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Yufeng Wang

TitleProfessor
InstitutionUniversity of Texas at San Antonio
DepartmentDepartment of biology
AddressUniversity of Texas at San Antonio
One UTSA Circle
San Antonio TX 78249
Phone(210) 458-6492
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    Research in Dr. Wang’s lab focuses on the comparative genomics, molecular evolution, and systems biology of gene families. Approaches range from the use of cutting edge bioinformatic and genomic tools to statistical modeling and analysis based on evolution and population genetics theory. The lab is particularly interested in the evolutionary mechanisms and systems biology of infectious diseases and the molecular evolution of vertebrate gene families.
    The lab uses genomic and related data, coupled with other biochemical and microbiological information, to identify new therapeutic targets and to further study the underlying evolutionary mechanisms in diseases such as malaria. Their research has a particular emphasis on the age distribution and functional divergence of duplicated genes, which are believed to provide the raw material for functional novelty in higher eukaryotes. They are also interested in the association between sequence evolution and gene network regulation.

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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
    Newest   |   Oldest   |   Most Cited   |   Most Discussed   |   Timeline   |   Field Summary   |   Plain Text
    PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. 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. PMID: 26974960.
      Citations: 3     Fields:    Translation:Animals
    2. 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:S1. PMID: 26100579.
      Citations: 1     Fields:    Translation:HumansAnimalsCells
    3. 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. PMID: 25861922.
      Citations:    Fields:    Translation:AnimalsCells
    4. 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. PMID: 25539848.
      Citations: 1     Fields:    Translation:AnimalsCells
    5. Wang HC, Greene WA, Kaini RR, Shen-Gunther J, Chen HI, Cai H, Wang Y. Profiling the microRNA Expression in Human iPS and iPS-derived Retinal Pigment Epithelium. Cancer Inform. 2014; 13(Suppl 5):25-35. PMID: 25392691.
      Citations:    
    6. Zhou Z, Li Y, Sun N, Sun Z, Lv L, Wang Y, Shen L, Li YQ. Function and evolution of two forms of SecDF homologs in Streptomyces coelicolor. PLoS One. 2014; 9(8):e105237. PMID: 25140821.
      Citations: 4     Fields:    Translation:Cells
    7. Foret MR, Sandstrom RS, Rhodes CT, Wang Y, Berger MS, Lin CH. Molecular targets of chromatin repressive mark H3K9me3 in primate progenitor cells within adult neurogenic niches. Front Genet. 2014; 5:252. PMID: 25126093.
      Citations:    
    8. Sandstrom RS, Foret MR, Grow DA, Haugen E, Rhodes CT, Cardona AE, Phelix CF, Wang Y, Berger MS, Lin CH. Epigenetic regulation by chromatin activation mark H3K4me3 in primate progenitor cells within adult neurogenic niche. Sci Rep. 2014 Jun 20; 4:5371. PMID: 24947819.
      Citations: 11     Fields:    Translation:AnimalsCells
    9. Cai H, Hong C, Lilburn TG, Rodriguez AL, Chen S, Gu J, Kuang R, Wang Y. A novel subnetwork alignment approach predicts new components of the cell cycle regulatory apparatus in Plasmodium falciparum. BMC Bioinformatics. 2013; 14 Suppl 12:S2. PMID: 24267797.
      Citations: 2     Fields:    Translation:AnimalsCells
    10. Cai H, Hong C, Gu J, Lilburn TG, Kuang R, Wang Y. Module-based subnetwork alignments reveal novel transcriptional regulators in malaria parasite Plasmodium falciparum. BMC Syst Biol. 2012; 6 Suppl 3:S5. PMID: 23282319.
      Citations: 8     Fields:    Translation:AnimalsCells
    11. Cai H, Zhou Z, Gu J, Wang Y. Comparative Genomics and Systems Biology of Malaria Parasites Plasmodium. Curr Bioinform. 2012 Dec 01; 7(4). PMID: 24298232.
      Citations:    
    12. Zhou Z, Gu J, Li YQ, Wang Y. Genome plasticity and systems evolution in Streptomyces. BMC Bioinformatics. 2012 Jun 25; 13 Suppl 10:S8. PMID: 22759432.
      Citations: 15     Fields:    Translation:Cells
    13. Lilburn TG, Cai H, Zhou Z, Wang Y. Protease-associated cellular networks in malaria parasite Plasmodium falciparum. BMC Genomics. 2011 Dec 23; 12 Suppl 5:S9. PMID: 22369208.
      Citations: 5     Fields:    Translation:AnimalsCells
    14. Coyne RS, Hannick L, Shanmugam D, Hostetler JB, Brami D, Joardar VS, Johnson J, Radune D, Singh I, Badger JH, 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, Wu M, Martens C, Van de Peer Y, Roos DS, Cassidy-Hanley DM, Clark TG. 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 Biol. 2011 Oct 17; 12(10):R100. PMID: 22004680.
      Citations: 30     Fields:    Translation:AnimalsCells
    15. Zhou Z, Gu J, Du YL, Li YQ, Wang Y. The -omics Era- Toward a Systems-Level Understanding of Streptomyces. Curr Genomics. 2011 Sep; 12(6):404-16. PMID: 22379394.
      Citations:    
    16. Cai H, Kuang R, Gu J, Wang Y. Proteases in malaria parasites - a phylogenomic perspective. Curr Genomics. 2011 Sep; 12(6):417-27. PMID: 22379395.
      Citations:    
    17. Cai H, Gu J, Wang Y. Core genome components and lineage specific expansions in malaria parasites plasmodium. BMC Genomics. 2010 Dec 01; 11 Suppl 3:S13. PMID: 21143780.
      Citations: 5     Fields:    Translation:HumansAnimals
    18. Roy Choudhury D, Small C, Wang Y, Mueller PR, Rebel VI, Griswold MD, McCarrey JR. Microarray-based analysis of cell-cycle gene expression during spermatogenesis in the mouse. Biol Reprod. 2010 Oct; 83(4):663-75. PMID: 20631398.
      Citations: 6     Fields:    Translation:AnimalsCells
    19. Lilburn TG, Gu J, Cai H, Wang Y. Comparative genomics of the family Vibrionaceae reveals the wide distribution of genes encoding virulence-associated proteins. BMC Genomics. 2010 Jun 10; 11:369. PMID: 20537180.
      Citations: 6     Fields:    Translation:Cells
    20. Gu J, Wang Y, Lilburn T. A comparative genomics, network-based approach to understanding virulence in Vibrio cholerae. J Bacteriol. 2009 Oct; 191(20):6262-72. PMID: 19666715.
      Citations: 5     Fields:    Translation:HumansCells
    21. Gu J, Neary J, Cai H, Moshfeghian A, Rodriguez SA, Lilburn TG, Wang Y. Genomic and systems evolution in Vibrionaceae species. BMC Genomics. 2009 Jul 07; 10 Suppl 1:S11. PMID: 19594870.
      Citations: 9     Fields:    Translation:Cells
    22. Wang Y, Lilburn TG. Biological Resource Centers and Systems Biology. Bioscience. 2009 Feb 11; 59(2):113-125. PMID: 20157346.
      Citations: 1     Fields:    
    23. Huang Y, Tienda-Luna IM, Wang Y. A Survey of Statistical Models for Reverse Engineering Gene Regulatory Networks. IEEE Signal Process Mag. 2009 Jan 01; 26(1):76-97. PMID: 20046885.
      Citations:    
    24. Kuang R, Gu J, Cai H, Wang Y. Improved prediction of malaria degradomes by supervised learning with SVM and profile kernel. Genetica. 2009 May; 136(1):189-209. PMID: 19057851.
      Citations: 10     Fields:    Translation:Animals
    25. Tienda-Luna IM, Yin Y, Huang Y, Padillo DP, Perez MC, Wang Y. Constructing gene networks using variational Bayesian variable selection. Artif Life. 2008; 14(1):65-79. PMID: 18171131.
      Citations:    Fields:    
    26. Tienda-Luna IM, Yin Y, Carrion MC, Huang Y, Cai H, Sanchez M, Wang Y. Inferring the skeleton cell cycle regulatory network of malaria parasite using comparative genomic and variational Bayesian approaches. Genetica. 2008 Feb; 132(2):131-42. PMID: 17562188.
      Citations: 5     Fields:    Translation:HumansAnimals
    27. Lu Y, Tian Q, Liu F, Sanchez M, Wang Y. Interactive semisupervised learning for microarray analysis. IEEE/ACM Trans Comput Biol Bioinform. 2007 Apr-Jun; 4(2):190-203. PMID: 17473313.
      Citations:    Fields:    
    28. Gu J, Neary JL, Sanchez M, Yu J, Lilburn TG, Wang Y. Genome evolution and functional divergence in Yersinia. J Exp Zool B Mol Dev Evol. 2007 Jan 15; 308(1):37-49. PMID: 16838303.
      Citations: 2     Fields:    Translation:Cells
    29. Eisen JA, Coyne RS, Wu M, Wu D, Thiagarajan M, Wortman JR, Badger JH, Ren Q, Amedeo P, Jones KM, Tallon LJ, Delcher AL, Salzberg SL, Silva JC, Haas BJ, Majoros WH, Farzad M, Carlton JM, Smith RK, Garg J, Pearlman RE, Karrer KM, Sun L, Manning G, Elde NC, Turkewitz AP, Asai DJ, Wilkes DE, Wang Y, Cai H, Collins K, Stewart BA, Lee SR, Wilamowska K, Weinberg Z, Ruzzo WL, Wloga D, Gaertig J, Frankel J, Tsao CC, Gorovsky MA, Keeling PJ, Waller RF, Patron NJ, Cherry JM, Stover NA, Krieger CJ, del Toro C, Ryder HF, Williamson SC, Barbeau RA, Hamilton EP, Orias E. Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote. PLoS Biol. 2006 Sep; 4(9):e286. PMID: 16933976.
      Citations: 250     Fields:    Translation:AnimalsCells
    30. Chen G, Zhu Y, Wang Y, Xu X, Lu T. Determination of bioactive constituents in traditional Chinese medicines by CE with electrochemical detection. Curr Med Chem. 2006; 13(21):2467-85. PMID: 17017905.
      Citations: 3     Fields:    
    31. Florens L, Liu X, Wang Y, Yang S, Schwartz O, Peglar M, Carucci DJ, Yates JR, Wu Y. Proteomics approach reveals novel proteins on the surface of malaria-infected erythrocytes. Mol Biochem Parasitol. 2004 May; 135(1):1-11. PMID: 15287581.
      Citations: 66     Fields:    Translation:AnimalsCells
    32. Wang Y, Wu Y. Computer assisted searches for drug targets with emphasis on malarial proteases and their inhibitors. Curr Drug Targets Infect Disord. 2004 Mar; 4(1):25-40. PMID: 15032632.
      Citations: 6     Fields:    Translation:HumansAnimals
    33. Feng X, Carlton JM, Joy DA, Mu J, Furuya T, Suh BB, Wang Y, Barnwell JW, Su XZ. Single-nucleotide polymorphisms and genome diversity in Plasmodium vivax. Proc Natl Acad Sci U S A. 2003 Jul 08; 100(14):8502-7. PMID: 12799466.
      Citations: 35     Fields:    Translation:AnimalsCells
    34. Wu Y, Wang X, Liu X, Wang Y. Data-mining approaches reveal hidden families of proteases in the genome of malaria parasite. Genome Res. 2003 Apr; 13(4):601-16. PMID: 12671001.
      Citations: 60     Fields:    Translation:HumansAnimalsCells
    35. Wang Y, Pollak E. The effective number of a population that varies cyclically in size. II. Overlapping generations. Math Biosci. 2002 Sep-Oct; 179(2):161-81. PMID: 12208614.
      Citations: 2     Fields:    Translation:Animals
    36. Gu J, Wang Y, Gu X. Evolutionary analysis for functional divergence of Jak protein kinase domains and tissue-specific genes. J Mol Evol. 2002 Jun; 54(6):725-33. PMID: 12029354.
      Citations: 7     Fields:    Translation:HumansAnimalsCells
    37. Gu X, Wang Y, Gu J. Age distribution of human gene families shows significant roles of both large- and small-scale duplications in vertebrate evolution. Nat Genet. 2002 Jun; 31(2):205-9. PMID: 12032571.
      Citations: 82     Fields:    Translation:HumansAnimals
    38. Wang Y, Pollak E. The effective number of a population that varies cyclically in size. I. Discrete generations. Math Biosci. 2000 Jul; 166(1):1-21. PMID: 10882797.
      Citations: 1     Fields:    Translation:Animals
    39. Wang Y, Gu X. Evolutionary patterns of gene families generated in the early stage of vertebrates. J Mol Evol. 2000 Jul; 51(1):88-96. PMID: 10903375.
      Citations: 26     Fields:    Translation:Animals
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