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David K. Gifford - Publications

Affiliations: 
Department of Electrical Engineering Stanford University, Palo Alto, CA 
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48 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2022 Hammelman J, Patel T, Closser M, Wichterle H, Gifford D. Ranking reprogramming factors for cell differentiation. Nature Methods. PMID 35710610 DOI: 10.1038/s41592-022-01522-2  0.317
2022 Krismer K, Hammelman J, Gifford DK. seqgra: Principled Selection of Neural Network Architectures for Genomics Prediction Tasks. Bioinformatics (Oxford, England). PMID 35191481 DOI: 10.1093/bioinformatics/btac101  0.781
2022 Hammelman J, Krismer K, Gifford DK. spatzie: an R package for identifying significant transcription factor motif co-enrichment from enhancer-promoter interactions. Nucleic Acids Research. PMID 35100401 DOI: 10.1093/nar/gkac036  0.799
2021 Hammelman J, Gifford DK. Discovering differential genome sequence activity with interpretable and efficient deep learning. Plos Computational Biology. 17: e1009282. PMID 34370721 DOI: 10.1371/journal.pcbi.1009282  0.312
2020 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 Reports. 33: 108426. PMID 33238122 DOI: 10.1016/j.celrep.2020.108426  0.307
2020 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 Research. PMID 32973041 DOI: 10.1101/gr.263228.120  0.801
2020 Krismer K, Guo Y, Gifford DK. IDR2D identifies reproducible genomic interactions. Nucleic Acids Research. PMID 32009147 DOI: 10.1093/nar/gkaa030  0.785
2019 Guo Y, Krismer K, Closser M, Wichterle H, Gifford DK. High resolution discovery of chromatin interactions. Nucleic Acids Research. 47: e35. PMID 30953075 DOI: 10.1093/Nar/Gkz051  0.78
2018 Mueller J, Jaakkola T, Gifford D. Modeling Persistent Trends in Distributions. Journal of the American Statistical Association. 113: 1296-1310. PMID 30906084 DOI: 10.1080/01621459.2017.1341412  0.579
2017 Kang D, Sherwood R, Barkal A, Hashimoto T, Engstrom L, Gifford D. DNase-capture reveals differential transcription factor binding modalities. Plos One. 12: e0187046. PMID 29284001 DOI: 10.1371/Journal.Pone.0187046  0.775
2017 Chen R, Gifford DK. Differential chromatin profiles partially determine transcription factor binding. Plos One. 12: e0179411. PMID 28704389 DOI: 10.1371/journal.pone.0179411  0.318
2017 Zeng H, Edwards MD, Guo Y, Gifford DK. Accurate eQTL prioritization with an ensemble-based framework. Human Mutation. PMID 28224684 DOI: 10.1002/humu.23198  0.32
2017 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, Goke J, Mueller NS, ... ... Gifford DK, et al. Predicting gene expression in massively parallel reporter assays: a comparative study. Human Mutation. PMID 28220625 DOI: 10.1002/Humu.23197  0.305
2016 Hashimoto TB, Sherwood R, Kang DD, Rajagopal N, Barkal AA, Zeng H, Emons BJ, Srinivasan S, Jaakkola T, Gifford D. A synergistic DNA logic predicts genome-wide chromatin accessibility. Genome Research. PMID 27456004 DOI: 10.1101/Gr.199778.115  0.78
2016 Barkal AA, Srinivasan S, Hashimoto T, Gifford DK, Sherwood RI. Cas9 Functionally Opens Chromatin. Plos One. 11: e0152683. PMID 27031353 DOI: 10.1371/Journal.Pone.0152683  0.765
2016 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. Nature Biotechnology. PMID 26807528 DOI: 10.1038/nbt.3468  0.333
2015 Zeng H, Hashimoto T, Kang DD, Gifford DK. GERV: a statistical method for generative evaluation of regulatory variants for transcription factor binding. Bioinformatics (Oxford, England). PMID 26476779 DOI: 10.1093/bioinformatics/btv565  0.755
2014 Hashimoto TB, Edwards MD, Gifford DK. Universal count correction for high-throughput sequencing. Plos Computational Biology. 10: e1003494. PMID 24603409 DOI: 10.1371/journal.pcbi.1003494  0.741
2014 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. Nature Biotechnology. 32: 171-8. PMID 24441470 DOI: 10.1038/Nbt.2798  0.797
2012 Guo Y, Mahony S, Gifford DK. High resolution genome wide binding event finding and motif discovery reveals transcription factor spatial binding constraints. Plos Computational Biology. 8: e1002638. PMID 22912568 DOI: 10.1371/journal.pcbi.1002638  0.354
2012 Hashimoto T, Jaakkola T, Sherwood R, Mazzoni EO, Wichterle H, Gifford D. Lineage-based identification of cellular states and expression programs. Bioinformatics (Oxford, England). 28: i250-7. PMID 22689769 DOI: 10.1093/Bioinformatics/Bts204  0.78
2011 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. Nature Methods. 8: 1056-8. PMID 22081127 DOI: 10.1038/Nmeth.1775  0.319
2010 Guo Y, Papachristoudis G, Altshuler RC, Gerber GK, Jaakkola TS, Gifford DK, Mahony S. Discovering homotypic binding events at high spatial resolution. Bioinformatics (Oxford, England). 26: 3028-34. PMID 20966006 DOI: 10.1093/Bioinformatics/Btq590  0.74
2008 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 Biology. 9: R126. PMID 18700969 DOI: 10.1186/Gb-2008-9-8-R126  0.358
2007 Gerber GK, Dowell RD, Jaakkola TS, Gifford DK. Automated discovery of functional generality of human gene expression programs. Plos Computational Biology. 3: e148. PMID 17696603 DOI: 10.1371/journal.pcbi.0030148  0.748
2006 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. Nature Biotechnology. 24: 963-70. PMID 16900145 DOI: 10.1038/Nbt1233  0.782
2006 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 (Oxford, England). 22: e417-23. PMID 16873502 DOI: 10.1093/bioinformatics/btl256  0.617
2006 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. Molecular Systems Biology. 2: 2006.0017. PMID 16738562 DOI: 10.1038/Msb4100059  0.315
2006 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. Proceedings of the National Academy of Sciences of the United States of America. 103: 5899-904. PMID 16595631 DOI: 10.1073/pnas.0510996103  0.666
2006 MacIsaac KD, Wang T, Gordon DB, Gifford DK, Stormo GD, Fraenkel E. An improved map of conserved regulatory sites for Saccharomyces cerevisiae. Bmc Bioinformatics. 7: 113. PMID 16522208 DOI: 10.1186/1471-2105-7-113  0.31
2006 Qi Y, Rolfe A, MacIsaac KD, Gerber GK, Pokholok D, Zeitlinger J, Danford T, Dowell RD, Fraenkel E, Jaakkola TS, Young RA, Gifford DK. Erratum: High-resolution computational models of genome binding events Nature Biotechnology. 24: 1293-1293. DOI: 10.1038/Nbt1006-1293A  0.718
2004 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, ... ... Gifford DK, et al. Transcriptional regulatory code of a eukaryotic genome. Nature. 431: 99-104. PMID 15343339 DOI: 10.1038/Nature02800  0.331
2004 Bar-Joseph Z, Farkash S, Gifford DK, Simon I, Rosenfeld R. Deconvolving cell cycle expression data with complementary information. Bioinformatics (Oxford, England). 20: i23-30. PMID 15262777 DOI: 10.1093/bioinformatics/bth915  0.517
2004 Sachs K, Perez OD, Pe'er D, Nolan GP, Gifford DK, Jaakkola TS, Lauffenburger DA. Analysis of signaling pathways in human T-cells using Bayesian network modeling of single cell data Proceedings - 2004 Ieee Computational Systems Bioinformatics Conference, Csb 2004. 644.  0.548
2003 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. Nature Biotechnology. 21: 1337-42. PMID 14555958 DOI: 10.1038/Nbt890  0.813
2003 Bar-Joseph Z, Gerber GK, Gifford DK, Jaakkola TS, Simon I. Continuous representations of time-series gene expression data. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 10: 341-56. PMID 12935332 DOI: 10.1089/10665270360688057  0.785
2003 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. Proceedings of the National Academy of Sciences of the United States of America. 100: 10146-51. PMID 12934016 DOI: 10.1073/Pnas.1732547100  0.801
2003 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 (Oxford, England). 19: 1070-8. PMID 12801867 DOI: 10.1093/Bioinformatics/Btg030  0.67
2002 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, ... ... Gifford DK, et al. Transcriptional regulatory networks in Saccharomyces cerevisiae. Science (New York, N.Y.). 298: 799-804. PMID 12399584 DOI: 10.1126/Science.1075090  0.753
2002 Sachs K, Gifford D, Jaakkola T, Sorger P, Lauffenburger DA. Bayesian network approach to cell signaling pathway modeling. Science's Stke : Signal Transduction Knowledge Environment. 2002: pe38. PMID 12209052 DOI: 10.1126/Stke.2002.148.Pe38  0.572
2002 Hartemink AJ, Gifford DK, Jaakkola TS, Young RA. Combining location and expression data for principled discovery of genetic regulatory network models. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 437-49. PMID 11928497  0.743
2002 Hartemink AJ, Gifford DK, Jaakkola TS, Young RA. Bayesian methods for elucidating genetic regulatory networks Ieee Intelligent Systems and Their Applications. 17: 37-43. DOI: 10.1109/5254.999218  0.712
2002 Bar-Joseph Z, Gerber G, Gifford DK, Jaakkola TS, Simon I. A new approach to analyzing gene expression time series data Proceedings of the Annual International Conference On Computational Molecular Biology, Recomb. 39-48.  0.74
2001 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. 106: 697-708. PMID 11572776 DOI: 10.1016/S0092-8674(01)00494-9  0.614
2001 Bar-Joseph Z, Gifford DK, Jaakkola TS. Fast optimal leaf ordering for hierarchical clustering. Bioinformatics (Oxford, England). 17: S22-9. PMID 11472989 DOI: 10.1093/Bioinformatics/17.Suppl_1.S22  0.661
2001 Hartemink AJ, Gifford DK, Jaakkola TS, Young RA. Using graphical models and genomic expression data to statistically validate models of genetic regulatory networks. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 422-33. PMID 11262961  0.758
2001 Hartemink AJ, Gifford DK, Jaakkola TS, Young RA. Maximum likelihood estimation of optimal scaling factors for expression array normalization Proceedings of Spie - the International Society For Optical Engineering. 4266: 132-140. DOI: 10.1117/12.427981  0.695
1999 Hartemink AJ, Gifford DK, Khodor J. Automated constraint-based nucleotide sequence selection for DNA computation. Bio Systems. 52: 227-35. PMID 10636048 DOI: 10.1016/S0303-2647(99)00050-7  0.6
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