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Results: 12

1.

Proteotyping of microbial communities by optimization of tandem mass spectrometry data interpretation.

Hugo A, Baxter DJ, Cannon WR, Kalyanaraman A, Kulkarni G, Callister SJ.

Pac Symp Biocomput. 2012:225-34.

PMID:
22174278
[PubMed - indexed for MEDLINE]
Free Article
2.

MapReduce implementation of a hybrid spectral library-database search method for large-scale peptide identification.

Kalyanaraman A, Cannon WR, Latt B, Baxter DJ.

Bioinformatics. 2011 Nov 1;27(21):3072-3. doi: 10.1093/bioinformatics/btr523. Epub 2011 Sep 16.

PMID:
21926122
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Attenuation of virulence in an apicomplexan hemoparasite results in reduced genome diversity at the population level.

Lau AO, Kalyanaraman A, Echaide I, Palmer GH, Bock R, Pedroni MJ, Rameshkumar M, Ferreira MB, Fletcher TI, McElwain TF.

BMC Genomics. 2011 Aug 12;12:410. doi: 10.1186/1471-2164-12-410.

PMID:
21838895
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

The genome of the domesticated apple (Malus × domestica Borkh.).

Velasco R, Zharkikh A, Affourtit J, Dhingra A, Cestaro A, Kalyanaraman A, Fontana P, Bhatnagar SK, Troggio M, Pruss D, Salvi S, Pindo M, Baldi P, Castelletti S, Cavaiuolo M, Coppola G, Costa F, Cova V, Dal Ri A, Goremykin V, Komjanc M, Longhi S, Magnago P, Malacarne G, Malnoy M, Micheletti D, Moretto M, Perazzolli M, Si-Ammour A, Vezzulli S, Zini E, Eldredge G, Fitzgerald LM, Gutin N, Lanchbury J, Macalma T, Mitchell JT, Reid J, Wardell B, Kodira C, Chen Z, Desany B, Niazi F, Palmer M, Koepke T, Jiwan D, Schaeffer S, Krishnan V, Wu C, Chu VT, King ST, Vick J, Tao Q, Mraz A, Stormo A, Stormo K, Bogden R, Ederle D, Stella A, Vecchietti A, Kater MM, Masiero S, Lasserre P, Lespinasse Y, Allan AC, Bus V, Chagné D, Crowhurst RN, Gleave AP, Lavezzo E, Fawcett JA, Proost S, Rouzé P, Sterck L, Toppo S, Lazzari B, Hellens RP, Durel CE, Gutin A, Bumgarner RE, Gardiner SE, Skolnick M, Egholm M, Van de Peer Y, Salamini F, Viola R.

Nat Genet. 2010 Oct;42(10):833-9. doi: 10.1038/ng.654. Epub 2010 Aug 29.

PMID:
20802477
[PubMed - indexed for MEDLINE]
5.

The B73 maize genome: complexity, diversity, and dynamics.

Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, Pasternak S, Liang C, Zhang J, Fulton L, Graves TA, Minx P, Reily AD, Courtney L, Kruchowski SS, Tomlinson C, Strong C, Delehaunty K, Fronick C, Courtney B, Rock SM, Belter E, Du F, Kim K, Abbott RM, Cotton M, Levy A, Marchetto P, Ochoa K, Jackson SM, Gillam B, Chen W, Yan L, Higginbotham J, Cardenas M, Waligorski J, Applebaum E, Phelps L, Falcone J, Kanchi K, Thane T, Scimone A, Thane N, Henke J, Wang T, Ruppert J, Shah N, Rotter K, Hodges J, Ingenthron E, Cordes M, Kohlberg S, Sgro J, Delgado B, Mead K, Chinwalla A, Leonard S, Crouse K, Collura K, Kudrna D, Currie J, He R, Angelova A, Rajasekar S, Mueller T, Lomeli R, Scara G, Ko A, Delaney K, Wissotski M, Lopez G, Campos D, Braidotti M, Ashley E, Golser W, Kim H, Lee S, Lin J, Dujmic Z, Kim W, Talag J, Zuccolo A, Fan C, Sebastian A, Kramer M, Spiegel L, Nascimento L, Zutavern T, Miller B, Ambroise C, Muller S, Spooner W, Narechania A, Ren L, Wei S, Kumari S, Faga B, Levy MJ, McMahan L, Van Buren P, Vaughn MW, Ying K, Yeh CT, Emrich SJ, Jia Y, Kalyanaraman A, Hsia AP, Barbazuk WB, Baucom RS, Brutnell TP, Carpita NC, Chaparro C, Chia JM, Deragon JM, Estill JC, Fu Y, Jeddeloh JA, Han Y, Lee H, Li P, Lisch DR, Liu S, Liu Z, Nagel DH, McCann MC, SanMiguel P, Myers AM, Nettleton D, Nguyen J, Penning BW, Ponnala L, Schneider KL, Schwartz DC, Sharma A, Soderlund C, Springer NM, Sun Q, Wang H, Waterman M, Westerman R, Wolfgruber TK, Yang L, Yu Y, Zhang L, Zhou S, Zhu Q, Bennetzen JL, Dawe RK, Jiang J, Jiang N, Presting GG, Wessler SR, Aluru S, Martienssen RA, Clifton SW, McCombie WR, Wing RA, Wilson RK.

Science. 2009 Nov 20;326(5956):1112-5. doi: 10.1126/science.1178534. Erratum in: Science. 2012 Aug 31;337(6098):1040.

PMID:
19965430
[PubMed - indexed for MEDLINE]
Free Article
6.

Detailed analysis of a contiguous 22-Mb region of the maize genome.

Wei F, Stein JC, Liang C, Zhang J, Fulton RS, Baucom RS, De Paoli E, Zhou S, Yang L, Han Y, Pasternak S, Narechania A, Zhang L, Yeh CT, Ying K, Nagel DH, Collura K, Kudrna D, Currie J, Lin J, Kim H, Angelova A, Scara G, Wissotski M, Golser W, Courtney L, Kruchowski S, Graves TA, Rock SM, Adams S, Fulton LA, Fronick C, Courtney W, Kramer M, Spiegel L, Nascimento L, Kalyanaraman A, Chaparro C, Deragon JM, Miguel PS, Jiang N, Wessler SR, Green PJ, Yu Y, Schwartz DC, Meyers BC, Bennetzen JL, Martienssen RA, McCombie WR, Aluru S, Clifton SW, Schnable PS, Ware D, Wilson RK, Wing RA.

PLoS Genet. 2009 Nov;5(11):e1000728. doi: 10.1371/journal.pgen.1000728. Epub 2009 Nov 20.

PMID:
19936048
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Turning repeats to advantage: scaffolding genomic contigs using LTR retrotransposons.

Kalyanaraman A, Aluru S, Schnable PS.

Comput Syst Bioinformatics Conf. 2006:167-78.

PMID:
17369635
[PubMed - indexed for MEDLINE]
Free Article
8.

Efficient algorithms and software for detection of full-length LTR retrotransposons.

Kalyanaraman A, Aluru S.

J Bioinform Comput Biol. 2006 Apr;4(2):197-216.

PMID:
16819780
[PubMed - indexed for MEDLINE]
9.

Space-conserving optimal DNA-protein alignment.

Ko P, Narayanan M, Kalyanaraman A, Aluru S.

Proc IEEE Comput Syst Bioinform Conf. 2004:80-8.

PMID:
16448002
[PubMed - indexed for MEDLINE]
10.

Efficient algorithms and software for detection of full-length LTR retrotransposons.

Kalyanaraman A, Aluru S.

Proc IEEE Comput Syst Bioinform Conf. 2005:56-64.

PMID:
16447962
[PubMed - indexed for MEDLINE]
11.

A survey of SL1-spliced transcripts from the root-lesion nematode Pratylenchus penetrans.

Mitreva M, Elling AA, Dante M, Kloek AP, Kalyanaraman A, Aluru S, Clifton SW, Bird DM, Baum TJ, McCarter JP.

Mol Genet Genomics. 2004 Sep;272(2):138-48. Epub 2004 Aug 28.

PMID:
15338281
[PubMed - indexed for MEDLINE]
12.

Efficient clustering of large EST data sets on parallel computers.

Kalyanaraman A, Aluru S, Kothari S, Brendel V.

Nucleic Acids Res. 2003 Jun 1;31(11):2963-74.

PMID:
12771222
[PubMed - indexed for MEDLINE]
Free PMC Article

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