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Genomic analysis of the causative agents of coccidiosis in domestic chickens.

Reid AJ, Blake DP, Ansari HR, Billington K, Browne HP, Bryant J, Dunn M, Hung SS, Kawahara F, Miranda-Saavedra D, Malas TB, Mourier T, Naghra H, Nair M, Otto TD, Rawlings ND, Rivailler P, Sanchez-Flores A, Sanders M, Subramaniam C, Tay YL, Woo Y, Wu X, Barrell B, Dear PH, Doerig C, Gruber A, Ivens AC, Parkinson J, Rajandream MA, Shirley MW, Wan KL, Berriman M, Tomley FM, Pain A.

Genome Res. 2014 Oct;24(10):1676-85. doi: 10.1101/gr.168955.113. Epub 2014 Jul 11.


IRS2 is a candidate driver oncogene on 13q34 in colorectal cancer.

Day E, Poulogiannis G, McCaughan F, Mulholland S, Arends MJ, Ibrahim AE, Dear PH.

Int J Exp Pathol. 2013 Jun;94(3):203-11. doi: 10.1111/iep.12021. Epub 2013 Apr 18.


Digital PCR strategies in the development and analysis of molecular biomarkers for personalized medicine.

Day E, Dear PH, McCaughan F.

Methods. 2013 Jan;59(1):101-7. doi: 10.1016/j.ymeth.2012.08.001. Epub 2012 Aug 19. Review.


Insights into the genome structure and copy-number variation of Eimeria tenella.

Lim LS, Tay YL, Alias H, Wan KL, Dear PH.

BMC Genomics. 2012 Aug 13;13:389. doi: 10.1186/1471-2164-13-389.


Numts help to reconstruct the demographic history of the ocellated lizard (Lacerta lepida) in a secondary contact zone.

Miraldo A, Hewitt GM, Dear PH, Paulo OS, Emerson BC.

Mol Ecol. 2012 Feb;21(4):1005-18. doi: 10.1111/j.1365-294X.2011.05422.x. Epub 2012 Jan 4.


Single-molecule analysis of genome rearrangements in cancer.

Pole JC, McCaughan F, Newman S, Howarth KD, Dear PH, Edwards PA.

Nucleic Acids Res. 2011 Jul;39(13):e85. doi: 10.1093/nar/gkr227. Epub 2011 Apr 27.


Genomic evidence of pre-invasive clonal expansion, dispersal and progression in bronchial dysplasia.

McCaughan F, Pipinikas CP, Janes SM, George PJ, Rabbitts PH, Dear PH.

J Pathol. 2011 Jun;224(2):153-9. doi: 10.1002/path.2887. Epub 2011 Apr 19.


Progressive 3q amplification consistently targets SOX2 in preinvasive squamous lung cancer.

McCaughan F, Pole JC, Bankier AT, Konfortov BA, Carroll B, Falzon M, Rabbitts TH, George PJ, Dear PH, Rabbitts PH.

Am J Respir Crit Care Med. 2010 Jul 1;182(1):83-91. doi: 10.1164/rccm.201001-0005OC. Epub 2010 Mar 18.


BAC-HAPPY mapping (BAP mapping): a new and efficient protocol for physical mapping.

Vu GT, Dear PH, Caligari PD, Wilkinson MJ.

PLoS One. 2010 Feb 8;5(2):e9089. doi: 10.1371/journal.pone.0009089.


Single-molecule genomics.

McCaughan F, Dear PH.

J Pathol. 2010 Jan;220(2):297-306. doi: 10.1002/path.2647.


Copy-number variation: the end of the human genome?

Dear PH.

Trends Biotechnol. 2009 Aug;27(8):448-54. doi: 10.1016/j.tibtech.2009.05.003. Epub 2009 Jul 1. Review.


Microdissection molecular copy-number counting (microMCC)--unlocking cancer archives with digital PCR.

McCaughan F, Darai-Ramqvist E, Bankier AT, Konfortov BA, Foster N, George PJ, Rabbitts TH, Kost-Alimova M, Rabbitts PH, Dear PH.

J Pathol. 2008 Nov;216(3):307-16. doi: 10.1002/path.2413.


Mitochondrial genomes reveal an explosive radiation of extinct and extant bears near the Miocene-Pliocene boundary.

Krause J, Unger T, Noçon A, Malaspinas AS, Kolokotronis SO, Stiller M, Soibelzon L, Spriggs H, Dear PH, Briggs AW, Bray SC, O'Brien SJ, Rabeder G, Matheus P, Cooper A, Slatkin M, Pääbo S, Hofreiter M.

BMC Evol Biol. 2008 Jul 28;8:220. doi: 10.1186/1471-2148-8-220.


Real-time PCRs and fingerprinting assays for the detection and characterization of Salmonella Genomic Island-1 encoding multidrug resistance: application to 445 European isolates of Salmonella, Escherichia coli, Shigella, and Proteus.

Amar CF, Arnold C, Bankier A, Dear PH, Guerra B, Hopkins KL, Liebana E, Mevius DJ, Threlfall EJ.

Microb Drug Resist. 2008 Jun;14(2):79-92. doi: 10.1089/mdr.2008.0812.


Multiplex amplification of ancient DNA.

Römpler H, Dear PH, Krause J, Meyer M, Rohland N, Schöneberg T, Spriggs H, Stiller M, Hofreiter M.

Nat Protoc. 2006;1(2):720-8.


Sequencing and analysis of chromosome 1 of Eimeria tenella reveals a unique segmental organization.

Ling KH, Rajandream MA, Rivailler P, Ivens A, Yap SJ, Madeira AM, Mungall K, Billington K, Yee WY, Bankier AT, Carroll F, Durham AM, Peters N, Loo SS, Isa MN, Novaes J, Quail M, Rosli R, Nor Shamsudin M, Sobreira TJ, Tivey AR, Wai SF, White S, Wu X, Kerhornou A, Blake D, Mohamed R, Shirley M, Gruber A, Berriman M, Tomley F, Dear PH, Wan KL.

Genome Res. 2007 Mar;17(3):311-9. Epub 2007 Feb 6.


An efficient method for multi-locus molecular haplotyping.

Konfortov BA, Bankier AT, Dear PH.

Nucleic Acids Res. 2007;35(1):e6. Epub 2006 Dec 7. Erratum in: Nucleic Acids Res. 2007;35(9):3165.


Use of HAPPY mapping for the higher order assembly of the Tetrahymena genome.

Hamilton EP, Dear PH, Rowland T, Saks K, Eisen JA, Orias E.

Genomics. 2006 Oct;88(4):443-51. Epub 2006 Jun 19.


Interrogation of genomes by molecular copy-number counting (MCC).

Daser A, Thangavelu M, Pannell R, Forster A, Sparrow L, Chung G, Dear PH, Rabbitts TH.

Nat Methods. 2006 Jun;3(6):447-53. Erratum in: Nat Methods. 2006 Jul;3(7):579.

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