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Interacting networks of resistance, virulence and core machinery genes identified by genome-wide epistasis analysis 期刊论文
PLOS GENETICS, 2017, 卷号: 13, 期号: 2, 页码: e1006508
Authors:  Skwark, MJ;  Croucher, NJ;  Puranen, S;  Chewapreecha, C;  Pesonen, M;  Xu, YY;  Turner, P;  Harris, SR;  Beres, SB;  Musser, JM;  Parkhill, J;  Bentley, SD;  Aurell, E;  Corander, J;  Corander, J (reprint author), Wellcome Trust Sanger Inst, Pathogen Gen, Cambridge, England.;  Aurell, E (reprint author), KTH Royal Inst Technol, Dept Computat Biol, Stockholm, Sweden.;  Aurell, E (reprint author), Aalto Univ, Dept Appl Phys & Comp Sci, Espoo, Finland.;  Aurell, E (reprint author), Chinese Acad Sci, Inst Theoret Phys, Beijing, Peoples R China.;  Corander, J (reprint author), Univ Helsinki, Dept Math & Stat, Helsinki, Finland.;  Corander, J (reprint author), Univ Oslo, Dept Biostat, Oslo, Norway.;  Corander, J (reprint author), Univ Cambridge, Dept Vet Med, Cambridge, England.
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Improving residue-residue contact prediction via low-rank and sparse decomposition of residue correlation matrix 期刊论文
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 2016, 卷号: 472, 期号: 1, 页码: 217-222
Authors:  Zhang, HC;  Gao, YJ;  Deng, MH;  Wang, C;  Zhu, JW;  Li, SC;  Zheng, WM;  Bu, DB;  Bu, DB (reprint author), Chinese Acad Sci, Inst Comp Technol, Key Lab Intelligent Informat Proc, Beijing, Peoples R China.;  Zheng, WM (reprint author), Chinese Acad Sci, Inst Theoret Phys, Beijing 100080, Peoples R China.
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Protein Contacts Prediction  Correlation Analysis  Background Correlation Removal  Low-rank And Sparse Matrix Decomposition  
Improving residue-residue contact prediction via low-rank and sparse decomposition of residue correlation matrix 期刊论文
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 2016, 卷号: 472, 期号: 1, 页码: 217-222
Authors:  Zhang, HC;  Gao, YJ;  Deng, MH;  Wang, C;  Zhu, JW;  Li, SC;  Zheng, WM;  Bu, DB
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Protein contacts prediction  MULTIPLE SEQUENCE ALIGNMENTS  Correlation analysis  COEVOLUTION  Background correlation removal  MUTATIONS  Low-rank and sparse matrix decomposition  PROTEINS  EVOLUTIONARY  INFORMATION  COVARIANCE  SEARCH  
Conditional entropy in variation-adjusted windows detects selection signatures associated with expression quantitative trait loci (eQTLs) 期刊论文
BMC GENOMICS, 2015, 卷号: 16, 期号: 0, 页码: S8
Authors:  Handelman, SK;  Seweryn, M;  Smith, RM;  Hartmann, K;  Wang, DX;  Pietrzak, M;  Johnson, AD;  Kloczkowski, A;  Sadee, W;  Handelman, SK (reprint author), Ohio State Univ, Coll Med, Ctr Pharmacogen, Graves Hall,330 W 10th Ave, Columbus, OH 43210 USA.
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Self-organizing approach for meta-genomes 期刊论文
COMPUTATIONAL BIOLOGY AND CHEMISTRY, 2014, 卷号: 53, 期号: Part A, 页码: 118-124
Authors:  Zhu, JF;  Zheng, WM;  Zheng, WM (reprint author), Acad Sinica, Inst Theoret Phys, Beijing 100190, Peoples R China.
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Protein-coding Regions  Microbial Genomes  Dna  Sequences  Diversity  Obesity  Flora  
Composition vector approach to whole-genome-based prokaryotic phylogeny: Success and foundations 期刊论文
JOURNAL OF BIOTECHNOLOGY, 2010, 卷号: 149, 期号: 3, 页码: 115-119
Authors:  Li, Qiang;  Xu, Zhao;  Hao, Bailin;  Hao, BL , Fudan Univ, Dept Phys, T Life Res Ctr, 220 Handan Rd, Shanghai 200433, Peoples R China
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Molecular Phylogeny  Trees  Reconstruction  Sequences  Evolution  Taxonomy  
CVTree update: a newly designed phylogenetic study platform using composition vectors and whole genomes 期刊论文
NUCLEIC ACIDS RESEARCH, 2009, 卷号: 37, 期号: suppl.2, 页码: W174-W178
Authors:  Xu, Zhao;  Hao, Bailin;  Xu, Z , Fudan Univ, T Life Res Ctr, 220 Handan Rd, Shanghai 200433, Peoples R China
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Prokaryote Phylogeny  Molecular Phylogeny  Trees  Reconstruction  Life  Tool  
Prokaryotic branch of the Tree of Life: A composition vector approach 期刊论文
JOURNAL OF SYSTEMATICS AND EVOLUTION, 2008, 卷号: 46, 期号: 3, 页码: 258-262
Authors:  Bai-Lin Hao;  Lei Gao;  Hao, BL , Fudan Univ, T Life Res Ctr, Shanghai 200433, Peoples R China
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Molecular Phylogeny  Sequence Alignment  Genomes  Reconstruction  Proteins  
Whole genome molecular phylogeny of large dsDNA viruses using composition vector method 期刊论文
BMC EVOLUTIONARY BIOLOGY, 2007, 卷号: 7, 期号: 1, 页码: -
Authors:  Gao, Lei;  Qi, Ji;  Gao, L , Acad Sinica, Inst Theoret Phys, Beijing 100080, Peoples R China
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World Monkey Adenovirus  Large Dna Viruses  Sequence-analysis  Cellular Genes  Common Origin  Evolution  Hosts  Herpesvirus  Baculovirus  Protein  
TreeFam: a curated database of phylogenetic trees of animal gene families 期刊论文
NUCLEIC ACIDS RESEARCH, 2006, 卷号: 34, 期号: 34, 页码: D572-D580
Authors:  Li, Heng;  Coghlan, Avril;  Ruan, Jue;  Coin, Lachlan James;  Heriche, Jean-Karim;  Osmotherly, Lara;  Li, Ruiqiang;  Liu, Tao;  Zhang, Zhang;  Bolund, Lars;  Wong, Gane Ka-Shu;  Zheng, Weimou;  Dehal, Paramvir;  Wang, Jun;  Durbin, Richard;  Durbin, R , Wellcome Trust Sanger Inst, Wellcome Trust Genome Campus, Cambridge CB10 1SA, England
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Protein Families  Multigene Family  Genome  Orthologs  Phylogenomics  Paralogs  Duplication  Vertebrate  Resources  Evolution