Progress: June 2014

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Publications Citing Koch Institute Faculty Members

1. Nanoporous networks: assembly of a bacteriophage-based template for the organization of materials into nanoporous networks. Courchesne NM, Klug MT, Chen PY, Kooi SE, Yun DS, Hong N, Fang NX, Belcher AM, Hammond PT. Adv Materpubmed:24891027;  doi:10.1002/adma.201470144

2. Dysregulated sphingolipid metabolism in endometriosis. Hou Lee Y, Wen Tan C, Venkatratnam A, Seng Tan C, Cui L, Feei Loh S, Griffith L, Tannenbaum SR, Kok Yen Chan J. J Clin Endocrinol Metabpubmed:24960545;  doi:10.1210/jc.2014-1340

3. Bone Repair: Osteotropic Therapy via Targeted Layer-by-Layer Nanoparticles. Morton SW, Shah NJ, Quadir MA, Deng ZJ, Poon Z, Hammond PT. Adv Healthc Mater.pubmed:24912883;  doi:10.1002/adhm.201470028

4. Quantitative Analysis of Signaling Networks Across Differentially Embedded Tumors Highlights Inter-Patient Heterogeneity in Human Glioblastoma. Johnson H, White FM. J Proteome Respubmed:24927040;  doi:10.1021/pr500418w

5. Silencing of CCR2 in myocarditis. Leuschner F, Courties G, Dutta P, Mortensen LJ, Gorbatov R, Sena B, Novobrantseva TI, Borodovsky A, Fitzgerald K, Koteliansky V, Iwamoto Y, Bohlender M, Meyer S, Lasitschka F, Meder B, Katus HA, Lin C, Libby P, Swirski FK, Anderson DG, Weissleder R, Nahrendorf M. Eur Heart Jpubmed:24950695;  doi:10.1093/eurheartj/ehu225

6. Genome editing with Cas9 in adult mice corrects a disease mutation and phenotype. Yin H, Xue W, Chen S, Bogorad RL, Benedetti E, Grompe M, Koteliansky V, Sharp PA, Jacks T, Anderson DG. Nat Biotechnolpubmed:24681508;  doi:10.1038/nbt.2884

7. Endothelial insights: the florian dialectic. Edelman ER. Sci Transl Medpubmed:24898742;  doi:10.1126/scitranslmed.3008664

8. Approaches to in vitro tissue regeneration with application for human disease modeling and drug development. Ebrahimkhani MR, Young CL, Lauffenburger DA, Griffith LG, Borenstein JT. Drug Discov Todaypubmed:24793141;  doi:10.1016/j.drudis.2014.04.017

9. Multilayer Films Assembled from Naturally-Derived Materials for Controlled Protein Release. Hsu BB, Hagerman SR, Jamieson KS, Veselinovic J, O'Neill N, Holler E, Ljubimova JY, Hammond PT. Biomacromoleculespubmed:24825478;  doi:10.1021/bm5001839

10. Osteotropic Therapy via Targeted Layer-by-Layer Nanoparticles. Morton SW, Shah NJ, Quadir MA, Deng ZJ, Poon Z, Hammond PT. Adv Healthc Mater.pubmed:24124132;  doi:10.1002/adhm.201300465

11. High throughput screening for biomaterials discovery. Algahtani MS, Scurr DJ, Hook AL, Anderson DG, Langer RS, Burley JC, Alexander MR, Davies MC. J Control Release.pubmed:24993427;  doi:10.1016/j.jconrel.2014.06.045

12. Ultra-High Throughput Synthesis of Nanoparticles with Homogeneous Size Distribution Using a Coaxial Turbulent Jet Mixer. Lim JM, Swami A, Gilson LM, Chopra S, Choi S, Wu J, Langer R, Karnik R, Farokhzad OC. ACS Nanopubmed:24824296;  doi:10.1021/nn501371n

13. Functionalizable Hydrogel Microparticles of Tunable Size and Stiffness for Soft-Tissue Filler Applications. Chan KM, Li RH, Chapman JW, Trac EM, Kobler JB, Zeitels SM, Langer R, Karajanagi SS. Acta Biomaterpubmed:24561708;  doi:10.1016/j.actbio.2014.02.021

14. A Small Molecule That Binds and Inhibits the ETV1 Transcription Factor Oncoprotein. Pop MS, Stransky N, Garvie CW, Theurillat JP, Hartman EC, Lewis TA, Zhong C, Culyba EK, Lin F, Daniels DS, Pagliarini R, Ronco L, Koehler AN, Garraway LA. Mol Cancer Therpubmed:24737027;  doi:10.1158/1535-7163.MCT-13-0689

15. Photothermally Targeted Thermosensitive Polymer-Masked Nanoparticles. Barhoumi A, Wang W, Zurakowski D, Langer RS, Kohane DS. Nano Lett.pubmed:24884872;  doi:10.1021/nl403733z

16. Materials for stem cell factories of the future. Celiz AD, Smith JG, Langer R, Anderson DG, Winkler DA, Barrett DA, Davies MC, Young LE, Denning C, Alexander MR. Nat Mater.pubmed:24845996;  doi:10.1038/nmat3972

17. Methods for time series analysis of RNA-seq data with application to human Th17 cell differentiation. Aijo T, Butty V, Chen Z, Salo V, Tripathi S, Burge CB, Lahesmaa R, Lahdesmaki H.Bioinformaticspubmed:24931974;  doi:10.1093/bioinformatics/btu274

18. Genetic and Chemical Correction of Cholesterol Accumulation and Impaired Autophagy in Hepatic and Neural Cells Derived from Niemann-Pick Type C Patient-Specific iPS Cells. Maetzel D, Sarkar S, Wang H, Abi-Mosleh L, Xu P, Cheng AW, Gao Q, Mitalipova M, Jaenisch R. Stem Cell Reportspubmed:24936472;  doi:10.1016/j.stemcr.2014.03.014

19. Human intestinal tissue with adult stem cell properties derived from pluripotent stem cells. Forster R, Chiba K, Schaeffer L, Regalado SG, Lai CS, Gao Q, Kiani S, Farin HF, Clevers H, Cost GJ, Chan A, Rebar EJ, Urnov FD, Gregory PD, Pachter L, Jaenisch R, Hockemeyer D. Stem Cell Reportspubmed:24936470;  doi:10.1016/j.stemcr.2014.05.001

20. Molecular Control of Induced Pluripotency. Theunissen TW, Jaenisch R. Cell Stem Cellpubmed:24905163;  doi:10.1016/j.stem.2014.05.002

21. Restarting stalled autophagy a potential therapeutic approach for the lipid storage disorder, Niemann-Pick type C1 disease. Sarkar S, Maetzel D, Korolchuk VI, Jaenisch R. Autophagy.pubmed:24879158;  doi:10.4161/auto.28623

22. Whole-exome sequencing and clinical interpretation of formalin-fixed, paraffin-embedded tumor samples to guide precision cancer medicine. Van Allen EM, Wagle N, Stojanov P, Perrin DL, Cibulskis K, Marlow S, Jane-Valbuena J, Friedrich DC, Kryukov G, Carter SL, McKenna A, Sivachenko A, Rosenberg M, Kiezun A, Voet D, Lawrence M, Lichtenstein LT, Gentry JG, Huang FW, Fostel J, Farlow D, Barbie D, Gandhi L, Lander ES, Gray SW, Joffe S, Janne P, Garber J, MacConaill L, Lindeman N, Rollins B, Kantoff P, Fisher SA, Gabriel S, Getz G, Garraway LA. Nat Medpubmed:24836576;  doi:10.1038/nm.3559

23. Development and Applications of CRISPR-Cas9 for Genome Engineering. Hsu PD, Lander ES, Zhang F. Cellpubmed:24906146;  doi:10.1016/j.cell.2014.05.010

24. Free IL-12p40 Monomer Is a Polyfunctional Adapter for Generating Novel IL-12-like Heterodimers Extracellularly. Abdi K, Singh NJ, Spooner E, Kessler BM, Radaev S, Lantz L, Xiao TS, Matzinger P, Sun PD, Ploegh HL. J Immunolpubmed:24821971;  doi:10.4049/jimmunol.1400159

25. Epithelial-to-mesenchymal transition activates PERK-eIF2a and sensitizes cells to endoplasmic reticulum stress. Feng Y, Sokol ES, Del Vecchio CA, Sanduja S, Claessen JH, Proia T, Jin DX, Reinhardt F, Ploegh HL, Wang Q, Gupta P. Cancer Discovpubmed:24705811;  doi:10.1158/2159-8290.CD-13-0945

26. Widespread Inhibition of Posttranscriptional Splicing Shapes the Cellular Transcriptome following Heat Shock. Shalgi R, Hurt JA, Lindquist S, Burge CB. Cell Rep.pubmed:24857664;  doi:10.1016/j.celrep.2014.04.044

27. Global analysis of induced transcription factors and cofactors identifies Tfdp2 as an essential coregulator during terminal erythropoiesis. Chen C, Lodish HF. Exp Hematol.pubmed:24607859;  doi:10.1016/j.exphem.2014.03.001

28. The Protein Synthesis Inhibitor Blasticidin S Enters Mammalian Cells via Leucine-Rich Repeat-Containing Protein 8D. Lee CC, Freinkman E, Sabatini DM, Ploegh HL. J Biol Chem.pubmed:24782309;  doi:10.1074/jbc.M114.571257

29. RNA Bind-n-Seq: Quantitative Assessment of the Sequence and Structural Binding Specificity of RNA Binding Proteins. Lambert N, Robertson A, Jangi M, McGeary S, Sharp PA, Burge CB. Mol Cellpubmed:24837674;  doi:10.1016/j.molcel.2014.04.016

30. LincRNA-p21 Activates p21 In cis to Promote Polycomb Target Gene Expression and to Enforce the G1/S Checkpoint. Dimitrova N, Zamudio JR, Jong RM, Soukup D, Resnick R, Sarma K, Ward AJ, Raj A, Lee JT, Sharp PA, Jacks T. Mol Cellpubmed:24857549;  doi:10.1016/j.molcel.2014.04.025

31. A Conditional System to Specifically Link Disruption of Protein-Coding Function with Reporter Expression in Mice. Chiou SH, Kim-Kiselak C, Risca VI, Heimann MK, Chuang CH, Burds AA, Greenleaf WJ, Jacks TE, Feldser DM, Winslow MM. Cell Reppubmed:24931605;  doi:10.1016/j.celrep.2014.05.031

32. Widespread Changes in the Posttranscriptional Landscape at the Drosophila Oocyte-to-Embryo Transition. Kronja I, Yuan B, Eichhorn SW, Dzeyk K, Krijgsveld J, Bartel DP, Orr-Weaver TL. Cell Reppubmed:24882012;  doi:10.1016/j.celrep.2014.05.002

33. IDH1 mutations alter citric acid cycle metabolism and increase dependence on oxidative mitochondrial metabolism. Grassian AR, Parker SJ, Davidson SM, Divakaruni AS, Green CR, Zhang X, Slocum KL, Pu M, Lin F, Vickers C, Joud-Caldwell C, Chung F, Yin H, Handly ED, Straub C, Growney JD, Vander Heiden MG, Murphy AN, Pagliarini R, Metallo CM. Cancer Res.pubmed:24755473;  doi:10.1158/0008-5472.CAN-14-0772-T

34. Targetable signaling pathway mutations are associated with malignant phenotype in IDH-mutant gliomas. Wakimoto H, Tanaka S, Curry WT, Loebel F, Zhao D, Tateishi K, Chen J, Klofas LK, Lelic N, Kim JC, Dias-Santagata D, Ellisen LW, Borger DR, Fendt SM, Vander Heiden M, Batchelor TT, Iafrate AJ, Cahill DP, Chi AS. Clin Cancer Res.pubmed:24714777;  doi:10.1158/1078-0432.CCR-13-3052

35. Combination PI3K/MEK inhibition promotes tumor apoptosis and regression in PIK3CA wild-type, KRAS mutant colorectal cancer. Roper J, Sinnamon MJ, Coffee EM, Belmont P, Keung L, Georgeon-Richard L, Wang WV, Faber AC, Yun J, Yilmaz OH, Bronson RT, Martin ES, Tsichlis PN, Hung KE. Cancer Lettpubmed:24576621;  doi:10.1016/j.canlet.2014.02.018

36. The Highly Conserved Bacterial RNase YbeY Is Essential in Vibrio cholerae, Playing a Critical Role in Virulence, Stress Regulation, and RNA Processing. Vercruysse M, Kohrer C, Davies BW, Arnold MF, Mekalanos JJ, RajBhandary UL, Walker GC. PLoS Pathogpubmed:24901994;  doi:10.1371/journal.ppat.1004175

37. Structural and mechanistic studies of polymerase eta bypass of phenanthriplatin DNA damage. Gregory MT, Park GY, Johnstone TC, Lee YS, Yang W, Lippard SJ. Proc Natl Acad Sci U S Apubmed:24927576;  doi:10.1073/pnas.1405739111

38. Pt(IV) Prodrugs Designed to Bind Non-Covalently to Human Serum Albumin for Drug Delivery. Zheng YR, Suntharalingam K, Johnstone TC, Yoo H, Lin W, Brooks JG, Lippard SJ. J Am Chem Socpubmed:24902769;  doi:10.1021/ja5038269

39. A Flexible Glutamine Regulates the Catalytic Activity of Toluene o-Xylene Monooxygenase. Liang AD, Wrobel AT, Lippard SJ. Biochemistrypubmed:24873259;  doi:10.1021/bi500387y

40. SpiroZin1: A Reversible and pH-Insensitive, Reaction-Based, Red-Fluorescent Probe for Imaging Biological Mobile Zinc. Rivera-Fuentes P, Lippard SJ. ChemMedChem.pubmed:24616292;  doi:10.1002/cmdc.201400014

41. Reinterpretation of the vibrational spectroscopy of the medicinal bioinorganic synthon c,c,t-[Pt(NH) Cl (OH) ]. Johnstone TC, Lippard SJ. J Biol Inorg Chem.pubmed:24515615;  doi:10.1007/s00775-014-1109-6

42. Alternative Splicing of Endothelial Fibronectin Is Induced by Disturbed Hemodynamics and Protects Against Hemorrhage of the Vessel Wall. Murphy PA, Hynes RO. Arterioscler Thromb Vasc Biolpubmed:24903094;  doi:10.1161/ATVBAHA.114.303879

43. Assembly of a Bacteriophage-Based Template for the Organization of Materials into Nanoporous Networks. Courchesne NM, Klug MT, Chen PY, Kooi SE, Yun DS, Hong N, Fang NX, Belcher AM, Hammond PT. Adv Materpubmed:24648015;  doi:10.1002/adma.201305928