Graduate MCO

Student Publications

Publications 2011

65 Publications listed for 2011:

  1. Ng, SL, Friedman, BA, Schmid, S, Gertz, J, Myers, RM, Tenoever, BR, and Maniatis, T. (2011) IκB kinase epsilon (IKK(epsilon)) regulates the balance between type I and type II interferon responses. Proc. Natl. Acad. Sci. U.S.A., 108(52):21170-5. PMID:22171011 PMC3248534
    Tom Maniatis Lab (MCB)
  2. Houck-Loomis, B, Durney, MA, Salguero, C, Shankar, N, Nagle, JM, Goff, SP, andD’Souza, VM. (2011) An equilibrium-dependent retroviral mRNA switch regulates translational recoding. Nature, 480(7378):561-4. PMID: 22121021PMC3582340
    Victoria D’Souza Lab (MCB)
  3. Mihalusova, M, Wu, JY, and Zhuang, X. (2011) Functional importance of telomerase pseudoknot revealed by single-molecule analysis. Proc. Natl. Acad. Sci. U.S.A., 108(51):20339-44. PMID: 21571642PMC3251044
    Xiaowei Zhuang Lab (CCB)
  4. Wang, X, Winter, D, Ashrafi, G, Schlehe, J, Wong, YL, Selkoe, D, Rice, S, Steen, J, LaVoie, MJ, and Schwarz, TL. (2011) PINK1 and Parkin target Miro for phosphorylation and degradation to arrest mitochondrial motility. Cell, 147(4):893-906. PMID:22078885 PMC3261796
    Thomas Schwarz Lab (HMS)
  5. Shaw, BF, Schneider, GF, Arthanari, H, Narovlyansky, M, Moustakas, D, Durazo, A, Wagner, G, and Whitesides, GM. (2011) Complexes of native ubiquitin and dodecyl sulfate illustrate the nature of hydrophobic and electrostatic interactions in the binding of proteins and surfactants. J. Am. Chem. Soc., 133(44):17681-95. PMID: 21939262PMC3209763
    George Whitesides Lab (CCB)
  6. Bianco, IH, Kampff, AR, and Engert, F. (2011) Prey capture behavior evoked by simple visual stimuli in larval zebrafish. Front Syst Neurosci, 5:101. PMID:22203793 PMC3240898
    Florian Engert Lab (MCB)
  7. Oman, TJ, Lupoli, TJ, Wang, TS, Kahne, D, Walker, S, and van der Donk, WA. (2011) Haloduracin α binds the peptidoglycan precursor lipid II with 2:1 stoichiometry. J. Am. Chem. Soc., 133(44):17544-7. PMID:22003874 PMC3206492
    Daniel Kahne Lab (CCB)
  8. Chand, NS, and Hung, DT. (2011) The two-component sensor kinase KinB acts as a non-canonical switch between acute and chronic infection. Virulence, 2(6):553-8. PMID: 21971182
    Deborah Hung Lab (HMS MICROBIO)
  9. Isogai, Y, Si, S, Pont-Lezica, L, Tan, T, Kapoor, V, Murthy, VN, and Dulac, C. (2011) Molecular organization of vomeronasal chemoreception. Nature, 478(7368):241-5. PMID: 21937988PMC3192931
    Catherine Dulac Lab (MCB)
  10. Kehayova, P, Monahan, K, Chen, W, andManiatis, T. (2011) Regulatory elements required for the activation and repression of the protocadherin-alpha gene cluster. Proc. Natl. Acad. Sci. U.S.A., 108(41):17195-200. PMID: 21949399 PMC3193253
    Tom Maniatis Lab (MCB)
  11. Nijhuis, CA, Reus, WF, Siegel, AC, andWhitesides, GM. (2011) A molecular half-wave rectifier. J. Am. Chem. Soc., 133(39):15397-411. PMID: 21842878
    George Whitesides Lab (CCB)
  12. Kummer, DA, Li, D, Dion, A, and Myers, AG. (2011) A practical, convergent route to the key precursor to the tetracycline antibiotics. Chem Sci, 2(9):1710-1718. PMID: 21949588 PMC3176682
    Andrew Myers Lab (CCB)
  13. Chang, BH, Gujral, TS, Karp, ES, BuKhalid, R, Grantcharova, VP, andMacBeath, G. (2011) A systematic family-wide investigation reveals that ~30% of mammalian PDZ domains engage in PDZ-PDZ interactions. Chem. Biol., 18(9):1143-52. PMID: 21944753 PMC3442787
    Gavin MacBeath Lab (HMS SYSBIO)
  14. Wang, W, Li, GW, Chen, C, Xie, XS, and Zhuang, X. (2011) Chromosome organization by a nucleoid-associated protein in live bacteria. Science, 333(6048):1445-9. PMID: 21903814PMC3329943
    X. Sunney Xie Lab (CCB)
  15. Son, EY, Ichida, JK, Wainger, BJ, Toma, JS, Rafuse, VF, Woolf, CJ, and Eggan, K. (2011) Conversion of mouse and human fibroblasts into functional spinal motor neurons. Cell Stem Cell, 9(3):205-18. PMID: 21852222 PMC3188987
    Kevin Eggan Lab (SCRB)
  16. Wang, F, Whynot, A, Tung, M, and Denic, V. (2011) The mechanism of tail-anchored protein insertion into the ER membrane. Mol. Cell, 43(5):738-50. PMID: 21835666PMC3614002
    Vlad Denic Lab (MCB)
  17. Dai, Q, Liu, W, Zhuang, X, Wu, J, Zhang, H, and Wang, P. (2011) Ratiometric fluorescence sensor based on a pyrene derivative and quantification detection of heparin in aqueous solution and serum. Anal. Chem., 83(17):6559-64. PMID:21800849
    Xiaowei Zhuang Lab (CCB)
  18. Yanik, MF, Rohde, CB, and Pardo-Martin, C. (2011) Technologies for micromanipulating, imaging, and phenotyping small invertebrates and vertebrates. Annu Rev Biomed Eng, 13:185-217. PMID: 21756142
    Mehmet Fatih Yanik Lab (MIT-NEURO)
  19. Lone, AM, Bachovchin, DA, Westwood, DB, Speers, AE, Spicer, TP, Fernandez-Vega, V, Chase, P, Hodder, PS, Rosen, H, Cravatt, BF, and Saghatelian, A. (2011) A substrate-free activity-based protein profiling screen for the discovery of selective PREPL inhibitors. J. Am. Chem. Soc., 133(30):11665-74. PMID: 21692504PMC3145007
    Alan Saghatelian Lab (CCB)
  20. Rogers, KW, and Schier, AF. (2011) Morphogen gradients: from generation to interpretation. Annu. Rev. Cell Dev. Biol., 27:377-407. PMID: 21801015
    Alex Schier Lab (MCB)
  21. Lupoli, TJ, Tsukamoto, H, Doud, EH, Wang, TS, Walker, S, and Kahne, D. (2011) Transpeptidase-mediated incorporation of D-amino acids into bacterial peptidoglycan. J. Am. Chem. Soc., 133(28):10748-51. PMID: 21682301 PMC3172152
    Daniel Kahne Lab (CCB)
  22. Wu, J, Sheng, R, Liu, W, Wang, P, Ma, J, Zhang, H, and Zhuang, X. (2011) Reversible fluorescent probe for highly selective and sensitive detection of mercapto biomolecules. Inorg Chem, 50(14):6543-51. PMID: 21692450
    Xiaowei Zhuang Lab (CCB)
  23. Saar, BG, Johnston, RS, Freudiger, CW,Xie, XS, and Seibel, EJ. (2011) Coherent Raman scanning fiber endoscopy. Opt Lett, 36(13):2396-8. PMID: 21725423PMC3164497
    X. Sunney Xie Lab (CCB)
  24. Zhou, X, and O’Shea, EK. (2011) Integrated approaches reveal determinants of genome-wide binding and function of the transcription factor Pho4. Mol. Cell, 42(6):826-36. PMID: 21700227PMC3127084
    Erin O’Shea Lab (MCB)
  25. Kleiner, RE, Dumelin, CE, and Liu, DR. (2011) Small-molecule discovery from DNA-encoded chemical libraries. Chem Soc Rev, 40(12):5707-17. PMID: 21674077
    David Liu Lab (CCB)
  26. Lang, GI, and Murray, AW. (2011) Mutation rates across budding yeast chromosome VI are correlated with replication timing. Genome Biol Evol, 3:799-811. PMID: 21666225 PMC3170098
    Andrew Murray Lab (MCB)
  27. Wang, TS, Lupoli, TJ, Sumida, Y, Tsukamoto, H, Wu, Y, Rebets, Y, Kahne, DE, and Walker, S. (2011) Primer preactivation of peptidoglycan polymerases. J. Am. Chem. Soc., 133(22):8528-30. PMID: 21568328 PMC3119865
    Daniel Kahne Lab (CCB)
  28. Jung, AS, Kaushansky, A, MacBeath, G, and Kaushansky, K. (2011) Tensin2 is a novel mediator in thrombopoietin (TPO)-induced cellular proliferation by promoting Akt signaling. Cell Cycle, 10(11):1838-44. PMID: 21527831 PMC3233486
    Gavin MacBeath Lab (HMS SYSBIO)
  29. Banse, AV, Hobbs, EC, and Losick, R. (2011) Phosphorylation of Spo0A by the histidine kinase KinD requires the lipoprotein med in Bacillus subtilis. J. Bacteriol., 193(15):3949-55. PMID:21622736 PMC3147521
    Richard Losick Lab (MCB)
  30. Galkin, VE, Britt, RL, Bane, LB, Yu, X, Cox, MM, and Egelman, EH. (2011) Two modes of binding of DinI to RecA filament provide a new insight into the regulation of SOS response by DinI protein. J. Mol. Biol., 408(5):815-24. PMID: 21458462PMC3089025
    Rachelle Gaudet Lab (MCB)
  31. Tan, KY, Eminli, S, Hettmer, S, Hochedlinger, K, and Wagers, AJ. (2011) Efficient generation of iPS cells from skeletal muscle stem cells. PLoS ONE, 6(10):e26406. PMID: 22028872PMC3196574
    Amy Wagers Lab (SCRB)
  32. Freudiger, CW, Roeffaers, MB, Zhang, X, Saar, BG, Min, W, and Xie, XS. (2011) Optical heterodyne-detected Raman-induced Kerr effect (OHD-RIKE) microscopy. J Phys Chem B, 115(18):5574-81. PMID: 21504149 PMC3412286
    X. Sunney Xie Lab (CCB)
  33. Esvelt, KM, Carlson, JC, and Liu, DR. (2011) A system for the continuous directed evolution of biomolecules. Nature, 472(7344):499-503. PMID: 21478873PMC3084352
    David Liu Lab (CCB)
  34. Pattanayak, V, Ramirez, CL, Joung, JK, and Liu, DR. (2011) Revealing off-target cleavage specificities of zinc-finger nucleases by in vitro selection. Nat. Methods, 8(9):765-70. PMID: 21822273PMC3164905
    David Liu Lab (CCB)
  35. Janas, MM, Khaled, M, Schubert, S, Bernstein, JG, Golan, D, Veguilla, RA,Fisher, DE, Shomron, N, Levy, C, and Novina, CD. (2011) Feed-forward microprocessing and splicing activities at a microRNA-containing intron. PLoS Genet., 7(10):e1002330. PMID: 22028668PMC3197686
    David Fisher Lab (MGH)
  36. Švenda, J, Hill, N, and Myers, AG. (2011) A multiply convergent platform for the synthesis of trioxacarcins. Proc. Natl. Acad. Sci. U.S.A., 108(17):6709-14. PMID:21245350 PMC3084144
    Andrew Myers Lab (CCB)
  37. Chand, NS, Lee, JS, Clatworthy, AE, Golas, AJ, Smith, RS, and Hung, DT. (2011) The sensor kinase KinB regulates virulence in acute Pseudomonas aeruginosa infection. J. Bacteriol., 193(12):2989-99. PMID:21515773 PMC3133189
    Deborah Hung Lab (HMS MICROBIO)
  38. Tang, Y, and Cohen, AE. (2011) Enhanced enantioselectivity in excitation of chiral molecules by superchiral light. Science, 332(6027):333-6. PMID: 21493854
    Adam Cohen Lab (CCB)
  39. Roeffaers, MB, Zhang, X, Freudiger, CW, Saar, BG, van Ruijven, M, van Dalen, G, Xiao, C, and Xie, XS. (2011) Label-free imaging of biomolecules in food products using stimulated Raman microscopy. J Biomed Opt, 16(2):021118. PMID: 21473164
    X. Sunney Xie Lab (CCB)
  40. Shih, JD, and Hunter, CP. (2011) SID-1 is a dsRNA-selective dsRNA-gated channel. RNA, 17(6):1057-65. PMID: 21474576PMC3096038
    Craig Hunter Lab (MCB)
  41. Min, W, Freudiger, CW, Lu, S, and Xie, XS. (2011) Coherent nonlinear optical imaging: beyond fluorescence microscopy. Annu Rev Phys Chem, 62:507-30. PMID:21453061 PMC3427791
    X. Sunney Xie Lab (CCB)
  42. Budin, I, and Szostak, JW. (2011) Physical effects underlying the transition from primitive to modern cell membranes. Proc. Natl. Acad. Sci. U.S.A., 108(13):5249-54. PMID: 21402937 PMC3069173
    Jack Szostak Lab (HMS GENETICS)
  43. Zhuang, X, Liu, W, Wu, J, Zhang, H, and Wang, P. (2011) A novel fluoride ion colorimetric chemosensor based on coumarin. Spectrochim Acta A Mol Biomol Spectrosc, 79(5):1352-5. PMID: 21689975
    Xiaowei Zhuang Lab (CCB)
  44. Thuo, MM, Reus, WF, Nijhuis, CA, Barber, JR, Kim, C, Schulz, MD, and Whitesides, GM. (2011) Odd-even effects in charge transport across self-assembled monolayers. J. Am. Chem. Soc., 133(9):2962-75. PMID: 21323319
    George Whitesides Lab (CCB)
  45. Zhuang, JJ, and Hunter, CP. (2011) Tissue specificity of Caenorhabditis elegans enhanced RNA interference mutants. Genetics, 188(1):235-7. PMID: 21385728PMC3120140
    Craig Hunter Lab (MCB)
  46. Ducat, DC, Sachdeva, G, and Silver, PA. (2011) Rewiring hydrogenase-dependent redox circuits in cyanobacteria. Proc. Natl. Acad. Sci. U.S.A., 108(10):3941-6. PMID:21368150 PMC3053959
    Pamela Silver Lab (HMS SYSBIO)
  47. Ramachandra, S, Schuermann, KC, Edafe, F, Belser, P, Nijhuis, CA, Reus, WF,Whitesides, GM, and De Cola, L. (2011) Luminescent ruthenium tripod complexes: properties in solution and on conductive surfaces. Inorg Chem, 50(5):1581-91. PMID:21194229
    George Whitesides Lab (CCB)
  48. Kay, JN, Voinescu, PE, Chu, MW, andSanes, JR. (2011) Neurod6 expression defines new retinal amacrine cell subtypes and regulates their fate. Nat. Neurosci., 14(8):965-72. PMID: 21743471PMC3144989
    Joshua Sanes Lab (MCB)
  49. Yang, D, and Arya, G. (2011) Structure and binding of the H4 histone tail and the effects of lysine 16 acetylation. Phys Chem Chem Phys, 13(7):2911-21. PMID: 21157623
    Mara Prentiss Lab (PHYSICS)
  50. Sherwood, RI, Maehr, R, Mazzoni, EO, and Melton, DA. (2011) Wnt signaling specifies and patterns intestinal endoderm. Mech. Dev., 128(7-10):387-400. PMID:21854845 PMC3223331
    Doug Melton Lab (SCRB)
  51. Burgett, AW, Poulsen, TB, Wangkanont, K, Anderson, DR, Kikuchi, C, Shimada, K, Okubo, S, Fortner, KC, Mimaki, Y, Kuroda, M, Murphy, JP, Schwalb, DJ, Petrella, EC, Cornella-Taracido, I, Schirle, M, Tallarico, JA, and Shair, MD. (2011) Natural products reveal cancer cell dependence on oxysterol-binding proteins. Nat. Chem. Biol., 7(9):639-47. PMID: 21822274 PMC3158287
    Matthew Shair Lab (CCB)
  52. Bock, C, Kiskinis, E, Verstappen, G, Gu, H,Boulting, G, Smith, ZD, Ziller, M, Croft, GF, Amoroso, MW, Oakley, DH, Gnirke, A,Eggan, K, and Meissner, A. (2011) Reference Maps of human ES and iPS cell variation enable high-throughput characterization of pluripotent cell lines. Cell, 144(3):439-52. PMID: 21295703PMC3063454
    Kevin Eggan Lab (SCRB)
  53. Lazarus, MB, Nam, Y, Jiang, J, Sliz, P, and Walker, S. (2011) Structure of human O-GlcNAc transferase and its complex with a peptide substrate. Nature, 469(7331):564-7. PMID: 21240259 PMC3064491
    Daniel Kahne Lab (CCB)
    Suzanne Walker Lab (HMS SYSBIO)
  54. Ayala, R, Zhang, C, Yang, D, Hwang, Y, Aung, A, Shroff, SS, Arce, FT, Lal, R, Arya, G, and Varghese, S. (2011) Engineering the cell-material interface for controlling stem cell adhesion, migration, and differentiation. Biomaterials, 32(15):3700-11. PMID: 21396708
    Mara Prentiss Lab (PHYSICS)
  55. Freudiger, CW, Min, W, Holtom, GR, Xu, B, Dantus, M, and Xie, XS. (2011) Highly specific label-free molecular imaging with spectrally tailored excitation stimulated Raman scattering (STE-SRS) microscopy. Nat Photonics, 5(2):103-109. PMID:23015809 PMC3454352
    X. Sunney Xie Lab (CCB)
  56. Rahn-Lee, L, Merrikh, H, Grossman, AD, and Losick, R. (2011) The sporulation protein SirA inhibits the binding of DnaA to the origin of replication by contacting a patch of clustered amino acids. J. Bacteriol., 193(6):1302-7. PMID: 21239581PMC3067619
    Richard Losick Lab (MCB)
  57. Groemer, G. E., Storrie-Lombardi, M., Sattler, B., Hauser, O., Bickert, K., Hauth, E., … Klauck, J. (2011). Reducing biological contamination by a space suited astronaut: Laboratory and field test results from Aouda.X. Acta Astronautica, 68(1-2), 218–225. doi:10.1016/j.actaastro.2010.08.018
    Martin Nowak Lab (OEB)
  58. Datta, SS, Gerrard, DD, Rhodes, TS, Mason, TG, Weitz, DA. 2011. Rheology of attractive emulsions. Phys Rev E Stat Nonlin Soft Matter Phys. 84(4 Pt 1):041404.
    David Weitz Lab (SEAS)
  59. Lin, A, Jimenez, J, Derr, J, Vera, P, Manapat, ML, Esvelt, KM, Villanueva, L,Liu, DR, and Chen, IA. (2011) Inhibition of bacterial conjugation by phage M13 and its protein g3p: quantitative analysis and model. PLoS ONE, 6(5):e19991. PMID:21637841 PMC3102678
    David Liu Lab (CCB)
  60. Green, DA, Sarikaya, DP, and Extavour, CG. (2011) Counting in oogenesis. Cell Tissue Res., 344(2):207-12. PMID:21384182
    Cassandra Extavour Lab (OEB)
  61. Krall, JA, Beyer, EM, and MacBeath, G. (2011) High- and low-affinity epidermal growth factor receptor-ligand interactions activate distinct signaling pathways. PLoS ONE, 6(1):e15945. PMID: 21264347PMC3018525
    Gavin MacBeath Lab (HMS SYSBIO)
  62. Boulting, GL, Kiskinis, E, Croft, GF, Amoroso, MW, Oakley, DH, Wainger, BJ, Williams, DJ, Kahler, DJ, Yamaki, M, Davidow, L, Rodolfa, CT, Dimos, JT, Mikkilineni, S, MacDermott, AB, Woolf, CJ, Henderson, CE, Wichterle, H, and Eggan, K. (2011) A functionally characterized test set of human induced pluripotent stem cells. Nat. Biotechnol., 29(3):279-86. PMID:21293464 PMC3229307
    Kevin Eggan Lab (SCRB)
  63. Wang, MC, Min, W, Freudiger, CW, Ruvkun, G, and Xie, XS. (2011) RNAi screening for fat regulatory genes with SRS microscopy. Nat. Methods, 8(2):135-8. PMID: 21240281 PMC3061290
    X. Sunney Xie Lab (CCB)
  64. Jones, SA, Shim, SH, He, J, and Zhuang, X. (2011) Fast, three-dimensional super-resolution imaging of live cells. Nat. Methods, 8(6):499-508. PMID: 21552254PMC3137767
    Xiaowei Zhuang Lab (CCB)
  65. Fame, RM, MacDonald, JL, and Macklis, JD. (2011) Development, specification, and diversity of callosal projection neurons. Trends Neurosci., 34(1):41-50. PMID:21129791 PMC3053014
    Jeffrey Macklis Lab (SCRB)