2008

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

Shi, P. and J. Zhang (2008) Extraordinary diversity of chemosensory receptor gene repertoires among vertebrates. Chemosensory Systems in Mammals, Fishes, and Insects. W. Meyerhof & S. Korsching, eds., Springer, in press. (Review)

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

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.

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. (Review)

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

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. (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. 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.