Publications

(last updated 05/16/2018) 

BOOKS AND BOOK CHAPTERS:
 

  1. Ventura IM, Long M. 2016. Connecting evolutionary genomics to cell biology. Encyclopedia of Cell Biology. Elsevier, volume 4, 153-159. DOI: 10.1016/B978-0-12-394447-4.40028-3.
     
  2. Long M., Vibranovski M.D., Zhang Y.E 2013. Evolution of New Genes. The Princeton Guide to Evolution. ISBN: 9780691149776(Editor-In-Chief: Jonathan Losos. Section Editor. Hopi Hoekstra).

  3. Long M, Vibranovski MD, Zhang YE, 2012. Evolutionary interactions between sex chromosomes and autosomes. In: Singh RS, Xu JP, Kulathinal RJ ed., Rapidly Evolving Genes and Genetic Systems. Oxford University Press, Oxford. P.101-114. pdf
  4. Long M, Gu HY, Zhou ZH ed. 2010, Darwin’s  Heritage  Today,  Proceedings  of  the  Darwin 200  Beijing  International  Conference.  Higher  Education  Press,  Beijing.  385  pages, 500,000 words.
  5. Long, M. ed. 2003 Origin and Evolution of New Gene Functions. (Volume 10, Contemporary Issues  in  Genetics  and  Evolution  and  Volume  118  (2-3),  Genetica).  Kluwer  Academic Publishers, The Netherlands. 202 pages 260,000 words.

ARTICLES:

  1. VanKuren NW and Long M, 2018. Gene duplicates resolving sexual conflict rapidly evolved essential gametogenesis functions. Nature Ecology & Evolution 2(4):705-712. doi: 10.1038/s41559-018-0471-0. Epub 2018 Feb 19        pdf

    • Related perspective:
      * Perry JC, 2018. News & Views: Duplication resolves conflict. Nature Ecology & Evolution 2, 597–598.       pdf

  2. VanKuren NW and Long M, 2018.VanKuren NW and Long M, 2017. Behind the paper: Species-specific duplicate genes
    help resolve sexual conflict while evolving essential. Nature Ecology & Evolution Community online February 19, 2018.      pdf

  3. Stein JC, Yu Y, Copetti D, ZwicklDJ, Zhang L, Zhang C , Chougule K, Gao D, Iwata A, Goicoechea JL, Wei S, Wang J, Liao Y, Wang M, Jacquemin J, Becker C, Kudrna D, Zhang J, Londono CEM, Song X, Lee S, Sanchez P, Zuccolo A, Ammiraju JSS, Talag J, Danowitz A, Rivera LF, Gschwend AR, Noutsos C, Wu CC, Kao SM, Zeng JW, Wei FJ, Zhao Q, Feng Q, El Baidouri M, Carpentier MC, Lasserre E, Cooke R, Rosa Farias DD, da Maia LC, Dos Santos RS, Nyberg KG, McNally KL, Mauleon R, Alexandrov N, Schmutz J, Flowers D, Fan C, Weigel D, Jena KK, Wicker T, Chen M, Han B, Henry R, Hsing YC, Kurata N, de Oliveira AC, Panaud O, Jackson SA, Machado CA, Sanderson MJ, Long M, Ware D and Wing RA, 2018. Sequence of 13 rice-related species unveils the Oryza pan-genome and the origin of genetic innovation. Nature Genetics 50, 285–296.      pdf

  4. Lee YCG, Yang Q, Chi W, Turkson SA, Du WA, Kemkemer C, Zeng Z-B, Long M, Zhuang X, 2017. Genetic architecture of natural variation underlying adult foraging behavior that is essential for survival of Drosophila melanogaster. Genome Biol & Evol 9(5):1357-1369      pdf

  5. Long M and Emerson JJ, 2017. The Gene Traffic in Evolution: the Compensational Role for the Meiotic Sex Chromosome Inactivation in Mammals. Current Biology 27 (11): R659-R661     pdf

  6. Chen Z, Oliver B, Gao G and Long M, 2017. Expressed Structurally Stable Inverted Duplicates in Mammalian Genomes as Functional Noncoding Elements. Genome Biol & Evol 9 (4): 981-992    pdf

  7. Tan S, Cardoso-Moreira M, Shi W, Zhang D, Huang J, Mao Y, Jia H, Zhang Y, Chen C, Shao Y, Leng L, Liu Z, Huang X, Long M, Zhang YE (2016). LTR-mediated retroposition as a mechanism of RNA-based duplication in metazoans. Genome Research, 26:1-13.   pdf

  8. Long M (2015). Evolution of New Genes. Oxford Bibliographies.   pdf

  9. Zhang W, Landback P, Gschwend AR, Shen B and Long M (2015). New genes drive the evolution of gene interaction networks in the human and mouse genomes. Genome Biology, 16:202.   pdf

  10. Zhang YE, Long M (2014).New genes contribute to genetic and phenotypic novelties in human evolution.Curr Opin Genet Dev. doi: 10.1016/j.gde.2014.08.013. pdf

  11. Wang M, Yu Y, Haberer G, Marri PR, Fan C, Goicoechea JL, Zuccolo A, Song X, Kudrna D, Ammiraju JS, Cossu RM, Maldonado C, Chen J, Lee S, Sisneros N, de Baynast K, Golser W, Wissotski M, Kim W, Sanchez P, Ndjiondjop MN, Sanni K, Long M, Carney J, Panaud O, Wicker T, Machado CA, Chen M, Mayer KF, Rounsley S, Wing RA (2014). The genome sequence of African rice (Oryza glaberrima) and evidence for independent domestication. Nat Genet. doi: 10.1038/ng.3044. pdf

  12. Kemkemer C, Long M (2014). New genes important for development. EMBO Rep doi: 10.1002/embr.201438787 pdf

  13. Zhang C, Gschwend RA, Ouyang Y, Long M (2014). Evolution of gene structural complexity: An alternative-splicing based model accounts for intron-containing retrogenes, Plant Physiology doi: 10.1104/pp.113.231696 pdf

  14. Gao G, Vibranovski MD, Zhang L, Li Z, Liu M, Zhang YE, Li X, Zhang W, Fan Q, Vankuren NW, Long M, Wei L, 2014. A long term demasculinization of X-linked intergenic noncoding RNAs in Drosophila melanogaster. Genome Res doi: 10.1101/gr.165837.113 pdf

  15. Krinsky B.H., 2013.NextGenVoices . Science pdf

  16. Zhang C*, Wang J*, Long M and Fan C, 2013. gKaKs: The pipeline for genome level Ka/Ks calculation. Bioinformatics doi: 10.1093/bioinformatics/btt009 pdf

  17. Zhang C*, Wang J*, Marowsky NC, Long M, Wing RA and Fan C, 2013. High Occurrence of Functional New Chimeric Genes in Survey of Rice Chromosome 3 Short Arm Genome Sequences. Genome Biology and Evolution. doi: 10.1093/gbe/evt071 pdf 

  18. Chen S, Krinsky BH, Long M, 2013. New genes as drivers of phenotypic evolution. Nature Reviews Genetics vol. 14:645-660 pdf

  19. Long M, VanKuren NW, Chen S, Vibranovski MD, 2013. New gene evolution: Little did we know. Annual Reviews Genet Vol. 47:325-351 pdf

  20. Chen Y, Dai HZ, Long M, 2013. The evolution of the modern RNA world. In Wu J, Editor, Posttranscriptional gene regulation – RNA processing in Eukaryotes. WileyBlackwell, Weinheim, Germany. P. 239-252.

  21. Vibranovski M.D., Zhang Y.E., Kemkemer C., Lopes H.F., Karr T.L. and Long M, 2012.Re-analysis of the larval testis data on meiotic sex chromosome inactivation revealed evidence for tissue-specific gene expression related to the drosophila X chromosome. BMC Biology vol. 10:49 pdf

  22. Wang J, Long M and Vibranovski M.D., 2012. Retrogenes Moved Out of the Z Chromosome in the Silkworm. J Mol Evol vol. 74:113–126 pdf

  23. Cardoso-Moreira M and Long M, 2012. The Origin and Evolution of New Genes. In: M Anisimova (ed.), Evolutionary Genomics: Statistical and Computational Methods. Methods in Molecular Biology, Springer Science vol. 856: 161-186 pdf

  24. Sidi Chen, Xiaochun Ni, Benjamin Krinsky, Yong E. Zhang, Maria Vibranovski, Kevin White and Manyuan Long. Integration of a Nascent Gene Reshaped Global Gene Network and Impacted Sex-biased Gene Expression. EMBO Journal (2012, in press) pdf

  25. Sidi Chen, Maria Spletter, Xiaochun Ni, Kevin White, Liqun Luo and Manyuan Long. Frequent recent origination of brain genes shaped the evolution of foraging behavior in Drosophila. Cell Reports, Volume 1, Issue 2, 118-132, 16 February 2012, 10.1016/j.celrep.2011.12.010 pdf

  26. Ni XC, Zhang YE, Negrè N, Chen SD, Long M, White KP, 2012. Adaptive Evolution and the Birth of CTCF Binding sites in the Drosophila Genome. PLoS Biology. pdf

  27. Zhang YE, Landback P, Vibranovski M, Long M, 2012. New genes expressed in human brains: Implications for annotating evolving genomes. BioEssays (published online September 24, 2012). pdf

  28. Vibranovski MD, Zhang YE, Kemkemer C, VanKuren NW, Lopes HF, Karr TL and Long M, 2012. Segmental dataset and whole body expression data do not support the hypothesis that non-random movement is an intrinsic property of Drosophila retrogenes. BMC Evolutionary Biology. 12: 169. (Published: 5 September 2012). pdf

  29. Long M, Zhang L, 2012. Why rodent pseudogenes refuse to retire. Genome Biology, 13:178. pdf

  30. Sidi Chen., Haiwang Yang, Benjamin H. Krinsky, Anthony Zhang and Manyuan Long. Roles of young serine-endopeptidase genes in survival and reproduction revealed rapid evolution of phenotypic effects at adult stages. Fly (Austin). 2011, 5(4):1-7. pdf

  31. Zhang C., Wang J., Xie W., Zhou G., Long M. and Zhang Q. Dynamic programming procedure for searching optimal models to estimate substitution rates based on the maximum-likelihood method. Proc Natl Acad Sci U S A. 2011, 108(19):7860-7865. pdf

  32. Cardoso-Moreira M., Emerson J.J., Clark A.G. and Long M. Drosophila Duplication Hotspots Are Associated with Late-Replicating Regions of the Genome. PLoS Genetics. 2011, 7(11):e1002340. pdf

  33. Zhang Y.E., Landback P., Vibranovski M.D. and Long M. Accelerated Recruitment of New Brain Development Genes into the Human Genome. PLoS Biology. 2011, 9(10):e1001179. pdf

    • Related perspective:

      • Konopka G. The Fetal Brain Provides a Raison dêtre for the Evolution of New Human Genes. Brain Behav Evol. 2012 (DOI: 10.1159/000336723). pdf
      • Ranz J.M., Parsch J. Newly evolved genes: Moving from comparative genomics to functional studies in model systems. Bioessays. 2012 (DOI: 10.1002/bies.201100177). pdf
  34. Zhang Y.E., Vibranovski M.D., Krinsky B.H. and Long M. A cautionary note for the retrocopy identification: DNA-based duplication of intron-containing genes significantly contributes to the origination of single exon genes. Bioinformatics. 2011, 27(13):1749-1753. pdf

  35. Chen Y., Dai H., Chen S., Zhang L. and Long M. Highly Tissue Specific Expression of Sphinx Supports Its Male Courtship Related Role in Drosophila melanogaster. PLoS One. 2011, 6(4):e18853. pdf

  36. Chen Z., Zhang Y.E., Vibranovski M.D., Luo J., Gao G. and Long M. Deficiency of X-linked inverted duplicates with male-biased expression and the underlying evolutionary mechanisms in the Drosophila genome. Mol Biol Evol. 2011, 28: 2823–2832. pdf

  37. Chen M., Zou M., Fu B., Li X., Vibranovski M.D., Gan X., Wang D., Wang W., Long M. and He S. Evolutionary Patterns of RNA-Based Duplication in Non-Mammalian Chordates. PLoS One. 2011, 6: e21466. pdf

  38. Sidi Chen, Yong Zhang and Manyuan Long. New Genes in Drosophila Quickly Become Essential. Science 17 December 2010: Vol. 330 no. 6011 pp. 1682-1685 DOI: 10.1126/science.1196380. pdf

  39. Zhang Y.E., Vibranovski M.D., Krinsky B.H. and Long M. Age-dependent chromosomal distribution of male-biased genes in Drosophila. Genome Res. 2010, 20: 1526-1533. pdf

  40. Zhang Y.E., Vibranovski M.D., Landback P., Marais G. and Long M. Chromosomal Redistribution of Male-Biased Genes in Mammalian Evolution with Two Bursts of Gene Gain on X chromosome. PLoS Biology 2010 8: e1000494. pdf

  41. Arguello J.R., Zhang Y., Kado T., Fan C., Zhao R., Innan H., Wang W. and Long M. Recombination yet inefficient selection along the Drosophila melanogaster subgroup's fourth chromosome. Mol. Biol. Evol. 2010 27(4):848-861. pdf

  42. Zhang J, Yang H, Long M, Li L, Dean AM. Evolution of enzymatic activities of testis-specific short-chain dehydrogenase /reductase in Drosophila. J Mol Evol. 2010 71:241-249. pdf

  43. Vibranovski M.D.*, Chalopin D.S.*, Lopes H.F., Long M. and Karr T.L. Direct evidence for postmeiotic transcription during Drosophila melanogaster spermatogenesis. Genetics. 2010 186:431-433. (* Equally contributed). pdf

  44. Cardoso-Moreira, M.M. and Long M. Mutational bias shaping fly copy number variation: implications for genome evolution. Trends Genet. 2010 26(6):243-247. pdf

  45. Kado T., Arguello J.R., Long M., Wang W. and Innan H. A method for estimating crossing-over and gene conversion rate. Genes & Genetic Systems 2009 84(6):467.

  46. Zhang Y, Lu S, Zhao S, Zheng X, Long M, et al. Positive selection for the male functionality of a co-retroposed gene in the hominoids. BMC Evol Biol 2009 9: 252. pdf

  47. Zhu Z., Zhang Y. and Long M. Extensive structural renovation of retrogenes in the evolution of the Populus genome. Plant Physiol. 2009 Dec; 151(4): 1943-1951. pdf

  48. Vibranovski M.D., Lopes H.F., Karr T.L. and Long M. Stage-specific expression profiling of Drosophila spermatogenesis suggests that meiotic sex chromosome inactivation drives genomic relocation of testis-expressed genes. PLoS Genet. 2009 Nov; 5(11): e1000731. pdf

  49. Vibranovski M.D., Zhang Y. and Long M. General gene movement off the X chromosome in the Drosophila genus. Genome Res. 2009 May;19(5):897-903. pdf

  50. Kaessmann H., Vinckenbosch N. and Long M. RNA-based gene duplication: mechanistic and evolutionary insights. Nat Rev Genet. 2009 Jan;10(1):19-31. pdf

  51. Fan, C.*, Zhang, Y.*, Yu, Y.*, Rounsley, S., Long, M. and Wing, R.A.The Subtelomere of Oryza sativa Chromosome 3 Short Arm as a Hot Bed of New Gene Origination in Rice. Mol Plant, 2008 ssn050. pdf

  52. Fan, Chuanzhu, Ying Chen, and Manyuan Long. Recurrent Tandem Gene Duplication Gave Rise to Functionally Divergent Genes in Drosophila. Mol Biol Evol. 2008 Jul;25(7):1451-8. pdf

  53. 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 2008, 320: 1629-1631. (* Equally contributed). pdf

  54. 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. Proc Natl Acad Sci USA, 2008, 105: 7478-7483. pdf

  55. 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

  56. 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, 2008, 4(1): e3. pdf

  57. Drosophila 12 Genomes Consortium. Evolution of genes and genomes on the Drosophila phylogeny. Nature, 2007, 450: 203-218. pdf

  58. 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.

  59. Long M. Journal Club: Mystery Genes-An evolutionary geneticist is surprised by genes of unknown origin. Nature, 2007, 449: 511. pdf

  60. Fan C., Vibranovski M.D., 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

  61. Vibranovski M.D., Sakabe N.J. and Long M, Birth and Evolution of Human Exons. Encyclopedia of Life Sciences, 2007. pdf

  62. 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

  63. Havlioglu N, Wang J, Kuo D, Fushimi K, Vibranovski MD, Kan Z, Gish W, Fedorov A, Long M and Wu JY. An Intronic Signal for Alternative Splicing in the Human Genome. PLoS One, 2007, 2(11): e1246. pdf

  64. Shiao MS, Khil PP, Smirnova NA, Camerini-Otero RD, Shiroishi T, Yu HT, Long M. Origins of New Male Germ-line Functions from X-Derived Autosomal Retrogenes in the Mouse. Mol Biol Evol, 2007, 24: 2242-2253. pdf

  65. 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

  66. 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. 

  67. 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

  68. Wen Wang, Hongkun Zheng, Chuanzhu Fan, Jun Li, Junjie Shi, Zhengqiu Cai, Guojie Zhang, Dongyuan Liu, Jianguo Zhang, S?ren 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

  69. 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

  70. 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

  71. 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

  72. Emerson JJ*, Kaessmann H*, Betran E, Long M. Extensive gene traffic on the mammalian X chromosome. Science. 2004, 303:537-40. (* Equally contributed). pdf

  73. 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

  74. 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

  75. 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

  76. International Chick Genome Sequencing Consortium. Sequencing and comparative analysis of the chicken genome. Nature, 2004, 432: 432:695-716. pdf

  77. 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

  78. 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

  79. 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

  80. Long, M., 2003. Preface, Origin and evolution of new gene functions. Genetica Contemporary Issues In Genetics and Evoluton 10: 97.

  81. Long, M. 2003. Fusion genes. Encyclopaedia of the Human Genome, Macmillan Reference Ltd, London.Nature Publishing Group. Macmillan Publishers Ltd, Nature Publishing Group.

  82. Long, M., E. Betrán, K. Thornton, and W. Wang. The origin of new genes: glimpses from the young and old. Nature Reviews Genetics 2003, 4: 865-875. pdf

  83. Betran E, Long M. Expansion of genome coding regions by acquisition of new genes. Genetica. 2002 May;115(1):65-80. pdf

  84. 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

  85. Betran E, Thornton K, Long M. Retroposed new genes out of the X in Drosophila. Genome Res. 2002 Dec;12(12):1854-9. pdf

  86. 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

  87. Long, M. and R. Cerff. Introns: Movement. Encyclopaedia of the Human Genome, 2002. Macmillan Reference Ltd, London.

  88. 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

  89. 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

  90. 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

  91. 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

  92. Long M. Evolution of novel genes. Curr Opin Genet Dev. 2001 Dec;11(6):673-80. pdf

  93. Long M., Thornton, K. Gene Duplication and Evolution (technical note) Science 31 August 2001:Vol. 293. no. 5535, p. 1551. pdf

  94. Long, M. Book review : "Adaptive evolution of genes and genomes" by Austin Hughes, Oxford University Press, New York. Persp. Biol. Med. 2001, 44: 460-464.

  95. Létitia J., M. Long, J. Young, P. Péry, F. Tomley AP genes from apicomplexan parasites: Evidence for evolution of the gene structure. Trends Paras. 17: 491-498. pdf

  96. 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

  97. Long M. A new function evolved from gene fusion. Genome Res. 2000 Nov;10(11):1655-7. pdf

  98. 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

  99. 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

  100. Long, M. Protein coding segments: evolution of exon-intron gene structure. Encyclopaedia of Life Science, 2000. Macmillan Reference Ltd, London. pdf

  101. 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

  102. 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

  103. Deutsch M, Long M. Intron-exon structures of eukaryotic model organisms. Nucleic Acids Res. 1999 Aug 1;27(15):3219-28. pdf

  104. 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

  105. Long, M. and S. J. de Souza Intron-exon structures: from molecular to population biology. Adv. Genome Biol: Genes and Genomes 5A: 143-178.

  106. 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

  107. De Souza, S. J., M. Long, R. J. Klein, S. Roy, S. Lin, W. Gilbert. Towards a resolution of the introns early/late debate. Only phase zero introns are correlated with the structure of ancient proteins. Proc. Natl. Acad. Sci. USA , 1998, 95: 5094-5099. pdf

  108. 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

  109. Gilbert W, de Souza SJ, Long M. Origin of Genes. Proc Natl Acad Sci U S A. 1997 Jul 22; 94(15): 7698-7703. pdf

  110. 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

  111. 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

  112. 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

  113. deSouza SJ, Long MY, Gilbert W Introns and gene evolution. Genes to Cells 1 (6): 493-505 JUN 1996. pdf

  114. 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

  115. DeSouza SJ, Long M, Schoenbach L, et al. Intron positions correlate with module boundaries in ancient proteins. Proc Natl Acad Sci U S A, 1996, 93: 14632-14636 DEC 10 1996 pdf

  116. Long MY, Rosenberg C, Gilbert W Intron phase correlations and the evolution of the intron exon structure of genes Proc Natl Acad Sci U S A. 1995, 92: 12495-12499 DEC 19 1995 pdf

  117. Gilbert, W., M. Long, C. Rosenberg, M. Glylias Tests of the exon theory of genes. In: Tracing Biological Evolution in Protein and Gene Structures. Ed. M. Go and P. Schimmel. Elsevier Science B. V., 1995, Amsterdam.

  118. Long, M, S. J. de Souza, W. Gilbert Evolution of intron/exon structure of eukaryotic genes. Curr. Opin. Genet. Dev. 1995, 5: 774-778. pdf

  119. 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

  120. Long, M., J. H. Gillespie 1991. Codon usage divergence of homologous vertebrate genes and codon usage clock. J Mol Evol 1991, 32: 6-15 JAN 1991 pdf

  121. Williamson, V. W., M. Long, G. Theodoris Isolation of Caenorhabditis elegans mutants lacking alcohol dehydrogenase activity. Biochem. Genet. 1991, 29: 313-323. pdf