software

Summary

Summary: Sequential operating instructions for a particular problem or function to be run on a digital computer.

Top Publications

  1. pmc The Sequence Alignment/Map format and SAMtools
    Heng Li
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA, UK, Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA
    Bioinformatics 25:2078-9. 2009
  2. pmc Fast and accurate short read alignment with Burrows-Wheeler transform
    Heng Li
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA, UK
    Bioinformatics 25:1754-60. 2009
  3. pmc MUSCLE: multiple sequence alignment with high accuracy and high throughput
    Robert C Edgar
    Nucleic Acids Res 32:1792-7. 2004
  4. pmc Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
    S F Altschul
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Nucleic Acids Res 25:3389-402. 1997
  5. ncbi Mapping and quantifying mammalian transcriptomes by RNA-Seq
    Ali Mortazavi
    Division of Biology, MC 156 29, California Institute of Technology, Pasadena, California 91125, USA
    Nat Methods 5:621-8. 2008
  6. pmc TopHat: discovering splice junctions with RNA-Seq
    Cole Trapnell
    Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA
    Bioinformatics 25:1105-11. 2009
  7. pmc Bioconductor: open software development for computational biology and bioinformatics
    Robert C Gentleman
    Department of Biostatistical Science, Dana Farber Cancer Institute, 44 Binney St, Boston, MA 02115, USA
    Genome Biol 5:R80. 2004
  8. ncbi DnaSP v5: a software for comprehensive analysis of DNA polymorphism data
    P Librado
    Departament de Genetica, Facultat de Biologia and Institut de Recerca de la Biodiversitat, Universitat de Barcelona, Barcelona, Spain
    Bioinformatics 25:1451-2. 2009
  9. ncbi Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study
    G Evanno
    Department of Ecology and Evolution, Biology Building, University of Lausanne, CH 1015 Lausanne, Switzerland
    Mol Ecol 14:2611-20. 2005
  10. pmc The Pfam protein families database
    Robert D Finn
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
    Nucleic Acids Res 38:D211-22. 2010

Detail Information

Publications230 found, 100 shown here

  1. pmc The Sequence Alignment/Map format and SAMtools
    Heng Li
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA, UK, Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA
    Bioinformatics 25:2078-9. 2009
    ..SAMtools implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments...
  2. pmc Fast and accurate short read alignment with Burrows-Wheeler transform
    Heng Li
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA, UK
    Bioinformatics 25:1754-60. 2009
    ..The speed of MAQ is also a concern when the alignment is scaled up to the resequencing of hundreds of individuals...
  3. pmc MUSCLE: multiple sequence alignment with high accuracy and high throughput
    Robert C Edgar
    Nucleic Acids Res 32:1792-7. 2004
    ..The MUSCLE program, source code and PREFAB test data are freely available at http://www.drive5. com/muscle...
  4. pmc Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
    S F Altschul
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Nucleic Acids Res 25:3389-402. 1997
    ..PSI-BLAST is used to uncover several new and interesting members of the BRCT superfamily...
  5. ncbi Mapping and quantifying mammalian transcriptomes by RNA-Seq
    Ali Mortazavi
    Division of Biology, MC 156 29, California Institute of Technology, Pasadena, California 91125, USA
    Nat Methods 5:621-8. 2008
    ..We observed 1.45 x 10(5) distinct splices, and alternative splices were prominent, with 3,500 different genes expressing one or more alternate internal splices...
  6. pmc TopHat: discovering splice junctions with RNA-Seq
    Cole Trapnell
    Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA
    Bioinformatics 25:1105-11. 2009
    ..However, current software for aligning RNA-Seq data to a genome relies on known splice junctions and cannot identify novel ones...
  7. pmc Bioconductor: open software development for computational biology and bioinformatics
    Robert C Gentleman
    Department of Biostatistical Science, Dana Farber Cancer Institute, 44 Binney St, Boston, MA 02115, USA
    Genome Biol 5:R80. 2004
    The Bioconductor project is an initiative for the collaborative creation of extensible software for computational biology and bioinformatics...
  8. ncbi DnaSP v5: a software for comprehensive analysis of DNA polymorphism data
    P Librado
    Departament de Genetica, Facultat de Biologia and Institut de Recerca de la Biodiversitat, Universitat de Barcelona, Barcelona, Spain
    Bioinformatics 25:1451-2. 2009
    DnaSP is a software package for a comprehensive analysis of DNA polymorphism data. Version 5 implements a number of new features and analytical methods allowing extensive DNA polymorphism analyses on large datasets...
  9. ncbi Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study
    G Evanno
    Department of Ecology and Evolution, Biology Building, University of Lausanne, CH 1015 Lausanne, Switzerland
    Mol Ecol 14:2611-20. 2005
    ..A recent Bayesian algorithm implemented in the software STRUCTURE allows the identification of such groups...
  10. pmc The Pfam protein families database
    Robert D Finn
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
    Nucleic Acids Res 38:D211-22. 2010
    ..This software is approximately 100 times faster than HMMER2 and is more sensitive due to the routine use of the forward ..
  11. pmc Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities
    Patrick D Schloss
    Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA
    Appl Environ Microbiol 75:7537-41. 2009
    mothur aims to be a comprehensive software package that allows users to use a single piece of software to analyze community sequence data...
  12. ncbi MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0
    Koichiro Tamura
    Center for Evolutionary Functional Genomics, The Biodesign Institute, Arizona State University, AZ, USA
    Mol Biol Evol 24:1596-9. 2007
    We announce the release of the fourth version of MEGA software, which expands on the existing facilities for editing DNA sequence data from autosequencers, mining Web-databases, performing automatic and manual sequence alignment, ..
  13. ncbi UCSF Chimera--a visualization system for exploratory research and analysis
    Eric F Pettersen
    Computer Graphics Laboratory, Department of Pharmaceutical Chemistry, University of California, 600 16th Street, San Francisco, California 94143 2240, USA
    J Comput Chem 25:1605-12. 2004
    ..Chimera includes full user documentation, is free to academic and nonprofit users, and is available for Microsoft Windows, Linux, Apple Mac OS X, SGI IRIX, and HP Tru64 Unix from http://www.cgl.ucsf.edu/chimera/...
  14. ncbi Basic local alignment search tool
    S F Altschul
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894
    J Mol Biol 215:403-10. 1990
    ..In addition to its flexibility and tractability to mathematical analysis, BLAST is an order of magnitude faster than existing sequence comparison tools of comparable sensitivity...
  15. pmc MAFFT multiple sequence alignment software version 7: improvements in performance and usability
    Kazutaka Katoh
    Immunology Frontier Research Center, Osaka University, Suita, Osaka, Japan
    Mol Biol Evol 30:772-80. 2013
    ..Some examples incorrectly aligned by MAFFT are also shown to clarify its limitations. We discuss how to avoid misalignments, and our ongoing efforts to overcome such limitations...
  16. pmc WebLogo: a sequence logo generator
    Gavin E Crooks
    Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
    Genome Res 14:1188-90. 2004
    ..A command line interface and the complete, open WebLogo source code are available for local installation and customization...
  17. pmc Mfold web server for nucleic acid folding and hybridization prediction
    Michael Zuker
    Department of Mathematical Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
    Nucleic Acids Res 31:3406-15. 2003
    The abbreviated name, 'mfold web server', describes a number of closely related software applications available on the World Wide Web (WWW) for the prediction of the secondary structure of single stranded nucleic acids...
  18. pmc BLAT--the BLAST-like alignment tool
    W James Kent
    Department of Biology and Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, CA 95064, USA
    Genome Res 12:656-64. 2002
    ..BLAT is compared with other alignment programs on various test sets and then used in several genome-wide applications. http://genome.ucsc.edu hosts a web-based BLAT server for the human genome...
  19. ncbi MRBAYES: Bayesian inference of phylogenetic trees
    J P Huelsenbeck
    Department of Biology, University of Rochester, Rochester, NY 14627, USA
    Bioinformatics 17:754-5. 2001
    ..The program MRBAYES performs Bayesian inference of phylogeny using a variant of Markov chain Monte Carlo...
  20. pmc The UCSC Genome Browser database: update 2011
    Pauline A Fujita
    Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
    Nucleic Acids Res 39:D876-82. 2011
    ..New data highlights include seven new genome assemblies, a Neandertal genome data portal, phenotype and disease association data, a human RNA editing track, and a zebrafish Conservation track. We also describe updates to existing tracks...
  21. pmc Jalview Version 2--a multiple sequence alignment editor and analysis workbench
    Andrew M Waterhouse
    School of Life Sciences Research, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
    Bioinformatics 25:1189-91. 2009
    ..53 compliant sequence or annotation server...
  22. ncbi SOAP2: an improved ultrafast tool for short read alignment
    Ruiqiang Li
    Beijing Genomics Institute at Shenzhen, Shenzhen, 518083, China
    Bioinformatics 25:1966-7. 2009
    ..Additionally, this tool now supports multiple text and compressed file formats. A consensus builder has also been developed for consensus assembly and SNP detection from alignment of short reads on a reference genome...
  23. pmc Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
    Cole Trapnell
    Department of Computer Science, University of Maryland, College Park, Maryland, USA
    Nat Biotechnol 28:511-5. 2010
    ..Here we introduce such algorithms in an open-source software program called Cufflinks...
  24. ncbi Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences
    Weizhong Li
    Burnham Institute for Medical Research La Jolla, CA 92037, USA
    Bioinformatics 22:1658-9. 2006
    ..All these programs can handle huge datasets with millions of sequences and can be hundreds of times faster than methods based on the popular sequence comparison and database search tools, such as BLAST...
  25. pmc The human genome browser at UCSC
    W James Kent
    Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Cruz, CA 95064, USA
    Genome Res 12:996-1006. 2002
    ..The conceptual and technical framework of the browser, its underlying MYSQL database, and overall use are described. The web site currently serves over 50,000 pages per day to over 3000 different users...
  26. pmc MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform
    Kazutaka Katoh
    Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606 8502, Japan
    Nucleic Acids Res 30:3059-66. 2002
    ..FFT-NS-i is over 100 times faster than T-COFFEE, when the number of input sequences exceeds 60, without sacrificing the accuracy...
  27. pmc KEGG for representation and analysis of molecular networks involving diseases and drugs
    Minoru Kanehisa
    Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611 0011, Japan
    Nucleic Acids Res 38:D355-60. 2010
    ..The new disease/drug information resource named KEGG MEDICUS can be used as a reference knowledge base for computational analysis of molecular networks, especially, by integrating large-scale experimental datasets...
  28. pmc The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data
    Aaron McKenna
    Program in Medical and Population Genetics, The Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
    Genome Res 20:1297-303. 2010
    ....
  29. ncbi Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes
    A Krogh
    Center for Biological Sequence Analysis, Technical University of Denmark, Building 208, 2800 Lyngby, Denmark
    J Mol Biol 305:567-80. 2001
    ..We discuss the possible relevance of this finding for our understanding of membrane protein assembly mechanisms. A TMHMM prediction service is available at http://www.cbs.dtu.dk/services/TMHMM/...
  30. ncbi Haploview: analysis and visualization of LD and haplotype maps
    J C Barrett
    Whitehead Institute for Biomedical Research Cambridge, MA 02142, USA
    Bioinformatics 21:263-5. 2005
    ..Haploview is a software package that provides computation of linkage disequilibrium statistics and population haplotype patterns from ..
  31. ncbi TM4: a free, open-source system for microarray data management and analysis
    A I Saeed
    Institute for Genomic Research, Rockville, MD, USA
    Biotechniques 34:374-8. 2003
  32. pmc Ensembl 2011
    Paul Flicek
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 39:D800-6. 2011
    ..Since our previous report, we have substantially improved the presentation and integration of both data of disease relevance and the regulatory state of different cell types...
  33. pmc Integrative genomics viewer
    James T Robinson
    Nat Biotechnol 29:24-6. 2011
  34. pmc The Ribosomal Database Project: improved alignments and new tools for rRNA analysis
    J R Cole
    Center for Microbial Ecology and Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
    Nucleic Acids Res 37:D141-5. 2009
    ..Details about RDP data and analytical functions can be found at http://rdp.cme.msu.edu/...
  35. pmc OrthoMCL: identification of ortholog groups for eukaryotic genomes
    Li Li
    Department of Biology and Genetics, Center for Bioinformatics, and Genomics Institute, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
    Genome Res 13:2178-89. 2003
    ..cbil.upenn.edu/gene-family). Analysis of clusters incorporating P. falciparum genes identifies numerous enzymes that were incompletely annotated in first-pass annotation of the parasite genome...
  36. pmc Cytoscape: a software environment for integrated models of biomolecular interaction networks
    Paul Shannon
    Institute for Systems Biology, Seattle, Washington 98103, USA
    Genome Res 13:2498-504. 2003
    Cytoscape is an open source software project for integrating biomolecular interaction networks with high-throughput expression data and other molecular states into a unified conceptual framework...
  37. pmc A framework for variation discovery and genotyping using next-generation DNA sequencing data
    Mark A DePristo
    Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
    Nat Genet 43:491-8. 2011
    ..We here discuss the application of these tools, instantiated in the Genome Analysis Toolkit, to deep whole-genome, whole-exome capture and multi-sample low-pass (∼4×) 1000 Genomes Project datasets...
  38. pmc BLAST+: architecture and applications
    Christiam Camacho
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
    BMC Bioinformatics 10:421. 2009
    ..Search Tool (BLAST) outperforms exact methods through its use of heuristics, the speed of the current BLAST software is suboptimal for very long queries or database sequences...
  39. ncbi Comparative protein modelling by satisfaction of spatial restraints
    A Sali
    Department of Crystallography, Birkbeck College, London, England
    J Mol Biol 234:779-815. 1993
    ..The method is automated and is illustrated by the modelling of trypsin from two other serine proteinases...
  40. pmc CAP3: A DNA sequence assembly program
    X Huang
    Department of Computer Science, Michigan Technological University, Houghton, Michigan 49931 USA
    Genome Res 9:868-77. 1999
    ..PHRAP often produces longer contigs than CAP3 whereas CAP3 often produces fewer errors in consensus sequences than PHRAP. It is easier to construct scaffolds with CAP3 than with PHRAP on low-pass data with forward-reverse constraints...
  41. ncbi MrBayes 3: Bayesian phylogenetic inference under mixed models
    Fredrik Ronquist
    Department of Systematic Zoology, Evolutionary Biology Centre, Uppsala University, Norbyv 18D, SE 752 36 Uppsala, Sweden
    Bioinformatics 19:1572-4. 2003
    ..g. morphological, nucleotide, and protein-and to explore a wide variety of structured models mixing partition-unique and shared parameters. The program employs MPI to parallelize Metropolis coupling on Macintosh or UNIX clusters...
  42. pmc MUSCLE: a multiple sequence alignment method with reduced time and space complexity
    Robert C Edgar
    Department of Plant and Microbial Biology, 461 Koshland Hall, University of California, Berkeley, CA 94720 3102, USA
    BMC Bioinformatics 5:113. 2004
    ..We introduce a new option, MUSCLE-fast, designed for high-throughput applications. We also describe a new protocol for evaluating objective functions that align two profiles...
  43. ncbi The VideoToolbox software for visual psychophysics: transforming numbers into movies
    D G Pelli
    Department of Psychology, New York University, NY 10003, USA
    Spat Vis 10:437-42. 1997
    ..Transcending the particular computer and language, we discuss the nature of the computer-display interface, and how to calibrate and control it...
  44. pmc SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB
    Elmar Pruesse
    Microbial Genomics Group, Max Planck Institute for Marine Microbiology
    Nucleic Acids Res 35:7188-96. 2007
    ..The ARB software suite with its corresponding rRNA datasets has been accepted by researchers worldwide as a standard tool for ..
  45. pmc Circos: an information aesthetic for comparative genomics
    Martin Krzywinski
    Canada s Michael Smith Genome Sciences Center, Vancouver, British Columbia V5Z 4S6, Canada
    Genome Res 19:1639-45. 2009
    ....
  46. pmc GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research--an update
    Rod Peakall
    Evolution, Ecology and Genetics, Research School of Biology, The Australian National University, Canberra ACT 0200, Australia
    Bioinformatics 28:2537-9. 2012
    ..Export to more than 30 other data formats is provided. Teaching tutorials and expanded step-by-step output options are included. The comprehensive guide has been fully revised...
  47. pmc MAFFT version 5: improvement in accuracy of multiple sequence alignment
    Kazutaka Katoh
    Bioinformatics Center, Institute for Chemical Research, Kyoto University Uji, Kyoto 611 0011, Japan
    Nucleic Acids Res 33:511-8. 2005
    ..Thus, we made a Ruby script, mafftE.rb, which aligns the input sequences together with their close homologues collected from SwissProt using NCBI-BLAST...
  48. pmc Tandem repeats finder: a program to analyze DNA sequences
    G Benson
    Department of Biomathematical Sciences, Mount Sinai School of Medicine, New York, NY 10029 6574, USA
    Nucleic Acids Res 27:573-80. 1999
    ..These sequences range in size from 3 kb up to 700 kb. A World Wide Web server interface atc3.biomath.mssm.edu/trf.html has been established for automated use of the program...
  49. pmc Versatile and open software for comparing large genomes
    Stefan Kurtz
    Center for Bioinformatics, University of Hamburg, Bundesstrasse 43, 20146 Hamburg, Germany
    Genome Biol 5:R12. 2004
    ..The new system is the first version of MUMmer to be released as open-source software. This allows other developers to contribute to the code base and freely redistribute the code...
  50. pmc ABySS: a parallel assembler for short read sequence data
    Jared T Simpson
    Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 4E6, Canada
    Genome Res 19:1117-23. 2009
    ..As a demonstration of the capability of our software, we assembled 3.5 billion paired-end reads from the genome of an African male publicly released by Illumina, Inc...
  51. ncbi TM4 microarray software suite
    Alexander I Saeed
    Department of Bioinformatics, The Institute for Genomic Research, Rockville, MD, USA
    Methods Enzymol 411:134-93. 2006
    Powerful specialized software is essential for managing, quantifying, and ultimately deriving scientific insight from results of a microarray experiment...
  52. pmc Relative expression software tool (REST) for group-wise comparison and statistical analysis of relative expression results in real-time PCR
    Michael W Pfaffl
    Institute of Physiology, FML Weihenstephan, Center of Life and Food Sciences, Technical University of Munich, Germany
    Nucleic Acids Res 30:e36. 2002
    ..Therefore a new software tool was established, named REST (relative expression software tool), which compares two groups, with up to 16 ..
  53. pmc Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB
    T Z DeSantis
    Center for Environmental Biotechnology, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Mail Stop 70A 3317, Berkeley, CA 94720, USA
    Appl Environ Microbiol 72:5069-72. 2006
    ..Putative chimeras were identified in 3% of environmental sequences and in 0.2% of records derived from isolates. Environmental sequences were classified into 100 phylum-level lineages in the Archaea and Bacteria...
  54. ncbi Determination of stable housekeeping genes, differentially regulated target genes and sample integrity: BestKeeper--Excel-based tool using pair-wise correlations
    Michael W Pfaffl
    Physiology, FML Weihenstephan, Centre of Life and Food Science, Technical University of Munich, Germany
    Biotechnol Lett 26:509-15. 2004
    ..The developed, and herein presented, software called BestKeeper determines the best suited standards, out of ten candidates, and combines them into an index...
  55. pmc Database resources of the National Center for Biotechnology Information
    Eric W Sayers
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Nucleic Acids Res 39:D38-51. 2011
    ..Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov...
  56. pmc The variant call format and VCFtools
    Petr Danecek
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK
    Bioinformatics 27:2156-8. 2011
    ..VCFtools is a software suite that implements various utilities for processing VCF files, including validation, merging, comparing and ..
  57. ncbi affy--analysis of Affymetrix GeneChip data at the probe level
    Laurent Gautier
    Center for Biological Sequence Analysis CBS, Technical University of Denmark, Building 208, 2800 Lyngby, Denmark
    Bioinformatics 20:307-15. 2004
    ..The processing of the Affymetrix GeneChip data has been a recent focus for data analysts. Alternatives to the original procedure have been proposed and some of these new methods are widely used...
  58. pmc miRBase: tools for microRNA genomics
    Sam Griffiths-Jones
    Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester, UK
    Nucleic Acids Res 36:D154-8. 2008
    ..miRBase is available at http://microrna.sanger.ac.uk/...
  59. ncbi Java Treeview--extensible visualization of microarray data
    Alok J Saldanha
    Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
    Bioinformatics 20:3246-8. 2004
    Open source software encourages innovation by allowing users to extend the functionality of existing applications...
  60. ncbi Artemis: sequence visualization and annotation
    K Rutherford
    The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
    Bioinformatics 16:944-5. 2000
    ..Sequences and annotation can be read and written directly in EMBL, GenBank and GFF format. AVAILABITLTY: Artemis is available under the GNU General Public License from http://www.sanger.ac.uk/Software/Artemis
  61. pmc MEME SUITE: tools for motif discovery and searching
    Timothy L Bailey
    Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
    Nucleic Acids Res 37:W202-8. 2009
    ..All of the motif-based tools are now implemented as web services via Opal. Source code, binaries and a web server are freely available for noncommercial use at http://meme.nbcr.net...
  62. pmc SIFT: Predicting amino acid changes that affect protein function
    Pauline C Ng
    Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue N A1 162, Seattle, WA 98109, USA
    Nucleic Acids Res 31:3812-4. 2003
    ..We have shown that SIFT can distinguish between functionally neutral and deleterious amino acid changes in mutagenesis studies and on human polymorphisms. SIFT is available at http://blocks.fhcrc.org/sift/SIFT.html...
  63. pmc GenBank
    Dennis A Benson
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Nucleic Acids Res 39:D32-7. 2011
    ..Complete bimonthly releases and daily updates of the GenBank database are available by FTP. To access GenBank and its related retrieval and analysis services, begin at the NCBI Homepage: www.ncbi.nlm.nih.gov...
  64. pmc A flexible and accurate genotype imputation method for the next generation of genome-wide association studies
    Bryan N Howie
    Department of Statistics, University of Oxford, Oxford, UK
    PLoS Genet 5:e1000529. 2009
    ....
  65. ncbi Recent developments in the MAFFT multiple sequence alignment program
    Kazutaka Katoh
    Digital Medicine Initiative, Kyushu University, Fukuoka 812 8582, Japan
    Brief Bioinform 9:286-98. 2008
    ..To rapidly construct a reasonable MSA, we developed the initial version of the MAFFT program in 2002. MSA software is now facing greater challenges in both scalability and accuracy than those of 5 years ago...
  66. pmc PLINK: a tool set for whole-genome association and population-based linkage analyses
    Shaun Purcell
    Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA
    Am J Hum Genet 81:559-75. 2007
    ..Analysis of the patterns of segmental sharing has the potential to map disease loci that contain multiple rare variants in a population-based linkage analysis...
  67. pmc FastTree 2--approximately maximum-likelihood trees for large alignments
    Morgan N Price
    Physical Biosciences Division, Lawrence Berkeley National Lab, Berkeley, California, United States of America
    PLoS ONE 5:e9490. 2010
    ..We recently described FastTree, a tool for inferring phylogenies for alignments with up to hundreds of thousands of sequences. Here, we describe improvements to FastTree that improve its accuracy without sacrificing scalability...
  68. pmc qBase relative quantification framework and software for management and automated analysis of real-time quantitative PCR data
    Jan Hellemans
    Center for Medical Genetics, Ghent University Hospital, De Pintelaan, B 9000 Ghent, Belgium
    Genome Biol 8:R19. 2007
    ..These models and algorithms are implemented in qBase, a free program for the management and automated analysis of qPCR data...
  69. ncbi Open source clustering software
    M J L de Hoon
    Human Genome Center, Institute of Medical Science, University of Tokyo, 4 6 1 Shirokanedai, Minato ku, Tokyo, 108 8639 Japan
    Bioinformatics 20:1453-4. 2004
    ..In addition, we generated a Python and a Perl interface to the C Clustering Library, thereby combining the flexibility of a scripting language with the speed of C...
  70. pmc Human MicroRNA targets
    Bino John
    Computational Biology Center, Memorial Sloan Kettering Cancer Center, New York, New York, USA
    PLoS Biol 2:e363. 2004
    ..Detailed information about target genes, target processes, and open-source software for target prediction (miRanda) is available at http://www.microrna.org...
  71. ncbi MapChart: software for the graphical presentation of linkage maps and QTLs
    R E Voorrips
    Plant Research International, P O Box 16, 6700 AA Wageningen, The Netherlands
    J Hered 93:77-8. 2002
  72. pmc InterProScan: protein domains identifier
    E Quevillon
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 33:W116-20. 2005
    ..O'Reilly Publishers, Sebastopol, CA, http://www.w3.org/TR/soap/] are also available to the users. Various output formats are supported and include text tables, XML documents, as well as various graphs to help interpret the results...
  73. pmc ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data
    Kai Wang
    Center for Applied Genomics, Children s Hospital of Philadelphia, PA 19104, USA
    Nucleic Acids Res 38:e164. 2010
    ..7 million variants, making it practical to handle hundreds of human genomes in a day. ANNOVAR is freely available at http://www.openbioinformatics.org/annovar/...
  74. pmc The UCSC Genome Browser database: update 2010
    Brooke Rhead
    Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
    Nucleic Acids Res 38:D613-9. 2010
    ....
  75. ncbi TASSEL: software for association mapping of complex traits in diverse samples
    Peter J Bradbury
    United States Department of Agriculture Agricultural Research Service, Institute for Genomic Diversity, Cornell University, Ithaca, New York, USA
    Bioinformatics 23:2633-5. 2007
    ..Other features include analyzing insertions/deletions, calculating diversity statistics, integration of phenotypic and genotypic data, imputing missing data and calculating principal components...
  76. ncbi MODELTEST: testing the model of DNA substitution
    D Posada
    Department of Zoology, Brigham Young University, 574 WIDB, Provo, UT 84602 5255, USA
    Bioinformatics 14:817-8. 1998
    ..The program MODELTEST uses log likelihood scores to establish the model of DNA evolution that best fits the data...
  77. pmc ARB: a software environment for sequence data
    Wolfgang Ludwig
    Lehrstuhl fur Mikrobiologie, Technische Universitat Munchen, D 853530 Freising, Germany
    Nucleic Acids Res 32:1363-71. 2004
    ..The ARB program package comprises a variety of directly interacting software tools for sequence database maintenance and analysis which are controlled by a common graphical user interface...
  78. pmc The HHpred interactive server for protein homology detection and structure prediction
    Johannes Söding
    Department of Protein Evolution, Max Planck Institute for Developmental Biology Spemannstrasse 35, 72076 Tubingen, Germany
    Nucleic Acids Res 33:W244-8. 2005
    ..templates selected from the search results, as well as 3D structural models that are calculated by the MODELLER software from these alignments. A detailed help facility is available...
  79. pmc The Amber biomolecular simulation programs
    David A Case
    Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Raod, TPC15, La Jolla, CA 92037, USA
    J Comput Chem 26:1668-88. 2005
    ....
  80. pmc The IntAct molecular interaction database in 2012
    Samuel Kerrien
    EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 40:D841-6. 2012
    ..IntAct is an active contributor to the IMEx consortium (http://www.imexconsortium.org). IntAct source code and data are freely available at http://www.ebi.ac.uk/intact...
  81. ncbi Clustal W and Clustal X version 2.0
    M A Larkin
    The Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
    Bioinformatics 23:2947-8. 2007
    ..ebi.ac.uk/tools/clustalw2. The source code and executables for Windows, Linux and Macintosh computers are available from the EBI ftp site ftp://ftp.ebi.ac.uk/pub/software/clustalw2/
  82. pmc MEGAN analysis of metagenomic data
    Daniel H Huson
    Center for Bioinformatics, Tubingen University, Sand 14, 72076 Tubingen, Germany
    Genome Res 17:377-86. 2007
    ..The software allows large data sets to be dissected without the need for assembly or the targeting of specific phylogenetic ..
  83. ncbi Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis
    J Castresana
    European Molecular Biology Laboratory, Heidelberg, Germany
    Mol Biol Evol 17:540-52. 2000
    ....
  84. pmc Database resources of the National Center for Biotechnology Information
    Eric W Sayers
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Nucleic Acids Res 38:D5-16. 2010
    ..Augmenting many of the web applications are custom implementations of the BLAST program optimized to search specialized data sets. All these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov...
  85. pmc The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes
    F Meyer
    Mathematics and Computer Science Division, Argonne National Laboratory, 9700 S Cass Avenue, Argonne, IL 60439, USA
    BMC Bioinformatics 9:386. 2008
    ..High-throughput, low-cost next-generation sequencing has provided access to metagenomics to a wide range of researchers...
  86. ncbi BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks
    Steven Maere
    Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology VIB, Ghent University, Technologiepark 927, B 9052, Ghent, Belgium
    Bioinformatics 21:3448-9. 2005
    ....
  87. ncbi Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research
    Ana Conesa
    Centro de Genomica, Instituto Valenciano de Investigaciones Agrarias, Moncada, Valencia, Spain
    Bioinformatics 21:3674-6. 2005
    ..This tool offers a suitable platform for functional genomics research in non-model species. B2G is an intuitive and interactive desktop application that allows monitoring and comprehension of the whole annotation and analysis process...
  88. pmc Ensembl's 10th year
    Paul Flicek
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 38:D557-62. 2010
    ..to Ensembl since our previous report include the incorporation of the human GRCh37 assembly, enhanced visualisation and data-mining options for the Ensembl regulatory features and continued development of our software infrastructure.
  89. pmc SMART 6: recent updates and new developments
    Ivica Letunic
    EMBL, Meyerhofstrasse 1, 69012 Heidelberg, Germany
    Nucleic Acids Res 37:D229-32. 2009
    ..In addition to the standard web access to the database, users can now query SMART using distributed annotation system (DAS) or through a simple object access protocol (SOAP) based web service...
  90. pmc Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists
    Da Wei Huang
    Laboratory of Immunopathogenesis and Bioinformatics, Clinical Services Program, SAIC Frederick, Inc, National Cancer Institute at Frederick, Frederick, MD 21702, USA
    Nucleic Acids Res 37:1-13. 2009
    ....
  91. pmc Mapping short DNA sequencing reads and calling variants using mapping quality scores
    Heng Li
    The Wellcome Trust Sanger Institute, Hinxton CB10 1SA, United Kingdom
    Genome Res 18:1851-8. 2008
    ..reads, typically of a few tens of base pairs, and to use these reads effectively requires new algorithms and software. In particular, there is a major issue in efficiently aligning short reads to a reference genome and handling ..
  92. pmc Reactome knowledgebase of human biological pathways and processes
    Lisa Matthews
    Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
    Nucleic Acids Res 37:D619-22. 2009
    ..Reactome's data content and software can all be freely used and redistributed under open source terms.
  93. pmc JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles
    Elodie Portales-Casamar
    Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, 950 West 28th Avenue, Vancouver, BC V5Z 4H4, Canada
    Nucleic Acids Res 38:D105-10. 2010
    ..Additionally, three new special collections provide matrix profile data produced by recent alternative high-throughput approaches...
  94. ncbi Profile hidden Markov models
    S R Eddy
    Department of Genetics, Washington University School of Medicine, 4566 Scott Avenue, St Louis, MO 63110, USA
    Bioinformatics 14:755-63. 1998
    The recent literature on profile hidden Markov model (profile HMM) methods and software is reviewed...
  95. pmc Integration of biological networks and gene expression data using Cytoscape
    Melissa S Cline
    Institut Pasteur, 25 28 Rue du Docteur Roux, 75724 Paris Cedex 15, France
    Nat Protoc 2:2366-82. 2007
    Cytoscape is a free software package for visualizing, modeling and analyzing molecular and genetic interaction networks...
  96. ncbi ProtTest: selection of best-fit models of protein evolution
    Federico Abascal
    Department of Biochemistry, Genetics and Immunology, Universidad de Vigo, Spain
    Bioinformatics 21:2104-5. 2005
    ..We have built a tool for the selection of the best-fit model of evolution, among a set of candidate models, for a given protein sequence alignment...
  97. pmc PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls
    Joel Rozowsky
    Molecular Biophysics and Biochemistry Dept, Yale University, PO Box 208114, New Haven, Connecticut 06520 8114, USA
    Nat Biotechnol 27:66-75. 2009
    ..Our scoring procedure enables us to optimize experimental design by estimating the depth of sequencing required for a desired level of coverage and demonstrating that more than two replicates provides only a marginal gain in information...
  98. pmc PANTHER: a library of protein families and subfamilies indexed by function
    Paul D Thomas
    Protein Informatics, Celera Genomics, Foster City, California 94404, USA
    Genome Res 13:2129-41. 2003
    ..Third, we use the family HMMs to rank missense single nucleotide polymorphisms (SNPs), on a database-wide scale, according to their likelihood of affecting protein function...
  99. pmc AmiGO: online access to ontology and annotation data
    Seth Carbon
    Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
    Bioinformatics 25:288-9. 2009
    ..AmiGO is free open source software developed and maintained by the GO Consortium.
  100. pmc BioMart Central Portal--unified access to biological data
    Syed Haider
    EMBL European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, Computer Laboratory, University of Cambridge, 15 JJ Thomson Avenue, Cambridge CB3 0FD, UK
    Nucleic Acids Res 37:W23-7. 2009
    ..The website is free and open to all users and there is no login requirement...

Research Grants90

  1. Functional discovery of Porphyromonas gingivalis genes
    Tsute Chen; Fiscal Year: 2006
    ..abstract_text> ..
  2. Single Molecule Studies of SNARE-Induced Vesicle Fusion
    Axel T Brunger; Fiscal Year: 2010
    ..Such a system could serve as an efficient model system for novel drug discovery. ..
  3. PERCEPTION AND PRODUCTION OF EXPRESSIVE MICROSTRUCTURE
    Bruno Repp; Fiscal Year: 2002
    ..This research is expected to provide new insights into the largely subconscious psychological processes underlying the flexible control of timing in both musical and nonmusical contexts. ..
  4. EEG BASED BRAIN COMPUTER INTERFACE
    JONATHAN WOLPAW; Fiscal Year: 2003
    ..If successful, this work is likely to improve performance and versatility of EEG-based communication and interface systems. ..
  5. Research Priorities in Ambulatory Management of Obstructive Sleep Apnea Workshop
    SAMUEL KUNA; Fiscal Year: 2007
    ..We submit that this workshop is an essential ?next step? to ensuring that there is[unreadable] substantive advancement of scientific knowledge in this important field. ..
  6. Sleep Apnea and Obesity: Cardiovascular Risk Assessment
    Atul Malhotra; Fiscal Year: 2008
    ..This data may have important implications for the diagnosis and treatment of these abnormalities. ..
  7. Genomewide discovery & analysis of alternative promoters
    Ramana Davuluri; Fiscal Year: 2009
    ....
  8. STATISTICAL APPROACHES TO THE STUDY OF GXE INTERACTIONS
    W Gauderman; Fiscal Year: 2002
    ..and evaluate methods of characterizing GxE interestion for a measured gene, and Develop algorithms and associated software for computing sample size and power in the context of gene-finding or gene-characterization studies...
  9. Methionine Recycling Pathways in Klebsiella
    Jeffrey Lawrence; Fiscal Year: 2006
    ..In this way, characterization of these pathways sheds light on the evolution of complex metabolism, and on the selective forces that lead to gene acquisition, gene loss, and genome change. ..
  10. METHODS FOR FUNCTIONAL/COMPARATIVE GENOMICS
    Xun Gu; Fiscal Year: 2003
    ..abstract_text> ..
  11. KNOWLEDGE MANAGEMENT OF THE NEUROSCIENTIFIC LITERATURE
    Gully Burns; Fiscal Year: 2005
    ....
  12. REDOX INTERACTIONS OF DT DIAPHORASE AND VITAMIN E
    DANIEL LIEBLER; Fiscal Year: 2002
    ..Answers to these questions are essential to improving our understanding of the interplay between cellular antioxidant defenses and their roles in human health and disease. ..
  13. Long-term Ambulatory Gait Monitor for Parkinson's Disease
    Steven Moore; Fiscal Year: 2007
    ..Linear acceleration and angular velocity of the measured leg are processed by SAGE software (SAGE-S) to provide an accurate measure of every stride taken by the subject, and the frequency characteristics ..
  14. Second Gordon Research Conference on Toxicogenomics
    DANIEL LIEBLER; Fiscal Year: 2005
    ..abstract_text> ..
  15. PROTEIN TARGETS OF ENVIRONMENTAL CHEMICALS
    DANIEL LIEBLER; Fiscal Year: 2008
    ..These studies will lay the groundwork for applying molecular target analysis to proteomes in toxicology. ..
  16. Aging Influence on the Development of Sleep Apnea
    Atul Malhotra; Fiscal Year: 2007
    ..abstract_text> ..
  17. CYTOCHROME P450 MODELS FOR RISK ASSESSMENT
    Jeffrey Jones; Fiscal Year: 2007
    ..Thus, this proposal also helps to train scientists in the use of multidisciplinary approaches, at the chemical/biological interface, to understanding a given scientific problem. [unreadable] [unreadable] [unreadable]..
  18. 2006 Diffraction Methods in Structual Biology Conference
    Paul Adams; Fiscal Year: 2006
    ..Junior participation will be encouraged with time for discussion after talks and a session devoted to talks selected from the poster-presentations. [unreadable] [unreadable] [unreadable] [unreadable]..
  19. Inferring the Roadmap of Bacterial Gene Transfer
    Jeffrey Lawrence; Fiscal Year: 2009
    ..This framework will allow us to test the hypothesis that gene transfer occurs more often between more closely related lineages. ..
  20. Cortisol Activity and Sexual Abuse
    Jennie Noll; Fiscal Year: 2006
    ..5) To provide a comprehensive evaluation of the effect of extrahypothalamic CRH regulated behaviors on cortisol concentrations and reactivity. ..
  21. Improving Bayesian Phylogeny
    Bret Larget; Fiscal Year: 2006
    ..abstract_text> ..
  22. Adverse Outcomes of Dual Use of Health Systems Among Older Male Veterans
    FREDRIC WOLINSKY; Fiscal Year: 2006
    ..unreadable] [unreadable] [unreadable] [unreadable]..
  23. Health and Health Services Use in the HRS/AHEAD
    FREDRIC WOLINSKY; Fiscal Year: 2008
    ..Linear and non-linear regression and random effects models will also be used where appropriate. [unreadable] [unreadable]..
  24. Genome Evolution in Pathogens: The roles of predator-prey interactions
    Jeffrey G Lawrence; Fiscal Year: 2010
    ....
  25. Wireless Digital Link Companion Microphone
    PAUL L GIBSON; Fiscal Year: 2010
    ..The proposed technology addresses these issues by miniaturizing the microphone and integrating a novel ultra-low-power UWB radio directly into the hearing aid with a minimal effect on battery life. ..
  26. Dynamin: Ligand Interactions and Conformational Dynamics
    David Jameson; Fiscal Year: 2009
    ..abstract_text> ..
  27. Comparative genomics with the VISTA/LAGAN computational system
    Inna Dubchak; Fiscal Year: 2009
    ..This proposal seeks support to create a stable stand-alone software system, based on improvements and modifications to our current tools, which a researcher could use in his own ..
  28. A Genome-wide Association Study of Childhood Respiratory Outcomes
    WILLIAM GAUDERMAN; Fiscal Year: 2009
    ..End of Abstract) ..
  29. Novel Druggable Exosites in Protein Kinases
    Ruben Abagyan; Fiscal Year: 2009
    ..The nature of the project is multi-disciplinary and we believe that the goals are within reach due to our combined expertise in computational, molecular and structural biology. ..
  30. LABELIT: Automated Diffraction Analysis for X-ray Crystallography
    Nicholas Sauter; Fiscal Year: 2009
    ..We recently introduced novel methods in our software package, LABELIT (Lawrence Berkeley Laboratory Indexing Toolbox), which we will further develop and extend...
  31. Diffraction Methods in Structural Biology 2008 Gordon Research Conference
    Paul Adams; Fiscal Year: 2008
    ..and Andrew Leslie (MRC-LMB, Cambridge, Vice-Chair) and will include presentations from many of the key software and hardware developers in the field...
  32. Cleveland Clinic Orthopaedic Research Training Grant
    JOSEPH IANNOTTI; Fiscal Year: 2008
    ..abstract_text> ..
  33. Combining Computational and Experimentation to Interrogate NF-kappaB Signaling
    Markus Covert; Fiscal Year: 2008
    ..We propose to use computer modeling and experiments to help us understand the NF-kappaB signaling network and its role in cancer development, particularly with regard to diffuse large B cell lymphomas. ..
  34. Continuity of Care and Health Outcomes: Does It Really Matter?
    FREDRIC WOLINSKY; Fiscal Year: 2008
    ..unreadable] [unreadable] [unreadable] [unreadable] [unreadable]..
  35. Ambulatory Real Time High Channel Count Electroencephalograph
    Paul Gibson; Fiscal Year: 2008
    ..The application of UWB to EEG monitoring is new and innovative. It will offer a significant improvement to the field over the slower existing technology. No comparable device is currently available. [unreadable] [unreadable] [unreadable]..
  36. DyNADS: A Dynamic Network Analysis Decision Support Tool for Nurse Managers
    Joyce A Verran; Fiscal Year: 2010
    ..3. Evaluate DyNADS'validity, scalability, and usefulness through a field test. 4. Evaluate the feasibility of implementing DyNADS or nursing units. ..
  37. PHYSIOLOGICAL BASES OF OTOTRAUMATIC INSULT
    Glen Martin; Fiscal Year: 2005
    ..The third hypothesis tests whether susceptibility to hearing loss or the prevention from it is associated with specific molecules in the cochlea. ..
  38. Covalent Binding Methods for Early Drug Development
    Jeffrey Jones; Fiscal Year: 2003
    ....
  39. COMPARATIVE GENOMIC ANALYSIS OF CARDIOVASCULAR GENE REGU
    Inna Dubchak; Fiscal Year: 2003
    ..6) The establishment of an educational program for cardiovascular researchers in the use of genomic databases and tools. ..
  40. PHARYNGEAL AIRWAY FUNCTION
    SAMUEL KUNA; Fiscal Year: 2003
    ....
  41. IDENTIFICATION OF CLINICALLY RELEVANT CHANGES IN HRQOL
    FREDRIC WOLINSKY; Fiscal Year: 2002
    ..abstract_text> ..
  42. Wireless Home Patient-Management Internet Appliances
    Paul Gibson; Fiscal Year: 2004
    ..Thorough testing established the feasibility of the system approach. In phase II, a production prototype home patient-management Internet appliance system will be developed and tested. ..
  43. Cross-species gene finding and annotation
    Lior Pachter; Fiscal Year: 2004
    ..The computational complexity of the problem is greatly reduced by the use of something we call an approximate alignment. ..
  44. RESPIRATORY RELATED MOTOR OUTPUT TO UPPER AIRWAY MUSLCES
    SAMUEL KUNA; Fiscal Year: 2003
    ..This work is an expansion of work conducted to date by the PI, who has recently relocated to the University of Pennsylvania. ..
  45. PERCEPTUAL MODEL FOR WORKSTATION DISPLAY OPTIMIZATION
    Dev Chakraborty; Fiscal Year: 2003
    ..It seeks to apply the powerful Visual Display Model (VDM) software, developed at Sarnoff over the last 20 years, to the problem of workstation optimization for digital mammography...
  46. DPOAE PHENOTYPING OF COCHLEAR FUNCTION
    Glen Martin; Fiscal Year: 2001
    ..The resulting data will be made widely available on the internet in the form of databases and the relevant training manuals. ..
  47. Splicing, Folding, and Stretching Nucleic Acids
    DANIEL AALBERTS; Fiscal Year: 2003
    ..Calculations are straightforward for this two-state model and preliminary results suggest they compare well with recent stretched DNA experiments. The SFJC is also handy for modeling single-stranded loop sections of RNA. ..
  48. TRIPLE QUADRUPOLE MASS SPECTROMETER
    Jeffrey Jones; Fiscal Year: 2001
    ..T specific DNA-binding properties of a human protein; and quantitation and identification of isoprostane biomarkers of oxidative stress. ..
  49. Serum albumin adducts in type 2 diabetes & prediabetes
    DANIEL LIEBLER; Fiscal Year: 2005
    ..These studies will bring the most sensitive and specific analytical proteomics technologies available to identify new markers for type 2 diabetes and pre-diabetes. ..
  50. COMPUTERIZED DETECTION OF PULMONARY NODULES
    Hiroyuki Yoshida; Fiscal Year: 2002
    ..Such a high-performance CAD scheme should advance the early detection of pulmonary nodules, and therefore has the potential to improve the prognosis for patients. ..
  51. Biologically Based Reaction Network Modeling of P4502E1
    Brad Reisfeld; Fiscal Year: 2005
    ....
  52. Offspring of Maltreated Mothers:Prenatal & Infant Health
    Jennie Noll; Fiscal Year: 2006
    ..The training component will involve extensive independent reading, coursework, seminars, conferences, and concentrated time with mentors. ..
  53. GENOME SCIENCE EDUCATION PROGRAM
    LOUISA STARK; Fiscal Year: 2006
    ..The GSEP project represents the development and functional testing of an innovative model for improving the science literacy of teachers, student and the lay public. ..
  54. Protein Damage in Oxidative Stress and Disease
    DANIEL LIEBLER; Fiscal Year: 2006
    ..These presentations collectively represent the state-of-the-art in the analysis protein damage and the exploration of protein damage as a cause of environmentally-related disease. [unreadable] [unreadable] [unreadable] [unreadable]..
  55. MOLECULAR DYNAMICS SIMULATIONS OF DNA OLIGONUCLEOTIDES
    David Beveridge; Fiscal Year: 2003
    ..abstract_text> ..
  56. PERCEPTUAL MODEL FOR WORKSTATION DISPLAY OPTIMIZATION
    Dev Chakraborty; Fiscal Year: 2002
    ..It seeks to apply the powerful Visual Display Model (VDM) software, developed at Sarnoff over the last 20 years, to the problem of workstation optimization for digital mammography...
  57. Wireless Digital Link Companion Microphone
    Paul Gibson; Fiscal Year: 2006
    ..These individuals have a reduced ability to understand speech in noise-filled environments. [unreadable] [unreadable] [unreadable]..
  58. Blood lead levels and development of asthma
    Christine Joseph; Fiscal Year: 2002
    ....
  59. Fragment assembly and metabolic/species diversity analysis for Human microbiome p
    Yuzhen Ye; Fiscal Year: 2010
    ..These software tools will enable researchers to efficiently and effectively analyze the data from HMP, which will enhance the ..
  60. Hierarchical Methods for Large BioMolecular Complexes
    Chandrajit L Bajaj; Fiscal Year: 2010
    ..In particular we propose the development of hierarchical computational representations, algorithms and software, which automates structural feature determination of LBCs as well as speeds up match and fitting techniques ..
  61. INCLUSION OF COMORBIDITY IN ONCOLOGY DATA REGISTRIES
    Jay Piccirillo; Fiscal Year: 2002
    ..An alternative, low-cost option to train registrars to code comorbidity and provide updated information is to use the Internet via the World Wide Web. ..
  62. Retinal Tracking for Enhances OCT Imaging
    R Ferguson; Fiscal Year: 2004
    ..Adjacent 2-D scans can be concatenated into 3-D data sets. Standard resolution and high resolution TOCT systems will be assembled and tested in clinical studies at New England Eye Center. ..
  63. Aerodynamic and Acoustic Models of Phonation
    Ronald Scherer; Fiscal Year: 2006
    ..This research program is a collaboration among laboratories at Bowling Green State University, Purdue University, the University of Toledo, and Washington University in Saint Louis. ..
  64. Computational Statistic Approaches to Gene-Environment Interaction
    SEBASTIAN ZOELLNER; Fiscal Year: 2009
    ..All the tools and methods we develop will be incorporated into publicly available software. We have access to genotype and phenotype data from the NIMH bipolar genetics initiative...
  65. Kidney Multiphoton Analysis of Therapeutic Agents
    Kenneth Dunn; Fiscal Year: 2007
    ..Since this is not possible with other imaging modalities, this approach complements and extends existing imaging technologies. [unreadable] [unreadable] [unreadable]..
  66. Targeted Alpha-Particle Emitter Therapy of Metastases
    George Sgouros; Fiscal Year: 2009
    ..The work described in this application is intended to develop and evaluate such an approach. ..
  67. Mixed Model Approach to Gene Mapping for Complex Traits
    Shizhong Xu; Fiscal Year: 2005
    ..The number, map positions and effects of QTL responsible for ethological divergence between species will be determined by associating mating behavior with polymorphic molecular markers in interspecific backcross hybrids. ..
  68. Statistical tests for association with X-linked genes
    Eden Martin; Fiscal Year: 2007
    ..Finally software to implement the novel methods for X-linked analysis will be developed and distributed...
  69. Functional Remapping of Hand Control
    FERDINANDO ALESSANDRO MUSSA IVALDI; Fiscal Year: 2010
    ..expected that this study will identify new means for exploiting the ability of the nervous system to reorganize itself so as to facilitate training novel hand movements and to recover skills lost to stroke and other neuromotor disorders ..
  70. Mechanism of Endotoxin's Effect On Allergy Risk
    Keoki Williams; Fiscal Year: 2008
    ..It is the hoped that understanding the mechanism of endotoxin's effect will establish new targets for the prevention of allergies. ..
  71. National Nutrient Databank Conference
    Phyllis Stumbo; Fiscal Year: 2004
    ..current information on analytical values for new food components; an overview of new nutrient calculation software; and national nutrition monitoring updates...
  72. HEARING: DEVELOPMENT OF SYNAPTIC CIRCUITS
    CRAIG HENKEL; Fiscal Year: 2005
    ....
  73. COMMUNITY STEPS TO MINORITY YOUTH FITNESS
    Antronette Yancey; Fiscal Year: 2002
    ..Mediating variables are self-report behaviors and attitudes. 4. Compile and distribute a resource book that includes those behavior change strategies that were observed to work best with this population. ..
  74. DELIVERY OF THE CGN INFORMATION RESOURCE DATABASE
    Prakash Nadkarni; Fiscal Year: 2006
    ..Informatics assistance will be provided to the individual nodes to assist the task of data exchange, and when necessary, to assist the design of local data collection systems. ..
  75. ROBUST QUERY OF HETEROGENEOUS CLINICAL DATABASES
    Prakash Nadkarni; Fiscal Year: 2002
    ..In particular, research will be performed on utilization of newer database technologies, such as new indexing methods, as well as parallel database implementations. ..
  76. DESIGN AND IMPLEMENTATION OF PHARMACOGENETIC DATABASE
    Prakash Nadkarni; Fiscal Year: 2002
    ..Informatics assistance will be provided to the individual nodes to assist the task of data exchange, and when necessary, to assist the design of local data collection systems. ..
  77. Randomized Trial of Tinnitus Retraining Therapy
    Richard Tyler; Fiscal Year: 2008
    ..If TRT is shown to be no more effective than masking or counseling, professionals should focus on more efficient therapeutic techniques. This experiment will test the neurophysiological model of tinnitus. [unreadable] [unreadable]..
  78. A Tailored Asthma Education Program for Urban Teens II
    Christine Joseph; Fiscal Year: 2009
    ..Puff City I software uses "tailoring" in conjunction with theoretical models of behavior change, to personalize health messages ..
  79. STRUCTURE AND PLASTICITY OF CENTRAL HEARING MECHANISMS
    CRAIG HENKEL; Fiscal Year: 2002
    ..Results should lead to a better understanding of the influence of experience on the development of these binaural sensory pathways. ..
  80. CHONDROPROTECTIVE EFFECTS OF SUPEROXIDE DISMUTASE
    Constance Chu; Fiscal Year: 2002
    ..These studies will also serve to improve understanding of the relative roles of NO and peroxynitrite on the pathophysiology of arthritis. ..
  81. ANGIOTENSIN-II BLOCKADE IN MITRAL REGURGITATION
    Maurice Enriquez Sarano; Fiscal Year: 2004
    ..The results of this clinical trial should provide strong evidence regarding medical treatment of patients with organic MR and define future strategies to minimize mortality and morbidity of organic MR. ..
  82. Encyclopedia of E. Coli Genes and Metabolism
    Peter Karp; Fiscal Year: 2005
    ..SRI further proposes to develop new bioinformatics methods for comparative genomics, and for predicting nutritional requirements and essential genes of an organism form its metabolic network. ..
  83. Robust Software Components for Model Organism Databases
    Peter Karp; Fiscal Year: 2003
    We propose to develop a set of robust software components for constructing model-organism databases (MODs)...
  84. Cognitive Processes in Smoking Cessation
    Andrew Waters; Fiscal Year: 2009
    ..Thus, results from this study may help us to identify individuals who are high risk for an early relapse, and facilitate the development of smoking cessation interventions. ..
  85. Home Automatic external Defibrillator Training
    Thomas Rea; Fiscal Year: 2007
    ..Alternatively, if nominal video-based approaches achieve comparable outcomes, training efforts can be streamlined at considerable cost savings with fewer impediments for distribution and dissemination. [unreadable] [unreadable]..
  86. AOSSM Post-Joint Injury Osteoarthritis Conference
    Constance Chu; Fiscal Year: 2008
    ..This symposium will bring doctors and scientists together to develop research plans to find new methods to prevent this from happening. [unreadable] [unreadable] [unreadable] [unreadable]..
  87. Pathway Prediction and Assessment Integrating Multiple Evidence Types
    Peter Karp; Fiscal Year: 2009
    ..We will search the MetaCyc reaction space (comprising almost 6000 reactions) for novel subpathways, explicitly constraining our search using organism-specific evidence (i.e., homology, experimental evidence, etc.) at each step. ..
  88. DEVELOPMENT OF THE METACYC METABOLIC PATHWAY DATABASE
    Peter Karp; Fiscal Year: 2003
    ..MetaCyc is accessed using the same query and visualization software as used for EcoCyc, which is called the Pathway Tools...