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Correlation-compressed direct-coupling analysis 期刊论文
PHYSICAL REVIEW E, 2018, 卷号: 98, 期号: 3, 页码: 32407
Authors:  Gao, CY;  Zhou, HJ;  Aurell, E
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STRUCTURE PREDICTION  PROTEIN-STRUCTURE  CONTACTS  IDENTIFICATION  MODEL  SEQUENCES  FAMILIES  HUMANS  
Template-based and free modeling of I-TASSER and QUARK pipelines using predicted contact maps in CASP12 期刊论文
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2018, 卷号: 86, 页码: 136-151
Authors:  Zhang, CX;  Mortuza, SM;  He, BJ;  Wang, YT;  Zhang, Y
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PROTEIN-STRUCTURE PREDICTION  RESIDUE CONTACTS  SEQUENCE  ALIGNMENTS  ACCURACY  NETWORKS  ROLL  
Improving protein fold recognition by extracting fold-specific features from predicted residue-residue contacts 期刊论文
BIOINFORMATICS, 2017, 卷号: 33, 期号: 23, 页码: 3749-3757
Authors:  Zhu, JW;  Zhang, HC;  Li, SC;  Wang, C;  Kong, LP;  Sun, SW;  Zheng, WM;  Bu, DB;  Bu, DB (reprint author), Chinese Acad Sci, Inst Comp Technol, Key Lab Intelligent Informat Proc, Beijing 100190, Peoples R China.;  Zheng, WM (reprint author), Chinese Acad Sci, Inst Theoret Phys, Beijing 100190, Peoples R China.
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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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NeBcon: protein contact map prediction using neural network training coupled with naiive Bayes classifiers 期刊论文
BIOINFORMATICS, 2017, 卷号: 33, 期号: 15, 页码: 2296-2306
Authors:  He, BJ;  Mortuza, SM;  Wang, YT;  Shen, HB;  Zhang, Y;  Zhang, Y (reprint author), Univ Michigan, Dept Computat Med & Bioinformat, Ann Arbor, MI 48109 USA.;  Zhang, Y (reprint author), Univ Michigan, Dept Biol Chem, Ann Arbor, MI 48109 USA.
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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  
Data quality for the inverse Ising problem 期刊论文
JOURNAL OF PHYSICS A-MATHEMATICAL AND THEORETICAL, 2016, 卷号: 49, 期号: 38, 页码: 384001
Authors:  Decelle, A;  Ricci-Tersenghi, F;  Zhang, P;  Ricci-Tersenghi, F (reprint author), Univ Roma La Sapienza, Dipartimento Fis, Ist Nazl Fis Nucl, Sez Roma1, Piazzale Aldo Moro 5, I-00185 Rome, Italy.;  Ricci-Tersenghi, F (reprint author), Univ Roma La Sapienza, CNR Nanotec, I-00185 Rome, Italy.
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Statistical Inference  Inverse Ising Problem  Big Data  Parallel Dynamics  Effective Rank  
Inference of the sparse kinetic Ising model using the decimation method 期刊论文
PHYSICAL REVIEW E, 2015, 卷号: 91, 期号: 5, 页码: 52136
Authors:  Decelle, A;  Zhang, P;  Decelle, A (reprint author), Univ Roma La Sapienza, Dipartimento Fis, Piazzale Aldo Moro 5, I-00185 Rome, Italy.
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Accurate disulfide-bonding network predictions improve ab initio structure prediction of cysteine-rich proteins 期刊论文
BIOINFORMATICS, 2015, 卷号: 31, 期号: 23, 页码: 3773-3781
Authors:  Yang, J;  He, BJ;  Jang, R;  Zhang, Y;  Shen, HB;  Zhang, Y (reprint author), Univ Michigan, Dept Computat Med & Bioinformat, Ann Arbor, MI 48109 USA.
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Quantifying the sequence-function relation in gene silencing by bacterial small RNAs 期刊论文
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2011, 卷号: 108, 期号: 30, 页码: 12473-12478
Authors:  Hao, Y;  Zhang, ZJ;  Erickson, DW;  Huang, M;  Huang, YW;  Li, JB;  Hwa, T;  Shi, HL;  Shi, HL (reprint author), Univ Calif San Diego, Div Biol Sci, Mol Biol Sect, La Jolla, CA 92093 USA.
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Small Regulatory Rnas  Small Noncoding Rnas  Messenger-rna  Escherichia-coli  Binding-sites  Soluble-rna  Translational Initiation  Vibrio-cholerae  Outer-membrane  Hfq-binding