Andrew D Smith

Summary

Affiliation: Cold Spring Harbor Laboratory
Country: USA

Publications

  1. pmc Using quality scores and longer reads improves accuracy of Solexa read mapping
    Andrew D Smith
    Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11274, USA
    BMC Bioinformatics 9:128. 2008
  2. pmc SIMPROT: using an empirically determined indel distribution in simulations of protein evolution
    Andy Pang
    Ontario Cancer Institute, University Health Network, Toronto, Ontario, Canada
    BMC Bioinformatics 6:236. 2005
  3. pmc Integrative bioinformatics analysis of transcriptional regulatory programs in breast cancer cells
    Atsushi Niida
    Laboratory of Molecular and Genetic Information, Institute of Molecular and Cellular Biosciences, The University of Tokyo, Bunkyo ku, Tokyo, 110 0032, Japan
    BMC Bioinformatics 9:404. 2008
  4. pmc Gene set-based module discovery in the breast cancer transcriptome
    Atsushi Niida
    Laboratory of Molecular and Genetic Information, Institute of Molecular and Cellular Biosciences, The University of Tokyo, 1 1 1 Yayoi, Bunkyo ku, Tokyo, Japan
    BMC Bioinformatics 10:71. 2009
  5. ncbi request reprint Mining ChIP-chip data for transcription factor and cofactor binding sites
    Andrew D Smith
    Cold Spring Harbor Laboratory 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
    Bioinformatics 21:i403-12. 2005
  6. pmc Statistical significance of cis-regulatory modules
    Dustin E Schones
    Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
    BMC Bioinformatics 8:19. 2007
  7. pmc De novo DNA demethylation and noncoding transcription define active intergenic regulatory elements
    Felix Schlesinger
    Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
    Genome Res 23:1601-14. 2013
  8. pmc Tissue-specific regulatory elements in mammalian promoters
    Andrew D Smith
    Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
    Mol Syst Biol 3:73. 2007
  9. ncbi request reprint DWE: discriminating word enumerator
    Pavel Sumazin
    Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
    Bioinformatics 21:31-8. 2005
  10. pmc Directional DNA methylation changes and complex intermediate states accompany lineage specificity in the adult hematopoietic compartment
    Emily Hodges
    Watson School of Biological Sciences, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
    Mol Cell 44:17-28. 2011

Collaborators

Detail Information

Publications23

  1. pmc Using quality scores and longer reads improves accuracy of Solexa read mapping
    Andrew D Smith
    Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11274, USA
    BMC Bioinformatics 9:128. 2008
    ..Two sources of information that are often ignored when mapping reads from the Solexa technology are the 3' ends of longer reads, which contain a much higher frequency of sequencing errors, and the base-call quality scores...
  2. pmc SIMPROT: using an empirically determined indel distribution in simulations of protein evolution
    Andy Pang
    Ontario Cancer Institute, University Health Network, Toronto, Ontario, Canada
    BMC Bioinformatics 6:236. 2005
    ..General protein evolution models help determine the baseline expectations for the evolution of sequences, and they have been extensively useful in sequence analysis and for the computer simulation of artificial sequence data sets...
  3. pmc Integrative bioinformatics analysis of transcriptional regulatory programs in breast cancer cells
    Atsushi Niida
    Laboratory of Molecular and Genetic Information, Institute of Molecular and Cellular Biosciences, The University of Tokyo, Bunkyo ku, Tokyo, 110 0032, Japan
    BMC Bioinformatics 9:404. 2008
    ..However, compared with the massive knowledge about the transcriptome, we have surprisingly little knowledge about regulatory mechanisms underling transcriptomic diversity...
  4. pmc Gene set-based module discovery in the breast cancer transcriptome
    Atsushi Niida
    Laboratory of Molecular and Genetic Information, Institute of Molecular and Cellular Biosciences, The University of Tokyo, 1 1 1 Yayoi, Bunkyo ku, Tokyo, Japan
    BMC Bioinformatics 10:71. 2009
    ..However, such module discovery methods are not applied cancer transcriptome data...
  5. ncbi request reprint Mining ChIP-chip data for transcription factor and cofactor binding sites
    Andrew D Smith
    Cold Spring Harbor Laboratory 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
    Bioinformatics 21:i403-12. 2005
    ..Identification of single motifs and motif pairs that can be used to predict transcription factor localization in ChIP-chip data, and gene expression in tissue-specific microarray data...
  6. pmc Statistical significance of cis-regulatory modules
    Dustin E Schones
    Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
    BMC Bioinformatics 8:19. 2007
    ..While various algorithms for this purpose have been introduced, most are not well suited for rapid, genome scale scanning...
  7. pmc De novo DNA demethylation and noncoding transcription define active intergenic regulatory elements
    Felix Schlesinger
    Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
    Genome Res 23:1601-14. 2013
    ....
  8. pmc Tissue-specific regulatory elements in mammalian promoters
    Andrew D Smith
    Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
    Mol Syst Biol 3:73. 2007
    ..In a broader context, methods used to construct the catalog provide a model for the analysis of genomic regions that regulate differentially expressed genes...
  9. ncbi request reprint DWE: discriminating word enumerator
    Pavel Sumazin
    Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
    Bioinformatics 21:31-8. 2005
    ..Tissue-specific transcription factor binding sites give insight into tissue-specific transcription regulation...
  10. pmc Directional DNA methylation changes and complex intermediate states accompany lineage specificity in the adult hematopoietic compartment
    Emily Hodges
    Watson School of Biological Sciences, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
    Mol Cell 44:17-28. 2011
    ..Overall, our studies represent an important reference data set and provide insights into directional changes in DNA methylation as cells adopt terminal fates...
  11. pmc Identifying tissue-selective transcription factor binding sites in vertebrate promoters
    Andrew D Smith
    Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11274, USA
    Proc Natl Acad Sci U S A 102:1560-5. 2005
    ....
  12. pmc DNA motifs in human and mouse proximal promoters predict tissue-specific expression
    Andrew D Smith
    Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
    Proc Natl Acad Sci U S A 103:6275-80. 2006
    ..The identification in proximal promoters of cis-regulatory modules with tissue-specific activity lays the groundwork for complete characterization and deciphering of cis-regulatory DNA code in mammalian genomes...
  13. pmc High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing
    Emily Hodges
    Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
    Genome Res 19:1593-605. 2009
    ..Methylation, along with specific histone marks, was enriched in exonic regions, suggesting that chromatin states can foreshadow the content of mature mRNAs...
  14. pmc Molecular hierarchy of mammary differentiation yields refined markers of mammary stem cells
    Camila O Dos Santos
    Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
    Proc Natl Acad Sci U S A 110:7123-30. 2013
    ..Collectively, our data provide tools for isolating a more precisely defined population of MaSCs and point to potentially critical factors for MaSC maintenance...
  15. pmc Site identification in high-throughput RNA-protein interaction data
    Philip J Uren
    Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
    Bioinformatics 28:3013-20. 2012
    ..Statistically robust, flexible computational methods for binding site identification from high-throughput immunoprecipitation assays are largely lacking however...
  16. pmc Sperm methylation profiles reveal features of epigenetic inheritance and evolution in primates
    Antoine Molaro
    Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
    Cell 146:1029-41. 2011
    ..Thus, the features that determine DNA methylation patterns differ between male germ cells and somatic cells, and elements of these features have diverged between humans and chimpanzees...
  17. pmc Diverse endonucleolytic cleavage sites in the mammalian transcriptome depend upon microRNAs, Drosha, and additional nucleases
    Fedor V Karginov
    Watson School of Biological Sciences, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
    Mol Cell 38:781-8. 2010
    ..Together, these results highlight the underappreciated role of endonucleolytic cleavage in controlling mRNA fates in mammals...
  18. ncbi request reprint Computational prediction of novel components of lung transcriptional networks
    M Juanita Martinez
    Lovelace Respiratory Research Institute, 2425 Ridgecrest Dr SE, Albuquerque, NM 87108, USA
    Bioinformatics 23:21-9. 2007
    ..Little is known regarding the transcriptional mechanisms involved in forming and maintaining epithelial cell lineages of the mammalian respiratory tract...
  19. pmc Genome-wide mapping and analysis of active promoters in mouse embryonic stem cells and adult organs
    Leah O Barrera
    Ludwig Institute for Cancer Research, UCSD School of Medicine, La Jolla, California 92093 0653, USA
    Genome Res 18:46-59. 2008
    ..Our results provide a resource for exploring promoter Polr2a binding and epigenetic states across pluripotent and differentiated cell types in mammals...
  20. pmc Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome
    Tae Hoon Kim
    Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA 92093 0653, USA
    Cell 128:1231-45. 2007
    ..In addition, CTCF localization is largely invariant across different cell types. Our results provide a resource for investigating insulator function and possible other general and evolutionarily conserved activities of CTCF sites...
  21. ncbi request reprint Use of exhaled nitric oxide measurements to guide treatment in chronic asthma
    Andrew D Smith
    Respiratory Research Unit, Department of Medicine, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
    N Engl J Med 352:2163-73. 2005
    ..Measurements of the fraction of exhaled nitric oxide (FE(NO)) constitute a noninvasive marker that may be a useful alternative for the adjustment of inhaled-corticosteroid treatment...
  22. ncbi request reprint Empirical models for substitution in ribosomal RNA
    Andrew D Smith
    Department of Medical Biophysics, University of Toronto, and Ontario Cancer Institute, University Health Network, Toronto, Ontario, Canada
    Mol Biol Evol 21:419-27. 2004
    ..In addition, the models are useful for simulating the evolution of RNA sequence and structure simultaneously...
  23. ncbi request reprint A biochemical characterization of the adeno-associated virus Rep40 helicase
    Roy F Collaco
    Department of Biochemistry and Molecular Biology, Medical College of Ohio, Toledo, Ohio 43614, USA
    J Biol Chem 278:34011-7. 2003
    ..These studies provide the first enzymatic characterization of the AAV Rep40 protein and elucidate important functional differences between the AAV helicases...