Joseph R. Ecker

Joseph Ecker is a pioneering plant and mammalian genomicist whose work has fundamentally shaped modern functional genomics. One of the earliest and most influential advocates for sequencing the *Arabidopsis thaliana* genome, he directed a major portion of that landmark effort and almost singlehandedly established *Arabidopsis* as the pre-eminent model organism for plant functional genomics. Among his most elegant contributions, Ecker and collaborators designed a set of GeneChips spanning the entire *Arabidopsis* genome, defining in a single experiment the vast majority of transcripts encoded by a plant genome. He and his team went on to determine the *Arabidopsis* methylome and applied these same technologies and analytical frameworks to characterize the human embryonic stem cell methylome — a breakthrough that bridged plant and mammalian epigenomics. Ecker revolutionized plant biology through the creation of a comprehensive collection of sequence-indexed insertion mutants covering every *Arabidopsis* gene. This resource transformed the field: researchers worldwide can now request a knockout mutant for virtually any *Arabidopsis* gene simply by email. Building on these foundations, Ecker's laboratory has emerged as a world leader in single-cell epigenomics, developing transformative technologies — including snmC-seq, snm3C-seq, and snmCT-seq — that simultaneously profile DNA methylation, chromatin conformation, and gene expression at single-cell resolution. These tools have powered a series of landmark atlases that are redefining our understanding of cellular diversity across the brain and body. As a core contributor to the NIH BRAIN Initiative Cell Census Network (BICAN), Ecker's laboratory has generated comprehensive epigenomic cell atlases of the mouse and human brain, cataloguing the full diversity of neuronal and non-neuronal cell types based on their distinct DNA methylation signatures and three-dimensional genome organization. These atlases have revealed how gene regulatory programs differ across hundreds of brain cell types, providing an unprecedented molecular framework for understanding brain development, function, and disease. Extending this work beyond the brain, Ecker and colleagues produced a human body single-cell atlas of 3D genome organization and DNA methylation — one of the most comprehensive maps of the human epigenome across tissues ever assembled. Together, these resources constitute a foundational reference for the field, enabling researchers to connect epigenomic variation to cell identity, gene regulation, and disease susceptibility at a resolution and scale previously unimaginable. Ecker holds the International Council Chair in Genetics at the Salk Institute