Responsible for implementing technology for high-throughput genomics, proteomics, clinical, wearable, single-cell, immunological, and microbiome assays, participating in organizational strategy, forming and managing strategic partnerships and collaborations, developing commercial opportunities, interfacing with the broader scientific community, participating in scientific interpretations, publications, and translation into clinical practice, and contributing to education and outreach to physicians, participants, and the public. Also a Senior Visiting Scientist at the Buck Institute for Research on Aging in Novato, CA.

Responsible for forming and managing strategic partnerships among PSJH clinicians and researchers, building outside collaborations, implementing technology for translational medicine, to include high-throughput genomics, proteomics, and single cell assays, developing commercial opportunities, and interfacing with the broader scientific community.

Led dozens of whole genome sequencing projects with both academic and corporate partners and built large-scale databases for their interpretation (see lists below under major scientific contributions).

Led JGI's transition from being a human genome sequencing facility to being a comparative genomics institute and JGI is, today, broadly acknowledged as premier in its sampling of phylogenetically diverse organisms and in their evolutionary comparisons. Led the development of the $20 million/year JGI Community Sequencing Program that provides genomic data to the scientific community through peer review.

Taught genome evolution, sponsored graduate students, postdoctoral researchers, and sabbatical visitors, managed many scientific collaborations with the national laboratory, and fully participated in academic life.

Led numerous whole genome sequencing projects, including those of the crustacean Daphnia pulex, the butterfly Danaus plexippus, the gastropod mollusks Potamopyrgus antipodarum, P. estuarinus and, P. kaitunuparaoa, the glaucophyte Cyanophora paradoxa, the moss Physcomitrella patens, the stramenopile alga Nannochloropsis gaditana, the green alga Chlorella vulgaris, and the oomycetes Phytophthora sojae and P. ramorum, and performed major parts of the analyses for the genomes of the fish Xiphophorus maculatus, the tunicate Ciona intestinalis, the bivalve mollusk Lottia gigantea, the annelids Helobdella robusta and Capitella teleta, and the oomycetes Pythium ultimum and Hyaloperonospora arabidopsidis.

Made significant contributions to understanding the genome duplications at the base of the vertebrates, the evolutionary transfer of genes among intracellular compartments, modes of genome rearrangement, mammalian sex chromosome evolution, Hox gene cluster evolution, recognizing regulatory elements in DNA sequences, using genome-level characters for reconstructing evolutionary relationships, evaluating changes in gene expression patterns, understanding the effects of various genome processes on DNA sequence evolution, and identifying the genomic underpinnings of plant pathogenesis and environmental adaptation, crop improvement, biofuels production, responses to environmental challenges, behavioral complexity, asexuality within lineages, and differential longevity among populations.

Early work on organellar genomes determined the complete mtDNA sequences of ~200 species and cpDNA sequences of ~100 species. The results addressed questions of genome evolution, deep evolutionary relationships, intron evolution, post-transcriptional modification of tRNAs, gene movements among intracellular compartments, changes in the genetic code, and the evolution of codon usage patterns.

Two examples of software created by my group include DOGMA (Dual Organellar Genome Annotator), which provides a semi-automated tool for identifying and annotating genes for mitochondrial and plastid genomes. Second is PHRINGE (Phylogenetic Resources for the Interpretation of Genomes), which accepts the complete gene sets of many genomes, clusters these into families using a unique algorithm, creates true phylogenetic trees for each cluster, and has an extensive set of databases, displays, and queries for comparing homologous genes across these genomes. This has been shown to be the most accurate method for assigning gene function based on inference of homology, the only possible evidence in the absence of genetic or biochemical experimentation.