Publications

  • Clemons, P.A., Wilson, J.A., Dančík, V., Muller, S., Carrinski, H.A., Wagner, B.K., Koehler, A.N., Schreiber, S.L. (2011). Quantifying structure and performance diversity for sets of small molecules comprising small-molecule screening collections. Proc. Natl. Acad. Sci. USA, 108: 6817-6822.
  • Hung, A.W., Ramek, A., Wang, Y., Kaya, T., Wilson, J.A., Clemons, P.A., Young, D.W. (2011). Route to three-dimensional fragments using diversity-oriented synthesis. Proc. Natl. Acad. Sci. USA, 108: 6799-6804.
  • Bochner, B.R., Siri, M., Huang, R.H., Noble, S., Lei, X.H., Clemons, P.A., Wagner, B.K. (2011). Assay of the multiple energy-producing pathways of mammalian cells. PLoS One, 6: e18147.
  • Kim Y.K., Lee, J.-S., Bi, X., Ha, H.-H., Ng, S.H., Ahn, Y., Lee J.-J., Wagner, B.K., Clemons, P.A., Chang, Y.-T. (2011). The binding of fluorophores to proteins depends on the cellular environment. Angew. Chem. Int. Ed., 50: 2761-2763.
  • Shaw S.Y., Blodgett D.M., Ma M.S., Westly E.C., Clemons P.A., Subramanian A., Schreiber S.L. (2011). Disease allele-dependent small-molecule sensitivities in blood cells from monogenic diabetes. Proc. Natl. Acad. Sci. USA, 108: 492-497. PMCID: PMC3021060
  • Muncipinto G., Kaya T., Wilson J.A., Kumagai N., Clemons P.A., Schreiber S.L. (2010). Expanding stereochemical and skeletal diversity using petasis reactions and 1,3-dipolar cycloadditions. Org. Lett., 12: 5230-5233. PMCID: PMC2979010
  • Clemons, P.A., Bodycombe, N.E., Carrinski, H.A., Wilson, J.A., Shamji, A.F., Wagner, B.K., Koehler, A.N., Schreiber S.L. (2010). Small molecules of different natural and synthetic origins have distinct distributions of structural complexity that correlate with protein-binding profiles. Proc. Natl. Acad. Sci. USA, 107: 18787-18792. PMCID: PMC2973913
  • Schreiber S.L., Shamji A.F., Clemons P.A., Hon C., Koehler A.N., Munoz B., Palmer M., Stern A.M., Wagner B.K., Powers S., Lowe S.W., Guo X., Krasnitz A., Sawey E.T., Sordella R., Stein L., Trotman L.C., Califano A., Dalla-Favera R., Ferrando A., Iavarone A., Pasqualucci L., Silva J., Stockwell B.R., Hahn W.C., Chin L., DePinho R.A., Boehm J.S., Gopal S., Huang A., Root D.E., Weir B.A., Gerhard D.S., Zenklusen J.-C., Roth M.G., White M.A., Minna J.D., MacMillan J.B., Posner B.A. (2010). Towards patient-based cancer therapeutics. Nat Biotechnol., 28: 904-906. PMCID: PMC2939009
  • Fomina-Yadlin, D., Kubicek, S., Walpita, D., Dančík, V., Hecksher-Sorensen, J., Bittker, J.A., Sharifnia, T., Shamji, A., Clemons, P.A., Wagner, B.K., Schreiber S.L. (2010). Small-molecule inducers of insulin expression in pancreatic alpha-cells. Proc. Natl. Acad. Sci. USA, 107: 15099-15104. PMCID: PMC2930573
  • Chou, D.H., Bodycombe, N.E., Carrinski, H.A., Lewis, T.A., Clemons, P.A., Schreiber, S.L., Wagner, B.K. (2010). Small-molecule suppressors of cytokine-induced beta-cell apoptosis. ACS Chem. Biol., 5: 729-734. PMCID: PMC2924935
  • Pizzirani, D., Kaya, T., Clemons, P.A., Schreiber, S.L. (2010). Stereochemical and skeletal diversity arising from amino propargylic alcohols. Org. Lett., 12: 2822-2825. PMCID: PMC2883853
  • Dančík, V., Seiler, K.P., Young, D.W., Schreiber, S.L., Clemons, P.A. (2010). Distinct biological network properties between the targets of natural products and disease genes. J. Am. Chem. Soc., 132: 9259-9261. PMCID: PMC2898216
  • Swamidass, S.J., Bittker, J.A., Bodycombe, N.E., Ryder, S.P., Clemons, P.A. (2010). An economic framework to prioritize confirmatory tests after a high-throughput screen. J. Biomol. Screen., 15: 680-686. PMID: 20547534
  • Clemons, P.A., Wagner, B.K. (2009). Connecting synthetic chemistry decisions to cell and genome biology using small-molecule phenotypic profiling. Curr. Opin. Chem. Biol. 13: 539-548. PMCID: PMC2787914
  • Wilson, J.A., Bender, A., Kaya, T., Clemons, P.A. (2009). Alpha shapes applied to molecular shape characterization exhibit novel properties compared to established shape descriptors. J. Chem. Inf. Model. 49: 2231-2241. PMID: 19775113
  • Clemons, P.A., Tolliday N.J., Wagner, B.K., eds. (2009). Cell-Based Assays for High-Throughput Screening; Humana Press; New York, NY, USA
  • Tanikawa, T., Fridman, M., Zhu, W., Faulk, B., Joseph, I.C., Kahne, D., Wagner, B.K., Clemons, P.A. (2009). Using biological performance similarity to inform disaccharide library design. J. Am. Chem. Soc. 131: 5075-5083. PMCID: PMC2730776
  • Kelly, K.A., Shaw, S.Y., Nahrendorf, M., Kristoff, K., Aikawa, E., Schreiber, S.L., Clemons, P.A., Weissleder, R. (2009). Unbiased discovery of in vivo imaging probes through in vitro profiling of nanoparticle libraries. Integr. Biol. 1: 311-317. PMCID: PMC2748356
  • Seiler, K.P., Kuehn, H., Happ, M.P., DeCaprio, D., Clemons, P.A. (2008). Using ChemBank to probe chemical biology. Curr. Protoc. Bioinformatics Chapter 14: Unit 14.5. PMID: 18551413
  • Wagner, B.K., Carrinski, H.A., Ahn, Y.-H., Kim, Y.K., Gilbert, T.J., Fomina, D.A., Schreiber, S.L., Chang, Y.-T., Clemons, P.A. (2008). Small-molecule fluorophores to detect cell-state switching in the context of high-throughput screening. J. Am. Chem. Soc. 130: 4208-4209. PMID: 18327938
  • Seiler, K.P., George, G.A., Happ, M.P., Bodycombe, N.E., Carrinski, H.A., Norton, S., Brudz, S., Sullivan, J.P., Muhlich, J., Serrano, M., Ferraiolo, P., Tolliday, N.J., Schreiber, S.L., Clemons, P.A. (2008). ChemBank: a small-molecule screening and cheminformatics resource database. Nucl. Acids Res. 36: D351-D359. PMCID: PMC2238881
  • Bender, A., Young, D.W., Jenkins, J.L., Serrano, M., Mikhailov, D., Clemons, P.A., Davies, J.W. (2007). Chemogenomic data analysis: prediction of small-molecule targets and the advent of biological fingerprints. Comb. Chem. High Throughput Screen. 10: 719-731. PMID: 18045083
  • Clemons, P.A. (2007). Chemical Informatics, in Chemical Biology: From small molecules to systems biology and drug design, Volume 2; Schreiber, S.L., Kapoor, T., Wess, G., eds., Wiley-VCH Verlag GmbH & Co., KGaA; Weinheim, Germany.
  • Duffner, J.L., Clemons, P.A., Koehler, A.N. (2007). A pipeline for ligand discovery using small-molecule microarrays. Curr. Opin. Chem. Biol. 11: 74-82.
  • Lamb, J., Crawford, E.D., Peck, D., Modell, J.W., Blat, I.C., Wrobel, M.J., Lerner, J., Brunet, J.-P., Subramanian, A., Ross, K.N., Reich, M., Hieronymus, H., Wei, G., Armstrong, S.A., Haggarty, S.J., Clemons, P.A., Wei, R., Carr, S.A., Lander, E.S., Golub, T.R. (2006). The Connectivity Map: Using gene-expression signatures to connect small molecules, genes, and disease. Science 313: 1929-1935. PMID: 17008526
  • Tolliday, N., Clemons, P.A., Ferraiolo, P., Koehler, A.N., Lewis, T.A., Li, X., Schreiber, S.L., Gerhard, D.S., Eliasof, S. (2006). Small molecules, big players: the National Cancer Institute's Initiative for Chemical Genetics. Cancer Res. 66: 8935-8942. PMID: 16982730
  • Kelly, K.A., Clemons, P.A., Yu, A.M., Weissleder R. (2006). High-throughput identification of phage-derived imaging agents. Mol. Imaging 5: 24-30. PMID: 16779967
  • Forman, J. J., Clemons, P.A., Schreiber, S.L., Haggarty, S.J. (2005). SpectralNET—an application for spectral graph analysis and visualization. BMC Bioinformatics 6: 260-272. PMCID: PMC1276787
  • Kim, Y.-K., Arai, M.A., Arai, T., Lamenzo, J.O., Dean, E.F., Patterson, N., Clemons, P.A., Schreiber, S.L. (2004). Relationship of stereochemical and skeletal diversity of small molecules to cellular measurement space. J. Am. Chem. Soc. 126: 14740-14746. PMID: 15535697
  • Haggarty, S.J., Wong, J.C., Clemons, P.A., Schreiber, S.L. (2004). Mapping chemical space using molecular descriptors and chemical genetics: deacetylase inhibitors. Comb. Chem. High Throughput Screen. 7: 669-676. PMID: 15578929
  • Wagner, B.K., Haggarty, S.J., Clemons, P.A. (2004). Chemical genomics: probing protein function using small molecules. Am. J. Pharmacogenomics 4: 313-320. PMID: 15462609
  • Clemons, P.A. (2004). Complex phenotypic assays in high-throughput screening. Curr. Opin. Chem. Biol. 8: 334-338. PMID: 15183333
  • Haggarty, S.J., Clemons, P.A., Schreiber, S.L. (2003). Chemical genomic profiling of biological networks using graph theory and combinations of small molecule perturbations. J. Am. Chem. Soc. 125: 10543-10545. PMID: 12940736
  • Clemons, P.A. (2003). Case Study: Collaborative Power. Biotech Tech. 2: 22-23.
  • Clemons, P.A. (2003). Cross-town traffic. Scientific Computing & Instrumentation 20: 36-42.
  • Wang, B., Nguyen, M., Breckenridge, D.G., Stojanovic, M., Clemons, P.A., Kuppig, S., Shore, G.C. (2003). Uncleaved BAP31 in association with A4 protein at the endoplasmic reticulum is an inhibitor of Fas-initiated release of cytochrome c from mitochondria. J. Biol. Chem. 278: 14461-14468. PMID: 12529377
  • Wagner, B.K., Clemons, P.A. (2002). Dual-purpose drug discovery. Trends Biotech. 20: 492-493.
  • Clemons, P.A., Gladstone, B.G., Seth, A., Chao, E.D., Foley, M.A., Schreiber, S.L. (2002). Synthesis of calcineurin-resistant derivatives of FK506 and selection of compensatory receptors. Chem. Biol. 9: 49-61. PMID: 11841938
  • Clemons, P.A. (2001). Systematic chemical genetic approaches to explore the roles of protein proximity in signal transduction. Ph.D. thesis, Harvard University.
  • Wagner, B.K., Clemons, P.A. (2001). An even-handed approach. Trends Biotech. 20: 53.
  • Clemons, P.A., Koehler, A.N., Wagner, B.K., Sprigings, T.G., Spring, D.R., King, R.W., Schreiber, S.L., Foley, M.A. (2001). A one-bead, one-stock solution approach to chemical genetics, part two. Chem. Biol. 8: 1183-1195. PMID: 11755397
  • Clemons, P.A., Wagner, B.K. (2001). Hay in a needlestack? Trends Biotech. 19: 435-436.
  • Blackwell, H.E., Clemons, P.A., Schreiber, S.L. (2001). Exploiting site-site interactions on solid support to generate dimeric molecules. Org. Lett. 3: 1185-1188. PMID: 11348190
  • Wagner, B.K., Clemons, P.A. (2001). Better signaling through chemistry. Trends Biotech. 19: 127.
  • Clemons, P.A. (2000). Be still my beating heart. Trends Biotech. 18: 407. PMID: 10998505
  • Clemons, P.A. (1999). Design and discovery of protein dimerizers. Curr. Opin. Chem. Biol. 3: 112-115. PMID: 10021413