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154 results on '"Hao, Bailin"'

1. Compositional representation of protein sequences and the number of Eulerian loops

Author

Hao, Bailin, Xie, Huimin, and Zhang, Shuyu

Subjects
Physics - Biological Physics, Quantitative Biology
Abstract

An amino acid sequence of a protein may be decomposed into consecutive overlapping strings of length K. How unique is the converse, i.e., reconstruction of amino acid sequences using the set of K-strings obtained in the decomposition? This problem may be transformed into the problem of counting the number of Eulerian loops in an Euler graph, though the well-known formula must be modified. By exhaustive enumeration and by using the modified formula we show that the reconstruction is unique at K equal or greater than 5 for an overwhelming majority of the proteins in the PDB.seq database. The corresponding Euler graphs provide a means to study the structure of repeated segments in protein sequences., Comment: 5 pages, no figure, 2 tables, RevTex3.1

Published
2001

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

Author

Wang, Hao, Xu, Zhao, Gao, Lei, and Hao, Bailin

Abstract

Abstract Background Molecular phylogenetics and phylogenomics have greatly revised and enriched the fungal systematics in the last two decades. Most of the analyses have been performed by comparing single or multiple orthologous gene regions. Sequence alignment has always been an essential element in tree construction. These alignment-based methods (to be called the standard methods hereafter) need independent verification in order to put the fungal Tree of Life (TOL) on a secure footing. The ever-increasing number of sequenced fungal genomes and the recent success of our newly proposed alignment-free composition vector tree (CVTree, see Methods) approach have made the verification feasible. Results In all, 82 fungal genomes covering 5 phyla were obtained from the relevant genome sequencing centers. An unscaled phylogenetic tree with 3 outgroup species was constructed by using the CVTree method. Overall, the resultant phylogeny infers all major groups in accordance with standard methods. Furthermore, the CVTree provides information on the placement of several currently unsettled groups. Within the sub-phylum Pezizomycotina, our phylogeny places the Dothideomycetes and Eurotiomycetes as sister taxa. Within the Sordariomycetes, it infers that Magnaporthe grisea and the Plectosphaerellaceae are closely related to the Sordariales and Hypocreales, respectively. Within the Eurotiales, it supports that Aspergillus nidulans is the early-branching species among the 8 aspergilli. Within the Onygenales, it groups Histoplasma and Paracoccidioides together, supporting that the Ajellomycetaceae is a distinct clade from Onygenaceae. Within the sub-phylum Saccharomycotina, the CVTree clearly resolves two clades: (1) species that translate CTG as serine instead of leucine (the CTG clade) and (2) species that have undergone whole-genome duplication (the WGD clade). It places Candida glabrata at the base of the WGD clade. Conclusion Using different input data and methodology, the CVTree approach is a good complement to the standard methods. The remarkable consistency between them has brought about more confidence to the current understanding of the fungal branch of TOL.

Published
2009

4. Advanced Topics in Bioinformatics and Computational Biology

Author

Hao, Bailin, Zhang, Chunting, Li, Yixue, Li, Hao, Wei, Liping, Kanehisa, Minoru, Lai, Luhua, Chen, Runsheng, Rajewsky, Nikolaus, Zhang, Michael Q., Han, Jingdong, Jiang, Rui, Zhang, Xuegong, Li, Yanda, Jiang, Rui, editor, Zhang, Xuegong, editor, and Zhang, Michael Q., editor

Published
2013
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15. The DNA sequence, annotation and analysis of human chromosome 3

Author

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

Subjects
Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): Donna M. Muzny [1]; Steven E. Scherer (corresponding author) [1]; Rajinder Kaul [2]; Jing Wang [3]; Jun Yu [3]; Ralf Sudbrak [4, 5]; Christian J. Buhay [1]; Rui Chen [...]

Published
2006
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18. A draft sequence of the rice (Oryza sativa ssp.indica) genome

Author

Yu, Jun, Hu, Songnian, Wang, Jun, Li, Songgang, Wong, Ka-Shu Gane, Liu, Bin, Deng, Yajun, Dai, Li, Zhou, Yan, Zhang, Xiuqing, Cao, Mengliang, Liu, Jing, Sun, Jiandong, Tang, Jiabin, Chen, Yanjiong, Huang, Xiaobing, Lin, Wei, Ye, Chen, Tong, Wei, Cong, Lijuan, Geng, Jianing, Han, Yujun, Li, Lin, Li, Wei, Hu, Guangqiang, Huang, Xiangang, Li, Wenjie, Li, Jian, Liu, Zhanwei, Li, Long, Liu, Jianping, Qi, Qiuhui, Liu, Jinsong, Li, Li, Wang, Xuegang, Lu, Hong, Wu, Tingting, Zhu, Miao, Ni, Peixiang, Han, Hua, Dong, Wei, Ren, Xiaoyu, Feng, Xiaoli, Cui, Peng, Li, Xianran, Wang, Hao, Xu, Xin, Zhai, Wenxue, Xu, Zhao, Zhang, Jinsong, He, Sijie, Zhang, Jianguo, Xu, Jichen, Zhang, Kunlin, Zheng, Xianwu, Dong, Jianhai, Zeng, Wanyong, Tao, Lin, Chen, Xuewei, He, Jun, Liu, Daofeng, Tian, Wei, Tian, Chaoguang, Xia, Hongai, Li, Gang, Gao, Hui, Li, Ping, Chen, Wei, Wang, Xudong, Zhang, Yong, Hu, Jianfei, Wang, Jing, Liu, Song, Yang, Jian, Zhang, Guangyu, Xiong, Yuqing, Li, Zhijie, Mao, Long, Zhou, Chengshu, Zhu, Zhen, Chen, Runsheng, Hao, Bailin, Zheng, Weimou, Chen, Shouyi, Guo, Wei, Li, Guojie, Liu, Siqi, Huang, Guyang, Tao, Ming, Wang, Jian, Zhu, Lihuang, Yuan, Longping, and Yang, Huanming

Published
2001
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22. Combinatorics from Bacterial Genomes

Author

Hao, Bailin, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Doug, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Dress, Andreas, editor, Xu, Yinfeng, editor, and Zhu, Binhai, editor

Published
2007
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24. A Draft Sequence of the Rice Genome (Oryza sativa L. ssp. indica)

Author

Yu, Jun, Hu, Songnian, Wang, Jun, Wong, Gane Ka-Shu, Li, Songgang, Liu, Bin, Deng, Yajun, Dai, Li, Zhou, Yan, Zhang, Xiuqing, Cao, Mengliang, Liu, Jing, Sun, Jiandong, Tang, Jiabin, Chen, Yanjiong, Huang, Xiaobing, Lin, Wei, Ye, Chen, Tong, Wei, Cong, Lijuan, Geng, Jianing, Han, Yujun, Li, Lin, Li, Wei, Hu, Guangqiang, Huang, Xiangang, Li, Wenjie, Li, Jian, Liu, Zhanwei, Li, Long, Liu, Jianping, Qi, Qiuhui, Liu, Jinsong, Li, Li, Li, Tao, Wang, Xuegang, Lu, Hong, Wu, Tingting, Zhu, Miao, Ni, Peixiang, Han, Hua, Dong, Wei, Ren, Xiaoyu, Feng, Xiaoli, Cui, Peng, Li, Xianran, Wang, Hao, Xu, Xin, Zhai, Wenxue, Xu, Zhao, Zhang, Jinsong, He, Sijie, Zhang, Jianguo, Xu, Jichen, Zhang, Kunlin, Zheng, Xianwu, Dong, Jianhai, Zeng, Wanyong, Tao, Lin, Ye, Jia, Tan, Jun, Ren, Xide, Chen, Xuewei, He, Jun, Liu, Daofeng, Tian, Wei, Tian, Chaoguang, Xia, Hongai, Bao, Qiyu, Li, Gang, Gao, Hui, Cao, Ting, Wang, Juan, Zhao, Wenming, Li, Ping, Chen, Wei, Wang, Xudong, Zhang, Yong, Hu, Jianfei, Wang, Jing, Liu, Song, Yang, Jian, Zhang, Guangyu, Xiong, Yuqing, Li, Zhijie, Mao, Long, Zhou, Chengshu, Zhu, Zhen, Chen, Runsheng, Hao, Bailin, Zheng, Weimou, Chen, Shouyi, Guo, Wei, Li, Guojie, Liu, Siqi, Tao, Ming, Wang, Jian, Zhu, Lihuang, Yuan, Longping, and Yang, Huanming

Published
2002

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

Author

Gao Lei, Xu Zhao, Wang Hao, and Hao Bailin

Subjects
Evolution, QH359-425
Abstract

Abstract Background Molecular phylogenetics and phylogenomics have greatly revised and enriched the fungal systematics in the last two decades. Most of the analyses have been performed by comparing single or multiple orthologous gene regions. Sequence alignment has always been an essential element in tree construction. These alignment-based methods (to be called the standard methods hereafter) need independent verification in order to put the fungal Tree of Life (TOL) on a secure footing. The ever-increasing number of sequenced fungal genomes and the recent success of our newly proposed alignment-free composition vector tree (CVTree, see Methods) approach have made the verification feasible. Results In all, 82 fungal genomes covering 5 phyla were obtained from the relevant genome sequencing centers. An unscaled phylogenetic tree with 3 outgroup species was constructed by using the CVTree method. Overall, the resultant phylogeny infers all major groups in accordance with standard methods. Furthermore, the CVTree provides information on the placement of several currently unsettled groups. Within the sub-phylum Pezizomycotina, our phylogeny places the Dothideomycetes and Eurotiomycetes as sister taxa. Within the Sordariomycetes, it infers that Magnaporthe grisea and the Plectosphaerellaceae are closely related to the Sordariales and Hypocreales, respectively. Within the Eurotiales, it supports that Aspergillus nidulans is the early-branching species among the 8 aspergilli. Within the Onygenales, it groups Histoplasma and Paracoccidioides together, supporting that the Ajellomycetaceae is a distinct clade from Onygenaceae. Within the sub-phylum Saccharomycotina, the CVTree clearly resolves two clades: (1) species that translate CTG as serine instead of leucine (the CTG clade) and (2) species that have undergone whole-genome duplication (the WGD clade). It places Candida glabrata at the base of the WGD clade. Conclusion Using different input data and methodology, the CVTree approach is a good complement to the standard methods. The remarkable consistency between them has brought about more confidence to the current understanding of the fungal branch of TOL.

Published
2009
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32. Polyphyly in 16S rRNA-based LVTree VersusMonophyly in Whole-genome-based CVTree

Author

Zuo, Guanghong, Qi, Ji, and Hao, Bailin

Abstract

We report an important but long-overlooked manifestation of low-resolution power of 16S rRNA sequenceanalysis at the species level, namely, in 16S rRNA-based phylogenetic trees polyphyletic placements of closely-related species are abundant compared to those in genome-based phylogeny. This phenomenon makes the demarcation of genera within many families ambiguous in the 16S rRNA-based taxonomy. In this study, we reconstructed phylogenetic relationship for more than ten thousand prokaryote genomes using the CVTreemethod, which is based on whole-genome information. And many such genera, which are polyphyletic in 16S rRNA-based trees, are well resolved as monophyletic clusters by CVTree. We believe that with genome sequencing of prokaryotes becoming a commonplace, genome-based phylogeny is doomed to play a definitive role in the construction of a natural and objective taxonomy.

Published
2024
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41. Polyphyly in 16S rRNA-Based LVTree VersusMonophyly in Whole-Genome-Based CVTree

Author

Zuo, Guanghong, Qi, Ji, and Hao, Bailin

Abstract

We report an important but long-overlooked manifestation of low-resolution power of 16S rRNA sequenceanalysis at the species level, namely, in 16S rRNA-based phylogenetic trees polyphyletic placements of closely-related species are abundant compared to those in genome-based phylogeny. This phenomenon makes the demarcation of genera within many families ambiguous in the 16S rRNA-based taxonomy. In this study, we reconstructed phylogenetic relationship for more than ten thousand prokaryote genomes using the CVTreemethod, which is based on whole-genome information. And many such genera, which are polyphyletic in 16S rRNA-based trees, are well resolved as monophyletic clusters by CVTree. We believe that with genome sequencing of prokaryotes becoming a commonplace, genome-based phylogeny is doomed to play a definitive role in the construction of a natural and objective taxonomy.

Published
2018
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45. A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms.

Author

Wong, Gane Ka-Shu, Liu, Bin, Wang, Jun, Zhang, Yong, Yang, Xu, Zhang, Zengjin, Meng, Qingshun, Zhou, Jun, Li, Dawei, Zhang, Jingjing, Ni, Peixiang, Li, Songgang, Ran, Longhua, Li, Heng, Zhang, Jianguo, Li, Ruiqiang, Li, Shengting, Zheng, Hongkun, Lin, Wei, Li, Guangyuan, Wang, Xiaoling, Zhao, Wenming, Li, Jun, Ye, Chen, Dai, Mingtao, Ruan, Jue, Zhou, Yan, Li, Yuanzhe, He, Ximiao, Zhang, Yunze, Wang, Jing, Huang, Xiangang, Tong, Wei, Chen, Jie, Ye, Jia, Chen, Chen, Wei, Ning, Li, Guoqing, Dong, Le, Lan, Fengdi, Sun, Yongqiao, Zhang, Zhenpeng, Yang, Zheng, Yu, Yingpu, Huang, Yanqing, He, Dandan, Xi, Yan, Wei, Dong, Qi, Qiuhui, Li, Wenjie, Shi, Jianping, Wang, Miaoheng, Xie, Fei, Wang, Jianjun, Zhang, Xiaowei, Wang, Pei, Zhao, Yiqiang, Li, Ning, Yang, Ning, Dong, Wei, Hu, Songnian, Zeng, Changqing, Zheng, Weimou, Hao, Bailin, Hillier, Ladeana W, Yang, Shiaw-Pyng, Warren, Wesley C, Wilson, Richard K, Brandström, Mikael, Ellegren, Hans, Crooijmans, Richard P M A, van der Poel, Jan J, Bovenhuis, Henk, Groenen, Martien A M, Ovcharenko, Ivan, Gordon, Laurie, Stubbs, Lisa, Lucas, Susan, Glavina, Tijana, Aerts, Andrea, Kaiser, Pete, Rothwell, Lisa, Young, John R, Rogers, Sally, Walker, Brian A, van Hateren, Andy, Kaufman, Jim, Bumstead, Nat, Lamont, Susan J, Zhou, Huaijun, Hocking, Paul M, Morrice, David, de Koning, Dirk-Jan, Law, Andy, Bartley, Neil, Burt, David W, Hunt, Henry, Cheng, Hans H, Gunnarsson, Ulrika, Wahlberg, Per, Andersson, Leif, Kindlund, Ellen, Tammi, Martti T, Andersson, Björn, Webber, Caleb, Ponting, Chris P, Overton, Ian M, Boardman, Paul E, Tang, Haizhou, Hubbard, Simon J, Wilson, Stuart A, Yu, Jun, Wang, Jian, Yang, Huanming, Wong, Gane Ka-Shu, Liu, Bin, Wang, Jun, Zhang, Yong, Yang, Xu, Zhang, Zengjin, Meng, Qingshun, Zhou, Jun, Li, Dawei, Zhang, Jingjing, Ni, Peixiang, Li, Songgang, Ran, Longhua, Li, Heng, Zhang, Jianguo, Li, Ruiqiang, Li, Shengting, Zheng, Hongkun, Lin, Wei, Li, Guangyuan, Wang, Xiaoling, Zhao, Wenming, Li, Jun, Ye, Chen, Dai, Mingtao, Ruan, Jue, Zhou, Yan, Li, Yuanzhe, He, Ximiao, Zhang, Yunze, Wang, Jing, Huang, Xiangang, Tong, Wei, Chen, Jie, Ye, Jia, Chen, Chen, Wei, Ning, Li, Guoqing, Dong, Le, Lan, Fengdi, Sun, Yongqiao, Zhang, Zhenpeng, Yang, Zheng, Yu, Yingpu, Huang, Yanqing, He, Dandan, Xi, Yan, Wei, Dong, Qi, Qiuhui, Li, Wenjie, Shi, Jianping, Wang, Miaoheng, Xie, Fei, Wang, Jianjun, Zhang, Xiaowei, Wang, Pei, Zhao, Yiqiang, Li, Ning, Yang, Ning, Dong, Wei, Hu, Songnian, Zeng, Changqing, Zheng, Weimou, Hao, Bailin, Hillier, Ladeana W, Yang, Shiaw-Pyng, Warren, Wesley C, Wilson, Richard K, Brandström, Mikael, Ellegren, Hans, Crooijmans, Richard P M A, van der Poel, Jan J, Bovenhuis, Henk, Groenen, Martien A M, Ovcharenko, Ivan, Gordon, Laurie, Stubbs, Lisa, Lucas, Susan, Glavina, Tijana, Aerts, Andrea, Kaiser, Pete, Rothwell, Lisa, Young, John R, Rogers, Sally, Walker, Brian A, van Hateren, Andy, Kaufman, Jim, Bumstead, Nat, Lamont, Susan J, Zhou, Huaijun, Hocking, Paul M, Morrice, David, de Koning, Dirk-Jan, Law, Andy, Bartley, Neil, Burt, David W, Hunt, Henry, Cheng, Hans H, Gunnarsson, Ulrika, Wahlberg, Per, Andersson, Leif, Kindlund, Ellen, Tammi, Martti T, Andersson, Björn, Webber, Caleb, Ponting, Chris P, Overton, Ian M, Boardman, Paul E, Tang, Haizhou, Hubbard, Simon J, Wilson, Stuart A, Yu, Jun, Wang, Jian, and Yang, Huanming

Published
2004

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