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Daniel Rokhsar

Daniel Rokhsar

University of California, Berkeley · Center for Computational Biology

Active 1984–2026

h-index155
Citations163.5k
Papers474125 last 5y
Funding$20.6M1 active

Academic metrics are sourced from OpenAlex and public funding records; values may differ from Google Scholar.

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About

Daniel Rokhsar is a Professor of Physics, Molecular & Cell Biology in the Division of Genetics, Genomics, Evolution, and Development at the University of California, Berkeley. His research focuses on advances at the interface between genetics, genomics, and computational biology, encompassing both applications and methodological development. His areas of interest include new model organism genome assembly and annotation for both plants and animals, the development of novel computational methods for analyzing sequencing data, and evolutionary genomics.

Research topics

  • Biology
  • Agronomy
  • Biotechnology
  • Botany
  • Genetics

Selected publications

  • Deeply conserved synteny resolves early events in vertebrate evolution

    Nature Ecology & Evolution · 2020-04-20 · 398 citations

    articleOpen accessSenior authorCorresponding

    Although it is widely believed that early vertebrate evolution was shaped by ancient whole-genome duplications, the number, timing and mechanism of these events remain elusive. Here, we infer the history of vertebrates through genomic comparisons with a new chromosome-scale sequence of the invertebrate chordate amphioxus. We show how the karyotypes of amphioxus and diverse vertebrates are derived from 17 ancestral chordate linkage groups (and 19 ancestral bilaterian groups) by fusion, rearrangem…

    PublisherOA PDFDOI

  • Ancient gene linkages support ctenophores as sister to other animals

    Nature · 2023-05-17 · 391 citations

    articleOpen accessSenior author

    Abstract A central question in evolutionary biology is whether sponges or ctenophores (comb jellies) are the sister group to all other animals. These alternative phylogenetic hypotheses imply different scenarios for the evolution of complex neural systems and other animal-specific traits 1–6 . Conventional phylogenetic approaches based on morphological characters and increasingly extensive gene sequence collections have not been able to definitively answer this question 7–11 . Here we develop ch…

    PublisherOA PDFDOI

  • Genomic mechanisms of climate adaptation in polyploid bioenergy switchgrass

    Nature · 2021-01-27 · 259 citations

    articleOpen access

    Abstract Long-term climate change and periodic environmental extremes threaten food and fuel security 1 and global crop productivity 2–4 . Although molecular and adaptive breeding strategies can buffer the effects of climatic stress and improve crop resilience 5 , these approaches require sufficient knowledge of the genes that underlie productivity and adaptation 6 —knowledge that has been limited to a small number of well-studied model systems. Here we present the assembly and annotation of the…

    PublisherOA PDFDOI

  • Genome biology of the paleotetraploid perennial biomass crop Miscanthus

    Nature Communications · 2020 · 126 citations

    Senior authorCorresponding

    Miscanthus is a perennial wild grass that is of global importance for paper production, roofing, horticultural plantings, and an emerging highly productive temperate biomass crop. We report a chromosome-scale assembly of the paleotetraploid M. sinensis genome, providing a resource for Miscanthus that links its chromosomes to the related diploid Sorghum and complex polyploid sugarcanes. The asymmetric distribution of transposons across the two homoeologous subgenomes proves Miscanthus paleo-allot…

    PublisherOA PDFDOI

  • The hagfish genome and the evolution of vertebrates

    Nature · 2024-01-23 · 103 citations

    articleOpen accessSenior authorCorresponding

    Abstract As the only surviving lineages of jawless fishes, hagfishes and lampreys provide a crucial window into early vertebrate evolution 1–3 . Here we investigate the complex history, timing and functional role of genome-wide duplications 4–7 and programmed DNA elimination 8,9 in vertebrates in the light of a chromosome-scale genome sequence for the brown hagfish Eptatretus atami . Combining evidence from syntenic and phylogenetic analyses, we establish a comprehensive picture of vertebrate ge…

    PublisherDOI

Recent grants

Frequent coauthors

  • Jeremy Schmutz

    HudsonAlpha Institute for Biotechnology

    265 shared

  • Jane Grimwood

    HudsonAlpha Institute for Biotechnology

    243 shared

  • Erika Lindquist

    Lawrence Berkeley National Laboratory

    179 shared

  • Igor V. Grigoriev

    Lawrence Berkeley National Laboratory

    160 shared

  • Astrid Terry

    Wellcome Centre for Molecular Parasitology

    154 shared

  • Simon Prochnik

    Lawrence Berkeley National Laboratory

    154 shared

  • Jarrod Chapman

    Joint Genome Institute

    149 shared

  • Asaf Salamov

    Joint Genome Institute

    146 shared

Education

  • Ph.D., Physics

    Cornell University

    1987

  • M.S., Physics

    Cornell University

    1985

  • A.B., Physics

    Princeton University

    1982

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