X
Univ of Michigan

Dept of Ecol & Evol Biol

b 2014 a

Qian, W., and J. Zhang (2014) Genomic evidence for adaptation by gene duplication. Genome Res., in press.

Yang, J.-R., S. Ruan, and J. Zhang (2014) Determinative developmental cell lineages are robust to cell deaths. PLoS Genet., 10:e1004501.pdf

Yang, J.-R., X. Chen, and J. Zhang (2014) Codon-by-codon modulation of translational speed and accuracy via mRNA folding. PLoS Biol., 12:e1001910.pdf

Xu, J., and J. Zhang (2014) Why human disease-associated residues appear as the wild-type in other species: genome-scale structural evidence for the compensation hypothesis. Mol. Biol. Evol., 31: 1787-1792.pdf

Ho, W.-C., and J. Zhang (2014) The genotype-phenotype map of yeast complex traits: basic parameters and the role of natural selection. Mol. Biol. Evol., 31: 1568-1580.pdf

Xu, G., and J. Zhang (2014) Human coding RNA editing is generally nonadaptive. Proc. Natl. Acad. Sci. USA, 111:3769-3774.pdf

Li, D., and J. Zhang (2014) Diet shapes the evolution of the vertebrate bitter taste receptor gene repertoire. Mol. Biol. Evol., 31:303-309.pdf

Zhang, J. (2014) Gene duplication. In Oxford Bibliographies in Evolutionary Biology (J. Losos, eds, Oxford University Press, Oxford), DOI: 10.1093/OBO/9780199941728-0002. (Review) pdf


b 2013 a

Zhang, J. (2013) Gene duplication. In Princeton Guide to Evolution (J. Losos, eds, Princeton University Press, Princeton, NJ), Pp 397-405. (Review) pdf

Chen, X., and J. Zhang (2013) Why are genes encoded on the lagging strand of the bacterial genome? Genome Biol. Evol., 5:2436-2439.pdf

Grus, W. E., and J. Zhang (2013) Human lineage-specific gene inactivation. Encyclopedia of Life Sciences. John Wiley & Sons, Chichester, UK, Pp 1-8. (Updated Review) pdf

Zhang, J., and G. P. Wagner (2013) On the definition and measurement of pleiotropy. Trends Genet., 29:383-384. (Letter to Editor)pdf

Li, C., Z. Wang, and J. Zhang. (2013) Toward genome-wide identification of Bateson-Dobzhansky-Muller incompatibilities in yeast: A simulation study. Genome Biol. Evol., 5:1261-1272.pdf

Chen, X., and J. Zhang (2013) No gene-specific optimization of mutation rate in Escherichia coli. Mol. Biol. Evol., 30:1559-1562.pdf

Park, C., X. Chen, J.-R. Yang, and J. Zhang (2013) Differential requirements for mRNA folding partially explain why highly expressed proteins evolve slowly. Proc. Natl. Acad. Sci. USA, 110:E678-E686.pdf


b 2012 a

Park, C., W. Qian, and J. Zhang (2012) Genomic evidence for elevated mutation rates in highly expressed genes. EMBO Rep., 13:1123-1129.pdf

Chen, X., and J. Zhang (2012) The ortholog conjecture is untestable by the current gene ontology but is supported by RNA sequencing data. PLoS Comput. Biol., 8:e1002784. pdf

Qian, W., D. Ma, C. Xiao, Z. Wang, and J. Zhang (2012) The genomic landscape and evolutionary resolution of antagonistic pleiotropy in yeast. Cell Rep., 2:1399-1410. pdf

Lin, F., K. Xing, J. Zhang, and X. He (2012) Expression reduction in mammalian X chromosome evolution refutes Ohno's hypothesis of dosage compensation. Proc. Natl. Acad. Sci. USA, 109:11752-11757. pdf

Zhao, H., and J. Zhang (2012) Mismatches between feeding ecology and taste receptor evolution: An inconvenient truth. Proc. Natl. Acad. Sci. USA, 109:E1464. (Letter to Editor) pdf

Park, C., and J. Zhang (2012) High expression hampers horizontal gene transfer. Genome Biol. Evol., 4:523-532. pdf

Yang, J.-R., B.-Y. Liao, S.-M. Zhuang, and J. Zhang (2012) Protein misinteraction avoidance causes highly expressed proteins to evolve slowly. Proc. Natl. Acad. Sci. USA., 109:E831-E840. pdf

Zhang, J. (2012) Genetic redundancies and their evolutionary maintenance. In Evolutionary Systems Biology (O. Soyer, eds, Springer), Pp 279-300. (Review) pdf

Wagner, G. P., and J. Zhang (2012) Universal pleiotropy is not a valid null hypothesis: Reply to Hill and Zhang. Nat. Rev. Genet., 13:296. pdf

Qian, W., J.-R. Yang, N. M. Pearson, C. Maclean, and J. Zhang (2012) Balanced codon usage optimizes eukaryotic translational efficiency. PLoS Genet., 8(3): e1002603. pdf

Zhao, H., D. Xu, S. Zhang, and J. Zhang (2012) Genomic and genetic evidence for the loss of umami taste in bats. Genome Biol. Evol., 4:73-79. pdf


b 2011 a

He, X. X. Chen, Y. Xiong, Z. Chen, X. Wang, S. Shi, X. Wang, and J. Zhang (2011) Response to the comments on "RNA sequencing shows no dosage compensation of the active X-chromosome". Nat Genet., 43:1171-1172. pdf

Zhang, J. (2011) A panorama of mammalian gene expression evolution. Mol. Syst. Biol., 7:552. (News & Views) pdf

Park, S. H., O. Podlaha, W. E. Grus, and J. Zhang (2011) The microevolution of V1r vomeronasal receptor genes in mice. Genome Biol. Evol., 3:401-412. pdf

Qian, W., X. He, E. Chan, H. Xu, and J. Zhang (2011) Measuring the evolutionary rate of protein-protein interaction. Proc. Natl. Acad. Sci. USA, 108:8725-8730. pdf

Wang, Z., and J. Zhang (2011) Impact of gene expression noise on organismal fitness and the efficacy of natural selection. Proc. Natl. Acad. Sci. USA. 108:E67-E76. pdf

Park, C., and J. Zhang (2011) Genome-wide evolutionary conservation of N-glycosylation sites. Mol. Biol. Evol. 28:2351-2357. pdf

Wagner, G. P., and J. Zhang (2011) The pleiotropic structure of the genotype-phenotype map: the evolvability of complex adaptations. Nat. Rev. Genet. 12:204-213. (Review) pdf

Zhao, H., D. Xu, S. Zhang, and J. Zhang (2011) Widespread losses of vomeronasal signal transduction in bats. Mol. Biol. Evol. 28:7-12. pdf


b 2010 a

Zhang, J. (2010) Positive Darwinian selection in gene evolution. In: Darwin's Heritage Today: Proceedings of the Darwin 200 Beijing International Conference. M. Long, et al., eds, High Education Press, Beijing, Pp. 288-309. (Review) pdf

Xiong, Y., X. Chen, Z. Chen, X. Wang, S. Shi, X. Wang, J. Zhang, and X. He (2010) RNA sequencing shows no dosage compensation of the active X-chromosome. Nat. Genet. 42:1043-1047. pdf

Wang, Z., B.-Y. Liao, and J. Zhang (2010) Genomic patterns of pleiotropy and the evolution of complexity. Proc. Natl. Acad. Sci. USA. 107:18034-18039. pdf

Yang, J.-R., S.-M. Zhuang, and J. Zhang (2010) Impact of translational error-induced and error-free misfolding on the rate of protein evolution. Mol. Syst. Biol. 6:421. pdf

Zhang, J. (2010) Evolutionary genetics: progress and challenges. In: Evolution Since Darwin: The First 150 Years. M. A. Bell, et al., eds., Sinauer, Sunderland, Mass. Pp. 87-118. (Review) pdf

Podlaha, O., and J. Zhang (2010) Pseudogenes and their evolution. Encyclopedia of Life Sciences. John Wiley & Sons, Chichester, UK, Pp. 1-8. (Review) a

Qian, W., B.-Y. Liao, A. Y.-F. Chang, and J. Zhang (2010) Maintenance of duplicate genes and their functional redundancy by reduced expression. Trends Genet., 26: 425-430. pdf

Zhao, H., Y. Zhou, C. M. Pinto, P. Charles-Dominique, J. Galindo-Gonzalez, S. Zhang, and J. Zhang (2010) Evolution of the sweet taste receptor gene Tas1r2 in bats. Mol Biol Evol. 27:2642-2650. pdf

Zhao, H., J.-R. Yang, H. Xu, and J. Zhang (2010) Pseudogenization of the umami taste receptor gene Tas1r1 in the giant panda coincided with its dietary switch to bamboo. Mol Biol Evol. 27:2669-2673. pdf

Liao, B.-Y., M.-P. Weng, and J. Zhang (2010) Contrasting genetic paths to morphological and physiological evolution. Proc Natl Acad Sci USA, 107: 7353-7358. pdf

He, X., W. Qian, Z. Wang, Y. Li, and J. Zhang (2010) Prevalent positive epistasis in Escherichia coli and Saccharomyces cerevisiae metabolic networks. Nat Genet, 42:272-276. pdf Nat Rev Genet (Additional Supplementary Materials)

Li, Y., Z. Liu, P. Shi, and J. Zhang (2010) The hearing gene Prestin unites
echolocating bats and whales. Curr Biol, 20: R55-R56. pdf Comments Science comments

Liao B.-Y., M.-P. Weng, and J. Zhang (2010) Impact of extracellularity on the evolutionary rate of mammalian proteins. Genome Biol Evol, 2010: 39-43. pdf


b 2009 a

Barkman, T., and J. Zhang (2009) Evidence for escape from adaptive conflict? Nature, 462:E1-E2. (Brief Communications Arising) a

Podlaha, O., and J. Zhang (2009) Processed pseudogenes: the 'fossilized footprints' of past gene expression. Trends Genet, 25: 429-434. a

Qian, W., and J. Zhang (2009) Protein subcellular relocalization in the evolution of yeast singleton and duplicate genes. Genome Biol Evol 1: 198-204. a

Zhang, Z., W. Qian, and J. Zhang (2009) Positive selection for elevated gene expression noise in yeast. Mol Syst Biol 5: 299. a

Zhang, J. (2009) Phylogenetic evidence for parallel adaptive origins of
digestive RNases in Asian and African leaf monkeys: a response to Xu et al., 2009. Mol Phylogenet Evol 53: 608-609. a

Shi, P., and J. Zhang (2009) Extraordinary diversity of chemosensory receptor gene repertoires among vertebrates. In: Chemosensory Systems in Mammals, Fishes, and Insects. W. Meyerhof & S. Korsching, eds., Springer, Berlin. Pp. 1-23 (Review) a

Zhang, Z., and J. Zhang (2009) A big world inside small-world networks. PLoS ONE 4: e5686. a

Wang, Z., and J. Zhang (2009) Abundant indispensable redundancies in cellular metabolic networks. Genome Biol Evol 1: 23-33. a

He, X., and J. Zhang (2009) On the growth of scientific knowledge: Yeast biology as a case study. PLoS Comput Biol 5: e1000320. a

Wang, Z., and J. Zhang (2009) Why is the correlation between gene importance and gene evolutionary rate so weak? PLoS Genet 5: e1000329. a

Grus, W. E., and J. Zhang (2009) Origin of the genetic components of the vomeronasal system in the common ancestor of all extant vertebrates. Mol Biol Evol 26: 407-419. a


2008

Zhang, J. (2008) Positive selection, not negative selection, in the pseudogenization of rcsA in Yersinia pestis. Proc Natl Acad Sci USA 105: E69. (Letter to Editor) a

Qian, W., and J. Zhang (2008) Gene dosage and gene duplicability. Genetics 179: 2319-2324. a

Grus, W. E., and J. Zhang (2008) Distinct evolutionary patterns between chemoreceptors of two vertebrate olfactory systems and the differential tuning hypothesis. Mol Biol Evol 25: 1593-1601. a

Bakewell, M. A., and J. Zhang (2008) Positive selection on genes in humans as
compared to chimpanzees. Encyclopedia of Life Sciences. John Wiley & Sons,
Chichester, UK, Pp1-7. (Review)
a

Liao, B.-Y., and J. Zhang (2008) Co-expression of linked genes in mammalian genomes is generally disadvantageous. Mol Biol Evol 25: 1555-1565. a

Zhang, Z., and J. Zhang (2008) Accuracy and application of the motif expression decomposition method in dissecting transcriptional regulation. Nucleic Acids Res 36: 3185-3193.

Liao, B.-Y., and J. Zhang (2008) Null mutations in human and mouse orthologs
frequently result in different phenotypes. Proc Natl Acad Sci USA 105: 6987-6992.

Grus, W. E., and J. Zhang (2008) Human lineage-specific gene inactivation.
Encyclopedia of Life Sciences. John Wiley & Sons, Chichester, UK, Pp1-6. (Review)

Qian, W., and J. Zhang (2008) Evolutionary dynamics of nematode operons: easy come, slow go. Genome Res 18: 412-421.


2007

Zhang, J. (2007) The drifting human genome. Proc Natl Acad Sci USA 104: 20147-20148. (Commentary)

Cho, S., Z. Y. Huang, and J. Zhang (2007) Sex-specific splicing of the
honey bee doublesex gene reveals 300 million years of evolution at the
bottom of the insect sex-determination pathway. Genetics 173: 1733-1741.

Grus, W. E., P. Shi, and J. Zhang (2007) Largest vertebrate vomeronasal type
1 receptor (V1R) gene repertoire in the semi-aquatic platypus. Mol Biol Evol 24: 2153-2157.

Wang, X., and J. Zhang (2007) Rapid evolution of primate ESX1, an X-linked
placenta- and testis-expressed homeobox gene. Hum Mol Genet 16: 2053-2060.

Liao, B.-Y., and J. Zhang (2007) Mouse duplicate genes are as essential as singleton genes. Trends Genet 23: 378-381.

Wang, Z., and J. Zhang (2007) In search of the biological significance of modular structurs in protein networks. PLoS Comput Biol 3: e107.

Cho, S., and J. Zhang (2007) Zebrafish ribonucleases are bactericidal: Implications for the origin of the vertebrate RNase A superfamily. Mol Biol Evol 24: 1259-1268.

Bakewell, M. A., P. Shi, and J. Zhang (2007) More genes underwent positive selection in chimpanzee evolution than in human evolution. Proc Natl Acad Sci USA 104: 7489-7494.

Shi, P., and J. Zhang (2007) Comparative genomic analysis identifies an evolutionary shift of vomeronasal receptor gene repertoires in the vertebrate transition from water to land. Genome Res 17: 166-174.

Zhang, J. (2007) Disulfide-bond reshuffling in the evolution of an ape
placental ribonuclease. Mol Biol Evol 24: 505-512.


2006

Cho, S., Z. Y. Huang, D. R. Green, D. R. Smith, and J. Zhang (2006) Evolution of the complementary sex-determination gene of honey bees: balancing selection and trans-species polymorphisms. Genome Res 16: 1366-1375.

Shi, P., M. A. Bakewell, and J. Zhang (2006) Did brain-specific genes evolve faster in humans than in chimpanzees? Trends Genet 22: 608-613.

Liao, B.-Y., N. M. Scott, and J. Zhang (2006) Impacts of gene essentiality, expression pattern, and gene compactness on the evolutionary rate of mammalian proteins. Mol Biol Evol 23: 2072-2080.

Podlaha, O., D. M. Webb, and J. Zhang (2006) Accelerated evolution and loss of a domain of the sperm-egg binding protein SED1 in ancestral primates.
Mol Biol Evol 23: 1828-1831.

He, X., and J. Zhang (2006) Toward a molecular understanding of pleiotropy. Genetics 173: 1885-1891.

Grus, W. E., and J. Zhang (2006) Origin and evolution of the vertebrate vomeronasal system viewed through system-specific genes. BioEssays 28: 709-718.

Zhang, J. (2006) Parallel adaptive origins of digestive RNases in Asian and African leaf monkeys. Nat Genet 38: 819-823.

Wang, X., and J. Zhang (2006) Remarkable expansions of an X-linked reproductive homeobox gene cluster in rodent evolution. Genomics 88: 34-43.

He, X., and J. Zhang (2006) Why do hubs tend to be essential in protein networks? PLoS Genet 2: e88.

Liao, B.-Y., and J. Zhang (2006) Low rates of expression-profile divergence in highly-expressed genes and tissue-specific genes during mammalian evolution. Mol Biol Evol 23: 1119-1128.

Cho, S., and J. Zhang (2006) Ancient expansion of the ribonuclease A superfamily revealed by genomic analysis of placental and marsupial mammals. Gene 373: 116-125.

He, X., and J. Zhang (2006) Transcriptional reprogramming and backup between duplicate genes: is it a genome-wide phenomenon? Genetics 172: 1363-1367.

Wang, X., W. E. Grus, and J. Zhang (2006) Gene losses during human origins. PLoS Biol 4: e52.

Liao, B.-Y., and J. Zhang (2006) Evolutionary conservation of expression profiles between human and mouse orthologous genes. Mol Biol Evol 23: 530-540.

Shi, P., and J. Zhang (2006) Contrasting Modes of Evolution Between Vertebrate Sweet/Umami Receptor Genes and Bitter Receptor Genes. Mol Biol Evol 23: 292-300.

He, X., and J. Zhang (2006) Higher duplicability of less important genes in yeast genomes. Mol Biol Evol 23: 144-151.


2005

Cho, S., J. J. Beintema, and J. Zhang (2005) The ribonuclease A superfamily of mammals and birds: identifying new members and tracing evolutionary histories. Genomics 85: 208-220.

Grus, W. E., P. Shi, Y. P. Zhang, and J. Zhang (2005) Dramatic variation of the vomeronasal pheromone receptor gene repertoire among five orders of placental and marsupial mammals. Proc Natl Acad Sci USA 102: 5767-5772.

He, X., and J. Zhang (2005) Gene complexity and gene duplicability. Curr Biol 15: 1016-1021.

He, X., and J. Zhang (2005) Rapid subfunctionalization accompanied by prolonged and substantial neofunctionalization in duplicate gene evolution. Genetics 169: 1157-1164.

Podlaha, O., D. M. Webb, P. K. Tucker, and J. Zhang (2005) Positive selection for indel substitutions in the rodent sperm protein catsper1. Mol Biol Evol 22: 1845-1852.

Webb, D. M., and J. Zhang (2005) FoxP2 in song-learning birds and vocal-learning mammals. J Hered 96: 212-216.

Yang, H., P. Shi, Y. P. Zhang, and J. Zhang (2005) Composition and evolution of the V2r vomeronasal receptor gene repertoire in mice and rats. Genomics 86: 306-315.

Zhang, J. (2005) On the evolution of codon volatility. Genetics 169: 495-501.

Zhang, J. (2005) Brain size (genetics). In: McGraw-Hill 2005 Yearbook of Science & Technology. McGraw-Hill, New York, Pp34-36. (Review)

Zhang, J. (2005) Evolution for bioinformaticians and bioinformatics for evolutionists. Evolution 59: 2281-2283. (Book review)

Zhang, J., and X. He (2005) Significant impact of protein dispensability on the instantaneous rate of protein evolution. Mol Biol Evol 22: 1147-1155.

Zhang, J., R. Nielsen, and Z. Yang (2005) Evaluation of an Improved Branch-Site Likelihood Method for Detecting Positive Selection at the Molecular Level. Mol Biol Evol 22: 2472-2479.


2004

Dyer, K. D., H. F. Rosenberg, and J. Zhang (2004) Isolation, characterization, and evolutionary divergence of mouse RNase 6: evidence for unusual evolution in rodents. J Mol Evol 59: 657-665.

Grus, W. E., and J. Zhang (2004) Rapid turnover and species-specificity of vomeronasal pheromone receptor genes in mice and rats. Gene 340: 303-312.

Podlaha, O., and J. Zhang (2004) Nonneutral evolution of the transcribed pseudogene Makorin1-p1 in mice. Mol Biol Evol 21: 2202-2209.

Wang, X., S. D. Thomas, and J. Zhang (2004) Relaxation of selective constraint and loss of function in the evolution of human bitter taste receptor genes. Hum Mol Genet 13: 2671-2678.

Wang, X., and J. Zhang (2004) Rapid evolution of mammalian X-linked testis-expressed homeobox genes. Genetics 167: 879-888.

Webb, D. M., L. Cortes-Ortiz, and J. Zhang (2004) Genetic evidence for the coexistence of pheromone perception and full trichromatic vision in howler monkeys. Mol Biol Evol 21: 697-704.

Zhang, J. (2004) Evolution of DMY, a newly emergent male sex-determination gene of medaka fish. Genetics 166: 1887-1895.

Zhang, J. (2004) The infancy of duplicate genes. Heredity 92:479-480. (News and Commentary)

Zhang, J. (2004) Frequent false detection of positive selection by the likelihood method with branch-site models. Mol Biol Evol 21: 1332-1339.

Zhang, J., X. Wang, and O. Podlaha (2004) Testing the chromosomal speciation hypothesis for humans and chimpanzees. Genome Res 14: 845-851.

Zhang, J., and D. M. Webb (2004) Rapid evolution of primate antiviral enzyme APOBEC3G. Hum Mol Genet 13: 1785-1791.


2003

Nei, M., and J. Zhang (2003) Evolutionary distance: estimation. Encyclopedia
of Life Sciences
. John Wiley & Sons, Chichester, UK, Pp1-4.  (Review)

Gao, L., and J. Zhang (2003) Why are some human disease-associated mutations fixed in mice? Trends Genet 19: 678-681.

Podlaha, O., and J. Zhang (2003) Positive selection on protein-length in the evolution of a primate sperm ion channel. Proc Natl Acad Sci USA 100: 12241-12246.

Shi, P., J. Zhang, H. Yang, and Y. P. Zhang (2003) Adaptive diversification of bitter taste receptor genes in Mammalian evolution. Mol Biol Evol 20: 805-814.

Zhang, J. (2003) Parallel functional changes in the digestive RNases of ruminants and colobines by divergent amino acid substitutions. Mol Biol Evol 20: 1310-1317.

Zhang, J. (2003) Evolution by gene duplication: an update. Trends Ecol Evol 18: 292-298.

Zhang, J. (2003) Evolution of the human ASPM gene, a major determinant of brain size. Genetics 165: 2063-2070.

Zhang, J. (2003) Paleomolecular biology unravels the evolutionary mystery of vertebrate UV vision. Proc Natl Acad Sci USA 100: 8045-8047. (Commentary)

Zhang, J., K. D. Dyer, and H. F. Rosenberg (2003) Human RNase 7: a new cationic ribonuclease of the RNase A superfamily. Nucleic Acids Res 31 :602-607.

Zhang, J., and D. M. Webb (2003) Evolutionary deterioration of the vomeronasal pheromone transduction pathway in catarrhine primates. Proc Natl Acad Sci USA 100: 8337-8341.

Zhang, J., and Y. P. Zhang (2003) Pseudogenization of the tumor-growth promoter angiogenin in a leaf-eating monkey. Gene 308: 95-101.


2002

Wang, X., J. Zhang, and Y. P. Zhang (2002) Erratic evolution of SRY in higher primates. Mol Biol Evol 19: 582-584.

Zhang, J., and H. F. Rosenberg (2002) Complementary advantageous substitutions in the evolution of an antiviral RNase of higher primates. Proc Natl Acad Sci USA 99: 5486-5491.

Zhang, J., and H. F. Rosenberg (2002) Diversifying selection of the tumor-growth promoter angiogenin in primate evolution. Mol Biol Evol 19: 438-445.

Zhang, J., K. D. Dyer, and H. F. Rosenberg (2002) RNase 8, a novel RNase A superfamily ribonuclease expressed uniquely in placenta. Nucleic Acids Res 30: 1169-1175.

Zhang, J., D. M. Webb, and O. Podlaha (2002) Accelerated protein evolution and origins of human-specific features: FOXP2 as an example. Genetics 162: 1825-1835.  

Zhang, J., Y. P. Zhang, and H. F. Rosenberg (2002) Adaptive evolution of a duplicated pancreatic ribonuclease gene in a leaf-eating monkey. Nat Genet 30: 411-415.


1996 - 2001

Rosenberg, H. F., J. Zhang, Y.-D. Liao, and K. D. Dyer (2001) Rapid diversification of RNase A superfamily ribonucleases from the bullfrog, Rana catesbeiana. J Mol Evol 53: 31-38.

Zhang, J. (2000) Rates of conservative and radical nonsynonymous nucleotide substitutions in mammalian nuclear genes. J Mol Evol 50: 56-68.

Zhang, J. (2000) Protein-length distributions for the three domains of life. Trends Genet 16: 107-109.

Zhang, J., and M. Nei (2000) Positive selection in the evolution of mammalian interleukin-2 genes. Mol Biol Evol 17: 1413-1416.

Zhang, J., and H. F. Rosenberg (2000) Sequence variation at two eosinophil-associated ribonuclease loci in humans. Genetics 156: 1949-1958.

Zhang, J., K. D. Dyer, and H. F. Rosenberg (2000) Evolution of the rodent eosinophil-associated RNase gene family by rapid gene sorting and positive selection. Proc Natl Acad Sci USA 97: 4701-4706.

Rooney, A. P., J. Zhang, and M. Nei (2000) An unusual form of purifying selection in a sperm protein. Mol Biol Evol 17: 278-283.

Zhang, J. (1999) Performance of likelihood ratio tests of evolutionary hypotheses under inadequate substitution models. Mol Biol Evol 16: 868-875.

Rooney, A. P., and J. Zhang (1999) Rapid evolution of a primate sperm protein: relaxation of functional constraint or positive Darwinian selection? Mol Biol Evol 16 :706-710.

Singhania, N. A., K. D. Dyer, J. Zhang, M. S. Deming, C. A. Bonville, J. B. Domachowske, and H. F. Rosenberg (1999) Rapid evolution of the Ribonuclease A superfamily: adaptive expansion of independent gene clusters in rats and mice. J Mol Evol 49: 721-728.

Zhang, J., and X. Gu (1998) Correlation between the substitution rate and rate variation among sites in protein evolution. Genetics 149: 1615-1625.

Zhang, J., H. F. Rosenberg, and M. Nei (1998) Positive Darwinian selection after gene duplication in primate ribonuclease genes. Proc Natl Acad Sci USA 95: 3708-3713.

Brown, J. R., J. Zhang, and J. E. Hodgson (1998) A bacterial antibiotic resistance gene with eukaryotic origins. Curr Biol 8 :R365-R367.

Nei, M., and J. Zhang (1998) Molecular origin of species. Science 282 :1428-1429. (Perspective)

Zhang, J., and M. Nei (1997) Accuracies of ancestral amino acid sequences inferred by parsimony, likelihood, and distance methods. J Mol Evol 44 :S139-S146.

Zhang, J., and S. Kumar (1997) Detection of convergent and parallel evolution at the amino acid sequence level. Mol Biol Evol 14: 527-536.

Zhang, J., S. Kumar, and M. Nei (1997) Small-sample tests of episodic adaptive evolution: a case study of primate lysozyme genes. Mol Biol Evol 14: 1335-1338.

Gu, X., and J. Zhang (1997) A simple method for estimating the parameter for substitution rate variation among sites. Mol Biol Evol 14: 1106-1113.

Nei, M., J. Zhang, and S. Yokoyama (1997) Color vision of ancestral organisms of higher primates. Mol Biol Evol 14: 611-618.

Zhang, J., and M. Nei (1996) Evolution of Antennapedia-class homeobox genes. Genetics 142: 295-303.

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