Progress: April 2013

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Publications Citing Koch Institute Faculty Members

1. A physical sciences network characterization of non-tumorigenic and metastatic cells. Agus DB, Alexander JF, Arap W, Ashili S, Aslan JE, Austin RH, Backman V, Bethel KJ, Bonneau R, Chen WC, Chen-Tanyolac C, Choi NC, Curley SA, Dallas M, Damania D, Davies PC, Decuzzi P, Dickinson L, Estevez-Salmeron L, Estrella V, Ferrari M, Fischbach C, Foo J, Fraley SI, Frantz C, Fuhrmann A, Gascard P, Gatenby RA, Geng Y, Gerecht S, Gillies RJ, Godin B, Grady WM, Greenfield A, Hemphill C, Hempstead BL, Hielscher A, Hillis WD, Holland EC, Ibrahim-Hashim A, Jacks T, Johnson RH, Joo A, Katz JE, Kelbauskas L, Kesselman C, King MR, Konstantopoulos K, Kraning-Rush CM, Kuhn P, Kung K, Kwee B, Lakins JN, Lambert G, Liao D, Licht JD, Liphardt JT, Liu L, Lloyd MC, Lyubimova A, Mallick P, Marko J, McCarty OJ, Meldrum DR, Michor F, Mumenthaler SM, Nandakumar V, O'Halloran TV, Oh S, Pasqualini R, Paszek MJ, Philips KG, Poultney CS, Rana K, Reinhart-King CA, Ros R, Semenza GL, Senechal P, Shuler ML, Srinivasan S, Staunton JR, Stypula Y, Subramanian H, Tlsty TD, Tormoen GW, Tseng Y, van Oudenaarden A, Verbridge SS, Wan JC, Weaver VM, Widom J, Will C, Wirtz D, Wojtkowiak J, Wu PH. Sci Rep. pubmed:23618955;  doi:10.1038/srep01449

2. Nkx2-1 Represses a Latent Gastric Differentiation Program in Lung Adenocarcinoma. Snyder EL, Watanabe H, Magendantz M, Hoersch S, Chen TA, Wang DG, Crowley D, Whittaker CA, Meyerson M, Kimura S, Jacks T. Mol Cell. pubmed:23523371;  doi:10.1016/j.molcel.2013.02.018

3. Genetically engineered mouse models of cancer reveal new insights about the antitumor immune response. Dupage M, Jacks T. Curr Opin Immunol. pubmed:23465466;  doi:10.1016/j.coi.2013.02.005

4. Chelators for investigating zinc metalloneurochemistry. Radford RJ, Lippard SJ. Curr Opin Chem Biol. pubmed:23478014;  doi:10.1016/j.cbpa.2013.01.009

5. Aging-associated enzyme human clock-1: substrate-mediated reduction of the diiron center for 5-demethoxyubiquinone hydroxylation. Lu TT, Lee SJ, Apfel UP, Lippard SJ. Biochemistry. pubmed:23445365;  doi:10.1021/bi301674p

6. Aag DNA glycosylase promotes alkylation-induced tissue damage mediated by parp1. Calvo JA, Moroski-Erkul CA, Lake A, Eichinger LW, Shah D, Jhun I, Limsirichai P, Bronson RT, Christiani DC, Meira LB, Samson LD. PLoS Genet. pubmed:23593019;  doi:10.1371/journal.pgen.1003413

7. Characterization of Torin2, an ATP-Competitive Inhibitor of mTOR, ATM, and ATR. Liu Q, Xu C, Kirubakaran S, Zhang X, Hur W, Liu Y, Kwiatkowski NP, Wang J, Westover KD, Gao P, Ercan D, Niepel M, Thoreen CC, Kang SA, Patricelli MP, Wang Y, Tupper T, Altabef A, Kawamura H, Held KD, Chou DM, Elledge SJ, Janne PA, Wong KK, Sabatini DM, Gray NS. Cancer Res. pubmed:23436801;  doi:10.1158/0008-5472.CAN-12-1702

8. Triptycene-based Bis(benzimidazole) Carboxylate-Bridged Biomimetic Diiron(II) Complexes. Li Y, Myae Soe CM, Wilson JJ, Tuang SL, Apfel UP, Lippard SJ. Eur J Inorg Chem. pubmed:23585728;  doi:10.1002/ejic.201201387

9. M13 Virus based detection of bacterial infections in living hosts. Bardhan NM, Ghosh D, Belcher AM. J Biophotonics. pubmed:23576418;  doi:10.1002/jbio.201300010

10. Polymer multilayer tattooing for enhanced DNA vaccination. Demuth PC, Min Y, Huang B, Kramer JA, Miller AD, Barouch DH, Hammond PT, Irvine DJ. Nat Mater. pubmed:23353628;  doi:10.1038/nmat3550

11. IDOL Stimulates Clathrin-Independent Endocytosis and Multivesicular Body-Mediated Lysosomal Degradation of the Low-Density Lipoprotein Receptor. Scotti E, Calamai M, Goulbourne CN, Zhang L, Hong C, Lin RR, Choi J, Pilch PF, Fong LG, Zou P, Ting AY, Pavone FS, Young SG, Tontonoz P. Mol Cell Biol. pubmed:23382078;  doi:10.1128/MCB.01716-12

12. Crosslinked linear polyethylenimine enhances delivery of DNA to the cytoplasm. Bonner DK, Zhao X, Buss H, Langer R, Hammond PT. J Control Release. pubmed:22995755;  doi:10.1016/j.jconrel.2012.09.004

13. Redesign of a cross-reactive antibody to dengue virus with broad-spectrum activity and increased in vivo potency. Tharakaraman K, Robinson LN, Hatas A, Chen YL, Siyue L, Raguram S, Sasisekharan V, Wogan GN, Sasisekharan R. Proc Natl Acad Sci U S A. pubmed:23569282;  doi:10.1073/pnas.1303645110

14. Modular glycosphere assays for high-throughput functional characterization of influenza viruses. Hobbie SN, Viswanathan K, Bachelet I, Aich U, Shriver Z, Subramanian V, Raman R, Sasisekharan R. BMC Biotechnol. pubmed:23587408;  doi:10.1186/1472-6750-13-34

15. Geometric control of vascular networks to enhance engineered tissue integration and function. Baranski JD, Chaturvedi RR, Stevens KR, Eyckmans J, Carvalho B, Solorzano RD, Yang MT, Miller JS, Bhatia SN, Chen CS. Proc Natl Acad Sci U S A. pubmed:23610423;  doi:10.1073/pnas.1217796110

16. Surface-structure-regulated cell-membrane penetration by monolayer-protected nanoparticles. Verma A, Uzun O, Hu Y, Hu Y, Han HS, Watson N, Chen S, Irvine DJ, Stellacci F. Nat Mater. pubmed:23511581;  doi:10.1038/nmat3593

17. Synergistic antitumor activity from two-stage delivery of targeted toxins and endosome-disrupting nanoparticles. Su X, Yang N, Wittrup KD, Irvine DJ. Biomacromolecules. pubmed:23444913;  doi:10.1021/bm3019906

18. Intercellular trafficking of the nuclear oncoprotein DEK. Saha AK, Kappes F, Mundade A, Deutzmann A, Rosmarin DM, Legendre M, Chatain N, Al-Obaidi Z, Adams BS, Ploegh HL, Ferrando-May E, Mor-Vaknin N, Markovitz DM. Proc Natl Acad Sci U S A. pubmed:23569252;  doi:10.1073/pnas.1220751110

19. SIRT1 Suppresses the Epithelial-to-Mesenchymal Transition in Cancer Metastasis and Organ Fibrosis. Simic P, Williams EO, Bell EL, Gong JJ, Bonkowski M, Guarente L. Cell Rep. pubmed:23583181;  doi:10.1016/j.celrep.2013.03.019

20. Discovery and characterization of artifactual mutations in deep coverage targeted capture sequencing data due to oxidative DNA damage during sample preparation. Costello M, Pugh TJ, Fennell TJ, Stewart C, Lichtenstein L, Meldrim JC, Fostel JL, Friedrich DC, Perrin D, Dionne D, Kim S, Gabriel SB, Lander ES, Fisher S, Getz G. Nucleic Acids Res. pubmed:23303777;  doi:10.1093/nar/gks1443

21. ATARiS: Computational quantification of gene suppression phenotypes from multisample RNAi screens. Shao DD, Tsherniak A, Gopal S, Weir BA, Tamayo P, Stransky N, Schumacher SE, Zack TI, Beroukhim R, Garraway LA, Margolin AA, Root DE, Hahn WC, Mesirov JP. Genome Res. pubmed:23269662;  doi:10.1101/gr.143586.112

22. Intact sphingomyelin biosynthetic pathway is essential for intracellular transport of influenza virus glycoproteins. Tafesse FG, Sanyal S, Ashour J, Guimaraes CP, Hermansson M, Somerharju P, Ploegh HL. Proc Natl Acad Sci U S A. pubmed:23576732;  doi:10.1073/pnas.1219909110

23. Molecular biology A circuitous route to noncoding RNA. Wilusz JE, Sharp PA. Science. pubmed:23620042;  doi:10.1126/science.1238522

24. Let-7 represses Nr6a1 and a mid-gestation developmental program in adult fibroblasts. Gurtan AM, Ravi A, Rahl PB, Bosson AD, Jnbaptiste CK, Bhutkar A, Whittaker CA, Young RA, Sharp PA. Genes Dev. pubmed:23630078;  doi:10.1101/gad.215376.113

25. Selective inhibition of tumor oncogenes by disruption of super-enhancers. Loven J, Hoke HA, Lin CY, Lau A, Orlando DA, Vakoc CR, Bradner JE, Lee TI, Young RA. Cell. pubmed:23582323;  doi:10.1016/j.cell.2013.03.036

26. Master transcription factors and mediator establish super-enhancers at key cell identity genes. Whyte WA, Orlando DA, Hnisz D, Abraham BJ, Lin CY, Kagey MH, Rahl PB, Lee TI, Young RA. Cell. pubmed:23582322;  doi:10.1016/j.cell.2013.03.035

27. Punctuated evolution of prostate cancer genomes. Baca SC, Prandi D, Lawrence MS, Mosquera JM, Romanel A, Drier Y, Park K, Kitabayashi N, Macdonald TY, Ghandi M, Van Allen E, Kryukov GV, Sboner A, Theurillat JP, Soong TD, Nickerson E, Auclair D, Tewari A, Beltran H, Onofrio RC, Boysen G, Guiducci C, Barbieri CE, Cibulskis K, Sivachenko A, Carter SL, Saksena G, Voet D, Ramos AH, Winckler W, Cipicchio M, Ardlie K, Kantoff PW, Berger MF, Gabriel SB, Golub TR, Meyerson M, Lander ES, Elemento O, Getz G, Demichelis F, Rubin MA, Garraway LA. Cell. pubmed:23622249;  doi:10.1016/j.cell.2013.03.021

28. The African coelacanth genome provides insights into tetrapod evolution. Amemiya CT, Alfoldi J, Lee AP, Fan S, Philippe H, Maccallum I, Braasch I, Manousaki T, Schneider I, Rohner N, Organ C, Chalopin D, Smith JJ, Robinson M, Dorrington RA, Gerdol M, Aken B, Biscotti MA, Barucca M, Baurain D, Berlin AM, Blatch GL, Buonocore F, Burmester T, Campbell MS, Canapa A, Cannon JP, Christoffels A, De Moro G, Edkins AL, Fan L, Fausto AM, Feiner N, Forconi M, Gamieldien J, Gnerre S, Gnirke A, Goldstone JV, Haerty W, Hahn ME, Hesse U, Hoffmann S, Johnson J, Karchner SI, Kuraku S, Lara M, Levin JZ, Litman GW, Mauceli E, Miyake T, Mueller MG, Nelson DR, Nitsche A, Olmo E, Ota T, Pallavicini A, Panji S, Picone B, Ponting CP, Prohaska SJ, Przybylski D, Saha NR, Ravi V, Ribeiro FJ, Sauka-Spengler T, Scapigliati G, Searle SM, Sharpe T, Simakov O, Stadler PF, Stegeman JJ, Sumiyama K, Tabbaa D, Tafer H, Turner-Maier J, van Heusden P, White S, Williams L, Yandell M, Brinkmann H, Volff JN, Tabin CJ, Shubin N, Schartl M, Jaffe DB, Postlethwait JH, Venkatesh B, Di Palma F, Lander ES, Meyer A, Lindblad-Toh K. Nature. pubmed:23598338;  doi:10.1038/nature12027

29. Spatiotemporal quantification of cell dynamics in the lung following influenza virus infection. Yin L, Xu S, Cheng J, Zheng D, Limmon GV, Leung NH, Rajapakse JC, Chow VT, Chen J, Yu H. J Biomed Opt. pubmed:23545853;  doi:10.1117/1.JBO.18.4.046001