It is the new dawn! Behind the sheer cliff rises the golden glory of the invisible sun. Almost falling Christophe at last reaches the bank, and he says to the child: "Here we are! How heavy thou wert! Child, who are thou?" And the child answers: "I am the day soon to be born." - Romain Rolland: Jean-Christophe

Manyuan Long, Ph.D.

The Edna K. Papazian Distinguished Service Professor

Updated: July 19, 2012



  • Postdoctoral fellow, July 1 1993 -- October 31, 1997, Departments of Molecular and Cellular Biology  and  Organismic  and  Evolutionary  Biology,  Joint  Appointment,  laboratories  of Professors  Walter  Gilbert  and  Richard  C.  Lewontin,  Harvard  University,  Cambridge,  MA 02138.  
  • Ph.D.,  Genetics,  University  of  California,  Davis.    Degree  received  December  12,  1992. Dissertation:  The  origin  and  evolutionary  mechanisms  of  new  genes.  Department  of Genetics.  Laboratory of Professor Charles Langley.  
  • M.S., Genetics, University of California, Davis.  1990.   
  • M.S., Plant Genetics, 1985, Sichuan Agricultural University, Ya’an, Sichuan. Plant Quantitative Genetics Institute led by Professor Zhiren Gao.
  • B.S., Agronomy, 1982, Sichuan Agricultural University, Ya’an, Sichuan




  • The Edna K. Papazian Distinguished Service Professor, Department of Ecology and Evolution, The University of Chicago, 2011.
  • Full professor with tenure, Department of Ecology and Evolution, Committees on Genetics and Evolutionary Biology, and The College, The University of Chicago. Started on January 1, 2005.
  • Senior Fellow, The Institute for Genomics & Systems Biology, The University of Chicago and Argonne National Laboratory, April 2007 – April 2012.
  • The Dean’s Chair Professor, Tuft University (offered and declined), 2004.
  • Associate  Professor  with  tenure,  Department  of  Ecology  and  Evolution,  Committees  on Genetics  and  Evolutionary  Biology,  and  The  College,  The  University  of  Chicago.  July  1, 2003 – December 31, 2004. 
  • Assistant  professor,  Department  of  Ecology  and  Evolution,  Committees  on  Genetics  and Evolutionary  Biology,  and  The  College,  The  University  of  Chicago.  November  1,  1997  – June 30, 2003.   
  • Postdoctoral  research  associate,  Joint  Appointment,  Department  of  Molecular  and  Cellular Biology  (Walter  Gilbert's  laboratory)  and  Department  of  Organismic  and  Evolutionary Biology (R.C. Lewontin's laboratory),  Harvard University, July 1993 -- October 31, 1997. 
  • Research  Assistant,  Department  of  Genetics  and  Center  for  Population  Biology,  UC  Davis, 1988--1992. 
  • Teaching Associate, Principles of Genetics, UC Davis, 1989--1992. 


  Origin and evolution of new genes: 

  • The phenotypic effects and functions of new genes and their roles in development.
  • Evolutionary analysis of gene interactions with new genes; 
  • Copy number variation within Drosophila populations; 
  • Evolution of sex chromosomes and sex-related genes;
  • Genes and Genomes in plants: high origination rate of chimeric genes in the grass family.

 Scientific impacts:

  • Recognized as the pioneer of the area of the origination and evolution of new genes.
  • His discovers written into the new chapters and sections about new gene evolution into major textbooks (e.g. Douglas Futuyma, 2005 and 2009, Evolution, Sinauer, Massachusetts; Wen-Hsiung Li, 1997, Molecular Evolution, Sinauer, Massachusetts; Roderic Page and Edward Holmes, 1998, Molecular Evolution. Blackwell Science London).

Social impacts: 

  • New York Times, Washington Times, Chicago Tribune, Sacramento Bee, La Vanguardia, New Scientist, Scientist, Discover, La Recherche, and other news media in US, Europe, China and Taiwan reported in various languages his scientific discovers and commentaries.
  • His research results summarized in a Nature Rev Genet article (Manyuan Long et al, 2003) were cited as major evidence in a successful defense of the First Amendment to the United States Constitution in the nationally famous case of Kitzmiller et al. vs. Dover Area School District in Pennsylvania in 2005.


  • The Edna K. Papazian Distinguished Service Professor, Department of Ecology and Evolution, The University of Chicago, 2011 (The honor as the “most distinguished members of faculty” at the University of Chicago).
  • Allen G. Marr Prize for the Best Ph.D. Dissertation of the University of California, Davis, 1993.
  • David and Lucile Packard Fellowship for Science and Engineering, 1998.
  • National Science Foundation CAREER award, 2003.
  • Elected as the council Secretary officer for the major international academic organization in the field of molecular and genomic evolution: Society of Molecular Biology and Evolution (SMBE), 2010-2012).
  • Elected as chair to organize the 21st International Conference of Molecular Biology and Evolution in 2013, Chicago.
  • Elected into the Board of Directors of the Chinese Biological Investigator Society (CBIS) in USA in 2009.




  • The Scientist (July 19, 2012). “Sex drives chromosome evolution” (by Ruth Williams).
  • PLoS Blogs (June 17, 2012) Tooth & Claw: “What’s in a (Gene) Name?” (By Hillary Rosner).
  • The Scientist (October 18, 2011). “New Genes, New Brain” (News & Opinion by Cristina     Luiggi).
  • The Fisher Scientific (October 25, 2011, UK). “Youngest genes ‘teach us the most about     the human brain’”(by Tania).
  • Bionews (October 24, 2011, UK). “Young genes in young humans provide clue to brain     evolution.” (By James Brooks).
  • The Huffington Post (October 19, 2011, UK). “Modern Human Brain Full Of New Genes” (By     Press-Association).
  • ScienceDaily (October 19, 2011). “Young Human-Specific Genes     Correlated With Brain     Evolution” (By Robert Mitchum).
  • BBC Radio Interview for The Naked Scientists (, October 18,     2011): “[our] current  findings on the genes involved in the evolution of the human     brain” (by Meera Senthilingam).
  • New  Scientist  (December  23,  2010):”New  genes  needed  for  survival  too”  (by  Debora MacKenzie).
  • ScienceDaily  (December  16,  2010):  “Age  Doesn't  Matter:  New  Genes  Are  as  Essential  as Ancient Ones” (by Robert Mitchum)
  • ScienceNews (July 16, 2009): “Old gene, short new trick” (By Laura Sanders)
  • GenomeWeb Daily News (June 5, 2008): “Copy Number Variation Subject to Natural Selection in Drosophila”( By Andrea Anderson).
  • Richard Dawkins.Net (May 27, 2008): “Courtship pattern shaped by emergence of gene in fruit flies”
  • The  New  York  Times  (May  6,  2008):  Opinion  \  The  Wild  Side:  Genes  Go  Retro  (by  Olivia Judson).
  • Discover  magazine  (May  27,  2008):  “A  team  of  scientists  led  by  Manyuan  Long  at  the University of Chicago call it the sphinx gene”  (By Andrew Moseman).
  • Discovery Channel (November 10, 2005): “Male Sexual Prowess Drives Evolution?”
  • La Vanguardia (August 28, 2004, Barcelona): “He sido el primero en ver cómo surge un gen”.
  • The Scientist (April 6, 2004, London): “Genes constantly evolve”.
  • The University of Chicago Chronicle (April 15, 2004): ”Gene ‘traffic’ study overturns claims of earlier research”;
  • Eesti Geenikeskus (Jan 22, 2004, Estonia), "X kromosoomi geenid ja meessoo n)rkus";
  • The Washington Times (January 22, 2004): "Gene traffic high on X chromosome";  
  • The Atlanta Journal-Constitution (January 22, 2004): "Male genes: The weaker sex?”
  • Wissenschaft-online (January 23, 2004, Heidelberg): “Ausgeprägter Genexport des X Chromosoms “;
  • La Recherche (N°374 - AVRIL 2004, Paris): “Attributs mâles protégés“;
  • Diario Medico (January 23, 2004, Spain): “El tráfico de genes en el X es superior a lo que se pensaba”;
  • The Scientist (February 2, 2004, London) : “Sex and the X”;
  • Sciscape (February 12, 2004, Taiwan): “Escaping from the X”;
  • Chicago Tribune (July 10: 2003): "Gene swap in plants surprises scientists"  
  • Hyde Park Herald (June 4, 2003): "Fruit fly evolution, the 2-million question for professor"  
  • The  University  of  Chicago  Chronicle  (May  29,  2003):  "  Long  receives  nearly  $2  million  in grant funding from NSF, NIH";
  • The  University  of  Chicago  Chronicle  (February  21,  2002):  "Variations  discovered  in  fourth chromosome of fruit fly";
  • Diario Medico (January 7, 2002, Spain): “El cromosoma 4 de la 'Drosophila' incluye regiones con historias evolutivas diferentes”;
  • Science (Volume 290: 1065-1066, November 10, 2000): "Twinned Genes Live Life in the Fast Lane” ;     
  • The  University  of  Chicago  Magazine  (December  1998)  and  The  University  of  Chicago Chronicle  (October  15,  1998):  "Packard Fellowship  Awarded to Professor Studying  Gene Fragments";
  • The  New  York  Times    (November  12,  1996):    "Reading  the  History  of  Life  in  the  Text  of Modern Genes";
  • Harvard Gazette  (December 12, 1996):  "Evidence Found for Origin of Genes";
  • The Sacramento Bee  (April 4, 1993): "UC Davis Student Stumbles Upon Boon for Darwin";
  • The Davis Enterprise  (April 2, 1993):  "UCD researchers study the origin of genes";
  • The California Aggie  (April 8, 1993):  "Imagination as important to discovery as facts";  
  • The Davis Enterprise (June 15, 1993): "Marr Prize goes to genetics researcher for top dissertation".




  • National Science Foundation, USA (Reviewers and Review Panel Member)
  • National Institutes of Health, USA
  • Austrian Science Foundation, Austria
  • Health Research Board, Dublin, Ireland
  • Canada Foundation for Innovation, Canada
  • The Netherlands Organisation for Scientific Research, Netherlands
  • National Natural Science Foundation, China




  • Genetics, the Genetics Society of America, Associate Editor (2008-2011).
  • Journal of Molecular Evolution, Associate Editor (2001-2008).
  • Faculty of 1000 biology (Section of Genetics and Evolution) (2002-2008; 2010-)
  • Proceedings of the National Academy of Sciences of the United States of America (Guest Editor, 2008);
  • PLoS Biology (Academic Editor; 2008);
  • Biology Direct (2005-)
  • Journal of Experimental Zoology – B. Developmental and Molecular Evolution (2006-)
  • Journal of Systematics and Evolution (2009-2011)
  • Journal of Genetics & Genomics and Hereditas (2005-2011)
  • Genetica and Contemporary Issues in Genetics and Evolution (2002-2003)




  • Biotechniques;
  • BMC Genomics;
  • Current Biology;
  • Evolution;
  • FASEB Journal;
  • Gene;
  • Genetica;
  • Genetical Research;
  • Genetics;
  • Genome Research;
  • Journal of Molecular Evolution;
  • Molecular Biology and Evolution;
  • Molecular Ecology;
  • Molecular Genetics and Genomics;
  • Molecular Phylogenetics and Evolution;
  • Nature;
  • Nature Genetics;
  • Nature Methods;
  • Nature Reviews Genetics;
  • Nature Communication; 
  • Nucleic Acid Research;
  • The Plant Cell; 
  • Plant Physiology;
  • PLoS Biology;
  • PLoS Genetics;
  • PLoS Computational Biology;
  • Plant Genome;
  • Proceedings of the National Academy of Sciences of the United States of America;
  • Quarterly Review of Biology;
  • Royal Society Proceedings B: Biological Letters;
  • Science;
  • Trends in Biotechnology;
  • Trends in Genetics;
  • Evolutionary biology textbook for Jones and Bartlett Publishers.




  • Genetics Society of America (GSA);
  • American Association for Advancement of Science;
  • The Society of Molecular Biology and Evolution;
  • The International Society of Molecular Evolution.




  • National Institutes of Health (1R01GM100768-01A1): PI (04/01/2012-03/31/2016)
  • National Science Foundation: PI (2011, Doctoral Dissertation Improvement Grant, Sidi Chen).
  • National Science Foundation (NSF1051826): PI (05/01/2011-04/31/2016).
  • National Institutes of Health (R01GM078070-03S1): PI (09/18/2009--04/30/2012);
  • National Institutes of Health (R01GM078070-01A1): PI (05/01/2007--04/30/2012);
  • National Science Foundation (NSF1026200): Co-PI (08/01/2010-07/31/2014, with PI, Rod Wing et al University of Arizona).
  • National Institutes of Health (R01GM078070-03S1): PI (09/18/2009--04/30/2012);
  • National Institutes of Health (R01GM078070-01A1): PI (05/01/2007--04/30/2012);
  • The Chicago Biomedical Consortium (Spark award), Co-I (03/01/2009-02/30/2011).
  • The Chicago Biomedical Consortium (Catalyst award C-006), Co-I   (08/01/2007-01/31/2009).
  • National Science Foundation (Dissertation Improvement Award for JJ Emerson) PI (10/01/2004-09/30/2005);
  • National Science Foundation CAREER Award: PI (04/01/2003 -- 03/31/2008);
  • National Institutes of Health (R01 GM065429-02S1): PI (10/01/2004-09/30/2006).  
  • National Institutes of Health (R01GM065429-01A1): PI (direct cost) (07/01/2003 -- 06/30/2007);
  • The David and Lucile Packard Foundation: PI (11/01/1998 – 10/31/2003;
  • National Science Foundation: PI (08/01/99 -- 07/31/2002);
  • Block fund award, The University of Chicago: PI (06/01/1998 -- 05/31/1999);
  • Block fund award, The University of Chicago: PI (06/01/2001 -- 05/31/2002);
  • The University of Chicago setup fund: PI.
  • Federal Training Grants (Genetics, GAAN, predoctoral fellowship)
  • International scholarships (European, South American, and Asian (2003-current).




  • Postdoctoral research associates (Past: 6; Current: 4)
  • Doctorial Graduate students (Past: 9; Current, 4)
  • Undergraduate research assistants (Past: 13)
  • Doctoral thesis committees (Having served for 23 Ph.D. graduate students; Currently, 2)
  • Visiting scholars (3)
  • Four doctoral students in my lab won the distinguished research awards: the best dissertation award at the Committee on Genetics, Genomics and Systems Biology (Kevin Thornton and Hongzheng Dai), the university-wide prestigious Harper Fellowship (Roman Arguello), and the best dissertation award in the Biological Science Division for 2011-2012 (Sidi Chen).  Two graduate students won the prestigious NSF Doctoral Dissertation Improvement Grants (JJ Emerson and Sidi Chen). One graduate student won prestigious NSF predoctotral fellowship (Nicholas VanKuren). The most of the students/postdocs I trained have been in various stages of successful career development in science, with 9 being tenured or tenure-tracked professors in research universities or institutes. Several former graduate students graduated in recent three years are postdoctoral research fellows in the top research universities in USA and UK. 



Undergraduate courses:

  • The Chicago curriculum “Big Problems” series: BP29100/BioSci 29319: What Do The Genomes Teach Us About Evolution? (Spring, 2009-2011, with James Shapiro and Robert Richards)
  • BioSci 23259: Molecular Evolution II, Spring 2009
  • BioSci  28401:  Introduction  to  Systems  Biology  II,  Spring  2007,  2008  (with  Hongyu  Zhao  of Yale)
  • BioSci 22600: Evolutionary Genomics (Computational Evolutionary Biology) (Spring 1999-2001; 2002-2005, with Thomas Nagylaki).


Graduate courses:

  • EE35900, Genomic Evolution (Spring 1998-2007, with Martin Kreitman);
  • EE35800, Classics of Evolutionary Genetics (Winter 1999-2001; 2002-2010, with Wen- Hsiung Li and Richard Hudson).
  • Reading Courses: EE497, Evolutionary Biology and History of Evolutionary Biology.




  • BSD Faculty Science Review Committee, 2009.  
  • Committee on Appointments and Promotions (CAOP), Division of Biological Sciences;
  • EE (Department of Ecology and Evolution) Admission committee (1997 – 1998; 2001 – 2002; 2009-2012);
  • EE Committee for recruitment of new faculty (1998 -- 1999);
  • EE Committee of Students Affairs (1998 -- 2000);
  • EE Committee for organizing the departmental seminars (1998 – 2000; 2002 -- 2003);
  • COG (Committee on Genetics) Admission Committee (1999 -- 2000).




  • 2011-2013,  Chair, Organizing Committee, The 21st Annual International Conference of     Molecular Biology and Evolution, Chicago (2013 Chicago SMBE meeting).
  • 2011    Co-organizer, the symposium of Gene Evolution and Phenotypic Evolution, the 19th Annual International Conference of Molecular Biology and Evolution, Kyoto.
  • 2011    the international organizing committee member, the 19th Annual International     Conference of Molecular Biology and Evolution, Kyoto.
  • 2010    Co-organizer, the symposium of Evolution of Sex chromsome and sex determination,  
  • 2010    Society of Molecular Biology and Evolution annual conference, Lyon.
  • 2010    Co-organizer, International Workshop of Evolution of Sex chromosomes and Sex determination, Functional Genomic Institut of Lyon, Ecole Normale Superieure.
  • 2010-2012,  The  administrative  council  Secretary  officer  of  the  international  organization Society  of  Molecular  Biology  and  Evolution  (SMBE),  elected  in  the  Iowa  city  annual conference of SMBE, 2009, to run secretary activities of SMBE.  
  • 2010-2012, The administrative board member of the Chinese Biological Investigator Society in USA (CBIS), elected in La Jolla biannual conference of CBIS.
  • 2010  Lectured  European  workshop  of  Genomic  Evolution,  sponsored  by  Ecole  Normale Supérieure, Lyon, France (01/2010).  
  • 2009    December 27-29 CBIS annual conference, co-chair, the session of Neuroscience, Development, Behaviors. Hilton Hotel, La Jolla, California.
  • 2009    Co-chair, organized the international conference: “Darwin’s Heritage Today,  Darwin 200 International Beijing conference”, sponsored by Peking University, Institute
  • of  Vertebrate  Paleontology  and  Paleoanthropology,  National  Key  Laboratories  of  Plant Systematics and Evolution, Beijing.
  • 2006 – 2009, Lectured Bio2000 Seminar series, organized by Professor Weimin Zhong at Yale University.
  • 2006    20012  Cheung Kong Scholars Chair Adjunct Professor, Peking University.
  • 2008    Chair of New Gene Evolution and Morphology, The 11th Chinese-American Frontiers  Sciences  Symposiums,  National  Academy  of  Science  USA  &  Chinese  Academy  of Sciences (Irvine, California, USA, 11/2008)
  • 2008    Guest Professor, Soochow University, Soochow.
  • 2007     2008  Panel  members  of  key  research  projects.  National  Natural  Science  Foundation, China (Beijing, Changchun).
  • 2006-2009  Visiting Professor, Zhejiang University, Hangzhou.
  • 2007-2010  Guest Professor, Huazhong Agricultural University, Wuhan.
  • 2006-2008  Professor  of  Graduate  Courses  in  Molecular  Biology:  Bio2000  for  Shanghai Institutes of Life Sciences, Tsinghua University and Peking University.
  • 2005  Co-chair,  organized  the  symposium  in  celebration  of  scientific  exploration  of  Walter Gilbert, Cold Spring Harbor Laboratory, 2005.
  • 2005    The section chair, the 14th International Congress of Origin of Life (Beijing, 06/2005). 
  • 2004    Lecture,  the  Southern  European  Evolutionary  Genomics  Workshop,  Barcelona,  Spain, 06/2004.
  • 2004 and 2008 Summer Training Class of Molecular Evolution, Kunming, Chinese Academy of Sciences, Kunming Zoology Institute.
  • 2004    Chair, Symposium of Genetics of Natural Selection (Chicago, 2004).
  • 2004-2006    Guest  Professor,  Institute  of  Genetics  and  Development,  Chinese  Academy  of Sciences. Beijing.
  • 2001-2002  Visiting assistant professor, Tonghai University, the Republic of China.
  • 1999-2000  The 8th and 9th SCBA international symposia of molecular evolution (Hong Kong, 1999; Taipei, 2000), co-chair.




  1. Ming,  D.  and  M.  Long    1985.  Mathematical  principle  and  application  of  canonical  correlation to quantitative genetic analysis.  J. of Sichuan Agri. Univ.  3: 250-255.
  2. Long, M.  1985.  A new method to measure the kernel volume of maize (Zea mays, L.).  J.of Sichuan Agri. Univ.  3: 415-420.
  3. Long, M. 1986.  On the application of fuzzy clustering to genetic analysis.  J. of Sichuan Agri. Univ.  4: 239-247.
  4.  Long,  M. 1987.    Study  on  the  relationship  between  genetic  distances  and  specific combining ability of yields in maize (Zea mays, L.).  Genetic Research in China.  5 (ed by Genetics Society of China)  (Hunan Press of Science and Technology, Changsha).
  5. Long, M. 1987.  The methods for measuring genetic distance and the relationship between yield heterosis/specific combining ability and genetic distance in maize (Zea mays, L.). Acta Agronomica Sinica 13: 193-200.
  6. Long, M. 1988.  Computational search of a special orthogonal experiment design scheme. J. of Sichuan Agri. Univ.  6: 100-103.
  7. Long, M.  1993.  Estimating genetic variation in restriction fragment length polymorphism of nucleic acids. Hereditas (Beijing) 15: 44-48.
  8. Long,  M.  1986. History  of  science:  G.  W.  Yule  ¨C  A  founder  of  polygene  hypothesis  of quantitative genetics who should not have been forgot. J of Sichuan Agri, Univ. Volume 4.
  9. Williamson,  V.  W.,  M.  Long,  G.  Theodoris  1991.  Isolation  of  Caenorhabditis  elegans mutants lacking alcohol dehydrogenase activity.  Biochem. Genet.  29: 313-323.
  10. Long, M., J. H. Gillespie 1991.  Codon usage divergence of homologous vertebrate genes and codon usage clock.  J. Mol. Evol. 32: 6-15.
  11. Long, M., C. H. Langley  1993.  Natural selection and the origin of jingwei, a chimeric processed functional gene in Drosophila.  Science  260: 91-95.
  12. Gilbert, W., M. Long, C. Rosenberg, M. Glylias  1995. 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., Amsterdam.
  13. Long, M, S. J. de Souza, W. Gilbert 1995. Evolution of intron/exon structure of eukaryotic genes.  Curr. Opin. Genet. Dev.  5: 774-778.
  14. Long, M., C. Rosenberg, W. Gilbert  1995.  Intron phase correlations and the evolution of intron/exon structure of genes.  Proc. Natl. Acad. Sci. USA  92: 12495-12499.
  15. De Souza, S. J., M. Long, L. Schoenbach,  W. Gilbert 1996. Intron positions correlate with module boundaries in ancient proteins. Proc. Natl. Acad. Sci. USA   93: 14632-14636.
  16. Long, M., S. J. De Souza, C. Rosenberg, W. Gilbert 1996. Exon shuffling and origin of plant mitochondrial targeting targeting in cytochrome c1 precursor. Proc. Natl. Acad. Sci. USA 93: 7727-7731.
  17. DeSouza, S. J., M. Long, and W. Gilbert 1996. Introns and gene evolution. Genes to Cells  1: 493-505.
  18. Richter, B., M. Long, R. C. Lewontin, E. Nitasaka 1997. Nucleotide polymorphism and evolution of the decapentaplegic gene in Drosophila.  Genetics  145: 311-323.
  19. Long, M., S.J. De Souza, W. Gilbert 1997. Delta-interacting protein A and the origin of hepatitis delta antigen. Science  276: 824-825.
  20. Gilbert, W., S.J. De Souza, M. Long 1997. Origin of genes. Proc. Natl. Acad. Sci. USA  94: 7698-7703.
  21. Long, M., S.J. De Souza, W. Gilbert 1997. The yeast  splice site revisited: A new exon consensus from genomic analysis.  Cell  91: 739-740.
  22. De Souza S.J., M. Long, L. Schoenbach, S.W. Roy, W. Gilbert 1997. The correlation between introns and the three-dimensional structure of proteins.  Gene  205: 141-144.
  23. Long, M., S.J. de Souza, W. Gilbert 1998. Relationship between "proto-splice sites" and intron phases: Evidence from Dicodon Analysis. Proc. Natl. Acad. Sci. USA  95: 219-223.
  24. De Souza, S. J., M. Long, R. J. Klein, S. Roy, S. Lin, W. Gilbert 1998. 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 95: 5094-5099.
  25. Long, M. and S. J. de Souza 1998. Intron-exon structures: from molecular to population biology.  Adv. Genome Biol: Genes and Genomes 5A: 143-178.
  26. Long, M., W. Wang, and J. Zhang 1999. Origin of New Genes and source for N-terminal domain of the chimerical gene, jingwei, in Drosophila.  Gene  238: 135-142.
  27. Long, M. and M. Deutsch 1999. Association of intron phases with conservation at splice site sequences and evolution of spliceosomal introns. Mol. Biol. Evol. 16: 1528-1534.
  28. Deutsch, M. and M. Long 1999. Intron-exon structures of model organisms. Nucl. Acid Research 27: 3219-3228.
  29. C¨¢ceres, M., J. M. Ranz, Barbadilla, M. Long, and A. Ruiz 1999, Generation of a widespread Drosophila inversion by a transposable element.  Science 285: 415-418.
  30. Sakharkar,M., M. Long, T. W. Tan, S. J. De Souza 2000. ExInt-an Exon/Intron database. Nucl. Acid Research 28: 191-192.
  31. Long, M. 2000. Protein coding segments: evolution of exon-intron gene structure. Encyclopaedia of Life Science, Macmillan Reference Ltd, London.
  32. Wang, W., J. Zhang, C. Alvarez, A. Llopart,  and M. Long 2000. The origin of the jingwei Gene  and the complex modular structure of its parental gene, yellow emperor, in D. Mol. Biol. Evol.  17:1294-1301.
  33. Sakharkar, M. K., P. Kangueane, T. W. Woon, T. W. Tan, P. R. Kolatkar, M. Long, and S. J. De Souza 2000. IE-Kb: intron exon knowledge base. Bioinformatics 16: 1151-1152.
  34. Long,  M.  2000.  A  new  function  evolved from  gene  fusion.  Genome  Research  10:  1655-
  35. Long, M. and C. Rosenberg 2000. Testing the "proto-splice sites" model of intron origin: Evidence from analysis of intron-phase correlations.  Mol. Biol. Evol. 17: 1789-1796.
  36. Long, M. 2001. Book review : "Adaptive evolution of genes and genomes" by Austin Hughes, Oxford University Press, New York. Persp. Biol. Med. 44, 460-464.
  37. Létitia J., M. Long, J. Young, P. Pery, F. Tomley 2001. AP genes from apicomplexan parasites: Evidence for evolution of the gene structure.  Trends Paras. 17: 491-498.
  38. Long, M., K. Thornton 2001. Gene duplication and evolution.  Science 293:1551. 
  39. Long, M. 2001. Evolution of novel genes.  Curr Opin Genet Dev 11:673-680. 
  40. Long, M. and R. Cerff. 2002. Introns: Movement. Encyclopaedia of the Human Genome, Macmillan Reference Ltd, London.
  41. Long, M. 2002.  Pseudoexons. Encyclopaedia of the Human Genome, Macmillan Reference Ltd, London. 
  42. Wang, W., K. Thornton, A. Berry, and M. Long. 2002. Nucleotide variation along the Drosophila melanogaster fourth chromosome. Science 295:134-137.
  43. Wang, W., F. G. Brunet, E. Nevo, M. Long 2002. Origin of sphinx, a young chimeric RNA gene in Drosophila melanogaster. Proc. Natl. Acad. Sci. USA.. 99: 4448-4453.
  44. Betran E., M. Long 2002. Expansion of genome coding regions by acquisition of new genes. Genetica 115: 65-80.
  45. Betran, E., W. Wang, L. Jin, M. Long 2002. Evolution of the phophoglycerate mutase processed gene in human and chimpanzee revealing the origin of a new primate gene.  Mol. Biol. Evol.. 19: 654-663.
  46. Thornton, K., M. Long 2002. Rapid divergence of gene duplicates on the Drosophila  X chromosome.  Mol. Biol. Evol. 19: 918-925.
  47. Betran, E., K. Thornton, and M. Long 2002. Retroposed new genes out of the X in Drosophila Genome Research. 12: 1854-1859.
  48. Llopart, A., J. M. Comeron, F. G. Brunet, D. Lachaise, M. Long 2002. Intron presence / absence polymorphism in Drosophila driven by positive Darwinian selection. Proc.  Natl. Acad. Sci. USA 99: 8121-8126.
  49. Sakharkar M, F. Passetti F, J. E. de Souza, M. Long, S. J. de Souza 2002. ExInt: an Exon Intron Database. Nucl. Acid. Research. 30:191-194.
  50. Betran, E., M. Long 2003. Dntf-2r, a young Drosophila retroposed gene with specific male expression under positive Darwinian selection. Genetics 164: 977-988
  51. Long, M., M. Deutsch, W. Wang, E. Betr¨¢n, F. Brunet, J. Zhang  2003. Origin of new genes: Results from experimental and computational analysis.  Genetica 118: 171-182.
  52. Long,  M.,  2003.    Preface,  Origin  and  evolution  of  new  gene  functions.  Contemporary Issues  In Genetics and Evoluton 10: 97.
  53. Long, M. 2003.  Fusion genes. Encyclopaedia of the Human Genome, Macmillan Reference Ltd, London.Nature Publishing Group. Macmillan Publishers Ltd, Nature Publishing Group.
  54. Long, M., E. Betran, K. Thornton, and W. Wang. 2003. The origin of new genes: glimpses from the young and old. Nature Reviews Genetics 4: 865-875.
  55. Wang, W, K. Thornton, J. J. Emerson, and M. Long 2004. Nucleotide Variation and Recombination  Along  the  Fourth  Chromosome  in  Drosophila  Simulans    Genetics  166:1783- 1794.
  56. Emerson J.J.*, H. Kaesmann*, E. Betran and M. Long 2004. Extensive gene traffic on the human X chromosome. Science  303: 537-540. (*Equal contribution).
  57. Wang,  W.,  H.  Yu  and  M.  Long  2004.  Duplication-degeneration  as  a  mechanism  of  gene fission and the origin of Drosophila new genes. Nature Genetics 36: 523 ¨C 527.
  58. Zhang, J., A. M. Dean, F. Brunet and M. Long 2004. Evolving functional diversity in new genes of Drosophila. Proc Natl Acad Sci USA. 101: 16246 -16250
  59. Betran,  E.,  J.J. Emerson,  H.  Kaessmann,  and  M.  Long  2004.  Sex  chromosomes  and  male functions: where do new genes go? Cell Cycle 3: 873-875.
  60. International  Chick  Genome  Sequencing  Consortium,  2004.  Sequencing  and  comparative analysis of the chicken genome. Nature 432: 432:695-716. 
  61. Thornton K, Long M. 2005.  Excess of Amino Acid Substitutions Relative to Polymorphism between X-linked Duplications in Drosophila melanogaster. Mol Biol Evol.22: 273-284.
  62. Zhang J,  Long M, and Li L, 2005. Translational effects of differential codon usage among intragenic domains of the young Drosophila gene. Biochim Biophys Acta 1728:135-142.
  63. Arguello JR, Chen Y, Yang S, Wang W, and Long M, 2006. An X-linked Testes Chimeric Gene by Illegitimate Recombination in Drosophila. PLoS Genetics 2: 0745-0754. e77.
  64. Wang  W,  Zheng  H,  Fan  C,  Li  J,  Shi  J,  Cai  Z,  et  al,  2006.  High  rate  of  chimeric  gene origination by retroposition in plant genomes. Plant Cell 18: 1791-1802.
  65. Dai  H,  Yoshimatsu  TF,  Long  M,  2006.  Retrogene  movement  within-  and  between-chromosomes  in  the  evolution  of  Drosophila  genomes.  Gene  (Special  Volume  for  6th Anton Dohrn Workshop: Genome Evolution). Gene 385: 96-102.
  66. Arguello JR, Fan C, Wang W and Long M (2006). Origination of Chimeric Genes through DNA-level  Recombination.  Genome  Dynamics:  Evolution  of  Gene  Functions.  Karger publishers. 3: 131-146.
  67. Fan  C  and  Long  M,  2007.  A  New  Retroposed  Gene  in  Drosophila  Heterochromatin Detected by Microarray-Based Comparative Genomic Hybridization. J Mol Evol  64:272-
  68. Shiao MS, Khil PP, Smirnova NA, Camerini-Otero RD, Shiroishi T, Yu HT, Long M. 2007. Natural  Selection  Targeting  on  Expression  Novelties  in  X-related  Retrogenes  in  Rodents. Mol Biol Evol 24: 2242-2253.
  69. Havlioglu  N,  Wang  J,  Kuo  D, Fushimi  K,  Vibranovski  MD,  Kan Z,  Gish  W, Fedorov A, Long M and Wu JY.  2007. Genomic Signal for Alternative Splicing of a Large Number of Gene Families in the Human Genome. PLoS One 2(11): e1246.
  70. Elde. NC, Long M, and Turkwitz AP. 2007. A role for convergent evolution in the secretory life of cells. Trends Cell Biol 17:157-164.
  71. Fan  C,  Vibranovsky  M,  Chen  Y  and  Long  M,  2007.  A  Microarray-based  genomic hybridization method for identification of new genes in plants: case analyses of Arabidopsis and Rice Journal of Integrative Plant Biology. 49: 915-926.
  72. Long  MY  and  Zhu  ZY,  2007.  Male  non-coding  RNA  genes  identified  by  comparative genomic analysis of the Drosophila genomes. Chinese Science Bulletin 52 :  721-724.
  73. Long M., 2007. Journal Club: Mystery Genes. Nature 449: 511. 
  74. Arguello JR, Fan C, Wang W, and Long M, 2007. Origination of Chimeric Genes through DNA-level Recombination. Genome Dynamics 3: 131-146. 
  75. Drosophila  12  Genomes  Consortium,  2007.  Evolution  of  genes  and  genomes  on  the Drosophila phylogeny. Nature  450: 203-218.
  76. Yang YF, Li Z, Fan QC, Long MY, and Zhang WX, 2007. Significant divergence of sex-related  non-coding  RNA  expression  patterns  among  closely  related  species  in  Drosophila. Chinese Science Bulletin 52: 748-754.
  77. Vibranovski  M,  Nobara,  M,  Long  M,  2007.  Birth  and  Evolution  of  Human  Exons. Encyclopedia of Life Sciences. A0020777. John Wiley & Sons, Ltd.
  78. Fan  C,  Emerson  JJ,  and  Long  M,  2007.  The  Origin  of  New  Genes.  In:  Evolutionary Genomics  and  Proteomics  Ed.  By  Mark  Pagel  and  Andrew  Pomiankowski.  Sinauer Associates.
  79. Long M, 2007.  Side effects of Tamiflu: clues from an Asian single nucleotide polymorphism. Cell Research 17: 309-310.
  80. Yang S., Arguello R, Li X, Ding Y, Zhou Q, Chen Y, Zhang Y, Zhao R, Brunet F, Peng L, Long  M,  Wang  W.,  2008.  Repetitive  Elements-mediated  Recombination  as  a  Mechanism for New Gene Origination in Drosophila  PLoS Genetics 4(1): e3. 0001-0010.
  81. Shiao  MS,  Liao  BY,  Long  M,  Yu  HT,  2008.  The  adaptive  evolution  of  insulin  two-gene system in rodents. Genetics online published February 2, 2008. 178: 1683-1691.
  82. Fan C, Chen Y, Long M, 2008. A Newly Tandem Duplicated Gene Cluster under Darwinian Positively  Selection  Evolved  a  Specific  Expression  Pattern  in  Reproductive  Organs  in Drosophila. Mol Biol Evol 25:1451-1458.
  83. Fan C, Zhang Y, Yu YS, Rounsley S, Long M, and Rod A, 2008. Wing The Subtelomere of Oryza sativa  Chromosome  3  Short  Arm  as  a  Hot  Bed  of  New  Gene  Origination  in  Rice. Molecular Plant 1: 839-850.
  84. Dai H, Chen Y, Chen S, Mao Q, Kennedy D, Landback P, Eyre-Walker A, Du D, Long M, The  evolution  of  courtship  behaviors  through  the  origination  of  a  new  gene  in Drosophila. Proc Natl Acad Sci USA. 105:7478-83.
  85. Emerson JJ*, Cardoso-Moreira M*, Borevitz JO, Long M, 2008. Natural selection shapes genome  wide  patterns  of  copy  number  polymorphism  in  D.  melanogaster.  Science 320:1629-1631. (* Equal contribution.)
  86. Xiao WF, Hongbo Liu HB, Wang L, Li XH, Xu CG, Long MY, Wang SP, 2009. A Rice Gene of De Novo Origin Negatively Regulates Pathogen-Induced Defense Response. PLoS One 4:e4603.
  87. Chen Y, Dai H, and Long M, 2010. The Evolution of the Modern RNA World. Ed, by Jane Wu   Post   Transcriptional   Gene   Regulation,   Wiley-Blackwell,   Weinheim,   Germany. (Accepted)
  88. Vibranovski MD, Zhang Y, Long M, 2009. General gene movement off the X chromosome in the Drosophila genus. Genome Research 19: 897-903.
  89. Kaessmann H, Vinckenbosch N, and Long M, 2009. RNA-based gene duplication. Nature Reviews Genetics 10: 19-31.
  90. Vibranovski MD, Lopes HF, Karr TL, Long M (2009) Stage-specific expression profiling of Drosophila  spermatogenesis  suggests  that  meiotic  sex  chromosome  inactivation  drives genomic relocation of testis expressed genes. PLoS Genet 5(11): e1000731.
  91. Li Z, Liu M, Zhang L, Zhang WX, Gao G, Zhu Z, Wei LP, Long M, Fan Q, 2008. Detection of Non-coding RNAs Encoded in the Intergenic Regions Expressed in Main Developmental Stages in Drosophila melanogaster Nucleic Acids Research 37:4308-4314.
  92. Zhu ZL, Zhang Y, and Long M, 2009. Structural Renovation of Retrogenes in Populus. Plant Physiology 151:1943-1951.
  93. Zhang Y, Lu S, Zhao S, Zheng X, Long M, and Wei LP, 2009. Positive selection for the male functionality of a co-retroposed gene in the hominoids. BMC Evol Biol 9: 252. doi: 10.1186/1471-2148-9-252.
  94. Kado T, Arguello JR, Long M, Wang W, and Innan H. 2009.  A method for estimating crossing-over and gene conversion rate. Genes & Genetic Systems  84:467-471.
  95. Arguello JR, Zhang Y, Kado T, Fan C, Zhao RP, Innan H, Wang W, and Long M, 2010. Recombination yet inefficient selection along the Drosophila melanogaster subgroup's fourth chromosome. Mol Biol Evol 27: 848-861.
  96. Raleigh DR, Marchiando AM, Zhang Y, Shen L, Sasaki H, Wang YM, Long M, Turner JR, Tissue Junction-associated MARVEL proteins marvelD3, tricellulin and occludin have distinct, but overlapping, functions. Mol Biol Cell 21: 1200-1213.
  97. Cardoso-Moreira M, Long M, 2010. Biased mutational processes influence the genomic composition of copy number variation in Drosophila melanogaster. Trend Genet 26: 243-247.
  98. Vibranovski MD, Chalopin DS, Lopes HF, Long M, Karr TL, 2010. Genome wide postmeiotic transcription in Drosophila melanogaster. Genetics. 186: 431 ¨C 433.
  99. Zhang Y, Vibranovski MD, Krinsky BH, Long M, 2010. Age-dependent chromosomal distribution of male-biased genes in Drosophila. Genome Research. Published in Advance August 26, 2010,  doi:10.1101/gr.107334.110. 20:  1526-1533.
  100. Zhang J, Yang H, Long M, Li L, Dean AM, 2010.  Evolution of enzymatic activities of testis-specific short-chain dehydrogenase /reductase in Drosophila. J Mol Evol. 71:241-249.
  101. Fu BD, Chen M, Zou M, Long M, He SP, 2010. The rapid generation of chimerical genes  expanding protein diversity in zebrafish. BMC Genomics  2010, 11:657,1-9.
  102. Zhang Y, Vibranovski MD, Landback P, Long M, 2010.  Chromosomal redistribution of male-biased genes in mammalian evolution with two bursts of gene gain on X chromosome. PLoS Biology 8(10): e1000494. doi:10.1371/journal.pbio.1000494.
  103. Chen S, Zhang Y, and Long M, 2010. New genes in Drosophila quickly become essential. Science 330: 1682-1685.
  104. Chen ZX, Zhang YE, Vibranovski M, Luo JC, Gao G, Long M, 2011. Deficiency of X-linked inverted duplicates with male-biased expression and the underlying evolutionary mechanisms in the Drosophila genome. Mol Biol Evol 28: 2823–2832.
  105. Chen Y, Dai HZ, Chen SD, Zhang L, Long M, 2011. The new gene, sphinx, evolved distinct     expression and interaction patterns supporting its male courtship related role in Drosophila     melanogaster. PLoS One 6:e18853.
  106. Zhang Y, Vibranovski MD, Krinsky BH, and Long M, 2011. A cautionary note for the     retrocopy identification: DNA-based duplication of intron-containing genes significantly contributes to the origination of single exon genes.  Bioinformatics (First published     online May 5, 2011. doi:10.1093). 27(13): 1749-1753.
  107. Chen M; Zou M; Fu Beide; Li X; Vibranovski MD, Gan XN, Wang DQ, Wang W, Long     MY, He SP, 2011. Evolutionary Patterns of RNA-Based Duplication in Non-    Mammalian Chordates. PLoS One 6: e21466.
  108. Zhang CJ, Wang J, Xie WB, Zhou G, Long M*, Zhang QF* (*co-corresponding authors),     2011. A dynamic programming procedure for searching optimal models to estimate     substitution rates based on the maximum-likelihood method. Proc Natl Acad Sci,     108:7860-7865.
  109. Zhang YE, Landback P, Vibranovski MD, Long M, 2011. Accelerated recruitment of new     brain development genes into the human genome. PLoS Biology 9: e1001179.
  110. Cardoso-Moreira M, Emerson JJ, Clark AG, Long M, 2011. Drosophila Duplication     Hotspots Are Associated with Late-Replicating Regions of the Genome. PLoS Genet     7: e1002340.
  111. Chen SD, Yang HW, Krinsky BH, Zhang A, Long M, 2011. Roles of young serine- endopeptidase genes in survival and reproduction revealed rapid evolution of phenotypic effects at adult stages. FLY 5(4): 1-7.
  112. Chen SD, Spletter M, Ni XC, White K, Luo LQ, Long M, 2012. Frequent Recent Origination of Brain Genes Shaped the Evolution of Foraging Behavior in Drosophila (Research Article). Cell Reports 1: 118-132
  113. Wang J, Long M and Vibranovski MD, 2012. Retrogenes Moved Out of the Z Chromosome in the Silkworm. J Mol Evol 74: 113-126.
  114. 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 (In Revision)
  115. Long M, Vibranovski MD, and Zhang YE, 2012. Evolutionary interactions between sex chromosomes and autosomes. In: Rapidly Evolving Genes and Genetic Systems. Ed. Robert Kulathinal, Jianping Xu and Rama Singh.  Oxford University Press, Longdon. (In press). 
  116. Chen SD, Ni XC, Krinsky BH, Zhang Y, Vibranovski M, White KP and Long M, 2012. Integration of a Nascent Gene Reshaped Global Gene Network and Impacted Sex-biased Gene Expression. EMBO J 31(12): 2798-2809.
  117. 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.
  118. Vibranovski MD, Zhang YE, Kemkemer C, Lopes HF, Karr TL 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. 10: 49.
  119. Chen SD, Yang HW, Krinsky BH, Pruett-Jones S and Long M, 2012. New Genes Drive Rapid Phenotypic Evolution in Males in Drosophila.  (In submission)
  120. Vibranovski MD, Zhang YE, Kemkemer C, Vankuren NW, Lopes HF, Karr TL, 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 Biology (In revision). 



  • 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.
  • 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.



  • 2012 – The public lecture of evolution in universe and organisms, Dayin Theater, Beijing. The Plenary Speaker, the 53rd Annual Drosophila Research Conference, the Genetics Society of America. Symposium of Copy Number Variation at the 23rd Annual Conference of Society of Molecular Biology and Evolution, Dublin, Ireland; Symposium in Celebration of Scientific Career of Wen-Hsiung Li, Dublin, Ireland. Departmental Seminar, Department of Plant Science, University of Illinois at Urbana-Champaign. Public Lecture, Division of Biological Sciences, The University of Chicago. Shanghai Institute of Neuroscience, Chinese Academy of Sciences. Systems Biomedicine Institute, Shanghai Jiaotong University, Shanghai; School of Life Sciences, Huanzhong Normal University, Wuhan.  School of Life Sciences, Shanghai Jiaotong University, Shanghai; Workshop on genomic evolution in agriculturally related species, sponsored by Ministry of Education, China, Wuhan; The Fifth National Conference of Systems Biology and Bioinformatics of China, Haerbin. 
  • 2011 –  The International Conference of Rice Functional Genomics, Taipei. Department of Evolutionary Genetics and Ecology, the University of Munster, Munster, Germany. Department of Biological Science, Poznan University, Poznan, Poland. Genetics & Biochemistry Branch, NIDDK, National Institutes of Health; Molecular Evolution in the Genomic Era, Roma Tre University, Genome Biology and Evolution and International Union of Biological Sciences, Rome, Italy; The Symposium of Gene Evolution and phenotypic Evolution, 19th International Conference of Society of Molecular Biology and Evolution, Kyoto; The Rice Genome Meeting, University of Arizona, Tucson; Plant and Animal Genome Conference, San Diego; The 1st Asian-Pacific Drosophila Conference, Taipei; Institute of Biological Diversity, Sinica Academia. Nankang, Taiwan. Shanghai JiaoTong University, Shanghai; Institute of Plant Genomes; Second International Symposium on Genomics and Crop Genetic Improvement, Wuhan. School of Biological Science, Shanxi University, Taiyuan, China. Institute of Systems Biology, Soozhou University, Soozhou.
  • 2010  –  Lecture  for  the  European  Genomic  Evolution  workshop,  Ecole  Normale  Supérieure, Lyon,  France;  Departmental  Seminar,  University  of  Lyon,  Lyon,  France;  53rd  annual conference of the Genetics Society of Canada, Hamilton, Canada; Symposium of Gene and Genome  Duplication,  The  2010  Annual  SMBE  conference,  Lyon,  France;  Institute  of Bioinformatics,  Department  of  Genetics,  North  Carolina  State  University,  Raleigh;  The University  of  Chicago  Beijing  Center  symposium,  Beijing;  Institute  of  Genetics  and Development,  CAS,  Beijing;  Institute  of  Biophysics,  CAS,  Beijing;  Institute  of  Botany, CAS,  Beijing;  National  Key  Laboratory  of  Crop  Genetics  and  Improvement,  Huazhong Agricultural University, Wuhan.
  • 2009  –  CBIS  conference,  La  Jolla,  California;  Graduate  Program  Research  Symposium  of Molecular  Genetics  and  Evolution,  the  University  of  Munich,  Germany;  School  of Biological Sciences, Zhejiang University, Hangzhou; Institute of Systems Biology, Suzhou University, Suzhou; Department of Biological Sciences, University of Texas at Arlington; “Graduate Student Sponsored Research Symposium”, Biochemistry and Molecular Biology, Oklahoma  State  University,  Stillwater;  The  100th  International  Titisee  Conference,  Black Forest, Germany; Life Science Seminar Series, South Dakota State University, Brookings; Journal  of  Systematics  and  Evolution  Symposia, Shenzhen  Fairylake  Botanical  Garden  & Beijing  Institute  of  Botany,  Shenzhen;  Theoretical  Center,  Academia  Sinica,  Taiwan; Institute   of   Zoology,   National   Taiwan   University,   Taiwan;   The   7th   International Bioinformatics  Workshop,  Suzhou;  Darwin-200  Lectureship,  Cheng  Gong  University, National  Research  Council;  Biodiversity  Center,  Academia  Sinica,  Taipei;  Bio2000, Shanghai; Institute of Zoology, Chinese Academy of Science; National Taiwan University, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; Taipei; University of Porto, Porto, Portugal.
  • 2008 –  Max-Planck-Institutes for Developmental Biology and for Biological Cybernetics and the Friedrich-Miescher Laboratory, Tübingen, Germany; Max-Plank Institute for Chemical Biology,  Jena,  Germany;  The  Section  of  Ecology,  Behavior,  &  Evolution,  University  of California,  San  Diego;  School  of  Life  Sciences,  Sichuan  University,  Sichuan;  National Natural Science Foundation of China, Changchun; Santa Barbara workshop of Theoretical Physical   Series:   Population   Genetics   and   New   Gene   Functions,   Kavli   Institute   for Theoretical Physics, University of California at Santa Barbara; The Peak Forum of Genetics, Institute  of  Genetics  and  Development,  Beijing;  Bio2000,  Shnaghai;  The  11th  Chinese American  Frontiers  of  Sciences  Symposiums,  National  Academy  of  Sciences  USA  and Chinese Academy of Science, Irvine, California.
  • 2007  –  Genome  Institute,  University  of  Lausanne,  Switzerland;  CNRS  /  Ecology  and Evolution,  University  of  Lyon,  Lyon,  France;  Evolution  of  Brain,  Behaviour  and Intelligence,  Welcome  Trust  Sanger  Institute,  Cambridge,  UK;  Programme  du  Colleloque en  L’Honneur  de  Daniel  Lachaise,  CNRS,  Paris,  France;  Santa  Barbara  workshop  of Theoretical  Physical  Series:  Gene  Duplication,  Kavli  Institute  for  Theoretical  Physics, University of California at Santa Barbara; The 5th International Bioinformatics Workshop, Weihai;  Bio2000,  Chinese  Academy  of  Sciences,  Beijing/Shanghai;  Graduate  Program  of Ecology   and   Evolution,   Michigan   State   University;   Department   of   Genetics,   Yale University; College of Life Sciences, Tongji University, Shanghai; College of Life Sciences, Soochow University, Soochow.
  • 2006  –  Division  of  Bioinformatics;  school  of  Life  Science,  Tsinghua  University;  Institute  of Molecular Medicine, Peking University; Institute of Zoology, National Taiwan University; Bio2000, Shanghai Instites of Life Sciences; Plant Genome Conference VII, Harbin, China; Gordon  Conference  Posttranscription  Regulation,  Queen’s  College,  Oxford,  UK;  The  31st Annual Conference of American Society of Andrology; The Argonne National Laboratory; Wenner-Gren  Foundations  International  Symposium  “Mutation,  Selection  and  Genome Evolution”, Stockholm, Sweden; Society of Molecular Biology and Evolution Symposium , Tampe; IGERT Symposium of Evolutionary Genomics, University of Arizona, Tucson.
  • 2005  –  National  Institutes  of  Health  USA;  the  7th  International  Conference  Bioinformatics (Tartum, Estonia); the 14th International Congress of the Origin of Life (Beijing); the 6th Anton Dohrn Worshop, Stazione Zoologica (Naples, Italy).
  • 2004   –   Tufts   University;   Harvard   University   (Dept   of   Systems   Biology);   Barcelona Autonomous University; Workshop of evolutionary genomics, Taiwan; The Second  International  Conference  of  Bioinformatics  and  Computational  Biology  (Rio  Janeiro); Northern Illinois University.  
  • 2003  –  Harvard  University  (Dept  of  Organismic Evolutionary  Biology);  North  Carolina  State University; Pennsylvania State University;  National Institute of Genetics, Japan; University of California, Riverside; Loyalo University of Chicago; University of Michigan, Ann Arbor.
  • 2002  –  CNRS,  Montpellier,  France;  CNRS,  Valbonne,  France;  University  of  Oklahoma; Gordon Conference on Genomic Evolution and Bioinformatics; Texas A & M University; National Singapore University.
  • 2001 – University of California, Davis. Jacques Monod Conference, Modane. CNRS, Gif-sur- Yvette,  France;  Loyola  University  of  Chicago;  Tunghai  University;  National  Taiwan University; Chinese National Natural Science Foundation; Beijing University.  
  • 2000  --  The  Salk  Institute  for  Biological  Research;  University  of  Oregon;  Academia  Sinica, Taiwan, ROC; National Taiwan University, ROC; Western Michigan University.
  • 1999  --  University  of  Nebraska;  Purdue  University;  Beijing  University,  PRC;  Zhejiang University,  PRC;  Eleventh  Annual  US  Frontier  of  Science  Symposium;  International Symposium on Molecular Evolution, Costa Rica.
  • 1998 -- Harvard University; University of California, Davis. 
  • 1997 -- State University of New York, Albany; University of Iowa; University of Rochester.
  • 1996 -- Wayne State University; University of Houston.
  • 1995 -- Fudan University, PRC; University of Missouri; University of Maryland.