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Optimal Allocation of Bacterial Protein Resources under Nonlethal Protein Maturation Stress 期刊论文
BIOPHYSICAL JOURNAL, 2018, 卷号: 115, 期号: 5, 页码: 896-910
Authors:  Zhang, Q;  Li, R;  Li, JB;  Shi, HL
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ESCHERICHIA-COLI PROTEOME  SIGMA-FACTOR COMPETITION  GENE-EXPRESSION  RNA-POLYMERASE  OXIDATIVE STRESS  GROWTH-INHIBITION  CELL-GROWTH  TRANSLATION  RATES  OVERPRODUCTION  
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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Effects of cooperation between translating ribosome and RNA polymerase on termination efficiency of the Rho-independent terminator 期刊论文
NUCLEIC ACIDS RESEARCH, 2016, 卷号: 44, 期号: 6, 页码: 2554-2563
Authors:  Li, R;  Zhang, Q;  Li, JB;  Shi, HL;  Shi, HL (reprint author), Chinese Acad Sci, Inst Theoret Phys, State Key Lab Theoret Phys, Beijing 100190, Peoples R China.;  Li, JB (reprint author), Chinese Acad Sci, Inst Chem, Beijing 100190, Peoples R China.;  Li, JB (reprint author), Natl Ctr Nanosci & Technol, Beijing 100190, Peoples R China.
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The bulk and the tail of minimal absent words in genome sequences 期刊论文
PHYSICAL BIOLOGY, 2016, 卷号: 13, 期号: 2, 页码: 26004
Authors:  Aurell, E;  Innocenti, N;  Zhou, HJ;  Innocenti, N (reprint author), Hebrew Univ Jerusalem, Sch Comp Sci & Engn, IL-91904 Jerusalem, Israel.
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Minimal Absent Words  Copy-mutation Evolution Model  Random Sequence  
Strategy of tuning gene expression ratio in prokaryotic cell from perspective of noise and correlation 期刊论文
JOURNAL OF THEORETICAL BIOLOGY, 2015, 卷号: 365, 期号: 0, 页码: 377-389
Authors:  Li, R;  Xu, LF;  Shi, HL;  Shi, HL (reprint author), Chinese Acad Sci, Inst Theoret Phys, State Key Lab Theoret Phys, Beijing 100190, Peoples R China.
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Polar Effect  The Two-state Promoter  Transcription Terminator  Gene Expression Correlation  Operon Structure  
Theoretical studies on sRNA-mediated regulation in bacteria 期刊论文
CHINESE PHYSICS B, 2015, 卷号: 24, 期号: 12, 页码: 128703
Authors:  Chang, XX;  Xu, LF;  Shi, HL;  Xu, LF (reprint author), Jilin Univ, Dept Phys, Changchun 130012, Peoples R China.
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Srna-mediated Regulation  Kinetic Model  Crosstalk  
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  
Theoretical Analysis of Catalytic-sRNA-Mediated Gene Silencing 期刊论文
JOURNAL OF MOLECULAR BIOLOGY, 2011, 卷号: 406, 期号: 1, 页码: 195-204
Authors:  Hao, Y;  Xu, LF;  Shi, HL;  Shi, HL (reprint author), Chinese Acad Sci, Inst Theoret Phys, Beijing 100190, Peoples R China.
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Transcriptional Regulation  Escherichia-coli  Regulatory Rnas  Bacteria  Expression  Noise  Consequences  Numbers  Stress  System