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Items: 1 to 50 of 107

1.

Predicting responses to platin chemotherapy agents with biochemically-inspired machine learning.

Mucaki EJ, Zhao JZL, Lizotte DJ, Rogan PK.

Signal Transduct Target Ther. 2019 Jan 11;4:1. doi: 10.1038/s41392-018-0034-5. eCollection 2019.

2.

RADIATION DOSE ESTIMATION BY COMPLETELY AUTOMATED INTERPRETATION OF THE DICENTRIC CHROMOSOME ASSAY.

Li Y, Shirley BC, Wilkins RC, Norton F, Knoll JHM, Rogan PK.

Radiat Prot Dosimetry. 2019 Jan 9. doi: 10.1093/rpd/ncy282. [Epub ahead of print]

PMID:
30624749
3.

Survival outcome differences based on treatments used and knowledge of the primary tumour site for patients with cancer of unknown and known primary in Ontario.

Kim CS, Hannouf MB, Sarma S, Rodrigues GB, Rogan PK, Mahmud SM, Winquist E, Brackstone M, Zaric GS.

Curr Oncol. 2018 Oct;25(5):307-316. doi: 10.3747/co.25.4003. Epub 2018 Oct 31.

4.

BRCA1 and BRCA2 5' noncoding region variants identified in breast cancer patients alter promoter activity and protein binding.

Burke LJ, Sevcik J, Gambino G, Tudini E, Mucaki EJ, Shirley BC, Whiley P, Parsons MT, De Leeneer K, Gutiérrez-Enríquez S, Santamariña M, Caputo SM, Santana Dos Santos E, Soukupova J, Janatova M, Zemankova P, Lhotova K, Stolarova L, Borecka M, Moles-Fernández A, Manoukian S, Bonanni B; ENIGMA Consortium, Edwards SL, Blok MJ, van Overeem Hansen T, Rossing M, Diez O, Vega A, Claes KBM, Goldgar DE, Rouleau E, Radice P, Peterlongo P, Rogan PK, Caligo M, Spurdle AB, Brown MA.

Hum Mutat. 2018 Dec;39(12):2025-2039. doi: 10.1002/humu.23652. Epub 2018 Sep 24.

5.

Predicting ionizing radiation exposure using biochemically-inspired genomic machine learning.

Zhao JZL, Mucaki EJ, Rogan PK.

Version 2. F1000Res. 2018 Feb 27 [revised 2018 Jan 1];7:233. doi: 10.12688/f1000research.14048.2. eCollection 2018.

6.

The Potential Clinical and Economic Value of Primary Tumour Identification in Metastatic Cancer of Unknown Primary Tumour: A Population-Based Retrospective Matched Cohort Study.

Hannouf MB, Winquist E, Mahmud SM, Brackstone M, Sarma S, Rodrigues G, Rogan PK, Hoch JS, Zaric GS.

Pharmacoecon Open. 2018 Sep;2(3):255-270. doi: 10.1007/s41669-017-0051-2.

7.

Assessment of the functional impact of germline BRCA1/2 variants located in non-coding regions in families with breast and/or ovarian cancer predisposition.

Dos Santos ES, Caputo SM, Castera L, Gendrot M, Briaux A, Breault M, Krieger S, Rogan PK, Mucaki EJ, Burke LJ; ENIGMA consortium, Bièche I, Houdayer C, Vaur D, Stoppa-Lyonnet D, Brown MA, Lallemand F, Rouleau E.

Breast Cancer Res Treat. 2018 Apr;168(2):311-325. doi: 10.1007/s10549-017-4602-0. Epub 2017 Dec 13.

PMID:
29236234
8.

The clinical significance of occult gynecologic primary tumours in metastatic cancer.

Hannouf MB, Winquist E, Mahmud SM, Brackstone M, Sarma S, Rodrigues G, Rogan PK, Hoch JS, Zaric GS.

Curr Oncol. 2017 Oct;24(5):e368-e378. doi: 10.3747/co.24.3594. Epub 2017 Oct 25.

9.

Accurate cytogenetic biodosimetry through automated dicentric chromosome curation and metaphase cell selection.

Liu J, Li Y, Wilkins R, Flegal F, Knoll JHM, Rogan PK.

F1000Res. 2017 Aug 9;6:1396. doi: 10.12688/f1000research.12226.1. eCollection 2017.

10.

Expedited Radiation Biodosimetry by Automated Dicentric Chromosome Identification (ADCI) and Dose Estimation.

Shirley B, Li Y, Knoll JHM, Rogan PK.

J Vis Exp. 2017 Sep 4;(127). doi: 10.3791/56245.

11.

Prevalence and spectrum of germline rare variants in BRCA1/2 and PALB2 among breast cancer cases in Sarawak, Malaysia.

Yang XR, Devi BCR, Sung H, Guida J, Mucaki EJ, Xiao Y, Best A, Garland L, Xie Y, Hu N, Rodriguez-Herrera M, Wang C, Jones K, Luo W, Hicks B, Tang TS, Moitra K, Rogan PK, Dean M.

Breast Cancer Res Treat. 2017 Oct;165(3):687-697. doi: 10.1007/s10549-017-4356-8. Epub 2017 Jun 29.

PMID:
28664506
12.

Predicting Outcomes of Hormone and Chemotherapy in the Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) Study by Biochemically-inspired Machine Learning.

Mucaki EJ, Baranova K, Pham HQ, Rezaeian I, Angelov D, Ngom A, Rueda L, Rogan PK.

Version 3. F1000Res. 2016 Aug 31 [revised 2017 Jan 1];5:2124. doi: 10.12688/f1000research.9417.3. eCollection 2016.

13.

The Clinical Significance of Occult Gastrointestinal Primary Tumours in Metastatic Cancer: A Population Retrospective Cohort Study.

Hannouf MB, Winquist E, Mahmud SM, Brackstone M, Sarma S, Rodrigues G, Rogan PK, Hoch JS, Zaric GS.

Cancer Res Treat. 2018 Jan;50(1):183-194. doi: 10.4143/crt.2016.532. Epub 2017 Mar 21.

14.

Proceedings of the third international molecular pathological epidemiology (MPE) meeting.

Campbell PT, Rebbeck TR, Nishihara R, Beck AH, Begg CB, Bogdanov AA, Cao Y, Coleman HG, Freeman GJ, Heng YJ, Huttenhower C, Irizarry RA, Kip NS, Michor F, Nevo D, Peters U, Phipps AI, Poole EM, Qian ZR, Quackenbush J, Robins H, Rogan PK, Slattery ML, Smith-Warner SA, Song M, VanderWeele TJ, Xia D, Zabor EC, Zhang X, Wang M, Ogino S.

Cancer Causes Control. 2017 Feb;28(2):167-176. doi: 10.1007/s10552-016-0845-z. Epub 2017 Jan 17. Review.

15.

Discovery and validation of information theory-based transcription factor and cofactor binding site motifs.

Lu R, Mucaki EJ, Rogan PK.

Nucleic Acids Res. 2017 Mar 17;45(5):e27. doi: 10.1093/nar/gkw1036.

16.

Radiation Dose Estimation by Automated Cytogenetic Biodosimetry.

Rogan PK, Li Y, Wilkins RC, Flegal FN, Knoll JH.

Radiat Prot Dosimetry. 2016 Dec;172(1-3):207-217. doi: 10.1093/rpd/ncw161. Epub 2016 Jul 13.

PMID:
27412514
17.

A unified analytic framework for prioritization of non-coding variants of uncertain significance in heritable breast and ovarian cancer.

Mucaki EJ, Caminsky NG, Perri AM, Lu R, Laederach A, Halvorsen M, Knoll JH, Rogan PK.

BMC Med Genomics. 2016 Apr 11;9:19. doi: 10.1186/s12920-016-0178-5.

18.

Automated discrimination of dicentric and monocentric chromosomes by machine learning-based image processing.

Li Y, Knoll JH, Wilkins RC, Flegal FN, Rogan PK.

Microsc Res Tech. 2016 May;79(5):393-402. doi: 10.1002/jemt.22642. Epub 2016 Mar 1.

PMID:
26929213
19.

Prioritizing Variants in Complete Hereditary Breast and Ovarian Cancer Genes in Patients Lacking Known BRCA Mutations.

Caminsky NG, Mucaki EJ, Perri AM, Lu R, Knoll JH, Rogan PK.

Hum Mutat. 2016 Jul;37(7):640-52. doi: 10.1002/humu.22972. Epub 2016 Mar 18.

PMID:
26898890
20.

Genomic signatures for paclitaxel and gemcitabine resistance in breast cancer derived by machine learning.

Dorman SN, Baranova K, Knoll JH, Urquhart BL, Mariani G, Carcangiu ML, Rogan PK.

Mol Oncol. 2016 Jan;10(1):85-100. doi: 10.1016/j.molonc.2015.07.006. Epub 2015 Aug 22.

21.

Reversing chromatin accessibility differences that distinguish homologous mitotic metaphase chromosomes.

Khan WA, Rogan PK, Knoll JH.

Mol Cytogenet. 2015 Aug 13;8:65. doi: 10.1186/s13039-015-0159-y. eCollection 2015.

22.

FANCM c.5791C>T nonsense mutation (rs144567652) induces exon skipping, affects DNA repair activity and is a familial breast cancer risk factor.

Peterlongo P, Catucci I, Colombo M, Caleca L, Mucaki E, Bogliolo M, Marin M, Damiola F, Bernard L, Pensotti V, Volorio S, Dall'Olio V, Meindl A, Bartram C, Sutter C, Surowy H, Sornin V, Dondon MG, Eon-Marchais S, Stoppa-Lyonnet D, Andrieu N, Sinilnikova OM; GENESIS, Mitchell G, James PA, Thompson E; kConFab; SWE-BRCA, Marchetti M, Verzeroli C, Tartari C, Capone GL, Putignano AL, Genuardi M, Medici V, Marchi I, Federico M, Tognazzo S, Matricardi L, Agata S, Dolcetti R, Della Puppa L, Cini G, Gismondi V, Viassolo V, Perfumo C, Mencarelli MA, Baldassarri M, Peissel B, Roversi G, Silvestri V, Rizzolo P, Spina F, Vivanet C, Tibiletti MG, Caligo MA, Gambino G, Tommasi S, Pilato B, Tondini C, Corna C, Bonanni B, Barile M, Osorio A, Benitez J, Balestrino L, Ottini L, Manoukian S, Pierotti MA, Renieri A, Varesco L, Couch FJ, Wang X, Devilee P, Hilbers FS, van Asperen CJ, Viel A, Montagna M, Cortesi L, Diez O, Balmaña J, Hauke J, Schmutzler RK, Papi L, Pujana MA, Lázaro C, Falanga A, Offit K, Vijai J, Campbell I, Burwinkel B, Kvist A, Ehrencrona H, Mazoyer S, Pizzamiglio S, Verderio P, Surralles J, Rogan PK, Radice P.

Hum Mol Genet. 2015 Sep 15;24(18):5345-55. doi: 10.1093/hmg/ddv251. Epub 2015 Jun 30.

23.

Identification and survival outcomes of a cohort of patients with cancer of unknown primary in Ontario, Canada.

Kim CS, Hannouf MB, Sarma S, Rodrigues GB, Rogan PK, Mahmud SM, Winquist E, Brackstone M, Zaric GS.

Acta Oncol. 2015 Nov;54(10):1781-7. doi: 10.3109/0284186X.2015.1020965. Epub 2015 Mar 31.

PMID:
25825957
24.

Interpretation of mRNA splicing mutations in genetic disease: review of the literature and guidelines for information-theoretical analysis.

Caminsky N, Mucaki EJ, Rogan PK.

F1000Res. 2014 Nov 18;3:282. doi: 10.12688/f1000research.5654.1. eCollection 2014. Review.

25.

Localized, non-random differences in chromatin accessibility between homologous metaphase chromosomes.

Khan WA, Rogan PK, Knoll JH.

Mol Cytogenet. 2014 Nov 19;7(1):70. doi: 10.1186/s13039-014-0070-y. eCollection 2014.

26.

Splicing mutation analysis reveals previously unrecognized pathways in lymph node-invasive breast cancer.

Dorman SN, Viner C, Rogan PK.

Sci Rep. 2014 Nov 14;4:7063. doi: 10.1038/srep07063.

27.

Automating dicentric chromosome detection from cytogenetic biodosimetry data.

Rogan PK, Li Y, Wickramasinghe A, Subasinghe A, Caminsky N, Khan W, Samarabandu J, Wilkins R, Flegal F, Knoll JH.

Radiat Prot Dosimetry. 2014 Jun;159(1-4):95-104. doi: 10.1093/rpd/ncu133. Epub 2014 Apr 21.

28.

Validation of predicted mRNA splicing mutations using high-throughput transcriptome data.

Viner C, Dorman SN, Shirley BC, Rogan PK.

Version 2. F1000Res. 2014 Jan 13 [revised 2014 Jan 1];3:8. doi: 10.12688/f1000research.3-8.v2. eCollection 2014.

29.

Best practices for evaluating mutation prediction methods.

Rogan PK, Zou GY.

Hum Mutat. 2013 Nov;34(11):1581-2. doi: 10.1002/humu.22401. Epub 2013 Sep 10. No abstract available.

PMID:
23955774
30.

Relating centromeric topography in fixed human chromosomes to α-satellite DNA and CENP-B distribution.

Khan WA, Chisholm R, Tadayyon S, Subasinghe A, Norton P, Samarabandu J, Johnston LJ, Knoll JH, Rogan PK.

Cytogenet Genome Res. 2013;139(4):234-42. doi: 10.1159/000348744. Epub 2013 Mar 23.

PMID:
23548580
31.

Interpretation, stratification and evidence for sequence variants affecting mRNA splicing in complete human genome sequences.

Shirley BC, Mucaki EJ, Whitehead T, Costea PI, Akan P, Rogan PK.

Genomics Proteomics Bioinformatics. 2013 Apr;11(2):77-85. doi: 10.1016/j.gpb.2013.01.008. Epub 2013 Mar 14.

32.

Intensity integrated Laplacian-based thickness measurement for detecting human metaphase chromosome centromere location.

Arachchige AS, Samarabandu J, Knoll JH, Rogan PK.

IEEE Trans Biomed Eng. 2013 Jul;60(7):2005-13. doi: 10.1109/TBME.2013.2248008. Epub 2013 Feb 20.

PMID:
23434602
33.

Expanding probe repertoire and improving reproducibility in human genomic hybridization.

Dorman SN, Shirley BC, Knoll JH, Rogan PK.

Nucleic Acids Res. 2013 Apr;41(7):e81. doi: 10.1093/nar/gkt048. Epub 2013 Feb 1.

34.

Prediction of mutant mRNA splice isoforms by information theory-based exon definition.

Mucaki EJ, Shirley BC, Rogan PK.

Hum Mutat. 2013 Apr;34(4):557-65. doi: 10.1002/humu.22277. Epub 2013 Feb 21.

PMID:
23348723
35.

Structural and genic characterization of stable genomic regions in breast cancer: relevance to chemotherapy.

Park NI, Rogan PK, Tarnowski HE, Knoll JH.

Mol Oncol. 2012 Jun;6(3):347-59. doi: 10.1016/j.molonc.2012.01.001. Epub 2012 Jan 15.

36.

Context-based FISH localization of genomic rearrangements within chromosome 15q11.2q13 duplicons.

Khan WA, Knoll JH, Rogan PK.

Mol Cytogenet. 2011 Aug 8;4(1):15. doi: 10.1186/1755-8166-4-15.

37.

Comprehensive prediction of mRNA splicing effects of BRCA1 and BRCA2 variants.

Mucaki EJ, Ainsworth P, Rogan PK.

Hum Mutat. 2011 Jul;32(7):735-42. doi: 10.1002/humu.21513. Epub 2011 May 5.

PMID:
21523855
38.

Usher syndrome splicing variants evaluated in nasal epithelial cells.

Rogan PK.

Hum Mutat. 2010 Jun;31(6):v. doi: 10.1002/humu.21291. No abstract available.

PMID:
20513139
39.

Deeper understanding of unclassified intronic variants and ESEs.

Rogan PK.

Hum Mutat. 2010 Apr;31(4):V. doi: 10.1002/humu.21247. No abstract available.

PMID:
20358580
40.

Predicting severity of haemophilia A and B splicing mutations by information analysis.

von Kodolitsch Y, Berger J, Rogan PK.

Haemophilia. 2006 May;12(3):258-62. Erratum in: Haemophilia. 2006 Jul;12(4):456.

PMID:
16643211
41.

Determination of genomic copy number with quantitative microsphere hybridization.

Newkirk HL, Rogan PK, Miralles M, Knoll JH.

Hum Mutat. 2006 Apr;27(4):376-86. Erratum in: Hum Mutat. 2006 Jun;27(6):597.

PMID:
16541397
42.

BIPAD: a web server for modeling bipartite sequence elements.

Bi C, Rogan PK.

BMC Bioinformatics. 2006 Feb 17;7:76.

43.

Dendrimer FISH detection of single-copy intervals in acute promyelocytic leukemia.

Mora JR, Knoll JH, Rogan PK, Getts RC, Wilson GS.

Mol Cell Probes. 2006 Apr;20(2):114-20. Epub 2006 Feb 7.

PMID:
16460913
44.
45.

A variant form of Oguchi disease mapped to 13q34 associated with partial deletion of GRK1 gene.

Zhang Q, Zulfiqar F, Riazuddin SA, Xiao X, Yasmeen A, Rogan PK, Caruso R, Sieving PA, Riazuddin S, Hejtmancik JF.

Mol Vis. 2005 Nov 14;11:977-85.

46.

Splice-site contribution in alternative splicing of PLP1 and DM20: molecular studies in oligodendrocytes.

Hobson GM, Huang Z, Sperle K, Sistermans E, Rogan PK, Garbern JY, Kolodny E, Naidu S, Cambi F.

Hum Mutat. 2006 Jan;27(1):69-77.

PMID:
16287154
47.

Tandem machine learning for the identification of genes regulated by transcription factors.

Dinakarpandian D, Raheja V, Mehta S, Schuetz EG, Rogan PK.

BMC Bioinformatics. 2005 Aug 22;6:204.

48.

Normal and abnormal mechanisms of gene splicing and relevance to inherited skin diseases.

Wessagowit V, Nalla VK, Rogan PK, McGrath JA.

J Dermatol Sci. 2005 Nov;40(2):73-84. Epub 2005 Jul 27. Review.

49.

Fish versus aCGH.

Rogan PK, Knoll JH.

MLO Med Lab Obs. 2005 May;37(5):8; author reply 8, 12. No abstract available.

PMID:
15960187
50.

Automated splicing mutation analysis by information theory.

Nalla VK, Rogan PK.

Hum Mutat. 2005 Apr;25(4):334-42. Erratum in: Hum Mutat. 2008 Sep;29(9): 1168.

PMID:
15776446

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