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- "The origins and functional effects of postzygotic mutations throughout the human life span" (Science, 2023)
- "A single-cell massively parallel reporter assay detects cell-type-specific gene regulation" (Nature Genetics, 2023)
- "A massively parallel reporter assay dissects the influence of chromatin structure on cis-regulatory activity" (Nature Biotechnology, 2019)
- "A Simple Grammar Defines Activating and Repressing cis-Regulatory Elements in Photoreceptors" (Cell Reports, 2016)
- "Single Nucleotide Variants in Transcription Factors Associate More Tightly with Phenotype than with Gene Expression" (PLOS Genetics, 2014)
- "A Computational Framework for Analyzing Stochasticity in Gene Expression" (PLOS Computational Biology, 2014)
- "Massively parallel in vivo enhancer assay reveals that highly local features determine the cis-regulatory function of ChIP-seq peaks" (PNAS, 2013)
- "Complex effects of nucleotide variants in a mammalian cis-regulatory element" (PNAS, 2012)
- "The cis-Regulatory Logic of Hedgehog Gradient Responses: Key Roles for Gli Binding Affinity, Competition, and Cooperativity" (Science Signaling, 2011)
- "Analysis of combinatorial cis-regulation in synthetic and genomic promoters" (Nature, 2009)
- "Genetic Interactions Between Transcription Factors Cause Natural Variation in Yeast" (Science, 2009)
- "The strength of selection on ultraconserved elements in the human genome" (American Journal Of Human Genetics, 2007)
- "Finding functional features in Saccharomyces genomes by phylogenetic footprinting" (Science, 2003)