Bernie Pope

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

Peter Georgeson, Anna Syme, Clare Sloggett, Jessica Chung, Harriet Dashnow, Michael Milton, Andrew Lonsdale, David Powell, Torsten Seemann, Bernard Pope

Journal article  |  2019  |  GigaScience

Hi-Plex2: a simple and robust approach to targeted sequencing-based genetic screening

Fleur Hammet, Khalid Mahmood, Thomas R Green, Nguyen-Dumont Tu, Melissa C Southey, Daniel D Buchanan, Andrew Lonie, Katherine L Nathanson, Fergus J Couch, Bernard J Pope, Daniel J Park

Journal article  |  2019  |  BioTechniques

We have previously reported Hi-Plex, a multiplex PCR methodology for building targeted DNA sequencing libraries that offers a low-..

Tumor mutational signatures in sebaceous skin lesions from individuals with Lynch syndrome

Peter Georgeson, Michael D Walsh, Mark Clendenning, Simin Daneshvar, Bernard J Pope, Khalid Mahmood, Jihoon E Joo, Harindra Jayasekara, Mark A Jenkins, Ingrid M Winship, Daniel D Buchanan

Journal article  |  2019  |  Molecular Genetics & Genomic Medicine

Annotation of the Giardia proteome through structure-based homology and machine learning

Brendan RE Ansell, Bernard J Pope, Peter Georgeson, Samantha J Emery-Corbin, Aaron R Jex

Journal article  |  2019  |  GigaScience

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

Chol-Hee Jung, Daniel J Park, Peter Georgeson, Khalid Mahmood, Roger L Milne, Melissa C Southey, Bernard J Pope

Journal article  |  2018  |  International Journal of Molecular Sciences

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

Daniel D Buchanan, Jenna R Stewart, Mark Clendenning, Christophe Rosty, Khalid Mahmood, Bernard J Pope, Mark A Jenkins, John L Hopper, Melissa C Southey, Finlay A Macrae, Ingrid M Winship, Aung Ko Win

Journal article  |  2018  |  Genet Med

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

Aleksander Myszka, Nguyen-Dumont Tu, Pawel Karpinski, Maria M Sasiadek, Hayane Akopyan, Fleur Hammet, Helen Tsimiklis, Daniel J Park, Bernard J Pope, Ryszard Slezak, Nataliya Kitsera, Aleksandra Siekierzynska, Melissa C Southey

Journal article  |  2018  |  Familial Cancer

Best practice data life cycle approaches for the life sciences

Philippa Griffin, Jyoti Khadake, Kate LeMay, Suzanna Lewis, Sandra Orchard, Andrew Pask, Bernard Pope, Ute Roessner, Keith Russell, Torsten Seemann, Andrew Treloar, Sonika Tyagi, Jeffrey Christiansen, Saravanan Dayalan, Simon Gladman, Sandra Hangartner, Helen Hayden, William WH Ho, Gabriel Keeble-Gagnère, Pasi Korhonen, et al.

Journal article  |  2018  |  F1000Research

Throughout history, the life sciences have been revolutionised by technological advances; in our era this is manifested by advance..

Is RNASEL:p.Glu265*a modifier of early-onset breast cancer risk for carriers of high-risk mutations?

Tu Nguyen-Dumont, Zhi L Teo, Fleur Hammet, Alexis Roberge, Maryam Mahmoodi, Helen Tsimiklis, Daniel J Park, Bernard J Pope, Andrew Lonie, Miroslav K Kapuscinski, Khalid Mahmood, David E Goldgar, Graham G Giles, Ingrid Winship, John L Hopper, Melissa C Southey

Journal article  |  2018  |  BMC Cancer

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

Nguyen-Dumont Tu, Aleksander Myszka, Pawel Karpinski, Maria M Sasiadek, Hayane Akopyan, Fleur Hammet, Helen Tsimiklis, Daniel J Park, Bernard J Pope, Ryszard Slezak, Nataliya Kitsera, Aleksandra Siekierzynska, Melissa C Southey

Journal article  |  2018  |  BMC Medical Genetics

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

Mark Clendenning, Alvin Huang, Harindra Jayasekara, Marie Lorans, Susan Preston, Neil O'Callaghan, Bernard J Pope, Finlay A Macrae, Ingrid M Winship, Roger L Milne, Graham G Giles, Dallas R English, John L Hopper, Aung K Win, Mark A Jenkins, Melissa C Southey, Christophe Rosty, Daniel D Buchanan

Journal article  |  2018  |  Familial Cancer

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

Bernard J Pope, Fleur Hammet, Tu Nguyen-Dumont, Daniel J Park

Book Chapter  |  2018  |  Methods in Molecular Biology

Hi-Plex is a suite of methods to enable simple, accurate, and cost-effective highly multiplex PCR-based targeted sequencing (Nguye..

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

Maria D Purice, Arpita Ray, Eva Jolanda Munzel, Bernard J Pope, Daniel J Park, Sean D Speese, Mary A Logan

Journal article  |  2017  |  eLife

Best Practice Data Life Cycle Approaches for the Life Sciences

Philippa Griffin, Jyoti Khadake, Kate LeMay, Suzanna Lewis, Sandra Orchard, Andrew Pask, Bernard Pope, Ute Roessner, Keith Russell, Torsten Seemann, Andrew Treloar, Sonika Tyagi, Jeffrey Christiansen, Saravanan Dayalan, Simon Gladman, Sandra Hangartner, Helen Hayden, William Ho, Gabriel Keeble-Gagnère, Pasi Korhonen, et al.

Journal article  |  2017  |  F1000Research

Abstract Throughout history, the life sciences have been revolutionised by technological advances; in our era this is manifested b..

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

Maryam Mahmoodi, Nguyen-Dumont Tu, Fleur Hammet, Bernard J Pope, Daniel J Park, Melissa C Southey, John M Darlow, Fiona Bruinsma, Ingrid Winship

Journal article  |  2017  |  Familial Cancer

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

Khalid Mahmood, Chol-hee Jung, Gayle Philip, Peter Georgeson, Jessica Chung, Bernard J Pope, Daniel J Park

Journal article  |  2017  |  Human Genomics

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

Bernard J Pope, Khalid Mahmood, Chol-hee Jung, Peter Georgeson, Daniel J Park

Journal article  |  2017  |  Genomics Data

Four simple recommendations to encourage best practices in research software.

Rafael C Jiménez, Mateusz Kuzak, Monther Alhamdoosh, Michelle Barker, Bérénice Batut, Mikael Borg, Salvador Capella-Gutierrez, Neil Chue Hong, Martin Cook, Manuel Corpas, Madison Flannery, Leyla Garcia, Josep Ll Gelpí, Simon Gladman, Carole Goble, Montserrat González Ferreiro, Alejandra Gonzalez-Beltran, Philippa C Griffin, Björn Grüning, Jonas Hagberg, et al.

Journal article  |  2017  |  F1000Research

Scientific research relies on computer software, yet software is not always developed following practices that ensure its quality ..

Best practice data life cycle approaches for the life sciences.

Philippa C Griffin, Jyoti Khadake, Kate S LeMay, Suzanna E Lewis, Sandra Orchard, Andrew Pask, Bernard Pope, Ute Roessner, Keith Russell, Torsten Seemann, Andrew Treloar, Sonika Tyagi, Jeffrey H Christiansen, Saravanan Dayalan, Simon Gladman, Sandra B Hangartner, Helen L Hayden, William WH Ho, Gabriel Keeble-Gagnère, Pasi K Korhonen, et al.

Journal article  |  2017  |  F1000Research

Throughout history, the life sciences have been revolutionised by technological advances; in our era this is manifested by advance..

Best practice data life cycle approaches for the life sciences.

Philippa C Griffin, Jyoti Khadake, Kate S LeMay, Suzanna E Lewis, Sandra Orchard, Andrew Pask, Bernard Pope, Ute Roessner, Keith Russell, Torsten Seemann, Andrew Treloar, Sonika Tyagi, Jeffrey H Christiansen, Saravanan Dayalan, Simon Gladman, Sandra B Hangartner, Helen L Hayden, William WH Ho, Gabriel Keeble-Gagnère, Pasi K Korhonen, et al.

Journal article  |  2017  |  F1000Research

Throughout history, the life sciences have been revolutionised by technological advances; in our era this is manifested by advance..

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

Bernard J Pope, Khalid Mahmood, Chol-hee Jung, Daniel J Park

Journal article  |  2016  |  Genomics Data

Proffered papers and posters presented at the Sixth International Symposium on Hereditary Breast and Ovarian Cancer—BRCA: Challenges and Opportunities: Presented by the Hereditary Breast and Ovarian Cancer Foundation in collaboration with the Program in Cancer Genetics, McGill University; Centre Mont-Royal, Montreal, QC; 10–13 May 2016.

Journal article  |  2016  |  Current Oncology

UNDR ROVER - a fast and accurate variant caller for targeted DNA sequencing

Daniel J Park, Roger Li, Edmund Lau, Peter Georgeson, Nguyen-Dumont Tu, Bernard J Pope

Journal article  |  2016  |  BMC Bioinformatics

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

Nicholas C Wong, Bernard J Pope, Ida L Candiloro, Darren Korbie, Matt Trau, Stephen Q Wong, Thomas Mikeska, Xinmin Zhang, Mark Pitman, Stefanie Eggers, Stephen R Doyle, Alexander Dobrovic

Journal article  |  2016  |  BMC Bioinformatics

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

Nicholas C Wong, Bernard J Pope, Ida Candiloro, Darren Korbie, Matt Trau, Stephen Q Wong, Thomas Mikeska, Bryce JW van Denderen, Erik W Thompson, Stefanie Eggers, Stephen R Doyle, Alexander Dobrovic

Journal article  |  2015  |  GigaScience

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

Michael G Leeming, Andrew P Isaac, Bernard J Pope, Noel Cranswick, Christine E Wright, James Ziogas, Richard AJ O'Hair, William A Donald

Journal article  |  2015  |  Analytical Chemistry

Abridged adapter primers increase the target scope of Hi-Plex

Nguyen-Dumont Tu, Fleur Hammet, Maryam Mahmoodi, Bernard J Pope, Graham G Giles, Graham G Hopper, Melissa C Southey, Daniel J Park

Journal article  |  2015  |  BioTechniques

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

Nguyen-Dumont Tu, Fleur Hammet, Maryam Mahmoodi, Helen Tsimiklis, Zhi L Teo, Roger Li, Bernard J Pope, Mary Beth Terry, Saundra S Buys, Mary Daly, John L Hopper, Ingrid Winship, David E Goldgar, Daniel J Park, Melissa C Southey

Journal article  |  2015  |  Breast Cancer Research and Treatment

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

Michael Inouye, Harriet Dashnow, Lesley-Ann Raven, Mark B Schultz, Bernard J Pope, Takehiro Tomita, Justin Zobel, Kathryn E Holt

Journal article  |  2014  |  Genome Medicine

Rare Mutations in RINT1 Predispose Carriers to Breast and Lynch Syndrome-Spectrum Cancers

Daniel J Park, Kayoko Tao, Florence Le Calvez-Kelm, Nguyen-Dumont Tu, Nivonirina Robinot, Fleur Hammet, Fabrice Odefrey, Helen Tsimiklis, Zhi L Teo, Louise B Thingholm, Erin L Young, Catherine Voegele, Andrew Lonie, Bernard J Pope, Terrell C Roane, Russell Bell, Hao Hu, undefined Shankaracharya, Chad D Huff, Jonathan Ellis, et al.

Journal article  |  2014  |  Cancer Discovery

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

Bernard J Pope, Tú Nguyen-Dumont, Fleur Hammet, Daniel J Park

Journal article  |  2014  |  Source Code for Biology and Medicine

BACKGROUND: We recently described Hi-Plex, a highly multiplexed PCR-based target-enrichment system for massively parallel sequenci..

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

Daniel J Park, Tú Nguyen-Dumont, Sori Kang, Karin Verspoor, Bernard J Pope

Journal article  |  2014  |  Source Code for Biology and Medicine

BackgroundThe NCBI Entrez Gene and PubMed databases contain a wealth of high-quality information about genes for many different or..

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

Nguyen-Dumont Tu, Bernard J Pope, Fleur Hammet, Maryam Mahmoodi, Helen Tsimiklis, Melissa C Southey, Daniel J Park

Journal article  |  2013  |  Analytical Biochemistry

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

Nguyen-Dumont Tu, Zhi L Teo, Bernard J Pope, Fleur Hammet, Maryam Mahmoodi, Helen Tsimiklis, Nelly Sabbaghian, Marc Tischkowitz, William D Foulkes, Graham G Giles, John L Hopper, Melissa C Southey, Daniel J Park

Journal article  |  2013  |  BMC Medical Genomics

MYRF Is a Membrane-Associated Transcription Factor That Autoproteolytically Cleaves to Directly Activate Myelin Genes

Helena Bujalka, Matthias Koenning, Stacey Jackson, Victoria M Perreau, Bernard Pope, Curtis M Hay, Stanlislaw Mitew, Andrew F Hill, Q Richard Lu, Michael Wegner, Rajini Srinivasan, John Svaren, Melanie Willingham, Ben A Barres, Ben Emery

Journal article  |  2013  |  PLoS Biology

A high-plex PCR approach for massively parallel sequencing

Nguyen-Dumont Tu, Bernard J Pope, Fleur Hammet, Melissa C Southey, Daniel J Park

Journal article  |  2013  |  Biotechniques

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

Bernard J Pope, Nguyen-Dumont Tu, Fabrice Odefrey, Fleur Hammet, Russell Bell, Kayoko Tao, Sean V Tavtigian, David E Goldgar, Andrew Lonie, Melissa C Southey, Daniel J Park

Journal article  |  2013  |  BMC Bioinformatics

Bpipe: a tool for running and managing bioinformatics pipelines

Simon P Sadedin, Bernard Pope, Alicia Oshlack

Journal article  |  2012  |  Bioinformatics

Rare Mutations in XRCC2 Increase the Risk of Breast Cancer

DJ Park, F Lesueur, T Nguyen-Dumont, M Pertesi, F Odefrey, F Hammet, SL Neuhausen, EM John, IL Andrulis, MB Terry, M Daly, S Buys, F Le Calvez-Kelm, A Lonie, BJ Pope, H Tsimiklis, C Voegele, FM Hilbers, N Hoogerbrugge, A Barroso, et al.

Journal article  |  2012  |  American Journal of Human Genetics

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

BJ Pope, BG Fitch, MC Pitman, JJ Rice, M Reumann

Journal article  |  2011  |  Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS

Performance of Hybrid Programming Models for Multiscale Cardiac Simulations: Preparing for Petascale Computation

Bernard J Pope, Blake G Fitch, Michael C Pitman, John J Rice, Matthias Reumann

Journal article  |  2011  |  IEEE Transactions on Biomedical Engineering

Precision Medicine: Dawn of Supercomputing in ‘omics Research

M Reumann, KE Holt, M Inouye, T Stinear, B Goudey, G Abraham, Q WANG, F Shi, A Kowalczyk, A Pearce, A Isaac, BJ Pope, H Butzkueven, J Wagner, S Moore, M Downton, PC Church, SJ Turner, J Field, M Southey, et al.

Conference Proceedings  |  2011

Petascale Computation Performance of Lightweight Multiscale Cardiac Models using Hybrid Programming Models

Bernard J Pope, Blake G Fitch, Michael C Pitman, John J Rice, Matthias Reumann

Conference Proceedings  |  2011  |  Proceedings the 33rd Annual International IEEE EMBC Conference

A Lightweight Interactive Debugger for Haskell

Simon Marlow, Jose Iborra, Bernard Pope, Andy Gill

Conference Proceedings  |  2007  |  Proceedings of the ACM SIGPLAN 2007 Haskell Worshop

Declarative debugging with Buddha

B Pope

Book Chapter  |  2004  |  Lecture Notes in Artificial Intelligence

Practical aspects of Declarative Debugging in Haskell 98

B Pope, L Naish

Conference Proceedings  |  2003  |  Proceedings of the Fifth ACM SIGPLAN Conference on Principles and Practice of Declarative Programming

A Program Transformation for Debugging Haskell 98

BJ Pope, L NAISH

Conference Proceedings  |  2003  |  Computer Science 2003: Proceedings of the Twenty-Sixth Australasian Computer Science Conference

Specialisation of higher-order functions for debugging

B Pope, L Naish

Conference Proceedings  |  2002  |  Electronic Notes in Theoretical Computer Science

Specialisation of Higher Order Functions for Debugging

B POPE, L NAISH

Conference Proceedings  |  2001  |  Proceedings of the International Workshop on Functional and (Constraint) Logic Programming