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Items: 1 to 50 of 87

1.

Best practices for benchmarking germline small-variant calls in human genomes.

Krusche P, Trigg L, Boutros PC, Mason CE, De La Vega FM, Moore BL, Gonzalez-Porta M, Eberle MA, Tezak Z, Lababidi S, Truty R, Asimenos G, Funke B, Fleharty M, Chapman BA, Salit M, Zook JM; Global Alliance for Genomics and Health Benchmarking Team.

Nat Biotechnol. 2019 Mar 11. doi: 10.1038/s41587-019-0054-x. [Epub ahead of print]

PMID:
30858580
2.

Bioconda: sustainable and comprehensive software distribution for the life sciences.

Grüning B, Dale R, Sjödin A, Chapman BA, Rowe J, Tomkins-Tinch CH, Valieris R, Köster J; Bioconda Team.

Nat Methods. 2018 Jul;15(7):475-476. doi: 10.1038/s41592-018-0046-7. No abstract available.

PMID:
29967506
3.

Prioritisation of structural variant calls in cancer genomes.

Ahdesmäki MJ, Chapman BA, Cingolani P, Hofmann O, Sidoruk A, Lai Z, Zakharov G, Rodichenko M, Alperovich M, Jenkins D, Carr TH, Stetson D, Dougherty B, Barrett JC, Johnson JH.

PeerJ. 2017 Apr 4;5:e3166. doi: 10.7717/peerj.3166. eCollection 2017.

4.

Community-driven development for computational biology at Sprints, Hackathons and Codefests.

Möller S, Afgan E, Banck M, Bonnal RJ, Booth T, Chilton J, Cock PJ, Gumbel M, Harris N, Holland R, Kalaš M, Kaján L, Kibukawa E, Powel DR, Prins P, Quinn J, Sallou O, Strozzi F, Seemann T, Sloggett C, Soiland-Reyes S, Spooner W, Steinbiss S, Tille A, Travis AJ, Guimera R, Katayama T, Chapman BA.

BMC Bioinformatics. 2014;15 Suppl 14:S7. doi: 10.1186/1471-2105-15-S14-S7. Epub 2014 Nov 27.

5.

The Bioinformatics Open Source Conference (BOSC) 2013.

Harris NL, Cock PJ, Chapman BA, Goecks J, Hotz HR, Lapp H.

Bioinformatics. 2015 Jan 15;31(2):299-300. doi: 10.1093/bioinformatics/btu413. Epub 2014 Jul 14. No abstract available.

6.

GEMINI: integrative exploration of genetic variation and genome annotations.

Paila U, Chapman BA, Kirchner R, Quinlan AR.

PLoS Comput Biol. 2013;9(7):e1003153. doi: 10.1371/journal.pcbi.1003153. Epub 2013 Jul 18.

7.

The low FODMAP diet improves gastrointestinal symptoms in patients with irritable bowel syndrome: a prospective study.

de Roest RH, Dobbs BR, Chapman BA, Batman B, O'Brien LA, Leeper JA, Hebblethwaite CR, Gearry RB.

Int J Clin Pract. 2013 Sep;67(9):895-903. doi: 10.1111/ijcp.12128. Epub 2013 May 23.

PMID:
23701141
8.

Targeted exome sequencing of suspected mitochondrial disorders.

Lieber DS, Calvo SE, Shanahan K, Slate NG, Liu S, Hershman SG, Gold NB, Chapman BA, Thorburn DR, Berry GT, Schmahmann JD, Borowsky ML, Mueller DM, Sims KB, Mootha VK.

Neurology. 2013 May 7;80(19):1762-70. doi: 10.1212/WNL.0b013e3182918c40. Epub 2013 Apr 17.

9.

Bio.Phylo: a unified toolkit for processing, analyzing and visualizing phylogenetic trees in Biopython.

Talevich E, Invergo BM, Cock PJ, Chapman BA.

BMC Bioinformatics. 2012 Aug 21;13:209. doi: 10.1186/1471-2105-13-209.

10.

A prospective study of endoscopist-blinded colonoscopy withdrawal times and polyp detection rates in a tertiary hospital.

Lim G, Viney SK, Chapman BA, Frizelle FA, Gearry RB.

N Z Med J. 2012 Jun 8;125(1356):52-9.

PMID:
22729059
11.

Histone H3R2 symmetric dimethylation and histone H3K4 trimethylation are tightly correlated in eukaryotic genomes.

Yuan CC, Matthews AG, Jin Y, Chen CF, Chapman BA, Ohsumi TK, Glass KC, Kutateladze TG, Borowsky ML, Struhl K, Oettinger MA.

Cell Rep. 2012 Feb 23;1(2):83-90.

12.

The genomic binding sites of a noncoding RNA.

Simon MD, Wang CI, Kharchenko PV, West JA, Chapman BA, Alekseyenko AA, Borowsky ML, Kuroda MI, Kingston RE.

Proc Natl Acad Sci U S A. 2011 Dec 20;108(51):20497-502. doi: 10.1073/pnas.1113536108. Epub 2011 Dec 5.

13.

Compaction of chromatin by diverse Polycomb group proteins requires localized regions of high charge.

Grau DJ, Chapman BA, Garlick JD, Borowsky M, Francis NJ, Kingston RE.

Genes Dev. 2011 Oct 15;25(20):2210-21. doi: 10.1101/gad.17288211.

14.

Potential interaction between valproic acid and doripenem.

Hellwig TR, Onisk ML, Chapman BA.

Curr Drug Saf. 2011 Feb 1;6(1):54-8.

PMID:
21241241
15.

Allopurinol might improve response to azathioprine and 6-mercaptopurine by correcting an unfavorable metabolite ratio.

Gardiner SJ, Gearry RB, Burt MJ, Chalmers-Watson T, Chapman BA, Ross AG, Stedman CA, Huelsen A, Barclay ML.

J Gastroenterol Hepatol. 2011 Jan;26(1):49-54. doi: 10.1111/j.1440-1746.2010.06489.x.

PMID:
21175793
16.

Engineering enzyme specificity using computational design of a defined-sequence library.

Lippow SM, Moon TS, Basu S, Yoon SH, Li X, Chapman BA, Robison K, Lipovšek D, Prather KL.

Chem Biol. 2010 Dec 22;17(12):1306-15. doi: 10.1016/j.chembiol.2010.10.012.

17.

Population-based epidemiology study of autoimmune hepatitis: a disease of older women?

Ngu JH, Bechly K, Chapman BA, Burt MJ, Barclay ML, Gearry RB, Stedman CA.

J Gastroenterol Hepatol. 2010 Oct;25(10):1681-6. doi: 10.1111/j.1440-1746.2010.06384.x.

PMID:
20880179
18.

Pairwise selection assembly for sequence-independent construction of long-length DNA.

Blake WJ, Chapman BA, Zindal A, Lee ME, Lippow SM, Baynes BM.

Nucleic Acids Res. 2010 May;38(8):2594-602. doi: 10.1093/nar/gkq123. Epub 2010 Mar 1.

19.

Limiting donation after cardiac death: questions on consent.

Chapman BA.

Health Law J. 2010;18:159-86. No abstract available.

PMID:
22125974
20.

Biopython: freely available Python tools for computational molecular biology and bioinformatics.

Cock PJ, Antao T, Chang JT, Chapman BA, Cox CJ, Dalke A, Friedberg I, Hamelryck T, Kauff F, Wilczynski B, de Hoon MJ.

Bioinformatics. 2009 Jun 1;25(11):1422-3. doi: 10.1093/bioinformatics/btp163. Epub 2009 Mar 20.

21.

Effect of inflammatory bowel disease classification changes on NOD2 genotype-phenotype associations in a population-based cohort.

Gearry RB, Roberts RL, Burt MJ, Frampton CM, Chapman BA, Collett JA, Shirley P, Allington MD, Kennedy MA, Barclay ML.

Inflamm Bowel Dis. 2007 Oct;13(10):1220-7.

PMID:
17538984
22.

Two cases of severe liver injury possibly related to 5-fluorouracil and calcium folinate.

Brooks AJ, Begg EJ, Chapman BA, Fitzharris BM.

Intern Med J. 2007 May;37(5):344-5. No abstract available.

PMID:
17504289
23.

High incidence of Crohn's disease in Canterbury, New Zealand: results of an epidemiologic study.

Gearry RB, Richardson A, Frampton CM, Collett JA, Burt MJ, Chapman BA, Barclay ML.

Inflamm Bowel Dis. 2006 Oct;12(10):936-43.

PMID:
17012964
24.

Many gene and domain families have convergent fates following independent whole-genome duplication events in Arabidopsis, Oryza, Saccharomyces and Tetraodon.

Paterson AH, Chapman BA, Kissinger JC, Bowers JE, Feltus FA, Estill JC.

Trends Genet. 2006 Nov;22(11):597-602. Epub 2006 Sep 18. Review.

PMID:
16979781
25.

Buffering of crucial functions by paleologous duplicated genes may contribute cyclicality to angiosperm genome duplication.

Chapman BA, Bowers JE, Feltus FA, Paterson AH.

Proc Natl Acad Sci U S A. 2006 Feb 21;103(8):2730-5. Epub 2006 Feb 8.

26.

Thiopurine drug adverse effects in a population of New Zealand patients with inflammatory bowel disease.

Gearry RB, Barclay ML, Burt MJ, Collett JA, Chapman BA.

Pharmacoepidemiol Drug Saf. 2004 Aug;13(8):563-7.

PMID:
15317038
27.

Ancient polyploidization predating divergence of the cereals, and its consequences for comparative genomics.

Paterson AH, Bowers JE, Chapman BA.

Proc Natl Acad Sci U S A. 2004 Jun 29;101(26):9903-8. Epub 2004 May 25.

28.

Comparative genome analysis of monocots and dicots, toward characterization of angiosperm diversity.

Paterson AH, Bowers JE, Chapman BA, Peterson DG, Rong J, Wicker TM.

Curr Opin Biotechnol. 2004 Apr;15(2):120-5. Review.

PMID:
15081049
29.

Surveillance for dysplasia in patients with inflammatory bowel disease: a national survey of colonoscopic practice in New Zealand.

Gearry RB, Wakeman CJ, Barclay ML, Chapman BA, Collett JA, Burt MJ, Frizelle FA.

Dis Colon Rectum. 2004 Mar;47(3):314-22.

PMID:
14991493
30.

A comparative phylogenetic approach for dating whole genome duplication events.

Chapman BA, Bowers JE, Schulze SR, Paterson AH.

Bioinformatics. 2004 Jan 22;20(2):180-5.

PMID:
14734308
31.

Structure and evolution of cereal genomes.

Paterson AH, Bowers JE, Peterson DG, Estill JC, Chapman BA.

Curr Opin Genet Dev. 2003 Dec;13(6):644-50. Review.

PMID:
14638328
32.

Thiopurine S-methyltransferase (TPMT) genotype does not predict adverse drug reactions to thiopurine drugs in patients with inflammatory bowel disease.

Gearry RB, Barclay ML, Burt MJ, Collett JA, Chapman BA, Roberts RL, Kennedy MA.

Aliment Pharmacol Ther. 2003 Aug 15;18(4):395-400.

33.

Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events.

Bowers JE, Chapman BA, Rong J, Paterson AH.

Nature. 2003 Mar 27;422(6930):433-8.

PMID:
12660784
34.

Influence of haemochromatosis gene mutations on treatment outcomes in patients with hepatitis C.

Chapman BA, Burt MJ, Frampton CM, Chapman TM, Whitehead MR, Upton JD, George PM.

Intern Med J. 2001 May-Jun;31(4):254-5. No abstract available.

PMID:
11456040
35.

Interferon-alpha2a/ribaviran versus interferon-alpha2a alone for the retreatment of hepatitis C patients who relapse after a standard course of interferon.

Chapman BA, Stace NH, Edgar CL, Bartlett SE, Frampton CM, Scahill SL, Jennings LC.

N Z Med J. 2001 Mar 23;114(1128):103-4.

PMID:
11346153
36.

The prevalence of viral hepatitis (HAV, HBV and HCV) in the Christchurch community.

Chapman BA, Burt MJ, Frampton CM, Collett JA, Yeo KH, Wilkinson ID, Cook HB, Barclay MJ, Ross AG, George PM.

N Z Med J. 2000 Sep 22;113(1118):394-6.

PMID:
11062814
37.

Adult coeliac disease: prevalence and clinical significance.

Cook HB, Burt MJ, Collett JA, Whitehead MR, Frampton CM, Chapman BA.

J Gastroenterol Hepatol. 2000 Sep;15(9):1032-6.

PMID:
11059933
38.
39.

Gallstone prevalence in Christchurch: risk factors and clinical significance.

Chapman BA, Frampton CM, Wilson IR, Chisholm RJ, Allan RB, Burt MJ.

N Z Med J. 2000 Feb 25;113(1104):46-8.

PMID:
10777222
40.

Seroprevalence of Helicobacter pylori in the adult population of Christchurch: risk factors and relationship to dyspeptic symptoms and iron studies.

Collett JA, Burt MJ, Frampton CM, Yeo KH, Chapman TM, Buttimore RC, Cook HB, Chapman BA.

N Z Med J. 1999 Aug 13;112(1093):292-5.

PMID:
10493426
41.

The significance of haemochromatosis gene mutations in the general population: implications for screening.

Burt MJ, George PM, Upton JD, Collett JA, Frampton CM, Chapman TM, Walmsley TA, Chapman BA.

Gut. 1998 Dec;43(6):830-6.

42.

Amphotericin B activation of human genes encoding for cytokines.

Rogers PD, Jenkins JK, Chapman SW, Ndebele K, Chapman BA, Cleary JD.

J Infect Dis. 1998 Dec;178(6):1726-33.

PMID:
9815226
43.
44.

Gallbladder polyps: prospective study.

Collett JA, Allan RB, Chisholm RJ, Wilson IR, Burt MJ, Chapman BA.

J Ultrasound Med. 1998 Apr;17(4):207-11.

PMID:
9544602
45.

Dissolution of gallstones with simvastatin, an HMG CoA reductase inhibitor.

Chapman BA, Burt MJ, Chisholm RJ, Allan RB, Yeo KH, Ross AG.

Dig Dis Sci. 1998 Feb;43(2):349-53.

PMID:
9512129
46.

Gallbladder volume: comparison of diabetics and controls.

Chapman BA, Chapman TM, Frampton CM, Chisholm RJ, Allan RB, Wilson IR, Burt MJ.

Dig Dis Sci. 1998 Feb;43(2):344-8.

PMID:
9512128
47.

Molecular analysis of HLA-H gene mutations in New Zealand patients with haemochromatosis.

Burt MJ, Upton JD, Morison IM, Chapman BA, Faed JM, George PM.

N Z Med J. 1997 Nov 28;110(1056):429-32.

PMID:
9418837
48.

37 kBq 14C-urea breath test and gastric biopsy analyses of H. pylori infection.

Allardyce RA, Chapman BA, Tie AB, Burt MJ, Yeo KJ, Keenan JI, Bagshaw PF.

Aust N Z J Surg. 1997 Jan;67(1):31-4.

PMID:
9033373
49.

Prevalence of gallbladder disease in diabetes mellitus.

Chapman BA, Wilson IR, Frampton CM, Chisholm RJ, Stewart NR, Eagar GM, Allan RB.

Dig Dis Sci. 1996 Nov;41(11):2222-8.

PMID:
8943976
50.

Evaluation of alpha interferon for the treatment of chronic hepatitis B infection in Christchurch.

Burt MJ, Ross AG, Schroeder BA, Chambers ST, Chapman BA.

N Z Med J. 1996 May 10;109(1021):162-4.

PMID:
8657367

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