Publications | J.W. Jenkinson Laboratory for Evolution and Development

Publications

Found 188 results
2017
Martin, K. J. and Holland, P. W. H. , Diversification of Hox Gene Clusters in Osteoglossomorph Fish in Comparison to Other Teleosts and the Spotted Gar Outgroup., J Exp Zool B Mol Dev Evol, 2017.
Holland, P. W. H. , Marlétaz, F. , Maeso, I. , Dunwell, T. L. , and Paps, J. , New genes from old: asymmetric divergence of gene duplicates and the evolution of development., Philos Trans R Soc Lond B Biol Sci, vol. 372, no. 1713, 2017.
Dunwell, T. L. and Holland, P. W. H. , A sister of NANOG regulates genes expressed in pre-implantation human development, Open Biology, 2017.
2016
Kenny, N. J. , Chan, K. W. , Nong, W. , Qu, Z. , Maeso, I. , Yip, H. Y. , Chan, T. F. , Kwan, H. S. , Holland, P. W. H. , Chu, K. H. , and Hui, J. H. L. , Ancestral whole-genome duplication in the marine chelicerate horseshoe crabs., Heredity (Edinb), vol. 116, no. 2, pp. 190-9, 2016.
Feuda, R. , Marlétaz, F. , Bentley, M. A. , and Holland, P. W. H. , Conservation, Duplication, and Divergence of Five Opsin Genes in Insect Evolution., Genome Biol Evol, vol. 8, no. 3, pp. 579-87, 2016.
Dunwell, T. L. and Holland, P. W. H. , Diversity of human and mouse homeobox gene expression in development and adult tissues., BMC Dev Biol, vol. 16, no. 1, p. 40, 2016.
Maeso, I. , Dunwell, T. L. , Wyatt, C. D. R. , Marlétaz, F. , Vető, B. , Bernal, J. A. , Quah, S. , Irimia, M. , and Holland, P. W. H. , Evolutionary origin and functional divergence of totipotent cell homeobox genes in eutherian mammals., BMC Biol, vol. 14, no. 1, p. 45, 2016.
Schierwater, B. , Holland, P. W. , Miller, D. J. , Stadler, P. F. , Wiegmann, B. M. , Worheide, G. , Wray, G. A. , and DeSalle, R. , Never ending analysis of a century old evolutionary debate: "unringing" the urmetazoon bell., frontiers in Ecology and Evolution, vol. 4, 2016.
Acemel, R. D. , Tena, J. J. , Irastorza-Azcarate, I. , Marlétaz, F. , Gómez-Marín, C. , de la Calle-Mustienes, E. , Bertrand, S. , Diaz, S. G. , Aldea, D. , Aury, J. - M. , Mangenot, S. , Holland, P. W. H. , Devos, D. P. , Maeso, I. , Escrivá, H. , and Gómez-Skarmeta, J. Luis, A single three-dimensional chromatin compartment in amphioxus indicates a stepwise evolution of vertebrate Hox bimodal regulation., Nat Genet, 2016.
Braasch, I. , Gehrke, A. R. , Smith, J. J. , Kawasaki, K. , Manousaki, T. , Pasquier, J. , Amores, A. , Desvignes, T. , Batzel, P. , Catchen, J. , Berlin, A. M. , Campbell, M. S. , Barrell, D. , Martin, K. J. , Mulley, J. F. , Ravi, V. , Lee, A. P. , Nakamura, T. , Chalopin, D. , Fan, S. , Wcisel, D. , Cañestro, C. , Sydes, J. , Beaudry, F. E. G. , Sun, Y. , Hertel, J. , Beam, M. J. , Fasold, M. , Ishiyama, M. , Johnson, J. , Kehr, S. , Lara, M. , Letaw, J. H. , Litman, G. W. , Litman, R. T. , Mikami, M. , Ota, T. , Saha, N. Ratan, Williams, L. , Stadler, P. F. , Wang, H. , Taylor, J. S. , Fontenot, Q. , Ferrara, A. , Searle, S. M. J. , Aken, B. , Yandell, M. , Schneider, I. , Yoder, J. A. , Volff, J. - N. , Meyer, A. , Amemiya, C. T. , Venkatesh, B. , Holland, P. W. H. , Guiguen, Y. , Bobe, J. , Shubin, N. H. , Di Palma, F. , Alföldi, J. , Lindblad-Toh, K. , and Postlethwait, J. H. , The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons., Nat Genet, 2016.
2015
Quah, S. , Hui, J. H. L. , and Holland, P. W. H. , A Burst of miRNA Innovation in the Early Evolution of Butterflies and Moths., Mol Biol Evol, vol. 32, no. 5, pp. 1161-74, 2015.
Marlétaz, F. , Maeso, I. , Faas, L. , Isaacs, H. V. , and Holland, P. W. H. , Cdx ParaHox genes acquired distinct developmental roles after gene duplication in vertebrate evolution., BMC Biol, vol. 13, p. 56, 2015.
Holland, P. W. H. , Did homeobox gene duplications contribute to the Cambrian explosion?, Zoological Lett, vol. 1, p. 1, 2015.
Quah, S. , Breuker, C. J. , and Holland, P. W. H. , A Diversity of Conserved and Novel Ovarian MicroRNAs in the Speckled Wood (Pararge aegeria)., PLoS One, vol. 10, no. 11, p. e0142243, 2015.
Quah, S. and Holland, P. W. H. , The Hox cluster microRNA miR-615: a case study of intronic microRNA evolution., Evodevo, vol. 6, p. 31, 2015.
Holland, P. W. H. , Observations on fragrance collection behaviour of euglossine bees (Hymenoptera, Apidae), Revista Brasileira de Entomologia , vol. 59, pp. 62-64, 2015.
Paps, J. , Xu, F. , Zhang, G. , and Holland, P. W. H. , Reinforcing the egg-timer: recruitment of novel lophotrochozoa homeobox genes to early and late development in the pacific oyster., Genome Biol Evol, vol. 7, no. 3, pp. 677-88, 2015.
Holland, N. D. , Holland, L. Z. , and Holland, P. W. H. , Scenarios for the making of vertebrates., Nature, vol. 520, no. 7548, pp. 450-5, 2015.
2014
Ferguson*, L. , Marlétaz*, F. , Carter*, J. - M. , Taylor, W. R. , Gibbs, M. , Breuker, C. J. , and Holland, P. W. H. , Ancient expansion of the hox cluster in lepidoptera generated four homeobox genes implicated in extra-embryonic tissue formation., PLoS Genet, vol. 10, no. 10, p. e1004698 (* joint first authors), 2014.
Marlétaz, F. , Paps, J. , Maeso, I. , and Holland, P. W. H. , Discovery and classification of homeobox genes in animal genomes., Methods Mol Biol, vol. 1196, pp. 3-18, 2014.
Martin, K. J. and Holland, P. W. H. , Enigmatic Orthology Relationships between Hox Clusters of the African Butterfly Fish and Other Teleosts Following Ancient Whole-Genome Duplication., Mol Biol Evol, vol. 31, no. 10, pp. 2592-611, 2014.
Mulley, J. F. and Holland, P. W. H. , Genomic organisation of the seven ParaHox genes of coelacanths., J Exp Zool B Mol Dev Evol, vol. 322, no. 6, pp. 352-8, 2014.
Boussau, B. , Walton, Z. , Delgado, J. A. , Collantes, F. , Beani, L. , Stewart, I. J. , Cameron, S. A. , Whitfield, J. B. , J Johnston, S. , Holland, P. W. H. , Bachtrog, D. , Kathirithamby, J. , and Huelsenbeck, J. P. , Strepsiptera, phylogenomics and the long branch attraction problem., PLoS One, vol. 9, no. 10, p. e107709, 2014.
2013
Barker, D. , Ferrier, D. Ek, Holland, P. Wh, Mitchell, J. Bo, Plaisier, H. , Ritchie, M. G. , and Smart, S. D. , 4273π: bioinformatics education on low cost ARM hardware., BMC Bioinformatics, vol. 14, p. 243, 2013.
Holland, P. W. H. , Evolution of homeobox genes., Wiley Interdiscip Rev Dev Biol, vol. 2, no. 1, pp. 31-45, 2013.
Marron, A. O. , Alston, M. J. , Heavens, D. , Akam, M. , Caccamo, M. , Holland, P. W. H. , and Walker, G. , A family of diatom-like silicon transporters in the siliceous loricate choanoflagellates., Proc Biol Sci, vol. 280, no. 1756, p. 20122543, 2013.
Tsai, I. J. , Zarowiecki, M. , Holroyd, N. , Garciarrubio, A. , Sanchez-Flores, A. , Brooks, K. L. , Tracey, A. , Bobes, R. J. , Fragoso, G. , Sciutto, E. , Aslett, M. , Beasley, H. , Bennett, H. M. , Cai, J. , Camicia, F. , Clark, R. , Cucher, M. , De Silva, N. , Day, T. A. , Deplazes, P. , Estrada, K. , Fernández, C. , Holland, P. W. H. , Hou, J. , Hu, S. , Huckvale, T. , Hung, S. S. , Kamenetzky, L. , Keane, J. A. , Kiss, F. , Koziol, U. , Lambert, O. , Liu, K. , Luo, X. , Luo, Y. , Macchiaroli, N. , Nichol, S. , Paps, J. , Parkinson, J. , Pouchkina-Stantcheva, N. , Riddiford, N. , Rosenzvit, M. , Salinas, G. , Wasmuth, J. D. , Zamanian, M. , Zheng, Y. , Cai, X. , Soberón, X. , Olson, P. D. , Laclette, J. P. , Brehm, K. , and Berriman, M. , The genomes of four tapeworm species reveal adaptations to parasitism., Nature, vol. 496, no. 7443, pp. 57-63, 2013.
Kenny, N. J. , Quah, S. , Holland, P. W. H. , Tobe, S. S. , and Hui, J. H. L. , How are comparative genomics and the study of microRNAs changing our views on arthropod endocrinology and adaptations to the environment?, Gen Comp Endocrinol, vol. 188, pp. 16-22, 2013.
2012
Butterfly genome reveals promiscuous exchange of mimicry adaptations among species., Nature, vol. 487, no. 7405, pp. 94-8, 2012.
Hui, J. H. L. , McDougall, C. , Monteiro, A. S. , Holland, P. W. H. , Arendt, D. , Balavoine, G. , and Ferrier, D. E. K. , Extensive chordate and annelid macrosynteny reveals ancestral homeobox gene organization., Mol Biol Evol, vol. 29, no. 1, pp. 157-65, 2012.
Paps, J. , Holland, P. W. H. , and Shimeld, S. M. , A genome-wide view of transcription factor gene diversity in chordate evolution: less gene loss in amphioxus?, Brief Funct Genomics, vol. 11, no. 2, pp. 177-86, 2012.
Zhang, G. , Fang, X. , Guo, X. , Li, L. , Luo, R. , Xu, F. , Yang, P. , Zhang, L. , Wang, X. , Qi, H. , Xiong, Z. , Que, H. , Xie, Y. , Holland, P. W. H. , Paps, J. , Zhu, Y. , Wu, F. , Chen, Y. , Wang, J. , Peng, C. , Meng, J. , Yang, L. , Liu, J. , Wen, B. , Zhang, N. , Huang, Z. , Zhu, Q. , Feng, Y. , Mount, A. , Hedgecock, D. , Xu, Z. , Liu, Y. , Domazet-Lošo, T. , Du, Y. , Sun, X. , Zhang, S. , Liu, B. , Cheng, P. , Jiang, X. , Li, J. , Fan, D. , Wang, W. , Fu, W. , Wang, T. , Wang, B. , Zhang, J. , Peng, Z. , Li, Y. , Li, N. , Wang, J. , Chen, M. , He, Y. , Tan, F. , Song, X. , Zheng, Q. , Huang, R. , Yang, H. , Du, X. , Chen, L. , Yang, M. , Gaffney, P. M. , Wang, S. , Luo, L. , She, Z. , Ming, Y. , Huang, W. , Zhang, S. , Huang, B. , Zhang, Y. , Qu, T. , Ni, P. , Miao, G. , Wang, J. , Wang, Q. , Steinberg, C. E. W. , Wang, H. , Li, N. , Qian, L. , Zhang, G. , Li, Y. , Yang, H. , Liu, X. , Wang, J. , Yin, Y. , and Wang, J. , The oyster genome reveals stress adaptation and complexity of shell formation., Nature, vol. 490, no. 7418, pp. 49-54, 2012.
2011
Holland, P. , The Animal Kingdom: a Very Short Introduction. Oxford: Oxford University Press, 2011.
Zhong, Y. - F. and Holland, P. W. H. , The dynamics of vertebrate homeobox gene evolution: gain and loss of genes in mouse and human lineages., BMC Evol Biol, vol. 11, p. 169, 2011.
McGonnell, I. M. , Graham, A. , Richardson, J. , Fish, J. L. , Depew, M. J. , Dee, C. T. , Holland, P. W. H. , and Takahashi, T. , Evolution of the Alx homeobox gene family: parallel retention and independent loss of the vertebrate Alx3 gene., Evol Dev, vol. 13, no. 4, pp. 343-51, 2011.
Zhong, Y. - F. and Holland, P. W. H. , HomeoDB2: functional expansion of a comparative homeobox gene database for evolutionary developmental biology., Evol Dev, vol. 13, no. 6, pp. 567-8, 2011.
Loenarz, C. , Coleman, M. L. , Boleininger, A. , Schierwater, B. , Holland, P. W. H. , Ratcliffe, P. J. , and Schofield, C. J. , The hypoxia-inducible transcription factor pathway regulates oxygen sensing in the simplest animal, Trichoplax adhaerens., EMBO Rep, vol. 12, no. 1, pp. 63-70, 2011.
Travillian, R. , Malone, J. , C., P. , Holland, P. W. H. , Schofield, P. , and Parkinson, H. , The Vertebrate Bridging Ontology (VBO)., Bio-Ontologies SIG, 2011.
2010
Butts, T. , Holland, P. W. H. , and Ferrier, D. E. K. , Ancient homeobox gene loss and the evolution of chordate brain and pharynx development: deductions from amphioxus gene expression., Proc Biol Sci, vol. 277, no. 1699, pp. 3381-9, 2010.
Li, G. and Holland, P. W. H. , The origin and evolution of ARGFX homeobox loci in mammalian radiation., BMC Evol Biol, vol. 10, p. 182, 2010.
Mulley, J. F. and Holland, P. W. H. , Parallel retention of Pdx2 genes in cartilaginous fish and coelacanths., Mol Biol Evol, vol. 27, no. 10, pp. 2386-91, 2010.
2009
Holland, P. W. H. , (2009) Foreword. In: Animal Evolution: Genomes, Fossils and Trees (eds. M.J. Telford and D.T.J. Littlewood), Oxford University Press, 2009.
Mulley, J. F. , Zhong, Y. - F. , and Holland, P. Wh, Comparative genomics of chondrichthyan Hoxa clusters., BMC Evol Biol, vol. 9, p. 218, 2009.
Sato, A. , White-Cooper, H. , Doggett, K. , and Holland, P. W. H. , Degenerate evolution of the hedgehog gene in a hemichordate lineage., Proc Natl Acad Sci U S A, vol. 106, no. 18, pp. 7491-4, 2009.
2008
Putnam, N. H. , Butts, T. , Ferrier, D. E. K. , Furlong, R. F. , Hellsten, U. , Kawashima, T. , Robinson-Rechavi, M. , Shoguchi, E. , Terry, A. , Yu, J. - K. , E Benito-Gutiérrez, L. , Dubchak, I. , Garcia-Fernàndez, J. , Gibson-Brown, J. J. , Grigoriev, I. V. , Horton, A. C. , de Jong, P. J. , Jurka, J. , Kapitonov, V. V. , Kohara, Y. , Kuroki, Y. , Lindquist, E. , Lucas, S. , Osoegawa, K. , Pennacchio, L. A. , Salamov, A. A. , Satou, Y. , Sauka-Spengler, T. , Schmutz, J. , Shin-I, T. , Toyoda, A. , Bronner-Fraser, M. , Fujiyama, A. , Holland, L. Z. , Holland, P. W. H. , Satoh, N. , and Rokhsar, D. S. , The amphioxus genome and the evolution of the chordate karyotype., Nature, vol. 453, no. 7198, pp. 1064-71, 2008.
Holland, L. Z. , Albalat, R. , Azumi, K. , Benito-Gutiérrez, E. , Blow, M. J. , Bronner-Fraser, M. , Brunet, F. , Butts, T. , Candiani, S. , Dishaw, L. J. , Ferrier, D. E. K. , Garcia-Fernàndez, J. , Gibson-Brown, J. J. , Gissi, C. , Godzik, A. , Hallböök, F. , Hirose, D. , Hosomichi, K. , Ikuta, T. , Inoko, H. , Kasahara, M. , Kasamatsu, J. , Kawashima, T. , Kimura, A. , Kobayashi, M. , Kozmik, Z. , Kubokawa, K. , Laudet, V. , Litman, G. W. , McHardy, A. C. , Meulemans, D. , Nonaka, M. , Olinski, R. P. , Pancer, Z. , Pennacchio, L. A. , Pestarino, M. , Rast, J. P. , Rigoutsos, I. , Robinson-Rechavi, M. , Roch, G. , Saiga, H. , Sasakura, Y. , Satake, M. , Satou, Y. , Schubert, M. , Sherwood, N. , Shiina, T. , Takatori, N. , Tello, J. , Vopalensky, P. , Wada, S. , Xu, A. , Ye, Y. , Yoshida, K. , Yoshizaki, F. , Yu, J. - K. , Zhang, Q. , Zmasek, C. M. , de Jong, P. J. , Osoegawa, K. , Putnam, N. H. , Rokhsar, D. S. , Satoh, N. , and Holland, P. W. H. , The amphioxus genome illuminates vertebrate origins and cephalochordate biology., Genome Res, vol. 18, no. 7, pp. 1100-11, 2008.
Sato, A. and Holland, P. W. H. , Asymmetry in a pterobranch hemichordate and the evolution of left-right patterning., Dev Dyn, vol. 237, no. 12, pp. 3634-9, 2008.
Takatori, N. , Butts, T. , Candiani, S. , Pestarino, M. , Ferrier, D. E. K. , Saiga, H. , and Holland, P. W. H. , Comprehensive survey and classification of homeobox genes in the genome of amphioxus, Branchiostoma floridae., Dev Genes Evol, vol. 218, no. 11-12, pp. 579-90, 2008.
Ho, S. Y. W. , Larson, G. , Edwards, C. J. , Heupink, T. H. , Lakin, K. E. , Holland, P. W. H. , and Shapiro, B. , Correlating Bayesian date estimates with climatic events and domestication using a bovine case study., Biol Lett, vol. 4, no. 4, pp. 370-4, 2008.
Sato, A. , Bishop, J. D. D. , and Holland, P. W. H. , Developmental biology of pterobranch hemichordates: history and perspectives., Genesis, vol. 46, no. 11, pp. 587-91, 2008.
Hui, J. H. L. , Holland, P. W. H. , and Ferrier, D. E. K. , Do cnidarians have a ParaHox cluster? Analysis of synteny around a Nematostella homeobox gene cluster., Evol Dev, vol. 10, no. 6, pp. 725-30, 2008.
Zhong, Y. - F. , Butts, T. , and Holland, P. W. H. , HomeoDB: a database of homeobox gene diversity., Evol Dev, vol. 10, no. 5, pp. 516-8, 2008.
Sato, A. , Richards, B. , and Holland, P. W. H. , The origins of graptolites and other pterobranchs: a journey from ‘Polyzoa', Lethaia, vol. 41, 2008.
Fonseca, N. A. , Vieira, C. P. , Holland, P. W. H. , and Vieira, J. , Protein evolution of ANTP and PRD homeobox genes., BMC Evol Biol, vol. 8, p. 200, 2008.
Holland, P. W. H. and Wada, H. , Protochordates., Methods Mol Biol, vol. 461, pp. 563-6, 2008.
Butts, T. , Holland, P. W. H. , and Ferrier, D. E. K. , The urbilaterian Super-Hox cluster., Trends Genet, vol. 24, no. 6, pp. 259-62, 2008.
Holland, P. W. H. , Wholemount in situ hybridization to amphioxus embryos., Methods Mol Biol, vol. 461, pp. 703-6, 2008.
2007
H Booth, A. F. and Holland, P. W. H. , Annotation, nomenclature and evolution of four novel homeobox genes expressed in the human germ line., Gene, vol. 387, no. 1-2, pp. 7-14, 2007.
Jiménez-Guri, E. , Philippe, H. , Okamura, B. , and Holland, P. W. H. , Buddenbrockia is a cnidarian worm., Science, vol. 317, no. 5834, pp. 116-8, 2007.
Herren, J. K. , Gordon, I. , Holland, P. W. H. , and Smith, D. , The butterfly Danaus chrysippus (Lepidoptera: Nymphalidae) in Kenya is variably infected with respect to genotype and body size by a maternally transmitted male-killing endosymbiont (Spiroplasma)., International Journal of Tropical Insect Science, vol. 27, no. 2, 2007.
Holland, P. W. H. , H Booth, A. F. , and Bruford, E. A. , Classification and nomenclature of all human homeobox genes., BMC Biol, vol. 5, p. 47, 2007.
Furlong, R. F. , Younger, R. , Kasahara, M. , Reinhardt, R. , Thorndyke, M. , and Holland, P. W. H. , A degenerate ParaHox gene cluster in a degenerate vertebrate., Mol Biol Evol, vol. 24, no. 12, pp. 2681-6, 2007.
Jiménez-Guri, E. , Okamura, B. , and Holland, P. W. H. , Origin and evolution of a myxozoan worm., Integr Comp Biol, vol. 47, no. 5, pp. 752-8, 2007.
Ruiz-Trillo, I. , Burger, G. , Holland, P. W. H. , King, N. , B Lang, F. , Roger, A. J. , and Gray, M. W. , The origins of multicellularity: a multi-taxon genome initiative., Trends Genet, vol. 23, no. 3, pp. 113-8, 2007.
2006
Mulley, J. F. , Chiu, C. -hua, and Holland, P. W. H. , Breakup of a homeobox cluster after genome duplication in teleosts., Proc Natl Acad Sci U S A, vol. 103, no. 27, pp. 10369-72, 2006.
L Castro, F. C. , Rasmussen, S. L. K. , Holland, P. W. H. , Holland, N. D. , and Holland, L. Z. , A Gbx homeobox gene in amphioxus: insights into ancestry of the ANTP class and evolution of the midbrain/hindbrain boundary., Dev Biol, vol. 295, no. 1, pp. 40-51, 2006.
Osborne, P. W. , Luke, G. N. , Holland, P. W. H. , and Ferrier, D. E. K. , Identification and characterisation of five novel miniature inverted-repeat transposable elements (MITEs) in amphioxus (Branchiostoma floridae)., Int J Biol Sci, vol. 2, no. 2, pp. 54-60, 2006.
Monteiro, A. S. , Schierwater, B. , Dellaporta, S. L. , and Holland, P. W. H. , A low diversity of ANTP class homeobox genes in Placozoa., Evol Dev, vol. 8, no. 2, pp. 174-82, 2006.
Holland, P. , Molecular phylogeny: My sister is a sea squirt?, Heredity (Edinb), vol. 96, no. 6, pp. 424-5, 2006.
Dearden, P. K. , Wilson, M. J. , Sablan, L. , Osborne, P. W. , Havler, M. , McNaughton, E. , Kimura, K. , Milshina, N. V. , Hasselmann, M. , Gempe, T. , Schioett, M. , Brown, S. J. , Elsik, C. G. , Holland, P. W. H. , Kadowaki, T. , and Beye, M. , Patterns of conservation and change in honey bee developmental genes., Genome Res, vol. 16, no. 11, pp. 1376-84, 2006.
Snell, E. A. , Brooke, N. M. , Taylor, W. R. , Casane, D. , Philippe, H. , and Holland, P. W. H. , An unusual choanoflagellate protein released by Hedgehog autocatalytic processing., Proc Biol Sci, vol. 273, no. 1585, pp. 401-7, 2006.
2005
Holland, P. W. H. and Takahashi, T. , The evolution of homeobox genes: Implications for the study of brain development., Brain Res Bull, vol. 66, no. 4-6, pp. 484-90, 2005.
Holland, P. W. H. , Evolutionary developmental biology. World English Edition of Encarta Encyclopedia., World English Edition of Encarta Encyclopedia. vol. 2005.
Dixon, D. R. , Jollivet, D. A. S. B. , Dixon, L. R. J. , Nott, J. A. , and Holland, P. W. H. , The molecular identification of early life-history stages of hydrothermal vent organisms In: Hydrothermal vents and processes. (Eds. Parson, L.M., Walker, C.L. and Dixon, D.R.), Geological Society Publishing House, 2005.
Minguillón, C. , Gardenyes, J. , Serra, E. , L Castro, F. C. , Hill-Force, A. , Holland, P. W. H. , Amemiya, C. T. , and Garcia-Fernàndez, J. , No more than 14: the end of the amphioxus Hox cluster., Int J Biol Sci, vol. 1, no. 1, pp. 19-23, 2005.
2004
Takahashi, T. and Holland, P. W. H. , Amphioxus and ascidian Dmbx homeobox genes give clues to the vertebrate origins of midbrain development., Development, vol. 131, no. 14, pp. 3285-94, 2004.
L Castro, F. C. , Furlong, R. F. , and Holland, P. W. H. , An antecedent of the MHC-linked genomic region in amphioxus., Immunogenetics, vol. 55, no. 11, pp. 782-4, 2004.
Mulley, J. and Holland, P. , Comparative genomics: small genome, big insights., Nature, vol. 431, no. 7011, pp. 916-7, 2004.
Holland, P. , Developmental biology. The ups and downs of a sea anemone., Science, vol. 304, no. 5675, pp. 1255-6, 2004.
H Booth, A. F. and Holland, P. W. H. , Eleven daughters of NANOG., Genomics, vol. 84, no. 2, pp. 229-38, 2004.
Holland, P. W. H. , The fall and rise of evolutionary developmental biology. CRC Press, 2004, pp. 261–275.
Philippe, H. , Snell, E. A. , Bapteste, E. , Lopez, P. , Holland, P. W. H. , and Casane, D. , Phylogenomics of eukaryotes: impact of missing data on large alignments., Mol Biol Evol, vol. 21, no. 9, pp. 1740-52, 2004.
Furlong, R. F. and Holland, P. W. H. , Polyploidy in vertebrate ancestry: Ohno and beyond, Biological Journal of the Linnean Society, vol. 82, no. 4, 2004.
Jakob, W. , Sagasser, S. , Dellaporta, S. , Holland, P. , Kuhn, K. , and Schierwater, B. , The Trox-2 Hox/ParaHox gene of Trichoplax (Placozoa) marks an epithelial boundary., Dev Genes Evol, vol. 214, no. 4, pp. 170-5, 2004.
2003
Castro, L. F. C. and Holland, P. W. H. , Chromosomal mapping of ANTP class homeobox genes in amphioxus: piecing together ancestral genomes., Evol Dev, vol. 5, no. 5, pp. 459-65, 2003.
Luke, G. N. , L Castro, F. C. , McLay, K. , Bird, C. , Coulson, A. , and Holland, P. W. H. , Dispersal of NK homeobox gene clusters in amphioxus and humans., Proc Natl Acad Sci U S A, vol. 100, no. 9, pp. 5292-5, 2003.
Brooke, N. M. and Holland, P. W. H. , The evolution of multicellularity and early animal genomes., Curr Opin Genet Dev, vol. 13, no. 6, pp. 599-603, 2003.
Holland, P. W. H. , More genes in vertebrates?, J Struct Funct Genomics, vol. 3, no. 1-4, pp. 75-84, 2003.
2002
Furlong, R. F. and Holland, P. W. H. , Bayesian phylogenetic analysis supports monophyly of ambulacraria and of cyclostomes., Zoolog Sci, vol. 19, no. 5, pp. 593-9, 2002.
Holland, P. W. H. , Ciona., Curr Biol, vol. 12, no. 18, p. R609, 2002.
Ferrier, D. E. K. and Holland, P. W. H. , Ciona intestinalis ParaHox genes: evolution of Hox/ParaHox cluster integrity, developmental mode, and temporal colinearity., Mol Phylogenet Evol, vol. 24, no. 3, pp. 412-7, 2002.
Holland, P. W. H. , Copley, R. R. , Snell, E. A. , Furlong, R. F. , and Agapow, P. M. , Exploiting genomics in evolutionary developmental biology In: Genome Science -Towards a New Paradigm?, International Congress Series, vol. 1246, 2002.
Castro, L. Filipe Cos and Holland, P. William Ha, Fluorescent in situ hybridisation to amphioxus chromosomes., Zoolog Sci, vol. 19, no. 12, pp. 1349-53, 2002.
Takahashi, T. , Holland, P. W. H. , Cohn, M. J. , Shimizu, K. , Kurokawa, M. , and Hirai, H. , An orphan PRD class homeobox gene expressed in mouse brain and limb development., Dev Genes Evol, vol. 212, no. 6, pp. 293-7, 2002.
Monteiro, A. Sara, Okamura, B. , and Holland, P. W. H. , Orphan worm finds a home: Buddenbrockia is a myxozoan., Mol Biol Evol, vol. 19, no. 6, pp. 968-71, 2002.
Furlong, R. F. and Holland, P. W. H. , Were vertebrates octoploid?, Philos Trans R Soc Lond B Biol Sci, vol. 357, no. 1420, pp. 531-44, 2002.
2001
Ferrier, D. E. and Holland, P. W. , Ancient origin of the Hox gene cluster., Nat Rev Genet, vol. 2, no. 1, pp. 33-8, 2001.
Holland, P. W. , Beyond the Hox: how widespread is homeobox gene clustering?, J Anat, vol. 199, no. Pt 1-2, pp. 13-23, 2001.
Snell, E. A. , Furlong, R. F. , and Holland, P. W. , Hsp70 sequences indicate that choanoflagellates are closely related to animals., Curr Biol, vol. 11, no. 12, pp. 967-70, 2001.
Ferrier, D. E. , Brooke, N. M. , Panopoulou, G. , and Holland, P. W. , The Mnx homeobox gene class defined by HB9, MNR2 and amphioxus AmphiMnx., Dev Genes Evol, vol. 211, no. 2, pp. 103-7, 2001.
Ferrier, D. E. and Holland, P. W. , Sipunculan ParaHox genes., Evol Dev, vol. 3, no. 4, pp. 263-70, 2001.
2000
Williams, N. A. and Holland, P. W. , An amphioxus Emx homeobox gene reveals duplication during vertebrate evolution., Mol Biol Evol, vol. 17, no. 10, pp. 1520-8, 2000.
Ferrier, D. E. , Minguillón, C. , Holland, P. W. , and Garcia-Fernàndez, J. , The amphioxus Hox cluster: deuterostome posterior flexibility and Hox14., Evol Dev, vol. 2, no. 5, pp. 284-93, 2000.
Knight, R. D. , Panopoulou, G. D. , Holland, P. W. , and Shimeld, S. M. , An amphioxus Krox gene: insights into vertebrate hindbrain evolution., Dev Genes Evol, vol. 210, no. 10, pp. 518-21, 2000.
Manzanares, M. , Wada, H. , Itasaki, N. , Trainor, P. A. , Krumlauf, R. , and Holland, P. W. , Conservation and elaboration of Hox gene regulation during evolution of the vertebrate head., Nature, vol. 408, no. 6814, pp. 854-7, 2000.
Holland, P. W. , Embryonic development of heads, skeletons and amphioxus: Edwin S. Goodrich revisited., Int J Dev Biol, vol. 44, no. 1, pp. 29-34, 2000.
Pollard, S. L. and Holland, P. W. , Evidence for 14 homeobox gene clusters in human genome ancestry., Curr Biol, vol. 10, no. 17, pp. 1059-62, 2000.
Rokas, A. and Holland, P. W. , Rare genomic changes as a tool for phylogenetics., Trends Ecol Evol, vol. 15, no. 11, pp. 454-459, 2000.
Shimeld, S. M. and Holland, P. W. , Vertebrate innovations., Proc Natl Acad Sci U S A, vol. 97, no. 9, pp. 4449-52, 2000.
1999
Sharman, A. C. , Shimeld, S. M. , and Holland, P. W. , An amphioxus Msx gene expressed predominantly in the dorsal neural tube., Dev Genes Evol, vol. 209, no. 4, pp. 260-3, 1999.
Luke, G. N. and Holland, P. W. , Amphioxus type I keratin cDNA and the evolution of intermediate filament genes., J Exp Zool, vol. 285, no. 1, pp. 50-6, 1999.
Wada, H. , Garcia-Fernàndez, J. , and Holland, P. W. , Colinear and segmental expression of amphioxus Hox genes., Dev Biol, vol. 213, no. 1, pp. 131-41, 1999.
Kobayashi, M. , Furuya, H. , and Holland, P. W. , Dicyemids are higher animals., Nature, vol. 401, no. 6755, p. 762, 1999.
Holland, P. W. , The effect of gene duplication on homology., Novartis Found Symp, vol. 222, pp. 226-36; discussion 236-42, 1999.
Snell, E. A. and Holland, P. W. H. , Evolution of the vertebrate fenome: clues from homeobox genes.In Recent Developments in Comparative Endocrinology and neurobiology (eds E.W. Roubos et al), Recent Developments in Comparative Endocrinology and Neurobiology, 1999.
Holland, P. W. , The future of evolutionary developmental biology., Nature, vol. 402, no. 6761 Suppl, pp. C41-4, 1999.
Holland, P. W. , Gene duplication: past, present and future., Semin Cell Dev Biol, vol. 10, no. 5, pp. 541-7, 1999.
Holland, P. W. , Introduction: gene duplication in development and evolution., Semin Cell Dev Biol, vol. 10, no. 5, pp. 515-6, 1999.
Rokas, A. , Kathirithamby, J. , and Holland, P. W. , Intron insertion as a phylogenetic character: the engrailed homeobox of Strepsiptera does not indicate affinity with Diptera., Insect Mol Biol, vol. 8, no. 4, pp. 527-30, 1999.
Holland, P. W. and Wada, H. , Protochordates., Methods Mol Biol, vol. 97, pp. 513-6, 1999.
Holland, P. W. H. , Whole-mount in situ hybridization: amphioxus. In: Molecular Embryology: Methods and Protocols (eds. P.T. Sharpe and I.J. Mason)., Molecular Embryology: Methods and Protocols (eds. P.T. Sharpe and I.J. Mason), vol. 97, 1999.
Holland, P. W. , Wholemount in situ hybridization to amphioxus embryos., Methods Mol Biol, vol. 97, pp. 641-4, 1999.
1998
Patton, S. J. , Luke, G. N. , and Holland, P. W. , Complex history of a chromosomal paralogy region: insights from amphioxus aromatic amino acid hydroxylase genes and insulin-related genes., Mol Biol Evol, vol. 15, no. 11, pp. 1373-80, 1998.
Sharman, A. C. and Holland, P. W. , Estimation of Hox gene cluster number in lampreys., Int J Dev Biol, vol. 42, no. 4, pp. 617-20, 1998.
Williams, N. A. and Holland, P. W. , Gene and domain duplication in the chordate Otx gene family: insights from amphioxus Otx., Mol Biol Evol, vol. 15, no. 5, pp. 600-7, 1998.
Holland, P. W. H. , Major transitions in animal evolution: a developmental genetic perspective., Ameican Zoologist, vol. 38, 1998.
Williams, N. A. and Holland, P. W. , Molecular evolution of the brain of chordates., Brain Behav Evol, vol. 52, no. 4-5, pp. 177-85, 1998.
Brooke, N. M. , Garcia-Fernàndez, J. , and Holland, P. W. , The ParaHox gene cluster is an evolutionary sister of the Hox gene cluster., Nature, vol. 392, no. 6679, pp. 920-2, 1998.
Wada, H. , Saiga, H. , Satoh, N. , and Holland, P. W. , Tripartite organization of the ancestral chordate brain and the antiquity of placodes: insights from ascidian Pax-2/5/8, Hox and Otx genes., Development, vol. 125, no. 6, pp. 1113-22, 1998.
1997
Sharman, A. C. , Hay-Schmidt, A. , and Holland, P. W. , Cloning and analysis of an HMG gene from the lamprey Lampetra fluviatilis: gene duplication in vertebrate evolution., Gene, vol. 184, no. 1, pp. 99-105, 1997.
Telford, M. J. and Holland, P. W. , Evolution of 28S ribosomal DNA in chaetognaths: duplicate genes and molecular phylogeny., J Mol Evol, vol. 44, no. 2, pp. 135-44, 1997.
Holland, P. W. H. , Patton, S. J. , Brooke, N. M. , and Garcia-Fernàndez, J. , Genetic patterning of ectoderm and endoderm in amphioxus: from homeobox genes to hormones. In: Advances in Comparative Endocrinology (ed. S. Kawashima and S. Kikuyama), Advances in Comparative Endocrinology (ed. S. Kawashima and S. Kikuyama), 1997.
Abouheif, E. , Akam, M. , Dickinson, W. J. , Holland, P. W. , Meyer, A. , Patel, N. H. , Raff, R. A. , Roth, V. L. , and Wray, G. A. , Homology and developmental genes., Trends Genet, vol. 13, no. 11, pp. 432-3, 1997.
Wada, H. , Holland, P. W. , Sato, S. , Yamamoto, H. , and Satoh, N. , Neural tube is partially dorsalized by overexpression of HrPax-37: the ascidian homologue of Pax-3 and Pax-7., Dev Biol, vol. 187, no. 2, pp. 240-52, 1997.
Holland, P. W. , Vertebrate evolution: something fishy about Hox genes., Curr Biol, vol. 7, no. 9, pp. R570-2, 1997.
1996
Garcia-Fernàndez, J. and Holland, P. W. , Amphioxus Hox genes: insights into evolution and development., Int J Dev Biol, vol. Suppl 1, p. 71S-72S, 1996.
Cooper, G. , Holland, P. W. H. , and Millter, P. T. , Captive breeding of Ischnura elegans (Vander Linden): observations on longevity, copulation and oviposition (Zygoptera: Coenagrionidae), Odontologica, vol. 25, 1996.
Sharman, A. C. and Holland, P. W. H. , Conservation, duplication and divergence of developmental genes during chordate evolution., Netherlands Journal of Zoology, vol. 46, 1996.
Holland, P. W. and Garcia-Fernàndez, J. , Hox genes and chordate evolution., Dev Biol, vol. 173, no. 2, pp. 382-95, 1996.
Garcia-Fernàndez, J. and Holland, P. W. H. , Hox genes and the origin of vertebrates., Cell Biology International, vol. 20, 1996.
Corte-Real, H. B. S. M. and Holland, P. W. H. , Intron-targeted PCR. In: PCR: Essential Techniques (ed. J.F. Burke)., in Intron-targeted PCR. In: PCR: Essential Techniques (ed. J.F. Burke)., Chichester: John Wiley & Sons, 1996, pp. 53-57.
Holland, P. W. H. , Molecular biology of lancelets: insights into development and evolution, Israel Journal of Zoology, vol. 42, 1996.
Cooper, G. , Miller, P. L. , and Holland, P. W. , Molecular genetic analysis of sperm competition in the damselfly Ischnura elegans (Vander Linden)., Proc Biol Sci, vol. 263, no. 1375, pp. 1343-9, 1996.
Williams, N. A. and Holland, P. W. H. , Old head on young shoulders, Nature, vol. 383, 1996.
Wada, H. , Holland, P. W. , and Satoh, N. , Origin of patterning in neural tubes., Nature, vol. 384, no. 6605, p. 123, 1996.
Holland, L. Z. , Holland, P. W. H. , and Holland, N. D. , Revealing homologies between body parts of distantly related animals by in situ hybridization to developmental genes: amphioxus vs vertebrates, Chapter 14 of Molecular Zoology: Advances, Strategies and Protocols, 1996.
Holland, P. W. , Unity or diversity?, Trends Genet, vol. 12, no. 8, p. 324, 1996.
1995
Holland, P. W. , Koschorz, B. , Holland, L. Z. , and Herrmann, B. G. , Conservation of Brachyury (T) genes in amphioxus and vertebrates: developmental and evolutionary implications., Development, vol. 121, no. 12, pp. 4283-91, 1995.
Holland, P. W. and Graham, A. , Evolution of regional identity in the vertebrate nervous system., Perspect Dev Neurobiol, vol. 3, no. 1, pp. 17-27, 1995.
Holland, P. W. H. , Head development and evolution, Gray's Anatomy (38th Edition), 1995.
Dixon, D. R. , Sole-Cava, A. M. , Pascoe, P. L. , and Holland, P. W. H. , Periostracal adventitious hairs on spat of the mussel Mytilus edulis., Journal of Marine Biological Association, vol. 75, 1995.
1994
Garcia-Fernàndez, J. and Holland, P. W. , Archetypal organization of the amphioxus Hox gene cluster., Nature, vol. 370, no. 6490, pp. 563-6, 1994.
Akam, M. E. , Holland, P. W. H. , Ingham, P. W. , and Wray, G. E. , The Evolution of Developmental Mechanisms. Cambridge: Company of Biologists, 1994, p. 241 p.
Holland, P. W. , Garcia-Fernàndez, J. , Williams, N. A. , and Sidow, A. , Gene duplications and the origins of vertebrate development., Dev Suppl, pp. 125-33, 1994.
Côrte-Real, H. B. S. M. , Holland, P. W. H. , and Dixon, D. R. , Inheritance of a nuclear DNA polymorphism assayed in single bivalve larvae., Marine Biology, vol. 120, 1994.
Côrte-Real, H. B. S. M. , Dixon, D. R. , and Holland, P. W. H. , Intron-targeted PCR: a new approach to survey neutral DNA polymorphism in bivalve populations, Marine Biology, vol. 120, no. 407-413, 1994.
Holland, P. W. H. , Garcia-Fernàndez, J. , Holland, L. Z. , Williams, N. A. , and Holland, N. D. , molecular control of spatial patterning in amphioxus., Journal of Marine Biological Association, vol. 74, 1994.
1993
Holland, P. W. H. , Cloning genes using PCR. In: Essential Developmental Biology: A Practical Approach Ed.: Stern, C.D. and Holland, P.W.H. IRl Press at Oxford University Press, 1993.
Essential Developmental Biology: A Practical Approach. Oxford: IRL Press at Oxford University Press, 1993, p. 368.
Holland, P. W. H. , Homeobox genes and homeodomain proteins. In: The Encyclopedia of Molecular Biology. Blackwell Scientific Publications, 1993.
Williams, N. A. , Dixon, D. R. , Southward, E. C. , and Holland, P. W. H. , Molecular evolution and diversification of the vestimentiferan tube worms, Journal of Marine Biological Association, vol. 73, 1993.
Telford, M. J. and Holland, P. W. , The phylogenetic affinities of the chaetognaths: a molecular analysis., Mol Biol Evol, vol. 10, no. 3, pp. 660-76, 1993.
Slack, J. M. , Holland, P. W. , and Graham, C. F. , The zootype and the phylotypic stage., Nature, vol. 361, no. 6412, pp. 490-2, 1993.
1992
Holland, P. W. , Holland, L. Z. , Williams, N. A. , and Holland, N. D. , An amphioxus homeobox gene: sequence conservation, spatial expression during development and insights into vertebrate evolution., Development, vol. 116, no. 3, pp. 653-61, 1992.
Holland, P. , Ingham, P. , and Krauss, S. , Development and evolution. Mice and flies head to head., Nature, vol. 358, no. 6388, pp. 627-8, 1992.
Kent, N. A. , Hill, M. R. , Keen, J. N. , Holland, P. W. , and Hart, B. J. , Molecular characterisation of group I allergen Eur m I from house dust mite Euroglyphus maynei., Int Arch Allergy Immunol, vol. 99, no. 1, pp. 150-2, 1992.
1991
Hill, M. R. , Kent, N. A. , Holland, P. W. H. , and Hart, B. J. , Characterization of Euroglyphus maynei allergens. In: Mite Allergens and Asthma, Mite Allergens and Asthma, 1991.
Holland, P. W. , Cloning and evolutionary analysis of msh-like homeobox genes from mouse, zebrafish and ascidian., Gene, vol. 98, no. 2, pp. 253-7, 1991.
Lanfear, J. , Jowett, T. , and Holland, P. W. , Cloning of fish zinc-finger genes related to Krox-20 and Krox-24., Biochem Biophys Res Commun, vol. 179, no. 3, pp. 1220-4, 1991.
Holland, P. W. , Williams, N. A. , and Lanfear, J. , Cloning of segment polarity gene homologues from the unsegmented brachiopod Terebratulina retusa (Linnaeus)., FEBS Lett, vol. 291, no. 2, pp. 211-3, 1991.
Willmer, P. G. and Holland, P. W. H. , Modern approaches to metazoan relationships. Journal of Zoology, Journal of Zoology, vol. 224, no. 4, 1991.
Holland, P. W. , Hacker, A. M. , and Williams, N. A. , A molecular analysis of the phylogenetic affinities of Saccoglossus cambrensis Brambell & Cole (Hemichordata)., Philos Trans R Soc Lond B Biol Sci, vol. 332, no. 1264, pp. 185-9, 1991.
Lanfear, J. and Holland, P. W. , The molecular evolution of ZFY-related genes in birds and mammals., J Mol Evol, vol. 32, no. 4, pp. 310-5, 1991.
1990
Holland, P. W. H. and Williams, N. A. , Conservation of engrailed-like homeobox sequences during vertebrate evolution., FEBS Lett, vol. 277, no. 1-2, pp. 250-2, 1990.
Holland, P. W. H. , Homeobox genes and segmentation: co-option, co-evolution, and convergence, Seminars in Developmental Biology, vol. 1, 1990.
Griffiths, R. and Holland, P. W. , A novel avian W chromosome DNA repeat sequence in the lesser black-backed gull (Larus fuscus)., Chromosoma, vol. 99, no. 4, pp. 243-50, 1990.
Hogan, B. L. M. , Holland, P. W. H. , and Engel, J. , Structure and expression of SPARC (osteonectin, BM-40): a secreted Ca++-binding glycoprotein associated with extracellular matrix production. In: Morphoregulatory Molecules. Eds. Edelman, G.M., Cunnningham, B.A. and Thiery, J.-P., Neurosciences Foundation., 1990.
1989
Holland, P. W. , Pursuing the functions of vertebrate homeobox genes: progress and prospects., Trends Neurosci, vol. 12, no. 6, pp. 206-9, 1989.
1988
Holland, P. W. H. and Hogan, B. L. M. , Expression of homeobox genes during mouse development: a review., Genes and Development, vol. 2, 1988.
Hogan, B. L. , Holland, P. W. , and Lumsden, A. , Expression of the homeobox gene, Hox 2.1, during mouse embryogenesis., Cell Differ Dev, vol. 25 Suppl, pp. 39-44, 1988.
Graham, A. , Holland, P. W. , Lumsden, A. , Krumlauf, R. , and Hogan, B. L. , Expression of the homeobox genes Hox 2.1 and 2.6 during mouse development., Curr Top Microbiol Immunol, vol. 137, pp. 87-93, 1988.
Holland, P. W. , Homeobox genes and the vertebrate head., Development, vol. 103 Suppl, pp. 17-24, 1988.
Holland, P. W. and Hogan, B. L. , Spatially restricted patterns of expression of the homeobox-containing gene Hox 2.1. during mouse embryogenesis., Development, vol. 102, no. 1, pp. 159-74, 1988.
1987
Krumlauf, R. , Holland, P. W. , McVey, J. H. , and Hogan, B. L. , Developmental and spatial patterns of expression of the mouse homeobox gene, Hox 2.1., Development, vol. 99, no. 4, pp. 603-17, 1987.
Holland, P. W. , Harper, S. J. , McVey, J. H. , and Hogan, B. L. , In vivo expression of mRNA for the Ca++-binding protein SPARC (osteonectin) revealed by in situ hybridization., J Cell Biol, vol. 105, no. 1, pp. 473-82, 1987.
1986
Holland, P. W. H. , Localization of gene transcripts in embryo sections: in situ hybridization with RNA probes. In: Manipulating the Mouse Embryo - a laboratory manual. Eds. Hogan, B.L.M., Constantini, F. and Lacy, E., in Manipulating the Mouse Embryo - a laboratory manual., New York, USA: Cold Spring Harbor Laboratory, 1986, pp. 228-242.
Holland, P. W. H. and Hogan, B. L. M. , Phylogenetic distribution of Antennapedia-like homeoboxes., nature, vol. 321, 1986.
1985
Hogan, B. L. M. , Holland, P. W. H. , and Schofield, P. N. , How is the mouse segmented?, Trends in Genetics, vol. 1, 1985.