Publishing Group evolution immunology patterning pub-model review tlr toll http://www.citeulike.org/user/asddd/article/2350761 <i>Nature Biotechnology, Vol. 26, No. 2., pp. 195-197.</i> What are artificial neural networks? Anders Krogh doi:10.1038/nbt1386 Nature Biotechnology, Vol. 26, No. 2., pp. 195-197. 2008-02-08T00:40:34-00:00 Nature Biotechnology 1087-0156 26 2 195 197 Nature Publishing Group algorithm network neural http://www.citeulike.org/user/asddd/article/1601330 <i>PLoS Biology, Vol. 5, No. 7. (1 July 2007), e194.</i> New Taxonomy and the Origin of Species Shai Meiri Georgina Mace doi:10.1371/journal.pbio.0050194 PLoS Biology, Vol. 5, No. 7. (1 July 2007), e194. 2007-08-28T16:42:20-00:00 2007 PLoS Biology 5 7 e194 evolution phylogeny tol http://www.citeulike.org/user/asddd/article/2437967 <i></i> Coalescent theory - Wikipedia 2008-02-27T18:30:13-00:00 bioinformatics coalescent genetics population wiki http://www.citeulike.org/user/asddd/article/1543464 <i>Bioinformatics, Vol. 23, No. 14. (1 July 2007), pp. 1713-1717.</i><br /><br />Motivation: The genome sequencing revolution is approaching a landmark figure of 1000 completely sequenced genomes. Coupled with fast-declining, per-base sequencing costs, this influx of DNA sequence data has encouraged laboratory scientists to engage large datasets in comparative sequence analyses for making evolutionary, functional and translational inferences. However, the majority of the scientists at the forefront of experimental research are not bioinformaticians, so a gap exists between the user-friendly software needed and the scripting/programming infrastructure often employed for the analysis of large numbers of genes, long genomic segments and groups of sequences. We see an urgent need for the expansion of the fundamental paradigms under which biologist-friendly software tools are designed and developed to fulfill the needs of biologists to analyze large datasets by using sophisticated computational methods. We argue that the design principles need to be sensitive to the reality that comparatively small teams of biologists have historically developed some of the most popular biological software packages in molecular evolutionary analysis. Furthermore, biological intuitiveness and investigator empowerment need to take precedence over the current supposition that biologists should re-tool and become programmers when analyzing genome scale datasets. Contact: s.kumar@asu.edu 10.1093/bioinformatics/btm239 Bioinformatics software for biologists in the genomics era Sudhir Kumar Joel Dudley doi:10.1093/bioinformatics/btm239 Bioinformatics, Vol. 23, No. 14. (1 July 2007), pp. 1713-1717. 2007-08-08T14:43:16-00:00 2007 Bioinformatics 23 14 1713 1717 bioinformatics genomics software http://www.citeulike.org/user/asddd/article/2084644 <i>PLoS Computational Biology, Vol. 3, No. 11. (1 November 2007), e237.</i><br /><br />“Phylogenetic profiling” is based on the hypothesis that during evolution functionally or physically interacting genes are likely to be inherited or eliminated in a codependent manner. Creating presence–absence profiles of orthologous genes is now a common and powerful way of identifying functionally associated genes. In this approach, correctly determining orthology, as a means of identifying functional equivalence between two genes, is a critical and nontrivial step and largely explains why previous work in this area has mainly focused on using presence–absence profiles in prokaryotic species. Here, we demonstrate that eukaryotic genomes have a high proportion of multigene families whose phylogenetic profile distributions are poor in presence–absence information content. This feature makes them prone to orthology mis-assignment and unsuited to standard profile-based prediction methods. Using CATH structural domain assignments from the Gene3D database for 13 complete eukaryotic genomes, we have developed a novel modification of the phylogenetic profiling method that uses genome copy number of each domain superfamily to predict functional relationships. In our approach, superfamilies are subclustered at ten levels of sequence identity—from 30% to 100%—and phylogenetic profiles built at each level. All the profiles are compared using normalised Euclidean distances to identify those with correlated changes in their domain copy number. We demonstrate that two protein families will “auto-tune” with strong co-evolutionary signals when their profiles are compared at the similarity levels that capture their functional relationship. Our method finds functional relationships that are not detectable by the conventional presence–absence profile comparisons, and it does not require a priori any fixed criteria to define orthologous genes. Predicting Protein Function with Hierarchical Phylogenetic Profiles: The Gene3D Phylo-Tuner Method Applied to Eukaryotic Genomes Juan Ranea Corin Yeats Alastair Grant Christine Orengo doi:10.1371/journal.pcbi.0030237 PLoS Computational Biology, Vol. 3, No. 11. (1 November 2007), e237. 2007-12-10T04:43:16-00:00 2007 PLoS Computational Biology 3 11 e237 bioinformatics eukaryota genome genomics hierarchical phylogeny prediction protein http://www.citeulike.org/user/asddd/article/1597743 <i>Current Biology, Vol. 17, No. 16. (21 August 2007), pp. 1420-1425.</i><br /><br />Summary Resolving the global phylogeny of eukaryotes has proven to be challenging. Among the eukaryotic groups of uncertain phylogenetic position are jakobids, a group of bacterivorous flagellates that possess the most bacteria-like mitochondrial genomes known and . Jakobids share several ultrastructural features with malawimonads and an assemblage of anaerobic protists (e.g., diplomonads and oxymonads) and . These lineages together with Euglenozoa and Heterolobosea have collectively been designated "excavates" . However, published molecular phylogenies based on the sequences of nuclear rRNAs , and and up to six nucleus-encoded proteins , and do not provide convincing support for the monophyly of excavates, nor do they uncover their relationship to other major eukaryotic groups , , , , and . Here, we report the first large-scale eukaryotic phylogeny, inferred from 143 nucleus-encoded proteins comprising 31,604 amino acid positions, that includes jakobids, malawimonads and cercozoans . We obtain compelling support for the monophyly of jakobids, Euglenozoa plus Heterolobosea (JEH group), and for the association of cercozoans with stramenopiles plus alveolates. Furthermore, we observe a sister-group relationship between the JEH group and malawimonads after removing fast-evolving species from the dataset. We discuss the implications of these results for the concept of "excavates" and for the elucidation of eukaryotic phylogeny in general. Toward Resolving the Eukaryotic Tree: The Phylogenetic Positions of Jakobids and Cercozoans Naiara Rodriguez-Ezpeleta Henner Brinkmann Gertraud Burger Andrew Roger Michael Gray Herve Philippe Franz Lang doi:10.1016/j.cub.2007.07.036 Current Biology, Vol. 17, No. 16. (21 August 2007), pp. 1420-1425. 2007-08-28T03:01:11-00:00 2007 Current Biology 17 16 1420 1425 eukaryota evolution phylogeny tol http://www.citeulike.org/user/asddd/article/2437692 <i>Genome Res., Vol. 16, No. 8. (1 August 2006), pp. 1046-1055.</i><br /><br />The distribution of cytosine methylation in 6.2 Mb of the mouse genome was tested using cohybridization of genomic representations from a methylation-sensitive restriction enzyme and its methylation-insensitive isoschizomer. This assay, termed HELP (HpaII tiny fragment Enrichment by Ligation-mediated PCR), allows both intragenomic profiling and intergenomic comparisons of cytosine methylation. The intragenomic profile shows most of the genome to be contiguous methylated sequence with occasional clusters of hypomethylated loci, usually but not exclusively at promoters and CpG islands. Intergenomic comparison found marked differences in cytosine methylation between spermatogenic and brain cells, identifying 223 new candidate tissue-specific differentially methylated regions (T-DMRs). Bisulfite pyrosequencing confirmed the four candidates tested to be T-DMRs, while quantitative RT-PCR for two genes with T-DMRs located at their promoters showed the HELP data to be correlated with gene activity at these loci. The HELP assay is robust, quantitative, and accurate and is providing new insights into the distribution and dynamic nature of cytosine methylation in the genome. 10.1101/gr.5273806 Comparative isoschizomer profiling of cytosine methylation: The HELP assay Batbayar Khulan Reid Thompson Kenny Ye Melissa Fazzari Masako Suzuki Edyta Stasiek Maria Figueroa Jacob Glass Quan Chen Cristina Montagna Eli Hatchwell Rebecca Selzer Todd Richmond Roland Green Ari Melnick John Greally doi:10.1101/gr.5273806 Genome Res., Vol. 16, No. 8. (1 August 2006), pp. 1046-1055. 2008-02-27T17:40:25-00:00 2006 Genome Res. 16 8 1046 1055 dna epigenetics methylation http://www.citeulike.org/user/asddd/article/1394974 <i>Science, Vol. 316, No. 5831. (15 June 2007), pp. 1556-1557.</i> Genomics. DNA study forces rethink of what it means to be a gene. E Pennisi doi:10.1126/science.316.5831.1556 Science, Vol. 316, No. 5831. (15 June 2007), pp. 1556-1557. 2007-06-17T11:22:39-00:00 2007 Science 1095-9203 316 5831 1556 1557 genetics genome transcription transcriptome http://www.citeulike.org/user/asddd/article/1288112 <i>Nat Rev Genet (8 May 2007)</i><br /><br />Recent evidence of genome-wide transcription in several species indicates that the amount of transcription that occurs cannot be entirely accounted for by current sets of genome-wide annotations. Evidence indicates that most of both strands of the human genome might be transcribed, implying extensive overlap of transcriptional units and regulatory elements. These observations suggest that genomic architecture is not colinear, but is instead interleaved and modular, and that the same genomic sequences are multifunctional: that is, used for multiple independently regulated transcripts and as regulatory regions. What are the implications and consequences of such an interleaved genomic architecture in terms of increased information content, transcriptional complexity, evolution and disease states? Genome-wide transcription and the implications for genomic organization. Philipp Kapranov Aarron T Willingham Thomas R Gingeras doi:10.1038/nrg2083 Nat Rev Genet (8 May 2007) 2007-05-10T13:57:03-00:00 2007 Nat Rev Genet 1471-0056 gene genome genome-wide genomics organization transcription transcriptome http://www.citeulike.org/user/asddd/article/1336057 <i>Science (17 May 2007), 1138341.</i><br /><br />Significant fractions of eukaryotic genomes give rise to RNA, much of which is unannotated and has reduced protein-coding potential. The genomic origins and the relations of human nuclear and cytosolic polyadenylated RNAs longer than 200 nucleotides and whole-cell RNAs less than 200 nt are investigated in this genome-wide study. Subcellular addresses for nucleotides present in detected RNAs were assigned, and their potential processing into short RNAs was investigated. Taken together, these observations suggest a role for some unannotated RNAs as primary transcripts for the production of short RNAs. Three novel potentially functional classes of RNAs have been identified, two of which are syntenically conserved and correlate with the expression state of protein-coding genes. These data support a highly interleaved organization of the human transcriptome. 10.1126/science.1138341 RNA Maps Reveal New RNA Classes and a Possible Function for Pervasive Transcription Philipp Kapranov Jill Cheng Sujit Dike David Nix Radharani Duttagupta Aarron Willingham Peter Stadler Jana Hertel Joerg Hackermueller Ivo Hofacker Ian Bell Evelyn Cheung Jorg Drenkow Erica Dumais Sandeep Patel Gregg Helt Madhavan Ganesh Srinka Ghosh Antonio Piccolboni Victor Sementchenko Hari Tammana Thomas Gingeras doi:10.1126/science.1138341 Science (17 May 2007), 1138341. 2007-05-27T00:42:53-00:00 2007 Science 1138341 classification expression genome ncrna non-coding noncoding_rna transcription transcriptome http://www.citeulike.org/user/asddd/article/1442986 <i>PLoS Computational Biology, Vol. 3, No. 6. (1 June 2007), e116.</i><br /><br />The term machine learning refers to a set of topics dealing with the creation and evaluation of algorithms that facilitate pattern recognition, classification, and prediction, based on models derived from existing data. Two facets of mechanization should be acknowledged when considering machine learning in broad terms. Firstly, it is intended that the classification and prediction tasks can be accomplished by a suitably programmed computing machine. That is, the product of machine learning is a classifier that can be feasibly used on available hardware. Secondly, it is intended that the creation of the classifier should itself be highly mechanized, and should not involve too much human input. This second facet is inevitably vague, but the basic objective is that the use of automatic algorithm construction methods can minimize the possibility that human biases could affect the selection and performance of the algorithm. Both the creation of the algorithm and its operation to classify objects or predict events are to be based on concrete, observable data. The history of relations between biology and the field of machine learning is long and complex. An early technique [1] for machine learning called the perceptron constituted an attempt to model actual neuronal behavior, and the field of artificial neural network (ANN) design emerged from this attempt. Early work on the analysis of translation initiation sequences [2] employed the perceptron to define criteria for start sites in Escherichia coli. Further artificial neural network architectures such as the adaptive resonance theory (ART) [3] and neocognitron [4] were inspired from the organization of the visual nervous system. In the intervening years, the flexibility of machine learning techniques has grown along with mathematical frameworks for measuring their reliability, and it is natural to hope that machine learning methods will improve the efficiency of discovery and understanding in the mounting volume and complexity of biological data. This tutorial is structured in four main components. Firstly, a brief section reviews definitions and mathematical prerequisites. Secondly, the field of supervised learning is described. Thirdly, methods of unsupervised learning are reviewed. Finally, a section reviews methods and examples as implemented in the open source data analysis and visualization language R (http://www.r-project.org). Machine Learning and Its Applications to Biology Adi Tarca Vincent Carey Xue-Wen Chen Roberto Romero Sorin Drăghici doi:10.1371/journal.pcbi.0030116 PLoS Computational Biology, Vol. 3, No. 6. (1 June 2007), e116. 2007-07-08T16:29:01-00:00 2007 PLoS Computational Biology 3 6 e116 algorithm analysis bioinformatics biology data machine_learning microarray pattern_recognition review http://www.citeulike.org/user/asddd/article/1336214 <i>Stat Appl Genet Mol Biol, Vol. 4 (2005)</i><br /><br />While scientific research and the methodologies involved have gone through substantial technological evolution the technology involved in the publication of the results of these endeavors has remained relatively stagnant. Publication is largely done in the same manner today as it was fifty years ago. Many journals have adopted electronic formats, however, their orientation and style is little different from a printed document. The documents tend to be static and take little advantage of computational resources that might be available. Recent work, Gentleman and Temple Lang (2003), suggests a methodology and basic infrastructure that can be used to publish documents in a substantially different way. Their approach is suitable for the publication of papers whose message relies on computation. Stated quite simply, Gentleman and Temple Lang (2003) propose a paradigm where documents are mixtures of code and text. Such documents may be self-contained or they may be a component of a compendium which provides the infrastructure needed to provide access to data and supporting software. These documents, or compendiums, can be processed in a number of different ways. One transformation will be to replace the code with its output -- thereby providing the familiar, but limited, static document. <p /> In this paper we apply these concepts to a seminal paper in bioinformatics, namely The Molecular Classification of Cancer, Golub et al (1999). The authors of that paper have generously provided data and other information that have allowed us to largely reproduce their results. Rather than reproduce this paper exactly we demonstrate that such a reproduction is possible and instead concentrate on demonstrating the usefulness of the compendium concept itself. Reproducible research: a bioinformatics case study. R Gentleman doi:10.2202/1544-6115.1034 Stat Appl Genet Mol Biol, Vol. 4 (2005) 2007-05-27T05:53:16-00:00 2005 Stat Appl Genet Mol Biol 1544-6115 4 bioinformatics publication reproducible research http://www.citeulike.org/user/asddd/article/1125833 <i>Library Review, Vol. 56, No. 1. (2007), pp. 12-23.</i><br /><br />Abstract: Purpose – To argue that unique contemporary cultural shifts are leading to a new form of librarianship that can be characterised as “postmodern” in nature, and that this form of professional specialism will be increasingly influential in the decades to come. Design/methodology/approach – A theoretical piece based on ideas from cultural history. Findings – That postmodern library and information science (LIS) concepts will be a vital new strand to professional practice, but they will most likely subsist alongside more familiar concepts of practice which have proved readily applicable in the early years of “first wave” web technologies. Research limitations/implications – These are purely conceptual approaches to LIS and need to be investigated evidentially. Practical implications – The change from “first wave” web technologies to Web 2.0 information technologies may have a greater impact on future techniques in digital librarianship than the change from print to the first electronic libraries in the 1990s. Originality/value – This LIS paper is distinctive in that it borrows original ideas from the humanities to offer an understanding of LIS practice in the context of broad “cultural theory”, rather than in the narrower context of change in mechanical and technological processes Digital libraries and the future of the library profession Nicholas Joint doi:10.1108/00242530710721989 Library Review, Vol. 56, No. 1. (2007), pp. 12-23. 2007-02-27T07:54:31-00:00 2007 Library Review 0024-2535 56 1 12 23 Emerald Group Publishing Limited digital_library librarianship library postmodernism http://www.citeulike.org/user/asddd/article/1442671 <i>PLoS Biology, Vol. 5, No. 7. (1 July 2007), e167.</i><br /><br />To determine whether the distinctive features of Caenorhabditis elegans chromosomal organization are shared with the C. briggsae genome, we constructed a single nucleotide polymorphism–based genetic map to order and orient the whole genome shotgun assembly along the six C. briggsae chromosomes. Although these species are of the same genus, their most recent common ancestor existed 80–110 million years ago, and thus they are more evolutionarily distant than, for example, human and mouse. We found that, like C. elegans chromosomes, C. briggsae chromosomes exhibit high levels of recombination on the arms along with higher repeat density, a higher fraction of intronic sequence, and a lower fraction of exonic sequence compared with chromosome centers. Despite extensive intrachromosomal rearrangements, 1:1 orthologs tend to remain in the same region of the chromosome, and colinear blocks of orthologs tend to be longer in chromosome centers compared with arms. More strikingly, the two species show an almost complete conservation of synteny, with 1:1 orthologs present on a single chromosome in one species also found on a single chromosome in the other. The conservation of both chromosomal organization and synteny between these two distantly related species suggests roles for chromosome organization in the fitness of an organism that are only poorly understood presently. Comparison of C. elegans and C. briggsae Genome Sequences Reveals Extensive Conservation of Chromosome Organization and Synteny Ladeana Hillier Raymond Miller Scott Baird Asif Chinwalla Lucinda Fulton Daniel Koboldt Robert Waterston doi:10.1371/journal.pbio.0050167 PLoS Biology, Vol. 5, No. 7. (1 July 2007), e167. 2007-07-08T12:29:07-00:00 2007 PLoS Biology 5 7 e167 comparative genomics synteny http://www.citeulike.org/user/asddd/article/1445051 <i>Genome Biol, Vol. 7, No. 1. (2006)</i><br /><br />BACKGROUND: The three consensus elements at the 3' end of human introns--the branch point sequence, the polypyrimidine tract, and the 3' splice site AG dinucleotide--are usually closely spaced within the final 40 nucleotides of the intron. However, the branch point sequence and polypyrimidine tract of a few known alternatively spliced exons lie up to 400 nucleotides upstream of the 3' splice site. The extended regions between the distant branch points (dBPs) and their 3' splice site are marked by the absence of other AG dinucleotides. In many cases alternative splicing regulatory elements are located within this region. RESULTS: We have applied a simple algorithm, based on AG dinucleotide exclusion zones (AGEZ), to a large data set of verified human exons. We found a substantial number of exons with large AGEZs, which represent candidate dBP exons. We verified the importance of the predicted dBPs for splicing of some of these exons. This group of exons exhibits a higher than average prevalence of observed alternative splicing, and many of the exons are in genes with some human disease association. CONCLUSION: The group of identified probable dBP exons are interesting first because they are likely to be alternatively spliced. Second, they are expected to be vulnerable to mutations within the entire extended AGEZ. Disruption of splicing of such exons, for example by mutations that lead to insertion of a new AG dinucleotide between the dBP and 3' splice site, could be readily understood even though the causative mutation might be remote from the conventional locations of splice site sequences. A class of human exons with predicted distant branch points revealed by analysis of AG dinucleotide exclusion zones. C Gooding F Clark MC Wollerton SN Grellscheid H Groom CW Smith doi:10.1186/gb-2006-7-1-r1 Genome Biol, Vol. 7, No. 1. (2006) 2007-07-09T23:01:29-00:00 2006 Genome Biol 1465-6914 7 1 exon intron prediction http://www.citeulike.org/user/asddd/article/1204540 <i>Theoretical Biology and Medical Modelling, Vol. 2, No. 1. (2005)</i><br /><br />BACKGROUND:Formal description of a cell's genetic information should provide the number of DNA molecules in that cell and their complete nucleotide sequences. We pose the formal problem: can the genome sequence forming the genotype of a given living cell be known with absolute certainty so that the cell's behaviour (phenotype) can be correlated to that genetic information? To answer this question, we propose a series of thought experiments.RESULTS:We show that the genome sequence of any actual living cell cannot physically be known with absolute certainty, independently of the method used. There is an associated uncertainty, in terms of base pairs, equal to or greater than mus (where mu is the mutation rate of the cell type and s is the cell's genome size).CONCLUSION:This finding establishes an "uncertainty principle" in genetics for the first time, and its analogy with the Heisenberg uncertainty principle in physics is discussed. The genetic information that makes living cells work is thus better represented by a probabilistic model rather than as a completely defined object. Uncertainty principle of genetic information in a living cell Pierluigi Strippoli Silvia Canaider Francesco Noferini Pietro D'Addabbo Lorenza Vitale Federica Facchin Luca Lenzi Raffaella Casadei Paolo Carinci Maria Zannotti Flavia Frabetti doi:10.1186/1742-4682-2-40 Theoretical Biology and Medical Modelling, Vol. 2, No. 1. (2005) 2007-04-03T14:33:56-00:00 2005 Theoretical Biology and Medical Modelling 2 1 bioinformatics biological_uncertainty_principle epigenetics genetics information modeling theoretical uncertainty http://www.citeulike.org/user/asddd/article/407130 <i>BMC Bioinformatics, Vol. 5 (19 April 2004)</i><br /><br />BACKGROUND: We present Pegasys--a flexible, modular and customizable software system that facilitates the execution and data integration from heterogeneous biological sequence analysis tools. RESULTS: The Pegasys system includes numerous tools for pair-wise and multiple sequence alignment, ab initio gene prediction, RNA gene detection, masking repetitive sequences in genomic DNA as well as filters for database formatting and processing raw output from various analysis tools. We introduce a novel data structure for creating workflows of sequence analyses and a unified data model to store its results. The software allows users to dynamically create analysis workflows at run-time by manipulating a graphical user interface. All non-serial dependent analyses are executed in parallel on a compute cluster for efficiency of data generation. The uniform data model and backend relational database management system of Pegasys allow for results of heterogeneous programs included in the workflow to be integrated and exported into General Feature Format for further analyses in GFF-dependent tools, or GAME XML for import into the Apollo genome editor. The modularity of the design allows for new tools to be added to the system with little programmer overhead. The database application programming interface allows programmatic access to the data stored in the backend through SQL queries. CONCLUSIONS: The Pegasys system enables biologists and bioinformaticians to create and manage sequence analysis workflows. The software is released under the Open Source GNU General Public License. All source code and documentation is available for download at http://bioinformatics.ubc.ca/pegasys/. Pegasys: software for executing and integrating analyses of biological sequences. SP Shah DY He JN Sawkins JC Druce G Quon D Lett GX Zheng T Xu BF Ouellette doi:10.1186/1471-2105-5-40 BMC Bioinformatics, Vol. 5 (19 April 2004) 2005-11-24T10:34:30-00:00 2004 BMC Bioinformatics 1471-2105 5 bioinformatics bio-tools combinatorial comparative genomics sequences software http://www.citeulike.org/user/asddd/article/1444976 <i>Bioinformatics (28 June 2007)</i><br /><br />SUMMARY: We have developed a quick web-based application for designing conserved genomic PCR and RT-PCR primers from multigenome alignments targeting specific exons or introns. We used Pygr (The Python Graph Database Framework for Bioinformatics) to query intervals from multigenome alignments, which gives us less than a millisecond access to any intervals of any genome within multigenome alignments. PRIMER3 was used to extract optimal primers from a gene of interest. QPRIMER creates an electronic genomic PCR image from a set of conserved primers as well as summary pages for primer alignments and products. QPRIMER supports human, mouse, rat, chicken, dog, zebrafish, and fruit fly. AVAILABILITY: http://www.bioinformatics.ucla.edu/QPRIMER/ QPRIMER: A Quick Web-based Application for Designing Conserved PCR Primers from Multigenome Alignments. Namshin Kim Christopher Lee doi:10.1093/bioinformatics/btm343 Bioinformatics (28 June 2007) 2007-07-09T21:53:25-00:00 2007 Bioinformatics 1460-2059 genomics methods pcr primers tools http://www.citeulike.org/user/asddd/article/1445114 <i>Genome Research, Vol. 14, No. 1. (January 2004), pp. 160-169.</i><br /><br />The EnsMart system (www.ensembl.org/EnsMart) provides a generic data warehousing solution for fast and flexible querying of large biological data sets and integration with third-party data and tools. The system consists of a query-optimized database and interactive, user-friendly interfaces. EnsMart has been applied to Ensembl, where it extends its genomic browser capabilities, facilitating rapid retrieval of customized data sets. A wide variety of complex queries, on various types of annotations, for numerous species are supported. These can be applied to many research problems, ranging from SNP selection for candidate gene screening, through cross-species evolutionary comparisons, to microarray annotation. Users can group and refine biological data according to many criteria, including cross-species analyses, disease links, sequence variations, and expression patterns. Both tabulated list data and biological sequence output can be generated dynamically, in HTML, text, Microsoft Excel, and compressed formats. A wide range of sequence types, such as cDNA, peptides, coding regions, UTRs, and exons, with additional upstream and downstream regions, can be retrieved. The EnsMart database can be accessed via a public Web site, or through a Java application suite. Both implementations and the database are freely available for local installation, and can be extended or adapted to 'non-Ensembl' data sets. EnsMart: A Generic System for Fast and Flexible Access to Biological Data A Kasprzyk D Keefe D Smedley D London W Spooner C Melsopp M Hammond P Rocca-Serra T Cox E Birney Genome Research, Vol. 14, No. 1. (January 2004), pp. 160-169. 2007-07-10T00:07:58-00:00 2004 Genome Research 14 1 160 169 bioinformatics ensembl genetics genomics science