Publications

1. Sundberg TB, Xavier RJ, Schreiber SL, and Shamji AF. Small-molecule control of cytokine function: new opportunities for treating immune disorders. Curr Opin Chem Biol. 2014;23C:23-30. PMCID: PMC Journal - In Process

2. Sundberg TB, Choi HG, Song JH, Russell CN, Hussain MM, Graham DB, Khor B, Gagnon J, O'Connell DJ, Narayan K, Dančík V, Perez JR, Reinecker HC, Gray NS, #Schreiber SL, #Xavier RJ, and #Shamji AF. Small-molecule screening identifies inhibition of salt-inducible kinases as a therapeutic strategy to enhance immunoregulatory functions of dendritic cells. Proc Natl Acad Sci USA. 2014;111(34):12468-73. PMCID: PMC4151730

3. Adams DJ, Ito D, Rees MG, Seashore-Ludlow B, Puyang X, Ramos AH, Cheah JH, Clemons PA, Warmuth M, #Zhu P, #Shamji AF, and Schreiber SL. NAMPT is the cellular target of STF-31-like small-molecule probes. ACS Chem Biol. 2014 [Epub ahead of print] PMCID: PMC Journal - In Process

4. Wawer MJ, Li K, Gustafsdottir SM, Ljosa V, Bodycombe NE, Marton MA, Sokolnicki KL, Bray MA, Kemp MM, Winchester E, Taylor B, Grant GB, Hon CS, Duvall JR, Wilson JA, Bittker JA, Dančík V, Narayan R, Subramanian A, Winckler W, Golub TR, Carpenter AE, Shamji AF, Schreiber SL, and Clemons PA. Toward performance-diverse small-molecule libraries for cell-based phenotypic screening using multiplexed high-dimensional profiling. Proc Natl Acad Sci USA. 2014;111(30):10911-6. PMCID: PMC4121832

5. Lassen KG, Kuballa P, Conway KL, Patel KK, Becker CE, Peloquin JM, Villablanca EJ, Norman JM, Liu TC, Heath RJ, Becker ML, Fagbami L, Horn H, Mercer J, Yilmaz OH, Jaffe JD, Shamji AF, Bhan AK, Carr SA, Daly MJ, Virgin HW, Schreiber SL, Stappenbeck TS, and Xavier RJ. Atg16L1 T300A variant decreases selective autophagy resulting in altered cytokine signaling and decreased antibacterial defense. Proc Natl Acad Sci USA. 2014;111(21):7741-6. PMCID: PMC4040621

6. Wawer MJ, Jaramillo DE, Dančík V, Fass DM, Haggarty SJ, Shamji AF, Wagner BK, Schreiber SL, and Clemons PA. Automated Structure-Activity Relationship Mining: Connecting Chemical Structure to Biological Profiles. J Biomol Screen. 2014;19(5):738-748. PMCID: PMC Journal - In Process

7. Dancík V, Carrel H, Bodycombe NE, Seiler KP, Fomina-Yadlin D, Kubicek ST, Hartwell K, Shamji AF, Wagner BK, and Clemons PA. Connecting Small Molecules with Similar Assay Performance Profiles Leads to New Biological Hypotheses. J Biomol Screen. 2014;19(5):771-781. Epub ahead of print. PMCID: PMC Journal - In Process

8. Yang WS, Sriramaratnam R, Welsch M, Shimada K, Skouta R, Viswanathan VS, Cheah JH, Clemons PA, Shamji AF, Clish CB, Brown LM, Girotti AW, Cornish VW, Schreiber SL, and Stockwell BR. Regulation of Ferroptotic Cancer Cell Death by GPX4. Cell. 2014;156(1-2):317-31. PMCID: PMC4076414

9. Shaw SY, Tran K, Castoreno AB, Peloquin JM, Lassen KG, Khor B, Aldrich LN, Tan PH, Graham DB, Kuballa P, Goel G, Daly MJ, Shamji AF, Schreiber SL, and Xavier RJ. Selective Modulation of Autophagy, Innate Immunity, and Adaptive Immunity by Small Molecules. ACS Chem Biol. 2013;8(12):2724-33. PMCID: PMC3951132

10. Conway KL, Kuballa P, Song JH, Patel KK, Castoreno AB, Yilmaz OH, Jijon HB, Zhang M, Aldrich LN, Villablanca EJ, Peloquin JM, Goel G, Lee IA, Mizoguchi E,Shi HN, Bhan AK, Shaw SY, Schreiber SL, Virgin HW, Shamji AF, Stappenbeck TS, Reinecker HC, and Xavier RJ. Atg16l1 is required for autophagy in intestinal epithelial cells and protection of mice from Salmonella infection. Gastroenterology. 2013;145(6):1347-57. PMCID: PMC3840157

11. Hartwell KA, Miller PG, Mukherjee S, Kahn AR, Stewart AL, Logan DJ, Negri JM, Duvet M, Järås M, Puram R, Dancik V, Al-Shahrour F, Kindler T, Tothova Z, Chattopadhyay S, Hasaka T, Narayan R, Dai M, Huang C, Shterental S, Chu LP, Haydu JE, Shieh JH, Steensma DP, Munoz B, Bittker JA, Shamji AF, Clemons PA, Tolliday NJ, Carpenter AE, Gilliland DG, Stern AM, Moore MA, Scadden DT, Schreiber SL, Ebert BL, and Golub TR. Niche-based screening identifies small-molecule inhibitors of leukemia stem cells. Nat Chem Biol. 2013;9(12):840-8. PMCID: PMC4009363

12. Basu A, Bodycombe NE, Cheah JH, Price EV, Liu K, Schaefer GI, Ebright RY, Stewart ML, Ito D, Wang S, Bracha AL, Liefeld T, Wawer M, Gilbert JC, Wilson AJ, Stransky N, Kryukov GV, Dancik V, Barretina J, Garraway LA, Hon CS, Munoz B, Bittker JA, Stockwell BR, Khabele D, Stern AM, Clemons PA, Shamji AF, and Schreiber SL. An interactive resource to identify cancer genetic and lineage dependencies targeted by small molecules. Cell. 2013;154(5):1151-61. PMCID: PMC3954635

13. Schaefer GI, Perez JR, Duvall JR, Stanton BZ, Shamji AF, and Schreiber SL. Discovery of small-molecule modulators of the Sonic Hedgehog pathway. J Am Chem Soc. 2013;135(26):9675-80. PMCID: PMC3703668

14. Yuan Y, Tang AJ, Castoreno AB, Kuo SY, Wang Q, Kuballa P, Xavier R, Shamji AF, Schreiber SL, and Wagner BK. Gossypol and an HMT G9a inhibitor act in synergy to induce cell death in pancreatic cancer cells. Cell Death Dis. 2013;4:e690. PMCID: PMC3702302

15. Adams DJ, Boskovic ZV, Theriault JR, Wang AJ, Stern AM, Wagner BK, Shamji AF, and Schreiber SL. Discovery of small-molecule enhancers of reactive oxygen species that are nontoxic or cause genotype-selective cell death ACS Chem Biol. 2013;8(5):923-9. PMCID: PMC3658551

16. Gustafsdottir SM, Ljosa V, Sokolnicki KL, Wilson JA, Walpita D, Kemp M, Seiler KP, Carrel HA, Golub TR, Schreiber SL, Clemons PA, Carpenter AE, and Shamji AF. Multiplex Cytological Profiling Assay to Measure Diverse Cellular States. PLoS ONE. 2013;8(12):e80999. PMCID: PMC3847047

17. Adams DJ, Dai M, Pellegrino G, Wagner BK, Stern A, Shamji AF, and Schreiber, SL. Synthesis, cellular evaluation, and mechanism of action of piperlongumine analogs. Proc Natl Acad Sci USA. 2012;109(38):15115-20. PMCID: PMC3458345

18. Yuan Y, Wang Q, Paulk J, Kubicek S, Kemp MM, Adams DJ, #Shamji AF, #Wagner BK, and #Schreiber SL. A Small-Molecule Probe of the Histone Methyltransferase G9a Induces Cellular Senescence in Pancreatic Adenocarcinoma. ACS Chem Biol. 2012;7(7):1152-7. Epub 2012 Apr 30. PMCID: PMC3401036

19. Kubicek S, Gilbert JC, Fomina-Yadlin D, Gitlin AD, Yuan Y, Wagner FF, Holson EB, Luo T, Lewis TA, Taylor B, Gupta S, Shamji AF, Wagner BK, Clemons PA, and Schreiber SL. Chromatin-targeting small molecules cause class-specific transcriptional changes in pancreatic endocrine cells. Proc Natl Acad Sci USA. 2012;109(14):5364-9. Epub 2012 Mar 20. PMCID: PMC3325696

20. Walpita D, Hasaka T, Spoonamore J, Vetere A, Takane KK, Fomina-Yadlin D, Fiaschi-Taesch N, Shamji AF, Clemons PA, Stewart AF, Schreiber SL, and Wagner BK. A Human Islet Culture System for High-Throughput Screening. J Biomol Screen 2012;17(4):509-18. Epub 2011 Dec 7. PMCID: PMC Journal - In Process

21. Raj L, Ide T, Gurkar AU, Foley M, Schenone M, Li X, Tolliday NJ, Golub TR, Carr SA, Shamji AF, Stern AM, Mandinova A, Schreiber SL, and Lee SW. Selective killing of cancer cells by a small molecule targeting the stress response to ROS. Nature 2011;475(7355):231-4. PMCID: PMC3316487

22. Clemons PA, Bodycombe NE, Carrinski HA, Wilson JA, Shamji AF, Wagner BK, Koehler AN, and Schreiber SL. Small molecules of different origins have distinct distributions of structural complexity that correlate with protein-binding profiles. Proc Natl Acad Sci USA. 2010;107(44):18787-92. PMCID: PMC2973913

23. Schreiber SL, Shamji AF, Clemons PA, Hon C, Koehler AN, Munoz B, Palmer M, Stern AM, Wagner BK, Powers S, Lowe SW, Guo X, Krasnitz A, Sawey ET, Sordella R, Stein L, Trotman LC, Califano A, Dalla-Favera R, Ferrando A, Iavarone A, Pasqualucci L, Silva J, Stockwell BR, Hahn WC, Chin L, DePinho RA, Boehm JS, Gopal S, Huang A, Root DE, Weir BA, Gerhard DS, Zenklusen JC, Roth MG, White MA, Minna JD, MacMillan JB, and Posner BA. Towards patient-based cancer therapeutics. Nat Biotechnol 2010;28(9):904-6. PMCID: PMC2939009

24. Fomina-Yadlin D, Kubicek S, Walpita D, Dancik V, Hecksher-Sørensen J, Bittker JA, Sharifnia T, Shamji AF, Clemons PA, Wagner BK, and Schreiber SL. Small-molecule inducers of insulin expression in pancreatic alpha-cells. Proc Natl Acad Sci USA. 2010;107(34):15099-104. PMCID: PMC2930573

25. Yang J, Shamji AF, Matchacheep S, and Schreiber SL. Identification of a small-molecule inhibitor of class Ia PI3Ks using cell-based screening. Chemistry and Biology 2007;14(4):371-377. 

26. *Humphrey EH, *Shamji AF, Bernstein BE, and Schreiber SL. Rpd3p relocation mediates a transcriptional response to rapamycin in yeast. Chemistry and Biology 2004;11(3):295-299.

27. Shamji AF, Nghiem P, and Schreiber SL. Integration of growth factor and nutrient signaling: implications for cancer biology (review). Molecular Cell 2003;12(2):271-280. 

28. Koehler AN, Shamji AF, and Schreiber SL. Discovery of an Inhibitor of a Transcription Factor Using Small Molecule Microarrays and Diversity-Oriented Synthesis. J Am Chem Soc 2003;125(28):8420-8421. 

29. Kuruvilla FG, *Shamji AF, *Sternson SM, Hergenrother PJ, and Schreiber SL. Dissecting glucose signaling using diversity-oriented synthesis and small molecule microarrays. Nature 2002;416(6881):653-657. 

30. Kuruvilla FG, Shamji AF, and Schreiber SL. Carbon- and nitrogen-quality signaling to translation are mediated by distinct GATA-type transcription factors. Proc Natl Acad Sci USA. 2001;98(13):7823-7828. PMCID: PMC34660

31. Shamji AF, Kuruvilla FG, and Schreiber SL. Partitioning the transcriptional program induced by rapamycin among the effectors of the Tor proteins. Current Biology 2000;10(24):1574-1581. 

32. Hardwick JS, Kuruvilla FG, Tong JK, Shamji AF, and Schreiber SL. Rapamycin-modulated transcription defines the subset of nutrient-sensitive signaling pathways directly controlled by the Tor proteins. Proc Natl Acad Sci USA. 1999;96(26):14866-14870. PMCID: PMC24739

*both authors contributed equally
#co-corresponding authors