Works by Manyuan Long

Results: 77

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

Published in:

Bioinformatics, 2013, v. 29, n. 5, p. 645, doi. 10.1093/bioinformatics/btt009

By:

Zhang, Chengjun;
Wang, Jun;
Long, Manyuan;
Fan, Chuanzhu

Publication type:

Article

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

Published in:

Bioinformatics, 2011, v. 27, n. 13, p. 1749, doi. 10.1093/bioinformatics/btr280

By:

Zhang, Yong E.;
Vibranovski, Maria D.;
Krinsky, Benjamin H.;
Long, Manyuan

Publication type:

Article

New genes as drivers of phenotypic evolution.

Published in:

Nature Reviews Genetics, 2013, v. 14, n. 10, p. 744, doi. 10.1038/nrg3584

By:

Chen, Sidi;
Krinsky, Benjamin H.;
Long, Manyuan

Publication type:

Article

Species-specific partial gene duplication in Arabidopsis thaliana evolved novel phenotypic effects on morphological traits under strong positive selection.

Published in:

Plant Cell, 2022, v. 34, n. 2, p. 802, doi. 10.1093/plcell/koab291

By:

Huang, Yuan;
Chen, Jiahui;
Dong, Chuan;
Sosa, Dylan;
Xia, Shengqian;
Ouyang, Yidan;
Fan, Chuanzhu;
Li, Dezhu;
Mortola, Emily;
Long, Manyuan;
Bergelson, Joy

Publication type:

Article

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

Published in:

Environmental Microbiology, 2019, v. 21, n. 3, p. 1124, doi. 10.1111/1462-2920.14542

By:

Li, Boqiang;
Chen, Yong;
Zong, Yuanyuan;
Shang, Yanjiao;
Zhang, Zhanquan;
Xu, Xiaodi;
Wang, Xiao;
Long, Manyuan;
Tian, Shiping

Publication type:

Article

Evolutionary New Genes in a Growing Paradigm.

Published in:

Genes, 2022, v. 13, n. 9, p. 1605, doi. 10.3390/genes13091605

By:

Betrán, Esther;
Long, Manyuan

Publication type:

Article

Retrogene Duplication and Expression Patterns Shaped by the Evolution of Sex Chromosomes in Malaria Mosquitoes.

Published in:

Genes, 2022, v. 13, n. 6, p. 968, doi. 10.3390/genes13060968

By:

Miller, Duncan;
Chen, Jianhai;
Liang, Jiangtao;
Betrán, Esther;
Long, Manyuan;
Sharakhov, Igor V.

Publication type:

Article

Rapid Cis–Trans Coevolution Driven by a Novel Gene Retroposed from a Eukaryotic Conserved CCR4–NOT Component in Drosophila.

Published in:

Genes, 2022, v. 13, n. 1, p. 57, doi. 10.3390/genes13010057

By:

Krinsky, Benjamin H.;
Arthur, Robert K.;
Xia, Shengqian;
Sosa, Dylan;
Arsala, Deanna;
White, Kevin P.;
Long, Manyuan

Publication type:

Article

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

Published in:

Nature Genetics, 2004, v. 36, n. 5, p. 523, doi. 10.1038/ng1338

By:

Wang, Wen;
Yu, Haijing;
Long, Manyuan

Publication type:

Article

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

Published in:

BMC Genomics, 2010, v. 11, p. 657, doi. 10.1186/1471-2164-11-657

By:

Beide Fu;
Ming Chen;
Ming Zou;
Manyuan Long;
Shunping He

Publication type:

Article

IE-Kb: intron exon knowledge base.

Published in:

Bioinformatics, 2000, v. 16, n. 12, p. 1151, doi. 10.1093/bioinformatics/16.12.1151

By:

Sakharkar, Meena K.;
Kangueane, Pandjassarame;
Woon, Tong W.;
Tan, Tin W.;
Kolatkar, Prasanna R.;
Long, Manyuan;
de Souza, Sandro J

Publication type:

Article

A zebrafish-specific chimeric gene evolved essential developmental functions: discussion of conceptual significance.

Published in:

SCIENCE CHINA Life Sciences, 2021, v. 64, n. 5, p. 840, doi. 10.1007/s11427-021-1884-2

By:

Long, Manyuan

Publication type:

Article

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

Published in:

SCIENCE CHINA Life Sciences, 2019, v. 62, n. 4, p. 594, doi. 10.1007/s11427-019-9483-6

By:

Zu, Jian;
Gu, Yuexi;
Li, Yu;
Li, Chentong;
Zhang, Wenyu;
Zhang, Yong E.;
Lee, UnJin;
Zhang, Li;
Long, Manyuan

Publication type:

Article

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

Published in:

SCIENCE CHINA Life Sciences, 2019, v. 62, n. 4, p. 579, doi. 10.1007/s11427-019-9482-0

By:

Zhang, Wenyu;
Gao, Yuanxiao;
Long, Manyuan;
Shen, Bairong

Publication type:

Article

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

Published in:

2019

By:

Long, Manyuan;
Shen, Bairong

Publication type:

Editorial

Gene fusion as an important mechanism to generate new genes in the genus Oryza.

Published in:

Genome Biology, 2022, v. 23, n. 1, p. 1, doi. 10.1186/s13059-022-02696-w

By:

Zhou, Yanli;
Zhang, Chengjun;
Zhang, Li;
Ye, Qiannan;
Liu, Ningyawen;
Wang, Muhua;
Long, Guangqiang;
Fan, Wei;
Long, Manyuan;
Wing, Rod A.

Publication type:

Article

Evolutionary Patterns of RNA-Based Duplication in Non- Mammalian Chordates.

Published in:

PLoS ONE, 2011, v. 6, n. 7, p. 1, doi. 10.1371/journal.pone.0021466

By:

Ming Chen;
Ming Zou;
Beide Fu;
Xin Li;
Vibranovski, Maria D.;
Xiaoni Gan;
Dengqiang Wang;
Wen Wang;
Manyuan Long;
Shunping He

Publication type:

Article

Highly Tissue Specific Expression of Sphinx Supports Its Male Courtship Related Role in Drosophila melanogaster.

Published in:

PLoS ONE, 2011, v. 6, n. 4, p. 1, doi. 10.1371/journal.pone.0018853

By:

Ying Chen;
Hongzheng Dai;
Sidi Chen;
Luoying Zhang;
Manyuan Long

Publication type:

Article

A Rice Gene of De Novo Origin Negatively Regulates Pathogen-Induced Defense Response.

Published in:

PLoS ONE, 2009, v. 4, n. 2, p. 1, doi. 10.1371/journal.pone.0004603

By:

Wenfei Xiao;
Hongbo Liu;
Yu Li1;
Xianghua Li;
Caiguo Xu;
Manyuan Long;
Shiping Wang

Publication type:

Article

Genomic analyses of new genes and their phenotypic effects reveal rapid evolution of essential functions in Drosophila development.

Published in:

PLoS Genetics, 2021, v. 17, n. 7, p. 1, doi. 10.1371/journal.pgen.1009654

By:

Xia, Shengqian;
VanKuren, Nicholas W.;
Chen, Chunyan;
Zhang, Li;
Kemkemer, Clause;
Shao, Yi;
Jia, Hangxing;
Lee, UnJin;
Advani, Alexander S.;
Gschwend, Andrea;
Vibranovski, Maria D.;
Chen, Sidi;
Zhang, Yong E.;
Long, Manyuan

Publication type:

Article

Adaptive Evolution of the Insulin Two-Gene System in Mouse.

Published in:

Genetics, 2008, v. 178, n. 3, p. 1683, doi. 10.1534/genetics.108.087023

By:

Meng-Shin Shiao;
Ben-Yang Liao;
Manyuan Long;
Hon-Tsen Yu

Publication type:

Article

Nucleotide Variation and Recombination Along the Fourth Chromosome in Drosophila simulans.

Published in:

Genetics, 2004, v. 166, n. 4, p. 1783, doi. 10.1534/genetics.166.4.1783

By:

Wen Wang;
Thornton, Kevin;
Emerson, J. J.;
Long, Manyuan

Publication type:

Article

Dntf-2r, a Young Drosophila Retroposed Gene With Specific Male Expression Under Positive Darwinian Selection.

Published in:

Genetics, 2003, v. 164, n. 3, p. 977, doi. 10.1093/genetics/164.3.977

By:

Bertán, Esther;
Long, Manyuan

Publication type:

Article

Adaptive Evolution and the Birth of CTCF Binding Sites in the <i>Drosophila</i> Genome

Published in:

PLoS Biology, 2012, v. 10, n. 11, p. 1, doi. 10.1371/journal.pbio.1001420

By:

Ni, Xiaochun;
Zhang, Yong E.;
Nègre, Nicolas;
Chen, Sidi;
Long, Manyuan;
White, Kevin P.

Publication type:

Article

Accelerated Recruitment of New Brain Development Genes into the Human Genome.

Published in:

PLoS Biology, 2011, v. 9, n. 10, p. 1, doi. 10.1371/journal.pbio.1001179

By:

Zhang, Yong E.;
Landback, Patrick;
Vibranovski, Maria D.;
Long, Manyuan

Publication type:

Article

Chromosomal Redistribution of Male-Biased Genes in Mammalian Evolution with Two Bursts of Gene Gain on the X Chromosome.

Published in:

PLoS Biology, 2010, v. 8, n. 10, p. 1, doi. 10.1371/journal.pbio.1000494

By:

Zhang, Yong E.;
Vibranovski, Maria D.;
Landback, Patrick;
Marais, Gabriel A. B.;
Long, Manyuan

Publication type:

Article

New genes important for development.

Published in:

EMBO Reports, 2014, v. 15, n. 5, p. 460, doi. 10.1002/embr.201438787

By:

Kemkemer, Claus;
Long, Manyuan

Publication type:

Article

New genes as drivers of phenotypic evolution.

Published in:

Nature Reviews Genetics, 2013, v. 14, n. 9, p. 645, doi. 10.1038/nrg3521

By:

Chen, Sidi;
Krinsky, Benjamin H.;
Long, Manyuan

Publication type:

Article

RNA-based gene duplication: mechanistic and evolutionary insights.

Published in:

2009

By:

Kaessmann, Henrik;
Vinckenbosch, Nicolas;
Long, Manyuan

Publication type:

journal article

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

Published in:

Nature Reviews Genetics, 2003, v. 4, n. 11, p. 865, doi. 10.1038/nrg1204

By:

Long, Manyuan;
Betrán, Esther;
Thornton, Kevin;
Wen Wang

Publication type:

Article

Whole genome-wide chromosome fusion and new gene birth in the Monopterus albus genome.

Published in:

Cell & Bioscience, 2020, v. 10, n. 1, p. 1, doi. 10.1186/s13578-020-00432-0

By:

Cheng, Yibin;
Shang, Dantong;
Luo, Majing;
Huang, Chunhua;
Lai, Fengling;
Wang, Xin;
Xu, Xu;
Ying, Ruhong;
Wang, Lingling;
Zhao, Yu;
Zhang, Li;
Long, Manyuan;
Cheng, Hanhua;
Zhou, Rongjia

Publication type:

Article

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

Published in:

BioEssays, 2012, v. 34, n. 11, p. 982, doi. 10.1002/bies.201200008

By:

Zhang, Yong E.;
Landback, Patrick;
Vibranovski, Maria;
Long, Manyuan

Publication type:

Article

Extensive Structural Renovation of Retrogenes in the Evolution of the Populus Genome.

Published in:

Plant Physiology, 2009, v. 151, n. 4, p. 1943, doi. 10.1104/pp.109.142984

By:

Zhenglin Zhu;
Zhang, Yong;
Long, Manyuan

Publication type:

Article

The Rapid Evolution of De Novo Proteins in Structure and Complex.

Published in:

Genome Biology & Evolution, 2024, v. 16, n. 6, p. 1, doi. 10.1093/gbe/evae107

By:

Chen, Jianhai;
Li, Qingrong;
Xia, Shengqian;
Arsala, Deanna;
Sosa, Dylan;
Wang, Dong;
Long, Manyuan

Publication type:

Article

High-Quality Genome Assemblies Reveal Evolutionary Dynamics of Repetitive DNA and Structural Rearrangements in the Drosophila virilis Subgroup.

Published in:

Genome Biology & Evolution, 2024, v. 16, n. 1, p. 1, doi. 10.1093/gbe/evad238

By:

Flynn, Jullien M;
Ahmed-Braimah, Yasir H;
Long, Manyuan;
Wing, Rod A;
Clark, Andrew G

Publication type:

Article

Human Gene Age Dating Reveals an Early and Rapid Evolutionary Construction of the Adaptive Immune System.

Published in:

Genome Biology & Evolution, 2023, v. 15, n. 5, p. 1, doi. 10.1093/gbe/evad081

By:

Zhang, Li;
Park, Jonathan J;
Dong, Matthew B;
Arsala, Deanna;
Xia, Shengqian;
Chen, Jianhai;
Sosa, Dylan;
Atlas, Jared E;
Long, Manyuan;
Chen, Sidi

Publication type:

Article

Genetic Architecture of Natural Variation Underlying Adult Foraging Behavior That Is Essential for Survival of Drosophila melanogaster.

Published in:

Genome Biology & Evolution, 2017, v. 9, n. 5, p. 1357, doi. 10.1093/gbe/evx089

By:

Lee, Yuh Chwen G.;
Qian Yang;
Wanhao Chi;
Turkson, Susie A.;
Du, Wei A.;
Kemkemer, Claus;
Zhao-Bang Zeng;
Manyuan Long;
Xiaoxi Zhuang

Publication type:

Article

Expressed Structurally Stable Inverted Duplicates in Mammalian Genomes as Functional Noncoding Elements.

Published in:

Genome Biology & Evolution, 2017, v. 9, n. 4, p. 981, doi. 10.1093/gbe/evx054

By:

Zhen-Xia Chen;
Oliver, Brian;
Zhang, Yong E.;
Ge Gao;
Manyuan Long

Publication type:

Article

Excess of Amino Acid Substitutions Relative to Polymorphism Between X-Linked Duplications in Drosophila melanogaster.

Published in:

Molecular Biology & Evolution, 2005, v. 22, n. 2, p. 273

By:

Thornton, Kevin;
Long, Manyuan

Publication type:

Article

Rapid Divergence of Gene Duplicates on the Drosophila melanogaster X Chromosome.

Published in:

Molecular Biology & Evolution, 2002, v. 19, n. 6, p. 918, doi. 10.1093/oxfordjournals.molbev.a004149

By:

Thornton, Kevin;
Long, Manyuan

Publication type:

Article

Evolution of the Phosphoglycerate mutase Processed Gene in Human and Chimpanzee Revealing the Origin of a New Primate Gene.

Published in:

Molecular Biology & Evolution, 2002, v. 19, n. 5, p. 654, doi. 10.1093/oxfordjournals.molbev.a004124

By:

Betrán, Esther;
Wang, Wen;
Jin, Li;
Long, Manyuan

Publication type:

Article

Testing the “Proto-splice Sites” Model of Intron Origin: Evidence from Analysis of Intron Phase Correlations.

Published in:

Molecular Biology & Evolution, 2000, v. 17, n. 12, p. 1789, doi. 10.1093/oxfordjournals.molbev.a026279

By:

Long, Manyuan;
Rosenberg, Carl

Publication type:

Article

The Origin of the Jingwei Gene and the Complex Modular Structure of Its Parental Gene, Yellow Emperor, in Drosophila melanogaster.

Published in:

Molecular Biology & Evolution, 2000, v. 17, n. 9, p. 1294, doi. 10.1093/oxfordjournals.molbev.a026413

By:

Wang, Wen;
Zhang, Jianming;
Alvarez, Carlos;
Llopart, Ana;
Long, Manyuan

Publication type:

Article

Journal club.

Published in:

Nature, 2007, v. 449, n. 7162, p. 511, doi. 10.1038/449511a

By:

Long, Manyuan

Publication type:

Article

Nucleotide variation and conservation at the dpp locus, a gene controlling early development in...

Published in:

Genetics, 1997, v. 145, n. 2, p. 311, doi. 10.1093/genetics/145.2.311

By:

Richter, Brent;
Long, Manyuan

Publication type:

Article

The concept of the sexual reproduction cycle and its evolutionary significance.

Published in:

Frontiers in Plant Science, 2015, v. 5, p. 1, doi. 10.3389/fpls.2015.00011

By:

Shu-Nong Bai;
Chong, Kang;
Dornelas, Marcelo Carnier;
Manyuan Long

Publication type:

Article

Intron–exon structures of eukaryotic model organisms.

Published in:

Nucleic Acids Research, 1999, v. 27, n. 15, p. 3219, doi. 10.1093/nar/27.15.3219

By:

Deutsch, Michael;
Long, Manyuan;
Hawkins, J.D.;
Dorit, R.L.;
Palmer, J.D.;
Mount, S.M.;
Fedorov, A.;
Das, S.;
Long, M.;
Sharp, P.A.;
Pearson, W.R.;
Boyce, F.M.;
Gilson, P.R.;
Russell, C.B;
Doolittle, W.F.;
Petrov, D.A.;
Moriyama, E.N.;
Hughes, A.L.;
Goffeau, A.;
Baxendale, S.

Publication type:

Article

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

Published in:

Genome Biology, 2015, v. 16, n. 1, p. 1, doi. 10.1186/s13059-015-0772-4

By:

Wenyu Zhang;
Landback, Patrick;
Gschwend, Andrea R.;
Bairong Shen;
Manyuan Long

Publication type:

Article

Why rodent pseudogenes refuse to retire.

Published in:

Genome Biology, 2012, v. 13, n. 11, p. 178, doi. 10.1186/gb-2012-13-11-178

By:

Manyuan Long;
Li Zhang

Publication type:

Article

High Occurrence of Functional New Chimeric Genes in Survey of Rice Chromosome 3 Short Arm Genome Sequences.

Published in:

Genome Biology & Evolution, 2013, v. 5, n. 5, p. 1038, doi. 10.1093/gbe/evt071

By:

Zhang, Chengjun;
Wang, Jun;
Marowsky, Nicholas C.;
Long, Manyuan;
Wing, Rod A.;
Fan, Chuanzhu

Publication type:

Article