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Realistic artificial DNA sequences as negative controls for computational genomics.

Caballero J, Smit AF, Hood L, Glusman G.

Nucleic Acids Res. 2014 Jul;42(12):e99. doi: 10.1093/nar/gku356. Epub 2014 May 6.


cnvOffSeq: detecting intergenic copy number variation using off-target exome sequencing data.

Bellos E, Coin LJ.

Bioinformatics. 2014 Sep 1;30(17):i639-45. doi: 10.1093/bioinformatics/btu475.


SnowyOwl: accurate prediction of fungal genes by using RNA-Seq and homology information to select among ab initio models.

Reid I, O'Toole N, Zabaneh O, Nourzadeh R, Dahdouli M, Abdellateef M, Gordon PM, Soh J, Butler G, Sensen CW, Tsang A.

BMC Bioinformatics. 2014 Jul 1;15:229. doi: 10.1186/1471-2105-15-229.


A BAC based physical map and genome survey of the rice false smut fungus Villosiclava virens.

Wang X, Liu Q, Wang H, Luo CX, Wang G, Luo M.

BMC Genomics. 2013 Dec 16;14:883. doi: 10.1186/1471-2164-14-883.


Identification of both copy number variation-type and constant-type core elements in a large segmental duplication region of the mouse genome.

Umemori J, Mori A, Ichiyanagi K, Uno T, Koide T.

BMC Genomics. 2013 Jul 8;14:455. doi: 10.1186/1471-2164-14-455.


Evidence for the dissemination of cryptic non-coding RNAs transcribed from intronic and intergenic segments by retroposition.

Hahn Y.

Bioinformatics. 2013 Jul 1;29(13):1593-9. doi: 10.1093/bioinformatics/btt258. Epub 2013 May 6.


Salamander Hox clusters contain repetitive DNA and expanded non-coding regions: a typical Hox structure for non-mammalian tetrapod vertebrates?

Voss SR, Putta S, Walker JA, Smith JJ, Maki N, Tsonis PA.

Hum Genomics. 2013 Apr 5;7:9. doi: 10.1186/1479-7364-7-9.


Elevated rate of fixation of endogenous retroviral elements in Haplorhini TRIM5 and TRIM22 genomic sequences: impact on transcriptional regulation.

Diehl WE, Johnson WE, Hunter E.

PLoS One. 2013;8(3):e58532. doi: 10.1371/journal.pone.0058532. Epub 2013 Mar 14.


Repeat or not repeat?--Statistical validation of tandem repeat prediction in genomic sequences.

Schaper E, Kajava AV, Hauser A, Anisimova M.

Nucleic Acids Res. 2012 Nov 1;40(20):10005-17. doi: 10.1093/nar/gks726. Epub 2012 Aug 25.


The complete chloroplast DNA sequence of Eleutherococcus senticosus (Araliaceae); comparative evolutionary analyses with other three asterids.

Yi DK, Lee HL, Sun BY, Chung MY, Kim KJ.

Mol Cells. 2012 May;33(5):497-508. doi: 10.1007/s10059-012-2281-6. Epub 2012 Apr 24.


MotifMap: integrative genome-wide maps of regulatory motif sites for model species.

Daily K, Patel VR, Rigor P, Xie X, Baldi P.

BMC Bioinformatics. 2011 Dec 30;12:495. doi: 10.1186/1471-2105-12-495.


AluScan: a method for genome-wide scanning of sequence and structure variations in the human genome.

Mei L, Ding X, Tsang SY, Pun FW, Ng SK, Yang J, Zhao C, Li D, Wan W, Yu CH, Tan TC, Poon WS, Leung GK, Ng HK, Zhang L, Xue H.

BMC Genomics. 2011 Nov 17;12:564. doi: 10.1186/1471-2164-12-564.


Genomic sequence around butterfly wing development genes: annotation and comparative analysis.

Conceição IC, Long AD, Gruber JD, Beldade P.

PLoS One. 2011;6(8):e23778. doi: 10.1371/journal.pone.0023778. Epub 2011 Aug 31.


Comparative genomics approach to detecting split-coding regions in a low-coverage genome: lessons from the chimaera Callorhinchus milii (Holocephali, Chondrichthyes).

Dessimoz C, Zoller S, Manousaki T, Qiu H, Meyer A, Kuraku S.

Brief Bioinform. 2011 Sep;12(5):474-84. doi: 10.1093/bib/bbr038. Epub 2011 Jun 28.


Analysis of BAC-end sequences in rainbow trout: content characterization and assessment of synteny between trout and other fish genomes.

Genet C, Dehais P, Palti Y, Gao G, Gavory F, Wincker P, Quillet E, Boussaha M.

BMC Genomics. 2011 Jun 14;12:314. doi: 10.1186/1471-2164-12-314.


Genomic MRI--a public resource for studying sequence patterns within genomic DNA.

Prakash A, Bechtel J, Fedorov A.

J Vis Exp. 2011 May 9;(51). pii: 2663. doi: 10.3791/2663.


Genomic insight into the common carp (Cyprinus carpio) genome by sequencing analysis of BAC-end sequences.

Xu P, Li J, Li Y, Cui R, Wang J, Wang J, Zhang Y, Zhao Z, Sun X.

BMC Genomics. 2011 Apr 14;12:188. doi: 10.1186/1471-2164-12-188.


TURNIP: tracking unresolved nucleotide polymorphisms in large hard-to-assemble regions of repetitive DNA sequence.

Davey RP, James SA, Dicks J, Roberts IN.

Bioinformatics. 2010 Nov 15;26(22):2908-9. doi: 10.1093/bioinformatics/btq557. Epub 2010 Oct 5.


MITE-Hunter: a program for discovering miniature inverted-repeat transposable elements from genomic sequences.

Han Y, Wessler SR.

Nucleic Acids Res. 2010 Dec;38(22):e199. doi: 10.1093/nar/gkq862. Epub 2010 Sep 29.


Sigma-2: Multiple sequence alignment of non-coding DNA via an evolutionary model.

Jayaraman G, Siddharthan R.

BMC Bioinformatics. 2010 Sep 16;11:464. doi: 10.1186/1471-2105-11-464.

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