Wen-Hsiung Li, Ph.D. - Publications

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

227 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
2021 Panibe JP, Wang L, Li J, Li MY, Lee YC, Wang CS, Ku MSB, Lu MJ, Li WH. Chromosomal-level genome assembly of the semi-dwarf rice Taichung Native 1, an initiator of Green Revolution. Genomics. PMID 34111524 DOI: 10.1016/j.ygeno.2021.06.006  1
2020 Wang WF, Lu MJ, Cheng TR, Tang YC, Teng YC, Hwa TY, Chen YH, Li MY, Wu MH, Chuang PC, Jou R, Wong CH, Li WH. Genomic analysis of Mycobacterium tuberculosis isolates and construction of a Beijing lineage reference genome. Genome Biology and Evolution. PMID 31971587 DOI: 10.1093/Gbe/Evaa009  1
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  0.64
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  0.52
2017 Su SC, Lin CW, Liu YF, Fan WL, Chen MK, Yu CP, Yang WE, Su CW, Chuang CY, Li WH, Chung WH, Yang SF. Exome Sequencing of Oral Squamous Cell Carcinoma Reveals Molecular Subgroups and Novel Therapeutic Opportunities. Theranostics. 7: 1088-1099. PMID 28435450 DOI: 10.7150/Thno.18551  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  1
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  0.64
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 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, ... Li WH, et al. 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. PMID 26561581 DOI: 10.1073/Pnas.1519556112  0.32
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  0.56
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
2015 Lin YL, Ma LT, Lee YR, Lin SS, Wang SY, Chang TT, Shaw JF, Li WH, Chu FH. MicroRNA-like small RNAs prediction in the development of Antrodia cinnamomea. Plos One. 10: e0123245. PMID 25860872 DOI: 10.1371/Journal.Pone.0123245  0.32
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  0.56
2014 Chang JJ, Ho CY, Mao CT, Barham N, Huang YR, Ho FJ, Wu YC, Hou YH, Shih MC, Li WH, Huang CC. A thermo- and toxin-tolerant kefir yeast for biorefinery and biofuel production Applied Energy. 132: 465-474. DOI: 10.1016/J.Apenergy.2014.06.081  1
2014 Lin Z, Li WH. Comparative genomics and evolutionary genetics of yeast carbon metabolism Molecular Mechanisms in Yeast Carbon Metabolism. 97-120. DOI: 10.1007/978-3-642-55013-3_5  1
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
2013 Shiao MS, Fan WL, Fang S, Lu MYJ, Kondo R, Li WH. Transcriptional profiling of adult drosophila antennae by high-throughput sequencing Zoological Studies. 52. DOI: 10.1186/1810-522X-52-42  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
2012 Ho CY, Chang JJ, Lee SC, Chin TY, Shih MC, Li WH, Huang CC. Development of cellulosic ethanol production process via co-culturing of artificial cellulosomal Bacillus and kefir yeast Applied Energy. 100: 27-32. DOI: 10.1016/J.Apenergy.2012.03.016  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
2011 Lin CW, Wu CH, Tran DT, Shih MC, Li WH, Wu CF. Mixed culture fermentation from lignocellulosic materials using thermophilic lignocellulose-degrading anaerobes Process Biochemistry. 46: 489-493. DOI: 10.1016/J.Procbio.2010.09.024  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: 10.7490/F1000Research.235.1  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
2010 Wang TY, Chen HL, Li WH, Sung HM, Shih MC. Omics Applications to Biofuel Research Biocatalysis and Biomolecular Engineering. 265-276. DOI: 10.1002/9780470608524.ch18  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 Tsai HK, Chou MY, Shih CH, Huang GT, Chang TH, Li WH. MYBS: a comprehensive web server for mining transcription factor binding sites in yeast. Nucleic Acids Research. 35: W221-6. PMID 17537814 DOI: 10.1093/Nar/Gkm379  0.32
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  0.6
2007 Chen FC, Chen CJ, Li WH, Chuang TJ. Human-specific insertions and deletions inferred from mammalian genome sequences. Genome Research. 17: 16-22. PMID 17095709 DOI: 10.1101/Gr.5429606  0.52
2007 Yi S, Li WH. Episodic molecular evolution of some protein hormones in primates and its implications for primate adaptation Primate Origins: Adaptations and Evolution. 739-773. DOI: 10.1007/978-0-387-33507-0_21  1
2006 Saunders MA, Good JM, Lawrence EC, Ferrell RE, Li WH, Nachman MW. Human adaptive evolution at Myostatin (GDF8), a regulator of muscle growth. American Journal of Human Genetics. 79: 1089-97. PMID 17186467 DOI: 10.1086/509707  1
2006 Hanada K, Gojobori T, Li WH. Radical amino acid change versus positive selection in the evolution of viral envelope proteins Gene. 385: 83-88. PMID 17014971 DOI: 10.1016/J.Gene.2006.06.029  1
2006 Kim J, Shiu SH, Thoma S, Li WH, Patterson SE. Patterns of expansion and expression divergence in the plant polygalacturonase gene family. Genome Biology. 7: R87. PMID 17010199 DOI: 10.1186/Gb-2006-7-9-R87  1
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 Tsai HK, Huang GT, Chou MY, Lu HH, Li WH. Method for identifying transcription factor binding sites in yeast. Bioinformatics (Oxford, England). 22: 1675-81. PMID 16644789 DOI: 10.1093/Bioinformatics/Btl160  0.4
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 Lin LH, Lee HC, Li WH, Chen BS. Dynamic modeling of cis-regulatory circuits and gene expression prediction via cross-gene identification. Bmc Bioinformatics. 6: 258. PMID 16232312 DOI: 10.1186/1471-2105-6-258  0.64
2005 Shiu SH, Shih MC, Li WH. Transcription factor families have much higher expansion rates in plants than in animals. Plant Physiology. 139: 18-26. PMID 16166257 DOI: 10.1104/Pp.105.065110  1
2005 Tsai HK, Lu HH, Li WH. Statistical methods for identifying yeast cell cycle transcription factors. Proceedings of the National Academy of Sciences of the United States of America. 102: 13532-7. PMID 16157877 DOI: 10.1073/Pnas.0505874102  0.4
2005 Li WH, Yang J, Gu X. Expression divergence between duplicate genes. Trends in Genetics : Tig. 21: 602-7. PMID 16140417 DOI: 10.1016/J.Tig.2005.08.006  0.64
2005 Yang J, Su AI, Li WH. Gene expression evolves faster in narrowly than in broadly expressed mammalian genes. Molecular Biology and Evolution. 22: 2113-8. PMID 15987875 DOI: 10.1093/Molbev/Msi206  0.64
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 Yi S, Li WH. Molecular evolution of recombination hotspots and highly recombining pseudoautosomal regions in hominoids. Molecular Biology and Evolution. 22: 1223-30. PMID 15703241 DOI: 10.1093/Molbev/Msi106  1
2005 Zhang L, Lu HH, Chung WY, Yang J, Li WH. Patterns of segmental duplication in the human genome. Molecular Biology and Evolution. 22: 135-41. PMID 15371527 DOI: 10.1093/Molbev/Msh262  0.64
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
2005 Byrnes JK, Li WH. Patterns of gene deletion following genome duplication in yeast 2005 Ieee Computational Systems Bioinformatics Conference, Workshops and Poster Abstracts. 25-26. DOI: 10.1109/CSBW.2005.104  1
2004 Qin H, Wu WB, Comeron JM, Kreitman M, Li WH. Intragenic spatial patterns of codon usage bias in prokaryotic and eukaryotic genomes. Genetics. 168: 2245-60. PMID 15611189 DOI: 10.1534/Genetics.104.030866  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 Zhang P, Min W, Li WH. Different age distribution patterns of human, nematode, and Arabidopsis duplicate genes. Gene. 342: 263-8. PMID 15527985 DOI: 10.1016/J.Gene.2004.08.001  0.6
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  0.64
2004 Chaw SM, Chang CC, Chen HL, Li WH. Dating the monocot-dicot divergence and the origin of core eudicots using whole chloroplast genomes. Journal of Molecular Evolution. 58: 424-41. PMID 15114421 DOI: 10.1007/S00239-003-2564-9  1
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
2004 Chen HC, Lee HC, Lin TY, Li WH, Chen BS. Quantitative characterization of the transcriptional regulatory network in the yeast cell cycle. Bioinformatics (Oxford, England). 20: 1914-27. PMID 15044243 DOI: 10.1093/Bioinformatics/Bth178  0.64
2004 Shiu SH, Li WH. Origins, lineage-specific expansions, and multiple losses of tyrosine kinases in eukaryotes. Molecular Biology and Evolution. 21: 828-40. PMID 14963097 DOI: 10.1093/Molbev/Msh077  1
2004 Yi S, Summers TJ, Pearson NM, Li WH. Recombination has little effect on the rate of sequence divergence in pseudoautosomal boundary 1 among humans and great apes. Genome Research. 14: 37-43. PMID 14672979 DOI: 10.1101/Gr.1777204  1
2004 Wang D, Oakley T, Mower J, Shimmin LC, Yim S, Honeycutt RL, Tsao H, Li WH. Molecular evolution of bat color vision genes. Molecular Biology and Evolution. 21: 295-302. PMID 14660703 DOI: 10.1093/Molbev/Msh015  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 Lu J, Li WH, Wu CI. Comment on "Chromosomal speciation and molecular divergence-accelerated evolution in rearranged chromosomes". Science (New York, N.Y.). 302: 988; author reply 98. PMID 14605352 DOI: 10.1126/Science.1088277  1
2003 Qin H, Lu HH, Wu WB, Li WH. Evolution of the yeast protein interaction network. Proceedings of the National Academy of Sciences of the United States of America. 100: 12820-4. PMID 14557537 DOI: 10.1073/Pnas.2235584100  0.4
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  0.64
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 DOI: 10.1111/J.1749-6632.2003.Tb03193.X  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 Nekrutenko A, Chung WY, Li WH. ETOPE: Evolutionary test of predicted exons. Nucleic Acids Research. 31: 3564-7. PMID 12824366 DOI: 10.1093/Nar/Gkg597  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  0.64
2003 Xia X, Xie Z, Li WH. Effects of GC content and mutational pressure on the lengths of exons and coding sequences. Journal of Molecular Evolution. 56: 362-70. PMID 12612839 DOI: 10.1007/S00239-002-2406-1  1
2003 Wolfe KH, Li WH. Molecular evolution meets the genomics revolution. Nature Genetics. 33: 255-65. PMID 12610535 DOI: 10.1038/Ng1088  1
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  0.64
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
2003 Yang YW, Chen Y, Li WH. The influence of adjacent nucleotides on the pattern of nucleotide substitution in mitochondrial introns of angiosperms. Journal of Molecular Evolution. 55: 111-5. PMID 12165848 DOI: 10.1007/S00239-001-2310-0  0.32
2002 Yi S, Ellsworth DL, Li WH. Slow molecular clocks in Old World monkeys, apes, and humans. Molecular Biology and Evolution. 19: 2191-8. PMID 12446810 DOI: 10.1093/Oxfordjournals.Molbev.A004043  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 Kaessmann H, Zöllner S, Nekrutenko A, Li WH. Signatures of domain shuffling in the human genome. Genome Research. 12: 1642-50. PMID 12421750 DOI: 10.1101/Gr.520702  1
2002 Sun H, Merugu S, Gu X, Kang YY, Dickinson DP, Callaerts P, Li WH. Identification of essential amino acid changes in paired domain evolution using a novel combination of evolutionary analysis and in vitro and in vivo studies. Molecular Biology and Evolution. 19: 1490-500. PMID 12200477 DOI: 10.1093/Oxfordjournals.Molbev.A004212  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 Yi S, Bernat B, Pál G, Kossiakoff A, Li WH. Functional promiscuity of squirrel monkey growth hormone receptor toward both primate and nonprimate growth hormones Molecular Biology and Evolution. 19: 1083-1092. PMID 12082127 DOI: 10.1093/Oxfordjournals.Molbev.A004166  1
2002 Yang YW, Tai PY, Chen Y, Li WH. A study of the phylogeny of Brassica rapa, B. nigra, Raphanus sativus, and their related genera using noncoding regions of chloroplast DNA. Molecular Phylogenetics and Evolution. 23: 268-75. PMID 12069556 DOI: 10.1016/S1055-7903(02)00026-X  0.44
2002 Cropp S, Boinski S, Li WH. Allelic variation in the squirrel monkey x-linked color vision gene: biogeographical and behavioral correlates. Journal of Molecular Evolution. 54: 734-45. PMID 12029355 DOI: 10.1007/S00239-001-0073-2  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 DOI: 10.1093/Oxfordjournals.Molbev.A004079  1
2002 Jacobs GH, Deegan JF, Tan Y, Li WH. Opsin gene and photopigment polymorphism in a prosimian primate. Vision Research. 42: 11-8. PMID 11804627 DOI: 10.1016/S0042-6989(01)00264-4  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
2001 Nekrutenko A, Li WH. Transposable elements are found in a large number of human protein-coding genes Trends in Genetics. 17: 619-621. PMID 11672845 DOI: 10.1016/S0168-9525(01)02445-3  1
2001 Sun H, Dickinson DP, Costello J, Li WH. Isolation of Cladonema Pax-B genes and studies of the DNA-binding properties of cnidarian Pax paired domains. Molecular Biology and Evolution. 18: 1905-18. PMID 11557796 DOI: 10.1093/Oxfordjournals.Molbev.A003731  1
2001 Liu JC, Makova KD, Adkins RM, Gibson S, Li WH. Episodic evolution of growth hormone in primates and emergence of the species specificity of human growth hormone receptor. Molecular Biology and Evolution. 18: 945-53. PMID 11371582 DOI: 10.1093/Oxfordjournals.Molbev.A003895  1
2001 Li WH, Gu Z, Wang H, Nekrutenko A. Evolutionary analyses of the human genome. Nature. 409: 847-9. PMID 11237007 DOI: 10.1038/35057039  1
2001 Adkins RM, Nekrutenko A, Li WH. Bushbaby growth hormone is much more similar to nonprimate growth hormones than to rhesus monkey and human growth hormones. Molecular Biology and Evolution. 18: 55-60. PMID 11141192 DOI: 10.1093/Oxfordjournals.Molbev.A003719  1
2000 Gu Z, Wang H, Nekrutenko A, Li WH. Densities, length proportions, and other distributional features of repetitive sequences in the human genome estimated from 430 megabases of genomic sequence. Gene. 259: 81-8. PMID 11163965 DOI: 10.1016/S0378-1119(00)00434-0  1
2000 Nekrutenko A, Li WH. Assessment of compositional heterogeneity within and between eukaryotic genomes Genome Research. 10: 1986-1995. PMID 11116093 DOI: 10.1101/Gr.10.12.1986  1
2000 Yu N, Zheng C, Zhang Y, Li W. Molecular systematics of pikas (genus Ochotona) inferred from mitochondrial DNA sequences. Molecular Phylogenetics and Evolution. 16: 85-95. PMID 10877942 DOI: 10.1006/Mpev.2000.0776  0.44
2000 Tourasse NJ, Li WH. Selective constraints, amino acid composition, and the rate of protein evolution. Molecular Biology and Evolution. 17: 656-64. PMID 10742056 DOI: 10.1093/Oxfordjournals.Molbev.A026344  1
1999 Callaerts P, Munoz-Marmol AM, Glardon S, Castillo E, Sun H, Li WH, Gehring WJ, Salo E. Isolation and expression of a Pax-6 gene in the regenerating and intact Planarian Dugesia(G)tigrina. Proceedings of the National Academy of Sciences of the United States of America. 96: 558-63. PMID 9892672 DOI: 10.1073/Pnas.96.2.558  1
1998 Hunt DM, Dulai KS, Cowing JA, Julliot C, Mollon JD, Bowmaker JK, Li WH, Hewett-Emmett D. Molecular evolution of trichromacy in primates. Vision Research. 38: 3299-306. PMID 9893841 DOI: 10.1016/S0042-6989(97)00443-4  1
1998 Xia X, Li WH. What amino acid properties affect protein evolution? Journal of Molecular Evolution. 47: 557-564. PMID 9797406 DOI: 10.1007/Pl00006412  1
1998 Shyue SK, Boissinot S, Schneider H, Sampaio I, Schneider MP, Abee CR, Williams L, Hewett-Emmett D, Sperling HG, Cowing JA, Dulai KS, Hunt DM, Li WH. Molecular genetics of spectral tuning in New World monkey color vision. Journal of Molecular Evolution. 46: 697-702. PMID 9608052 DOI: 10.1007/Pl00006350  1
1998 Gu X, Li W. Estimation of evolutionary distances under stationary and nonstationary models of nucleotide substitution Proceedings of the National Academy of Sciences of the United States of America. 95: 5899-5905. PMID 9600890 DOI: 10.1073/Pnas.95.11.5899  0.44
1998 Zhao Z, Hewett-Emmett D, Li WH. Frequent gene conversion between human red and green opsin genes. Journal of Molecular Evolution. 46: 494-6. PMID 9541545 DOI: 10.1007/Pl00013147  0.48
1998 Gu X, Hewett-Emmett D, Li W. Directional mutational pressure affects the amino acid composition and hydrophobicity of proteins in bacteria Genetica. 102: 383-391. DOI: 10.1007/978-94-011-5210-5_31  0.44
1997 Zhou YH, Hewett-Emmett D, Ward JP, Li WH. Unexpected conservation of the X-linked color vision gene in nocturnal prosimians: evidence from two bush babies. Journal of Molecular Evolution. 45: 610-8. PMID 9419238 DOI: 10.1007/Pl00006265  1
1997 Sun H, Rodin A, Zhou Y, Dickinson DP, Harper DE, Hewett-Emmett D, Li WH. Evolution of paired domains: isolation and sequencing of jellyfish and hydra Pax genes related to Pax-5 and Pax-6. Proceedings of the National Academy of Sciences of the United States of America. 94: 5156-61. PMID 9144207 DOI: 10.1073/Pnas.94.10.5156  1
1996 Li W, Gu X. Estimating evolutionary distances between DNA sequences. Methods in Enzymology. 266: 449-459. PMID 8743699 DOI: 10.1016/S0076-6879(96)66028-5  0.44
1996 Gu X, Li W. A general additive distance with time-reversibility and rate variation among nucleotide sites Proceedings of the National Academy of Sciences of the United States of America. 93: 4671-4676. PMID 8643462 DOI: 10.1073/Pnas.93.10.4671  0.44
1995 Gu X, Fu Y, Li W. Maximum likelihood estimation of the heterogeneity of substitution rate among nucleotide sites. Molecular Biology and Evolution. 12: 546-557. PMID 7659011 DOI: 10.1093/Oxfordjournals.Molbev.A040235  0.44
1995 Shyue SK, Hewett-Emmett D, Sperling HG, Hunt DM, Bowmaker JK, Mollon JD, Li WH. Adaptive evolution of color vision genes in higher primates. Science (New York, N.Y.). 269: 1265-7. PMID 7652574 DOI: 10.1126/Science.7652574  1
1992 Gu X, Li W. Higher rates of amino acid substitution in rodents than in humans. Molecular Phylogenetics and Evolution. 1: 211-214. PMID 1342937 DOI: 10.1016/1055-7903(92)90017-B  0.44
1991 Graur D, Hide WA, Li WH. Is the guinea-pig a rodent? Nature. 351: 649-52. PMID 2052090 DOI: 10.1038/351649A0  1
1991 Graur D, Li WH. Neutral mutation hypothesis test [10] Nature. 354: 114-115. PMID 1944591 DOI: 10.1038/354114E0  1
1990 Li WH, Gouy M. Statistical tests of molecular phylogenies. Methods in Enzymology. 183: 645-59. PMID 2314297 DOI: 10.1016/0076-6879(90)83042-8  1
1990 Gouy M, Li W. Archaebacterial or eocyte tree Nature. 343: 419-419. DOI: 10.1038/343419A0  1
1989 Wolfe KH, Sharp PM, Li WH. Mutation rates differ among regions of the mammalian genome. Nature. 337: 283-5. PMID 2911369 DOI: 10.1038/337283A0  1
1989 Wolfe KH, Gouy M, Yang YW, Sharp PM, Li WH. Date of the monocot-dicot divergence estimated from chloroplast DNA sequence data. Proceedings of the National Academy of Sciences of the United States of America. 86: 6201-5. PMID 2762323 DOI: 10.1073/Pnas.86.16.6201  1
1989 Sharp PM, Shields DC, Wolfe KH, Li WH. Chromosomal location and evolutionary rate variation in enterobacterial genes. Science (New York, N.Y.). 246: 808-10. PMID 2683084 DOI: 10.1126/Science.2683084  1
1989 Sharp PM, Li WH. On the rate of DNA sequence evolution in Drosophila Journal of Molecular Evolution. 28: 398-402. PMID 2501501 DOI: 10.1007/Bf02603075  1
1989 Graur D, Shuali Y, Li WH. Deletions in processed pseudogenes accumulate faster in rodents than in humans. Journal of Molecular Evolution. 28: 279-85. PMID 2499684 DOI: 10.1007/Bf02103423  1
1989 Gouy M, Li WH. Phylogenetic analysis based on rRNA sequences supports the archaebacterial rather than the eocyte tree. Nature. 339: 145-7. PMID 2497353 DOI: 10.1038/339145A0  1
1989 Gouy M, Li WH. Molecular phylogeny of the kingdoms Animalia, Plantae, and Fungi. Molecular Biology and Evolution. 6: 109-22. PMID 2469937 DOI: 10.1093/Oxfordjournals.Molbev.A040536  1
1989 Wolfe KH, Sharp PM, Li WH. Rates of synonymous substitution in plant nuclear genes Journal of Molecular Evolution. 29: 208-211. DOI: 10.1007/Bf02100204  1
1988 Li WH, Tanimura M, Sharp PM. Rates and dates of divergence between AIDS virus nucleotide sequences Molecular Biology and Evolution. 5: 313-330. PMID 3405075 DOI: 10.1093/Oxfordjournals.Molbev.A040503  1
1988 Sharp PM, Li WH. Understanding the origins of AIDS viruses [4] Nature. 336: 315. PMID 3194016 DOI: 10.1038/336315A0  1
1988 Graur D, Li WH. Evolution of protein inhibitors of serine proteinases: positive Darwinian selection or compositional effects? Journal of Molecular Evolution. 28: 131-5. PMID 3148733 DOI: 10.1007/Bf02143504  1
1987 Pamilo P, Nei M, Li WH. Accumulation of mutations in sexual and asexual populations Genetical Research. 49: 135-146. PMID 3596234 DOI: 10.1017/S0016672300026938  1
1987 Sharp PM, Li WH. The codon adaptation index-a measure of directional synonymous codon usage bias, and its potential applications Nucleic Acids Research. 15: 1281-1295. PMID 3547335 DOI: 10.1093/Nar/15.3.1281  1
1987 Wolfe KH, Li WH, Sharp PM. Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast, and nuclear DNAs. Proceedings of the National Academy of Sciences of the United States of America. 84: 9054-8. PMID 3480529 DOI: 10.1073/Pnas.84.24.9054  1
1987 Sharp PM, Li WH. The Rate of synonymous substitution in enterobacterial genes is inversely related to codon usage bias Molecular Biology and Evolution. 4: 222-230. PMID 3328816 DOI: 10.1093/Oxfordjournals.Molbev.A040443  1
1987 Li WH, Tanimura M, Sharp PM. An evaluation of the molecular clock hypothesis using mammalian DNA sequences Journal of Molecular Evolution. 25: 330-342. PMID 3118047 DOI: 10.1007/Bf02603118  1
1987 Sharp PM, Li WH. Ubiquitin genes as a paradigm of concerted evolution of tandem repeats Journal of Molecular Evolution. 25: 58-64. PMID 3041010 DOI: 10.1007/Bf02100041  1
1987 Sharp PM, Li WH. Molecular evolution of ubiquitin genes Trends in Ecology and Evolution. 2: 328-332. DOI: 10.1016/0169-5347(87)90108-X  1
1986 Sharp PM, Li WH. Codon usage in regulatory genes in Escherichia coli does not reflect selection for 'rare' codons Nucleic Acids Research. 14: 7737-7749. PMID 3534792 DOI: 10.1093/Nar/14.19.7737  1
1986 Sharp PM, Li WH. An evolutionary perspective on synonymous codon usage in unicellular organisms Journal of Molecular Evolution. 24: 28-38. PMID 3104616 DOI: 10.1007/Bf02099948  1
1986 Luo CC, Li WH, Moore MN, Chan L. Structure and evolution of the apolipoprotein multigene family. Journal of Molecular Biology. 187: 325-40. PMID 3084795 DOI: 10.1016/0022-2836(86)90436-5  1
1985 Wei CF, Chen SH, Yang CY, Marcel YL, Milne RW, Li WH, Sparrow JT, Gotto AM, Chan L. Molecular cloning and expression of partial cDNAs and deduced amino acid sequence of a carboxyl-terminal fragment of human apolipoprotein B-100. Proceedings of the National Academy of Sciences of the United States of America. 82: 7265-9. PMID 2932736 DOI: 10.1073/Pnas.82.21.7265  1
1984 Lopez LC, Li WH, Frazier ML, Luo CC, Saunders GF. Evolution of glucagon genes Molecular Biology and Evolution. 1: 335-344. PMID 6599970 DOI: 10.1093/Oxfordjournals.Molbev.A040322  1
1983 Griffiths RC, Li WH. Simulating allele frequencies in a population and the genetic differentiation of populations under mutation pressure Theoretical Population Biology. 23: 19-33. PMID 6857548 DOI: 10.1016/0040-5809(83)90003-5  1
1982 Gojobori T, Li WH, Graur D. Patterns of nucleotide substitution in pseudogenes and functional genes Journal of Molecular Evolution. 18: 360-369. PMID 7120431 DOI: 10.1007/Bf01733904  1
1980 Ewens WJ, Li WH. Frequency spectra of neutral and deleterious alleles in a finite population Journal of Mathematical Biology. 10: 155-166. DOI: 10.1007/BF00275839  1
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