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From systems to structure: bridging networks and mechanism
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3558917
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22 February 2020
review article
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title
From systems to structure: bridging networks and mechanism
(English)
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PubMed
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Europe PubMed Central
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3558917
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22 February 2020
author
James S Fraser
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1
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Europe PubMed Central
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3558917
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22 February 2020
Nevan Krogan
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Nevan J Krogan
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Europe PubMed Central
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3558917
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22 February 2020
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John D Gross
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2
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Europe PubMed Central
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3558917
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22 February 2020
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English
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1 January 2013
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22 February 2020
published in
Molecular Cell
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Europe PubMed Central
PMC publication ID
3558917
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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23352243%20AND%20SRC:MED&resulttype=core&format=json
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22 February 2020
volume
49
2 references
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Europe PubMed Central
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3558917
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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23352243%20AND%20SRC:MED&resulttype=core&format=json
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22 February 2020
issue
2
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PubMed
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Europe PubMed Central
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3558917
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22 February 2020
page(s)
222-231
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Europe PubMed Central
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3558917
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22 February 2020
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28 September 2017
The spatial architecture of protein function and adaptation
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28 September 2017
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28 September 2017
Interaction landscape of membrane-protein complexes in Saccharomyces cerevisiae
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28 September 2017
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IDH1(R132H) mutation increases murine haematopoietic progenitors and alters epigenetics
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Functional dissection of lysine deacetylases reveals that HDAC1 and p300 regulate AMPK
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Vif hijacks CBF-β to degrade APOBEC3G and promote HIV-1 infection
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Mapping of signaling networks through synthetic genetic interaction analysis by RNAi
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Rewiring of genetic networks in response to DNA damage.
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Interplay of transcription factors in T-cell differentiation and function: the role of Runx
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The beginning of a beautiful friendship: cross-linking/mass spectrometry and modelling of proteins and multi-protein complexes
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28 September 2017
The next frontier of systems biology: higher-order and interspecies interactions.
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28 September 2017
Drug interactions and the evolution of antibiotic resistance
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28 September 2017
High-throughput, quantitative analyses of genetic interactions in E. coli
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Characterizing heterogeneous cellular responses to perturbations
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3558917
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28 September 2017
Protein kinase R reveals an evolutionary model for defeating viral mimicry
1 reference
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3558917
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28 September 2017
Conservation and rewiring of functional modules revealed by an epistasis map in fission yeast.
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3558917
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28 September 2017
Understanding and predicting protein assemblies with 3D structures
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3558917
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28 September 2017
Rewiring the specificity of two-component signal transduction systems
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3558917
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28 September 2017
Defining genetic interaction
1 reference
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3558917
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28 September 2017
Principles underlying energetic coupling along an allosteric communication trajectory of a voltage-activated K+ channel
1 reference
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3558917
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28 September 2017
Determining the architectures of macromolecular assemblies
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3558917
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28 September 2017
Evolutionary constraints on chaperone-mediated folding provide an antiviral approach refractory to development of drug resistance
1 reference
stated in
PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3558917
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28 September 2017
Relating three-dimensional structures to protein networks provides evolutionary insights
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3558917
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28 September 2017
Robustness-epistasis link shapes the fitness landscape of a randomly drifting protein.
1 reference
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3558917
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28 September 2017
The biochemical architecture of an ancient adaptive landscape
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28 September 2017
SNPs, protein structure, and disease.
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3558917
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28 September 2017
Lessons learned from BRCA1 and BRCA2.
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3558917
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28 September 2017
Double-mutant cycles: a powerful tool for analyzing protein structure and function
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3558917
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28 September 2017
Quantitative genetic interaction mapping using the E-MAP approach
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31 May 2018
Quantitative genetic interactions reveal biological modularity
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3558917
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31 May 2018
Combinatorial RNA interference in Caenorhabditis elegans reveals that redundancy between gene duplicates can be maintained for more than 80 million years of evolution
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3558917
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31 May 2018
Additivity of mutational effects in proteins
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3558917
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31 May 2018
Long-range electrostatic interactions can influence the folding, stability, and cooperativity of dihydrofolate reductase.
1 reference
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3558917
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19 June 2018
Epistasis as the primary factor in molecular evolution
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3558917
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28 November 2018
Contingency and statistical laws in replicate microbial closed ecosystems.
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3558917
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28 November 2018
The molecular diversity of adaptive convergence.
1 reference
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3558917
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28 November 2018
Protein-protein interactions and networks: forward and reverse edgetics.
1 reference
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3558917
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28 November 2018
Systematic bioinformatics and experimental validation of yeast complexes reduces the rate of attrition during structural investigations.
1 reference
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3558917
retrieved
28 November 2018
Understanding modularity in molecular networks requires dynamics
1 reference
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3558917
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28 November 2018
Structure-based assembly of protein complexes in yeast
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3558917
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28 November 2018
Energetics of protein-protein interactions: analysis of the barnase-barstar interface by single mutations and double mutant cycles.
1 reference
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3558917
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28 November 2018
The combinatorial distance geometry method for the calculation of molecular conformation. I. A new approach to an old problem.
1 reference
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3558917
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28 November 2018
Strategy for analysing the co-operativity of intramolecular interactions in peptides and proteins
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https://pubmed.ncbi.nlm.nih.gov/23352243
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12 December 2020
based on heuristic
inferred from PubMed ID database lookup
Non-additivity in protein-protein interactions
1 reference
stated in
PubMed
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https://pubmed.ncbi.nlm.nih.gov/23352243
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12 December 2020
based on heuristic
inferred from PubMed ID database lookup
Structural Probing of a Protein Phosphatase 2A Network by Chemical Cross-Linking and Mass Spectrometry
1 reference
stated in
PubMed
reference URL
https://pubmed.ncbi.nlm.nih.gov/23352243
retrieved
12 December 2020
based on heuristic
inferred from PubMed ID database lookup
The use of double mutants to detect structural changes in the active site of the tyrosyl-tRNA synthetase (Bacillus stearothermophilus)
1 reference
stated in
PubMed
reference URL
https://pubmed.ncbi.nlm.nih.gov/23352243
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12 December 2020
based on heuristic
inferred from PubMed ID database lookup
CBFβ stabilizes HIV Vif to counteract APOBEC3 at the expense of RUNX1 target gene expression.
1 reference
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Crossref
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https://api.crossref.org/works/10.1016%2FJ.MOLCEL.2013.01.003
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7 January 2021
based on heuristic
inferred from DOI database lookup
Design principles of regulatory networks: searching for the molecular algorithms of the cell
1 reference
stated in
Crossref
reference URL
https://api.crossref.org/works/10.1016%2FJ.MOLCEL.2013.01.003
retrieved
7 January 2021
based on heuristic
inferred from DOI database lookup
Identifiers
DOI
10.1016/J.MOLCEL.2013.01.003
1 reference
stated in
Europe PubMed Central
PMC publication ID
3558917
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23352243%20AND%20SRC:MED&resulttype=core&format=json
retrieved
22 February 2020
PMC publication ID
3558917
2 references
stated in
PubMed
stated in
Europe PubMed Central
PMC publication ID
3558917
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23352243%20AND%20SRC:MED&resulttype=core&format=json
retrieved
22 February 2020
PubMed publication ID
23352243
2 references
stated in
PubMed
stated in
Europe PubMed Central
PMC publication ID
3558917
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23352243%20AND%20SRC:MED&resulttype=core&format=json
retrieved
22 February 2020
ResearchGate publication ID
235374365
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