SELECTED
PUBLICATIONS |
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| PUBLISHED
OR IN PRESS |
| 2006 |
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H Zhou,
J Gu, S J. Lamont, Gu X * (2006) Evolutionary analysis
for functional divergence of Toll-like receptor gene family
and altered functional constraints. Journal of Molecular
Evolution (in press) |
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Leebens-Mack,
J, Vision T, Brenner E,…Gu X … (2006) Taking
the first steps towards a standard for reporting on phylogenies:
Minimal Information About a Phylogenetic Analysis (MIAPA).
OMIC Integrated Biology (in press). |
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Guo,
H, Weiss R. E., Gu, X, and Suchard, M. A. (2006) Time
Squared: Repeated Measures on Phylogenies. Molecular
Biology and Evolution (in press). |
|
Gu
X. (2006) A Simple Statistical Method for Estimating
Type-II (Cluster-Specific) Functional Divergence of Protein
Sequences. Mol Biol Evol. Jul 24; [Epub ahead of print]
 |
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Lin
H, Zhu W, Silva JC, Gu X, Buell CR. (2006)
Intron gain and loss in segmentally duplicated genes
in rice. Genome Biol. 7(5):R41. |
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Su
Z, Wang J, Yu J, Huang X and Gu X*(2006) Evolution of
Alternative Splicing after Gene Duplications. Genome
Res. 16(2):182-9. |
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Wu
Q, Gu X, Wang Y, Li N, Liu X, Wu C, Yu L, Gu X. (2006) Neurotransmitter
inactivation is important for the origin of nerve system in
animal early evolution: a suggestion from genomic comparison.
Prog Neurobiol. 78(6):390-5.
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| 2005 |
|
Gu X and Su Z (2005) Web-base resources for comparative
genomics. Human Genomics, Vol. 2, No. 3, 187-190. |
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Li,
W-H, Yang J, and Gu, X(2005) Expression Divergence between
Duplicate Genes. Trends in Genetics 21:602-607. |
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Gao
X, Vander Velden KA, Voytas DF and Gu X* (2005) SplitTester:
software to identify domains responsible for functional divergence
in protein family BMC Bioinformatics 2005, 6:137 |
|
Wu,
S, Gu, X (2005) Gene Network: Model, dynamics and simulation.
Lecture Notes on Computer Science, 3595: pp.12-21. |
|
Gu,
X*, Zhang, Z., Huang, W. (2005) Rapid Evolution of Expression
and Regulatory Divergences after Yeast Gene Duplications. PNAS.
102:707-712. |
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Gu,
X*, Huang, W., Xu, D., Zhang, H.(2005) GeneContent:
software for whole-genome phylogenetic analysis. Bioinformatics
21(8):1713-1714. |
2004 |
|
Sen,
T*, Kloczkowski, A., Jernigan, R., Yan, C., Honavar, V., Ho,
K., Wang, C., Ihm, Y. Cao, H., Dobbs, D.,Gu, X. (2004) Prediction
of binding sites of hydrolase-inhibitor complexes by combining
several methods.BMC Bioinformatics. 5:205. |
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Zhang,
H, and Gu, X* (2004) Maximum Likelihood for Genome Phylogeny
on Gene Content. Statistical Applications in Genetics
and Molecular Biology. |
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Zhang,
Z, Gu, J and Gu, X* (2004) How much expression divergence
after yeast gene duplication could be explained by regulatory
motif evolution? Trends in Genetics 20:403-407. |
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Jiang,
C., Gu, J., Gu, X., and T. Peterson (2004). Ordered
origin of the typical two- and three-repeat Myb genes.
Gene 326:13-22 |
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Guo
J, Zhu P, Chen S, Chen L, Wu C, Yu L, Zhao S , Gu X. (2004)
In silico analysis indicates a similar gene expression
pattern between human brain and testis. Cytogenetic
and Genome Research 103:58-62. |
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Gu,
X* (2004) Statistical framework for phylogenetic analysis
of expression profiles. Genetics 167:531-542. |
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Gu,
J and Gu, X* (2004) Further statistical analysis for
genome-wide expression evolution in primate brain/liver/fibroblast
tissues. Human Genomics 1:247-254. |
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Gu,
X*, Zhang H (2004) Genome phylogeny inference based
on gene contents. Mol Biol Evol 21:1401-1408. |
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Jiang,
C., Gu X., and T. Peterson (2004) Functional classification
and prediction of Myb gene family in Arabidopsis and Rice.
Genome Biology 5(7):R46. |
2003
|
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Gu,
X (2003) Functional divergence in protein (family) sequence
evolution. Genetica 118:133-141. |
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Gu,
J, Gu, X* (2003) Induced gene expression in human brain
after the split from chimpanzee. Trend in Genetics
19:63-65. |
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Gu,
Z, Steinmetz, LM, Gu, X, Scharfe, C., Davis RD, Li, WH (2003)
Role of duplicate genes in genetic robustness against
null mutations. Nature 421:63-66. |
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Gu,
J, Gu, X (2003) Natural history and functional divergence
of protein tyrosine kinases. Gene 317:49-57. |
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Gu,
X. 2003. Genetic buffering, gene duplication, and evolution.
Trend in Genetic 19:354-356. |
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Wu,
S, Gu, X (2003) Algorithms for multiple genome rearrangement
by signed reversals. Pacific Symposium on Biocomputing
(PSB) 8:363-374 |
2002 |
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Huang,
W, Nattleton D, Gu, X (2002) Expression pattern of yeast
sporulation: A case study for regulatory changes after yeast
genome duplication. Information Sciences 145:261-269. |
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Zhou,
Y. H., Zheng, J.B., Gu, X, Saunders, G. F., Yung W-K F (2002)
Novel PAX6 binding sites in human genome and the role
of SINE in the evolution of gene regulation. Genome
Res 12:1716-1722. |
|
Gu,
J, Gu, X (2002) Functional divergence in TGF-b signaling
pathway. Information Sciences 145:195-204. |
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Wang,
Y, Gu, X (2002) Evolutionary analysis for developmental
profile of gene family expression in central nervous system.
Information Sciences 145:215-223. |
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Sun,
H., Merugu S., Gu, X. Kang, Y. Dickinson, DP., Callaerts, P.
and Li W-H. (2002) Identification of essential amino
acid changes in paired domain evolution using a novel combination
of evolutionary analysis and in vitro and in vivo studies.
Mol. Biol. Evol. 19:1490-1500. |
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Gu,
X, Wang Y, Gu, J (2002) Age-distribution of human gene
families showing equal roles of large and small-scale duplications
in vertebrate evolution. Nature Genetics 31:205-209. |
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Gaucher
EA, Gu X, Miyamoto, M, Benner, S. (2002) Predicting
functional divergence in protein evolution by site-specific
rate shifts. Trend in Biochemical Sciences (TiBS) 27:315-321. |
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Wu,
S, Gu, X (2002) Random shuffling permutations of nucleotides.
Journal of Systemics, Cybernetics and Informatics. V1 N4: 308-313.
ISBN: 980-8150-1. |
|
Gu,
X, Wang Y, Gu, J, Vander Velden K (2002) Evolutionary
perspective for functional divergence of gene families and applications
in functional genomics. Current Genomics. 3:201-212. |
|
Gu,
X. Huang W (2002) Testing the parsimony test of genome
duplications: A counterexample. Genome Research. 12:1-2. |
|
Gu,
J, Wang Y, Gu X (2002) Pattern of Functional divergence
in JAK tyrosine protein kinase family. Journal of Molecular
Evolution. 54:725-733. |
|
Gu,
X, Vander Velden K (2002) DIVERGE: Phylogeny-based Analysis
for Functional-Structural Divergence of a Protein Family.
Bioinformatics 18:500-501. |
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Wu,
S, Gu, X (2002) Multiple Genome Rearrangement By Reversals.
Pacific Symposium on Biocomputing (PSB) 7:259-270. |
2001 |
|
Gu,
X (2001) A site-specific measure for rate-difference
after gene duplication or speciation. Mol Biol Evol
18:2327-2330. |
|
Gu
X (2001) Mathematical Modeling for Functional Divergence
after Gene Duplication. Journal Computational Biology.
8:221-234. |
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Wu,
S, Gu, X (2001) A greedy algorithm for optimal recombination.
Lecture Notes on Computer Science (LNCS). 2108: 86-90. |
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Wang
Y, Gu X (2001) Predicting functional divergence of caspase
gene family. Genetics. 158:1311-1320. |
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Kumar
S, Gadagkar S, Filipski A, Gu, X (2001) Determination
of the Number of Conserved Chromosomal Segments between Species.
Genetics 157:1387-1395 |
|
Wang
Y, Gu J, Gu X (2001) Patterns of Functional Divergence
after Gene Duplications in Vertebrate Gene Families: Altered
Functional Constraints. In: Proceedings of the Atlantic
Symposium on Computational Biology, Genome Information Systems
& Technology. Pp.181-185. |
|
Gu.
J, Wang Y , Gu X (2001) Statistical Testing for Protein
Functional Divergence after Major Evolutionary Events.
In: Proceedings of the Atlantic Symposium on Computational Biology,
Genome Information Systems & Technology. Pp.176-180 |
|
Gu
X (2001) Maximum likelihood approach for gene family
evolution under functional divergence. Molecular Biology
and Evolution. 18: 453-464 |
2000 |
|
Wang
Y, Gu X (2000) Evolutionary patterns of gene families
generated in the early stage of vertebrates. Journal
of Molecular Evolution. 51:88-96. |
|
Gu
X (2000) A simple evolutionary model for genome phylogeny
inference based on gene content. Comparative genomics
(ed. Sankoff and Nadeau) Pp.515-524. Kluwer Academic Publishers.
|
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Zhou
YH, Zheng JB, Gu X, Li WH, Saunders GF (2000) A novel
Pax-6 binding site in rodent B1 repetitive elements: coevolution
between developmental regulation and repeated elements?
Gene 245:319-328. |
1999
|
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Gu
X (1999) Statistical methods for testing functional
divergence after gene duplication. Molecular Biology
and Evolution 16:1664-1674. |
|
Su
C, Jakobsen I, Gu X, Nei M (1999) Diversity and evolution
of T-cell receptor variable region genes in mammals and birds.
Immunogenetics 50:301-308. |
|
Gu
X, Nei M (1999) Locus-specificity of polymorphic alleles
and evolution by birth-and-death process in mammalian MHC genes.
Molecular Biology and Evolution 16:147-156. |
1998 |
|
Gu
X, Hewett-Emmett D, Li WH (1998) Directional mutational
pressure affects the amino acid composition and hydrophobicity
of proteins in bacteria. Genetica 102/103; 383-391 |
|
Gu
X (1998) Early metazoan divergence is about 830 million
years ago.Journal of Molecular Evolution 47:369-371 |
|
Zhang
J, Gu X (1998) Correlation between substitution rate
and rate variation among sites. Genetics 149:1615-1625 |
|
Gu
X, Li WH (1998) Evolutionary distances under stationary
and nonstationary models of nucleotide substitutions.
PNAS 95: 5899-5905. |
|
Huang
W, Yun-Xin Fu, Chang B HJ, Gu X, Jorde LB, Li WH (1998) Sequence
variation in ZFX introns in human populations. Molecular
Biology and Evolution 15:138-142. |
1997
|
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Gu
X, Zhang J (1997) A simple method for estimating the
parameter of substitution rate variation among sites.
Molecular Biology and Evolution. 14:1106-1113. |
|
Nei
M, Gu X, Stinikova T (1997) Evolution by the birth-and-death
process in multigene families of the vertebrate immune systems.
PNAS 94:7799-7806. |
|
Gu
X(1997) The age of common ancestor of eukaryotes and
prokaryotes. Molecular Biology and Evolution 14:861-866. |
|
Huang
W, Chang B HJ, Gu X, Hewett-Emmett D, Li WH (1997) Sex
differences in mutation rate in higher primates estimated from
AMG intron sequences. Journal of Molecular Evolution.
44:463-465. |
1996 |
|
Gu
X, Li WH (1996) Bias-corrected paralinear and LogDet
distances and tests of molecular clocks and phylogenies under
nonstationary nucleotide frequencies. Molecular Biology
and Evolution. 13:1375-1383. |
|
Gu
X, Zera AJ (1996) Quantitative genetics of juvenile
hormone esterase, juvenile hormone binding and general esterase
activity in the cricket, Gryllus assimilis. Heredity.
76:136-142. |
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Li
WH, Gu X (1996) Estimating evolutionary distances.
Methods in Enzymology 266:449-459. Academic Press, Inc. |
|
Gu
X, Li WH (1996) A general additive distance with time-reversibility
and rate variation among nucleotide sites. PNAS 93:4671-4676. |
1995 and before |
|
Li
WH, Gu X (1995) Statistical models for studying DNA
sequence evolution. Physica A. 221:159-167 |
|
Gu
X, Li WH (1995) The size distribution of insertions
and deletions in human and rodent pseudogenes suggests the logarithmic
gap penalty for sequence alignment. Journal of Molecular
Evolution 40:464-473 |
|
Gu
X, Fu YX, Li WH (1995) Maximum likelihood estimation
of the heterogeneity of substitution rate among nucleotide sites.
Molecular Biology and Evolution 12: 546-557. |
|
Gu
X, Zera AJ (1994) Developmental profiles and characteristics
of hemolymph juvenile hormone esterase, general esterase and
juvenile hormone binding in the cricket, Gryllus assimilis.
Comparative Biochemistry and Physiology 107B:553-560 |
|
Gu
X, Li WH (1994) A model for the correlation of mutation
rate with GC content and the origin GC-rich isochores.
Journal of Molecular Evolution 38:468-475 |
|
Zera
AJ, Gu X, Zeisset M (1992) Characterization of juvenile
hormone esterase from genetically-determined wing morphs of
the cricket, Gryllus Rubens. Insect Biochemistry and
Molecular Biology 22:829-839 |
|
Gu
X, Li WH (1992) Higher rates of amino acid substitution
in rodents than in humans. Molecular Phylogenetics
and Evolution 1:211-214 |
|
Gu
X (1988) The stable selection and genetic information
threshold in Mendelian population. Bulletin of Science,
Sinica 33:1792-1795 |
|
Gu
X, Liu TT (1988) The diffusion model of gene in the
population with overlapping generations and its heterozygosity.
Bulletin of Science, Sinica 33:1641-1645 |
|
Gu
X, Xu JG (1987) The diffusion model on the competition
among subpopulations under the group selection. Bulletin
of Science, Sinica 32:537-540 |
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