Publications 2012

73 publications listed for 2012:

  1. Budin, I, Debnath, A, and Szostak, JW. (2012) Concentration-driven growth of model protocell membranes. J. Am. Chem. Soc., 134(51):20812-9. PMID: 23198690PMC3530389
    Jack Szostak Lab (HMS GENETICS)
  2. Guo, Y, Monahan, K, Wu, H, Gertz, J, Varley, KE, Li, W, Myers, RM, Maniatis, T, and Wu, Q. (2012) CTCF/cohesin-mediated DNA looping is required for protocadherin α promoter choice. Proc. Natl. Acad. Sci. U.S.A., 109(51):21081-6. PMID: 23204437PMC3529044
    Tom Maniatis Lab (MCB)
  3. Peterson, KA, Nishi, Y, Ma, W, Vedenko, A, Shokri, L, Zhang, X, McFarlane, M, Baizabal, JM, Junker, JP, van Oudenaarden, A, Mikkelsen, T, Bernstein, BE, Bailey, TL, Bulyk, ML, Wong, WH, andMcMahon, AP. (2012) Neural-specific Sox2 input and differential Gli-binding affinity provide context and positional information in Shh-directed neural patterning. Genes Dev., 26(24):2802-16. PMID: 23249739PMC3533082
    Andrew McMahon Lab (MCB)
  4. Ewen-Campen, B, Srouji, JR, Schwager, EE, and Extavour, CG. (2012) Oskar predates the evolution of germ plasm in insects. Curr. Biol., 22(23):2278-83. PMID:23122849
    Cassandra Extavour Lab (OEB)
    Andres Leschziner Lab (MCB)
  5. Green, DA, and Extavour, CG. (2012) Convergent evolution of a reproductive trait through distinct developmental mechanisms in Drosophila. Dev. Biol., 372(1):120-30. PMID: 23022298
    Cassandra Extavour Lab (OEB)
  6. Didovyk, A, and Verdine, GL. (2012) Structural origins of DNA target selection and nucleobase extrusion by a DNA cytosine methyltransferase. J. Biol. Chem., 287(48):40099-105. PMID: 23012373PMC3504724
    Gregory Verdine Lab (SCRB)
  7. Peacock-Villada, A, Yang, D, Danilowicz, C, Feinstein, E, Pollock, N, McShan, S, Coljee, V, and Prentiss, M. (2012) Complementary strand relocation may play vital roles in RecA-based homology recognition. Nucleic Acids Res., 40(20):10441-51. PMID: 22941658PMC3488227
    Mara Prentiss Lab (PHYSICS)
  8. De la Huerta, I, Kim, IJ, Voinescu, PE, and Sanes, JR. (2012) Direction-selective retinal ganglion cells arise from molecularly specified multipotential progenitors. Proc. Natl. Acad. Sci. U.S.A., 109(43):17663-8. PMID: 23045641 PMC3491461
    Joshua Sanes Lab (MCB)
  9. Zhuang, JJ, and Hunter, CP. (2012) The Influence of Competition Among C. elegans Small RNA Pathways on Development. Genes (Basel), 3(4). PMID: 23483754PMC3592204
    Craig Hunter Lab (MCB)
  10. Zhang, X, and Zhang, Y. (2012) DBL-1, a TGF-β, is essential for Caenorhabditis elegans aversive olfactory learning. Proc. Natl. Acad. Sci. U.S.A., 109(42):17081-6. PMID: 23019581 PMC3479501
    Yun Zhang Lab (OEB)
  11. Kocabas, A, Shen, CH, Guo, ZV, andRamanathan, S. (2012) Controlling interneuron activity in Caenorhabditis elegans to evoke chemotactic behaviour. Nature, 490(7419):273-7. PMID: 23000898
    Sharad Ramanathan Lab (MCB)
  12. Nannas, NJ, and Murray, AW. (2012) Complications dawn for kinetochore regulation by Aurora. Proc. Natl. Acad. Sci. U.S.A., 109(40):15972-3. PMID: 22991465PMC3479548
    Andrew Murray Lab (MCB)
  13. Gleason, EJ, and Kramer, EM. (2012) Characterization of Aquilegia Polycomb Repressive Complex 2 homologs reveals absence of imprinting. Gene, 507(1):54-60. PMID: 22796128
    Elena Kramer Lab (OEB)
  14. Chand, NS, Clatworthy, AE, and Hung, DT. (2012) The two-component sensor KinB acts as a phosphatase to regulate Pseudomonas aeruginosa Virulence. J. Bacteriol., 194(23):6537-47. PMID:23024348 PMC3497526
    Deborah Hung Lab (HMS MICROBIO)
  15. Datta, SS, Kim, SH, Paulose, J, Abbaspourrad, A, Nelson, DR, and Weitz, DA. (2012) Delayed buckling and guided folding of inhomogeneous capsules. Phys. Rev. Lett., 109(13):134302. PMID:23030092
    David Weitz Lab (SEAS)
  16. McEwan, DL, Weisman, AS, and Hunter, CP. (2012) Uptake of extracellular double-stranded RNA by SID-2. Mol. Cell, 47(5):746-54. PMID: 22902558PMC3488460
    Craig Hunter Lab (MCB)
  17. Gujral, TS, Karp, RL, Finski, A, Chan, M, Schwartz, PE, MacBeath, G, and Sorger, P. (2012) Profiling phospho-signaling networks in breast cancer using reverse-phase protein arrays. Oncogene, . PMID:22945653
    Gavin MacBeath Lab (HMS SYSBIO)
  18. Carter-O’Connell, I, Peel, MT, Wykoff, DD, and O’Shea, EK. (2012) Genome-Wide Characterization of the Phosphate Starvation Response in Schizosaccharomyces pombe. BMC Genomics, 13:697. PMID: 23231582PMC3556104
    Erin O’Shea Lab (MCB)
  19. Freudiger, CW, Pfannl, R, Orringer, DA, Saar, BG, Ji, M, Zeng, Q, Ottoboni, L, Wei, Y, Ying, W, Waeber, C, Sims, JR, De Jager, PL, Sagher, O, Philbert, MA, Xu, X, Kesari, S, Xie, XS, and Young, GS. (2012) Multicolored stain-free histopathology with coherent Raman imaging. Lab. Invest., 92(10):1492-502. PMID: 22906986PMC3622202
    X. Sunney Xie Lab (CCB)
  20. Kao, RM, Vasilyev, A, Miyawaki, A, Drummond, IA, and McMahon, AP. (2012) Invasion of distal nephron precursors associates with tubular interconnection during nephrogenesis. J. Am. Soc. Nephrol., 23(10):1682-90. PMID: 22904347PMC3458467
    Andrew McMahon Lab (MCB)
  21. Hsu, PD, and Zhang, F. (2012) Dissecting neural function using targeted genome engineering technologies. ACS Chem Neurosci, 3(8):603-10. PMID: 22896804PMC3419454
    Xiaowei Zhuang Lab (CCB)
    Feng Zhang Lab (BROAD)
  22. Lo, SM, McElroy, KA, and Francis, NJ. (2012) Chromatin modification by PSC occurs at one PSC per nucleosome and does not require the acidic patch of histone H2A. PLoS ONE, 7(10):e47162. PMID: 23071745PMC3469540
    Nicole Francis Lab (MCB)
    Mitzi Kuroda Lab (HMS GENETICS)
  23. Grant, SS, Kaufmann, BB, Chand, NS, Haseley, N, and Hung, DT. (2012) Eradication of bacterial persisters with antibiotic-generated hydroxyl radicals. Proc. Natl. Acad. Sci. U.S.A., 109(30):12147-52. PMID: 22778419 PMC3409745
    Deborah Hung Lab (HMS MICROBIO)
  24. Bianco, IH, Ma, LH, Schoppik, D, Robson, DN, Orger, MB, Beck, JC, Li, JM, Schier, AF, Engert, F, and Baker, R. (2012) The tangential nucleus controls a gravito-inertial vestibulo-ocular reflex. Curr. Biol., 22(14):1285-95. PMID: 22704987
    Alex Schier Lab (MCB)
  25. Crenshaw, CM, Nam, K, Oo, K, Kutchukian, PS, Bowman, BR, Karplus, M, and Verdine, GL. (2012) Enforced presentation of an extrahelical guanine to the lesion recognition pocket of human 8-oxoguanine glycosylase, hOGG1. J. Biol. Chem., 287(30):24916-28. PMID: 22511791PMC3408145
    Gregory Verdine Lab (SCRB)
  26. Carrasquillo, R, Tian, D, Krishna, S,Pollak, MR, Greka, A, and Schlöndorff, J. (2012) SNF8, a member of the ESCRT-II complex, interacts with TRPC6 and enhances its channel activity. BMC Cell Biol., 13:33. PMID: 23171048 PMC3520717
    Martin Pollak Lab (HMS BBS)
  27. Thuo, MM, Reus, WF, Simeone, FC, Kim, C, Schulz, MD, Yoon, HJ, and Whitesides, GM. (2012) Replacing -CH2CH2- with -CONH- does not significantly change rates of charge transport through Ag(TS)-SAM//Ga2O3/EGaIn junctions. J. Am. Chem. Soc., 134(26):10876-84. PMID:22676159
    George Whitesides Lab (CCB)
  28. Lo, SM, Follmer, NE, Lengsfeld, BM, Madamba, EV, Seong, S, Grau, DJ, andFrancis, NJ. (2012) A bridging model for persistence of a polycomb group protein complex through DNA replication in vitro. Mol. Cell, 46(6):784-96. PMID: 22749399PMC3389374
    Nicole Francis Lab (MCB)
  29. Reus, WF, Thuo, MM, Shapiro, ND, Nijhuis, CA, and Whitesides, GM. (2012) The SAM, not the electrodes, dominates charge transport in metal-monolayer//Ga2O3/gallium-indium eutectic junctions. ACS Nano, 6(6):4806-22. PMID: 22548354
    George Whitesides Lab (CCB)
  30. Monahan, K, Rudnick, ND, Kehayova, PD, Pauli, F, Newberry, KM, Myers, RM, andManiatis, T. (2012) Role of CCCTC binding factor (CTCF) and cohesin in the generation of single-cell diversity of protocadherin-α gene expression. Proc. Natl. Acad. Sci. U.S.A., 109(23):9125-30. PMID: 22550178PMC3384188
    Tom Maniatis Lab (MCB)
  31. Rosains, J, and Mango, SE. (2012) Genetic characterization of smg-8 mutants reveals no role in C. elegans nonsense mediated decay. PLoS ONE, 7(11):e49490. PMID:23166684 PMC3500306
    Susan Mango Lab (MCB)
  32. Lazarus, MB, Jiang, J, Gloster, TM, Zandberg, WF, Whitworth, GE, Vocadlo, DJ, and Walker, S. (2012) Structural snapshots of the reaction coordinate for O-GlcNAc transferase. Nat. Chem. Biol., 8(12):966-8. PMID: 23103939PMC3508357
    Suzanne Walker Lab (HMS SYSBIO)
    Daniel Kahne Lab (CCB)
  33. Kim, YG, Lone, AM, Nolte, WM, andSaghatelian, A. (2012) Peptidomics approach to elucidate the proteolytic regulation of bioactive peptides. Proc. Natl. Acad. Sci. U.S.A., 109(22):8523-7. PMID:22586115 PMC3365226
    Alan Saghatelian Lab (CCB)
  34. Cook, KE, and O’Shea, EK. (2012) Hog1 controls global reallocation of RNA Pol II upon osmotic shock in Saccharomyces cerevisiae. G3 (Bethesda), 2(9):1129-36. PMID: 22973550 PMC3429927
    Erin O’Shea Lab (MCB)
  35. Hacisuleyman, E, Cabili, MN, and Rinn, JL. (2012) A Keystone for ncRNA. Genome Biol., 13(5):315. PMID: 22632630PMC3446285
    John Rinn Lab (SCRB)
  36. Sung, RJ, Zhang, M, Qi, Y, and Verdine, GL. (2012) Sequence-dependent structural variation in DNA undergoing intrahelical inspection by the DNA glycosylase MutM. J. Biol. Chem., 287(22):18044-54. PMID:22465958 PMC3365742
    Gregory Verdine Lab (SCRB)
  37. Gude, L, Berkovitch, SS, Santos, WL, Kutchukian, PS, Pawloski, AR, Kuimelis, R, McGall, G, and Verdine, GL. (2012) Mapping targetable sites on human telomerase RNA pseudoknot/template domain using 2′-OMe RNA-interacting polynucleotide (RIPtide) microarrays. J. Biol. Chem., 287(22):18843-53. PMID:22451672 PMC3365779
    Gregory Verdine Lab (SCRB)
  38. Grama, A, and Engert, F. (2012) Direction selectivity in the larval zebrafish tectum is mediated by asymmetric inhibition. Front Neural Circuits, 6:59. PMID: 22969706PMC3432856
    Florian Engert Lab (MCB)
  39. Ahrens, MB, Li, JM, Orger, MB, Robson, DN, Schier, AF, Engert, F, and Portugues, R. (2012) Brain-wide neuronal dynamics during motor adaptation in zebrafish. Nature, 485(7399):471-7. PMID: 22622571
    Alex Schier Lab (MCB)
  40. Loy, RE, Lueck, JD, Mostajo-Radji, MA, Carrell, EM, and Dirksen, RT. (2012) Allele-specific gene silencing in two mouse models of autosomal dominant skeletal myopathy. PLoS ONE, 7(11):e49757. PMID: 23152933PMC3495761
    Paola Arlotta Lab (SCRB)
  41. Müller, P, Rogers, KW, Jordan, BM, Lee, JS, Robson, D, Ramanathan, S, andSchier, AF. (2012) Differential diffusivity of Nodal and Lefty underlies a reaction-diffusion patterning system. Science, 336(6082):721-4. PMID: 22499809PMC3525670
    Alex Schier Lab (MCB)
  42. Lee, MJ, Ye, AS, Gardino, AK, Heijink, AM, Sorger, PK, MacBeath, G, and Yaffe, MB. (2012) Sequential application of anticancer drugs enhances cell death by rewiring apoptotic signaling networks. Cell, 149(4):780-94. PMID: 22579283
    Gavin MacBeath Lab (HMS SYSBIO)
  43. Mekhoubad, S, Bock, C, de Boer, AS, Kiskinis, E, Meissner, A, and Eggan, K. (2012) Erosion of dosage compensation impacts human iPSC disease modeling. Cell Stem Cell, 10(5):595-609. PMID: 22560080
    Kevin Eggan Lab (SCRB)
  44. Moffitt, JR, Lee, JB, and Cluzel, P. (2012) The single-cell chemostat: an agarose-based, microfluidic device for high-throughput, single-cell studies of bacteria and bacterial communities. Lab Chip, 12(8):1487-94. PMID: 22395180
    Sharad Ramanathan Lab (MCB)
  45. Vigneault, F, Ter-Ovanesyan, D, Alon, S, Eminaga, S, C Christodoulou, D, Seidman, JG, Eisenberg, E, and M Church, G. (2012) High-throughput multiplex sequencing of miRNA. Curr Protoc Hum Genet, Chapter 11:Unit 11.12.1-10. PMID: 22470142
    George Church Lab (HMS GENETICS)
  46. Kubicek, S, Gilbert, JC, Fomina-Yadlin, D, Gitlin, AD, Yuan, Y, Wagner, FF, Holson, EB, Luo, T, Lewis, TA, Taylor, B, Gupta, S, Shamji, AF, Wagner, BK, Clemons, PA, andSchreiber, SL. (2012) Chromatin-targeting small molecules cause class-specific transcriptional changes in pancreatic endocrine cells. Proc. Natl. Acad. Sci. U.S.A., 109(14):5364-9. PMID: 22434908PMC3325696
    Stuart Schreiber Lab (CCB)
  47. Banse, SA, and Hunter, CP. (2012) Vampiric isolation of extracellular fluid from Caenorhabditis elegans. J Vis Exp, (61). PMID: 22453516
    Craig Hunter Lab (MCB)
  48. Kuballa, P, Nolte, WM, Castoreno, AB, and Xavier, RJ. (2012) Autophagy and the immune system. Annu. Rev. Immunol., 30:611-46. PMID: 22449030
    Alan Saghatelian Lab (CCB)
  49. Sarikaya, DP, Belay, AA, Ahuja, A, Dorta, A,Green, DA, and Extavour, CG. (2012) The roles of cell size and cell number in determining ovariole number in Drosophila. Dev. Biol., 363(1):279-89. PMID: 22200592
    Cassandra Extavour Lab (OEB)
  50. Fu, D, Lu, FK, Zhang, X, Freudiger, C, Pernik, DR, Holtom, G, and Xie, XS. (2012) Quantitative chemical imaging with multiplex stimulated Raman scattering microscopy. J. Am. Chem. Soc., 134(8):3623-6. PMID: 22316340PMC3396204
    X. Sunney Xie Lab (CCB)
  51. Chang, TY, Pardo-Martin, C, Allalou, A, Wählby, C, and Yanik, MF. (2012) Fully automated cellular-resolution vertebrate screening platform with parallel animal processing. Lab Chip, 12(4):711-6. PMID:22159032 PMC3415711
    Mehmet Fatih Yanik Lab (MIT-NEURO)
  52. Kolinski, JM, Rubinstein, SM, Mandre, S, Brenner, MP, Weitz, DA, and Mahadevan, L. (2012) Skating on a film of air: drops impacting on a surface. Phys. Rev. Lett., 108(7):074503. PMID: 22401209
    L Mahadevan Lab (SEAS)
  53. Akopian, V, Chan, MM, Clement, K, Galonska, C, Gifford, CA, Lehtola, E, Liao, J, Samavarchi-Tehrani, P, Sindhu, C, Smith, ZD, Tsankov, AM, Webster, J, Zhang, Y, Ziller, MJ, and Meissner, A. (2012) Epigenomics and chromatin dynamics. Genome Biol., 13(2):313. PMID: 22364154PMC3334565
    Alex Meissner Lab (SCRB)
  54. Song, E, de Bivort, B, Dan, C, and Kunes, S. (2012) Determinants of the Drosophila odorant receptor pattern. Dev. Cell, 22(2):363-76. PMID: 22340498
    Sam Kunes Lab (MCB)
  55. Beyer, EM, and MacBeath, G. (2012) Cross-talk between receptor tyrosine kinase and tumor necrosis factor-α signaling networks regulates apoptosis but not proliferation. Mol. Cell Proteomics, 11(6):M111.013292. PMID: 22323825PMC3433887
    Gavin MacBeath Lab (HMS SYSBIO)
  56. Lau, DT, and Murray, AW. (2012) Mad2 and Mad3 cooperate to arrest budding yeast in mitosis. Curr. Biol., 22(3):180-90. PMID:22209528 PMC3277655
    Andrew Murray Lab (MCB)
  57. Qi, Y, Nam, K, Spong, MC, Banerjee, A,Sung, RJ, Zhang, M, Karplus, M, andVerdine, GL. (2012) Strandwise translocation of a DNA glycosylase on undamaged DNA. Proc. Natl. Acad. Sci. U.S.A., 109(4):1086-91. PMID: 22219368PMC3268267
    Gregory Verdine Lab (SCRB)
  58. Verdine, GL, and Hilinski, GJ. (2012) Stapled peptides for intracellular drug targets. Meth. Enzymol., 503:3-33. PMID:22230563
    Gregory Verdine Lab (SCRB)
  59. Dearborn, RE, Dai, Y, Reed, B, Karian, T,Gray, J, and Kunes, S. (2012) Reph, a regulator of Eph receptor expression in the Drosophila melanogaster optic lobe. PLoS ONE, 7(5):e37303. PMID: 22615969PMC3353934
    Sam Kunes Lab (MCB)
  60. Hou, J, Cohen, A. E., Motion induced by asymmetric degradation of hydrogels, Soft Matter, 8, 4616-4624, 2012
    Adam Cohen Lab (CCB)
  61. Datta, SS, Kim, S-H, Paulose, J, Abbaspourrad, A, Nelson, DR, Weitz, DA. (2012) How does a porous shell collapse? Delayed buckling and guided folding of inhomogeneous capsules. Physical Review Letters 109: 134302.
    David Weitz Lab (SEAS)
  62. Fung, J, Perry, RW, Dimiduk, TG,Manoharan, VN. 2012. Imaging multiple colloidal particles by fitting electromagnetic scattering solutions to digital holograms J Quant Spectroscopy Rad Transfer 113(18): 212-9.
    Vinothan Manoharan Lab (SEAS)
  63. Jepsen, RA, Roberts, JD, Kearney, SP,Dimiduk, TG, O’Hern, TJ, Gailani, JZ. 2012. Shear Stress Measurements and Erosion Implications for Wave and Combined Wave-Current Generated Flows. J Wateray Port Coastal Ocean Engin-ASCE 138(4): 323-9.
    Vinothan Manoharan Lab (SEAS)
  64. Perry, RW, Meng, G, Dimiduk, TG, Fung, J, Manoharan, VN. 2012. Real-space studies of the structure and dynamics of self-assembled colloidal clusters. Faraday Discussions 159: 211-234.
    Vinothan Manoharan Lab (SEAS)
  65. Ferreira, LM, Floriddia, EM, Quadrato, G, and Di Giovanni, S. (2012) Neural regeneration: lessons from regenerating and non-regenerating systems. Mol. Neurobiol., 46(2):227-41. PMID: 22717989
    Chad Cowan Lab (SCRB)
    Jack Strominger Lab (MCB)
  66. Walpita, D, Hasaka, T, Spoonamore, J, Vetere, A, Takane, KK, Fomina-Yadlin, D, Fiaschi-Taesch, N, Shamji, A, Clemons, PA, Stewart, AF, Schreiber, SL, and Wagner, BK. (2012) A human islet cell culture system for high-throughput screening. J Biomol Screen, 17(4):509-18. PMID: 22156222
    Stuart Schreiber Lab (CCB)
  67. Zhuang, JJ, and Hunter, CP. (2012) RNA interference in Caenorhabditis elegans: uptake, mechanism, and regulation. Parasitology, 139(5):560-73. PMID:22075748
    Craig Hunter Lab (MCB)
  68. Zhang, X, Roeffaers, MB, Basu, S, Daniele, JR, Fu, D, Freudiger, CW, Holtom, GR, and Xie, XS. (2012) Label-free live-cell imaging of nucleic acids using stimulated Raman scattering microscopy. Chemphyschem, 13(4):1054-9. PMID:22368112 PMC3516876
    Tom Maniatis Lab (MCB)
    X. Sunney Xie Lab (CCB)
  69. Pakotiprapha, D, Samuels, M, Shen, K, Hu, JH, and Jeruzalmi, D. (2012) Structure and mechanism of the UvrA-UvrB DNA damage sensor. Nat. Struct. Mol. Biol., 19(3):291-8. PMID: 22307053
    David Jeruzalmi Lab (MCB)
  70. Georghiou, G, Kleiner, RE, Pulkoski-Gross, M, Liu, DR, and Seeliger, MA. (2012) Highly specific, bisubstrate-competitive Src inhibitors from DNA-templated macrocycles. Nat. Chem. Biol., 8(4):366-74. PMID: 22344177 PMC3307835
    David Liu Lab (CCB)
  71. Jabaudon, D, Shnider, SJ, Tischfield, DJ, Galazo, MJ, and Macklis, JD. (2012) RORβ induces barrel-like neuronal clusters in the developing neocortex. Cereb. Cortex, 22(5):996-1006. PMID: 21799210PMC3328343
    Jeffrey Macklis Lab (SCRB)
  72. Fomina-Yadlin, D, Kubicek, S, Vetere, A, He, KH, He, KH, Schreiber, SL, and Wagner, BK. (2012) GW8510 increases insulin expression in pancreatic alpha cells through activation of p53 transcriptional activity. PLoS ONE, 7(1):e28808. PMID:22242153 PMC3252286
    Stuart Schreiber Lab (CCB)
  73. Jiang, J, Lazarus, MB, Pasquina, L, Sliz, P, and Walker, S. (2012) A neutral diphosphate mimic crosslinks the active site of human O-GlcNAc transferase. Nat. Chem. Biol., 8(1):72-7. PMID: 22082911PMC3241908
    Suzanne Walker Lab (HMS SYSBIO)
    Daniel Kahne Lab (CCB)