Publications (last updated 6/23/08)
2008
Maria D. Vibranovski, Hedibert F. Lopes, Timothy L. Karr, Manyuan Long
Male germline X inactivation and its consequences on the evolution of male related genes in Drosophila
(submitted)
Fan, Chuanzhu, Ying Chen, and Manyuan Long.
Recurrent Tandem Gene Duplication Gave Rise to Functionally Divergent Genes in Drosophila.
(submitted).
Fan C and Long M
A Newly Tandem Duplicated Gene Cluster under Darwinian Positively Selection Evolved a Specific Expression Pattern in Reproductive Organs in Drosophila.
(Submitted).
J.J. Emerson., Margarida Cardoso-Moreira, M., Borevitz, J.O., Long, M.
Natural Selection Shapes Genome Wide Patterns of Copy Number Polymorphism in D. melanogaster
Science 20 June 2008: 1629-1631. pdf
Hongzheng, D., Chen, Y., Chen, S., Mao, Q., Kennedy, D., Landback, P., Eyre-Walker, A., Du, W., Long, M.
The evolution of courship behaviors through the origination of a new gene in Drosophila.
PNAS, 2008 105: 7478-7483. pdf
Meng-Shin Shiao, Ben-Yang Liao, Manyuan Long, and Hon-Tsen Yu
Adaptive Evolution of the Insulin Two-Gene System in Mouse.
Genetics, 2008, 178: 1683-1691. pdf
Yang S., Arguello R, Li X, Ding Y, Zhou Q, Chen Y, Zhang Y, Zhao R, Brunet F, Peng L, Long M, Wang W.
Repetitive Elements-mediated Recombination as a Mechanism for New Gene Origination in Drosophila
PLoS Genetics 4(1): e3. pdf
2007
Drosophila 12 Genomes Consortium
Evolution of genes and genomes on the Drosophila phylogeny.
Nature, 2007, 450: 203-218. pdf
Fan, Chuanzhu, J. J. Emerson, Manyuan Long, The origin of new genes.
Evolutionary Genomics and Proteomics, Mark Pagel & Andrew Pomiankowski (eds.). Sinauer Associates, Inc., Sunderland, Massachusetts, USA. Pp27-44.
Long M.
Journal Club: Mystery Genes.
Nature, 2007, 449: 511. pdf
Fan C, Vibranovski M, Chen Y and Long M,
A Microarray-based genomic hybridization method for identification of new genes in plants: case analyses of Arabidopsis and Rice
Journal of Integrative Plant Biology. 2007 49: 915-926. pdf
Elde. NC, Long M, and Turkwitz AP.
A role for convergent evolution in the secretory life of cells.
Trends in Cell Biology, 2007, 17:157-164. pdf
Havlioglu N, Wang J, Kuo D, Fushimi K, Vibranovski MD, Kan Z, Gish W, Fedorov A, Long M and Wu JY.
Genomic Signal for Alternative Splicing of a Large Number of Gene Families in the Human Genome.
PLoS One, 2007, 2(11): e1246. pdf
Shiao MS, Khil PP, Smirnova NA, Camerini-Otero RD, Shiroishi T, Yu HT, Long M.
Natural Selection Targeting on Expression Novelties in X-related Retrogenes in Rodents.
Mol Biol Evol, 2007, 24: 2242-2253. pdf
Fan C and Long M.
A New Retroposed Gene in Drosophila Heterochromatin Detected by Microarray-Based Comparative Genomic Hybridization.
J Mol Evol, 2007, 64:272-283. pdf
Arguello JR, Fan C, Wang W and Long M.
Origination of Chimeric Genes through DNA-level Recombination (review).
Genome Dynamics : Protein and Gene Evolution, Volume 3, Karger publishers. pdf
Dai H, Yoshimatsu TF, Long M.
Retrogene movement within- and between-chromosomes in the evolution of Drosophila genomes.
Gene (Special Volume for "6 th Anton Dohrn Workshop: Genome Evolution), 2007, 385: 96-102. pdf
2006
Wen Wang, Hongkun Zheng, Chuanzhu Fan, Jun Li, Junjie Shi, Zhengqiu Cai, Guojie Zhang, Dongyuan Liu, Jianguo Zhang, Søren Vang, Zhike Lu, Gane Ka-Shu Wong, Manyuan Long, and Jun Wang.
High Rate of Chimeric Gene Origination by Retroposition in Plant Genomes
Plant Cell. 2006, 18: 1791-1802. pdf
Arguello JR, Chen Y, Yang S, Wang W, Long M.
Origination of an X-linked testes chimeric gene by illegitimate recombination in Drosophila.
PLoS Genet. 2006 May;2(5):e77. pdf
2005
Thornton K, Long M.
Excess of amino acid substitutions relative to polymorphism between X-linked duplications in Drosophila melanogaster.
Mol Biol Evol. 2005 Feb;22(2):273-84. pdf
Zhang J, Long M, Li L.
Translational effects of differential codon usage among intragenic domains of new genes in Drosophila.
Biochim Biophys Acta. 2005 May 1;1728(3):135-42. pdf
2004
Emerson JJ, Kaessmann H, Betran E, Long M.
Extensive gene traffic on the mammalian X chromosome.
Science. 2004 Jan 23;303(5657):537-40. pdf
Wang W, Thornton K, Emerson JJ, Long M.
Nucleotide variation and recombination along the fourth chromosome in Drosophila simulans.
Genetics. 2004 Apr;166(4):1783-94. pdf
Betran E, Emerson JJ, Kaessmann H, Long M.
Sex chromosomes and male functions: where do new genes go?
Cell Cycle. 2004 Jul;3(7):873-5. Epub 2004 Jul 5. pdf
Long M, Betran E, Thornton K, Wang W.
The origin of new genes: glimpses from the young and old.
Nat Rev Genet. 2003 Nov;4(11):865-75. pdf
Zhang J, Dean AM, Brunet F, Long M.
Evolving protein functional diversity in new genes of Drosophila.
Proc Natl Acad Sci U S A. 2004 Nov 16;101(46):16246-50. pdf
Wang W, Yu H, Long M.
Duplication-degeneration as a mechanism of gene fission and the origin of new genes in Drosophila species.
Nat Genet. 2004 May;36(5):523-7. pdf
2003
Long M, Deutsch M, Wang W, Betran E, Brunet FG, Zhang J.
Origin of new genes: evidence from experimental and computational analyses.
Genetica. 2003 Jul;118(2-3):171-82. pdf
Betran E, Long M.
Dntf-2r, a young Drosophila retroposed gene with specific male expression under positive Darwinian selection.
Genetics. 2003 Jul;164(3):977-88. pdf
2002
Betran E, Long M.
Expansion of genome coding regions by acquisition of new genes.
Genetica. 2002 May;115(1):65-80. pdf
Wen Wang, Frédéric G. Brunet, Eviatar Nevo, and Manyuan Long
Origin of sphinx, a young chimeric RNA gene in Drosophila melanogaster
Proc Natl Acad Sci U S A. 2002 April 2; 99(7): 4448–4453. pdf
Betran E, Thornton K, Long M.
Retroposed new genes out of the X in Drosophila.
Genome Res. 2002 Dec;12(12):1854-9. pdf
Thornton K, Long M.
Rapid divergence of gene duplicates on the Drosophila melanogaster X chromosome.
Mol Biol Evol. 2002 Jun;19(6):918-25. pdf
Betran E, Wang W, Jin L, Long M.
Evolution of the phosphoglycerate mutase processed gene in human and chimpanzee revealing the origin of a new primate gene.
Mol Biol Evol. 2002 May;19(5):654-63. pdf
Wang W, Thornton K, Berry A, Long M.
Nucleotide variation along the Drosophila melanogaster fourth chromosome.
Science. 2002 Jan 4;295(5552):134-7. pdf
Sakharkar M, Passetti F, de Souza JE, Long M, de Souza SJ.
ExInt: an Exon Intron Database.
Nucleic Acids Res. 2002 Jan 1;30(1):191-4. pdf
Llopart A, Comeron JM, Brunet FG, Lachaise D, Long M.
Intron presence-absence polymorphism in Drosophila driven by positive Darwinian selection.
Proc Natl Acad Sci U S A. 2002 Jun 11;99(12):8121-6. pdf
2001
Long M.
Evolution of novel genes.
Curr Opin Genet Dev. 2001 Dec;11(6):673-80. pdf
Long M., Thornton, K.
Gene Duplication and Evolution (technical note)
Science 31 August 2001:Vol. 293. no. 5535, p. 1551. pdf
2000
Long M, Rosenberg C.
Testing the "proto-splice sites" model of intron origin: evidence from analysis of intron phase correlations.
Mol Biol Evol. 2000 Dec;17(12):1789-96. pdf
Long M.
A new function evolved from gene fusion.
Genome Res. 2000 Nov;10(11):1655-7. pdf
Wang W, Zhang J, Alvarez C, Llopart A, Long M.
The origin of the Jingwei gene and the complex modular structure of its parental gene, yellow emperor, in Drosophila melanogaster.
Mol Biol Evol. 2000 Sep;17(9):1294-301. pdf
Sakharkar MK, Kangueane P, Woon TW, Tan TW, Kolatkar PR, Long M, de Souza SJ.
IE-Kb: intron exon knowledge base.
Bioinformatics. 2000 Dec;16(12):1151-2. pdf
1999
M Long and M Deutsch
Association of intron phases with conservation at splice site sequences and evolution of spliceosomal introns
Mol. Bio. Evol. 1999, Vol 16, 1528-1534. pdf
Long M, Wang W, Zhang J.
Origin of new genes and source for N-terminal domain of the chimerical gene, jingwei, in Drosophila.
Gene 1999, Sep 30;238(1):135-41. pdf
Deutsch M, Long M.
Intron-exon structures of eukaryotic model organisms.
Nucleic Acids Res. 1999 Aug 1;27(15):3219-28. pdf
Caceres M, Ranz JM, Barbadilla A, Long M, Ruiz A.
Generation of a widespread Drosophila inversion by a transposable element.
Science. 1999 Jul 16;285(5426):415-8. pdf
1998
M Long, C Rosenberg and W Gilbert
Intron Phase Correlations and the Evolution of the Intron/Exon Structure of Genes
Proc Natl Acad Sci U S A. 1995, Vol 92, 12495-12499. pdf
Long M, de Souza SJ, Rosenberg C, Gilbert W.
Relationship between "proto-splice sites" and intron phases: evidence from dicodon analysis.
Proc Natl Acad Sci U S A. 1998 Jan 6;95(1):219-23. pdf
1997
Long M, deSouza SJ, Gilbert W
Delta-interacting protein A and the origin of hepatitis delta antigen
SCIENCE 276 (5313): 824-825 MAY 2 1997. pdf
Origin of Genes.
Gilbert W, de Souza SJ, Long M.
Proc Natl Acad Sci U S A. 1997 Jul 22; 94(15): 7698-7703. pdf
Richter B, Long M, Lewontin RC, Nitasaka E.
Nucleotide variation and conservation at the dpp locus, a gene controlling early development in Drosophila.
Genetics. 1997 Feb;145(2):311-23. pdf
Long M, de Souza SJ, Gilbert W.
The yeast splice site revisited: new exon consensus from genomic analysis.
Cell. 1997 Dec 12;91(6):739-40. pdf
Souza S.J. Long M.; Schoenbach L. Roy S.W. Gilbert W.
The correlation between introns and the three-dimensional structure of proteinsde
Gene, Volume 205, Number 1, 31 December 1997, pp. 141-144(4) pdf
1996
deSouza SJ, Long MY, Gilbert W
Introns and gene evolution
GENES TO CELLS 1 (6): 493-505 JUN 1996. pdf
Exon shuffling and the origin of the mitochondrial targeting function in plant cytochrome c1 precursor.
Long M, de Souza SJ, Rosenberg C, Gilbert W.
Proc Natl Acad Sci U S A. 1996 Jul 23; 93(15): 7727-7731. pdf
deSouza SJ, Long M, Schoenbach L, et al.
Intron positions correlate with module boundaries in ancient proteins
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 93 (25): 14632-14636 DEC 10 1996 pdf
1995
Long MY, Rosenberg C, Gilbert W
Intron phase correlations and the evolution of the intron exon structure of genes
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 92 (26): 12495-12499 DEC 19 1995 pdf
1993
Long M, Langley CH.
Natural selection and the origin of jingwei, a chimeric processed functional gene in Drosophila.
Science.1993 Apr 2;260(5104):91-5. pdf
1991
LONG MY, GILLESPIE JH
CODON USAGE DIVERGENCE OF HOMOLOGOUS VERTEBRATE GENES AND CODON USAGE CLOCK
JOURNAL OF MOLECULAR EVOLUTION 32 (1): 6-15 JAN 1991 pdf