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Items: 1 to 50 of 58

1.

Northern Spotted Owl (Strix occidentalis caurina) Genome: Divergence with the Barred Owl (Strix varia) and Characterization of Light-Associated Genes.

Hanna ZR, Henderson JB, Wall JD, Emerling CA, Fuchs J, Runckel C, Mindell DP, Bowie RCK, DeRisi JL, Dumbacher JP.

Genome Biol Evol. 2017 Oct 1;9(10):2522-2545. doi: 10.1093/gbe/evx158.

2.

Multi-locus phylogenetic inference among New World Vultures (Aves: Cathartidae).

Johnson JA, Brown JW, Fuchs J, Mindell DP.

Mol Phylogenet Evol. 2016 Dec;105:193-199. doi: 10.1016/j.ympev.2016.08.025. Epub 2016 Sep 4.

PMID:
27601346
3.

Response to Comment on "Whole-genome analyses resolve early branches in the tree of life of modern birds".

Cracraft J, Houde P, Ho SY, Mindell DP, Fjeldså J, Lindow B, Edwards SV, Rahbek C, Mirarab S, Warnow T, Gilbert MT, Zhang G, Braun EL, Jarvis ED.

Science. 2015 Sep 25;349(6255):1460. doi: 10.1126/science.aab1578.

PMID:
26404820
4.

Isolation of a Complete Circular Virus Genome Sequence from an Alaskan Black-Capped Chickadee (Poecile atricapillus) Gastrointestinal Tract Sample.

Hanna ZR, Runckel C, Fuchs J, DeRisi JL, Mindell DP, Van Hemert C, Handel CM, Dumbacher JP.

Genome Announc. 2015 Sep 24;3(5). pii: e01081-15. doi: 10.1128/genomeA.01081-15.

5.

Phylogenomic analyses data of the avian phylogenomics project.

Jarvis ED, Mirarab S, Aberer AJ, Li B, Houde P, Li C, Ho SY, Faircloth BC, Nabholz B, Howard JT, Suh A, Weber CC, da Fonseca RR, Alfaro-Núñez A, Narula N, Liu L, Burt D, Ellegren H, Edwards SV, Stamatakis A, Mindell DP, Cracraft J, Braun EL, Warnow T, Jun W, Gilbert MT, Zhang G; Avian Phylogenomics Consortium.

Gigascience. 2015 Feb 12;4:4. doi: 10.1186/s13742-014-0038-1. eCollection 2015.

6.

Whole-genome analyses resolve early branches in the tree of life of modern birds.

Jarvis ED, Mirarab S, Aberer AJ, Li B, Houde P, Li C, Ho SY, Faircloth BC, Nabholz B, Howard JT, Suh A, Weber CC, da Fonseca RR, Li J, Zhang F, Li H, Zhou L, Narula N, Liu L, Ganapathy G, Boussau B, Bayzid MS, Zavidovych V, Subramanian S, Gabaldón T, Capella-Gutiérrez S, Huerta-Cepas J, Rekepalli B, Munch K, Schierup M, Lindow B, Warren WC, Ray D, Green RE, Bruford MW, Zhan X, Dixon A, Li S, Li N, Huang Y, Derryberry EP, Bertelsen MF, Sheldon FH, Brumfield RT, Mello CV, Lovell PV, Wirthlin M, Schneider MP, Prosdocimi F, Samaniego JA, Vargas Velazquez AM, Alfaro-Núñez A, Campos PF, Petersen B, Sicheritz-Ponten T, Pas A, Bailey T, Scofield P, Bunce M, Lambert DM, Zhou Q, Perelman P, Driskell AC, Shapiro B, Xiong Z, Zeng Y, Liu S, Li Z, Liu B, Wu K, Xiao J, Yinqi X, Zheng Q, Zhang Y, Yang H, Wang J, Smeds L, Rheindt FE, Braun M, Fjeldsa J, Orlando L, Barker FK, Jønsson KA, Johnson W, Koepfli KP, O'Brien S, Haussler D, Ryder OA, Rahbek C, Willerslev E, Graves GR, Glenn TC, McCormack J, Burt D, Ellegren H, Alström P, Edwards SV, Stamatakis A, Mindell DP, Cracraft J, Braun EL, Warnow T, Jun W, Gilbert MT, Zhang G.

Science. 2014 Dec 12;346(6215):1320-31. doi: 10.1126/science.1253451.

7.

Comparative genomics reveals insights into avian genome evolution and adaptation.

Zhang G, Li C, Li Q, Li B, Larkin DM, Lee C, Storz JF, Antunes A, Greenwold MJ, Meredith RW, Ödeen A, Cui J, Zhou Q, Xu L, Pan H, Wang Z, Jin L, Zhang P, Hu H, Yang W, Hu J, Xiao J, Yang Z, Liu Y, Xie Q, Yu H, Lian J, Wen P, Zhang F, Li H, Zeng Y, Xiong Z, Liu S, Zhou L, Huang Z, An N, Wang J, Zheng Q, Xiong Y, Wang G, Wang B, Wang J, Fan Y, da Fonseca RR, Alfaro-Núñez A, Schubert M, Orlando L, Mourier T, Howard JT, Ganapathy G, Pfenning A, Whitney O, Rivas MV, Hara E, Smith J, Farré M, Narayan J, Slavov G, Romanov MN, Borges R, Machado JP, Khan I, Springer MS, Gatesy J, Hoffmann FG, Opazo JC, Håstad O, Sawyer RH, Kim H, Kim KW, Kim HJ, Cho S, Li N, Huang Y, Bruford MW, Zhan X, Dixon A, Bertelsen MF, Derryberry E, Warren W, Wilson RK, Li S, Ray DA, Green RE, O'Brien SJ, Griffin D, Johnson WE, Haussler D, Ryder OA, Willerslev E, Graves GR, Alström P, Fjeldså J, Mindell DP, Edwards SV, Braun EL, Rahbek C, Burt DW, Houde P, Zhang Y, Yang H, Wang J; Avian Genome Consortium, Jarvis ED, Gilbert MT, Wang J.

Science. 2014 Dec 12;346(6215):1311-20. doi: 10.1126/science.1251385. Epub 2014 Dec 11.

8.

Rapid diversification of falcons (Aves: Falconidae) due to expansion of open habitats in the Late Miocene.

Fuchs J, Johnson JA, Mindell DP.

Mol Phylogenet Evol. 2015 Jan;82 Pt A:166-82. doi: 10.1016/j.ympev.2014.08.010. Epub 2014 Sep 23.

PMID:
25256056
9.

Evolutionary biology for the 21st century.

Losos JB, Arnold SJ, Bejerano G, Brodie ED 3rd, Hibbett D, Hoekstra HE, Mindell DP, Monteiro A, Moritz C, Orr HA, Petrov DA, Renner SS, Ricklefs RE, Soltis PS, Turner TL.

PLoS Biol. 2013;11(1):e1001466. doi: 10.1371/journal.pbio.1001466. Epub 2013 Jan 8. No abstract available.

10.

The tree of life: metaphor, model, and heuristic device.

Mindell DP.

Syst Biol. 2013 May 1;62(3):479-89. doi: 10.1093/sysbio/sys115. Epub 2013 Jan 3. No abstract available.

PMID:
23291311
11.

Approaching a state shift in Earth's biosphere.

Barnosky AD, Hadly EA, Bascompte J, Berlow EL, Brown JH, Fortelius M, Getz WM, Harte J, Hastings A, Marquet PA, Martinez ND, Mooers A, Roopnarine P, Vermeij G, Williams JW, Gillespie R, Kitzes J, Marshall C, Matzke N, Mindell DP, Revilla E, Smith AB.

Nature. 2012 Jun 6;486(7401):52-8. doi: 10.1038/nature11018. Review.

PMID:
22678279
12.

Aggregating, tagging and integrating biodiversity research.

Mindell DP, Fisher BL, Roopnarine P, Eisen J, Mace GM, Page RD, Pyle RL.

PLoS One. 2011;6(8):e19491. doi: 10.1371/journal.pone.0019491. Epub 2011 Aug 1. No abstract available.

13.

Pliocene diversification within the South American Forest falcons (Falconidae: Micrastur).

Fuchs J, Chen S, Johnson JA, Mindell DP.

Mol Phylogenet Evol. 2011 Sep;60(3):398-407. doi: 10.1016/j.ympev.2011.05.008. Epub 2011 May 20.

PMID:
21621621
14.

The use of genetics for the management of a recovering population: temporal assessment of migratory peregrine falcons in North America.

Johnson JA, Talbot SL, Sage GK, Burnham KK, Brown JW, Maechtle TL, Seegar WS, Yates MA, Anderson B, Mindell DP.

PLoS One. 2010 Nov 18;5(11):e14042. doi: 10.1371/journal.pone.0014042.

15.

Population structure and plumage polymorphism: The intraspecific evolutionary relationships of a polymorphic raptor, Buteo jamaicensis harlani.

Hull JM, Mindell DP, Talbot SL, Kay EH, Hoekstra HE, Ernest HB.

BMC Evol Biol. 2010 Jul 22;10:224. doi: 10.1186/1471-2148-10-224.

16.

It's not too late for the harpy eagle (Harpia harpyja): high levels of genetic diversity and differentiation can fuel conservation programs.

Lerner HR, Johnson JA, Lindsay AR, Kiff LF, Mindell DP.

PLoS One. 2009 Oct 5;4(10):e7336. doi: 10.1371/journal.pone.0007336.

17.

Evolution in the everyday world.

Mindell DP.

Sci Am. 2009 Jan;300(1):82-9. No abstract available.

PMID:
19186754
18.

Long-term survival despite low genetic diversity in the critically endangered Madagascar fish-eagle.

Johnson JA, Tingay RE, Culver M, Hailer F, Clarke ML, Mindell DP.

Mol Ecol. 2009 Jan;18(1):54-63. doi: 10.1111/j.1365-294X.2008.04012.x.

PMID:
19140964
19.

Strong mitochondrial DNA support for a Cretaceous origin of modern avian lineages.

Brown JW, Rest JS, García-Moreno J, Sorenson MD, Mindell DP.

BMC Biol. 2008 Jan 28;6:6. doi: 10.1186/1741-7007-6-6.

20.

Genetic structure among continental and island populations of gyrfalcons.

Johnson JA, Burnham KK, Burnham WA, Mindell DP.

Mol Ecol. 2007 Aug;16(15):3145-60.

21.

Nuclear DNA does not reconcile 'rocks' and 'clocks' in Neoaves: a comment on Ericson et al.

Brown JW, Payne RB, Mindell DP.

Biol Lett. 2007 Jun 22;3(3):257-9; discussion 260-1. No abstract available.

22.

The rise and fall of the CR1 subfamily in the lineage leading to penguins.

Watanabe M, Nikaido M, Tsuda TT, Inoko H, Mindell DP, Murata K, Okada N.

Gene. 2006 Jan 3;365:57-66. Epub 2005 Dec 20.

PMID:
16368202
23.

Prioritizing species conservation: does the Cape Verde kite exist?

Johnson JA, Watson RT, Mindell DP.

Proc Biol Sci. 2005 Jul 7;272(1570):1365-71.

24.

Phylogeny of eagles, Old World vultures, and other Accipitridae based on nuclear and mitochondrial DNA.

Lerner HR, Mindell DP.

Mol Phylogenet Evol. 2005 Nov;37(2):327-46. Epub 2005 May 31.

PMID:
15925523
25.

Don't forget about viruses.

Mindell DP, Villarreal LP.

Science. 2003 Dec 5;302(5651):1677. No abstract available.

PMID:
14657474
26.
27.

Molecular systematics of primary reptilian lineages and the tuatara mitochondrial genome.

Rest JS, Ast JC, Austin CC, Waddell PJ, Tibbetts EA, Hay JM, Mindell DP.

Mol Phylogenet Evol. 2003 Nov;29(2):289-97.

PMID:
13678684
28.

Phylogeny of magpies (genus Pica) inferred from mtDNA data.

Lee SI, Parr CS, Hwang Y, Mindell DP, Choe JC.

Mol Phylogenet Evol. 2003 Nov;29(2):250-7.

PMID:
13678680
29.

Congruent avian phylogenies inferred from mitochondrial and nuclear DNA sequences.

García-Moreno J, Sorenson MD, Mindell DP.

J Mol Evol. 2003 Jul;57(1):27-37.

30.

Retroids in archaea: phylogeny and lateral origins.

Rest JS, Mindell DP.

Mol Biol Evol. 2003 Jul;20(7):1134-42. Epub 2003 May 30.

PMID:
12777534
31.

More taxa, more characters: the hoatzin problem is still unresolved.

Sorenson MD, Oneal E, Garcia-Moreno J, Mindell DP.

Mol Biol Evol. 2003 Sep;20(9):1484-98. Epub 2003 May 30.

PMID:
12777516
32.

An extra nucleotide is not translated in mitochondrial ND3 of some birds and turtles.

Mindell DP, Sorenson MD, Dimcheff DE.

Mol Biol Evol. 1998 Nov;15(11):1568-71. No abstract available.

PMID:
12572620
33.

Molecular evidence of HIV-1 transmission in a criminal case.

Metzker ML, Mindell DP, Liu XM, Ptak RG, Gibbs RA, Hillis DM.

Proc Natl Acad Sci U S A. 2002 Oct 29;99(22):14292-7. Epub 2002 Oct 18.

34.

rtREV: an amino acid substitution matrix for inference of retrovirus and reverse transcriptase phylogeny.

Dimmic MW, Rest JS, Mindell DP, Goldstein RA.

J Mol Evol. 2002 Jul;55(1):65-73.

35.

Phylogeny of Tetraoninae and other galliform birds using mitochondrial 12S and ND2 genes.

Dimcheff DE, Drovetski SV, Mindell DP.

Mol Phylogenet Evol. 2002 Aug;24(2):203-15.

PMID:
12144757
36.

Interordinal relationships of birds and other reptiles based on whole mitochondrial genomes.

Mindell DP, Sorenson MD, Dimcheff DE, Hasegawa M, Ast JC, Yuri T.

Syst Biol. 1999 Mar;48(1):138-52.

PMID:
12078637
37.

Assessing the Cretaceous superordinal divergence times within birds and placental mammals by using whole mitochondrial protein sequences and an extended statistical framework.

Waddell PJ, Cao Y, Hasegawa M, Mindell DP.

Syst Biol. 1999 Mar;48(1):119-37. Erratum in: Syst Biol 1999 Sep;48(3):681.

PMID:
12078636
38.
39.

Phylogenetic position of turtles among amniotes: evidence from mitochondrial and nuclear genes.

Cao Y, Sorenson MD, Kumazawa Y, Mindell DP, Hasegawa M.

Gene. 2000 Dec 23;259(1-2):139-48.

PMID:
11163971
40.
41.

Cospeciation and horizontal transmission of avian sarcoma and leukosis virus gag genes in galliform birds.

Dimcheff DE, Drovetski SV, Krishnan M, Mindell DP.

J Virol. 2000 May;74(9):3984-95.

42.
43.

Modeling evolution at the protein level using an adjustable amino acid fitness model.

Dimmic MW, Mindell DP, Goldstein RA.

Pac Symp Biocomput. 2000:18-29.

44.

Primers for a PCR-based approach to mitochondrial genome sequencing in birds and other vertebrates.

Sorenson MD, Ast JC, Dimcheff DE, Yuri T, Mindell DP.

Mol Phylogenet Evol. 1999 Jul;12(2):105-14.

PMID:
10381314
45.

Using physical-chemistry-based substitution models in phylogenetic analyses of HIV-1 subtypes.

Koshi JM, Mindell DP, Goldstein RA.

Mol Biol Evol. 1999 Feb;16(2):173-9.

PMID:
10028285
46.

Multiple independent origins of mitochondrial gene order in birds.

Mindell DP, Sorenson MD, Dimcheff DE.

Proc Natl Acad Sci U S A. 1998 Sep 1;95(18):10693-7.

47.

"Misleading" molecules?

Mindell DP.

Science. 1997 Jun 13;276(5319):1629. No abstract available.

PMID:
9206819
48.

Dihydropteroate synthase polymorphisms in Pneumocystis carinii.

Lane BR, Ast JC, Hossler PA, Mindell DP, Bartlett MS, Smith JW, Meshnick SR.

J Infect Dis. 1997 Feb;175(2):482-5.

PMID:
9203679
49.

Beyond Mutation Matrices: Physical-Chemistry Based Evolutionary Models.

Koshi JM, Mindell DP, Goldstein RA.

Genome Inform Ser Workshop Genome Inform. 1997;8:80-89.

PMID:
11072308
50.

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