Jianzhi Zhang

Summary

Affiliation: University of Michigan
Country: USA

Publications

  1. ncbi request reprint Frequent false detection of positive selection by the likelihood method with branch-site models
    Jianzhi Zhang
    Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
    Mol Biol Evol 21:1332-9. 2004
  2. pmc Accuracy and application of the motif expression decomposition method in dissecting transcriptional regulation
    Zhihua Zhang
    Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor MI 48109, USA
    Nucleic Acids Res 36:3185-93. 2008
  3. pmc High expression hampers horizontal gene transfer
    Chungoo Park
    Department of Ecology and Evolutionary Biology, University of Michigan, MI, USA
    Genome Biol Evol 4:523-32. 2012
  4. pmc Why is the correlation between gene importance and gene evolutionary rate so weak?
    Zhi Wang
    Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, United States of America
    PLoS Genet 5:e1000329. 2009
  5. pmc Positive selection for elevated gene expression noise in yeast
    Zhihua Zhang
    Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
    Mol Syst Biol 5:299. 2009
  6. pmc Prevalent positive epistasis in Escherichia coli and Saccharomyces cerevisiae metabolic networks
    Xionglei He
    Department of Ecology and Evolutionary Biology, Ann Arbor, Michigan, USA
    Nat Genet 42:272-6. 2010
  7. pmc The microevolution of V1r vomeronasal receptor genes in mice
    Seong Hwan Park
    Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
    Genome Biol Evol 3:401-12. 2011
  8. pmc Toward genome-wide identification of Bateson-Dobzhansky-Muller incompatibilities in yeast: a simulation study
    Chuan Li
    Department of Ecology and Evolutionary Biology, University of Michigan, USA
    Genome Biol Evol 5:1261-72. 2013
  9. pmc Why are genes encoded on the lagging strand of the bacterial genome?
    Xiaoshu Chen
    Department of Ecology and Evolutionary Biology, University of Michigan
    Genome Biol Evol 5:2436-9. 2013
  10. pmc A big world inside small-world networks
    Zhihua Zhang
    Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, United States of America
    PLoS ONE 4:e5686. 2009

Research Grants

Collaborators

Detail Information

Publications88

  1. ncbi request reprint Frequent false detection of positive selection by the likelihood method with branch-site models
    Jianzhi Zhang
    Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
    Mol Biol Evol 21:1332-9. 2004
    ....
  2. pmc Accuracy and application of the motif expression decomposition method in dissecting transcriptional regulation
    Zhihua Zhang
    Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor MI 48109, USA
    Nucleic Acids Res 36:3185-93. 2008
    ..As an example, MED results are used to demonstrate that motifs generally have higher binding strengths when appearing in multiple copies than appearing in one copy per promoter...
  3. pmc High expression hampers horizontal gene transfer
    Chungoo Park
    Department of Ecology and Evolutionary Biology, University of Michigan, MI, USA
    Genome Biol Evol 4:523-32. 2012
    ..They also suggest that most successful HGTs are initially slightly deleterious, fixed because of their negligibly low costs rather than high benefits to the recipient...
  4. pmc Why is the correlation between gene importance and gene evolutionary rate so weak?
    Zhi Wang
    Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, United States of America
    PLoS Genet 5:e1000329. 2009
    ....
  5. pmc Positive selection for elevated gene expression noise in yeast
    Zhihua Zhang
    Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
    Mol Syst Biol 5:299. 2009
    ....
  6. pmc Prevalent positive epistasis in Escherichia coli and Saccharomyces cerevisiae metabolic networks
    Xionglei He
    Department of Ecology and Evolutionary Biology, Ann Arbor, Michigan, USA
    Nat Genet 42:272-6. 2010
    ..We offer mechanistic explanations of these findings and experimentally validate them for 61 S. cerevisiae gene pairs...
  7. pmc The microevolution of V1r vomeronasal receptor genes in mice
    Seong Hwan Park
    Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
    Genome Biol Evol 3:401-12. 2011
    ..These findings have broad implications for understanding the driving forces of rapid gene turnovers that are often observed in the evolution of large gene families...
  8. pmc Toward genome-wide identification of Bateson-Dobzhansky-Muller incompatibilities in yeast: a simulation study
    Chuan Li
    Department of Ecology and Evolutionary Biology, University of Michigan, USA
    Genome Biol Evol 5:1261-72. 2013
    ..The improved methodology developed here is, in principle, applicable to other organisms and can help detect epistasis in general. ..
  9. pmc Why are genes encoded on the lagging strand of the bacterial genome?
    Xiaoshu Chen
    Department of Ecology and Evolutionary Biology, University of Michigan
    Genome Biol Evol 5:2436-9. 2013
    ..Therefore, the adaptive hypothesis is neither theoretically needed nor empirically supported...
  10. pmc A big world inside small-world networks
    Zhihua Zhang
    Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, United States of America
    PLoS ONE 4:e5686. 2009
    ..Hence, short diameters appear to be sacrificed for high modularities, suggesting a tradeoff between network efficiency and advantages offered by modularity (e.g., multi-functionality, robustness, and/or evolvability)...
  11. pmc Abundant indispensable redundancies in cellular metabolic networks
    Zhi Wang
    Department of Ecology and Evolutionary Biology, University of Michigan
    Genome Biol Evol 2009:23-33. 2009
    ..Taken together, our results strongly suggest that redundant reactions are not kept as backups and that the genetic robustness of metabolic networks is an evolutionary by-product...
  12. pmc Protein subcellular relocalization in the evolution of yeast singleton and duplicate genes
    Wenfeng Qian
    Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor
    Genome Biol Evol 2009:198-204. 2009
    ..These results suggest that subcellular relocalization is unlikely to have been a major mechanism for duplicate gene retention and functional divergence at the genomic scale...
  13. pmc Impact of translational error-induced and error-free misfolding on the rate of protein evolution
    Jian Rong Yang
    Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat Sen University, Guangzhou, PR China
    Mol Syst Biol 6:421. 2010
    ..These findings provide unambiguous support to the role of protein-misfolding-avoidance in determining the rate of protein sequence evolution...
  14. pmc Balanced codon usage optimizes eukaryotic translational efficiency
    Wenfeng Qian
    Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, United States of America
    PLoS Genet 8:e1002603. 2012
    ....
  15. doi request reprint Genetic redundancies and their evolutionary maintenance
    Jianzhi Zhang
    Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
    Adv Exp Med Biol 751:279-300. 2012
    ..The studies summarized here illustrate the utility of systems analysis for understanding evolutionary phenomena and the importance of evolutionary thinking in uncovering the functions and origins of systemic properties...
  16. ncbi request reprint Significant impact of protein dispensability on the instantaneous rate of protein evolution
    Jianzhi Zhang
    Department of Ecology and Evolutionary Biology, University of Michigan, USA
    Mol Biol Evol 22:1147-55. 2005
    ..A comparison of the fitness contributions of orthologous genes in yeast and nematode supports this conclusion...
  17. ncbi request reprint Parallel adaptive origins of digestive RNases in Asian and African leaf monkeys
    Jianzhi Zhang
    Department of Ecology and Evolutionary Biology, University of Michigan, 1075 Natural Science Building, 830 North University Avenue, Ann Arbor, Michigan 48109, USA
    Nat Genet 38:819-23. 2006
    ..These results demonstrate that despite the overall stochasticity, even molecular evolution has a certain degree of repeatability and predictability under the pressures of natural selection...
  18. pmc Paleomolecular biology unravels the evolutionary mystery of vertebrate UV vision
    Jianzhi Zhang
    Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
    Proc Natl Acad Sci U S A 100:8045-7. 2003
  19. ncbi request reprint Disulfide-bond reshuffling in the evolution of an ape placental ribonuclease
    Jianzhi Zhang
    Department of Ecology and Evolutionary Biology, University of Michigan, USA
    Mol Biol Evol 24:505-12. 2007
    ..Our results provide the foundation for detailed analysis toward understanding the impact of disulfide-bond reshuffling on the structure, function, and evolution of proteins in general and human RNase 8 in particular...
  20. pmc The drifting human genome
    Jianzhi Zhang
    Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
    Proc Natl Acad Sci U S A 104:20147-8. 2007
  21. pmc On the evolution of codon volatility
    Jianzhi Zhang
    Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109, USA
    Genetics 169:495-501. 2005
    ..These and other considerations suggest that codon volatility has only limited utility for detecting positive selection at the DNA sequence level...
  22. ncbi request reprint Pseudogenization of the tumor-growth promoter angiogenin in a leaf-eating monkey
    Jianzhi Zhang
    Department of Ecology and Evolutionary Biology, University of Michigan, 3003 Natural Sciences Building, 830 North University Avenue, Ann Arbor, MI 48109, USA
    Gene 308:95-101. 2003
    ..Our findings also provide a strong case for the importance of evolutionary analysis in biomedical studies of gene functions...
  23. pmc Accelerated protein evolution and origins of human-specific features: Foxp2 as an example
    Jianzhi Zhang
    Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109, USA
    Genetics 162:1825-35. 2002
    ..Taken together, our results suggest an important role that FOXP2 may have played in the origin of human speech and demonstrate a strategy for identifying candidate genes underlying the emergences of human-specific features...
  24. pmc Evolution of DMY, a newly emergent male sex-determination gene of medaka fish
    Jianzhi Zhang
    Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109, USA
    Genetics 166:1887-95. 2004
    ....
  25. ncbi request reprint Parallel functional changes in the digestive RNases of ruminants and colobines by divergent amino acid substitutions
    Jianzhi Zhang
    Department of Ecology and Evolutionary Biology, University of Michigan, USA
    Mol Biol Evol 20:1310-7. 2003
    ....
  26. pmc Evolutionary deterioration of the vomeronasal pheromone transduction pathway in catarrhine primates
    Jianzhi Zhang
    Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
    Proc Natl Acad Sci U S A 100:8337-41. 2003
    ....
  27. pmc Testing the chromosomal speciation hypothesis for humans and chimpanzees
    Jianzhi Zhang
    Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109, USA
    Genome Res 14:845-51. 2004
    ....
  28. pmc Evolution of the human ASPM gene, a major determinant of brain size
    Jianzhi Zhang
    Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109, USA
    Genetics 165:2063-70. 2003
    ....
  29. ncbi request reprint Rapid evolution of primate antiviral enzyme APOBEC3G
    Jianzhi Zhang
    Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor 48109, USA
    Hum Mol Genet 13:1785-91. 2004
    ..The identification of pervasive positive selection for charge-altering amino acid substitutions supports the hypothesis of electrostatic interactions between APOBEC3G and vif or its functional equivalents...
  30. pmc Complementary advantageous substitutions in the evolution of an antiviral RNase of higher primates
    Jianzhi Zhang
    Laboratory of Host Defenses, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
    Proc Natl Acad Sci U S A 99:5486-91. 2002
    ..Overall, our study illustrates the power of the "paleomolecular biochemistry" approach in delineating the complex interplays of amino acid substitutions in evolution and in identifying the molecular basis of biological innovation...
  31. pmc RNase 8, a novel RNase A superfamily ribonuclease expressed uniquely in placenta
    Jianzhi Zhang
    Laboratory of Host Defenses, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
    Nucleic Acids Res 30:1169-75. 2002
    ..The rapid evolution, species-limited deactivation and tissue-specific expression of RNase 8 suggest a unique physiological function and reiterates the evolutionary plasticity of the RNase A superfamily...
  32. pmc Human RNase 7: a new cationic ribonuclease of the RNase A superfamily
    Jianzhi Zhang
    Department of Ecology and Evolutionary Biology, University of Michigan, 3003 Natural Science Building, 830 North University Avenue, Ann Arbor, MI 48109, USA
    Nucleic Acids Res 31:602-7. 2003
    ....
  33. pmc Rapid subfunctionalization accompanied by prolonged and substantial neofunctionalization in duplicate gene evolution
    Xionglei He
    Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109, USA
    Genetics 169:1157-64. 2005
    ..Our results demonstrate that enormous numbers of new functions have originated via gene duplication...
  34. ncbi request reprint Ancient expansion of the ribonuclease A superfamily revealed by genomic analysis of placental and marsupial mammals
    Soochin Cho
    Department of Ecology and Evolutionary Biology, University of Michigan, 1075 Natural Science Building, 830 North University Avenue, Ann Arbor, MI 48109, USA
    Gene 373:116-25. 2006
    ....
  35. ncbi request reprint Rapid evolution of primate ESX1, an X-linked placenta- and testis-expressed homeobox gene
    Xiaoxia Wang
    Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
    Hum Mol Genet 16:2053-60. 2007
    ..These and other results suggest that even the fundamental process of spermatogenesis has been targeted by positive selection in primate and human evolution and that mouse may not be a suitable model for studying human reproduction...
  36. pmc Dramatic variation of the vomeronasal pheromone receptor gene repertoire among five orders of placental and marsupial mammals
    Wendy E Grus
    Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
    Proc Natl Acad Sci U S A 102:5767-72. 2005
    ..In sum, our results demonstrate tremendous diversity and rapid evolution of mammalian V1R gene inventories and caution the generalization of VNO biology from rodents to all mammals...
  37. ncbi request reprint Isolation, characterization, and evolutionary divergence of mouse RNase 6: evidence for unusual evolution in rodents
    Kimberly D Dyer
    Eosinophil Biology Section, Laboratory of Allergic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
    J Mol Evol 59:657-65. 2004
    ..66. These data suggest that the ancestral rodent RNase 6 was subject to accelerated evolution, resulting in the conserved modern gene, which most likely plays an important role in mouse physiology...
  38. ncbi request reprint Zebrafish ribonucleases are bactericidal: implications for the origin of the vertebrate RNase A superfamily
    Soochin Cho
    Department of Ecology and Evolutionary Biology, University of Michigan, USA
    Mol Biol Evol 24:1259-68. 2007
    ..These results, together with the presence of antibacterial and/or antiviral activities in multiple distantly related mammalian RNases, strongly suggest that the superfamily started as a host-defense mechanism in vertebrate evolution...
  39. ncbi request reprint Rapid turnover and species-specificity of vomeronasal pheromone receptor genes in mice and rats
    Wendy E Grus
    Department of Ecology and Evolutionary Biology, University of Michigan, 3003 Natural Science Building, 830 North University Avenue, Ann Arbor, MI 48109, USA
    Gene 340:303-12. 2004
    ..Our results show that the evolution of the V1r repertoire is characterized by exceptionally fast gene turnover via gains and losses of individual genes, suggesting rapid and substantial changes in pheromone communication between species...
  40. pmc Why do hubs tend to be essential in protein networks?
    Xionglei He
    Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
    PLoS Genet 2:e88. 2006
    ..These and other findings provide new perspectives on the biological relevance of network structure and robustness...
  41. pmc Sex-specific splicing of the honeybee doublesex gene reveals 300 million years of evolution at the bottom of the insect sex-determination pathway
    Soochin Cho
    Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109, USA
    Genetics 177:1733-41. 2007
    ..Thus, it is likely that the dsx splicing activator system in flies, where the male form is the default, arose during early dipteran evolution...
  42. ncbi request reprint Genetic evidence for the coexistence of pheromone perception and full trichromatic vision in howler monkeys
    David M Webb
    Department of Ecology and Evolutionary Biology, University of Michigan, USA
    Mol Biol Evol 21:697-704. 2004
    ..We suggest that the ecological differences between OW and NW primates, particularly in habitat selection, may have also affected the evolution of pheromone perception...
  43. ncbi request reprint Higher duplicability of less important genes in yeast genomes
    Xionglei He
    Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, USA
    Mol Biol Evol 23:144-51. 2006
    ....
  44. ncbi request reprint Nonneutral evolution of the transcribed pseudogene Makorin1-p1 in mice
    Ondrej Podlaha
    Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, USA
    Mol Biol Evol 21:2202-9. 2004
    ..Our results illustrate the potential of using evolutionary analysis to identify such pseudogenes from genome sequences...
  45. pmc Distinct evolutionary patterns between chemoreceptors of 2 vertebrate olfactory systems and the differential tuning hypothesis
    Wendy E Grus
    Department of Ecology and Evolutionary Biology, University of Michigan, USA
    Mol Biol Evol 25:1593-601. 2008
    ....
  46. doi request reprint RNA sequencing shows no dosage compensation of the active X-chromosome
    Yuanyan Xiong
    State Key Laboratory of Biocontrol, College of Life Sciences, Sun Yat Sen University, Guangzhou, China
    Nat Genet 42:1043-7. 2010
    ..Together, our findings reject Ohno’s hypothesis, necessitating a major revision of the current model of dosage compensation in the evolution of sex chromosomes...
  47. pmc Null mutations in human and mouse orthologs frequently result in different phenotypes
    Ben Yang Liao
    Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
    Proc Natl Acad Sci U S A 105:6987-92. 2008
    ....
  48. ncbi request reprint Adaptive evolution of a duplicated pancreatic ribonuclease gene in a leaf-eating monkey
    Jianzhi Zhang
    Laboratory of Host Defenses, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
    Nat Genet 30:411-5. 2002
    ..Our findings demonstrate the contribution of gene duplication to organismal adaptation and show the power of combining sequence analysis and functional assays in delineating the molecular basis of adaptive evolution...
  49. pmc Gene dosage and gene duplicability
    Wenfeng Qian
    Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109, USA
    Genetics 179:2319-24. 2008
    ..On the basis of these and other results, we conclude that selection for higher gene dosage does not play a major role in driving the fixation of duplication genes...
  50. pmc Positive selection for indel substitutions in the rodent sperm protein catsper1
    Ondrej Podlaha
    Department of Ecology and Evolutionary Biology, University of Michigan, USA
    Mol Biol Evol 22:1845-52. 2005
    ..Our findings provide a necessary foundation for future experimental investigations of Catsper1's function in sperm physiology and role in sperm competition using rodent models...
  51. pmc Evolution of the complementary sex-determination gene of honey bees: balancing selection and trans-species polymorphisms
    Soochin Cho
    Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109, USA
    Genome Res 16:1366-75. 2006
    ..Our results provide a definitive demonstration of balancing selection acting at the honey bee csd gene, offer insights into the molecular determinants of csd allelic specificities, and help avoid homozygosity in bee breeding...
  52. pmc The ortholog conjecture is untestable by the current gene ontology but is supported by RNA sequencing data
    Xiaoshu Chen
    Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, United States of America
    PLoS Comput Biol 8:e1002784. 2012
    ..We conclude that the ortholog conjecture remains largely valid to the extent that it has been tested, but further scrutiny using more and better functional data is needed...
  53. pmc Protein misinteraction avoidance causes highly expressed proteins to evolve slowly
    Jian Rong Yang
    Key Laboratory of Gene Engineering of the Ministry of Education, School of Life Sciences, Sun Yat Sen University, Guangzhou 510275, China
    Proc Natl Acad Sci U S A 109:E831-40. 2012
    ..These findings show a pluralistic origin of the E-R anticorrelation and reveal the role of protein misinteraction, an inherent property of complex cellular systems, in constraining protein evolution...
  54. ncbi request reprint Evolutionary conservation of expression profiles between human and mouse orthologous genes
    Ben Yang Liao
    Department of Ecology and Evolutionary Biology, University of Michigan, USA
    Mol Biol Evol 23:530-40. 2006
    ..These results highlight the importance of proper consideration of various estimation errors in comparing the microarray data between species...
  55. pmc Toward a molecular understanding of pleiotropy
    Xionglei He
    Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109, USA
    Genetics 173:1885-91. 2006
    ..We also provide genomewide evidence that the evolutionary conservation of genes and gene sequences positively correlates with the level of gene pleiotropy...
  56. ncbi request reprint Gene complexity and gene duplicability
    Xionglei He
    Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor 48109, USA
    Curr Biol 15:1016-21. 2005
    ..Thus, gene duplication increases both gene number and gene complexity, two important factors in the origin of genomic and organismal complexity...
  57. pmc Gene losses during human origins
    Xiaoxia Wang
    Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
    PLoS Biol 4:e52. 2006
    ....
  58. pmc Coexpression of linked genes in Mammalian genomes is generally disadvantageous
    Ben Yang Liao
    Department of Ecology and Evolutionary Biology, University of Michigan, USA
    Mol Biol Evol 25:1555-65. 2008
    ....
  59. ncbi request reprint The ribonuclease A superfamily of mammals and birds: identifying new members and tracing evolutionary histories
    Soochin Cho
    Department of Ecology and Evolutionary Biology, University of Michigan, 3003 Natural Science Building, 830 North University Avenue, Ann Arbor, MI 48109, USA
    Genomics 85:208-20. 2005
    ..Consistent with this hypothesis, all members of the superfamily exhibit high rates of amino acid substitution as is commonly observed in immunity genes...
  60. pmc Measuring the evolutionary rate of protein-protein interaction
    Wenfeng Qian
    Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
    Proc Natl Acad Sci U S A 108:8725-30. 2011
    ..The extremely slow evolution of protein molecular function may account for the remarkable conservation of life at molecular and cellular levels and allow for studying the mechanistic basis of human disease in much simpler organisms...
  61. ncbi request reprint Relaxation of selective constraint and loss of function in the evolution of human bitter taste receptor genes
    Xiaoxia Wang
    Department of Ecology and Evolutionary Biology, University of Michigan, 830 North University Avenue, Ann Arbor, MI 48109, USA
    Hum Mol Genet 13:2671-8. 2004
    ....
  62. pmc Positive selection on protein-length in the evolution of a primate sperm ion channel
    Ondrej Podlaha
    Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
    Proc Natl Acad Sci U S A 100:12241-6. 2003
    ..This finding suggests that the selection detected may be related to the regulation of the CATSPER1 channel, which can affect sperm motility, an important determinant in sperm competition...
  63. pmc Origin of the genetic components of the vomeronasal system in the common ancestor of all extant vertebrates
    Wendy E Grus
    Department of Ecology and Evolutionary Biology, University of Michigan, USA
    Mol Biol Evol 26:407-19. 2009
    ..These findings are important for understanding the evolution of vertebrate sensory systems and illustrate the utility of the genome sequences of early diverging vertebrates for uncovering the evolution of vertebrate-specific traits...
  64. ncbi request reprint Remarkable expansions of an X-linked reproductive homeobox gene cluster in rodent evolution
    Xiaoxia Wang
    Department of Ecology and Evolutionary Biology, University of Michigan, 1075 Natural Science Building, 830 North University Avenue, Ann Arbor, MI 48109, USA
    Genomics 88:34-43. 2006
    ....
  65. pmc Comparative genomic analysis identifies an evolutionary shift of vomeronasal receptor gene repertoires in the vertebrate transition from water to land
    Peng Shi
    Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109, USA
    Genome Res 17:166-74. 2007
    ..Taken together, our results demonstrate the exceptional evolutionary fluidity of vomeronasal receptors, making them excellent targets for studying the molecular basis of physiological and behavioral diversity and adaptation...
  66. pmc The genomic landscape and evolutionary resolution of antagonistic pleiotropy in yeast
    Wenfeng Qian
    Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
    Cell Rep 2:1399-410. 2012
    ..These findings provide an empirical foundation for AP-dependent theories and have broad biomedical and evolutionary implications...
  67. pmc More genes underwent positive selection in chimpanzee evolution than in human evolution
    Margaret A Bakewell
    Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
    Proc Natl Acad Sci U S A 104:7489-94. 2007
    ....
  68. ncbi request reprint Contrasting modes of evolution between vertebrate sweet/umami receptor genes and bitter receptor genes
    Peng Shi
    Department of Ecology and Evolutionary Biology, University of Michigan, USA
    Mol Biol Evol 23:292-300. 2006
    ..Thus, functional divergence and specialization of taste receptors generally occurred via adaptive evolution...
  69. pmc Maintenance of duplicate genes and their functional redundancy by reduced expression
    Wenfeng Qian
    Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
    Trends Genet 26:425-30. 2010
    ..Whereas the majority of the expression reductions are likely to be neutral, some are apparently beneficial to rebalancing gene dosage after duplication...
  70. ncbi request reprint Impacts of gene essentiality, expression pattern, and gene compactness on the evolutionary rate of mammalian proteins
    Ben Yang Liao
    Department of Ecology and Evolutionary Biology, University of Michigan, USA
    Mol Biol Evol 23:2072-80. 2006
    ..Our results suggest a considerable variation in rate determinants between unicellular organisms such as the yeast and multicellular organisms such as mammals...
  71. ncbi request reprint Diversifying selection of the tumor-growth promoter angiogenin in primate evolution
    Jianzhi Zhang
    Laboratory of Host Defenses, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Building 10, Rm 11 N 104, 9000 Rockville Pike, Bethesda, MD 20892, USA
    Mol Biol Evol 19:438-45. 2002
    ....
  72. ncbi request reprint Low rates of expression profile divergence in highly expressed genes and tissue-specific genes during mammalian evolution
    Ben Yang Liao
    Department of Ecology and Evolutionary Biology, University of Michigan, USA
    Mol Biol Evol 23:1119-28. 2006
    ..Thus, different forces and selective constraints must underlie the evolution of gene sequence and that of gene expression...
  73. pmc Genomic evidence for elevated mutation rates in highly expressed genes
    Chungoo Park
    Department of Ecology and Evolutionary Biology, University of Michigan, 1075 Natural Science Building, 830 North University Avenue, Ann Arbor, Michigan 48109, USA
    EMBO Rep 13:1123-9. 2012
    ..A significant positive correlation is also detected between the human germline mutation rate and expression level. These results indicate that transcription is overall mutagenic...
  74. ncbi request reprint Did brain-specific genes evolve faster in humans than in chimpanzees?
    Peng Shi
    Department of Ecology and Evolutionary Biology, University of Michigan, 1075 Natural Science Building, 830 North University Avenue, Ann Arbor, MI 48109, USA
    Trends Genet 22:608-13. 2006
    ..Our results suggest that the unique features of the human brain did not arise by a large number of adaptive amino acid changes in many proteins...
  75. ncbi request reprint Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level
    Jianzhi Zhang
    Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, USA
    Mol Biol Evol 22:2472-9. 2005
    ..Bayes empirical Bayes identification of amino acid sites under positive selection along the foreground branches was found to be reliable, but lacked power...
  76. pmc Genome-wide evolutionary conservation of N-glycosylation sites
    Chungoo Park
    Department of Ecology and Evolutionary Biology, University of Michigan, USA
    Mol Biol Evol 28:2351-7. 2011
    ..Because the majority of N-glycosylation occurs at solvent accessible sites, our results show an overall functional importance for N-glycosylation...
  77. pmc Transcriptional reprogramming and backup between duplicate genes: is it a genomewide phenomenon?
    Xionglei He
    Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109, USA
    Genetics 172:1363-7. 2006
    ..There is little evidence supporting widespread functional compensation of divergently expressed duplicate genes by transcriptional reprogramming...
  78. ncbi request reprint Why are some human disease-associated mutations fixed in mice?
    Lizhi Gao
    Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
    Trends Genet 19:678-81. 2003
  79. ncbi request reprint Mouse duplicate genes are as essential as singletons
    Ben Yang Liao
    Department of Ecology and Evolutionary Biology, University of Michigan, 1075 Natural Science Building, 830 North University Avenue, Ann Arbor, MI 48109, USA
    Trends Genet 23:378-81. 2007
    ..This suggests that mammalian duplicates rarely compensate for each other, and that the absence of phenotypes in mice deficient for a duplicate gene should not be automatically attributed to paralogous compensation...
  80. pmc Rapid evolution of mammalian X-linked testis-expressed homeobox genes
    Xiaoxia Wang
    Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109, USA
    Genetics 167:879-88. 2004
    ....
  81. ncbi request reprint Origin and evolution of the vertebrate vomeronasal system viewed through system-specific genes
    Wendy E Grus
    Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
    Bioessays 28:709-18. 2006
    ..We propose that a VNS precursor exists in teleosts and that its evolutionary origin predated the separation between teleosts and tetrapods...
  82. pmc In search of the biological significance of modular structures in protein networks
    Zhi Wang
    Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, United States of America
    PLoS Comput Biol 3:e107. 2007
    ..Taken together, our results suggest the intriguing possibility that the structural modules in the PPI network originated as an evolutionary byproduct without biological significance...
  83. ncbi request reprint Composition and evolution of the V2r vomeronasal receptor gene repertoire in mice and rats
    Hui Yang
    Laboratory of Cellular and Molecular Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
    Genomics 86:306-15. 2005
    ..The identification of the entire V2r repertoire opens the door to genomic-level studies of the structure, function, and evolution of this diverse group of sensory receptors...
  84. ncbi request reprint Adaptive diversification of bitter taste receptor genes in Mammalian evolution
    Peng Shi
    Laboratory of Molecular Evolution and Genome Diversity, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
    Mol Biol Evol 20:805-14. 2003
    ....
  85. ncbi request reprint Accelerated evolution and loss of a domain of the sperm-egg-binding protein SED1 in ancestral primates
    Ondrej Podlaha
    Mol Biol Evol 23:1828-31. 2006
    ..These results reveal a different evolutionary pattern of SED1 from that of many other sperm-egg-binding proteins, which often show diversifying selection occurring in multiple lineages...
  86. ncbi request reprint Erratic evolution of SRY in higher primates
    Xiaoxia Wang
    Mol Biol Evol 19:582-4. 2002
  87. ncbi request reprint Largest vertebrate vomeronasal type 1 receptor gene repertoire in the semiaquatic platypus
    Wendy E Grus
    Mol Biol Evol 24:2153-7. 2007
    ..Our results challenge the view that olfaction is unimportant to aquatic mammals and call for further study into the role of vomeronasal reception in platypus physiology and behavior...

Research Grants13

  1. RNases for understanding the origin of new gene function
    Jianzhi Zhang; Fiscal Year: 2003
    ....
  2. Evolution of vertebrate sensory genes
    Jianzhi Zhang; Fiscal Year: 2010
    ..These studies will also help understand human smell and taste variations and disorders. ..
  3. Functional genomic approaches to duplicate gene evolution
    Jianzhi Zhang; Fiscal Year: 2010
    ..A clear understanding of these relationships helps clarify the exact molecular basis of human diseases, a necessary step in the treatment and prevention of these diseases. ..
  4. Functional genomic approaches to duplicate gene evolution
    Jianzhi Zhang; Fiscal Year: 2009
    ..A clear understanding of these relationships helps clarify the exact molecular basis of human diseases, a necessary step in the treatment and prevention of these diseases. ..
  5. Evolution of vertebrate sensory genes
    Jianzhi Zhang; Fiscal Year: 2009
    ..These studies will also help understand human smell and taste variations and disorders. ..
  6. Evolution of vertebrate sensory genes
    Jianzhi Zhang; Fiscal Year: 2007
    ..These studies will also help understand human smell and taste variations and disorders. ..
  7. RNases for understanding the origin of new gene function
    Jianzhi Zhang; Fiscal Year: 2007
    ..abstract_text> ..
  8. RNases for understanding the origin of new gene function
    Jianzhi Zhang; Fiscal Year: 2006
    ..abstract_text> ..
  9. Functional genomic approaches to duplicate gene evolution
    Jianzhi Zhang; Fiscal Year: 2010
    ..A clear understanding of these relationships helps clarify the exact molecular basis of human diseases, a necessary step in the treatment and prevention of these diseases. ..