Faculty list

Dr. Wen-Hsiung Li

Distinguished Research Fellow
Brown University, Providence, RI, USA Ph.D.
Research Fields
Evolutionary Genomics, Molecular Evolution, Bioinformatics, Population Genetics, Synthetic Biology
Major Research Achievements (2013-2017)
Research Interests
  • I. Evolution of gene regulation: The importance of regulatory evolution has been proposed long ago (for instance, in the conspicuous morphological differences between human and chimp), but it has not been well studied due to experimental limitations. Making use of recent advances we are pursuing the following studies:
     (1) Evolution of gene regulation in yeast strains and species. Our major question is whether evolution of gene regulation is mainly due to changes in cis elements or in trans factors. We are using NGS sequencing and real time PCR to study expression differences, computational analysis of genomic data to identify sites of interest, and site-directed mutagenesis and fitness assays to test effects of regulatory changes.
     (2) Evolution of cis-regulatory modules and gene networks. Using statistical and experimental approaches we are identifying cis elements and gene networks, and studying how they have evolved.
  • II. Development of statistical methods and computational analysis of genomic data.
     The huge amount of genomic data currently available is a tremendous resource for understanding the organization and evolution of genomes. We are currently developing tools for analysis of segmental duplications, protein interaction data, and genomic data.
  • III. Synthetic biology.
     Synthetic biology is a new approach to biotechnology, using a combination of DNA technology, systems biology, and bioinformatics tools to construct novel biological systems in a microbe to produce desirable products such as proteins or metabolites. This approach can save land space and reduce pollution and negative impacts on biodiversity.
    Ongoing projects
    Publications (2009-2017)
    1. Ke HM, Prachumwat A, Yu CP, Yang YT, Promsri V, Liu KF, Lo CF, Lu MYJ, Lai MC, Tsai IJ, Li WH*, 2017, “Comparative genomics of Vibrio campbellii strains and core species of the Vibrio Harveyi clade”, Scientific Reports, 7, 41394. (SCI) (IF: 5.228; SCI ranking: 11.1%)
    2. Chen CK, Yu CP, Li SC, Wu SM, Lu MJ, Chen YH, Chen DR, Ng CS, Ting CT, Li WH, 2017, “Identification and evolutionary analysis of long non-coding RNAs in zebra finch.”, BMC genomics, 18(1), 117. (SCI) (IF: 3.867; SCI ranking: 25.9%,19.9%)
    3. Li H, Xiang-Yu J, Dai G, Gu Z, Ming C, Yang Z, Ryder OA, Li WH*, Fu YX, Zhang YP, 2016, “Large numbers of vertebrates began rapid population decline in the late 19th century.”, Proceedings of the National Academy of Sciences of the United States of America, 113(49), 14079-14084. (SCI) (IF: 9.423; SCI ranking: 6.3%)
    4. Tsai KJ, Lu MJ, Yang KJ, Li M, Teng Y, Chen S, Ku MS, Li WH*, 2016, “Assembling the Setaria italica L. Beauv. genome into nine chromosomes and insights into regions affecting growth and drought tolerance.”, Scientific reports, 6, 35076. (SCI) (IF: 5.228; SCI ranking: 11.1%)
    5. Bhattacharjee MJ, Yu CP, Lin JJ, Ng CS, Wang TY, Lin HH, Li WH*, 2016, “Regulatory Divergence among Beta-Keratin Genes during Bird Evolution.”, Molecular biology and evolution, 33(11), 2769-2780. (SCI) (IF: 13.649; SCI ranking: 1.7%,2.4%,4.3%)
    6. Chen CK, Ng CS, Wu SM, Chen JJ, Cheng PL, Wu P, Lu MY, Chen DR, Chuong CM, Cheng HC, Ting CT, Li WH*, 2016, “Regulatory Differences in Natal Down Development between Altricial Zebra Finch and Precocial Chicken.”, Molecular biology and evolution, 33(8), 2030-2043. (SCI) (IF: 13.649; SCI ranking: 1.7%,2.4%,4.3%)
    7. Mei-Ju May Chen, Li-Kai Chen, Yu-Shing Lai, Yu-Yu Lin, Dung-Chi Wu, Yi-An Tung, Kwei-Yan Liu, Hsueh-Tzu Shih, Yi-Jyun Chen, Yan-Liang Lin, Li-Ting Ma, Jian-Long Huang, Po-Chun Wu, Ming-Yi Hong, Fang-Hua Chu, June-Tai Wu, Wen-Hsiung Li* and Chien-Yu Chen*, 2016, “Integrating RNA-seq and ChIP-seq data to characterize long non-coding RNAs in Drosophila melanogaster”, BMC Genomics, 17, 220. (SCI) (IF: 3.867; SCI ranking: 25.9%,19.9%)
    8. Huang CF, Chang YM, Lin JJ, Yu CP, Lin HH, Liu WY, Yeh S, Tu SL, Wu SH, Ku MS, Li WH*, 2016, “Insights into the regulation of C leaf development from comparative transcriptomic analysis.”, Current opinion in plant biology, 30, 1-10. (SCI) (IF: 6.78; SCI ranking: 3.3%)
    9. Yu CP, Lin JJ, Li WH*, 2016, “Positional distribution of transcription factor binding sites in Arabidopsis thaliana.”, Scientific reports, 6, 25164. (SCI) (IF: 5.228; SCI ranking: 11.1%)
    10. Su-Ying Yeh, Hau-Wen Chen, Chun-Yeung Ng, Chu-Yin Lin, Tung-Hai Tseng, Wen-Hsiung Li, Maurice S. B. Ku, 2015, “Down-Regulation of Cytokinin Oxidase 2 Expression Increases Tiller Number and Improves Rice Yield”, Rice, 8(1), 36. (SCI) (IF: 3.417; SCI ranking: 8.4%)
    11. Chen Siang Ng, Chih-Kuan Chen, Wen-Lang Fan, Ping Wu, Siao-Man Wu, Jiun-Jie Chen, Yu-Ting Lai, Chi-Tang Mao, Mei-Yeh Jade Lu, Di-Rong Chen, Ze-Shiang Lin, Kai-Jung Yang, Yuan-An Sha, Tsung-Che Tu, Chih-Feng Chen, Cheng-Ming Chuong and Wen-Hsiung Li*, 2015, “Transcriptomic analyses of regenerating adult feathers in chicken”, BMC Genomics, 16, 756. (SCI) (IF: 3.867; SCI ranking: 25.9%,19.9%)
    12. Jui-Jen Chang, Caroline Thia, Hao-Yeh Lin, Hsien-Lin Liu, Feng-Ju Ho, Jiunn-Tzong Wu, Ming-Che Shih, Wen-Hsiung Li, Chieh-Chen Huang, 2015, “Integrating an algal β-carotene hydroxylase gene into a designed carotenoid-biosynthesis pathway increases carotenoid production in yeast”, Bioresource Technology, 184, 2-8. (SCI) (IF: 4.917; SCI ranking: 10.6%,7.1%,12.5%)
    13. Lin YL, Ma LT, Lee YR, Lin SS, Wang SY, Chang TT, Shaw JF, Li WH, Chu FH, 2015, “MicroRNA-Like Small RNAs Prediction in the Development of Antrodia cinnamomea”, PLoS One, 10(4), e0123245. (SCI) (IF: 3.057; SCI ranking: 17.5%)
    14. Cheng F, Liu C, Lin CC, Zhao J, Jia P, Li WH, Zhao Z, 2015, “A Gene Gravity Model for the Evolution of Cancer Genomes: A Study of 3,000 Cancer Genomes across 9 Cancer Types.”, PLoS computational biology, 11(9), e1004497. (SCI) (IF: 4.587; SCI ranking: 11.7%,8.9%)
    15. Chen SC, Tsai TH, Chung CH, Li WH, 2015, “Dynamic association rules for gene expression data analysis.”, BMC genomics, 16, 786. (SCI) (IF: 3.867; SCI ranking: 25.9%,19.9%)
    16. Shiao MS, Chang JM, Fan WL, Lu MY, Notredame C, Fang S, Kondo R, Li WH*, 2015, “Expression Divergence of Chemosensory Genes between Drosophila sechellia and Its Sibling Species and Its Implications for Host Shift.”, Genome biology and evolution, 7(10), 2843-58. (SCI) (IF: 4.098; SCI ranking: 19.9%,21.7%)
    17. Ling S, Hu Z, Yang Z, Yang F, Li Y, Lin P, Chen K, Dong L, Cao L, Tao Y, Hao L, Chen Q, Gong Q, Wu D, Li W, Zhao W, Tian X, Hao C, Hungate EA, Catenacci DV, Hudson RR, Li WH*, Lu X, Wu CI, 2015, “Extremely high genetic diversity in a single tumor points to prevalence of non-Darwinian cell evolution.”, Proceedings of the National Academy of Sciences of the United States of America, 112(47), E6496-E6505. (SCI) (IF: 9.423; SCI ranking: 6.3%)
    18. Schaefke B, Wang TY, Wang CY, Li WH*, 2015, “Gains and Losses of Transcription Factor Binding Sites in Saccharomyces cerevisiae and Saccharomyces paradoxus.”, Genome biology and evolution, 7(8), 2245-2257. (SCI) (IF: 4.098; SCI ranking: 19.9%,21.7%)
    19. Wu P, Ng CS, Yan J, Lai YC, Chen CK, Lai YT, Wu SM, Chen JJ, Luo W, Widelitz RB, Li WH*, Chuong CM, 2015, “Topographical mapping of alpha- and beta-keratins on developing chicken skin integuments: Functional interaction and evolutionary perspectives.”, Proceedings of the National Academy of Sciences of the United States of America, 112(49), E6770-E6779. (SCI) (IF: 9.423; SCI ranking: 6.3%)
    20. Yu CP, Chen SC, Chang YM, Liu WY, Lin HH, Lin JJ, Chen HJ, Lu YJ, Wu YH, Lu MY, Lu CH, Shih AC, Ku MS, Shiu SH, Wu SH, Li WH*, 2015, “Transcriptome dynamics of developing maize leaves and genomewide prediction of cis elements and their cognate transcription factors.”, Proceedings of the National Academy of Sciences of the United States of America, 112(19), E2477-86. (SCI) (IF: 9.423; SCI ranking: 6.3%)
    21. Tsai DY, Hung KH, Lin IY, Su ST, Wu SY, Chung CH, Wang TC, Li WH, Shih AC, Lin KI, 2015, “Uncovering MicroRNA Regulatory Hubs that Modulate Plasma Cell Differentiation.”, Scientific reports, 5, 17957. (SCI) (IF: 5.228; SCI ranking: 11.1%)
    22. Lin CC, Chang YM, Pan CT, Chen CC, Ling L, Tsao KC, Yang RB, Li WH*, 2014, “Functional Evolution of cardiac microRNAs in heart development and functions.”, Mol Biol Evol., 31(10), 2722-2734. (SCI) (IF: 13.649; SCI ranking: 1.7%,2.4%,4.3%)
    23. Chang JJ, C. Y. Ho, C. T. Mao, N. Barham, Y. R. Huang, F. J. Ho, Y. C. Wu, Y. H. Hou, M. C. Shih, W. H. Li, C. C. Huang, 2014, “A thermo- and toxin-tolerant kefir yeast for biorefinery and biofuel production”, Applied Energy, 132, 465-474. (SCI) (IF: 5.746; SCI ranking: 4.4%,11.4%)
    24. Lu MY, Fan WL, Wang WF, Chen T, Tang YC, Chu FH, Chang TT, Wang SY, Li MY, Chen YH, Lin ZS, Yang KJ, Chen SM, Teng YC, Lin YL, Shaw JF, Wang TF, Li WH*, 2014, “Genomic and transcriptomic analyses of the medicinal fungus Antrodia cinnamomea for its metabolite biosynthesis and sexual development.”, Proceedings of the National Academy of Sciences of the United States of America, 111(44), E4743-E4752. (SCI) (IF: 9.423; SCI ranking: 6.3%)
    25. Ng CS, Wu P, Fan WL, Yan J, Chen CK, Lai YT, Wu SM, Mao CT, Chen JJ, Lu MY, Ho MR, Widelitz RB, Chen CF, Chuong CM, Li WH*, 2014, “Genomic Organization, Transcriptomic Analysis, and Functional Characterization of Avian alpha- and beta-Keratins in Diverse Feather Forms.”, Genome biology and evolution, 6(9), 2258-73. (SCI) (IF: 4.098; SCI ranking: 19.9%,21.7%)
    26. Lin JJ, Yu CP, Chang YM, Chen SC, Li WH*, 2014, “Maize and millet transcription factors annotated using comparative genomic and transcriptomic data.”, BMC genomics, 15, 818. (SCI) (IF: 3.867; SCI ranking: 25.9%,19.9%)
    27. Cheng F, Jia P, Wang Q, Lin CC, Li WH, Zhao Z., 2014, “Studying tumorigenesis through network evolution and somatic mutational perturbations in the cancer interactome.”, Mol Biol Evol., 31, 2156-2169. (SCI) (IF: 13.649; SCI ranking: 1.7%,2.4%,4.3%)
    28. Yang YT, Lee DY, Wang Y, Hu JM, Li WH, Leu JH, Chang GD, Ke HM, Kang ST, Lin SS, Kou GH, Lo CF, 2014, “The genome and occlusion bodies of marine Penaeus monodon nudivirus (PmNV, also known as MBV and PemoNPV) suggest that it should be assigned to a new nudivirus genus that is distinct from the terrestrial nudiviruses.”, BMC genomics, 15, 628. (SCI) (IF: 3.867; SCI ranking: 25.9%,19.9%)
    29. Chang CH, Fan TC, Yu JC, Liao GS, Lin YC, Shih A, Li WH* and Yu A.*, 2014, “The prognostic significance of RUNX2 and miR-10a/10b and their inter-relationship in breast cancer”, Journal of Translational Medicine, 12, 257. (SCI) (IF: 3.694; SCI ranking: 24.2%)
    30. Wang TY, Huang CJ, Chen HL, Ho PC, Ke HM, Cho HY, Ruan SK, Hung KY, Wang IL, Cai YW, Sung HM, Li WH*, Shih MC*, 2013, “Systematic screening of glycosylation- and trafficking-associated gene knockouts in Saccharomyces cerevisiae identifies mutants with improved heterologous exocellulase activity and host secretion”, BMC Biotechnology, 13(1), 71. (SCI) (IF: 2.452; SCI ranking: 39.1%)
    31. Liu WY, Chang YM, Chen SC, Lu CH, Wu YH, Lu MY, Chen DR, Shih AC, Sheue CR, Huang HC, Yu CP, Lin HH, Shiu SH, Sun-Ben Ku M, Li WH*, 2013, “Anatomical and transcriptional dynamics of maize embryonic leaves during seed germination.”, Proceedings of the National Academy of Sciences of the United States of America, 110(10), 3979-3984. (SCI) (IF: 9.423; SCI ranking: 6.3%)
    32. Chu TC, Lu CH, Liu T, Lee GC, Li WH, Shih AC*, 2013, “Assembler for de novo assembly of large genomes”, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, E3417-E3424. (SCI) (IF: 9.423; SCI ranking: 6.3%)
    33. Chang JJ, Ho FJ, Ho CY, Wu YC, Hou YH, Huang CC, Shih MC, Li WH*, 2013, “Assembling a cellulase cocktail and a cellodextrin transporter into a yeast host for CBP ethanol production.”, Biotechnology for biofuels, 6(1), 19. (SCI) (IF: 6.444; SCI ranking: 7.5%,8%)
    34. Wang HC, Chu FH, Chien SC, Liao JW, Hsieh HW, Li WH, Lin CC, Shaw JF, Kuo YH, Wang SY, 2013, “Establishment of the metabolite profile for an Antrodia cinnamomea health food product and investigation of its chemoprevention activity.”, Journal of agricultural and food chemistry, 61(36), 8556-64. (SCI) (IF: 2.857; SCI ranking: 5.3%,19.4%,16%)
    35. Fan WL, Ng CS, Chen CF, Lu MY, Chen YH, Liu CJ, Wu SM, Chen CK, Chen JJ, Mao CT, Lai YT, Lo WS, Chang WH, Li WH*, 2013, “Genome-wide patterns of genetic variation in two domestic chickens”, Genome Biol Evol., 5, 1376-1392. (SCI) (IF: 4.098; SCI ranking: 19.9%,21.7%)
    36. Chang YM, Chang CL, Li WH, Shih AC, 2013, “Historical profiling of maize duplicate genes sheds light on the evolution of C4 photosynthesis in grasses.”, Molecular phylogenetics and evolution, 66(2), 453-462. (SCI) (IF: 3.792; SCI ranking: 27.7%,28.3%,29.1%)
    37. Lin Z, Wang TY, Tsai BS, Wu FT, Yu FJ, Tseng YJ, Sung HM, Li WH*, 2013, “Identifying cis-regulatory changes involved in the evolution of aerobic fermentation in yeasts”, Genome Biol Evol, 6, 1065-1078. (SCI) (IF: 4.098; SCI ranking: 19.9%,21.7%)
    38. Schaefke B, Emerson JJ, Wang TY, Lu MY, Hsieh LC, Li WH*, 2013, “Inheritance of gene expression level and selective constraints on trans- and cis-regulatory changes in yeast”, Mol Biol Evol., 30, 2121-2133. (SCI) (IF: 13.649; SCI ranking: 1.7%,2.4%,4.3%)
    39. Ha M, Hong S, Li WH* , 2013, “Predicting the probability of H3K4me3 occupation at a base pair from the genome sequence context”, Bioinformatics, 29, 1199-11205. (SCI) (IF: 5.766; SCI ranking: 9.1%,5.4%,9.3%)
    40. Shiao MS, Fan WL, Fang S, Lu MYJ, Kondo R, Li WH*, 2013, “Transcriptional profiling of chemosensory genes in adult Drosophila antennae by High Throughput Sequencing”, ZOOLOGICAL STUDIES, 52, 42. (SCI) (IF: 0.885; SCI ranking: 56.5%)
    41. Chen HL, Chen YC, Lu MY, Chang JJ, Wang HT, Ke HM, Wang TY, Ruan SK, Wang TY, Hung KY, Cho HY, Lin WT, Shih MC, Li WH*, 2012, “A highly efficient beta-glucosidase from the buffalo rumen fungus Neocallimastix patriciarum W5.”, Biotechnology for biofuels, 5(1), 24. (SCI) (IF: 6.444; SCI ranking: 7.5%,8%)
    42. Chang YM, Liu WY, Shih AC, Shen MN, Lu CH, Lu MY, Yang HW, Wang TY, Chen SC, Chen SM, Li WH*, Ku MS, 2012, “Characterizing regulatory and functional differentiation between maize mesophyll and bundle sheath cells by transcriptomic analysis.”, Plant physiology, 160(1), 165-177. (SCI) (IF: 6.28; SCI ranking: 3.8%)
    43. Tseng YY, Li WH*, 2012, “Classification of protein functional surfaces using structural characteristics.”, Proceedings of the National Academy of Sciences of the United States of America, 109(4), 1170-1175. (SCI) (IF: 9.423; SCI ranking: 6.3%)
    44. Chang HT, Li SC, Ho MR, Pan HW, Ger LP, Hu LY, Yu SY, Li WH, Tsai KW, 2012, “Comprehensive analysis of microRNAs in breast cancer.”, BMC genomics, 13 Suppl 7, S18. (SCI) (IF: 3.867; SCI ranking: 25.9%,19.9%)
    45. Rest JS, Bullaughey K, Morris GP, Li WH*, 2012, “Contribution of transcription factor binding site motif variants to condition-specific gene expression patterns in budding yeast.”, PloS one, 7(2), e32274. (SCI) (IF: 3.057; SCI ranking: 17.5%)
    46. Ho CY, Chang JJ, Lee SC, Chin TY, Shih MC, Li WH, Huang CC, 2012, “Development of cellulosic ethanol production process via co-culturing of artificial cellulosomal Bacillus and kefir yeast”, Applied Energy, 100,27-32. (SCI) (IF: 5.746; SCI ranking: 4.4%,11.4%)
    47. Woo YH, Li WH*, 2012, “DNA replication timing and selection shape the landscape of nucleotide variation in cancer genomes.”, Nature communications, 3, 1004. (SCI) (IF: 11.329; SCI ranking: 4.8%)
    48. Lin Z, Li WH*, 2012, “Evolution of 5' untranslated region length and gene expression reprogramming in yeasts.”, Molecular biology and evolution, 29(1), 81-89. (SCI) (IF: 13.649; SCI ranking: 1.7%,2.4%,4.3%)
    49. Woo YH, Li WH*, 2012, “Evolutionary conservation of histone modifications in mammals.”, Molecular biology and evolution, 29(7), 1757-1767. (SCI) (IF: 13.649; SCI ranking: 1.7%,2.4%,4.3%)
    50. Li SC, Tsai KW, Pan HW, Jeng YM, Ho MR, Li WH*, 2012, “MicroRNA 3' end nucleotide modification patterns and arm selection preference in liver tissues.”, BMC systems biology, 6 Suppl 2, S14. (SCI) (IF: 2.208; SCI ranking: 19.6%)
    51. Chang JJ, Ho CY, Ho FJ, Tsai TY, Ke HM, Wang CH, Chen HL, Shih MC, Huang CC, Li WH*, 2012, “PGASO: A synthetic biology tool for engineering a cellulolytic yeast.”, Biotechnology for biofuels, 5(1), 53. (SCI) (IF: 6.444; SCI ranking: 7.5%,8%)
    52. Tseng YY, Li WH*, 2012, “PSC: protein surface classification.”, Nucleic acids research, 40(W1), W435-W439. (SCI) (IF: 9.202; SCI ranking: 6.2%)
    53. Tseng CW, Huang HC, Shih AC, Chang YY, Hsu CC, Chang JY, Li WH, Juan HF, 2012, “Revealing the anti-tumor effect of artificial miRNA p-27-5p on human breast carcinoma cell line T-47D.”, International journal of molecular sciences, 13(5), 6352-69. (SCI) (IF: 3.257; SCI ranking: 38.1%,31.9%)
    54. Ng CS, Wu P, Foley J, Foley A, McDonald ML, Juan WT, Huang CJ, Lai YT, Lo WS, Chen CF, Leal SM, Zhang H, Widelitz RB, Patel PI, Li WH*, Chuong CM, 2012, “The chicken frizzle feather is due to an alpha-keratin (KRT75) mutation that causes a defective rachis.”, PLoS genetics, 8(7), e1002748. (SCI) (IF: 6.661; SCI ranking: 9%)
    55. Shiao MS, Chang AY, Liao BY, Ching YH, Lu MY, Chen SM, Li WH*, 2012, “Transcriptomes of mouse olfactory epithelium reveal sexual differences in odorant detection.”, Genome biology and evolution, 4(5), 703-712. (SCI) (IF: 4.098; SCI ranking: 19.9%,21.7%)
    56. Lin YS, Liu FG, Wang TY, Pan CT, Chang WT, Li WH, 2011, “A simple method using PyrosequencingTM to identify de novo SNPs in pooled DNA samples.”, Nucleic acids research, 39(5), e28. (SCI) (IF: 9.202; SCI ranking: 6.2%)
    57. Kumar KJ, Chu FH, Hsieh HW, Liao JW, Li WH, Lin JC, Shaw JF, Wang SY, 2011, “Antroquinonol from ethanolic extract of mycelium of Antrodia cinnamomea protects hepatic cells from ethanol-induced oxidative stress through Nrf-2 activation.”, Journal of Ethnopharmacology, 136(1), 168-177. (SCI) (IF: 3.055; SCI ranking: 17.2%,28.6%,27.1%,8.3%)
    58. Ha M, Ng DW, Li WH, Chen ZJ, 2011, “Coordinated histone modifications are associated with gene expression variation within and between species.”, Genome research, 21(4), 590-598. (SCI) (IF: 11.351; SCI ranking: 3.6%,2.5%,3.5%)
    59. Tseng YY, Li WH*, 2011, “Evolutionary approach to predicting the binding site residues of a protein from its primary sequence.”, Proceedings of the National Academy of Sciences of the United States of America, 108(13), 5313-5318. (SCI) (IF: 9.423; SCI ranking: 6.3%)
    60. Lin Z, Li WH*, 2011, “Expansion of hexose transporter genes was associated with the evolution of aerobic fermentation in yeasts.”, Molecular biology and evolution, 28(1), 131-42. (SCI) (IF: 13.649; SCI ranking: 1.7%,2.4%,4.3%)
    61. Wang TY, Chen HL, Lu MY, Chen YC, Sung HM, Mao CT, Cho HY, Ke HM, Hwa TY, Ruan SK, Hung KY, Chen CK, Li JY, Wu YC, Chen YH, Chou SP, Tsai YW, Chu TC, Shih CC, Li WH*, Shih MC, 2011, “Functional characterization of cellulases identified from the cow rumen fungus Neocallimastix patriciarum W5 by transcriptomic and secretomic analyses.”, Biotechnology for biofuels, 4, 24. (SCI) (IF: 6.444; SCI ranking: 7.5%,8%)
    62. Hanada K, Sawada Y, Kuromori T, Klausnitzer R, Saito K, Toyoda T, Shinozaki K, Li WH*, Hirai MY, 2011, “Functional compensation of primary and secondary metabolites by duplicate genes in Arabidopsis thaliana.”, Molecular biology and evolution, 28(1):377-382. (SCI) (IF: 13.649; SCI ranking: 1.7%,2.4%,4.3%)
    63. Woo YH, Li WH*, 2011, “Gene clustering pattern, promoter architecture, and gene expression stability in eukaryotic genomes.”, Proceedings of the National Academy of Sciences of the United States of America, 108(8), 3306-3311. (SCI) (IF: 9.423; SCI ranking: 6.3%)
    64. Nikaido M, Sasaki T, Emerson JJ, Aibara M, Mzighani SI, Budeba YL, Ngatunga BP, Iwata M, Abe Y, Li WH*, Okada N, 2011, “Genetically distinct coelacanth population off the northern Tanzanian coast.”, Proceedings of the National Academy of Sciences of the United States of America, 108(44), 18009-18013. (SCI) (IF: 9.423; SCI ranking: 6.3%)
    65. Lin TY, Chen CY, Chien SC, Hsiao WW, Chu FH, Li WH, Lin CC, Shaw JF, Wang SY, 2011, “Metabolite Profiles for Antrodia cinnamomea Fruiting Bodies Harvested at Different Culture Ages and from Different Wood Substrates.”, Journal of agricultural and food chemistry, 59(14), 7626-7635. (SCI) (IF: 2.857; SCI ranking: 5.3%,19.4%,16%)
    66. Yun J, Frankenberger CA, Kuo WL, Boelens MC, Eves EM, Cheng N, Liang H, Li WH, Ishwaran H, Minn AJ, Rosner MR, 2011, “Signalling pathway for RKIP and Let-7 regulates and predicts metastatic breast cancer.”, The EMBO journal, 30(21), 4500-14. (SCI) (IF: 9.643; SCI ranking: 5.2%,8%)
    67. Lin Z, Li WH*, 2011, “The evolution of aerobic fermentation in Schizosaccharomyces pombe was associated with regulatory reprogramming but not nucleosome reorganization.”, Molecular biology and evolution, 28(4), 1407-1413. (SCI) (IF: 13.649; SCI ranking: 1.7%,2.4%,4.3%)
    68. Chen SC, Chuang TJ, Li WH*, 2011, “The Relationships Among MicroRNA Regulation, Intrinsically Disordered Regions, and Other Indicators of Protein Evolutionary Rate.”, Molecular biology and evolution, 28(9), 2513-2520. (SCI) (IF: 13.649; SCI ranking: 1.7%,2.4%,4.3%)
    69. Tang T, Kumar S, Shen Y, Lu J, Wu ML, Shi S, Li WH, Wu CI, 2010, “Adverse interactions between micro-RNAs and target genes from different species.”, Proceedings of the National Academy of Sciences of the United States of America, 107(29), 12935-12940. (SCI) (IF: 9.423; SCI ranking: 6.3%)
    70. Tseng YY, Chen ZJ, Li WH*, 2010, “fPOP: footprinting functional pockets of proteins by comparative spatial patterns.”, Nucleic acids research, 38(Database issue), D288-95. (SCI) (IF: 9.202; SCI ranking: 6.2%)
    71. Chen FC, Chen CJ, Li WH, Chuang TJ, 2010, “Gene family size conservation is a good indicator of evolutionary rates.”, Molecular biology and evolution, 27:1750-1758. (SCI) (IF: 13.649; SCI ranking: 1.7%,2.4%,4.3%)
    72. Emerson JJ, Hsieh LC, Sung HM, Wang TY, Huang CJ, Lu HH, Lu MY, Wu SH, Li WH*, 2010, “Natural selection on cis and trans regulation in yeasts.”, Genome research, 20(6), 826-836. (SCI) (IF: 11.351; SCI ranking: 3.6%,2.5%,3.5%)
    73. Chen SC, Chen FC, Li WH*, 2010, “Phosphorylated and non-phosphorylated serine and threonine residues evolve at different rates in mammals.”, Molecular biology and evolution, 27(11), 2548-2554. (SCI) (IF: 13.649; SCI ranking: 1.7%,2.4%,4.3%)
    74. Lin Z, Wu WS, Liang H, Woo Y, Li WH*, 2010, “The spatial distribution of cis regulatory elements in yeast promoters and its implications for transcriptional regulation.”, BMC genomics, 11, 581. (SCI) (IF: 3.867; SCI ranking: 25.9%,19.9%)
    75. Bradley, M.E., J. S. Rest JS, W.-H. Li, N.B. Schwartz, 2009, “Sulfate activation enzymes: phylogeny and association with pyrophosphatase.”, J. Mol. Evol., 68:1-13.. (SCI) (IF: 1.847; SCI ranking: 73.9%,73.7%,72.3%)
    76. Kuo MW, Wang SH, Chang JC, Chang CH, Huang LJ, Lin HH, Yu AL, Li WH, Yu J, 2009, “A novel puf-A gene predicted from evolutionary analysis is involved in the development of eyes and primordial germ-cells.”, PloS one, 4(3), e4980. (SCI) (IF: 3.057; SCI ranking: 17.5%)
    77. Wang D, Wang TY, Weng LC, Emori Y, Tseng CS and Li WH, 2009, “Evolution of Olfactory Receptor Genes in East Asian Loaches”, Zoological Studies, 48(2): 223-237. (SCI) (IF: 0.885; SCI ranking: 56.5%)
    78. Hanada K, Kuromori T, Myouga F, Toyoda T, Li WH, Shinozaki K, 2009, “Evolutionary persistence of functional compensation by duplicate genes in Arabidopsis.”, Genome biology and evolution, 2009, 409-14. (SCI) (IF: 4.098; SCI ranking: 19.9%,21.7%)
    79. Liang H, Li WH, 2009, “Functional compensation by duplicated genes in mouse.”, Trends in genetics : TIG, 25(10), 441-2. (SCI) (IF: 9.858; SCI ranking: 6%)
    80. Wang H, Li WH, 2009, “Increasing MicroRNA target prediction confidence by the relative R(2) method.”, Journal of theoretical biology, 259(4), 793-798. (SCI) (IF: 2.049; SCI ranking: 29.1%,25%)
    81. Liang H, Li WH, 2009, “Lowly expressed human microRNA genes evolve rapidly.”, Molecular biology and evolution, 26(6), 1195-1198. (SCI) (IF: 13.649; SCI ranking: 1.7%,2.4%,4.3%)
    82. Sung HM, Wang TY, Wang D, Huang YS, Wu JP, Tsai HK, Tzeng J, Huang CJ, Lee YC, Yang P, Hsu J, Chang T, Cho CY, Weng LC, Lee TC, Chang TH, Li WH, Shih MC, 2009, “Roles of trans and cis variation in yeast intraspecies evolution of gene expression.”, Molecular biology and evolution, 26(11), 2533-8. (SCI) (IF: 13.649; SCI ranking: 1.7%,2.4%,4.3%)
    83. Tseng YY, Dupree C, Chen ZJ, Li WH, 2009, “SplitPocket: identification of protein functional surfaces and characterization of their spatial patterns.”, Nucleic acids research, 37(Web Server issue), W384-9. (SCI) (IF: 9.202; SCI ranking: 6.2%)
    84. Hsieh LC, Lin SI, Shih AC, Chen JW, Lin WY, Tseng CY, Li WH, Chiou TJ, 2009, “Uncovering small RNA-mediated responses to phosphate deficiency in Arabidopsis by deep sequencing.”, Plant physiology, 151(4), 2120-32. (SCI) (IF: 6.28; SCI ranking: 3.8%)