Progress: August 2013

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Publications Citing Koch Institute Faculty Members

1. PTEN-null Tumors Cohabiting the Same Lung Display Differential Akt Activation and Sensitivity to Dietary Restriction. Curry NL, Mino-Kenudson M, Oliver TG, Yilmaz OH, Yilmaz VO, Moon JY, Jacks T, Sabatini DM, Kalaany NY. Cancer Discov. pubmed:23719831;  doi:10.1158/2159-8290.CD-12-0507

2. Integrated Network Analyses for Functional Genomic Studies in Cancer. Wilson JL, Hemann MT, Fraenkel E, Lauffenburger DA. Semin Cancer Biol. pubmed:23811269;  doi:10.1016/j.semcancer.2013.06.004

3. An Sp1 transcription factor coordinates caspase-dependent and -independent apoptotic pathways. Hirose T, Horvitz HR. Nature. pubmed:23851392;  doi:10.1038/nature12329

4. Cytochrome P450 Drives a HIF-Regulated Behavioral Response to Reoxygenation by C elegans. Ma DK, Rothe M, Zheng S, Bhatla N, Pender CL, Menzel R, Horvitz HR. Science. pubmed:23811225;  doi:10.1126/science.1235753

5. Targeting H3K4 trimethylation in Huntington disease. Vashishtha M, Ng CW, Yildirim F, Gipson TA, Kratter IH, Bodai L, Song W, Lau A, Labadorf A, Vogel-Ciernia A, Troncosco J, Ross CA, Bates GP, Krainc D, Sadri-Vakili G, Finkbeiner S, Marsh JL, Housman DE, Fraenkel E, Thompson LM. Proc Natl Acad Sci U S A. pubmed:23872847;  doi:10.1073/pnas.1311323110

6. Drosophila Embryonic Cell Cycle Mutants. Unhavaithaya Y, Park EA, Royzman I, Orr-Weaver TL. G3 (Bethesda). pubmed:23979936;  doi:10.1534/g3.113.007880

7. Polo kinase Cdc5 is a central regulator of meiosis I. Attner MA, Miller MP, Ee LS, Elkin SK, Amon A. Proc Natl Acad Sci U S A. pubmed:23918381;  doi:10.1073/pnas.1311845110

8. Meiosis I: when chromosomes undergo extreme makeover. Miller MP, Amon A, Unal E. Curr Opin Cell Biol. pubmed:23916768;  doi:10.1016/

9. Comparative oncogenomic analysis of copy number alterations in human and zebrafish tumors enables cancer driver discovery. Zhang G, Hoersch S, Amsterdam A, Whittaker CA, Beert E, Catchen JM, Farrington S, Postlethwait JH, Legius E, Hopkins N, Lees JA. PLoS Genet. pubmed:24009526;  doi:10.1371/journal.pgen.1003734

10. Multiplexed activation of endogenous genes by CRISPR-on, an RNA-guided transcriptional activator system. Cheng AW, Wang H, Yang H, Shi L, Katz Y, Theunissen TW, Rangarajan S, Shivalila CS, Dadon DB, Jaenisch R. Cell Res. pubmed:23979020;  doi:10.1038/cr.2013.122

11. MicroRNA-126-mediated control of cell fate in B-cell myeloid progenitors as a potential alternative to transcriptional factors. Okuyama K, Ikawa T, Gentner B, Hozumi K, Harnprasopwat R, Lu J, Yamashita R, Ha D, Toyoshima T, Chanda B, Kawamata T, Yokoyama K, Wang S, Ando K, Lodish HF, Tojo A, Kawamoto H, Kotani A. Proc Natl Acad Sci U S A. pubmed:23893300;  doi:10.1073/pnas.1220710110

12. Young and old genetically heterogeneous HET3 mice on a rapamycin diet are glucose intolerant but insulin sensitive. Lamming DW, Ye L, Astle MC, Baur JA, Sabatini DM, Harrison DE. Aging Cell. pubmed:23648089;  doi:10.1111/acel.12097

13. A systematic analysis of the PARP protein family identifies new functions critical for cell physiology. Vyas S, Chesarone-Cataldo M, Todorova T, Huang YH, Chang P. Nat Commun. pubmed:23917125;  doi:10.1038/ncomms3240

14. HIV-1 infection induces strong production of IP-10 through TLR7/9-dependent pathways. Simmons RP, Scully EP, Groden EE, Arnold KB, Chang JJ, Lane K, Lifson J, Rosenberg E, Lauffenburger DA, Altfeld M. AIDS. pubmed:23835503;  doi:10.1097/01.aids.0000432456.14099.c7

15. Peptide-based Targeting of Fluorescent Zinc Sensors to the Plasma Membrane of Live Cells. Radford RJ, Chyan W, Lippard SJ. Chem Sci. pubmed:23878718;  doi:10.1039/C3SC50974E

16. A Central Role for mTOR in Lipid Homeostasis. Lamming DW, Sabatini DM. Cell Metab. pubmed:23973332;  doi:10.1016/j.cmet.2013.08.002

17. Nutrients and growth factors in mTORC1 activation. Efeyan A, Sabatini DM. Biochem Soc Trans. pubmed:23863153;  doi:10.1042/BST20130063

18. Genome-wide single-cell-level screen for protein abundance and localization changes in response to DNA damage in S cerevisiae. Mazumder A, Pesudo LQ, McRee S, Bathe M, Samson LD. Nucleic Acids Res. pubmed:23935119;  doi:10.1093/nar/gkt715

19. Mechanical and Transport Properties of Layer-by-Layer Electrospun Composite Proton Exchange Membranes for Fuel Cell Applications. Mannarino MM, Liu DS, Hammond PT, Rutledge GC. ACS Appl Mater Interfaces. pubmed:23876250;  doi:10.1021/am402204v

20. N-linked Glycosylation of the hemagglutinin protein influences virulence and antigenicity of the 1918 pandemic and seasonal H1N1 influenza A viruses. Sun X, Jayaraman A, Maniprasad P, Raman R, Houser KV, Pappas C, Zeng H, Sasisekharan R, Katz JM, Tumpey TM. J Virol. pubmed:23740978;  doi:10.1128/JVI.00593-13

21. Allele-specific detection of single mRNA molecules in situ. Hansen CH, van Oudenaarden A. Nat Methods. pubmed:23934076;  doi:10.1038/nmeth.2601

22. Microneedle Electrodes Toward an Amperometric Glucose-Sensing Smart Patch. Invernale MA, Tang BC, York RL, Le L, Hou DY, Anderson DG. Adv Healthc Mater. pubmed:24039157;  doi:10.1002/adhm.201300142

23. Plasmonic Photothermal Heating of Intraperitoneal Tumors through the Use of an Implanted Near-Infrared Source. Bagley AF, Hill S, Rogers GS, Bhatia SN. ACS Nano. pubmed:23961973;  doi:10.1021/nn4033757

24. Identification of small molecules for human hepatocyte expansion and iPS differentiation. Shan J, Schwartz RE, Ross NT, Logan DJ, Thomas D, Duncan SA, North TE, Goessling W, Carpenter AE, Bhatia SN. Nat Chem Biol. pubmed:23728495;  doi:10.1038/nchembio.1270

25. Modifications of Microvascular EC Surface Modulate Phototoxicity of a Porphycene anti-ICAM-1 Immunoconjugate; Therapeutic Implications. Rosas E, Santoma P, Duran-Frigola M, Hernandez B, Llinas MC, Ruiz-Gonzalez R, Nonell S, Sanchez-Garcia D, Edelman ER, Balcells M. Langmuir. pubmed:23844929;  doi:10.1021/la401067d

26. A Versatile Three-Dimensional Virus-Based Template for Dye-Sensitized Solar Cells with Improved Electron Transport and Light Harvesting. Chen PY, Dang X, Klug MT, Qi J, Courchesne NM, Burpo FJ, Fang N, Hammond PT, Belcher AM. ACS Nano. pubmed:23808626;  doi:10.1021/nn4014164

27. 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

28. Parallel Microfluidic Synthesis of Size-Tunable Polymeric Nanoparticles Using 3D Flow Focusing towards In Vivo Study. Lim JM, Bertrand N, Valencia PM, Rhee M, Langer R, Jon S, Farokhzad OC, Karnik R. Nanomedicine. pubmed:23969105;  doi:10.1016/j.nano.2013.08.003

29. Drug Delivery Interfaces in the 21st Century: From Science Fiction Ideas to Viable Technologies. Chertok B, Webber MJ, Succi MD, Langer R. Mol Pharm. pubmed:23915375;  doi:10.1021/mp4003283

30. Multiparametric approach for the evaluation of lipid nanoparticles for siRNA delivery. Alabi CA, Love KT, Sahay G, Yin H, Luly KM, Langer R, Anderson DG. Proc Natl Acad Sci U S A. pubmed:23882076;  doi:10.1073/pnas.1306529110

31. 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

32. Single cells from human primary colorectal tumors exhibit polyfunctional heterogeneity in secretions of ELR+ CXC chemokines. Adalsteinsson VA, Tahirova N, Tallapragada N, Yao X, Campion L, Angelini A, Douce TB, Huang C, Bowman B, Williamson CA, Kwon DS, Wittrup KD, Love JC. Integr Biol (Camb). pubmed:23995780;  doi:10.1039/c3ib40059j

33. Emergent Properties of Nanosensor Arrays: Applications for Monitoring IgG Affinity Distributions, Weakly Affined Hypermannosylation, and Colony Selection for Biomanufacturing. Reuel NF, Grassbaugh B, Kruss S, Mundy JZ, Opel C, Ogunniyi AO, Egodage K, Wahl R, Helk B, Zhang J, Kalcioglu ZI, Tvrdy K, Bellisario DO, Mu B, Blake SS, Van Vliet KJ, Love JC, Wittrup KD, Strano MS. ACS Nano. pubmed:23909808;  doi:10.1021/nn403215e

34. Heparin sensing: Blue-chip binding. Shriver Z, Sasisekharan R. Nat Chem. pubmed:23881491;  doi:10.1038/nchem.1701

35. Site-specific protein labeling using PRIME and chelation-assisted click chemistry. Uttamapinant C, Sanchez MI, Liu DS, Yao JZ, Ting AY. Nat Protoc. pubmed:23887180;  doi:10.1038/nprot.2013.096

36. 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

37. Oocyte differentiation is genetically dissociable from meiosis in mice. Dokshin GA, Baltus AE, Eppig JJ, Page DC. Nat Genet. pubmed:23770609;  doi:10.1038/ng.2672

38. Conjugation to polymeric chains of influenza drugs targeting M2 ion channels partially restores inhibition of drug-resistant mutants. Larson AM, Chen J, Klibanov AM. J Pharm Sci. pubmed:23832466;  doi:10.1002/jps.23644

39. The Xist lncRNA Exploits Three-Dimensional Genome Architecture to Spread Across the X Chromosome. Engreitz JM, Pandya-Jones A, McDonel P, Shishkin A, Sirokman K, Surka C, Kadri S, Xing J, Goren A, Lander ES, Plath K, Guttman M. Science. pubmed:23828888;  doi:10.1126/science.1237973

40. Independent specialization of the human and mouse X chromosomes for the male germ line. Mueller JL, Skaletsky H, Brown LG, Zaghlul S, Rock S, Graves T, Auger K, Warren WC, Wilson RK, Page DC. Nat Genet. pubmed:23872635;  doi:10.1038/ng.2705

41. Sirtuins and ageing-new findings. Guarente L. EMBO Rep. pubmed:23928812;  doi:10.1038/embor.2013.121

42. Integrative radiogenomic profiling of squamous cell lung cancer. Abazeed ME, Adams DJ, Hurov KE, Tamayo P, Creighton CJ, Sonkin D, Giacomelli AO, Du C, Fries DF, Wong KK, Mesirov JP, Loeffler JS, Schreiber SL, Hammerman PS, Meyerson M. Cancer Res. pubmed:23980093;  doi:10.1158/0008-5472.CAN-13-1616

43. H2A.Z Acidic Patch Couples Chromatin Dynamics to Regulation of Gene Expression Programs during ESC Differentiation. Subramanian V, Mazumder A, Surface LE, Butty VL, Fields PA, Alwan A, Torrey L, Thai KK, Levine SS, Bathe M, Boyer LA. PLoS Genet. pubmed:23990805;  doi:10.1371/journal.pgen.1003725