Manyuan Long

Manyuan Long

UNVERIFIED PROFILE

Are you Manyuan Long?   Register this Author

Register author
Manyuan Long

Manyuan Long

Publications by authors named "Manyuan Long"

Are you Manyuan Long?   Register this Author

90Publications

1035Reads

14Profile Views

Evolutionary dynamics of abundant 7 bp satellites in the genome of Drosophila virilis.

Mol Biol Evol 2020 Jan 21. Epub 2020 Jan 21.

Department of Molecular Biology and Genetics, Cornell University, Ithaca, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/molbev/msaa010DOI Listing
January 2020

GenTree, an integrated resource for analyzing the evolution and function of primate-specific coding genes.

Genome Res 2019 04 12;29(4):682-696. Epub 2019 Mar 12.

Key Laboratory of Zoological Systematics and Evolution and State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1101/gr.238733.118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6442393PMC
April 2019

Topological evolution of coexpression networks by new gene integration maintains the hierarchical and modular structures in human ancestors.

Sci China Life Sci 2019 Apr 21;62(4):594-608. Epub 2019 Mar 21.

Department of Ecology and Evolution, The University of Chicago, Chicago, Illinois, 60637, USA.

View Article

Download full-text PDF

Source
http://link.springer.com/10.1007/s11427-019-9483-6
Publisher Site
http://dx.doi.org/10.1007/s11427-019-9483-6DOI Listing
April 2019

Origination and evolution of orphan genes and de novo genes in the genome of Caenorhabditis elegans.

Sci China Life Sci 2019 Apr 21;62(4):579-593. Epub 2019 Mar 21.

Institutes for Systems Genetics, West China Hospital, Sichuan University, Chengdu, 610041, China.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/s11427-019-9482-0DOI Listing
April 2019

Evolution of genes and genomes: an emerging paradigm in life science.

Sci China Life Sci 2019 04 16;62(4):435-436. Epub 2019 Apr 16.

Institutes for Systems Genetics, West China Hospital, Sichuan University, Chengdu, 610041, China.

View Article

Download full-text PDF

Source
http://link.springer.com/10.1007/s11427-018-9448-x
Publisher Site
http://dx.doi.org/10.1007/s11427-018-9448-xDOI Listing
April 2019

Dissection of patulin biosynthesis, spatial control and regulation mechanism in Penicillium expansum.

Environ Microbiol 2019 Mar 6;21(3):1124-1139. Epub 2019 Mar 6.

Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.

View Article

Download full-text PDF

Source
http://doi.wiley.com/10.1111/1462-2920.14542
Publisher Site
http://dx.doi.org/10.1111/1462-2920.14542DOI Listing
March 2019

Gene duplicates resolving sexual conflict rapidly evolved essential gametogenesis functions.

Nat Ecol Evol 2018 04 19;2(4):705-712. Epub 2018 Feb 19.

Department of Ecology and Evolution, The University of Chicago, Chicago, IL, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41559-018-0471-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5866764PMC
April 2018

Meiotic Sex Chromosome Inactivation: Compensation by Gene Traffic.

Curr Biol 2017 07;27(13):R659-R661

Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697, USA; Center for Complex Biological Systems, University of California, Irvine, Irvine, CA 92697, USA. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.cub.2017.05.077DOI Listing
July 2017

LTR-mediated retroposition as a mechanism of RNA-based duplication in metazoans.

Genome Res 2016 12 20;26(12):1663-1675. Epub 2016 Oct 20.

Key Laboratory of Zoological Systematics and Evolution and State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1101/gr.204925.116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5131818PMC
December 2016

New genes drive the evolution of gene interaction networks in the human and mouse genomes.

Genome Biol 2015 Oct 1;16:202. Epub 2015 Oct 1.

Department of Ecology and Evolution, The University of Chicago, Chicago, IL, 60637, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s13059-015-0772-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4590697PMC
October 2015

New genes contribute to genetic and phenotypic novelties in human evolution.

Curr Opin Genet Dev 2014 Dec 16;29:90-6. Epub 2014 Sep 16.

Department of Ecology and Evolution, The University of Chicago, Chicago, USA. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.gde.2014.08.013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4631527PMC
December 2014

Evolution of gene structural complexity: an alternative-splicing-based model accounts for intron-containing retrogenes.

Plant Physiol 2014 May 11;165(1):412-23. Epub 2014 Feb 11.

Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1104/pp.113.231696DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4012599PMC
May 2014

New genes important for development.

EMBO Rep 2014 May 10;15(5):460-1. Epub 2014 Apr 10.

Department of Ecology and Evolution, The University of Chicago, Chicago, IL, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1002/embr.201438787DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4210085PMC
May 2014

New gene evolution: little did we know.

Annu Rev Genet 2013 13;47:307-33. Epub 2013 Sep 13.

Department of Ecology and Evolution, The University of Chicago, Chicago, Illinois 60637; email:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1146/annurev-genet-111212-133301DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4281893PMC
April 2014

A long-term demasculinization of X-linked intergenic noncoding RNAs in Drosophila melanogaster.

Genome Res 2014 04 9;24(4):629-38. Epub 2014 Jan 9.

State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences and Center for Bioinformatics, Peking University, Beijing 100871, China;

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1101/gr.165837.113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3975062PMC
April 2014

Roles of young serine-endopeptidase genes in survival and reproduction revealed rapid evolution of phenotypic effects at adult stages.

Fly (Austin) 2011 Oct-Dec;5(4):345-51. Epub 2011 Oct 1.

Department of Biology, and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.4161/fly.5.4.17808DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3266076PMC
January 2014

New genes as drivers of phenotypic evolution.

Nat Rev Genet 2013 Sep;14(9):645-60

1] Department of Ecology and Evolution, The University of Chicago, 1101 East 57th Street, Chicago, Illinois 60637, USA. [2] Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nrg3521DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4236023PMC
September 2013

Adaptive evolution and the birth of CTCF binding sites in the Drosophila genome.

PLoS Biol 2012 6;10(11):e1001420. Epub 2012 Nov 6.

Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pbio.1001420DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3491045PMC
April 2013

gKaKs: the pipeline for genome-level Ka/Ks calculation.

Bioinformatics 2013 Mar 12;29(5):645-6. Epub 2013 Jan 12.

Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA.

View Article

Download full-text PDF

Source
http://bioinformatics.oxfordjournals.org/content/29/5/645.fu
Web Search
http://bioinformatics.oxfordjournals.org/cgi/doi/10.1093/bio
Publisher Site
http://dx.doi.org/10.1093/bioinformatics/btt009DOI Listing
March 2013

New genes expressed in human brains: implications for annotating evolving genomes.

Bioessays 2012 Nov 24;34(11):982-91. Epub 2012 Sep 24.

Key Laboratory of the Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, P.R. China.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1002/bies.201200008DOI Listing
November 2012

Why rodent pseudogenes refuse to retire.

Genome Biol 2012 Nov 20;13(11):178. Epub 2012 Nov 20.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/gb4060DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3580489PMC
November 2012

The origin and evolution of new genes.

Methods Mol Biol 2012 ;856:161-86

Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/978-1-61779-585-5_7DOI Listing
July 2012

Retrogenes moved out of the z chromosome in the silkworm.

J Mol Evol 2012 Apr 26;74(3-4):113-26. Epub 2012 Apr 26.

Department of Ecology and Evolution, The University of Chicago, Chicago, IL 60637, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/s00239-012-9499-yDOI Listing
April 2012

Frequent recent origination of brain genes shaped the evolution of foraging behavior in Drosophila.

Cell Rep 2012 Feb 16;1(2):118-32. Epub 2012 Feb 16.

Department of Ecology and Evolution, The University of Chicago, Chicago, IL 60637, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.celrep.2011.12.010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4382513PMC
February 2012

Evolutionary patterns of RNA-based duplication in non-mammalian chordates.

PLoS One 2011 11;6(7):e21466. Epub 2011 Jul 11.

Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, People's Republic of China.

View Article

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0021466PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3136929PMC
November 2011

Drosophila duplication hotspots are associated with late-replicating regions of the genome.

PLoS Genet 2011 Nov 3;7(11):e1002340. Epub 2011 Nov 3.

Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pgen.1002340DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3207856PMC
November 2011

Deficiency of X-linked inverted duplicates with male-biased expression and the underlying evolutionary mechanisms in the Drosophila genome.

Mol Biol Evol 2011 Oct 5;28(10):2823-32. Epub 2011 May 5.

Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, PR China.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/molbev/msr101DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3176832PMC
October 2011

Accelerated recruitment of new brain development genes into the human genome.

PLoS Biol 2011 Oct 18;9(10):e1001179. Epub 2011 Oct 18.

Department of Ecology and Evolution, The University of Chicago, Illinois, United States of America.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pbio.1001179DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3196496PMC
October 2011

A cautionary note for retrocopy identification: DNA-based duplication of intron-containing genes significantly contributes to the origination of single exon genes.

Bioinformatics 2011 Jul 5;27(13):1749-53. Epub 2011 May 5.

Department of Ecology and Evolution, The University of Chicago, 1101 E 57th Street, Chicago, IL 60637, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/btr280DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3117337PMC
July 2011

Dynamic programming procedure for searching optimal models to estimate substitution rates based on the maximum-likelihood method.

Proc Natl Acad Sci U S A 2011 May 26;108(19):7860-5. Epub 2011 Apr 26.

National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research Wuhan, Huazhong Agricultural University, Wuhan 430070, China.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1073/pnas.1018621108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3093512PMC
May 2011

Highly tissue specific expression of Sphinx supports its male courtship related role in Drosophila melanogaster.

PLoS One 2011 Apr 26;6(4):e18853. Epub 2011 Apr 26.

Committee on Genetics, University of Chicago, Chicago, Illinois, United States of America.

View Article

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0018853PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3082539PMC
April 2011

New genes in Drosophila quickly become essential.

Science 2010 Dec;330(6011):1682-5

Department of Ecology and Evolution, The University of Chicago, 1101 East 57th Street, Chicago, IL 60637, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1126/science.1196380DOI Listing
December 2010

Age-dependent chromosomal distribution of male-biased genes in Drosophila.

Genome Res 2010 Nov 26;20(11):1526-33. Epub 2010 Aug 26.

Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637, USA.

View Article

Download full-text PDF

Source
http://genome.cshlp.org/cgi/doi/10.1101/gr.107334.110
Publisher Site
http://dx.doi.org/10.1101/gr.107334.110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2963816PMC
November 2010

The rapid generation of chimerical genes expanding protein diversity in zebrafish.

BMC Genomics 2010 Nov 24;11:657. Epub 2010 Nov 24.

Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P R China.

View Article

Download full-text PDF

Source
http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2
Publisher Site
http://dx.doi.org/10.1186/1471-2164-11-657DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3091775PMC
November 2010

Evolution of enzymatic activities of testis-specific short-chain dehydrogenase/reductase in Drosophila.

J Mol Evol 2010 Oct 31;71(4):241-9. Epub 2010 Aug 31.

Department of Ecology and Evolution, The University of Chicago, Chicago, IL 60637, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/s00239-010-9384-5DOI Listing
October 2010

Chromosomal redistribution of male-biased genes in mammalian evolution with two bursts of gene gain on the X chromosome.

PLoS Biol 2010 Oct 5;8(10). Epub 2010 Oct 5.

Department of Ecology and Evolution, the University of Chicago, Chicago, Illinois, United States of America.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pbio.1000494DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2950125PMC
October 2010

Direct evidence for postmeiotic transcription during Drosophila melanogaster spermatogenesis.

Genetics 2010 Sep 6;186(1):431-3. Epub 2010 Jul 6.

Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, 60637, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1534/genetics.110.118919DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2940308PMC
September 2010

Mutational bias shaping fly copy number variation: implications for genome evolution.

Trends Genet 2010 Jun 21;26(6):243-7. Epub 2010 Apr 21.

Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA.

View Article

Download full-text PDF

Source
https://linkinghub.elsevier.com/retrieve/pii/S01689525100006
Publisher Site
http://dx.doi.org/10.1016/j.tig.2010.03.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2878862PMC
June 2010

Recombination yet inefficient selection along the Drosophila melanogaster subgroup's fourth chromosome.

Mol Biol Evol 2010 Apr 14;27(4):848-61. Epub 2009 Dec 14.

Committee on Evolutionary Biology, University of Chicago, Chicago, IL, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/molbev/msp291DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2877538PMC
April 2010

Extensive structural renovation of retrogenes in the evolution of the Populus genome.

Plant Physiol 2009 Dec 29;151(4):1943-51. Epub 2009 Sep 29.

Center for Bioinformatics, College of Life Sciences, Peking University, Beijing 100871, China.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1104/pp.109.142984DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2785971PMC
December 2009

Positive selection for the male functionality of a co-retroposed gene in the hominoids.

BMC Evol Biol 2009 Oct 15;9:252. Epub 2009 Oct 15.

Center for Bioinformatics, National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing, 100871, PR China.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/1471-2148-9-252DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2773790PMC
October 2009

Detection of intergenic non-coding RNAs expressed in the main developmental stages in Drosophila melanogaster.

Nucleic Acids Res 2009 Jul 18;37(13):4308-14. Epub 2009 May 18.

Center of Developmental Biology and Genetics, School of Life Sciences, Peking University, Beijing, China.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/nar/gkp334DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2715228PMC
July 2009

General gene movement off the X chromosome in the Drosophila genus.

Genome Res 2009 May 27;19(5):897-903. Epub 2009 Feb 27.

Department of Ecology and Evolution, The University of Chicago, Chicago, IL 60637, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1101/gr.088609.108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2675978PMC
May 2009

A rice gene of de novo origin negatively regulates pathogen-induced defense response.

PLoS One 2009 25;4(2):e4603. Epub 2009 Feb 25.

National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China.

View Article

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0004603PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2643483PMC
April 2009

RNA-based gene duplication: mechanistic and evolutionary insights.

Nat Rev Genet 2009 Jan;10(1):19-31

Center for Integrative Genomics, University of Lausanne, Genopode, CH-1015 Lausanne, Switzerland.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nrg2487DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3690669PMC
January 2009

The subtelomere of Oryza sativa chromosome 3 short arm as a hot bed of new gene origination in rice.

Mol Plant 2008 Sep 22;1(5):839-50. Epub 2008 Aug 22.

Arizona Genomics Institute, Department of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA.

View Article

Download full-text PDF

Source
http://linkinghub.elsevier.com/retrieve/pii/S167420521460360
Publisher Site
http://dx.doi.org/10.1093/mp/ssn050DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2902912PMC
September 2008

Recurrent tandem gene duplication gave rise to functionally divergent genes in Drosophila.

Mol Biol Evol 2008 Jul 11;25(7):1451-8. Epub 2008 Apr 11.

Department of Ecology and Evolution, The University of Chicago, Chicago, IL, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/molbev/msn089DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2878002PMC
July 2008

Natural selection shapes genome-wide patterns of copy-number polymorphism in Drosophila melanogaster.

Science 2008 Jun 5;320(5883):1629-31. Epub 2008 Jun 5.

Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA.

View Article

Download full-text PDF

Source
http://www.sciencemag.org/cgi/doi/10.1126/science.1158078
Publisher Site
http://dx.doi.org/10.1126/science.1158078DOI Listing
June 2008

The evolution of courtship behaviors through the origination of a new gene in Drosophila.

Proc Natl Acad Sci U S A 2008 May 27;105(21):7478-83. Epub 2008 May 27.

Committee on Genetics, University of Chicago, 920 East 58th Street, Chicago, IL 60637, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1073/pnas.0800693105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2396706PMC
May 2008

Adaptive evolution of the insulin two-gene system in mouse.

Genetics 2008 Mar 1;178(3):1683-91. Epub 2008 Feb 1.

Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1534/genetics.108.087023DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2278064PMC
March 2008

Repetitive element-mediated recombination as a mechanism for new gene origination in Drosophila.

PLoS Genet 2008 Jan 27;4(1):e3. Epub 2007 Nov 27.

Chinese Academy of Sciences-Max Planck Junior Research Group, Key Laboratory of Cellular and Molecular Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pgen.0040003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2211543PMC
January 2008

Evolution of genes and genomes on the Drosophila phylogeny.

Authors:
Andrew G Clark Michael B Eisen Douglas R Smith Casey M Bergman Brian Oliver Therese A Markow Thomas C Kaufman Manolis Kellis William Gelbart Venky N Iyer Daniel A Pollard Timothy B Sackton Amanda M Larracuente Nadia D Singh Jose P Abad Dawn N Abt Boris Adryan Montserrat Aguade Hiroshi Akashi Wyatt W Anderson Charles F Aquadro David H Ardell Roman Arguello Carlo G Artieri Daniel A Barbash Daniel Barker Paolo Barsanti Phil Batterham Serafim Batzoglou Dave Begun Arjun Bhutkar Enrico Blanco Stephanie A Bosak Robert K Bradley Adrianne D Brand Michael R Brent Angela N Brooks Randall H Brown Roger K Butlin Corrado Caggese Brian R Calvi A Bernardo de Carvalho Anat Caspi Sergio Castrezana Susan E Celniker Jean L Chang Charles Chapple Sourav Chatterji Asif Chinwalla Alberto Civetta Sandra W Clifton Josep M Comeron James C Costello Jerry A Coyne Jennifer Daub Robert G David Arthur L Delcher Kim Delehaunty Chuong B Do Heather Ebling Kevin Edwards Thomas Eickbush Jay D Evans Alan Filipski Sven Findeiss Eva Freyhult Lucinda Fulton Robert Fulton Ana C L Garcia Anastasia Gardiner David A Garfield Barry E Garvin Greg Gibson Don Gilbert Sante Gnerre Jennifer Godfrey Robert Good Valer Gotea Brenton Gravely Anthony J Greenberg Sam Griffiths-Jones Samuel Gross Roderic Guigo Erik A Gustafson Wilfried Haerty Matthew W Hahn Daniel L Halligan Aaron L Halpern Gillian M Halter Mira V Han Andreas Heger LaDeana Hillier Angie S Hinrichs Ian Holmes Roger A Hoskins Melissa J Hubisz Dan Hultmark Melanie A Huntley David B Jaffe Santosh Jagadeeshan William R Jeck Justin Johnson Corbin D Jones William C Jordan Gary H Karpen Eiko Kataoka Peter D Keightley Pouya Kheradpour Ewen F Kirkness Leonardo B Koerich Karsten Kristiansen Dave Kudrna Rob J Kulathinal Sudhir Kumar Roberta Kwok Eric Lander Charles H Langley Richard Lapoint Brian P Lazzaro So-Jeong Lee Lisa Levesque Ruiqiang Li Chiao-Feng Lin Michael F Lin Kerstin Lindblad-Toh Ana Llopart Manyuan Long Lloyd Low Elena Lozovsky Jian Lu Meizhong Luo Carlos A Machado Wojciech Makalowski Mar Marzo Muneo Matsuda Luciano Matzkin Bryant McAllister Carolyn S McBride Brendan McKernan Kevin McKernan Maria Mendez-Lago Patrick Minx Michael U Mollenhauer Kristi Montooth Stephen M Mount Xu Mu Eugene Myers Barbara Negre Stuart Newfeld Rasmus Nielsen Mohamed A F Noor Patrick O'Grady Lior Pachter Montserrat Papaceit Matthew J Parisi Michael Parisi Leopold Parts Jakob S Pedersen Graziano Pesole Adam M Phillippy Chris P Ponting Mihai Pop Damiano Porcelli Jeffrey R Powell Sonja Prohaska Kim Pruitt Marta Puig Hadi Quesneville Kristipati Ravi Ram David Rand Matthew D Rasmussen Laura K Reed Robert Reenan Amy Reily Karin A Remington Tania T Rieger Michael G Ritchie Charles Robin Yu-Hui Rogers Claudia Rohde Julio Rozas Marc J Rubenfield Alfredo Ruiz Susan Russo Steven L Salzberg Alejandro Sanchez-Gracia David J Saranga Hajime Sato Stephen W Schaeffer Michael C Schatz Todd Schlenke Russell Schwartz Carmen Segarra Rama S Singh Laura Sirot Marina Sirota Nicholas B Sisneros Chris D Smith Temple F Smith John Spieth Deborah E Stage Alexander Stark Wolfgang Stephan Robert L Strausberg Sebastian Strempel David Sturgill Granger Sutton Granger G Sutton Wei Tao Sarah Teichmann Yoshiko N Tobari Yoshihiko Tomimura Jason M Tsolas Vera L S Valente Eli Venter J Craig Venter Saverio Vicario Filipe G Vieira Albert J Vilella Alfredo Villasante Brian Walenz Jun Wang Marvin Wasserman Thomas Watts Derek Wilson Richard K Wilson Rod A Wing Mariana F Wolfner Alex Wong Gane Ka-Shu Wong Chung-I Wu Gabriel Wu Daisuke Yamamoto Hsiao-Pei Yang Shiaw-Pyng Yang James A Yorke Kiyohito Yoshida Evgeny Zdobnov Peili Zhang Yu Zhang Aleksey V Zimin Jennifer Baldwin Amr Abdouelleil Jamal Abdulkadir Adal Abebe Brikti Abera Justin Abreu St Christophe Acer Lynne Aftuck Allen Alexander Peter An Erica Anderson Scott Anderson Harindra Arachi Marc Azer Pasang Bachantsang Andrew Barry Tashi Bayul Aaron Berlin Daniel Bessette Toby Bloom Jason Blye Leonid Boguslavskiy Claude Bonnet Boris Boukhgalter Imane Bourzgui Adam Brown Patrick Cahill Sheridon Channer Yama Cheshatsang Lisa Chuda Mieke Citroen Alville Collymore Patrick Cooke Maura Costello Katie D'Aco Riza Daza Georgius De Haan Stuart DeGray Christina DeMaso Norbu Dhargay Kimberly Dooley Erin Dooley Missole Doricent Passang Dorje Kunsang Dorjee Alan Dupes Richard Elong Jill Falk Abderrahim Farina Susan Faro Diallo Ferguson Sheila Fisher Chelsea D Foley Alicia Franke Dennis Friedrich Loryn Gadbois Gary Gearin Christina R Gearin Georgia Giannoukos Tina Goode Joseph Graham Edward Grandbois Sharleen Grewal Kunsang Gyaltsen Nabil Hafez Birhane Hagos Jennifer Hall Charlotte Henson Andrew Hollinger Tracey Honan Monika D Huard Leanne Hughes Brian Hurhula M Erii Husby Asha Kamat Ben Kanga Seva Kashin Dmitry Khazanovich Peter Kisner Krista Lance Marcia Lara William Lee Niall Lennon Frances Letendre Rosie LeVine Alex Lipovsky Xiaohong Liu Jinlei Liu Shangtao Liu Tashi Lokyitsang Yeshi Lokyitsang Rakela Lubonja Annie Lui Pen MacDonald Vasilia Magnisalis Kebede Maru Charles Matthews William McCusker Susan McDonough Teena Mehta James Meldrim Louis Meneus Oana Mihai Atanas Mihalev Tanya Mihova Rachel Mittelman Valentine Mlenga Anna Montmayeur Leonidas Mulrain Adam Navidi Jerome Naylor Tamrat Negash Thu Nguyen Nga Nguyen Robert Nicol Choe Norbu Nyima Norbu Nathaniel Novod Barry O'Neill Sahal Osman Eva Markiewicz Otero L Oyono Christopher Patti Pema Phunkhang Fritz Pierre Margaret Priest Sujaa Raghuraman Filip Rege Rebecca Reyes Cecil Rise Peter Rogov Keenan Ross Elizabeth Ryan Sampath Settipalli Terry Shea Ngawang Sherpa Lu Shi Diana Shih Todd Sparrow Jessica Spaulding John Stalker Nicole Stange-Thomann Sharon Stavropoulos Catherine Stone Christopher Strader Senait Tesfaye Talene Thomson Yama Thoulutsang Dawa Thoulutsang Kerri Topham Ira Topping Tsamla Tsamla Helen Vassiliev Andy Vo Tsering Wangchuk Tsering Wangdi Michael Weiand Jane Wilkinson Adam Wilson Shailendra Yadav Geneva Young Qing Yu Lisa Zembek Danni Zhong Andrew Zimmer Zac Zwirko David B Jaffe Pablo Alvarez Will Brockman Jonathan Butler CheeWhye Chin Sante Gnerre Manfred Grabherr Michael Kleber Evan Mauceli Iain MacCallum

Nature 2007 Nov;450(7167):203-18

Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nature06341DOI Listing
November 2007

An intronic signal for alternative splicing in the human genome.

PLoS One 2007 Nov 28;2(11):e1246. Epub 2007 Nov 28.

Department of Pathology, Saint Louis University, St. Louis, Missouri, United States of America.

View Article

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0001246PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2082412PMC
November 2007

Origins of new male germ-line functions from X-derived autosomal retrogenes in the mouse.

Mol Biol Evol 2007 Oct 23;24(10):2242-53. Epub 2007 Jul 23.

Department of Ecology and Evolution, University of Chicago, USA.

View Article

Download full-text PDF

Source
https://academic.oup.com/mbe/article-lookup/doi/10.1093/molb
Publisher Site
http://dx.doi.org/10.1093/molbev/msm153DOI Listing
October 2007

A role for convergent evolution in the secretory life of cells.

Trends Cell Biol 2007 Apr 27;17(4):157-64. Epub 2007 Feb 27.

Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.tcb.2007.02.007DOI Listing
April 2007

Side effects of Tamiflu: clues from an Asian single nucleotide polymorphism.

Authors:
Manyuan Long

Cell Res 2007 Apr;17(4):309-10

Department of Ecology and Evolution, The University of Chicago, 1101 East 57th Street, Chicago, IL 60637, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/cr.2007.30DOI Listing
April 2007

A new retroposed gene in Drosophila heterochromatin detected by microarray-based comparative genomic hybridization.

J Mol Evol 2007 Feb 19;64(2):272-83. Epub 2006 Dec 19.

Department of Ecology and Evolution, The University of Chicago, 1101 East 57th Street, Chicago, IL 60637, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/s00239-006-0169-9DOI Listing
February 2007

Retrogene movement within- and between-chromosomes in the evolution of Drosophila genomes.

Gene 2006 Dec 23;385:96-102. Epub 2006 Sep 23.

Committee on Genetics, The University of Chicago, 1101 E 57th Street, Chicago, IL 60637, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.gene.2006.04.033DOI Listing
December 2006

High rate of chimeric gene origination by retroposition in plant genomes.

Plant Cell 2006 Aug 7;18(8):1791-802. Epub 2006 Jul 7.

CAS-Max-Plank Junior Research Group, Key Laboratory of Cellular and Molecular Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.

View Article

Download full-text PDF

Source
http://www.plantcell.org/cgi/doi/10.1105/tpc.106.041905
Publisher Site
http://dx.doi.org/10.1105/tpc.106.041905DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1533979PMC
August 2006

Origination of an X-linked testes chimeric gene by illegitimate recombination in Drosophila.

PLoS Genet 2006 May 19;2(5):e77. Epub 2006 May 19.

Committee on Evolutionary Biology, University of Chicago, Chicago, Illinois, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pgen.0020077DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1463047PMC
May 2006

Translational effects of differential codon usage among intragenic domains of new genes in Drosophila.

Biochim Biophys Acta 2005 May 2;1728(3):135-42. Epub 2005 Mar 2.

Department of Ecology and Evolution, The University of Chicago, Chicago, IL 60637, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.bbaexp.2005.02.004DOI Listing
May 2005

Excess of amino acid substitutions relative to polymorphism between X-linked duplications in Drosophila melanogaster.

Mol Biol Evol 2005 Feb 13;22(2):273-84. Epub 2004 Oct 13.

Department of Ecology and Evolution and the Committee on Genetiecs, University of Chicago, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/molbev/msi015DOI Listing
February 2005

Evolving protein functional diversity in new genes of Drosophila.

Proc Natl Acad Sci U S A 2004 Nov 8;101(46):16246-50. Epub 2004 Nov 8.

Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1073/pnas.0407066101DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC528974PMC
November 2004

Sex chromosomes and male functions: where do new genes go?

Cell Cycle 2004 Jul 5;3(7):873-5. Epub 2004 Jul 5.

Department of Biology, University of Texas at Arlington, Arlington, Texas, USA.

View Article

Download full-text PDF

Source
July 2004

Duplication-degeneration as a mechanism of gene fission and the origin of new genes in Drosophila species.

Nat Genet 2004 May 4;36(5):523-7. Epub 2004 Apr 4.

CAS-Max Planck Junior Scientist Group, Key Laboratory of Cellular and Molecular Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.

View Article

Download full-text PDF

Source
http://www.nature.com/articles/ng1338
Publisher Site
http://dx.doi.org/10.1038/ng1338DOI Listing
May 2004

Nucleotide variation and recombination along the fourth chromosome in Drosophila simulans.

Genetics 2004 Apr;166(4):1783-94

Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637, USA.

View Article

Download full-text PDF

Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1470817PMC
http://dx.doi.org/10.1534/genetics.166.4.1783DOI Listing
April 2004

Extensive gene traffic on the mammalian X chromosome.

Science 2004 Jan;303(5657):537-40

Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1126/science.1090042DOI Listing
January 2004

The origin of new genes: glimpses from the young and old.

Nat Rev Genet 2003 Nov;4(11):865-75

Department of Ecology and Evolution, The University of Chicago, 1101 East 57th Street, Chicago, Illinois 60637, USA.

View Article

Download full-text PDF

Source
http://www.nature.com/articles/nrg1204
Publisher Site
http://dx.doi.org/10.1038/nrg1204DOI Listing
November 2003

Origin of new genes: evidence from experimental and computational analyses.

Genetica 2003 Jul;118(2-3):171-82

Department of Ecology and Evolution, The University of Chicago, 1101 East 57th Street, Chicago, IL 60637, USA.

View Article

Download full-text PDF

Source
July 2003

Dntf-2r, a young Drosophila retroposed gene with specific male expression under positive Darwinian selection.

Genetics 2003 Jul;164(3):977-88

Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637, USA.

View Article

Download full-text PDF

Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1462638PMC
July 2003

Retroposed new genes out of the X in Drosophila.

Genome Res 2002 Dec;12(12):1854-9

Department of Ecology and Evolution, The University of Chicago, Chicago, Illinois 60637, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1101/gr.6049DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC187566PMC
December 2002

Rapid divergence of gene duplicates on the Drosophila melanogaster X chromosome.

Mol Biol Evol 2002 Jun;19(6):918-25

Committee on Genetics, University of Chicago.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/oxfordjournals.molbev.a004149DOI Listing
June 2002

Intron presence-absence polymorphism in Drosophila driven by positive Darwinian selection.

Proc Natl Acad Sci U S A 2002 Jun;99(12):8121-6

Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA.

View Article

Download full-text PDF

Source
http://www.pnas.org/cgi/doi/10.1073/pnas.122570299
Publisher Site
http://dx.doi.org/10.1073/pnas.122570299DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC123031PMC
June 2002

Evolution of the phosphoglycerate mutase processed gene in human and chimpanzee revealing the origin of a new primate gene.

Mol Biol Evol 2002 May;19(5):654-63

Department of Ecology and Evolution, The University of Chicago, 1101 East 57th Street, Chicago, IL 60637, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/oxfordjournals.molbev.a004124DOI Listing
May 2002

Expansion of genome coding regions by acquisition of new genes.

Genetica 2002 May;115(1):65-80

Department of Ecology and Evolution, The University of Chicago, IL 60637, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1023/a:1016024131097DOI Listing
May 2002

Origin of sphinx, a young chimeric RNA gene in Drosophila melanogaster.

Proc Natl Acad Sci U S A 2002 Apr 19;99(7):4448-53. Epub 2002 Mar 19.

Department of Ecology and Evolution, University of Chicago, 1101 East 57th Street, Chicago, IL 60637, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1073/pnas.072066399DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC123668PMC
April 2002

Nucleotide variation along the Drosophila melanogaster fourth chromosome.

Science 2002 Jan;295(5552):134-7

Department of Ecology and Evolution, Committee on Genetics, University of Chicago, 1101 East 57 Street, Chicago, IL 60637, USA.

View Article

Download full-text PDF

Source
http://www.sciencemag.org/cgi/doi/10.1126/science.1064521
Publisher Site
http://dx.doi.org/10.1126/science.1064521DOI Listing
January 2002