List of works - Andy G. Lynch

5-hydroxymethylcytosine marks promoters in colon that resist DNA hypermethylation in cancer

scientific article published on April 2015

A comparative analysis of whole genome sequencing of esophageal adenocarcinoma pre- and post-chemotherapy

scientific article

A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing.

scientific article

A re-annotation pipeline for Illumina BeadArrays: improving the interpretation of gene expression data

scientific article

A study of the characteristics of single-injection insulated block needles in a biologic model

scientific article published in September 2004

Appraising the relevance of DNA copy number loss and gain in prostate cancer using whole genome DNA sequence data

scientific article published on 25 September 2017

Assessing agreement between multiple raters with missing rating information, applied to breast cancer tumour grading

scientific article

BASH: a tool for managing BeadArray spatial artefacts

scientific article published on 25 October 2008

BayesPeak--an R package for analysing ChIP-seq data

scientific article

BayesPeak: Bayesian analysis of ChIP-seq data

scientific article

BeadArray expression analysis using bioconductor.

scientific article published on December 2011

Breaking the waves: improved detection of copy number variation from microarray-based comparative genomic hybridization.

scientific article

Calling sample mix-ups in cancer population studies

scientific article

Choline Kinase Alpha as an Androgen Receptor Chaperone and Prostate Cancer Therapeutic Target

scientific article published on 11 December 2015

Crambled: A Shiny application to enable intuitive resolution of conflicting cellularity estimates

scientific article

DESNT: A Poor Prognosis Category of Human Prostate Cancer.

scientific article

Deciphering the genomic, epigenomic, and transcriptomic landscapes of pre-invasive lung cancer lesions

scientific article published on 21 January 2019

Different laterality indexes are poorly correlated with one another but consistently show the tendency of males and females to be more left- and right-lateralized, respectively

scientific article published on 15 April 2020

Does the Use of a Handheld Fan Improve Chronic Dyspnea? A Randomized, Controlled, Crossover Trial

scientific article published on 01 May 2010

Driver mutations in TP53 are ubiquitous in high grade serous carcinoma of the ovary

scientific article

Early radiotherapy dose response and lack of hypersensitivity effect in normal brain tissue: a sequential dynamic susceptibility imaging study of cerebral perfusion.

scientific article

Effective gene therapy in an authentic model of Tay-Sachs-related diseases

scientific article

Genomic Evolution of Breast Cancer Metastasis and Relapse

scientific article published on August 2017

HES5 silencing is an early and recurrent change in prostate tumourigenesis

scientific article

Hemodynamic steroid responsiveness is predictive of neurological outcome after traumatic brain injury.

scientific article published in January 2006

Hidden copy number variation in the HapMap population.

scholarly article

Integration of copy number and transcriptomics provides risk stratification in prostate cancer: A discovery and validation cohort study

scientific article

Mining Human Prostate Cancer Datasets: The "camcAPP" Shiny App.

scientific article

Missing channels in two-colour microarray experiments: combining single-channel and two-channel data

scientific article

Multicenter Validation of the CamGFR Model for Estimated Glomerular Filtration Rate

scientific article published on 19 September 2019

Mutational signatures in esophageal adenocarcinoma define etiologically distinct subgroups with therapeutic relevance.

scientific article published on 5 September 2016

New Model for Estimating Glomerular Filtration Rate in Patients With Cancer

scientific article published on 7 July 2017

New androgen receptor genomic targets show an interaction with the ETS1 transcription factor.

scientific article published on 17 August 2007

Numbers of copy-number variations and false-negative rates will be underestimated if we do not account for the dependence between repeated experiments

scientific article published on August 2007

Ordering of mutations in preinvasive disease stages of esophageal carcinogenesis.

scientific article

Origins and functional consequences of somatic mitochondrial DNA mutations in human cancer

scientific article

Overnight intensive recovery: elective open aortic surgery without a routine ICU bed.

scientific article published on 15 April 2005

Phenotype specific analyses reveal distinct regulatory mechanism for chronically activated p53

scientific article

Publisher Correction: Telomerecat: A ploidy-agnostic method for estimating telomere length from whole genome sequencing data ⬇️

scientific article published in Scientific Reports

Publisher Correction: Whole-genome sequencing of a sporadic primary immunodeficiency cohort

scientific article published on 17 July 2020

Quantifying the impact of inter-site heterogeneity on the distribution of ChIP-seq data

scientific article

Resolving the immune landscape of human prostate at a single-cell level in health and cancer

scientific article published on 01 December 2021

Sequencing of prostate cancers identifies new cancer genes, routes of progression and drug targets

scientific article published on 16 April 2018

Serum albumin level as a predictor of outcome in traumatic brain injury: potential for treatment

scientific article published in April 2008

Spike-in validation of an Illumina-specific variance-stabilizing transformation

scientific article

Statistical issues in the analysis of Illumina data

scientific article

Suprarenal endograft fixation and medium-term renal function: systematic review and meta-analysis.

scientific article published on 14 February 2008

Symptom classification in irritable bowel syndrome as a guide to treatment

scientific article published on 01 January 2009

Synthetic lethality between androgen receptor signalling and the PARP pathway in prostate cancer

scientific article published on 29 August 2017

Telomerecat: A ploidy-agnostic method for estimating telomere length from whole genome sequencing data ⬇️

scientific article published on 22 January 2018

The Early Effects of Rapid Androgen Deprivation on Human Prostate Cancer

scientific article

The androgen receptor fuels prostate cancer by regulating central metabolism and biosynthesis

scientific article published on 20 May 2011

The pitfalls of platform comparison: DNA copy number array technologies assessed

scientific article

The role of TET-mediated DNA hydroxymethylation in prostate cancer

scientific article published in September 2017

Timing the Landmark Events in the Evolution of Clear Cell Renal Cell Cancer: TRACERx Renal

scientific article published on 4 April 2018

Utility of HLAMatchmaker and single-antigen HLA-antibody detection beads for identification of acceptable mismatches in highly sensitized patients awaiting kidney transplantation

scientific article published in May 2006

Variation of the distal metatarsal articular angle with axial rotation and inclination of the first metatarsal.

scientific article published on December 2006

Whole blood mRNA in prostate cancer reveals a four-gene androgen regulated panel

scientific article

Whole-genome sequencing of a sporadic primary immunodeficiency cohort

scientific article published on 06 May 2020

Whole-genome sequencing of nine esophageal adenocarcinoma cell lines

scientific article published on 10 June 2016

Whole-genome sequencing provides new insights into the clonal architecture of Barrett's esophagus and esophageal adenocarcinoma

scientific article

ZNF703 is a common Luminal B breast cancer oncogene that differentially regulates luminal and basal progenitors in human mammary epithelium

scientific article

multiSNV: a probabilistic approach for improving detection of somatic point mutations from multiple related tumour samples

scientific article published on 26 February 2015

List of works by Andy G. Lynch

5-hydroxymethylcytosine marks promoters in colon that resist DNA hypermethylation in cancer

A comparative analysis of whole genome sequencing of esophageal adenocarcinoma pre- and post-chemotherapy

A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing.

A re-annotation pipeline for Illumina BeadArrays: improving the interpretation of gene expression data

A study of the characteristics of single-injection insulated block needles in a biologic model

Appraising the relevance of DNA copy number loss and gain in prostate cancer using whole genome DNA sequence data

Assessing agreement between multiple raters with missing rating information, applied to breast cancer tumour grading

BASH: a tool for managing BeadArray spatial artefacts

BayesPeak--an R package for analysing ChIP-seq data

BayesPeak: Bayesian analysis of ChIP-seq data

BeadArray expression analysis using bioconductor.

Breaking the waves: improved detection of copy number variation from microarray-based comparative genomic hybridization.

Calling sample mix-ups in cancer population studies

Choline Kinase Alpha as an Androgen Receptor Chaperone and Prostate Cancer Therapeutic Target

Crambled: A Shiny application to enable intuitive resolution of conflicting cellularity estimates

DESNT: A Poor Prognosis Category of Human Prostate Cancer.

Deciphering the genomic, epigenomic, and transcriptomic landscapes of pre-invasive lung cancer lesions

Different laterality indexes are poorly correlated with one another but consistently show the tendency of males and females to be more left- and right-lateralized, respectively

Does the Use of a Handheld Fan Improve Chronic Dyspnea? A Randomized, Controlled, Crossover Trial

Driver mutations in TP53 are ubiquitous in high grade serous carcinoma of the ovary

Early radiotherapy dose response and lack of hypersensitivity effect in normal brain tissue: a sequential dynamic susceptibility imaging study of cerebral perfusion.

Effective gene therapy in an authentic model of Tay-Sachs-related diseases

Genomic Evolution of Breast Cancer Metastasis and Relapse

HES5 silencing is an early and recurrent change in prostate tumourigenesis

Hemodynamic steroid responsiveness is predictive of neurological outcome after traumatic brain injury.

Hidden copy number variation in the HapMap population.

Integration of copy number and transcriptomics provides risk stratification in prostate cancer: A discovery and validation cohort study

Mining Human Prostate Cancer Datasets: The "camcAPP" Shiny App.

Missing channels in two-colour microarray experiments: combining single-channel and two-channel data

Multicenter Validation of the CamGFR Model for Estimated Glomerular Filtration Rate

Mutational signatures in esophageal adenocarcinoma define etiologically distinct subgroups with therapeutic relevance.

New Model for Estimating Glomerular Filtration Rate in Patients With Cancer

New androgen receptor genomic targets show an interaction with the ETS1 transcription factor.

Numbers of copy-number variations and false-negative rates will be underestimated if we do not account for the dependence between repeated experiments

Ordering of mutations in preinvasive disease stages of esophageal carcinogenesis.

Origins and functional consequences of somatic mitochondrial DNA mutations in human cancer

Overnight intensive recovery: elective open aortic surgery without a routine ICU bed.

Phenotype specific analyses reveal distinct regulatory mechanism for chronically activated p53

Publisher Correction: Telomerecat: A ploidy-agnostic method for estimating telomere length from whole genome sequencing data ⬇️

Publisher Correction: Whole-genome sequencing of a sporadic primary immunodeficiency cohort

Quantifying the impact of inter-site heterogeneity on the distribution of ChIP-seq data

Resolving the immune landscape of human prostate at a single-cell level in health and cancer

Sequencing of prostate cancers identifies new cancer genes, routes of progression and drug targets

Serum albumin level as a predictor of outcome in traumatic brain injury: potential for treatment

Spike-in validation of an Illumina-specific variance-stabilizing transformation

Statistical issues in the analysis of Illumina data

Suprarenal endograft fixation and medium-term renal function: systematic review and meta-analysis.

Symptom classification in irritable bowel syndrome as a guide to treatment

Synthetic lethality between androgen receptor signalling and the PARP pathway in prostate cancer

Telomerecat: A ploidy-agnostic method for estimating telomere length from whole genome sequencing data ⬇️

The Early Effects of Rapid Androgen Deprivation on Human Prostate Cancer

The androgen receptor fuels prostate cancer by regulating central metabolism and biosynthesis

The pitfalls of platform comparison: DNA copy number array technologies assessed

The role of TET-mediated DNA hydroxymethylation in prostate cancer

Timing the Landmark Events in the Evolution of Clear Cell Renal Cell Cancer: TRACERx Renal

Utility of HLAMatchmaker and single-antigen HLA-antibody detection beads for identification of acceptable mismatches in highly sensitized patients awaiting kidney transplantation

Variation of the distal metatarsal articular angle with axial rotation and inclination of the first metatarsal.

Whole blood mRNA in prostate cancer reveals a four-gene androgen regulated panel

Whole-genome sequencing of a sporadic primary immunodeficiency cohort

Whole-genome sequencing of nine esophageal adenocarcinoma cell lines

Whole-genome sequencing provides new insights into the clonal architecture of Barrett's esophagus and esophageal adenocarcinoma

ZNF703 is a common Luminal B breast cancer oncogene that differentially regulates luminal and basal progenitors in human mammary epithelium

multiSNV: a probabilistic approach for improving detection of somatic point mutations from multiple related tumour samples