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The Code of Silence: Widespread Associations Between Synonymous Codon Biases and Gene Function

Journal of Molecular Evolution, 2016-01, Vol.82 (1), p.65-73

Supek, Fran

2016

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DNA mismatch repair promotes APOBEC3-mediated diffuse hypermutation in human cancers

Nature genetics, 2020-09, Vol.52 (9), p.958-968

2020

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Scales and mechanisms of somatic mutation rate variation across the human genome

DNA repair, 2019-09, Vol.81, p.102647-102647, Article 102647

2019

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Genomics reveal unknown mutation-promoting agents at global sites

Nature (London), 2024-05, Vol.629 (8013), p.767-768

2024

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Differential DNA mismatch repair underlies mutation rate variation across the human genome

Nature (London), 2015-05, Vol.521 (7550), p.81-84

2015

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Mutational signatures are markers of drug sensitivity of cancer cells

Nature communications, 2022-05, Vol.13 (1), p.2926-19, Article 2926

2022

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Clustered Mutation Signatures Reveal that Error-Prone DNA Repair Targets Mutations to Active Genes

Cell, 2017-07, Vol.170 (3), p.534-547.e23

2017

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Higher order genetic interactions switch cancer genes from two-hit to one-hit drivers

Nature communications, 2021-12, Vol.12 (1), p.7051-10, Article 7051

2021

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Copy number losses of oncogenes and gains of tumor suppressor genes generate common driver mutations

Nature communications, 2024-07, Vol.15 (1), p.6139-20, Article 6139

2024

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The rules and impact of nonsense-mediated mRNA decay in human cancers

Nature genetics, 2016-10, Vol.48 (10), p.1112-1118

2016

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Synonymous Mutations Frequently Act as Driver Mutations in Human Cancers

Cell, 2014-03, Vol.156 (6), p.1324-1335

2014

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The impact of nonsense-mediated mRNA decay on genetic disease, gene editing and cancer immunotherapy

Nature genetics, 2019-11, Vol.51 (11), p.1645-1651

2019

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Systematic discovery of germline cancer predisposition genes through the identification of somatic second hits

Nature communications, 2018-07, Vol.9 (1), p.2601-13, Article 2601

2018

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Genome-scale quantification and prediction of pathogenic stop codon readthrough by small molecules

Nature genetics, 2024-09, Vol.56 (9), p.1914-1924

2024

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Passenger mutations accurately classify human tumors

PLoS computational biology, 2019-04, Vol.15 (4), p.e1006953

2019

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A framework for mutational signature analysis based on DNA shape parameters

PloS one, 2022-01, Vol.17 (1), p.e0262495

2022

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Whole genome DNA sequencing provides an atlas of somatic mutagenesis in healthy human cells and identifies a tumor-prone cell type

Genome Biology, 2019-12, Vol.20 (1), p.285-22, Article 285

2019

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MUFFINN: cancer gene discovery via network analysis of somatic mutation data

Genome Biology, 2016-06, Vol.17 (1), p.129-129, Article 129

2016

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Spectrum of DNA mismatch repair failures viewed through the lens of cancer genomics and implications for therapy

Clinical science (1979), 2022-03, Vol.136 (5), p.383-404

2022

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Hydroxymethylated cytosines are associated with elevated C to G transversion rates

PLoS genetics, 2014-09, Vol.10 (9), p.e1004585-e1004585

2014

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Prevalence, causes and impact of TP53-loss phenocopying events in human tumors

BMC biology, 2023-04, Vol.21 (1), p.92-92, Article 92

2023

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Proton and alpha radiation-induced mutational profiles in human cells

Scientific reports, 2023-06, Vol.13 (1), p.9791-19, Article 9791

2023

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Targeting the ERAD pathway via inhibition of signal peptide peptidase for antiparasitic therapeutic design

Proceedings of the National Academy of Sciences - PNAS, 2012-12, Vol.109 (52), p.21486-21491

2012

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A large-scale evaluation of computational protein function prediction

Nature methods, 2013-03, Vol.10 (3), p.221-227

2013

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The Code of Silence: Widespread Associations Between Synonymous Codon Biases and Gene Function

DNA mismatch repair promotes APOBEC3-mediated diffuse hypermutation in human cancers

Scales and mechanisms of somatic mutation rate variation across the human genome

Genomics reveal unknown mutation-promoting agents at global sites

Differential DNA mismatch repair underlies mutation rate variation across the human genome

Mutational signatures are markers of drug sensitivity of cancer cells

Clustered Mutation Signatures Reveal that Error-Prone DNA Repair Targets Mutations to Active Genes

Higher order genetic interactions switch cancer genes from two-hit to one-hit drivers

Copy number losses of oncogenes and gains of tumor suppressor genes generate common driver mutations

The rules and impact of nonsense-mediated mRNA decay in human cancers

Synonymous Mutations Frequently Act as Driver Mutations in Human Cancers

The impact of nonsense-mediated mRNA decay on genetic disease, gene editing and cancer immunotherapy

Systematic discovery of germline cancer predisposition genes through the identification of somatic second hits

Genome-scale quantification and prediction of pathogenic stop codon readthrough by small molecules

Passenger mutations accurately classify human tumors

A framework for mutational signature analysis based on DNA shape parameters

Whole genome DNA sequencing provides an atlas of somatic mutagenesis in healthy human cells and identifies a tumor-prone cell type

MUFFINN: cancer gene discovery via network analysis of somatic mutation data

Spectrum of DNA mismatch repair failures viewed through the lens of cancer genomics and implications for therapy

Hydroxymethylated cytosines are associated with elevated C to G transversion rates

Prevalence, causes and impact of TP53-loss phenocopying events in human tumors

Proton and alpha radiation-induced mutational profiles in human cells

Selective and Specific Inhibition of the Plasmodium falciparum Lysyl-tRNA Synthetase by the Fungal Secondary Metabolite Cladosporin

Targeting the ERAD pathway via inhibition of signal peptide peptidase for antiparasitic therapeutic design

A large-scale evaluation of computational protein function prediction

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