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Evaluation of microRNA alignment techniques.

Ziemann M, Kaspi A, El-Osta A.

RNA. 2016 Aug;22(8):1120-38. doi: 10.1261/rna.055509.115.


Alignment of Short Reads: A Crucial Step for Application of Next-Generation Sequencing Data in Precision Medicine.

Ye H, Meehan J, Tong W, Hong H.

Pharmaceutics. 2015 Nov 23;7(4):523-41. doi: 10.3390/pharmaceutics7040523. Review.


Heterozygous genome assembly via binary classification of homologous sequence.

Bodily PM, Fujimoto M, Ortega C, Okuda N, Price JC, Clement MJ, Snell Q.

BMC Bioinformatics. 2015;16 Suppl 7:S5. doi: 10.1186/1471-2105-16-S7-S5.


Genome-wide profiling of the C. elegans dsRNAome.

Whipple JM, Youssef OA, Aruscavage PJ, Nix DA, Hong C, Johnson WE, Bass BL.

RNA. 2015 May;21(5):786-800. doi: 10.1261/rna.048801.114.


ADaM: augmenting existing approximate fast matching algorithms with efficient and exact range queries.

Clement NL, Thompson LP, Miranker DP.

BMC Bioinformatics. 2014;15 Suppl 7:S1. doi: 10.1186/1471-2105-15-S7-S1.


Validation and assessment of variant calling pipelines for next-generation sequencing.

Pirooznia M, Kramer M, Parla J, Goes FS, Potash JB, McCombie WR, Zandi PP.

Hum Genomics. 2014 Jul 30;8:14. doi: 10.1186/1479-7364-8-14.


Evaluation and comparison of multiple aligners for next-generation sequencing data analysis.

Shang J, Zhu F, Vongsangnak W, Tang Y, Zhang W, Shen B.

Biomed Res Int. 2014;2014:309650. doi: 10.1155/2014/309650.


RNA-Seq technology and its application in fish transcriptomics.

Qian X, Ba Y, Zhuang Q, Zhong G.

OMICS. 2014 Feb;18(2):98-110. doi: 10.1089/omi.2013.0110. Review.


Probabilistic alignment leads to improved accuracy and read coverage for bisulfite sequencing data.

Hong C, Clement NL, Clement S, Hammoud SS, Carrell DT, Cairns BR, Snell Q, Clement MJ, Johnson WE.

BMC Bioinformatics. 2013 Nov 21;14:337. doi: 10.1186/1471-2105-14-337.


Multiplatform single-sample estimates of transcriptional activation.

Piccolo SR, Withers MR, Francis OE, Bild AH, Johnson WE.

Proc Natl Acad Sci U S A. 2013 Oct 29;110(44):17778-83. doi: 10.1073/pnas.1305823110.


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.


Low concordance of multiple variant-calling pipelines: practical implications for exome and genome sequencing.

O'Rawe J, Jiang T, Sun G, Wu Y, Wang W, Hu J, Bodily P, Tian L, Hakonarson H, Johnson WE, Wei Z, Wang K, Lyon GJ.

Genome Med. 2013 Mar 27;5(3):28. doi: 10.1186/gm432.


Parallel Mapping Approaches for GNUMAP.

Clement NL, Clement MJ, Snell Q, Johnson WE.

IPDPS. 2011:435-443.


A comprehensive evaluation of alignment algorithms in the context of RNA-seq.

Lindner R, Friedel CC.

PLoS One. 2012;7(12):e52403. doi: 10.1371/journal.pone.0052403.


Rhizobial plasmids that cause impaired symbiotic nitrogen fixation and enhanced host invasion.

Crook MB, Lindsay DP, Biggs MB, Bentley JS, Price JC, Clement SC, Clement MJ, Long SR, Griffitts JS.

Mol Plant Microbe Interact. 2012 Aug;25(8):1026-33. doi: 10.1094/MPMI-02-12-0052-R.


Effects of ADARs on small RNA processing pathways in C. elegans.

Warf MB, Shepherd BA, Johnson WE, Bass BL.

Genome Res. 2012 Aug;22(8):1488-98. doi: 10.1101/gr.134841.111.


De novo assembly of the carrot mitochondrial genome using next generation sequencing of whole genomic DNA provides first evidence of DNA transfer into an angiosperm plastid genome.

Iorizzo M, Senalik D, Szklarczyk M, Grzebelus D, Spooner D, Simon P.

BMC Plant Biol. 2012 May 1;12:61. doi: 10.1186/1471-2229-12-61.


A novel application of pattern recognition for accurate SNP and indel discovery from high-throughput data: targeted resequencing of the glucocorticoid receptor co-chaperone FKBP5 in a Caucasian population.

Pelleymounter LL, Moon I, Johnson JA, Laederach A, Halvorsen M, Eckloff B, Abo R, Rossetti S.

Mol Genet Metab. 2011 Dec;104(4):457-69. doi: 10.1016/j.ymgme.2011.08.019.


Exome sequencing and unrelated findings in the context of complex disease research: ethical and clinical implications.

Lyon GJ, Jiang T, Van Wijk R, Wang W, Bodily PM, Xing J, Tian L, Robison RJ, Clement M, Lin Y, Zhang P, Liu Y, Moore B, Glessner JT, Elia J, Reimherr F, van Solinge WW, Yandell M, Hakonarson H, Wang J, Johnson WE, Wei Z, Wang K.

Discov Med. 2011 Jul;12(62):41-55.


Using VAAST to identify an X-linked disorder resulting in lethality in male infants due to N-terminal acetyltransferase deficiency.

Rope AF, Wang K, Evjenth R, Xing J, Johnston JJ, Swensen JJ, Johnson WE, Moore B, Huff CD, Bird LM, Carey JC, Opitz JM, Stevens CA, Jiang T, Schank C, Fain HD, Robison R, Dalley B, Chin S, South ST, Pysher TJ, Jorde LB, Hakonarson H, Lillehaug JR, Biesecker LG, Yandell M, Arnesen T, Lyon GJ.

Am J Hum Genet. 2011 Jul 15;89(1):28-43. doi: 10.1016/j.ajhg.2011.05.017. Erratum in: Am J Hum Genet. 2011 Aug 12;89(2):345.

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