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Found 1346 results
2006
Salgado H, Gama-Castro S, Peralta-Gil M, Díaz-Peredo E, Sánchez-Solano F, Santos-Zavaleta A, Martínez-Flores I, Jiménez-Jacinto V, Bonavides-Martínez C, Segura-Salazar J et al..  2006.  RegulonDB (version 5.0): Escherichia coli K-12 transcriptional regulatory network, operon organization, and growth conditions.. Nucleic Acids Res. 34(Database issue):D394-7.
Lucier J-F, Bergeron LJunior, Brière FP, Ouellette R, Elela SAbou, Perreault J-P.  2006.  RiboSubstrates: a web application addressing the cleavage specificities of ribozymes in designated genomes.. BMC Bioinformatics. 7:480.
Krüger J, Rehmsmeier M.  2006.  RNAhybrid: microRNA target prediction easy, fast and flexible.. Nucleic Acids Res. 34(Web Server issue):W451-4.
Olson A, Sheth N, Lee JS, Hannon G, Sachidanandam R.  2006.  RNAi Codex: a portal/database for short-hairpin RNA (shRNA) gene-silencing constructs.. Nucleic Acids Res. 34(Database issue):D153-7.
Alkan C, Karakoç E, Nadeau JH, S Sahinalp C, Zhang K.  2006.  RNA-RNA interaction prediction and antisense RNA target search.. J Comput Biol. 13(2):267-82.
Ren Y, Gong W, Xu Q, Zheng X, Lin D, Wang Y, Li T.  2006.  siRecords: an extensive database of mammalian siRNAs with efficacy ratings.. Bioinformatics. 22(8):1027-8.
Naito Y, Ui-Tei K, Nishikawa T, Takebe Y, Saigo K.  2006.  siVirus: web-based antiviral siRNA design software for highly divergent viral sequences.. Nucleic Acids Res. 34(Web Server issue):W448-50.
Marinescu VD, Kohane IS, Kim T-K, Harmin DA, Greenberg ME, Riva A.  2006.  START: an automated tool for serial analysis of chromatin occupancy data.. Bioinformatics. 22(8):999-1001.
Sethupathy P, Corda B, Hatzigeorgiou AG.  2006.  TarBase: A comprehensive database of experimentally supported animal microRNA targets.. RNA. 12(2):192-7.
Jacobs GH, Stockwell PA, Tate WP, Brown CM.  2006.  Transterm--extended search facilities and improved integration with other databases.. Nucleic Acids Res. 34(Database issue):D37-40.
Cheung THiu, Kwan YLam, Hamady M, Liu X.  2006.  Unraveling transcriptional control and cis-regulatory codes using the software suite GeneACT.. Genome Biol. 7(10):R97.
2005
Yamada T, Morishita S.  2005.  Accelerated off-target search algorithm for siRNA.. Bioinformatics. 21(8):1316-24.
Dror O, Nussinov R, Wolfson H.  2005.  ARTS: alignment of RNA tertiary structures.. Bioinformatics. 21 Suppl 2:ii47-53.
Gustafson AM, Allen E, Givan S, Smith D, Carrington JC, Kasschau KD.  2005.  ASRP: the Arabidopsis Small RNA Project Database.. Nucleic Acids Res. 33(Database issue):D637-40.
Fox JA, Butland SL, McMillan S, Campbell G, Ouellette BFFrancis.  2005.  The Bioinformatics Links Directory: a compilation of molecular biology web servers.. Nucleic Acids Res. 33(Web Server issue):W3-24.
Xue C, Li F, He T, Liu G-P, Li Y, Zhang X.  2005.  Classification of real and pseudo microRNA precursors using local structure-sequence features and support vector machine.. BMC Bioinformatics. 6:310.
Krek A, Grün D, Poy MN, Wolf R, Rosenberg L, Epstein EJ, MacMenamin P, da Piedade I, Gunsalus KC, Stoffel M et al..  2005.  Combinatorial microRNA target predictions.. Nat Genet. 37(5):495-500.
Dieterich C, Grossmann S, Tanzer A, Röpcke S, Arndt PF, Stadler PF, Vingron M.  2005.  Comparative promoter region analysis powered by CORG.. BMC Genomics. 6:24.
Adai A, Johnson C, Mlotshwa S, Archer-Evans S, Manocha V, Vance V, Sundaresan V.  2005.  Computational prediction of miRNAs in Arabidopsis thaliana.. Genome Res. 15(1):78-91.
Lewis BP, Burge CB, Bartel DP.  2005.  Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets.. Cell. 120(1):15-20.
Naito Y, Yamada T, Matsumiya T, Ui-Tei K, Saigo K, Morishita S.  2005.  dsCheck: highly sensitive off-target search software for double-stranded RNA-mediated RNA interference.. Nucleic Acids Res. 33(Web Server issue):W589-91.
Arziman Z, Horn T, Boutros M.  2005.  E-RNAi: a web application to design optimized RNAi constructs.. Nucleic Acids Res. 33(Web Server issue):W582-8.
Watt TJ, Doyle DF.  2005.  ESPSearch: a program for finding exact sequences and patterns in DNA, RNA, or protein.. Biotechniques. 38(1):109-15.
Washietl S, Hofacker IL, Stadler PF.  2005.  Fast and reliable prediction of noncoding RNAs.. Proc Natl Acad Sci U S A. 102(7):2454-9.
Yiu SM, Wong PWH, Lam TW, Mui YC, Kung HF, Lin M, Cheung YT.  2005.  Filtering of ineffective siRNAs and improved siRNA design tool.. Bioinformatics. 21(2):144-51.

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