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 2012

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Publications Citing Intramural Faculty

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

1.  Rapid casting of patterned vascular networks for perfusable engineered three-dimensional tissues
Miller JS, Stevens KR, Yang MT, Baker BM, Nguyen DH, Cohen DM, Toro E, Chen AA, Galie PA, Yu X, Chaturvedi R, Bhatia SN, Chen CS
Publication: Nature Materials
DOI: 10.1038/nmat3357
E-Publication Date: July 1, 2012

*2.  Highly transparent mixed electron and proton conducting polymer membranes
Liu J, Davis NR, Liu DS, Hammond PT
Publication: Journal of Materials Chemistry
DOI: 10.1039/C2JM32296J
E-Publication Date: July 5, 2012

3.  M13 bacteriophage display framework that allows sortase-mediated modification of surface-accessible phage proteins
Hess GT, Cragnolini JJ, Popp MW, Allen MA, Dougan SK, Spooner E, Ploegh HL, Belcher AM, Guimaraes CP
Publication: Bioconjugate Chemistry
DOI: 10.1021/bc300130z
E-Publication Date: July 6, 2012

*4.  In Vitro-In Vivo Translation of Lipid Nanoparticles for Hepatocellular siRNA Delivery
Whitehead KA, Matthews J, Chang PH, Niroui F, Dorkin JR, Severgnini M, Anderson DG
Publication: ACS Nano
DOI: 10.1021/nn301922x
E-Publication Date: July 6, 2012

*5.  New Insights into the Troubles of Aneuploidy
Siegel JJ, Amon A
Publication: Annual Review of Cell and Developmental Biology
DOI: 10.1146/annurev-cellbio-101011-155807
E-Publication Date: July 9, 2012

6.  Conjugating drug candidates to polymeric chains does not necessarily enhance anti-influenza activity
Larson AM, Wang H, Cao Y, Jiang T, Chen J, M Klibanov A
Publication: Journal of Pharmaceutical Sciences
DOI: 10.1002/jps.23253
E-Publication Date: July 11, 2012

*7.  Differential Requirement for CD70 and CD80/CD86 in Dendritic Cell-Mediated Activation of Tumor-Tolerized CD8 T Cells
Bak SP, Barnkob MS, Bai A, Higham EM, Wittrup KD, Chen J
Publication: Journal of Immunology
DOI: 10.4049/jimmunol.1201271
E-Publication Date: July 13, 2012

*8.  Robust co-regulation of tyrosine phosphorylation sites on proteins reveals novel protein interactions
Naegle KM, White FM, Lauffenburger DA, Yaffe MB
Publication: Molecular BioSystems
DOI: 10.1039/C2MB25200G
E-Publication Date: July 13, 2012

*9.  Transcriptional consequences of aneuploidy
Sheltzer JM, Torres EM, Dunham MJ, Amon A
Publication: Proceedings of the National Academy of Sciences of the United States of America
DOI: 10.1073/pnas.1209227109
E-Publication Date: July 16, 2012

*10.  Continuous intravesical lidocaine treatment for interstitial cystitis/bladder pain syndrome: safety and efficacy of a new drug delivery device
Nickel JC, Jain P, Shore N, Anderson J, Giesing D, Lee H, Kim G, Daniel K, White S, Larrivee-Elkins C, Lekstrom-Himes J, Cima M
Publication: Science Translational Medicine
DOI: 10.1126/scitranslmed.3003804
E-Publication Date: July 18, 2012

*11.  A 3D Interconnected Microchannel Network Formed in Gelatin by Sacrificial Shellac Microfibers
Bellan LM, Pearsall M, Cropek DM, Langer R
Publication: Advanced Materials
DOI: 10.1002/adma.201200810
E-Publication Date: July 24, 2012

12.  The smartest materials: the future of nanoelectronics in medicine
Cohen-Karni T, Langer R, Kohane DS
Publication: ACS Nano
DOI: 10.1021/nn302915s
E-Publication Date: July 31, 2012

Publications Citing Extramural Faculty

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

13.  AraPath: a knowledgebase for pathway analysis in Arabidopsis
Lai L, Liberzon A, Hennessey J, Jiang G, Qi J, Mesirov JP, Ge SX
Publication: Bioinformatics
DOI: 10.1093/bioinformatics/bts421
E-Publication Date: July 3, 2012

*14.  Cancer-stimulated mesenchymal stem cells create a carcinoma stem-cell niche via Prostaglandin E2 signaling
Li HJ, Reinhardt F, Herschman HR, Weinberg RA
Publication: Cancer Discovery
DOI: 10.1158/2159-8290.CD-12-0101
E-Publication Date: July 3, 2012

15.  The Polycomb Group Protein L3mbtl2 Assembles an Atypical PRC1-Family Complex that Is Essential in Pluripotent Stem Cells and Early Development
Qin J, Whyte WA, Anderssen E, Apostolou E, Chen HH, Akbarian S, Bronson RT, Hochedlinger K, Ramaswamy S, Young RA, Hock H
Publication: Cell Stem Cell
DOI: 10.1016/j.stem.2012.06.002
E-Publication Date: July 5, 2012

16.  Untuning the tumor metabolic machine: Targeting cancer metabolism: a bedside lesson
Birsoy K, Sabatini DM, Possemato R
Publication: Nature Medicine
DOI: 10.1038/nm.2870
E-Publication Date: July 6, 2012

*17.  Phenanthriplatin, a monofunctional DNA-binding platinum anticancer drug candidate with unusual potency and cellular activity profile
Park GY, Wilson JJ, Song Y, Lippard SJ
Publication: Proceedings of the National Academy of Sciences of the United States of America
DOI: 10.1073/pnas.1207670109
E-Publication Date: July 6, 2012

*18.  Preparation of unnatural N-to-N and C-to-C protein fusions
Witte MD, Cragnolini JJ, Dougan SK, Yoder NC, Popp MW, Ploegh HL
Publication: Proceedings of the National Academy of Sciences of the United States of America
DOI: 10.1073/pnas.1205427109
E-Publication Date: July 9, 2012

*19.  Programmed elimination of cells by caspase-independent cell extrusion in C. elegans
Denning DP, Hatch V, Horvitz HR
Publication: Nature
DOI: 10.1038/nature11240
E-Publication Date: July 15, 2012

*20.  Transcriptional Profiling of Plasmodium falciparum Parasites from Patients with Severe Malaria Identifies Distinct Low vs. High Parasitemic Clusters
Milner DA Jr, Pochet N, Krupka M, Williams C, Seydel K, Taylor TE, Van de Peer Y, Regev A, Wirth D, Daily JP, Mesirov JP
Publication: PLoS One
DOI: 10.1371/journal.pone.0040739
E-Publication Date: July 18, 2012

21.  BAY61-3606 Affects the Viability of Colon Cancer Cells in a Genotype-Directed Manner
Lau KS, Zhang T, Kendall KR, Lauffenburger D, Gray NS, Haigis KM
Publication: PLoS One
DOI: 10.1371/journal.pone.0041343
E-Publication Date: July 18, 2012

22.  A landscape of driver mutations in melanoma
Hodis E, Watson IR, Kryukov GV, Arold ST, Imielinski M, Theurillat JP, Nickerson E, Auclair D, Li L, Place C, Dicara D, Ramos AH, Lawrence MS, Cibulskis K, Sivachenko A, Voet D, Saksena G, Stransky N, Onofrio RC, Winckler W, Ardlie K, Wagle N, Wargo J, Chong K, Morton DL, Stemke-Hale K, Chen G, Noble M, Meyerson M, Ladbury JE, Davies MA, Gershenwald JE, Wagner SN, Hoon DS, Schadendorf D, Lander ES, Gabriel SB, Getz G, Garraway LA, Chin L
Publication: Cell
DOI: 10.1016/j.cell.2012.06.024
E-Publication Date: July 19, 2012

*23.  CpG island structure and trithorax/polycomb chromatin domains in human cells
Orlando DA, Guenther MG, Frampton GM, Young RA
Publication: Genomics
DOI: 10.1016/j.ygeno.2012.07.006
E-Publication Date: July 20, 2012

24.  Medulloblastoma exome sequencing uncovers subtype-specific somatic mutations
Pugh TJ, Weeraratne SD, Archer TC, Pomeranz Krummel DA, Auclair D, Bochicchio J, Carneiro MO, Carter SL, Cibulskis K, Erlich RL, Greulich H, Lawrence MS, Lennon NJ, McKenna A, Meldrim J, Ramos AH, Ross MG, Russ C, Shefler E, Sivachenko A, Sogoloff B, Stojanov P, Tamayo P, Mesirov JP, Amani V, Teider N, Sengupta S, Francois JP, Northcott PA, Taylor MD, Yu F, Crabtree GR, Kautzman AG, Gabriel SB, Getz G, Jäger N, Jones DT, Lichter P, Pfister SM, Roberts TM, Meyerson M, Pomeroy SL, Cho YJ
Publication: Nature
DOI: 10.1038/nature11329
E-Publication Date: July 22, 2012

*25.  X-linked H3K27me3 demethylase Utx is required for embryonic development in a sex-specific manner
Welstead GG, Creyghton MP, Bilodeau S, Cheng AW, Markoulaki S, Young RA, Jaenisch R
Publication: Proceedings of the National Academy of Sciences of the United States of America
DOI: 10.1073/pnas.1210787109
E-Publication Date: July 23, 2012

26.  Modular Design of Artificial Tissue Homeostasis: Robust Control through Synthetic Cellular Heterogeneity
Miller M, Hafner M, Sontag E, Davidsohn N, Subramanian S, Purnick PE, Lauffenburger D, Weiss R
Publication: PLoS Computational Biology
DOI: 10.1371/journal.pcbi.1002579
E-Publication Date: July 19, 2012 

*27.  The Caenorhabditis elegans Gene mfap-1 Encodes a Nuclear Protein That Affects Alternative Splicing
Ma L, Gao X, Luo J, Huang L, Teng Y, Horvitz HR
Publication: PLoS Genetics
DOI: 10.1371/journal.pgen.1002827
E-Publication Date: July 19, 2012

*28.  Deviation of innate circadian period from 24 h reduces longevity in mice
Libert S, Bonkowski MS, Pointer K, Pletcher SD, Guarente L
Publication: Aging Cell
DOI: 10.1111/j.1474-9726.2012.00846.x
E-Publication Date: July 12, 2012

29.  Comprehensive molecular characterization of human colon and rectal cancer
The Cancer Genome Atlas Network
Publication: Nature
DOI: 10.1038/nature11252
E-Publication Date: July 18, 2012