Contact, publication, and social network information about Harvard faculty and fellows. Harvard Catalyst Profiles
Keywords
Last Name
Institution

David Kenneth Gifford, Ph.D.

TitleMember of the Affiliated Faculty of the Harvard-MIT Division of Health Sciences and Technology
InstitutionMassachusetts Institute of Technology
DepartmentHealth Sciences and Technology
AddressDavid Gifford
Sherman Fairchild Biochemistry Bldg
7 Divinity Ave
Cambridge MA 02138
Phone617/253-6039
Other Positions
TitleVisiting Scholar in Stem Cell & Regenerative Biology (EXT)
InstitutionFaculty of Arts & Sciences
DepartmentStem Cell and Regenerative Biology


 Bibliographic 
 selected publications
Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
List All   |   Timeline
  1. Paik EJ, Mahony S, White RM, Price EN, Dibiase A, Dorjsuren B, Mosimann C, Davidson AJ, Gifford D, Zon LI. A cdx4-sall4 regulatory module controls the transition from mesoderm formation to embryonic hematopoiesis. Stem Cell Reports. 2013; 1(5):425-36.
    View in: PubMed
  2. Mazzoni EO, Mahony S, Peljto M, Patel T, Thornton SR, McCuine S, Reeder C, Boyer LA, Young RA, Gifford DK, Wichterle H. Saltatory remodeling of Hox chromatin in response to rostrocaudal patterning signals. Nat Neurosci. 2013 Sep; 16(9):1191-8.
    View in: PubMed
  3. Wichterle H, Gifford D, Mazzoni E. Neuroscience. Mapping neuronal diversity one cell at a time. Science. 2013 Aug 16; 341(6147):726-7.
    View in: PubMed
  4. Mazzoni EO, Mahony S, Closser M, Morrison CA, Nedelec S, Williams DJ, An D, Gifford DK, Wichterle H. Synergistic binding of transcription factors to cell-specific enhancers programs motor neuron identity. Nat Neurosci. 2013 Sep; 16(9):1219-27.
    View in: PubMed
  5. Arbab M, Mahony S, Cho H, Chick JM, Rolfe PA, van Hoff JP, Morris VW, Gygi SP, Maas RL, Gifford DK, Sherwood RI. A multi-parametric flow cytometric assay to analyze DNA-protein interactions. Nucleic Acids Res. 2013 Jan 1; 41(2):e38.
    View in: PubMed
  6. Ryan O, Shapiro RS, Kurat CF, Mayhew D, Baryshnikova A, Chin B, Lin ZY, Cox MJ, Vizeacoumar F, Cheung D, Bahr S, Tsui K, Tebbji F, Sellam A, Istel F, Schwarzm├╝ller T, Reynolds TB, Kuchler K, Gifford DK, Whiteway M, Giaever G, Nislow C, Costanzo M, Gingras AC, Mitra RD, Andrews B, Fink GR, Cowen LE, Boone C. Global gene deletion analysis exploring yeast filamentous growth. Science. 2012 Sep 14; 337(6100):1353-6.
    View in: PubMed
  7. Rolfe PA, Bernstein DA, Grisafi P, Fink GR, Gifford DK. Ruler arrays reveal haploid genomic structural variation. PLoS One. 2012; 7(8):e43210.
    View in: PubMed
  8. Guo Y, Mahony S, Gifford DK. High resolution genome wide binding event finding and motif discovery reveals transcription factor spatial binding constraints. PLoS Comput Biol. 2012; 8(8):e1002638.
    View in: PubMed
  9. Hashimoto T, Jaakkola T, Sherwood R, Mazzoni EO, Wichterle H, Gifford D. Lineage-based identification of cellular states and expression programs. Bioinformatics. 2012 Jun 15; 28(12):i250-7.
    View in: PubMed
  10. Edwards MD, Gifford DK. High-resolution genetic mapping with pooled sequencing. BMC Bioinformatics. 2012; 13 Suppl 6:S8.
    View in: PubMed
  11. Mazzoni EO, Mahony S, Iacovino M, Morrison CA, Mountoufaris G, Closser M, Whyte WA, Young RA, Kyba M, Gifford DK, Wichterle H. Embryonic stem cell-based mapping of developmental transcriptional programs. Nat Methods. 2011 Dec; 8(12):1056-8.
    View in: PubMed
  12. Rolfe PA, Gifford DK. ReadDB provides efficient storage for mapped short reads. BMC Bioinformatics. 2011; 12:278.
    View in: PubMed
  13. Danford T, Dowell R, Agarwala S, Grisafi P, Fink G, Gifford D. Discovering regulatory overlapping RNA transcripts. J Comput Biol. 2011 Mar; 18(3):295-303.
    View in: PubMed
  14. Mahony S, Mazzoni EO, McCuine S, Young RA, Wichterle H, Gifford DK. Ligand-dependent dynamics of retinoic acid receptor binding during early neurogenesis. Genome Biol. 2011; 12(1):R2.
    View in: PubMed
  15. Wu CY, Rolfe PA, Gifford DK, Fink GR. Control of transcription by cell size. PLoS Biol. 2010; 8(11):e1000523.
    View in: PubMed
  16. Williams AL, Housman DE, Rinard MC, Gifford DK. Rapid haplotype inference for nuclear families. Genome Biol. 2010; 11(10):R108.
    View in: PubMed
  17. Guo Y, Papachristoudis G, Altshuler RC, Gerber GK, Jaakkola TS, Gifford DK, Mahony S. Discovering homotypic binding events at high spatial resolution. Bioinformatics. 2010 Dec 15; 26(24):3028-34.
    View in: PubMed
  18. Jung H, Lacombe J, Mazzoni EO, Liem KF, Grinstein J, Mahony S, Mukhopadhyay D, Gifford DK, Young RA, Anderson KV, Wichterle H, Dasen JS. Global control of motor neuron topography mediated by the repressive actions of a single hox gene. Neuron. 2010 Sep 9; 67(5):781-96.
    View in: PubMed
  19. Dowell RD, Ryan O, Jansen A, Cheung D, Agarwala S, Danford T, Bernstein DA, Rolfe PA, Heisler LE, Chin B, Nislow C, Giaever G, Phillips PC, Fink GR, Gifford DK, Boone C. Genotype to phenotype: a complex problem. Science. 2010 Apr 23; 328(5977):469.
    View in: PubMed
  20. Wolf JJ, Dowell RD, Mahony S, Rabani M, Gifford DK, Fink GR. Feed-forward regulation of a cell fate determinant by an RNA-binding protein generates asymmetry in yeast. Genetics. 2010 Jun; 185(2):513-22.
    View in: PubMed
  21. Bumgarner SL, Dowell RD, Grisafi P, Gifford DK, Fink GR. Toggle involving cis-interfering noncoding RNAs controls variegated gene expression in yeast. Proc Natl Acad Sci U S A. 2009 Oct 27; 106(43):18321-6.
    View in: PubMed
  22. Mathur D, Danford TW, Boyer LA, Young RA, Gifford DK, Jaenisch R. Analysis of the mouse embryonic stem cell regulatory networks obtained by ChIP-chip and ChIP-PET. Genome Biol. 2008; 9(8):R126.
    View in: PubMed
  23. Danford T, Rolfe A, Gifford D. GSE: a comprehensive database system for the representation, retrieval, and analysis of microarray data. Pac Symp Biocomput. 2008; 539-50.
    View in: PubMed
  24. Gerber GK, Dowell RD, Jaakkola TS, Gifford DK. Automated discovery of functional generality of human gene expression programs. PLoS Comput Biol. 2007 Aug; 3(8):e148.
    View in: PubMed
  25. Odom DT, Dowell RD, Jacobsen ES, Gordon W, Danford TW, MacIsaac KD, Rolfe PA, Conboy CM, Gifford DK, Fraenkel E. Tissue-specific transcriptional regulation has diverged significantly between human and mouse. Nat Genet. 2007 Jun; 39(6):730-2.
    View in: PubMed
  26. Qi Y, Rolfe A, MacIsaac KD, Gerber GK, Pokholok D, Zeitlinger J, Danford T, Dowell RD, Fraenkel E, Jaakkola TS, Young RA, Gifford DK. High-resolution computational models of genome binding events. Nat Biotechnol. 2006 Aug; 24(8):963-70.
    View in: PubMed
  27. Qi Y, Missiuro PE, Kapoor A, Hunter CP, Jaakkola TS, Gifford DK, Ge H. Semi-supervised analysis of gene expression profiles for lineage-specific development in the Caenorhabditis elegans embryo. Bioinformatics. 2006 Jul 15; 22(14):e417-23.
    View in: PubMed
  28. Odom DT, Dowell RD, Jacobsen ES, Nekludova L, Rolfe PA, Danford TW, Gifford DK, Fraenkel E, Bell GI, Young RA. Core transcriptional regulatory circuitry in human hepatocytes. Mol Syst Biol. 2006; 2:2006.0017.
    View in: PubMed
  29. Lee TI, Jenner RG, Boyer LA, Guenther MG, Levine SS, Kumar RM, Chevalier B, Johnstone SE, Cole MF, Isono K, Koseki H, Fuchikami T, Abe K, Murray HL, Zucker JP, Yuan B, Bell GW, Herbolsheimer E, Hannett NM, Sun K, Odom DT, Otte AP, Volkert TL, Bartel DP, Melton DA, Gifford DK, Jaenisch R, Young RA. Control of developmental regulators by Polycomb in human embryonic stem cells. Cell. 2006 Apr 21; 125(2):301-13.
    View in: PubMed
  30. Boyer LA, Plath K, Zeitlinger J, Brambrink T, Medeiros LA, Lee TI, Levine SS, Wernig M, Tajonar A, Ray MK, Bell GW, Otte AP, Vidal M, Gifford DK, Young RA, Jaenisch R. Polycomb complexes repress developmental regulators in murine embryonic stem cells. Nature. 2006 May 18; 441(7091):349-53.
    View in: PubMed
  31. Schreiber J, Jenner RG, Murray HL, Gerber GK, Gifford DK, Young RA. Coordinated binding of NF-kappaB family members in the response of human cells to lipopolysaccharide. Proc Natl Acad Sci U S A. 2006 Apr 11; 103(15):5899-904.
    View in: PubMed
  32. MacIsaac KD, Wang T, Gordon DB, Gifford DK, Stormo GD, Fraenkel E. An improved map of conserved regulatory sites for Saccharomyces cerevisiae. BMC Bioinformatics. 2006; 7:113.
    View in: PubMed
  33. Macisaac KD, Gordon DB, Nekludova L, Odom DT, Schreiber J, Gifford DK, Young RA, Fraenkel E. A hypothesis-based approach for identifying the binding specificity of regulatory proteins from chromatin immunoprecipitation data. Bioinformatics. 2006 Feb 15; 22(4):423-9.
    View in: PubMed
  34. Boyer LA, Lee TI, Cole MF, Johnstone SE, Levine SS, Zucker JP, Guenther MG, Kumar RM, Murray HL, Jenner RG, Gifford DK, Melton DA, Jaenisch R, Young RA. Core transcriptional regulatory circuitry in human embryonic stem cells. Cell. 2005 Sep 23; 122(6):947-56.
    View in: PubMed
  35. Pokholok DK, Harbison CT, Levine S, Cole M, Hannett NM, Lee TI, Bell GW, Walker K, Rolfe PA, Herbolsheimer E, Zeitlinger J, Lewitter F, Gifford DK, Young RA. Genome-wide map of nucleosome acetylation and methylation in yeast. Cell. 2005 Aug 26; 122(4):517-27.
    View in: PubMed
  36. Robert F, Pokholok DK, Hannett NM, Rinaldi NJ, Chandy M, Rolfe A, Workman JL, Gifford DK, Young RA. Global position and recruitment of HATs and HDACs in the yeast genome. Mol Cell. 2004 Oct 22; 16(2):199-209.
    View in: PubMed
  37. Harbison CT, Gordon DB, Lee TI, Rinaldi NJ, Macisaac KD, Danford TW, Hannett NM, Tagne JB, Reynolds DB, Yoo J, Jennings EG, Zeitlinger J, Pokholok DK, Kellis M, Rolfe PA, Takusagawa KT, Lander ES, Gifford DK, Fraenkel E, Young RA. Transcriptional regulatory code of a eukaryotic genome. Nature. 2004 Sep 2; 431(7004):99-104.
    View in: PubMed
  38. Bar-Joseph Z, Farkash S, Gifford DK, Simon I, Rosenfeld R. Deconvolving cell cycle expression data with complementary information. Bioinformatics. 2004 Aug 4; 20 Suppl 1:i23-30.
    View in: PubMed
  39. Sciamanna CN, Gifford DR, Smith RJ. Design and acceptability of patient-oriented computerized diabetes care reminders for use at the point of care. Med Inform Internet Med. 2004 Jun; 29(2):157-68.
    View in: PubMed
  40. Fairchild DG, Benjamin EM, Gifford DR, Huot SJ. Physician leadership: enhancing the career development of academic physician administrators and leaders. Acad Med. 2004 Mar; 79(3):214-8.
    View in: PubMed
  41. Odom DT, Zizlsperger N, Gordon DB, Bell GW, Rinaldi NJ, Murray HL, Volkert TL, Schreiber J, Rolfe PA, Gifford DK, Fraenkel E, Bell GI, Young RA. Control of pancreas and liver gene expression by HNF transcription factors. Science. 2004 Feb 27; 303(5662):1378-81.
    View in: PubMed
  42. Takusagawa KT, Gifford DK. Negative information for motif discovery. Pac Symp Biocomput. 2004; 360-71.
    View in: PubMed
  43. Bar-Joseph Z, Gerber GK, Lee TI, Rinaldi NJ, Yoo JY, Robert F, Gordon DB, Fraenkel E, Jaakkola TS, Young RA, Gifford DK. Computational discovery of gene modules and regulatory networks. Nat Biotechnol. 2003 Nov; 21(11):1337-42.
    View in: PubMed
  44. Bar-Joseph Z, Gerber G, Simon I, Gifford DK, Jaakkola TS. Comparing the continuous representation of time-series expression profiles to identify differentially expressed genes. Proc Natl Acad Sci U S A. 2003 Sep 2; 100(18):10146-51.
    View in: PubMed
  45. Bar-Joseph Z, Demaine ED, Gifford DK, Srebro N, Hamel AM, Jaakkola TS. K-ary clustering with optimal leaf ordering for gene expression data. Bioinformatics. 2003 Jun 12; 19(9):1070-8.
    View in: PubMed
  46. Bar-Joseph Z, Gerber GK, Gifford DK, Jaakkola TS, Simon I. Continuous representations of time-series gene expression data. J Comput Biol. 2003; 10(3-4):341-56.
    View in: PubMed
  47. Lee TI, Rinaldi NJ, Robert F, Odom DT, Bar-Joseph Z, Gerber GK, Hannett NM, Harbison CT, Thompson CM, Simon I, Zeitlinger J, Jennings EG, Murray HL, Gordon DB, Ren B, Wyrick JJ, Tagne JB, Volkert TL, Fraenkel E, Gifford DK, Young RA. Transcriptional regulatory networks in Saccharomyces cerevisiae. Science. 2002 Oct 25; 298(5594):799-804.
    View in: PubMed
  48. Sachs K, Gifford D, Jaakkola T, Sorger P, Lauffenburger DA. Bayesian network approach to cell signaling pathway modeling. Sci STKE. 2002 Sep 3; 2002(148):pe38.
    View in: PubMed
  49. Hartemink AJ, Gifford DK, Jaakkola TS, Young RA. Combining location and expression data for principled discovery of genetic regulatory network models. Pac Symp Biocomput. 2002; 437-49.
    View in: PubMed
  50. Simon I, Barnett J, Hannett N, Harbison CT, Rinaldi NJ, Volkert TL, Wyrick JJ, Zeitlinger J, Gifford DK, Jaakkola TS, Young RA. Serial regulation of transcriptional regulators in the yeast cell cycle. Cell. 2001 Sep 21; 106(6):697-708.
    View in: PubMed
  51. Gifford DK. Blazing pathways through genetic mountains. Science. 2001 Sep 14; 293(5537):2049-51.
    View in: PubMed
  52. Hartemink AJ, Gifford DK, Jaakkola TS, Young RA. Using graphical models and genomic expression data to statistically validate models of genetic regulatory networks. Pac Symp Biocomput. 2001; 422-33.
    View in: PubMed
  53. Bar-Joseph Z, Gifford DK, Jaakkola TS. Fast optimal leaf ordering for hierarchical clustering. Bioinformatics. 2001; 17 Suppl 1:S22-9.
    View in: PubMed
  54. Hartemink AJ, Gifford DK, Khodor J. Automated constraint-based nucleotide sequence selection for DNA computation. Biosystems. 1999 Oct; 52(1-3):227-35.
    View in: PubMed
  55. Khodor J, Gifford DK. Design and implementation of computational systems based on programmed mutagenesis. Biosystems. 1999 Oct; 52(1-3):93-7.
    View in: PubMed
  56. Gifford DK. On the path to computation with DNA. Science. 1994 Nov 11; 266(5187):993-4.
    View in: PubMed
Local representatives can answer questions about the Profiles website or help with editing a profile or issues with profile data. For assistance with this profile: HMS/HSDM faculty should contact Human Resources at faculty_serviceshms.harvard.edu. FAS faculty should contact the Office for Scholarly Communication (oschulmail.harvard.edu) for general questions about Profiles. For data questions, please contact Raelyn Lincoln (raelyn_lincolnharvard.edu) from the FAS Division of Science; Jennifer Shephard (jmshephfas.harvard.edu) from the FAS Division of Social Science; or Alexander Parker (afparkerfas.harvard.edu) from the FAS Division of Arts and Humanities.
Gifford's Networks
Click the "See All" links for more information and interactive visualizations!
Concepts
_
Co-Authors
_
Similar People
_
Same Department
Physical Neighbors
_