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.

CD8+ lymphocytes are critical for early control of tuberculosis in macaques
  • Winchell et al.,
  • Journal of Experimental Medicine,
  • 2023
  • Infectious Disease
  • Medicine
  • Computational Methods
  • Josh Bromley
  • Sarah Nyquist
  • Alex K. Shalek
  • Marc Wadsworth II
  • Travis Hughes
Identification and characterization of the T cell receptor (TCR) repertoire of the cynomolgus macaque (Macaca Fascicularis)
  • Jaiswal et al.,
  • BMC Genomics,
  • 2023
  • Immunology
  • Infectious Disease
  • Cell Atlas
  • Computational Methods
  • Biology
  • Genomics
  • R&D
  • Sarah Nyquist
  • Tasneem Jivanjee
  • Samira Ibrahim
  • Josh Bromley
  • James Gatter
  • Alex K. Shalek
HIV specific CD8+ TRM-like cells in tonsils express exhaustive signatures in the absence of natural HIV control
  • Fardoos et al.,
  • Frontiers in Immunology,
  • Genomics
  • Immunology
  • Biology
  • Infectious Disease
  • Sarah Nyquist
  • Sam Kazer
  • Son Nguyen
  • Alex K. Shalek
Multimodal profiling of lung granulomas in macaques reveals cellular correlates of tuberculosis control
  • Gideon et al.,
  • Immunity,
  • 2022
  • Biology
  • Cell Atlas
  • Microbiology
  • Immunology
  • Infectious Disease
  • Genomics
  • Travis Hughes
  • Constantine Tzouanas
  • Marc Wadsworth II
  • Conner Kummerlowe
  • Sarah Nyquist
  • Samira Ibrahim
  • José Ordovas-Montañes
  • Alex K. Shalek
Cellular and transcriptional diversity over the course of human lactation
  • Nyquist et al.,
  • PNAS,
  • 2022
  • Medicine
  • Immunology
  • Cell Atlas
  • Genomics
  • Biology
  • Sarah Nyquist
  • Patricia Gao
  • Riley Drake
  • Kellie Kolb
  • Ben Mead
  • Alex K. Shalek
  • Brittany Goods
HIV infection drives interferon signaling within intestinal SARS-CoV-2 target cells
  • Fardoos et al.,
  • JCI Insight,
  • 2021
  • Immunology
  • Infectious Disease
  • Genomics
  • Sarah Nyquist
  • Alex K. Shalek
Human airway mast cells proliferate and acquire distinct inflammation-driven phenotypes during type 2 inflammation
  • Dwyer et al.,
  • Science Immunology,
  • 2021
  • Immunology
  • Biology
  • Genomics
  • José Ordovas-Montañes
  • Sam Allon
  • Marko Vukovic
  • Travis Hughes
  • Sarah Nyquist
  • Alex K. Shalek
Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics
  • Muus et al.,
  • Nature Medicine,
  • 2021
  • Infectious Disease
  • Immunology
  • Cell Atlas
  • Statistics
  • Genomics
  • Computational Methods
  • Sam Allon
  • Sarah Nyquist
  • Marc Wadsworth II
  • Carly Ziegler
  • Alex K. Shalek
Single-cell profiling of tuberculosis lung granulomas reveals functional lymphocyte signatures of bacterial control
  • Gideon et al.,
  • bioRxiv,
  • 2020
  • Genomics
  • Biology
  • Immunology
  • Cell Atlas
  • Infectious Disease
  • Travis Hughes
  • Marc Wadsworth II
  • Conner Kummerlowe
  • Sarah Nyquist
  • José Ordovas-Montañes
  • Alex K. Shalek
Improved haplotype inference by exploiting long-range linking and allelic imbalance in RNA-seq datasets
  • Berger et al.,
  • Nature Communications,
  • 2020
  • Computational Methods
  • Biology
  • Statistics
  • Sarah Nyquist
  • Alex K. Shalek
Computational Methods for Single-Cell RNA Sequencing
  • Hie et al.,
  • Annual Reviews,
  • 2020
  • Genomics
  • Computational Methods
  • Biology
  • Sarah Nyquist
  • Alex K. Shalek
SARS-CoV-2 receptor ACE2 is an interferon-stimulated gene in human airway epithelial cells and is detected in specific cell subsets across tissues
  • Ziegler et al.,
  • Cell,
  • 2020
  • Infectious Disease
  • Immunology
  • Cell Atlas
  • Biology
  • Statistics
  • Genomics
  • Carly Ziegler
  • Sam Allon
  • Sarah Nyquist
  • Vincent Miao
  • Constantine Tzouanas
  • Marc Wadsworth II
  • Sam Kazer
  • Travis Hughes
  • Benjamin Doran
  • James Gatter
  • Marko Vukovic
  • Ben Mead
  • Shaina Carroll
  • Alex K. Shalek
  • José Ordovas-Montañes
Integrated analyses of single-cell atlases reveal age, gender, and smoking status associations with cell type-specific expression of mediators of SARS-CoV-2 viral entry and highlights inflammatory programs in putative target cells
  • Muus et al.,
  • bioRxiv,
  • Computational Methods
  • Statistics
  • Infectious Disease
  • Genomics
  • Biology
  • Cell Atlas
  • Immunology
  • Sam Allon
  • Sarah Nyquist
  • José Ordovas-Montañes
  • Marc Wadsworth II
  • Carly Ziegler
  • Alex K. Shalek
Integrated single-cell analysis of multicellular immune dynamics during hyperacute HIV-1 infection
  • Kazer et al.,
  • Nature Medicine,
  • 2020
  • Computational Methods
  • Genomics
  • Infectious Disease
  • Biology
  • Immunology
  • Statistics
  • Sam Kazer
  • Toby Aicher
  • Shaina Carroll
  • José Ordovas-Montañes
  • Vincent Miao
  • Carly Ziegler
  • Sarah Nyquist
  • Alex K. Shalek
SARS-CoV-2 receptor ACE2 is an interferon-stimulated gene in human airway epithelial cells and is enriched in specific cell subsets across tissues
  • Ziegler et al.,
  • SSRN,
  • Computational Methods
  • Biology
  • Immunology
  • Medicine
  • Cell Atlas
  • Genomics
  • Infectious Disease
  • Carly Ziegler
  • Sam Allon
  • Sarah Nyquist
  • Vincent Miao
  • Marc Wadsworth II
  • Sam Kazer
  • Travis Hughes
  • Benjamin Doran
  • James Gatter
  • Marko Vukovic
  • Constantine Tzouanas
  • Shaina Carroll
  • Alex K. Shalek
  • José Ordovas-Montañes
Integrated Single-Cell Analysis of Multicellular Immune Dynamics during Hyper-Acute HIV-1 Infection
  • Kazer S.W. et al.,
  • bioRxiv,
  • 2019
  • Infectious Disease
  • Genomics
  • Immunology
  • Biology
  • Sam Kazer
  • Toby Aicher
  • Shaina Carroll
  • José Ordovas-Montañes
  • Carly Ziegler
  • Sarah Nyquist
  • Alex K. Shalek
Allergic Inflammatory Memory in Human Respiratory Epithelial Progenitor Cells
  • Ordovas-Montanes et al.,
  • Nature,
  • 2018
  • Medicine
  • Biology
  • Cell Atlas
  • Immunology
  • José Ordovas-Montañes
  • Sarah Nyquist
  • Marko Vukovic
  • Marc Wadsworth II
  • Travis Hughes
  • Sam Kazer
  • Alex K. Shalek
Reduced cellular diversity and an altered basal progenitor cell state inform epithelial barrier dysfunction in human type 2 immunity
  • Jose Ordovas-Montanes et al.,
  • BioRxiv,
  • 2017
  • Immunology
  • Cell Atlas
  • Medicine
  • José Ordovas-Montañes
  • Sarah Nyquist
  • Marc Wadsworth II
  • Travis Hughes
  • Sam Kazer
  • Alex K. Shalek