2009

Zhang, Z., J. Zhang (2009) A Big World Inside Small-World Networks. PLoS ONE, 4: e5686.

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

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

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

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.

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)

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.