Publications

Scholarly Journals--Published

• Boutrin MC, Mishra A, Wang C, Dou Y, Fletcher HM. The involvement of CdhR in Porphyromonas gingivalis during nitric oxide stress. Mol Oral Microbiol. 2023 May 3. doi: 10.1111/omi.12414. Epub ahead of print. PMID: 37134265 (05/2023) (link)
• Oyefeso FA, Goldberg G, Opoku NYPS, Vazquez M, Bertucci A, Chen Z, Wang C, Muotri AR, Pecaut MJ. Effects of acute low-moderate dose ionizing radiation to human brain organoids. PLoS One. 2023 May 31;18(5):e0282958. doi: 10.1371/journal.pone.0282958. PMID: 37256873; PMCID: PMC10231836. (05/2023) (link)
• Chen W, Wang C, Yang ZX, Zhang F, Wen W, Schaniel C, Mi X, Bock M, Zhang XB, Qiu H, Wang C (corresponding). Reprogramming of human peripheral blood mononuclear cells into induced mesenchymal stromal cells using non-integrating vectors. Commun Biol. 2023 Apr 11;6(1):393. doi: 10.1038/s42003-023-04737-x. PMID: 37041280; PMCID: PMC10090171. (04/2023) (link)
• Liu T, Chen Z, Chen W, Evans R, Xu J, Reeves ME, de Vera ME, Wang C (corresponding). Dysregulated miRNAs modulate tumor microenvironment associated signaling networks in pancreatic ductal adenocarcinoma. Precis Clin Med. 2023 Mar 10;6(1):pbad004. doi: 10.1093/pcmedi/pbad004. PMID: 37007745; PMCID: PMC10052370. (03/2023) (link)
• Kremsky I, Ma Q, Li B, Dasgupta C, Chen X, Ali S, Angeloni S, Wang C, Zhang L. Fetal hypoxia results in sex- and cell type-specific alterations in neonatal transcription in rat oligodendrocyte precursor cells, microglia, neurons, and oligodendrocytes. Cell Biosci. 2023 Mar 17;13(1):58. doi: 10.1186/s13578-023-01012-8. PMID: 36932456; PMCID: PMC10022003 (03/2023) (link)
• Ximinies AD, Dou Y, Mishra A, Zhang K, Deivanayagam C, Wang C, Fletcher HM. The Oxidative Stress-Induced Hypothetical Protein PG_0686 in Porphyromonas gingivalis W83 Is a Novel Diguanylate Cyclase. Microbiol Spectr. 2023 Jan 31;11(2):e0441122. doi: 10.1128/spectrum.04411-22. Epub ahead of print. PMID: 36719196; PMCID: PMC10101095. (01/2023) (link)
• Daneshgaran G, Gardner DJ, Chen HA, Niknam-Bienia S, Soundararajan V, Raghuram AC, Kim GH, Labaj P, Kreil DP, Wang C, Hong YK, Wong AK. Silicone Breast Implant Surface Texture Impacts Gene Expression in Periprosthetic Fibrous Capsules. Plast Reconstr Surg. 2023 Jan 1;151(1):85-95. doi: 10.1097/PRS.0000000000009800. Epub 2022 Oct 7. PMID: 36205692. (01/2023) (link)
• Talsania K, Shen TW, Chen X, Jaeger E, Li Z, Chen Z, Chen W, Tran B, Kusko R, Wang L, Pang AWC, Yang Z, Choudhari S, Colgan M, Fang LT, Carroll A, Shetty J, Kriga Y, German O, Smirnova T, Liu T, Li J, Kellman B, Hong K, Hastie AR, Natarajan A, Moshrefi A, Granat A, Truong T, Bombardi R, Mankinen V, Meerzaman D, Mason CE, Collins J, Stahlberg E, Xiao C, Wang C (co-corresponding), Xiao W, Zhao Y. Structural variant analysis of a cancer reference cell line sample using multiple sequencing technologies. Genome Biol. 2022 Dec 13;23(1):255. doi: 10.1186/s13059-022-02816-6. PMID: 36514120; PMCID: PMC9746098. (12/2022) (link)
• Xiao C, Chen Z, Chen W, Padilla C, Colgan M, Wu W, Fang LT, Liu T, Yang Y, Schneider V, Wang C (co-corresponding), Xiao W. Personalized genome assembly for accurate cancer somatic mutation discovery using tumor-normal paired reference samples. Genome Biol. 2022 Nov 9;23(1):237. doi: 10.1186/s13059-022-02803-x. PMID: 36352452; PMCID: PMC9648002. (11/2022) (link)
• Yang Z, Chen Z, Lin X, Yao S, Xian M, Ning X, Fu W, Jiang M, Li N, Xiao X, Feng M, Lian Z, Yang W, Ren X, Zheng Z, Zhao J, Wei N, Lu W, Roponen M, Schaub B, Wong GWK, Su Z, Wang C (co-corresponding), Li J. Rural environment reduces allergic inflammation by modulating the gut microbiota. Gut Microbes. 2022 Jan-Dec;14(1):2125733. doi: 10.1080/19490976.2022.2125733. PMID: 36193874; PMCID: PMC9542937. 122. (10/2022) (link)
• Mavingire, N., Campbell, P, Liu, Tiantian, Wooten, J, Chen, X., Wang, C. (co-corresponding), and Brantley, E. (2022). Aminoflavone upregulates miR-125b-2-3p to inhibit luminal breast cancer stem cell-like properties. Precision Clinical Medicine, Volume 5, Issue 2, June 2022, pbac008, https://doi.org/10.1093/pcmedi/pbac008 (06/2022) (link)
• Chen Z, Wang C, Blood A, Bragg S, Mata-Greenwood E. Renal functional, transcriptome, and methylome adaptations in pregnant Sprague Dawley and Brown Norway rats. PLoS One. 2022 Jun 16;17(6):e0269792. doi: 10.1371/journal.pone.0269792. PMID: 35709218; PMCID: PMC9202892. (06/2022) (link)
• Li, X.; Wang, X.; Huang, R.; Stucky, A.; Chen, X.; Sun, L.; Wen, Q.; Zeng, Y.; Fletcher, H.; Wang, C.; Xu, Y.; Cao, H.; Sun, F.; Li, S.C.; Zhang, X.; Zhong, J.F. The Machine-Learning-Mediated Interface of Microbiome and Genetic Risk Stratification in Neuroblastoma Reveals Molecular Pathways Related to Patient Survival. Cancers 2022, 14, 2874. https://doi.org/10.3390/cancers14122874 (06/2022) (link)
• Wang Z, Zhang C, Warden CD, Liu Z, Yuan YC, Guo C, Wang C, Wang J, Wu X, Ermel R, Vonderfecht SL, Wang X, Brown C, Forman S, Yang Y, James You M, Chen W. Loss of SIRT1 inhibits hematopoietic stem cell aging and age-dependent mixed phenotype acute leukemia. Commun Biol. 2022 Apr 28;5(1):396. doi: 10.1038/s42003-022-03340-w. PMID: 35484199; PMCID: PMC9051098. (04/2022) (link)
• Mandy M Liu, Tiantian Liu, Steven Yeung, Zhijun Wang, Bradley Andresen, Cyrus Parsa, Robert Orlando, Bingsen Zhou, Wei Wu, Xia Li, Yilong Zhang, Charles Wang* (co-corresponding), Ying Huang. Inhibitory activity of medicinal mushroom Ganoderma lucidum on colorectal cancer by attenuating inflammation.  Precision Clinical Medicine, Volume 4, Issue 4, December 2021, Pages 231–245. (12/2021) (link)
• Jonathan Foox, Jessica Nordlund, Claudia Lalancette, Ting Gong, Michelle Lacey, Samantha Lent, Bradley W. Langhorst, V. K. Chaithanya Ponnaluri, Louise Williams, Karthik Ramaswamy Padmanabhan, Raymond Cavalcante, Anders Lundmark, Daniel Butler, Christopher Mozsary, Justin Gurvitch, John M. Greally, Masako Suzuki, Mark Menor, Masaki Nasu, Alicia Alonso, Caroline Sheridan, Andreas Scherer, Stephen Bruinsma, Gosia Golda, Agata Muszynska, Pawel P. Labaj, Matthew A. Campbell, Frank Wos, Amanda Raine, Ulrika Liljedahl, Tomas Axelsson, Charles Wang, Zhong Chen, Zhaowei Yang, Jing Li, ……Youping Deng & Christopher E. Mason. The SEQC2 epigenomics quality control (EpiQC) study. Genome Biol 22, 332 (2021). doi.org/10.1186/s13059-021-02529-2. (12/2021) (link)
• Yongmei Zhao, Li Tai Fang, Tsai-wei Shen, Sulbha Choudhari, Keyur Talsania, Xiongfong Chen, Jyoti Shetty, Yuliya Kriga, Bao Tran, Bin Zhu, Zhong Chen, Wanqiu Chen, Charles Wang, Erich Jaeger……. Christopher E. Mason, Chunlin Xiao, Huixiao Hong & Wenming Xiao et al. Whole genome and exome sequencing reference datasets from a multi-center and cross-platform benchmark study. Sci Data 8, 296 (2021). doi.org/10.1038/s41597-021-01077-5. (11/2021) (link)
• Wenqian Wu, Xiaonan Sun, Xiaomeng Shi, Lo Lai, Charles Wang, Mingxin Xie, Gangjian Qin, Hongyu Qiu. Hsp22 Deficiency Induces Age-Dependent Cardiac Dilation and Dysfunction by Impairing Autophagy, Metabolism, and Oxidative Response. Antioxidants (Basel) 2021 Sep 29;10(10):1550. doi: 10.3390/antiox10101550. (09/2021) (link)
• Chen W, Zhao Y, Chen X, Yang Z, Xu X, Bi Y, Chen V, Li J, Choi H, Ernest B, Tran B, Mehta M, Kumar P, Farmer A, Mir A, Mehra UA, Li JL, Moos M Jr, Xiao W, Wang C (corresponding). A multicenter study benchmarking single-cell RNA sequencing technologies using reference samples. Nat Biotechnol 39, 1103–1114 (2021). doi.org/10.1038/s41587-020-00748-92020 (Received the Best Paper Award, 2021 MAQC Society Meeting) (09/2021) (link)
• Xiao W, Ren L, Chen Z,….Wang C* (co-corresponding), and Shi L. Towards best practice in cancer mutation detection with whole-genome and whole-exome sequencing. Nat Biotechnol 39, 1141–1150 (2021). doi.org/10.1038/s41587-021-00994-5 (09/2021) (link)
• Fang LT, Zhu B, Zhao Y, Chen W, Yang Z,…Shi L, Wang* C (co-corresponding), and Xiao W. Establishing community reference samples, data and call sets for benchmarking cancer mutation detection using whole-genome sequencing. Nat Biotechnol 39, 1151–1160 (2021). doi.org/10.1038/s41587-021-00993-6 (09/2021) (link)
• Tiantian Liu, Zhong Chen, Wanqiu Chen, Xin Chen, Maryam Hosseini, Zhaowei Yang, Jing Li, Diana Ho, David Turay, Ciprian Gheorghe, Wendell Jones, Charles Wang (corresponding). A benchmarking study of SARS-CoV-2 whole-genome sequencing protocols using COVID-19 patient samples. iScience, Volume 24, Issue 8, 20 August 2021, 102892. doi.org/10.1016/j.isci.2021.102892. (08/2021) (link)
• Gatto, N.M., Garcia-Cano, J., Irani, C., Jaceldo-Siegl, K., Liu, Tiantian., Chen, Z., Paul, J., Fraser, G., Wang, C., and Lee, G.J. Vegetarian Dietary Patterns and Cognitive Function among Older Adults: The Adventist Health Study-2. J Nutr Gerontol Geriatr, Aug 19, 2021, 40 (4): 197-214. (08/2021) (link)
• Maryam Hosseini, Wanqiu Chen, Daliao Xiao, Charles Wang. Computational molecular docking and virtual screening revealed promising SARS-CoV-2 drugs, Precision Clinical Medicine, Volume 4, Issue 1, March 2021 (03/2021) (link)
• Chen X, Yang Z, Chen W, Zhao Y, Farmer A, Tran B, Furtak V, Moos M Jr, Xiao W, Wang C. A multi-center cross-platform single-cell RNA sequencing reference dataset. Sci Data. 2021 Feb 2;8(1):39 (02/2021) (link)
• Jonathan Foox, Jessica Nordlund, Claudia Lalancette, Ting Gong, Michelle Lacey, Samantha Lent, Bradley W. Langhorst, V. K. Chaithanya Ponnaluri, Louise Williams, Karthik Ramaswamy Padmanabhan, Raymond Cavalcante, Anders Lundmark, Daniel Butler, Christopher Mozsary, Justin Gurvitch, John M. Greally, Masako Suzuki, Mark Menor, Masaki Nasu, Alicia Alonso, Caroline Sheridan, Andreas Scherer, Stephen Bruinsma, Gosia Golda, Agata Muszynska, Pawel P. Labaj, Matthew A. Campbell, Frank Wos, Amanda Raine, Ulrika Liljedahl, Tomas Axelsson, Charles Wang, Zhong Chen, Zhaowei Yang, Jing Li, ……Youping Deng & Christopher E. Mason. The SEQC2 epigenomics quality control (EpiQC) study. Genome Biol 22, 332 (2021). doi.org/10.1186/s13059-021-02529-2. (02/2021) (link)
• Zhang, JP, Yang ZX, Zhang F, Fu YW, Dai XY, Wen W, Zhang B, Choi H, Chen W, Brown M, Baylink D, Zhang L, Qiu H, Wang C, Cheng T, Zhang XB. HDAC inhibitors improve CRISPR-mediated HDR editing efficiency in iPSCs. Sci China Life Sci. 2021 Jan 6. (01/2021) (link)
• Filippov V, Jaceldo-Siegl K, Eroshkin A, Loskutov V, Chen X, Wang C, Duerksen-Hughes PJ. Methylomes in Vegans versus Pescatarians and Nonvegetarians. Epigenomes. 2020; 4(4):28. (12/2020) (link)
• Siddiqui SS, Vaill M, Do R, Khan N, Verhagen AL, Zhang W, Lenz HJ, Johnson-Pais TL, Leach RJ, Fraser G, Wang C, Feng GS, Varki N, Varki A. Human-specific polymorphic pseudogenization of SIGLEC12 protects against advanced cancer progression. FASEB Bio Adv. 2020 Dec 8;3(2):69-82. (12/2020) (link)
• Liu T, Gatto NM, Chen Z, Qiu H, Lee G, Duerksen-Hughes P, Fraser G, Wang C. Vegetarian diets, circulating miRNA expression and healthspan in subjects living in the Blue Zone. Precis Clin Med. 2020 Dec;3(4):245-259. (12/2020) (link)
• Chen W, Zhao Y, Chen X, Yang Z, Xu X, Bi Y, Chen V, Li J, Choi H, Ernest B, Tran B, Mehta M, Kumar P, Farmer A, Mir A, Mehra UA, Li JL, Moos M Jr, Xiao W, Wang C. A multicenter study benchmarking single-cell RNA sequencing technologies using reference samples. Nat Biotechnology. 2020 Dec 21.  https://www.nature.com/articles/s41587-020-00748-9 This paper recieved the 2021 MAQC Society the Best Paper Award (Inaguration Award)! (12/2020) (link)
• Miles FL, Mashchak A, Filippov V, Orlich MJ, Duerksen-Hughes P, Chen X, Wang C, Siegmund K, Fraser GE. DNA Methylation Profiles of Vegans and Non-Vegetarians in the Adventist Health Study-2 Cohort. Nutrients. 2020 Nov 30;12(12):3697. (11/2020) (link)
• Lin X, Ren X, Xiao X, Yang Z, Yao S, Wong GW, Liu Z, Wang C, Su Z, Li J.   Important Role of Immunological Responses to Environmental Exposure in the Development of Allergic Asthma.   Allergy Asthma Immunol Research. 2020 Nov;12(6):934-948 (11/2020) (link)
• Zhou N, Chen X, Xi J, Ma B, Leimena C, Stoll S, Qin G, Wang* C, Qiu H. Novel genomic targets of valosin-containing protein in protecting pathological cardiac hypertrophy. Scientific Reports, October 22, 2020 (co-corresponding) (10/2020) (link)
• Eric Chang, Cong Fu, Steven L. Coon, Shahar Alon, Marjan Bozinoski, Matthew Breymaier, Diego M. Bustos, Samuel J. Clokie, Yoav Gothilf, Caroline Esnault, P. Michael Iuvone, Christopher E. Mason, 8 Margaret J. Ochocinska, Adi Tovin, Charles Wang, Pinxian Xu, Jinhang Zhu, Ryan Dale, and David C. Klein, Resource: A multi-species multi-timepoint transcriptome database and webpage for the pineal gland and retina, Journal of Pineal Research, July 8, 2020 (10/2020) (link)
• Ning Zhou, Xin Chen, Jing Xi, Ben Ma, Christiana Leimena, Shaunrick Stoll, Gangjian Qin, Charles Wang*, Hongyu Qiu, Genomic characterization reveals novel mechanisms underlying the valosin-containing protein-mediated cardiac protection against heart failure, Redox Biology, Volume 36, September 2020 (co-corresponding)   (09/2020) (link)
• Gatto, N. M., Garcia-Cano, J., Irani, C., Liu, T., Arakaki, C., Fraser, G., Wang, C., & Lee, G. J., Observed Physical Function Is Associated With Better Cognition Among Elderly Adults: The Adventist Health Study-2. American Journal of Alzheimer’s Disease & Other Dementias, September 30, 2020 (09/2020) (link)
• Chen, X., Zhang*, L. & Wang*, C. Prenatal hypoxia-induced epigenomic and transcriptomic reprogramming in rat fetal and adult offspring hearts. Scientific Data (10/2019)
• Eliah Overbey, Willian Abraham da Silveira, Seta Stanbouly, Nina Nishiyama, Gina Roque-Torres, Michael Pecaut, David Zawieja, Charles Wang, Jeffrey Willey, Michael Delp, Gary Hardiman, and Xiao Mao. Spaceflight influences gene expression, photoreceptor integrity, and oxidative stress-related damage in the murine retina. Scientific Reports (09/2019)
• Eliah G. Overbey, Amber M. Paul, Willian A. da Silveira, Candice G.T. Tahimic, Sigrid S. Reinsch, Nathaniel Szewczyk, Seta Stanbouly, Charles Wang, Jonathan M. Galazka, and Xiao Wen Mao. Mice Exposed to Combined Chronic Low-Dose Irradiation and Modeled Microgravity Develop Long-Term Neurological Sequelae. International Journal of Molecular Science (08/2019)
• Johnson, M., Niknam-Bienia, S., Soundararajan, V., Pang, B., Jung, E., Park, S., Perrauts, D., Wang, C., Baker, R., Chen, M., Hong, Y., Li, W., Gardner, D. and Wong, A. Mesenchymal stem cells isolated from irradiated human skin have diminished capacity for proliferation, differentiation, colony formation, and paracrine stimulation. Stem Cells Translational Medicine (01/2019)
• Christina K. Cajigas-Du Ross, Shannalee R. Martinez, Leanne Woods-Burnham, Alfonso M. Durán, Sourav Roy, Anamika Basu, Joshua A. Ramirez, Greisha L. Ortiz-Hernández, Leslimar Ríos-Colón, Juli Unternaehrer, Ubaldo Soto, Celine Greco, Claude Boucheix, Xin Chen, Charles Wang, Carlos A. Casiano. RNA sequencing reveals upregulation of a cancer stem cell transcriptomic program in metastatic prostate cancer cells selected for taxane resistance. Oncotarget, July 2018, Vol. 9, (No. 54), pp: 30363-30384. (07/2018)
• Lei Huang, Xin Chen, Chiranjib Dasgupta, Wanqiu Chen, Rui Song, Charles Wang* (co-corresponding) and Lubo Zhang*. Fetal Hypoxia Impacts Methylome and Transcriptome in Developmental Programming of Heart Disease. Cardiovascular Research (07/2018)