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MACSE v2: Toolkit for the Alignment of Coding Sequences Accounting for Frameshifts and Stop Codons

Molecular biology and evolution, 2018-10, Vol.35 (10), p.2582-2584

2018

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Systematic humanization of yeast genes reveals conserved functions and genetic modularity

Science (American Association for the Advancement of Science), 2015-05, Vol.348 (6237), p.921-925

2015

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Divergent Allele Advantage at Human MHC Genes: Signatures of Past and Ongoing Selection

Molecular biology and evolution, 2018-09, Vol.35 (9), p.2145-2158

2018

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Predicting the Landscape of Recombination Using Deep Learning

Molecular biology and evolution, 2020-06, Vol.37 (6), p.1790-1808

2020

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A systematic analysis of the beta hairpin motif in the Protein Data Bank

Protein science, 2021-03, Vol.30 (3), p.613-623

2021

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Translationally Optimal Codons Associate with Structurally Sensitive Sites in Proteins

Molecular biology and evolution, 2009-07, Vol.26 (7), p.1571-1580

2009

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A single determinant dominates the rate of yeast protein evolution

Molecular biology and evolution, 2006-02, Vol.23 (2), p.327-337

2006

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Pinetree: a step-wise gene expression simulator with codon-specific translation rates

Bioinformatics, 2019-10, Vol.35 (20), p.4176-4178

2019

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Substitutions at Nonconserved Rheostat Positions Modulate Function by Rewiring Long-Range, Dynamic Interactions

Molecular biology and evolution, 2021-01, Vol.38 (1), p.201-214

2021

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Growth-dependent Gene Expression Variation Influences the Strength of Codon Usage Biases

Molecular biology and evolution, 2023-09, Vol.40 (9)

2023

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Physical Constraints on Epistasis

Molecular biology and evolution, 2020-10, Vol.37 (10), p.2865-2874

2020

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Biophysical Inference of Epistasis and the Effects of Mutations on Protein Stability and Function

Molecular biology and evolution, 2018-10, Vol.35 (10), p.2345-2354

2018

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Extensively Parameterized Mutation-Selection Models Reliably Capture Site-Specific Selective Constraint

Molecular biology and evolution, 2016-11, Vol.33 (11), p.2990-3002

2016

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Adaptive Changes in Hemoglobin Function in High-Altitude Tibetan Canids Were Derived via Gene Conversion and Introgression

Molecular biology and evolution, 2019-10, Vol.36 (10), p.2227-2237

2019

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Colocality to Cofunctionality: Eukaryotic Gene Neighborhoods as a Resource for Function Discovery

Molecular biology and evolution, 2021-02, Vol.38 (2), p.650-662

2021

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Adaptive Landscapes in the Age of Synthetic Biology

Molecular biology and evolution, 2019-05, Vol.36 (5), p.890-907

2019

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Repeated Evolution of Inactive Pseudonucleases in a Fungal Branch of the Dis3/RNase II Family of Nucleases

Molecular biology and evolution, 2021-05, Vol.38 (5), p.1837-1846

2021

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The Many Nuanced Evolutionary Consequences of Duplicated Genes

Molecular biology and evolution, 2019-02, Vol.36 (2), p.304-314

2019

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Archaeal Ribosomal Proteins Possess Nuclear Localization Signal-Type Motifs: Implications for the Origin of the Cell Nucleus

Molecular biology and evolution, 2020-01, Vol.37 (1), p.124-133

2020

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Physicochemical Amino Acid Properties Better Describe Substitution Rates in Large Populations

Molecular biology and evolution, 2019-04, Vol.36 (4), p.679-690

2019

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Runaway GC Evolution in Gerbil Genomes

Molecular biology and evolution, 2020-08, Vol.37 (8), p.2197-2210

2020

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The Evolution of Gene Expression Underlying Vision Loss in Cave Animals

Molecular biology and evolution, 2018-08, Vol.35 (8), p.2005-2014

2018

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Structural Phylogenetics with Confidence

Molecular biology and evolution, 2020-09, Vol.37 (9), p.2711-2726

2020

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Effective Population Size Predicts Local Rates but Not Local Mitigation of Read-through Errors

Molecular biology and evolution, 2021-01, Vol.38 (1), p.244-262

2021

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Rapid Accumulation of Mutations in Growing Mycelia of a Hypervariable Fungus Schizophyllum commune

Molecular biology and evolution, 2020-08, Vol.37 (8), p.2279-2286

2020

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MACSE v2: Toolkit for the Alignment of Coding Sequences Accounting for Frameshifts and Stop Codons

Systematic humanization of yeast genes reveals conserved functions and genetic modularity

Divergent Allele Advantage at Human MHC Genes: Signatures of Past and Ongoing Selection

Predicting the Landscape of Recombination Using Deep Learning

A systematic analysis of the beta hairpin motif in the Protein Data Bank

Translationally Optimal Codons Associate with Structurally Sensitive Sites in Proteins

A single determinant dominates the rate of yeast protein evolution

Pinetree: a step-wise gene expression simulator with codon-specific translation rates

Substitutions at Nonconserved Rheostat Positions Modulate Function by Rewiring Long-Range, Dynamic Interactions

Growth-dependent Gene Expression Variation Influences the Strength of Codon Usage Biases

Physical Constraints on Epistasis

Biophysical Inference of Epistasis and the Effects of Mutations on Protein Stability and Function

Extensively Parameterized Mutation-Selection Models Reliably Capture Site-Specific Selective Constraint

Adaptive Changes in Hemoglobin Function in High-Altitude Tibetan Canids Were Derived via Gene Conversion and Introgression

Colocality to Cofunctionality: Eukaryotic Gene Neighborhoods as a Resource for Function Discovery

Adaptive Landscapes in the Age of Synthetic Biology

Repeated Evolution of Inactive Pseudonucleases in a Fungal Branch of the Dis3/RNase II Family of Nucleases

The Many Nuanced Evolutionary Consequences of Duplicated Genes

Archaeal Ribosomal Proteins Possess Nuclear Localization Signal-Type Motifs: Implications for the Origin of the Cell Nucleus

Physicochemical Amino Acid Properties Better Describe Substitution Rates in Large Populations

Runaway GC Evolution in Gerbil Genomes

The Evolution of Gene Expression Underlying Vision Loss in Cave Animals

Structural Phylogenetics with Confidence

Effective Population Size Predicts Local Rates but Not Local Mitigation of Read-through Errors

Rapid Accumulation of Mutations in Growing Mycelia of a Hypervariable Fungus Schizophyllum commune

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