My Bibliography

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Roman MA, Porszasz J, Cao R, Rennard SI, Ma S, Kiledjian R, Casaburi R. An Efficient New Method For Determining Oxygen Uptake Kinetics During Exercise: The Chirp Waveform. American Thoracic Society 2012 International Conference; 2012 May 20; San Francisco, CA, USA.

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Hecht A, Ma S, Porszasz J, Casaburi R. Methodology for using long-term accelerometry monitoring to describe daily activity patterns in COPD. COPD. 2009 Apr;6(2):121-9. doi: 10.1080/15412550902755044. PubMed PMID: 19378225; PubMed Central PMCID: PMC2862250.

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Ma S, Hecht A, Varga J, Rambod M, Morford S, Goto S, Casaburi R, Porszasz J. Breath-by-breath quantification of progressive airflow limitation during exercise in COPD: a new method. Respir Med. 2010 Mar;104(3):389-96. doi: 10.1016/j.rmed.2009.10.014. PubMed PMID: 19931441.

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Ma S, Rossiter HB, Barstow TJ, Casaburi R, Porszasz J. Clarifying the equation for modeling of VO2 kinetics above the lactate threshold. J Appl Physiol (1985). 2010 Oct;109(4):1283-4. doi: 10.1152/japplphysiol.00459.2010. PubMed PMID: 20940444.

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Ma S, Funk CC, Price ND. Systems approaches to molecular cancer diagnostics. Discov Med. 2010 Dec;10(55):531-42. Review. PubMed PMID: 21189224; PubMed Central PMCID: PMC3155470.

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Li Q, Singh CR, Ma S, Price ND, Jagannath C. Label-free proteomics and systems biology analysis of mycobacterial phagosomes in dendritic cells and macrophages. J Proteome Res. 2011 May 6;10(5):2425-39. doi: 10.1021/pr101245u. Epub 2011 Mar 30. PubMed PMID: 21413810; PubMed Central PMCID: PMC3090528.

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Porszasz J, Rambod M, van der Vaart H, Rossiter HB, Ma S, Kiledjian R, Casaburi R. Sinusoidal high-intensity exercise does not elicit ventilatory limitation in chronic obstructive pulmonary disease. Exp Physiol. 2013 Jun;98(6):1102-14. doi: 10.1113/expphysiol.2012.070375. Epub 2013 Jan 18. PubMed PMID: 23335005.

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Sung J, Kim PJ, Ma S, Funk CC, Magis AT, Wang Y, Hood L, Geman D, Price ND. Multi-study integration of brain cancer transcriptomes reveals organ-level molecular signatures. PLoS Comput Biol. 2013;9(7):e1003148. doi: 10.1371/journal.pcbi.1003148. Epub 2013 Jul 25. PubMed PMID: 23935471; PubMed Central PMCID: PMC3723500.

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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. Genome Biol. 2014;15(11):502. doi: 10.1186/PREACCEPT-1701638048134699. PubMed PMID: 25380655; PubMed Central PMCID: PMC4249609.

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Ma S, Sung J, Magis AT, Wang Y, Geman D, Price ND. Measuring the effect of inter-study variability on estimating prediction error. PLoS One. 2014;9(10):e110840. doi: 10.1371/journal.pone.0110840. eCollection 2014. PubMed PMID: 25330348; PubMed Central PMCID: PMC4201588.

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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. Nat Commun. 2015 Jan 12;6:5829. doi: 10.1038/ncomms6829. PubMed PMID: 25581030; PubMed Central PMCID: PMC4301838.

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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. Sci Data. 2015;2:150010. doi: 10.1038/sdata.2015.10. eCollection 2015. PubMed PMID: 25977815; PubMed Central PMCID: PMC4413241.

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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. PLoS Comput Biol. 2015 Nov;11(11):e1004543. doi: 10.1371/journal.pcbi.1004543. eCollection 2015 Nov. PubMed PMID: 26618656; PubMed Central PMCID: PMC4664399.

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Peterson EJR, Ma S, Sherman DR, Baliga NS. Network analysis identifies Rv0324 and Rv0880 as regulators of bedaquiline tolerance in Mycobacterium tuberculosis. Nat Microbiol. 2016 Jun 6;1(8):16078. doi: 10.1038/nmicrobiol.2016.78. PubMed PMID: 27573104; PubMed Central PMCID: PMC5010021.

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Varga J, Casaburi R, Ma S, Hecht A, Hsia D, Somfay A, Porszasz J. Relation of concavity in the expiratory flow-volume loop to dynamic hyperinflation during exercise in COPD. Respir Physiol Neurobiol. 2016 Dec;234:79-84. doi: 10.1016/j.resp.2016.08.005. Epub 2016 Aug 26. PubMed PMID: 27575552.

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Ma S, Earls JC, Eddy JA, Price ND. Using Integrative Omics Approaches in Network Medicine. In: Loscalzo J, Barabási A, Silverman EK, editors. Network Medicine: Complex Systems in Human Disease and Therapeutics Cambridge, Massachusetts: Harvard University Press; 2017. Chapter 12. 500p.

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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. PLoS Comput Biol. 2017 May;13(5):e1005489. doi: 10.1371/journal.pcbi.1005489. eCollection 2017 May. PubMed PMID: 28520713; PubMed Central PMCID: PMC5453602.

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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. Cell Host Microbe. 2017 Jun 14;21(6):695-706.e5. doi: 10.1016/j.chom.2017.05.012. PubMed PMID: 28618268; PubMed Central PMCID: PMC5533182.

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Porszasz J, Carraro N, Cao R, Gore A, Ma S, Jiang T, Maltais F, Ferguson GT, O'Donnell DE, Shaikh A, Rossiter HB, Casaburi R. Effect of tiotropium on spontaneous expiratory flow-volume curves during exercise in GOLD 1-2 COPD. Respir Physiol Neurobiol. 2018 May;251:8-15. doi: 10.1016/j.resp.2018.02.006. Epub 2018 Feb 10. PubMed PMID: 29438808.

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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. Bacterial Factors That Predict Relapse after Tuberculosis Therapy. N Engl J Med. 2018 Aug 30;379(9):823-833. doi: 10.1056/NEJMoa1715849. PubMed PMID: 30157391; PubMed Central PMCID: PMC6317071.

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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. Clin Microbiol Rev. 2018 Oct;31(4). doi: 10.1128/CMR.00021-18. Print 2018 Oct. Review. PubMed PMID: 30021818; PubMed Central PMCID: PMC6148193.

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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. Proc Natl Acad Sci U S A. 2019 Sep 24;116(39):19665-19674. doi: 10.1073/pnas.1907631116. Epub 2019 Sep 5. PubMed PMID: 31488707; PubMed Central PMCID: PMC6765255.

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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. mBio. 2019 Nov 12;10(6). doi: 10.1128/mBio.02627-19. PubMed PMID: 31719182; PubMed Central PMCID: PMC6851285.

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Wang Y, Ma S, Ruzzo WL. Spatial modeling of prostate cancer metabolic gene expression reveals extensive heterogeneity and selective vulnerabilities. Sci Rep. 2020 Feb 26;10(1):3490. doi: 10.1038/s41598-020-60384-w. PubMed PMID: 32103057; PubMed Central PMCID: PMC7044328.

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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. Antimicrob Agents Chemother. 2020 Aug 20;64(9). doi: 10.1128/AAC.00213-20. Print 2020 Aug 20. PubMed PMID: 32571828; PubMed Central PMCID: PMC7449195.

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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. Annu Rev Genet. 2020 Nov 23;54:511-537. doi: 10.1146/annurev-genet-022820-085940. Epub 2020 Sep 14. Review. PubMed PMID: 32926793.

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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. Nat Microbiol. 2021 Jan;6(1):44-50. doi: 10.1038/s41564-020-00810-x. Epub 2020 Nov 16. PubMed PMID: 33199862; PubMed Central PMCID: PMC8331221.

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Ma S, Jones RM Jr, Gleason NS, Farrow-Johnson J, Sherman DR. Experimental and Computational Workflow for RNA Sequencing in Mycobacterium tuberculosis : From Total RNA to Differentially Expressed Genes. Methods Mol Biol. 2021;2314:481-512. doi: 10.1007/978-1-0716-1460-0_21. PubMed PMID: 34235667.

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Lovey A, Verma S, Kaipilyawar V, Ribeiro-Rodrigues R, Husain S, Palaci M, Dietze R, Ma S, Morrison RD, Sherman DR, Ellner JJ, Salgame P. Early alveolar macrophage response and IL-1R-dependent T cell priming determine transmissibility of Mycobacterium tuberculosis strains. Nat Commun. 2022 Feb 16;13(1):884. doi: 10.1038/s41467-022-28506-2. PubMed PMID: 35173157; PubMed Central PMCID: PMC8850437.

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Frando A, Boradia V, Gritsenko M, Beltejar C, Day L, Sherman DR, Ma S, Jacobs JM, Grundner C. The Mycobacterium tuberculosis protein O-phosphorylation landscape. Nat Microbiol. 2023 Mar;8(3):548-561. doi: 10.1038/s41564-022-01313-7. Epub 2023 Jan 23. PubMed PMID: 36690861.