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The David H. Koch Institute for Integrative Cancer Research at MITThe David H. Koch Institute for Integrative Cancer Research at MIT

Massachusetts Institute of Technology

National Cancer Institute Cancer Center

Science + Engineering... Conquering Cancer Together

Progress: July 2014

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Publications Citing Koch Institute Faculty Members

1. Ordered and Kinetically Discrete Sequential Protein Release from Biodegradable Thin Films. Hsu BB, Jamieson KS, Hagerman SR, Holler E, Ljubimova JY, Hammond PT. Angew Chem Int Ed Englpubmed:24938739;  doi:10.1002/anie.201403702

2. Niemann-Pick C1 Affects the Gene Delivery Efficacy of Degradable Polymeric Nanoparticles. Eltoukhy AA, Sahay G, Cunningham JM, Anderson DG. ACS Nanopubmed:25010491;  doi:10.1021/nn501630h

3. Thermally Switchable Polymers Achieve Controlled Escherichia coli Detachment. Hook AL, Chang CY, Scurr DJ, Langer R, Anderson DG, Williams P, Davies MC, Alexander MR. Adv Healthc Materpubmed:24497458;  doi:10.1002/adhm.201300518

4. Insights into Human Glycan Receptor conformation of 1918 Pandemic Haemagglutinin-Glycan Complexes derived from NMR and MD studies. Elli S, Macchi E, Rudd TR, Raman R, Sassaki GL, Viswanathan K, Yates EA, Shriver Z, Naggi A, Torri G, Sasisekharan R, Guerrini M. Biochemistrypubmed:24878075;  doi:10.1021/bi500338r

5. Design of Lipid Nanocapsule Delivery Vehicles for Multivalent Display of Recombinant Env Trimers in HIV Vaccination. Pejawar-Gaddy S, Kovacs JM, Barouch DH, Chen B, Irvine DJ.Bioconjug Chempubmed:25020048;  doi:10.1021/bc5002246

6. Antigen Delivery by Lipid-enveloped PLGA Microparticle Vaccines Mediated by in situ Vesicle Shedding. Hanson MC, Bershteyn A, Crespo MP, Irvine DJ. Biomacromolecules.pubmed:24894061;  doi:10.1021/bm500337r

7. Enhanced immune activation linked to endotoxemiain HIV-1 seronegative MSM. Palmer CD, Tomassilli J, Sirignano M, Tejeda MR, Arnold KB, Che D, Lauffenburger DA, Jost S, Allen T, Mayer KH, Altfeld M. AIDSpubmed:25003719;  doi:10.1097/QAD.0000000000000386

8. Intratumor heterogeneity alters most effective drugs in designed combinations. Zhao B, Hemann MT, Lauffenburger DA. Proc Natl Acad Sci U S Apubmed:25002493;  doi:10.1073/pnas.1323934111

9. Cell-specific labeling enzymes for analysis of cell-cell communication in continuous co-culture. Tape CJ, Norrie IC, Worboys JD, Lim L, Lauffenburger DA, Jorgensen C. Mol Cell Proteomicspubmed:24820872;  doi:10.1074/mcp.O113.037119

10. Inter-individual variation in DNA repair capacity: A need for multi-pathway functional assays to promote translational DNA repair research. Nagel ZD, Chaim IA, Samson LD. DNA Repair (Amst)pubmed:24780560;  doi:10.1016/j.dnarep.2014.03.009

11. Ischemia in tumors induces early and sustained phosphorylation changes in stress kinase pathways but does not affect global protein levels. Mertins P, Yang F, Liu T, Mani DR, Petyuk VA, Gillette MA, Clauser KR, Qiao JW, Gritsenko MA, Moore RJ, Levine DA, Townsend R, Erdmann-Gilmore P, Snider JE, Davies SA, Ruggles KV, Fenyo D, Kitchens RT, Li S, Olvera N, Dao F, Rodriguez H, Chan DW, Liebler D, White F, Rodland KD, Mills GB, Smith RD, Paulovich AG, Ellis M, Carr SA. Mol Cell Proteomicspubmed:24719451;  doi:10.1074/mcp.M113.036392

12. M13 virus directed synthesis of nanostructured metal oxides for Li-oxygen batteries. Oh D, Qi J, Han B, Zhang G, Carney TJ, Ohmura J, Zhang Y, Shao-Horn Y, Belcher AM. Nano Lett.pubmed:25058851;  doi:10.1021/nl502078m

13. Mechanisms of cooperation in cancer nanomedicine: towards systems nanotechnology. Hauert S, Bhatia SN. Trends Biotechnolpubmed:25086728;  doi:10.1016/j.tibtech.2014.06.010

14. Cell and tissue engineering for liver disease. Bhatia SN, Underhill GH, Zaret KS, Fox IJ. Sci Transl Medpubmed:25031271;  doi:10.1126/scitranslmed.3005975

15. Next-generation wearable electronics. Cima MJ. Nat Biotechnolpubmed:25004232;  doi:10.1038/nbt.2952

16. Extent of flow recirculation governs expression of atherosclerotic and thrombotic biomarkers in arterial bifurcations. Martorell J, Santoma P, Kolandaivelu K, Kolachalama VB, Melgar-Lesmes P, Molins JJ, Garcia L, Edelman ER, Balcells M. Cardiovasc Respubmed:24841070;  doi:10.1093/cvr/cvu124

17. Capillary Flow Layer-by-Layer: A Microfluidic Platform for the High Throughput Assembly and Screening of Nanolayered Film Libraries. Castleberry SA, Li W, Deng D, Mayner S, Hammond PT. ACS Nanopubmed:24836460;  doi:10.1021/nn501963q

18. PEG-polypeptide Block Copolymers as pH-responsive Endosome-Solubilizing Drug Nanocarriers. Quadir MA, Morton SW, Deng ZJ, Shopsowitz KE, Murphy RP, Epps Iii TH, Hammond PT. Mol Pharmpubmed:24813025;  doi:10.1021/mp500162w

19. CRISPR transcriptional repression devices and layered circuits in mammalian cells. Kiani S, Beal J, Ebrahimkhani MR, Huh J, Hall RN, Xie Z, Li Y, Weiss R. Nat Methods.pubmed:24797424;  doi:10.1038/nmeth.2969

20. MicroRNAs are required for the feature maintenance and differentiation of brown adipocytes. Kim HJ, Cho H, Alexander R, Patterson HC, Gu M, Lo KA, Xu D, Goh VJ, Nguyen LN, Chai X, Huang CX, Kovalik JP, Ghosh S, Trajkovski M, Silver DL, Lodish H, Sun L. Diabetespubmed:25008181;  doi:10.2337/db14-0466

21. Genome-wide binding of the CRISPR endonuclease Cas9 in mammalian cells. Wu X, Scott DA, Kriz AJ, Chiu AC, Hsu PD, Dadon DB, Cheng AW, Trevino AE, Konermann S, Chen S, Jaenisch R, Zhang F, Sharp PA. Nat Biotechnolpubmed:24752079;  doi:10.1038/nbt.2889

22. A melanoma cell state distinction influences sensitivity to MAPK pathway inhibitors. Konieczkowski DJ, Johannessen CM, Abudayyeh O, Kim JW, Cooper ZA, Piris A, Frederick DT, Barzily-Rokni M, Straussman R, Haq R, Fisher DE, Mesirov JP, Hahn WC, Flaherty KT, Wargo JA, Tamayo P, Garraway LA. Cancer Discovpubmed:24771846;  doi:10.1158/2159-8290.CD-13-0424

23. Muscleblind-like 1 (Mbnl1) regulates pre-mRNA alternative splicing during terminal erythropoiesis. Cheng AW, Shi J, Wong P, Luo KL, Trepman P, Wang ET, Choi H, Burge CB, Lodish HF. Bloodpubmed:24869935;  doi:10.1182/blood-2013-12-542209

24. Engineered red blood cells as carriers for systemic delivery of a wide array of functional probes. Shi J, Kundrat L, Pishesha N, Bilate A, Theile C, Maruyama T, Dougan SK, Ploegh HL, Lodish HF. Proc Natl Acad Sci U S Apubmed:24982154;  doi:10.1073/pnas.1409861111

25. Altered translation of GATA1 in Diamond-Blackfan anemia. Ludwig LS, Gazda HT, Eng JC, Eichhorn SW, Thiru P, Ghazvinian R, George TI, Gotlib JR, Beggs AH, Sieff CA, Lodish HF, Lander ES, Sankaran VG. Nat Medpubmed:24952648;  doi:10.1038/nm.3557

26. Perturbation of m6A Writers Reveals Two Distinct Classes of mRNA Methylation at Internal and 5' Sites. Schwartz S, Mumbach MR, Jovanovic M, Wang T, Maciag K, Bushkin GG, Mertins P, Ter-Ovanesyan D, Habib N, Cacchiarelli D, Sanjana NE, Freinkman E, Pacold ME, Satija R, Mikkelsen TS, Hacohen N, Zhang F, Carr SA, Lander ES, Regev A. Cell Rep.pubmed:24981863;  doi:10.1016/j.celrep.2014.05.048

27. Systematic identification of personal tumor-specific neoantigens in chronic lymphocytic leukemia. Rajasagi M, Shukla SA, Fritsch EF, Keskin DB, DeLuca D, Carmona E, Zhang W, Sougnez C, Cibulskis K, Sidney J, Stevenson K, Ritz J, Neuberg D, Brusic V, Gabriel S, Lander ES, Getz G, Hacohen N, Wu CJ. Bloodpubmed:24891321;  doi:10.1182/blood-2014-04-567933

28. Targeting transcription regulation in cancer with a covalent CDK7 inhibitor. Kwiatkowski N, Zhang T, Rahl PB, Abraham BJ, Reddy J, Ficarro SB, Dastur A, Amzallag A, Ramaswamy S, Tesar B, Jenkins CE, Hannett NM, McMillin D, Sanda T, Sim T, Kim ND, Look T, Mitsiades CS, Weng AP, Brown JR, Benes CH, Marto JA, Young RA, Gray NS. Nature.pubmed:25043025;  doi:10.1038/nature13393

29. Systematic Identification of Culture Conditions for Induction and Maintenance of Naive Human Pluripotency. Theunissen TW, Powell BE, Wang H, Mitalipova M, Faddah DA, Reddy J, Fan ZP, Maetzel D, Ganz K, Shi L, Lungjangwa T, Imsoonthornruksa S, Stelzer Y, Rangarajan S, D'Alessio A, Zhang J, Gao Q, Dawlaty MM, Young RA, Gray NS, Jaenisch R. Cell Stem Cell.pubmed:25090446;  doi:10.1016/j.stem.2014.07.002

30. D-Cyclins Repress Apoptosis in Hematopoietic Cells by Controlling Death Receptor Fas and Its Ligand FasL. Choi YJ, Saez B, Anders L, Hydbring P, Stefano J, Bacon NA, Cook C, Kalaszczynska I, Signoretti S, Young RA, Scadden DT, Sicinski P. Dev Cellpubmed:25087893;  doi:10.1016/j.devcel.2014.06.015

31. Regulation of Centromere Localization of the Drosophila Shugoshin MEI-S332 and Sister-Chromatid Cohesion in Meiosis. Nogueira C, Kashevsky H, Pinto B, Clarke A, Orr-Weaver TL.G3 (Bethesda)pubmed:25081981;  doi:10.1534/g3.114.012823

32. Muscle-Specific SIRT1 Gain-of-Function Increases Slow-Twitch Fibers and Ameliorates Pathophysiology in a Mouse Model of Duchenne Muscular Dystrophy. Chalkiadaki A, Igarashi M, Nasamu AS, Knezevic J, Guarente L. PLoS Genetpubmed:25032964;  doi:10.1371/journal.pgen.1004490

33. SnapShot: Sirtuins, NAD, and Aging. Nakagawa T, Guarente L. Cell Metabpubmed:24988458;  doi:10.1016/j.cmet.2014.06.001

34. Quantitative proteomic analysis reveals posttranslational responses to aneuploidy in yeast. Dephoure N, Hwang S, O'Sullivan C, Dodgson SE, Gygi SP, Amon A, Torres EM. Elife (Cambridge)pubmed:25073701;  doi:10.7554/eLife.03023

35. Multiple Functions for Mcm2-7 ATPase Motifs during Replication Initiation. Kang S, Warner MD, Bell SP. Mol Cellpubmed:25087876;  doi:10.1016/j.molcel.2014.06.033

36. KRAS and YAP1 Converge to Regulate EMT and Tumor Survival. Shao DD, Xue W, Krall EB, Bhutkar A, Piccioni F, Wang X, Schinzel AC, Sood S, Rosenbluh J, Kim JW, Zwang Y, Roberts TM, Root DE, Jacks T, Hahn WC. Cellpubmed:24954536;  doi:10.1016/j.cell.2014.06.004

37. The Reprogramming of Tumor Stroma by HSF1 Is a Potent Enabler of Malignancy. Scherz-Shouval R, Santagata S, Mendillo ML, Sholl LM, Ben-Aharon I, Beck AH, Dias-Santagata D, Koeva M, Stemmer SM, Whitesell L, Lindquist S. Cellpubmed:25083868;  doi:10.1016/j.cell.2014.05.045

38. A quantitative chaperone interaction network reveals the architecture of cellular protein homeostasis pathways. Taipale M, Tucker G, Peng J, Krykbaeva I, Lin ZY, Larsen B, Choi H, Berger B, Gingras AC, Lindquist S. Cellpubmed:25036637;  doi:10.1016/j.cell.2014.05.039

39. Regulation of mTORC1 by amino acids. Bar-Peled L, Sabatini DM. Trends Cell Biolpubmed:24698685;  doi:10.1016/j.tcb.2014.03.003

40. Tracing Compartmentalized NADPH Metabolism in the Cytosol and Mitochondria of Mammalian Cells. Lewis CA, Parker SJ, Fiske BP, McCloskey D, Gui DY, Green CR, Vokes NI, Feist AM, Vander Heiden MG, Metallo CM. Mol Cellpubmed:24882210;  doi:10.1016/j.molcel.2014.05.008

41. Depletion of Rictor, an essential protein component of mTORC2, decreases male lifespan. Lamming DW, Mihaylova MM, Katajisto P, Baar EL, Yilmaz OH, Hutchins A, Gultekin Y, Gaither R, Sabatini DM. Aging Cellpubmed:25059582;  doi:10.1111/acel.12256

42. New PARP targets for cancer therapy. Vyas S, Chang P. Nat Rev Cancerpubmed:24898058;  doi:10.1038/nrc3748

43. Ena/VASP regulates mDia2-initiated filopodial length, dynamics, and function. Barzik M, McClain LM, Gupton SL, Gertler FB. Mol Biol Cellpubmed:24989797;  doi:10.1091/mbc.E14-02-0712

44. Platelets guide the formation of early metastatic niches. Labelle M, Begum S, Hynes RO. Proc Natl Acad Sci U S Apubmed:25024172;  doi:10.1073/pnas.1411082111

45. Electron transfer control in soluble methane monooxygenase. Wang W, Iacob RE, Luoh RP, Engen JR, Lippard SJ. J Am Chem Socpubmed:24937475;  doi:10.1021/ja504688z

46. Addition of a Second Binding Site Increases the Dynamic Range but Alters the Cellular Localization of a Red Fluorescent Probe for Mobile Zinc. Loas A, Radford RJ, Lippard SJ. Inorg Chempubmed:24915285;  doi:10.1021/ic500732z

47. Biological cost of pyocin production during the SOS response in Pseudomonas aeruginosa. Penterman J, Singh PK, Walker GC. J Bacteriolpubmed:25022851;  doi:10.1128/JB.01889-14

48. Tackling the cancer stem cells - what challenges do they pose?. Pattabiraman DR, Weinberg RA. Nat Rev Drug Discovpubmed:24981363;  doi:10.1038/nrd4253

49. Proteomic Mapping of the Human Mitochondrial Intermembrane Space in Live Cells via Ratiometric APEX Tagging. Hung V, Zou P, Rhee HW, Udeshi ND, Cracan V, Svinkina T, Carr SA, Mootha VK, Ting AY. Mol Cellpubmed:25002142;  doi:10.1016/j.molcel.2014.06.003