List of works - Bernard Pope

A high-plex PCR approach for massively parallel sequencing.

scientific article published on August 2013

A novel Drosophila injury model reveals severed axons are cleared through a Draper/MMP-1 signaling cascade.

scientific article published on 21 August 2017

Abridged adapter primers increase the target scope of Hi-Plex

scientific article published in January 2015

Annokey: an annotation tool based on key term search of the NCBI Entrez Gene database.

scientific article published on 26 June 2014

Best Practice Data Life Cycle Approaches for the Life Sciences

scholarly article

Best practice data life cycle approaches for the life sciences

article

Bionitio: demonstrating and facilitating best practices for bioinformatics command-line software

scientific article published on 01 September 2019

Bpipe: a tool for running and managing bioinformatics pipelines

scientific article

Corrigendum: Risk of colorectal cancer for carriers of a germ-line mutation in POLE or POLD1.

scientific article published in February 2018

Cross-platform compatibility of Hi-Plex, a streamlined approach for targeted massively parallel sequencing.

scientific article

Exemplary multiplex bisulfite amplicon data used to demonstrate the utility of Methpat

scientific article

Expanded genetic analysis of a PALB2 c.3113G>A mutation carrying multiple-case breast cancer family via exome sequencing

scientific article published on 12 April 2012

FANCM and RECQL genetic variants and breast cancer susceptibility: relevance to South Poland and West Ukraine

scientific article published on 19 January 2018

FAVR (Filtering and Annotation of Variants that are Rare): methods to facilitate the analysis of rare germline genetic variants from massively parallel sequencing datasets

scientific article published on 25 February 2013

Fine resolution mapping of double-strand break sites for human ribosomal DNA units

scientific article

Four simple recommendations to encourage best practices in research software

scientific article

Genetic testing in Poland and Ukraine: should comprehensive germline testing of BRCA1 and BRCA2 be recommended for women with breast and ovarian cancer?

scientific article published on 10 August 2020

Hi-Plex for Simple, Accurate, and Cost-Effective Amplicon-based Targeted DNA Sequencing

scientific article published in January 2018

Hi-Plex for high-throughput mutation screening: application to the breast cancer susceptibility gene PALB2

scientific article

High-resolution twin-ion metabolite extraction (HiTIME) mass spectrometry: nontargeted detection of unknown drug metabolites by isotope labeling, liquid chromatography mass spectrometry, and automated high-performance computing.

scientific article published on 8 April 2015

Identification of new breast cancer predisposition genes via whole exome sequencing

scientific article published on 12 April 2012

MYRF is a membrane-associated transcription factor that autoproteolytically cleaves to directly activate myelin genes

scientific article published on 13 August 2013

MethPat: a tool for the analysis and visualisation of complex methylation patterns obtained by massively parallel sequencing

scientific article

Mismatch repair gene pathogenic germline variants in a population-based cohort of breast cancer

scientific article published on 14 February 2020

Mutation screening of ACKR3 and COPS8 in kidney cancer cases from the CONFIRM study.

scientific article

Mutation screening of PALB2 in clinically ascertained families from the Breast Cancer Family Registry

scientific article

Performance of hybrid programming models for multiscale cardiac simulations: preparing for petascale computation

scientific article published on 14 July 2011

Perish and publish: Dynamics of biomedical publications by deceased authors

scientific article published in 2022

Petascale computation performance of lightweight multiscale cardiac models using hybrid programming models

scientific article published on January 2011

ROVER variant caller: read-pair overlap considerate variant-calling software applied to PCR-based massively parallel sequencing datasets.

scientific article published on 24 January 2014

Rare mutations in RINT1 predispose carriers to breast and Lynch syndrome-spectrum cancers

scientific article

Risk of colorectal cancer for carriers of a germ-line mutation in POLE or POLD1.

scientific article published on 9 November 2017

SRST2: Rapid genomic surveillance for public health and hospital microbiology labs

scientific article

Single nucleotide-level mapping of DNA double-strand breaks in human HEK293T cells

scientific article published on 11 November 2016

Somatic mutations of the coding microsatellites within the beta-2-microglobulin gene in mismatch repair-deficient colorectal cancers and adenomas

scientific article

Targeted massively parallel sequencing characterises the mutation spectrum of PALB2 in breast and ovarian cancer cases from Poland and Ukraine

scientific article

Variant effect prediction tools assessed using independent, functional assay-based datasets: implications for discovery and diagnostics

scientific article published on 16 May 2017

sEst: Accurate Sex-Estimation and Abnormality Detection in Methylation Microarray Data

scholarly article by Chol-Hee Jung published in October 2018

List of works by Bernard Pope

A high-plex PCR approach for massively parallel sequencing.

A novel Drosophila injury model reveals severed axons are cleared through a Draper/MMP-1 signaling cascade.

Abridged adapter primers increase the target scope of Hi-Plex

Annokey: an annotation tool based on key term search of the NCBI Entrez Gene database.

Best Practice Data Life Cycle Approaches for the Life Sciences

Best practice data life cycle approaches for the life sciences

Bionitio: demonstrating and facilitating best practices for bioinformatics command-line software

Bpipe: a tool for running and managing bioinformatics pipelines

Corrigendum: Risk of colorectal cancer for carriers of a germ-line mutation in POLE or POLD1.

Cross-platform compatibility of Hi-Plex, a streamlined approach for targeted massively parallel sequencing.

Exemplary multiplex bisulfite amplicon data used to demonstrate the utility of Methpat

Expanded genetic analysis of a PALB2 c.3113G>A mutation carrying multiple-case breast cancer family via exome sequencing

FANCM and RECQL genetic variants and breast cancer susceptibility: relevance to South Poland and West Ukraine

FAVR (Filtering and Annotation of Variants that are Rare): methods to facilitate the analysis of rare germline genetic variants from massively parallel sequencing datasets

Fine resolution mapping of double-strand break sites for human ribosomal DNA units

Four simple recommendations to encourage best practices in research software

Genetic testing in Poland and Ukraine: should comprehensive germline testing of BRCA1 and BRCA2 be recommended for women with breast and ovarian cancer?

Hi-Plex for Simple, Accurate, and Cost-Effective Amplicon-based Targeted DNA Sequencing

Hi-Plex for high-throughput mutation screening: application to the breast cancer susceptibility gene PALB2

High-resolution twin-ion metabolite extraction (HiTIME) mass spectrometry: nontargeted detection of unknown drug metabolites by isotope labeling, liquid chromatography mass spectrometry, and automated high-performance computing.

Identification of new breast cancer predisposition genes via whole exome sequencing

MYRF is a membrane-associated transcription factor that autoproteolytically cleaves to directly activate myelin genes

MethPat: a tool for the analysis and visualisation of complex methylation patterns obtained by massively parallel sequencing

Mismatch repair gene pathogenic germline variants in a population-based cohort of breast cancer

Mutation screening of ACKR3 and COPS8 in kidney cancer cases from the CONFIRM study.

Mutation screening of PALB2 in clinically ascertained families from the Breast Cancer Family Registry

Performance of hybrid programming models for multiscale cardiac simulations: preparing for petascale computation

Perish and publish: Dynamics of biomedical publications by deceased authors

Petascale computation performance of lightweight multiscale cardiac models using hybrid programming models

ROVER variant caller: read-pair overlap considerate variant-calling software applied to PCR-based massively parallel sequencing datasets.

Rare mutations in RINT1 predispose carriers to breast and Lynch syndrome-spectrum cancers

Risk of colorectal cancer for carriers of a germ-line mutation in POLE or POLD1.

SRST2: Rapid genomic surveillance for public health and hospital microbiology labs

Single nucleotide-level mapping of DNA double-strand breaks in human HEK293T cells

Somatic mutations of the coding microsatellites within the beta-2-microglobulin gene in mismatch repair-deficient colorectal cancers and adenomas

Targeted massively parallel sequencing characterises the mutation spectrum of PALB2 in breast and ovarian cancer cases from Poland and Ukraine

Variant effect prediction tools assessed using independent, functional assay-based datasets: implications for discovery and diagnostics

sEst: Accurate Sex-Estimation and Abnormality Detection in Methylation Microarray Data