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: November 2011

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Publications Citing Intramural Faculty

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

1.  Exon-centric regulation of pyruvate kinase M alternative splicing via mutually exclusive exons
Zhenxun Wang, Deblina Chatterjee, Hyun Yong Jeon, Martin Akerman, Matthew G. Vander Heiden, Lewis C. Cantley and Adrian R. Krainer
Publication: Journal of Molecular Cell Biology
DOI: 10.1093/jmcb/mjr030
E-Publication Date: November 1, 2011

2.  Inhibition of Pyruvate Kinase M2 by Reactive Oxygen Species Contributes to Antioxidant Responses
Dimitrios Anastasiou, George Poulogiannis, John M. Asara, Matthew B. Boxer, Jian-kang Jiang, Min Shen, Gary Bellinger, Atsuo T. Sasaki, Jason W. Locasale, Douglas S. Auld, Craig J. Thomas, Matthew G. Vander Heiden, Lewis C. Cantley
Publication: Science
DOI: 10.1126/science.1211485
E-Publication Date: November 3, 2011

*3.  Dose dependence of intratumoral perivascular distribution of monoclonal antibodies
John J. Rhoden and Karl Dane Wittrup
Publication: Journal of Pharmaceutical Sciences
DOI: 10.1002/jps.22801
E-Publication Date: November 4, 2011

4.  Systematic phosphorylation analysis of human mitotic protein complexes
Björn Hegemann, James R. A. Hutchins, Otto Hudecz, Maria Novatchkova, Jonathan Rameseder, Martina M. Sykora, Sihan Liu, Michael Mazanek, Péter Lénárt, Jean-Karim Hériché, Ina Poser, Norbert Kraut, Anthony A. Hyman, Michael B. Yaffe, Karl Mechtler and Jan-Michael Peters
Publication: Science Signaling
DOI: 10.1126/scisignal.2001993
E-Publication Date: November 8, 2011

*5.  Aerobic glycolysis: meeting the metabolic requirements of cell proliferation
Sophia Y. Lunt and Matthew G. Vander Heiden
Publication: Annual Review of Cell and Developmental Biology
DOI: 10.1146/annurev-cellbio-092910-154237
E-Publication Date: November, 2011

*6.  tRNAs marked with CCACCA are targeted for degradation
Jeremy E. Wilusz, Joseph M. Whipple, Eric M. Phizicky and Phillip A. Sharp
Publication: Journal of Molecular Cell Biology
DOI: 10.1126/science.1213671
E-Publication Date: November 11, 2011

7.  A physical mechanism to explain the delivery of chemical penetration enhancers into skin during transdermal sonophoresis - Insight into the observed synergism
Polat BE, Deen WM, Langer R, Blankschtein D
Publication: Journal of Controlled Release
DOI: 10.1016/j.jconrel.2011.11.008
E-Publication Date: November 12, 2011

*8.  Direct Signaling between Platelets and Cancer Cells Induces an Epithelial-Mesenchymal-Like Transition and Promotes Metastasis
Myriam Labelle, Shahinoor Begum and Richard O. Hynes
Publication: Cancer Cell
DOI: 10.1016/j.ccr.2011.09.009
E-Publication Date: November 15, 2011

*9.  In vivo prevention of arterial restenosis with paclitaxel-encapsulated targeted lipid-polymeric nanoparticles
Chan JM, Rhee JW, Drum CL, Bronson RT, Golomb G, Langer R, Farokhzad OC
Publication: Proceedings of the National Academy of Sciences of the United States of America
DOI: 10.1073/pnas.1115945108
E-Publication Date: November 15, 2011

10.  Interaction of Streptavidin-Based Peptide-MHC Oligomers (Tetramers) with Cell-Surface TCRs
Jennifer D. Stone, Maxim N. Artyomov, Adam S. Chervin, Arup K. Chakraborty, Herman N. Eisen and David M. Kranz
Publication: Journal of Immunology
DOI: 10.4049/jimmunol.1101734
E-Publication Date: November 18, 2011

11.  Reductive glutamine metabolism by IDH1 mediates lipogenesis under hypoxia
Christian M. Metallo, Paulo A. Gameiro, Eric L. Bell, Katherine R. Mattaini, Juanjuan Yang, Karsten Hiller, Christopher M. Jewell, Zachary R. Johnson, Darrell J. Irvine, Leonard Guarente, Joanne K. Kelleher, Matthew G. Vander Heiden, Othon Iliopoulos and Gregory Stephanopoulos
Publication: Nature
DOI: 10.1038/nature10602
E-Publication Date: November 20, 2011

12.  Chemical Genetic Screen for AMPKα2 Substrates Uncovers a Network of Proteins Involved in Mitosis
Max R. Banko, Jasmina J. Allen, Bethany E. Schaffer, Erik W. Wilker, Peiling Tsou, Jamie L. White, Judit Villén, Beatrice Wang, Sara R. Kim, Kei Sakamoto, Steven P. Gygi, Lewis C. Cantley, Michael B. Yaffe, Kevan M. Shokat and Anne Brunet
Publication: Molecular Cell
DOI: 10.1016/j.molcel.2011.11.005
E-Publication Date: November 30, 2011

Publications Citing Extramural Faculty

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

*13.  Multiple Cdt1 molecules act at each origin to load replication-competent Mcm2-7 helicases
Thomas J Takara and Stephen P Bell
Publication: The EMBO Journal
DOI: 10.1038/emboj.2011.394
E-Publication Date: November 1, 2011

*14.  Protein quality control in the ER: balancing the ubiquitin checkbook
Jasper H.L. Claessen, Lenka Kundrat and Hidde L. Ploegh
Publication: Biotechnology Journal
DOI: 10.1016/j.tcb.2011.09.010
E-Publication Date: November 3, 2011

*15.  mTORC1 senses lysosomal amino acids through an inside-out mechanism that requires the vacuolar H⁺-ATPase
Roberto Zoncu, Liron Bar-Peled, Alejo Efeyan, Shuyu Wang, Yasemin Sancak and David M. Sabatini
Publication: Science
DOI: 10.1126/science.1207056
E-Publication Date: November 4, 2011

*16.  Surface-engineered substrates for improved human pluripotent stem cell culture under fully defined conditions
Krishanu Sahaa, Ying Meib, Colin M. Reisterer, Neena Kenton Pyzocha, Jing Yang, Julien Muffat, Martyn C. Davies, Morgan R. Alexander, Robert Langer, Daniel G. Anderson and Rudolf Jaenisch
Publication: Proceedings of the National Academy of Sciences of the United States of America
DOI: 10.1073/pnas.1114854108
E-Publication Date: November 7, 2011 

*17.  Direct repair of 3,N(4)-ethenocytosine by the human ALKBH2 dioxygenase is blocked by the AAG/MPG glycosylase
Dragony Fu and Leona D. Samson
Publication: DNA Repair
DOI: 10.1016/j.dnarep.2011.10.004
E-Publication Date: November 10, 2011

18.  Lipids promote survival, proliferation, and maintenance of differentiation of rat liver sinusoidal endothelial cells in vitro
Ta-Chun Hang, Douglas A. Lauffenburger, Linda G. Griffith and Donna B. Stolz
Publication: American Journal of Physiology: Gastrointestinal and Liver Physiology
DOI: 10.1152/ajpgi.00288.2011
E-Publication Date: November 10, 2011

19.  Competencies: a cure for pre-med curriculum
Winston A. Anderson, Richard M. Amasino, Manuel Ares Jr., Utpal Banerjee, Bonnie Bartel, Victor G. Corces, Catherine L. Drennan, Sarah C. R. Elgin, Irving R. Epstein, Ellen Fanning, Louis J. Guillette Jr., Jo Handelsman, Graham F. Hatfull, Ronald Raymond Hoy, Darcy Kelley, Leslie A. Leinwand, Richard Losick, Yi Lu, David G. Lynn, Claudia Neuhauser, Diane K. O'Dowd, Toto Olivera, Pavel Pevzner, Rebecca R. Richards-Kortum, Jasper Rine, Robert L. Sah, Scott A. Strobel, Graham C. Walker, David R. Walt, Isiah M. Warner, Sue Wessler, Huntington F. Willard and Richard N. Zare
Publication: Science
DOI: 10.1126/science.334.6057.760-b
E-Publication Date: November 11, 2011

20.  Embryonic stem cell-based mapping of developmental transcriptional programs
Esteban O Mazzoni, Shaun Mahony, Michelina Iacovino, Carolyn A Morrison, George Mountoufaris, Michael Closser, Warren A Whyte, Richard A Young, Michael Kyba, David K Gifford and Hynek Wichterle
Publication: Nature Methods
DOI: 10.1038/nmeth.1775
E-Publication Date: November 13, 2011

*21.  Developmental control of gene copy number by repression of replication initiation and fork progression
Noa Sher, George W. Bell, Sharon Li, Jared Nordman, Thomas Eng, Matthew L. Eaton, David M. MacAlpine and Terry L. Orr-Weaver
Publication: Genome Research
DOI: 10.1101/gr.126003.111
E-Publication Date: November 16, 2011

22.  STITCHER: Dynamic assembly of likely amyloid and prion β-structures from secondary structure predictions
Allen W. Bryan Jr., Charles W. O'Donnell, Matthew Menke, Lenore J. Cowen, Susan Lindquist and Bonnie Berger
Publication: Proteins
DOI: 10.1002/prot.23203
E-Publication Date: November 17, 2011

*23.  Imaging Protein-Protein Interactions inside Living Cells via Interaction-Dependent Fluorophore Ligation
Sarah A. Slavoff, Daniel S. Liu, Justin D. Cohen and Alice Y. Ting
Publication: Journal of the American Chemical Society
DOI: 10.1021/ja206435e
E-Publication Date: November 18, 2011

24.  Lyapunov exponents and phase diagrams reveal multi-factorial control over TRAIL-induced apoptosis
Bree B Aldridge, Suzanne Gaudet, Douglas A Lauffenburger and Peter K Sorger
Publication: Molecular Systems Biology
DOI: 10.1038/msb.2011.85
E-Publication Date: November 22, 2011

*25.  Sirtuins, Aging, and Metabolism
Leonard Guarente
Publication: Cold Spring Harbor Symposia on Quantitative Biology
DOI: 10.1101/sqb.2011.76.010629
E-Publication Date: November 23, 2011

26.  Road to ruin: targeting proteins for degradation in the endoplasmic reticulum
Melanie H. Smith, Hidde L. Ploegh, Jonathan S. Weissman
Publication: Science
DOI: 10.1126/science.1209235
E-Publication Date: November 25, 2011

*27.  Single-molecule transcript counting of stem-cell markers in the mouse intestine
Itzkovitz S, Lyubimova A, Blat IC, Maynard M, van Es J, Lees J, Jacks T, Clevers H, van Oudenaarden A
Publication: Nature Cell Biology
DOI: 10.1038/ncb2384
E-Publication Date: November 27, 2011

*28.  Identification of host cell factors required for intoxication through use of modified cholera toxin
Carla P. Guimaraes, Jan E. Carette, Malini Varadarajan, John Antos, Maximilian W. Popp, Eric Spooner, Thijn R. Brummelkamp and Hidde L. Ploegh
Publication: Journal of Cell Biology
DOI: 10.1083/jcb.201108103
E-Publication Date: November 28, 2011

*29.  A rapid survival assay to measure drug-induced cytotoxicity and cell cycle effects
Chandni Valiathan, Jose L. McFaline and Leona D. Samson
Publication: DNA Repair
DOI: 10.1016/j.dnarep.2011.11.002
E-Publication Date: November 29, 2011

*30.  Querying Quantitative Logic Models (Q2LM) to study intracellular signaling networks and cell/cytokine interactions
Melody K. Morris, Zachary Shriver, Ram Sasisekharan and Douglas A. Lauffenburger
Publication: Biotechnology Journal
DOI: 10.1002/biot.201100222
E-Publication Date: November 29, 2011

*31.  mTOR Signaling
Mathieu Laplante and David M. Sabatini
Publication: Cold Spring Harbor Perspectives in Biology
DOI: 10.1101/cshperspect.a011593
E-Publication Date: November 30, 2011

32.  Using the Heat-Shock Response To Discover Anticancer Compounds that Target Protein Homeostasis
Sandro Santagata, Ya-ming Xu, E. M. Kithsiri Wijeratne, Renee Kontnik, Christine Rooney, Casey C. Perley, Hyoungtae Kwon, Jon Clardy, Santosh Kesari, Luke Whitesell, Susan Lindquist and A. A. Leslie Gunatilaka
Publication: ACS Chemical Biology
DOI: 10.1021/cb200353m
E-Publication Date: November 30, 2011