publications

publications by categories in reversed chronological order. generated by jekyll-scholar.

2024

  1. Contrastive linear regression
    Boyang Zhang, Sarah Nyquist, Andrew Jones, Barbara E Engelhardt, and Didong Li
    arXiv preprint arXiv:2401.03106, 2024
    Article Code

2023

  1. CD4+ T cells are homeostatic regulators during Mtb reinfection
    Joshua D Bromley*, Sharie Keanne C Ganchua*, Sarah K Nyquist, Pauline Maiello, Michael Chao, H Jacob Borish, Mark Rodgers, Jaime Tomko, Kara Kracinovsky, Douaa Mugahid, and  others
    bioRxiv, 2023
    Article
  2. CD8+ lymphocytes are critical for early control of tuberculosis in macaques
    Caylin G Winchell*, Sarah K Nyquist*, Michael C Chao, Pauline Maiello, Amy J Myers, Forrest Hopkins, Michael Chase, Hannah P Gideon, Kush V Patel, Joshua D Bromley, and  others
    Journal of Experimental Medicine, 2023
    Article Code
  3. Protective intravenous BCG vaccination induces enhanced immune signaling in the airways
    Joshua M Peters, Edward B Irvine, Jacob M Rosenberg, Marc H Wadsworth, Travis K Hughes, Matthew Sutton, Sarah K Nyquist, Joshua D Bromley, Rajib Mondal, Mario Roederer, and  others
    bioRxiv, 2023
    Article

2022

  1. Differential analysis of scRNA-Seq data to characterize epithelial cells in health and disease
    Sarah Kate Nyquist
    Massachusetts Institute of Technology, 2022
    Article
  2. Cellular and transcriptional diversity over the course of human lactation
    Sarah K Nyquist, Patricia Gao, Tessa KJ Haining, Michael R Retchin, Yarden Golan, Riley S Drake, Kellie Kolb, Benjamin E Mead, Nadav Ahituv, Micaela E Martinez, and  others
    Proceedings of the National Academy of Sciences, 2022
    Article Explore Data
  3. Identification and characterization of the T cell receptor (TCR) repertoire of the cynomolgus macaque (Macaca Fascicularis)
    Swati Jaiswal, Sarah K Nyquist, Shayla Boyce, Tasneem Jivanjee, Samira Ibrahim, Joshua D Bromley, G James Gatter, Hannah Gideon, Kush Patel, Sharie Keanne Ganchua, and  others
    BMC Genomics, 2022
    Article
  4. Multimodal profiling of lung granulomas in macaques reveals cellular correlates of tuberculosis control
    Hannah P Gideon*, Travis K Hughes*, Constantine N Tzouanas, Marc H Wadsworth II, Ang Andy Tu, Todd M Gierahn, Joshua M Peters, Forrest F Hopkins, Jun-Rong Wei, Conner Kummerlowe, and  others
    Immunity, 2022
    Article Explore Data
  5. Enriching and Characterizing T-Cell Repertoires from 3’Barcoded Single-Cell Whole Transcriptome Amplification Products
    Tasneem Jivanjee*, Samira Ibrahim*, Sarah K Nyquist, G James Gatter, Joshua D Bromley, Swati Jaiswal, Bonnie Berger, Samuel M Behar, J Christopher Love, and Alex K Shalek
    arXiv preprint arXiv:2203.11266, 2022
    Article Code

2021

  1. Human airway mast cells proliferate and acquire distinct inflammation-driven phenotypes during type 2 inflammation
    Daniel F Dwyer, Jose Ordovas-Montanes, Samuel J Allon, Kathleen M Buchheit, Marko Vukovic, Tahereh Derakhshan, Chunli Feng, Juying Lai, Travis K Hughes, Sarah K Nyquist, and  others
    Science Immunology, 2021
    Article
  2. HIV infection drives interferon signaling within intestinal SARS-CoV-2 target cells
    Rabiah Fardoos, Osaretin E Asowata, Nicholas Herbert, Sarah K Nyquist, Yenzekile Zungu, Alveera Singh, Abigail Ngoepe, Ian M Mbano, Ntombifuthi Mthabela, Dirhona Ramjit, and  others
    JCI Insight, 2021
    Article
  3. Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics
    Christoph Muus, Malte D Luecken, Gökcen Eraslan, Lisa Sikkema, Avinash Waghray, Graham Heimberg, Yoshihiko Kobayashi, Eeshit Dhaval Vaishnav, Ayshwarya Subramanian, Christopher Smillie, and  others
    Nature Medicine, 2021
    Article

2020

  1. Improved haplotype inference by exploiting long-range linking and allelic imbalance in RNA-seq datasets
    Emily Berger, Deniz Yorukoglu, Lillian Zhang, Sarah K Nyquist, Alex K Shalek, Manolis Kellis, Ibrahim Numanagić, and Bonnie Berger
    Nature Communications, 2020
    Article Code
  2. Computational methods for single-cell RNA sequencing
    Brian Hie*, Joshua Peters*, Sarah K Nyquist*, Alex K Shalek, Bonnie Berger, and Bryan D Bryson
    Annual Review of Biomedical Data Science, 2020
    Article
  3. Integrated single-cell analysis of multicellular immune dynamics during hyperacute HIV-1 infection
    Samuel W Kazer, Toby P Aicher, Daniel M Muema, Shaina L Carroll, Jose Ordovas-Montanes, Vincent N Miao, Ang A Tu, Carly GK Ziegler, Sarah K Nyquist, Emily B Wong, and  others
    Nature medicine, 2020
    Article Explore Data
  4. SARS-CoV-2 receptor ACE2 is an interferon-stimulated gene in human airway epithelial cells and is detected in specific cell subsets across tissues
    Carly GK Ziegler*, Samuel J Allon*, Sarah K Nyquist*, Ian M Mbano*, Vincent N Miao, Constantine N Tzouanas, Yuming Cao, Ashraf S Yousif, Julia Bals, Blake M Hauser, and  others
    Cell, 2020
    Article Blog Explore Data

2019

  1. Mast cell hyperplasia in human type 2 inflammation: insights from single cell RNA sequencing
    Daniel F Dwyer, Jose Ordovas-Montanes, Sarah K Nyquist, Kathleen M Buchheit, Howard R Katz, Neil Bhattacharyya, Tanya M Laidlaw, Joshua A Boyce, Alex K Shalek, and Nora A Barrett
    Journal of Allergy and Clinical Immunology, 2019
    Article

2018

  1. Allergic inflammatory memory in human respiratory epithelial progenitor cells
    Jose Ordovas-Montanes*, Daniel F Dwyer*, Sarah K Nyquist, Kathleen M Buchheit, Marko Vukovic, Chaarushena Deb, Marc H Wadsworth, Travis K Hughes, Samuel W Kazer, Eri Yoshimoto, and  others
    Nature, 2018
    Article Explore Data
  2. The Juicebox Assembly Tools module facilitates de novo assembly of mammalian genomes with chromosome-length scaffolds for under $1000
    Olga Dudchenko, Muhammad S Shamim, Sanjit S Batra, Neva C Durand, Nathaniel T Musial, Ragib Mostofa, Melanie Pham, Brian Glenn St Hilaire, Weijie Yao, Elena Stamenova, and  others
    bioRxiv, 2018
    Article
  3. Hi-C yields chromosome-length scaffolds for a legume genome, Trifolium subterraneum
    Olga Dudchenko, Melanie Pham, Christopher Lui, Sanjit S Batra, Marie Hoeger, Sarah K Nyquist, Neva C Durand, Muhammad S Shamim, Ido Machol, William Erskine, and  others
    bioRxiv, 2018
    Article

2017

  1. De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds
    Olga Dudchenko*, Sanjit S Batra*, Arina D Omer, Sarah K Nyquist, Marie Hoeger, Neva C Durand, Muhammad S Shamim, Ido Machol, Eric S Lander, Aviva Presser Aiden, and  others
    Science, 2017
    Article