Gifford, David K.

Core Transcriptional Regulatory Circuitry in Human Embryonic Stem Cells

Boyer, L. A., Lee, T. I., Cole, M. F., Johnstone, S. E., Levine, S. S., Zucker, J. P., Guenther, M. G., Kumar, R. M., Murray, H. L., Jenner, R. G., et al. (2005) · Cell

Pluripotent Stem Cells ResearchDevelopmental Biology and Gene Regulation

Cited by 4,505

Transcriptional Regulatory Networks in Saccharomyces cerevisiae

Lee, T. I., Rinaldi, N. J., Robert, F., Odom, D. T., Bar-Joseph, Z., Gerber, G. K., Hannett, N. M., Harbison, C. T., Thompson, C. M., Simon, I., et al. (2002) · Science

Gene Regulatory Network AnalysisFungal and yeast genetics research

Cited by 2,956

Expanded encyclopaedias of DNA elements in the human and mouse genomes

The ENCODE Project Consortium, Abascal, F., Acosta, R., Addleman, N. J., Adrian, J., Afzal, V., Ai, R., Aken, B., Akiyama, J. A., Jammal, O. A., et al. (2020) · Nature

Genomics and Chromatin DynamicsEpigenetics and DNA Methylation

Cited by 2,378

Predictable and precise template-free CRISPR editing of pathogenic variants

Shen, M. W., Arbab, M., Hsu, J. Y., Worstell, D., Culbertson, S. J., Krabbe, O., Cassa, C. A., Liu, D. R., Gifford, D. K., & Sherwood, R. I. (2018) · Nature

CRISPR and Genetic EngineeringRNA regulation and disease

Cited by 569

Tissue-specific transcriptional regulation has diverged significantly between human and mouse

Odom, D. T., Dowell, R. D., Jacobsen, E. S., Gordon, W., Danford, T. W., MacIsaac, K. D., Rolfe, P. A., Conboy, C. M., Gifford, D. K., & Fraenkel, E. (2007) · Nature Genetics

Genomics and Chromatin DynamicsGenomics and Phylogenetic Studies

Cited by 506

Differentiated human stem cells resemble fetal, not adult, β cells

Hrvatin, S., O’Donnell, C. W., Deng, F., Millman, J. R., Pagliuca, F. W., DiIorio, P., Rezania, A., Gifford, D. K., & Melton, D. A. (2014) · Proceedings of the National Academy of Sciences

Pancreatic function and diabetesPluripotent Stem Cells Research

Cited by 302

High-throughput mapping of regulatory DNA

Rajagopal, N., Srinivasan, S., Kooshesh, K., Guo, Y., Edwards, M. D., Banerjee, B., Syed, T., Emons, B. J. M., Gifford, D. K., & Sherwood, R. I. (2016) · Nature Biotechnology

CRISPR and Genetic EngineeringGenomics and Chromatin Dynamics

Cited by 238

Antibody complementarity determining region design using high-capacity machine learning

Liu, G., Zeng, H., Mueller, J., Carter, B., Wang, Z., Schilz, J., Horny, G., Birnbaum, M. E., Ewert, S., & Gifford, D. K. (2020) · Bioinformatics

Monoclonal and Polyclonal Antibodies Researchvaccines and immunoinformatics approaches

Cited by 157

Ligand-dependent dynamics of retinoic acid receptor binding during early neurogenesis

Mahony, S., Mazzoni, E. O., McCuine, S., Young, R. A., Wichterle, H., & Gifford, D. K. (2011) · Genome Biology

Genomics and Chromatin DynamicsRetinoids in leukemia and cellular processes

Cited by 142

Generative modeling of single-cell time series with PRESCIENT enables prediction of cell trajectories with interventions

Yeo, G. H. T., Saksena, S. D., & Gifford, D. K. (2021) · Nature Communications

Single-cell and spatial transcriptomicsGene Regulatory Network Analysis

Cited by 103

An improved map of conserved regulatory sites for Saccharomyces cerevisiae

MacIsaac, K. D., Wang, T., Gordon, D. B., Gifford, D. K., Stormo, G. D., & Fraenkel, E. (2006) · BMC Bioinformatics

Genomics and Chromatin DynamicsFungal and yeast genetics research

Cited by 9

Maximizing Overall Diversity for Improved Uncertainty Estimates in Deep Ensembles

Jain, S., Liu, G., Mueller, J., & Gifford, D. (2019) · arXiv

Adversarial Robustness in Machine LearningMachine Learning and Data Classification

Cited by 8