Benjamin Doughty

2 months ago | cell.com | Gabriella E Martyn |Michael Montgomery |Hank Jones |Katherine Guo |Benjamin Doughty |Johannes Linder | +14 more

1Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA 2Basic Science and Engineering Initiative, Stanford Children’s Health, Betty Irene Moore Children’s Heart Center, Stanford, CA 94305, USA 3Calico Life Sciences LLC, South San Francisco, CA 94080, USA 4Department of Genitourinary Medical Oncology, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA 5Department of Genomic Medicine, The University of Texas...

Mar 19, 2024 | nature.com | David Yao |Josh Tycko |Lexi R. Bounds |Benjamin Doughty |Alexander White |Xingjie Ren | +16 more

AbstractThe ENCODE Consortium’s efforts to annotate noncoding cis-regulatory elements (CREs) have advanced our understanding of gene regulatory landscapes. Pooled, noncoding CRISPR screens offer a systematic approach to investigate cis-regulatory mechanisms. The ENCODE4 Functional Characterization Centers conducted 108 screens in human cell lines, comprising >540,000 perturbations across 24.85 megabases of the genome.

Nov 2, 2023 | biorxiv.org | Georgi K. Marinov |Benjamin Doughty |Anshul Kundaje |William J. Greenleaf

AbstractHistone proteins have traditionally been thought to be restricted to eukaryotes and most archaea, with eukaryotic nucleosomal histones deriving from their archaeal ancestors. In contrast, bacteria lack histones as a rule. However, histone proteins have recently been identified in a few bacterial clades, most notably the phylum Bdellovibrionota, and these histones have been proposed to exhibit a range of divergent features compared to histones in archaea and eukaryotes.