Publications
Jones, P.T., Dear, P.H., Foote, J., Neuberger, M.S. and Winter, G. (1986) Replacing the complementarity-determining regions in a human antibody with those from a mouse Nature 321, 522-525.PDF
Dear, P.H. and Cook, P.R. (1989) HAPPY mapping - a proposal for linkage mapping the human genome Nucleic Acids Res. 17, 6795-6807. PDF
Dear, P.H. and Cook, P.R. (1991) Cellular gels - purifying and mapping long DNA molecules Biochem. J. 273, 695-699. PDF
Dear, P.H. and Cook, P.R. (1993) HAPPY mapping - linkage mapping using a physical analog of meiosis Nucleic Acids Res. 21, 13-20. PDF
Walter, G., Tomlinson, I.M., Cook, G.P., Winter, G., Rabbitts, T.H. and Dear, P.H. (1993) HAPPY mapping of a YAC reveals alternative haplotypes in the human immunoglobulin Vh locus Nucleic Acids Res., 21, 4524-4529. PDF
Walter, G., Tomlinson, I.M., Dear, P.H., Sonnhammer, E.L.L., Cook, G.P. and Winter, G. (1995) Comparison of the human germline and rearranged Vh repertoire reveals complementarity between germline variability and somatic mutation Ann. N.Y. Acad. Sci. 764, 180-182. PDF
Tomlinson, I.M., Walter, G., Jones, P.T., Dear, P.H., Sonnhammer, E.L.L. and Winter, G. (1996) The imprint of somatic hypermutation on the repertoire of human germline V genes J. Mol. Biol. 256, 813-817. PDF
Trusov, Y.A. and Dear, P.H. (1996) A molecular clock based on the expansion of gene families Nucleic Acids Res. 24, 995-999. PDF
Dear, P.H., Bankier, A.T. and Piper, M.B. (1998) A high-resolution metric HAPPY map of human chromosome 14 Genomics 48, 232-241PDF
Lynch, R., Piper, M., Bankier, A.T., Bhugra, B., Surti, U., Liu, J., Buckler, A., Dear, P.H., and Menon, A.G. (1998) Genomic and functional map of the t(12;14) breakpoint cluster region in uterine leiomyoma Genomics 52, 17-26. PDF
Deming, M.S., Dyer, K.D., Bankier, A.T., Piper, M.B., Dear, P.H. and Rosenberg, H.F. (1998) Ribonuclease k6: chromosomal mapping and divergent rates of evolution within the RNase A gene superfamily Genome Research 8, 599-607. PDF
Piper, M.B., Bankier, A.T. and Dear, P.H. (1998) Construction and characterization of a genomic PAC library of the intestinal parasite Cryptosporidium parvum. Mol. Biochem. Parasitol 95, 147-151. PDF
Piper, M.B., Bankier, A.T. and Dear, P.H. (1998) A HAPPY map of Cryptosporidium parvum. Genome Res. 8, 1299-1307. PDF
Biunno, I., Bernard, L., Dear, P., Cattaneo, M., Volorio, S., Zannini, L., Bankier, A. and Zollo, M. (2000) SEL1, the human homolog of C. elegans sel-1: refined physical mapping, gene structure and identification of polymorphic markers. Hum. Genet. 106, 227-235. PDF
Konfortov, B.A., Cohen, H.M., Bankier, A.T. and Dear, P.H. (2000) A high-resolution HAPPY map of Dictyostelium discoideum chromosome 6. Genome Res. 10, 1737-1742. PDF
Amar, C. F., Dear, P.H., Pedraza-Diaz, S., Looker, N., Linnane, E. and McLauchlin, J. (2002) Sensitive PCR-restriction fragment length polymorphism assay for detection and genotyping of Giardia duodenalis in human feces. J Clin Microbiol. 40, 446-452. PDF
Glöckner, G., Eichinger, E., Szafranski K., Pachebat, J.A., Bankier, A.T., Dear, P.H., Lehmann, R., Baumgart, C., Parra, G., Abril, J.F., Guigó, R., Kumpf, K., Tunggal, B., the Dictyostelium Genome Sequencing Consortium, Cox, E., Quail, M., Platzer, M., Rosenthal, A. and Noegel, A.A. (2002) Sequence and Analysis of Chromosome 2 of Dictyostelium discoideum. Nature 418, 79-85. PDF
Waugh, R., Dear, P.H., Powell, W. and Machray, G.C. (2002) Physical education - new technologies for mapping plant genomes. Trends Plant Sci. 7, 521
Hall, N., Pain, A., Berriman, M., Churcher, C., Harris, B., Harris, D., Mungall, K., Bowman, S., Atkin, R., Baker, S., Barron, A., Brooks, K., Buckee, C.O., Burrows, C., Cherevach, I., Chillingworth, C., Chillingworth, T., Christodoulou, Z., Clark, L., Clark, R., Corton, C., Cronin, A., Davies, R., Davis, P., Dear, P., Dearden, F., Doggett, J., Feltwell, T., Goble, A., Goodhead, I., Gwilliam, R., Hamlin, N., Hance, Z., Harper, D., Hauser, H., Hornsby, T., Holroyd, S., Horrocks, P., Humphray, S., Jagels, K., James, K.D., Johnson, D., Kerhornou, A., Knights, A., Konfortov, B., Kyes, S., Larke, N., Lawson, D., Lennard, N., Line, A., Maddison, M., McLean, J., Mooney, P., Moule, S., Murphy, L., Oliver, K., Ormond, D., Price, C., Quail, M.A., Rabbinowitsch, E., Rajandream, M.A., Rutter, S., Rutherford, K.M., Sanders, M., Simmonds, M., Seeger, K., Sharp, S., Smith, R., Squares, R., Squares, S., Stevens, K., Taylor, K., Tivey, A., Unwin, L., Whitehead, S., Woodward, J., Sulston, J.E., Craig, A., Newbold, C. and Barrell, B.G. (2002) Sequence of Plasmodium falciparum chromosomes 1, 3-9 and 13. Nature 419, 527-531. PDF
Thangavelu, M., James, A.B., Bankier, A., Bryan, G.J., Dear, P.H. and Waugh, R. (2003) HAPPY mapping in a plant genome: reconstruction and analysis of a high-resolution physical map of a 1.9Mbp region of Arabidopsis thaliana chromosome 4 Plant Biotech. J. 1, 23-31.PDF
Dear, P.H. (2003) One by one: single-molecular tools for genomics. Briefings in Functional Genomics 1, 397-416. PDF
Amar, C.F.L., Dear, P.H. and McLauchlin, J. (2003) Detection and genotyping by real-time PCR/RFLP analyses of Giardia duedenalis from human faeces. J. Med. Microbiol. 52, 681-683. PDF
Bankier, A.T., Spriggs, H.F., Fartmann, B., Konfortov, B.A., Madera, M., Vogel, C., Teichmann, S.A., Ivens, A. and Dear, P.H. (2003) Integrated mapping, chromosomal sequencing and sequence analysis of Cryptosporidium parvum. Genomics 1, 1787-99. PDF
Amar, C.F., Dear, P.H. and McLauchlin, J. (2004) Detection and identification by real time PCR/RFLP analyses of Cryptosporidium species from human faeces. Lett. Appl. Microbiol. 38, 217-22. PDF
Abrahamsen, M.S., Templeton, T.J., Enomoto, S., Abrahante, J.E., Zhu, G., Lancto, C.A., Deng, M., Liu, C., Widmer, G., Tzipori, S., Buck, G.A., Xu, P., Bankier, A.T., Dear, P.H., Konfortov, B.A., Spriggs, H.F., Iyer, L., Anantharaman, V., Aravind, L., and Kapur, V. (2004) Complete genome sequence of the apicomplexan, Cryptosporidium parvum. Science. 304, 441-445. PDF
Shirley, M.W., Ivens, A., Gruber, A., Madeira, A.M., Wan, K.L., Dear, P.H., and Tomley, F.M. (2004) The Eimeria genome projects: a sequence of events. Trends Parasitol. 20, 199-201. PDF
Xu, P., Widmer, G., Wang, Y., Ozaki, L.S., Alves, J.M., Serrano, M.G., Puiu, D., Manque, P., Akiyoshi, D., Mackey, A.J., Pearson, W.R., Dear, P.H., Bankier, A.T., Peterson, D.L., Abrahamsen, M.S., Kapur, V., Tzipori, S. and Buck, G.A. (2004) The genome of Cryptosporidium hominis. Nature 431, 1107-1112. PDF
L. Eichinger, J.A. Pachebat, G. Glöckner, M.-A. Rajandream, R. Sucgang, M. Berriman, J. Song, R. Olsen, K. Szafranski, Q. Xu, B. Tunggal, S. Kummerfeld, M. Madera, B. A. Konfortov, F. Rivero, A. T. Bankier, R. Lehmann, N. Hamlin, R. Davies, P. Gaudet, P. Fey , K. Pilcher, G. Chen, D. Saunders, E. Sodergren, P. Davis, A. Kerhornou, X. Nie, N. Hall, C. Anjard, L. Hemphill, N. Bason, P. Farbrother, B. Desany, E. Just, T. Morio, R. Rost, C. Churcher, J. Cooper, S. Haydock, N. van Driessche, A. Cronin, I. Goodhead, D. Muzny, T. Mourier, A. Pain, M. Lu, D. Harper, R. Lindsay, H. Hauser, K. James, M. Quiles, M. Madan Babu, T. Saito, C. Buchrieser, A. Wardroper, M. Felder, M. Thangavelu, D. Johnson, A. Knights, H. Loulseged, K. Mungall, K. Oliver, C. Price, M.A. Quail, H. Urushihara, J. Hernandez, E. Rabbinowitsch, D. Steffen, M. Sanders, J. Ma, Y. Kohara, S. Sharp, M. Simmonds, S. Spiegler, A. Tivey, S. Sugano, B. White, D. Walker, J. Woodward, T. Winckler, Y. Tanaka, G. Shaulsky, M. Schleicher, G. Weinstock, A. Rosenthal, E.C. Cox, R. L. Chisholm, R. Gibbs, W. F. Loomis, M. Platzer, R. R. Kay, J. Williams, P. H. Dear, A. A. Noegel, B. Barrell and A. Kuspa (2005) The genome of the social amoeba Dictyostelium discoideum. Nature 435, 43-57. PDF
Daser, A., Thangavelu, M., Pannell, R., Forster, A., Sparrow, L., Chung, G., Dear, P.H. and Rabbitts, T.H. (2006) Interrogation of genomes by molecular copy-number counting (MCC) Nature Methods 3, 447-453. PDF
Hamilton, E.P., Dear P.H., Rowland, T., Saks, K., Eisen, J.A. and Orias, E. (2006) Use of HAPPY mapping for higher order assembly of the Tetrahymena genome. Genomics 88, 443-451. PDF
Krause, J., Dear, P.H., Pollack, J.L., Slatkin, M. ,Spriggs, H., Barnes, I., Lister, A.M., Ebersberger, I.,Pääbo, S. and Hofreiter, M. (2006) Multiplex amplification of the mammoth mitochondrial genome and the evolution of Elephantidae. Nature 439, 724-727.
Rompler, H., Dear, P.H., Krause, J., Meyer, M., Rohland, N., Schoneberg, T., Spriggs, H., Stiller, M. and Hofreiter, M. (2006) Multiplex amplification of ancient DNA. Nat. Protoc. 1, 720-728. PDF
Konfortov, B.A., Bankier, A.T. and Dear, P.H. (2007) An efficient method for molecular haplotyping. Nucleic Acids Res. 35, e6. PDF
Ling, K.H., Rajandream, M.A., Rivailler, P., Ivens, A., Yap, S.J., Madeira, A.M., Mungall, K., Billington, K., Yee, W.Y., Bankier, A.T., Carroll, F., Durham, A.M., Peters, N., Loo, S.S., Isa, M.N., Novaes, J., Quail, M., Rosli, R., Nor Shamsudin, M., Sobreira, T.J., Tivey, A.R., Wai, S.F., White, S., Wu, X., Kerhornou, A., Blake, D., Mohamed, R., Shirley, M., Gruber, A., Berriman, M., Tomley, F., Dear, P.H. and Wan, K.L. (2007) Sequencing and analysis of chromosome 1 of Eimeria tenella reveals a unique segmental organization. Genome Res. 17, 311-319. PDF
McCaughan, F., Darai-Ramqvist, E., Bankier, A.T., Konfortov, B.A., Foster, N., George, P.J., Rabbitts, T.H., Kost-Alimova, M., Rabbitts, P.H. and Dear, P.H. (2008) Microdissection molecular copy-number counting (microMCC) - unlocking cancer archives with digital PCR. J Pathol. 216, 307-16. PDF
Krause, J., Unger, T., Noçon, A., Malaspinas, A.S., Kolokotronis, S.O., Stiller, M., Soibelzon, L., Spriggs, H., Dear, P.H., Briggs, A.W., Bray, S.C., O'Brien, S.J., Rabeder, G., Matheus, P., Cooper, A., Slatkin, M., Pääbo, S. and Hofreiter, M. (2008) Mitochondrial genomes reveal an explosive radiation of extinct and extant bears near the Miocene-Pliocene boundary. BMC Evol. Biol. 8, 220. PDF
Amar, C.F., Arnold, C., Bankier, A., Dear, P.H., Guerra, B., Hopkins, K.L., Liebana, E., Mevius, D.J. and Threlfall, E.J. (2008) 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. Microb. Drug. Resist. 14, 79-92. PDF
Dear, P.H. (2009) Copy-number variation: the end of the human genome? Trends Biotech. 27, 448-454. PDF
McCaughan, F. and Dear, P.H. (2010) Single-molecule genomics. J. Pathol. 220, 297-306.PDF
Vu, G.T., Dear, P.H., Caligari, P.D. and Wilkinson, M.J. (2010) BAC-HAPPY mapping (BAP mapping): a new and efficient protocol for physical mapping. PLoS One 8, e9089. PDF
Ramsay, N., Jemth, A.-S., Brown, A., Crampton, N., Dear, P. and Holliger, P. (2010) CyDNA: Synthesis and Replication of Highly Cy-Dye Substituted DNA by an Evolved Polymerase. J. Amer. Chem. Soc.,132, 5096-5104. PDF
McCaughan, F., Pole, J.C., Bankier, A.T., Konfortov, B.A., Carroll, B., Falzon, M., Rabbitts, T.H., George, P.J., Dear, P.H. and Rabbitts, P.H. (2010) Progressive 3q amplification consistently targets SOX2 in preinvasive squamous lung cancer. Am. J. Respir. Crit. Care Med., 182, 83-9. PDF
McCaughan, F., Pipinikas, C.P., Janes, S.M., George, P.J., Rabbitts, P.H. and Dear, P.H. (2011) Genomic evidence for pre-invasive clonal expansion, dispersal and progression in bronchial dysplasia. J. Pathol. 224, 153-159. PDF
Pole, J.C., McCaughan, F., Newman, S., Howarth, K.D., Dear, P.H. and Edwards, P.A. (2011) Single-molecule analysis of genome rearrangements in cancer. Nucleic Acids Res. 39, e85.PDF
Miraldo, A., Hewitt, G.M., Dear, P.H., Paulo, O.S. and Emerson, B.C. (2012) NUMTS help to reconstruct the demographic history of the ocellated lizard (Lacerta lepida) in a secondary contact zone. Mol. Ecol. 21, 1005-1018.PDF
Lim, L.S., Tay, Y.L., Alias, H., Wan, K.L. and Dear, P.H. (2012) Insights into the genome structure and copy-number variation of Eimeria tenella. BMC Genomics 13:389.PDF
Day, E., Dear, P.H. and McCaughan, F. (2012) Digital PCR strategies in the development and analysis of molecular biomarkers for personalized medicine. Methods, 59, 101-107.PDF
Ali, H., Daser, A., Dear, P., Wood, H., Rabbitts, P. and Rabbitts, T. (2012) Nonreciprocal chromosomal translocations in renal cancer involve multiple DSBs and NHEJ associated with breakpoint inversion but not necessarily with transcription. Genes Chromosomes Cancer PDF
Day, E., Poulogiannis, G., McCaughan, F., Mulholland, S., Arends, M., Ibrahim, A.E.K. and Dear, P.H. (2013) IRS2 is a candidate driver oncogene on 13q34 in colorectal cancer. Int. J. Exp. Path. PDF
Dear, P.H. (ed.) (1997) Genome Mapping: A Practical Approach IRL Press, Oxford. Amazon
Cooper, D.N. et al (eds) (2003) Nature Encyclopedia of the Human Genome Nature Publishing Group (Area Editor mapping and sequencing). Amazon
Dear, P.H. (ed.) (2007) Bioinformatics: Methods Express Scion Press, Oxford. Amazon
Book chapters:
Dear, P.H. (2003) Single-molecule PCR – basic protocols and applications in “PCR Technology – Current Innovations”, pp245-257, 2nd Edn. (Eds. Weissensteiner, T., Griffin, H. and Griffin, A.), CRC Press
Dear, P.H. (2003) 12 articles in: Encyclopedia of the Human Genome. Nature Publishing Group.
US 20040248153A1 , US 2005/0003379 and US 20040224324A1 relate to genome mapping
US 20090191556A1 describes a method for determining copy-number
US 20010023012A1 describes a modular gel casette