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Significant associations between driver gene mutations and DNA methylation alterations across many cancer types

PLoS computational biology, 2017-11, Vol.13 (11), p.e1005840-e1005840

2017

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Characterization and clustering of kinase isoform expression in metastatic melanoma

PLoS computational biology, 2022-05, Vol.18 (5), p.e1010065-e1010065

2022

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Homotypic clusters of transcription factor binding sites are a key component of human promoters and enhancers

Genome research, 2010-05, Vol.20 (5), p.565-577

2010

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Differential gene expression identifies a transcriptional regulatory network involving ER-alpha and PITX1 in invasive epithelial ovarian cancer

BMC cancer, 2021-07, Vol.21 (1), p.1-768, Article 768

2021

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Tissue-specific and ubiquitous expression patterns from alternative promoters of human genes

PloS one, 2010-08, Vol.5 (8), p.e12274-e12274

2010

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Pan-cancer stratification of solid human epithelial tumors and cancer cell lines reveals commonalities and tissue-specific features of the CpG island methylator phenotype

Epigenetics & chromatin, 2015-04, Vol.8 (1), p.14-14, Article 14

2015

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Bidirectional promoters as important drivers for the emergence of species-specific transcripts

PloS one, 2013-02, Vol.8 (2), p.e57323-e57323

2013

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A Case of IL-7R Deficiency Caused by a Novel Synonymous Mutation and Implications for Mutation Screening in SCID Diagnosis

Frontiers in immunology, 2016-10, Vol.7, p.443-443

2016

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CpG island methylator phenotype in adenocarcinomas from the digestive tract:Methods,conclusions,and controversies

World journal of gastrointestinal oncology, 2017-03, Vol.9 (3), p.105-120

2017

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CAGI experiments: Modeling sequence variant impact on gene splicing using predictions from computational tools

Human mutation, 2019-09, Vol.40 (9), p.1252-1260

2019

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DiRE: identifying distant regulatory elements of co-expressed genes

Nucleic acids research, 2008-07, Vol.36 (Web Server issue), p.W133-W139

2008

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Ascertaining regions affected by GC-biased gene conversion through weak-to-strong mutational hotspots

Genomics (San Diego, Calif.), 2014-05, Vol.103 (5-6), p.349-356

2014

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Transposable Elements: Classification, Identification, and Their Use As a Tool For Comparative Genomics

Methods in molecular biology (Clifton, N.J.), 2019, Vol.1910, p.177

2019

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The functional relevance of somatic synonymous mutations in melanoma and other cancers

Pigment cell and melanoma research, 2015-11, Vol.28 (6), p.673-684

2015

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The Megacomplex protects ER-alpha from degradation by Fulvestrant in epithelial ovarian cancer

Cancer letters, 2024-07, p.217129, Article 217129

2024

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Abstract 2137: Differential gene expression identifies a transcriptional regulatory network involving ESR1and PITX1 in invasive epithelial ovarian cancer

Cancer research (Chicago, Ill.), 2021-07, Vol.81 (13_Supplement), p.2137-2137

2021

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A novel role for nucleolin in splice site selection

RNA biology, 2022-12, Vol.19 (1), p.333-352

2022

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CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods

Genome Biology, 2024-02, Vol.25 (1), p.53-46, Article 53

2024

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Do transposable elements really contribute to proteomes?

Trends in genetics, 2006-05, Vol.22 (5), p.260-267

2006

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Whole-genome sequencing identifies a recurrent functional synonymous mutation in melanoma

Proceedings of the National Academy of Sciences - PNAS, 2013-08, Vol.110 (33), p.13481-13486

2013

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Abstract 2003: Chromatin based targeting of a master regulatory complex in estrogen receptor epithelial ovarian cancer

Cancer research (Chicago, Ill.), 2024-03, Vol.84 (6_Supplement), p.2003-2003

2024

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Transposable elements as a significant source of transcription regulating signals

Gene, 2006-01, Vol.365, p.104-110

2006

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Assessing predictions of the impact of variants on splicing in CAGI5

Human mutation, 2019-09, Vol.40 (9), p.1215-1224

2019

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Recurrent patterns of DNA methylation in the ZNF154, CASP8, and VHL promoters across a wide spectrum of human solid epithelial tumors and cancer cell lines

Epigenetics, 2013-12, Vol.8 (12), p.1355-1372

2013

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Functional analysis of synonymous substitutions predicted to affect splicing of the CFTR gene

Journal of cystic fibrosis, 2012-12, Vol.11 (6), p.511-517

2012

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Significant associations between driver gene mutations and DNA methylation alterations across many cancer types

Characterization and clustering of kinase isoform expression in metastatic melanoma

Homotypic clusters of transcription factor binding sites are a key component of human promoters and enhancers

Differential gene expression identifies a transcriptional regulatory network involving ER-alpha and PITX1 in invasive epithelial ovarian cancer

Tissue-specific and ubiquitous expression patterns from alternative promoters of human genes

Pan-cancer stratification of solid human epithelial tumors and cancer cell lines reveals commonalities and tissue-specific features of the CpG island methylator phenotype

Bidirectional promoters as important drivers for the emergence of species-specific transcripts

A Case of IL-7R Deficiency Caused by a Novel Synonymous Mutation and Implications for Mutation Screening in SCID Diagnosis

CpG island methylator phenotype in adenocarcinomas from the digestive tract:Methods,conclusions,and controversies

CAGI experiments: Modeling sequence variant impact on gene splicing using predictions from computational tools

DiRE: identifying distant regulatory elements of co-expressed genes

Ascertaining regions affected by GC-biased gene conversion through weak-to-strong mutational hotspots

Transposable Elements: Classification, Identification, and Their Use As a Tool For Comparative Genomics

The functional relevance of somatic synonymous mutations in melanoma and other cancers

The Megacomplex protects ER-alpha from degradation by Fulvestrant in epithelial ovarian cancer

Abstract 2137: Differential gene expression identifies a transcriptional regulatory network involving ESR1and PITX1 in invasive epithelial ovarian cancer

A novel role for nucleolin in splice site selection

CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods

Do transposable elements really contribute to proteomes?

Whole-genome sequencing identifies a recurrent functional synonymous mutation in melanoma

Abstract 2003: Chromatin based targeting of a master regulatory complex in estrogen receptor epithelial ovarian cancer

Transposable elements as a significant source of transcription regulating signals

Assessing predictions of the impact of variants on splicing in CAGI5

Recurrent patterns of DNA methylation in the ZNF154, CASP8, and VHL promoters across a wide spectrum of human solid epithelial tumors and cancer cell lines

Functional analysis of synonymous substitutions predicted to affect splicing of the CFTR gene

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