Publications

Grouped By Research Topic

FUNCTION OF KERATINS IN CELL ADHESION AND PROLIFERATION

34.   Dong Y, Elgerbi A, Xie B, Choy JS, Sivasankar S. Desmoplakin is a desmosomal mechanosensor. (Under Review April 2024)

33.   Del Puerto HL, Miranda AP, Qutob D, Ferreira E, Silva F, Lima BM, Cervalho BA, Souza BR, Gutseit E, Castro DC, Pozzolini ET, Duarte NO, Lopes T, Taborda D, Quirino SM, Elgerbi A, Choy JS, Underwood A. Clinical correlation of transcription factor SOX3 in cancer: Unveiling its role in tumorigenesis. Genes 2024 Jun 13;15(6):777. doi: 10.3390/genes15060777

MECHANISMS OF SARS-COV-2 PATHOGENESIS AND DRUG RESISTANCE

32.   Liang S, Bao C, Yang Z, iu S, Cao W, Schwantes-An TH, Choy JS, Naidu S, Luo A, Yin W, Black S Wang J, Ran P, Deai AA and Tang H. SARS-CoV-2 spike protein induces IL-18-mediated cardiopulmonary inflammation via reduced mitophagy. Signal Transduct Target Ther. (Accepted Feb 2023)

31.   Hu Y, Lewandowski EM, Tan H, Zhang X, Morgan RT, Zhang X, Jacobs LMC, Butler SG, Gongora MV, Choy JS, Deng X, Chen Y, Wang J. Naturally occurring mutations of SARS-CoV-2 main protease confer drug resistance to nirmatrelvir. bioRxiv. 2022 Sep 6;. doi: 10.1101/2022.06.28.497978. (under review at ACS)

30.   Ou J, Lewandowski EM, Hu Y, Lipinski AA, Morgan RT, Jacobs LMC, Zhang X, Bikowitz MJ, Langlais P, Tan H, Wang J, Chen Y, Choy JS*. A yeast-based system to study SARS-CoV-2 M pro structure and to identify nirmatrelvir resistant mutations. bioRxiv. 2022 Aug 8;. doi: 10.1101/2022.08.06.503039. (under review at PLoS Pathogens)

IDENTIFYING MICROBIAL TARGETS OF PHARMACEUTICALS AND RESISTANCE

MECHANISMS

29.   Ou J, Elizalde P, Guo HB, Qin H, Tobe BTD, Choy JS*. TCA and SSRI Antidepressants Exert Selection Pressure for Efflux-Dependent Antibiotic Resistance Mechanisms in Escherichia coli. mBio. 2022 Dec 20;13(6):e0219122. doi: 10.1128/mbio.02191-22. Epub 2022 Nov 14 (Selected by editors as a “Highlighted” article)

28.   Alhumaidi M, Nentwig LM, Rahman H, Schmitt L, Rudrow A, Harris A, Dillon C, Restrepo L, Lamping E, Arya N, Ambudkar SV, Choy JS, Golin J. Residues forming the gating regions of asymmetric multidrug transporter Pdr5 also play roles in conformational switching and protein folding. J Biol Chem. 2022 Dec;298(12):102689. doi: 10.1016/j.jbc.2022.102689. Epub 2022 Nov 10.

27.   Rahman H, Rudrow A, Carneglia J, Joly SSP, Nicotera D, Naldrett M, Choy JS, Ambudkar SV, Golin J. Nonsynonymous Mutations in Linker-2 of the Pdr5 Multidrug Transporter Identify a New RNA Stability Element. G3 (Bethesda). 2020 Jan 7;10(1):357-369. doi: 10.1534/g3.119.400863.

26.   Rahman H, Carneglia J, Lausten M, Robertello M, Choy JS, Golin J. Robust, pleiotropic drug resistance 5 (Pdr5)-mediated multidrug resistance is vigorously maintained in Saccharomyces cerevisiae cells during glucose and nitrogen limitation. FEMS Yeast Res. 2018 Jun 1;18(4). doi: 10.1093/femsyr/foy029.

ENGINEERING MICROFLUIDIC PLATFORMS TO STUDY THE DYNAMICS OF

MICROBIAL COMMUNITIES

25.   Pham LHP, Ly KL, Colon-Ascanio M, Ou J, Wang H, Lee SW, Wang Y, Choy JS*, Phillips KS, Luo X. Dissolvable alginate hydrogel-based biofilm microreactors for antibiotic susceptibility assays. Biofilm. 2023 Dec;5:100103. doi: 10.1016/j.bioflm.2022.100103.

24.   Pham LHP, Colon-Ascanio M, Ou J, Ly K, Hu P, Choy JS*, Luo X. Probing mutual interactions between Pseudomonas aeruginosa and Candida albicans in a biofabricated membrane-based microfluidic platform. Lab Chip. 2022 Nov 8;22(22):4349-4358. doi: 10.1039/d2lc00728b.

23.   Hu P, Raub CB, Choy JS, Luo X. Modulating the properties of flow-assembled chitosan membranes in microfluidics with glutaraldehyde crosslinking. J Mater Chem B. 2020 Mar 25;8(12):2519-2529. doi: 10.1039/c9tb02527h.

22.   Vo T, Shah SB, Choy JS*, Luo X. Chemotropism among populations of yeast cells with spatiotemporal resolution in a biofabricated microfluidic platform. Biomicrofluidics. 2020 Jan;14(1):014108. doi: 10.1063/1.5128739. eCollection 2020 Jan.

21.   Pham PL, Rooholghodos SA, Choy JS*, Luo X. Constructing Synthetic Ecosystems with Biopolymer Fluitrodes. Advanced biosystems. 2018 February. doi: 10.1002/adbi.201700180.

20.   Luo X, Vo T, Jambi F, Pham P, Choy JS. Microfluidic partition with in situ biofabricated semipermeable biopolymer membranes for static gradient generation. Lab Chip. 2016 Sep 21;16(19):3815-3823. doi: 10.1039/c6lc00742b.

BIOPHYSICS OF CHROMATIN AND GENE EXPRESSSION AT SINGLE MOLECULE AND

SINGLE CELL RESOLUTION

19.   Wadsworth GM, Parikh RY, Choy JS, Kim HD. mRNA detection in budding yeast with single fluorophores. Nucleic Acids Res. 2017 Sep 6;45(15):e141. doi: 10.1093/nar/gkx568.

18.   Choy JS, Lee TH. Structural dynamics of nucleosomes at single-molecule resolution. Trends Biochem Sci. 2012 Oct;37(10):425-35. doi: 10.1016/j.tibs.2012.06.006. Epub 2012 Jul 23.

17.   Choy JS, Wei S, Lee JY, Tan S, Chu S, Lee TH. DNA methylation increases nucleosome compaction and rigidity. J Am Chem Soc. 2010 Feb 17;132(6):1782-3. doi: 10.1021/ja910264z.

GENOME-WIDE STUDIES OF CHROMOSOME SEGREGATION

16.   Choy JS*, Qadri B, Henry L, Shroff K, Bifarin O, Basrai MA. A Genome-Wide Screen with Nicotinamide to Identify Sirtuin-Dependent Pathways in Saccharomyces cerevisiae. G3 (Bethesda). 2015 Dec 8;6(2):485-94. doi: 10.1534/g3.115.022244.

15.   Choy JS, O'Toole E, Schuster BM, Crisp MJ, Karpova TS, McNally JG, Winey M, Gardner MK, Basrai MA. Genome-wide haploinsufficiency screen reveals a novel role for γ-TuSC in spindle organization and genome stability. Mol Biol Cell. 2013 Sep;24(17):2753-63. doi: 10.1091/mbc.E12-12-0902. Epub 2013 Jul 3.

14.   Choy JS, Acuña R, Au WC, Basrai MA. A role for histone H4K16 hypoacetylation in Saccharomyces cerevisiae kinetochore function. Genetics. 2011 Sep;189(1):11-21. doi: 10.1534/genetics.111.130781. Epub 2011 Jun 6.

13.   Magtanong L, Ho CH, Barker SL, Jiao W, Baryshnikova A, Bahr S, Smith AM, Heisler LE, Choy JS, Kuzmin E, Andrusiak K, Kobylianski A, Li Z, Costanzo M, Basrai MA, Giaever G, Nislow C, Andrews B, Boone C. Dosage suppression genetic interaction networks enhance functional wiring diagrams of the cell. Nat Biotechnol. 2011 May 15;29(6):505-11. doi: 10.1038/nbt.1855.

ELUCIDATING MECHANISMS OF CHROMOSOME SEGREGATION

12.   Shah SB, Parmiter D, Constantine C, Elizalde P, Naldrett M, Karpova TS, Choy JS*. Glucose Signaling Is Connected to Chromosome Segregation Through Protein Kinase A Phosphorylation of the Dam1 Kinetochore Subunit in Saccharomycescerevisiae. Genetics. 2019 Feb;211(2):531-547. doi: 10.1534/genetics.118.301727. Epub 2018 Dec 13. (Selected by editors as a “Highlighted” article)

11.   Boeckmann L, Takahashi Y, Au WC, Mishra PK, Choy JS, Dawson AR, Szeto MY, Waybright TJ, Heger C, McAndrew C, Goldsmith PK, Veenstra TD, Baker RE, Basrai MA. Phosphorylation of centromeric histone H3 variant regulates chromosome segregation in Saccharomyces cerevisiae. Mol Biol Cell. 2013 Jun;24(12):2034-44. doi: 10.1091/mbc.E12-12-0893. Epub 2013 May 1.

10.   Choy JS, Mishra PK, Au WC, Basrai MA. Insights into assembly and regulation of centromeric chromatin in Saccharomyces cerevisiae. Biochim Biophys Acta. 2012 Jul;1819(7):776-83. doi: 10.1016/j.bbagrm.2012.02.008. Epub 2012 Feb 16.

9.    Mishra PK, Au WC, Choy JS, Kuich PH, Baker RE, Foltz DR, Basrai MA. Misregulation of Scm3p/HJURP causes chromosome instability in Saccharomyces cerevisiae and human cells. PLoS Genet. 2011 Sep;7(9):e1002303. doi: 10.1371/journal.pgen.1002303. Epub 2011 Sep 29.

MODELING DISEASES USING STEM CELLS AND YEAST

8.    Qanash H, Li Y, Smith RH, Linask K, Young-Baird S, Hakami W, Keyvanfar K, Choy JS, Zou J, Larochelle A. Eltrombopag Improves Erythroid Differentiation in a Human Induced Pluripotent Stem Cell Model of Diamond Blackfan Anemia. Cells. 2021 Mar 26;10(4). doi: 10.3390/cells10040734.

7.    Vander Heiden MG, Choy JS, VanderWeele DJ, Brace JL, Harris MH, Bauer DE, Prange B, Kron SJ, Thompson CB, Rudin CM. Bcl-x(L) complements Saccharomyces cerevisiae genes that facilitate the switch from glycolytic to oxidative metabolism. J Biol Chem. 2002 Nov 22;277(47):44870-6. doi: 10.1074/jbc.M204888200. Epub 2002 Sep 19.

EPIGENETIC REGULATION OF GENOME INTEGRITY AND CELL PROLIFERATION IN

HUMAN AND YEAST CELLS

6.    Tobe BT, Kitazono AA, Garcia JS, Gerber RA, Bevis BJ, Choy JS, Chasman D, Kron SJ. Morphogenesis signaling components influence cell cycle regulation by cyclin dependent kinase. Cell Div. 2009 Jul 1;4:12. doi: 10.1186/1747-1028-4-12.

5.    Taneja N, Davis M, Choy JS, Beckett MA, Singh R, Kron SJ, Weichselbaum RR. Histone H2AX phosphorylation as a predictor of radiosensitivity and target for radiotherapy. J Biol Chem. 2004 Jan 16;279(3):2273-80. doi: 10.1074/jbc.M310030200. Epub 2003 Oct 15.

4.    Choy JS, Kron SJ. NuA4 subunit Yng2 function in intra-S-phase DNA damage response. Mol Cell Biol. 2002 Dec;22(23):8215-25. doi: 10.1128/MCB.22.23.8215-8225.2002.

3.    Choy JS, Tobe BT, Huh JH, Kron SJ. Yng2p-dependent NuA4 histone H4 acetylation activity is required for mitotic and meiotic progression. J Biol Chem. 2001 Nov 23;276(47):43653-62. doi: 10.1074/jbc.M102531200. Epub 2001 Sep 5.

MECHANISMS OF HYPERTENSION IN RAT MODELS

2.    Madden JA, Keller PA, Choy JS, Alvarez TA, Hacker AD. L-arginine-related responses to pressure and vasoactive agents in monocrotaline-treated rat pulmonary arteries. J Appl Physiol (1985). 1995 Aug;79(2):589-93. doi: 10.1152/jappl.1995.79.2.589.

1.    Madden JA, Keller PA, Effros RM, Seavitte C, Choy JS, Hacker AD. Responses to pressure and vasoactive agents by isolated pulmonary arteries from monocrotaline-treated rats. J Appl Physiol (1985). 1994 Apr;76(4):1589-93. doi: 10.1152/jappl.1994.76.4.1589.

(*Corresponding author)