cluster analysis

Summary

Summary: A set of statistical methods used to group variables or observations into strongly inter-related subgroups. In epidemiology, it may be used to analyze a closely grouped series of events or cases of disease or other health-related phenomenon with well-defined distribution patterns in relation to time or place or both.

Top Publications

  1. 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
  2. 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
  3. 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
  4. 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
  5. ncbi CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure
    Mattias Jakobsson
    Center for Computational Medicine and Biology, Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
    Bioinformatics 23:1801-6. 2007
  6. 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
  7. pmc Bacterial community variation in human body habitats across space and time
    Elizabeth K Costello
    Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA
    Science 326:1694-7. 2009
  8. ncbi Gene expression profiling predicts clinical outcome of breast cancer
    Laura J van 't Veer
    Division of Diagnostic Oncology, The Netherlands Cancer Institute, 121 Plesmanlaan, 1066 CX Amsterdam, The Netherlands
    Nature 415:530-6. 2002
  9. 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
  10. pmc Ironing out the wrinkles in the rare biosphere through improved OTU clustering
    Susan M Huse
    Josephine Bay Paul Center, Marine Biological Laboratory at Woods Hole, 7 MBL Street, Woods Hole, MA 02543, USA
    Environ Microbiol 12:1889-98. 2010

Detail Information

Publications340 found, 100 shown here

  1. 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...
  2. 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...
  3. 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...
  4. 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...
  5. ncbi CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure
    Mattias Jakobsson
    Center for Computational Medicine and Biology, Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
    Bioinformatics 23:1801-6. 2007
    ....
  6. 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/..
  7. pmc Bacterial community variation in human body habitats across space and time
    Elizabeth K Costello
    Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA
    Science 326:1694-7. 2009
    ..These results indicate that our microbiota, although personalized, varies systematically across body habitats and time; such trends may ultimately reveal how microbiome changes cause or prevent disease...
  8. ncbi Gene expression profiling predicts clinical outcome of breast cancer
    Laura J van 't Veer
    Division of Diagnostic Oncology, The Netherlands Cancer Institute, 121 Plesmanlaan, 1066 CX Amsterdam, The Netherlands
    Nature 415:530-6. 2002
    ..This gene expression profile will outperform all currently used clinical parameters in predicting disease outcome. Our findings provide a strategy to select patients who would benefit from adjuvant therapy...
  9. 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...
  10. pmc Ironing out the wrinkles in the rare biosphere through improved OTU clustering
    Susan M Huse
    Josephine Bay Paul Center, Marine Biological Laboratory at Woods Hole, 7 MBL Street, Woods Hole, MA 02543, USA
    Environ Microbiol 12:1889-98. 2010
    ..This new clustering method can reduce the OTU richness in environmental samples by as much as 30-60% but does not reduce the fraction of OTUs in long-tailed rank abundance curves that defines the rare biosphere...
  11. ncbi Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates
    Victor Kunin
    Microbial Ecology Program, DOE Joint Genome Institute, Walnut Creek, CA 94598, USA
    Environ Microbiol 12:118-23. 2010
    ..We suggest that stringent quality-based trimming of 16S pyrotags and clustering thresholds no greater than 97% identity should be used to avoid overestimates of the rare biosphere...
  12. ncbi TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets
    Geo Pertea
    The Institute for Genomic Research, Rockville, MD 20850, USA
    Bioinformatics 19:651-2. 2003
    ..The system can run on multi-CPU architectures including SMP and PVM...
  13. pmc CONSORT statement: extension to cluster randomised trials
    Marion K Campbell
    Health Services Research Unit, University of Aberdeen, Aberdeen, AB25 2ZD
    BMJ 328:702-8. 2004
  14. pmc Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data
    Micah Hamady
    Department of Computer Science, University of Colorado, Boulder, CO, USA
    ISME J 4:17-27. 2010
    ..Together, these case studies point the way toward a broad range of applications and show some of the new features of Fast UniFrac...
  15. 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...
  16. ncbi Functional profiling of the Saccharomyces cerevisiae genome
    Guri Giaever
    Stanford Genome Technology Center, Stanford University, Palo Alto, California 94304, USA
    Nature 418:387-91. 2002
    ..Our results validate the yeast gene-deletion collection as a valuable resource for functional genomics...
  17. pmc CD-HIT Suite: a web server for clustering and comparing biological sequences
    Ying Huang
    California Institute for Telecommunications and Information Technology, University of California San Diego, La Jolla, CA, USA
    Bioinformatics 26:680-2. 2010
    ..Users can now interactively explore the clusters within web browsers. We also provide downloadable clusters for several public databases (NCBI NR, Swissprot and PDB) at different identity levels...
  18. pmc De novo characterization of a whitefly transcriptome and analysis of its gene expression during development
    Xiao Wei Wang
    Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou 310029, China
    BMC Genomics 11:400. 2010
    ..Yet little is understood about its genes involved in development, insecticide resistance, host range plasticity and virus transmission...
  19. pmc Proposal for standardization of optimized mycobacterial interspersed repetitive unit-variable-number tandem repeat typing of Mycobacterium tuberculosis
    Philip Supply
    INSERM U629, Institut Pasteur de Lille, 1, Rue du Prof Calmette, F 59019 Lille cedex, France
    J Clin Microbiol 44:4498-510. 2006
    ..This 15-locus system is therefore proposed as the new standard for routine epidemiological discrimination of M. tuberculosis isolates and the 24-locus system as a high-resolution tool for phylogenetic studies...
  20. pmc Sequencing and de novo analysis of a coral larval transcriptome using 454 GSFlx
    Eli Meyer
    University of Texas at Austin, 1 University Station C0930, Austin, TX 78712, USA
    BMC Genomics 10:219. 2009
    ..We have applied these methods to sequence the transcriptome of planulae larvae from the coral Acropora millepora...
  21. ncbi Neighbor-net: an agglomerative method for the construction of phylogenetic networks
    David Bryant
    McGill Centre for Bioinformatics, Montreal, Quebec, Canada
    Mol Biol Evol 21:255-65. 2004
    ..and a collection of 12 Archeal chaperonin sequences demonstrating strong evidence for gene conversion. Neighbor-Net is available as part of the SplitsTree4 software package...
  22. ncbi Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments
    Gerard Talavera
    Department of Physiology, Institute of Molecular Biology of Barcelona, Barcelona, Spain
    Syst Biol 56:564-77. 2007
    ..This indicates that divergent and problematic alignment regions may lead, when present, to apparently better supported although, in fact, more biased topologies...
  23. ncbi Pvclust: an R package for assessing the uncertainty in hierarchical clustering
    Ryota Suzuki
    Department of Mathematical and Computing Sciences, Tokyo Institute of Technology 2 12 1 Ookayama, Meguro ku, Tokyo 152 8552, Japan
    Bioinformatics 22:1540-2. 2006
    Pvclust is an add-on package for a statistical software R to assess the uncertainty in hierarchical cluster analysis. Pvclust can be used easily for general statistical problems, such as DNA microarray analysis, to perform the bootstrap ..
  24. ncbi Genes that act downstream of DAF-16 to influence the lifespan of Caenorhabditis elegans
    Coleen T Murphy
    Department of Biochemistry and Biophysics, University of California, San Francisco, California 94143 2200, USA
    Nature 424:277-83. 2003
    ....
  25. pmc Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes
    Ken Kurokawa
    Laboratory of Comparative Genomics, Graduate School of Information Science, Nara Institute of Science and Technology, Ikoma, Nara, Japan
    DNA Res 14:169-81. 2007
    ..In addition, we discovered a conjugative transposon family explosively amplified in human gut microbiomes, which strongly suggests that the intestine is a 'hot spot' for horizontal gene transfer between microbes...
  26. pmc Deep sequencing of the Camellia sinensis transcriptome revealed candidate genes for major metabolic pathways of tea-specific compounds
    Cheng Ying Shi
    Key Laboratory of Tea Biochemistry and Biotechnology, Ministry of Education, Ministry of Agriculture, Anhui Agricultural University, Hefei, 230036, PR China
    BMC Genomics 12:131. 2011
    ....
  27. pmc Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data
    Manhong Dai
    Molecular and Behavioural Neuroscience Institute and Department of Psychiatry, University of Michigan, Ann Arbor, MI 48109, USA
    Nucleic Acids Res 33:e175. 2005
    ..It will be beneficial to re-analyze existing GeneChip data with updated probe set definitions...
  28. ncbi Community genomics among stratified microbial assemblages in the ocean's interior
    Edward F DeLong
    Massachusetts Institute of Technology, Cambridge, MA 02139, USA
    Science 311:496-503. 2006
    ..Comparative genomic analyses of stratified microbial communities have the potential to provide significant insight into higher-order community organization and dynamics...
  29. ncbi Effect of community-based newborn-care intervention package implemented through two service-delivery strategies in Sylhet district, Bangladesh: a cluster-randomised controlled trial
    Abdullah H Baqui
    Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
    Lancet 371:1936-44. 2008
    ..Therefore the project for advancing the health of newborns and mothers (Projahnmo) implemented a community-based intervention package through government and non-government organisation infrastructures to reduce neonatal mortality...
  30. pmc UniFrac--an online tool for comparing microbial community diversity in a phylogenetic context
    Catherine Lozupone
    Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
    BMC Bioinformatics 7:371. 2006
    ..Techniques that allow microbial communities to be compared in a phylogenetic context are rapidly gaining acceptance, but the widespread application of these techniques has been hindered by the difficulty of performing the analyses...
  31. pmc Combinatorial patterns of histone acetylations and methylations in the human genome
    Zhibin Wang
    Laboratory of Molecular Immunology, National Heart, Lung, and Blood Institute, US National Institutes of Health, Bethesda, Maryland 20892, USA
    Nat Genet 40:897-903. 2008
    ..Our data suggest that these histone modifications may act cooperatively to prepare chromatin for transcriptional activation...
  32. ncbi Clustering by passing messages between data points
    Brendan J Frey
    Department of Electrical and Computer Engineering, University of Toronto, 10 King s College Road, Toronto, Ontario M5S 3G4, Canada
    Science 315:972-6. 2007
    ..Affinity propagation found clusters with much lower error than other methods, and it did so in less than one-hundredth the amount of time...
  33. pmc Detecting overlapping protein complexes in protein-protein interaction networks
    Tamás Nepusz
    Department of Computer Science, Centre for Systems and Synthetic Biology, Royal Holloway, University of London, Egham Hill, Egham, UK
    Nat Methods 9:471-2. 2012
    ..The results also showed a high extent of functional homogeneity...
  34. ncbi The humoral immune system has a key prognostic impact in node-negative breast cancer
    Marcus Schmidt
    Department of Obstetrics and Gynecology, Medical School, Johannes Gutenberg University, Mainz, Germany
    Cancer Res 68:5405-13. 2008
    ..After performing hierarchical cluster analysis, we identified coregulated genes related to the biological process of proliferation, steroid hormone receptor ..
  35. ncbi Small-world networks and functional connectivity in Alzheimer's disease
    C J Stam
    Department of Clinical Neurophysiology, VU University Medical Center, 1007 MB Amsterdam, The Netherlands
    Cereb Cortex 17:92-9. 2007
    ..Graph theoretical analysis may be a useful approach to study the complexity of patterns of interrelations between EEG channels...
  36. ncbi Standardization of pulsed-field gel electrophoresis protocols for the subtyping of Escherichia coli O157:H7, Salmonella, and Shigella for PulseNet
    Efrain M Ribot
    Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
    Foodborne Pathog Dis 3:59-67. 2006
    ....
  37. pmc Identification of conserved gene expression features between murine mammary carcinoma models and human breast tumors
    Jason I Herschkowitz
    Lineberger Comprehensive Cancer Center
    Genome Biol 8:R76. 2007
    ..To address this need, we characterized mammary tumor gene expression profiles from 13 different murine models using DNA microarrays and compared the resulting data to those from human breast tumors...
  38. pmc Ubiquity and diversity of ammonia-oxidizing archaea in water columns and sediments of the ocean
    Christopher A Francis
    Department of Geological and Environmental Sciences, Stanford University, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 102:14683-8. 2005
    ..Considering the abundance of nonextremophilic archaea in the ocean, our results suggest that AOA may play a significant, but previously unrecognized, role in the global nitrogen cycle...
  39. ncbi Design and analysis of stepped wedge cluster randomized trials
    Michael A Hussey
    Fred Hutchinson Cancer Research Center, Seattle, WA, United States
    Contemp Clin Trials 28:182-91. 2007
    ..In this article we discuss the design and analysis of a particular type of crossover CRT - the stepped wedge - and provide an example of its use...
  40. pmc An automated method for finding molecular complexes in large protein interaction networks
    Gary D Bader
    Samuel Lunenfeld Research Institute, MT, Sinai Hospital, Toronto ON Canada M5G 1X5, Dept, of Biochemistry, University of Toronto, Toronto ON Canada M5S 1A8
    BMC Bioinformatics 4:2. 2003
    ..As the size of the interaction set increases, databases and computational methods will be required to store, visualize and analyze the information in order to effectively aid in knowledge discovery...
  41. ncbi Exploiting indirect neighbours and topological weight to predict protein function from protein-protein interactions
    Hon Nian Chua
    Graduate School for Integrated Sciences and Engineering, National University of Singapore, Singapore
    Bioinformatics 22:1623-30. 2006
    ..We are interested in finding out how significant is functional association between level-2 neighbours and how they can be exploited for protein function prediction...
  42. 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...
  43. ncbi Neurophysiological architecture of functional magnetic resonance images of human brain
    Raymond Salvador
    Brain Mapping Unit and Wolfson Brain Imaging Centre, University of Cambridge, Addenbrooke s Hospital, Cambridge CB2 2QQ, UK
    Cereb Cortex 15:1332-42. 2005
    ....
  44. ncbi Characterization of microRNA expression levels and their biological correlates in human cancer cell lines
    Arti Gaur
    Norris Cotton Cancer Center, Dartmouth Medical School, Lebanon, New Hampshire 03755, USA
    Cancer Res 67:2456-68. 2007
    ..These findings call attention to the potential of microRNAs to provide etiologic insights as well as to serve as both diagnostic markers and therapeutic targets for many different tumor types...
  45. pmc Defining the healthy "core microbiome" of oral microbial communities
    Egija Zaura
    Department of Cariology, Academic Centre for Dentistry Amsterdam ACTA, University of Amsterdam and Free University Amsterdam, The Netherlands
    BMC Microbiol 9:259. 2009
    ..The aim of this study therefore was to define the healthy oral microbiome using recent advances in sequencing technology (454 pyrosequencing)...
  46. pmc Geometric interpretation of gene coexpression network analysis
    Steve Horvath
    Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, California, United States of America
    PLoS Comput Biol 4:e1000117. 2008
    ..The unification of coexpression network methods with traditional data mining methods can inform the application and development of systems biologic methods...
  47. pmc Enhanced Bayesian modelling in BAPS software for learning genetic structures of populations
    Jukka Corander
    Department of Mathematics, Fänriksgatan 3B, Abo Akademi University, Abo, Finland
    BMC Bioinformatics 9:539. 2008
    ..However, the complexity of biological problems related to genetic structure analysis keeps increasing such that in many cases the current methods may provide either inappropriate or insufficient solutions...
  48. pmc Quantitative and qualitative beta diversity measures lead to different insights into factors that structure microbial communities
    Catherine A Lozupone
    Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
    Appl Environ Microbiol 73:1576-85. 2007
    ..We also demonstrate that both weighted and unweighted UniFrac measurements are robust to the methods used to build the underlying phylogeny...
  49. 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
    ..Additionally, mapping of gene expression data onto chromosomal sequences was implemented to enhance promoter analysis and investigation of transcriptional control mechanisms...
  50. ncbi Defining clusters from a hierarchical cluster tree: the Dynamic Tree Cut package for R
    Peter Langfelder
    Department of Human Genetics, University of California at Los Angeles, CA 90095 7088, USA
    Bioinformatics 24:719-20. 2008
    ..We illustrate the use of these methods by applying them to protein-protein interaction network data and to a simulated gene expression data set...
  51. pmc MetaboAnalyst: a web server for metabolomic data analysis and interpretation
    Jianguo Xia
    Department of Biological Sciences, University of Alberta, Edmonton AB T6G 2E8, Canada
    Nucleic Acids Res 37:W652-60. 2009
    ..MetaboAnalyst is capable of handling most kinds of metabolomic data and was designed to perform most of the common kinds of metabolomic data analyses. MetaboAnalyst is accessible at http://www.metaboanalyst.ca...
  52. pmc Meta-analysis of gene expression profiles in breast cancer: toward a unified understanding of breast cancer subtyping and prognosis signatures
    Pratyaksha Wirapati
    Swiss Institute of Bioinformatics, Batiment Genopode, University of Lausanne, 1015 Lausanne, Switzerland
    Breast Cancer Res 10:R65. 2008
    ....
  53. pmc ESPRIT-Tree: hierarchical clustering analysis of millions of 16S rRNA pyrosequences in quasilinear computational time
    Yunpeng Cai
    Interdisciplinary Center for Biotechnology Research University of Florida, Gainesville, FL 32610, USA
    Nucleic Acids Res 39:e95. 2011
    ..The new algorithm exhibits a quasilinear time and space complexity comparable to greedy heuristic clustering algorithms, while achieving a similar accuracy to the standard hierarchical clustering algorithm...
  54. ncbi Assessing genetic diversity and population structure in a citrus germplasm collection utilizing simple sequence repeat markers (SSRs)
    Noelle A Barkley
    Department of Botany and Plant Sciences and Graduate Program in Genetics, Genomics, and Bioinformatics, University of California, Riverside, CA 92521, USA
    Theor Appl Genet 112:1519-31. 2006
    ....
  55. pmc The molecular portraits of breast tumors are conserved across microarray platforms
    Zhiyuan Hu
    Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
    BMC Genomics 7:96. 2006
    ..To overcome this problem we used publicly available breast cancer gene expression data sets and a novel approach to data fusion, in order to validate a new breast tumor intrinsic list...
  56. pmc Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms
    M C Maiden
    Wellcome Trust Centre for the Epidemiology of Infectious Disease, Department of Zoology, University of Oxford, Oxford OX1 3PS, United Kingdom
    Proc Natl Acad Sci U S A 95:3140-5. 1998
    ..numbers and dendrograms were constructed from the pairwise differences in multilocus allelic profiles by cluster analysis. The strain associations obtained were consistent with clonal groupings previously determined by multilocus ..
  57. ncbi Effect of community-based behaviour change management on neonatal mortality in Shivgarh, Uttar Pradesh, India: a cluster-randomised controlled trial
    Vishwajeet Kumar
    International Center for Advancing Neonatal Health, Department of International Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
    Lancet 372:1151-62. 2008
    ..We developed an intervention of behaviour change management, with a focus on prevention of hypothermia, aimed at modifying practices and reducing neonatal mortality...
  58. ncbi Patterns of intra-cluster correlation from primary care research to inform study design and analysis
    Geoffrey Adams
    Department of Public Health Sciences, King s College London, Capital House, 42 Weston Street, London SE1 3QD, UK
    J Clin Epidemiol 57:785-94. 2004
    ..To provide information concerning the magnitude of the intraclass correlation coefficient (ICC) for cluster-based studies set in primary care...
  59. ncbi The AtGenExpress hormone and chemical treatment data set: experimental design, data evaluation, model data analysis and data access
    Hideki Goda
    RIKEN Plant Science Center, Tsurumi, Yokohama, Kanagawa 230 0045, Japan
    Plant J 55:526-42. 2008
    ..Genome-wide transcriptional gene-to-gene correlations, analyzed by hierarchical cluster analysis (HCA), indicated that our data set is useful for identification of clusters of co-expressed genes, and to ..
  60. pmc Assessing and improving methods used in operational taxonomic unit-based approaches for 16S rRNA gene sequence analysis
    Patrick D Schloss
    Department of Microbiology and Immunology University of Michigan, Ann Arbor, MI 48109, USA
    Appl Environ Microbiol 77:3219-26. 2011
    ..The ability to quickly and accurately assign sequences to OTUs and then obtain taxonomic information for those OTUs will greatly improve OTU-based analyses and overcome many of the challenges encountered with phylotype-based methods...
  61. ncbi Contemporary cryptic sexuality in Trypanosoma cruzi
    Juan David Ramírez
    Centro de Investigaciones en Microbiologia y Parasitologia Tropical, Universidad de Los Andes, Bogota, Colombia
    Mol Ecol 21:4216-26. 2012
    ....
  62. ncbi A global test for groups of genes: testing association with a clinical outcome
    Jelle J Goeman
    Department of Medical Statistics, Leiden University Medical Center, P O Box 9604, 2300 RC Leiden, The Netherlands
    Bioinformatics 20:93-9. 2004
    ..Groups of genes may be any size from a single gene to all genes on the chip (e.g. known pathways, specific areas of the genome or clusters from a cluster analysis).
  63. pmc Transcriptomic and metabolite analyses of Cabernet Sauvignon grape berry development
    Laurent G Deluc
    Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Nevada 89557 0014, USA
    BMC Genomics 8:429. 2007
    ....
  64. pmc A large-scale benchmark study of existing algorithms for taxonomy-independent microbial community analysis
    Yijun Sun
    Interdisciplinary Center for Biotechnology Research, University of Florida, PO Box 103622, Gainesville, FL 32610 3622, USA
    Brief Bioinform 13:107-21. 2012
    ....
  65. pmc Reemergence of enterovirus 71 in 2008 in taiwan: dynamics of genetic and antigenic evolution from 1998 to 2008
    Sheng Wen Huang
    Department of Medical Laboratory Science and Biotechnology, National Cheng Kung University, One University Road, Tainan, 701, Taiwan
    J Clin Microbiol 47:3653-62. 2009
    ..Therefore, continuous surveillance of EV71 including the monitoring of genetic evolution and antigenic changes is recommended and may contribute to the development of a vaccine for EV71...
  66. ncbi Logic of the yeast metabolic cycle: temporal compartmentalization of cellular processes
    Benjamin P Tu
    Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, L3 124, Dallas, TX 75390, USA
    Science 310:1152-8. 2005
    ..Essential cellular and metabolic events occur in synchrony with the metabolic cycle, demonstrating that key processes in a simple eukaryotic cell are compartmentalized in time...
  67. ncbi Genetic structure of human populations
    Noah A Rosenberg
    Molecular and Computational Biology, 1042 West 36th Place DRB 289, University of Southern California, Los Angeles, CA 90089, USA
    Science 298:2381-5. 2002
    ..General agreement of genetic and predefined populations suggests that self-reported ancestry can facilitate assessments of epidemiological risks but does not obviate the need to use genetic information in genetic association studies...
  68. ncbi Complex discovery from weighted PPI networks
    Guimei Liu
    School of Computing, National University of Singapore, Singapore and Institute for Infocomm Research, Singapore
    Bioinformatics 25:1891-7. 2009
    ..However, protein interaction data produced by high-throughput experiments are often associated with high false positive and false negative rates, which makes it difficult to predict complexes accurately...
  69. pmc Inference of bacterial microevolution using multilocus sequence data
    Xavier Didelot
    Department of Statistics, University of Oxford, Oxford OX1 3SY, United Kingdom
    Genetics 175:1251-66. 2007
    ..The software used in this article, ClonalFrame, is available from http://bacteria.stats.ox.ac.uk/...
  70. ncbi ClustalW-MPI: ClustalW analysis using distributed and parallel computing
    Kuo Bin Li
    Bioinformatics Institute, 30 Medical Drive, Singapore 117609, Republic of Singapore
    Bioinformatics 19:1585-6. 2003
    ..The software uses a message-passing library called MPI (Message Passing Interface) and runs on distributed workstation clusters as well as on traditional parallel computers...
  71. pmc Brain anatomical network and intelligence
    Yonghui Li
    LIAMA Center for Computational Medicine, National Laboratory of Pattern Recognition, Institute of Automation, Chinese Academy of Sciences, Beijing, China
    PLoS Comput Biol 5:e1000395. 2009
    ..Our findings suggest that the efficiency of brain structural organization may be an important biological basis for intelligence...
  72. pmc A Markov chain Monte Carlo approach for joint inference of population structure and inbreeding rates from multilocus genotype data
    Hong Gao
    Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14853, USA
    Genetics 176:1635-51. 2007
    ..48-0.70)...
  73. ncbi Network visualization and analysis of gene expression data using BioLayout Express(3D)
    Athanasios Theocharidis
    The Roslin Institute, R D SVS, University of Edinburgh, Roslin Biocentre, Midlothian, Scotland, UK
    Nat Protoc 4:1535-50. 2009
    ....
  74. pmc Coordination of growth rate, cell cycle, stress response, and metabolic activity in yeast
    Matthew J Brauer
    Lewis Sigler Institute for Integrative Genomics and Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
    Mol Biol Cell 19:352-67. 2008
    ..This concept is useful in interpreting the system-level connections among growth rate, metabolism, stress, and the cell cycle...
  75. ncbi Gene expression analyses reveal molecular relationships among 20 regions of the human CNS
    Richard B Roth
    Department of Molecular Medicine, Neurocrine Biosciences, Incorporated, 12790 El Camino Real, San Diego, CA 92130, USA
    Neurogenetics 7:67-80. 2006
    ..In summary, we have generated a database of gene expression that can be used to gain valuable insight into the molecular characterization of functions carried out by different sites of the human CNS...
  76. pmc The evolutionary genetics and emergence of avian influenza viruses in wild birds
    Vivien G Dugan
    Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
    PLoS Pathog 4:e1000076. 2008
    ....
  77. ncbi Subtypes of breast cancer show preferential site of relapse
    Marcel Smid
    Department of Medical Oncology, Erasmus MC, Josephine Nefkens Institute, Rotterdam, The Netherlands
    Cancer Res 68:3108-14. 2008
    ..The five major molecular subtypes in breast cancer are evidently different with regard to their ability to metastasize to distant organ(s), and share biological features and pathways with their preferred distant metastatic site...
  78. pmc Colloquium paper: genome-wide patterns of population structure and admixture among Hispanic/Latino populations
    Katarzyna Bryc
    Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14850, USA
    Proc Natl Acad Sci U S A 107:8954-61. 2010
    ....
  79. ncbi Empirically derived eating patterns using factor or cluster analysis: a review
    P K Newby
    Jean Mayer USDA Human Nutrition Research Center on Aging, Tufts University, Boston, MA 02111, USA
    Nutr Rev 62:177-203. 2004
    ..Although the research considered herein has created a meaningful body of literature, refining both the factor and cluster analysis methods will help to further establish eating patterns as a sound dietary assessment method.
  80. ncbi A novel prognostic subtype of human hepatocellular carcinoma derived from hepatic progenitor cells
    Ju Seog Lee
    Lab of Experimental Carcinogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Room 4146, Bethesda, Maryland 20892, USA
    Nat Med 12:410-6. 2006
    ..Analyses of gene networks showed that activation of AP-1 transcription factors in this newly identified HCC subtype might have key roles in tumor development...
  81. pmc Microbial community resemblance methods differ in their ability to detect biologically relevant patterns
    Justin Kuczynski
    Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Colorado, USA
    Nat Methods 7:813-9. 2010
    ..These results also provide a basis for understanding tradeoffs between number of samples and depth of coverage, tradeoffs that are important to consider when designing studies to characterize microbial communities...
  82. ncbi Micro-RNA profiling in kidney and bladder cancers
    Fedra Gottardo
    Department of Urology, Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA
    Urol Oncol 25:387-92. 2007
    ..To study the role of the micro-RNAs in human kidney and bladder cancer, we analyzed the expression profile of 245 micro-RNAs in kidney and bladder primary tumors...
  83. ncbi MicroRNA expression profiles for the NCI-60 cancer cell panel
    Paul E Blower
    Program of Pharmacogenomics, Department of Pharmacology and the Comprehensive Cancer Center, College of Medicine, The Ohio State University, 5072 Graves Hall, 333 West 10th Avenue, Columbus, OH 43210, USA
    Mol Cancer Ther 6:1483-91. 2007
    ..Combined with gene expression and other biological data using multivariate analysis, microRNA expression profiles may provide a critical link for understanding mechanisms involved in chemosensitivity and chemoresistance...
  84. pmc Effectiveness of the diabetes education and self management for ongoing and newly diagnosed (DESMOND) programme for people with newly diagnosed type 2 diabetes: cluster randomised controlled trial
    M J Davies
    Department of Cardiovascular Sciences, University of Leicester, Leicester LE1 5WW
    BMJ 336:491-5. 2008
    ..To evaluate the effectiveness of a structured group education programme on biomedical, psychosocial, and lifestyle measures in people with newly diagnosed type 2 diabetes...
  85. pmc Gene expression programs in response to hypoxia: cell type specificity and prognostic significance in human cancers
    Jen Tsan Chi
    Department of Biochemistry, Stanford University School of Medicine, Palo Alto, California, United States of America
    PLoS Med 3:e47. 2006
    ....
  86. pmc Finding statistically significant communities in networks
    Andrea Lancichinetti
    Complex Networks and Systems Lagrange Laboratory, Institute for Scientific Interchange, Torino, Italy
    PLoS ONE 6:e18961. 2011
    ..Several applications on real networks are shown as well. OSLOM is implemented in a freely available software (http://www.oslom.org), and we believe it will be a valuable tool in the analysis of networks...
  87. ncbi A note on robust variance estimation for cluster-correlated data
    R L Williams
    Research Triangle Institute, Research Triangle Park, North Carolina 27709 2194, USA
    Biometrics 56:645-6. 2000
    ..The result is not new, but a simple and general reference is not readily available. The use of the method will benefit from a general explanation of its wide applicability...
  88. pmc Human enterovirus 109: a novel interspecies recombinant enterovirus isolated from a case of acute pediatric respiratory illness in Nicaragua
    Nathan L Yozwiak
    Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, California, USA
    J Virol 84:9047-58. 2010
    ..Further experimentation is required to more fully characterize the pathogenic role, disease associations, and global distribution of EV109...
  89. pmc Arabidopsis gene co-expression network and its functional modules
    Linyong Mao
    Virtual Reality Applications Center, Iowa State University, Ames, IA 50010, USA
    BMC Bioinformatics 10:346. 2009
    ..The organization of gene functional modules was also investigated...
  90. pmc A comprehensive survey of soil acidobacterial diversity using pyrosequencing and clone library analyses
    Ryan T Jones
    Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309, USA
    ISME J 3:442-53. 2009
    ....
  91. ncbi An information-intensive approach to the molecular pharmacology of cancer
    J N Weinstein
    Laboratory of Molecular Pharmacology LMP, Division of Basic Science, National Cancer Institute NCI, National Institutes of Health, Bethesda, MD 20892, USA
    Science 275:343-9. 1997
    ..It remains to be seen how effective this information-intensive strategy will be at generating new clinically active agents...
  92. ncbi A microarray-based DNA methylation study of glioblastoma multiforme
    Ramon Martinez
    Department of Neurosurgery, University of Goettingen, Goettingen WT 084071, Germany
    Epigenetics 4:255-64. 2009
    ..Furthermore, we identified that promoter hypermethylation of the transcription factor gene GATA6 (occurring in 30% of GBM) was significantly associated with unfavorable patient survival...
  93. pmc Two hybridization events define the population structure of Trypanosoma cruzi
    Scott J Westenberger
    Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, 90095, USA
    Genetics 171:527-43. 2005
    ..The second hybridization between DTU IIb and IIc strains that generated DTUs IId and IIe resulted in extensive heterozygosity with subsequent recombination of parental genotypes...
  94. ncbi Molecular profiling of diffuse large B-cell lymphoma identifies robust subtypes including one characterized by host inflammatory response
    Stefano Monti
    The Broad Institute, Cambridge, MA, USA
    Blood 105:1851-61. 2005
    ..These studies identify tumor microenvironment and host inflammatory response as defining features in DLBCL and suggest rational treatment targets in specific DLBCL subsets...
  95. pmc A unique H3K4me2 profile marks tissue-specific gene regulation
    Aleksandra Pekowska
    Centre d immunologie de Marseille Luminy, Universite Aix Marseille, Marseille 13009, France
    Genome Res 20:1493-502. 2010
    ..We propose that this epigenetic feature reflects the activity of an as yet unrecognized, intragenic cis-regulatory platform dedicated to refining tissue-specificity in gene expression...
  96. ncbi Gene expression signatures for predicting prognosis of squamous cell and adenocarcinomas of the lung
    Mitch Raponi
    Molecular Diagnostics, Veridex LLC a Johnson and Johnson Company, 3210 Merryfriend Row, San Diego, CA 92121, USA
    Cancer Res 66:7466-72. 2006
    ..0002; HR, 3.54; 95% CI, 1.74-7.19). This prognostic signature could be used to identify patients with early-stage high-risk NSCLC who might benefit from adjuvant therapy following surgery...
  97. pmc Coexpression analysis of human genes across many microarray data sets
    Homin K Lee
    Columbia Genome Center, Columbia University, New York, New York 10032, USA
    Genome Res 14:1085-94. 2004
    ..confirmation of coexpression in multiple data sets is correlated with functional relatedness, and show how cluster analysis of the network can reveal functionally coherent groups of genes...
  98. pmc TACOA: taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach
    Naryttza N Diaz
    Center for Biotechnology CeBiTec, Bielefeld University, Bielefeld, Germany
    BMC Bioinformatics 10:56. 2009
    ..We present a novel strategy to predict the taxonomic origin of environmental genomic fragments. The proposed classifier combines the idea of the k-nearest neighbor with strategies from kernel-based learning...
  99. ncbi Reverse engineering of regulatory networks in human B cells
    Katia Basso
    Institute for Cancer Genetics, 1300 St Nicholas Avenue, Room 912, New York, New York 10032, USA
    Nat Genet 37:382-90. 2005
    ..The newly identified MYC targets include some major hubs. This approach can be generally useful for the analysis of normal and pathologic networks in mammalian cells...
  100. pmc Network-based prediction of protein function
    Roded Sharan
    School of Computer Science, Tel Aviv University, Tel Aviv, Israel
    Mol Syst Biol 3:88. 2007
    ..Although a broad variety of interesting approaches has been developed, further progress in the field will depend on systematic evaluation of the methods and their dissemination in the biological community...
  101. ncbi Human epicardial adipose tissue is a source of inflammatory mediators
    Tomasz Mazurek
    Department of Surgery, Thomas Jefferson University, Suite 623, 1025 Walnut St, Philadelphia, PA 19107, USA
    Circulation 108:2460-6. 2003
    ..In this study, we sought to compare expression of inflammatory mediators in epicardial and subcutaneous adipose stores in patients with critical CAD...

Research Grants72

  1. 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...
  2. Vascular and Skeletal Muscle Function in Gulf War Veterans Illness
    Scott Kinlay; Fiscal Year: 2013
    ..for GWVI are based on chronic multisystem illness (CMI) criteria, which are based on statistical symptom cluster analysis resulting in three categories: fatigue, mood/ cognition, and musculoskeletal symptoms...
  3. Climate Change and Adverse Birth Outcomes: Assessing the Vulnerability of Pregnan
    Shao Lin; Fiscal Year: 2013
    ..K-means cluster analysis and Monte Carlo methods will be used to estimate weather factor clusters and uncertainty, respectively...
  4. Molecular Determinants Affecting FLT-PET in Colorectal Cancer
    HENRY C MANNING; Fiscal Year: 2010
    ..Genes identified qualitatively via cluster analysis will be quantified using qRT-PCR...
  5. Dietary patterns and root caries risk
    ELIZABETH A KAYE; Fiscal Year: 2010
    ..To address this hypothesis, we will use cluster analysis to identify dietary patterns from food frequency questionnaires in the DLS that are associated with reduced ..
  6. Measuring Altered Social Behavior in Neurodegenerative Disease
    Katherine P Rankin; Fiscal Year: 2013
    ..We will also use cluster analysis to determine whether cognitive deficits in non-social domains such as memory, language, etc...
  7. STUDIES IN GLAUCOMATOUS OPTIC NERVE DAMAGE
    John C Morrison; Fiscal Year: 2013
    ..We will then (b) use a microarray cluster analysis to determine the chronological cascade of gene expression changes to CEI 60-8, with (c) confirmation by qPCR ..
  8. Molecular Phenotyping of NOD Mice
    Ivan C Gerling; Fiscal Year: 2010
    ..To reveal molecular network associations between specific proteins and gene expression by conducting cluster analysis on combined molecular phenotype data files (using and further developing some novel analysis and mining ..
  9. Metabolic Screening: Prioritizing Implementation Strategies for Mental Health
    Elaine H Morrato; Fiscal Year: 2013
    ..Results of Aim 1 will inform the selection of segmentation factors used in the Aim 2 cluster analysis. Split-sample validation will be used to assess the stability of the segments...
  10. Genetic Predisposition & Prevention of Neural Tube Defects (NTDs)
    MARGARET ELIZABETH contact ROSS; Fiscal Year: 2010
    ..Gene transcript arrays will examine expression in the neural tube during closure in these mutants using cluster analysis to compare patterns in the mutant vs. wildtype siblings...
  11. Adapting Electronic Medical Record to Measure Medical Outcomes in ASD Populations
    RUTH ANN BUSH; Fiscal Year: 2013
    ..Aim 2: To measure utilization patterns among patients with ASD and to identify, using cluster analysis, health care utilization subgroups...
  12. Multi-center Structural &Functional Quantitative CT Pulmonary Phenotyping
    ERIC ALFRED HOFFMAN; Fiscal Year: 2012
    ..segments as the standard region of interest;4) test the application of a novel statistica approach to cluster analysis such that the measures from quantitative CT fully account for specific phenotypes for disease subgroups and ..
  13. Human immunoglobulin Fc receptor functions in sarcoidosis
    Jianming Wu; Fiscal Year: 2013
    ..In addition, our study may lead to the development of new strategies for the prediction and treatment of other immunoglobulin-mediated inflammatory diseases. ..
  14. Glycoprotein Signatures as Biomarkers for Breast Cancer
    ROBERT YEN; Fiscal Year: 2012
    ..Aim 1 will be accomplished using a mass spectrometry-based protocol, coupled with hierarchical cluster analysis, previously demonstrated in the applicant's hands to result in a glycoprotein signature that ..
  15. Pharmacodynamics of Biased G protein-Coupled Receptor Agonism
    Louis M Luttrell; Fiscal Year: 2013
    ..Using bioinformatic metabolic pathways and gene cluster analysis, we found that the arrestin-selective PTH1R agonist produces a unique genomic 'footprint'at the ..
  16. Family Cluster Analysis of Norovirus Variants by Multiple-region Sequence Typing
    Robert H Gilman; Fiscal Year: 2013
    ..Index case families will be compared with two age-matched control families by cluster analysis. We will determine the prevalence of family members infected with the same or different NV genotypic strains...
  17. UNCLASSIFIED SPIROMETRIC ABNORMALITIES: RADIOLOGY, EPIDEMIOLOGY, AND GENETICS
    Edwin K Silverman; Fiscal Year: 2010
    ..Finally, cluster analysis of the CT, physiological, and epidemiological data will be performed, and genetic association analysis using ..
  18. Characterization of Symptom Occurrence in Persons with Multiple Sclerosis
    Pamela K Newland; Fiscal Year: 2012
    ..Aim 1) in patients with RRMS patients not involved with the focus groups, and 3): to determine, using cluster analysis, if there are symptom clusters in patients with RRMS and, if there are clusters, to examine the relationships ..
  19. HIV Transmission Cluster Analysis to Inform Prevention
    Hong Ha M Truong; Fiscal Year: 2013
    ..Real-time analysis of HIV transmission cluster data will place us on the leading edge of the epidemic and enable assessment of how high-risk clusters and current prevention strategies affect transmission patterns. ..
  20. Infant Assessment of Early Communication Risk Factors: The ECBS
    Cynthia J Cress; Fiscal Year: 2011
    ..of typically developing infants using correlational analyses, including exploratory factor analysis and cluster analysis. PUBLIC HEALTH RELEVANCE: We have recognized the need for detecting communication problems as early as ..
  21. Longitudinal Phenomics and Genetics of Severe Asthma
    Deborah A Meyers; Fiscal Year: 2013
    ..When the total population has been studied, a new cluster analysis will be performed for comparison with the current clusters, including additional biomarkers and CT imaging...
  22. The Effects of Acute Events on ADL Trajectories of Nursing Home Residents
    Robin L Kruse; Fiscal Year: 2010
    ..Using the output from these analyses, cluster analysis will be employed to identify ADL trajectory categories (1) preceding and following hospital stays and (2) ..
  23. Morphine undermines recovery of function after SCI: Neurobiological mechanisms
    Michelle A Hook; Fiscal Year: 2013
    ..For this third aim, we plan to target specific receptor systems, and use a cluster analysis to ascertain which molecular end-points co-vary with specific consequences of morphine administration...
  24. Differential Approach to the Postural Tachycardia Syndrome
    Wolfgang Singer; Fiscal Year: 2013
    ..for each patient reflecting different pathomechanisms with the goal to identify distinct subtypes using cluster analysis. Methods will include microneurography, blood volume estimation, exercise testing, and measurements of nerve ..
  25. Human Reservoirs of Plasmodium vivax Transmission in the Peruvian Amazon
    Joseph M Vinetz; Fiscal Year: 2010
    ..using geographic spatio- temporal analysis of circulating genotypes using spatial statistical modeling and cluster analysis. These analyses will distinguish whether circulating P...
  26. MULTIPLE RISKS, DECISIONS & BEHAVIORS IN THE GENOMIC ERA
    Karen E Hurley; Fiscal Year: 2010
    ..b>Cluster analysis will yield a taxonomy of perceived/risk worry types (e.g., selective worry about one type of cancer vs...
  27. Symptoms Clusters in Oncology Patients Receiving Chemotherapy
    Christine A Miaskowski; Fiscal Year: 2013
    ..In addition, cluster analysis procedures will be employed to create subgroups of patients based on their experience with the symptoms of ..
  28. Symptoms of Lower Urinary Tract Dysfunction Research Network (LURN)Data Coordinat
    Robert M Merion; Fiscal Year: 2013
    ..analysis methods;2) development of deep phenotyping of patient cohorts with relevant LUTD symptoms using cluster analysis, classification and regression trees, and other data mining methods;and 3) identification of biomarkers ..
  29. NanoGenomics to study molecular mechanisms of neurodegeneration in human cells
    Nader Pourmand; Fiscal Year: 2013
    ..Using informatics, we will relate this cluster analysis to cellular pathways dysregulated in HD i- neurons. The WTA results will be verified by qPCR...
  30. Gene Networks for Prostate Cancer Progression
    Leif Peterson; Fiscal Year: 2005
    ..Microarray data analysis will include fold-change analysis, cluster analysis, and principal component analysis to identify (a) unique patterns of expression (strongly up or downregulated)..
  31. Disparities in Health and Academics of Sexual Minorities in Urban Middle Schools
    Negin Ghavami; Fiscal Year: 2013
    ..A combination of cluster analysis, hierarchical linear modeling and SEM multiple group analysis will be used to test the hypotheses in both ..
  32. Molecular mechanisms of altered calcium sensing in human parathyroid disease
    John A Olson; Fiscal Year: 2013
    ..Second, cluster analysis of transcriptional microarray data generated in our laboratory reveals at least three distinct subtypes of ..
  33. Affect and Cerebral Asymmetry: A Developmental Approach
    Nathan A Fox; Fiscal Year: 2010
    ..Our proposed study will attempt an innovativeanalytical approach, growth modeling with latent cluster analysis so that we might identify clusters of children who show particularpatterns of change or continuity in the ..
  34. In Vivo Imaging of Neuronal Plasticity in Mouse Visual Cortex
    Elly Nedivi; Fiscal Year: 2012
    ..Principle component analysis and cluster analysis will be used to quantitatively classify and analyze the morphological and cellular characteristics of imaged ..
  35. Effect of non genetic factors on genetic signatures of complex traits
    Paola Sebastiani; Fiscal Year: 2013
    ..We demonstrated that cluster analysis of the genetic risk profiles can help dissect the complex phenotype of exceptional longevity into sub-..
  36. Framework for a perceptually-driven taxonomy of dysarthric speech
    KAITLIN LORRAINE LANSFORD; Fiscal Year: 2011
    ..correlates to perceptual dimensions associated with dysarthric speaker similarity will be investigated using cluster analysis and multidimensional scaling methods...
  37. Effective Observational Strategies for Health Survey Interviewers
    Brady T West; Fiscal Year: 2013
    ..by NSFG interviewers for their observations on two key features of all sampled NSFG households;2) use cluster analysis techniques to determine whether unique subgroups of NSFG interviewers exist based on the observational ..
  38. Neuropathologic Abnormalities Define A Subgroup of Patients with CFS
    Nora Weiduschat; Fiscal Year: 2012
    ..Our second Aim will use the results from the first Aim in a cluster analysis to attempt objective, data-driven classification of the CFS subjects into subtypes, and then compare the ..
  39. Communication in Infants and Social Screener : The CISS
    Cynthia J Cress; Fiscal Year: 2013
    ..Establish reliability and validity of CISS cluster and composite scores in new as well as videotaped samples of TD and at-risk infants using correlational analyses, including exploratory factor analysis and cluster analysis.
  40. Clinical Cytometry Analysis Software with Automated Gating
    Adam S Treister; Fiscal Year: 2011
    ..Using Magnetic Gating, Probability Clustering, Subtractive Cluster Analysis, Artificial Neural Networks, and Support Vector Machines (SVM), Tree Star software will analyze the cell ..
  41. DEVELOPMENT AND REORGANIZATION OF PRENATAL VISUAL SYSTEM
    Barbara Chapman; Fiscal Year: 2010
    ..A cluster analysis of multiple morphometric measures obtained on a preliminary sample of cells suggests that the mouse ganglion ..
  42. Phenomics: Joint clustering to associate changes in allergy and asthma over time
    Hongmei Zhang; Fiscal Year: 2013
    ..b>Cluster analysis is one type of pattern analysis...
  43. AIDS Related Candidiasis: Dynamic Expression of Drug Resistant Genes
    Theodore C White; Fiscal Year: 2010
    ..Representative strains from the cluster analysis in Aim 1 will be expression profiled using microarrays to identify and characterize the gene induction ..
  44. Metabolic biomarkers for early detection of women at risk for Alzheimer's disease
    JAMAICA RETTBERG; Fiscal Year: 2013
    ..analysis ranging from simple ANOVA/ANCOVA analyses to complex mixed linear effects modeling and K-means cluster analysis will be employed...
  45. Gross morphological correlates to the minicolumnopathy of autism
    Manuel F Casanova; Fiscal Year: 2010
    ..and white matter distribution in the brains of postmortem autistic patients and controls, and 3) To perform a cluster analysis of autism diagnostic criteria and morphometric measurements...
  46. An Investigation Into Atypical Alzheimer's Disease
    JENNIFER LOUISE WHITWELL; Fiscal Year: 2011
    ..Statistical analysis will be performed to compare results across groups for aims 1 and 2 and to perform cluster analysis for aim 3...
  47. Personal Perspective and Provider Communication of Genomic Risk for T2DM
    Sandra Daack-Hirsch; Fiscal Year: 2013
    ..Thematic and cluster analysis will used to analyze the qualitative data...
  48. Statistical Analysis of Epigenomics Data
    Kimberly D Siegmund; Fiscal Year: 2013
    ..a. To develop novel filters to select loci for cluster analysis that consider the outcome, proportion DNA methylation, to follow a Beta distribution with variance a function ..
  49. Cluster Based Selection of Candidate Genes in Genome Wide Association Studies.
    Laura Kelly Vaughan; Fiscal Year: 2011
    ..The proposed research introduces the use of cluster analysis in GWA studies, which will group genes together based on their similarity derived from functional annotations ..
  50. Relationship between adolescent weight, sexual behavior and reproductive outcomes
    Aletha Y Akers; Fiscal Year: 2012
    ..We perform cluster analysis to identify subgroups of youth at highest risk for engaging in sexual risk behaviors based on their actual or ..
  51. A taste for tastes?The spread of food choices & health behaviors in networks
    MARK ANDREW PACHUCKI; Fiscal Year: 2010
    ..A three-stage analysis is proposed. In the first stage, cluster analysis and individuals'scoring on an index of "healthy eating" are used to describe individuals'eating ..
  52. The role of the thalamus in human olfactory processing
    CHRISTINA MARIA ZELANO; Fiscal Year: 2012
    ..In Aim 2, I will use fMRI to Using hierarchical cluster analysis and a general linear model approach to data analysis, I will be able to distinguish between olfactory brain ..
  53. Physical Activity Patterns via New Dimension-Informative Cluster Models.
    Mitchell S Elkind; Fiscal Year: 2013
    ..Goals of this proposal are to develop new cluster analysis methods to accommodate special features of physical activity data arising from questionnaire and ..
  54. Survival Bump Hunting for Finding Informative Subgroups in High Dimensional Data.
    J Sunil Rao; Fiscal Year: 2013
    ..Typically this has been done with various forms of cluster analysis (both supervised and unsupervised)...
  55. Identification of Clinically Relevant TMD Subtypes Using Cluster Analysis
    Eric Bair; Fiscal Year: 2013
    ..Our proposed study is to reanalyze the data collected in OPPERA using cluster analysis and other machine learning methods to identify clinically relevant subtypes of TMD and TMD-like symptoms...
  56. Multiparametric MRI characterization of breast tissue
    Michael Jacobs; Fiscal Year: 2009
    ..dynamic contrast enhanced gadolinium (GdDTPA), soditma, and spectroscopic MR images] in conjunction with cluster analysis methods (ISODATA and angle analysis) into a single vector, to improve differentiation between benign or ..
  57. The Influence of Gender on Symptom Characteristics During Acute Coronary Syndrome
    Holli A DeVon; Fiscal Year: 2013
    ..Symptom clusters will be examined using agglomerative cluster analysis, and patient outcomes will be evaluated using linear mixed methods...
  58. Prediction of Pathologic Complete Response by Gene Expression Profiling in Esopha
    Jaffer A Ajani; Fiscal Year: 2013
    ..In our 19-patient gene expression profiling study, the unsupervised hierarchical cluster analysis segregated cancers into two subtypes...
  59. STD/HIV Prevention Training Center
    Robert J Reed; Fiscal Year: 2010
    ..year, the NYS PTC will have developed and piloted a draft curriculum for a new course on Social Network and Cluster Analysis. Three additional training objectives related to data and evaluation are included in the Training Objectives ..
  60. The Etiology of Successful Aging
    S CONSTANCE WANG; Fiscal Year: 2010
    ..RF), in comparison with existing state-of-the-art statistical methods for longitudinal data analysis and cluster analysis. The overall goal of this strategy is to facilitate the development of simplified ways in which computational ..
  61. GLYCOSYLTRANSFERASE INHIBITORS AS ANTIFUNGAL AGENTS
    Nathaniel Finney; Fiscal Year: 2003
    ..The first of these is the emergence of hydrophobic cluster analysis (HCA) as a widely-used and widely-accepted computational method for identifying structural similarities ..
  62. Chronic Alcohol Effects on Transcriptional Regulation in Liver Regeneration
    Rajanikanth Vadigepalli; Fiscal Year: 2009
    ..the time series gene expression data in order to identify differentially expressed genes and a subsequent cluster analysis to derive temporal expression patterns...
  63. Alzheimer's Diagnosis: Leukocyte Multigene Signatures.
    JAMES CLELLAND; Fiscal Year: 2006
    ..Initial results from this expression study have been striking: Supervised cluster analysis of peripheral leukocyte gene expression data, using transcript level measurements of thousands of genes from ..
  64. Identification of Metastasis-related Gene in Oral Cancer
    Zhuo Chen; Fiscal Year: 2004
    ..DNA microarray and data mining methods such as cluster analysis and feature selection will be used to compare gene expression in highly metastatic primary tumor cells with ..
  65. EVOLUTION OF GROUP A STREPTOCOCCI
    DEBRA BESSEN; Fiscal Year: 2004
    ..Additional emmst will be performed. The data will be analyzed by cluster analysis of differences in alleles, indices of association, and phylogenetic trees to determine how important the role ..
  66. FUNCTIONAL GENOMICS OF HEARING
    Zheng Yi Chen; Fiscal Year: 2005
    ..1. Cluster analysis will be used to identify the expression pattern of candidate genes during development...
  67. PARENTING, CULTURE, NEIGHBORHOODS & ANTISOCIAL BEHAVIOR
    Elizabeth Roberts; Fiscal Year: 2001
    ..Exploratory cluster analysis of the resulting parenting scales will then allow potentially unique holistic patterns of parenting behaviors ..
  68. Adaptive Modeling of Longitudinal Health Outcomes for MACS Participants
    George Knafl; Fiscal Year: 2009
    ..Current LCV-based ASM methods support adaptive forms of classification, cluster analysis, factor analysis, and regression involving univariate or repeated outcome measurements with normal, logistic, ..
  69. Breast Cancer Therapy by Differentiation Gene Activation
    Irma Russo; Fiscal Year: 2006
    ..b>Cluster analysis of mammary gland RNAs obtained during and after pregnancy or hCG treatment and that were hybridized to cDNA ..
  70. SOCIO-ECONOMIC IMPACT OF GATED COMMUNITIES ON AMERICAN CITIES
    ELENA VESSELINOV; Fiscal Year: 2009
    ..We further apply hierarchical cluster analysis to test a typology of gated communities developed through our theoretical model...
  71. Proteomics Approaches to Interstitial Cystitis.
    Brian Liu; Fiscal Year: 2006
    ..e., hierarchical cluster analysis and K-means methods, canonical correlations, discriminant analysis, Bayesian statistics, self-organizing maps ..
  72. Detecting Antidepressant Response Trajectory Shapes in the STAR*D Cohort
    Aimee Hunter; Fiscal Year: 2009
    ..In this vein, growth mixture modeling (GMM), a multilevel modeling technique that incorporates features of cluster analysis, can be applied to longitudinal data to identify latent "classes" or patterns of change in symptom severity ..