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.

Single-cell profiling of tuberculosis lung granulomas reveals functional lymphocyte signatures of bacterial control
  • Gideon et al.,
  • bioRxiv,
  • 2020
  • Genomics
  • Biology
  • Infectious Disease
  • Immunology
  • Cell Atlas
  • 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
  • Biology
  • Statistics
  • Computational Methods
  • 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
  • Immunology
  • Biology
  • Cell Atlas
  • Infectious Disease
  • 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
  • Genomics
  • Infectious Disease
  • Biology
  • Statistics
  • Immunology
  • Cell Atlas
  • 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
  • Statistics
  • Infectious Disease
  • Immunology
  • Genomics
  • Biology
  • 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,
  • Immunology
  • Cell Atlas
  • Computational Methods
  • Biology
  • Infectious Disease
  • Medicine
  • Genomics
  • 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
  • Biology
  • Immunology
  • Genomics
  • Infectious Disease
  • 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
  • Biology
  • Immunology
  • Medicine
  • Cell Atlas
  • 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
  • Medicine
  • Cell Atlas
  • José Ordovas-Montañes
  • Sarah Nyquist
  • Marc Wadsworth II
  • Travis Hughes
  • Sam Kazer
  • Alex K. Shalek