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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: August 2011

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Publications Citing Intramural Faculty

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

1.  Progressive genomic instability in the FVB/KrasLA2 mouse model of lung cancer
Minh D. To, David A. Quigley, Jian-Hua Mao, Reyno Del Rosario, Jeff Hsu, Graeme Hodgson, Tyler Jacks and Allan Balmain
Publication: Molecular Cancer Research
DOI: 10.1158/1541-7786.MCR-11-0219
E-Publication Date: August 1, 2011

2.  Polydopamine Coatings Enhance Biointegration of a Model Polymeric Implant
Kyung Jae Jeong, Liqiang Wang, Cristina F. Stefanescu, Michael W. Lawlor, Julia Polat, Claes H. Dohlman, Robert S. Langer and Daniel S. Kohane
Publication: Soft Matter
DOI: 10.1039/C1SM05918A
E-Publication Date: August 1, 2011

*3.  Immuno-hybridization chain reaction enhances detection of individual cytokine-secreting human peripheral mononuclear cells
Jonghoon Choi, Kerry Routenberg Love, Yuan Gong, Todd M. Gierahn and J. Christopher Love
Publication: Analytical Chemistry
DOI: 10.1021/ac2013916
E-Publication Date: August 3, 2011

*4.  Highly Efficient Plasmon-Enhanced Dye-Sensitized Solar Cells through Metal Oxide Core-Shell Nanostructure
Jifa Qi, Xiangnan Dang, Paula T. Hammond and Angela M. Belcher
Publication: ACS Nano
DOI: 10.1021/nn201808g
E-Publication Date: August 4, 2011

5.  T Cell Receptor Internalization from the Immunological Synapse Is Mediated by TC21 and RhoG GTPase-Dependent Phagocytosis modeling
Nuria Martínez-Martín, Elena Fernández-Arenas, Saso Cemerski, Pilar Delgado, Martin Turner, John Heuser, Darrell J. Irvine, Bonnie Huang, Xosé R. Bustelo, Andrey Shaw and Balbino Alarcón
Publication: Immunity
DOI: 10.1016/j.immuni.2011.06.003
E-Publication Date: August 4, 2011

6.  Energy dissipation in microfluidic beam resonators: Effect of Poisson's ratio
John E. Sader, Thomas P. Burg, Jungchul Lee and Scott R. Manalis
Publication: Physical Review E - Statistical, Nonlinear, and Soft Matter Physics
DOI: 10.1103/PhysRevE.84.026304
E-Publication Date: August 5, 2011

7.  Facilitated Ion Transport in All-Solid-State Flexible Supercapacitors
Bong Gill Choi, Jinkee Hong, Won Hi Hong, Paula T. Hammond and HoSeok Park
Publication: ACS Nano
DOI: 10.1021/nn202020w
E-Publication Date: August 10, 2011

*8.  Directing human embryonic stem cell differentiation by non-viral delivery of siRNA in 3D culture
Janet Zoldan, Abigail K.R. Lytton-Jean, Emmanouil D. Karagiannis, Kaila Deiorio-Haggar, Leon M. Bellan, Robert Langer and Daniel G. Anderson
Publication: Biomaterials
DOI: 10.1016/j.biomaterials.2011.06.057
E-Publication Date: August 11, 2011

*9.  An EMT-Driven Alternative Splicing Program Occurs in Human Breast Cancer and Modulates Cellular Phenotype
Irina M. Shapiro, Albert W. Cheng, Nicholas C. Flytzanis, Michele Balsamo, John S. Condeelis, Maja H. Oktay, Christopher B. Burge and Frank B. Gertler
Publication: PLoS Genetics
DOI: 10.1371/journal.pgen.1002218
E-Publication Date: August 18, 2011

10.  Metabolic Regulation of Protein N-Alpha-Acetylation by Bcl-xL Promotes Cell Survival
Caroline H. Yi, Heling Pan, Jan Seebacher, Il-Ho Jang, Sven G. Hyberts, Gregory J. Heffron, Matthew G. Vander Heiden, Renliang Yang, Fupeng Li, Jason W. Locasale, Hadar Sharfi, Bo Zhai, Ricard Rodriguez-Mias, Harry Luithardt, Lewis C. Cantley, George Q. Daley, John M. Asara, Steven P. Gygi, Gerhard Wagner, Chuan-Fa Liu and Junying Yuan
Publication: Cell
DOI: 10.1016/j.cell.2011.06.050
E-Publication Date: August 18, 2011

*11.  Aneuploidy drives genomic instability in yeast
Jason M. Sheltzer, Heidi M. Blank, Sarah J. Pfau, Yoshie Tange, Benson M. George, Timothy J. Humpton, Ilana L. Brito, Yasushi Hiraoka, Osami Niwa and Angelika Amon
Publication: Science
DOI: 10.1126/science.1206412
E-Publication Date: August 19, 2011

12.  Quantitative phospho-proteomics to investigate the Polo-like kinase 1-dependent phospho-proteome
Karin Grosstessner-Hain, Björn Hegemann, Maria Novatchkova, Jonathan Rameseder, Brian A. Joughin, Otto Hudecz, Elisabeth Roitinger, Peter Pichler, Norbert Kraut, Michael B. Yaffe, Jan-Michael Peters and Karl Mechtler
Publication: Molecular and Cell Proteomics
DOI: 10.1074/mcp.M111.008540
E-Publication Date: August 21, 2011

*13.  Competitive Inhibition of Heparinase by Persulfonated Glycosaminoglycans: A Tool to Detect Heparin Contamination
Udayanath Aich, Zachary Shriver, Kannan Tharakaraman, Rahul Raman and Ram Sasisekharan
Publication: Analytical Chemistry
DOI: 10.1021/ac201498a
E-Publication Date: August 24, 2011

14.  Coordinate loss of a microRNA and protein-coding gene cooperate in the pathogenesis of 5q- syndrome
Madhu S. Kumar, Anupama Narla, Atsushi Nonami, Ann Mullally, Nadya Dimitrova, Brian Ball, J. Randall McAuley, Luke Poveromo, Jeffrey L. Kutok, Naomi Galili, Azra Raza, Eyal Attar, D. Gary Gilliland, Tyler Jacks and Benjamin L. Ebert
Publication: Blood
DOI: 10.1182/blood-2010-12-324715
E-Publication Date: August 26, 2011

*15.  The aneuploidy paradox: costs and benefits of an incorrect karyotype
Jason M. Sheltzer and Angelika Amon
Publication: Trends in Genetics
DOI: 10.1016/j.tig.2011.07.003
E-Publication Date: August 26, 2011

*16.  Targeting cancer metabolism: a therapeutic window opens
Matthew G. Vander Heiden
Publication: Nature Reviews Drug Discovery
DOI: 10.1038/nrd3504
E-Publication Date: August 31, 2011

17.  Integrin-dependent and -independent functions of astrocytic fibronectin in retinal angiogenesis
Denise Stenzel, Andrea Lundkvist, Dominique Sauvaget, Marta Busse, Mariona Graupera, Arjan van der Flier, Errol S. Wijelath, Jacqueline Murray, Michael Sobel, Mercedes Costell, Seiichiro Takahashi, Reinhard Fässler, Yu Yamaguchi, David H. Gutmann, Richard O. Hynes and Holger Gerhardt
Publication: Development
DOI: 10.1242/dev.071381
E-Publication Date: August 31, 2011

Publications Citing Extramural Faculty

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

*18.  Hunting the elusive oncogene: a stroke of good luck
Robert A. Weinberg
Publication: Nature Cell Biology
DOI: 10.1038/ncb2302
E-Publication Date: August 1, 2011

*19.  The logic linking protein acetylation and metabolism
Leonard Guarente
Publication: Cell Metabolism
DOI: 10.1016/j.cmet.2011.07.007
E-Publication Date: August 2, 2011

*20.  Tet1 is dispensable for maintaining pluripotency and its loss is compatible with embryonic and postnatal development
Meelad M. Dawlaty, Kibibi Ganz, Benjamin E. Powell, Yueh-Chiang Hu, Styliani Markoulaki, Albert W. Cheng, Qing Gao, Jongpil Kim, Sang-Woon Choi, David C. Page and Rudolf Jaenisch
Publication: Cell Stem Cell
DOI: 10.1016/j.stem.2011.07.010
E-Publication Date: August 4, 2011

*21.  mTOR Complex 1 Regulates Lipin 1 Localization to Control the SREBP Pathway
Timothy R. Peterson, Shomit S. Sengupta, Thurl E. Harris, Anne E. Carmack, Seong A. Kang, Eric Balderas, David A. Guertin, Katherine L. Madden, Anne E. Carpenter, Brian N. Finck and David M. Sabatini
Publication: Cell
DOI: 10.1016/j.cell.2011.06.034
E-Publication Date: August 4, 2011

22.  Fungal recognition is mediated by the association of dectin-1 and galectin-3 in macrophages
Alexandre Esteban, Maximilian W. Popp, Valmik K. Vyas, Karin Strijbis, Hidde L. Ploegh and Gerald R. Fink
Publication: Proceedings of the National Academy of Sciences of the United States of America
DOI: 10.1073/pnas.1111415108
E-Publication Date: August 8, 2011

*23.  Synthesis, Photophysics, Electrochemistry, and Electrogenerated Chemiluminescence of a Homologous Set of BODIPY-Appended Bipyridine Derivatives
Joel Rosenthal, Alexander B. Nepomnyashchii, Julia Kozhukh, Allen J. Bard and Stephen J. Lippard
Publication: Journal of Physical Chemistry C
DOI: 10.1021/jp204487r
E-Publication Date: August 10, 2011

*24.  Signaling network state predicts Twist-mediated effects on breast cell migration across diverse growth factor contexts
Hyung-Do Kim, Aaron S. Meyer, Joel P. Wagner, Shannon K. Alford, Alan Wells, Frank B. Gertler and Douglas A. Lauffenburger
Publication: Mol Cell Proteomics
DOI: 10.1074/mcp.M111.008433
E-Publication Date: August 10, 2011

*25.  Mir-290-295 deficiency in mice results in partially penetrant embryonic lethality and germ cell defects
Lea A. Medeiros, Lucas M. Dennis, Mark E. Gill, Hristo Houbaviy, Styliani Markoulaki, Dongdong Fu, Amy C. White, Oktay Kirak, Phillip A. Sharp, David C. Page and Rudolf Jaenisch
Publication: Proceedings of the National Academy of Sciences of the United States of America
DOI: 10.1073/pnas.1111241108
E-Publication Date: August 15, 2011

26.  The Msx1 Homeoprotein Recruits Polycomb to the Nuclear Periphery during Development
Jingqiang Wang, Roshan M. Kumar, Vanessa J. Biggs, Hansol Lee, Yun Chen, Michael H. Kagey, Richard A. Young and Cory Abate-Shen
Publication: Nature
DOI: 10.1016/j.devcel.2011.07.003
E-Publication Date: August 18, 2011

*27.  Functional genomics reveal that the serine synthesis pathway is essential in breast cancer
Richard Possemato, Kevin M. Marks, Yoav D. Shaul, Michael E. Pacold, Dohoon Kim, Kıvanç Birsoy, Shalini Sethumadhavan, Hin-Koon Woo, Hyun G. Jang, Abhishek K. Jha, Walter W. Chen, Francesca G. Barrett, Nicolas Stransky, Zhi-Yang Tsun, Glenn S. Cowley, Jordi Barretina, Nada Y. Kalaany, Peggy P. Hsu, Kathleen Ottina, Albert M. Chan, Bingbing Yuan, Levi A. Garraway, David E. Root, Mari Mino-Kenudson, Elena F. Brachtel, Edward M. Driggers and David M. Sabatini
Publication: Nature
DOI: 10.1038/nature10350
E-Publication Date: August 18, 2011

*28.  Stochastic state transitions give rise to phenotypic equilibrium in populations of cancer cells
Piyush B. Gupta1, Christine M. Fillmore, Guozhi Jiang, Sagi D. Shapira, Kai Tao, Charlotte Kuperwasser and Eric S. Lander
Publication: Cell
DOI: 10.1016/j.cell.2011.07.026
E-Publication Date: August 18, 2011

29.  SIRT1 mediated acute cardioprotection
Sergiy M. Nadtochiy, Hongwei Yao, Michael W. McBurney, Wei Gu, Leonard Guarente, Irfan Rahman and Paul S. Brookes
Publication: American Journal of Physiology - Heart and Circulatory Physiology
DOI: 10.1152/ajpheart.00587.2011
E-Publication Date: August 19, 2011

30.  Evidence That Gene Activation and Silencing during Stem Cell Differentiation Requires a Transcriptionally Paused Intermediate State
Jonathan L. Golob, Roshan M. Kumar, Matthew G. Guenther, Lil M. Pabon, Gabriel A. Pratt, Jeanne F. Loring, Louise C. Laurent, Richard A. Young and Charles E. Murry
Publication: PLoS One
DOI: 10.1371/journal.pone.0022416
E-Publication Date: August 19, 2011

*31.  MicroRNAs can generate thresholds in target gene expression
Shankar Mukherji, Margaret S Ebert, Grace X Y Zheng, John S Tsang, Phillip A Sharp and Alexander van Oudenaarden
Publication: Nature Genetics
DOI: 10.1038/ng.905
E-Publication Date: August 21, 2011

32.  Tracking a defined route for O2 migration in a dioxygen-activating diiron enzyme
Woon Ju Song, Grant Gucinski, Matthew H. Sazinsky and Stephen J. Lippard
Publication: Proceedings of the National Academy of Sciences of the United States of America
DOI: 10.1073/pnas.1106514108
E-Publication Date: August 22, 2011

*33.  Drosophila Inducer of Meiosis 4 (IME4) is required for Notch signaling during oogenesis
Cintia F. Hongay and Terry L. Orr-Weaver
Publication: Proceedings of the National Academy of Sciences of the United States of America
DOI: 10.1073/pnas.1111577108
E-Publication Date: August 22, 2011

*34.  Gene induction and repression during terminal erythropoiesis are mediated by distinct epigenetic changes
Piu Wong, Shilpa M. Hattangadi, Albert W. Cheng, Garrett M. Frampton, Richard A. Young and Harvey F. Lodish
Publication: Blood
DOI: 10.1182/blood-2011-03-341404
E-Publication Date: August 22, 2011

35.  Structure-Guided Engineering of a Pacific Blue Fluorophore Ligase for Specific Protein Imaging in Living Cells
Justin D. Cohen, Samuel Thompson, and Alice Y. Ting
Publication: Biochemistry
DOI: 10.1021/bi201037r
E-Publication Date: August 23, 2011

*36.  Immobilization, Trapping, and Anion Exchange of Perrhenate Ion Using Copper-Based Tripodal Complexes
Rui Cao, Brian D. McCarthy and Stephen J. Lippard
Publication: Inorganic Chemistry
DOI: 10.1021/ic201172r
E-Publication Date: August 26, 2011

37.  CD8α(+) Dendritic Cells Are the Critical Source of Interleukin-12 that Controls Acute Infection by Toxoplasma gondii Tachyzoites
Mona Mashayekhi, Michelle M. Sandau, Ildiko R. Dunay, Eva M. Frickel, Asis Khan, Romina S. Goldszmid, Alan Sher, Hidde L. Ploegh, Theresa L. Murphy, L. David Sibley and Kenneth M. Murphy
Publication: Immunity
DOI: 10.1016/j.immuni.2011.08.008
E-Publication Date: August 26, 2011

*38.  lincRNAs act in the circuitry controlling pluripotency and differentiation
Mitchell Guttman, Julie Donaghey, Bryce W. Carey, Manuel Garber, Jennifer K. Grenier, Glen Munson, Geneva Young, Anne Bergstrom Lucas, Robert Ach, Laurakay Bruhn, Xiaoping Yang, Ido Amit, Alexander Meissner, Aviv Regev, John L. Rinn, David E. Root and Eric S. Lander
Publication: Nature
DOI: 10.1038/nature10398
E-Publication Date: August 28, 2011

39.  Functional characterization of bacterial sRNAs using a network biology approach
Sheetal R. Modi, Diogo M. Camacho, Michael A. Kohanski, Graham C. Walker and James J. Collins
Publication: Proceedings of the National Academy of Sciences of the United States of America
DOI: 10.1073/pnas.1104318108
E-Publication Date: August 29, 2011

40.  Phenotypic plasticity and epithelial-mesenchymal transitions in cancer and normal stem cells?
Christina Scheel and Robert A. Weinberg
Publication: International Journal of Cancer
DOI: 10.1002/ijc.26311
E-Publication Date: August 29, 2011

*41.  Design and Synthesis of a Novel Triptycene-Based Ligand for Modeling Carboxylate-Bridged Diiron Enzyme Active Sites
Yang Li, Rui Cao and Stephen J. Lippard
Publication: Organic Letters
DOI: 10.1021/ol201882v
E-Publication Date: August 29, 2011

*42.  The dual role of ancient ubiquitous protein 1 (AUP1) in lipid droplet accumulation and ER protein quality control
Elizabeth J. Klemm, Eric Spooner and Hidde L. Ploegh
Publication: The Journal of Biological Chemistry
DOI: 10.1074/jbc.M111.284794
E-Publication Date: August 30, 2011

43.  The genome of the green anole lizard and a comparative analysis with birds and mammals
Jessica Alföldi, Federica Di Palma, Manfred Grabherr, Christina Williams, Lesheng Kong, Evan Mauceli, Pamela Russell, Craig B. Lowe, Richard E. Glor, Jacob D. Jaffe, David A. Ray, Stephane Boissinot, Andrew M. Shedlock, Christopher Botka, Todd A. Castoe, John K. Colbourne, Matthew K. Fujita, Ricardo Godinez Moreno, Boudewijn F. ten Hallers, David Haussler, Andreas Heger, David Heiman, Daniel E. Janes, Jeremy Johnson, Pieter J. de Jong, Maxim Y. Koriabine, Marcia Lara, Peter A. Novick, Chris L. Organ, Sally E. Peach, Steven Poe, David D. Pollock, Kevin de Queiroz, Thomas Sanger, Steve Searle, Jeremy D. Smith, Zachary Smith, Ross Swofford, Jason Turner-Maier, Juli Wade, Sarah Young, Amonida Zadissa, Scott V. Edwards, Travis C. Glenn, Christopher J. Schneider, Jonathan B. Losos, Eric S. Lander, Matthew Breen, Chris P. Ponting and Kerstin Lindblad-Toh
Publication: Nature
DOI: 10.1038/nature10390
E-Publication Date: August 31, 2011