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Publications by Year: 2012

2012
C911 Calculator. 2012;
Haystack Analysis Web Server. 2012;
Buehler E, Khan AA, Marine S, Rajaram M, Bahl A, Burchard J, Ferrer M. siRNA off-target effects in genome-wide screens identify signaling pathway members. Sci Rep 2012;2(428)
Sigoillot FD, Lyman S, Huckins JF, Adamson B, Chung E, Quattrochi B, King RW. A bioinformatics method identifies prominent off-targeted transcripts in RNAi screens. Nat Methods 2012;9(4):363-6.Abstract
Because off-target effects hamper interpretation and validation of RNAi screen data, we developed a bioinformatics method, genome-wide enrichment of seed sequence matches (GESS), to identify candidate off-targeted transcripts in primary screening data. GESS analysis revealed a prominent off-targeted transcript in several screens, including MAD2 (MAD2L1) in a screen for genes required for the spindle assembly checkpoint. GESS analysis results can enhance the validation rate in RNAi screens.
Buehler E, Chen Y-C, Martin ST. C911: A bench-level control for sequence specific siRNA off-target effects. PLoS One 2012;7(12):e51942.
Snijder B, Sacher R, Rämö P, Liberali P, Mench K, Wolfrum N, Burleigh L, Scott CC, Verheije MH, Mercer J, Moese S, Heger T, Theusner K, Jurgeit A, Lamparter D, Balistreri G, Schelhaas M, De Haan CAM, Marjomäki V, Hyypiä T, Rottier PJM, Sodeik B, Marsh M, Gruenberg J, Amara A, Greber U, Helenius A, Pelkmans L. Single-cell analysis of population context advances RNAi screening at multiple levels. Mol Syst Biol 2012;8:579.
Thorn N, Shen M, Lea WA, Simeonov A, Lovell S, Auld DS, Inglese J. Firefly luciferase in chemical biology: a compendium of inhibitors, mechanistic evaluation of chemotypes, and suggested use as a reporter. . Chem Biol 2012;19(8):1060-72.
Tardiff DF, Tucci ML, Caldwell KA, Caldwell GA, Lindquist S. Different 8-hydroxyquinolines protect models of TDP-43 protein, α-synuclein, and polyglutamine proteotoxicity through distinct mechanisms [Internet]. 2012; The Journal of biological chemistry 287, 4107-20.
Rogers MS, Cryan LM, Habeshian KA, Bazinet L, Caldwell TP, Ackroyd PC, Christensen KA. A FRET-based high throughput screening assay to identify inhibitors of anthrax protective antigen binding to capillary morphogenesis gene 2 protein [Internet]. 2012; PLoS One 7(6):e39911.
Ymele-Leki P, Cao S, Sharp J, Lambert KG, McAdam AJ, Husson RN, Tamayo G, Clardy J, Watnick PI. A high-throughput screen identifies a new natural product with broad-spectrum antibacterial activity [Internet]. 2012; PLoS One 7(2):e31307.
Stahla-Beek HJ, April DG, Saeedi BJ, Hannah AM, Keenan SM, Geiss BJ. Identification of a novel antiviral inhibitor of the flavivirus guanylyltransferase enzyme [Internet]. 2012; J Virol 86(16):8730-9.
Wahome PG, Ahlawat S, Mantis NJ. Identification of small molecules that suppress ricin-induced stress-activated signaling pathways [Internet]. 2012; PLoS One 7(11):e49075.
Ortigoza MB, Dibben O, Maamary J, Martinez-Gil L, Leyva-Grado VH, Abreu P, Ayllon J, Palese P, Shaw ML. A novel small molecule inhibitor of influenza A viruses that targets polymerase function and indirectly induces interferon [Internet]. 2012; PLoS Pathog 8(4):e1002668
Schmidt AG, Lee K, Yang PL, Harrison SC. Small-molecule inhibitors of dengue-virus entry [Internet]. 2012; PLoS Pathog 8(4):e1002627.
Tan X, Hu L, Luquette LJ 3rd, Gao G, Liu Y, Qu H, Xi R, Lu ZJ, Park PJ, Elledge SJ. Systematic identification of synergistic drug pairs targeting HIV [Internet]. 2012; Nat Biotechnol 30(11):1125-30.
Ezgimen M, Lai H, Mueller NH, Lee K, Cuny G, Ostrov DA, Padmanabhan R. Characterization of the 8-hydroxyquinoline scaffold for inhibitors of West Nile virus serine protease [Internet]. 2012; Antiviral Res 94(1):18-24.
Cohen NA, Stewart ML, Gavathiotis E, Tepper JL, Bruekner SR, Koss B, Opferman JT, Walensky LD. A competitive stapled peptide screen identifies a selective small molecule that overcomes MCL-1-dependent leukemia cell survival [Internet]. 2012; Chemistry & biology 19, 1175-86.
Lee BH, Finley D, King RW. A High-Throughput Screening Method for Identification of Inhibitors of the Deubiquitinating Enzyme USP14 [Internet]. 2012; Current protocols in chemical biology 4, 311-30.
Ceyhan O, Birsoy K, Hoffman CS. Identification of biologically active PDE11-selective inhibitors using a yeast-based high throughput screen [Internet]. 2012; Chemistry & Biology, 19:155-163.
Ellenbecker M, Lanchy JM, Lodmell JS. Identification of Rift Valley Fever virus nucleocapsid protein-RNA binding inhibitors using a high-throughput screening assay [Internet]. 2012; J Biomol Screen 17(8): 1062-70.

PubChem URL Data from this screen has been deposited in PubChem Bioassay. AID #651828

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