Progress: January 2013

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Publications Citing Koch Institute Faculty Members

1. Systematic identification of combinatorial drivers and targets in cancer cell lines. Tabchy A, Eltonsy N, Housman DE, Mills GB. PLoS One. pubmed:23577104;  doi:10.1371/journal.pone.0060339

2. Characterization of FUS Mutations in Amyotrophic Lateral Sclerosis Using RNA-Seq. van Blitterswijk M, Wang ET, Friedman BA, Keagle PJ, Lowe P, Leclerc AL, van den Berg LH, Housman DE, Veldink JH, Landers JE. PLoS One. pubmed:23577159;  doi:10.1371/journal.pone.0060788

3. Integrated cistromic and expression analysis of amplified NKX2-1 in lung adenocarcinoma identifies LMO3 as a functional transcriptional target. Watanabe H, Francis JM, Woo MS, Etemad B, Lin W, Fries DF, Peng S, Snyder EL, Tata PR, Izzo F, Schinzel AC, Cho J, Hammerman PS, Verhaak RG, Hahn WC, Rajagopal J, Jacks T, Meyerson M. Genes Dev. pubmed:23322301;  doi:10.1101/gad.203208.112

4. Helicase Loading at Chromosomal Origins of Replication. Bell SP, Kaguni JM. Cold Spring Harb Perspect Biol. pubmed:23613349;  doi:10.1101/cshperspect.a010124

5. Gene copy-number alterations: a cost-benefit analysis. Tang YC, Amon A. Cell. pubmed:23374337;  doi:10.1016/j.cell.2012.11.043

6. A role for PVRL4-driven cell-cell interactions in tumorigenesis. Pavlova NN, Pallasch C, Elia AE, Braun CJ, Westbrook TF, Hemann M, Elledge SJ. Elife. pubmed:23682311;  doi:10.7554/eLife.00358

7. Phenotypic screens for compounds that target the cellular pathologies underlying Parkinson's Disease. Tardiff DF, Lindquist S. Drug Discov Today Technol. pubmed:23644949;  doi:10.1016/j.ddtec.2012.02.003

8. Defining principles of combination drug mechanisms of action. Pritchard JR, Bruno PM, Gilbert LA, Capron KL, Lauffenburger DA, Hemann MT. Proc Natl Acad Sci U S A. pubmed:23251029;  doi:10.1073/pnas.1210419110

9. Both the Caspase CSP-1 and a Caspase-Independent Pathway Promote Programmed Cell Death in Parallel to the Canonical Pathway for Apoptosis in Caenorhabditis elegans. Denning DP, Hatch V, Horvitz HR. PLoS Genet. pubmed:23505386;  doi:10.1371/journal.pgen.1003341

10. The scientific drunk and the lamppost: massive sequencing efforts in cancer discovery and treatment. Yaffe MB. Sci Signal. pubmed:23550209;  doi:10.1126/scisignal.2003684

11. 2012: Signaling breakthroughs of the year. Yaffe MB, Gough NR. Sci Signal. pubmed:23281367;  doi:10.1126/scisignal.2003881

12. Linking proteomic and transcriptional data through the interactome and epigenome reveals a map of oncogene-induced signaling. Huang SS, Clarke DC, Gosline SJ, Labadorf A, Chouinard CR, Gordon W, Lauffenburger DA, Fraenkel E. PLoS Comput Biol. pubmed:23408876;  doi:10.1371/journal.pcbi.1002887

13. Normalization and statistical analysis of multiplexed bead-based immunoassay data using mixed-effects modeling. Clarke DC, Morris MK, Lauffenburger DA. Mol Cell Proteomics. pubmed:23071098;  doi:10.1074/mcp.M112.018655

14. Insights into proteomic immune cell signaling and communication via data-driven modeling. Benedict KF, Lauffenburger DA. Curr Top Microbiol Immunol. pubmed:22878785;  doi:10.1007/82_2012_249

15. Physical and structural properties of [Cu(BOT1)Cl]Cl, a fluorescent imaging probe for HNO. Royzen M, Wilson JJ, Lippard SJ. J Inorg Biochem. pubmed:23102502;  doi:10.1016/j.jinorgbio.2012.08.025

16. Regulation of mTORC1 by the Rag GTPases is necessary for neonatal autophagy and survival. Efeyan A, Zoncu R, Chang S, Gumper I, Snitkin H, Wolfson RL, Kirak O, Sabatini DD, Sabatini DM. Nature. pubmed:23263183;  doi:10.1038/nature11745

17. MCT1-mediated transport of a toxic molecule is an effective strategy for targeting glycolytic tumors. Birsoy K, Wang T, Possemato R, Yilmaz OH, Koch CE, Chen WW, Hutchins AW, Gultekin Y, Peterson TR, Carette JE, Brummelkamp TR, Clish CB, Sabatini DM. Nat Genet. pubmed:23202129;  doi:10.1038/ng.2471

18. Our new look at biology. Lauffenburger DA. Integr Biol (Camb). pubmed:23223812;  doi:10.1039/c2ib90056d

19. Cell plasticity and heterogeneity in cancer. Marjanovic ND, Weinberg RA, Chaffer CL. Clin Chem. pubmed:23220226;  doi:10.1373/clinchem.2012.184655

20. SOX2 co-occupies distal enhancer elements with distinct POU factors in ESCs and NPCs to specify cell state. Lodato MA, Ng CW, Wamstad JA, Cheng AW, Thai KK, Fraenkel E, Jaenisch R, Boyer LA. PLoS Genet. pubmed:23437007;  doi:10.1371/journal.pgen.1003288

21. Cell-specific TLR9 trafficking in primary APCs of transgenic TLR9-GFP mice. Avalos AM, Kirak O, Oelkers JM, Pils MC, Kim YM, Ottinger M, Jaenisch R, Ploegh HL, Brinkmann MM. J Immunol. pubmed:23241879;  doi:10.4049/jimmunol.1202342

22. Dual roles for PARP1 during heat shock: transcriptional activator and posttranscriptional inhibitor of gene expression. Vyas S, Chang P. Mol Cell. pubmed:23312545;  doi:10.1016/j.molcel.2012.12.017

23. Dose-dependent roles for canonical Wnt signalling in de novo crypt formation and cell cycle properties of the colonic epithelium. Hirata A, Utikal J, Yamashita S, Aoki H, Watanabe A, Yamamoto T, Okano H, Bardeesy N, Kunisada T, Ushijima T, Hara A, Jaenisch R, Hochedlinger K, Yamada Y. Development. pubmed:23222438;  doi:10.1242/dev.084103

24. High throughput discovery of thermo-responsive materials using water contact angle measurements and time-of-flight secondary ion mass spectrometry. Hook AL, Scurr DJ, Anderson DG, Langer R, Williams P, Davies M, Alexander M. Surf Interface Anal. pubmed:23450147;  doi:10.1002/sia.4910

25. Strategies for MCR image analysis of large hyperspectral data-sets. Scurr DJ, Hook AL, Burley JA, Williams PM, Anderson DG, Langer RC, Davies MC, Alexander MR. Surf Interface Anal. pubmed:23450109;  doi:10.1002/sia.5040

26. DNA nanotherapy for pre-neoplastic cervical lesions. Peng W, Dunton C, Holtz D, Parva M, Stampler K, Forwood M, Gogoi R, Lace MJ, Anderson DG, Sawicki JA. Gynecol Oncol. pubmed:23103931;  doi:10.1016/j.ygyno.2012.10.018

27. Mass-encoded synthetic biomarkers for multiplexed urinary monitoring of disease. Kwong GA, von Maltzahn G, Murugappan G, Abudayyeh O, Mo S, Papayannopoulos IA, Sverdlov DY, Liu SB, Warren AD, Popov Y, Schuppan D, Bhatia SN. Nat Biotechnol. pubmed:23242163;  doi:10.1038/nbt.2464

28. models for liver toxicity testing. Soldatow VY, Lecluyse EL, Griffith LG, Rusyn I. Toxicol Res (Camb). pubmed:23495363;  doi:10.1039/C2TX20051A

29. Uremic serum and solutes increase post-vascular interventional thrombotic risk through altered stability of smooth muscle cell tissue factor. Chitalia VC, Shivanna S, Martorell J, Balcells M, Bosch I, Kolandaivelu K, Edelman ER. Circulation. pubmed:23269489;  doi:10.1161/CIRCULATIONAHA.112.118174

30. The effect of substrate modulus on the growth and function of matrix-embedded endothelial cells. Murikipudi S, Methe H, Edelman ER. Biomaterials. pubmed:23102623;  doi:10.1016/j.biomaterials.2012.09.079

31. Composite dissolving microneedles for coordinated control of antigen and adjuvant delivery kinetics in transcutaneous vaccination. Demuth PC, Garcia-Beltran WF, Ai-Ling ML, Hammond PT, Irvine DJ. Adv Funct Mater. pubmed:23503923;  doi:10.1002/adfm.201201512

32. Bio-inspired polymer composite actuator and generator driven by water gradients. Ma M, Guo L, Anderson DG, Langer R. Science. pubmed:23307738;  doi:10.1126/science.1230262

33. Robustness and epistasis in the C elegans vulval signaling network revealed by pathway dosage modulation. Barkoulas M, van Zon JS, Milloz J, van Oudenaarden A, Felix MA. Dev Cell. pubmed:23328399;  doi:10.1016/j.devcel.2012.12.001

34. Formulations for trans-tympanic antibiotic delivery. Khoo X, Simons EJ, Chiang HH, Hickey JM, Sabharwal V, Pelton SI, Rosowski JJ, Langer R, Kohane DS. Biomaterials. pubmed:23146430;  doi:10.1016/j.biomaterials.2012.10.025

35. Deconvolving the roles of Wnt ligands and receptors in sensing and amplification. Tan RZ, Ji N, Mentink RA, Korswagen HC, van Oudenaarden A. Mol Syst Biol. pubmed:23295860;  doi:10.1038/msb.2012.64

36. Development of siRNA-probes for studying intracellular trafficking of siRNA nanoparticles. Alabi CA, Sahay G, Langer R, Anderson DG. Integr Biol (Camb). pubmed:23014672;  doi:10.1039/c2ib20155k

37. Functional single-cell analysis of T-cell activation by supported lipid bilayer-tethered ligands on arrays of nanowells. Torres AJ, Contento RL, Gordo S, Wucherpfennig KW, Love JC. Lab Chip. pubmed:23070211;  doi:10.1039/c2lc40869d

38. Imaging trans-cellular neurexin-neuroligin interactions by enzymatic probe ligation. Liu DS, Loh KH, Lam SS, White KA, Ting AY. PLoS One. pubmed:23457442;  doi:10.1371/journal.pone.0052823

39. Quantitative Characterization of Glycan-Receptor Binding of H9N2 Influenza A Virus Hemagglutinin. Srinivasan K, Raman R, Jayaraman A, Viswanathan K, Sasisekharan R. PLoS One. pubmed:23626667;  doi:10.1371/journal.pone.0059550

40. Quantitative description of glycan-receptor binding of influenza a virus h7 hemagglutinin. Srinivasan K, Raman R, Jayaraman A, Viswanathan K, Sasisekharan R. PLoS One. pubmed:23437033;  doi:10.1371/journal.pone.0049597

41. Single-Cell Analysis Reveals Isotype-Specific Autoreactive B Cell Repertoires in Sjogren's Syndrome. Nguyen CQ, Ogunniyi AO, Karabiyik A, Love JC. PLoS One. pubmed:23516437;  doi:10.1371/journal.pone.0058127

42. A phase II, sham-controlled, double-blinded study testing the safety and efficacy of the coronary sinus reducer in patients with refractory angina: study protocol for a randomized controlled trial. Jolicoeur EM, Banai S, Henry TD, Schwartz M, Doucet S, White CJ, Edelman E, Verheye S. Trials. pubmed:23413981;  doi:10.1186/1745-6215-14-46

43. Surface tethered epidermal growth factor protects proliferating and differentiating multipotential stromal cells from FasL-induced apoptosis. Rodrigues M, Blair H, Stockdale L, Griffith L, Wells A. Stem Cells. pubmed:22948863;  doi:10.1002/stem.1215

44. Benchtop fabrication of microfluidic systems based on curable polymers with improved solvent compatibility. Hashimoto M, Langer R, Kohane DS. Lab Chip. pubmed:23192674;  doi:10.1039/c2lc40888k

45. Engineering fibronectin-based binding proteins by yeast surface display. Chen TF, de Picciotto S, Hackel BJ, Wittrup KD. Methods Enzymol. pubmed:23422436;  doi:10.1016/B978-0-12-394292-0.00014-X

46. Rapid conformational epitope mapping of anti-gp120 antibodies with a designed mutant panel displayed on yeast. Mata-Fink J, Kriegsman B, Yu HX, Zhu H, Hanson MC, Irvine DJ, Wittrup KD. J Mol Biol. pubmed:23159556;  doi:10.1016/j.jmb.2012.11.010

47. Prognostically relevant gene signatures of high-grade serous ovarian carcinoma. Verhaak RG, Tamayo P, Yang JY, Hubbard D, Zhang H, Creighton CJ, Fereday S, Lawrence M, Carter SL, Mermel CH, Kostic AD, Etemadmoghadam D, Saksena G, Cibulskis K, Duraisamy S, Levanon K, Sougnez C, Tsherniak A, Gomez S, Onofrio R, Gabriel S, Chin L, Zhang N, Spellman PT, Zhang Y, Akbani R, Hoadley KA, Kahn A, Kobel M, Huntsman D, Soslow RA, Defazio A, Birrer MJ, Gray JW, Weinstein JN, Bowtell DD, Drapkin R, Mesirov JP, Getz G, Levine DA, Meyerson M. J Clin Invest. pubmed:23257362;  doi:10.1172/JCI65833

48. Monovalent and multivalent ligation of the B cell receptor exhibit differential dependence upon Syk and Src family kinases. Mukherjee S, Zhu J, Zikherman J, Parameswaran R, Kadlecek TA, Wang Q, Au-Yeung B, Ploegh H, Kuriyan J, Das J, Weiss A. Sci Signal. pubmed:23281368;  doi:10.1126/scisignal.2003220

49. Quantifying Argonaute proteins in and out of GW/P-bodies: implications in microRNA activities. Leung AK, Sharp PA. Adv Exp Med Biol. pubmed:23224970;  doi:10.1007/978-1-4614-5107-5_10

50. Braveheart, a long noncoding RNA required for cardiovascular lineage commitment. Klattenhoff CA, Scheuermann JC, Surface LE, Bradley RK, Fields PA, Steinhauser ML, Ding H, Butty VL, Torrey L, Haas S, Abo R, Tabebordbar M, Lee RT, Burge CB, Boyer LA. Cell. pubmed:23352431;  doi:10.1016/j.cell.2013.01.003

51. Immunopaleontology reveals how affinity enhancement is achieved during affinity maturation of antibodies to influenza virus. Eisen HN, Chakraborty AK. Proc Natl Acad Sci U S A. pubmed:23284164;  doi:10.1073/pnas.1219396110

52. The Ligand Binding Domain of GCNF Is Not Required for Repression of Pluripotency Genes in Mouse Fetal Ovarian Germ Cells. Okumura LM, Lesch BJ, Page DC. PLoS One. pubmed:23762465;  doi:10.1371/journal.pone.0066062

53. Sortase-mediated modification of alphaDEC205 affords optimization of antigen presentation and immunization against a set of viral epitopes. Swee LK, Guimaraes CP, Sehrawat S, Spooner E, Barrasa MI, Ploegh HL. Proc Natl Acad Sci U S A. pubmed:23297227;  doi:10.1073/pnas.1214994110

54. Metabolic and neuropsychiatric effects of calorie restriction and sirtuins. Libert S, Guarente L. Annu Rev Physiol. pubmed:23043250;  doi:10.1146/annurev-physiol-030212-183800

55. A complex network of factors with overlapping affinities represses splicing through intronic elements. Wang Y, Xiao X, Zhang J, Choudhury R, Robertson A, Li K, Ma M, Burge CB, Wang Z. Nat Struct Mol Biol. pubmed:23241926;  doi:10.1038/nsmb.2459

56. Integrated genomic analysis of the 8q24 amplification in endometrial cancers identifies ATAD2 as essential to MYC-dependent cancers. Raeder MB, Birkeland E, Trovik J, Krakstad C, Shehata S, Schumacher S, Zack TI, Krohn A, Werner HM, Moody SE, Wik E, Stefansson IM, Holst F, Oyan AM, Tamayo P, Mesirov JP, Kalland KH, Akslen LA, Simon R, Beroukhim R, Salvesen HB. PLoS One. pubmed:23393560;  doi:10.1371/journal.pone.0054873