Bernie Pope

Dr

20122018
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Research Output 2012 2018

  • 21 Article
  • 2 Review Article
  • 1 Chapter (Book)
  • 1 Comment / Debate
2018
3 Citations (Scopus)

Best practice data life cycle approaches for the life sciences

Griffin, P. C., Khadake, J., LeMay, K. S., Lewis, S. E., Orchard, S., Pask, A., Pope, B., Roessner, U., Russell, K., Seemann, T., Treloar, A., Tyagi, S., Christiansen, J. H., Dayalan, S., Gladman, S., Hangartner, S. B., Hayden, H. L., Ho, W. W. H., Keeble-Gagnère, G., Korhonen, P. K. & 7 others, Neish, P., Prestes, P. R., Richardson, M. F., Watson-Haigh, N. S., Wyres, K. L., Young, N. D. & Schneider, M. V., 4 Jun 2018, In : F1000Research. 6, 22 p., 1618.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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Correction to: Risk of colorectal cancer for carriers of a germ-line mutation in POLE or POLD1 (Genetics in Medicine, (2018), 20, 8, (890-895), 10.1038/gim.2017.185)

Buchanan, D. D., Stewart, J. R., Clendenning, M., Rosty, C., Mahmood, K., Pope, B. J., Jenkins, M. A., Hopper, J. L., Southey, M. C., Macrae, F. A., Winship, I. M. & Win, A. K., 1 Oct 2018, In : Genetics in Medicine. 20, 10, 1 p.

Research output: Contribution to journalComment / DebateOtherpeer-review

Open Access
5 Citations (Scopus)

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

Nguyen-Dumont, T., Myszka, A., Karpinski, P., Sasiadek, M. M., Akopyan, H., Hammet, F., Tsimiklis, H., Park, D. J., Pope, B. J., Slezak, R., Kitsera, N., Siekierzynska, A. & Southey, M. C., 19 Jan 2018, In : BMC Medical Genetics. 19, 1, 7 p., 12.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File
1 Citation (Scopus)

Hi-plex for simple, accurate, and cost-effective amplicon-based targeted DNA sequencing

Pope, B. J., Hammet, F., Nguyen-Dumont, T. & Park, D. J., 2018, Next Generation Sequencing: Methods and Protocols. Head, S. R., Ordoukhanian, P. & Salomon, D. R. (eds.). Humana Press, p. 53-70 18 p. (Methods in Molecular Biology; vol. 1712).

Research output: Chapter in Book/Report/Conference proceedingChapter (Book)Otherpeer-review

1 Citation (Scopus)

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

Nguyen-Dumont, T., Teo, Z. L., Hammet, F., Roberge, A., Mahmoodi, M., Tsimiklis, H., Park, D. J., Pope, B. J., Lonie, A., Kapuscinski, M. K., Mahmood, K., ABCFR, Goldgar, D. E., Giles, G. G., Winship, I., Hopper, J. L. & Southey, M. C., 8 Feb 2018, In : BMC Cancer. 18, 1, 7 p., 165.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File
9 Citations (Scopus)

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

Buchanan, D. D., Stewart, J., Clendenning, M., Rosty, C., Mahmood, K., Pope, B., Jenkins, M., Hopper, J. L., Southey, M. C., Macrae, F. A., Winship, I. M. & Win, A. K., 1 Aug 2018, In : Genetics in Medicine. 20, 8, p. 890-895 6 p.

Research output: Contribution to journalArticleResearchpeer-review

sEst: Accurate sex-estimation and abnormality detection in methylation microarray data

Jung, C. H., Park, D. J., Georgeson, P., Mahmood, K., Milne, R. L., Southey, M. C. & Pope, B. J., 15 Oct 2018, In : International Journal of Molecular Sciences. 19, 10, 11 p., 3172.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File
1 Citation (Scopus)

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

Clendenning, M., Huang, A., Jayasekara, H., Lorans, M., Preston, S., O’Callaghan, N., Pope, B. J., Macrae, F. A., Winship, I. M., Milne, R. L., Giles, G. G., English, D. R., Hopper, J. L., Win, A. K., Jenkins, M. A., Southey, M. C., Rosty, C., Buchanan, D. D. & On Behalf Of Investigators From The Melbourne Collaborative Cohort Study And The Australasian Colorectal Cancer Family Registry Cohort, Jan 2018, In : Familial Cancer. 17, 1, p. 91-100 10 p.

Research output: Contribution to journalArticleResearchpeer-review

4 Citations (Scopus)

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

Myszka, A., Nguyen-Dumont, T., Karpinski, P., Sasiadek, M. M., Akopyan, H., Hammet, F., Tsimiklis, H., Park, D. J., Pope, B. J., Slezak, R., Kitsera, N., Siekierzynska, A. & Southey, M. C., Jul 2018, In : Familial Cancer. 17, 3, p. 345-349 5 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File
2017
14 Citations (Scopus)

Four simple recommendations to encourage best practices in research software

Jiménez, R. C., Kuzak, M., Alhamdoosh, M., Barker, M., Batut, B., Borg, M., Capella-Gutierrez, S., Chue Hong, N., Cook, M., Corpas, M., Flannery, M., Garcia, L., Gelpí, J. L., Gladman, S., Goble, C., González Ferreiro, M., Gonzalez-Beltran, A., Griffin, P. C., Grüning, B., Hagberg, J. & 29 others, Holub, P., Hooft, R., Ison, J., Katz, D. S., Leskošek, B., López Gómez, F., Oliveira, L. J., Mellor, D., Mosbergen, R., Mulder, N., Perez-Riverol, Y., Pergl, R., Pichler, H., Pope, B., Sanz, F., Schneider, M. V., Stodden, V., Suchecki, R., Svobodová Vařeková, R., Talvik, H. A., Todorov, I., Treloar, A., Tyagi, S., van Gompel, M., Vaughan, D., Via, A., Wang, X., Watson-Haigh, N. S. & Crouch, S., 2017, In : F1000Research. 6, 13 p., 876.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File
2 Citations (Scopus)

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

Mahmoodi, M., Nguyen-Dumont, T., Hammet, F., Pope, B. J., Park, D. J., Southey, M. C., Darlow, J. M., Bruinsma, F. & Winship, I., 1 Jul 2017, In : Familial Cancer. 16, 3, p. 411-416 6 p.

Research output: Contribution to journalArticleResearchpeer-review

2016
8 Citations (Scopus)

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

Wong, N. C., Pope, B. J., Candiloro, I. L., Korbie, D., Trau, M., Wong, S. Q., Mikeska, T., Zhang, X., Pitman, M., Eggers, S., Doyle, S. R. & Dobrovic, A., 24 Feb 2016, In : BMC Bioinformatics. 17, 1, 14 p., 98.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File
3 Citations (Scopus)

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

Park, D. J., Li, R., Lau, E., Georgeson, P., Nguyen-Dumont, T. & Pope, B. J., 16 Apr 2016, In : BMC Bioinformatics. 17, 1, 7 p., 165.

Research output: Contribution to journalArticleOtherpeer-review

Open Access
2015
7 Citations (Scopus)

Abridged adapter primers increase the target scope of Hi-Plex

Nguyen-Dumont, T., Hammet, F., Mahmoodi, M., Pope, B. J., Giles, G. G., Hopper, J. L., Southey, M. C. & Park, D. J., 1 Jan 2015, In : BioTechniques. 58, 1, p. 33-36 4 p.

Research output: Contribution to journalArticleOtherpeer-review

Open Access
File
2 Citations (Scopus)

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

Wong, N. C., Pope, B. J., Candiloro, I., Korbie, D., Trau, M., Wong, S. Q., Mikeska, T., Bryce, B. J., Thompson, E. W., Eggers, S., Doyle, S. R. & Dobrovic, A., 1 Jan 2015, In : GigaScience. 4, 1, 8 p., 55.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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18 Citations (Scopus)

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

Nguyen-Dumont, T., Hammet, F., Mahmoodi, M., Tsimiklis, H., Teo, Z. L., Li, R., Pope, B. J., Terry, M. B., Buys, S. S., Daly, M., Hopper, J. L., Winship, I., Goldgar, D. E., Park, D. J. & Southey, M. C., 2015, In : Breast Cancer Research and Treatment. 149, 2, p. 547-554 8 p.

Research output: Contribution to journalArticleResearchpeer-review

2014
3 Citations (Scopus)

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

Park, D. J., Nguyen-Dumont, T., Kang, S., Verspoor, K. & Pope, B. J., 26 Jun 2014, In : Source Code for Biology and Medicine. 9, 1, 9 p., 15.

Research output: Contribution to journalReview ArticleOtherpeer-review

Open Access
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23 Citations (Scopus)

Rare mutations in RINT1 predispose carriers to breast and lynch syndrome-Spectrum cancers

Park, D. J., Tao, K., Le Calvez-Kelm, F. L., Nguyen-Dumont, T., Robinot, N., Hammet, F., Odefrey, F., Tsimiklis, H., Teo, Z. L., Thingholm, L. B., Young, E. L., Voegele, C., Lonie, A., Pope, B. J., Roane, T. C., Bell, R., Hu, H., Shankaracharya, Huff, C. D., Ellis, J. & 17 others, Li, J., Makunin, I. V., John, E. M., Andrulis, I. L., Terry, M. B., Daly, M. B., Buys, S. S., Snyder, C., Lynch, H. T., Devilee, P., Giles, G. G., Hopper, J. L., Feng, B. J., Lesueur, F., Tavtigian, S. V., Southey, M. C. & Goldgar, D. E., Jul 2014, In : Cancer Discovery. 4, 7, p. 804-815 12 p.

Research output: Contribution to journalArticleResearchpeer-review

11 Citations (Scopus)

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

Pope, B. J., Nguyen-Dumont, T., Hammet, F. & Park, D. J., 24 Jan 2014, In : Source Code for Biology and Medicine. 9, 1, 5 p., 3.

Research output: Contribution to journalReview ArticleOtherpeer-review

Open Access
File
294 Citations (Scopus)

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

Inouye, M., Dashnow, H., Raven, L. A., Schultz, M. B., Pope, B. J., Tomita, T., Zobel, J. & Holt, K. E., 20 Nov 2014, In : Genome Medicine. 6, 11, 16 p., 90.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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2013
23 Citations (Scopus)

A high-plex PCR approach for massively parallel sequencing

Nguyen-Dumont, T., Pope, B. J., Hammet, F., Southey, M. C. & Park, D. J., Aug 2013, In : BioTechniques. 55, 2, p. 69-74 6 p.

Research output: Contribution to journalArticleResearchpeer-review

9 Citations (Scopus)

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

Nguyen-Dumont, T., Pope, B. J., Hammet, F., Mahmoodi, M., Tsimiklis, H., Southey, M. C. & Park, D. J., 2013, In : Analytical Biochemistry. 442, 2, p. 127-129 3 p.

Research output: Contribution to journalArticleOtherpeer-review

7 Citations (Scopus)

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

Pope, B. J., Nguyen-Dumont, T., Odefrey, F., Hammet, F., Bell, R., Tao, K., Tavtigian, S. V., Goldgar, D. E., Lonie, A., Southey, M. C. & Park, D. J., 25 Feb 2013, In : BMC Bioinformatics. 14, 1, 9 p., 65.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File
11 Citations (Scopus)

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

Nguyen-Dumont, T., Teo, Z. L., Pope, B. J., Hammet, F., Mahmoodi, M., Tsimiklis, H., Sabbaghian, N., Tischkowitz, M., Foulkes, W. D., Giles, G. G., Hopper, J. L., Australian Breast Cancer Family Registry, Southey, M. C. & Park, D. J., 2013, In : BMC Medical Genomics. 6, 1, 5 p., 48.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File
2012
114 Citations (Scopus)

Rare mutations in XRCC2 increase the risk of breast cancer

Park, D. J., Lesueur, F., Nguyen-Dumont, T., Pertesi, M., Odefrey, F., Hammet, F., Neuhausen, S. L., John, E. M., Andrulis, I. L., Terry, M. B., Daly, T. M., Buys, S. S., Le Calvez-Kelm, F. L., Lonie, A., Pope, B. J., Tsimiklis, H., Voegele, C., Hilbers, F. M., Hoogerbrugge, N., Barroso, A. & 8 others, Osorio, A., Giles, G. G., Devilee, P., Benitez, J., Hopper, J. L., Tavtigian, S. V., Goldgar, D. E. & Southey, M. C., 6 Apr 2012, In : American Journal of Human Genetics. 90, 4, p. 734-739 6 p.

Research output: Contribution to journalArticleResearchpeer-review