Progress: June 2013

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Publications Citing Koch Institute Faculty Members

1. Helicase Loading at Chromosomal Origins of Replication. Bell SP, Kaguni JM. Cold Spring Harb Perspect Biol. pubmed:23613349;  doi:10.1101/cshperspect.a010124

2. Dominant Role of Oncogene Dosage and Absence of Tumor Suppressor Activity in Nras-Driven Hematopoietic Transformation. Xu J, Haigis KM, Firestone AJ, McNerney ME, Li Q, Davis E, Chen SC, Nakitandwe J, Downing J, Jacks T, Le Beau MM, Shannon K. Cancer Discov. pubmed:23733505;  doi:10.1158/2159-8290.CD-13-0096

3. Fundamental differences in endoreplication in mammals and Drosophila revealed by analysis of endocycling and endomitotic cells. Sher N, Von Stetina JR, Bell GW, Matsuura S, Ravid K, Orr-Weaver TL. Proc Natl Acad Sci U S A. pubmed:23613587;  doi:10.1073/pnas.1304889110

4. Unraveling Tumor Suppressor Networks with In Vivo RNAi. Braun CJ, Hemann MT. Cell Stem Cell. pubmed:23746971;  doi:10.1016/j.stem.2013.05.020

5. Blessings in disguise: biological benefits of prion-like mechanisms. Newby GA, Lindquist S. Trends Cell Biol. pubmed:23485338;  doi:10.1016/j.tcb.2013.01.007

6. Mechanisms and models of somatic cell reprogramming. Buganim Y, Faddah DA, Jaenisch R. Nat Rev Genet. pubmed:23681063;  doi:10.1038/nrg3473

7. Matrix Remodeling Maintains ESC Self-Renewal by Activating Stat3. Przybyla LM, Theunissen TW, Jaenisch R, Voldman J. Stem Cells. pubmed:23404867;  doi:10.1002/stem.1360

8. TALEN-mediated editing of the mouse Y chromosome. Wang H, Hu YC, Markoulaki S, Welstead GG, Cheng AW, Shivalila CS, Pyntikova T, Dadon DB, Voytas DF, Bogdanove AJ, Page DC, Jaenisch R. Nat Biotechnol. pubmed:23666012;  doi:10.1038/nbt.2595

9. Determination of 35 cell surface antigen levels in malignant pleural effusions identifies CD24 as a marker of disseminated tumor cells. Yao X, Labelle M, Lamb CR, Dugan JM, Williamson CA, Spencer DR, Christ KR, Keating RO, Lee WD, Paradis GA, Begum S, Hynes RO, Wittrup KD. Int J Cancer. pubmed:23775727;  doi:10.1002/ijc.28312

10. Monofunctional and Higher-Valent Platinum Anticancer Agents. Johnstone TC, Wilson JJ, Lippard SJ. Inorg Chem. pubmed:23738524;  doi:10.1021/ic400538c

11. Tris(2-pyridylmethyl)amine (TPA) as a membrane-permeable chelator for interception of biological mobile zinc. Huang Z, Zhang XA, Bosch M, Smith SJ, Lippard SJ. Metallomics. pubmed:23715510;  doi:10.1039/c3mt00103b

12. MicroRNA networks regulate development of brown adipocytes. Trajkovski M, Lodish H. Trends Endocrinol Metab. pubmed:23809233;  doi:10.1016/j.tem.2013.05.002

13. Regulated ADAM17-dependent EGF family ligand release by substrate-selecting signaling pathways. Dang M, Armbruster N, Miller MA, Cermeno E, Hartmann M, Bell GW, Root DE, Lauffenburger DA, Lodish HF, Herrlich A. Proc Natl Acad Sci U S A. pubmed:23720309;  doi:10.1073/pnas.1307478110

14. Heterogeneity of tumor-induced gene expression changes in the human metabolic network. Hu J, Locasale JW, Bielas JH, O'Sullivan J, Sheahan K, Cantley LC, Vander Heiden MG, Vitkup D. Nat Biotechnol. pubmed:23604282;  doi:10.1038/nbt.2530

15. Development of a Colon Cancer GEMM-Derived Orthotopic Transplant Model for Drug Discovery and Validation. Martin ES, Belmont PJ, Sinnamon MJ, Georgeon Richard L, Yuan J, Coffee EM, Roper J, Lee L, Heidari P, Lunt SY, Goel G, Ji C, Xie J, Xie T, Lamb J, Weinrich S, Vanarsdale TL, Bronson RT, Xavier RJ, Vander Heiden M, Kan JL, Mahmood U, Hung KE. Clin Cancer Res. pubmed:23403635;  doi:10.1158/1078-0432.CCR-12-2307

16. Pyruvate as a pivot point for oncogene-induced senescence. Olenchock BA, Vander Heiden MG. Cell. pubmed:23791173;  doi:10.1016/j.cell.2013.06.001

17. The bromodomain protein Brd4 insulates chromatin from DNA damage signalling. Floyd SR, Pacold ME, Huang Q, Clarke SM, Lam FC, Cannell IG, Bryson BD, Rameseder J, Lee MJ, Blake EJ, Fydrych A, Ho R, Greenberger BA, Chen GC, Maffa A, Del Rosario AM, Root DE, Carpenter AE, Hahn WC, Sabatini DM, Chen CC, White FM, Bradner JE, Yaffe MB. Nature. pubmed:23728299;  doi:10.1038/nature12147

18. Computer aided manual validation of mass spectrometry-based proteomic data. Curran TG, Bryson BD, Reigelhaupt M, Johnson H, White FM. Methods. pubmed:23500044;  doi:10.1016/j.ymeth.2013.03.004

19. Microfluidic genome-wide profiling of intrinsic electrical properties in Saccharomyces cerevisiae. Vahey MD, Quiros Pesudo L, Svensson JP, Samson LD, Voldman J. Lab Chip. pubmed:23661198;  doi:10.1039/c3lc50162k

20. Lipid-Modified Aminoglycoside Derivatives for in vivo siRNA Delivery. Zhang Y, Pelet JM, Heller DA, Dong Y, Chen D, Gu Z, Joseph BJ, Wallas J, Anderson DG. Adv Mater. pubmed:23813808;  doi:10.1002/adma.201301917

21. A personal account of translating discoveries in an academic lab. Langer R. Nat Biotechnol. pubmed:23752424;  doi:10.1038/nbt.2609

22. Surface-mediated bone tissue morphogenesis from tunable nanolayered implant coatings. Shah NJ, Hyder MN, Moskowitz JS, Quadir MA, Morton SW, Seeherman HJ, Padera RF, Spector M, Hammond PT. Sci Transl Med. pubmed:23803705;  doi:10.1126/scitranslmed.3005576

23. Fluorescent Multiblock pi-Conjugated Polymer Nanoparticles for In Vivo Tumor Targeting. Ahmed E, Morton SW, Hammond PT, Swager TM. Adv Mater. pubmed:23794490;  doi:10.1002/adma.201301656

24. Nano-Layered siRNA Dressing for Sustained Localized Knockdown. Castleberry S, Wang M, Hammond PT. ACS Nano. pubmed:23672676;  doi:10.1021/nn401011n

25. 3D Structural Patterns in Scalable, Elastomeric Scaffolds Guide Engineered Tissue Architecture. Kolewe ME, Park H, Gray C, Ye X, Langer R, Freed LE. Adv Mater. pubmed:23765688;  doi:10.1002/adma.201301016

26. Glycan Receptor Binding of the Influenza A Virus H7N9 Hemagglutinin. Tharakaraman K, Jayaraman A, Raman R, Viswanathan K, Stebbins NW, Johnson D, Shriver Z, Sasisekharan V, Sasisekharan R. Cell. pubmed:23746830;  doi:10.1016/j.cell.2013.05.034

27. Structural Determinants for Naturally Evolving H5N1 Hemagglutinin to Switch Its Receptor Specificity. Tharakaraman K, Raman R, Viswanathan K, Stebbins NW, Jayaraman A, Krishnan A, Sasisekharan V, Sasisekharan R. Cell. pubmed:23746829;  doi:10.1016/j.cell.2013.05.035

28. Impact of flow pulsatility on arterial drug distribution in stent-based therapy. O'Brien CC, Kolachalama VB, Barber TJ, Simmons A, Edelman ER. J Control Release. pubmed:23541929;  doi:10.1016/j.jconrel.2013.03.014

29. In vivo targeting of adoptively transferred T-cells with antibody- and cytokine-conjugated liposomes. Zheng Y, Stephan M, Gai SA, Abraham W, Shearer A, Irvine DJ. J Control Release. pubmed:23770010;  doi:10.1016/j.jconrel.2013.05.037

30. B7-H5 costimulates human T cells via CD28H. Zhu Y, Yao S, Iliopoulou BP, Han X, Augustine MM, Xu H, Phennicie RT, Flies SJ, Broadwater M, Ruff W, Taube JM, Zheng L, Luo L, Zhu G, Chen J, Chen L. Nat Commun. pubmed:23784006;  doi:10.1038/ncomms3043

31. Global analyses of UPF1 binding and function reveals expanded scope of nonsense-mediated mRNA decay. Hurt JA, Robertson AD, Burge CB. Genome Res. pubmed:23766421;  doi:10.1101/gr.157354.113

32. MBNL proteins repress ES-cell-specific alternative splicing and reprogramming. Han H, Irimia M, Ross PJ, Sung HK, Alipanahi B, David L, Golipour A, Gabut M, Michael IP, Nachman EN, Wang E, Trcka D, Thompson T, O'Hanlon D, Slobodeniuc V, Barbosa-Morais NL, Burge CB, Moffat J, Frey BJ, Nagy A, Ellis J, Wrana JL, Blencowe BJ. Nature. pubmed:23739326;  doi:10.1038/nature12270

33. SIRT1 Mediates Central Circadian Control in the SCN by a Mechanism that Decays with Aging. Chang HC, Guarente L. Cell. pubmed:23791176;  doi:10.1016/j.cell.2013.05.027

34. Sirtuin deacetylases in neurodegenerative diseases of aging. Herskovits AZ, Guarente L. Cell Res. pubmed:23689277;  doi:10.1038/cr.2013.70

35. Bruton's Tyrosine Kinase (BTK) and Vav1 Contribute to Dectin1-Dependent Phagocytosis of Candida albicans in Macrophages. Strijbis K, Tafesse FG, Fairn GD, Witte MD, Dougan SK, Watson N, Spooner E, Esteban A, Vyas VK, Fink GR, Grinstein S, Ploegh HL. PLoS Pathog. pubmed:23825946;  doi:10.1371/journal.ppat.1003446

36. Systematic interrogation of 3q26 identifies TLOC1 and SKIL as cancer drivers. Hagerstrand D, Tong A, Schumacher SE, Ilic N, Shen RR, Cheung HW, Vazquez F, Shrestha Y, Kim SY, Giacomelli AO, Rosenbluh J, Schinzel AC, Spardy NA, Barbie DA, Mermel CH, Weir BA, Garraway LA, Tamayo P, Mesirov JP, Beroukhim R, Hahn WC. Cancer Discov. pubmed:23764425;  doi:10.1158/2159-8290.CD-12-0592