Christopher Francis

About

Christopher Francis is a Professor of Earth System Science, specializing in Oceans, and a Senior Fellow at the Woods Institute for the Environment at Stanford University. He holds a Ph.D. in Marine Biology from the Scripps Institution of Oceanography, University of California, San Diego, earned in 2000, and a B.A. in Biology with Highest Honors from the University of California, Santa Cruz, obtained in 1994. His academic and research focus encompasses the Earth system, with particular emphasis on oceanic processes and environmental microbiology. As a faculty member, he contributes to the university's efforts in understanding complex environmental systems and advancing sustainability initiatives.

Research topics

• Biology
• Computational biology
• Genetics
• Computer Science
• Evolutionary biology
• Astronomy
• Ecology
• Library science
• Data science
• Neuroscience

Selected publications

• A genomic catalog of Earth’s microbiomes

  Nature Biotechnology · 2020 · 963 citations

  The reconstruction of bacterial and archaeal genomes from shotgun metagenomes has enabled insights into the ecology and evolution of environmental and host-associated microbiomes. Here we applied this approach to >10,000 metagenomes collected from diverse habitats covering all of Earth's continents and oceans, including metagenomes from human and animal hosts, engineered environments, and natural and agricultural soils, to capture extant microbial, metabolic and functional potential. This compre…

  PublisherOA PDFDOI

• Unraveling the functional dark matter through global metagenomics

  Nature · 2023 · 193 citations

  . Using massively parallel graph-based clustering, we group these proteins into 106,198 novel sequence clusters with more than 100 members, doubling the number of protein families obtained from the reference genomes clustered using the same approach. We annotate these families on the basis of their taxonomic, habitat, geographical and gene neighbourhood distributions and, where sufficient sequence diversity is available, predict protein three-dimensional models, revealing novel structures. Overa…

  PublisherOA PDFDOI

• Metagenome-assembled genomes reveal unique metabolic adaptations of a basal marine Thaumarchaeota lineage

  The ISME Journal · 2020 · 68 citations

  Senior authorCorresponding

  assimilation mediated by RuBisCO, which may be linked to the central carbon metabolism. We conclude that these genomes represent a hitherto unrecognized evolutionary link between predominantly anaerobic basal thaumarchaeal lineages and mesophilic marine AOA, with important implications for diversification within the phylum Thaumarchaeota.

  DOI

• Thousands of small, novel genes predicted in global phage genomes

  Cell Reports · 2022 · 55 citations

  Small genes (<150 nucleotides) have been systematically overlooked in phage genomes. We employ a large-scale comparative genomics approach to predict >40,000 small-gene families in ∼2.3 million phage genome contigs. We find that small genes in phage genomes are approximately 3-fold more prevalent than in host prokaryotic genomes. Our approach enriches for small genes that are translated in microbiomes, suggesting the small genes identified are coding. More than 9,000 families encode potentially…

  PublisherOA PDFDOI

• Globally distributed marine Gemmatimonadota have unique genomic potentials

  Microbiome · 2024-08-10 · 38 citations

  articleOpen access

  BACKGROUND: Gemmatimonadota bacteria are widely distributed in nature, but their metabolic potential and ecological roles in marine environments are poorly understood. RESULTS: Here, we obtained 495 metagenome-assembled genomes (MAGs), and associated viruses, from coastal to deep-sea sediments around the world. We used this expanded genomic catalog to compare the protein composition and update the phylogeny of these bacteria. The marine Gemmatimonadota are phylogenetically different from those p…

  PublisherOA PDFDOI

Recent grants

• MIP: Re-evaluating Ammonia Oxidation in Coastal Estuarine Sediments: Assessing the Relative Diversity, Abundance, and Activity of Ammonia-oxidizing Archaea and Bacteria

  NSF · $374k · 2006–2010

• Starter Grant: Diversity and Activity of Denitrifiers Across Estuarine Gradients

  NSF · $50k · 2004–2007

• COLLABORATIVE RESEARCH: The role of marine Crenarchaeota in nitrification and links among biogeochemical processes in the eastern tropical North Pacific and Gulf of California

  NSF · $264k · 2008–2013

Frequent coauthors

• Scott Fendorf

  Stanford University

  80 shared

• Bradley B. Tolar

  Stanford University

  73 shared

• Vanessa Bailey

  72 shared

• Marco Keiluweit

  72 shared

• Christian Dewey

  University of Minnesota

  72 shared

• Anne Dekas

  Stanford University

  72 shared

• Soichi Wakatsuki

  Stanford University

  63 shared

• Yasuo Yoshikuni

  Joint Genome Institute

  59 shared

Labs

• Environmental MicrobiologyPI

  1-2 sentence research focus

Education

• PhD, Marine Biology Research Division

  University of California San Diego Scripps Institution of Oceanography

  2000

• B.A., Biology

  University of California Santa Cruz

  1994

Similar researchers at Stanford University

• Eric Lambinh-130
• David Lobellh-115