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 2012

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Publications Citing Intramural Faculty

*Indicates publications for which a KI intramural faculty member is senior author

*1.  Recent developments in multifunctional hybrid nanoparticles: opportunities and challenges in cancer therapy
Carolina Salvador Morales, Pedro M. Valencia, Anjali B. Thakkar, Edward Swanson and Robert Langer
Publication: Frontiers in Bioscience
DOI: 10.2741/398
E-Publication Date: January 1, 2012

2.  Correlated Immunohistochemical and Cytological Assays for the Prediction of Hematogenous Dissemination of Breast Cancer
Maja H. Oktay, Frank B. Gertler, Yi-Fang Liu, Thomas E. Rohan, John S. Condeelis and Joan G. Jones
Publication: The Journal of Histochemistry and Cytochemistry
DOI: 10.1369/0022155411435153
E-Publication Date: January 3, 2012

3.  Engineering of Targeted Nanoparticles for Cancer Therapy Using Internalizing Aptamers Isolated by Cell-Uptake Selection
Xiao Z, Levy-Nissenbaum E, Alexis F, Lupták A, Teply BA, Chan JM, Shi J, Digga E, Cheng J, Langer R, Farokhzad OC
Publication: ACS Nano
DOI: 10.1021/nn204165v
E-Publication Date: January 3, 2012

4.  A passion for science without barriers. Interview by Adrianne Appel.
Interview with Nancy Hopkins
Publication: Nature
DOI: 10.1038/481013a
E-Publication Date: January 4, 2012

*5.  Progress in the Tissue Engineering and Stem Cell Industry
Ana Jaklenec, Andrea Stamp, Elizabeth Deweerd, Angela Sherwin and Robert Langer
Publication: Tissue Engineering Part B, Reviews
DOI: 10.1089/ten.TEB.2011.0553
E-Publication Date: January 5, 2012

6.  14-3-3 fusion oncogenes in high-grade endometrial stromal sarcoma
Cheng-Han Lee, Wen-Bin Ou, Adrian Mariño-Enriquez, Meijun Zhu, Mark Mayeda, Yuexiang Wang, Xiangqian Guo, Alayne L. Brunner, Frédéric Amant, Christopher A. French, Robert B. West, Jessica N. McAlpine, C. Blake Gilks, Michael B. Yaffe, Leah M. Prentice, Andrew McPherson, Steven J. M. Jones, Marco A. Marra, Sohrab P. Shah, Matt van de Rijn, David G. Huntsman, Paola Dal Cin, Maria Debiec-Rychter, Marisa R. Nucci and Jonathan A. Fletcher
Publication: Proceedings of the National Academy of Sciences of the United States of America
DOI: 10.1073/pnas.1115528109
E-Publication Date: January 5, 2012

7.  Practical theoretic guidance for the design of tumor-targeting agents
K. Dane Wittrup, Greg M. Thurber, Michael M. Schmidt and John J. Rhoden
Publication: Methods in Enzymology
DOI: 10.1016/B978-0-12-396962-0.00010-0
E-Publication Date: January 8, 2012

8.  Cotransplantation of Ex Vivo Expanded and Unexpanded Cord Blood Units in Immunodeficient Mice Using Insulin Growth Factor Binding Protein-2–Augmented Mesenchymal Cell Cocultures
Li Ming Ong, Xiubo Fan, Pat Pak Yan Chu, Florence Pik Hoon Gay, Sudipto Bari, Justina May Lynn Ang, Zhihong Li, Jianzhu Chen, Sai Kiang Lim, Ralph Milford Bunte, William Ying Khee Hwang
Publication: Biology of Blood and Marrow Transplantation
DOI: 10.1016/j.bbmt.2012.01.001
E-Publication Date: January 9, 2012

9.  Querying quantitative logic models (Q2LM) to study intracellular signaling networks and cell-cytokine interactions
Melody K. Morris, Zachary Shriver, Ram Sasisekharan, Douglas A. Lauffenburger
Publication: Biotechnology Journal
DOI: 10.1002/biot.201100222
E-Publication Date: January 10, 2012

10.  Superstructure based on β-CD self-assembly induced by a small guest molecule
Frederico B. De Sousa ,  Ana C. Lima ,  Ângelo M. L. Denadai ,  Cleber P. A. Anconi ,  Wagner B. De Almeida ,  Willian T. G. Novato ,  Hélio F. Dos Santos ,  Chester L. Drum ,  Robert Langer and Rubén D. Sinisterra
Publication: Physical Chemistry Chemical Physics
DOI: 10.1039/C2CP22768A
E-Publication Date: January 10, 2012

11.  Detection of 2-Hydroxyglutarate in IDH-Mutated Glioma Patients by In Vivo Spectral-Editing and 2D Correlation Magnetic Resonance Spectroscopy
Ovidiu C. Andronesi, Grace S. Kim, Elizabeth Gerstner, Tracy Batchelor, Aria A. Tzika, Valeria R. Fantin, Matthew G. Vander Heiden and A. Gregory Sorensen
Publication: Science Translational Medicine
DOI: 10.1126/scitranslmed.3002693
E-Publication Date: January 11, 2012

*12.  Enhancing humoral responses to a malaria antigen with nanoparticle vaccines that expand Tfh cells and promote germinal center induction
James J. Moon, Heikyung Suh, Adrienne V. Li, Christian F. Ockenhouse, Anjali Yadava and Darrell J. Irvine
Publication: Proceedings of the National Academy of Sciences of the United States of America
DOI: 10.1073/pnas.1112648109
E-Publication Date: January 12, 2012

*13.  Quantifying Particle Coatings Using High-Precision Mass Measurements
Scott M. Knudsen, Marcio G. von Muhlen and Scott R. Manalis
Publication: Analytical Chemistry
DOI: 10.1021/ac300034r
E-Publication Date: January 17, 2012

*14.  Action and Reaction: The Biological Response to siRNA and Its Delivery Vehicles
Rosemary L Kanasty, Kathryn A Whitehead, Arturo J Vegas and Daniel G Anderson
Publication: Molecular Therapy
DOI: 10.1038/mt.2011.294
E-Publication Date: January 17, 2012

*15.  Continuous and long-term volume measurements with a commercial coulter counter
Andrea K. Bryan, Alex Engler, Amneet Gulati, Scott R. Manalis
Publication: PLoS One
DOI: 10.1371/journal.pone.0029866
E-Publication Date: January 17, 2012

*16.  Automated ARGET ATRP Accelerates Catalyst Optimization for the Synthesis of Thiol-Functionalized Polymers
Daniel J. Siegwart, Matthias Leiendecker, Robert Langer and Daniel G. Anderson
Publication: Macromolecules
DOI: 10.1021/ma3000219
E-Publication Date: January 20, 2012

17.  Fabrication of a hybrid microfluidic system incorporating both lithographically patterned microchannels and a 3D fiber-formed microfluidic network
Leon M. Bellan, Tatiana Kniazeva, Ernest S. Kim, Alla A. Epshteyn, Donald M. Cropek, Robert Langer and Jeffrey T. Borenstein
Publication: Advanced Healthcare Materials
DOI: 10.1002/adhm.201100052
E-Publication Date: January 20, 2012

*18.  Pyruvate kinase M2-specific siRNA induces apoptosis and tumor regression
Michael S. Goldberg and Phillip A. Sharp
Publication: The Journal of Experimental Medicine
DOI: 10.1084/jem.20111487
E-Publication Date: January 23, 2012

*19.  M13 Phage-Functionalized Single-Walled Carbon Nanotubes As Nanoprobes for Second Near-Infrared Window Fluorescence Imaging of Targeted Tumors
Hyunjung Yi, Debadyuti Ghosh, Moon-Ho Ham, Jifa Qi, Paul W. Barone, Michael S. Strano and Angela M. Belcher
Publication: Nano Letters
DOI: 10.1021/nl2031663
E-Publication Date: January 23, 2012 

20.  Recycling is not always good: the dangers of self-plagiarism
Dawn A. Bonnell, Jillian M. Buriak, Jason H. Hafner, Paula T. Hammond, Mark C. Hersam, Ali Javey, Nicholas A. Kotov, Peter Nordlander, Wolfgang J. Parak, Andrey L. Rogach, Raymond E. Schaak, Molly M. Stevens, Andrew T. S. Wee, C. Grant Willson and Paul S. Weiss
Publication: ACS Nano
DOI: 10.1021/nn3000912
E-Publication Date: January 24, 2012

21.  Polymer microarrays for high throughput discovery of biomaterials
Andrew L. Hook, Chien-Yi Chang, Jing Yang, David J. Scurr, Robert Langer, Daniel G. Anderson, Steve Atkinson, Paul Williams, Martyn C. Davies and Morgan R. Alexander
Publication: Journal of Visualized Experiments
DOI: 10.3791/3636
E-Publication Date: January 25, 2012

22.  Origins of tumor-associated macrophages and neutrophils
Virna Cortez-Retamozo, Martin Etzrodt, Andita Newton, Philipp J. Rauch, Aleksey Chudnovskiy, Cedric Berger, Russell J. H. Ryan, Yoshiko Iwamoto, Brett Marinelli, Rostic Gorbatov, Reza Forghani, Tatiana I. Novobrantseva, Victor Koteliansky, Jose-Luiz Figueiredo, John W. Chen, Daniel G. Anderson, Matthias Nahrendorf, Filip K. Swirski, Ralph Weissleder and Mikael J. Pittet
Publication: Proceedings of the National Academy of Sciences of the United States of America
DOI: 10.1073/pnas.1113744109
E-Publication Date: January 30, 2012

*23.  Modeling hepatitis C virus infection using human induced pluripotent stem cells
Robert E. Schwartz, Kartik Trehan, Linda Andrus, Timothy P. Sheahan, Alexander Ploss, Stephen A. Duncan, Charles M. Rice, and Sangeeta N. Bhatia
Publication: Proceedings of the National Academy of Sciences of the United States of America
DOI: 10.1073/pnas.1121400109
E-Publication Date: January 30, 2012

24.  Identification of High Affinity Polo-like Kinase 1 (Plk1) Polo-box Domain Binding Peptides Using Oxime-based Diversification.
Fa Liu, Jung-Eun Park, Wen-Jian Qian, Dan Lim, Andrej Scharow, Thorsten Berg, Michael B. Yaffe, Kyung S. Lee, and Terrence R. Burke, Jr.
Publication: ACS Chemical Biology
DOI: 10.1021/cb200469a
E-Publication Date: January 31, 2012

*25.  Combined experimental and computational analysis of DNA damage signaling reveals context-dependent roles for Erk in apoptosis and G1/S arrest after genotoxic stress
Andrea R Tentner, Michael J Lee, Gerry J Ostheimer, Leona D Samson, Douglas A Lauffenburger and Michael B Yaffe
Publication: Molecular Systems Biology
DOI: 10.1038/msb.2012.1
E-Publication Date: January 31, 2012

Publications Citing Extramural Faculty

*Indicates publications for which a KI extramural faculty member is senior author

*26.  Polyploidization of glia in neural development links tissue growth to blood-brain barrier integrity
Yingdee Unhavaithaya and Terry L. Orr-Weaver
Publication: Genes and Development
DOI: 10.1101/gad.177436.111
E-Publication Date: January 1, 2012

*27.  Alternative splicing of RNA triplets is often regulated and accelerates proteome evolution
Robert K. Bradley, Jason Merkin, Nicole J. Lambert and Christopher B. Burge
Publication: PLoS Biology
DOI: 10.1371/journal.pbio.1001229
E-Publication Date: January 3, 2012

*28.  Modulation of ligand fluorescence by the Pt(II)/Pt(IV) redox couple
Wilson JJ, Lippard SJ
Publication: Inorganica Chimica Acta
DOI: 10.1016/j.ica.2011.12.034
E-Publication Date: January 3, 2012

*29.  SIRT1 Protects against α-Synuclein Aggregation by Activating Molecular Chaperones
Gizem Donmez, Anirudh Arun, Chee-Yeun Chung, Pamela J. McLean, Susan Lindquist and Leonard Guarente
Publication: The Journal of Neuroscience
DOI: 10.1523/JNEUROSCI.3442-11.2012
E-Publication Date: January 4, 2012

*30.  Fluorophore targeting to cellular proteins via enzyme-mediated azide ligation and strain-promoted cycloaddition
Jennifer Z. Yao, Chayasith Uttamapinant, Andrei Poloukhtine, Jeremy M. Baskin, Julian A. Codelli, Ellen M. Sletten, Carolyn R. Bertozzi, Vladimir V. Popik and Alice Y. Ting
Publication: Journal of the American Chemical Society
DOI: 10.1021/ja208090p
E-Publication Date: January 4, 2012

31.  Kinome-wide selectivity profiling of ATP-competitive mTOR (mammalian target of rapamycin) inhibitors and characterization of their binding kinetics
Qingsong Liu, Sivapriya Kirubakaran, Wooyoung Hur, Mario Niepel, Kenneth Westover, Carson C. Thoreen, Jinhua Wang, Jing Ni, Matthew P. Patricelli, Kurt Vogel, Steve Riddle, David L. Waller, Ryan Traynor, Takaomi Sanda, Zheng Zhao, Seong A. Kang, Jean Zhao, A. Thomas Look, Peter K. Sorger, David M. Sabatini and Nathanael S. Gray
Publication: The Journal of Biological Chemistry
DOI: 10.1074/jbc.M111.304485
E-Publication Date: January 5, 2012

*32.  The mystery of missing heritability: Genetic interactions create phantom heritability
Or Zuk, Eliana Hechter, Shamil R. Sunyaev, and Eric S. Lander
Publication: Proceedings of the National Academy of Sciences of the United States of America
DOI: 10.1073/pnas.1119675109
E-Publication Date: January 5, 2012

*33.  Balancing repair and tolerance of DNA damage caused by alkylating agents
Dragony Fu, Jennifer A. Calvo & Leona D. Samson
Publication: Nature Reviews Cancer
DOI: 10.1038/nrc3185
E-Publication Date: January 12, 2012

34.  Functional Association of Gdown1 with RNA Polymerase II Poised on Human Genes
Bo Cheng, Tiandao Li, Peter B. Rahl, Todd E. Adamson, Nicholas B. Loudas, Jiannan Guo, Katayoun Varzavand, Jeffrey J. Cooper, Xiaopeng Hu, Averell Gnatt, Richard A. Young, David H. Price
Publication: Molecular Cell
DOI: 10.1016/j.molcel.2011.10.022
E-Publication Date: January 13, 2012

35.  Sirtuins mediate mammalian metabolic responses to nutrient availability
Angeliki Chalkiadaki and Leonard Guarente
Publication: Nature Reviews Endocrinology
DOI: 10.1038/nrendo.2011.225
E-Publication Date: January 17, 2012

36. Single-Cell Analysis Reveals that Noncoding RNAs Contribute to Clonal Heterogeneity by Modulating Transcription Factor Recruitment
Stacie L. Bumgarner, Gregor Neuert, Benjamin F. Voight, Anna Symbor-Nagrabska, Paula Grisafi, Alexander van Oudenaarden, Gerald R. Fink
Publication: Molecular Cell
DOI: 10.1016/j.molcel.2011.11.029
E-Publication Date: January 18, 2012

*37.  Evaluating the Identity and Diiron Core Transformations of a (μ-Oxo)diiron(III) Complex Supported by Electron-Rich Tris(pyridyl-2-methyl)amine Ligands
Loi H. Do, Genqiang Xue, Lawrence Que, Jr. and Stephen J. Lippard
Publication: Inorganic Chemistry
DOI: 10.1021/ic202379b
E-Publication Date: January 20, 2012

38.  Cholera toxin activates nonconventional adjuvant pathways that induce protective CD8 T-cell responses after epicutaneous vaccination
Irlanda Olvera-Gomez, Sara E. Hamilton, Zhengguo Xiao, Carla P. Guimaraes, Hidde L. Ploegh, Kristin A. Hogquist, Liangchun Wang and Stephen C. Jameson
Publication: Proceedings of the National Academy of Sciences of the United States of America
DOI: 10.1073/pnas.1105771109
E-Publication Date: January 23, 2012

*39.  Quantitative analysis of gradient sensing: towards building predictive models of chemotaxis in cancer
Shannon K Hughes-Alford and Douglas A Lauffenburger
Publication: Current Opinion in Cell Biology
DOI: 10.1016/
E-Publication Date: January 25, 2012

*40.  Redox activation of metal-based prodrugs as a strategy for drug delivery
Nora Graf and Stephen J. Lippard
Publication: Advanced Drug Delivery Reviews
DOI: 10.1016/j.addr.2012.01.007
E-Publication Date: January 25, 2012

41.  Class II MHC Self-Antigen Presentation in Human B and T Lymphocytes
Cristina Maria Costantino, Eric Spooner, Hidde L. Ploegh and David A. Hafler
Publication: PLoS One
DOI: 10.1371/journal.pone.0029805
E-Publication Date: January 27, 2012