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A computational model for bacteriophage ϕX174 gene expression.
- Published in:
- PLoS ONE, 2024, v. 19, n. 10, p. 1, doi. 10.1371/journal.pone.0313039
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- Article
Functional Sites Induce Long-Range Evolutionary Constraints in Enzymes.
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- PLoS Biology, 2016, v. 14, n. 5, p. 1, doi. 10.1371/journal.pbio.1002452
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- Article
Humanization of yeast genes with multiple human orthologs reveals functional divergence between paralogs.
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- PLoS Biology, 2020, v. 18, n. 5, p. 1, doi. 10.1371/journal.pbio.3000627
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- Article
Transcript degradation and codon usage regulate gene expression in a lytic phage.
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- Virus Evolution, 2019, v. 5, n. 2, p. N.PAG, doi. 10.1093/ve/vez055
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- Article
Influenza passaging annotations: what they tell us and why we should listen.
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- Virus Evolution, 2019, v. 5, n. 1, p. N.PAG, doi. 10.1093/ve/vez016
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- Article
The Relationship Between Relative Solvent Accessibility and Evolutionary Rate in Protein Evolution.
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- Genetics, 2011, v. 188, n. 2, p. 479, doi. 10.1534/genetics.111.128025
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- Article
Lethal Mutagenesis of Bacteria.
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- Genetics, 2008, v. 180, n. 2, p. 1061, doi. 10.1534/genetics.108.091413
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- Article
The Stochastic Edge in Adaptive Evolution.
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- Genetics, 2008, v. 179, n. 1, p. 603, doi. 10.1534/genetics.107.079319
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- Article
Thermodynamics of Neutral Protein Evolution.
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- Genetics, 2007, v. 175, n. 1, p. 255, doi. 10.1534/genetics.106.061754
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- Article
Population Genetics of Translational Robustness.
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- Genetics, 2006, v. 173, n. 1, p. 473, doi. 10.1534/genetics.105.051300
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- Publication type:
- Article
Co-infection Weakens Selection Against Epistatic Mutations in RNA Viruses.
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- Genetics, 2004, v. 168, n. 1, p. 9, doi. 10.1534/genetics.104.030205
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- Article
The Speed of Adaptation in Large Asexual Populations.
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- Genetics, 2004, v. 167, n. 4, p. 2045, doi. 10.1534/genetics.104.027136
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- Article
Probability of Fixation of an Advantageous Mutant in a Viral Quasispecies.
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- Genetics, 2003, v. 163, n. 2, p. 467, doi. 10.1093/genetics/163.2.467
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- Article
A new twist in measuring mutation rates.
- Published in:
- eLife, 2017, p. 1, doi. 10.7554/eLife.29586
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- Article
Viral factors in influenza pandemic risk assessment.
- Published in:
- eLife, 2016, p. 1, doi. 10.7554/eLife.18491
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- Article
At the mercy of viruses.
- Published in:
- eLife, 2016, p. 1, doi. 10.7554/eLife.16758
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- Article
Socioeconomic disparities in the presentation of acute bacterial sinusitis complications in children.
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- Laryngoscope, 2014, v. 124, n. 7, p. 1700, doi. 10.1002/lary.24492
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- Article
The E. coli molecular phenotype under different growth conditions.
- Published in:
- Scientific Reports, 2017, p. 45303, doi. 10.1038/srep45303
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- Article
INTERACTIONS BETWEEN EVOLUTIONARY PROCESSES AT HIGH MUTATION RATES.
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- Evolution, 2012, v. 66, n. 7, p. 2303, doi. 10.1111/j.1558-5646.2012.01596.x
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- Article
EFFECTS OF POPULATION SIZE AND MUTATION RATE ON THE EVOLUTION OF MUTATIONAL ROBUSTNESS.
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- Evolution, 2007, v. 61, n. 3, p. 666, doi. 10.1111/j.1558-5646.2007.00064.x
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- Publication type:
- Article
REPLICATION AT PERIODICALLY CHANGING MULTIPLICITY OF INFECTION PROMOTES STABLE COEXISTENCE OF COMPETING VIRAL POPULATIONS.
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- Evolution, 2004, v. 58, n. 4, p. 900, doi. 10.1554/03-652
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- Publication type:
- Article
SELECTION FOR FITNESS VERSUS SELECTION FOR ROBUSTNESS IN RNA SECONDARY STRUCTURE FOLDING.
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- Evolution, 2001, v. 55, n. 12, p. 2412, doi. 10.1554/0014-3820(2001)055[2412:SFFVSF]2.0.CO;2
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- Article
Robustness and Evolvability in Living Systems.
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- 2006
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- Publication type:
- Book Review
Pyvolve: A Flexible Python Module for Simulating Sequences along Phylogenies.
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- PLoS ONE, 2015, v. 10, n. 9, p. 1, doi. 10.1371/journal.pone.0139047
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- Publication type:
- Article
Predicting Growth Conditions from Internal Metabolic Fluxes in an In-Silico Model of E. coli.
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- PLoS ONE, 2014, v. 9, n. 12, p. 1, doi. 10.1371/journal.pone.0114608
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- Article
Maximum Allowed Solvent Accessibilites of Residues in Proteins.
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- PLoS ONE, 2013, v. 8, n. 11, p. 1, doi. 10.1371/journal.pone.0080635
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- Article
Principal-Oscillation-Pattern Analysis of Gene Expression.
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- PLoS ONE, 2012, v. 7, n. 1, p. 1, doi. 10.1371/journal.pone.0028805
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- Article
The Phenotype-Fitness Map in Experimental Evolution of Phages.
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- PLoS ONE, 2011, v. 6, n. 11, p. 1, doi. 10.1371/journal.pone.0027796
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- Article
Detecting Clusters of Mutations.
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- PLoS ONE, 2008, v. 3, n. 11, p. 1, doi. 10.1371/journal.pone.0003765
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- Publication type:
- Article
Dissecting the roles of local packing density and longer-range effects in protein sequence evolution.
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- Proteins, 2016, v. 84, n. 6, p. 841, doi. 10.1002/prot.25034
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- Article
Low-level HIV-1 replication and the dynamics of the resting CD4+ T cell reservoir for HIV-1 in the setting of HAART.
- Published in:
- 2008
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- Publication type:
- journal article
Low-level HIV-1 replication and the dynamics of the resting CD4<sup>+</sup> T cell reservoir for HIV-1 in the setting of HAART.
- Published in:
- BMC Infectious Diseases, 2008, v. 8, n. 1, p. 1, doi. 10.1186/1471-2334-8-2
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- Publication type:
- Article
Translationally optimal codons associate with aggregation-prone sites in proteins.
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- Proteomics, 2010, v. 10, n. 23, p. 4163, doi. 10.1002/pmic.201000229
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- Article
The evolutionary consequences of erroneous protein synthesis.
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- 2009
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- Publication type:
- journal article
Growth-dependent Gene Expression Variation Influences the Strength of Codon Usage Biases.
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- Molecular Biology & Evolution, 2023, v. 40, n. 9, p. 1, doi. 10.1093/molbev/msad189
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- Article
Many Nuanced Evolutionary Consequences of Duplicated Genes.
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- Molecular Biology & Evolution, 2019, v. 36, n. 2, p. 304, doi. 10.1093/molbev/msy210
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- Article
Withdrawn as Duplicate: The many nuanced evolutionary consequences of duplicated genes.
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- Molecular Biology & Evolution, 2018, v. 35, n. 12, p. e1, doi. 10.1093/molbev/msy216
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- Article
Within-Gene Shine–Dalgarno Sequences Are Not Selected for Function.
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- Molecular Biology & Evolution, 2018, v. 35, n. 10, p. 2487, doi. 10.1093/molbev/msy150
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- Article
Extensively Parameterized Mutation-Selection Models Reliably Capture Site-Specific Selective Constraint.
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- Molecular Biology & Evolution, 2016, v. 33, n. 11, p. 2990, doi. 10.1093/molbev/msw171
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- Article
The Relationship between dN/dS and Scaled Selection Coefficients.
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- Molecular Biology & Evolution, 2015, v. 32, n. 4, p. 1097, doi. 10.1093/molbev/msv003
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- Publication type:
- Article
Limited Utility of Residue Masking for Positive-Selection Inference.
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- Molecular Biology & Evolution, 2014, v. 31, n. 9, p. 2496, doi. 10.1093/molbev/msu183
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- Article
Integrating Sequence Variation and Protein Structure to Identify Sites under Selection.
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- Molecular Biology & Evolution, 2013, v. 30, n. 1, p. 36, doi. 10.1093/molbev/mss217
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- Publication type:
- Article
Reduced Protein Expression in a Virus Attenuated by Codon Deoptimization.
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- G3: Genes | Genomes | Genetics, 2017, v. 7, n. 9, p. 2957, doi. 10.1534/g3.117.041020
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- Article
Molecular clock in neutral protein evolution.
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- BMC Genetics, 2004, v. 5, p. 25, doi. 10.1186/1471-2156-5-25
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- Article
Breaking proteins with mutations: threads and thresholds in evolution.
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- Molecular Systems Biology, 2007, v. 3, n. 1, p. 76, doi. 10.1038/msb4100119
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- Publication type:
- Article
Limits on Replenishment of the Resting CD4<sup>+</sup> T Cell Reservoir for HIV in Patients on HAART.
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- PLoS Pathogens, 2007, v. 3, n. 8, p. 1165, doi. 10.1371/journal.ppat.0030122
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- Publication type:
- Article
Controlled Measurement and Comparative Analysis of Cellular Components in E. coli Reveals Broad Regulatory Changes in Response to Glucose Starvation.
- Published in:
- PLoS Computational Biology, 2015, v. 11, n. 8, p. 1, doi. 10.1371/journal.pcbi.1004400
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- Article
Bringing Molecules Back into Molecular Evolution.
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- PLoS Computational Biology, 2012, v. 8, n. 6, p. 1, doi. 10.1371/journal.pcbi.1002572
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- Article
Does Mutational Robustness Inhibit Extinction by Lethal Mutagenesis in Viral Populations?
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- PLoS Computational Biology, 2010, v. 6, n. 6, p. 1, doi. 10.1371/journal.pcbi.1000811
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- Publication type:
- Article
A Universal Trend of Reduced mRNA Stability near the Translation-Initiation Site in Prokaryotes and Eukaryotes.
- Published in:
- PLoS Computational Biology, 2010, v. 6, n. 2, p. 1, doi. 10.1371/journal.pcbi.1000664
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- Article