Bailin Hao

Bailin Hao

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Bailin Hao

Bailin Hao

Publications by authors named "Bailin Hao"

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27Publications

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Polyphyly in 16S rRNA-based LVTree Versus Monophyly in Whole-genome-based CVTree.

Genomics Proteomics Bioinformatics 2018 10 11;16(5):310-319. Epub 2018 Dec 11.

T-Life Research Center, Department of Physics, Fudan University, Shanghai 200433, China.

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http://dx.doi.org/10.1016/j.gpb.2018.06.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6364046PMC
October 2018

On monospecific genera in prokaryotic taxonomy.

Synth Syst Biotechnol 2017 Sep 2;2(3):226-235. Epub 2017 Sep 2.

T-Life Research Center and Department of Physics, Fudan University, Shanghai 200433, China.

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http://dx.doi.org/10.1016/j.synbio.2017.08.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5655349PMC
September 2017

Whole-genome-based phylogeny supports the objections against the reclassification of Eubacterium rectale to Agathobacter rectalis.

Int J Syst Evol Microbiol 2016 Jun 31;66(6):2451. Epub 2016 Mar 31.

T-Life Research Center, Fudan University, Shanghai 200433, PR China.

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http://dx.doi.org/10.1099/ijsem.0.001047DOI Listing
June 2016

LVTree Viewer: An Interactive Display for the All-Species Living Tree Incorporating Automatic Comparison with Prokaryotic Systematics.

Genomics Proteomics Bioinformatics 2016 04 25;14(2):94-102. Epub 2016 Mar 25.

T-Life Research Center, Department of Physics, Fudan University, Shanghai 200433, China. Electronic address:

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http://dx.doi.org/10.1016/j.gpb.2015.12.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4880948PMC
April 2016

CVTree3 Web Server for Whole-genome-based and Alignment-free Prokaryotic Phylogeny and Taxonomy.

Genomics Proteomics Bioinformatics 2015 Oct 10;13(5):321-31. Epub 2015 Nov 10.

T-Life Research Center, Department of Physics, Fudan University, Shanghai 200433, China. Electronic address:

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http://dx.doi.org/10.1016/j.gpb.2015.08.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4678791PMC
October 2015

Phylogeny and Taxonomy of Archaea: A Comparison of the Whole-Genome-Based CVTree Approach with 16S rRNA Sequence Analysis.

Life (Basel) 2015 Mar 17;5(1):949-68. Epub 2015 Mar 17.

Life Research Center and Department of Physics, Fudan University, 220 Handan Road, Shanghai 200433, China.

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http://dx.doi.org/10.3390/life5010949DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4390887PMC
March 2015

On K-peptide length in composition vector phylogeny of prokaryotes.

Comput Biol Chem 2014 Dec 20;53 Pt A:166-73. Epub 2014 Aug 20.

T-Life Research Center, Fudan University, Shanghai 200433, China. Electronic address:

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http://dx.doi.org/10.1016/j.compbiolchem.2014.08.021DOI Listing
December 2014

Geographic divergence of "Sulfolobus islandicus" strains assessed by genomic analyses including electronic DNA hybridization confirms they are geovars.

Antonie Van Leeuwenhoek 2014 Feb 4;105(2):431-5. Epub 2013 Dec 4.

T-Life Research Center, Fudan University, Shanghai, 200433, China.

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http://dx.doi.org/10.1007/s10482-013-0081-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893479PMC
February 2014

Shigella strains are not clones of Escherichia coli but sister species in the genus Escherichia.

Genomics Proteomics Bioinformatics 2013 Feb 29;11(1):61-5. Epub 2012 Dec 29.

T-Life Research Center and Department of Physics, Fudan University, Shanghai 200433, China.

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http://dx.doi.org/10.1016/j.gpb.2012.11.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4357666PMC
February 2013

Jackknife and bootstrap tests of the composition vector trees.

Genomics Proteomics Bioinformatics 2010 Dec;8(4):262-7

T-Life Research Center & Department of Physics, Fudan University, Shanghai 200433, China.

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http://dx.doi.org/10.1016/S1672-0229(10)60028-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5054193PMC
December 2010

Composition vector approach to whole-genome-based prokaryotic phylogeny: success and foundations.

J Biotechnol 2010 Sep 29;149(3):115-9. Epub 2009 Dec 29.

T-Life Research Center, Fudan University, Shanghai 200433, China.

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http://dx.doi.org/10.1016/j.jbiotec.2009.12.015DOI Listing
September 2010

A fungal phylogeny based on 82 complete genomes using the composition vector method.

BMC Evol Biol 2009 Aug 10;9:195. Epub 2009 Aug 10.

T-life Research Center, Department of Physics, Fudan University, Shanghai 200433, PR China.

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http://bmcevolbiol.biomedcentral.com/articles/10.1186/1471-2
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http://dx.doi.org/10.1186/1471-2148-9-195DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3087519PMC
August 2009

A simple method for phylogenomic inference using the information of gene content of genomes.

Gene 2009 Jul 17;441(1-2):163-8. Epub 2008 Jul 17.

Department of Epidemiology and Biostatistics, University of South Carolina, Columbia, SC 29208, USA.

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http://dx.doi.org/10.1016/j.gene.2008.07.008DOI Listing
July 2009

CVTree update: a newly designed phylogenetic study platform using composition vectors and whole genomes.

Authors:
Zhao Xu Bailin Hao

Nucleic Acids Res 2009 Jul 26;37(Web Server issue):W174-8. Epub 2009 Apr 26.

T-Life Research Center, Fudan University, 220 Handan Road, Shanghai 200433, China.

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http://dx.doi.org/10.1093/nar/gkp278DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2703908PMC
July 2009

Prokaryote phylogeny meets taxonomy: an exhaustive comparison of composition vector trees with systematic bacteriology.

Sci China C Life Sci 2007 Oct;50(5):587-99

Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing 100080, China.

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http://dx.doi.org/10.1007/s11427-007-0084-3DOI Listing
October 2007

Prokaryote phylogeny without sequence alignment: from avoidance signature to composition distance.

Authors:
Bailin Hao Ji Qi

Proc IEEE Comput Soc Bioinform Conf 2003 ;2:375-84

T-Life Research Center, Fudan University, Shanghai, 200433, China.

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August 2006

The DNA sequence, annotation and analysis of human chromosome 3.

Authors:
Donna M Muzny Steven E Scherer Rajinder Kaul Jing Wang Jun Yu Ralf Sudbrak Christian J Buhay Rui Chen Andrew Cree Yan Ding Shannon Dugan-Rocha Rachel Gill Preethi Gunaratne R Alan Harris Alicia C Hawes Judith Hernandez Anne V Hodgson Jennifer Hume Andrew Jackson Ziad Mohid Khan Christie Kovar-Smith Lora R Lewis Ryan J Lozado Michael L Metzker Aleksandar Milosavljevic George R Miner Margaret B Morgan Lynne V Nazareth Graham Scott Erica Sodergren Xing-Zhi Song David Steffen Sharon Wei David A Wheeler Mathew W Wright Kim C Worley Ye Yuan Zhengdong Zhang Charles Q Adams M Ali Ansari-Lari Mulu Ayele Mary J Brown Guan Chen Zhijian Chen James Clendenning Kerstin P Clerc-Blankenburg Runsheng Chen Zhu Chen Clay Davis Oliver Delgado Huyen H Dinh Wei Dong Heather Draper Stephen Ernst Gang Fu Manuel L Gonzalez-Garay Dawn K Garcia Will Gillett Jun Gu Bailin Hao Eric Haugen Paul Havlak Xin He Steffen Hennig Songnian Hu Wei Huang Laronda R Jackson Leni S Jacob Susan H Kelly Michael Kube Ruth Levy Zhangwan Li Bin Liu Jing Liu Wen Liu Jing Lu Manjula Maheshwari Bao-Viet Nguyen Geoffrey O Okwuonu Anthony Palmeiri Shiran Pasternak Lesette M Perez Karen A Phelps Farah J H Plopper Boqin Qiang Christopher Raymond Ruben Rodriguez Channakhone Saenphimmachak Jireh Santibanez Hua Shen Yan Shen Sandhya Subramanian Paul E Tabor Daniel Verduzco Lenee Waldron Jian Wang Jun Wang Qiaoyan Wang Gabrielle A Williams Gane K-S Wong Zhijian Yao JingKun Zhang Xiuqing Zhang Guoping Zhao Jianling Zhou Yang Zhou David Nelson Hans Lehrach Richard Reinhardt Susan L Naylor Huanming Yang Maynard Olson George Weinstock Richard A Gibbs

Nature 2006 Apr;440(7088):1194-8

Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.

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http://dx.doi.org/10.1038/nature04728DOI Listing
April 2006

Visualization of K-tuple distribution in procaryote complete genomes and their randomized counterparts.

Proc IEEE Comput Soc Bioinform Conf 2002 ;1:31-42

Department of Mathematics, Suzhou University, Suzhou, 215006, China.

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May 2005

Duplication and DNA segmental loss in the rice genome: implications for diploidization.

New Phytol 2005 Mar;165(3):937-46

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

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http://dx.doi.org/10.1111/j.1469-8137.2004.01293.xDOI Listing
March 2005

The Genomes of Oryza sativa: a history of duplications.

PLoS Biol 2005 Feb 1;3(2):e38. Epub 2005 Feb 1.

Beijing Institute of Genomics of the Chinese Academy of Sciences, Beijing Genomics Institute, Beijing Proteomics Institute, China.

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http://dx.doi.org/10.1371/journal.pbio.0030038DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC546038PMC
February 2005

A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms.

Nature 2004 Dec;432(7018):717-22

Beijing Institute of Genomics of Chinese Academy of Sciences, Beijing Genomics Institute, Beijing Proteomics Institute, Beijing 101300, China.

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http://dx.doi.org/10.1038/nature03156DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2263125PMC
December 2004

Prokaryote phylogeny based on ribosomal proteins and aminoacyl tRNA synthetases by using the compositional distance approach.

Sci China C Life Sci 2004 Aug;47(4):313-21

College of Life Sciences, Zhejiang University, Hangzhou 310027, China.

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August 2004

SeeDNA: a visualization tool for K-string content of long DNA sequences and their randomized counterparts.

Genomics Proteomics Bioinformatics 2004 Aug;2(3):192-6

Department of Computer Science, Zhejiang University, Hangzhou 310027, China.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5172470PMC
http://dx.doi.org/10.1016/s1672-0229(04)02025-xDOI Listing
August 2004

CVTree: a phylogenetic tree reconstruction tool based on whole genomes.

Nucleic Acids Res 2004 Jul;32(Web Server issue):W45-7

The Institute of Theoretical Physics, Academia Sinica, Beijing 100080, China.

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http://dx.doi.org/10.1093/nar/gkh362DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC441500PMC
July 2004

Prokaryote phylogeny without sequence alignment: from avoidance signature to composition distance.

Authors:
Bailin Hao Ji Qi

J Bioinform Comput Biol 2004 Mar;2(1):1-19

T-Life Research Center, Fudan University, Shanghai 200433, China.

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March 2004

The transfer RNA genes in Oryza sativa L. ssp. indica.

Sci China C Life Sci 2002 Oct;45(5):504-11

College of Life Science, Peking University, 100871, Beijing, China.

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http://dx.doi.org/10.1360/02yc9055DOI Listing
October 2002