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Items: 1 to 50 of 123

1.

Publisher Correction: The sea lamprey germline genome provides insights into programmed genome rearrangement and vertebrate evolution.

Smith JJ, Timoshevskaya N, Ye C, Holt C, Keinath MC, Parker HJ, Cook ME, Hess JE, Narum SR, Lamanna F, Kaessmann H, Timoshevskiy VA, Waterbury CKM, Saraceno C, Wiedemann LM, Robb SMC, Baker C, Eichler EE, Hockman D, Sauka-Spengler T, Yandell M, Krumlauf R, Elgar G, Amemiya CT.

Nat Genet. 2018 Nov;50(11):1617. doi: 10.1038/s41588-018-0199-4.

PMID:
30224652
2.

Pillars Article: Somatic Diversification of Variable Lymphocyte Receptors in the Agnathan Sea Lamprey. Nature. 2004. 430: 174-180.

Pancer Z, Amemiya CT, Ehrhardt GRA, Ceitlin J, Gartland GL, Cooper MD.

J Immunol. 2018 Sep 1;201(5):1336-1342. No abstract available.

PMID:
30127063
3.

Publisher Correction: The sea lamprey germline genome provides insights into programmed genome rearrangement and vertebrate evolution.

Smith JJ, Timoshevskaya N, Ye C, Holt C, Keinath MC, Parker HJ, Cook ME, Hess JE, Narum SR, Lamanna F, Kaessmann H, Timoshevskiy VA, Waterbury CKM, Saraceno C, Wiedemann LM, Robb SMC, Baker C, Eichler EE, Hockman D, Sauka-Spengler T, Yandell M, Krumlauf R, Elgar G, Amemiya CT.

Nat Genet. 2018 May;50(5):768. doi: 10.1038/s41588-018-0075-2.

PMID:
29674745
4.

The sea lamprey germline genome provides insights into programmed genome rearrangement and vertebrate evolution.

Smith JJ, Timoshevskaya N, Ye C, Holt C, Keinath MC, Parker HJ, Cook ME, Hess JE, Narum SR, Lamanna F, Kaessmann H, Timoshevskiy VA, Waterbury CKM, Saraceno C, Wiedemann LM, Robb SMC, Baker C, Eichler EE, Hockman D, Sauka-Spengler T, Yandell M, Krumlauf R, Elgar G, Amemiya CT.

Nat Genet. 2018 Feb;50(2):270-277. doi: 10.1038/s41588-017-0036-1. Epub 2018 Jan 22. Erratum in: Nat Genet. 2018 Apr 19;:. Nat Genet. 2018 Nov;50(11):1617.

5.

On chemistry of γ-chitin.

Kaya M, Mujtaba M, Ehrlich H, Salaberria AM, Baran T, Amemiya CT, Galli R, Akyuz L, Sargin I, Labidi J.

Carbohydr Polym. 2017 Nov 15;176:177-186. doi: 10.1016/j.carbpol.2017.08.076. Epub 2017 Aug 23.

PMID:
28927596
6.

Biochemical Regulatory Features of Activation-Induced Cytidine Deaminase Remain Conserved from Lampreys to Humans.

Quinlan EM, King JJ, Amemiya CT, Hsu E, Larijani M.

Mol Cell Biol. 2017 Sep 26;37(20). pii: e00077-17. doi: 10.1128/MCB.00077-17. Print 2017 Oct 15.

7.

Molecular cytogenetic differentiation of paralogs of Hox paralogs in duplicated and re-diploidized genome of the North American paddlefish (Polyodon spathula).

Symonová R, Havelka M, Amemiya CT, Howell WM, Kořínková T, Flajšhans M, Gela D, Ráb P.

BMC Genet. 2017 Mar 2;18(1):19. doi: 10.1186/s12863-017-0484-8.

8.

Establishing and maintaining primary cell cultures derived from the ctenophore Mnemiopsis leidyi.

Vandepas LE, Warren KJ, Amemiya CT, Browne WE.

J Exp Biol. 2017 Apr 1;220(Pt 7):1197-1201. doi: 10.1242/jeb.152371. Epub 2017 Jan 30.

9.

Discovery of large genomic inversions using long range information.

Eslami Rasekh M, Chiatante G, Miroballo M, Tang J, Ventura M, Amemiya CT, Eichler EE, Antonacci F, Alkan C.

BMC Genomics. 2017 Jan 10;18(1):65. doi: 10.1186/s12864-016-3444-1.

10.

Morphological And Molecular Analyses of an Anatomical Novelty: The Pelvic Fin Filaments of the South American Lungfish.

Lima SQ, Costa CM, Amemiya CT, Schneider I.

J Exp Zool B Mol Dev Evol. 2017 Jan;328(1-2):97-105. doi: 10.1002/jez.b.22711. Epub 2016 Nov 9.

PMID:
27862964
11.

Tetrapod limb and sarcopterygian fin regeneration share a core genetic programme.

Nogueira AF, Costa CM, Lorena J, Moreira RN, Frota-Lima GN, Furtado C, Robinson M, Amemiya CT, Darnet S, Schneider I.

Nat Commun. 2016 Nov 2;7:13364. doi: 10.1038/ncomms13364.

12.

The Presence of a Functionally Tripartite Through-Gut in Ctenophora Has Implications for Metazoan Character Trait Evolution.

Presnell JS, Vandepas LE, Warren KJ, Swalla BJ, Amemiya CT, Browne WE.

Curr Biol. 2016 Oct 24;26(20):2814-2820. doi: 10.1016/j.cub.2016.08.019. Epub 2016 Aug 25.

13.

Unusual Diversity of Myoglobin Genes in the Lungfish.

Koch J, Lüdemann J, Spies R, Last M, Amemiya CT, Burmester T.

Mol Biol Evol. 2016 Dec;33(12):3033-3041. Epub 2016 Aug 10.

PMID:
27512111
14.

Emergence of a Homo sapiens-specific gene family and chromosome 16p11.2 CNV susceptibility.

Nuttle X, Giannuzzi G, Duyzend MH, Schraiber JG, Narvaiza I, Sudmant PH, Penn O, Chiatante G, Malig M, Huddleston J, Benner C, Camponeschi F, Ciofi-Baffoni S, Stessman HA, Marchetto MC, Denman L, Harshman L, Baker C, Raja A, Penewit K, Janke N, Tang WJ, Ventura M, Banci L, Antonacci F, Akey JM, Amemiya CT, Gage FH, Reymond A, Eichler EE.

Nature. 2016 Aug 11;536(7615):205-9. Epub 2016 Aug 3.

15.

Proton conductivity in ampullae of Lorenzini jelly.

Josberger EE, Hassanzadeh P, Deng Y, Sohn J, Rego MJ, Amemiya CT, Rolandi M.

Sci Adv. 2016 May 13;2(5):e1600112. doi: 10.1126/sciadv.1600112. eCollection 2016 May.

16.

Characterization of Somatically-Eliminated Genes During Development of the Sea Lamprey (Petromyzon marinus).

Bryant SA, Herdy JR, Amemiya CT, Smith JJ.

Mol Biol Evol. 2016 Sep;33(9):2337-44. doi: 10.1093/molbev/msw104. Epub 2016 Jun 10.

17.

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
18.

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.

19.

African Lungfish Reveal the Evolutionary Origins of Organized Mucosal Lymphoid Tissue in Vertebrates.

Tacchi L, Larragoite ET, Muñoz P, Amemiya CT, Salinas I.

Curr Biol. 2015 Sep 21;25(18):2417-24. doi: 10.1016/j.cub.2015.07.066. Epub 2015 Sep 3.

20.

Chitin is endogenously produced in vertebrates.

Tang WJ, Fernandez J, Sohn JJ, Amemiya CT.

Curr Biol. 2015 Mar 30;25(7):897-900. doi: 10.1016/j.cub.2015.01.058. Epub 2015 Mar 12.

21.

Palindromic GOLGA8 core duplicons promote chromosome 15q13.3 microdeletion and evolutionary instability.

Antonacci F, Dennis MY, Huddleston J, Sudmant PH, Steinberg KM, Rosenfeld JA, Miroballo M, Graves TA, Vives L, Malig M, Denman L, Raja A, Stuart A, Tang J, Munson B, Shaffer LG, Amemiya CT, Wilson RK, Eichler EE.

Nat Genet. 2014 Dec;46(12):1293-302. doi: 10.1038/ng.3120. Epub 2014 Oct 19.

22.

SCPP genes in the coelacanth: tissue mineralization genes shared by sarcopterygians.

Kawasaki K, Amemiya CT.

J Exp Zool B Mol Dev Evol. 2014 Sep;322(6):390-402.

PMID:
25243252
23.

The architecture of a scrambled genome reveals massive levels of genomic rearrangement during development.

Chen X, Bracht JR, Goldman AD, Dolzhenko E, Clay DM, Swart EC, Perlman DH, Doak TG, Stuart A, Amemiya CT, Sebra RP, Landweber LF.

Cell. 2014 Aug 28;158(5):1187-1198. doi: 10.1016/j.cell.2014.07.034.

24.

The coelacanth and its genome.

Amemiya CT, Dorrington R, Meyer A.

J Exp Zool B Mol Dev Evol. 2014 Sep;322(6):317-21. doi: 10.1002/jez.b.22583. Epub 2014 Jul 25. No abstract available.

PMID:
25059403
25.

Genome complexity in the coelacanth is reflected in its adaptive immune system.

Saha NR, Ota T, Litman GW, Hansen J, Parra Z, Hsu E, Buonocore F, Canapa A, Cheng JF, Amemiya CT.

J Exp Zool B Mol Dev Evol. 2014 Sep;322(6):438-63. doi: 10.1002/jez.b.22558. Epub 2014 Jan 24.

26.

Coelacanths.

Robinson M, Amemiya CT.

Curr Biol. 2014 Jan 20;24(2):R62-3. doi: 10.1016/j.cub.2013.10.027. No abstract available.

27.

Atypical RNAs in the coelacanth transcriptome.

Nitsche A, Doose G, Tafer H, Robinson M, Saha NR, Gerdol M, Canapa A, Hoffmann S, Amemiya CT, Stadler PF.

J Exp Zool B Mol Dev Evol. 2014 Sep;322(6):342-51. doi: 10.1002/jez.b.22542. Epub 2013 Oct 30.

PMID:
24174405
28.

Francis (Frank) Hugh Ruddle (1929-2013).

Amemiya CT, Wagner GP.

J Exp Zool B Mol Dev Evol. 2013 Jul;320(5):273-5. doi: 10.1002/jez.b.22509. Epub 2013 May 6. No abstract available.

PMID:
23650107
29.

The African coelacanth genome provides insights into tetrapod evolution.

Amemiya CT, Alföldi J, Lee AP, Fan S, Philippe H, Maccallum I, Braasch I, Manousaki T, Schneider I, Rohner N, Organ C, Chalopin D, Smith JJ, Robinson M, Dorrington RA, Gerdol M, Aken B, Biscotti MA, Barucca M, Baurain D, Berlin AM, Blatch GL, Buonocore F, Burmester T, Campbell MS, Canapa A, Cannon JP, Christoffels A, De Moro G, Edkins AL, Fan L, Fausto AM, Feiner N, Forconi M, Gamieldien J, Gnerre S, Gnirke A, Goldstone JV, Haerty W, Hahn ME, Hesse U, Hoffmann S, Johnson J, Karchner SI, Kuraku S, Lara M, Levin JZ, Litman GW, Mauceli E, Miyake T, Mueller MG, Nelson DR, Nitsche A, Olmo E, Ota T, Pallavicini A, Panji S, Picone B, Ponting CP, Prohaska SJ, Przybylski D, Saha NR, Ravi V, Ribeiro FJ, Sauka-Spengler T, Scapigliati G, Searle SM, Sharpe T, Simakov O, Stadler PF, Stegeman JJ, Sumiyama K, Tabbaa D, Tafer H, Turner-Maier J, van Heusden P, White S, Williams L, Yandell M, Brinkmann H, Volff JN, Tabin CJ, Shubin N, Schartl M, Jaffe DB, Postlethwait JH, Venkatesh B, Di Palma F, Lander ES, Meyer A, Lindblad-Toh K.

Nature. 2013 Apr 18;496(7445):311-6. doi: 10.1038/nature12027.

30.

The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage.

Shaffer HB, Minx P, Warren DE, Shedlock AM, Thomson RC, Valenzuela N, Abramyan J, Amemiya CT, Badenhorst D, Biggar KK, Borchert GM, Botka CW, Bowden RM, Braun EL, Bronikowski AM, Bruneau BG, Buck LT, Capel B, Castoe TA, Czerwinski M, Delehaunty KD, Edwards SV, Fronick CC, Fujita MK, Fulton L, Graves TA, Green RE, Haerty W, Hariharan R, Hernandez O, Hillier LW, Holloway AK, Janes D, Janzen FJ, Kandoth C, Kong L, de Koning AP, Li Y, Literman R, McGaugh SE, Mork L, O'Laughlin M, Paitz RT, Pollock DD, Ponting CP, Radhakrishnan S, Raney BJ, Richman JM, St John J, Schwartz T, Sethuraman A, Spinks PQ, Storey KB, Thane N, Vinar T, Zimmerman LM, Warren WC, Mardis ER, Wilson RK.

Genome Biol. 2013 Mar 28;14(3):R28. doi: 10.1186/gb-2013-14-3-r28.

31.

Sequencing of the sea lamprey (Petromyzon marinus) genome provides insights into vertebrate evolution.

Smith JJ, Kuraku S, Holt C, Sauka-Spengler T, Jiang N, Campbell MS, Yandell MD, Manousaki T, Meyer A, Bloom OE, Morgan JR, Buxbaum JD, Sachidanandam R, Sims C, Garruss AS, Cook M, Krumlauf R, Wiedemann LM, Sower SA, Decatur WA, Hall JA, Amemiya CT, Saha NR, Buckley KM, Rast JP, Das S, Hirano M, McCurley N, Guo P, Rohner N, Tabin CJ, Piccinelli P, Elgar G, Ruffier M, Aken BL, Searle SM, Muffato M, Pignatelli M, Herrero J, Jones M, Brown CT, Chung-Davidson YW, Nanlohy KG, Libants SV, Yeh CY, McCauley DW, Langeland JA, Pancer Z, Fritzsch B, de Jong PJ, Zhu B, Fulton LL, Theising B, Flicek P, Bronner ME, Warren WC, Clifton SW, Wilson RK, Li W.

Nat Genet. 2013 Apr;45(4):415-21, 421e1-2. doi: 10.1038/ng.2568. Epub 2013 Feb 24.

32.

Theria-specific homeodomain and cis-regulatory element evolution of the Dlx3-4 bigene cluster in 12 different mammalian species.

Sumiyama K, Miyake T, Grimwood J, Stuart A, Dickson M, Schmutz J, Ruddle FH, Myers RM, Amemiya CT.

J Exp Zool B Mol Dev Evol. 2012 Dec;318(8):639-50. doi: 10.1002/jez.b.22469. Epub 2012 Sep 5.

33.

An independent genome duplication inferred from Hox paralogs in the American paddlefish--a representative basal ray-finned fish and important comparative reference.

Crow KD, Smith CD, Cheng JF, Wagner GP, Amemiya CT.

Genome Biol Evol. 2012;4(9):937-53. doi: 10.1093/gbe/evs067. Epub 2012 Jul 31.

34.

Genetic consequences of programmed genome rearrangement.

Smith JJ, Baker C, Eichler EE, Amemiya CT.

Curr Biol. 2012 Aug 21;22(16):1524-9. doi: 10.1016/j.cub.2012.06.028. Epub 2012 Jul 19.

35.

Antigen-presenting genes and genomic copy number variations in the Tasmanian devil MHC.

Cheng Y, Stuart A, Morris K, Taylor R, Siddle H, Deakin J, Jones M, Amemiya CT, Belov K.

BMC Genomics. 2012 Mar 12;13:87. doi: 10.1186/1471-2164-13-87.

36.

Genomic restructuring in the Tasmanian devil facial tumour: chromosome painting and gene mapping provide clues to evolution of a transmissible tumour.

Deakin JE, Bender HS, Pearse AM, Rens W, O'Brien PC, Ferguson-Smith MA, Cheng Y, Morris K, Taylor R, Stuart A, Belov K, Amemiya CT, Murchison EP, Papenfuss AT, Graves JA.

PLoS Genet. 2012;8(2):e1002483. doi: 10.1371/journal.pgen.1002483. Epub 2012 Feb 16. Erratum in: PLoS Genet. 2014 Oct;10(10):e1004840.

37.

A living fossil in the genome of a living fossil: Harbinger transposons in the coelacanth genome.

Smith JJ, Sumiyama K, Amemiya CT.

Mol Biol Evol. 2012 Mar;29(3):985-93. doi: 10.1093/molbev/msr267. Epub 2011 Oct 31.

38.

Hox clusters of the bichir (Actinopterygii, Polypterus senegalus) highlight unique patterns of sequence evolution in gnathostome phylogeny.

Raincrow JD, Dewar K, Stocsits C, Prohaska SJ, Amemiya CT, Stadler PF, Chiu CH.

J Exp Zool B Mol Dev Evol. 2011 Sep 15;316(6):451-64. doi: 10.1002/jez.b.21420. Epub 2011 Jun 17.

PMID:
21688387
39.

Genome biology of the cyclostomes and insights into the evolutionary biology of vertebrate genomes.

Smith JJ, Saha NR, Amemiya CT.

Integr Comp Biol. 2010 Jul;50(1):130-7. doi: 10.1093/icb/icq023. Epub 2010 Apr 19.

40.

Comparative analyses of vertebrate posterior HoxD clusters reveal atypical cluster architecture in the caecilian Typhlonectes natans.

Mannaert A, Amemiya CT, Bossuyt F.

BMC Genomics. 2010 Nov 24;11:658. doi: 10.1186/1471-2164-11-658.

41.

Antarctic notothenioid fishes: genomic resources and strategies for analyzing an adaptive radiation.

Detrich HW 3rd, Amemiya CT.

Integr Comp Biol. 2010 Dec;50(6):1009-17. doi: 10.1093/icb/icq071. Epub 2010 Jul 12.

42.

Conservation of shh cis-regulatory architecture of the coelacanth is consistent with its ancestral phylogenetic position.

Lang M, Hadzhiev Y, Siegel N, Amemiya CT, Parada C, Strähle U, Becker MB, Müller F, Meyer A.

Evodevo. 2010 Nov 3;1(1):11. doi: 10.1186/2041-9139-1-11.

43.

Mouse and zebrafish Hoxa3 orthologues have nonequivalent in vivo protein function.

Chen L, Zhao P, Wells L, Amemiya CT, Condie BG, Manley NR.

Proc Natl Acad Sci U S A. 2010 Jun 8;107(23):10555-60. doi: 10.1073/pnas.1005129107. Epub 2010 May 24.

44.

BAC library for the amphipod crustacean, Parhyale hawaiensis.

Parchem RJ, Poulin F, Stuart AB, Amemiya CT, Patel NH.

Genomics. 2010 May;95(5):261-7. doi: 10.1016/j.ygeno.2010.03.005. Epub 2010 Mar 16.

45.

Genome enablement of the notothenioidei: genome size estimates from 11 species and BAC libraries from 2 representative taxa.

Detrich HW, Stuart A, Schoenborn M, Parker SK, Methé BA, Amemiya CT.

J Exp Zool B Mol Dev Evol. 2010 Jul 15;314(5):369-81. doi: 10.1002/jez.b.21341.

46.

Development and analysis of a germline BAC resource for the sea lamprey, a vertebrate that undergoes substantial chromatin diminution.

Smith JJ, Stuart AB, Sauka-Spengler T, Clifton SW, Amemiya CT.

Chromosoma. 2010 Aug;119(4):381-9. doi: 10.1007/s00412-010-0263-z. Epub 2010 Mar 2.

47.

Complete HOX cluster characterization of the coelacanth provides further evidence for slow evolution of its genome.

Amemiya CT, Powers TP, Prohaska SJ, Grimwood J, Schmutz J, Dickson M, Miyake T, Schoenborn MA, Myers RM, Ruddle FH, Stadler PF.

Proc Natl Acad Sci U S A. 2010 Feb 23;107(8):3622-7. doi: 10.1073/pnas.0914312107. Epub 2010 Feb 5.

48.

Evolution of adaptive immune recognition in jawless vertebrates.

Saha NR, Smith J, Amemiya CT.

Semin Immunol. 2010 Feb;22(1):25-33. doi: 10.1016/j.smim.2009.12.002. Epub 2010 Jan 6. Review.

49.

Going adaptive: the saga of antibodies.

Danilova N, Amemiya CT.

Ann N Y Acad Sci. 2009 Jun;1168:130-55. doi: 10.1111/j.1749-6632.2009.04881.x. Review.

PMID:
19566706
50.

Programmed loss of millions of base pairs from a vertebrate genome.

Smith JJ, Antonacci F, Eichler EE, Amemiya CT.

Proc Natl Acad Sci U S A. 2009 Jul 7;106(27):11212-7. doi: 10.1073/pnas.0902358106. Epub 2009 Jun 26.

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