David K Gifford

Summary

Affiliation: Massachusetts Institute of Technology
Country: USA

Publications

  1. pmc ReadDB provides efficient storage for mapped short reads
    P Alexander Rolfe
    Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
    BMC Bioinformatics 12:278. 2011
  2. pmc Ruler arrays reveal haploid genomic structural variation
    P Alexander Rolfe
    Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
    PLoS ONE 7:e43210. 2012
  3. pmc Discovering homotypic binding events at high spatial resolution
    Yuchun Guo
    MIT Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, MA 02139, USA
    Bioinformatics 26:3028-34. 2010
  4. ncbi request reprint Transcriptional regulatory networks in Saccharomyces cerevisiae
    Tong Ihn Lee
    Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, MA 02142, USA
    Science 298:799-804. 2002
  5. pmc Ligand-dependent dynamics of retinoic acid receptor binding during early neurogenesis
    Shaun Mahony
    Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
    Genome Biol 12:R2. 2011
  6. pmc High resolution genome wide binding event finding and motif discovery reveals transcription factor spatial binding constraints
    Yuchun Guo
    Computational and Systems Biology Program, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
    PLoS Comput Biol 8:e1002638. 2012
  7. pmc Control of transcription by cell size
    Chia Yung Wu
    Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
    PLoS Biol 8:e1000523. 2010
  8. pmc Feed-forward regulation of a cell fate determinant by an RNA-binding protein generates asymmetry in yeast
    Joshua J Wolf
    Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
    Genetics 185:513-22. 2010
  9. ncbi request reprint Computational discovery of gene modules and regulatory networks
    Ziv Bar-Joseph
    MIT Computer Science and Artificial Intelligence Laboratory, 200 Technology Square, Cambridge, Massachusetts 02139, USA
    Nat Biotechnol 21:1337-42. 2003
  10. ncbi request reprint A hypothesis-based approach for identifying the binding specificity of regulatory proteins from chromatin immunoprecipitation data
    Kenzie D Macisaac
    MIT Computer Science and Artificial Intelligence, Laboratory 32, Vassar Street, Cambridge, MA 02139, USA
    Bioinformatics 22:423-9. 2006

Collaborators

Detail Information

Publications33

  1. pmc ReadDB provides efficient storage for mapped short reads
    P Alexander Rolfe
    Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
    BMC Bioinformatics 12:278. 2011
    ..We present ReadDB, a network accessible column store database system for aligned high-throughput read datasets...
  2. pmc Ruler arrays reveal haploid genomic structural variation
    P Alexander Rolfe
    Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
    PLoS ONE 7:e43210. 2012
    ..In an empirical test between two closely related haploid strains of yeast ruler arrays detected 78% of the structural variants larger than 100 bp...
  3. pmc Discovering homotypic binding events at high spatial resolution
    Yuchun Guo
    MIT Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, MA 02139, USA
    Bioinformatics 26:3028-34. 2010
    ..However, detecting closely spaced homotypic events from ChIP-Seq data is challenging because random variation in the ChIP fragmentation process obscures event locations...
  4. ncbi request reprint Transcriptional regulatory networks in Saccharomyces cerevisiae
    Tong Ihn Lee
    Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, MA 02142, USA
    Science 298:799-804. 2002
    ..Our results reveal that eukaryotic cellular functions are highly connected through networks of transcriptional regulators that regulate other transcriptional regulators...
  5. pmc Ligand-dependent dynamics of retinoic acid receptor binding during early neurogenesis
    Shaun Mahony
    Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
    Genome Biol 12:R2. 2011
    ..RAR is thought to bind the genome constitutively, and only induce transcription in the presence of the retinoid ligand. However, little is known about where RAR binds to the genome or how it selects target sites...
  6. pmc High resolution genome wide binding event finding and motif discovery reveals transcription factor spatial binding constraints
    Yuchun Guo
    Computational and Systems Biology Program, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
    PLoS Comput Biol 8:e1002638. 2012
    ....
  7. pmc Control of transcription by cell size
    Chia Yung Wu
    Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
    PLoS Biol 8:e1000523. 2010
    ..The causal relationship between cell size and transcription suggests that cell size homeostasis serves a regulatory role in transcriptome maintenance...
  8. pmc Feed-forward regulation of a cell fate determinant by an RNA-binding protein generates asymmetry in yeast
    Joshua J Wolf
    Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
    Genetics 185:513-22. 2010
    ..This regulation enables changes in FLO11 expression between mother and daughter cells, which establishes the asymmetry required for the developmental transition between yeast form and filamentous growth...
  9. ncbi request reprint Computational discovery of gene modules and regulatory networks
    Ziv Bar-Joseph
    MIT Computer Science and Artificial Intelligence Laboratory, 200 Technology Square, Cambridge, Massachusetts 02139, USA
    Nat Biotechnol 21:1337-42. 2003
    ..We also present a genome-wide location analysis data set for regulators in yeast cells treated with rapamycin, and use the GRAM algorithm to provide biological insights into this regulatory network..
  10. ncbi request reprint A hypothesis-based approach for identifying the binding specificity of regulatory proteins from chromatin immunoprecipitation data
    Kenzie D Macisaac
    MIT Computer Science and Artificial Intelligence, Laboratory 32, Vassar Street, Cambridge, MA 02139, USA
    Bioinformatics 22:423-9. 2006
    ..However, the discovered motifs often do not agree with the binding specificity of the protein, when it is known...
  11. pmc Comparing the continuous representation of time-series expression profiles to identify differentially expressed genes
    Ziv Bar-Joseph
    Laboratory for Computer Science, Massachusetts Institute of Technology, 200 Technology Square, Cambridge, MA 02139, USA
    Proc Natl Acad Sci U S A 100:10146-51. 2003
    ..This set of genes is significantly correlated in a set of independent expression experiments, suggesting additional roles for the transcription factors Fkh1 and Fkh2 in controlling cellular activity in yeast...
  12. pmc An improved map of conserved regulatory sites for Saccharomyces cerevisiae
    Kenzie D Macisaac
    Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, MA 02142, USA
    BMC Bioinformatics 7:113. 2006
    ..Using these programs, we create a refined regulatory map for S. cerevisiae by reanalyzing the same chromatin immunoprecipitation data...
  13. ncbi request reprint K-ary clustering with optimal leaf ordering for gene expression data
    Ziv Bar-Joseph
    Laboratory for Computer Science, MIT, 545 Technology Square, Cambridge, MA 02139, USA
    Bioinformatics 19:1070-8. 2003
    ..In this paper we propose a new hierarchical clustering algorithm which reduces susceptibility to noise, permits up to k siblings to be directly related, and provides a single optimal order for the resulting tree...
  14. ncbi request reprint Continuous representations of time-series gene expression data
    Ziv Bar-Joseph
    MIT Laboratory for Computer Science, 200 Technology Square, Cambridge, MA 02139, USA
    J Comput Biol 10:341-56. 2003
    ..We demonstrate that our algorithm produces stable low-error alignments on real expression data and further show a specific application to yeast knock-out data that produces biologically meaningful results...
  15. pmc Control of pancreas and liver gene expression by HNF transcription factors
    Duncan T Odom
    Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA
    Science 303:1378-81. 2004
    ..Our results suggest how misregulation of HNF4alpha can contribute to type 2 diabetes...
  16. ncbi request reprint Genome-wide map of nucleosome acetylation and methylation in yeast
    Dmitry K Pokholok
    Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, Massachusetts 02142, USA
    Cell 122:517-27. 2005
    ..These maps provide the foundation for further understanding the roles of chromatin in gene expression and genome maintenance...
  17. pmc High-resolution genetic mapping with pooled sequencing
    Matthew D Edwards
    Computer Science and Artificial Intelligence Laboratory, Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
    BMC Bioinformatics 13:S8. 2012
    ..However, the uncertainty from pooling and the challenge of noisy sequencing data demand advanced computational methods...
  18. pmc Rapid haplotype inference for nuclear families
    Amy L Williams
    Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, 32 Vassar Street, Cambridge, MA 02139, USA
    Genome Biol 11:R108. 2010
    ..Because Hapi infers both minimum-recombinant and maximum likelihood haplotypes and applies to related individuals, the haplotypes it infers are highly accurate over extended genomic distances...
  19. pmc Toggle involving cis-interfering noncoding RNAs controls variegated gene expression in yeast
    Stacie L Bumgarner
    Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA
    Proc Natl Acad Sci U S A 106:18321-6. 2009
    ....
  20. pmc Tissue-specific transcriptional regulation has diverged significantly between human and mouse
    Duncan T Odom
    Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nat Genet 39:730-2. 2007
    ..When the same protein binds the promoters of orthologous genes, approximately two-thirds of the binding sites do not align...
  21. ncbi request reprint High-resolution computational models of genome binding events
    Yuan Qi
    Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, 32 Vassar Street, Cambridge, MA 02139, USA
    Nat Biotechnol 24:963-70. 2006
    ..We present results on the yeast transcription factors Gcn4 and Mig2 to demonstrate JBD's spatial resolution capabilities and show that positional priors allow computational discovery of the Mig2 motif when a standard approach fails...
  22. pmc Global position and recruitment of HATs and HDACs in the yeast genome
    Francois Robert
    Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, MA 02142, USA
    Mol Cell 16:199-209. 2004
    ....
  23. pmc Core transcriptional regulatory circuitry in human embryonic stem cells
    Laurie A Boyer
    Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Cell 122:947-56. 2005
    ..These results provide new insights into the transcriptional regulation of stem cells and reveal how OCT4, SOX2, and NANOG contribute to pluripotency and self-renewal...
  24. pmc Interactions between chromosomal and nonchromosomal elements reveal missing heritability
    Matthew D Edwards
    Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139
    Proc Natl Acad Sci U S A 111:7719-22. 2014
    ..Taken together, our results highlight the importance of including all sources of heritable information in genetic studies and suggest a possible avenue of attack for finding additional missing heritability. ..
  25. pmc A multi-parametric flow cytometric assay to analyze DNA-protein interactions
    Mandana Arbab
    Division of Genetics, Department of Medicine, Brigham and Women s Hospital and Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
    Nucleic Acids Res 41:e38. 2013
    ..Combinatorial fluorescent staining allows simultaneous analysis of sequence-specific TF-DNA interaction and chromatin modification. MagPIE provides a simple and robust method to analyze complex epigenetic interactions in vitro...
  26. pmc Transcriptional regulatory code of a eukaryotic genome
    Christopher T Harbison
    Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nature 431:99-104. 2004
    ..We find that environment-specific use of regulatory elements predicts mechanistic models for the function of a large population of yeast's transcriptional regulators...
  27. pmc Control of developmental regulators by Polycomb in human embryonic stem cells
    Tong Ihn Lee
    Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA
    Cell 125:301-13. 2006
    ..These results indicate that PRC2 occupies a special set of developmental genes in ES cells that must be repressed to maintain pluripotency and that are poised for activation during ES cell differentiation...
  28. ncbi request reprint Semi-supervised analysis of gene expression profiles for lineage-specific development in the Caenorhabditis elegans embryo
    Yuan Qi
    Massachusetts Institute of Technology, Computer Science and Artificial Intelligence Laboratory, 32 Vassar Street, Cambridge, MA 02139, USA
    Bioinformatics 22:e417-23. 2006
    ..However, for many biological problems, little prior knowledge is available, which limits the prediction performance of most supervised methods...
  29. pmc Universal count correction for high-throughput sequencing
    Tatsunori B Hashimoto
    Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
    PLoS Comput Biol 10:e1003494. 2014
    ..We demonstrate that FIXSEQ substantially improves the performance of existing RNA-seq, DNase-seq, and ChIP-seq analysis tools when compared with existing alternatives...
  30. pmc Analysis of the mouse embryonic stem cell regulatory networks obtained by ChIP-chip and ChIP-PET
    Divya Mathur
    Department of Biology, Massachusetts Institute of Technology, Ames Street, Cambridge, MA 02139, USA
    Genome Biol 9:R126. 2008
    ..Recent evidence with comparing multiple technologies suggests that expanding these datasets using different platforms would be a useful resource for examining the mechanisms underlying pluripotency regulation...
  31. ncbi request reprint Genotype to phenotype: a complex problem
    Robin D Dowell
    Computer Science and Artificial Intelligence Laboratory, Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology MIT, Cambridge, MA 02139, USA
    Science 328:469. 2010
    ..Our comprehensive analysis suggests that the presence of a complex set of modifiers will often underlie the phenotypic differences between individuals...
  32. pmc Automated discovery of functional generality of human gene expression programs
    Georg K Gerber
    Department of Computer Science and Electrical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
    PLoS Comput Biol 3:e148. 2007
    ..Further, our method is multipurpose, and can be applied readily to novel compendia of biological data...
  33. pmc Core transcriptional regulatory circuitry in human hepatocytes
    Duncan T Odom
    Young Laboratory, Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA
    Mol Syst Biol 2:2006.0017. 2006
    ..Our studies reveal portions of the core circuitry of human hepatocytes...