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Results: 1 to 20 of 70

1.

Using phylogenetically-informed annotation (PIA) to search for light-interacting genes in transcriptomes from non-model organisms.

Speiser DI, Pankey M, Zaharoff AK, Battelle BA, Bracken-Grissom HD, Breinholt JW, Bybee SM, Cronin TW, Garm A, Lindgren AR, Patel NH, Porter ML, Protas ME, Rivera AS, Serb JM, Zigler KS, Crandall KA, Oakley TH.

BMC Bioinformatics. 2014 Nov 19;15(1):350. [Epub ahead of print]

PMID:
25407802
[PubMed - as supplied by publisher]
Free Article
2.

Predictable transcriptome evolution in the convergent and complex bioluminescent organs of squid.

Pankey MS, Minin VN, Imholte GC, Suchard MA, Oakley TH.

Proc Natl Acad Sci U S A. 2014 Nov 4;111(44):E4736-42. doi: 10.1073/pnas.1416574111. Epub 2014 Oct 21.

PMID:
25336755
[PubMed - in process]
3.

New joints, same moves: the ossification of community psychiatry.

Oakley T.

Psychiatr Bull (2014). 2014 Feb;38(1):45. doi: 10.1192/pb.38.1.45. No abstract available.

PMID:
25237491
[PubMed]
Free PMC Article
4.

Occurrence of hemocyanin in ostracod crustaceans.

Marxen JC, Pick C, Oakley TH, Burmester T.

J Mol Evol. 2014 Aug;79(1-2):3-11. doi: 10.1007/s00239-014-9636-x. Epub 2014 Aug 19.

PMID:
25135304
[PubMed - in process]
5.

The comb jelly opsins and the origins of animal phototransduction.

Feuda R, Rota-Stabelli O, Oakley TH, Pisani D.

Genome Biol Evol. 2014 Jul 24;6(8):1964-71. doi: 10.1093/gbe/evu154.

PMID:
25062921
[PubMed - in process]
Free PMC Article
6.

Evolutionary history and the strength of species interactions: testing the phylogenetic limiting similarity hypothesis.

Fritschie KJ, Cardinale BJ, Alexandrou MA, Oakley TH.

Ecology. 2014 May;95(5):1407-17.

PMID:
25000771
[PubMed - indexed for MEDLINE]
7.

Osiris: accessible and reproducible phylogenetic and phylogenomic analyses within the Galaxy workflow management system.

Oakley TH, Alexandrou MA, Ngo R, Pankey MS, Churchill CK, Chen W, Lopker KB.

BMC Bioinformatics. 2014 Jul 2;15:230. doi: 10.1186/1471-2105-15-230.

PMID:
24990571
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Ocular and extraocular expression of opsins in the rhopalium of Tripedalia cystophora (Cnidaria: Cubozoa).

Bielecki J, Zaharoff AK, Leung NY, Garm A, Oakley TH.

PLoS One. 2014 Jun 5;9(6):e98870. doi: 10.1371/journal.pone.0098870. eCollection 2014.

PMID:
24901369
[PubMed - in process]
Free PMC Article
9.

Two new sympatric species of Eusarsiella (Ostracoda: Myodocopida: Sarsiellidae) from the Florida Keys with a morphological phylogeny of Sarsiellinae.

Churchill CK, Ellis EA, Pique AE, Oakley TH.

Zootaxa. 2014 May 28;(3802):444-58. doi: 10.11646/zootaxa.3802.4.3.

PMID:
24871023
[PubMed - indexed for MEDLINE]
10.

The Global Invertebrate Genomics Alliance (GIGA): developing community resources to study diverse invertebrate genomes.

GIGA Community of Scientists, Bracken-Grissom H, Collins AG, Collins T, Crandall K, Distel D, Dunn C, Giribet G, Haddock S, Knowlton N, Martindale M, Medina M, Messing C, O'Brien SJ, Paulay G, Putnam N, Ravasi T, Rouse GW, Ryan JF, Schulze A, W├Ârheide G, Adamska M, Bailly X, Breinholt J, Browne WE, Diaz MC, Evans N, Flot JF, Fogarty N, Johnston M, Kamel B, Kawahara AY, Laberge T, Lavrov D, Michonneau F, Moroz LL, Oakley T, Osborne K, Pomponi SA, Rhodes A, Santos SR, Satoh N, Thacker RW, Van de Peer Y, Voolstra CR, Welch DM, Winston J, Zhou X.

J Hered. 2014 Jan-Feb;105(1):1-18. doi: 10.1093/jhered/est084.

PMID:
24336862
[PubMed - indexed for MEDLINE]
11.

Eye-specification genes in the bacterial light organ of the bobtail squid Euprymna scolopes, and their expression in response to symbiont cues.

Peyer SM, Pankey MS, Oakley TH, McFall-Ngai MJ.

Mech Dev. 2014 Feb;131:111-26. doi: 10.1016/j.mod.2013.09.004. Epub 2013 Oct 21.

PMID:
24157521
[PubMed - indexed for MEDLINE]
12.

Experimental evidence that evolutionary relatedness does not affect the ecological mechanisms of coexistence in freshwater green algae.

Narwani A, Alexandrou MA, Oakley TH, Carroll IT, Cardinale BJ.

Ecol Lett. 2013 Nov;16(11):1373-81. doi: 10.1111/ele.12182. Epub 2013 Sep 23.

PMID:
24112458
[PubMed - indexed for MEDLINE]
13.

The risks and benefits of glucocorticoid treatment for tendinopathy: a systematic review of the effects of local glucocorticoid on tendon.

Dean BJ, Lostis E, Oakley T, Rombach I, Morrey ME, Carr AJ.

Semin Arthritis Rheum. 2014 Feb;43(4):570-6. doi: 10.1016/j.semarthrit.2013.08.006. Epub 2013 Sep 26. Review.

PMID:
24074644
[PubMed - indexed for MEDLINE]
14.

Shared ancestry influences community stability by altering competitive interactions: evidence from a laboratory microcosm experiment using freshwater green algae.

Venail PA, Alexandrou MA, Oakley TH, Cardinale BJ.

Proc Biol Sci. 2013 Aug 14;280(1768):20131548. doi: 10.1098/rspb.2013.1548. Print 2013 Oct 7.

PMID:
23945692
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Genome duplication and multiple evolutionary origins of complex migratory behavior in Salmonidae.

Alexandrou MA, Swartz BA, Matzke NJ, Oakley TH.

Mol Phylogenet Evol. 2013 Dec;69(3):514-23. doi: 10.1016/j.ympev.2013.07.026. Epub 2013 Aug 7.

PMID:
23933489
[PubMed - indexed for MEDLINE]
16.

The evolution of complexity in the visual systems of stomatopods: insights from transcriptomics.

Porter ML, Speiser DI, Zaharoff AK, Caldwell RL, Cronin TW, Oakley TH.

Integr Comp Biol. 2013 Jul;53(1):39-49. doi: 10.1093/icb/ict060. Epub 2013 May 31.

PMID:
23727979
[PubMed - indexed for MEDLINE]
Free Article
17.

Evasion of predators contributes to the maintenance of male eyes in sexually dimorphic Euphilomedes ostracods (Crustacea).

Speiser DI, Lampe RI, Lovdahl VR, Carrillo-Zazueta B, Rivera AS, Oakley TH.

Integr Comp Biol. 2013 Jul;53(1):78-88. doi: 10.1093/icb/ict025. Epub 2013 May 7.

PMID:
23652199
[PubMed - indexed for MEDLINE]
Free Article
18.

Phylotranscriptomics to bring the understudied into the fold: monophyletic ostracoda, fossil placement, and pancrustacean phylogeny.

Oakley TH, Wolfe JM, Lindgren AR, Zaharoff AK.

Mol Biol Evol. 2013 Jan;30(1):215-33. doi: 10.1093/molbev/mss216. Epub 2012 Sep 12.

PMID:
22977117
[PubMed - indexed for MEDLINE]
Free Article
19.

A multi-gene phylogeny of Cephalopoda supports convergent morphological evolution in association with multiple habitat shifts in the marine environment.

Lindgren AR, Pankey MS, Hochberg FG, Oakley TH.

BMC Evol Biol. 2012 Jul 28;12:129.

PMID:
22839506
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Blue-light-receptive cryptochrome is expressed in a sponge eye lacking neurons and opsin.

Rivera AS, Ozturk N, Fahey B, Plachetzki DC, Degnan BM, Sancar A, Oakley TH.

J Exp Biol. 2012 Apr 15;215(Pt 8):1278-86. doi: 10.1242/jeb.067140.

PMID:
22442365
[PubMed - indexed for MEDLINE]
Free PMC Article

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