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Items: 1 to 20 of 136

1.

Integrating microbial and host transcriptomics to characterize asthma-associated microbial communities.

Castro-Nallar E, Shen Y, Freishtat RJ, Pérez-Losada M, Manimaran S, Liu G, Johnson WE, Crandall KA.

BMC Med Genomics. 2015 Aug 16;8:50. doi: 10.1186/s12920-015-0121-1.

2.

Dual Transcriptomic Profiling of Host and Microbiota during Health and Disease in Pediatric Asthma.

Pérez-Losada M, Castro-Nallar E, Bendall ML, Freishtat RJ, Crandall KA.

PLoS One. 2015 Jun 30;10(6):e0131819. doi: 10.1371/journal.pone.0131819. eCollection 2015.

3.

Concordance and discordance of sequence survey methods for molecular epidemiology.

Castro-Nallar E, Hasan NA, Cebula TA, Colwell RR, Robison RA, Johnson WE, Crandall KA.

PeerJ. 2015 Feb 17;3:e761. doi: 10.7717/peerj.761. eCollection 2015.

4.

Multiple drivers of decline in the global status of freshwater crayfish (Decapoda: Astacidea).

Richman NI, Böhm M, Adams SB, Alvarez F, Bergey EA, Bunn JJ, Burnham Q, Cordeiro J, Coughran J, Crandall KA, Dawkins KL, DiStefano RJ, Doran NE, Edsman L, Eversole AG, Füreder L, Furse JM, Gherardi F, Hamr P, Holdich DM, Horwitz P, Johnston K, Jones CM, Jones JP, Jones RL, Jones TG, Kawai T, Lawler S, López-Mejía M, Miller RM, Pedraza-Lara C, Reynolds JD, Richardson AM, Schultz MB, Schuster GA, Sibley PJ, Souty-Grosset C, Taylor CA, Thoma RF, Walls J, Walsh TS, Collen B.

Philos Trans R Soc Lond B Biol Sci. 2015 Feb 19;370(1662):20140060. doi: 10.1098/rstb.2014.0060.

5.

A synthetic phylogeny of freshwater crayfish: insights for conservation.

Owen CL, Bracken-Grissom H, Stern D, Crandall KA.

Philos Trans R Soc Lond B Biol Sci. 2015 Feb 19;370(1662):20140009. doi: 10.1098/rstb.2014.0009.

PMID:
25561670
6.

Phylogeny, extinction and conservation: embracing uncertainties in a time of urgency.

Forest F, Crandall KA, Chase MW, Faith DP.

Philos Trans R Soc Lond B Biol Sci. 2015 Feb 19;370(1662):20140002. doi: 10.1098/rstb.2014.0002.

7.

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

Speiser DI, Pankey MS, 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;15:350. doi: 10.1186/s12859-014-0350-x.

8.

Characteristics of equipartition for RNA structure.

Li H, Zhu D, Zhang C, Han H, Crandall KA.

BMC Proc. 2014 Oct 13;8(Suppl 6 Proceedings of the Great Lakes Bioinformatics Confer):S3. doi: 10.1186/1753-6561-8-S6-S3. eCollection 2014.

9.

Molecular phylogeny, systematics and morphological evolution of the acorn barnacles (Thoracica: Sessilia: Balanomorpha).

Pérez-Losada M, Høeg JT, Simon-Blecher N, Achituv Y, Jones D, Crandall KA.

Mol Phylogenet Evol. 2014 Dec;81:147-58. doi: 10.1016/j.ympev.2014.09.013. Epub 2014 Sep 27.

PMID:
25261121
10.

PathoScope 2.0: a complete computational framework for strain identification in environmental or clinical sequencing samples.

Hong C, Manimaran S, Shen Y, Perez-Rogers JF, Byrd AL, Castro-Nallar E, Crandall KA, Johnson WE.

Microbiome. 2014 Sep 5;2:33. doi: 10.1186/2049-2618-2-33. eCollection 2014.

11.

Single-molecule long-read 16S sequencing to characterize the lung microbiome from mechanically ventilated patients with suspected pneumonia.

Toma I, Siegel MO, Keiser J, Yakovleva A, Kim A, Davenport L, Devaney J, Hoffman EP, Alsubail R, Crandall KA, Castro-Nallar E, Pérez-Losada M, Hilton SK, Chawla LS, McCaffrey TA, Simon GL.

J Clin Microbiol. 2014 Nov;52(11):3913-21. doi: 10.1128/JCM.01678-14. Epub 2014 Aug 20.

12.

Characteristics and prediction of RNA structure.

Li H, Zhu D, Zhang C, Han H, Crandall KA.

Biomed Res Int. 2014;2014:690340. doi: 10.1155/2014/690340. Epub 2014 Jul 6.

13.

Clinical PathoScope: rapid alignment and filtration for accurate pathogen identification in clinical samples using unassembled sequencing data.

Byrd AL, Perez-Rogers JF, Manimaran S, Castro-Nallar E, Toma I, McCaffrey T, Siegel M, Benson G, Crandall KA, Johnson WE.

BMC Bioinformatics. 2014 Aug 4;15:262. doi: 10.1186/1471-2105-15-262.

14.

Whole genome single-nucleotide variation profile-based phylogenetic tree building methods for analysis of viral, bacterial and human genomes.

Faison WJ, Rostovtsev A, Castro-Nallar E, Crandall KA, Chumakov K, Simonyan V, Mazumder R.

Genomics. 2014 Jul;104(1):1-7. doi: 10.1016/j.ygeno.2014.06.001. Epub 2014 Jun 12.

PMID:
24930720
15.

Life in extreme environments: microbial diversity in Great Salt Lake, Utah.

Tazi L, Breakwell DP, Harker AR, Crandall KA.

Extremophiles. 2014 May;18(3):525-35. doi: 10.1007/s00792-014-0637-x. Epub 2014 Mar 30.

PMID:
24682608
16.

The emergence of lobsters: phylogenetic relationships, morphological evolution and divergence time comparisons of an ancient group (decapoda: achelata, astacidea, glypheidea, polychelida).

Bracken-Grissom HD, Ahyong ST, Wilkinson RD, Feldmann RM, Schweitzer CE, Breinholt JW, Bendall M, Palero F, Chan TY, Felder DL, Robles R, Chu KH, Tsang LM, Kim D, Martin JW, Crandall KA.

Syst Biol. 2014 Jul;63(4):457-79. doi: 10.1093/sysbio/syu008. Epub 2014 Feb 20.

PMID:
24562813
17.

Lost branches on the tree of life.

Drew BT, Gazis R, Cabezas P, Swithers KS, Deng J, Rodriguez R, Katz LA, Crandall KA, Hibbett DS, Soltis DE.

PLoS Biol. 2013 Sep;11(9):e1001636. doi: 10.1371/journal.pbio.1001636. Epub 2013 Sep 3. No abstract available.

18.

Pathoscope: species identification and strain attribution with unassembled sequencing data.

Francis OE, Bendall M, Manimaran S, Hong C, Clement NL, Castro-Nallar E, Snell Q, Schaalje GB, Clement MJ, Crandall KA, Johnson WE.

Genome Res. 2013 Oct;23(10):1721-9. doi: 10.1101/gr.150151.112. Epub 2013 Jul 10.

19.

A comprehensive and integrative reconstruction of evolutionary history for Anomura (Crustacea: Decapoda).

Bracken-Grissom HD, Cannon ME, Cabezas P, Feldmann RM, Schweitzer CE, Ahyong ST, Felder DL, Lemaitre R, Crandall KA.

BMC Evol Biol. 2013 Jun 20;13:128. doi: 10.1186/1471-2148-13-128.

20.

Pathogen typing in the genomics era: MLST and the future of molecular epidemiology.

Pérez-Losada M, Cabezas P, Castro-Nallar E, Crandall KA.

Infect Genet Evol. 2013 Jun;16:38-53. doi: 10.1016/j.meegid.2013.01.009. Epub 2013 Jan 26. Review.

PMID:
23357583
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