List of works by Aedin C Culhane

A multivariate analysis approach to the integration of proteomic and gene expression data

scientific article

A multivariate approach to the integration of multi-omics datasets

scientific article

A three-gene model to robustly identify breast cancer molecular subtypes

scientific article published on 18 January 2012

Altered cytoplasmic-to-nuclear ratio of survivin is a prognostic indicator in breast cancer

scientific article

An international characterisation of patients hospitalised with COVID-19 and a comparison with those previously hospitalised with influenza

scientific article published on 26 April 2020

Analysis of differential gene expression in colorectal cancer and stroma using fluorescence-activated cell sorting purification

scientific article published on May 2009

Angiogenic mRNA and microRNA gene expression signature predicts a novel subtype of serous ovarian cancer

scientific article (publication date: 2012)

Apoptosis: molecular regulation of cell death

scientific journal article

Application of DNA microarray technology in determining breast cancer prognosis and therapeutic response

scientific article

BRCA1-IRIS promotes human tumor progression through PTEN blockade and HIF-1α activation

article published in the Proceedings of the National Academy of Sciences of the United States of America

Between-group analysis of microarray data

scientific article

CENP-F expression is associated with poor prognosis and chromosomal instability in patients with primary breast cancer

scientific article published on April 2007

Cloning of rat brain interleukin-18 cDNA.

scientific article published in July 1998

Community-wide hackathons to identify central themes in single-cell multi-omics

publication published in 2021

Comparative meta-analysis of prognostic gene signatures for late-stage ovarian cancer

scientific article

Comparison and evaluation of methods for generating differentially expressed gene lists from microarray data.

scientific article

Confounding effects in "A six-gene signature predicting breast cancer lung metastasis".

scientific article published on September 2009

Cross-platform comparison and visualisation of gene expression data using co-inertia analysis

scientific article

Curated single cell multimodal landmark datasets for R/Bioconductor

scientific article published on 25 August 2023

DNA Microarray-Based Gene Expression Profiling in Cancer: Aiding Cancer Diagnosis, Assessing Prognosis and Predicting Response to Therapy

article

Deep phenotyping of 34,128 adult patients hospitalised with COVID-19 in an international network study

scientific article published on 06 October 2020

Detection of the interleukin 18 family in rat brain by RT-PCR

scientific article published on 01 May 2000

Dimension reduction techniques for the integrative analysis of multi-omics data

scientific article

Enter the Matrix: Factorization Uncovers Knowledge from Omics

scientific article published on 22 August 2018

Epithelial progeny of estrogen-exposed breast progenitor cells display a cancer-like methylome

scientific article

Expression Profiler: next generation--an online platform for analysis of microarray data

scientific article (publication date: July 2004)

Functional classification analysis of somatically mutated genes in human breast and colorectal cancers

scientific article published on 22 April 2008

Gene Expression Atlas update--a value-added database of microarray and sequencing-based functional genomics experiments

scientific article

GeneSigDB--a curated database of gene expression signatures

scientific article

GeneSigDB: a manually curated database and resource for analysis of gene expression signatures

scientific article published on 21 November 2011

Identification of novel kinase targets for the treatment of estrogen receptor-negative breast cancer

scientific article published on 06 October 2009

Identification of transcription factors associated with castration-resistance: is the serum responsive factor a potential therapeutic target?

scientific article

In Reply

Integrated analysis of multiple microarray datasets identifies a reproducible survival predictor in ovarian cancer

scientific article

Integrating postgraduate and undergraduate general practice education: qualitative study.

scientific article published in May 2013

Integrating transcription factor binding site information with gene expression datasets

scientific article published on 24 November 2006

Integrative Exploratory Analysis of Two or More Genomic Datasets

scientific article published on January 2016

MADE4: an R package for multivariate analysis of gene expression data

scientific article

MECP2 Is a Frequently Amplified Oncogene with a Novel Epigenetic Mechanism That Mimics the Role of Activated RAS in Malignancy

scientific article published on 6 November 2015

MOGSA: Integrative Single Sample Gene-set Analysis of Multiple Omics Data

scientific article published on 26 June 2019

Mechanisms driving local breast cancer recurrence in a model of breast-conserving surgery.

scientific article published on 12 July 2008

MicroRNA paraffin-based studies in osteosarcoma reveal reproducible independent prognostic profiles at 14q32.

scientific article published on 22 January 2013

Molecular Subtypes Improve Prognostic Value of International Metastatic Renal Cell Carcinoma Database Consortium Prognostic Model

scientific article published on 20 February 2017

Multiple markers for melanoma progression regulated by DNA methylation: insights from transcriptomic studies

scientific article published on 15 June 2005

Oligonucleotide microarray analysis of gene expression in neuroblastoma displaying loss of chromosome 11q.

scientific article published on 16 April 2004

Optimized between-group classification: a new jackknife-based gene selection procedure for genome-wide expression data

scientific article

Pleiotropic mechanisms drive endocrine resistance in the three-dimensional bone microenvironment

scientific article published on 28 August 2020

Profiles of genomic instability in high-grade serous ovarian cancer predict treatment outcome

scientific article

Proliferative genes dominate malignancy-risk gene signature in histologically-normal breast tissue

scientific article published on 06 March 2009

Public data and open source tools for multi-assay genomic investigation of disease

scientific article

RAP80 targets BRCA1 to specific ubiquitin structures at DNA damage sites

scientific article

RamiGO: an R/Bioconductor package providing an AmiGO visualize interface

scientific article published on 6 January 2013

RelA-Induced Interferon Response Negatively Regulates Proliferation

scientific article published on 13 October 2015

Repeatability of published microarray gene expression analyses

scientific article

Risk of hydroxychloroquine alone and in combination with azithromycin in the treatment of rheumatoid arthritis: a multinational, retrospective study

scientific article published on 21 August 2020

Risk prediction for late-stage ovarian cancer by meta-analysis of 1525 patient samples.

scientific article

Safety of hydroxychloroquine, alone and in combination with azithromycin, in light of rapid wide-spread use for COVID-19: a multinational, network cohort and self-controlled case series study

scientific article published on 11 April 2020

Significance analysis of prognostic signatures

scientific article

Software for the Integration of Multiomics Experiments in Bioconductor

scientific article

Stem cell-like gene expression in ovarian cancer predicts type II subtype and prognosis

scientific article

Taxonomy of breast cancer based on normal cell phenotype predicts outcome.

scientific article published on 27 January 2014

The Immune Landscape of Cancer

scientific article published on 01 August 2019

The Immune Landscape of Cancer.

scientific article published on 4 April 2018

The Impact of Stroma Admixture on Molecular Subtypes and Prognostic Gene Signatures in Serous Ovarian Cancer

scientific article published on 23 December 2019

The Stem Cell Discovery Engine: an integrated repository and analysis system for cancer stem cell comparisons

scientific article published on 24 November 2011

The cocaine- and amphetamine-regulated transcript mediates ligand-independent activation of ERα, and is an independent prognostic factor in node-negative breast cancer.

scientific article

Therapeutic implications of GIPC1 silencing in cancer

scientific article

Towards vertical integration in general practice education: literature review and discussion paper.

scientific article published on 25 December 2012

iBBiG: iterative binary bi-clustering of gene sets

scientific article

moGSA: integrative single sample gene-set analysis of multiple omics data

article

survcomp: an R/Bioconductor package for performance assessment and comparison of survival models

scientific article published on 7 September 2011

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