My Bibliography

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Najnin T, Saimon SH, Zand M, Adnan N, Liu Z, Huang TH, Ruan J. An Integrated Approach to Knowledge and Prediction Modeling of Breast Cancer Metastasis Using Gene Regulatory Networks. IEEE Trans Comput Biol Bioinform. 2026 May-Jun;23(3):985-995. doi: 10.1109/TCBBIO.2025.3647659. PubMed PMID: 41433163; PubMed Central PMCID: PMC13344502.

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Kleynhans L, Kunsevi-Kilola C, Tshivhula H, Webber T, Keyser A, Prins N, Snyders CI, Shabangu A, Rozot V, Kidd M, Zhang H, Cai H, Wang Y, Ewing AD, Malherbe ST, Azad AK, Arnett E, Restrepo BI, Schlesinger LS, Ronacher K. Human alveolar macrophage function is impaired in tuberculosis contacts with diabetes. EBioMedicine. 2025 Dec;122:106050. doi: 10.1016/j.ebiom.2025.106050. Epub 2025 Dec 1. PubMed PMID: 41330113; PubMed Central PMCID: PMC12719684.

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Stanton V, Himes B, Mejia-Santana A, Eppinger M, Romo J, Xing J, Zhulin IB, Cai H, Wang Y, Inniss Nl, Minasov G, Satchell KJF, Klose KE. The PAS domain of the polarly localized histidine kinase FlrB in Vibrio cholerae controls class III flagellar transcription and contributes to intestinal colonization. mBio. 2025 Nov 12;16(11):e0237925. doi: 10.1128/mbio.02379-25. Epub 2025 Sep 22. PubMed PMID: 40981415; PubMed Central PMCID: PMC12607845.

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Lin CA, Lin C, Rhodes CT, Moseley MC, Wang Y, Berger MS. Takeaways from meta-analysis: indications of combinational treatments for glioblastoma. J Neurooncol. 2025 Dec;175(3):1199-1209. doi: 10.1007/s11060-025-05205-8. Epub 2025 Aug 21. PubMed PMID: 40839241.

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Shen-Gunther J, Xia Q, Cai H, Wang Y. Cervicovaginal Microbiome and HPV: A Standardized Approach to 16S/ITS NGS and Microbial Community Profiling for Viral Association. Int J Mol Sci. 2025 Aug 21;26(16). doi: 10.3390/ijms26168090. PubMed PMID: 40869406; PubMed Central PMCID: PMC12386612.

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Sadee W, Cheeseman IH, Papp A, Pietrzak M, Seweryn M, Zhou X, Lin S, Williams AM, Wewers MD, Curry HM, Zhang H, Cai H, Kunsevi-Kilola C, Tshivhula H, Walzl G, Restrepo BI, Kleynhans L, Ronacher K, Wang Y, Arnett E, Azad AK, Schlesinger LS. Human alveolar macrophage response to Mycobacterium tuberculosis: immune characteristics underlying large inter-individual variability. Commun Biol. 2025 Jun 23;8(1):950. doi: 10.1038/s42003-025-08337-9. PubMed PMID: 40550843; PubMed Central PMCID: PMC12185700.

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Shen-Gunther J, Cai H, Wang Y. Genomic and Antigenic Differences Between Monkeypox Virus and Vaccinia Vaccines: Insights and Implications for Vaccinology. Int J Mol Sci. 2025 Feb 8;26(4). doi: 10.3390/ijms26041428. PubMed PMID: 40003895; PubMed Central PMCID: PMC11855751.

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Rorex C, Cardona SM, Church KA, Rodriguez D, Vanegas D, Saldivar RA, El-Sheikh A, Wang Y, Gyoneva S, Cotleur AC, Cardona AE. CX3CR1-Fractalkine Dysregulation Affects Retinal GFAP Expression, Inflammatory Gene Induction, and LPS Response in a Mouse Model of Hypoxic Retinopathy. Int J Mol Sci. 2025 Jan 28;26(3). doi: 10.3390/ijms26031131. PubMed PMID: 39940901; PubMed Central PMCID: PMC11817233.

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Olmo-Fontánez AM, Allué-Guardia A, Garcia-Vilanova A, Glenn J, Wang S-H, Merritt RE, Schlesinger LS, Turner J, Wang Y, Torrelles JB. Impact of the elderly lung mucosa on Mycobacterium tuberculosis transcriptional adaptation during infection of alveolar epithelial cells. Microbiol Spectr. 2024 Dec 5;12(12):e0179024. doi: 10.1128/spectrum.01790-24. Epub 2024 Nov 8. PubMed PMID: 39513699; PubMed Central PMCID: PMC11619525.

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Rhodes CT, Wang Y, Lin CA. Differential Gene Expression in MRI-classified Glioblastoma. bioRxiv. 2024 Jun 27;. doi: 10.1101/2024.06.21.600091. PubMed PMID: 38979247; PubMed Central PMCID: PMC11230240.

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Headley CA, Gautam S, Olmo-Fontanez A, Garcia-Vilanova A, Dwivedi V, Akhter A, Schami A, Chiem K, Ault R, Zhang H, Cai H, Whigham A, Delgado J, Hicks A, Tsao PS, Gelfond J, Martinez-Sobrido L, Wang Y, Torrelles JB, Turner J. Extracellular Delivery of Functional Mitochondria Rescues the Dysfunction of CD4(+) T Cells in Aging. Adv Sci (Weinh). 2024 Feb;11(5):e2303664. doi: 10.1002/advs.202303664. Epub 2023 Nov 21. PubMed PMID: 37990641; PubMed Central PMCID: PMC10837346.

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Allué-Guardia A, Garcia-Vilanova A, Schami AM, Olmo-Fontánez AM, Hicks A, Peters J, Maselli DJ, Wewers MD, Wang Y, Torrelles JB. Exposure of Mycobacterium tuberculosis to human alveolar lining fluid shows temporal and strain-specific adaptation to the lung environment. bioRxiv. 2023 Sep 28;. doi: 10.1101/2023.09.27.559381. PubMed PMID: 37808780; PubMed Central PMCID: PMC10557635.

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Piergallini TJ, Scordo JM, Allué-Guardia A, Pino PA, Zhang H, Cai H, Wang Y, Schlesinger LS, Torrelles JB, Turner J. Acute inflammation alters lung lymphocytes and potentiates innate-like behavior in young mouse lung CD8 T cells, resembling lung CD8 T cells from old mice. J Leukoc Biol. 2023 Sep 1;114(3):237-249. doi: 10.1093/jleuko/qiad060. PubMed PMID: 37196159; PubMed Central PMCID: PMC10473256.

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Shen-Gunther J, Gunther RS, Cai H, Wang Y. A Customized Human Mitochondrial DNA Database (hMITO DB v1.0) for Rapid Sequence Analysis, Haplotyping and Geo-Mapping. Int J Mol Sci. 2023 Aug 31;24(17). doi: 10.3390/ijms241713505. PubMed PMID: 37686313; PubMed Central PMCID: PMC10488239.

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Pahari S, Arnett E, Simper J, Azad A, Guerrero-Arguero I, Ye C, Zhang H, Cai H, Wang Y, Lai Z, Jarvis N, Lumbreras M, Maselli DJ, Peters J, Torrelles JB, Martinez-Sobrido L, Schlesinger LS. A new tractable method for generating human alveolar macrophage-like cells in vitro to study lung inflammatory processes and diseases. mBio. 2023 Aug 31;14(4):e0083423. doi: 10.1128/mbio.00834-23. Epub 2023 Jun 8. PubMed PMID: 37288969; PubMed Central PMCID: PMC10470505.

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Sadee W, Cheeseman IH, Papp A, Pietrzak M, Seweryn M, Zhou X, Lin S, Williams AM, Wewers MD, Curry HM, Zhang H, Cai H, Kunsevi-Kilola C, Tshivhula H, Walzl G, Restrepo BI, Kleynhans L, Ronacher K, Wang Y, Arnett E, Azad AK, Schlesinger LS. Human alveolar macrophage response to Mycobacterium tuberculosis: immune characteristics underlying large inter-individual variability. Res Sq. 2023 Jun 8;. doi: 10.21203/rs.3.rs-2986649/v1. PubMed PMID: 37333188; PubMed Central PMCID: PMC10275041.

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Pahari S, Arnett E, Simper J, Azad A, Guerrero-Arguero I, Ye C, Zhang H, Cai H, Wang Y, Lai Z, Jarvis N, Lumbreras M, Maselli-Caceres DJ, Peters J, Torrelles JB, Martinez-Sobrido L, Schlesinger LS. A new tractable method for generating Human Alveolar Macrophage Like cells in vitro to study lung inflammatory processes and diseases. bioRxiv. 2023 Apr 6;. doi: 10.1101/2023.04.05.535806. PubMed PMID: 37066199; PubMed Central PMCID: PMC10104118.

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Zhou Z, Gu J, Wang Y. Editorial: Evolutionary mechanisms of infectious diseases, volume II. Front Microbiol. 2023;14:1192566. doi: 10.3389/fmicb.2023.1192566. eCollection 2023. PubMed PMID: 37077239; PubMed Central PMCID: PMC10106751.

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Shen-Gunther J, Cai H, Wang Y. A Customized Monkeypox Virus Genomic Database (MPXV DB v1.0) for Rapid Sequence Analysis and Phylogenomic Discoveries in CLC Microbial Genomics. Viruses. 2022 Dec 22;15(1). doi: 10.3390/v15010040. PubMed PMID: 36680080; PubMed Central PMCID: PMC9861985.

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Cai H, Zhang H, Guo DH, Wang Y, Gu J. Genomic Data Mining Reveals Abundant Uncharacterized Transporters in Coccidioides immitis and Coccidioides posadasii. J Fungi (Basel). 2022 Oct 10;8(10). doi: 10.3390/jof8101064. PubMed PMID: 36294626; PubMed Central PMCID: PMC9604845.

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Garcia-Vilanova A, Olmo-Fontánez AM, Moliva JI, Allué-Guardia A, Singh H, Merritt RE, Maselli DJ, Peters JI, Restrepo BI, Wang Y, Schlesinger LS, Turner J, Weintraub ST, Torrelles JB. The Aging Human Lung Mucosa: A Proteomics Study. J Gerontol A Biol Sci Med Sci. 2022 Oct 6;77(10):1969-1974. doi: 10.1093/gerona/glac091. PubMed PMID: 35460553; PubMed Central PMCID: PMC9536443.

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Shen-Gunther J, Cai H, Wang Y. HPV Integration Site Mapping: A Rapid Method of Viral Integration Site (VIS) Analysis and Visualization Using Automated Workflows in CLC Microbial Genomics. Int J Mol Sci. 2022 Jul 23;23(15). doi: 10.3390/ijms23158132. PubMed PMID: 35897706; PubMed Central PMCID: PMC9331699.

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Allué-Guardia A, Garcia-Vilanova A, Olmo-Fontánez AM, Peters J, Maselli DJ, Wang Y, Turner J, Schlesinger LS, Torrelles JB. Host- and Age-Dependent Transcriptional Changes in Mycobacterium tuberculosis Cell Envelope Biosynthesis Genes after Exposure to Human Alveolar Lining Fluid. Int J Mol Sci. 2022 Jan 17;23(2). doi: 10.3390/ijms23020983. PubMed PMID: 35055170; PubMed Central PMCID: PMC8780516.

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Shen-Gunther J, Xia Q, Cai H, Wang Y. HPV DeepSeq: An Ultra-Fast Method of NGS Data Analysis and Visualization Using Automated Workflows and a Customized Papillomavirus Database in CLC Genomics Workbench. Pathogens. 2021 Aug 13;10(8). doi: 10.3390/pathogens10081026. PubMed PMID: 34451490; PubMed Central PMCID: PMC8398645.

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Gu J, Zhou Z, Wang Y. Editorial: Evolutionary Mechanisms of Infectious Diseases. Front Microbiol. 2021;12:667561. doi: 10.3389/fmicb.2021.667561. eCollection 2021. PubMed PMID: 34054775; PubMed Central PMCID: PMC8155310.

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Mori Y, Ogonuki N, Hasegawa A, Kanatsu-Shinohara M, Ogura A, Wang Y, McCarrey JR, Shinohara T. OGG1 protects mouse spermatogonial stem cells from reactive oxygen species in culture†. Biol Reprod. 2021 Mar 11;104(3):706-716. doi: 10.1093/biolre/ioaa216. PubMed PMID: 33252132.

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Tian Q, Zhou Z, Wang L, Abu-Khdeir AH, Huo Z, Sun X, Zhang N, Schenken R, Wang Y, Xue M, Zhong G. Gastrointestinal Coinfection Promotes Chlamydial Pathogenicity in the Genital Tract. Infect Immun. 2020 Mar 23;88(4). doi: 10.1128/IAI.00905-19. Print 2020 Mar 23. PubMed PMID: 31988173; PubMed Central PMCID: PMC7093119.

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Romo JA, Zhang H, Cai H, Kadosh D, Koehler JR, Saville SP, Wang Y, Lopez-Ribot JL. Global Transcriptomic Analysis of the Candida albicans Response to Treatment with a Novel Inhibitor of Filamentation. mSphere. 2019 Sep 11;4(5). doi: 10.1128/mSphere.00620-19. PubMed PMID: 31511371; PubMed Central PMCID: PMC6739497.

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Hole CR, Wager CML, Castro-Lopez N, Campuzano A, Cai H, Wozniak KL, Wang Y, Wormley FL Jr. Induction of memory-like dendritic cell responses in vivo. Nat Commun. 2019 Jul 4;10(1):2955. doi: 10.1038/s41467-019-10486-5. PubMed PMID: 31273203; PubMed Central PMCID: PMC6609631.

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May HC, Yu JJ, Zhang H, Wang Y, Cap AP, Chambers JP, Guentzel MN, Arulanandam BP. Thioredoxin-A is a virulence factor and mediator of the type IV pilus system in Acinetobacter baumannii. PLoS One. 2019;14(7):e0218505. doi: 10.1371/journal.pone.0218505. eCollection 2019. PubMed PMID: 31265467; PubMed Central PMCID: PMC6605650.

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Moliva JI, Duncan MA, Olmo-Fontánez A, Akhter A, Arnett E, Scordo JM, Ault R, Sasindran SJ, Azad AK, Montoya MJ, Reinhold-Larsson N, Rajaram MVS, Merrit RE, Lafuse WP, Zhang L, Wang SH, Beamer G, Wang Y, Proud K, Maselli DJ, Peters J, Weintraub ST, Turner J, Schlesinger LS, Torrelles JB. The Lung Mucosa Environment in the Elderly Increases Host Susceptibility to Mycobacterium tuberculosis Infection. J Infect Dis. 2019 Jul 2;220(3):514-523. doi: 10.1093/infdis/jiz138. PubMed PMID: 30923818; PubMed Central PMCID: PMC6603975.

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Mueller KD, Zhang H, Serrano CR, Billmyre RB, Huh EY, Wiemann P, Keller NP, Wang Y, Heitman J, Lee SC. Gastrointestinal microbiota alteration induced by Mucor circinelloides in a murine model. J Microbiol. 2019 Jun;57(6):509-520. doi: 10.1007/s12275-019-8682-x. Epub 2019 May 27. PubMed PMID: 31012059; PubMed Central PMCID: PMC6737537.

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Shen-Gunther J, Cai H, Zhang H, Wang Y. Abundance of HPV L1 Intra-Genotype Variants With Capsid Epitopic Modifications Found Within Low- and High-Grade Pap Smears With Potential Implications for Vaccinology. Front Genet. 2019;10:489. doi: 10.3389/fgene.2019.00489. eCollection 2019. PubMed PMID: 31231420; PubMed Central PMCID: PMC6558378.

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Leopold Wager CM, Hole CR, Campuzano A, Castro-Lopez N, Cai H, Caballero Van Dyke MC, Wozniak KL, Wang Y, Wormley FL Jr. IFN-γ immune priming of macrophages in vivo induces prolonged STAT1 binding and protection against Cryptococcus neoformans. PLoS Pathog. 2018 Oct;14(10):e1007358. doi: 10.1371/journal.ppat.1007358. eCollection 2018 Oct. PubMed PMID: 30304063; PubMed Central PMCID: PMC6197699.

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Lee GC, Dallas SD, Wang Y, Olsen RJ, Lawson KA, Wilson J, Frei CR. Emerging multidrug resistance in community-associated Staphylococcus aureus involved in skin and soft tissue infections and nasal colonization. J Antimicrob Chemother. 2017 Sep 1;72(9):2461-2468. doi: 10.1093/jac/dkx200. PubMed PMID: 28859442; PubMed Central PMCID: PMC5890715.

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Wang P, Yu Z, Santangelo TJ, Olesik J, Wang Y, Heldwein E, Li X. BosR Is A Novel Fur Family Member Responsive to Copper and Regulating Copper Homeostasis in Borrelia burgdorferi. J Bacteriol. 2017 Aug 15;199(16). doi: 10.1128/JB.00276-17. Print 2017 Aug 15. PubMed PMID: 28583949; PubMed Central PMCID: PMC5527378.

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Raphael I, Webb J, Gomez-Rivera F, Chase Huizar CA, Gupta R, Arulanandam BP, Wang Y, Haskins WE, Forsthuber TG. Serum Neuroinflammatory Disease-Induced Central Nervous System Proteins Predict Clinical Onset of Experimental Autoimmune Encephalomyelitis. Front Immunol. 2017;8:812. doi: 10.3389/fimmu.2017.00812. eCollection 2017. PubMed PMID: 28769926; PubMed Central PMCID: PMC5512177.

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Zhou Z, Wu S, Lai J, Shi Y, Qiu C, Chen Z, Wang Y, Gu X, Zhou J, Chen S. Identification of trunk mutations in gastric carcinoma: a case study. BMC Med Genomics. 2017 Jul 17;10(1):49. doi: 10.1186/s12920-017-0285-y. PubMed PMID: 28716121; PubMed Central PMCID: PMC5520061.

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Shen-Gunther J, Wang Y, Lai Z, Poage GM, Perez L, Huang TH. Deep sequencing of HPV E6/E7 genes reveals loss of genotypic diversity and gain of clonal dominance in high-grade intraepithelial lesions of the cervix. BMC Genomics. 2017 Mar 14;18(1):231. doi: 10.1186/s12864-017-3612-y. PubMed PMID: 28288568; PubMed Central PMCID: PMC5348809.

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Cooper DJ, Chen IC, Hernandez C, Wang Y, Walter CA, McCarrey JR. Pluripotent cells display enhanced resistance to mutagenesis. Stem Cell Res. 2017 Mar;19:113-117. doi: 10.1016/j.scr.2016.12.029. Epub 2017 Jan 6. PubMed PMID: 28129601.

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McCarrey JR, Lehle JD, Raju SS, Wang Y, Nilsson EE, Skinner MK. Tertiary Epimutations - A Novel Aspect of Epigenetic Transgenerational Inheritance Promoting Genome Instability. PLoS One. 2016;11(12):e0168038. doi: 10.1371/journal.pone.0168038. eCollection 2016. PubMed PMID: 27992467; PubMed Central PMCID: PMC5167269.

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Lee GC, Hall RG, Boyd NK, Dallas SD, Du LC, Treviño LB, Treviño SB, Retzloff C, Lawson KA, Wilson J, Olsen RJ, Wang Y, Frei CR. A prospective observational cohort study in primary care practices to identify factors associated with treatment failure in Staphylococcus aureus skin and soft tissue infections. Ann Clin Microbiol Antimicrob. 2016 Nov 22;15(1):58. doi: 10.1186/s12941-016-0175-8. PubMed PMID: 27876059; PubMed Central PMCID: PMC5120512.

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Chen IC, Hernandez C, Xu X, Cooney A, Wang Y, McCarrey JR. Dynamic Variations in Genetic Integrity Accompany Changes in Cell Fate. Stem Cells Dev. 2016 Nov 15;25(22):1698-1708. doi: 10.1089/scd.2016.0221. Epub 2016 Oct 12. PubMed PMID: 27627671; PubMed Central PMCID: PMC6453492.

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Zhou Z, Sun N, Wu S, Li YQ, Wang Y. Genomic data mining reveals a rich repertoire of transport proteins in Streptomyces. BMC Genomics. 2016 Aug 22;17 Suppl 7(Suppl 7):510. doi: 10.1186/s12864-016-2899-4. PubMed PMID: 27557108; PubMed Central PMCID: PMC5001237.

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Lee GC, Hall RG, Boyd NK, Dallas SD, Du LC, Treviño LB, Retzloff C, Treviño SB, Lawson KA, Wilson JP, Olsen RJ, Wang Y, Frei CR. Predictors of community-associated Staphylococcus aureus, methicillin-resistant and methicillin-susceptible Staphylococcus aureus skin and soft tissue infections in primary-care settings. Epidemiol Infect. 2016 Nov;144(15):3198-3204. doi: 10.1017/S0950268816001709. Epub 2016 Aug 4. PubMed PMID: 27489019; PubMed Central PMCID: PMC9150203.

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Rhodes CT, Sandstrom RS, Huang SA, Wang Y, Schotta G, Berger MS, Lin CA. Cross-species Analyses Unravel the Complexity of H3K27me3 and H4K20me3 in the Context of Neural Stem Progenitor Cells. Neuroepigenetics. 2016 Jun;6:10-25. doi: 10.1016/j.nepig.2016.04.001. Epub 2016 May 3. PubMed PMID: 27429906; PubMed Central PMCID: PMC4941106.

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Zhang Y, He J, Jia LJ, Yuan TL, Zhang D, Guo Y, Wang Y, Tang WH. Cellular Tracking and Gene Profiling of Fusarium graminearum during Maize Stalk Rot Disease Development Elucidates Its Strategies in Confronting Phosphorus Limitation in the Host Apoplast. PLoS Pathog. 2016 Mar;12(3):e1005485. doi: 10.1371/journal.ppat.1005485. eCollection 2016 Mar. PubMed PMID: 26974960; PubMed Central PMCID: PMC4790934.

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Cai H, Lilburn TG, Hong C, Gu J, Kuang R, Wang Y. Predicting and exploring network components involved in pathogenesis in the malaria parasite via novel subnetwork alignments. BMC Syst Biol. 2015;9 Suppl 4(Suppl 4):S1. doi: 10.1186/1752-0509-9-S4-S1. Epub 2015 Jun 11. PubMed PMID: 26100579; PubMed Central PMCID: PMC4474416.

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Yu X, Korkmaz T, Lilburn TG, Cai H, Gu J, Wang Y. Heavy path mining of protein-protein associations in the malaria parasite. Methods. 2015 Jul 15;83:63-70. doi: 10.1016/j.ymeth.2015.04.002. Epub 2015 Apr 7. PubMed PMID: 25861922; PubMed Central PMCID: PMC4510024.

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Lilburn TG, Cai H, Gu J, Zhou Z, Wang Y. Exploring systems affected by the heat shock response in Plasmodium falciparum via protein association networks. Int J Comput Biol Drug Des. 2014;7(4):369-83. doi: 10.1504/IJCBDD.2014.066554. Epub 2014 Dec 25. PubMed PMID: 25539848; PubMed Central PMCID: PMC4492993.