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Found 1346 results
2011
Kadri S, Hinman VF, Benos PV.  2011.  RNA deep sequencing reveals differential microRNA expression during development of sea urchin and sea star.. PLoS One. 6(12):e29217.
Bateman A, Agrawal S, Birney E, Bruford EA, Bujnicki JM, Cochrane G, Cole JR, Dinger ME, Enright AJ, Gardner PP et al..  2011.  RNAcentral: A vision for an international database of RNA sequences.. RNA. 17(11):1941-6.
Xu G, Deng N, Zhao Z, Judeh T, Flemington E, Zhu D.  2011.  SAMMate: a GUI tool for processing short read alignments in SAM/BAM format.. Source Code Biol Med. 6(1):2.
Bao E, Jiang T, Kaloshian I, Girke T.  2011.  SEED: efficient clustering of next-generation sequences.. Bioinformatics. 27(18):2502-9.
David M, Dzamba M, Lister D, Ilie L, Brudno M.  2011.  SHRiMP2: sensitive yet practical SHort Read Mapping.. Bioinformatics. 27(7):1011-2.
Thieme CJ, Gramzow L, Lobbes D, Theissen G.  2011.  SplamiR--prediction of spliced miRNAs in plants.. Bioinformatics. 27(9):1215-23.
Yang J-H, Li J-H, Shao P, Zhou H, Chen Y-Q, Qu L-H.  2011.  starBase: a database for exploring microRNA-mRNA interaction maps from Argonaute CLIP-Seq and Degradome-Seq data.. Nucleic Acids Res. 39(Database issue):D202-9.
Fei Z, Joung J-G, Tang X, Zheng Y, Huang M, Lee JMin, McQuinn R, Tieman DM, Alba R, Klee HJ et al..  2011.  Tomato Functional Genomics Database: a comprehensive resource and analysis package for tomato functional genomics.. Nucleic Acids Res. 39(Database issue):D1156-63.
Cutts RJ, Gadaleta E, Lemoine NR, Chelala C.  2011.  Using BioMart as a framework to manage and query pancreatic cancer data.. Database (Oxford). 2011:bar024.
Lorenz R, Bernhart SH, Siederdissen CHöner Zu, Tafer H, Flamm C, Stadler PF, Hofacker IL.  2011.  ViennaRNA Package 2.0.. Algorithms Mol Biol. 6:26.
Zhao W, Liu W, Tian D, Tang B, Wang Y, Yu C, Li R, Ling Y, Wu J, Song S et al..  2011.  wapRNA: a web-based application for the processing of RNA sequences.. Bioinformatics. 27(21):3076-7.
Garcia DM, Baek D, Shin C, Bell GW, Grimson A, Bartel DP.  2011.  Weak seed-pairing stability and high target-site abundance decrease the proficiency of lsy-6 and other microRNAs.. Nat Struct Mol Biol. 18(10):1139-46.
Hackenberg M, Carpena P, Bernaola-Galván P, Barturen G, Alganza AM, Oliver JL.  2011.  WordCluster: detecting clusters of DNA words and genomic elements.. Algorithms Mol Biol. 6:2.
2010
Emig D, Salomonis N, Baumbach J, Lengauer T, Conklin BR, Albrecht M.  2010.  AltAnalyze and DomainGraph: analyzing and visualizing exon expression data.. Nucleic Acids Res. 38(Web Server issue):W755-62.
Jin P, Ji X, Wang H, Li-Ling J, Ma F.  2010.  AmphiEST: Enabling comparative analysis of ESTs from five developmental stages of amphioxus.. Mar Genomics. 3(3-4):151-5.
Vaz C, Ahmad HM, Sharma P, Gupta R, Kumar L, Kulshreshtha R, Bhattacharya A.  2010.  Analysis of microRNA transcriptome by deep sequencing of small RNA libraries of peripheral blood.. BMC Genomics. 11:288.
Liu H, Yue D, Zhang L, Chen Y, Gao S-J, Huang Y.  2010.  A Bayesian approach for identifying miRNA targets by combining sequence prediction and gene expression profiling.. BMC Genomics. 11 Suppl 3:S12.
Friard O, Re A, Taverna D, De Bortoli M, Corá D.  2010.  CircuitsDB: a database of mixed microRNA/transcription factor feed-forward regulatory circuits in human and mouse.. BMC Bioinformatics. 11:435.
Forman JJ, Coller HA.  2010.  The code within the code: microRNAs target coding regions.. Cell Cycle. 9(8):1533-41.
Dassanayake M, Haas JS, Bohnert HJ, Cheeseman JM.  2010.  Comparative transcriptomics for mangrove species: an expanding resource.. Funct Integr Genomics. 10(4):523-32.
Lee LWee, Zhang S, Etheridge A, Ma L, Martin D, Galas D, Wang K.  2010.  Complexity of the microRNA repertoire revealed by next-generation sequencing.. RNA. 16(11):2170-80.
Betel D, Koppal A, Agius P, Sander C, Leslie C.  2010.  Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites.. Genome Biol. 11(8):R90.
Liu G, Ding M, Chen J, Huang J, Wang H, Jing Q, Shen B.  2010.  Computational analysis of microRNA function in heart development.. Acta Biochim Biophys Sin (Shanghai). 42(9):662-70.
Li L, Xu J, Yang D, Tan X, Wang H.  2010.  Computational approaches for microRNA studies: a review.. Mamm Genome. 21(1-2):1-12.
Mahalingam G, Meyers BC.  2010.  Computational methods for comparative analysis of plant small RNAs.. Methods Mol Biol. 592:163-81.

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