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
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
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. Science313: 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. Imaging5: 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 Bioinformatics6: 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. Pharmacogenomics4: 313-320. PMID: 15462609
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.
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
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.