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Matthew Daugherty - UC San Diego. San Diego, CA, US

Matthew Daugherty Matthew Daugherty

Assistant Professor | UC San Diego


Evolution of host-pathogen interactions; innate antiviral immunity; how SARS-CoV-2 & other viruses enter the human population





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A Deep Look into the Biology and Evolution of COVID-19




Matt Daugherty received his undergraduate degree from Wesleyan University and then spent three years working for a start-up biotech company in Chicago. He received his Ph.D. from UC San Francisco and did his postdoctoral training at the Fred Hutchinson Cancer Research Center in Seattle WA. He joined the Division of Biological Sciences at UCSD in 2016.

Areas of Expertise (4)

Host-Pathogen Interactions


Innate Immunity

Evolutionary Genomics

Education (2)

University of California, San Francisco: Ph.D. 2009

Wesleyan University: B.A., Biochemistry, Neuroscience 1999

Media Appearances (1)

A Deep Look into the Biology and Evolution of COVID-19

UC San Diego Health  online


Matt Daugherty, an assistant professor in the Section of Molecular Biology, studies the evolutionary arms race that pits the immune systems of hosts on one hand and pathogens on the other.

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Research Focus (2)

Pathogen-Driven Evolution of Innate Antiviral Defense Mechanisms

NIH R35GM133633

2019-2024 Role: Principal Investigator

Consequences of IFIT Gene Evolution on Species-Specific Antiviral Immunity

NIH K22AI119017

2016 - 2018 Role: Principal Investigator

Articles (5)

RNA-binding protein isoforms ZAP-S and ZAP-L have distinct antiviral and immune resolution functions.

Nat Immunol.

2019 The initial response to viral infection is anticipatory, with host antiviral restriction factors and pathogen sensors constantly surveying the cell to rapidly mount an antiviral response through the synthesis and downstream activity of interferons. After pathogen clearance, the host's ability to resolve this antiviral response and return to homeostasis is critical.

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Diversification of the Caenorhabditis heat shock response by Helitron transposable elements.


2019 Heat Shock Factor 1 (HSF-1) is a key regulator of the heat shock response (HSR). Upon heat shock, HSF-1 binds well-conserved motifs, called Heat Shock Elements (HSEs), and drives expression of genes important for cellular protection during this stress. Remarkably, we found that substantial numbers of HSEs in multiple Caenorhabditis species reside within Helitrons, a type of DNA transposon.

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Gene conversion generates evolutionary novelty that fuels genetic conflicts.

Curr Opin Genet Dev.

2019 Genetic conflicts arise when the evolutionary interests of two genetic elements are not aligned. Conflicts between genomes (e.g. pathogen versus host) or within the same genome (e.g. internal parasitic DNA sequences versus the rest of the host genome) can both foster 'molecular arms races', in which genes on both sides of the conflict rapidly evolve due to bouts of adaptation and counter-adaptation.

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ICTV Virus Taxonomy Profile: Polyomaviridae.

J Gen Virol.

2017 The Polyomaviridae is a family of small, non-enveloped viruses with circular dsDNA genomes of approximately 5 kbp. The family includes four genera whose members have restricted host range, infecting mammals and birds. Polyomavirus genomes have also been detected recently in fish.

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Functional and Evolutionary Analyses Identify Proteolysis as a General Mechanism for NLRP1 Inflammasome Activation.

PLoS Pathog.

2016 Inflammasomes are cytosolic multi-protein complexes that initiate immune responses to infection by recruiting and activating the Caspase-1 protease. Human NLRP1 was the first protein shown to form an inflammasome, but its physiological mechanism of activation remains unknown.

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