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Structured RNAs and synteny regions in the pig genome.

Anthon C, Tafer H, Havgaard JH, Thomsen B, Hedegaard J, Seemann SE, Pundhir S, Kehr S, Bartschat S, Nielsen M, Nielsen RO, Fredholm M, Stadler PF, Gorodkin J.

BMC Genomics. 2014 Jun 10;15:459. doi: 10.1186/1471-2164-15-459.


Detection of RNA structures in porcine EST data and related mammals.

Seemann SE, Gilchrist MJ, Hofacker IL, Stadler PF, Gorodkin J.

BMC Genomics. 2007 Sep 10;8:316.


Automated detection of ncRNAs in the draft genome sequence of a colonial tunicate: the carpet sea squirt Didemnum vexillum.

Velandia-Huerto CA, Gittenberger AA, Brown FD, Stadler PF, Bermúdez-Santana CI.

BMC Genomics. 2016 Aug 30;17:691. doi: 10.1186/s12864-016-2934-5.


Homology-based annotation of non-coding RNAs in the genomes of Schistosoma mansoni and Schistosoma japonicum.

Copeland CS, Marz M, Rose D, Hertel J, Brindley PJ, Santana CB, Kehr S, Attolini CS, Stadler PF.

BMC Genomics. 2009 Oct 8;10:464. doi: 10.1186/1471-2164-10-464.


nocoRNAc: characterization of non-coding RNAs in prokaryotes.

Herbig A, Nieselt K.

BMC Bioinformatics. 2011 Jan 31;12:40. doi: 10.1186/1471-2105-12-40.


Identification and characterisation of non-coding small RNAs in the pathogenic filamentous fungus Trichophyton rubrum.

Liu T, Ren X, Xiao T, Yang J, Xu X, Dong J, Sun L, Chen R, Jin Q.

BMC Genomics. 2013 Dec 30;14:931. doi: 10.1186/1471-2164-14-931.


Conservation and losses of non-coding RNAs in avian genomes.

Gardner PP, Fasold M, Burge SW, Ninova M, Hertel J, Kehr S, Steeves TE, Griffiths-Jones S, Stadler PF.

PLoS One. 2015 Mar 30;10(3):e0121797. doi: 10.1371/journal.pone.0121797.


MicroRNA discovery by similarity search to a database of RNA-seq profiles.

Pundhir S, Gorodkin J.

Front Genet. 2013 Jul 11;4:133. doi: 10.3389/fgene.2013.00133.


Identification and annotation of noncoding RNAs in Saccharomycotina.

Cruz JA, Westhof E.

C R Biol. 2011 Aug-Sep;334(8-9):671-8. doi: 10.1016/j.crvi.2011.05.016. Review.


Plant noncoding RNA gene discovery by "single-genome comparative genomics".

Chen CJ, Zhou H, Chen YQ, Qu LH, Gautheret D.

RNA. 2011 Mar;17(3):390-400. doi: 10.1261/rna.2426511.


Identification and profiling of novel microRNAs in the Brassica rapa genome based on small RNA deep sequencing.

Kim B, Yu HJ, Park SG, Shin JY, Oh M, Kim N, Mun JH.

BMC Plant Biol. 2012 Nov 19;12:218. doi: 10.1186/1471-2229-12-218.


Structure-based whole-genome realignment reveals many novel noncoding RNAs.

Will S, Yu M, Berger B.

Genome Res. 2013 Jun;23(6):1018-27. doi: 10.1101/gr.137091.111.


Computational RNomics of drosophilids.

Rose D, Hackermüller J, Washietl S, Reiche K, Hertel J, Findeiss S, Stadler PF, Prohaska SJ.

BMC Genomics. 2007 Nov 8;8:406.


Prediction of structured non-coding RNAs in the genomes of the nematodes Caenorhabditis elegans and Caenorhabditis briggsae.

Missal K, Zhu X, Rose D, Deng W, Skogerbø G, Chen R, Stadler PF.

J Exp Zool B Mol Dev Evol. 2006 Jul 15;306(4):379-92.


Comparative analysis of structured RNAs in S. cerevisiae indicates a multitude of different functions.

Steigele S, Huber W, Stocsits C, Stadler PF, Nieselt K.

BMC Biol. 2007 Jun 18;5:25.


Genome-scale NCRNA homology search using a Hamming distance-based filtration strategy.

Sun Y, Aljawad O, Lei J, Liu A.

BMC Bioinformatics. 2012 Mar 21;13 Suppl 3:S12. doi: 10.1186/1471-2105-13-S3-S12.


Non-coding RNA annotation of the genome of Trichoplax adhaerens.

Hertel J, de Jong D, Marz M, Rose D, Tafer H, Tanzer A, Schierwater B, Stadler PF.

Nucleic Acids Res. 2009 Apr;37(5):1602-15. doi: 10.1093/nar/gkn1084.


De novo search for non-coding RNA genes in the AT-rich genome of Dictyostelium discoideum: performance of Markov-dependent genome feature scoring.

Larsson P, Hinas A, Ardell DH, Kirsebom LA, Virtanen A, Söderbom F.

Genome Res. 2008 Jun;18(6):888-99. doi: 10.1101/gr.069104.107.


ShortStack: comprehensive annotation and quantification of small RNA genes.

Axtell MJ.

RNA. 2013 Jun;19(6):740-51. doi: 10.1261/rna.035279.112.

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