Manyuan Long

 

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

 

Update: May 1, 2018

 

 

 

 

EDUCATION

 

  • Postdoctoral fellow, July 1 1993 -- October 31, 1997, Departments of Molecular and Cellular Biology and Organismic and Evolutionary Biology, a joint appointment, with mentors Walter Gilbert and Richard Lewontin, at 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. With mentor Charles Langley, Department of Genetics, University of California at Davis.
  • M.S., Genetics, University of California, Davis.  1990.  
  • M.S. & B.S., Plant Genetics & Breeding, 1985, 1982, Sichuan Agricultural University, Ya’an, Sichuan. Plant Quantitative Genetics Institute, Sichuan Agricultural University. With mentor Zhiren Gao and supervisor Daoxu Ming.  

 

PROFESSIONAL EXPERIENCE

 

  • Edna K. Papazian Distinguished Service Professor, Department of Ecology and Evolution and the College, The University of Chicago; a faculty member of the Committees on Genetics and Evolutionary Biology, The University of Chicago.    Started July 1, 2011, the permanent appointment.
  • Full professor with tenure, Department of Ecology and Evolution and The College, The University of Chicago; a faculty member of the Committees on Genetics and Evolutionary Biology, The University of Chicago.   January 2005 – June 2011.
  • Senior Fellow, The Institute for Genomics & Systems Biology, The University of Chicago and Argonne National Laboratory, April 2007 – current.
  • The Dean’s Chair Professor, Tuft University (offered and declined), 2004.
  • Associate Professor with tenure, Department of Ecology and Evolution and The College, The University of Chicago; a faculty member of the Committees on Genetics and Evolutionary Biology, The University of Chicago.  July 1, 2003 – December 31, 2004.
  • Assistant professor, Department of Ecology and Evolution and the College; A faculty member of the Committees on Genetics and Evolutionary Biology, The University of Chicago. November 1, 1997 – June 30, 2003.  
  • Postdoctoral research associate, a 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 (Charles Langley’s laboratory and John Gillespie’s laboratory), University of California, Davis, 1988--1992.
  • Teaching Assistant and Teaching Associate, Principles of Genetics; Population Genetics; Evolutionary Quantitative Genetics.  Department of Genetics, University of California, Davis, 1989--1992.

 

 

RESEARCH INTERESTS AND IMPACTS

  •  
  • Since the graduate school in California in the early 1990s, Long has been focusing on the study of a new and major scientific problem: How does a new gene originate and evolve?  The approaches Long has developed and are being used to investigate the new gene problem include theoretical, computational, and molecular experimental approaches.

 

Origin and evolution of new genes:

 

  • Evolution of gene expression networks by integration of new genes;
  • Phenotypic effects and functions of new genes;
  • 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:

 

 The American Association for the Advancement of Science (AAAS) summarized my contribution when conferring Long with a fellow honor (2014 AAAS Fellow) as “You

are being honored: For distinguished contributions to the fields of molecular evolution and genetics, particularly for starting and leading the area of new gene evolution using experimental and computational genomics and molecular biology”.

 

 Long’s discovers have helped shape the new chapters and sections about new gene evolution   in major textbooks pf evolutionary biology (e.g. Douglas Futuyma, 2013, 2009 and 2005, Evolution, Sinauer, Massachusetts; Michael Lynch, 2007, The Origins of Genome   Architecture, Sinauer, Massachesetts; 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, The Huffington Post, La VanguardiatheNew Scientist, the Scientist, DiscoverLa Recherche, Wen Hui Bao, and other news media in US, Europe, East Asia reported in various languages Long’s scientific discovers.

 

 Long’s research results summarized in a Nature Rev Genet article (Manyuan Long et al, 2003) were cited as major evidence for a successful defense of Amendment I to the United States Constitution in the nationally concerned case of Kitzmiller et al. vs. Dover Area School District in Pennsylvania in 2005.

 

 

HONORS

 

  • AAAS Fellow by the American Association for the Advancement of Science (AAAS),  2014.
  • Appointed by National Institute of Genetics, Japan, as one of two visiting professors (with an Austrian scholar in Vienna) to its Division of Theoretical Genetics (a major international power house for the neutral theory of molecular evolution), 2013-2016.
  • European Molecular Biological Organization, Advisory Editorial Board for EMBO Reports, 2013-2015; 2017-2020.
  • International Review Experts Board, Chinese Academy of Sciences, 2014-2017.
  • Edna K. Papazian Distinguished Service Professor, Department of Ecology and Evolution and the College, the University of Chicago. The inaugural honorific professorship started July 1, 2011 as a permanent appointment by the University of Chicago Board of Trustees and the University president Robert J. Zimmer.
  • Elected as chair to organize the 21st International Conference of Molecular Biology and Evolution in 2013, Chicago.
  • 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).
  • David and Lucile Packard Fellow for Science and Engineering, 1998 ~ 2008.
  • National Science Foundation CAREER award2003 ~ 2008.
  • Allen G. Marr Prize for the Best Ph.D. Dissertation of the University of California, Davis, 1993.

 

INTERVIEWS AND NEWS MEDIA

 

  • PanSci (March 30, 2018, Taipei).  “果蠅基因兩性互相傷害?一個基因不,那就複製一個!” (by 寒波).
  • Arstechnica (February 23, 2018, Splitsville). “A battle between the sexes in a single gene ” (By John Timmer).
  • Scientias (Marchh 16, 2018. Netherland). “Hoe lossen fruitvliegjess seksuele conflicten op?” (By Jente Ottenburghs).
  • ScienceDaily (February 19, 2018). “Duplicate genes help animals resolve sexual conflict” (By Matt Wood).
  • Guangming News Media Network (光明网 科普中国- September 23, 2015, Beijing).  “The way of scientific research of Manyuan Long” (by Pu Xiao).
  • Genome Biology and Evolution (October 1, 2014). “Highlight: The “Out of Pollen” Hypothesis—In Plants, Animals New Genes Originate in Male Sex Tissue” (by Danielle Venton).
  • New Scientist (January 16, 2013, London). “Genes from nowhere: Orphans with a surprising story” (by Helen Pilcher).
  • Wen Hui Bao (汇报Wenhui Review, April 15, 2013, Shanghai). “The Life has no progress but evolution” (by Chunyi Li).
  • 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).
  • PLoS Blogs (February 7, 2011). Tooth & CLAW: “Of bad odors and good yarns” (By Hillary Rosner).
  • BBC Radio Interview for The Naked Scientists (www.thenakedscientists.comOctober 18, 2011): “[The Manyuan Long group’s] 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, New York): “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, New York) : “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".

 

  • SERVICE AND HONORARY APPOINTMENTS
    • NATIONAL / INTERNATIONAL ACADEMIC ACTIVTIES
      • Chair, International Symposium on Evolution of Genes and Genomes, sponsored by Science China Life Sciences and West China School of Medicine, Sichuan University, Chengdu (April 22-25, 2018).
      • Organizer, Section S20 of the 1st Asian Conference of Evolutionary Biology (AsiaEvo 1), Symposium on Molecular Mechanism of Evolution and Section of banquet dinner talks (April 18-20, 2018).
      • Specially Appointed Expert of Hundreds of Scholars Program, Northwest University and Shaanxi Province Government, Xi’an, China (hosted by Aigen Fu, Institute of Frontier of Biological Sciences, Northwest University (2017-2022).
      • International Member, the Committee of the Ohta Fund, which was donated by the Crafoord Prize (2015) winner Tomoko Ohta to promote education and research of evolutionary genetics in Japan and Asia, housed in the Association for Propagation of the Knowledge  of Genetics (The Idengaku-fukyukai) and the National Institute of Genetics, Mishima, Japan.(Invited by Hiroshi Akashi, NIG in 2017)
      •  Chair, the 21st annual international conference of molecular biology and evolution (2013, Chicago), the international Society of Molecular Biology and Evolution.
      • Chair, the Darwin 200 International Beijing conferencesponsored by Peking University, Institute of Vertebrate Paleontology and Paleoanthropology, National Key Laboratories of Plant Systematics and Evolution, Beijing.
      • Secretary, the international Society of Molecular Biology and Evolution (2010-2012).
      • Board of Directors of the Chinese Biological Investigator Society (CBIS) in USA 2010-2015.
      • Changjiang Scholar Chair Professorship, Peking University, 2006-2015.
      • Organizer, Macrobiology Course International Team, Zhiyuan College, Shanghai Jiaotong University, 2011-2018.
      • Education reform committee oversea member, Shanghai Jiaotong University, 2015 – 2018/
      • Invited Expert for Faculty Promotion in the Center for Biological Diversity and the Institute of Molecular Biology, Academia Sinica, Taiwan (2009-2014).
      • Chair, the Darwin 200 Beijing International Conference (2009, Beijing).
      • Bio-2000 course series, Shanghai Institutes of Life Sciences, Chinese Academy of Sciences, Qinghua University and Peking University (2008-2011).
      • Member, the Conference Committee, The Genetics Society of America (2013-2016).
      • Co-organizer, The Course of Biological Thoughts and Concepts, Peking University (2008-2013)
      • The academic evaluation expert, the State Science and Technology Prizes, the State Council of the People’s Republic of China (2012-2013).
      • Evaluation Committee on the five-year academic progress of Institute of Zoology, Chinese Academy of Sciences, Beijing (November 6-9, 2014).
    • PANEL MEMBER / GRANT REVIEWER
      • National Science Foundation, USA (Reviewers and Review Panels)
      • National Institutes of Health, USA (R01 and Predoctoral and Postdoctoral Fellowships Applications)
      • Austrian Science Foundation, Austria
      • Health Research Board, Dublin, Ireland
      • Canada Foundation for Innovation, Canada
      • Canada Research Chairs Program, Canada
      • The Netherlands Organization for Scientific Research, Netherlands
      • National Natural Science Foundation, China
      • Chicago Biomedical Consortium, Chicago
      • Danish National Research Foundation (evaluated applications for the Centers of Excellence),
      •           Copenhagen
      • National Centre for Biological Sciences, Department of Atomic Energy, Bangalore, India
      • National Science Foundation China, Beijing.
    • THE UNIVERSITY OF CHICAGO SERVICE:
      • The Dean’s Advisory Committee, Biological Science Division (2009).
      • Faculty Advisory Committee (FAC), Biological Science Division (2014-2017).
      • Committee on Appointments and Promotions (COAP) Committee, Biological Science Division, ad hoc member (2005-2013).
    • EDITORIAL BOARD SERVICE
      • SCIENCE CHINA Life Sciences (Sci China Life Sci), Editorial Board Member (North America Office) (2016-)
      • EMBO Reports, the European Molecular Biology Organization, published by Nature Publishing Group, Advisory Editorial Board (2013-2016; 2017-2010);
      • BMC Genomics, Associate Editor (2012-2016);
      • 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 (Editor, 2008, 2015, 2016, 2018);
      • Journal of Systematics and Evolution (2010-2017);
      • International Journal of Biological Sciences (2011);
      • PLoS Biology (Academic Editor; 2008);
      • Biology Direct (2005-);
      • Journal of Experimental Zoology – B. Developmental and Molecular Evolution (2006-2016).
      • Journal of Systematics and Evolution (2009-2016);
      • Journal of Genetics & Genomics and Hereditas (2005-2011);
      • Genetica and Contemporary Issues in Genetics and Evolution (2002-2003).

 

JOURNAL AND BOOK REVIEWER

 

Biotechniques; BMC Genomics; Cell; Cell Reports; Current Biology; Development; Evolution; EMBO Reports; FASEB Journal; Gene; Genetica; G3; Genetical Research; Genetics; Genome Research; Genome BiologyGenome Biology and Evolution; Journal of Molecular Evolution; Journal of Genomics; Molecular Biology and Evolution; Molecular Ecology; Molecular Genetics and Genomics; Molecular Phylogenetics and Evolution; Nature; Nature Genetics; Nature Methods; Nature Reviews Genetics; Nature Communications; Nature Plants; Nature Ecology & Evolution; Nucleic Acid Research; The Plant Cell; Plant Physiology; PLoS Biology; PLoS Genetics; PLoS Computational Biology; Plant Genome; PNAS; Quarterly Review of Biology; Biological Letters; Proceedings of the Royal Society B; Science; Scientific Reports; Trends in Biotechnology; Trends in Genetics; Genome Biology and Evolution; Mammalian Genome; Progress in Neurobiology.

 

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;
  • International Society of Molecular Evolution.

RESEARCH SUPPORT BY

 

  • National Institute of Health (1R01GM116113-01A1): Multiple PI (09/08/2016 – 08/31/2020).
  • National Institutes of Health (1R01GM100768-01A1): Multiple PI (04/01/2012-03/31/2016)
  • National Science Foundation: PI (2011, Doctoral Dissertation Improvement Grant, Sidi Chen).
  • National Science Foundation (NSF1051826): PI (05/01/2011-04/30/2017).
  • 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 (08/15/2010-07/31/2015, with PI, Rod Wing et al University of Arizona);
  • Edna K. Papazian Distinguished Service Professorship, The University of Chicago (since July 1, 2011).
  • National Institute of Health Grant of NRSA Postdoctoral Fellowship F32 GM109676 (Sponsor, 2014-2016; Trainee: Grace Lee);
  • National Institute of Health Grant of NRSA Postdoctoral Fellowship F32 GM115100-01 (Sponsor, 2015-2016; Trainee: Andrea Gschwend);
  • The Chicago Biomedical Consortium Postdoctoral Research Grant (PI, 2014-2016);
  • 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);
  • 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: PI (2004, Doctoral Dissertation Improvement Grant, JJ Emerson);
  • 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 – 10/31/2008);
  • 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 fellowships)
  • International scholarships (European, South American, and Asian (2003-current).

 

 

MAIN COLLABORATORS

 

Antony Dean (2000-, University of Minnesota), Kevin White (2008-, University of Chicago), Liqun Luo (2008-2012, Stanford University), Liping Wei (2006-, Peking University), Hongya Gu (2008-, Peking University), Jerrold Turner (2008, University of Chicago Medical School),

 

 

Jon Staley (2008, University of Chicago), Steve Pruit-Jones (2013-, University of Chicago), Rod Wing (2010-, University of Arizona Tucson), Bairong Shen (2007-, Suzhou University).

 

STUDENTS / POSTDOCTORAL RESEARCH ASSOCIATES / VISITING SCHOLARS

  • Postdoctoral research associates (Past: 11; Current: 2)
  • Doctorial Graduate students (Past: 12; Current, 4)

 

  • Visiting scientists (Past: 6; Current: 1)
  • Undergraduate research assistants (Past: 15)

 

Doctoral thesis committees (Having served for 23 Ph.D. graduate students e.g. Zhiyue Gao, Rob Arthur, Alice McQueen; Currently, 3: Chun Wai Kwan, Wenhan Chang, Kathleen Beilsmith).

 

Five doctoral students won the distinguished research awards: the best dissertation award at the Committee on Genetics, Genomics and Systems Biology (Kevin Thornton, Hongzheng Dai and Nicholas VanKuren), the university-wide prestigious Harper Fellowship (Roman Arguello) and the best dissertation award at the University of Chicago (Biological Science) 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) and two postdoctoral associates won prestigious NIH postdoctoral Fellowships, National Research Service Award (NRSA), (Grace Lee and Andrea Gschwend). The most of the students/postdocs I trained have been in various stages of successful

 

career development in science, with 12 being tenured or tenure-tracked faculty members (the rank of assistant professors to full professors) in major research universities or institutes in Europe, USA, South America and Asia, e.g. Yale University, University of California, University of Texas, University of Sao Paulo, and Chinese Academy of sciences. Several former doctoral students graduated in recent three years are postdoctoral research fellows in the top research universities in USA and Europe.

 

The former lab members (graduate students, postdoctorial fellows and visiting scholars) who have been faculty members (or rank-equivalent) of research universities:

 

Graduate students and postdoctoral fellows:

  • Esther Betran, Full Professor with Tenure, University of Texas at Arlington, USA
  • Wen Wang, Professor and Director, Northwest Poly-technology University, China
  • Ana Llopart, Associate Professor with Tenure, University of Iowa, USA
  • Frederic Brunet, Research Fellow, Lyon Superior Normal University, France
  • Kevin Thorton, Associate Professor with Tenure, University of California at Irvine, USA
  • Chuanzhu Fan, Assistant Professor in tenure track, Wayne University, USA
  • Yong E Zhang, Professor, Beijing Institute of Zoology, Chinese Academy of Sciences, China
  • Meng-Shin Shiao, Senior Researcher and Vice Dean, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand.
  • JJ Emerson, Associate Professor with tenure, University of California at Irvine, USA
  • Grace Lee, Assistant Professor in tenure track, University of Toronto, Canada
  • Andrea Gschwend, Assistant Professor in tenure track, Ohio State University, USA
  • Roman Arguello, Assistant Professor in tenure track, University of Lausanne, Switzerland
  • Chengjun Zhang, Professor, Institute of Botany, Chinese Academy of Sciences, China
  • Maria Vibranovski, Assistant Professor in tenure track, University of Sao Paulo, Brazil
  • Jianming Zhang, Professor, Shanghai Jiaotong University, Shanghai
  • Soojin Yi, Associate Professor with tenure, Georgia Institute of Technology, USA
  • Zhengxia Chen, Professor, Huazhong Agricultural University, Wuhan, China
  • Sidi Chen, Assistant Professor, Yale University, USA
  • Zhengling Zhu, Associate Professor, Qiongqing University, Qiongqing, China
  • Benyang Liao, Investigator (Professor), Institute of Population Health Sciences, National Health Research Institutes,Taipei
  • Hongzheng Dai, ABMGG Clinical Molecular Genetics & Genomics Fellow, Baylor College of Medicine, USA
  • Ben Krinsky, Senior Science Affairs Officer, Senior Legislative Affairs Officer at Federation of American Societies for Experimental Biology (FASEB), Washington D.C., USA

 

Lists of postdoctoral fellows, graduate students, and visiting scholars (including sabbatical scholars):

 

Postdoctoral fellows:

 

Esther Betran (1999-2003); Wen Wang (1999-2003); Frederic Brunet (1998-2002); Ana Llopart (1999-2001); Ying Chen (2003-2005); Chuanzhu Fan (2004-2007); Maria Vibranovski (2006-2012); Yong Zhang (2007-2011); Claus Kemkemer (2011-2015); Li Zhang (2012-2018); Chengjun Zhang (2012-); Grace Lee (2012-2016); Andrea Gschwend (2012-2017);

 

Graduate students (the vast majority for doctoral degrees)

 

Jianming Zhang (1998-); Kevin Thornton (1999-); Mario Caceras*(2000-); JJ Emerson (2001-); Roman Arguello (2002-); Benyang Liao (2002-)*; James O’Conner (2003-2015); Hongzheng Dai (2003-2009); Mengshin Hsiao (2003-2008); Ying Chen (2003-2009); Sidi Chen (2005-2010); Magarida Moreira-Cardoso (2005-2010); Benjamin krinsky (2009-2015); Patrick Landback (2009-2015); Haiwang Yang (2010-)*; Nick VanKuren (2010-2016); Alexander Advani (2012-); Qian Yang* (2012-); Iuri Ventura (2014-); Unjin Lee (2015-); Zhengling Zhu (2008-)**; Zhengxia Chen (2009-)**; Li Zhang (2007-). (*: part time students from the labs in other Universities); **: trained in the adjunct Changjiang Chair professorship program in the Peking University graduate school, Beijing).

 

Visiting scholars:

    • Shunping He, Professor and director, Museum, Wuhan Institute of Hydrobiology, Chinese Academy of Sciences, China
    • Yidan Ouyang, Professor, Huazhong Agricultural University, China
    • Yuan Huang, Associate Professor, Kunming Normal University, China
    • Robin M. Bush, Associate Professor, University of California at Irvine, USA
    • Hon-Tsen Yu, Professor, National Taiwan University, Taipei
    • Jing Yang, Associate Professor, Central North China University, Taiyuan, China
    • Jian Zu, Associate Professor, Xi’an Jiaotong University, China

 

 

College/High School Lab Training and Interns:

 

Michael Deutsch (Chicago, 1998-); Cutter Makens (Chicago, 1999-); Maia Dorsett (Chicago, 2000-); Megan Noe (Kalamazoo, 2004-); Toshio Yoshimatsu (Chicago, 2006-); Michael Jackson Jr (Chicago, 2008-2009); Warren McCauley (Chicago, 2008-2009); CheeHyurng Park (Chicago, 2008-2010); David Liu (Chicago, 2008 with Sidi Chen); Jason Aerni (Chicago, 2011-); Brandon Amos (Chicago State, 2013-); Jiawei Liu (PKU, 2015-); Dan Downie (UIUC, 2015-2016); Nina Sun (Carmel Middle School, 2012-); Lora Lin (2015-); Yugan Sakthi (IMSA, 2015-); Baihe Yu (Whitney Young, 2015-2016); Emma Litchter (Chicago, 2017-)

 

 

TEACHING

 

 

 

Undergraduate courses:

 

  • The Chicago curriculum “Big Problems” series:
  • BP29100/BioSci 29319: What Do The Genomes Teach Us About Evolution? (Spring, 2009-2012, with James Shapiro)
  • 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).
  • Undergraduate round-table research meetings.

 

 

Graduate courses:

 

  • ECEV36100, Genetic Networks in Molecular Evolution: Theories and Empirical Data (2014, Spring; 2016).
  • ECEV35901, Genomic Evolution: New Gene Problems (2013, Fall)
  • ECEV35901, Genomic Evolution: The Underlying Networks (2016, Fall; with Stefano Allesina and Chung-I Wu. Drs. Jian Zu and Nick vanKuren each gave one lecture).
  • ECEV35901, Genomic Evolution: Problems and Approaches (2017, Fall; with Chung-I Wu)
  • EE35900, Genomic Evolution (Since Spring 1998, odd years, with Martin Kreitman, until 2016; with John Reinitz, since 2014 Autumn);
  • EE35800, Classics of Evolutionary Genetics (Since Winter 1998, until 2017. Participating in various years: Marty Kreitman, Wenhsiung Li, Richard Hudson, Chung-I Wu and John Reinitz).
  • Reading Courses: EE497, Evolutionary Biology and History of Evolutionary Biology.

 

 

WITHIN-CAMPUS ADMINISTRATIVE SERVICE

 

  • BSD Faculty Advisory Committee, 2014-2017.
  • BSD Faculty Science Review Committee, 2009.
  • Committee on Appointments and Promotions (COAP), Division of Biological Sciences, Ad Hoc;
  • 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; 2009-2011);
  • EE Committee for organizing the departmental seminars (1998 – 2000;2002 – 2003; 2011- 2012);
  • COG (Committee on Genetics) Admission Committee (1999 -- 2000).
  • Faculty review committee to select the candidates to represent the University of Chicago for nomination for the 2016 Packard Foundation Fellowships in Science and Engineering. (2016).
  • Admission Committee, the Committee on Genetics, Genomics and Systems Biology. 2016-2017.

 

 

OTHER HONORARY APPOINTMENTS

 

2016 Advisory Board member, International Conferences of Genomics, Beijing Genome Institute at Shenzhen (BGI-Shenzhen).

2016-2018 International member, Teaching Reform Committee, Biology, Zhiyuan College, Shanghai Jiaotong University, 2015-2016.

2015 Organizer, International Symposium of Molecular Population Genetics and Evolution: Genes, Genomes and Models, Genetics Society of America and the University of California at Davis, Asilomar, Montery, California.

2013 Organizing Committee of the National Institute of Genetics, Japan/SMBE international meeting in Mishima, Japan, “Causes of Genome Evolution”.

2013- External Advisory Board, School of Life Sciences, Peking University, Beijing.

2011 Co-organizer, the symposium of Gene Evolution and Phenotypic Evolution, the

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, the 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 Chair, the 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 Professorship, 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 Organizer, 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.

20004 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, Taiwan, the Republic of China.

1999-2000 The 8th and 9th SCBA international symposia of molecular evolution (Hong Kong.

1999; Taipei, 2000), co-chair.

 

 

PUBLICATIONS

 

  1. Ming, D. and Long, M. 1985. Mathematical principle and application of canonical correlation to quantitative genetic analysis. J. of Sichuan Agri. Univ. 3: 250-255.

 

  1. Long, M. 1985. A new method to measure the kernel volume of maize (Zea mays, L.). J. of Sichuan Agri. Univ. 3: 415-420.

 

  1. Long, M. 1986. On the application of fuzzy clustering to genetic analysis. J. of Sichuan Agri. Univ. 4: 239-247.

 

  1. 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) (Hunnan 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 – 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., 1992. The origin and evolutionary mechanism of new genes. Ph.D. thesis. University of California at Davis.

 

12. Long, M., C. H. Langley 1993. Natural selection and the origin of jingwei, a chimeric processed functional gene in Drosophila Science  260: 91-95.

 

13.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.

 

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

 

15. 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.

 

16. 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.

 

 

17. 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.

 

18. DeSouza, S. J., M. Long, and W. Gilbert 1996. Introns and gene evolution. Genes to Cells 1: 493-505.

 

19. Richter, B., M. Long, R. C. Lewontin, E. Nitasaka 1997. Nucleotide polymorphism and evolution of the decapentaplegic gene in Drosophila Genetics 145: 311-323.

 

20. Long, M., S.J. De Souza, W. Gilbert 1997. Delta-interacting protein A and the origin of hepatitis delta antigen. Science  276: 824-825.

 

21. Gilbert, W., S.J. De Souza, M. Long 1997. Origin of genes. Proc. Natl. Acad. Sci. USA 94: 7698-7703.

 

22. 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.

 

23. 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.

 

24. 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.

 

25. 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.

 

26. 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.

 

27. 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.

 

28. 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.

 

29. Deutsch, M. and M. Long 1999. Intron-exon structures of model organisms. Nucl. Acid Research 27: 3219-3228.

 

30. Cáceres, 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.

 

31. Sakharkar,M., M. Long, T. W. Tan, S. J. De Souza 2000. ExInt-an Exon/Intron database. Nucl. Acid Research 28: 191-192.

 

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

 

33. 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. melanogaster. Mol. Biol. Evol. 17:1294-1301.

 

34. 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.

 

35. Long, M. 2000. A new function evolved from gene fusion. Genome Research 10: 1655-1657.

 

36. 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.

 

37. 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.

 

38. Létitia J., M. Long, J. Young, P. Péry, F. Tomley 2001. AP genes from apicomplexan parasites: Evidence for evolution of the gene structure.  Trends Paras. 17: 491-498.

 

39. Long, M., K. Thornton 2001. Gene duplication and evolution.  Science 293:1551.

 

40. Long, M. 2001. Evolution of novel genes.  Curr Opin Genet Dev 11:673-680.

 

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

 

42. Long, M. 2002. Pseudoexons. Encyclopaedia of the Human Genome, Macmillan Reference Ltd, London.

 

43. Wang, W., K. Thornton, A. Berry, and M. Long. 2002. Nucleotide variation along the Drosophila melanogaster fourth chromosome. Science 295:134-137. (Highlighted by Nature Rev Genet (Vol. 3(3): 158).

 

44. 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.

 

45. Betrán E., M. Long 2002. Expansion of genome coding regions by acquisition of new genes. Genetica 115: 65-80.

 

46. Betrán, 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.

 

47. Thornton, K., M. Long 2002. Rapid divergence of gene duplicates on the Drosophila X chromosome. Mol. Biol. Evol. 19: 918-925.

 

48. Betrán, E., K. Thornton, and M. Long 2002. Retroposed new genes out of the X in Drosophila Genome Research. 12: 1854-1859.

 

 

49. 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.

 

50. 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.

 

51. Betran, E., M. Long 2003. Dntf-2r, a young Drosophila retroposed gene with specific male expression under positive Darwinian selection. Genetics 164: 977-988

 

52. Long, M., M. Deutsch, W. Wang, E. Betrán, F. Brunet, J. Zhang 2003. Origin of new  genes: Results from experimental and computational analysis. Genetica 118: 171-182.

 

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

 

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

 

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

 

56. 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.

 

57. Emerson J.J.*, H. Kaesmann*, E. Betrán and M. Long 2004. Extensive gene traffic on the human X chromosome. Science 303: 537-540. (*Equal contribution). (Highlighted by Nature Rev Genet (Vol. 5(3):164).

 

58. Wang, W., H. Yu and M. Long 2004. Duplication-degeneration as a mechanism of gene fission and the origin of Drosophila new genes. NatureGenetics 36: 523 – 527.

 

59. 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.

 

60. Betrán, 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.

 

61. International Chick Genome Sequencing Consortium (the Long lab as a consortium member), 2004. Sequencing and comparative analysis of the chicken genome. Nature 432: 432:695-716.

 

62. 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.

 

63. 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.

 

64. 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.

 

65. 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.

 

66. Dai H, Yoshimatsu TF, Long M, 2007. 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.

 

67. Arguello JR, Fan C, Wang W and Long M (2007). Origination of Chimeric Genes through

DNA-level Recombination. Genome Dynamics: Evolution of Gene Functions. Karger publishers. 3: 131-146.

 

 

68. Fan C and Long M, 2007. A New Retroposed Gene in Drosophila Heterochromatin Detected by Microarray-Based Comparative Genomic Hybridization. J Mol Evol 64:272-283.

 

69. 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.

 

70. 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.

 

71. 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.

 

72. 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.

 

73. 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.

 

74. Long M., 2007. Journal Club: Mystery Genes. Nature 449: 511.

 

75. Arguello JR, Fan C, Wang W, and Long M, 2007. Origination of Chimeric Genes through DNA-level Recombination. Genome Dynamics 3: 131-146.

 

76. Drosophila 12 Genomes Consortium (the Long lab as a consortium member), 2007. Evolution of genes and genomes on the Drosophila phylogeny. Nature 450: 203-218.

 

77. 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.

 

78. 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

 

79. 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.

 

80. Long M, 2007. Side effects of Tamiflu: clues from an Asian single nucleotide polymorphism. Cell Research 17: 309-310.

 

81. 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.

 

82. 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.

 

 

83. 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.

 

84. Fan C, Zhang Y, Yu YS, Rounsley S, Long M, and Rod A, 2008. The Subtelomere of Oryza sativa Chromosome 3 Short Arm as a Hot Bed of New Gene Origination in Rice. Molecular Plant 1: 839-850.

 

85. Dai H, Chen Y, Chen S, Mao Q, Kennedy D, Landback P, Eyre-Walker A, Du D, Long M, 2008. The evolution of courtship behaviors through the origination of a new gene in Drosophila. Proc Natl Acad Sci USA. 105:7478-83.

 

86. 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. (* Equally contributed.) (Highlighted by Nature Rev Genet (Vol. 9(7): 497)).

 

87. 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.

 

88. 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.

 

89. Vibranovski MD, Zhang Y, Long M, 2009. General gene movement off the X chromosome in the Drosophila genus. Genome Research 19: 897-903.

 

90. Kaessmann H, Vinckenbosch N, and Long M, 2009. RNA-based gene duplication. Nature Reviews Genetics 10: 19-31.

 

91. 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.

 

92. Li Z, Liu M, Zhang L, Zhang WX, Gao G, Zhu Z, Wei LP, Fan Q, Long M, 2009. Detection of intergenic non-coding RNAs Expressed in the main developmental stages in Drosophila melanogaster Nucleic Acids Research 37:4308-4314.

 

93. Zhu ZL, Zhang Y, and Long M, 2009. Structural Renovation of Retrogenes in Populus. Plant Physiology 151:1943-1951.

 

94. 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.

 

95. 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.

 

96. 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.

 

97. Raleigh DR, Marchiando AM, Zhang Y, Shen L, Sasaki H, Wang YM, Long M, Turner JR, 2010. Tissue Junction-associated MARVEL proteins marvelD3, tricellulin and occludin have distinct, but overlapping, functions. Mol Biol Cell 21: 1200-1213.

 

98. 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.

 

99. Vibranovski MD*, Chalopin DS*, Lopes HF, Long M, Karr TL, 2010. Genome wide postmeiotic transcription in Drosophila melanogaster. Genetics. 186: 431 – 433. (* Equally contributed).

 

100. 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.

 

101. 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.

 

102. 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.

 

103. 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.

 

104. Chen S, Zhang Y, and Long M, 2010. New genes in Drosophila quickly become essential. Science 330: 1682-1685. Highlighted by Nature Rev Genet (Vol. 12(1):79) and Bioessay (March 28, 2012).

105. 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.

 

106. 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.

 

107. 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.

 

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

 

109. Zhang CJ, Wang J, Xie WB, Zhou G, Long M*, Zhang QF* (*co-corresponding authors), 2011. A dynamic programming procedure for searching optimal models estimate substitution rates based on the maximum-likelihood method. Proc Natl Acad Sci USA, 108:7860-7865.

 

110. Zhang YE, Landback P, Vibranovski MD, Long M, 2011. Accelerated recruitment of new brain development genes into the human genome. PLoS Biology 9(10): e1001179.

(Highlighted by Nature Rev Genet (Vol. 12 (12): 805), Science (Vol 334 (6056): 570), Bioessay (March 28, 2012), Brain, Behavior and Evolution (March 6, 2012))

 

111. 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.

 

112. 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.

 

113. 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

 

114. Wang J, Long M and Vibranovski MD, 2012. Retrogenes Moved Out of the Z Chromosome in the Silkworm. J Mol Evol 74: 113-126.

 

115. 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.

 

116. 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.

 

117. 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.

 

118. 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 Evolutionary Biology 12: 169.

 

119. Zhang YE, Landback P, Vibranovski M, Long M, 2012. New genes expressed in human brains: Implications for annotating evolving genomes. BioEssays 34(11): 982-991.

 

120. Long M, 2013. The Evolution of New Genes. In. Losos JB,editor in chief; Hoekstra H &  Peichel C, section editors, Princeton Guide to Evolution. Princeton University Press, Princeton, NJ.

 

121. 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.

 

122. 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 10(11): e1001420.

 

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

 

124. 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.

 

125. Long M, VanKuren N, Chen SD, Vibranovski M, 2013. New Gene Evolution: Little Did We Know. Annual Review of Genetics 47: 325-351.

 

126. Chen SD, Krinsky B, Long M, 2013. New genes as drivers of phenotypic evolution. Nature Reviews Genetics 14 (9): 645-660.

 

127. Zhang CJ, Wang J, Long M and Fan C, 2013. gKaKs: the pipeline for genome level Ka/Ks calculation. Bioinformatics Published online January 12, 2013.

 

128. Zhang CJ, Wang J, Marowsky NC, Long M, Wing R and Fan CZ, 2013. High Occurrence of Functional New Chimeric Genes in Survey of Rice Chromosome 3 Short Arm Genome Sequences. Genome Biol Evol. Published online May 7, 2013. 5:1038-1048.

 

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

 

 

130. Long M, 2014. Evolution of New Genes. In Losos JB, editor-in-chief, Oxford Bibliographies in Evolutionary Biology. Oxford University Press.

 

131. Kemkemer C, Long M, 2014. Opinion: New genes important for development. EMBO Reports. Published online April 10, 2014. DOI: 10.1002/embr.201438787

 

132. Zhang C, Gschwend AR, Ouyang Y and Long M, 2014. Evolution of gene structural complexity: An alternative-splicing based model accounts for intron-containing retrogenes. Plant Physiology 165: 412-423.

 

133. Gao G, Vibranovski MD, Zhang L, Li Z, Liu M, Zhang YE, Li X, Zhang W, Fan Q, VanKuren NW, Long M, Wei L, 2014. A long term demasculinization of X-linked intergenic noncoding RNAs in Drosophila melanogaster. Genome Research 24: 629–638.

 

134. Wang M, Yu Y, Haberer G, Marri PR, Fan C, Goicoechea JL, Zuccolo A, Song X, Kudrna D, Ammiraju JS, Cossu RM, Maldonado C, Chen JF, Lee S, Sisneros N, de Baynast K, Golser W, Wissotski M, Kim W, Sanchez P, Ndjiondjop M-N, Sanni K, Long M, Carney J, Panaud O, Wicker T, Machado CA, Chen M, Mayer K, Rounsley S & Wing RA, 2014. The genome of African rice (Oryza glaberrima): Evidence for independent domestication. Nature Genetics Published online 27 July 2014, doi:10.1038/ng.3044. 46: 982–988.

 

135. Zhang Y and Long M, 2014. New genes contribute to genetic and phenotypic novelties in human evolution. Curr Opin Genet Dev 29: 90–96.

 

136. Zhang C, Li Zhang L, Gschwend AR, Song X, Chougule K, Wang M, Dario Copetti D, Long M and Wing RA, 2014. Gene Fusion as an Important Mechanism to Generate New

Genes in the Oryza Genomes. (A Special Volume for Oryza Genome Evolution for Genome Research, submitted).

 

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

 

138. Ventura IM and Long M, 2015. Connecting evolutionary genomics to cell biology. The Encyclopedia of Cell Biology. Elsevier, 153-159. 

 

139. Vibranovski M and Long M, 2016. Origination and Evolution of Genes on the Sex Chromosomes. In: ed. Kliman RM, The Encyclopedia of Evolutionary Biology. Elsevier. PP 117-126.

 

140. Zhang C, Zhang L, Wing R and Long M, 2018. High rate of gene recombination in Oryza genome. (submitted)

 

141. Tan S, Cardoso-Moreira M, Shi W, Zhang D, Huang J, Mao Y, Jia H, Zhang Y, Liu Z, Huang X, Long M, Zhang YE, 2016. LTR-mediated retroposition as a mechanism of RNA-based duplication in metazoans. Genome Research 26:1663–1675 .

 

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

 

143. Huang Y, Ouyang YD, Fan C, Li DZ, Bergelson J, and Long M, 2015. A young gene in Arabidopsis thaliana evolved strong phenotypic effects on morphological traits under positive selection. (Commissioned by Molecular Plants).

 

144. Zhang L, Ren Y, Yang T, Li G, Chen J, Gschwend AR, Yu Y, Hou G, Zi J, Zhou R, Wen B, Zhang J, Chougule K, Wang M, Copetti D, Jin G, Peng Z, Zhang C, Ouyang Y, Wing RA, Liu S, Long M, 2017. Rapid evolution of protein diversity by de novo origination in Oryza. Submitted.

 

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

 

146. VanKuren NW and Long M, 2018. Drosophila melanogaster-specific genes rapidly became essential for fly development. (submitted).

 

147. Luo M, Zhao X, Sheng Y , Min J, Bai M, Yang Y, Cheng Y, He C, Chen F, Li Z, Liu J, Huang C, Jian J, Xu M, Li X, Wang Y, Ming Y,  Hu Z, Shi Q, Gao Q,  Fang X, Zhong P, Yu C, Zhang L, Long M, Wang J, Cheng H, Zhou R, 2017. Developmental activation of male through Z1Z2 sex chromosome system. (Submitted).

 

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

 

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

 

150. Gschwend AR, Mihaljevic J, VanKuren N, Allesina S, Pruett-Jones S, Long M, 2018. Newly evolved genes play important roles in male and female reproductive fitness in Drosophila melanogaster. (to be Submitted)

 

151. Zhang L, Gschwend A, Wing R and Long M, 2017. Rapid gene evolution driven by adaptation and domestication in Oryza. Submitted.

 

152. VanKuren NW and Long M, 2018. Gene duplicates resolving sexual conflict rapidly evolved essential gametogenesis functions. Nature Ecology & Evolution 2(4):705-712. doi: 10.1038/s41559-018-0471-0. Epub 2018 Feb 19, with a News & Views commentary in the same issue.

 

153. VanKuren NW and Long M, 2017. Behind the paper: Species-specific duplicate genes help resolve sexual conflict while evolving essential Nature Ecology & Evolution Community. https://natureecoevocommunity.nature.com/users/81959-nicholas-vankuren.

 

154. Zhang L, Gschwend AR, Wing RA and Long M, 2018. Rapid gene evolution driven by adaptation and domestication in Oryza. Submitted to Nature Plants.

 

155. Lee G, Ventura IM, Rice GR, Chen D, Long M, 2018. Rapid evolution of gained essential developmental functions of a young gene via interactions with other essential genes. Reviewed and invited to revise by PNAS.

 

156. VanKuren NW, Chen C, Xia S, Shao Y, Vibranovski M, Chen S, Zhang Y and Long M, 2018. Complement Knockdown and Knockout: Evolutionary Roles of New Essential Genes Revisited. Submitted to Genes & Development

 

 

 

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.

 

Gilbert W and Long M, 2018. Walter Gilbert: Selected Works. The Nobel Prize Laureates series by the World Scientific, Singapore. 650 pages.

 

Long M and Shen B ed. 2018. Evolution of Genes and Genomes. Science China Life Science, Beijing.

 

 

 

INVITED SEMINARS/LECTURES

 

(250 seminars, lectures, and talks until 2018 in major scientific research institutes and universities in western countries and China).

 

 

2018 Fralin Life Science Institute, Virginia Tech, Blacksburg; School of Life Sciences, Peing University, 07/16-07/22, Beijing; Department of Biological Sciences Molecular, Cell and Developmental Biology, University of Illinois at Chicago, Chicago, 04/10; First Asian Conference of Evolutionary Biology (AsiaEvo 1), Shenzhen, China, 04/18-20; Institute of Systems Biology, Suzhou University, 03/12-15, Suzhou; International Symposium of Evolution of Genes and Genomes, Science China Biological Sciences and West China School of Medicine of Sichuan University, Chengdu, 04/22-04/26; School of Biological Sciences, Zhejiang University, Hangzhou, China, 05/29-05/31; Amazon Valley Expedition of Biological Diversity, Brazilian Federal University of Natal, Belem, Brazil 07/03-07/06; The 8th National Conference of Bioinformatics and Systems Biology, Aomen/Macau, 10/22-10/24; International Conference on Bioinformatics and Systems Biology (BSB-2018), the center of excellence in Information Technology, Government of India, Allahabad, 10/26-10/28.

 

2017 – School of Applied Mathematics and Statistics, Xi’an Jiaotong University, 11/15/17; Institute of Frontiers of Life Science, Northwest University, Xi’an, 11/13/17; The School Lecture, School of Life Sciences, Northwest University, Xi’an, 11/14/17; Michigan State University, the Annual Research Conference Keynote Seminar, The graduate program of

Ecology, Evolutionary Biology, and Behavior (EEBB), East Lansing, 05/01-05/02; Symposium of Systems Biology, Natal, Brazil (05/30-06/03); Department of Genetics and Evolutionary Biology, University of Sao Paulo, Sao Paulo, Brazil, 05/28-05/29; Gordon Research Conference of Molecular Mechanisms in Evolution, Stonehill College, Easton, Massachusetts, 06/11/-06/16; School of Life Sciences, Peking University, Beijing, Summer school lectures, Logics of Life; Hydrobiology Research Institute, CAS, China, 01/02-01/07; Qiushi Advanced Undergraduate Program, Zhejiang University, Hangzhou, 04/15-04/17; The Second Oceanographic Research Institute, Hangzhou, 04/17; West China Medical

School, Chengdu, 05/05-05/10; School of Life Sciences, Sichuan University, Chengdu, 05/10; The 4th International Conference of Geobiology, Wuhan, 06/24-06/26; Institute of Vertebrate Paleontology and Paleoanthropology, CAS, Beijing, summer seminar; Zhiyuan College, Shanghai Jiaotong University, Shanghai, 03/04-03/17; Institute of Hydrobiology, CAS, Wuhan, 01/06-01/08. Annual Conference of Precision Medicine, West China Medical School, Chengdu, 09/xx.

 

2016 – Symposium of Sex determination and evolution, the XXIV Conference of Plant and Animal Genomes, San Diego, 01/10; Departments of Crop Science and Plant Biology, University of Illinois Urbana, 04/13; The 1866th Biological Symposium, National Institute of Genetics, Mishima, Japan, 03/04; Department of Biology, Faculty of Science, Kyushu University, Fukuoka, Japan, 03/08; Department of Evolutionary Biology, Graduate University for Advanced Studies, (SOKENDAI), Hayama, Japan, 03/09; Bioengineering and Bioinformatics, Graduate School of Information Science and Technology, University of Hokkaido, Sapporo, Japan, 03/10; Seminar, National Institute of Genetics, 03/11; Departments of Plant Biology and Crop Sciences, University of Illinois at Urbana-Champaign, 04/13; School of Life Sciences and Bioengineering, Beijing Jiaotong University,

04/22; Institute of Applied Mathematics and Systems Sciences, CAS, Beijing; School of Biological Sciences, Fudan University, 06/01; Institute of Biological Medical Engineering, Chinese Academy of Science, 05/27; School of Life Sciences, Northwest University, Xi’an,

 

06/21; Institute of Molecular Ecology, Lanzhou University, 06/22; School of Life Sciences, Lanzhou University, Lanzhou, 06/23; Northwest Normal University, Lanzhou, 06/24; School of Life Science, Huazhong Agricultural University, Wuhan, 08/13; School of Animal Sciences, Huazhong Agricultural University, Wuhan, 08/14; School of Life Science,

Xingjiang University, Urumqi, 08/16; School of Life Science, Xingjiang Normal University, Urumqi, 08/16; Symposium of Systems Biology,10th International BGRS Multiconference 2016, Institute of Cytology and Genetics, Novosibirsk, Russia, 08/29-09/02; Laval

University, Quebec City, Canada, 09/22; the 11th Annual International Conference on Genomics (ICG-11), Beijing Genome Institute, Shenzhen, 11/03-11/06; CoyneFest: the symposium in honor of Jerry Coyne, the University of Chicago, Chicago, 11/14-11/15; School of Life Sciences, Peking University, 12/16; Graduate School, Chinese Academy of Agricultural Sciences, Beijing.

 

2015 – Department of Biology, Indiana State University, Terre Haute; Department of Biological Sciences, University of Wisconsin, Milwaukee; Schools of Medicine and Arts and Sciences, Johns Hopkins University; Institute of Biology, Chinese Academy of Sciences (CAS),

Chengdu; Marine Biology Laboratories, Woods Hole, Massachusetts; Shanghai Institute of Technology (ShanghaiTech), Shanghai; Systems Biological Laboratories, Institutes of Life

Sciences, CAS, Shanghai; Institute of Zoology, CAS, Beijing; School of Biological Sciences, Wuhan University; National Institute of Genetics, Mishima, Japan; International

Symposium of Molecular Population Genetics and Evolution: Genes, Genomes and Models, Genetics Society of America and the University of California at Davis, Asilomar, Montery, California; School of Mathematics and Statistics, Xi-An Jiaotong University, Xi-An; FAFU

Summer & Symposium on Plant Biology, Lecture for Summer Classes, Fujian Agricultural & Forestry University, Fuzhou; FAFU Summer & Symposium on Plant Biology, Symposium, Fujian Agricultural & Forestry University, Fuzhou; Special session 1 of Chinese Conference of Complex Networks (CCCN) 2015, the 8th  

International Congress on Industrial and Applied Mathematics, Beijing; The Conference of Genomics and its Application to the Plant and Animal Breeding, Chengdu; The School of

Life Sciences, Zhejiang University, Hangzhou; The Second Institute of Oceangraphy, Hangzhou.

 

2014 – Centre of Social Evolution, University of Copenhagen, Denmark; The Theory Lunch, Department of Systems Biology, Harvard Medical School; The 9th Genomic Conference,

BGI, Shenzhen; Modern Insights into Evolutionary Genetics, Training Program in Genetics, the University of Michigan, Ann Arbor; Center of Computational Biology, the University of Toledo, Toledo, Ohio; the 18th Evolutionary Biology Meeting, Marseille, the Association for the Study of Biology Evolution; Symposium for The Causes of Genome Evolution, Society of Molecular Biology and Evolution, Mishima, Japan; the 1738th Biological Symposium seminar, National Institute of Genetics, Mishima, Japan; Kunming Botany Institute, Kunming, Chinese Academy of Sciences; Undergraduate Lecture, Qinghua

University, Bejing; Integration of Molecular Genetics and Paleontology, Xiangshan Scientific Meeting, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese

Academy of Science, Beijing; The Zhiyuan College, Shanghai Jiao Tong University; The Cold Spring Harbor Conference Asia-Evolutionary Genetics and Genomics, Suzhou, Cold

 

 

Spring Harbor Laboratory; Bioinformatics and Proteomics/Genomics Program, The University of Toledo.

 

2013 – Department of Molecular, Cellular and Developmental Biology, Yale University; Institute of Biochemistry and Cellular Biology, Shanghai; School of Life Science, Shanghai

Jiaotong University; Graduate student-invited talk, Molecular Cluster Retreat, the University of Chicago, Galena, Illinois; International Conference of Bioinformatics and

Systems Biology and Translational Studies, Taicang, Suzhou; STEM (Science/Math), Global Citizenship Experience, Chicago; Graduate School of Life Science, Chinese Academy of Science, Shanghai; 2013 International Symposium on Evolutionary Genomics

and Bioinformatics, Taichung, Taiwan; Institute of Biological Diversity Graduate Program,

Academia Sinica, Nankang, Taiwan; The Mini-Symposium on Conservation Biology, Ecology & Biological Evolution, College of Life Sciences, Peking University; Minilecture series of New Gene Evolution to graduate students, College of Life Sciences, Peking University.

 

2012 – 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; International Symposium of Copy Number Variation at the 23rd Annual

Conference of Society of Molecular Biology and Evolution, 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; International Symposium of Genetics Development & Evolution, Institute of Zoology, Kunmin; Graduate Student Seminar, Ecology Evolution & Population Biology,

Washington University, St. Louis; Public lecture: The meanings of evolution and the origins of genes, the University Library, Beijing Normal University; Phenopic Evolution by New Gene Origination, Institute of Vertebrate Paleontology and Paleoanthropology, Beijing.

 

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 conferenceof the Genetics Society of Canada, Hamilton, Canada; Symposium of Gene and

GenomeDuplication, The 2010 Annual SMBE conference, Lyon, France; Institute of Bioinformatics, Department of Genetics, North Carolina State University, Raleigh; The

University of ChicagoBeijing 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; Darwin 200 International Beijing conference, Beijing.

 

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, Shanghai; 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, Shanghai; University of Missouri; University of Maryland; Sichuan Agricultural University.

 

1993 – The Society of Chinese Biologists conference, University of Maryland, Baltimore.