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报 告 人: Dr. Manyuan Long
The Edna K. Papazian Distinguished Service Professor
DEPARTMENT OF ECOLOGY AND EVOLUTION
1101 EAST 57TH STREET, CHICAGO, IL 60637
TEL (773)702-0557; FAX (773)702-9740
Webpage: http://longlab.uchicago.edu/
报告题目: New Genes as Drivers of Phenotypic Evolution
报告时间: 2013年3月14日（星期四）下午14:30时
报告地点: 上海交通大学生命学院3-105会议室
联系人：张大兵 教授
报告人背景介绍：
EDUCATION
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
PROFESSIONAL EXPERIENCE
The Edna K. Papazian Distinguished Service Professor, Department of Ecology and Evolution, and The College, The University of Chicago. Started on July 1, 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.
HONORS
The Edna K. Papazian Distinguished Service Professor, The University of Chicago, 2011.
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.
INTERVIEWS AND NEWS MEDIA
New Scientist (January 24, 2013). “Genes from nowhere: Orphans with a surprising story” (by Helen Pilcher)
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 (www.thenakedscientists.com, 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".
PANEL MEMBER / GRANT REVIEWER
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
EDITORIAL BOARD SERVICE
EMBO Reports, Advisory editorial board (2013-2015)
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 (2006-2015)
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)
JOURNAL AND BOOK REVIEWER
Biotechniques;
Current Biology;
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;
Nucleic Acid Research;
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.
PROFESSIONAL AFFILIATIONS
Genetics Society of America (GSA);
American Association for Advancement of Science;
The Society of Molecular Biology and Evolution;
The International Society of Molecular Evolution.
RESEARCH SUPPORT
National Science Foundation: PI (2011, Doctoral Dissertation Improvement Grant, Graduate student Sidi Chen).)
National Science Foundation: PI (05/01/2011-04/31/2016).
National Institutes of Health (R01GM078070-03S1): PI (09/18/2009 -- 04/30/2011);
National Institutes of Health (R01GM078070-01A1): PI (05/01/2007 -- 04/30/2011);
National Science Foundation: Co-PI (08/01/2010-07/31/2014).
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).
LAB MEMBERS
Postdoctoral research associates (Past: 6; Current: 5)
Doctorial Graduate students (Past: 8; Current, 5)
Visiting Scientists (Past: 5; Current 2)
Undergraduate research assistants (Past: 13; Current 2)
Doctoral thesis committees (Having served for 23 Ph.D. graduate students; Currently, 2)
Visiting scholars (3)
Three doctoral students in my lab won the distinguished research awards at the Committee on Genetics and university-wide prestigious Harper Fellowship at the University of Chicago.The most of the students/postdocs I trained have been in various stages of successful career development in science, with ten being tenured or tenure-tracked professors in research universities or institutes. Several former graduate students graduated in three years are postdoctoral research fellows in the top research universities in USA and UK.
TEACHING SERVICE
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.
ADMINISTRATIVE SERVICE
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);
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);
EE Admission Committee (2001 -- 2002);
COG (Committee on Genetics) Admission Committee (1999 -- 2000).
ACADEMIC ACTIVITIES AND HONORABLE APPOINTMENTS
2013-2016, Genetics Society of America, the Conferences Committee
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 --20015 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.
PUBLICATIONS
Ming, D. and M. Long 1985. Mathematical principle and application of canonical correlation to quantitative genetic analysis. J. Sichuan Agri. Univ. 3: 250-255.
Long, M. 1985. A new method to measure the kernel volume of maize (Zea mays, L.). J. Sichuan Agri. Univ. 3: 415-420.
Long, M. 1986. On the application of fuzzy clustering to genetic analysis. J. Sichuan Agri. Univ. 4: 239-247.
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).
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.
Long, M. 1988. Computational search of a special orthogonal experiment design scheme. J. of Sichuan Agri. Univ. 6: 100-103.
Long, M. 1993. Estimating genetic variation in restriction fragment length polymorphism of nucleic acids. Hereditas (Beijing) 15: 44-48.
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 Sichuan Agri, Univ. Volume 4.
Williamson, V. W., M. Long, G. Theodoris 1991. Isolation of Caenorhabditis elegans mutants lacking alcohol dehydrogenase activity. Biochem. Genet. 29: 313-323.
Long, M., J. H. Gillespie 1991. Codon usage divergence of homologous vertebrate genes and codon usage clock. J. Mol. Evol. 32: 6-15.
Long, M., C. H. Langley 1993. Natural selection and the origin of jingwei, a chimeric processed functional gene in Drosophila. Science 260: 91-95.
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.
Long, M, S. J. de Souza, W. Gilbert 1995. Evolution of intron/exon structure of eukaryotic genes. Curr. Opin. Genet. Dev. 5: 774-778.
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.
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.
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.
DeSouza, S. J., M. Long, and W. Gilbert 1996. Introns and gene evolution. Genes to Cells 1: 493-505.
Richter, B., M. Long, R. C. Lewontin, E. Nitasaka 1997. Nucleotide polymorphism and evolution of the decapentaplegic gene in Drosophila. Genetics 145: 311-323.
Long, M., S.J. De Souza, W. Gilbert 1997. Delta-interacting protein A and the origin of hepatitis delta antigen. Science 276: 824-825.
Gilbert, W., S.J. De Souza, M. Long 1997. Origin of genes. Proc. Natl. Acad. Sci. USA 94: 7698-7703.
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.
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.
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.
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.
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.
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.
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.
Deutsch, M. and M. Long 1999. Intron-exon structures of model organisms. Nucl. Acid Research 27: 3219-3228.
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.
Sakharkar,M., M. Long, T. W. Tan, S. J. De Souza 2000. ExInt-an Exon/Intron database. Nucl. Acid Research 28: 191-192.
Long, M. 2000. Protein coding segments: evolution of exon-intron gene structure. Encyclopaedia of Life Science, Macmillan Reference Ltd, London.
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 Drosophila. Mol. Biol. Evol. 17:1294-1301.
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.
Long, M. 2000. A new function evolved from gene fusion. Genome Research 10: 1655-
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.
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.
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.
Long, M., K. Thornton 2001. Gene duplication and evolution. Science 293:1551.
Long, M. 2001. Evolution of novel genes. Curr Opin Genet Dev 11:673-680.
Long, M. and R. Cerff. 2002. Introns: Movement. Encyclopaedia of the Human Genome, Macmillan Reference Ltd, London.
Long, M. 2002. Pseudoexons. Encyclopaedia of the Human Genome, Macmillan Reference Ltd, London.
Wang, W., K. Thornton, A. Berry, and M. Long. 2002. Nucleotide variation along the Drosophila melanogaster fourth chromosome. Science 295:134-137.
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.
Betran E., M. Long 2002. Expansion of genome coding regions by acquisition of new genes. Genetica 115: 65-80.
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.
Thornton, K., M. Long 2002. Rapid divergence of gene duplicates on the Drosophila X chromosome. Mol. Biol. Evol. 19: 918-925.
Betran, E., K. Thornton, and M. Long 2002. Retroposed new genes out of the X in Drosophila Genome Research. 12: 1854-1859.
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.
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.
Betran, E., M. Long 2003. Dntf-2r, a young Drosophila retroposed gene with specific male expression under positive Darwinian selection. Genetics 164: 977-988
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.
Long, M., 2003. Preface, Origin and evolution of new gene functions. Contemporary Issues in Genetics and Evoluton 10: 97.
Long, M. 2003. Fusion genes. Encyclopaedia of the Human Genome, Macmillan Reference Ltd, London. Nature Publishing Group. Macmillan Publishers Ltd, Nature Publishing Group.
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.
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.
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).
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.
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
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.
International Chick Genome Sequencing Consortium, 2004. Sequencing and comparative analysis of the chicken genome. Nature 432: 432:695-716.
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.
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.
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.
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.
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.
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.
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-
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.
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.
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.
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.
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.
Long M., 2007. Journal Club: Mystery Genes. Nature 449: 511.
Arguello JR, Fan C, Wang W, and Long M, 2007. Origination of Chimeric Genes through DNA-level Recombination. Genome Dynamics 3: 131-146.
Drosophila 12 Genomes Consortium, 2007. Evolution of genes and genomes on the Drosophila phylogeny. Nature 450: 203-218.
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.
Vibranovski M, Nobara, M, Long M, 2007. Birth and Evolution of Human Exons. Encyclopedia of Life Sciences. A0020777. John Wiley & Sons, Ltd. www.els.net
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.
Long M, 2007. Side effects of Tamiflu: clues from an Asian single nucleotide polymorphism. Cell Research 17: 309-310.
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.
Shiao MS, Liao BY, Long M, Yu HT, 2008. The adaptive evolution of insulin two-gene system in rodents. Genetics 178: 1683-1691.
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.
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.
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.
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.)
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.
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.
Vibranovski MD, Zhang Y, Long M, 2009. General gene movement off the X chromosome in the Drosophila genus. Genome Research 19: 897-903.
Kaessmann H, Vinckenbosch N, and Long M, 2009. RNA-based gene duplication. Nature Reviews Genetics 10: 19-31.
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.
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.
Zhu ZL, Zhang Y, and Long M, 2009. Structural Renovation of Retrogenes in Populus. Plant Physiology 151:1943-1951.
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.
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.
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.
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.
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.
Vibranovski MD, Chalopin DS, Lopes HF, Long M, Karr TL, 2010. Genome wide postmeiotic transcription in Drosophila melanogaster. Genetics. 186: 431 ¨C 433.
Zhang Y, Vibranovski MD, Krinsky BH, Long M, 2010. Age-dependent chromosomal distribution of male-biased genes in Drosophila. Genome Research. 20: 1526-1533.
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.
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.
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.
Chen S, Zhang Y, and Long M, 2010. New genes in Drosophila quickly become essential. Science 330: 1682-1685.
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.
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.
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 27(13): 1749-1753.
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.
Long M, Vibranovski M, Zhang Y, 2011. Evolution of New Genes. The Princeton Guide to Evolution (Editor-In-Chief: Jonathan Losos. Section Editor. Hopi Hoekstra).
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, USA 108:7860-7865.
Zhang YE, Landback P, Vibranovski MD, Long M, 2011. Accelerated recruitment of new brain development genes into the human genome. PLoS Biology 9: e1001179.
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.
Chen SD,Spletter M, Ni XC,White KP, Luo LQ, Long M. 2012. Frequent Recent Origination of Brain Genes Shaped the Evolution of Foraging Behavior in Drosophila. Cell Reports. 1: 118-132.
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.
Wang J, Long M and Vibranovski M.D., 2012. Retrogenes Moved Out of the Z Chromosome in the Silkworm. J Mol Evol 74:113–126.
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.
Sidi Chen, Xiaochun Ni, Benjamin Krinsky, Yong E. Zhang, Maria Vibranovski, Kevin White and Manyuan Long, 2012. Integration of a Nascent Gene Reshaped Global Gene Network and Impacted Sex-biased Gene Expression. EMBO Journal 31: 2798-2809
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.
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).
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.
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.
Long M, Zhang L, 2012. Why rodent pseudogenes refuse to retire. Genome Biology 13: 178.
Zhang CJ, Wang J, Long M and Tan CZ, 2013. gKaKs: The pipeline for genome level Ka/Ks calculation. Bioinformatics. First published online: January 12, 2013 .
Chen SD, Krinsky B and Long M, 2013. New genes as drivers of phenotypic evolution. Nature Reviews Genetics (Accepted).
Long M, VanKuren N, Chen SD and Vibranovski M, 2013. Annual Review of Genetics (Accepted)
Books:
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.
INVITED SEMINARS/LECTURES
2013 – Natural Science Research Academy, Shanghai Jiaotong University; EMBO Conference, Rome, Italy.
2012 – Public Lecture in Daying Theatre, Shongshuhui, Beijing; Division of Biological Science, The University of Chicago; Plenary Talk, the 53rd Drosophila Annual Research Conferences; Department of Plant Science, University of Illinois Urbana-Champaign; International Symposium of Copy Number Variation, Dublin, Ireland; International Symposium in Celebration of W-H Li’s Scientific Career, Dublin, Ireland; Shanghai Neuroscience Research Institute, Chinese Academy of Science, Shanghai.
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.
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