Harvard Catalyst Profiles

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David Kenneth Gifford, Ph.D.

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Research
The research activities and funding listed below are automatically derived from NIH ExPORTER and other sources, which might result in incorrect or missing items. Faculty can login to make corrections and additions.
  1. R01CA218094 (GIFFORD, DAVID K) Mar 9, 2018 - Feb 28, 2023
    NIH/NCI
    Deep learning based antibody design using high-throughput affinity testing of synthetic sequences
    Role: Principal Investigator
  2. R01HG008754 (GIFFORD, DAVID K) Sep 9, 2016 - Jun 30, 2020
    NIH/NHGRI
    High-Throughput Native Context Mapping and Modeling of Regulatory DNA
    Role: Principal Investigator
  3. R01HG008363 (GIFFORD, DAVID K) May 13, 2015 - Apr 30, 2018
    NIH/NHGRI
    High-throughput methods for elucidating the control of chromatin accessibility
    Role: Principal Investigator
  4. U01HG007037 (GIFFORD, DAVID K.) Sep 17, 2012 - Jun 30, 2016
    NIH/NHGRI
    Integrated Genome Discovery at Single Base Pair Resolution
    Role: Principal Investigator
  5. T32HG004947 (GIFFORD, DAVID K.) Jul 8, 2009 - Jun 30, 2014
    NIH/NHGRI
    MIT/Whitehead/Broad Computational Genetics Training Program
    Role: Principal Investigator

Bibliographic
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.
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PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
  1. Hammelman J, Krismer K, Banerjee B, Gifford DK, Sherwood RI. Identification of determinants of differential chromatin accessibility through a massively parallel genome-integrated reporter assay. Genome Res. 2020 Oct; 30(10):1468-1480. PMID: 32973041.
    Citations:    Fields:    
  2. Liu G, Carter B, Bricken T, Jain S, Viard M, Carrington M, Gifford DK. Computationally Optimized SARS-CoV-2 MHC Class I and II Vaccine Formulations Predicted to Target Human Haplotype Distributions. Cell Syst. 2020 08 26; 11(2):131-144.e6. PMID: 32721383.
    Citations: 1     Fields:    Translation:HumansCells
  3. Yeo GHT, Lin L, Qi CY, Cha M, Gifford DK, Sherwood RI. A Multiplexed Barcodelet Single-Cell RNA-Seq Approach Elucidates Combinatorial Signaling Pathways that Drive ESC Differentiation. Cell Stem Cell. 2020 06 04; 26(6):938-950.e6. PMID: 32459995.
    Citations:    Fields:    
  4. Liu G, Carter B, Bricken T, Jain S, Viard M, Carrington M, Gifford DK. Robust computational design and evaluation of peptide vaccines for cellular immunity with application to SARS-CoV-2. bioRxiv. 2020 May 17. PMID: 32511351.
    Citations:    
  5. Krismer K, Guo Y, Gifford DK. IDR2D identifies reproducible genomic interactions. Nucleic Acids Res. 2020 04 06; 48(6):e31. PMID: 32009147.
    Citations:    Fields:    Translation:Cells
  6. Liu G, Zeng H, Mueller J, Carter B, Wang Z, Schilz J, Horny G, Birnbaum ME, Ewert S, Gifford DK. Antibody complementarity determining region design using high-capacity machine learning. Bioinformatics. 2020 04 01; 36(7):2126-2133. PMID: 31778140.
    Citations: 4     Fields:    Translation:HumansCells
  7. Liu G, Zeng H, Gifford DK. Visualizing complex feature interactions and feature sharing in genomic deep neural networks. BMC Bioinformatics. 2019 Jul 19; 20(1):401. PMID: 31324140.
    Citations: 2     Fields:    Translation:Cells
  8. Zeng H, Gifford DK. DeepLigand: accurate prediction of MHC class I ligands using peptide embedding. Bioinformatics. 2019 07 15; 35(14):i278-i283. PMID: 31510651.
    Citations: 2     Fields:    Translation:Cells
  9. Zeng H, Gifford DK. Quantification of Uncertainty in Peptide-MHC Binding Prediction Improves High-Affinity Peptide Selection for Therapeutic Design. Cell Syst. 2019 08 28; 9(2):159-166.e3. PMID: 31176619.
    Citations: 3     Fields:    Translation:HumansCells
  10. Sharon N, Vanderhooft J, Straubhaar J, Mueller J, Chawla R, Zhou Q, Engquist EN, Trapnell C, Gifford DK, Melton DA. Wnt Signaling Separates the Progenitor and Endocrine Compartments during Pancreas Development. Cell Rep. 2019 05 21; 27(8):2281-2291.e5. PMID: 31116975.
    Citations: 5     Fields:    Translation:HumansCells
  11. Guo Y, Krismer K, Closser M, Wichterle H, Gifford DK. High resolution discovery of chromatin interactions. Nucleic Acids Res. 2019 04 08; 47(6):e35. PMID: 30953075.
    Citations:    Fields:    Translation:HumansCells
  12. Shen MW, Arbab M, Hsu JY, Worstell D, Culbertson SJ, Krabbe O, Cassa CA, Liu DR, Gifford DK, Sherwood RI. Author Correction: Predictable and precise template-free CRISPR editing of pathogenic variants. Nature. 2019 03; 567(7746):E1-E2. PMID: 30765887.
    Citations: 3     Fields:    
  13. Sharon N, Chawla R, Mueller J, Vanderhooft J, Whitehorn LJ, Rosenthal B, Gürtler M, Estanboulieh RR, Shvartsman D, Gifford DK, Trapnell C, Melton D. A Peninsular Structure Coordinates Asynchronous Differentiation with Morphogenesis to Generate Pancreatic Islets. Cell. 2019 02 07; 176(4):790-804.e13. PMID: 30661759.
    Citations: 10     Fields:    Translation:HumansAnimalsCells
  14. Shen MW, Arbab M, Hsu JY, Worstell D, Culbertson SJ, Krabbe O, Cassa CA, Liu DR, Gifford DK, Sherwood RI. Predictable and precise template-free CRISPR editing of pathogenic variants. Nature. 2018 11; 563(7733):646-651. PMID: 30405244.
    Citations: 42     Fields:    Translation:HumansCells
  15. Mueller J, Jaakkola T, Gifford D. Modeling Persistent Trends in Distributions. J Am Stat Assoc. 2018; 113(523):1296-1310. PMID: 30906084.
    Citations:    
  16. Guo Y, Tian K, Zeng H, Guo X, Gifford DK. A novel k-mer set memory (KSM) motif representation improves regulatory variant prediction. Genome Res. 2018 06; 28(6):891-900. PMID: 29654070.
    Citations: 2     Fields:    Translation:HumansCells
  17. Kang D, Sherwood R, Barkal A, Hashimoto T, Engstrom L, Gifford D. DNase-capture reveals differential transcription factor binding modalities. PLoS One. 2017; 12(12):e0187046. PMID: 29284001.
    Citations:    Fields:    Translation:Cells
  18. Chen R, Gifford DK. Differential chromatin profiles partially determine transcription factor binding. PLoS One. 2017; 12(7):e0179411. PMID: 28704389.
    Citations: 2     Fields:    Translation:HumansCells
  19. Daneshjou R, Wang Y, Bromberg Y, Bovo S, Martelli PL, Babbi G, Lena PD, Casadio R, Edwards M, Gifford D, Jones DT, Sundaram L, Bhat RR, Li X, Pal LR, Kundu K, Yin Y, Moult J, Jiang Y, Pejaver V, Pagel KA, Li B, Mooney SD, Radivojac P, Shah S, Carraro M, Gasparini A, Leonardi E, Giollo M, Ferrari C, Tosatto SCE, Bachar E, Azaria JR, Ofran Y, Unger R, Niroula A, Vihinen M, Chang B, Wang MH, Franke A, Petersen BS, Pirooznia M, Zandi P, McCombie R, Potash JB, Altman RB, Klein TE, Hoskins RA, Repo S, Brenner SE, Morgan AA. Working toward precision medicine: Predicting phenotypes from exomes in the Critical Assessment of Genome Interpretation (CAGI) challenges. Hum Mutat. 2017 09; 38(9):1182-1192. PMID: 28634997.
    Citations: 4     Fields:    Translation:Humans
  20. Zeng H, Gifford DK. Predicting the impact of non-coding variants on DNA methylation. Nucleic Acids Res. 2017 Jun 20; 45(11):e99. PMID: 28334830.
    Citations: 11     Fields:    Translation:Cells
  21. Zeng H, Edwards MD, Guo Y, Gifford DK. Accurate eQTL prioritization with an ensemble-based framework. Hum Mutat. 2017 09; 38(9):1259-1265. PMID: 28224684.
    Citations: 4     Fields:    Translation:Humans
  22. Kreimer A, Zeng H, Edwards MD, Guo Y, Tian K, Shin S, Welch R, Wainberg M, Mohan R, Sinnott-Armstrong NA, Li Y, Eraslan G, Amin TB, Tewhey R, Sabeti PC, Goke J, Mueller NS, Kellis M, Kundaje A, Beer MA, Keles S, Gifford DK, Yosef N. Predicting gene expression in massively parallel reporter assays: A comparative study. Hum Mutat. 2017 09; 38(9):1240-1250. PMID: 28220625.
    Citations: 10     Fields:    Translation:Humans
  23. Guo Y, Gifford DK. Modular combinatorial binding among human trans-acting factors reveals direct and indirect factor binding. BMC Genomics. 2017 01 06; 18(1):45. PMID: 28061806.
    Citations: 4     Fields:    Translation:HumansCells
  24. Rhee HS, Closser M, Guo Y, Bashkirova EV, Tan GC, Gifford DK, Wichterle H. Expression of Terminal Effector Genes in Mammalian Neurons Is Maintained by a Dynamic Relay of Transient Enhancers. Neuron. 2016 Dec 21; 92(6):1252-1265. PMID: 27939581.
    Citations: 17     Fields:    Translation:AnimalsCells
  25. Gould GM, Paggi JM, Guo Y, Phizicky DV, Zinshteyn B, Wang ET, Gilbert WV, Gifford DK, Burge CB. Identification of new branch points and unconventional introns in Saccharomyces cerevisiae. RNA. 2016 10; 22(10):1522-34. PMID: 27473169.
    Citations: 13     Fields:    Translation:AnimalsCells
  26. Hashimoto T, Sherwood RI, Kang DD, Rajagopal N, Barkal AA, Zeng H, Emons BJ, Srinivasan S, Jaakkola T, Gifford DK. A synergistic DNA logic predicts genome-wide chromatin accessibility. Genome Res. 2016 10; 26(10):1430-1440. PMID: 27456004.
    Citations: 9     Fields:    Translation:HumansAnimalsCells
  27. Zeng H, Edwards MD, Liu G, Gifford DK. Convolutional neural network architectures for predicting DNA-protein binding. Bioinformatics. 2016 06 15; 32(12):i121-i127. PMID: 27307608.
    Citations: 43     Fields:    Translation:Cells
  28. Ferreira LM, Meissner TB, Mikkelsen TS, Mallard W, O'Donnell CW, Tilburgs T, Gomes HA, Camahort R, Sherwood RI, Gifford DK, Rinn JL, Cowan CA, Strominger JL. A distant trophoblast-specific enhancer controls HLA-G expression at the maternal-fetal interface. Proc Natl Acad Sci U S A. 2016 May 10; 113(19):5364-9. PMID: 27078102.
    Citations: 21     Fields:    Translation:HumansCells
  29. Barkal AA, Srinivasan S, Hashimoto T, Gifford DK, Sherwood RI. Cas9 Functionally Opens Chromatin. PLoS One. 2016; 11(3):e0152683. PMID: 27031353.
    Citations: 6     Fields:    Translation:AnimalsCells
  30. Rajagopal N, Srinivasan S, Kooshesh K, Guo Y, Edwards MD, Banerjee B, Syed T, Emons BJ, Gifford DK, Sherwood RI. High-throughput mapping of regulatory DNA. Nat Biotechnol. 2016 Feb; 34(2):167-74. PMID: 26807528.
    Citations: 63     Fields:    Translation:Animals
  31. Zeng H, Hashimoto T, Kang DD, Gifford DK. GERV: a statistical method for generative evaluation of regulatory variants for transcription factor binding. Bioinformatics. 2016 Feb 15; 32(4):490-6. PMID: 26476779.
    Citations: 14     Fields:    Translation:HumansCells
  32. Li W, Cavelti-Weder C, Zhang Y, Clement K, Donovan S, Gonzalez G, Zhu J, Stemann M, Xu K, Hashimoto T, Yamada T, Nakanishi M, Zhang Y, Zeng S, Gifford D, Meissner A, Weir G, Zhou Q. Corrigendum: Long-term persistence and development of induced pancreatic beta cells generated by lineage conversion of acinar cells. Nat Biotechnol. 2015 Aug; 33(8):882. PMID: 26252147.
    Citations:    Fields:    
  33. Reeder C, Closser M, Poh HM, Sandhu K, Wichterle H, Gifford D. High resolution mapping of enhancer-promoter interactions. PLoS One. 2015; 10(5):e0122420. PMID: 25970635.
    Citations:    Fields:    Translation:AnimalsCells
  34. Li W, Cavelti-Weder C, Zhang Y, Zhang Y, Clement K, Donovan S, Gonzalez G, Zhu J, Stemann M, Xu K, Hashimoto T, Yamada T, Nakanishi M, Zhang Y, Zeng S, Gifford D, Meissner A, Weir G, Zhou Q. Long-term persistence and development of induced pancreatic beta cells generated by lineage conversion of acinar cells. Nat Biotechnol. 2014 Dec; 32(12):1223-30. PMID: 25402613.
    Citations: 33     Fields:    Translation:HumansAnimalsCells
  35. Lodato S, Molyneaux BJ, Zuccaro E, Goff LA, Chen HH, Yuan W, Meleski A, Takahashi E, Mahony S, Rinn JL, Gifford DK, Arlotta P. Gene co-regulation by Fezf2 selects neurotransmitter identity and connectivity of corticospinal neurons. Nat Neurosci. 2014 Aug; 17(8):1046-54. PMID: 24997765.
    Citations: 33     Fields:    Translation:AnimalsCells
  36. Edwards MD, Symbor-Nagrabska A, Dollard L, Gifford DK, Fink GR. Interactions between chromosomal and nonchromosomal elements reveal missing heritability. Proc Natl Acad Sci U S A. 2014 May 27; 111(21):7719-22. PMID: 24825890.
    Citations: 8     Fields:    Translation:HumansAnimalsCells
  37. Mahony S, Edwards MD, Mazzoni EO, Sherwood RI, Kakumanu A, Morrison CA, Wichterle H, Gifford DK. An integrated model of multiple-condition ChIP-Seq data reveals predeterminants of Cdx2 binding. PLoS Comput Biol. 2014 Mar; 10(3):e1003501. PMID: 24675637.
    Citations: 17     Fields:    Translation:AnimalsCells
  38. Hashimoto TB, Edwards MD, Gifford DK. Universal count correction for high-throughput sequencing. PLoS Comput Biol. 2014 Mar; 10(3):e1003494. PMID: 24603409.
    Citations: 5     Fields:    Translation:HumansCells
  39. Hrvatin S, Deng F, O'Donnell CW, Gifford DK, Melton DA. MARIS: method for analyzing RNA following intracellular sorting. PLoS One. 2014; 9(3):e89459. PMID: 24594682.
    Citations: 40     Fields:    Translation:HumansCells
  40. Hrvatin S, O'Donnell CW, Deng F, Millman JR, Pagliuca FW, DiIorio P, Rezania A, Gifford DK, Melton DA. Differentiated human stem cells resemble fetal, not adult, ß cells. Proc Natl Acad Sci U S A. 2014 Feb 25; 111(8):3038-43. PMID: 24516164.
    Citations: 77     Fields:    Translation:HumansCells
  41. Sherwood RI, Hashimoto T, O'Donnell CW, Lewis S, Barkal AA, van Hoff JP, Karun V, Jaakkola T, Gifford DK. Discovery of directional and nondirectional pioneer transcription factors by modeling DNase profile magnitude and shape. Nat Biotechnol. 2014 Feb; 32(2):171-178. PMID: 24441470.
    Citations: 145     Fields:    Translation:Cells
  42. 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. PMID: 24286030.
    Citations: 11     Fields:    Translation:Animals
  43. 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):1191-1198. PMID: 23955559.
    Citations: 42     Fields:    Translation:HumansAnimalsCells
  44. Wichterle H, Gifford D, Mazzoni E. Neuroscience. Mapping neuronal diversity one cell at a time. Science. 2013 Aug 16; 341(6147):726-7. PMID: 23950522.
    Citations: 18     Fields:    Translation:HumansCells
  45. 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. PMID: 23872598.
    Citations: 68     Fields:    Translation:AnimalsCells
  46. 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; 41(2):e38. PMID: 23143268.
    Citations:    Fields:    Translation:AnimalsCells
  47. 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, Schwarzmüller 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. PMID: 22984072.
    Citations: 85     Fields:    Translation:AnimalsCells
  48. Rolfe PA, Bernstein DA, Grisafi P, Fink GR, Gifford DK. Ruler arrays reveal haploid genomic structural variation. PLoS One. 2012; 7(8):e43210. PMID: 22952647.
    Citations:    Fields:    Translation:Animals
  49. 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. PMID: 22912568.
    Citations: 83     Fields:    Translation:HumansCells
  50. 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. PMID: 22689769.
    Citations: 1     Fields:    Translation:Animals
  51. Edwards MD, Gifford DK. High-resolution genetic mapping with pooled sequencing. BMC Bioinformatics. 2012 Apr 19; 13 Suppl 6:S8. PMID: 22537047.
    Citations: 19     Fields:    Translation:HumansAnimals
  52. 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 Nov 13; 8(12):1056-8. PMID: 22081127.
    Citations: 30     Fields:    Translation:AnimalsCells
  53. Rolfe PA, Gifford DK. ReadDB provides efficient storage for mapped short reads. BMC Bioinformatics. 2011 Jul 07; 12:278. PMID: 21736741.
    Citations:    Fields:    Translation:Humans
  54. 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. PMID: 21385035.
    Citations:    Fields:    Translation:AnimalsCells
  55. 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. PMID: 21232103.
    Citations: 44     Fields:    Translation:Cells
  56. Wu CY, Rolfe PA, Gifford DK, Fink GR. Control of transcription by cell size. PLoS Biol. 2010 Nov 02; 8(11):e1000523. PMID: 21072241.
    Citations: 41     Fields:    Translation:AnimalsCells
  57. Williams AL, Housman DE, Rinard MC, Gifford DK. Rapid haplotype inference for nuclear families. Genome Biol. 2010; 11(10):R108. PMID: 21034477.
    Citations: 12     Fields:    Translation:Humans
  58. 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. PMID: 20966006.
    Citations: 29     Fields:    Translation:Cells
  59. 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 09; 67(5):781-96. PMID: 20826310.
    Citations: 56     Fields:    Translation:AnimalsCells
  60. 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. PMID: 20413493.
    Citations: 166     Fields:    Translation:Animals
  61. 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. PMID: 20382833.
    Citations: 13     Fields:    Translation:Animals
  62. 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. PMID: 19805129.
    Citations: 87     Fields:    Translation:AnimalsCells
  63. 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. PMID: 18700969.
    Citations: 29     Fields:    Translation:AnimalsCells
  64. 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. PMID: 18229714.
    Citations: 4     Fields:    
  65. 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. PMID: 17696603.
    Citations: 12     Fields:    Translation:Cells
  66. 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. PMID: 17529977.
    Citations: 264     Fields:    Translation:HumansAnimalsCells
  67. 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. PMID: 16900145.
    Citations: 42     Fields:    Translation:Cells
  68. 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. PMID: 16873502.
    Citations: 3     Fields:    Translation:Animals
  69. 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. PMID: 16738562.
    Citations: 96     Fields:    Translation:HumansCells
  70. 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. PMID: 16630818.
    Citations: 972     Fields:    Translation:HumansAnimalsCells
  71. 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. PMID: 16625203.
    Citations: 1056     Fields:    Translation:AnimalsCells
  72. 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. PMID: 16595631.
    Citations: 73     Fields:    Translation:HumansCells
  73. 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 Mar 07; 7:113. PMID: 16522208.
    Citations: 358     Fields:    Translation:AnimalsCells
  74. 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. PMID: 16332710.
    Citations: 46     Fields:    Translation:HumansAnimalsCells
  75. 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. PMID: 16153702.
    Citations: 1618     Fields:    Translation:HumansAnimalsCells
  76. 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. PMID: 16122420.
    Citations: 639     Fields:    Translation:AnimalsCells
  77. 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. PMID: 15494307.
    Citations: 129     Fields:    Translation:AnimalsCells
  78. 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 02; 431(7004):99-104. PMID: 15343339.
    Citations: 1002     Fields:    Translation:AnimalsCells
  79. Bar-Joseph Z, Farkash S, Gifford DK, Simon I, Rosenfeld R. Deconvolving cell cycle expression data with complementary information. Bioinformatics. 2004 Aug 04; 20 Suppl 1:i23-30. PMID: 15262777.
    Citations: 23     Fields:    Translation:Animals
  80. 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. PMID: 15370995.
    Citations: 3     Fields:    Translation:Humans
  81. 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. PMID: 14985193.
    Citations: 9     Fields:    Translation:Humans
  82. 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. PMID: 14988562.
    Citations: 474     Fields:    Translation:HumansCells
  83. Takusagawa KT, Gifford DK. Negative information for motif discovery. Pac Symp Biocomput. 2004; 360-71. PMID: 14992517.
    Citations: 7     Fields:    Translation:Cells
  84. 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. PMID: 14555958.
    Citations: 183     Fields:    Translation:AnimalsCells
  85. 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 02; 100(18):10146-51. PMID: 12934016.
    Citations: 38     Fields:    Translation:Animals
  86. 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. PMID: 12801867.
    Citations: 17     Fields:    Translation:Animals
  87. 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. PMID: 12935332.
    Citations: 70     Fields:    Translation:Animals
  88. 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. PMID: 12399584.
    Citations: 967     Fields:    Translation:AnimalsCells
  89. Sachs K, Gifford D, Jaakkola T, Sorger P, Lauffenburger DA. Bayesian network approach to cell signaling pathway modeling. Sci STKE. 2002 Sep 03; 2002(148):pe38. PMID: 12209052.
    Citations: 37     Fields:    Translation:HumansCells
  90. 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. PMID: 11928497.
    Citations: 60     Fields:    Translation:Cells
  91. 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. PMID: 11572776.
    Citations: 236     Fields:    Translation:Animals
  92. Gifford DK. Blazing pathways through genetic mountains. Science. 2001 Sep 14; 293(5537):2049-51. PMID: 11557882.
    Citations: 3     Fields:    Translation:HumansAnimals
  93. 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. PMID: 11262961.
    Citations: 73     Fields:    Translation:Animals
  94. Bar-Joseph Z, Gifford DK, Jaakkola TS. Fast optimal leaf ordering for hierarchical clustering. Bioinformatics. 2001; 17 Suppl 1:S22-9. PMID: 11472989.
    Citations: 76     Fields:    Translation:Animals
  95. Hartemink AJ, Gifford DK, Khodor J. Automated constraint-based nucleotide sequence selection for DNA computation. Biosystems. 1999 Oct; 52(1-3):227-35. PMID: 10636048.
    Citations: 1     Fields:    Translation:HumansAnimals
  96. Khodor J, Gifford DK. Design and implementation of computational systems based on programmed mutagenesis. Biosystems. 1999 Oct; 52(1-3):93-7. PMID: 10636034.
    Citations: 4     Fields:    Translation:HumansAnimals
  97. Gifford DK. On the path to computation with DNA. Science. 1994 Nov 11; 266(5187):993-4. PMID: 7973681.
    Citations: 2     Fields:    
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Funded by the NIH National Center for Advancing Translational Sciences through its Clinical and Translational Science Awards Program, grant number UL1TR002541.