Chung-I Wu

Chung-I Wu

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Chung-I Wu

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Molecular Evolution in Small Steps under Prevailing Negative Selection: A Nearly Universal Rule of Codon Substitution.

Authors:
Qingjian Chen Ao Lan Xu Shen Chung-I Wu

Genome Biol Evol 2019 Oct;11(10):2702-2712

State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.

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http://dx.doi.org/10.1093/gbe/evz192DOI Listing
October 2019

Molecular Evolution in Large Steps-Codon Substitutions under Positive Selection.

Authors:
Qingjian Chen Ziwen He Ao Lan Xu Shen Haijun Wen Chung-I Wu

Mol Biol Evol 2019 09;36(9):1862-1873

State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China.

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http://dx.doi.org/10.1093/molbev/msz108DOI Listing
September 2019

Weak Regulation of Many Targets Is Cumulatively Powerful-A Reply to Seitz on microRNA Functionality.

Authors:
Yixin Zhao Xu Shen Tian Tang Chung-I Wu

Mol Biol Evol 2019 07;36(7):1598-1599

State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China.

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http://dx.doi.org/10.1093/molbev/msz055DOI Listing
July 2019

Tumorigenesis as the Paradigm of Quasi-neutral Molecular Evolution.

Authors:
Bingjie Chen Zongkun Shi Qingjian Chen Xu Shen Darryl Shibata Haijun Wen Chung-I Wu

Mol Biol Evol 2019 07;36(7):1430-1441

State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.

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https://academic.oup.com/mbe/advance-article/doi/10.1093/mol
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http://dx.doi.org/10.1093/molbev/msz075DOI Listing
July 2019

Speciation with gene flow via cycles of isolation and migration: insights from multiple mangrove taxa.

Authors:
Ziwen He Xinnian Li Ming Yang Xinfeng Wang Cairong Zhong Norman C Duke Chung-I Wu Suhua Shi

Natl Sci Rev 2019 Mar 24;6(2):275-288. Epub 2018 Jul 24.

State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China.

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http://dx.doi.org/10.1093/nsr/nwy078DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6599600PMC
March 2019

Small Segmental Duplications in Drosophila-High Rate of Emergence and Elimination.

Authors:
Juan Li Lan Jiang Chung-I Wu Xuemei Lu Shu Fang Chau-Ti Ting

Genome Biol Evol 2019 02;11(2):486-496

Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, Taiwan.

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http://dx.doi.org/10.1093/gbe/evz011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6380325PMC
February 2019

The heterogeneity of plasma miRNA profiles in hepatocellular carcinoma patients and the exploration of diagnostic circulating miRNAs for hepatocellular carcinoma.

Authors:
Xue Bai Zhenzhen Liu Xiaojian Shao Di Wang Encheng Dong Yan Wang Chung-I Wu Yunfei Yuan Xuemei Lu Chunyan Li

PLoS One 2019 5;14(2):e0211581. Epub 2019 Feb 5.

Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0211581PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6363174PMC
February 2019

Death of new microRNA genes in via gradual loss of fitness advantages.

Authors:
Guang-An Lu Yixin Zhao Hao Yang Ao Lan Suhua Shi Zhongqi Liufu Yumei Huang Tian Tang Jin Xu Xu Shen Chung-I Wu

Genome Res 2018 09 26;28(9):1309-1318. Epub 2018 Jul 26.

State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, Guangdong, China.

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http://dx.doi.org/10.1101/gr.233809.117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6120634PMC
September 2018

On the low reproducibility of cancer studies.

Authors:
Haijun Wen Hurng-Yi Wang Xionglei He Chung-I Wu

Natl Sci Rev 2018 Sep 2;5(5):619-624. Epub 2018 Feb 2.

State Key Laboratory of Biocontrol, College of Ecology and Evolution, Sun Yat-Sen University, Guangzhou.

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http://dx.doi.org/10.1093/nsr/nwy021DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6599599PMC
September 2018

Direct measurement of pervasive weak repression by microRNAs and their role at the network level.

Authors:
Fuqiang Ma Pei Lin Qingjian Chen Xuemei Lu Yong E Zhang Chung-I Wu

BMC Genomics 2018 May 15;19(1):362. Epub 2018 May 15.

Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.

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http://dx.doi.org/10.1186/s12864-018-4757-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5952853PMC
May 2018

On the possibility of death of new genes - evidence from the deletion of de novo microRNAs.

Authors:
Guang-An Lu Yixin Zhao Zhongqi Liufu Chung-I Wu

BMC Genomics 2018 May 23;19(1):388. Epub 2018 May 23.

State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, Guangdong, China.

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http://dx.doi.org/10.1186/s12864-018-4755-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5966946PMC
May 2018

Extremely low genetic diversity across mangrove taxa reflects past sea level changes and hints at poor future responses.

Authors:
Zixiao Guo Xinnian Li Ziwen He Yuchen Yang Wenqing Wang Cairong Zhong Anthony J Greenberg Chung-I Wu Norman C Duke Suhua Shi

Glob Chang Biol 2018 04 28;24(4):1741-1748. Epub 2017 Nov 28.

State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, School of Life Science, Sun Yat-Sen University, Guangzhou, Guangdong, China.

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http://dx.doi.org/10.1111/gcb.13968DOI Listing
April 2018

Regulation of Large Number of Weak Targets-New Insights from Twin-microRNAs.

Authors:
Yixin Zhao Pei Lin Zhongqi Liufu Hao Yang Yang Lyu Xu Shen Chung-I Wu Tian Tang

Genome Biol Evol 2018 04;10(5):1255-1264

State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China.

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http://dx.doi.org/10.1093/gbe/evy079DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5963297PMC
April 2018

Convergent adaptive evolution in marginal environments: unloading transposable elements as a common strategy among mangrove genomes.

Authors:
Haomin Lyu Ziwen He Chung-I Wu Suhua Shi

New Phytol 2018 Jan 27;217(1):428-438. Epub 2017 Sep 27.

State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, 510275, China.

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http://dx.doi.org/10.1111/nph.14784DOI Listing
January 2018

Weak Regulation of Many Targets Is Cumulatively Powerful-An Evolutionary Perspective on microRNA Functionality.

Authors:
Yixin Zhao Xu Shen Tian Tang Chung-I Wu

Mol Biol Evol 2017 Dec;34(12):3041-3046

State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China.

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http://dx.doi.org/10.1093/molbev/msx260DOI Listing
December 2017

Free-living human cells reconfigure their chromosomes in the evolution back to uni-cellularity.

Authors:
Jin Xu Xinxin Peng Yuxin Chen Yuezheng Zhang Qin Ma Liang Liang Ava C Carter Xuemei Lu Chung-I Wu

Elife 2017 12 18;6. Epub 2017 Dec 18.

Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.

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https://elifesciences.org/articles/28070
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http://dx.doi.org/10.7554/eLife.28070DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5734875PMC
December 2017

Genomic sequencing identifies a few mutations driving the independent origin of primary liver tumors in a chronic hepatitis murine model.

Authors:
Zuyu Yang Mingming Jia Guojing Liu Huaining Hao Li Chen Guanghao Li Sixue Liu Yawei Li Chung-I Wu Xuemei Lu Shengdian Wang

PLoS One 2017 8;12(11):e0187551. Epub 2017 Nov 8.

Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China, University of Chinese Academy of Sciences, Beijing, China.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0187551PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5678715PMC
November 2017

The genotype-phenotype relationships in the light of natural selection.

Authors:
Han Chen Chung-I Wu Xionglei He

Mol Biol Evol 2017 Nov 9. Epub 2017 Nov 9.

State Key Laboratory of Bio-control, College of Ecology and Evolution, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.

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http://dx.doi.org/10.1093/molbev/msx288DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5850688PMC
November 2017

Redundant and incoherent regulations of multiple phenotypes suggest microRNAs' role in stability control.

Authors:
Zhongqi Liufu Yixin Zhao Li Guo Guangxia Miao Juan Xiao Yang Lyu Yuxin Chen Suhua Shi Tian Tang Chung-I Wu

Genome Res 2017 10 13;27(10):1665-1673. Epub 2017 Sep 13.

State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, Guangdong, China.

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http://dx.doi.org/10.1101/gr.222505.117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5630030PMC
October 2017

Classifying the evolutionary and ecological features of neoplasms.

Authors:
Carlo C Maley Athena Aktipis Trevor A Graham Andrea Sottoriva Amy M Boddy Michalina Janiszewska Ariosto S Silva Marco Gerlinger Yinyin Yuan Kenneth J Pienta Karen S Anderson Robert Gatenby Charles Swanton David Posada Chung-I Wu Joshua D Schiffman E Shelley Hwang Kornelia Polyak Alexander R A Anderson Joel S Brown Mel Greaves Darryl Shibata

Nat Rev Cancer 2017 10 15;17(10):605-619. Epub 2017 Sep 15.

Department of Pathology, Norris Comprehensive Cancer Center, University of Southern California, 1441 Eastlake Avenue, NOR2424, Los Angeles, California 90033, USA.

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http://dx.doi.org/10.1038/nrc.2017.69DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5811185PMC
October 2017

The origin, diversification and adaptation of a major mangrove clade (Rhizophoreae) revealed by whole-genome sequencing.

Authors:
Shaohua Xu Ziwen He Zhang Zhang Zixiao Guo Wuxia Guo Haomin Lyu Jianfang Li Ming Yang Zhenglin Du Yelin Huang Renchao Zhou Cairong Zhong David E Boufford Manuel Lerdau Chung-I Wu Norman C Duke Suhua Shi

Natl Sci Rev 2017 Sep 5;4(5):721-734. Epub 2017 Jun 5.

State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China.

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http://dx.doi.org/10.1093/nsr/nwx065DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6599620PMC
September 2017

A New Formulation of Random Genetic Drift and Its Application to the Evolution of Cell Populations.

Authors:
Yuxin Chen Ding Tong Chung-I Wu

Mol Biol Evol 2017 08;34(8):2057-2064

State Key Laboratory of Bio-control, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong, China.

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http://dx.doi.org/10.1093/molbev/msx161DOI Listing
August 2017

A Direct Test of Selection in Cell Populations Using the Diversity in Gene Expression within Tumors.

Authors:
Chunyan Li Yali Hou Jin Xu Aiqun Zhang Zhenzhen Liu Furong Qi Zuyu Yang Ke Chen Sixue Liu Huanwei Huang Qianfei Wang Jiahong Dong Chung-I Wu Xuemei Lu

Mol Biol Evol 2017 07;34(7):1730-1742

Key Laboratory of Genomic and Precision Medicine, China Gastrointestinal Cancer Research Center, Beijing Institute of Genomics, Chinese Academy of Sciences and University of Chinese Academy of Sciences, Beijing, China.

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http://dx.doi.org/10.1093/molbev/msx115DOI Listing
July 2017

The emergence of the hyperinvasive vine, Mikania micrantha (Asteraceae), via admixture and founder events inferred from population transcriptomics.

Authors:
Ming Yang Ziwen He Yelin Huang Lu Lu Yubin Yan Lan Hong Hao Shen Ying Liu Qiang Guo Lu Jiang Yanwu Zhang Anthony J Greenberg Renchao Zhou Xuejun Ge Chung-I Wu Suhua Shi

Mol Ecol 2017 Jul 19;26(13):3405-3423. Epub 2017 Apr 19.

State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, China.

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http://dx.doi.org/10.1111/mec.14124DOI Listing
July 2017

Can genomic data alone tell us whether speciation happened with gene flow?

Authors:
Ming Yang Ziwen He Suhua Shi Chung-I Wu

Mol Ecol 2017 Jun 19;26(11):2845-2849. Epub 2017 Apr 19.

State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.

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http://dx.doi.org/10.1111/mec.14117DOI Listing
June 2017

A mathematical theory of the transcription repression (TR) therapy of cancer - whether and how it may work.

Authors:
Yuxin Chen Haijun Wen Chung-I Wu

Oncotarget 2017 Jun;8(24):38642-38649

State Key Laboratory of Bio-control, School of Life Science, Sun Yat-Sen University, Guangzhou, China.

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http://dx.doi.org/10.18632/oncotarget.16957DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5503560PMC
June 2017

Ultrasensitive and high-efficiency screen of de novo low-frequency mutations by o2n-seq.

Authors:
Kaile Wang Shujuan Lai Xiaoxu Yang Tianqi Zhu Xuemei Lu Chung-I Wu Jue Ruan

Nat Commun 2017 05 22;8:15335. Epub 2017 May 22.

Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Pengfei Road No. 7, Dapeng New District, Shenzhen, Guangdong 518120, China.

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http://dx.doi.org/10.1038/ncomms15335DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5458117PMC
May 2017

Genome-Wide Convergence during Evolution of Mangroves from Woody Plants.

Authors:
Shaohua Xu Ziwen He Zixiao Guo Zhang Zhang Gerald J Wyckoff Anthony Greenberg Chung-I Wu Suhua Shi

Mol Biol Evol 2017 04;34(4):1008-1015

State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong, China.

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https://academic.oup.com/mbe/article-lookup/doi/10.1093/molb
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http://dx.doi.org/10.1093/molbev/msw277DOI Listing
April 2017

The Ecology and Evolution of Cancer: The Ultra-Microevolutionary Process.

Authors:
Chung-I Wu Hurng-Yi Wang Shaoping Ling Xuemei Lu

Annu Rev Genet 2016 Nov 28;50:347-369. Epub 2016 Sep 28.

CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; email:

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http://dx.doi.org/10.1146/annurev-genet-112414-054842DOI Listing
November 2016

Genomic analysis of snub-nosed monkeys (Rhinopithecus) identifies genes and processes related to high-altitude adaptation.

Authors:
Li Yu Guo-Dong Wang Jue Ruan Yong-Bin Chen Cui-Ping Yang Xue Cao Hong Wu Yan-Hu Liu Zheng-Lin Du Xiao-Ping Wang Jing Yang Shao-Chen Cheng Li Zhong Lu Wang Xuan Wang Jing-Yang Hu Lu Fang Bing Bai Kai-Le Wang Na Yuan Shi-Fang Wu Bao-Guo Li Jin-Guo Zhang Ye-Qin Yang Cheng-Lin Zhang Yong-Cheng Long Hai-Shu Li Jing-Yuan Yang David M Irwin Oliver A Ryder Ying Li Chung-I Wu Ya-Ping Zhang

Nat Genet 2016 08 11;48(8):947-52. Epub 2016 Jul 11.

State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.

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http://dx.doi.org/10.1038/ng.3615DOI Listing
August 2016

Erratum to: 'Ultra-precise detection of mutations by droplet-based amplification of circularized DNA'.

Authors:
Kaile Wang Qin Ma Lan Jiang Shujuan Lai Xuemei Lu Yali Hou Chung-I Wu Jue Ruan

BMC Genomics 2016 Jun 2;17(1):421. Epub 2016 Jun 2.

Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.

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http://dx.doi.org/10.1186/s12864-016-2683-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4891909PMC
June 2016

Small RNA transcriptomes of mangroves evolve adaptively in extreme environments.

Authors:
Ming Wen Xingqin Lin Munan Xie Yushuai Wang Xu Shen Zhongqi Liufu Chung-I Wu Suhua Shi Tian Tang

Sci Rep 2016 06 9;6:27551. Epub 2016 Jun 9.

State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, Guangdong, China.

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http://dx.doi.org/10.1038/srep27551DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4899726PMC
June 2016

Reminder to deposit DNA sequences.

Authors:
Mark Blaxter Antoine Danchin Babis Savakis Kaoru Fukami-Kobayashi Ken Kurokawa Sumio Sugano Richard J Roberts Steven L Salzberg Chung-I Wu

Science 2016 May 11;352(6287):780. Epub 2016 May 11.

Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA. Beijing Institute of Genomics, Beijing, 100101, China.

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http://dx.doi.org/10.1126/science.aaf7672DOI Listing
May 2016

Using ultra-sensitive next generation sequencing to dissect DNA damage-induced mutagenesis.

Authors:
Kaile Wang Xiaolu Ma Xue Zhang Dafei Wu Chenyi Sun Yazhou Sun Xuemei Lu Chung-I Wu Caixia Guo Jue Ruan

Sci Rep 2016 04 28;6:25310. Epub 2016 Apr 28.

Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.

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http://dx.doi.org/10.1038/srep25310DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4848531PMC
April 2016

Ultra-precise detection of mutations by droplet-based amplification of circularized DNA.

Authors:
Kaile Wang Qin Ma Lan Jiang Shujuan Lai Xuemei Lu Yali Hou Chung-I Wu Jue Ruan

BMC Genomics 2016 Mar 9;17:214. Epub 2016 Mar 9.

Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.

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http://dx.doi.org/10.1186/s12864-016-2480-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4784281PMC
March 2016

Out of southern East Asia: the natural history of domestic dogs across the world.

Authors:
Guo-Dong Wang Weiwei Zhai He-Chuan Yang Lu Wang Li Zhong Yan-Hu Liu Ruo-Xi Fan Ting-Ting Yin Chun-Ling Zhu Andrei D Poyarkov David M Irwin Marjo K Hytönen Hannes Lohi Chung-I Wu Peter Savolainen Ya-Ping Zhang

Cell Res 2016 Jan 15;26(1):21-33. Epub 2015 Dec 15.

State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.

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http://dx.doi.org/10.1038/cr.2015.147DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4816135PMC
January 2016

Functional Conservation of Both CDS- and 3'-UTR-Located MicroRNA Binding Sites between Species.

Authors:
Liu Guojing Rui Zhang Jin Xu Chung-I Wu Xuemei Lu

Mol Biol Evol 2015 Dec 29;32(12):3276. Epub 2015 Sep 29.

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http://dx.doi.org/10.1093/molbev/msv192DOI Listing
December 2015

Extremely high genetic diversity in a single tumor points to prevalence of non-Darwinian cell evolution.

Authors:
Shaoping Ling Zheng Hu Zuyu Yang Fang Yang Yawei Li Pei Lin Ke Chen Lili Dong Lihua Cao Yong Tao Lingtong Hao Qingjian Chen Qiang Gong Dafei Wu Wenjie Li Wenming Zhao Xiuyun Tian Chunyi Hao Eric A Hungate Daniel V T Catenacci Richard R Hudson Wen-Hsiung Li Xuemei Lu Chung-I Wu

Proc Natl Acad Sci U S A 2015 Nov 11;112(47):E6496-505. Epub 2015 Nov 11.

Key Laboratory of Genomics and Precision Medicine, China Gastrointestinal Cancer Research Center, Beijing Institute of Genomics, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Beijing 100101, People's Republic of China; State Key Laboratory of Biocontrol, College of Ecology and Evolution, Sun Yat-Sen University, Guangzhou 510275, People's Republic of China; Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637;

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http://dx.doi.org/10.1073/pnas.1519556112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4664355PMC
November 2015

siRNAs with decreased off-target effect facilitate the identification of essential genes in cancer cells.

Authors:
Chunyan Li Zhenzhen Liu Fang Yang Wensheng Liu Di Wang Encheng Dong Yu Wang Chung-I Wu Xuemei Lu

Oncotarget 2015 Aug;6(25):21603-13

CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Chaoyang District, Beijing, P. R. China.

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http://dx.doi.org/10.18632/oncotarget.4269DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4673289PMC
August 2015

Functional conservation of both CDS- and 3'-UTR-located microRNA binding sites between species.

Authors:
Guojing Liu Rui Zhang Jin Xu Chung-I Wu Xuemei Lu

Mol Biol Evol 2015 Mar 19;32(3):623-8. Epub 2014 Nov 19.

Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China University of Chinese Academy of Sciences, Beijing, China

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http://dx.doi.org/10.1093/molbev/msu323DOI Listing
March 2015

Genetic convergence in the adaptation of dogs and humans to the high-altitude environment of the tibetan plateau.

Authors:
Guo-Dong Wang Ruo-Xi Fan Weiwei Zhai Fei Liu Lu Wang Li Zhong Hong Wu He-Chuan Yang Shi-Fang Wu Chun-Ling Zhu Yan Li Yun Gao Ri-Li Ge Chung-I Wu Ya-Ping Zhang

Genome Biol Evol 2014 Aug;6(8):2122-8

State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China Laboratory for Conservation and Utilization of Bio-resources, Yunnan University, Kunming, China Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore

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http://dx.doi.org/10.1093/gbe/evu162DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4231634PMC
August 2014

Exome sequencing identifies frequent mutation of MLL2 in non-small cell lung carcinoma from Chinese patients.

Authors:
Shanye Yin Jing Yang Bin Lin Wenjun Deng Yuchao Zhang Xianfu Yi Yufang Shi Yong Tao Jun Cai Chung-I Wu Guoping Zhao Laurence D Hurst Jie Zhang Landian Hu Xiangyin Kong

Sci Rep 2014 Aug 12;4:6036. Epub 2014 Aug 12.

State Key Laboratory of Medical Genomics, Institute of Health Sciences, Shanghai Jiao Tong University School of Medicine and Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200025, People's Republic of China.

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http://dx.doi.org/10.1038/srep06036DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5381403PMC
August 2014

Reply to Liu: Amino acid 104 asparagine/glutamic acid of p53 is an adaptively selected site for extreme environments in mammals of the Tibet plateau.

Authors:
Yang Zhao Ji-Long Ren Ming-Yang Wang Sheng-Ting Zhang Yu Liu Min Li Yi-Bin Cao Hu-Yue Zu Xiao-Cheng Chen Chung-I Wu Eviatar Nevo Xue-Qun Chen Ji-Zeng Du

Proc Natl Acad Sci U S A 2014 Jun;111(23):E2358

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4060686PMC
http://dx.doi.org/10.1073/pnas.1403299111DOI Listing
June 2014

New microRNAs in Drosophila--birth, death and cycles of adaptive evolution.

Authors:
Yang Lyu Yang Shen Heng Li Yuxin Chen Li Guo Yixin Zhao Eric Hungate Suhua Shi Chung-I Wu Tian Tang

PLoS Genet 2014 Jan 23;10(1):e1004096. Epub 2014 Jan 23.

State Key Laboratory of Biocontrol, Key Laboratory of Gene Engineering of the Ministry of Education, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China ; Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China ; Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, Sun Yat-sen University, Guangzhou, Guangdong, China.

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http://dx.doi.org/10.1371/journal.pgen.1004096DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3900394PMC
January 2014

The genomics of selection in dogs and the parallel evolution between dogs and humans.

Authors:
Guo-dong Wang Weiwei Zhai He-chuan Yang Ruo-xi Fan Xue Cao Li Zhong Lu Wang Fei Liu Hong Wu Lu-guang Cheng Andrei D Poyarkov Nikolai A Poyarkov Shu-sheng Tang Wen-ming Zhao Yun Gao Xue-mei Lv David M Irwin Peter Savolainen Chung-I Wu Ya-ping Zhang

Nat Commun 2013 ;4:1860

State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, No. 32 Jiaochang Donglu, Kunming 650223, China.

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http://dx.doi.org/10.1038/ncomms2814DOI Listing
December 2013

The evolution of small insertions and deletions in the coding genes of Drosophila melanogaster.

Authors:
Zechen Chong Weiwei Zhai Chunyan Li Min Gao Qiang Gong Jue Ruan Juan Li Lan Jiang Xuemei Lv Eric Hungate Chung-I Wu

Mol Biol Evol 2013 Dec 26;30(12):2699-708. Epub 2013 Sep 26.

Center for Computational Biology and Laboratory of Disease Genomics and Individualized Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.

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http://dx.doi.org/10.1093/molbev/mst167DOI Listing
December 2013

Codon 104 variation of p53 gene provides adaptive apoptotic responses to extreme environments in mammals of the Tibet plateau.

Authors:
Yang Zhao Ji-Long Ren Ming-Yang Wang Sheng-Ting Zhang Yu Liu Min Li Yi-Bin Cao Hu-Yue Zu Xiao-Cheng Chen Chung-I Wu Eviatar Nevo Xue-Qun Chen Ji-Zeng Du

Proc Natl Acad Sci U S A 2013 Dec 2;110(51):20639-44. Epub 2013 Dec 2.

Division of Neurobiology and Physiology, Department of Basic Medical Sciences, School of Medicine, Zhejiang University, Hangzhou 310058, China.

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http://dx.doi.org/10.1073/pnas.1320369110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3870672PMC
December 2013

Determination of genomic copy number alteration emphasizing a restriction site-based strategy of genome re-sequencing.

Authors:
Caihong Zheng Xuexia Miao Yanen Li Ying Huang Jue Ruan Xi Ma Li Wang Chung-I Wu Jun Cai

Bioinformatics 2013 Nov 20;29(22):2813-21. Epub 2013 Aug 20.

Laboratory of Disease Genomics and Personalized Medicine & Center of Computational Biology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China, University of Chinese Academy of Sciences, Beijing 100049, China, Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA, Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, USA, Department of Epidemiology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing 100730, China and Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA.

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http://dx.doi.org/10.1093/bioinformatics/btt481DOI Listing
November 2013

A locus in Drosophila sechellia affecting tolerance of a host plant toxin.

Authors:
Eric A Hungate Eric J Earley Ian A Boussy David A Turissini Chau-Ti Ting Jennifer R Moran Mao-Lien Wu Chung-I Wu Corbin D Jones

Genetics 2013 Nov 13;195(3):1063-75. Epub 2013 Sep 13.

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

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http://dx.doi.org/10.1534/genetics.113.154773DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3813837PMC
November 2013

The evolution of evolvability in microRNA target sites in vertebrates.

Authors:
Jin Xu Rui Zhang Yang Shen Guojing Liu Xuemei Lu Chung-I Wu

Genome Res 2013 Nov 27;23(11):1810-6. Epub 2013 Sep 27.

Laboratory of Disease Genomics and Individualized Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China;

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http://dx.doi.org/10.1101/gr.148916.112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3814881PMC
November 2013

Pseudo-Sanger sequencing: massively parallel production of long and near error-free reads using NGS technology.

Authors:
Jue Ruan Lan Jiang Zechen Chong Qiang Gong Heng Li Chunyan Li Yong Tao Caihong Zheng Weiwei Zhai David Turissini Charles H Cannon Xuemei Lu Chung-I Wu

BMC Genomics 2013 Oct 17;14:711. Epub 2013 Oct 17.

Laboratory of Disease Genomics and Individualized Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, People's Republic of China.

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http://dx.doi.org/10.1186/1471-2164-14-711DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4046676PMC
October 2013

Estimating DNA polymorphism from next generation sequencing data with high error rate by dual sequencing applications.

Authors:
Ziwen He Xinnian Li Shaoping Ling Yun-Xin Fu Eric Hungate Suhua Shi Chung-I Wu

BMC Genomics 2013 Aug 7;14:535. Epub 2013 Aug 7.

State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, Sun Yat-sen University, 135 Xingang West Road, Guangzhou 510275, China.

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http://dx.doi.org/10.1186/1471-2164-14-535DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3750404PMC
August 2013

Age-dependent transition from cell-level to population-level control in murine intestinal homeostasis revealed by coalescence analysis.

Authors:
Zheng Hu Yun-Xin Fu Anthony J Greenberg Chung-I Wu Weiwei Zhai

PLoS Genet 2013 28;9(2):e1003326. Epub 2013 Feb 28.

Center for Computational Biology and Laboratory of Disease Genomics and Individualized Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.

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http://dx.doi.org/10.1371/journal.pgen.1003326DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3585040PMC
June 2013

Sperm, but not oocyte, DNA methylome is inherited by zebrafish early embryos.

Authors:
Lan Jiang Jing Zhang Jing-Jing Wang Lu Wang Li Zhang Guoqiang Li Xiaodan Yang Xin Ma Xin Sun Jun Cai Jun Zhang Xingxu Huang Miao Yu Xuegeng Wang Feng Liu Chung-I Wu Chuan He Bo Zhang Weimin Ci Jiang Liu

Cell 2013 May;153(4):773-84

CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.

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http://dx.doi.org/10.1016/j.cell.2013.04.041DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4081501PMC
May 2013

Targeted disruption in mice of a neural stem cell-maintaining, KRAB-Zn finger-encoding gene that has rapidly evolved in the human lineage.

Authors:
Huan-Chieh Chien Hurng-Yi Wang Yi-Ning Su Kuan-Yu Lai Li-Chen Lu Pau-Chung Chen Shih-Feng Tsai Chung-I Wu Wu-Shiun Hsieh Che-Kun James Shen

PLoS One 2012 10;7(10):e47481. Epub 2012 Oct 10.

Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, Taiwan, Republic of China.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0047481PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3468564PMC
February 2013

Identification of medium-sized genomic deletions with low coverage, mate-paired restricted tags.

Authors:
Qiang Gong Yong Tao Jian-Rong Yang Jun Cai Yunfei Yuan Jue Ruan Jin Yang Hailiang Liu Wanghua Li Xuemei Lu Shi-Mei Zhuang San Ming Wang Chung-I Wu

BMC Genomics 2013 Jan 24;14:51. Epub 2013 Jan 24.

Laboratory of Disease Genomics and Individualized Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, PR China.

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http://dx.doi.org/10.1186/1471-2164-14-51DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3608957PMC
January 2013

Rainbow: an integrated tool for efficient clustering and assembling RAD-seq reads.

Authors:
Zechen Chong Jue Ruan Chung-I Wu

Bioinformatics 2012 Nov 1;28(21):2732-7. Epub 2012 Sep 1.

Laboratory of Disease Genomics and Individualized Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, People's Republic of China.

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http://dx.doi.org/10.1093/bioinformatics/bts482DOI Listing
November 2012

Incompatibility and competitive exclusion of genomic segments between sibling Drosophila species.

Authors:
Shu Fang Roman Yukilevich Ying Chen David A Turissini Kai Zeng Ian A Boussy Chung-I Wu

PLoS Genet 2012 Jun 28;8(6):e1002795. Epub 2012 Jun 28.

Biodiversity Research Center, Academia Sinica, Taipei, Taiwan, Republic of China.

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http://dx.doi.org/10.1371/journal.pgen.1002795DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3386244PMC
June 2012

Population genetics in nonmodel organisms: II. natural selection in marginal habitats revealed by deep sequencing on dual platforms.

Authors:
Renchao Zhou Shaoping Ling Wenming Zhao Naoki Osada Sufang Chen Meng Zhang Ziwen He Hua Bao Cairong Zhong Bing Zhang Xuemei Lu David Turissini Norman C Duke Jian Lu Suhua Shi Chung-I Wu

Mol Biol Evol 2011 Oct 18;28(10):2833-42. Epub 2011 Apr 18.

State Key Laboratory of Biocontrol and Key Laboratory of Gene Engineering of the Ministry of Education, Sun Yat-sen University, Guangzhou, China.

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http://dx.doi.org/10.1093/molbev/msr102DOI Listing
October 2011

Testing hypotheses on the rate of molecular evolution in relation to gene expression using microRNAs.

Authors:
Yang Shen Yang Lv Lei Huang Wensheng Liu Ming Wen Tian Tang Rui Zhang Eric Hungate Suhua Shi Chung-I Wu

Proc Natl Acad Sci U S A 2011 Sep 12;108(38):15942-7. Epub 2011 Sep 12.

State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen (Zhongshan) University, Guangzhou 510275, China.

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http://dx.doi.org/10.1073/pnas.1110098108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3179107PMC
September 2011

Rapid growth of a hepatocellular carcinoma and the driving mutations revealed by cell-population genetic analysis of whole-genome data.

Authors:
Yong Tao Jue Ruan Shiou-Hwei Yeh Xuemei Lu Yu Wang Weiwei Zhai Jun Cai Shaoping Ling Qiang Gong Zecheng Chong Zhengzhong Qu Qianqian Li Jiang Liu Jin Yang Caihong Zheng Changqing Zeng Hurng-Yi Wang Jing Zhang Sheng-Han Wang Lingtong Hao Lili Dong Wenjie Li Min Sun Wei Zou Caixia Yu Chaohua Li Guojing Liu Lan Jiang Jin Xu Huanwei Huang Chunyan Li Shuangli Mi Bing Zhang Baoxian Chen Wenming Zhao Songnian Hu Shi-Mei Zhuang Yang Shen Suhua Shi Christopher Brown Kevin P White Ding-Shinn Chen Pei-Jer Chen Chung-I Wu

Proc Natl Acad Sci U S A 2011 Jul 5;108(29):12042-7. Epub 2011 Jul 5.

Laboratory of Disease Genomics and Individualized Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, People's Republic of China.

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http://dx.doi.org/10.1073/pnas.1108715108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3141952PMC
July 2011

Two evolutionary histories in the genome of rice: the roles of domestication genes.

Authors:
Ziwen He Weiwei Zhai Haijun Wen Tian Tang Yu Wang Xuemei Lu Anthony J Greenberg Richard R Hudson Chung-I Wu Suhua Shi

PLoS Genet 2011 Jun 9;7(6):e1002100. Epub 2011 Jun 9.

State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, Sun Yat-Sen University, Guangzhou, China.

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http://dx.doi.org/10.1371/journal.pgen.1002100DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3111475PMC
June 2011

Sex, sex chromosomes and gene expression.

Authors:
Xuemei Lu Chung-I Wu

BMC Biol 2011 May 4;9:30. Epub 2011 May 4.

Laboratory of Disease Genomics and Individualized Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beichen West Road, Chaoyang, Beijing, China.

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http://dx.doi.org/10.1186/1741-7007-9-30DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3087707PMC
May 2011

Genome-wide misexpression of X-linked versus autosomal genes associated with hybrid male sterility.

Authors:
Xuemei Lu Joshua A Shapiro Chau-Ti Ting Yan Li Chunyan Li Jin Xu Huanwei Huang Ya-Jen Cheng Anthony J Greenberg Shou-Hsien Li Mao-Lien Wu Yang Shen Chung-I Wu

Genome Res 2010 Aug 28;20(8):1097-102. Epub 2010 May 28.

CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, People's Republic of China.

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http://dx.doi.org/10.1101/gr.076620.108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2909572PMC
August 2010

Adverse interactions between micro-RNAs and target genes from different species.

Authors:
Tian Tang Supriya Kumar Yang Shen Jian Lu Mao-Lien Wu Suhua Shi Wen-Hsiung Li Chung-I Wu

Proc Natl Acad Sci U S A 2010 Jul 6;107(29):12935-40. Epub 2010 Jul 6.

State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.

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http://dx.doi.org/10.1073/pnas.1007591107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2919947PMC
July 2010

Reply to evolutionary flux of canonical microRNAs and mirtrons in Drosophila.

Authors:
Jian Lu Yang Shen Richard W Carthew San Ming Wang Chung-I Wu

Nat Genet 2010 Jan;42(1):9-10

Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, USA ; State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen (Zhongshan) University, Guangzhou, China ; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.

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http://dx.doi.org/10.1038/ng0110-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4108203PMC
January 2010

Evolution under canalization and the dual roles of microRNAs: a hypothesis.

Authors:
Chung-I Wu Yang Shen Tian Tang

Genome Res 2009 May;19(5):734-43

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

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http://dx.doi.org/10.1101/gr.084640.108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3647535PMC
May 2009

Independent losses of function in a polyphenol oxidase in rice: differentiation in grain discoloration between subspecies and the role of positive selection under domestication.

Authors:
Yanchun Yu Tian Tang Qian Qian Yonghong Wang Meixian Yan Dali Zeng Bin Han Chung-I Wu Suhua Shi Jiayang Li

Plant Cell 2008 Nov 25;20(11):2946-59. Epub 2008 Nov 25.

State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.

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http://dx.doi.org/10.1105/tpc.108.060426DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2613672PMC
November 2008

Poly A- transcripts expressed in HeLa cells.

Authors:
Qingfa Wu Yeong C Kim Jian Lu Zhenyu Xuan Jun Chen Yonglan Zheng Tom Zhou Michael Q Zhang Chung-I Wu San Ming Wang

PLoS One 2008 Jul 30;3(7):e2803. Epub 2008 Jul 30.

Center for Functional Genomics, Division of Medical Genetics, Department of Medicine, ENH Research Institute, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0002803PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2481391PMC
July 2008

Decoupled differentiation of gene expression and coding sequence among Drosophila populations.

Authors:
Michael H Kohn Joshua Shapiro Chung-I Wu

Genes Genet Syst 2008 Jun;83(3):265-73

Department of Ecology & Evolutionary Biology, Rice University, Houston, TX 77005, USA.

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June 2008

Adaptive evolution of newly emerged micro-RNA genes in Drosophila.

Authors:
Jian Lu Yonggui Fu Supriya Kumar Yang Shen Kai Zeng Anlong Xu Richard Carthew Chung-I Wu

Mol Biol Evol 2008 May 22;25(5):929-38. Epub 2008 Feb 22.

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

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http://dx.doi.org/10.1093/molbev/msn040DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3707409PMC
May 2008

Testing a hypothesis of unidirectional hybridization in plants: observations on Sonneratia, Bruguiera and Ligularia.

Authors:
Renchao Zhou Xun Gong David Boufford Chung-I Wu Suhua Shi

BMC Evol Biol 2008 May 16;8:149. Epub 2008 May 16.

State Key Laboratory of Biocontrol and Key Laboratory of Gene Engineering of Ministry of Education, Sun Yat-Sen University, Guangzhou 510275, PR China.

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http://dx.doi.org/10.1186/1471-2148-8-149DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2409324PMC
May 2008

Complex genetic interactions underlying expression differences between Drosophila races: analysis of chromosome substitutions.

Authors:
Hurng-Yi Wang Yonggui Fu Mary Sara McPeek Xuemei Lu Sergey Nuzhdin Anlong Xu Jian Lu Mao-Lien Wu Chung-I Wu

Proc Natl Acad Sci U S A 2008 Apr 22;105(17):6362-7. Epub 2008 Apr 22.

Graduate Institute of Clinical Medicine, National Taiwan University, 7 Chung-Shan South Road, Taipei 100, Taiwan.

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http://dx.doi.org/10.1073/pnas.0711774105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2359775PMC
April 2008

The birth and death of microRNA genes in Drosophila.

Authors:
Jian Lu Yang Shen Qingfa Wu Supriya Kumar Bin He Suhua Shi Richard W Carthew San Ming Wang Chung-I Wu

Nat Genet 2008 Mar 17;40(3):351-5. Epub 2008 Feb 17.

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

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http://dx.doi.org/10.1038/ng.73DOI Listing
March 2008

Population genetics of speciation in nonmodel organisms: I. Ancestral polymorphism in mangroves.

Authors:
Renchao Zhou Kai Zeng Wei Wu Xiaoshu Chen Ziheng Yang Suhua Shi Chung-I Wu

Mol Biol Evol 2007 Dec 28;24(12):2746-54. Epub 2007 Sep 28.

State Key Laboratory of Biocontrol and Key Laboratory of Gene Engineering of the Ministry of Education, Sun Yat-Sen University, Guangzhou, China.

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http://dx.doi.org/10.1093/molbev/msm209DOI Listing
December 2007

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

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

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November 2007

Transcriptional regulation of human eosinophil RNases by an evolutionary- conserved sequence motif in primate genome.

Authors:
Hsiu-Yu Wang Hao-Teng Chang Tun-Wen Pai Chung-I Wu Yuan-Hung Lee Yen-Hsin Chang Hsiu-Ling Tai Chuan-Yi Tang Wei-Yao Chou Margaret Dah-Tsyr Chang

BMC Mol Biol 2007 Oct 11;8:89. Epub 2007 Oct 11.

Institute of Molecular and Cellular Biology & Department of Life Science, National Tsing Hua University, Hsinchu, Taiwan 30013, Republic of China.

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http://dx.doi.org/10.1186/1471-2199-8-89DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2174947PMC
October 2007

Compound tests for the detection of hitchhiking under positive selection.

Authors:
Kai Zeng Suhua Shi Chung-I Wu

Mol Biol Evol 2007 Aug 8;24(8):1898-908. Epub 2007 Jun 8.

State Key Laboratory of Biocontrol and Key Laboratory of Gene Engineering of the Ministry of Education, Sun Yat-Sen University, Guangzhou, China.

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http://dx.doi.org/10.1093/molbev/msm119DOI Listing
August 2007

Comparisons of site- and haplotype-frequency methods for detecting positive selection.

Authors:
Kai Zeng Shuhei Mano Suhua Shi Chung-I Wu

Mol Biol Evol 2007 Jul 21;24(7):1562-74. Epub 2007 Apr 21.

State Key Laboratory of Biocontrol and Key Laboratory of Gene Engineering of the Ministry of Education, Sun Yat-sen University, Guangzhou, China.

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http://dx.doi.org/10.1093/molbev/msm078DOI Listing
July 2007

Low concentrations of resveratrol potentiate the antiplatelet effect of prostaglandins.

Authors:
Chin-Chung Wu Chung-I Wu Wei-Ya Wang Yang-Chang Wu

Planta Med 2007 May;73(5):439-43

Graduate Institute of Nature Products, Kaohsiung Medical University, Kaohsiung City, Taiwan, ROC.

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http://dx.doi.org/10.1055/s-2007-967173DOI Listing
May 2007

The evaluation and structure-activity relationships of 2-benzoylaminobenzoic esters and their analogues as anti-inflammatory and anti-platelet aggregation agents.

Authors:
Pei-Wen Hsieh Tsong-Long Hwang Chin-Chung Wu Shin-Zan Chiang Chung-I Wu Yang-Chang Wu

Bioorg Med Chem Lett 2007 Mar 15;17(6):1812-7. Epub 2006 Dec 15.

Graduate Institute of Natural Products, Kaohsiung Medical University, Kaohsiung 807, Taiwan.

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http://dx.doi.org/10.1016/j.bmcl.2006.12.038DOI Listing
March 2007

Adaptive evolution in humans revealed by the negative correlation between the polymorphism and fixation phases of evolution.

Authors:
Jun Gojobori Hua Tang Joshua M Akey Chung-I Wu

Proc Natl Acad Sci U S A 2007 Mar 26;104(10):3907-12. Epub 2007 Feb 26.

Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.

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http://dx.doi.org/10.1073/pnas.0605565104DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1820682PMC
March 2007

Rate of evolution in brain-expressed genes in humans and other primates.

Authors:
Hurng-Yi Wang Huan-Chieh Chien Naoki Osada Katsuyuki Hashimoto Sumio Sugano Takashi Gojobori Chen-Kung Chou Shih-Feng Tsai Chung-I Wu C-K James Shen

PLoS Biol 2007 Feb;5(2):e13

Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan.

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http://dx.doi.org/10.1371/journal.pbio.0050013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1717015PMC
February 2007

Adaptive genic evolution in the Drosophila genomes.

Authors:
Joshua A Shapiro Wei Huang Chenhui Zhang Melissa J Hubisz Jian Lu David A Turissini Shu Fang Hurng-Yi Wang Richard R Hudson Rasmus Nielsen Zhu Chen Chung-I Wu

Proc Natl Acad Sci U S A 2007 Feb 6;104(7):2271-6. Epub 2007 Feb 6.

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

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http://dx.doi.org/10.1073/pnas.0610385104DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1892965PMC
February 2007

Statistical tests for detecting positive selection by utilizing high-frequency variants.

Authors:
Kai Zeng Yun-Xin Fu Suhua Shi Chung-I Wu

Genetics 2006 Nov 1;174(3):1431-9. Epub 2006 Sep 1.

State Key Laboratory of Biocontrol, Ministry of Education, Sun Yat-sen University, Guangzhou, China.

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http://dx.doi.org/10.1534/genetics.106.061432DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1667063PMC
November 2006

Genomic variation in rice: genesis of highly polymorphic linkage blocks during domestication.

Authors:
Tian Tang Jian Lu Jianzi Huang Jinghong He Susan R McCouch Yang Shen Zeng Kai Michael D Purugganan Suhua Shi Chung-I Wu

PLoS Genet 2006 Nov;2(11):e199

State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen (Zhongshan) University, Guangzhou, People's Republic of China.

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http://dx.doi.org/10.1371/journal.pgen.0020199DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1636696PMC
November 2006

Genomic inferences of the cis-regulatory nucleotide polymorphisms underlying gene expression differences between Drosophila melanogaster mating races.

Authors:
Naoki Osada Michael H Kohn Chung-I Wu

Mol Biol Evol 2006 Aug 5;23(8):1585-91. Epub 2006 Jun 5.

Division of Biomedical Research Resources, National Institute of Biomedical Innovation, Ibaraki, Osaka, Japan.

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http://academic.oup.com/mbe/article/23/8/1585/967525/Genomic
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http://dx.doi.org/10.1093/molbev/msl023DOI Listing
August 2006

Proceedings of the SMBE Tri-National Young Investigators' Workshop 2005. Molecular genetics of natural populations.

Authors:
Anthony J Greenberg Chung-I Wu

Mol Biol Evol 2006 May 16;23(5):883-6. Epub 2005 Dec 16.

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

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http://dx.doi.org/10.1093/molbev/msj077DOI Listing
May 2006

The accumulation of deleterious mutations in rice genomes: a hypothesis on the cost of domestication.

Authors:
Jian Lu Tian Tang Hua Tang Jianzi Huang Suhua Shi Chung-I Wu

Trends Genet 2006 Mar 27;22(3):126-31. Epub 2006 Jan 27.

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

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http://dx.doi.org/10.1016/j.tig.2006.01.004DOI Listing
March 2006

An ancient balanced polymorphism in a regulatory region of human major histocompatibility complex is retained in Chinese minorities but lost worldwide.

Authors:
Xiaoyi Liu Yonggui Fu Zehuan Liu Bin Lin Yi Xie Yin Liu Yunpin Xu Jianghai Lin Xinlan Fan Meiling Dong Kai Zeng Chung-I Wu Anlong Xu

Am J Hum Genet 2006 Mar 19;78(3):393-400. Epub 2006 Jan 19.

State Key Laboratory for Biocontrol, Department of Biochemistry, Key Laboratory of Genetic Engineering of the Ministry of Education, College of Life Sciences, Sun Yat-sen Zhongshan University, Guangzhou, China.

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http://dx.doi.org/10.1086/500593DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1380283PMC
March 2006

Proper control of genetic background with precise allele substitution: a comment on Coyne and Elwyn.

Authors:
Anthony J Greenberg Jennifer R Moran Chung-I Wu

Evolution 2006 Mar;60(3):623-5; discussion 626-7

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

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March 2006

A new method for estimating nonsynonymous substitutions and its applications to detecting positive selection.

Authors:
Hua Tang Chung-I Wu

Mol Biol Evol 2006 Feb 19;23(2):372-9. Epub 2005 Oct 19.

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

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http://dx.doi.org/10.1093/molbev/msj043DOI Listing
February 2006

Adaptive loss of an old duplicated gene during incipient speciation.

Authors:
Anthony J Greenberg Jennifer R Moran Shu Fang Chung-I Wu

Mol Biol Evol 2006 Feb 26;23(2):401-10. Epub 2005 Oct 26.

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

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http://dx.doi.org/10.1093/molbev/msj045DOI Listing
February 2006

Substitution rate and structural divergence of 5'UTR evolution: comparative analysis between human and cynomolgus monkey cDNAs.

Authors:
Naoki Osada Makoto Hirata Reiko Tanuma Jun Kusuda Munetomo Hida Yutaka Suzuki Sumio Sugano Takashi Gojobori C-K James Shen Chung-I Wu Katsuyuki Hashimoto

Mol Biol Evol 2005 Oct 8;22(10):1976-82. Epub 2005 Jun 8.

Division of Genetic Resources, National Institute of Infectious Diseases, Tokyo, Japan.

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http://dx.doi.org/10.1093/molbev/msi187DOI Listing
October 2005

Molecular criteria for determining new hybrid species--an application to the Sonneratia hybrids.

Authors:
Renchao Zhou Suhua Shi Chung-I Wu

Mol Phylogenet Evol 2005 Jun 11;35(3):595-601. Epub 2005 Apr 11.

State Key Laboratory of Biocontrol and Key Laboratory of Gene Engineering of the Ministry of Education, Zhongshan University, Guangzhou 510275, People's Republic of China.

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http://dx.doi.org/10.1016/j.ympev.2005.03.012DOI Listing
June 2005

Detecting novel low-abundant transcripts in Drosophila.

Authors:
Sanggyu Lee Jingyue Bao Guolin Zhou Joshua Shapiro Jinhua Xu Run Zhang Shi Xuemei Lu Terry Clark Deborah Johnson Yeong C Kim Claudia Wing Charles Tseng Min Sun Wei Lin Jun Wang Huanming Yang Jian Wang Wei Du Chung-I Wu Xiuqing Zhang San Ming Wang

RNA 2005 Jun;11(6):939-46

Department of Medicine, University of Chicago, IL 60637, USA.

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http://dx.doi.org/10.1261/rna.7239605DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1370778PMC
June 2005

Evolution of sexual isolation during secondary contact: genotypic versus phenotypic changes in laboratory populations.

Authors:
Julie A Alipaz Shu Fang Naoki Osada Chung-I Wu

Am Nat 2005 Apr 28;165(4):420-8. Epub 2005 Feb 28.

Committee on Evolutionary Biology, University of Chicago, Chicago, Illinois 60637, USA.

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http://dx.doi.org/10.1086/428388DOI Listing
April 2005

Evolution of sexual isolation in laboratory populations: fitness differences between mating types and the associated hybrid incompatibilities.

Authors:
Julie A Alipaz Timothy L Karr Chung-I Wu

Am Nat 2005 Apr 28;165(4):429-38. Epub 2005 Feb 28.

Committee on Evolutionary Biology, University of Chicago, Chicago, Illinois 60637, USA.

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http://dx.doi.org/10.1086/428407DOI Listing
April 2005

Weak selection revealed by the whole-genome comparison of the X chromosome and autosomes of human and chimpanzee.

Authors:
Jian Lu Chung-I Wu

Proc Natl Acad Sci U S A 2005 Mar 23;102(11):4063-7. Epub 2005 Feb 23.

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

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http://dx.doi.org/10.1073/pnas.0500436102DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC554819PMC
March 2005

Cross-host evolution of severe acute respiratory syndrome coronavirus in palm civet and human.

Authors:
Huai-Dong Song Chang-Chun Tu Guo-Wei Zhang Sheng-Yue Wang Kui Zheng Lian-Cheng Lei Qiu-Xia Chen Yu-Wei Gao Hui-Qiong Zhou Hua Xiang Hua-Jun Zheng Shur-Wern Wang Chern Feng Cheng Chun-Ming Pan Hua Xuan Sai-Juan Chen Hui-Ming Luo Duan-Hua Zhou Yu-Fei Liu Jian-Feng He Peng-Zhe Qin Ling-Hui Li Yu-Qi Ren Wen-Jia Liang Ye-Dong Yu Larry Anderson Ming Wang Rui-Heng Xu Xin-Wei Wu Huan-Ying Zheng Jin-Ding Chen Guodong Liang Yang Gao Ming Liao Ling Fang Li-Yun Jiang Hui Li Fang Chen Biao Di Li-Juan He Jin-Yan Lin Suxiang Tong Xiangang Kong Lin Du Pei Hao Hua Tang Andrea Bernini Xiao-Jing Yu Ottavia Spiga Zong-Ming Guo Hai-Yan Pan Wei-Zhong He Jean-Claude Manuguerra Arnaud Fontanet Antoine Danchin Neri Niccolai Yi-Xue Li Chung-I Wu Guo-Ping Zhao

Proc Natl Acad Sci U S A 2005 Feb 4;102(7):2430-5. Epub 2005 Feb 4.

State Key Laboratory for Medical Genomics/Pôle Sino-Français de Recherche en Sciences du Vivant et Génomique, Ruijin Hospital Affiliated to Shanghai Second Medical University, 197 Rui Jin Road II, Shanghai 200025, China.

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http://dx.doi.org/10.1073/pnas.0409608102DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC548959PMC
February 2005