Chuanzhu Fan

Chuanzhu Fan

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Chuanzhu Fan

Chuanzhu Fan

Publications by authors named "Chuanzhu Fan"

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31Publications

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Phylogenomic Analysis and Dynamic Evolution of Chloroplast Genomes in Salicaceae.

Front Plant Sci 2017 20;8:1050. Epub 2017 Jun 20.

Key Laboratory for Plant Diversity and Biogeography of East Asia, Chinese Academy of SciencesKunming, China.

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http://dx.doi.org/10.3389/fpls.2017.01050DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5476734PMC
June 2017

Evolutionary Fates and Dynamic Functionalization of Young Duplicate Genes in Arabidopsis Genomes.

Plant Physiol 2016 09 2;172(1):427-40. Epub 2016 Aug 2.

Department of Biological Sciences, Wayne State University, Detroit, Michigan 48202

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http://dx.doi.org/10.1104/pp.16.01177DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5074645PMC
September 2016

DNA methylation changes facilitated evolution of genes derived from Mutator-like transposable elements.

Genome Biol 2016 05 6;17(1):92. Epub 2016 May 6.

Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, Detroit, MI, 48202, USA.

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http://dx.doi.org/10.1186/s13059-016-0954-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4858842PMC
May 2016

Divergence of gene body DNA methylation and evolution of plant duplicate genes.

PLoS One 2014 13;9(10):e110357. Epub 2014 Oct 13.

Department of Biological Sciences, Wayne State University, Detroit, Michigan, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0110357PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4195714PMC
December 2015

Detection, characterization and evolution of internal repeats in Chitinases of known 3-D structure.

PLoS One 2014 17;9(3):e91915. Epub 2014 Mar 17.

Department of Biological Sciences, Wayne State University, Detroit, Michigan, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0091915PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3956812PMC
January 2015

A neutrality test for detecting selection on DNA methylation using single methylation polymorphism frequency spectrum.

Genome Biol Evol 2014 Dec 23;7(1):154-71. Epub 2014 Dec 23.

Department of Biological Sciences, Wayne State University

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http://dx.doi.org/10.1093/gbe/evu271DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4316624PMC
December 2014

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.

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

Conservation and purifying selection of transcribed genes located in a rice centromere.

Plant Cell 2011 Aug 19;23(8):2821-30. Epub 2011 Aug 19.

Arizona Genomics Institute, School of Plant Sciences, Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA.

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http://dx.doi.org/10.1105/tpc.111.085605DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3180794PMC
August 2011

Spatio-temporal patterns of genome evolution in allotetraploid species of the genus Oryza.

Plant J 2010 Aug 6;63(3):430-42. Epub 2010 May 6.

Arizona Genomics Institute, School of Plant Sciences, BIO5 Institute, University of Arizona, Tucson, AZ 85721, USABiodiversity Synthesis Center, Field Museum of Natural History, 1400 South Lake Shore Drive, Chicago, IL 60605, USADepartment of Genetics, University of Georgia, Athens, GA 30602-7223, USAState Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, ChinaDepartment of Agronomy, Purdue University, West Lafayette, IN 47907-2054, USADepartment of Horticulture, Michigan State University, East Lansing, MI 48823, USA.

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http://dx.doi.org/10.1111/j.1365-313X.2010.04251.xDOI Listing
August 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.

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

A lineage-specific centromere retrotransposon in Oryza brachyantha.

Plant J 2009 Dec 21;60(5):820-31. Epub 2009 Aug 21.

Molecular and Evolutionary Genetics, Purdue University, 915 W. State Street, West Lafayette, IN 47907, USA.

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http://dx.doi.org/10.1111/j.1365-313X.2009.04005.xDOI Listing
December 2009

The B73 maize genome: complexity, diversity, and dynamics.

Authors:
Patrick S Schnable Doreen Ware Robert S Fulton Joshua C Stein Fusheng Wei Shiran Pasternak Chengzhi Liang Jianwei Zhang Lucinda Fulton Tina A Graves Patrick Minx Amy Denise Reily Laura Courtney Scott S Kruchowski Chad Tomlinson Cindy Strong Kim Delehaunty Catrina Fronick Bill Courtney Susan M Rock Eddie Belter Feiyu Du Kyung Kim Rachel M Abbott Marc Cotton Andy Levy Pamela Marchetto Kerri Ochoa Stephanie M Jackson Barbara Gillam Weizu Chen Le Yan Jamey Higginbotham Marco Cardenas Jason Waligorski Elizabeth Applebaum Lindsey Phelps Jason Falcone Krishna Kanchi Thynn Thane Adam Scimone Nay Thane Jessica Henke Tom Wang Jessica Ruppert Neha Shah Kelsi Rotter Jennifer Hodges Elizabeth Ingenthron Matt Cordes Sara Kohlberg Jennifer Sgro Brandon Delgado Kelly Mead Asif Chinwalla Shawn Leonard Kevin Crouse Kristi Collura Dave Kudrna Jennifer Currie Ruifeng He Angelina Angelova Shanmugam Rajasekar Teri Mueller Rene Lomeli Gabriel Scara Ara Ko Krista Delaney Marina Wissotski Georgina Lopez David Campos Michele Braidotti Elizabeth Ashley Wolfgang Golser HyeRan Kim Seunghee Lee Jinke Lin Zeljko Dujmic Woojin Kim Jayson Talag Andrea Zuccolo Chuanzhu Fan Aswathy Sebastian Melissa Kramer Lori Spiegel Lidia Nascimento Theresa Zutavern Beth Miller Claude Ambroise Stephanie Muller Will Spooner Apurva Narechania Liya Ren Sharon Wei Sunita Kumari Ben Faga Michael J Levy Linda McMahan Peter Van Buren Matthew W Vaughn Kai Ying Cheng-Ting Yeh Scott J Emrich Yi Jia Ananth Kalyanaraman An-Ping Hsia W Brad Barbazuk Regina S Baucom Thomas P Brutnell Nicholas C Carpita Cristian Chaparro Jer-Ming Chia Jean-Marc Deragon James C Estill Yan Fu Jeffrey A Jeddeloh Yujun Han Hyeran Lee Pinghua Li Damon R Lisch Sanzhen Liu Zhijie Liu Dawn Holligan Nagel Maureen C McCann Phillip SanMiguel Alan M Myers Dan Nettleton John Nguyen Bryan W Penning Lalit Ponnala Kevin L Schneider David C Schwartz Anupma Sharma Carol Soderlund Nathan M Springer Qi Sun Hao Wang Michael Waterman Richard Westerman Thomas K Wolfgruber Lixing Yang Yeisoo Yu Lifang Zhang Shiguo Zhou Qihui Zhu Jeffrey L Bennetzen R Kelly Dawe Jiming Jiang Ning Jiang Gernot G Presting Susan R Wessler Srinivas Aluru Robert A Martienssen Sandra W Clifton W Richard McCombie Rod A Wing Richard K Wilson

Science 2009 Nov;326(5956):1112-5

Center for Plant Genomics, Iowa State University, Ames, IA 50011, USA.

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http://www.dawelab.org/wp-content/uploads/2011/03/schnable-2
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http://www.sciencemag.org/cgi/doi/10.1126/science.1178534
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http://dx.doi.org/10.1126/science.1178534DOI Listing
November 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.

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http://linkinghub.elsevier.com/retrieve/pii/S167420521460360
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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.

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

Comprehensive sequence and expression profile analysis of PEX11 gene family in rice.

Gene 2008 Apr 26;412(1-2):59-70. Epub 2008 Jan 26.

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

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http://linkinghub.elsevier.com/retrieve/pii/S037811190800025
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http://dx.doi.org/10.1016/j.gene.2008.01.006DOI Listing
April 2008

Evolutionary patterns in the antR-Cor gene in the dwarf dogwood complex (Cornus, Cornaceae).

Genetica 2007 May 19;130(1):19-34. Epub 2006 Aug 19.

Department of Botany, North Carolina State University, Raleigh, NC 27695-7612, USA.

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http://dx.doi.org/10.1007/s10709-006-0016-3DOI Listing
May 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.

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

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.

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

Ancestral chloroplast polymorphism and historical secondary contact in a broad hybrid zone of Aesculus (Sapindaceae).

Am J Bot 2006 Mar;93(3):377-88

Department of Botany, North Carolina State University, Raleigh, North Carolina 27695-7612 USA.

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http://dx.doi.org/10.3732/ajb.93.3.377DOI Listing
March 2006

Phylogeny, biogeography, and molecular dating of cornelian cherries (Cornus, Cornaceae): tracking Tertiary plant migration.

Evolution 2005 Aug;59(8):1685-700

Department of Botany, North Carolina State University, Raleigh 27695-7612, USA.

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August 2005

Heterogeneous evolution of the Myc-like Anthocyanin regulatory gene and its phylogenetic utility in Cornus L. (Cornaceae).

Mol Phylogenet Evol 2004 Dec;33(3):580-94

Department of Botany, North Carolina State University, Raleigh, NC 27695-7612, USA.

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http://dx.doi.org/10.1016/j.ympev.2004.08.002DOI Listing
December 2004

Phylogenetic analyses of Cornales based on 26S rRNA and combined 26S rDNA-MATK-RBCL sequence data.

Am J Bot 2003 Sep;90(9):1357-72

Department of Botany, North Carolina State University, Campus Box 7612, Raleigh, North Carolina 27695-7612 USA.

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http://dx.doi.org/10.3732/ajb.90.9.1357DOI Listing
September 2003