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Publications

2013
Lee K, Ren T, Côté M, Gholamreza B, Misasi J, Bruchez A, Cunningham J. Inhibition of Ebola virus infection: identification of Niemann-Pick C1 as the target by optimization of a chemical probe. ACS Med Chem Lett 2013;4(2):239-243.
Lee Y, Mootien S, Shoen C, Destefano M, Cirillo P, Asojo OA, Yeung KR, Ledizet M, Cynamon MH, Aristoff PA, Koski RA, Kaplan PA, Anthony KG. Inhibition of mycobacterial alanine racemase activity and growth by thiadiazolidinones [Internet]. 2013; Biochem Pharmacol. Jul 15;86(2):222-30.
Le X, Pugach EK, Hettmer S, Storer NY, Liu J, Wills AA, DiBiase A, Chen EY, Ignatius MS, Poss KD, Wagers AJ, Langenau DM, Zon L. A novel chemical screening strategy in zebrafish identifies common pathways in embryogenesis and rhabdomyosarcoma development [Internet]. 2013; Development (Cambridge, England) 140, 2354-64
Chamoun-Emanuelli AM, Pecheur EI, Simeon RL, Huang D, Cremers PS, Chen Z. Phenothiazines inhibit hepatitis C virus entry, likely by increasing the fluidity of cholesterol-rich membranes [Internet]. 2013; Antimicrob Agents Chemother. Jun;57(6):2571-81.
Lafleur MD, Sun L, Lister I, Keating J, Nantel A, Long L, Ghannoum M, North J, Lee RE, Coleman K, Dahl T, Lewis K. Potention of azole antifungals by 2-adamantanamine [Internet]. 2013; Antimicrob Agents Chemother Aug;57(8):3585-92.
Kirienko NV, Kirienko DR, Larkins-Ford J, Wählby C, Ruvkun G, Ausubel FM. Pseudomonas aeruginosa Disrupts Caenorhabditis elegans Iron Homeostasis, Causing a Hypoxic Response and Death [Internet]. 2013; Cell host & microbe 13, 406-16.

Data from this screen has been deposited in PubChem Bioassay. AID #651566

Chen C, Shanmugasundaram K, Rigby AC, Kung AL. Shikonin, a natural product from the root of Lithospermum erythrorhizon, is a cytotoxic DNA-binding agent [Internet]. 2013; Eur J Pharm Sci Apr 11;49(1):18-26.
Lu L, Hannoush RN, Goess BC, Varadarajan S, Shair MD, Kirchhausen T. The small molecule dispergo tubulates the endoplasmic reticulum and inhibits export [Internet]. 2013; Molecular biology of the cell 24, 1020-9.
Richter SG, Elli D, Kim HK, Hendrickx AP, Sorg JA, Schneewind O, Missiakas D. Small molecule inhibitor of lipoteichoic acid synthesis is an antibiotic for Gram-positive bacteria [Internet]. 2013; Proc Natl Acad Sci U S A 110(9):3531-6.

Data from this screen has been deposited in PubChem Bioassay. AID #720641

Gampe CM, Tsukamoto H, Doud EH, Walker S, Kahne D. Tuning the moenomycin pharmacophore to enable discovery of bacterial cell wall synthesis inhibitors [Internet]. 2013; J Am Chem Soc 135(10):3776-9.
Demirbas D, Wyman AR, Shimizu-Albergine M, Cakici O, Beavo JA, Hoffman CS. A Yeast-Based Chemical Screen Identifies A PDE Inhibitor That Elevates Steroidogenesis In Mouse Leydig Cells via PDE8 And PDE4 Inhibition [Internet]. 2013; PLoS One. 2013;8(8):e71279.
Fusco DN, Brisac C, John SP, Huang YW, Chin CR, Xie T, Zhao H, Zhang L, Chevalier S, Wambua D, Lin W, Peng L, Chung RT, Brass AL. A genetic screen identifies interferon-α effector genes required to suppress hepatitis C virus replication. Gastroenterology 2013;Jun; 144(7):1438-49.
Petrocca F, Altschuler G, Tan SM, Mendillo ML, Yan H, Jerry DJ, Kung AL, Hide W, Ince TA, Lieberman J. A genome-wide siRNA screen identifies proteasome addiction as a vulnerability of basal-like triple-negative breast cancer cells. Cancer Cell 2013;24(2):182-96.
Caradonna KL, Engel JC, Jacobi D, Lee CH, Burleigh BA. Host metabolism regulates intracellular growth of Trypanosoma cruzi. Cell Host Microbe 2013;Jan 16;13(1):108-17.
Lee MN, Roy M, Ong SE, Mertins P, Villani AC, Li W, Dotiwala F, Sen J, Doench JG, Orzalli MH, Kramnik I, Knipe DM, Lieberman J, Carr SA, Hacohen N. Identification of regulators of the innate immune response to cytosolic DNA and retroviral infection by an integrative approach [Internet]. 2013; Nat Immunol Feb;14(2):179-85.
Sharma S, Quintana A, Findlay GM, Mettlen M, Baust B, Jain M, Nilsson R, Rao A, Hogan PG. An siRNA screen for NFAT activation identifies septins as coordinators of store-operated Ca2+ entry. Nature 2013;Jul 11; 499(7457):238-42.
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.

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