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Items: 1 to 50 of 154

1.

Mouse Obox and Crxos modulate preimplantation transcriptional profiles revealing similarity between paralogous mouse and human homeobox genes.

Royall AH, Maeso I, Dunwell TL, Holland PWH.

Evodevo. 2018 Jan 27;9:2. doi: 10.1186/s13227-018-0091-4. eCollection 2018.

2.

Novel and divergent genes in the evolution of placental mammals.

Dunwell TL, Paps J, Holland PWH.

Proc Biol Sci. 2017 Oct 11;284(1864). pii: 20171357. doi: 10.1098/rspb.2017.1357.

PMID:
28978728
3.

Ancestral whole-genome duplication in the marine chelicerate horseshoe crabs.

Kenny NJ, Chan KW, Nong W, Qu Z, Maeso I, Yip HY, Chan TF, Kwan HS, Holland PWH, Chu KH, Hui JHL.

Heredity (Edinb). 2017 Nov;119(5):388. doi: 10.1038/hdy.2017.38. Epub 2017 Aug 9.

4.

Genome sequence of a diabetes-prone rodent reveals a mutation hotspot around the ParaHox gene cluster.

Hargreaves AD, Zhou L, Christensen J, Marlétaz F, Liu S, Li F, Jansen PG, Spiga E, Hansen MT, Pedersen SVH, Biswas S, Serikawa K, Fox BA, Taylor WR, Mulley JF, Zhang G, Heller RS, Holland PWH.

Proc Natl Acad Sci U S A. 2017 Jul 18;114(29):7677-7682. doi: 10.1073/pnas.1702930114. Epub 2017 Jul 3.

5.

Lineage-specific rediploidization is a mechanism to explain time-lags between genome duplication and evolutionary diversification.

Robertson FM, Gundappa MK, Grammes F, Hvidsten TR, Redmond AK, Lien S, Martin SAM, Holland PWH, Sandve SR, Macqueen DJ.

Genome Biol. 2017 Jun 14;18(1):111. doi: 10.1186/s13059-017-1241-z.

6.

A sister of NANOG regulates genes expressed in pre-implantation human development.

Dunwell TL, Holland PWH.

Open Biol. 2017 Apr;7(4). pii: 170027. doi: 10.1098/rsob.170027.

7.

Diversification of Hox Gene Clusters in Osteoglossomorph Fish in Comparison to Other Teleosts and the Spotted Gar Outgroup.

Martin KJ, Holland PWH.

J Exp Zool B Mol Dev Evol. 2017 Nov;328(7):638-644. doi: 10.1002/jez.b.22726. Epub 2017 Feb 23.

PMID:
28229564
8.

New genes from old: asymmetric divergence of gene duplicates and the evolution of development.

Holland PW, Marlétaz F, Maeso I, Dunwell TL, Paps J.

Philos Trans R Soc Lond B Biol Sci. 2017 Feb 5;372(1713). pii: 20150480. Review.

9.
10.

Evolutionary origin and functional divergence of totipotent cell homeobox genes in eutherian mammals.

Maeso I, Dunwell TL, Wyatt CD, Marlétaz F, Vető B, Bernal JA, Quah S, Irimia M, Holland PW.

BMC Biol. 2016 Jun 13;14:45. doi: 10.1186/s12915-016-0267-0.

11.

Corrigendum: The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons.

Braasch I, Gehrke AR, Smith JJ, Kawasaki K, Manousaki T, Pasquier J, Amores A, Desvignes T, Batzel P, Catchen J, Berlin AM, Campbell MS, Barrell D, Martin KJ, Mulley JF, Ravi V, Lee AP, Nakamura T, Chalopin D, Fan S, Wcisel D, Cañestro C, Sydes J, Beaudry FE, Sun Y, Hertel J, Beam MJ, Fasold M, Ishiyama M, Johnson J, Kehr S, Lara M, Letaw JH, Litman GW, Litman RT, Mikami M, Ota T, Saha NR, Williams L, Stadler PF, Wang H, Taylor JS, Fontenot Q, Ferrara A, Searle SM, Aken B, Yandell M, Schneider I, Yoder JA, Volff JN, Meyer A, Amemiya CT, Venkatesh B, Holland PW, Guiguen Y, Bobe J, Shubin NH, Di Palma F, Alfo Ldi J, Lindblad-Toh K, Postlethwait JH.

Nat Genet. 2016 May 27;48(6):700. doi: 10.1038/ng0616-700c. No abstract available.

PMID:
27230688
12.

The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons.

Braasch I, Gehrke AR, Smith JJ, Kawasaki K, Manousaki T, Pasquier J, Amores A, Desvignes T, Batzel P, Catchen J, Berlin AM, Campbell MS, Barrell D, Martin KJ, Mulley JF, Ravi V, Lee AP, Nakamura T, Chalopin D, Fan S, Wcisel D, Cañestro C, Sydes J, Beaudry FE, Sun Y, Hertel J, Beam MJ, Fasold M, Ishiyama M, Johnson J, Kehr S, Lara M, Letaw JH, Litman GW, Litman RT, Mikami M, Ota T, Saha NR, Williams L, Stadler PF, Wang H, Taylor JS, Fontenot Q, Ferrara A, Searle SM, Aken B, Yandell M, Schneider I, Yoder JA, Volff JN, Meyer A, Amemiya CT, Venkatesh B, Holland PW, Guiguen Y, Bobe J, Shubin NH, Di Palma F, Alföldi J, Lindblad-Toh K, Postlethwait JH.

Nat Genet. 2016 Apr;48(4):427-37. doi: 10.1038/ng.3526. Epub 2016 Mar 7.

13.

Conservation, Duplication, and Divergence of Five Opsin Genes in Insect Evolution.

Feuda R, Marlétaz F, Bentley MA, Holland PW.

Genome Biol Evol. 2016 Feb 9;8(3):579-87. doi: 10.1093/gbe/evw015.

14.

A single three-dimensional chromatin compartment in amphioxus indicates a stepwise evolution of vertebrate Hox bimodal regulation.

Acemel RD, Tena JJ, Irastorza-Azcarate I, Marlétaz F, Gómez-Marín C, de la Calle-Mustienes E, Bertrand S, Diaz SG, Aldea D, Aury JM, Mangenot S, Holland PW, Devos DP, Maeso I, Escrivá H, Gómez-Skarmeta JL.

Nat Genet. 2016 Mar;48(3):336-41. doi: 10.1038/ng.3497. Epub 2016 Feb 1.

PMID:
26829752
15.

Did homeobox gene duplications contribute to the Cambrian explosion?

Holland PW.

Zoological Lett. 2015 Jan 13;1:1. doi: 10.1186/s40851-014-0004-x. eCollection 2015. Review.

16.

A Diversity of Conserved and Novel Ovarian MicroRNAs in the Speckled Wood (Pararge aegeria).

Quah S, Breuker CJ, Holland PW.

PLoS One. 2015 Nov 10;10(11):e0142243. doi: 10.1371/journal.pone.0142243. eCollection 2015.

17.

The Hox cluster microRNA miR-615: a case study of intronic microRNA evolution.

Quah S, Holland PW.

Evodevo. 2015 Oct 7;6:31. doi: 10.1186/s13227-015-0027-1. eCollection 2015.

18.

Ancestral whole-genome duplication in the marine chelicerate horseshoe crabs.

Kenny NJ, Chan KW, Nong W, Qu Z, Maeso I, Yip HY, Chan TF, Kwan HS, Holland PW, Chu KH, Hui JH.

Heredity (Edinb). 2016 Feb;116(2):190-9. doi: 10.1038/hdy.2015.89. Epub 2015 Sep 30. Erratum in: Heredity (Edinb). 2017 Aug 09;:.

19.

Cdx ParaHox genes acquired distinct developmental roles after gene duplication in vertebrate evolution.

Marlétaz F, Maeso I, Faas L, Isaacs HV, Holland PW.

BMC Biol. 2015 Aug 1;13:56. doi: 10.1186/s12915-015-0165-x.

20.

Scenarios for the making of vertebrates.

Holland ND, Holland LZ, Holland PW.

Nature. 2015 Apr 23;520(7548):450-5. doi: 10.1038/nature14433. Review.

PMID:
25903626
21.

Reinforcing the egg-timer: recruitment of novel lophotrochozoa homeobox genes to early and late development in the pacific oyster.

Paps J, Xu F, Zhang G, Holland PW.

Genome Biol Evol. 2015 Jan 27;7(3):677-88. doi: 10.1093/gbe/evv018.

22.

A Burst of miRNA Innovation in the Early Evolution of Butterflies and Moths.

Quah S, Hui JH, Holland PW.

Mol Biol Evol. 2015 May;32(5):1161-74. doi: 10.1093/molbev/msv004. Epub 2015 Jan 8.

23.

Ancient expansion of the hox cluster in lepidoptera generated four homeobox genes implicated in extra-embryonic tissue formation.

Ferguson L, Marlétaz F, Carter JM, Taylor WR, Gibbs M, Breuker CJ, Holland PW.

PLoS Genet. 2014 Oct 23;10(10):e1004698. doi: 10.1371/journal.pgen.1004698. eCollection 2014 Oct.

24.

Strepsiptera, phylogenomics and the long branch attraction problem.

Boussau B, Walton Z, Delgado JA, Collantes F, Beani L, Stewart IJ, Cameron SA, Whitfield JB, Johnston JS, Holland PW, Bachtrog D, Kathirithamby J, Huelsenbeck JP.

PLoS One. 2014 Oct 1;9(10):e107709. doi: 10.1371/journal.pone.0107709. eCollection 2014.

25.

Discovery and classification of homeobox genes in animal genomes.

Marlétaz F, Paps J, Maeso I, Holland PW.

Methods Mol Biol. 2014;1196:3-18. doi: 10.1007/978-1-4939-1242-1_1.

PMID:
25151154
26.

Enigmatic orthology relationships between Hox clusters of the African butterfly fish and other teleosts following ancient whole-genome duplication.

Martin KJ, Holland PW.

Mol Biol Evol. 2014 Oct;31(10):2592-611. doi: 10.1093/molbev/msu202. Epub 2014 Jun 27.

27.

4273π: bioinformatics education on low cost ARM hardware.

Barker D, Ferrier DE, Holland PW, Mitchell JB, Plaisier H, Ritchie MG, Smart SD.

BMC Bioinformatics. 2013 Aug 12;14:243. doi: 10.1186/1471-2105-14-243.

28.

Evolution of homeobox genes.

Holland PW.

Wiley Interdiscip Rev Dev Biol. 2013 Jan-Feb;2(1):31-45. doi: 10.1002/wdev.78. Epub 2012 Sep 10. Review.

PMID:
23799629
29.

Genomic organisation of the seven ParaHox genes of coelacanths.

Mulley JF, Holland PW.

J Exp Zool B Mol Dev Evol. 2014 Sep;322(6):352-8. doi: 10.1002/jez.b.22513. Epub 2013 Jun 17.

30.

The genomes of four tapeworm species reveal adaptations to parasitism.

Tsai IJ, Zarowiecki M, Holroyd N, Garciarrubio A, Sánchez-Flores A, Brooks KL, Tracey A, Bobes RJ, Fragoso G, Sciutto E, Aslett M, Beasley H, Bennett HM, Cai X, Camicia F, Clark R, Cucher M, De Silva N, Day TA, Deplazes P, Estrada K, Fernández C, Holland PWH, Hou J, Hu S, Huckvale T, Hung SS, Kamenetzky L, Keane JA, 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 JD, Zamanian M, Zheng Y; Taenia solium Genome Consortium, Cai J, Soberón X, Olson PD, Laclette JP, Brehm K, Berriman M.

Nature. 2013 Apr 4;496(7443):57-63. doi: 10.1038/nature12031. Epub 2013 Mar 13.

31.

How are comparative genomics and the study of microRNAs changing our views on arthropod endocrinology and adaptations to the environment?

Kenny NJ, Quah S, Holland PW, Tobe SS, Hui JH.

Gen Comp Endocrinol. 2013 Jul 1;188:16-22. doi: 10.1016/j.ygcen.2013.02.013. Epub 2013 Mar 7. Review.

PMID:
23480873
32.

A family of diatom-like silicon transporters in the siliceous loricate choanoflagellates.

Marron AO, Alston MJ, Heavens D, Akam M, Caccamo M, Holland PW, Walker G.

Proc Biol Sci. 2013 Feb 13;280(1756):20122543. doi: 10.1098/rspb.2012.2543. Print 2013 Apr 7.

33.

HomeoDB2: functional expansion of a comparative homeobox gene database for evolutionary developmental biology.

Zhong YF, Holland PW.

Evol Dev. 2011 Nov-Dec;13(6):567-8. doi: 10.1111/j.1525-142X.2011.00513.x.

34.

The oyster genome reveals stress adaptation and complexity of shell formation.

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 PW, 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 PM, 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 CE, Wang H, Li N, Qian L, Zhang G, Li Y, Yang H, Liu X, Wang J, Yin Y, Wang J.

Nature. 2012 Oct 4;490(7418):49-54. doi: 10.1038/nature11413. Epub 2012 Sep 19.

PMID:
22992520
35.

A genome-wide view of transcription factor gene diversity in chordate evolution: less gene loss in amphioxus?

Paps J, Holland PW, Shimeld SM.

Brief Funct Genomics. 2012 Mar;11(2):177-86. doi: 10.1093/bfgp/els012. Review.

PMID:
22441554
36.

Evolution of the Alx homeobox gene family: parallel retention and independent loss of the vertebrate Alx3 gene.

McGonnell IM, Graham A, Richardson J, Fish JL, Depew MJ, Dee CT, Holland PW, Takahashi T.

Evol Dev. 2011 Jul-Aug;13(4):343-51. doi: 10.1111/j.1525-142X.2011.00489.x.

37.

Extensive chordate and annelid macrosynteny reveals ancestral homeobox gene organization.

Hui JH, McDougall C, Monteiro AS, Holland PW, Arendt D, Balavoine G, Ferrier DE.

Mol Biol Evol. 2012 Jan;29(1):157-65. doi: 10.1093/molbev/msr175. Epub 2011 Jul 4.

PMID:
21727239
38.

The dynamics of vertebrate homeobox gene evolution: gain and loss of genes in mouse and human lineages.

Zhong YF, Holland PW.

BMC Evol Biol. 2011 Jun 16;11:169. doi: 10.1186/1471-2148-11-169. Erratum in: BMC Evol Biol. 2011;11:204.

39.

The hypoxia-inducible transcription factor pathway regulates oxygen sensing in the simplest animal, Trichoplax adhaerens.

Loenarz C, Coleman ML, Boleininger A, Schierwater B, Holland PW, Ratcliffe PJ, Schofield CJ.

EMBO Rep. 2011 Jan;12(1):63-70. doi: 10.1038/embor.2010.170. Epub 2010 Nov 26.

40.

The origin and evolution of ARGFX homeobox loci in mammalian radiation.

Li G, Holland PW.

BMC Evol Biol. 2010 Jun 17;10:182. doi: 10.1186/1471-2148-10-182.

41.

Ancient homeobox gene loss and the evolution of chordate brain and pharynx development: deductions from amphioxus gene expression.

Butts T, Holland PW, Ferrier DE.

Proc Biol Sci. 2010 Nov 22;277(1699):3381-9. doi: 10.1098/rspb.2010.0647. Epub 2010 Jun 16.

42.

Parallel retention of Pdx2 genes in cartilaginous fish and coelacanths.

Mulley JF, Holland PW.

Mol Biol Evol. 2010 Oct;27(10):2386-91. doi: 10.1093/molbev/msq121. Epub 2010 May 12.

43.

A comparison of statistical selection strategies for univariate and bivariate log-linear models.

Moses T, Holland PW.

Br J Math Stat Psychol. 2010 Nov;63(Pt 3):557-74. doi: 10.1348/000711009X478580. Epub 2009 Dec 22.

PMID:
20030964
44.

Comparative genomics of chondrichthyan Hoxa clusters.

Mulley JF, Zhong YF, Holland PW.

BMC Evol Biol. 2009 Sep 2;9:218. doi: 10.1186/1471-2148-9-218.

45.

Degenerate evolution of the hedgehog gene in a hemichordate lineage.

Sato A, White-Cooper H, Doggett K, Holland PW.

Proc Natl Acad Sci U S A. 2009 May 5;106(18):7491-4. doi: 10.1073/pnas.0810430106. Epub 2009 Apr 20.

46.

Wholemount in situ hybridization to amphioxus embryos.

Holland PW.

Methods Mol Biol. 2008;461:703-6. doi: 10.1007/978-1-60327-483-8_48. No abstract available.

PMID:
19030833
47.

Protochordates.

Holland PW, Wada H.

Methods Mol Biol. 2008;461:563-6. doi: 10.1007/978-1-60327-483-8_38. No abstract available.

PMID:
19030823
48.

Do cnidarians have a ParaHox cluster? Analysis of synteny around a Nematostella homeobox gene cluster.

Hui JH, Holland PW, Ferrier DE.

Evol Dev. 2008 Nov-Dec;10(6):725-30. doi: 10.1111/j.1525-142X.2008.00286.x.

PMID:
19021743
49.

HomeoDB: a database of homeobox gene diversity.

Zhong YF, Butts T, Holland PW.

Evol Dev. 2008 Sep-Oct;10(5):516-8. doi: 10.1111/j.1525-142X.2008.00266.x.

PMID:
18803769
50.

Developmental biology of pterobranch hemichordates: history and perspectives.

Sato A, Bishop JD, Holland PW.

Genesis. 2008 Nov;46(11):587-91. doi: 10.1002/dvg.20395.

PMID:
18798243

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