algorithms

Summary

Summary: A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.

Top Publications

  1. pmc Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
    Ben Langmead
    Center for Bioinformatics and Computational Biology, Institute for Advanced Computer Studies, University of Maryland, College Park, MD 20742, USA
    Genome Biol 10:R25. 2009
  2. pmc MUSCLE: multiple sequence alignment with high accuracy and high throughput
    Robert C Edgar
    Nucleic Acids Res 32:1792-7. 2004
  3. 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
  4. 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
  5. pmc Velvet: algorithms for de novo short read assembly using de Bruijn graphs
    Daniel R Zerbino
    EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
    Genome Res 18:821-9. 2008
  6. 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
  7. ncbi New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0
    Stephane Guindon
    Méthodes et Algorithmes pour la Bioinformatique, LIRMM, Centre National de la Recherche Scientifique, Universite de Montpellier, Montpellier Cedex 5, France
    Syst Biol 59:307-21. 2010
  8. ncbi Exploration, normalization, and summaries of high density oligonucleotide array probe level data
    Rafael A Irizarry
    Department of Biostatistics, Johns Hopkins University, Baltimore, MD 21205, USA
    Biostatistics 4:249-64. 2003
  9. 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
  10. pmc Model-based analysis of ChIP-Seq (MACS)
    Yong Zhang
    Department of Biostatistics and Computational Biology, Dana Farber Cancer Institute and Harvard School of Public Health, Boston, MA 02115, USA
    Genome Biol 9:R137. 2008

Detail Information

Publications237 found, 100 shown here

  1. pmc Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
    Ben Langmead
    Center for Bioinformatics and Computational Biology, Institute for Advanced Computer Studies, University of Maryland, College Park, MD 20742, USA
    Genome Biol 10:R25. 2009
    ..Multiple processor cores can be used simultaneously to achieve even greater alignment speeds. Bowtie is open source (http://bowtie.cbcb.umd.edu)...
  2. 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...
  3. 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...
  4. 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...
  5. pmc Velvet: algorithms for de novo short read assembly using de Bruijn graphs
    Daniel R Zerbino
    EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
    Genome Res 18:821-9. 2008
    We have developed a new set of algorithms, collectively called "Velvet," to manipulate de Bruijn graphs for genomic sequence assembly...
  6. 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...
  7. ncbi New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0
    Stephane Guindon
    Méthodes et Algorithmes pour la Bioinformatique, LIRMM, Centre National de la Recherche Scientifique, Universite de Montpellier, Montpellier Cedex 5, France
    Syst Biol 59:307-21. 2010
    ..In the meantime, research around PhyML has continued, and this article describes the new algorithms and methods implemented in the program...
  8. ncbi Exploration, normalization, and summaries of high density oligonucleotide array probe level data
    Rafael A Irizarry
    Department of Biostatistics, Johns Hopkins University, Baltimore, MD 21205, USA
    Biostatistics 4:249-64. 2003
    ..Finally, we evaluate the algorithms in terms of their ability to detect known levels of differential expression using the spike-in data...
  9. 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...
  10. pmc Model-based analysis of ChIP-Seq (MACS)
    Yong Zhang
    Department of Biostatistics and Computational Biology, Dana Farber Cancer Institute and Harvard School of Public Health, Boston, MA 02115, USA
    Genome Biol 9:R137. 2008
    ..MACS also uses a dynamic Poisson distribution to effectively capture local biases in the genome, allowing for more robust predictions. MACS compares favorably to existing ChIP-Seq peak-finding algorithms, and is freely available.
  11. 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...
  12. ncbi Principal components analysis corrects for stratification in genome-wide association studies
    Alkes L Price
    Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
    Nat Genet 38:904-9. 2006
    ..Our simple, efficient approach can easily be applied to disease studies with hundreds of thousands of markers...
  13. pmc Statistical significance for genomewide studies
    John D Storey
    Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
    Proc Natl Acad Sci U S A 100:9440-5. 2003
    ..Our approach avoids a flood of false positive results, while offering a more liberal criterion than what has been used in genome scans for linkage...
  14. 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...
  15. ncbi A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood
    Stephane Guindon
    LIRMM, CNRS, 161 rue Ada, 34392, Montpellier Cedex 5, France
    Syst Biol 52:696-704. 2003
    ..pairs from plant plastids, thus reaching a speed of the same order as some popular distance-based and parsimony algorithms. This new method is implemented in the PHYML program, which is freely available on our web page: http://www...
  16. 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...
  17. pmc Inference of population structure using multilocus genotype data
    J K Pritchard
    Department of Statistics, University of Oxford, United Kingdom
    Genetics 155:945-59. 2000
    ..g. , seven microsatellite loci in an example using genotype data from an endangered bird species. The software used for this article is available from http://www.stats.ox.ac.uk/ approximately pritch/home. html...
  18. 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 primary genotype data in a visually appealing and interactive interface...
  19. pmc Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications
    T Sørlie
    Department of Genetics, The Norwegian Radium Hospital, Montebello, N 0310 Oslo, Norway
    Proc Natl Acad Sci U S A 98:10869-74. 2001
    ....
  20. 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
    ....
  21. 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...
  22. pmc Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies
    Daniel Falush
    Department of Molecular Biology, Max Planck Institut für Infektionsbiologie, Schumann Strasse 21 22, 10117 Berlin, Germany
    Genetics 164:1567-87. 2003
    ..The methods are implemented in a program, structure, version 2.0, which is available at http://pritch.bsd.uchicago.edu...
  23. 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...
  24. ncbi Combinatorial microRNA target predictions
    Azra Krek
    Center for Comparative Functional Genomics, Department of Biology, New York University, 100 Washington Square East, New York, New York 10003, USA
    Nat Genet 37:495-500. 2005
    ..In particular, we experimentally validate common regulation of Mtpn by miR-375, miR-124 and let-7b and thus provide evidence for coordinate microRNA control in mammals...
  25. ncbi A comparison of normalization methods for high density oligonucleotide array data based on variance and bias
    B M Bolstad
    Group in Biostatistics, University of California, Berkeley, CA 94720, USA
    Bioinformatics 19:185-93. 2003
    ..Normalization is a process for reducing this variation. It is common to see non-linear relations between arrays and the standard normalization provided by Affymetrix does not perform well in these situations...
  26. ncbi Prediction of mammalian microRNA targets
    Benjamin P Lewis
    Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
    Cell 115:787-98. 2003
    ..The predicted regulatory targets of mammalian miRNAs were enriched for genes involved in transcriptional regulation but also encompassed an unexpectedly broad range of other functions...
  27. 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...
  28. ncbi RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
    Alexandros Stamatakis
    Swiss Federal Institute of Technology Lausanne, School of Computer and Communication Sciences Lab Prof Moret, Station 14, CH 1015 Lausanne, Switzerland
    Bioinformatics 22:2688-90. 2006
    ..The program has been used to compute ML trees on two of the largest alignments to date containing 25,057 (1463 bp) and 2182 (51,089 bp) taxa, respectively...
  29. 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
    ..acid (DNA) sequencing instruments has prompted the recent development of de novo short read assembly algorithms. A common shortcoming of the available tools is their inability to efficiently assemble vast amounts of data ..
  30. ncbi Search and clustering orders of magnitude faster than BLAST
    Robert C Edgar
    Tiburon, CA 94920, USA
    Bioinformatics 26:2460-1. 2010
    ..Biological sequence data is accumulating rapidly, motivating the development of improved high-throughput methods for sequence classification...
  31. 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
    ..TopHat is an efficient read-mapping algorithm designed to align reads from an RNA-Seq experiment to a reference genome without relying on known splice sites...
  32. pmc Fast and accurate long-read alignment with Burrows-Wheeler transform
    Heng Li
    Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
    Bioinformatics 26:589-95. 2010
    ..of them are very efficient for short reads but inefficient or not applicable for reads >200 bp because the algorithms are heavily and specifically tuned for short queries with low sequencing error rate...
  33. 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...
  34. ncbi Fast robust automated brain extraction
    Stephen M Smith
    Oxford Centre for Functional Magnetic Resonance Imaging of the Brain, Department of Clinical Neurology, Oxford University, John Radcliffe Hospital, Headington, Oxford, United Kingdom
    Hum Brain Mapp 17:143-55. 2002
    ..We describe the new method and give examples of results and the results of extensive quantitative testing against "gold-standard" hand segmentations, and two other popular automated methods...
  35. 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
    ..We review these and other techniques that MAFFT uses and suggest possible future directions of MSA software as a basis of comparative analyses. MAFFT is available at http://align.bmr.kyushu-u.ac.jp/mafft/software/...
  36. pmc The transcriptional landscape of the yeast genome defined by RNA sequencing
    Ugrappa Nagalakshmi
    Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA
    Science 320:1344-9. 2008
    ..We also found unexpected 3'-end heterogeneity and the presence of many overlapping genes. These results indicate that the yeast transcriptome is more complex than previously appreciated...
  37. 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...
  38. pmc Human MicroRNA targets
    Bino John
    Computational Biology Center, Memorial Sloan Kettering Cancer Center, New York, New York, USA
    PLoS Biol 2:e363. 2004
    ..microrna.org. Our analysis suggests that miRNA genes, which are about 1% of all human genes, regulate protein production for 10% or more of all human genes...
  39. 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...
  40. pmc Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy
    Qiong Wang
    Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824, USA
    Appl Environ Microbiol 73:5261-7. 2007
    ..It combines the RDP Classifier with a statistical test to flag taxa differentially represented between samples. The RDP Classifier and RDP Library Compare are available online at http://rdp.cme.msu.edu/...
  41. 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...
  42. 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
    ....
  43. pmc EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates
    Albert J Vilella
    EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
    Genome Res 19:327-35. 2009
    ..All data are made available in a number of formats and will be kept up to date with the Ensembl project...
  44. 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
    ....
  45. ncbi Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search
    Andrew Keller
    Institute for Systems Biology, Seattle, Washington 98103, USA
    Anal Chem 74:5383-92. 2002
    ..This analysis makes it possible to filter large volumes of MS/MS database search results with predictable false identification error rates and can serve as a common standard by which the results of different research groups are compared...
  46. ncbi Protein secondary structure prediction based on position-specific scoring matrices
    D T Jones
    Department of Biological Sciences, University of Warwick, Coventry, CV4 7AL, United Kingdom
    J Mol Biol 292:195-202. 1999
    ..Given the success of the method in CASP3, it is reasonable to be confident that the evaluation presented here gives a fair indication of the performance of the method in general...
  47. pmc An efficient algorithm for large-scale detection of protein families
    A J Enright
    Computational Genomics Group, The European Bioinformatics Institute, EMBL Cambridge Outstation, Cambridge CB10 1SD, UK
    Nucleic Acids Res 30:1575-84. 2002
    ..This novel approach does not suffer from the problems that normally hinder other protein sequence clustering algorithms, such as the presence of multi-domain proteins, promiscuous domains and fragmented proteins...
  48. 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
    ..This will facilitate the further development of the alignment algorithms in the future and has allowed proper porting of the programs to the latest versions of Linux, Macintosh and ..
  49. ncbi A multigene assay to predict recurrence of tamoxifen-treated, node-negative breast cancer
    Soonmyung Paik
    Division of Pathology, Operation Center, and the Biostatistics Center, National Surgical Adjuvant Breast and Bowel Project, Pittsburgh 15212, USA
    N Engl J Med 351:2817-26. 2004
    ..The likelihood of distant recurrence in patients with breast cancer who have no involved lymph nodes and estrogen-receptor-positive tumors is poorly defined by clinical and histopathological measures...
  50. pmc Identifying bacterial genes and endosymbiont DNA with Glimmer
    Arthur L Delcher
    Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA
    Bioinformatics 23:673-9. 2007
    ..This module was developed in response to the discovery that eukaryotic genome sequencing projects sometimes inadvertently capture the DNA of intracellular bacteria living in the host...
  51. 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...
  52. pmc Fast and effective prediction of microRNA/target duplexes
    Marc Rehmsmeier
    Universitat Bielefeld, International NRW Graduate School in Bioinformatics and Genome Research, Postfach 10 01 31, 33501 Bielefeld, Germany
    RNA 10:1507-17. 2004
    ..RNAhybrid, with its accompanying programs RNAcalibrate and RNAeffective, is available for download and as a Web tool on the Bielefeld Bioinformatics Server (http://bibiserv.techfak.uni-bielefeld.de/rnahybrid/)...
  53. pmc GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists
    Eran Eden
    Molecular Cell Biology Department, Weizmann Institute of Science, Rehovot, Israel
    BMC Bioinformatics 10:48. 2009
    ..A few tools also exist that support analyzing ranked lists. The latter typically rely on simulations or on union-bound correction for assigning statistical significance to the results...
  54. ncbi Unified segmentation
    John Ashburner
    Wellcome Department of Imaging Neuroscience, 12 Queen Square, London, WC1N 3BG, UK
    Neuroimage 26:839-51. 2005
    ..A strategy for optimising the model parameters is described, along with the requisite partial derivatives of the objective function...
  55. ncbi Genome-wide mapping of in vivo protein-DNA interactions
    David S Johnson
    Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305 5120, USA
    Science 316:1497-502. 2007
    ..96] and statistical confidence (P <10(-4)), properties that were important for inferring new candidate interactions. These include key transcription factors in the gene network that regulates pancreatic islet cell development...
  56. pmc WGCNA: an R package for weighted correlation network analysis
    Peter Langfelder
    Department of Human Genetics and Department of Biostatistics, University of California, Los Angeles, CA 90095, USA
    BMC Bioinformatics 9:559. 2008
    ..While parts of the correlation network methodology have been described in separate publications, there is a need to provide a user-friendly, comprehensive, and consistent software implementation and an accompanying tutorial...
  57. ncbi A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach
    S Whelan
    Department of Zoology, University of Cambridge, Cambridge, England
    Mol Biol Evol 18:691-9. 2001
    ....
  58. ncbi Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome
    Nathaniel D Heintzman
    Ludwig Institute for Cancer Research, University of California San Diego UCSD School of Medicine, 9500 Gilman Drive, La Jolla, California 92093 0653 USA
    Nat Genet 39:311-8. 2007
    ..We developed computational algorithms using these distinct chromatin signatures to identify new regulatory elements, predicting over 200 promoters and ..
  59. ncbi Protein homology detection by HMM-HMM comparison
    Johannes Söding
    Department of Protein Evolution, Max Planck Institute for Developmental Biology Spemannstrasse 35, D 72076 Tubingen, Germany
    Bioinformatics 21:951-60. 2005
    ..Protein homology detection and sequence alignment are at the basis of protein structure prediction, function prediction and evolution...
  60. pmc Removing noise from pyrosequenced amplicons
    Christopher Quince
    Department of Civil Engineering, University of Glasgow, Rankine Building, Oakfield Avenue, Glasgow G12 8LT, UK
    BMC Bioinformatics 12:38. 2011
    ..We use data sets where samples of known diversity have been amplified and sequenced to quantify the effect of each of the sources of error on OTU inflation and to validate these algorithms.
  61. ncbi Coding algorithms for defining comorbidities in ICD-9-CM and ICD-10 administrative data
    Hude Quan
    Department of Community Health Sciences, University of Calgary, Calgary, Alberta, Canada
    Med Care 43:1130-9. 2005
    ..Recognizing this, we conducted a multistep process to develop ICD-10 coding algorithms to define Charlson and Elixhauser comorbidities in administrative data and assess the performance of the ..
  62. ncbi Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry
    Joshua E Elias
    Department of Cell Biology, 240 Longwood Avenue, Harvard Medical School, Boston, Massachusetts 02115, USA
    Nat Methods 4:207-14. 2007
    ....
  63. ncbi R/qtl: QTL mapping in experimental crosses
    Karl W Broman
    Department of Biostatistics, Johns Hopkins University, 615 N Wolfe St, Baltimore, MD 21205, USA
    Bioinformatics 19:889-90. 2003
    ....
  64. 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...
  65. 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
    ..produce very short reads, typically of a few tens of base pairs, and to use these reads effectively requires new algorithms and software...
  66. pmc A comparison of bayesian methods for haplotype reconstruction from population genotype data
    Matthew Stephens
    Department of Statistics, University of Washington, Seattle, WA 98195 4322, USA
    Am J Hum Genet 73:1162-9. 2003
    ..The new algorithm is included in the software package PHASE, version 2.0, available online (http://www.stat.washington.edu/stephens/software.html)...
  67. pmc InParanoid 7: new algorithms and tools for eukaryotic orthology analysis
    Gabriel Ostlund
    Department of Biochemistry and Biophysics, Stockholm Bioinformatics Centre, AlbaNova University Centre, Stockholm University, SE 10691 Stockholm, Sweden
    Nucleic Acids Res 38:D196-203. 2010
    ..To facilitate data exchange and comparisons among ortholog databases, we have developed and are making available two XML schemas: SeqXML for the input sequences and OrthoXML for the output ortholog clusters...
  68. ncbi Improved prediction of signal peptides: SignalP 3.0
    Jannick Dyrløv Bendtsen
    Center for Biological Sequence Analysis, BioCentrum DTU, Building 208, Technical University of Denmark, DK 2800 Lyngby, Denmark
    J Mol Biol 340:783-95. 2004
    ..SignalP consists of two different predictors based on neural network and hidden Markov model algorithms, where both components have been updated...
  69. ncbi T-Coffee: A novel method for fast and accurate multiple sequence alignment
    C Notredame
    National Institute for Medical Research, The Ridgeway, London, NW7 1AA, UK
    J Mol Biol 302:205-17. 2000
    ..The improvement, especially clear with the more difficult test cases, is always visible, regardless of the phylogenetic spread of the sequences in the tests...
  70. ncbi MatInspector and beyond: promoter analysis based on transcription factor binding sites
    K Cartharius
    Genomatix Software GmbH Landsberger Strasse 6, 80339 München, Germany
    Bioinformatics 21:2933-42. 2005
    ..The next steps in promoter analysis can be tackled only with reliable predictions, e.g. finding phylogenetically conserved patterns or identifying higher order combinations of sites in promoters of co-regulated genes...
  71. ncbi RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees
    A Stamatakis
    Department of Computer Science, Technical University of Munich Boltzmannstrasse 3, D 85748 München, Germany
    Bioinformatics 21:456-63. 2005
    ..Due to the combinatorial and computational complexity the size of trees which can be computed on a Biologist's PC workstation within reasonable time is limited to trees containing approximately 100 taxa...
  72. ncbi Imaging intracellular fluorescent proteins at nanometer resolution
    Eric Betzig
    Howard Hughes Medical Institute, Janelia Farm Research Campus, Ashburn, VA 20147, USA
    Science 313:1642-5. 2006
    ....
  73. pmc A new statistical method for haplotype reconstruction from population data
    M Stephens
    Department of Statistics, University of Oxford
    Am J Hum Genet 68:978-89. 2001
    ..applicable to genotype data at linked loci from a population sample, that improves substantially on current algorithms; often, error rates are reduced by > 50%, relative to its nearest competitor...
  74. ncbi Improved scoring of functional groups from gene expression data by decorrelating GO graph structure
    Adrian Alexa
    Max Planck Institute for Informatics Stuhlsatzenhausweg 85, D 66123 Saarbrucken, Germany
    Bioinformatics 22:1600-7. 2006
    ..g. based on Gene Ontology (GO). We develop methods that increase the explanatory power of this approach by integrating knowledge about relationships between the GO terms into the calculation of the statistical significance...
  75. ncbi Rank products: a simple, yet powerful, new method to detect differentially regulated genes in replicated microarray experiments
    Rainer Breitling
    Plant Science Group, Institute of Biomedical and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
    FEBS Lett 573:83-92. 2004
    ..In addition, using RP can lead to a sharp reduction in the number of replicate experiments needed to obtain reproducible results...
  76. pmc SNP detection for massively parallel whole-genome resequencing
    Ruiqiang Li
    Beijing Genomics Institute at Shenzhen, Shenzhen 518000, China
    Genome Res 19:1124-32. 2009
    ..Our analyses demonstrate that our method has a very low false call rate at any sequencing depth and excellent genome coverage at a high sequencing depth...
  77. ncbi A neural substrate of prediction and reward
    W Schultz
    Institute of Physiology, University of Fribourg, CH 1700 Fribourg, Switzerland
    Science 275:1593-9. 1997
    ..Taken together, these findings can be understood through quantitative theories of adaptive optimizing control...
  78. ncbi Accurate determination of microbial diversity from 454 pyrosequencing data
    Christopher Quince
    Department of Civil Engineering, Rankine Building, University of Glasgow, Glasgow, UK
    Nat Methods 6:639-41. 2009
    ..We pyrosequenced a known mixture of microbial 16S rDNA sequences extracted from a lake and found that without noise reduction the number of operational taxonomic units is overestimated but using PyroNoise it can be accurately calculated...
  79. pmc Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering
    Sharon R Browning
    Department of Statistics, The University of Auckland, Auckland, New Zealand
    Am J Hum Genet 81:1084-97. 2007
    ..1 days of computing time, with 99% of masked alleles imputed correctly. Our method is implemented in the Beagle software package, which is freely available...
  80. pmc High-quality draft assemblies of mammalian genomes from massively parallel sequence data
    Sante Gnerre
    Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
    Proc Natl Acad Sci U S A 108:1513-8. 2011
    ..The ALLPATHS-LG program is available at http://www.broadinstitute.org/science/programs/genome-biology/crd...
  81. pmc PROSITE, a protein domain database for functional characterization and annotation
    Christian J A Sigrist
    Structural Biology and Bioinformatics Department, University of Geneva, Swiss Institute of Bioinformatics, Centre Medical Universitaire, CH 1211 Geneva 4, Switzerland
    Nucleic Acids Res 38:D161-6. 2010
    ..The latest version of PROSITE (release 20.54, of 22 September 2009) contains 1308 patterns, 863 profiles and 869 ProRules. PROSITE is accessible at: http://www.expasy.org/prosite/...
  82. ncbi GROMACS: fast, flexible, and free
    David van der Spoel
    Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box 596, S 75124 Uppsala, Sweden
    J Comput Chem 26:1701-18. 2005
    ..It is maintained by a group of developers from the Universities of Groningen, Uppsala, and Stockholm, and the Max Planck Institute for Polymer Research in Mainz. Its Web site is http://www.gromacs.org...
  83. ncbi Discovering microRNAs from deep sequencing data using miRDeep
    Marc R Friedländer
    Max Delbruck Centrum fur Molekulare Medizin, Robert Rossle Strasse 10, D 13125 Berlin Buch, Germany
    Nat Biotechnol 26:407-15. 2008
    ..miRDeep reports altogether approximately 230 previously unannotated miRNAs, of which four novel C. elegans miRNAs are validated by northern blot analysis...
  84. pmc The sequence and de novo assembly of the giant panda genome
    Ruiqiang Li
    BGI Shenzhen, Shenzhen 518083, China
    Nature 463:311-7. 2010
    ....
  85. pmc Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes
    Jo Vandesompele
    Center for Medical Genetics, Ghent University Hospital 1K5, De Pintelaan 185, B 9000 Ghent, Belgium
    Genome Biol 3:RESEARCH0034. 2002
    ....
  86. 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...
  87. 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
    ..Tools are uniquely categorized into three major classes, according to their underlying enrichment algorithms. The comprehensive collections, unique tool classifications and associated questions/issues will provide a more ..
  88. ncbi A pattern-based method for the identification of MicroRNA binding sites and their corresponding heteroduplexes
    Kevin C Miranda
    Bioinformatics and Pattern Discovery Group, IBM Thomas J Watson Research Center, Yorktown Heights, P O Box 218, NY 10598, USA
    Cell 126:1203-17. 2006
    ..We also extended the method's key idea to a low-error microRNA-precursor-discovery scheme; our studies suggest that the number of microRNA precursors in mammalian genomes likely ranges in the tens of thousands...
  89. pmc ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context
    Adam A Margolin
    Department of Biomedical Informatics, Columbia University, New York, NY 10032, USA
    BMC Bioinformatics 7:S7. 2006
    ..This method uses an information theoretic approach to eliminate the majority of indirect interactions inferred by co-expression methods...
  90. ncbi Using GOstats to test gene lists for GO term association
    S Falcon
    Fred Hutchison Cancer Research Center, Program Computational Biology, 1100 Fairview Avenue North P O Box 19024, Seattle, WA 98109, USA
    Bioinformatics 23:257-8. 2007
    ..In this paper we report significant improvements and extensions such as support for conditional testing...
  91. pmc Scalable molecular dynamics with NAMD
    James C Phillips
    Beckman Institute, University of Illinois at Urbana Champaign, Urbana, IL 61801, USA
    J Comput Chem 26:1781-802. 2005
    ..force field, equations of motion, and integration methods along with the efficient electrostatics evaluation algorithms employed and temperature and pressure controls used...
  92. pmc Bayesian inference of species trees from multilocus data
    Joseph Heled
    Department of Computer Science, University of Auckland, New Zealand
    Mol Biol Evol 27:570-80. 2010
    ..We demonstrate that both BEST and our method have much better estimation accuracy for species tree topology than concatenation, and our method outperforms BEST in divergence time and population size estimation...
  93. 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
    ..Three sequence scanning algorithms--MAST, FIMO and GLAM2SCAN--allow scanning numerous DNA and protein sequence databases for motifs discovered by ..
  94. ncbi Bayesian inference of phylogeny and its impact on evolutionary biology
    J P Huelsenbeck
    Department of Biology, University of Rochester, Rochester, NY 14627, USA
    Science 294:2310-4. 2001
    ....
  95. pmc Assembly algorithms for next-generation sequencing data
    Jason R Miller
    J Craig Venter Institute, Rockville, MD 20850 3343, USA
    Genomics 95:315-27. 2010
    ..emergence of next-generation sequencing platforms led to resurgence of research in whole-genome shotgun assembly algorithms and software...
  96. pmc High-resolution mapping and characterization of open chromatin across the genome
    Alan P Boyle
    Institute for Genome Sciences and Policy, Duke University, Durham, NC 27708, USA
    Cell 132:311-22. 2008
    ..In addition, and unexpectedly, our analyses have uncovered detailed features of nucleosome structure...
  97. pmc Improved microbial gene identification with GLIMMER
    A L Delcher
    Department of Computer Science, Loyola College in Maryland, Baltimore, MD 21210, USA
    Nucleic Acids Res 27:4636-41. 1999
    ..When the analysis is restricted to genes that have significant homology to genes in other organisms, GLIMMER misses <1% of known genes...
  98. ncbi IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content
    Zsuzsanna Dosztanyi
    Institute of Enzymology, BRC, Hungarian Academy of Sciences, PO Box 7, H 1518 Budapest, Hungary
    Bioinformatics 21:3433-4. 2005
    ..Optional to the prediction are built-in parameter sets optimized for predicting short or long disordered regions and structured domains...
  99. ncbi HyPhy: hypothesis testing using phylogenies
    Sergei L Kosakovsky Pond
    Antiviral Research Center, University of California San Diego San Diego, CA 92103, USA
    Bioinformatics 21:676-9. 2005
    ..AVAILABILITY: http://www.hyphy.org CONTACT: muse@stat.ncsu.edu SUPPLEMENTARY INFORMATION: HyPhydocumentation and tutorials are available at http://www.hyphy.org...
  100. ncbi Genesis: cluster analysis of microarray data
    Alexander Sturn
    Institute of Biomedical Engineering, Graz University of Technology, Krenngasse 37, 8010 Graz, Austria
    Bioinformatics 18:207-8. 2002
    ..analysis such as filters, normalization and visualization tools, distance measures as well as common clustering algorithms including hierarchical clustering, self-organizing maps, k-means, principal component analysis, and support ..
  101. ncbi A fast diffeomorphic image registration algorithm
    John Ashburner
    Wellcome Trust Centre for Neuroimaging, 12 Queen Square, London, UK
    Neuroimage 38:95-113. 2007
    ....

Research Grants80

  1. Visualization of Pelvic Floor Reflexes
    CHRISTOS EURIPIDES CONSTANTINOU; Fiscal Year: 2010
    ..Movement detection, including motion tracking algorithms and segmentation algorithms will be developed to acquire new parameters of trajectory, displacement, velocity ..
  2. Understanding/ Treating Neuropsychiatric Symptoms of Pediatric Physical Illness
    Eva Szigethy; Fiscal Year: 2009
    ..abstract_text> ..
  3. Genetic variation and regulatory networks: Mechanisms and complexity
    DANA PE ER; Fiscal Year: 2009
    ..We will develop computational algorithms that integrate genotype, gene expression and phenotype data to construct models that describe how sequence ..
  4. Novel TIRF microscopy analyzing trafficking & signaling at the cell cortex
    Derek Toomre; Fiscal Year: 2009
    ..Consistent with the recovery act's goal, this funding will provide full-time summer employment for 4 undergraduate students and accelerate scientific achievement of the parent DP2 award...
  5. Improving TB Diagnosis in Children with and without HIV in Kenya
    Rinn Song; Fiscal Year: 2013
    ..In practice, diagnosis is often based on clinical judgment or insufficiently validated diagnostic algorithms. Moreover, pediatric data on the diagnostic utility of promising emerging diagnostic tools for TB, including the ..
  6. Computer/Electrical Engineering
    Theodore Raphan; Fiscal Year: 2011
    ..7. Utilize the Kunin/Raphan algorithms developed for humans and for head-fixed monkeys on a linear sled to determine the binocular fixation point of ..
  7. A Computational Framework for Mapping Long Range Genetic Circuits
    Tolga Tasdizen; Fiscal Year: 2010
    ..g., informatics tools, implementation of data analytic algorithms), hardware-based (e.g., instrumentation or devices), or biology-based (e.g...
  8. Multivariate CART for survival with dental applications
    Martha E Nunn; Fiscal Year: 2013
    ..We also plan to refine computer algorithms we developed for multivariate CART for survival to increase computing efficiency and further extend Bayesian ..
  9. Optical Molecular Tomography for Regenerative Medicine
    Ge Wang; Fiscal Year: 2013
    ..Innovative algorithms will be developed to reconstruct 3D distributions of multiple fluorescent probes...
  10. Vitamin D3 Regulation of the Hypothalamic-Pituitary-Gonadal Axis
    Genevieve S Neal-Perry; Fiscal Year: 2012
    ..This project may provide a foundation for the institution of screening algorithms for at risk populations and the development of a relatively safe, inexpensive, biologically plausible yet simple ..
  11. EEG Synchrony, perinatal risk and outcome: analysis of CHIME data
    PHILIP GEORGE GRIEVE; Fiscal Year: 2010
    ..To evaluate this hypothesis we will develop new algorithms to compute measures of synchrony and nonlinear coupling in CHIME EEG waveforms using recently developed theory ..
  12. Diagnostic array for aseptic encephalitis
    Darrell P Chandler; Fiscal Year: 2011
    ..to demonstrate assay reproducibility, repeatability, sensitivity and specificity;and developing automated algorithms and decision rules for assay data analysis and reporting...
  13. STRAW+10: Addressing the Unfinished Agenda of Staging Reproductive Aging - RESUBM
    Sioban D Harlow; Fiscal Year: 2011
    ..hormone and inhibin-B;to assess how to include women with higher body-mass-index and who smoke in staging algorithms;to provide recommendations regarding staging of women following gynecological surgery, chemotherapy, and hormone ..
  14. Decompressive craniotomy versus medical therapy for refractory intracranial hyper
    Raminder Nirula; Fiscal Year: 2010
    ..More recently, DC has been incorporated into intracranial pressure treatment algorithms at an earlier time point in centers with aggressive neurocritical care units with some encouraging results...
  15. Optically-Guided Bladder Biopsy Using Polarized Elastic Scattering Spectroscopy
    FREDERICK GEORGE BARGOOT; Fiscal Year: 2010
    ..A successful Phase 1 outcome will lead to a broader multi-center Phase II clinical study, refined algorithms for tissue classification, and commercialization of the integrated optically-guided biopsy forceps...
  16. Biomarkers of Sudden Death and Progressive Heart Failure
    GORDON FRANK TOMASELLI; Fiscal Year: 2010
    ..this strategy reflects major limitations in the current understanding of SCD, as existing risk-stratification algorithms (based largely on ejection fraction) are neither sensitive nor specific;they require implantation of more than ..
  17. Advanced Magnetization Transfer Imaging in Multiple Sclerosis Disease
    Alexey Samsonov; Fiscal Year: 2012
    ..but more importantly provides a foundation for accelerating qMTI through model-based image reconstruction algorithms developed in the second aim...
  18. A geostatistical framework for the multi-scale boundary analysis of space-time tr
    PIERRE E GOOVAERTS; Fiscal Year: 2013
    ..2. Explore the use of diffusion of innovation theory and simulated annealing-based spatial aggregation algorithms for the representation and exploratory data analysis of temporal trends in health outcomes and their ..
  19. Seriodiagnostic arrays for biodefense and emerging infectious diseases
    DAVID HUW DAVIES; Fiscal Year: 2010
    ..By using statistical and bioinformatic algorithms, we can derive antigen sets that, when combined, can provide the basis for serological tests able to ..
  20. 3D Single Fiber Endoscope for Minimally Invasive Surgeries
    Jason Geng; Fiscal Year: 2013
    ..who have developed multiple versions of working 2D scanning fiber endoscopes, we will develop full scale design, algorithms, hardware, software, and packaging for the 3D-SFE system, making it an integrated endoscopic image-guided system ..
  21. Fluorescence enhanced optical tomography
    Eva M Sevick-Muraca; Fiscal Year: 2012
    ..respiratory gating;(3) Integrate FDPM data acquisition software and Transpire/BCM RTE-based optical tomography algorithms for determination of percent injected dose per gram of tissue (%ID/gm) for comparison to PET values;(4) Optimize ..
  22. Symbiotic Rickettsia Species as a Model System for the Study of Folate Biosynthes
    Jianmin Zhong; Fiscal Year: 2012
    ..Using freely available computer software, as well as computer algorithms written in our lab, we have discovered all six genes involved in the vitamin B9 biosynthetic pathway...
  23. CRCNS: Theory and experiment of neural circuit mapping by DNA sequencing
    Anthony M Zador; Fiscal Year: 2013
    ..models against experimental data, and use the resulting expertise to design accurate and efficient computational algorithms. Because of the need for feedback between theory, computational algorithms, and experiments, our project is ..
  24. Optical spectroscopy to study mitochondrial function within replicating cells
    Roger J Springett; Fiscal Year: 2010
    ..3) Develop and validate spectral analysis algorithms to calculate the absolute cytochrome oxidation state instead of our current measure of oxidation changes...
  25. Self-Sensing Physiologic Control of a Rotary Mag Lev LVAD
    JAMES FARLEY WALTON; Fiscal Year: 2010
    ..System (MCS) will be modified to more accurately model left ventricle hemodynamics, the physiologic control algorithms having differential pressure, flow and suction avoidance objective functions will be implemented in the ..
  26. HALF-PINT: Heart and Lung Failure - Pediatric INsulin Titration trial - CCC
    Vinay M Nadkarni; Fiscal Year: 2013
    ..significant increases in mortality and hypoglycemia when TGC is deployed without adequately explicit algorithms or continuous glucose monitoring...
  27. MicroRNA Modulation of Immune Function in Multiple Sclerosis
    Caroline C Whitacre; Fiscal Year: 2012
    ..Using target prediction algorithms, we found that the miR-29 family (miR-29a, miR-29b, miR-29c) is predicted to target both IFN3, the prototypical ..
  28. Mapping Expression Quantitative Trait Loci with Next Generation Sequencing in SLE
    Min Chen; Fiscal Year: 2013
    ..We have three specific aims: (1) Aim 1: To develop and implement computational and statistical algorithms to build a pipeline for processing RNA and DNA sequencing data...
  29. HIV, HCV and Liver Disease Among Injection Drug Users in Chennai, India
    Shruti H Mehta; Fiscal Year: 2013
    ..1: To validate existing diagnostic algorithms for steatosis and fibrosis and to compare the predictive accuracy of existing panels (e.g...
  30. DECISION SUPPORT SYSTEM TO GUIDE PEDIATRIC PHARMACOTHERAPY
    JEFFREY SCOTT BARRETT; Fiscal Year: 2010
    ..solution beyond CHOP boundaries, provide the appropriate test data to qualify/validate the prediction algorithms and generate the clinical experience with the PPDSS that will encourage other therapeutic areas and institutions ..
  31. Prognostic markers in metastatic melanoma
    BONNIE ELYSSA GOULDROTHBERG; Fiscal Year: 2013
    ..immunohistochemical methods on a cohort of 192 primary melanoma patients, on executing multivariate statistical algorithms to develop a multi-marker prognostic model and validating the model in a separate cohort of 246 cases of primary ..
  32. Sleep, Arousal, and Spontaneous Movements in Opioid Exposed Infants
    Marie J Hayes; Fiscal Year: 2010
    ..Demographically similar infants (G3, n=20) will be compared to exposure groups using algorithms developed in our laboratory to detect the periodicity and bout structure of spontaneous movements (SM) a ..
  33. Identification of a Multi-Analyte Profile for Primary Hyperoxaluria
    James P Mapes; Fiscal Year: 2012
    ..can be used as a reference for future studies and for the development of both a diagnostic test and therapeutic algorithms. The identification of novel biomarker patterns of individuals with PH1, as well as, individuals at high risk ..
  34. Improved Source Localization for Pediatric Epilepsy
    Damon Hyde; Fiscal Year: 2013
    ..My graduate work focused on the development of algorithms to improve pre-clinical imaging of fluorescent proteins in small animals...
  35. HALF-PINT: Heart And Lung Failure - Pediatric INsulin Titration trial - DCC
    David Wypij; Fiscal Year: 2013
    ..significant increases in mortality and hypoglycemia when TGC is deployed without adequately explicit algorithms or continuous glucose monitoring...
  36. A Proteomic Approach to Biomarker Discovery in Prion Disease
    Lingjun Li; Fiscal Year: 2009
    ..isotopic labeling strategy for quantitative analyses, tandem mass spectrometry, and a suite of machine-learning algorithms will provide a unique and integrated platform to identify and characterize these diagnostic protein markers with ..
  37. Pre-osteoclast fusion
    Paul R Odgren; Fiscal Year: 2013
    ..topology of both OC- and DC-STAMP (DC- STAMP has been reported to be a 7-TM superfamily member, yet different algorithms predict different topologies)...
  38. Prediction of Physiological Events in People with Sleep Disordered Breathing
    Jonathan A Waxman; Fiscal Year: 2011
    ..Our novel prediction algorithms track the interactions between several physiological systems and reveal the most important predictors...
  39. Immunopathological basis of PTSD
    Prakash S Nagarkatti; Fiscal Year: 2013
    ..The miRNA data generated will be used in silico algorithms for related target gene prediction and pathways that are dysregulated...
  40. Human iPS/ES Cell-Based Models for Predictive Neural Toxicity and Teratogenicity
    JAMES ALEXANDER THOMSON; Fiscal Year: 2013
    ..Database, and the EPA's Toxicity Reference Database as training sets, we will develop machine learning algorithms to predict neural toxicity of blinded drugs known to have failed in late stage animal testing or human clinical ..
  41. High Resolution Peripheral Quantitative CT
    MARY BETH LEONARD; Fiscal Year: 2013
    ..multidisciplinary collaboration among (1) investigators dedicated to the development of new image-processing algorithms and ?-FEA models for the quantitative assessment of the structural and mechanical implications of bone disease, ..
  42. Predict Near Future Bed Exit for Effective Intervention to Avoid Nighttime Falls
    THOMAS HENRY WHALEN; Fiscal Year: 2012
    ..The intended system is an application of automated pattern-recognition algorithms to an electronic medical record (EMR) in order to provide predictive capability, thus prompting timely ..
  43. Molecular epidemiology of non-Hodgkin lymphoma prognosis and prevention
    Sophia Wang; Fiscal Year: 2013
    ..A number of tumor marker algorithms based on immunohistochemical (IHC) staining have been developed to simulate these molecular subtypes but ..
  44. Telehealth-Enabled Ultrasound-Bioimpedance Viscoelastographic Edema Monitoring
    William F Weitzel; Fiscal Year: 2013
    ..b>Algorithms and models based on the collected data will be developed and validated using PIV, load cell, and pressure ..
  45. Genetic Analysis of the Nucleosome and RNA Polymerase II: A Systems Approach
    Nevan J Krogan; Fiscal Year: 2012
    ..We will also employ newly developed algorithms that identify functionally related sets of genes (or modules) from large-scale interaction datasets and allows ..
  46. PHASE II TRIAL OF SLEEP APNEA TREATMENT TO REDUCE CARDIOVASCULAR MORBIDITY
    SUSAN S REDLINE; Fiscal Year: 2010
    ..Suboptimal case-identification and treatment of patients with OSA is, in part, from the complexity of diagnostic algorithms and the perceived burden of using a nightly appliance, which in some individuals results in discomfort and sleep ..
  47. Establichment of CHLA's ChilDREN Clinical Center
    KASPER SAONUN WANG; Fiscal Year: 2013
    ..sufficient experience to make meaningful scientific contributions which are the basis for the management algorithms of these diseases...
  48. Sound Source Segregation
    Mark A Bee; Fiscal Year: 2013
    ..Similarly, computer algorithms for automated speech recognition (ASR) also have persistent difficulty segregating multiple sources...
  49. RISK FACTORS AS PREDICTORS OF ECTOPIC PREGNANCY
    Kurt T Barnhart; Fiscal Year: 2010
    ..There are limitations in the strategies currently employed to diagnose EP. Even with the use of diagnostic algorithms that systematically evaluate all women at risk for an EP, only 50 percent of women with an EP can be diagnosed ..
  50. WEARABLE SENSOR FOR CONTINUOUS NONINVASIVE MONITORING OF PULSE PRESSURE
    Sridhar Madala; Fiscal Year: 2010
    ..a multi-element Doppler transducer and bench top wired Pulsed Doppler electronics, 2) validate the technique and algorithms with in-vivo animal studies, and 3) demonstrate pulse pressure measurement in humans by comparison with snapshot ..
  51. Genetic Epidemiology of Osteosarcoma
    Logan G Spector; Fiscal Year: 2010
    ..SNP in public databases, 2) coding non-synonymous SNPs with deleterious function predicted by sequence homology algorithms, 3) effect of variant on protein function or expression reported in the literature...
  52. Impact of a New Molecular TB Test on TB/HIV Outcomes among HIV-Infected Malawians
    Richard E Chaisson; Fiscal Year: 2013
    ..this proposal is to conduct a cluster randomized trial of the relative impact and costeffectiveness of screening algorithms based on symptom screening, point-of-care GeneXpert TB testing and sputum smear microscopy versus a routine ..
  53. A Haplotype Map for Multiple Sclerosis
    Stephen L Hauser; Fiscal Year: 2013
    ..Using the meta-analysis-derived genotypes, together with open databases and novel algorithms, we will develop a composite global map of the effects of epistatic interactions and biochemical networks of ..
  54. Genome-wide identification of cis-regulatory polymorphisms in S. cerevisiae
    Kevin Chen; Fiscal Year: 2011
    ..A deeper understanding of cis-regulatory variafion will also facilitate the design of better algorithms for predicting cis-regulatory sites and help us elucidate the impact of changes in gene regulafion on ..
  55. Genome Transplant Dynamics: non-invasive sequencing-based diagnosis of rejection
    HANNAH AUGUSTA contact VALANTINE; Fiscal Year: 2010
    ..generation DNA sequencing methods to perform low cost, noninvasive analysis of donor DNA load;(2) bioinformatic algorithms that maximize the sensitivity to discriminate donor and recipient DNA;(3) sensitivity of a defined single ..
  56. Genetic Discovery and Application in a Clinical Setting Continuing a Partnership
    Eric B Larson; Fiscal Year: 2013
    ..b>Algorithms developed in eMERGE I will be used to combine genome-wide association studies with phenotypes mined from EMRs to ..
  57. Modular Chimeric Vaccines tailored for malaria parasites
    Alberto Moreno; Fiscal Year: 2010
    ..MCVs will be designed in silico using computer-assisted algorithms to predict molecular conformation and stability characteristics and to induce immune responses to several stages ..
  58. Remote food photography for the real-time measurement of children's food intake
    Corby K Martin; Fiscal Year: 2013
    ..to manage EMA methods and to automatically identify foods and estimate food intake using computer imaging algorithms. Data are collected and analyzed quickly and efficiently, allowing near real-time food intake measurement...
  59. Patient-Oriented Research on Hepatitis in Special Populations
    Raymond T Chung; Fiscal Year: 2013
    ..In this regard, Aim 1, development of clinical prediction models and disease management algorithms that incorporate fundamental discoveries such as genetic markers, will be an important focus for young clinical ..
  60. Comprehensive studies of novel SNPs affecting warfarin dose in African Americans
    Minoli Perera; Fiscal Year: 2012
    ..Currently, algorithms using polymorphisms in the CYP2C9 and VKORC1 genes have been developed to predict the correct maintenance dose ..
  61. Combination immunotherapy for neuroblastoma: model of innate tumor immunity
    Shakeel Modak; Fiscal Year: 2013
    ..Correlating donor-recipient KIR/HLA effects with outcome will clarify donor prioritization algorithms and provide prognostic value for future NK immunotherapy studies.
  62. Computer-Aided Detection of Pulmonary Embolism on CT Pulmonary Angiography
    Chuan Zhou; Fiscal Year: 2012
    ..The specific aims of this project include (1) collecting a large data set to develop and evaluate our CAD algorithms and systems, (2) establishing "gold standard" for performance evaluation, (3) developing robust pulmonary vessel ..
  63. A high-resolution in situ proteomics atlas of salivary gland development
    Melinda Larsen; Fiscal Year: 2010
    ..tracking dozens of proteins within single formalin-fixed, paraffin-embedded tissue sections and novel software algorithms for quantifying and categorizing protein localization patterns for these markers at the subcellular level...
  64. Non-intrusive Locomotion and Gait Stability Analysis Monitoring System for the El
    Sunil Saxena; Fiscal Year: 2007
    ..Using specific patented and tested algorithms the system will be able to give the user the following information on a monitored individual: 1...
  65. Outbreak detection:combinatorial tests for small samples
    SCOTT D FERSON; Fiscal Year: 2010
    ..This project will formulate computational algorithms and develop convenient software that implements ten exact combinatorial statistical tests for real-time use by ..
  66. Advanced Computational Framework for Decision Support in Critically Ill Children
    Randall C Wetzel; Fiscal Year: 2010
    ..While such algorithms have successful applications in business, industry, physical sciences and in parts of health care, several ..
  67. STRUCTURED ANALYSIS OF THE RETINA
    Michael Goldbaum; Fiscal Year: 1992
    ..Specialized image-processing algorithms form groups of pixels that have common attributes, such as texture or a range of brightness or color...
  68. AD classification algorithms using ADNI multi-modal image data
    Vikas Singh; Fiscal Year: 2010
    ..In parallel, automated image analysis algorithms must be developed to enable not only accurate localization and characterization of changes but also identify ..
  69. Breast Cancer Diagnosis by Electrical Impedance Imaging
    JONATHAN NEWELL; Fiscal Year: 2009
    ..currents to flow in the body and the voltage and current values at the electrodes are used by mathematical algorithms to reconstruct the values of the electrical conductivity and permittivity inside the body...
  70. Statistical Functional Data Analysis Models of Glucose and Insulin Kinetics
    Inna Chervoneva; Fiscal Year: 2010
    ..Appropriate physiologically justified algorithms for the controller are crucial for a successful mechanical artificial pancreas...
  71. Combined OCT/FLIM Biochemical and Anatomical Imaging for Early Cancer Diagnosis
    Javier Jo; Fiscal Year: 2009
    ..The ultimate goal of this line of research is to develop a novel optical imaging system and associated algorithms for noninvasive optical biopsy in oral cancer...
  72. Automatic Insulin Dosage Adjustment to Improve Glycemic Control of Diabetic Patie
    RICHARD MAURITZ BERGENSTAL; Fiscal Year: 2010
    ..The already developed software algorithms are based on the way an endocrinologist evaluates and frequently adjusts insulin in a diabetic patient...
  73. Airway Navigational System
    JENELLE GANATRA; Fiscal Year: 2007
    ..In this Phase I feasibility project, we propose four specific aims: Specific Aim 1: Refine the algorithms needed for the magnetic tracking of a bronchoscope tip during an endoscopic procedure...
  74. Reducing Antimicrobial Use Associated with Ventilator Associated Pneumonia and Ca
    SARA ELIZABETH COSGROVE; Fiscal Year: 2010
    ..The goals of this project are to develop, implement and evaluate algorithms for both the diagnosis and treatment of ventilator-associated pneumonia (VAP) and catheter- associated urinary ..
  75. Image Reconstruction Algorithms for Optical Tomography
    JOHN SCHOTLAND; Fiscal Year: 2009
    ..of the proposed research is to solve the problem of developing computationally efficient image reconstruction algorithms for noncontact optical tomography (OT) with large data sets...
  76. Splicing, Folding, and Stretching Nucleic Acids
    DANIEL AALBERTS; Fiscal Year: 2003
    ..1) Gene finding algorithms are currently statistics based. We, like cells, favor a thermodynamics-based approach to locating splice sites...
  77. Comorbidity Algorithms Project (COMAP)
    Steven Shon; Fiscal Year: 2002
    ..The purpose of this R13 conference grant is to develop evidence-based, consensually derived medication treatment algorithms for co-occurring mental illness and substance abuse...
  78. 3-D Microwave Imaging System for Breast Cancer Detection
    Qing Liu; Fiscal Year: 2006
    ..array microwave imaging system for breast imaging, with fast 3-D forward and nonlinear inverse scattering algorithms for image reconstruction...
  79. ALGORITHMS, THERMODYNAMICS AND STATISTICS FOR RNA FOLDIN
    Michael Zuker; Fiscal Year: 2003
    ..The long term goal of this work is to develop the best possible algorithms for predicting nucleic acid secondary structure by free energy minimization using the most up-to-date ..
  80. Accuracy of Diffuse Optical Tomography Using 3d camera
    STEVEN YI; Fiscal Year: 2006
    ..To fully exploit the advantages to these sophisticated algorithms, accurate 3D boundary geometry of the subject has to be extracted in practical, real-time, and in vivo manner...