Sarah Nyquist

Sarah Nyquist

Former Graduate Student

Degrees & Affiliations

BA, Computer Science - Rice University PhD Candidate, Computational & Systems Biology - MIT

Background & Interests

Biology Biology
Computational Methods Computational Methods
Genomics Genomics
I Want a Hot Body, but I also Want Tacos I Want a Hot Body, but I also Want Tacos
Outdoor Adventures Outdoor Adventures
Statistics Statistics

Biography

Sarah is a third year graduate student in the Computational and Systems Biology
program co-advised by Professors Alex Shalek and Bonnie Berger. She is interested
in applying machine learning methods to better understand single cell genomic
data.

Before starting at MIT, Sarah studied computer science at Rice University where
she worked on genome assembly algorithms. In her free time Sarah likes to
explore art museums, make crafts, and go for very slow runs.

Publications

Systematic deconstruction of myeloid cell signaling in tuberculosis granulomas reveals IFN-γ, TGF-β, and time are associated with conserved myeloid diversity
Systematic deconstruction of myeloid cell signaling in tuberculosis granulomas reveals IFN-γ, TGF-β, and time are associated with conserved myeloid diversity
  • Peters et al.,
  • biorxiv,
  • 2024
Alex K. Shalek Alex K. Shalek
Josh Bromley Josh Bromley
Sarah Nyquist Sarah Nyquist
Travis Hughes Travis Hughes
CD4 + T cells are homeostatic regulators during Mtb reinfection
CD4 + T cells are homeostatic regulators during Mtb reinfection
  • Bromley et al.,
  • bioRxiv,
  • 2024
Biology Biology
Computational Methods Computational Methods
Immunology Immunology
Infectious Disease Infectious Disease
Alex K. Shalek Alex K. Shalek
Dennis Wang Dennis Wang
Josh Bromley Josh Bromley
Sarah Nyquist Sarah Nyquist
Son Nguyen Son Nguyen
CD8+ lymphocytes are critical for early control of tuberculosis in macaques
CD8+ lymphocytes are critical for early control of tuberculosis in macaques
  • Winchell et al.,
  • Journal of Experimental Medicine,
  • 2023
Computational Methods Computational Methods
Infectious Disease Infectious Disease
Medicine Medicine
Alex K. Shalek Alex K. Shalek
Josh Bromley Josh Bromley
Marc Wadsworth II Marc Wadsworth II
Sarah Nyquist Sarah Nyquist
Travis Hughes Travis Hughes
Identification and characterization of the T cell receptor (TCR) repertoire of the cynomolgus macaque (Macaca Fascicularis)
Identification and characterization of the T cell receptor (TCR) repertoire of the cynomolgus macaque (Macaca Fascicularis)
  • Jaiswal et al.,
  • BMC Genomics,
  • 2023
Biology Biology
Cell Atlas Cell Atlas
Computational Methods Computational Methods
Genomics Genomics
Immunology Immunology
Infectious Disease Infectious Disease
R&D R&D
Alex K. Shalek Alex K. Shalek
James Gatter James Gatter
Josh Bromley Josh Bromley
Samira Ibrahim Samira Ibrahim
Sarah Nyquist Sarah Nyquist
Tasneem Jivanjee Tasneem Jivanjee
HIV specific CD8+ TRM-like cells in tonsils express exhaustive signatures in the absence of natural HIV control
HIV specific CD8+ TRM-like cells in tonsils express exhaustive signatures in the absence of natural HIV control
  • Fardoos et al.,
  • Frontiers in Immunology,
  • 2023
Biology Biology
Genomics Genomics
Immunology Immunology
Infectious Disease Infectious Disease
Alex K. Shalek Alex K. Shalek
Sam Kazer Sam Kazer
Sarah Nyquist Sarah Nyquist
Son Nguyen Son Nguyen
Multimodal profiling of lung granulomas in macaques reveals cellular correlates of tuberculosis control
Multimodal profiling of lung granulomas in macaques reveals cellular correlates of tuberculosis control
  • Gideon et al.,
  • Immunity,
  • 2022
Biology Biology
Cell Atlas Cell Atlas
Genomics Genomics
Immunology Immunology
Infectious Disease Infectious Disease
Microbiology Microbiology
Alex K. Shalek Alex K. Shalek
Conner Kummerlowe Conner Kummerlowe
Constantine Tzouanas Constantine Tzouanas
José Ordovas-Montañes José Ordovas-Montañes
Marc Wadsworth II Marc Wadsworth II
Samira Ibrahim Samira Ibrahim
Sarah Nyquist Sarah Nyquist
Travis Hughes Travis Hughes
Cellular and transcriptional diversity over the course of human lactation
Cellular and transcriptional diversity over the course of human lactation
  • Nyquist et al.,
  • PNAS,
  • 2022
Biology Biology
Cell Atlas Cell Atlas
Genomics Genomics
Immunology Immunology
Medicine Medicine
Alex K. Shalek Alex K. Shalek
Ben Mead Ben Mead
Brittany Goods Brittany Goods
Kellie Kolb Kellie Kolb
Patricia Gao Patricia Gao
Riley Drake Riley Drake
Sarah Nyquist Sarah Nyquist
HIV infection drives interferon signaling within intestinal SARS-CoV-2 target cells
HIV infection drives interferon signaling within intestinal SARS-CoV-2 target cells
  • Fardoos et al.,
  • JCI Insight,
  • 2021
Genomics Genomics
Immunology Immunology
Infectious Disease Infectious Disease
Alex K. Shalek Alex K. Shalek
Sarah Nyquist Sarah Nyquist
Human airway mast cells proliferate and acquire distinct inflammation-driven phenotypes during type 2 inflammation
Human airway mast cells proliferate and acquire distinct inflammation-driven phenotypes during type 2 inflammation
  • Dwyer et al.,
  • Science Immunology,
  • 2021
Biology Biology
Genomics Genomics
Immunology Immunology
Alex K. Shalek Alex K. Shalek
José Ordovas-Montañes José Ordovas-Montañes
Marko Vukovic Marko Vukovic
Sam Allon Sam Allon
Sarah Nyquist Sarah Nyquist
Travis Hughes Travis Hughes
Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics
Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics
  • Muus et al.,
  • Nature Medicine,
  • 2021
Cell Atlas Cell Atlas
Computational Methods Computational Methods
Genomics Genomics
Immunology Immunology
Infectious Disease Infectious Disease
Statistics Statistics
Alex K. Shalek Alex K. Shalek
Carly Ziegler Carly Ziegler
Marc Wadsworth II Marc Wadsworth II
Sam Allon Sam Allon
Sarah Nyquist Sarah Nyquist