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A universal trend of reduced mRNA stability near the translation-initiation site in prokaryotes and eukaryotes

PLoS computational biology, 2010-02, Vol.6 (2), p.e1000664-e1000664

2010

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Bringing molecules back into molecular evolution

PLoS computational biology, 2012-06, Vol.8 (6), p.e1002572-e1002572

2012

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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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Controlled Measurement and Comparative Analysis of Cellular Components in E. coli Reveals Broad Regulatory Changes in Response to Glucose Starvation

PLoS computational biology, 2015-08, Vol.11 (8), p.e1004400-e1004400

2015

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Why do eukaryotic proteins contain more intrinsically disordered regions?

PLoS computational biology, 2019-07, Vol.15 (7), p.e1007186-e1007186

2019

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Widespread position-specific conservation of synonymous rare codons within coding sequences

PLoS computational biology, 2017-05, Vol.13 (5), p.e1005531-e1005531

2017

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Inferring interaction partners from protein sequences using mutual information

PLoS computational biology, 2018-11, Vol.14 (11), p.e1006401-e1006401

2018

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Translationally optimal codons associate with aggregation-prone sites in proteins

Proteomics (Weinheim), 2010-12, Vol.10 (23), p.4163-4171

2010

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Extrapolating weak selection in evolutionary games

PLoS computational biology, 2013-12, Vol.9 (12), p.e1003381-e1003381

2013

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Evolutionary accessibility of mutational pathways

PLoS computational biology, 2011-08, Vol.7 (8), p.e1002134

2011

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Estimating time of HIV-1 infection from next-generation sequence diversity

PLoS computational biology, 2017-10, Vol.13 (10), p.e1005775-e1005775

2017

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Multiscale modeling of influenza A virus replication in cell cultures predicts infection dynamics for highly different infection conditions

PLoS computational biology, 2019-02, Vol.15 (2), p.e1006819-e1006819

2019

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Optimal number of spacers in CRISPR arrays

PLoS computational biology, 2017-12, Vol.13 (12), p.e1005891-e1005891

2017

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A computational framework to assess genome-wide distribution of polymorphic human endogenous retrovirus-K In human populations

PLoS computational biology, 2019-03, Vol.15 (3), p.e1006564-e1006564

2019

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Discerning evolutionary trends in post-translational modification and the effect of intrinsic disorder: Analysis of methylation, acetylation and ubiquitination sites in human proteins

PLoS computational biology, 2018-08, Vol.14 (8), p.e1006349-e1006349

2018

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Protein sectors: statistical coupling analysis versus conservation

PLoS computational biology, 2015-02, Vol.11 (2), p.e1004091-e1004091

2015

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Neutral Models of Microbiome Evolution

PLoS computational biology, 2015-07, Vol.11 (7), p.e1004365

2015

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Does mutational robustness inhibit extinction by lethal mutagenesis in viral populations?

PLoS computational biology, 2010-06, Vol.6 (6), p.e1000811

2010

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Retrospective Parameter Estimation and Forecast of Respiratory Syncytial Virus in the United States

PLoS computational biology, 2016-10, Vol.12 (10), p.e1005133

2016

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The genotype-phenotype map of an evolving digital organism

PLoS computational biology, 2017-02, Vol.13 (2), p.e1005414-e1005414

2017

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Effects of Darwinian Selection and Mutability on Rate of Broadly Neutralizing Antibody Evolution during HIV-1 Infection

PLoS computational biology, 2016-05, Vol.12 (5), p.e1004940-e1004940

2016

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Co-operation between Polymerases and Nucleotide Synthetases in the RNA World

PLoS computational biology, 2016-11, Vol.12 (11), p.e1005161-e1005161

2016

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Phenotypic Heterogeneity and the Evolution of Bacterial Life Cycles

PLoS computational biology, 2016-02, Vol.12 (2), p.e1004764-e1004764

2016

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Viral proteins originated de novo by overprinting can be identified by codon usage: application to the "gene nursery" of Deltaretroviruses

PLoS computational biology, 2013-08, Vol.9 (8), p.e1003162-e1003162

2013

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Stress-induced mutagenesis: Stress diversity facilitates the persistence of mutator genes

PLoS computational biology, 2017-07, Vol.13 (7), p.e1005609-e1005609

2017

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A universal trend of reduced mRNA stability near the translation-initiation site in prokaryotes and eukaryotes

Bringing molecules back into molecular evolution

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

Controlled Measurement and Comparative Analysis of Cellular Components in E. coli Reveals Broad Regulatory Changes in Response to Glucose Starvation

Why do eukaryotic proteins contain more intrinsically disordered regions?

Widespread position-specific conservation of synonymous rare codons within coding sequences

Inferring interaction partners from protein sequences using mutual information

Translationally optimal codons associate with aggregation-prone sites in proteins

Extrapolating weak selection in evolutionary games

Evolutionary accessibility of mutational pathways

Estimating time of HIV-1 infection from next-generation sequence diversity

Multiscale modeling of influenza A virus replication in cell cultures predicts infection dynamics for highly different infection conditions

Optimal number of spacers in CRISPR arrays

A computational framework to assess genome-wide distribution of polymorphic human endogenous retrovirus-K In human populations

Discerning evolutionary trends in post-translational modification and the effect of intrinsic disorder: Analysis of methylation, acetylation and ubiquitination sites in human proteins

Protein sectors: statistical coupling analysis versus conservation

Neutral Models of Microbiome Evolution

Does mutational robustness inhibit extinction by lethal mutagenesis in viral populations?

Retrospective Parameter Estimation and Forecast of Respiratory Syncytial Virus in the United States

The genotype-phenotype map of an evolving digital organism

Effects of Darwinian Selection and Mutability on Rate of Broadly Neutralizing Antibody Evolution during HIV-1 Infection

Co-operation between Polymerases and Nucleotide Synthetases in the RNA World

Phenotypic Heterogeneity and the Evolution of Bacterial Life Cycles

Viral proteins originated de novo by overprinting can be identified by codon usage: application to the "gene nursery" of Deltaretroviruses

Stress-induced mutagenesis: Stress diversity facilitates the persistence of mutator genes

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