List of works - Sean Davis

A molecular function map of Ewing's sarcoma

scientific article published on 30 April 2009

A polymorphism in IRF4 affects human pigmentation through a tyrosinase-dependent MITF/TFAP2A pathway

scientific article

A single IGF1 allele is a major determinant of small size in dogs

scientific article

Advanced bone formation in mice with a dominant-negative mutation in the thyroid hormone receptor β gene due to activation of Wnt/β-catenin protein signaling.

scientific article

Analysis of bipolar disorder using affected relatives

scientific article published on January 1997

Analysis of complex oligogenic disease

scientific article published on 01 January 1997

Analysis of complex oligogenic disease

Analysis of the matrix metalloproteinase family reveals that MMP8 is often mutated in melanoma

scientific article published on 29 March 2009

Antagonistic cross-regulation between Sox9 and Sox10 controls an anti-tumorigenic program in melanoma.

scientific article

Assessment of automated image analysis of breast cancer tissue microarrays for epidemiologic studies

scientific article

BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis

scientific article

CHEK2 genomic and proteomic analyses reveal genetic inactivation or endogenous activation across the 60 cell lines of the US National Cancer Institute.

scientific article

Canine tumor cross-species genomics uncovers targets linked to osteosarcoma progression

scientific article

Chromothripsis and focal copy number alterations determine poor outcome in malignant melanoma

scientific article

Comparative exome sequencing of metastatic lesions provides insights into the mutational progression of melanoma ⬇️

scientific article published on September 24, 2012

Comparison of nonparametric statistics for detection of linkage in nuclear families: single-marker evaluation

scientific article published on December 1997

Constitutive Fms-like tyrosine kinase 3 activation results in specific changes in gene expression in myeloid leukaemic cells

article

DNase-chip: a high-resolution method to identify DNase I hypersensitive sites using tiled microarrays

scientific article

Database of mRNA gene expression profiles of multiple human organs

scientific article

Detection of novel amplicons in prostate cancer by comprehensive genomic profiling of prostate cancer cell lines using oligonucleotide-based arrayCGH.

scientific article

Downregulation of IGFBP2 is associated with resistance to IGF1R therapy in rhabdomyosarcoma.

scientific article published on 2 December 2013

Epigenomic alterations and gene expression profiles in respiratory epithelia exposed to cigarette smoke condensate.

scientific article

Evidence for an unanticipated relationship between undifferentiated pleomorphic sarcoma and embryonal rhabdomyosarcoma

scientific article

Ewing's sarcoma: general insights from a rare model.

scientific article

Exclusion of the 750-kb genetically unstable region at Xq27 as a candidate locus for prostate malignancy in HPCX1-linked families.

scientific article

Exome sequencing identifies GRIN2A as frequently mutated in melanoma

scientific article

GEOmetadb: powerful alternative search engine for the Gene Expression Omnibus

scientific article published on 07 October 2008

Gene expression profiling of human sarcomas: insights into sarcoma biology

scientific article published on October 2005

Genetic susceptibility for human familial essential hypertension in a region of homology with blood pressure linkage on rat chromosome 10.

scientific article published in November 1997

Genome-wide analysis of menin binding provides insights into MEN1 tumorigenesis

scientific article

Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS)

scientific article

Genome-wide methylation patterns in papillary thyroid cancer are distinct based on histological subtype and tumor genotype.

scientific article published on 11 December 2013

Genome-wide methylation profiling in archival formalin-fixed paraffin-embedded tissue samples

scientific article published on January 2012

Harnessing genomics to identify environmental determinants of heritable disease

journal article published in 2013

High prevalence of MAP2K1 mutations in variant and IGHV4-34-expressing hairy-cell leukemias

scientific article

High-resolution mapping and characterization of open chromatin across the genome

scientific article

Homozygosity mapping of Hallervorden-Spatz syndrome to chromosome 20p12.3-p13

scientific article

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

scientific article published in June 2007

Identification of an inhibitor of the EWS-FLI1 oncogenic transcription factor by high-throughput screening.

scientific article

Impact of overlapping recruitment on linkage analysis of complex disorders: simulation studies

scientific article published in March 2001

In Vivo Role of Alternative Splicing and Serine Phosphorylation of the Microphthalmia-Associated Transcription Factor ⬇️

scientific article published on February 23, 2012

Integrated analysis of DNA methylation, immunohistochemistry and mRNA expression, data identifies a methylation expression index (MEI) robustly associated with survival of ER-positive breast cancer patients

scientific article

Interaction of the glucocorticoid receptor with the chromatin landscape

scientific article

Interferon-γ links ultraviolet radiation to melanomagenesis in mice

scientific article

Kinetic complexity of the global response to glucocorticoid receptor action.

scientific article published on 08 January 2009

Large-scale profiling of archival lymph nodes reveals pervasive remodeling of the follicular lymphoma methylome

scientific article published on 20 January 2009

Lineage of origin in rhabdomyosarcoma informs pharmacological response

scientific article

Linkage and association between inflammatory bowel disease and a locus on chromosome 12

scientific article

Melanoblast transcriptome analysis reveals pathways promoting melanoma metastasis

scientific article published on 16 January 2020

Modeling synovial sarcoma: timing is everything

scientific article published in April 2007

Molecular Grading of Ductal Carcinoma In situ of the Breast

scientific article published on 01 December 2008

NCBI GEO: archive for functional genomics data sets--update

scientific article

NCI-60 whole exome sequencing and pharmacological CellMiner analyses

scientific article (publication date: 2014)

On the Selective Packaging of Genomic RNA by HIV-1

scientific article

Orchestrating a community-developed computational workshop and accompanying training materials

scientific article published on 17 October 2018

Orchestrating high-throughput genomic analysis with Bioconductor

scientific article

Preferential Localization of Human Origins of DNA Replication at the 5′-Ends of Expressed Genes and at Evolutionarily Conserved DNA Sequences ⬇️

scientific article published on May 13, 2011

Prohibitin expression is associated with high grade breast cancer but is not a driver of amplification at 17q21.33.

scientific article published on December 2013

RARRES2 functions as a tumor suppressor by promoting β-catenin phosphorylation/degradation and inhibiting p38 phosphorylation in adrenocortical carcinoma

scientific article

RCircos: an R package for Circos 2D track plots.

scientific article

Rare structural variants disrupt multiple genes in neurodevelopmental pathways in schizophrenia

scientific article

Rb1 loss modifies but does not initiate alveolar rhabdomyosarcoma

scientific article

SRAdb: query and use public next-generation sequencing data from within R.

scientific article

Super-enhancers delineate disease-associated regulatory nodes in T cells

scientific article

Suppressor role of activating transcription factor 2 (ATF2) in skin cancer

scientific article

Ten simple rules for large-scale data processing

scientific article published on 10 February 2022

The Bioconductor channel in F1000Research

scientific article published on 10 July 2015

The exomes of the NCI-60 panel: a genomic resource for cancer biology and systems pharmacology

scientific article published on 15 July 2013

Upregulation of IFN-Inducible and Damage-Response Pathways in Chronic Graft-versus-Host Disease.

scientific article published on 30 September 2016

Vorinostat inhibits brain metastatic colonization in a model of triple-negative breast cancer and induces DNA double-strand breaks

scientific article published on 29 September 2009

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

scientific article published on 30 July 2013

miR30a inhibits LOX expression and anaplastic thyroid cancer progression.

scientific article published on 8 December 2014

recount-brain: a curated repository of human brain RNA-seq datasets metadata

scholarly article published 24 April 2019

List of works by Sean Davis

A molecular function map of Ewing's sarcoma

A polymorphism in IRF4 affects human pigmentation through a tyrosinase-dependent MITF/TFAP2A pathway

A single IGF1 allele is a major determinant of small size in dogs

Advanced bone formation in mice with a dominant-negative mutation in the thyroid hormone receptor β gene due to activation of Wnt/β-catenin protein signaling.

Analysis of bipolar disorder using affected relatives

Analysis of complex oligogenic disease

Analysis of complex oligogenic disease

Analysis of the matrix metalloproteinase family reveals that MMP8 is often mutated in melanoma

Antagonistic cross-regulation between Sox9 and Sox10 controls an anti-tumorigenic program in melanoma.

Assessment of automated image analysis of breast cancer tissue microarrays for epidemiologic studies

BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis

CHEK2 genomic and proteomic analyses reveal genetic inactivation or endogenous activation across the 60 cell lines of the US National Cancer Institute.

Canine tumor cross-species genomics uncovers targets linked to osteosarcoma progression

Chromothripsis and focal copy number alterations determine poor outcome in malignant melanoma

Comparative exome sequencing of metastatic lesions provides insights into the mutational progression of melanoma ⬇️

Comparison of nonparametric statistics for detection of linkage in nuclear families: single-marker evaluation

Constitutive Fms-like tyrosine kinase 3 activation results in specific changes in gene expression in myeloid leukaemic cells

DNase-chip: a high-resolution method to identify DNase I hypersensitive sites using tiled microarrays

Database of mRNA gene expression profiles of multiple human organs

Detection of novel amplicons in prostate cancer by comprehensive genomic profiling of prostate cancer cell lines using oligonucleotide-based arrayCGH.

Downregulation of IGFBP2 is associated with resistance to IGF1R therapy in rhabdomyosarcoma.

Epigenomic alterations and gene expression profiles in respiratory epithelia exposed to cigarette smoke condensate.

Evidence for an unanticipated relationship between undifferentiated pleomorphic sarcoma and embryonal rhabdomyosarcoma

Ewing's sarcoma: general insights from a rare model.

Exclusion of the 750-kb genetically unstable region at Xq27 as a candidate locus for prostate malignancy in HPCX1-linked families.

Exome sequencing identifies GRIN2A as frequently mutated in melanoma

GEOmetadb: powerful alternative search engine for the Gene Expression Omnibus

Gene expression profiling of human sarcomas: insights into sarcoma biology

Genetic susceptibility for human familial essential hypertension in a region of homology with blood pressure linkage on rat chromosome 10.

Genome-wide analysis of menin binding provides insights into MEN1 tumorigenesis

Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS)

Genome-wide methylation patterns in papillary thyroid cancer are distinct based on histological subtype and tumor genotype.

Genome-wide methylation profiling in archival formalin-fixed paraffin-embedded tissue samples

Harnessing genomics to identify environmental determinants of heritable disease

High prevalence of MAP2K1 mutations in variant and IGHV4-34-expressing hairy-cell leukemias

High-resolution mapping and characterization of open chromatin across the genome

Homozygosity mapping of Hallervorden-Spatz syndrome to chromosome 20p12.3-p13

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

Identification of an inhibitor of the EWS-FLI1 oncogenic transcription factor by high-throughput screening.

Impact of overlapping recruitment on linkage analysis of complex disorders: simulation studies

In Vivo Role of Alternative Splicing and Serine Phosphorylation of the Microphthalmia-Associated Transcription Factor ⬇️

Integrated analysis of DNA methylation, immunohistochemistry and mRNA expression, data identifies a methylation expression index (MEI) robustly associated with survival of ER-positive breast cancer patients

Interaction of the glucocorticoid receptor with the chromatin landscape

Interferon-γ links ultraviolet radiation to melanomagenesis in mice

Kinetic complexity of the global response to glucocorticoid receptor action.

Large-scale profiling of archival lymph nodes reveals pervasive remodeling of the follicular lymphoma methylome

Lineage of origin in rhabdomyosarcoma informs pharmacological response

Linkage and association between inflammatory bowel disease and a locus on chromosome 12

Melanoblast transcriptome analysis reveals pathways promoting melanoma metastasis

Modeling synovial sarcoma: timing is everything

Molecular Grading of Ductal Carcinoma In situ of the Breast

NCBI GEO: archive for functional genomics data sets--update

NCI-60 whole exome sequencing and pharmacological CellMiner analyses

On the Selective Packaging of Genomic RNA by HIV-1

Orchestrating a community-developed computational workshop and accompanying training materials

Orchestrating high-throughput genomic analysis with Bioconductor

Preferential Localization of Human Origins of DNA Replication at the 5′-Ends of Expressed Genes and at Evolutionarily Conserved DNA Sequences ⬇️

Prohibitin expression is associated with high grade breast cancer but is not a driver of amplification at 17q21.33.

RARRES2 functions as a tumor suppressor by promoting β-catenin phosphorylation/degradation and inhibiting p38 phosphorylation in adrenocortical carcinoma

RCircos: an R package for Circos 2D track plots.

Rare structural variants disrupt multiple genes in neurodevelopmental pathways in schizophrenia

Rb1 loss modifies but does not initiate alveolar rhabdomyosarcoma

SRAdb: query and use public next-generation sequencing data from within R.

Super-enhancers delineate disease-associated regulatory nodes in T cells

Suppressor role of activating transcription factor 2 (ATF2) in skin cancer

Ten simple rules for large-scale data processing

The Bioconductor channel in F1000Research

The exomes of the NCI-60 panel: a genomic resource for cancer biology and systems pharmacology

Upregulation of IFN-Inducible and Damage-Response Pathways in Chronic Graft-versus-Host Disease.

Vorinostat inhibits brain metastatic colonization in a model of triple-negative breast cancer and induces DNA double-strand breaks

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

miR30a inhibits LOX expression and anaplastic thyroid cancer progression.

recount-brain: a curated repository of human brain RNA-seq datasets metadata