Kaz A, Rhodes C, Lin CW, Wong C-J, Sandstrom R, Wang Y, Chak A, Willis J, Grady W, Lin CHA (2018) Case Report of Molecular Signature in Poorly Differentiated Esophageal Adenocarcinoma. Cancer Research Frontiers. 3(1): 170-191.
Leopold Wager CM, Hole CR, Campuzano A, Castro-Lopez N, Cai H, Caballero Van Dyke MC, Wozniak KL, Wang Y, Wormley FL Jr. (2018) IFN-γ immune priming of macrophages in vivo induces prolonged STAT1 binding and protection against Cryptococcus neoformans. PLoS Pathogens. Oct 10;14(10):e1007358. doi: 10.1371/journal.ppat.1007358. [Epub ahead of print]
Lee GC, Steven D, Wang Y, Randall O, Kenneth L, James W, Christopher F (2017) Emerging Multidrug Resistance in Community-Associated Staphylococcus aureus involved in Skin and Soft Tissue Infections and Nasal Colonization. Journal of Antimicrobial Chemotherapy. dkx200. doi: 10.1093/jac/dkx200.
Shen-Gunther J, Wang Y, Lai Z, Poage GM, Perez L, Huang THM (2017) 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. 18(1):231.
Wang P, Santangelo TJ, Olesik J, Heldwein E, Wang Y, Li X. (2017) BosR Is A Novel Fur Family Member Responsive to Copper and Regulating Copper Homeostasis in Borrelia burgdorferi. Journal of Bacteriology. pii: JB.00276-17. doi: 10.1128/JB.00276-17.
Raphael I, Webb J, Gomez-Rivera F, Huizar CA, Gupta R, Arulanandam BP, Wang Y, Haskins WE, Forsthuber TG (2017) Serum Neuroinflammatory Disease-Induced Central Nervous System Proteins Predict Clinical Onset of Experimental Autoimmune Encephalomyelitis. Frontiers in Immunology. 17 July 2017, https://doi.org/10.3389/fimmu.2017.00812
Zhou Z, Wu S, Lai J, Shi Y, Qiu C, Chen Z, Wang Y, Gu X, Zhou J, Chen S (2017) Identification of trunk mutations in gastric carcinoma: a case study. BMC Medical Genomics. Jul 17;10(1):49. doi: 10.1186/s12920-017-0285-y.
Yu X, Zhang H, Lilburn TG, Cai H, Gu J, Korkmaz T, Wang Y (2017) Transcriptomic and network analyses combine to identify genes that drive the red blood cell cycle of Plasmodium falciparum. International Journal of Data Mining and Bioinformatics. Accepted.
Cooper DJ, Chen I-C, Hernandez C, Wang Y, Walter CA, McCarrey JR (2017) Pluripotent Cells Display Enhanced Resistance to Mutagenesis. Stem Cell Research. 19:113-117.
McCarrey JR, Lehle JD, Raju SS, Wang Y, Nilsson EE, Skinner MK (2017) Tertiary Epimutations - A Novel Aspect of Epigenetic Transgenerational Inheritance Promoting Genome Instability. PLoS One. 11(12):e0168038.
Yu X, Lilburn TG, Cai H, Gu J, Korkmaz T, Wang Y (2017) PageRank influence analysis of protein-protein association networks in the malaria parasite Plasmodium falciparum. International Journal of Computational Biology and Drug Design. 10(2):137-156.
Zhang Y, He J, Jia LJ, Yuan TL, Zhang D, Guo Y, Wang Y, Tang WH (2016) 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 Pathogens. 12(3):e1005485.
Zhou Z, Sun N, Wu S, Li YQ, Wang Y. (2016) Genomic data mining reveals a rich repertoire of transport proteins in Streptomyces. BMC Genomics. 17 (S7):510.
Lee GC, Hall RG, Boyd RK, Dallas SK, Du LC, Treveno LB, Retzloff C, Trevino SB, Lawson KA, Wilson JP, Olsen RJ, Wang Y, Frei CR (2016) Predictors of community-associated Staphylococcus aureus, methicillin-resistant and methicillin-susceptible Staphylococcus aureus skin and soft tissue infections in primary-care settings. Epidemiol. Infect. 4:1-7.
Rhodes CT, Sandstrom R, Huang S, Wang Y, Schotta G, Berger MS, Lin CH (2016). Cross-species analyses unravel the complexity of H3K27me3 and H4K20me3 in the context of neural stem progenitor cells. Neuroepigenetics.6:15.
Cai H, Luo MH, Wang Y, Tang Q (2016) Diversity of and Implications from the Viral Genomes and Viral Proteins of Zika Virus. J Virol Antivir Res 2016, 5:3.
Chen I-C, Hernandez C, Xu X, Cooney A, Wang Y, McCarrey JR. (2016) Dynamic variations in genetic integrity accompany changes in cell fate. Stem Cells and Development. 25(22):1698-1708.
Lee GC, Hall RG, Boyd NK, Dallas SD, Du LC, Trevino LB, Trevino, SB, Retzloff C, Lawson KA, Wilson J, Olsen RJ, Wang Y, Frei CR (2016) A prospective observational cohort study in primary care practices to identify factors associated with treatment failure in Staphylococcus aureus skin and soft tissue infections. Annals of Clinical Microbiology and Antimicrobials. In press.
Yu X, Korkmaz T, Lilburn TG, Cai H, Gu J, Wang Y. (2015) Heavy path mining of protein-protein associations in the malaria parasite. Methods. (Elsevier). 83:63-70.
Cai H, Lilburn TG, Hong C, Gu J, Kuang R, Wang Y (2015) Predicting and exploring network components involved in pathogenesis in the malaria parasite via novel subnetwork alignments. BMC Systems Biology. 9(Suppl 4):S1.
Sandstrom RS, Foret MR, Grow DA, Haugen E, Rhodes CT, Cardona AE, Phelix CF, Wang Y, Berger MS, Lin CH.(2014) Epigenetic Regulation by Chromatin Activation Mark H3K4me3 in Primate Progenitor Cells within Adult Neurogenic Niche. Sci Rep. 2014 Jun 20;4:5371.
Lilburn TG, Cai H, Gu J, Zhou Z, Wang Y (2014) Exploring systems affected by the heat shock response in Plasmodium falciparum via protein association networks. International Journal of Computational Biology and Drug Design. (4):369-383..
Zhou Z, Li Y, Sun N, Sun Z, Lv L, Wang Y, Shen L, Li YQ. (2014) Function and Evolution of Two Forms of SecDF Homologs in Streptomyces coelicolor. PLoS One. 2014 Aug 20;9(8):e105237.
Foret MR, Sandstrom RS, Rhodes CT, Wang Y, Berger MS, Lin CH. (2014) Molecular targets of chromatin repressive mark H3K9me3 in primate progenitor cells within adult neurogenic niches. Front Genet. 2014 Jul 30;5:252.
Wang HC, Greene WA, Kaini RR, Shen-Gunther J, Chen HH, Cai H, Wang Y. (2014) Profiling the microRNA expression in human iPS and iPS-derived retinal pigment epithelium. Cancer Informatics. 13(Suppl 5):25-35.
Cai H, Hong C, Lilburn TG, Rodriguez AL, Chen S, Gu J, Kuang R, Wang Y (2013) A novel subnetwork alignment approach predicts new components of the cell cycle regulatory apparatus in Plasmodium falciparum. BMC Bioinformatics. 14(Suppl 12):S2.
Lilburn TG, Wang Y, Cai H, Hong C, Gu J (2013) Protein Families in Plasmodium Parasites - A Network Perspective. In “Comparative genomics in human neglected parasites”. Editors: Marchat LA and López-Camarillo C. 1-17.
Cai H, Hong C, Gu J, Lilburn TG, Kuang R, Wang Y (2012) Module-based Subnetwork Alignments Reveal Novel Transcriptional Regulators in Malaria Parasite Plasmodium falciparum. BMC Systems Biology. 6(Suppl3):S5
Zhou Z, Gu J, Li YQ, Wang Y (2012) Genome plasticity and systems evolution in Streptomyces. BMC Bioinformatics. 13(Suppl 10):S8.
Cai H, Zhou Z, Gu J, Wang Y (2012) Comparative Genomics and Systems Biology of Malaria Parasites Plasmodium. Current Bioinformatics. 7 (4):478-489.
Lilburn TG, Cai H, Zhou Z, Wang Y (2011) Protease-associated Cellular Networks in Malaria Parasite Plasmodium falciparum. BMC Genomics. 12(Suppl 5):S9.
Coyne RS, Hannick L, Shanmugam D, Hostetler JB, Brami D, Joardar VS, Johnson J, Radune D, Singh I, Kumar U, Saier M, Wang Y, Cai H, Gu J, Mather MW, Vaidya AB, Wilkes DE, Rajagopalan V, Asai DJ, Pearson CG, Findly RC, Dickerson HW, Badger JH, Wu M, Martens C, Van de Peer Y, Roos DS, Cassidy-Hanley DM, Clark TG. (2011) Comparative genomics of the pathogenic ciliate Ichthyophthirius multifiliis, its free-living relatives and a host species provide insights into adoption of a parasitic lifestyle and prospects for disease control. Genome Biology. 12:R100
Cai H, Kuang R, Gu J, Wang Y (2011) Proteases in Malaria Parasites - a Phylogenomic Perspective. Current Genomics. 12(6) 417-427.
Zhou Z, Gu J, Li Y, Li YQ, Wang Y (2011) The -omics Era- Toward a Systems-Level Understanding of Streptomyces. Current Genomics. 12(6) 404-416.Lilburn TG, Gu J, Cai H, Wang Y (2010) Comparative genomics of the family Vibrionaceae reveals the wide distribution of genes encoding virulence-associated proteins. BMC Genomics. 11:369.
Cai H, Gu J, Wang Y (2010). Core Genome Components and Lineage Specific Expansions in Malaria Parasites Plasmodium. BMC Genomics. 11(Suppl 3):S13.
RoyChoudhury D, Small C, Wang Y, Mueller P, Rebel V, Griswold MD, McCarrey JR (2010) Microarray-Based Analysis of Cell Cycle Gene Expression During Spermatogenesis in the Mouse. Biology of Reproduction. 83(4):663-75. Epub 2010 Jul 14.
Gu J*, Wang Y*, Lilburn TG (2009). A Comparative Genomics, Network-based Approach to Understanding Virulence in Vibriocholerae. Journal of Bacteriology. 191:6262-6272.(*: Equally contributed)
Gu J*, Neary JL*, Cai H, Moshfeghian A, Rodriguez SA, Lilburn TG, Wang Y (2009). Genomic and Systems Evolution in Vibrionaceae species. BMC Genomics. 10(Suppl 1):S11. (*: Equally contributed)
Kuang R, Gu J, Cai H, Wang Y (2009). Improved Prediction of Malaria Degradomes by Supervised Learning with SVM and Profile Kernel. Genetica. 136:189-209.
Wang Y, Lilburn TG (2009). Systems Biology and Biological Resource Centers . BioScience. 59(2):113-125.
Huang Y, Tienda Luna I, Wang Y (2009). Reverse engineering gene regulatory networks: A survey of statistical models. IEEE Signal Processing. 26(1):76-97.
Lu Y, Tian Q, Neary J, Liu F, Wang Y (2008) Adaptive Discriminant Analysis for Microarray-based Classification. ACM Transactions on Knowledge Discovery from Data (TKDD). Special Issue on Bioinformatics. 2:5(1-20).
Tienda-Luna IM, Yin Y, Carrion MC, Huang Y, Cai H, Sanchez M, Wang Y (2008) Inferring the skeleton cell cycle regulatory network of malaria parasite using comparative genomic and variational Bayesian approaches. Genetica. 132:131–142.
Tienda-Luna IM, Yin Y, Huang Y, Padillo DPR, Wang Y. (2008) Constructing Gene Networks Using Variational Bayesian Variable Selection. Artificial Life. Special Issue on Systems Biology. 14(1):65-79.
Lu Y, Tian Q, Liu F, Sanchez M, Wang Y (2007) Interactive Semi-Supervised Learning for Microarray Analysis. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 4(2): 190-203.
Lu Y, Tian Q, Sanchez M, Neary J, Liu F, Wang Y (2007) Learning Microarray Gene Expression Data by Hybrid Discriminant Analysis. IEEE Multimedia. Special Issue on Multimedia Signal Processing and Systems in Healthcare and Life Sciences. 14(4):22-31.
Huang Y, Wang J, Zhang J, Sanchez M, Wang Y (2007) Bayesian Inference of Genetic Regulatory Networks from Time Series Microarray Data Using Dynamic Bayesian Networks. Journal of Multimedia. 2: 46-56.
Gu J*, Neary JL*, Sanchez M, Yu J, Lilburn TG, Wang Y (2007) Genome Evolution and Functional Divergence in Yersinia. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution. 308:37-49. (*: Equally contributed)
Lilburn TG, Wang Y (2006) Systems biology and computer aided drug discovery. Current Computer-Aided Drug Design. 2:267-274.
Chen G, Zhu Y, Wang Y, Xu X, Lu T (2006) Determination of bioactive constituents in traditional Chinese medicines by CE with electrochemical detection. Current Medicinal Chemistry 13:2467-2485.
Gu X, Wang Y, Gu J, Velden KV, Xu DP (2006) Predicting Type-I (Rate-Shift) Functional Divergence of Protein Sequences and Applications in Functional Genomics. Current Genomics. 7: 87-96.
Eisen JA, Wu M, Wu D, Thiagarajan M, Wortman JR, Badger JH, Ren Q, Amedeo P, Jones KM, Tallon LJ, Delcher AL, Salzberg SL, delToro C, Ryder HF, Williamson SC, Barbeau RA, Silva1 JC, Haas BJ, Majoros WH, Farzad M, Carlton JM, Garg J, Pearlman RE, Karrer KM, Sun L, Smith RK, Manning G, Elde NC, Turkewitz AP, Asai DJ, Wilkes DE, Wang Y, Cai H, Collins K, Wilamowska K, Ruzzo WL, Weinberg Z, Stewart BA, Lee SL, Wloga D, Rogowski K, Frankel J, Gaertig J, Tsao C, Gorovsky MA, Keeling PJ, Waller RF, Patron NJ, Cherry JM, Stover NA, Krieger CJ, Hamilton EP, Orias E, Coyne RS. (2006) Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote. PLoS Biology. 4(9):e286.
Florens L, Liu X, Wang Y, Yang S, Schwartz O, Peglar M, Carucci DJ, Yates JR 3rd, Wu Y (2004) Proteomics approach reveals novel proteins on the surface of malaria-infected erythrocytes. Molecular and Biochemical Parasitology. 135(1):1-11.
Wang Y, Wu Y(2004) Computer assisted searches for drug targets with emphasis on malarial proteases and their inhibitors. Current Drug Targets: Infectious Disorders. 4(1):25-40.
Feng X, Carlton JM, Joy DA, Mu J, Furuya T, Suh B, Wang Y, Barnwell JW, Su X-Z. (2003) Genome diversity and the origin of Plasmodium vivax. Proc. Natl. Acad. Sci. USA. 100:8502-8507.
Wu Y, Wang X, Liu X, Wang Y (2003) Data-mining approaches reveal hidden families of proteases in the genome of Malaria parasite. Genome Research. 13: 601-616.
Wang Y, Pollak E (2002) The effective number of a population that varies cyclically in size. II. Continuous generations. Mathematical Biosciences. 179: 161-181.Wang Y, Gu X (2002) Evolutionary and expression profiles of gene families crucial for central nervous system development. Information Sciences. 145:215-223.
Gu X, Wang Y, Gu J (2002) Age-distribution of human gene families showing equal roles of large and small-scale duplications in vertebrate evolution. Nature Genetics. 31:205-209.
Gu J, Wang Y, Gu X (2002) Functional divergence of Jak gene family: an evolutionary perspective. Journal of Molecular Evolution. 54:725-733.
Gu X, Wang Y, Gu J (2002) Evolutionary perspective for functional divergence of gene family and Applications in functional genomics. Current Genomics. 3:201-211.
Wang Y, Gu X (2001) Functional divergence in caspase gene family and altered functional constraints: statistical analysis and prediction. Genetics. 158: 1311-1320.
Wang Y, Pollak E (2000) The effective number of a population that varies cyclically in size. I. Discrete generations. Mathematical Biosciences. 166: 1-21.
Wang Y, Gu X (2000) Evolutionary patterns of gene families generated in the early stage of vertebrates. Journal of Molecular Evolution. 51:88-96.