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
    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, 2021
    NIH
    High-Throughput Native Context Mapping and Modeling of Regulatory DNA
    Role: Principal Investigator
  3. R01HG008363 (GIFFORD, DAVID K) May 13, 2015 - Apr 30, 2020
    NIH
    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
    Integrated Genome Discovery at Single Base Pair Resolution
    Role: Principal Investigator
  5. T32HG004947 (GIFFORD, DAVID K) Jul 8, 2009 - Aug 31, 2016
    NIH
    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. Berry SD, Johnson KS, Myles L, Herndon L, Montoya A, Fashaw S, Gifford D. Lessons learned from frontline skilled nursing facility staff regarding COVID-19 vaccine hesitancy. J Am Geriatr Soc. 2021 Mar 25. PMID: 33764497.
    Citations:    Fields:    
  2. Harrison J, Berry S, Mor V, Gifford D. "Somebody Like Me": Understanding COVID-19 Vaccine Hesitancy Among Staff in Skilled Nursing Facilities. J Am Med Dir Assoc. 2021 Mar 20. PMID: 33861978.
    Citations:    Fields:    
  3. Yeo GHT, Juez O, Chen Q, Banerjee B, Chu L, Shen MW, Sabry M, Logister I, Sherwood RI, Gifford DK. Detection of gene cis-regulatory element perturbations in single-cell transcriptomes. PLoS Comput Biol. 2021 Mar; 17(3):e1008789. PMID: 33711017.
    Citations:    Fields:    
  4. Dai Z, Huisman BD, Zeng H, Carter B, Jain S, Birnbaum ME, Gifford DK. Machine learning optimization of peptides for presentation by class II MHCs. Bioinformatics. 2021 Mar 10. PMID: 33705522.
    Citations:    Fields:    
  5. Gharpure R, Guo A, Bishnoi CK, Patel U, Gifford D, Tippins A, Jaffe A, Shulman E, Stone N, Mungai E, Bagchi S, Bell J, Srinivasan A, Patel A, Link-Gelles R. Early COVID-19 First-Dose Vaccination Coverage Among Residents and Staff Members of Skilled Nursing Facilities Participating in the Pharmacy Partnership for Long-Term Care Program - United States, December 2020-January 2021. MMWR Morb Mortal Wkly Rep. 2021 Feb 05; 70(5):178-182. PMID: 33539332.
    Citations: 5     Fields:    Translation:Humans
  6. Louie W, Shen MW, Tahiry Z, Zhang S, Worstell D, Cassa CA, Sherwood RI, Gifford DK. Machine learning based CRISPR gRNA design for therapeutic exon skipping. PLoS Comput Biol. 2021 Jan; 17(1):e1008605. PMID: 33417623.
    Citations:    Fields:    
  7. Liu G, Carter B, Gifford DK. Predicted Cellular Immunity Population Coverage Gaps for SARS-CoV-2 Subunit Vaccines and Their Augmentation by Compact Peptide Sets. Cell Syst. 2021 01 20; 12(1):102-107.e4. PMID: 33321075.
    Citations:    Fields:    Translation:Humans
  8. Lin L, Holmes B, Shen MW, Kammeron D, Geijsen N, Gifford DK, Sherwood RI. Comprehensive Mapping of Key Regulatory Networks that Drive Oncogene Expression. Cell Rep. 2020 11 24; 33(8):108426. PMID: 33238122.
    Citations: 1     Fields:    
  9. Sreekanth V, Zhou Q, Kokkonda P, Bermudez-Cabrera HC, Lim D, Law BK, Holmes BR, Chaudhary SK, Pergu R, Leger BS, Walker JA, Gifford DK, Sherwood RI, Choudhary A. Chemogenetic System Demonstrates That Cas9 Longevity Impacts Genome Editing Outcomes. ACS Cent Sci. 2020 Dec 23; 6(12):2228-2237. PMID: 33376784.
    Citations:    
  10. 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 10; 30(10):1468-1480. PMID: 32973041.
    Citations:    Fields:    
  11. 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: 5     Fields:    Translation:HumansCells
  12. 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:    Translation:Cells
  13. 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:    
  14. Krismer K, Guo Y, Gifford DK. IDR2D identifies reproducible genomic interactions. Nucleic Acids Res. 2020 04 06; 48(6):e31. PMID: 32009147.
    Citations: 2     Fields:    Translation:Cells
  15. 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: 8     Fields:    Translation:HumansCells
  16. 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: 3     Fields:    Translation:Cells
  17. 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: 4     Fields:    Translation:Cells
  18. 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: 6     Fields:    Translation:HumansCells
  19. 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: 17     Fields:    Translation:HumansCells
  20. 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
  21. 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:    
  22. 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: 18     Fields:    Translation:HumansAnimalsCells
  23. 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: 99     Fields:    Translation:HumansCells
  24. Mueller J, Jaakkola T, Gifford D. Modeling Persistent Trends in Distributions. J Am Stat Assoc. 2018; 113(523):1296-1310. PMID: 30906084.
    Citations:    
  25. 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: 5     Fields:    Translation:HumansCells
  26. 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
  27. 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
  28. 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: 9     Fields:    Translation:Humans
  29. 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: 16     Fields:    Translation:Cells
  30. 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: 6     Fields:    Translation:Humans
  31. 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: 17     Fields:    Translation:Humans
  32. 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: 7     Fields:    Translation:HumansCells
  33. 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: 24     Fields:    Translation:AnimalsCells
  34. 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: 15     Fields:    Translation:AnimalsCells
  35. 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
  36. 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: 61     Fields:    Translation:Cells
  37. 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: 27     Fields:    Translation:HumansCells
  38. Barkal AA, Srinivasan S, Hashimoto T, Gifford DK, Sherwood RI. Cas9 Functionally Opens Chromatin. PLoS One. 2016; 11(3):e0152683. PMID: 27031353.
    Citations: 8     Fields:    Translation:AnimalsCells
  39. 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: 79     Fields:    Translation:Animals
  40. 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: 17     Fields:    Translation:HumansCells
  41. 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:    
  42. 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
  43. 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: 44     Fields:    Translation:HumansAnimalsCells
  44. 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: 37     Fields:    Translation:AnimalsCells
  45. 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: 10     Fields:    Translation:HumansAnimalsCells
  46. 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: 25     Fields:    Translation:AnimalsCells
  47. Hashimoto TB, Edwards MD, Gifford DK. Universal count correction for high-throughput sequencing. PLoS Comput Biol. 2014 Mar; 10(3):e1003494. PMID: 24603409.
    Citations: 6     Fields:    Translation:HumansCells
  48. 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: 49     Fields:    Translation:HumansCells
  49. 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: 102     Fields:    Translation:HumansCells
  50. 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: 176     Fields:    Translation:Cells
  51. 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: 13     Fields:    Translation:Animals
  52. 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: 50     Fields:    Translation:HumansAnimalsCells
  53. 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: 19     Fields:    Translation:HumansCells
  54. 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: 82     Fields:    Translation:AnimalsCells
  55. 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
  56. 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: 94     Fields:    Translation:AnimalsCells
  57. 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
  58. 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: 99     Fields:    Translation:HumansCells
  59. 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
  60. Edwards MD, Gifford DK. High-resolution genetic mapping with pooled sequencing. BMC Bioinformatics. 2012 Apr 19; 13 Suppl 6:S8. PMID: 22537047.
    Citations: 23     Fields:    Translation:HumansAnimals
  61. 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: 40     Fields:    Translation:AnimalsCells
  62. 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
  63. 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
  64. 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: 50     Fields:    Translation:Cells
  65. 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: 43     Fields:    Translation:AnimalsCells
  66. Williams AL, Housman DE, Rinard MC, Gifford DK. Rapid haplotype inference for nuclear families. Genome Biol. 2010; 11(10):R108. PMID: 21034477.
    Citations: 13     Fields:    Translation:Humans
  67. 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: 31     Fields:    Translation:Cells
  68. 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: 59     Fields:    Translation:AnimalsCells
  69. 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: 178     Fields:    Translation:Animals
  70. 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
  71. 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: 95     Fields:    Translation:AnimalsCells
  72. 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
  73. 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: 6     Fields:    
  74. Lynn J, West J, Hausmann S, Gifford D, Nelson R, McGann P, Bergstrom N, Ryan JA. Collaborative clinical quality improvement for pressure ulcers in nursing homes. J Am Geriatr Soc. 2007 Oct; 55(10):1663-9. PMID: 17714457.
    Citations: 13     Fields:    Translation:Humans
  75. 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: 13     Fields:    Translation:Cells
  76. 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: 270     Fields:    Translation:HumansAnimalsCells
  77. 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
  78. 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
  79. 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: 99     Fields:    Translation:HumansCells
  80. 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: 1020     Fields:    Translation:HumansAnimalsCells
  81. 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: 1117     Fields:    Translation:AnimalsCells
  82. 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: 77     Fields:    Translation:HumansCells
  83. 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: 378     Fields:    Translation:AnimalsCells
  84. 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
  85. 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: 1719     Fields:    Translation:HumansAnimalsCells
  86. 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: 661     Fields:    Translation:AnimalsCells
  87. McNicoll L, Pisani MA, Ely EW, Gifford D, Inouye SK. Detection of delirium in the intensive care unit: comparison of confusion assessment method for the intensive care unit with confusion assessment method ratings. J Am Geriatr Soc. 2005 Mar; 53(3):495-500. PMID: 15743296.
    Citations: 30     Fields:    Translation:Humans
  88. 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: 133     Fields:    Translation:AnimalsCells
  89. 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: 1019     Fields:    Translation:AnimalsCells
  90. 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
  91. 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
  92. 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
  93. 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: 497     Fields:    Translation:HumansCells
  94. Takusagawa KT, Gifford DK. Negative information for motif discovery. Pac Symp Biocomput. 2004; 360-71. PMID: 14992517.
    Citations: 7     Fields:    Translation:Cells
  95. 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: 184     Fields:    Translation:AnimalsCells
  96. 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: 39     Fields:    Translation:Animals
  97. 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: 18     Fields:    Translation:Animals
  98. Kissam S, Gifford D, Parks P, Patry G, Palmer L, Wilkes L, Fitzgerald M, Petrulis AS, Barnette L. Approaches to quality improvement in nursing homes: lessons learned from the six-state pilot of CMS's Nursing Home Quality Initiative. BMC Geriatr. 2003 May 16; 3:2. PMID: 12753699.
    Citations: 4     Fields:    
  99. 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: 74     Fields:    Translation:Animals
  100. 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: 982     Fields:    Translation:AnimalsCells
  101. 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: 38     Fields:    Translation:HumansCells
  102. 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: 61     Fields:    Translation:Cells
  103. 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: 239     Fields:    Translation:Animals
  104. Gifford DK. Blazing pathways through genetic mountains. Science. 2001 Sep 14; 293(5537):2049-51. PMID: 11557882.
    Citations: 3     Fields:    Translation:HumansAnimals
  105. 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: 75     Fields:    Translation:Animals
  106. Bar-Joseph Z, Gifford DK, Jaakkola TS. Fast optimal leaf ordering for hierarchical clustering. Bioinformatics. 2001; 17 Suppl 1:S22-9. PMID: 11472989.
    Citations: 86     Fields:    Translation:Animals
  107. 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
  108. 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
  109. 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.