Wen Hsiung Li

Summary

Affiliation: University of Chicago
Country: USA

Publications

  1. ncbi CpG island density and its correlations with genomic features in mammalian genomes
    Leng Han
    Department of Psychiatry, Virginia Commonwealth University, Richmond, VA 23298, USA
    Genome Biol 9:R79. 2008
  2. ncbi Overlapping genes in the human and mouse genomes
    Chaitanya R Sanna
    Department of Computer Science, Virginia Tech, Blacksburg, USA
    BMC Genomics 9:169. 2008
  3. ncbi Identifying regulatory targets of cell cycle transcription factors using gene expression and ChIP-chip data
    Wei Sheng Wu
    Lab of Control and Systems Biology, Department of Electrical Engineering, National Tsing Hua University, Hsinchu, Taiwan
    BMC Bioinformatics 8:188. 2007
  4. ncbi Dynamic modeling of cis-regulatory circuits and gene expression prediction via cross-gene identification
    Li Hsieh Lin
    Lab of System Biology, National Tsing Hua University, Hsinchu, 300, Taiwan
    BMC Bioinformatics 6:258. 2005
  5. ncbi Multidimensional scaling for large genomic data sets
    Jengnan Tzeng
    Genomics Research Center, Academia Sinica, Taipei, 115 Taiwan
    BMC Bioinformatics 9:179. 2008
  6. ncbi A systematic approach to detecting transcription factors in response to environmental stresses
    Li Hsieh Lin
    Lab of Systems Biology, Department of Electronical Engineering, National Tsing Hua University, 101, Sec 2, Kuang Fu Hsinchu, 300, Taiwan
    BMC Bioinformatics 8:473. 2007
  7. ncbi Detection of gene duplications and block duplications in eukaryotic genomes
    Wen Hsiung Li
    Department of Ecology and Evolution, University of Chicago, 1101 East 57th Street, Chicago, IL 60637, USA
    J Struct Funct Genomics 3:27-34. 2003
  8. ncbi Functional characterization of cellulases identified from the cow rumen fungus Neocallimastix patriciarum W5 by transcriptomic and secretomic analyses
    Tzi Yuan Wang
    Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
    Biotechnol Biofuels 4:24. 2011
  9. ncbi Different evolutionary patterns between young duplicate genes in the human genome
    Peng Zhang
    Department of Ecology and Evolution, University of Chicago, East 57th Street, Chicago, IL 60637, USA
    Genome Biol 4:R56. 2003
  10. ncbi Functional promiscuity of squirrel monkey growth hormone receptor toward both primate and nonprimate growth hormones
    Soojin Yi
    Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637, USA
    Mol Biol Evol 19:1083-92. 2002

Research Grants

  1. Cis-regulatory motif variants and evolution of gene regulation in yeasts
    Wen Hsiung Li; Fiscal Year: 2007
  2. STATISTICAL STUDIES OF DNA EVOLUTION
    Wen Hsiung Li; Fiscal Year: 2007
  3. Evolution of Duplicate Genes at the Genomic Level
    Wen Hsiung Li; Fiscal Year: 2005
  4. Mutation Rate Variation Among Human Genomic Regions
    Wen Hsiung Li; Fiscal Year: 2004
  5. MOLECULAR COEVOLUTION OF GROWTH HORMONE AND ITS RECEPTOR
    Wen Hsiung Li; Fiscal Year: 2002
  6. HUMAN DNA POLYMORPHISM AND EVOLUTION
    Wen Hsiung Li; Fiscal Year: 2001
  7. Cis-regulatory motif variants and evolution of gene regulation in yeasts
    Wen Hsiung Li; Fiscal Year: 2009

Collaborators

Detail Information

Publications116 found, 100 shown here

  1. ncbi CpG island density and its correlations with genomic features in mammalian genomes
    Leng Han
    Department of Psychiatry, Virginia Commonwealth University, Richmond, VA 23298, USA
    Genome Biol 9:R79. 2008
    ..To date, there seems to be no comparative analysis of CpG islands and their density at the DNA sequence level among mammalian genomes and of their correlations with other genome features...
  2. ncbi Overlapping genes in the human and mouse genomes
    Chaitanya R Sanna
    Department of Computer Science, Virginia Tech, Blacksburg, USA
    BMC Genomics 9:169. 2008
    ..In this study we identified and characterized the overlapping genes in a set of 13,484 pairs of human-mouse orthologous genes...
  3. ncbi Identifying regulatory targets of cell cycle transcription factors using gene expression and ChIP-chip data
    Wei Sheng Wu
    Lab of Control and Systems Biology, Department of Electrical Engineering, National Tsing Hua University, Hsinchu, Taiwan
    BMC Bioinformatics 8:188. 2007
    ..However, the binding of a TF to a gene does not necessarily imply regulation. Thus, it is important to develop methods to identify regulatory targets of TFs from ChIP-chip data...
  4. ncbi Dynamic modeling of cis-regulatory circuits and gene expression prediction via cross-gene identification
    Li Hsieh Lin
    Lab of System Biology, National Tsing Hua University, Hsinchu, 300, Taiwan
    BMC Bioinformatics 6:258. 2005
    ..This is in contrast to traditional approaches where a cis-regulatory circuit is constructed by a mutagenesis or motif-deletion scheme. We estimate the regulatory functions of cis-regulatory circuits using microarray data...
  5. ncbi Multidimensional scaling for large genomic data sets
    Jengnan Tzeng
    Genomics Research Center, Academia Sinica, Taipei, 115 Taiwan
    BMC Bioinformatics 9:179. 2008
    ..The computational complexity of most metric MDS methods is over O(N2), so that it is difficult to process a data set of a large number of genes N, such as in the case of whole genome microarray data...
  6. ncbi A systematic approach to detecting transcription factors in response to environmental stresses
    Li Hsieh Lin
    Lab of Systems Biology, Department of Electronical Engineering, National Tsing Hua University, 101, Sec 2, Kuang Fu Hsinchu, 300, Taiwan
    BMC Bioinformatics 8:473. 2007
    ..In this study, a novel efficient method is proposed to detect the TFs and their interactivities that regulate yeast genes that respond to any specific environment change...
  7. ncbi Detection of gene duplications and block duplications in eukaryotic genomes
    Wen Hsiung Li
    Department of Ecology and Evolution, University of Chicago, 1101 East 57th Street, Chicago, IL 60637, USA
    J Struct Funct Genomics 3:27-34. 2003
    ..Moreover, in yeast the majority of block duplications occurred between chromosomes, while in nematode most block duplications occurred within chromosomes...
  8. ncbi Functional characterization of cellulases identified from the cow rumen fungus Neocallimastix patriciarum W5 by transcriptomic and secretomic analyses
    Tzi Yuan Wang
    Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
    Biotechnol Biofuels 4:24. 2011
    ..abstract:..
  9. ncbi Different evolutionary patterns between young duplicate genes in the human genome
    Peng Zhang
    Department of Ecology and Evolution, University of Chicago, East 57th Street, Chicago, IL 60637, USA
    Genome Biol 4:R56. 2003
    ..In order to resolve this issue, by providing a general picture, we studied 250 independent pairs of young duplicate genes from the whole human genome...
  10. ncbi Functional promiscuity of squirrel monkey growth hormone receptor toward both primate and nonprimate growth hormones
    Soojin Yi
    Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637, USA
    Mol Biol Evol 19:1083-92. 2002
    ..Interestingly, the altered residue Arg at position 43 of the smGHR does not lead to an increased binding affinity. The implications of these results on the evolution of the GH:GHR interaction and on functional evolution are discussed...
  11. ncbi Rate of protein evolution versus fitness effect of gene deletion
    Jing Yang
    Department of Ecology and Evolution, The University of Chicago, USA
    Mol Biol Evol 20:772-4. 2003
    ....
  12. ncbi Male-driven evolution
    Wen Hsiung Li
    Department of Ecology and Evolution University of Chicago 1101 East 57th Street, Chicago, Illinois 60637, USA
    Curr Opin Genet Dev 12:650-6. 2002
    ....
  13. ncbi Expression divergence between duplicate genes
    Wen Hsiung Li
    Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA
    Trends Genet 21:602-7. 2005
    ..In addition, the relationship between gene duplication and evolution of transcriptional regulatory networks is largely unexplored...
  14. ncbi Evolutionary analyses of the human genome
    W H Li
    Ecology and Evolution, University of Chicago, Illinois 60637, USA
    Nature 409:847-9. 2001
    ..Here we present some first glimpses of these features...
  15. ncbi fPOP: footprinting functional pockets of proteins by comparative spatial patterns
    Yan Yuan Tseng
    Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA
    Nucleic Acids Res 38:D288-95. 2010
    ..Finally, our approach provides a framework for classification of proteins into families on the basis of their functional surfaces...
  16. ncbi ETOPE: Evolutionary test of predicted exons
    Anton Nekrutenko
    Department of Ecology and Evolution, The University of Chicago, 1101 East 57th Street, Chicago, IL 60637, USA
    Nucleic Acids Res 31:3564-7. 2003
    ..It has been previously shown, by empirical data and computer simulation, to be a powerful criterion for identifying protein-coding regions. The ETOPE is available at http://nekrut.uchicago.edu/etope/...
  17. ncbi Expression evolution in yeast genes of single-input modules is mainly due to changes in trans-acting factors
    Daryi Wang
    Research Center for Biodiversity, Academia Sinica, Taipei, Taiwan
    Genome Res 17:1161-9. 2007
    ..In summary, our study suggests that trans-acting factors play the major role in expression evolution between yeast strains, but the role of cis variation is also important...
  18. ncbi Natural selection on cis and trans regulation in yeasts
    J J Emerson
    Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
    Genome Res 20:826-36. 2010
    ..A further examination of correlation between polymorphism and divergence within each category suggests that cis divergence is more frequently mediated by positive Darwinian selection than is trans divergence...
  19. ncbi Protein under-wrapping causes dosage sensitivity and decreases gene duplicability
    Han Liang
    Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, United States of America
    PLoS Genet 4:e11. 2008
    ..Our under-wrapping analysis of more than 12,000 protein structures strongly supports these predictions and further reveals that the effect of dosage sensitivity on gene duplicability decreases with increasing organismal complexity...
  20. ncbi The spatial distribution of cis regulatory elements in yeast promoters and its implications for transcriptional regulation
    Zhenguo Lin
    Department of Ecology and Evolution, University of Chicago, 1101 East 57th Street, Chicago, IL 60637, USA
    BMC Genomics 11:581. 2010
    ..In this study, we reexamined the spatial distribution of TFBSs, investigated various promoter features that may affect the distribution, and studied the effect of TFBS distribution on transcriptional regulation...
  21. ncbi Expansion of hexose transporter genes was associated with the evolution of aerobic fermentation in yeasts
    Zhenguo Lin
    Department of Ecology and Evolution, University of Chicago, USA
    Mol Biol Evol 28:131-42. 2011
    ..Our study reveals a strong positive correlation between the copy number of HXT genes and the strength of aerobic fermentation, suggesting that HXT gene expansion has facilitated the evolution of aerobic fermentation...
  22. ncbi Uncovering small RNA-mediated responses to phosphate deficiency in Arabidopsis by deep sequencing
    Li Ching Hsieh
    Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
    Plant Physiol 151:2120-32. 2009
    ..This study represents a comprehensive expression profiling of Pi-responsive small RNAs and advances our understanding of the regulation of Pi homeostasis mediated by small RNAs...
  23. ncbi Signatures of domain shuffling in the human genome
    Henrik Kaessmann
    Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637, USA
    Genome Res 12:1642-50. 2002
    ..elegans genes. [The following individuals kindly provided reagents, samples, or unpublished information as indicated in the paper: Z. Gu and R. Stevens.]..
  24. ncbi Comparative analysis of the receptor-like kinase family in Arabidopsis and rice
    Shin Han Shiu
    Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637, USA
    Plant Cell 16:1220-34. 2004
    ..These findings led us to hypothesize that most of the recent expansions of the RLK/Pelle family have involved defense/resistance-related genes...
  25. ncbi Comparative methods for the analysis of gene-expression evolution: an example using yeast functional genomic data
    Todd H Oakley
    Ecology and Evolution, University of Chicago, USA
    Mol Biol Evol 22:40-50. 2005
    ..The comparative methods presented here are general enough to test a wide range of evolutionary hypotheses using genomic-scale data from any organism...
  26. ncbi A study of the phylogeny of Brassica rapa, B. nigra, Raphanus sativus, and their related genera using noncoding regions of chloroplast DNA
    Yau Wen Yang
    Institute of Botany, Academia Sinica, Taipei 11529, Taiwan
    Mol Phylogenet Evol 23:268-75. 2002
    ..The rate of nucleotide substitution in the rapa/oleracea lineage is at least 1.5 times that in the nigra lineage...
  27. ncbi Roles of trans and cis variation in yeast intraspecies evolution of gene expression
    Huang Mo Sung
    Genomics Research Center, Academia Sinica, Taipei, Taiwan
    Mol Biol Evol 26:2533-8. 2009
    ..Moreover, MIM genes are, on average, subject to stronger trans effects than SIM genes, though the difference between the two types of genes is not conspicuous...
  28. ncbi The evolution of aerobic fermentation in Schizosaccharomyces pombe was associated with regulatory reprogramming but not nucleosome reorganization
    Zhenguo Lin
    Department of Ecology and Evolution, University of Chicago, USA
    Mol Biol Evol 28:1407-13. 2011
    ..However, we found no significant nucleosome organization change in the promoter of respiration-related gene in Sch. pombe...
  29. ncbi Origins, lineage-specific expansions, and multiple losses of tyrosine kinases in eukaryotes
    Shin-Han Shiu
    Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
    Mol Biol Evol 21:828-40. 2004
    ....
  30. ncbi Transcription factor families have much higher expansion rates in plants than in animals
    Shin-Han Shiu
    Department of Ecology and Evolution, University of Chicago, Illinois 60637, USA
    Plant Physiol 139:18-26. 2005
    ..The high rate of expansion among plant TF genes and their propensity for parallel expansion suggest frequent adaptive responses to selection pressure common among higher plants...
  31. ncbi Molecular evolution of recombination hotspots and highly recombining pseudoautosomal regions in hominoids
    Soojin Yi
    Department of Ecology and Evolution, University of Chicago, USA
    Mol Biol Evol 22:1223-30. 2005
    ..We hypothesize that sudden changes in recombination rate have caused the changes in substitution rate at this locus...
  32. ncbi Human TRIM71 and its nematode homologue are targets of let-7 microRNA and its zebrafish orthologue is essential for development
    You Chin Lin
    Genomics Research Center, Academia Sinica, Taipei, Taiwan
    Mol Biol Evol 24:2525-34. 2007
    ..Taken together, our results suggest that the regulation of TRIM71 expression by let-7 has been evolutionarily conserved and that TRIM71 likely plays an important role in development...
  33. ncbi Allelic variation in the squirrel monkey x-linked color vision gene: biogeographical and behavioral correlates
    Susan Cropp
    Department of Ecology and Evolution, University of Chicago, IL 60637, USA
    J Mol Evol 54:734-45. 2002
    ....
  34. ncbi Gene number expansion and contraction in vertebrate genomes with respect to invertebrate genomes
    Anuphap Prachumwat
    Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637, USA
    Genome Res 18:221-32. 2008
    ..e., the number of singletons plus the number of gene families) tends to be over-represented in Vonly, but under-represented in V.MCL. Our study suggests that gene function is a major determinant of gene family size...
  35. ncbi Evolution of the hominoid semenogelin genes, the major proteins of ejaculated semen
    Michael I Jensen-Seaman
    Department of Ecology and Evolution, University of Chicago, 1101 East 57th Street, Chicago, IL 60637, USA
    J Mol Evol 57:261-70. 2003
    ....
  36. ncbi Gene essentiality, gene duplicability and protein connectivity in human and mouse
    Han Liang
    Department of Ecology and Evolution, University of Chicago, 1101 East 57th Street, Chicago, IL 60637, USA
    Trends Genet 23:375-8. 2007
    ....
  37. ncbi The K(A)/K(S) ratio test for assessing the protein-coding potential of genomic regions: an empirical and simulation study
    Anton Nekrutenko
    Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637, USA
    Genome Res 12:198-202. 2002
    ....
  38. ncbi Classification of protein functional surfaces using structural characteristics
    Yan Yuan Tseng
    Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA
    Proc Natl Acad Sci U S A 109:1170-5. 2012
    ..As an expandable library, PSC provides a resource of spatial patterns for studying the evolution of protein structure and function...
  39. ncbi The genetic basis of evolutionary change in gene expression levels
    J J Emerson
    Genomics Research Center, Academia Sinica, Taipei 115, Taiwan, Republic of China
    Philos Trans R Soc Lond B Biol Sci 365:2581-90. 2010
    ....
  40. ncbi Systematic identification of yeast cell cycle transcription factors using multiple data sources
    Wei Sheng Wu
    Department of Evolution and Ecology, University of Chicago, Chicago, IL 60637, USA
    BMC Bioinformatics 9:522. 2008
    ..To understand the cell cycle process, it is important to identify the cell cycle transcription factors (TFs) that regulate the expression of cell cycle-regulated genes...
  41. ncbi Identifying gene regulatory modules of heat shock response in yeast
    Wei Sheng Wu
    Department of Evolution and Ecology, University of Chicago, Chicago, IL 60637, USA
    BMC Genomics 9:439. 2008
    ..By organizing the genome into GRMs, a living cell can coordinate the activities of many genes in response to various internal and external stimuli. Therefore, identifying GRMs is helpful for understanding gene regulation...
  42. ncbi An evolutionary approach reveals a high protein-coding capacity of the human genome
    Anton Nekrutenko
    Department of Ecology and Evolution, The University of Chicago, 1101 East 57th Street, Chicago, IL 60637, USA
    Trends Genet 19:306-10. 2003
    ..Of these, 13700 satisfied very stringent criteria and can with confidence be considered as novel exons. Evidently, a large number of new human genes can be identified using evolutionary approaches...
  43. ncbi MicroRNA regulation of human protein protein interaction network
    Han Liang
    Department of Ecology and Evolution, University of Chicago, IL 60637, USA
    RNA 13:1402-8. 2007
    ..Taken together, our study provides the first evidence for global correlation between microRNA repression and protein-protein interactions...
  44. ncbi Human polymorphism at microRNAs and microRNA target sites
    Matthew A Saunders
    Department of Ecology and Evolution, University of Chicago, 1101 East 57th Street, Chicago, IL 60637, USA
    Proc Natl Acad Sci U S A 104:3300-5. 2007
    ....
  45. ncbi Roles of cis- and trans-changes in the regulatory evolution of genes in the gluconeogenic pathway in yeast
    Ya Wen Chang
    Department of Ecology and Evolution, University of Chicago, USA
    Mol Biol Evol 25:1863-75. 2008
    ....
  46. ncbi Fast evolution of core promoters in primate genomes
    Han Liang
    Department of Ecology and Evolution, University of Chicago, USA
    Mol Biol Evol 25:1239-44. 2008
    ..Taken together, our results suggest that positive selection has played a substantial role in the evolution of transcriptional regulation in primates...
  47. ncbi Simultaneous amino acid substitutions at antigenic sites drive influenza A hemagglutinin evolution
    Arthur Chun Chieh Shih
    Institute of Information Science, Academia Sinica, Nankang, Taipei 115, Taiwan
    Proc Natl Acad Sci U S A 104:6283-8. 2007
    ....
  48. ncbi Low nucleotide diversity in chimpanzees and bonobos
    Ning Yu
    Department of Ecology and Evolution, University of Chicago, 1101 E. 57th Street, Chicago, IL 60637, USA
    Genetics 164:1511-8. 2003
    ..Sequence data from this article have been deposited with the GenBank Data libraries under accession nos. AY 275957-AY 277244...
  49. ncbi Role of duplicate genes in genetic robustness against null mutations
    Zhenglong Gu
    Department of Ecology and Evolution, University of Chicago, 1101 East 57th Street, Chicago, Illinois 60637, USA
    Nature 421:63-6. 2003
    ..We estimate that in S. cerevisiae at least a quarter of those gene deletions that have no phenotype are compensated by duplicate genes...
  50. ncbi Patterns of gene duplication in Saccharomyces cerevisiae and Caenorhabditis elegans
    Andre R O Cavalcanti
    Department of Ecology and Evolution, University of Chicago, 1101 East 57th Street, Chicago, IL 60637, USA
    J Mol Evol 56:28-37. 2003
    ..Moreover, in the yeast the majority of block duplications occurred between chromosomes, while in the nematode most block duplications occurred within chromosomes...
  51. ncbi Extent of gene duplication in the genomes of Drosophila, nematode, and yeast
    Zhenglong Gu
    Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA
    Mol Biol Evol 19:256-62. 2002
    ..elegans were probably largely caused by block duplications. At any rate, it is clear that the genome of Drosophila melanogaster has undergone few gene duplications in the recent past and has much fewer gene families than C. elegans...
  52. ncbi Duplicate genes increase gene expression diversity within and between species
    Zhenglong Gu
    Department of Ecology and Evolution, University of Chicago, 1101 East 57th Street, Chicago, Illinois 60637, USA
    Nat Genet 36:577-9. 2004
    ..We show further that duplicate genes tend to cause expression divergences between Drosophila species (or strains) to evolve faster than do single-copy genes. This conclusion is also supported by data from different yeast strains...
  53. ncbi The nonsynonymous/synonymous substitution rate ratio versus the radical/conservative replacement rate ratio in the evolution of mammalian genes
    Kousuke Hanada
    Department of Ecology and Evolution, University of Chicago, USA
    Mol Biol Evol 24:2235-41. 2007
    ....
  54. ncbi SplitPocket: identification of protein functional surfaces and characterization of their spatial patterns
    Yan Yuan Tseng
    Department of Ecology and Evolution, University of Chicago, 1101 East 57th Street, Chicago, IL 60637, USA
    Nucleic Acids Res 37:W384-9. 2009
    ..These spatial patterns should also be useful for protein functional inference, structural evolution and drug design...
  55. ncbi Dating the monocot-dicot divergence and the origin of core eudicots using whole chloroplast genomes
    Shu Miaw Chaw
    Institute of Botany, Academia Sinica, 128 Sec 2 Academy Road, Taipei 115, Taiwan
    J Mol Evol 58:424-41. 2004
    ..These estimates indicate that both the monocot-dicot divergence and the core eudicot's age are older than their respective fossil records...
  56. ncbi Evolutionary diversification of DNA methyltransferases in eukaryotic genomes
    Loic Ponger
    Department of Ecology and Evolution, University of Chicago, USA
    Mol Biol Evol 22:1119-28. 2005
    ..Our results also suggest acquisitions and losses of different MTases in every eukaryotic lineage studied and that some eukaryotes appear to be devoid of methylation...
  57. ncbi Human adaptive evolution at Myostatin (GDF8), a regulator of muscle growth
    Matthew A Saunders
    Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA
    Am J Hum Genet 79:1089-97. 2006
    ..Both mutations are rare among non-Africans yet are at frequencies of up to 31% in sub-Saharan Africans. These signatures of selection at the molecular level suggest that human variation at GDF8 is associated with functional differences...
  58. ncbi Coordinated histone modifications are associated with gene expression variation within and between species
    Misook Ha
    Institute for Cellular and Molecular Biology and Center for Computational Biology and Bioinformatics, University of Texas, Austin, TX 78712, USA
    Genome Res 21:590-8. 2011
    ..The data suggest that genome-wide coordinated modifications of histone acetylation and methylation provide a general mechanism for gene expression changes within and between species and in allopolyploids...
  59. ncbi Are GC-rich isochores vanishing in mammals?
    Jianying Gu
    Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA
    Gene 385:50-6. 2006
    ..Since many eutherian mammals still maintain a fairly large number of chromosomes, it is unlikely that GC-rich isochores are vanishing in these mammals...
  60. ncbi Larger genetic differences within africans than between Africans and Eurasians
    Ning Yu
    Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637, USA
    Genetics 161:269-74. 2002
    ..Clearly, one must specify the geographic origins of the individuals sampled when studying pi or SNP density...
  61. ncbi Comment on "Chromosomal speciation and molecular divergence-accelerated evolution in rearranged chromosomes"
    Jian Lu
    Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA
    Science 302:988; author reply 988. 2003
  62. ncbi Role of positive selection in the retention of duplicate genes in mammalian genomes
    Shin-Han Shiu
    Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA
    Proc Natl Acad Sci U S A 103:2232-6. 2006
    ..In addition, certain functional categories show a higher tendency of lineage-specific expansion than expected, suggesting lineage-specific selection or functional bias in retained duplicates...
  63. ncbi Different age distribution patterns of human, nematode, and Arabidopsis duplicate genes
    Peng Zhang
    Department of Ecology and Evolution, University of Chicago, 1101 East 57th Street, Chicago, IL 60637, USA
    Gene 342:263-8. 2004
    ..One possible explanation of the decreasing rate of loss of duplicate genes over time could be rapid functional divergence between duplicate genes, providing an advantage for the retention of both duplicates...
  64. ncbi Organismal complexity, protein complexity, and gene duplicability
    Jing Yang
    Department of Ecology and Evolution, University of Chicago, 1101 East 57th Street, Chicago, IL 60637, USA
    Proc Natl Acad Sci U S A 100:15661-5. 2003
    ..The same conclusion is reached from a comparison of family sizes in yeast and human...
  65. ncbi Rapid divergence in expression between duplicate genes inferred from microarray data
    Zhenglong Gu
    Dept of Ecology and Evolution, University of Chicago, 1101 East 57th Street, 60637, Chicago, IL, USA
    Trends Genet 18:609-13. 2002
    ..Indeed, more than 40% of gene pairs show expression divergence even when K(S) is </= 0.10, and this proportion becomes >80% for K(S) > 1.5. Only a small fraction of ancient gene pairs do not show expression divergence...
  66. ncbi Signalling pathway for RKIP and Let-7 regulates and predicts metastatic breast cancer
    Jieun Yun
    Ben May Department for Cancer Research, University of Chicago, IL, USA
    EMBO J 30:4500-14. 2011
    ....
  67. ncbi Evolutionary approach to predicting the binding site residues of a protein from its primary sequence
    Yan Yuan Tseng
    Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA
    Proc Natl Acad Sci U S A 108:5313-8. 2011
    ..An automated computational pipeline was developed for our method. A performance evaluation shows that our method achieves a 70% precision in predicting binding site residues at 60% sensitivity...
  68. ncbi Sulfate activation enzymes: phylogeny and association with pyrophosphatase
    Michael E Bradley
    Department of Pediatrics, University of Chicago, 5841 South Maryland Avenue, WCH C519A, Chicago, IL, 60637, USA
    J Mol Evol 68:1-13. 2009
    ....
  69. ncbi The influence of adjacent nucleotides on the pattern of nucleotide substitution in mitochondrial introns of angiosperms
    Yau Wen Yang
    Institute of Botany, Academia Sinica, Taipei 11529, Taiwan
    J Mol Evol 55:111-5. 2002
    ..This might be due largely to the difference in the AT content (0.48 vs. 0.72) between the mitochondrial first nad4 intron and the chloroplast DNA regions studied...
  70. ncbi Mammalian housekeeping genes evolve more slowly than tissue-specific genes
    Liqing Zhang
    Department of Ecology and Evolution, University of Chicago, USA
    Mol Biol Evol 21:236-9. 2004
    ..Therefore, the stronger selective constraints on housekeeping genes are not due to a lower degree of genetic redundancy...
  71. ncbi Recombination has little effect on the rate of sequence divergence in pseudoautosomal boundary 1 among humans and great apes
    Soojin Yi
    Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637, USA
    Genome Res 14:37-43. 2004
    ..Therefore, the mutagenic effect of recombination is far weaker than previously proposed, at least in hominoid PABs...
  72. ncbi Evolution of the yeast protein interaction network
    Hong Qin
    Department of Ecology and Evolution, University of Chicago, 1101 East 57th Street, Chicago, IL 60637, USA
    Proc Natl Acad Sci U S A 100:12820-4. 2003
    ..These observations suggest synergistic selection during network evolution and provide insights into the hierarchical modularity of cellular networks...
  73. ncbi How strong is the mutagenicity of recombination in mammals?
    Shiao-Wei Huang
    Department of Ecology and Evolution, University of Chicago, Chicago, USA
    Mol Biol Evol 22:426-31. 2005
    ..In addition, contrary to a previous study, we found no Fxy duplicate in Mus spretus...
  74. ncbi Reorganization of adjacent gene relationships in yeast genomes by whole-genome duplication and gene deletion
    Jake K Byrnes
    Department of Ecology and Evolution, University of Chicago, USA
    Mol Biol Evol 23:1136-43. 2006
    ..Newly created adjacent gene pairs also have an initial increase in mean log2 expression ratios and maximal expression levels, suggesting that increased intergenic spacing caused a genome-wide reduction in transcriptional interference...
  75. ncbi Patterns of segmental duplication in the human genome
    Liqing Zhang
    Department of Ecology and Evolution, University of Chicago, USA
    Mol Biol Evol 22:135-41. 2005
    ..Our simulation suggests that many duplications containing genes have been selectively maintained in the genome...
  76. ncbi Parallel evolution between aromatase and androgen receptor in the animal kingdom
    Basant Tiwary
    Department of Ecology and Evolution, University of Chicago, USA
    Mol Biol Evol 26:123-9. 2009
    ..Finally, we found evidence supporting the hypothesis that the androgen-to-estrogen ratio determines the gonadal sex in all metazoans...
  77. ncbi Whole genome transcriptome polymorphisms in Arabidopsis thaliana
    Xu Zhang
    Department of Ecology and Evolution, University of Chicago, 1101 E, 57th Street, Chicago, IL 60637, USA
    Genome Biol 9:R165. 2008
    ..Our study demonstrates that whole genome tiling arrays are a powerful platform for dissecting natural transcriptome variation at multi-dimension and high resolution...
  78. ncbi Historical contingency in the evolution of primate color vision
    Nathaniel J Dominy
    Department of Ecology and Evolution, University of Chicago, 1101 East 57th Street, 60637, Chicago, IL, USA
    J Hum Evol 44:25-45. 2003
    ..These results imply a link between the differential evolution of primate color vision and climatic changes during the Eocene-Oligocene transition...
  79. ncbi Improved variance estimators for one- and two-parameter models of nucleotide substitution
    Hsiuying Wang
    Institute of Statistical Science, Academia Sinica, Taipei, Taiwan
    J Theor Biol 254:164-7. 2008
    ..In this paper, we developed improved variance estimators, using a higher-order Taylor expansion and empirical methods. The new estimators outperform the conventional estimators and provide accurate estimates of the true variances...
  80. ncbi Gene clustering pattern, promoter architecture, and gene expression stability in eukaryotic genomes
    Yong H Woo
    Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA
    Proc Natl Acad Sci U S A 108:3306-11. 2011
    ..In complex organisms such as mammals, only a small fraction of head-to-tail genes have retained a short upstream distance, probably because the promoter may not be flanked by a strongly positioned nucleosome on the upstream side...
  81. ncbi Divergence in the spatial pattern of gene expression between human duplicate genes
    Kateryna D Makova
    Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637, USA
    Genome Res 13:1638-45. 2003
    ..Finally,we compare the functions of those duplicate genes that show rapid divergence in spatial expression pattern with the functions of those duplicate genes that show no or little divergence in spatial expression...
  82. ncbi Codon-usage bias versus gene conversion in the evolution of yeast duplicate genes
    Yeong-Shin Lin
    Department of Ecology and Evolution, University of Chicago, 1101 East 57th Street, Chicago, IL 60637, USA
    Proc Natl Acad Sci U S A 103:14412-6. 2006
    ....
  83. ncbi Slow molecular clocks in Old World monkeys, apes, and humans
    Soojin Yi
    Department of Ecology and Evolution, University of Chicago, 1101 East 57th Street, Chicago, IL 60637, USA
    Mol Biol Evol 19:2191-8. 2002
    ....
  84. ncbi Intragenic spatial patterns of codon usage bias in prokaryotic and eukaryotic genomes
    Hong Qin
    Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637, USA
    Genetics 168:2245-60. 2004
    ..Effect of expression level on the strength of codon usage bias is more conspicuous than its effect on the shape of the spatial distribution...
  85. ncbi Developmental constraint on gene duplicability in fruit flies and nematodes
    Jing Yang
    Department of Ecology and Evolution, The University of Chicago, Chicago, IL 60637, USA
    Gene 340:237-40. 2004
    ..Thus, although developmental constraint does appear to reduce gene duplicability, the effect seems weak or at best moderate...
  86. ncbi Strong male-driven evolution of DNA sequences in humans and apes
    Kateryna D Makova
    Department of Ecology and Evolution, University of Chicago, IL 60637, USA
    Nature 416:624-6. 2002
    ..Moreover, we provide an explanation for the small estimate of alpha in a previous study. Our study reinstates a high alpha in hominoids and supports the view that DNA replication errors are the primary source of germline mutation...
  87. ncbi Evidence from opsin genes rejects nocturnality in ancestral primates
    Ying Tan
    Department of Ecology and Evolution, University of Chicago, 1101 East 57th Street, Chicago, IL 60637, USA
    Proc Natl Acad Sci U S A 102:14712-6. 2005
    ..This view is further supported by the distribution pattern of the middle-wavelength (M) and long-wavelength (L) opsin genes among prosimians...
  88. ncbi Radical amino acid change versus positive selection in the evolution of viral envelope proteins
    Kousuke Hanada
    Department of Ecology and Evolution, University of Chicago 1101 East 57th Street, Chicago, IL, 60637, USA
    Gene 385:83-8. 2006
    ....
  89. ncbi Gene expression evolves faster in narrowly than in broadly expressed mammalian genes
    Jing Yang
    Department of Ecology and Evolution, University of Chicago, USA
    Mol Biol Evol 22:2113-8. 2005
    ..In addition, we find a rapid decrease in ECI with the synonymous divergence between duplicate genes, suggesting fast divergence in tissue expression between duplicate genes...
  90. ncbi Contribution of transcription factor binding site motif variants to condition-specific gene expression patterns in budding yeast
    Joshua S Rest
    Department of Ecology and Evolution, The University of Chicago, Chicago, Illinois, United States of America
    PLoS ONE 7:e32274. 2012
    ....
  91. ncbi Evolution of 5' untranslated region length and gene expression reprogramming in yeasts
    Zhenguo Lin
    Department of Ecology and Evolution, University of Chicago, USA
    Mol Biol Evol 29:81-9. 2012
    ..Finally, we found that an increase in 5' UTR length may decrease the +1 nucleosome occupancy. This study provides a new angle to understand the role of 5' UTR in gene expression regulation and evolution...
  92. ncbi Identification of protein functional surfaces by the concept of a split pocket
    Yan Yuan Tseng
    Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637, USA
    Proteins 76:959-76. 2009
    ..Our study demonstrates the power of geometric and evolutionary matching for studying protein functional evolution and provides a framework for classifying protein functions by local spatial patterns of functional surfaces...
  93. ncbi A novel puf-A gene predicted from evolutionary analysis is involved in the development of eyes and primordial germ-cells
    Ming Wei Kuo
    Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
    PLoS ONE 4:e4980. 2009
    ..These studies represent an exemplary implementation of a unique platform to uncover unknown function(s) of human genes and their roles in development regulation...
  94. ncbi Prediction of human miRNAs using tissue-selective motifs in 3' UTRs
    Yao Ming Chang
    Institute of Information Science, Innovation Research Center, and Biodiversity Research Center and Genomics Research Center, Academia Sinica, Nankang, Taipei, Taiwan
    Proc Natl Acad Sci U S A 105:17061-6. 2008
    ....
  95. ncbi Protein function, connectivity, and duplicability in yeast
    Anuphap Prachumwat
    Committee on Genetics, University of Chicago, USA
    Mol Biol Evol 23:30-9. 2006
    ..g., transcription, RNA and DNA metabolisms, and ribosome biogenesis and assembly) are highly connected but have a low duplicability. Finally, we found a negative correlation between protein connectivity and duplicability...
  96. ncbi Comparison of three methods for estimating rates of synonymous and nonsynonymous nucleotide substitutions
    Yun-Huei Tzeng
    Department of Ecology and Evolution, University of Chicago, USA
    Mol Biol Evol 21:2290-8. 2004
    ....
  97. ncbi DNA polymorphism in a worldwide sample of human X chromosomes
    Ning Yu
    Department of Ecology and Evolution, University of Chicago, 1101 East 57th Street, Chicago, IL 60637, USA
    Mol Biol Evol 19:2131-41. 2002
    ..Moreover, this haplotype and all other haplotypes coalesced to the most recent common ancestor of the sample, which was estimated to be older than 490,000 years. Therefore, this region may have a long history in Eurasia...
  98. ncbi Nucleotide diversity in gorillas
    Ning Yu
    Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637, USA
    Genetics 166:1375-83. 2004
    ..From the nuclear DNA pi values, we estimated that the long-term effective population sizes of humans, bonobos, chimpanzees, and gorillas are, respectively, 10,400, 12,300, 21,300, and 25,200...
  99. ncbi Molecular evolution of bat color vision genes
    Daryi Wang
    Institute of Zoology, Academic Sinica, Taipei, Taiwan
    Mol Biol Evol 21:295-302. 2004
    ..Some of these observations are unexpected and may provide insights into the effect of nocturnal life on the evolution of opsin genes in mammals and the evolution of the life history traits of bats in general...
  100. ncbi Features and trend of loss of promoter-associated CpG islands in the human and mouse genomes
    Cizhong Jiang
    Department of Psychiatry and Center for the Study of Biological Complexity, Virginia Commonwealth, USA
    Mol Biol Evol 24:1991-2000. 2007
    ..Our study provides a detailed view of the evolution of promoter-associated CGIs in the human and mouse genomes and our findings are helpful for understanding the evolution of mammalian genomes and the role of CGIs in gene function...
  101. ncbi Method for identifying transcription factor binding sites in yeast
    Huai-Kuang Tsai
    Genomics Research Center, Academia Sinica, Taipei, 115 Taiwan
    Bioinformatics 22:1675-81. 2006
    ..For synthetic data and yeast cell cycle TFs, TFBSfinder identifies motifs that are highly similar to known consensuses. Moreover, TFBSfinder outperforms well-known methods. AVAILABILITY: http://cg1.iis.sinica.edu.tw/~TFBSfinder/...

Research Grants19

  1. Cis-regulatory motif variants and evolution of gene regulation in yeasts
    Wen Hsiung Li; Fiscal Year: 2007
    ....
  2. STATISTICAL STUDIES OF DNA EVOLUTION
    Wen Hsiung Li; Fiscal Year: 2007
    ..5. To introduce the neural network approach into phylogenetic study; this approach has proved extremely powerful in many branches of science and engineering. ..
  3. Evolution of Duplicate Genes at the Genomic Level
    Wen Hsiung Li; Fiscal Year: 2005
    ..5. To study the mechanisms of evolution of duplicate genes or how duplicate genes evolve following the duplication event. We shall examine various models for the retention and evolution of duplicate genes. ..
  4. Mutation Rate Variation Among Human Genomic Regions
    Wen Hsiung Li; Fiscal Year: 2004
    ..Sequence each of them in chimpanzee, gorilla, orangutan, siamang, baboon and colobus. 4. To conduct statistical analyses of the new and existing data to address the above issues. ..
  5. MOLECULAR COEVOLUTION OF GROWTH HORMONE AND ITS RECEPTOR
    Wen Hsiung Li; Fiscal Year: 2002
    ..For amino acid differences with observed significant effects on binding, determine their collective effect in combinations. 6. Conduct statistical analyses of data to characterize evolution of GH and GHR. ..
  6. HUMAN DNA POLYMORPHISM AND EVOLUTION
    Wen Hsiung Li; Fiscal Year: 2001
    ..The new methods and some existing methods will used to analyze the data to be obtained. The new methods will be accessible on the World Wide Web. ..
  7. Cis-regulatory motif variants and evolution of gene regulation in yeasts
    Wen Hsiung Li; Fiscal Year: 2009
    ....