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X chromosomes show relaxed selection and complete somatic dosage compensation across Timema stick insect species

Journal of evolutionary biology, 2022-12, Vol.35 (12), p.1734-1750

2022

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Rhythmicity is linked to expression cost at the protein level but to expression precision at the mRNA level

PLoS computational biology, 2022-09, Vol.18 (9), p.e1010399-e1010399

2022

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Genomic changes underlying host specialization in the bee gut symbiont Lactobacillus Firm5

Molecular ecology, 2019-05, Vol.28 (9), p.2224-2237

2019

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What to compare and how: Comparative transcriptomics for Evo-Devo

Journal of experimental zoology. Part B, Molecular and developmental evolution, 2015-06, Vol.324 (4), p.372-382

2015

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Performance of a phylogenetic independent contrast method and an improved pairwise comparison under different scenarios of trait evolution after speciation and duplication

Methods in ecology and evolution, 2021-10, Vol.12 (10), p.1875-1887

2021

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Comparative genome analysis of Pseudomonas knackmussii B13, the first bacterium known to degrade chloroaromatic compounds

Environmental microbiology, 2015-01, Vol.17 (1), p.91-104

2015

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Tissue-Specificity of Gene Expression Diverges Slowly between Orthologs, and Rapidly between Paralogs

PLoS computational biology, 2016-12, Vol.12 (12), p.e1005274-e1005274

2016

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Methods detecting rhythmic gene expression are biologically relevant only for strong signal

PLoS computational biology, 2020-03, Vol.16 (3), p.e1007666-e1007666

2020

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Selective Constraints on Coding Sequences of Nervous System Genes Are a Major Determinant of Duplicate Gene Retention in Vertebrates

Molecular biology and evolution, 2017-11, Vol.34 (11), p.2773-2791

2017

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The lineage-specific evolution of aquaporin gene clusters facilitated tetrapod terrestrial adaptation

PloS one, 2014-11, Vol.9 (11), p.e113686-e113686

2014

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Tissue-Specific Evolution of Protein Coding Genes in Human and Mouse

PloS one, 2015-06, Vol.10 (6), p.e0131673-e0131673

2015

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The complete mitochondrial genome of Calyptogena marissinica (Heterodonta: Veneroida: Vesicomyidae): Insight into the deep-sea adaptive evolution of vesicomyids

PloS one, 2019-09, Vol.14 (9), p.e0217952

2019

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Genomic Features of Parthenogenetic Animals

The Journal of heredity, 2021-03, Vol.112 (1), p.19-33

2021

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The lasting after-effects of an ancient polyploidy on the genomes of teleosts

PloS one, 2020-04, Vol.15 (4), p.e0231356-e0231356

2020

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Resolving the ortholog conjecture: orthologs tend to be weakly, but significantly, more similar in function than paralogs

PLoS computational biology, 2012-05, Vol.8 (5), p.e1002514-e1002514

2012

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Molecular signaling in zebrafish development and the vertebrate phylotypic period

Evolution & development, 2010-03, Vol.12 (2), p.144-156

2010

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Inter-embryo gene expression variability recapitulates the hourglass pattern of evo-devo

BMC biology, 2020-09, Vol.18 (1), p.129-129, Article 129

2020

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Pyvolve: A Flexible Python Module for Simulating Sequences along Phylogenies

PloS one, 2015-09, Vol.10 (9), p.e0139047

2015

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Enrichment on steps, not genes, improves inference of differentially expressed pathways

PLoS computational biology, 2024-03, Vol.20 (3), p.e1011968-e1011968

2024

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Bias in the arrival of variation can dominate over natural selection in Richard Dawkins's biomorphs

PLoS computational biology, 2024-03, Vol.20 (3), p.e1011893-e1011893

2024

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Using digital organisms to study the evolutionary consequences of whole genome duplication and polyploidy

PloS one, 2019-07, Vol.14 (7), p.e0220257-e0220257

2019

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Evolution of the modular, disordered stress proteins known as dehydrins

PloS one, 2019-02, Vol.14 (2), p.e0211813-e0211813

2019

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Transcript assembly and annotations: Bias and adjustment

PLoS computational biology, 2023-12, Vol.19 (12), p.e1011734-e1011734

2023

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X chromosomes show relaxed selection and complete somatic dosage compensation across Timema stick insect species

Rhythmicity is linked to expression cost at the protein level but to expression precision at the mRNA level

Genomic changes underlying host specialization in the bee gut symbiont Lactobacillus Firm5

The amphioxus genome and the evolution of the chordate karyotype

What to compare and how: Comparative transcriptomics for Evo-Devo

An ancient truncated duplication of the anti‐Müllerian hormone receptor type 2 gene is a potential conserved master sex determinant in the Pangasiidae catfish family

Performance of a phylogenetic independent contrast method and an improved pairwise comparison under different scenarios of trait evolution after speciation and duplication

Comparative genome analysis of Pseudomonas knackmussii B13, the first bacterium known to degrade chloroaromatic compounds

Tissue-Specificity of Gene Expression Diverges Slowly between Orthologs, and Rapidly between Paralogs

Methods detecting rhythmic gene expression are biologically relevant only for strong signal

Selective Constraints on Coding Sequences of Nervous System Genes Are a Major Determinant of Duplicate Gene Retention in Vertebrates

The lineage-specific evolution of aquaporin gene clusters facilitated tetrapod terrestrial adaptation

Tissue-Specific Evolution of Protein Coding Genes in Human and Mouse

The complete mitochondrial genome of Calyptogena marissinica (Heterodonta: Veneroida: Vesicomyidae): Insight into the deep-sea adaptive evolution of vesicomyids

Genomic Features of Parthenogenetic Animals

The lasting after-effects of an ancient polyploidy on the genomes of teleosts

Resolving the ortholog conjecture: orthologs tend to be weakly, but significantly, more similar in function than paralogs

Molecular signaling in zebrafish development and the vertebrate phylotypic period

Inter-embryo gene expression variability recapitulates the hourglass pattern of evo-devo

Pyvolve: A Flexible Python Module for Simulating Sequences along Phylogenies

Enrichment on steps, not genes, improves inference of differentially expressed pathways

Bias in the arrival of variation can dominate over natural selection in Richard Dawkins's biomorphs

Using digital organisms to study the evolutionary consequences of whole genome duplication and polyploidy

Evolution of the modular, disordered stress proteins known as dehydrins

Transcript assembly and annotations: Bias and adjustment

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