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: January 2014

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Publications Citing Koch Institute Faculty Members

1. Implantable Silk Composite Microneedles for Programmable Vaccine Release Kinetics and Enhanced Immunogenicity in Transcutaneous Immunization. Demuth PC, Min Y, Irvine DJ, Hammond PT. Adv Healthc Mater. pubmed:23847143;  doi:10.1002/adhm.201300139

2. Addressing genetic tumor heterogeneity through computationally predictive combination therapy. Zhao B, Pritchard JR, Lauffenburger DA, Hemann MT. Cancer Discov. pubmed:24318931;  doi:10.1158/2159-8290.CD-13-0465

3. System level dynamics of post-translational modifications. Gajadhar AS, White FM. Curr Opin Biotechnol. pubmed:24441143;  doi:10.1016/j.copbio.2013.12.009

4. Qualitatively Different T Cell Phenotypic Responses to IL-2 versus IL-15 Are Unified by Identical Dependences on Receptor Signal Strength and Duration. Arneja A, Johnson H, Gabrovsek L, Lauffenburger DA, White FM. J Immunol. pubmed:24298013;  doi:10.4049/jimmunol.1302291

5. Role of fluid dynamics and inflammation in intracranial aneurysm formation. Turjman AS, Turjman F, Edelman ER. Circulation. pubmed:24446407;  doi:10.1161/CIRCULATIONAHA.113.001444

6. Tailoring Chimeric Ligands for Studying and Biasing ErbB Receptor Family Interactions. Krueger AT, Kroll C, Sanchez E, Griffith LG, Imperiali B. Angew Chem Int Ed Engl. pubmed:24481645;  doi:10.1002/anie.201307869

7. The influence of transition metal oxides on the kinetics of LiO oxidation in Li-O batteries: high activity of chromium oxides. Yao KP, Lu YC, Amanchukwu CV, Kwabi DG, Risch M, Zhou J, Grimaud A, Hammond PT, Barde F, Shao-Horn Y. Phys Chem Chem Phys. pubmed:24352578;  doi:10.1039/c3cp53330a

8. Skin permeabilization for transdermal drug delivery: recent advances and future prospects. Schoellhammer CM, Blankschtein D, Langer R. Expert Opin Drug Deliv. pubmed:24392787;  doi:10.1517/17425247.2014.875528

9. Niche-independent high-purity cultures of Lgr5 intestinal stem cells and their progeny. Yin X, Farin HF, van Es JH, Clevers H, Langer R, Karp JM. Nat Methods. pubmed:24292484;  doi:10.1038/nmeth.2737

10. In vivo discovery of immunotherapy targets in the tumour microenvironment. Zhou P, Shaffer DR, Alvarez Arias DA, Nakazaki Y, Pos W, Torres AJ, Cremasco V, Dougan SK, Cowley GS, Elpek K, Brogdon J, Lamb J, Turley SJ, Ploegh HL, Root DE, Love JC, Dranoff G, Hacohen N, Cantor H, Wucherpfennig KW. Nature. pubmed:24476824;  doi:10.1038/nature12988

11. Single-cell technologies for monitoring immune systems. Chattopadhyay PK, Gierahn TM, Roederer M, Love JC. Nat Immunol. pubmed:24448570;  doi:10.1038/ni.2796

12. Crossword: A Fully Automated Algorithm for the Segmentation and Quality Control of Protein Microarray Images. Gierahn TM, Loginov D, Love JC. J Proteome Res. pubmed:24417579;  doi:10.1021/pr401167h

13. Weighing nanoparticles in solution at the attogram scale. Olcum S, Cermak N, Wasserman SC, Christine KS, Atsumi H, Payer KR, Shen W, Lee J, Belcher AM, Bhatia SN, Manalis SR. Proc Natl Acad Sci U S A. pubmed:24474753;  doi:10.1073/pnas.1318602111

14. A stochastic model dissects cell states in biological transition processes. Armond JW, Saha K, Rana AA, Oates CJ, Jaenisch R, Nicodemi M, Mukherjee S. Sci Rep. pubmed:24435049;  doi:10.1038/srep03692

15. A polygenic burden of rare disruptive mutations in schizophrenia. Purcell SM, Moran JL, Fromer M, Ruderfer D, Solovieff N, Roussos P, O'Dushlaine C, Chambert K, Bergen SE, Kahler A, Duncan L, Stahl E, Genovese G, Fernandez E, Collins MO, Komiyama NH, Choudhary JS, Magnusson PK, Banks E, Shakir K, Garimella K, Fennell T, Depristo M, Grant SG, Haggarty SJ, Gabriel S, Scolnick EM, Lander ES, Hultman CM, Sullivan PF, McCarroll SA, Sklar P. Nature. pubmed:24463508;  doi:10.1038/nature12975

16. Searching for missing heritability: Designing rare variant association studies. Zuk O, Schaffner SF, Samocha K, Do R, Hechter E, Kathiresan S, Daly MJ, Neale BM, Sunyaev SR, Lander ES. Proc Natl Acad Sci U S A. pubmed:24443550;  doi:10.1073/pnas.1322563111

17. Gene signatures related to B-cell proliferation predict influenza vaccine-induced antibody response. Tan Y, Tamayo P, Nakaya H, Pulendran B, Mesirov JP, Haining WN. Eur J Immunol. pubmed:24136404;  doi:10.1002/eji.201343657

18. MYC and Transcription Elongation. Rahl PB, Young RA. Cold Spring Harb Perspect Med. pubmed:24384817;  doi:10.1101/cshperspect.a020990

19. Genome-wide localization of small molecules. Anders L, Guenther MG, Qi J, Fan ZP, Marineau JJ, Rahl PB, Loven J, Sigova AA, Smith WB, Lee TI, Bradner JE, Young RA. Nat Biotechnol. pubmed:24336317;  doi:10.1038/nbt.2776

20. Sensitizing protective tumor microenvironments to antibody-mediated therapy. Pallasch CP, Leskov I, Braun CJ, Vorholt D, Drake A, Soto-Feliciano YM, Bent EH, Schwamb J, Iliopoulou B, Kutsch N, van Rooijen N, Frenzel LP, Wendtner CM, Heukamp L, Kreuzer KA, Hallek M, Chen J, Hemann MT. Cell. pubmed:24485462;  doi:10.1016/j.cell.2013.12.041

21. ZFHX4 Interacts with the NuRD Core Member CHD4 and Regulates the Glioblastoma Tumor-Initiating Cell State. Chudnovsky Y, Kim D, Zheng S, Whyte WA, Bansal M, Bray MA, Gopal S, Theisen MA, Bilodeau S, Thiru P, Muffat J, Yilmaz OH, Mitalipova M, Woolard K, Lee J, Nishimura R, Sakata N, Fine HA, Carpenter AE, Silver SJ, Verhaak RG, Califano A, Young RA, Ligon KL, Mellinghoff IK, Root DE, Sabatini DM, Hahn WC, Chheda MG. Cell Rep. pubmed:24440720;  doi:10.1016/j.celrep.2013.12.032

22. Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre. Hacisuleyman E, Goff LA, Trapnell C, Williams A, Henao-Mejia J, Sun L, McClanahan P, Hendrickson DG, Sauvageau M, Kelley DR, Morse M, Engreitz J, Lander ES, Guttman M, Lodish HF, Flavell R, Raj A, Rinn JL. Nat Struct Mol Biol. pubmed:24463464;  doi:10.1038/nsmb.2764

23. Global discovery of erythroid long non-coding RNAs reveals novel regulators of red cell maturation. Alvarez-Dominguez JR, Hu W, Yuan B, Shi J, Park SS, Gromatzky AA, van Oudenaarden A, Lodish HF. Blood. pubmed:24200680;  doi:10.1182/blood-2013-10-530683

24. Genetic Screens in Human Cells Using the CRISPR/Cas9 System. Wang T, Wei JJ, Sabatini DM, Lander ES. Science. pubmed:24336569;  doi:10.1126/science.1246981

25. Discovery and saturation analysis of cancer genes across 21 tumour types. Lawrence MS, Stojanov P, Mermel CH, Robinson JT, Garraway LA, Golub TR, Meyerson M, Gabriel SB, Lander ES, Getz G. Nature. pubmed:24390350;  doi:10.1038/nature12912

26. Small-Molecule Allosteric Activators of Sirtuins. Sinclair DA, Guarente L. Annu Rev Pharmacol Toxicol. pubmed:24160699;  doi:10.1146/annurev-pharmtox-010611-134657

27. Hepatic signaling by the mechanistic target of rapamycin complex 2 (mTORC2). Lamming DW, Demirkan G, Boylan JM, Mihaylova MM, Peng T, Ferreira J, Neretti N, Salomon A, Sabatini DM, Gruppuso PA. FASEB J. pubmed:24072782;  doi:10.1096/fj.13-237743

28. The Many Faces of Sirtuins: Sirtuins and the Warburg effect. Guarente L. Nat Med. pubmed:24398961;  doi:10.1038/nm.3438

29. Distinct Prion Strains Are Defined by Amyloid Core Structure and Chaperone Binding Site Dynamics. Frederick KK, Debelouchina GT, Kayatekin C, Dorminy T, Jacavone AC, Griffin RG, Lindquist S. Chem Biol. pubmed:24485763;  doi:10.1016/j.chembiol.2013.12.013

30. Diiron Oxidation State Control of Substrate Access to the Active Site of Soluble Methane Monooxygenase Mediated by the Regulatory Component. Wang W, Lippard SJ. J Am Chem Soc. pubmed:24476336;  doi:10.1021/ja412351b

31. Conjugation of vitamin E analog alpha-TOS to Pt(iv) complexes for dual-targeting anticancer therapy. Suntharalingam K, Song Y, Lippard SJ. Chem Commun (Camb). pubmed:24452361;  doi:10.1039/c3cc48740g

32. The Chiral Potential of Phenanthriplatin and Its Influence on Guanine Binding. Johnstone TC, Lippard SJ. J Am Chem Soc. pubmed:24417436;  doi:10.1021/ja4125115

33. Understanding and improving platinum anticancer drugs - phenanthriplatin. Johnstone TC, Park GY, Lippard SJ. Anticancer Res. pubmed:24403503;  

34. Effects of Monofunctional Platinum Agents on Bacterial Growth: A Retrospective Study. Johnstone TC, Alexander SM, Lin W, Lippard SJ. J Am Chem Soc. pubmed:24364388;  doi:10.1021/ja411742c

35. Versatile Reactivity of a Solvent-Coordinated Diiron(II) Compound: Synthesis and Dioxygen Reactivity of a Mixed-Valent FeFe Species. Majumdar A, Apfel UP, Jiang Y, Moenne-Loccoz P, Lippard SJ. Inorg Chem. pubmed:24359397;  doi:10.1021/ic4019585

36. Reaction-based fluorescent sensor for investigating mobile Zn2+ in mitochondria of healthy versus cancerous prostate cells. Chyan W, Zhang DY, Lippard SJ, Radford RJ. Proc Natl Acad Sci U S A. pubmed:24335702;  doi:10.1073/pnas.1310583110

37. Inference of Tumor Evolution during Chemotherapy by Computational Modeling and In Situ Analysis of Genetic and Phenotypic Cellular Diversity. Almendro V, Cheng YK, Randles A, Itzkovitz S, Marusyk A, Ametller E, Gonzalez-Farre X, Munoz M, Russnes HG, Helland A, Rye IH, Borresen-Dale AL, Maruyama R, van Oudenaarden A, Dowsett M, Jones RL, Reis-Filho J, Gascon P, Gonen M, Michor F, Polyak K. Cell Rep. pubmed:24462293;  doi:10.1016/j.celrep.2013.12.041

38. FuseFISH: Robust Detection of Transcribed Gene Fusions in Single Cells. Semrau S, Crosetto N, Bienko M, Boni M, Bernasconi P, Chiarle R, van Oudenaarden A. Cell Rep. pubmed:24373969;  doi:10.1016/j.celrep.2013.12.002