Wen-Hsiung Li, Ph.D. - Publications

Affiliations: 
Ecology and Evolution University of Chicago, Chicago, IL 
Area:
Molecular Evolution
Website:
http://pondside.uchicago.edu/~lilab/

129 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Wang L, Zhao L, Zhang X, Zhang Q, Jia Y, Wang G, Li S, Tian D, Li WH, Yang S. Large-scale identification and functional analysis of genes in blast resistance in the Tetep rice genome sequence. Proceedings of the National Academy of Sciences of the United States of America. PMID 31451649 DOI: 10.1073/pnas.1910229116  0.4
2019 Gómez Luciano LB, Jason Tsai I, Chuma I, Tosa Y, Chen YH, Li JY, Li MY, Jade Lu MY, Nakayashiki H, Li WH. Blast fungal genomes show frequent chromosomal changes, gene gains and losses, and effector gene turnover. Molecular Biology and Evolution. PMID 30835262 DOI: 10.1093/molbev/msz045  0.56
2017 Wu P, Yan J, Lai YC, Ng CS, Li A, Jiang X, Elsey R, Widelitz R, Bajpai R, Li WH, Chuong CM. Multiple regulatory modules are required for scale-to-feather conversion. Molecular Biology and Evolution. PMID 29177513 DOI: 10.1093/molbev/msx295  0.32
2017 Ke HM, Prachumwat A, Yu CP, Yang YT, Promsri S, Liu KF, Lo CF, Lu MJ, Lai MC, Tsai IJ, Li WH. Comparative genomics of Vibrio campbellii strains and core species of the Vibrio Harveyi clade. Scientific Reports. 7: 41394. PMID 28145490 DOI: 10.1038/srep41394  1
2017 Chen CK, Yu CP, Li SC, Wu SM, Lu MJ, Chen YH, Chen DR, Ng CS, Ting CT, Li WH. Identification and evolutionary analysis of long non-coding RNAs in zebra finch. Bmc Genomics. 18: 117. PMID 28143393 DOI: 10.1186/s12864-017-3506-z  0.56
2016 Li H, Xiang-Yu J, Dai G, Gu Z, Ming C, Yang Z, Ryder OA, Li WH, Fu YX, Zhang YP. 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. PMID 27872315 DOI: 10.1073/pnas.1616804113  0.6
2016 Tsai KJ, Lu MJ, Yang KJ, Li M, Teng Y, Chen S, Ku MS, Li WH. Assembling the Setaria italica L. Beauv. genome into nine chromosomes and insights into regions affecting growth and drought tolerance. Scientific Reports. 6: 35076. PMID 27734962 DOI: 10.1038/srep35076  1
2016 Chen CK, Ng CS, Wu SM, Chen JJ, Cheng PL, Wu P, Lu MJ, Chen DR, Chuong CM, Cheng HC, Ting CT, Li WH. Regulatory Differences in Natal Down Development between Altricial Zebra Finch and Precocial Chicken. Molecular Biology and Evolution. PMID 27189543 DOI: 10.1093/molbev/msw085  1
2016 Yu CP, Lin JJ, Li WH. Positional distribution of transcription factor binding sites in Arabidopsis thaliana. Scientific Reports. 6: 25164. PMID 27117388 DOI: 10.1038/srep25164  1
2016 Chen MM, Chen LK, Lai YS, Lin YY, Wu DC, Tung YA, Liu KY, Shih HT, Chen YJ, Lin YL, Ma LT, Huang JL, Wu PC, Hong MY, Chu FH, ... ... Li WH, et al. Integrating RNA-seq and ChIP-seq data to characterize long non-coding RNAs in Drosophila melanogaster. Bmc Genomics. 17: 220. PMID 26969372 DOI: 10.1186/s12864-016-2457-0  1
2016 Huang CF, Chang YM, Lin JJ, Yu CP, Lin HH, Liu WY, Yeh S, Tu SL, Wu SH, Ku MS, Li WH. Insights into the regulation of C4 leaf development from comparative transcriptomic analysis. Current Opinion in Plant Biology. 30: 1-10. PMID 26828378 DOI: 10.1016/j.pbi.2015.12.011  1
2015 Wu P, Ng CS, Yan J, Lai YC, Chen CK, Lai YT, Wu SM, Chen JJ, Luo W, Widelitz RB, Li WH, Chuong CM. Topographical mapping of α- and β-keratins on developing chicken skin integuments: Functional interaction and evolutionary perspectives. Proceedings of the National Academy of Sciences of the United States of America. PMID 26598683 DOI: 10.1073/pnas.1520566112  1
2015 Chen SC, Tsai TH, Chung CH, Li WH. Dynamic association rules for gene expression data analysis. Bmc Genomics. 16: 786. PMID 26467206 DOI: 10.1186/s12864-015-1970-x  1
2015 Ng CS, Chen CK, Fan WL, Wu P, Wu SM, Chen JJ, Lai YT, Mao CT, Lu MY, Chen DR, Lin ZS, Yang KJ, Sha YA, Tu TC, Chen CF, ... ... Li WH, et al. Transcriptomic analyses of regenerating adult feathers in chicken. Bmc Genomics. 16: 756. PMID 26445093 DOI: 10.1186/s12864-015-1966-6  1
2015 Cheng F, Liu C, Lin CC, Zhao J, Jia P, Li WH, Zhao Z. 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: e1004497. PMID 26352260 DOI: 10.1371/journal.pcbi.1004497  0.44
2015 Schaefke B, Wang TY, Wang CY, Li WH. Gains and Losses of Transcription Factor Binding Sites in Saccharomyces cerevisiae and S. paradoxus. Genome Biology and Evolution. PMID 26220934 DOI: 10.1093/gbe/evv138  1
2015 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, et al. 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: E2477-86. PMID 25918418 DOI: 10.1073/pnas.1500605112  1
2014 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, ... ... Li WH, et al. 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: E4743-52. PMID 25336756 DOI: 10.1073/pnas.1417570111  1
2014 Chang CH, Fan TC, Yu JC, Liao GS, Lin YC, Shih AC, Li WH, Yu AL. The prognostic significance of RUNX2 and miR-10a/10b and their inter-relationship in breast cancer. Journal of Translational Medicine. 12: 257. PMID 25266482 DOI: 10.1186/s12967-014-0257-3  1
2014 Lin JJ, Yu CP, Chang YM, Chen SC, Li WH. Maize and millet transcription factors annotated using comparative genomic and transcriptomic data. Bmc Genomics. 15: 818. PMID 25261191 DOI: 10.1186/1471-2164-15-818  1
2014 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. Genomic organization, transcriptomic analysis, and functional characterization of avian α- and β-keratins in diverse feather forms. Genome Biology and Evolution. 6: 2258-73. PMID 25152353 DOI: 10.1093/gbe/evu181  1
2014 Lin CC, Chang YM, Pan CT, Chen CC, Ling L, Tsao KC, Yang RB, Li WH. Functional evolution of cardiac microRNAs in heart development and functions. Molecular Biology and Evolution. 31: 2722-34. PMID 25063441 DOI: 10.1093/molbev/msu217  1
2014 Yang YT, Lee DY, Wang Y, Hu JM, Li WH, Leu JH, Chang GD, Ke HM, Kang ST, Lin SS, Kou GH, Lo CF. 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. PMID 25063321 DOI: 10.1186/1471-2164-15-628  1
2014 Cheng F, Jia P, Wang Q, Lin CC, Li WH, Zhao Z. Studying tumorigenesis through network evolution and somatic mutational perturbations in the cancer interactome. Molecular Biology and Evolution. 31: 2156-69. PMID 24881052 DOI: 10.1093/molbev/msu167  0.44
2013 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. 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: 71. PMID 24004614 DOI: 10.1186/1472-6750-13-71  1
2013 Chu TC, Lu CH, Liu T, Lee GC, Li WH, Shih AC. Assembler for de novo assembly of large genomes. Proceedings of the National Academy of Sciences of the United States of America. 110: E3417-24. PMID 23966565 DOI: 10.1073/pnas.1314090110  1
2013 Wang HC, Chu FH, Chien SC, Liao JW, Hsieh HW, Li WH, Lin CC, Shaw JF, Kuo YH, Wang SY. 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: 8556-64. PMID 23957814 DOI: 10.1021/jf402849b  1
2013 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. Genome-wide patterns of genetic variation in two domestic chickens. Genome Biology and Evolution. 5: 1376-92. PMID 23814129 DOI: 10.1093/gbe/evt097  1
2013 Schaefke B, Emerson JJ, Wang TY, Lu MY, Hsieh LC, Li WH. Inheritance of gene expression level and selective constraints on trans- and cis-regulatory changes in yeast. Molecular Biology and Evolution. 30: 2121-33. PMID 23793114 DOI: 10.1093/molbev/mst114  1
2013 Lin Z, Wang TY, Tsai BS, Wu FT, Yu FJ, Tseng YJ, Sung HM, Li WH. Identifying cis-regulatory changes involved in the evolution of aerobic fermentation in yeasts. Genome Biology and Evolution. 5: 1065-78. PMID 23650209 DOI: 10.1093/gbe/evt067  1
2013 Ha M, Hong S, Li WH. Predicting the probability of H3K4me3 occupation at a base pair from the genome sequence context. Bioinformatics (Oxford, England). 29: 1199-205. PMID 23511541 DOI: 10.1093/bioinformatics/btt126  1
2013 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, Ku MS, Li WH. 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: 3979-84. PMID 23431200 DOI: 10.1073/pnas.1301009110  1
2013 Chang JJ, Ho FJ, Ho CY, Wu YC, Hou YH, Huang CC, Shih MC, Li WH. Assembling a cellulase cocktail and a cellodextrin transporter into a yeast host for CBP ethanol production. Biotechnology For Biofuels. 6: 19. PMID 23374631 DOI: 10.1186/1754-6834-6-19  1
2013 Chang YM, Chang CL, Li WH, Shih AC. Historical profiling of maize duplicate genes sheds light on the evolution of C4 photosynthesis in grasses. Molecular Phylogenetics and Evolution. 66: 453-62. PMID 22960144 DOI: 10.1016/j.ympev.2012.08.009  1
2012 Li SC, Tsai KW, Pan HW, Jeng YM, Ho MR, Li WH. MicroRNA 3' end nucleotide modification patterns and arm selection preference in liver tissues. Bmc Systems Biology. 6: S14. PMID 23282006 DOI: 10.1186/1752-0509-6-S2-S14  1
2012 Chang HT, Li SC, Ho MR, Pan HW, Ger LP, Hu LY, Yu SY, Li WH, Tsai KW. Comprehensive analysis of microRNAs in breast cancer. Bmc Genomics. 13: S18. PMID 23281739 DOI: 10.1186/1471-2164-13-S7-S18  1
2012 Woo YH, Li WH. DNA replication timing and selection shape the landscape of nucleotide variation in cancer genomes. Nature Communications. 3: 1004. PMID 22893128 DOI: 10.1038/ncomms1982  1
2012 Chang JJ, Ho CY, Ho FJ, Tsai TY, Ke HM, Wang CH, Chen HL, Shih MC, Huang CC, Li WH. PGASO: A synthetic biology tool for engineering a cellulolytic yeast. Biotechnology For Biofuels. 5: 53. PMID 22839502 DOI: 10.1186/1754-6834-5-53  1
2012 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, et al. The chicken frizzle feather is due to an α-keratin (KRT75) mutation that causes a defective rachis. Plos Genetics. 8: e1002748. PMID 22829773 DOI: 10.1371/journal.pgen.1002748  1
2012 Chang YM, Liu WY, Shih AC, Shen MN, Lu CH, Lu MY, Yang HW, Wang TY, Chen SC, Chen SM, Li WH, Ku MS. Characterizing regulatory and functional differentiation between maize mesophyll and bundle sheath cells by transcriptomic analysis. Plant Physiology. 160: 165-77. PMID 22829318 DOI: 10.1104/pp.112.203810  1
2012 Tseng CW, Huang HC, Shih AC, Chang YY, Hsu CC, Chang JY, Li WH, Juan HF. 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: 6352-69. PMID 22754369 DOI: 10.3390/ijms13056352  1
2012 Tseng YY, Li WH. PSC: protein surface classification. Nucleic Acids Research. 40: W435-9. PMID 22669905 DOI: 10.1093/nar/gks495  1
2012 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. A highly efficient β-glucosidase from the buffalo rumen fungus Neocallimastix patriciarum W5. Biotechnology For Biofuels. 5: 24. PMID 22515264 DOI: 10.1186/1754-6834-5-24  1
2012 Shiao MS, Chang AY, Liao BY, Ching YH, Lu MY, Chen SM, Li WH. Transcriptomes of mouse olfactory epithelium reveal sexual differences in odorant detection. Genome Biology and Evolution. 4: 703-12. PMID 22511034 DOI: 10.1093/gbe/evs039  1
2012 Rest JS, Bullaughey K, Morris GP, Li WH. Contribution of transcription factor binding site motif variants to condition-specific gene expression patterns in budding yeast. Plos One. 7: e32274. PMID 22384202 DOI: 10.1371/journal.pone.0032274  1
2012 Woo YH, Li WH. Evolutionary conservation of histone modifications in mammals. Molecular Biology and Evolution. 29: 1757-67. PMID 22319170 DOI: 10.1093/molbev/mss022  1
2012 Tseng YY, Li WH. Classification of protein functional surfaces using structural characteristics. Proceedings of the National Academy of Sciences of the United States of America. 109: 1170-5. PMID 22238424 DOI: 10.1073/pnas.1119684109  1
2012 Lin Z, Li WH. Evolution of 5' untranslated region length and gene expression reprogramming in yeasts. Molecular Biology and Evolution. 29: 81-9. PMID 21965341 DOI: 10.1093/molbev/msr143  1
2011 Nikaido M, Sasaki T, Emerson JJ, Aibara M, Mzighani SI, Budeba YL, Ngatunga BP, Iwata M, Abe Y, Li WH, Okada N. Genetically distinct coelacanth population off the northern Tanzanian coast. Proceedings of the National Academy of Sciences of the United States of America. 108: 18009-13. PMID 22025696 DOI: 10.1073/pnas.1115675108  1
2011 Yun J, Frankenberger CA, Kuo WL, Boelens MC, Eves EM, Cheng N, Liang H, Li WH, Ishwaran H, Minn AJ, Rosner MR. Signalling pathway for RKIP and Let-7 regulates and predicts metastatic breast cancer. The Embo Journal. 30: 4500-14. PMID 21873975 DOI: 10.1038/emboj.2011.312  1
2011 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, ... ... Li WH, et al. Functional characterization of cellulases identified from the cow rumen fungus Neocallimastix patriciarum W5 by transcriptomic and secretomic analyses. Biotechnology For Biofuels. 4: 24. PMID 21849025 DOI: 10.1186/1754-6834-4-24  1
2011 Lin TY, Chen CY, Chien SC, Hsiao WW, Chu FH, Li WH, Lin CC, Shaw JF, Wang SY. Metabolite profiles for Antrodia cinnamomea fruiting bodies harvested at different culture ages and from different wood substrates. Journal of Agricultural and Food Chemistry. 59: 7626-35. PMID 21668009 DOI: 10.1021/jf201632w  1
2011 Kumar KJ, Chu FH, Hsieh HW, Liao JW, Li WH, Lin JC, Shaw JF, Wang SY. 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: 168-77. PMID 21540101 DOI: 10.1016/j.jep.2011.04.030  1
2011 Tseng YY, Li WH. 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: 5313-8. PMID 21402946 DOI: 10.1073/pnas.1102210108  1
2011 Chen SC, Chuang TJ, Li WH. The relationships among microRNA regulation, intrinsically disordered regions, and other indicators of protein evolutionary rate. Molecular Biology and Evolution. 28: 2513-20. PMID 21398349 DOI: 10.1093/molbev/msr068  1
2011 Ha M, Ng DW, Li WH, Chen ZJ. Coordinated histone modifications are associated with gene expression variation within and between species. Genome Research. 21: 590-8. PMID 21324879 DOI: 10.1101/gr.116467.110  1
2011 Woo YH, Li WH. 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: 3306-11. PMID 21300882 DOI: 10.1073/pnas.1100210108  1
2011 Lin YS, Liu FG, Wang TY, Pan CT, Chang WT, Li WH. A simple method using PyrosequencingTM to identify de novo SNPs in pooled DNA samples. Nucleic Acids Research. 39: e28. PMID 21131285 DOI: 10.1093/nar/gkq1249  1
2011 Lin Z, Li WH. The evolution of aerobic fermentation in Schizosaccharomyces pombe was associated with regulatory reprogramming but not nucleosome reorganization. Molecular Biology and Evolution. 28: 1407-13. PMID 21127171 DOI: 10.1093/molbev/msq324  1
2011 Hanada K, Sawada Y, Kuromori T, Klausnitzer R, Saito K, Toyoda T, Shinozaki K, Li WH, Hirai MY. Functional compensation of primary and secondary metabolites by duplicate genes in Arabidopsis thaliana. Molecular Biology and Evolution. 28: 377-82. PMID 20736450 DOI: 10.1093/molbev/msq204  1
2011 Lin Z, Li WH. Expansion of hexose transporter genes was associated with the evolution of aerobic fermentation in yeasts. Molecular Biology and Evolution. 28: 131-42. PMID 20660490 DOI: 10.1093/molbev/msq184  1
2010 Lin Z, Wu WS, Liang H, Woo Y, Li WH. The spatial distribution of cis regulatory elements in yeast promoters and its implications for transcriptional regulation. Bmc Genomics. 11: 581. PMID 20958978 DOI: 10.1186/1471-2164-11-581  1
2010 Emerson JJ, Li WH. The genetic basis of evolutionary change in gene expression levels. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 365: 2581-90. PMID 20643748 DOI: 10.1098/rstb.2010.0005  1
2010 Tang T, Kumar S, Shen Y, Lu J, Wu ML, Shi S, Li WH, Wu CI. 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: 12935-40. PMID 20615957 DOI: 10.1073/pnas.1007591107  1
2010 Chen SC, Chen FC, Li WH. Phosphorylated and nonphosphorylated serine and threonine residues evolve at different rates in mammals. Molecular Biology and Evolution. 27: 2548-54. PMID 20534707 DOI: 10.1093/molbev/msq142  1
2010 Emerson JJ, Hsieh LC, Sung HM, Wang TY, Huang CJ, Lu HH, Lu MY, Wu SH, Li WH. Natural selection on cis and trans regulation in yeasts. Genome Research. 20: 826-36. PMID 20445163 DOI: 10.1101/gr.101576.109  1
2010 Chen FC, Chen CJ, Li WH, Chuang TJ. Gene family size conservation is a good indicator of evolutionary rates. Molecular Biology and Evolution. 27: 1750-8. PMID 20194423 DOI: 10.1093/molbev/msq055  1
2010 Tseng YY, Chen ZJ, Li WH. fPOP: footprinting functional pockets of proteins by comparative spatial patterns. Nucleic Acids Research. 38: D288-95. PMID 19880384 DOI: 10.1093/nar/gkp900  1
2009 Hsieh LC, Lin SI, Shih AC, Chen JW, Lin WY, Tseng CY, Li WH, Chiou TJ. Uncovering small RNA-mediated responses to phosphate deficiency in Arabidopsis by deep sequencing. Plant Physiology. 151: 2120-32. PMID 19854858 DOI: 10.1104/pp.109.147280  1
2009 Liang H, Li WH. Functional compensation by duplicated genes in mouse. Trends in Genetics : Tig. 25: 441-2. PMID 19783063 DOI: 10.1016/j.tig.2009.08.001  1
2009 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, ... ... Li WH, et al. Roles of trans and cis variation in yeast intraspecies evolution of gene expression. Molecular Biology and Evolution. 26: 2533-8. PMID 19648464 DOI: 10.1093/molbev/msp171  1
2009 Wang H, Li WH. Increasing MicroRNA target prediction confidence by the relative R(2) method. Journal of Theoretical Biology. 259: 793-8. PMID 19463832 DOI: 10.1016/j.jtbi.2009.05.007  1
2009 Tseng YY, Dupree C, Chen ZJ, Li WH. SplitPocket: identification of protein functional surfaces and characterization of their spatial patterns. Nucleic Acids Research. 37: W384-9. PMID 19406922 DOI: 10.1093/nar/gkp308  1
2009 Tseng YY, Li WH. Identification of protein functional surfaces by the concept of a split pocket. Proteins. 76: 959-76. PMID 19326458 DOI: 10.1002/prot.22402  1
2009 Kuo MW, Wang SH, Chang JC, Chang CH, Huang LJ, Lin HH, Yu AL, Li WH, Yu J. A novel puf-A gene predicted from evolutionary analysis is involved in the development of eyes and primordial germ-cells. Plos One. 4: e4980. PMID 19319195 DOI: 10.1371/journal.pone.0004980  1
2009 Liang H, Li WH. Lowly expressed human microRNA genes evolve rapidly. Molecular Biology and Evolution. 26: 1195-8. PMID 19299536 DOI: 10.1093/molbev/msp053  1
2009 Bradley ME, Rest JS, Li WH, Schwartz NB. Sulfate activation enzymes: phylogeny and association with pyrophosphatase. Journal of Molecular Evolution. 68: 1-13. PMID 19067028 DOI: 10.1007/s00239-008-9181-6  1
2009 Tiwary B, Tiwary BK, Li WH. Parallel evolution between aromatase and androgen receptor in the animal kingdom. Molecular Biology and Evolution. 26: 123-9. PMID 18936441 DOI: 10.1093/molbev/msn233  1
2008 Wu WS, Li WH, Chen BS. Reconstructing a network of stress-response regulators via dynamic system modeling of gene regulation. Gene Regulation and Systems Biology. 2: 53-62. PMID 19787074  1
2008 Wu WS, Li WH. Systematic identification of yeast cell cycle transcription factors using multiple data sources. Bmc Bioinformatics. 9: 522. PMID 19061501 DOI: 10.1186/1471-2105-9-522  1
2008 Zhang X, Byrnes JK, Gal TS, Li WH, Borevitz JO. Whole genome transcriptome polymorphisms in Arabidopsis thaliana. Genome Biology. 9: R165. PMID 19025653 DOI: 10.1186/gb-2008-9-11-r165  1
2008 Chang YM, Juan HF, Lee TY, Chang YY, Yeh YM, Li WH, Shih AC. Prediction of human miRNAs using tissue-selective motifs in 3' UTRs. Proceedings of the National Academy of Sciences of the United States of America. 105: 17061-6. PMID 18952845 DOI: 10.1073/pnas.0809151105  1
2008 Wu WS, Li WH. Identifying gene regulatory modules of heat shock response in yeast. Bmc Genomics. 9: 439. PMID 18811975 DOI: 10.1186/1471-2164-9-439  1
2008 Chang YW, Robert Liu FG, Yu N, Sung HM, Yang P, Wang D, Huang CJ, Shih MC, Li WH. Roles of cis- and trans-changes in the regulatory evolution of genes in the gluconeogenic pathway in yeast. Molecular Biology and Evolution. 25: 1863-75. PMID 18573843 DOI: 10.1093/molbev/msn138  1
2008 Wang H, Tzeng YH, Li WH. Improved variance estimators for one- and two-parameter models of nucleotide substitution. Journal of Theoretical Biology. 254: 164-7. PMID 18571203 DOI: 10.1016/j.jtbi.2008.04.034  1
2008 Han L, Su B, Li WH, Zhao Z. CpG island density and its correlations with genomic features in mammalian genomes. Genome Biology. 9: R79. PMID 18477403 DOI: 10.1186/gb-2008-9-5-r79  1
2008 Sanna CR, Li WH, Zhang L. Overlapping genes in the human and mouse genomes. Bmc Genomics. 9: 169. PMID 18410680 DOI: 10.1186/1471-2164-9-169  1
2008 Tzeng J, Lu HH, Li WH. Multidimensional scaling for large genomic data sets. Bmc Bioinformatics. 9: 179. PMID 18394154 DOI: 10.1186/1471-2105-9-179  1
2008 Zhang C, Li WH, Krainer AR, Zhang MQ. RNA landscape of evolution for optimal exon and intron discrimination. Proceedings of the National Academy of Sciences of the United States of America. 105: 5797-802. PMID 18391195 DOI: 10.1073/pnas.0801692105  1
2008 Liang H, Lin YS, Li WH. Fast evolution of core promoters in primate genomes. Molecular Biology and Evolution. 25: 1239-44. PMID 18367463 DOI: 10.1093/molbev/msn072  1
2008 Chen CY, Tsai HK, Hsu CM, May Chen MJ, Hung HG, Huang GT, Li WH. Discovering gapped binding sites of yeast transcription factors. Proceedings of the National Academy of Sciences of the United States of America. 105: 2527-32. PMID 18272477 DOI: 10.1073/pnas.0712188105  1
2008 Liang H, Plazonic KR, Chen J, Li WH, Fernández A. Protein under-wrapping causes dosage sensitivity and decreases gene duplicability. Plos Genetics. 4: e11. PMID 18208334 DOI: 10.1371/journal.pgen.0040011  1
2008 Prachumwat A, Li WH. Gene number expansion and contraction in vertebrate genomes with respect to invertebrate genomes. Genome Research. 18: 221-32. PMID 18083775 DOI: 10.1101/gr.7046608  1
2007 Chen BS, Wu WS, Wu WS, Li WH. On the adaptive design rules of biochemical networks in evolution. Evolutionary Bioinformatics Online. 3: 27-39. PMID 19430602  1
2007 Lin LH, Lee HC, Li WH, Chen BS. A systematic approach to detecting transcription factors in response to environmental stresses. Bmc Bioinformatics. 8: 473. PMID 18067669 DOI: 10.1186/1471-2105-8-473  1
2007 Lin YC, Hsieh LC, Kuo MW, Yu J, Kuo HH, Lo WL, Lin RJ, Yu AL, Li WH. Human TRIM71 and its nematode homologue are targets of let-7 microRNA and its zebrafish orthologue is essential for development. Molecular Biology and Evolution. 24: 2525-34. PMID 17890240 DOI: 10.1093/molbev/msm195  1
2007 Hanada K, Shiu SH, Li WH. The nonsynonymous/synonymous substitution rate ratio versus the radical/conservative replacement rate ratio in the evolution of mammalian genes. Molecular Biology and Evolution. 24: 2235-41. PMID 17652332 DOI: 10.1093/molbev/msm152  1
2007 Liang H, Li WH. MicroRNA regulation of human protein protein interaction network. Rna (New York, N.Y.). 13: 1402-8. PMID 17652130 DOI: 10.1261/rna.634607  1
2007 Wang D, Sung HM, Wang TY, Huang CJ, Yang P, Chang T, Wang YC, Tseng DL, Wu JP, Lee TC, Shih MC, Li WH. Expression evolution in yeast genes of single-input modules is mainly due to changes in trans-acting factors. Genome Research. 17: 1161-9. PMID 17615293 DOI: 10.1101/gr.6328907  1
2007 Jiang C, Han L, Su B, Li WH, Zhao Z. Features and trend of loss of promoter-associated CpG islands in the human and mouse genomes. Molecular Biology and Evolution. 24: 1991-2000. PMID 17591602 DOI: 10.1093/molbev/msm128  1
2007 Wu WS, Li WH, Chen BS. Identifying regulatory targets of cell cycle transcription factors using gene expression and ChIP-chip data. Bmc Bioinformatics. 8: 188. PMID 17559637 DOI: 10.1186/1471-2105-8-188  1
2007 Liang H, Li WH. Gene essentiality, gene duplicability and protein connectivity in human and mouse. Trends in Genetics : Tig. 23: 375-8. PMID 17512629 DOI: 10.1016/j.tig.2007.04.005  1
2007 Hanada K, Zhang X, Borevitz JO, Li WH, Shiu SH. A large number of novel coding small open reading frames in the intergenic regions of the Arabidopsis thaliana genome are transcribed and/or under purifying selection. Genome Research. 17: 632-40. PMID 17395691 DOI: 10.1101/gr.5836207  1
2007 Saunders MA, Liang H, Li WH. Human polymorphism at microRNAs and microRNA target sites. Proceedings of the National Academy of Sciences of the United States of America. 104: 3300-5. PMID 17360642 DOI: 10.1073/pnas.0611347104  0.44
2006 Wu WS, Li WH, Chen BS. Computational reconstruction of transcriptional regulatory modules of the yeast cell cycle. Bmc Bioinformatics. 7: 421. PMID 17010188 DOI: 10.1186/1471-2105-7-421  1
2006 Lin YS, Byrnes JK, Hwang JK, Li WH. Codon-usage bias versus gene conversion in the evolution of yeast duplicate genes. Proceedings of the National Academy of Sciences of the United States of America. 103: 14412-6. PMID 16971485 DOI: 10.1073/pnas.0606348103  1
2006 Byrnes JK, Morris GP, Li WH. Reorganization of adjacent gene relationships in yeast genomes by whole-genome duplication and gene deletion. Molecular Biology and Evolution. 23: 1136-43. PMID 16527865 DOI: 10.1093/molbev/msj121  1
2006 Shiu SH, Byrnes JK, Pan R, Zhang P, Li WH. Role of positive selection in the retention of duplicate genes in mammalian genomes. Proceedings of the National Academy of Sciences of the United States of America. 103: 2232-6. PMID 16461903 DOI: 10.1073/pnas.0510388103  1
2006 Prachumwat A, Li WH. Protein function, connectivity, and duplicability in yeast. Molecular Biology and Evolution. 23: 30-9. PMID 16120800 DOI: 10.1093/molbev/msi249  1
2005 Chen BS, Wang YC, Wu WS, Li WH. A new measure of the robustness of biochemical networks. Bioinformatics (Oxford, England). 21: 2698-705. PMID 15731208 DOI: 10.1093/bioinformatics/bti348  1
2005 Oakley TH, Gu Z, Abouheif E, Patel NH, Li WH. Comparative methods for the analysis of gene-expression evolution: an example using yeast functional genomic data. Molecular Biology and Evolution. 22: 40-50. PMID 15356281 DOI: 10.1093/molbev/msh257  1
2004 Marland E, Prachumwat A, Maltsev N, Gu Z, Li WH. Higher gene duplicabilities for metabolic proteins than for nonmetabolic proteins in yeast and E. coli. Journal of Molecular Evolution. 59: 806-14. PMID 15599512 DOI: 10.1007/s00239-004-0068-x  1
2004 Gu Z, Rifkin SA, White KP, Li WH. Duplicate genes increase gene expression diversity within and between species. Nature Genetics. 36: 577-9. PMID 15122255 DOI: 10.1038/ng1355  0.6
2004 Yu N, Jensen-Seaman MI, Chemnick L, Ryder O, Li WH. Nucleotide diversity in gorillas. Genetics. 166: 1375-83. PMID 15082556 DOI: 10.1534/genetics.166.3.1375  1
2003 Jensen-Seaman MI, Li WH. Evolution of the hominoid semenogelin genes, the major proteins of ejaculated semen. Journal of Molecular Evolution. 57: 261-70. PMID 14629036 DOI: 10.1007/s00239-003-2474-x  1
2003 Zhang P, Gu Z, Li WH. Different evolutionary patterns between young duplicate genes in the human genome. Genome Biology. 4: R56. PMID 12952535 DOI: 10.1186/gb-2003-4-9-r56  0.6
2003 Yu N, Jensen-Seaman MI, Chemnick L, Kidd JR, Deinard AS, Ryder O, Kidd KK, Li WH. Low nucleotide diversity in chimpanzees and bonobos. Genetics. 164: 1511-8. PMID 12930756  1
2003 John PR, Makova K, Li WH, Jenkins T, Ramsay M. DNA polymorphism and selection at the melanocortin-1 receptor gene in normally pigmented southern African individuals. Annals of the New York Academy of Sciences. 994: 299-306. PMID 12851329  1
2003 Makova KD, Li WH. Divergence in the spatial pattern of gene expression between human duplicate genes. Genome Research. 13: 1638-45. PMID 12840042 DOI: 10.1101/gr.1133803  1
2003 Li WH, Gu Z, Cavalcanti AR, Nekrutenko A. Detection of gene duplications and block duplications in eukaryotic genomes. Journal of Structural and Functional Genomics. 3: 27-34. PMID 12836682 DOI: 10.1023/A:1022644628861  1
2003 Yang J, Gu Z, Li WH. Rate of protein evolution versus fitness effect of gene deletion. Molecular Biology and Evolution. 20: 772-4. PMID 12679525 DOI: 10.1093/molbev/msg078  0.6
2003 Cavalcanti AR, Ferreira R, Gu Z, Li WH. Patterns of gene duplication in Saccharomyces cerevisiae and Caenorhabditis elegans. Journal of Molecular Evolution. 56: 28-37. PMID 12569420 DOI: 10.1007/s00239-002-2377-2  0.6
2003 Gu Z, Steinmetz LM, Gu X, Scharfe C, Davis RW, Li WH. Role of duplicate genes in genetic robustness against null mutations. Nature. 421: 63-6. PMID 12511954 DOI: 10.1038/nature01198  1
2002 Gu Z, Nicolae D, Lu HH, Li WH. Rapid divergence in expression between duplicate genes inferred from microarray data. Trends in Genetics : Tig. 18: 609-13. PMID 12446139 DOI: 10.1016/S0168-9525(02)02837-8  1
2002 Li WH, Yi S, Makova K. Male-driven evolution. Current Opinion in Genetics & Development. 12: 650-6. PMID 12433577 DOI: 10.1016/S0959-437X(02)00354-4  1
2002 Mu J, Duan J, Makova KD, Joy DA, Huynh CQ, Branch OH, Li WH, Su XZ. Chromosome-wide SNPs reveal an ancient origin for Plasmodium falciparum. Nature. 418: 323-6. PMID 12124624 DOI: 10.1038/nature00836  1
2002 Makova KD, Li WH. Strong male-driven evolution of DNA sequences in humans and apes. Nature. 416: 624-6. PMID 11948348 DOI: 10.1038/416624a  1
2002 Gu Z, Cavalcanti A, Chen FC, Bouman P, Li WH. Extent of gene duplication in the genomes of Drosophila, nematode, and yeast. Molecular Biology and Evolution. 19: 256-62. PMID 11861885  1
2002 Nekrutenko A, Makova KD, Li WH. The K(A)/K(S) ratio test for assessing the protein-coding potential of genomic regions: an empirical and simulation study. Genome Research. 12: 198-202. PMID 11779845 DOI: 10.1101/gr.200901  1
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