My Bibliography

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Ambati S, Pham T, Lewis ZA, Lin X, Meagher RB. DC-SIGN targets amphotericin B-loaded liposomes to diverse pathogenic fungi. Fungal Biol Biotechnol. 2021 Dec 24;8(1):22. doi: 10.1186/s40694-021-00126-3. PubMed PMID: 34952645; PubMed Central PMCID: PMC8709943.

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Ambati S, Pham T, Lewis ZA, Lin X, Meagher RB. DectiSomes: Glycan Targeting of Liposomal Drugs Improves the Treatment of Disseminated Candidiasis. Antimicrob Agents Chemother. 2022 Jan 18;66(1):e0146721. doi: 10.1128/AAC.01467-21. Epub 2021 Oct 11. PubMed PMID: 34633846; PubMed Central PMCID: PMC8765427.

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Meagher RB, Lewis ZA, Ambati S, Lin X. Aiming for a bull's-eye: Targeting antifungals to fungi with dectin-decorated liposomes. PLoS Pathog. 2021 Jul;17(7):e1009699. doi: 10.1371/journal.ppat.1009699. eCollection 2021 Jul. Review. PubMed PMID: 34293050; PubMed Central PMCID: PMC8297870.

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Ferraro AR, Ameri AJ, Lu Z, Kamei M, Schmitz RJ, Lewis ZA. Chromatin accessibility profiling in Neurospora crassa reveals molecular features associated with accessible and inaccessible chromatin. BMC Genomics. 2021 Jun 19;22(1):459. doi: 10.1186/s12864-021-07774-0. PubMed PMID: 34147068; PubMed Central PMCID: PMC8214302.

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Kamei M, Ameri AJ, Ferraro AR, Bar-Peled Y, Zhao F, Ethridge CL, Lail K, Amirebrahimi M, Lipzen A, Ng V, Grigoriev IV, Schmitz RJ, Liu Y, Lewis ZA. IMITATION SWITCH is required for normal chromatin structure and gene repression in PRC2 target domains. Proc Natl Acad Sci U S A. 2021 Jan 26;118(4). doi: 10.1073/pnas.2010003118. PubMed PMID: 33468665; PubMed Central PMCID: PMC7848606.

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Ma Y, Zhang X, Alsaidan OA, Yang X, Sulejmani E, Zha J, Beharry Z, Huang H, Bartlett M, Lewis Z, Cai H. Long-Chain Acyl-CoA Synthetase 4-Mediated Fatty Acid Metabolism Sustains Androgen Receptor Pathway-Independent Prostate Cancer. Mol Cancer Res. 2021 Jan;19(1):124-135. doi: 10.1158/1541-7786.MCR-20-0379. Epub 2020 Oct 19. PubMed PMID: 33077484; PubMed Central PMCID: PMC7785683.

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Courtney AJ, Kamei M, Ferraro AR, Gai K, He Q, Honda S, Lewis ZA. Normal Patterns of Histone H3K27 Methylation Require the Histone Variant H2A.Z in Neurospora crassa. Genetics. 2020 Sep;216(1):51-66. doi: 10.1534/genetics.120.303442. Epub 2020 Jul 10. PubMed PMID: 32651262; PubMed Central PMCID: PMC7463285.

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Lin J, Zhao Y, Ferraro AR, Yang E, Lewis ZA, Lin X. Transcription factor Znf2 coordinates with the chromatin remodeling SWI/SNF complex to regulate cryptococcal cellular differentiation. Commun Biol. 2019;2:412. doi: 10.1038/s42003-019-0665-2. eCollection 2019. PubMed PMID: 31754642; PubMed Central PMCID: PMC6856107.

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Ambati S, Ellis EC, Lin J, Lin X, Lewis ZA, Meagher RB. Dectin-2-Targeted Antifungal Liposomes Exhibit Enhanced Efficacy. mSphere. 2019 Oct 30;4(5). doi: 10.1128/mSphere.00715-19. PubMed PMID: 31666315; PubMed Central PMCID: PMC6821932.

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Schmitz RJ, Lewis ZA, Goll MG. DNA Methylation: Shared and Divergent Features across Eukaryotes. Trends Genet. 2019 Nov;35(11):818-827. doi: 10.1016/j.tig.2019.07.007. Epub 2019 Aug 6. Review. PubMed PMID: 31399242; PubMed Central PMCID: PMC6825889.

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Laue K, Rajshekar S, Courtney AJ, Lewis ZA, Goll MG. The maternal to zygotic transition regulates genome-wide heterochromatin establishment in the zebrafish embryo. Nat Commun. 2019 Apr 4;10(1):1551. doi: 10.1038/s41467-019-09582-3. PubMed PMID: 30948728; PubMed Central PMCID: PMC6449393.

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Ambati S, Ferarro AR, Kang SE, Lin J, Lin X, Momany M, Lewis ZA, Meagher RB. Dectin-1-Targeted Antifungal Liposomes Exhibit Enhanced Efficacy. mSphere. 2019 Feb 13;4(1). doi: 10.1128/mSphere.00025-19. PubMed PMID: 30760610; PubMed Central PMCID: PMC6374590.

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Ferraro AR, Lewis ZA. ChIP-Seq Analysis in Neurospora crassa. Methods Mol Biol. 2018;1775:241-250. doi: 10.1007/978-1-4939-7804-5_19. PubMed PMID: 29876822; PubMed Central PMCID: PMC10911069.

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Lewis ZA. Polycomb Group Systems in Fungi: New Models for Understanding Polycomb Repressive Complex 2. Trends Genet. 2017 Mar;33(3):220-231. doi: 10.1016/j.tig.2017.01.006. Epub 2017 Feb 11. Review. PubMed PMID: 28196760.

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Gacek-Matthews A, Berger H, Sasaki T, Wittstein K, Gruber C, Lewis ZA, Strauss J. KdmB, a Jumonji Histone H3 Demethylase, Regulates Genome-Wide H3K4 Trimethylation and Is Required for Normal Induction of Secondary Metabolism in Aspergillus nidulans. PLoS Genet. 2016 Aug;12(8):e1006222. doi: 10.1371/journal.pgen.1006222. eCollection 2016 Aug. PubMed PMID: 27548260; PubMed Central PMCID: PMC4993369.

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Seymour M, Ji L, Santos AM, Kamei M, Sasaki T, Basenko EY, Schmitz RJ, Zhang X, Lewis ZA. Histone H1 Limits DNA Methylation in Neurospora crassa. G3 (Bethesda). 2016 Jul 7;6(7):1879-89. doi: 10.1534/g3.116.028324. PubMed PMID: 27172195; PubMed Central PMCID: PMC4938642.

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Basenko EY, Kamei M, Ji L, Schmitz RJ, Lewis ZA. The LSH/DDM1 Homolog MUS-30 Is Required for Genome Stability, but Not for DNA Methylation in Neurospora crassa. PLoS Genet. 2016 Jan;12(1):e1005790. doi: 10.1371/journal.pgen.1005790. eCollection 2016 Jan. PubMed PMID: 26771905; PubMed Central PMCID: PMC4714748.

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Basenko EY, Sasaki T, Ji L, Prybol CJ, Burckhardt RM, Schmitz RJ, Lewis ZA. Genome-wide redistribution of H3K27me3 is linked to genotoxic stress and defective growth. Proc Natl Acad Sci U S A. 2015 Nov 17;112(46):E6339-48. doi: 10.1073/pnas.1511377112. Epub 2015 Nov 2. PubMed PMID: 26578794; PubMed Central PMCID: PMC4655558.

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Adhvaryu KK, Gessaman JD, Honda S, Lewis ZA, Grisafi PL, Selker EU. The cullin-4 complex DCDC does not require E3 ubiquitin ligase elements to control heterochromatin in Neurospora crassa. Eukaryot Cell. 2015 Jan;14(1):25-8. doi: 10.1128/EC.00212-14. Epub 2014 Oct 31. PubMed PMID: 25362134; PubMed Central PMCID: PMC4279019.

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Ji L, Sasaki T, Sun X, Ma P, Lewis ZA, Schmitz RJ. Methylated DNA is over-represented in whole-genome bisulfite sequencing data. Front Genet. 2014;5:341. doi: 10.3389/fgene.2014.00341. eCollection 2014. PubMed PMID: 25374580; PubMed Central PMCID: PMC4204604.

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Sasaki T, Lynch KL, Mueller CV, Friedman S, Freitag M, Lewis ZA. Heterochromatin controls γH2A localization in Neurospora crassa. Eukaryot Cell. 2014 Aug;13(8):990-1000. doi: 10.1128/EC.00117-14. Epub 2014 May 30. PubMed PMID: 24879124; PubMed Central PMCID: PMC4135800.

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Jamieson K, Rountree MR, Lewis ZA, Stajich JE, Selker EU. Regional control of histone H3 lysine 27 methylation in Neurospora. Proc Natl Acad Sci U S A. 2013 Apr 9;110(15):6027-32. doi: 10.1073/pnas.1303750110. Epub 2013 Mar 25. PubMed PMID: 23530226; PubMed Central PMCID: PMC3625340.

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Honda S, Lewis ZA, Shimada K, Fischle W, Sack R, Selker EU. Heterochromatin protein 1 forms distinct complexes to direct histone deacetylation and DNA methylation. Nat Struct Mol Biol. 2012 Apr 15;19(5):471-7, S1. doi: 10.1038/nsmb.2274. PubMed PMID: 22504884; PubMed Central PMCID: PMC4957970.

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Belden WJ, Lewis ZA, Selker EU, Loros JJ, Dunlap JC. CHD1 remodels chromatin and influences transient DNA methylation at the clock gene frequency. PLoS Genet. 2011 Jul;7(7):e1002166. doi: 10.1371/journal.pgen.1002166. Epub 2011 Jul 21. PubMed PMID: 21811413; PubMed Central PMCID: PMC3140994.

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Lewis ZA, Adhvaryu KK, Honda S, Shiver AL, Knip M, Sack R, Selker EU. DNA methylation and normal chromosome behavior in Neurospora depend on five components of a histone methyltransferase complex, DCDC. PLoS Genet. 2010 Nov 4;6(11):e1001196. doi: 10.1371/journal.pgen.1001196. PubMed PMID: 21079689; PubMed Central PMCID: PMC2973830.

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Lee HC, Li L, Gu W, Xue Z, Crosthwaite SK, Pertsemlidis A, Lewis ZA, Freitag M, Selker EU, Mello CC, Liu Y. Diverse pathways generate microRNA-like RNAs and Dicer-independent small interfering RNAs in fungi. Mol Cell. 2010 Jun 25;38(6):803-14. doi: 10.1016/j.molcel.2010.04.005. Epub 2010 Apr 22. PubMed PMID: 20417140; PubMed Central PMCID: PMC2902691.

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Lewis ZA, Adhvaryu KK, Honda S, Shiver AL, Selker EU. Identification of DIM-7, a protein required to target the DIM-5 H3 methyltransferase to chromatin. Proc Natl Acad Sci U S A. 2010 May 4;107(18):8310-5. doi: 10.1073/pnas.1000328107. Epub 2010 Apr 19. PubMed PMID: 20404183; PubMed Central PMCID: PMC2889519.

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Honda S, Lewis ZA, Huarte M, Cho LY, David LL, Shi Y, Selker EU. The DMM complex prevents spreading of DNA methylation from transposons to nearby genes in Neurospora crassa. Genes Dev. 2010 Mar 1;24(5):443-54. doi: 10.1101/gad.1893210. Epub 2010 Feb 5. PubMed PMID: 20139222; PubMed Central PMCID: PMC2827840.

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Lewis ZA, Honda S, Khlafallah TK, Jeffress JK, Freitag M, Mohn F, Schübeler D, Selker EU. Relics of repeat-induced point mutation direct heterochromatin formation in Neurospora crassa. Genome Res. 2009 Mar;19(3):427-37. doi: 10.1101/gr.086231.108. Epub 2008 Dec 17. PubMed PMID: 19092133; PubMed Central PMCID: PMC2661801.

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Baird NA, Etter PD, Atwood TS, Currey MC, Shiver AL, Lewis ZA, Selker EU, Cresko WA, Johnson EA. Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS One. 2008;3(10):e3376. doi: 10.1371/journal.pone.0003376. Epub 2008 Oct 13. PubMed PMID: 18852878; PubMed Central PMCID: PMC2557064.

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Lewis ZA, Shiver AL, Stiffler N, Miller MR, Johnson EA, Selker EU. High-density detection of restriction-site-associated DNA markers for rapid mapping of mutated loci in Neurospora. Genetics. 2007 Oct;177(2):1163-71. doi: 10.1534/genetics.107.078147. Epub 2007 Jul 29. PubMed PMID: 17660537; PubMed Central PMCID: PMC2034621.

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de Paula RM, Lewis ZA, Greene AV, Seo KS, Morgan LW, Vitalini MW, Bennett L, Gomer RH, Bell-Pedersen D. Two circadian timing circuits in Neurospora crassa cells share components and regulate distinct rhythmic processes. J Biol Rhythms. 2006 Jun;21(3):159-68. doi: 10.1177/0748730406288338. PubMed PMID: 16731655.

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Xie X, Wilkinson HH, Correa A, Lewis ZA, Bell-Pedersen D, Ebbole DJ. Transcriptional response to glucose starvation and functional analysis of a glucose transporter of Neurospora crassa. Fungal Genet Biol. 2004 Dec;41(12):1104-19. doi: 10.1016/j.fgb.2004.08.009. PubMed PMID: 15531214.

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Correa A, Lewis ZA, Greene AV, March IJ, Gomer RH, Bell-Pedersen D. Multiple oscillators regulate circadian gene expression in Neurospora. Proc Natl Acad Sci U S A. 2003 Nov 11;100(23):13597-602. doi: 10.1073/pnas.2233734100. Epub 2003 Nov 3. PubMed PMID: 14597725; PubMed Central PMCID: PMC263859.

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Lewis ZA, Correa A, Schwerdtfeger C, Link KL, Xie X, Gomer RH, Thomas T, Ebbole DJ, Bell-Pedersen D. Overexpression of White Collar-1 (WC-1) activates circadian clock-associated genes, but is not sufficient to induce most light-regulated gene expression in Neurospora crassa. Mol Microbiol. 2002 Aug;45(4):917-31. doi: 10.1046/j.1365-2958.2002.03074.x. PubMed PMID: 12180913.

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Bell-Pedersen D, Lewis ZA, Loros JJ, Dunlap JC. The Neurospora circadian clock regulates a transcription factor that controls rhythmic expression of the output eas(ccg-2) gene. Mol Microbiol. 2001 Aug;41(4):897-909. doi: 10.1046/j.1365-2958.2001.02558.x. PubMed PMID: 11532152.

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Shrode LB, Lewis ZA, White LD, Bell-Pedersen D, Ebbole DJ. vvd is required for light adaptation of conidiation-specific genes of Neurospora crassa, but not circadian conidiation. Fungal Genet Biol. 2001 Apr;32(3):169-81. doi: 10.1006/fgbi.2001.1264. PubMed PMID: 11343403.