Shuyi Ma, PhD

Shuyi Ma, PhD

Children's Title: Principal Investigator, Supervisor, Center for Global Infectious Disease Research

Academic Title: Assistant Professor, UW Department of Pediatrics; Adjunct Assistant Professor, UW Department of Chemical Engineering

Research Center: Center for Global Infectious Disease Research

    • Related Pages

    • Ma Lab Website

      In the Ma Lab, we combine computational and experimental network biology approaches to understand the molecular interactions that determine infection and treatment fate in tuberculosis.

  • Manuscripts in Refereed Journals

    • Ma S, Morrison R, Hobbs SJ, Soni V, Farrow-Johnson J, Frando A, Fleck N, Grundner C, Rhee KY, Rustad TR, Sherman DR
      Transcriptional regulator-induced phenotype screen reveals drug potentiators in Mycobacterium tuberculosis.
      33199862 Nature microbiology, 2021 Jan. : 6(1)44-50
    • Peters JS, Ismail N, Dippenaar A, Ma S, Sherman DR, Warren RM, Kana BD
      Genetic Diversity in Mycobacterium tuberculosis Clinical Isolates and Resulting Outcomes of Tuberculosis Infection and Disease.
      32926793 Annual review of genetics, 2020 Nov. 23 : 54511-537
    • Safi H, Lingaraju S, Ma S, Husain S, Hoque M, Soteropoulos P, Rustad T, Sherman DR, Alland D
      Rapidly Correcting Frameshift Mutations in the Mycobacterium tuberculosis orn Gene Produce Reversible Ethambutol Resistance and Small-Colony-Variant Morphology.
      32571828 Antimicrobial agents and chemotherapy, 2020 Aug. 20 : 64(9) PMCID:PMC7449195
    • Ma S, Jaipalli S, Larkins-Ford J, Lohmiller J, Aldridge BB, Sherman DR, Chandrasekaran S
      Transcriptomic Signatures Predict Regulators of Drug Synergy and Clinical Regimen Efficacy against Tuberculosis.
      31719182 mBio, 2019 Nov. 12 : 10(6) PMCID:PMC6851285
    • Safi H, Gopal P, Lingaraju S, Ma S, Levine C, Dartois V, Yee M, Li L, Blanc L, Ho Liang HP, Husain S, Hoque M, Soteropoulos P, Rustad T, Sherman DR, Dick T, Alland D
      Phase variation in Mycobacterium tuberculosis glpK produces transiently heritable drug tolerance.
      31488707 Proceedings of the National Academy of Sciences of the United States of America, 2019 Sept. 24 : 116(39)19665-19674 PMCID:PMC6765255
    • Drain PK, Bajema KL, Dowdy D, Dheda K, Naidoo K, Schumacher SG, Ma S, Meermeier E, Lewinsohn DM, Sherman DR
      Incipient and Subclinical Tuberculosis: a Clinical Review of Early Stages and Progression of Infection.
      30021818 Clinical microbiology reviews, 2018 Oct. : 31(4) PMCID:PMC6148193
    • Colangeli R, Jedrey H, Kim S, Connell R, Ma S, Chippada Venkata UD, Chakravorty S, Gupta A, Sizemore EE, Diem L, Sherman DR, Okwera A, Dietze R, Boom WH, Johnson JL, Mac Kenzie WR, Alland D, DMID 01-009/Tuberculosis Trials Consortium Study 22 Teams.
      Bacterial Factors That Predict Relapse after Tuberculosis Therapy.
      30157391 The New England journal of medicine, 2018 Aug. 30 : 379(9)823-833 PMCID:PMC6317071
    • Moguche AO, Musvosvi M, Penn-Nicholson A, Plumlee CR, Mearns H, Geldenhuys H, Smit E, Abrahams D, Rozot V, Dintwe O, Hoff ST, Kromann I, Ruhwald M, Bang P, Larson RP, Shafiani S, Ma S, Sherman DR, Sette A, Lindestam Arlehamn CS, McKinney DM, Maecker H, Hanekom WA, Hatherill M, Andersen P, Scriba TJ, Urdahl KB
      Antigen Availability Shapes T Cell Differentiation and Function during Tuberculosis.
      28618268 Cell host & microbe, 2017 June 14 : 21(6)695-706.e5 PMCID:PMC5533182
    • Wang Z, Danziger SA, Heavner BD, Ma S, Smith JJ, Li S, Herricks T, Simeonidis E, Baliga NS, Aitchison JD, Price ND
      Combining inferred regulatory and reconstructed metabolic networks enhances phenotype prediction in yeast.
      28520713 PLoS computational biology, 2017 May : 13(5)e1005489 PMCID:PMC5453602
    • Peterson EJR, Ma S, Sherman DR, Baliga NS
      Network analysis identifies Rv0324 and Rv0880 as regulators of bedaquiline tolerance in Mycobacterium tuberculosis.
      27573104 Nature microbiology, 2016 June 6 : 1(8)16078 PMCID:PMC5010021
    • Ma S, Minch KJ, Rustad TR, Hobbs S, Zhou SL, Sherman DR, Price ND
      Integrated Modeling of Gene Regulatory and Metabolic Networks in Mycobacterium tuberculosis.
      26618656 PLoS computational biology, 2015 Nov. : 11(11)e1004543 PMCID:PMC4664399
    • Minch KJ, Rustad TR, Peterson EJ, Winkler J, Reiss DJ, Ma S, Hickey M, Brabant W, Morrison B, Turkarslan S, Mawhinney C, Galagan JE, Price ND, Baliga NS, Sherman DR
      The DNA-binding network of Mycobacterium tuberculosis.
      25581030 Nature communications, 2015 Jan. 12 : 65829 PMCID:PMC4301838
    • Turkarslan S, Peterson EJ, Rustad TR, Minch KJ, Reiss DJ, Morrison R, Ma S, Price ND, Sherman DR, Baliga NS
      A comprehensive map of genome-wide gene regulation in Mycobacterium tuberculosis.
      25977815 Scientific data, 2015 : 2150010 PMCID:PMC4413241
    • Ma S, Sung J, Magis AT, Wang Y, Geman D, Price ND
      Measuring the effect of inter-study variability on estimating prediction error.
      25330348 PloS one, 2014 : 9(10)e110840 PMCID:PMC4201588
    • Rustad TR, Minch KJ, Ma S, Winkler JK, Hobbs S, Hickey M, Brabant W, Turkarslan S, Price ND, Baliga NS, Sherman DR
      Mapping and manipulating the Mycobacterium tuberculosis transcriptome using a transcription factor overexpression-derived regulatory network.
      25380655 Genome biology, 2014 : 15(11)502 PMCID:PMC4249609
    • Ma S, Funk CC, Price ND
      Systems approaches to molecular cancer diagnostics.
      21189224 Discovery medicine, 2010 Dec. : 10(55)531-42 PMCID:PMC3155470