Graduate MCO

Student Publications

Publications 2013

68 publications listed for 2013

  1. Sauvageau, M, Goff, LA, Lodato, S, Bonev, B, Groff, AF, Gerhardinger, C, Sanchez-Gomez, DB, Hacisuleyman, E, Li, E, Spence, M, Liapis, SC, Mallard, W, Morse, M, Swerdel, MR, D’Ecclessis, MF, Moore, JC, Lai, V, Gong, G, Yancopoulos, GD, Frendewey, D, Kellis, M, Hart, RP, Valenzuela, DM, Arlotta, P, and Rinn, JL. (2013) Multiple knockout mouse models reveal lincRNAs are required for life and brain development. Elife, 2:e01749. PMID:24381249 PMC3874104
    John Rinn Lab (SCRB)
  2. Hill, AF, Pegtel, DM, Lambertz, U, Leonardi, T, O’Driscoll, L, Pluchino, S, Ter-Ovanesyan, D, and Nolte-‘t Hoen, EN. (2013) ISEV position paper: extracellular vesicle RNA analysis and bioinformatics. J Extracell Vesicles, 2. PMID: 24376909PMC3873759
    George Church Lab (HMS GENETICS)
  3. Subramaniam, AR, DeLoughery, A, Bradshaw, N, Chen, Y, O’Shea, E, Losick, R, and Chai, Y. (2013) A serine sensor for multicellularity in a bacterium. Elife, 2:e01501. PMID: 24347549 PMC3862929
    Richard Losick Lab (MCB)
  4. Markson, JS, Piechura, JR, Puszynska, AM, and O’Shea, EK. (2013) Circadian control of global gene expression by the cyanobacterial master regulator RpaA. Cell, 155(6):1396-408. PMID: 24315105
    Erin O’Shea Lab (MCB)
  5. MacDonald J.L., Fame R.M., Azim E., Shnider S.J., Molyneaux B.J., Arlotta P. and Macklis J.D. (2013) Specification of Cortical Projection Neurons. In: RUBENSTEIN J. L. R. and RAKIC P. (ed.) Comprehensive Developmental Neuroscience: Patterning and Cell Type Specification in the Developing CNS and PNS, volume 1, pp. 475-502 Amsterdam: Elsevier.
    Jeffrey Macklis Lab (SCRB)
  6. López-Sagaseta, J, Dulberger, CL,McFedries, A, Cushman, M, Saghatelian, A, and Adams, EJ. (2013) MAIT recognition of a stimulatory bacterial antigen bound to MR1. J. Immunol., 191(10):5268-77. PMID:24108697 PMC3819123
    Alan Saghatelian Lab (CCB)
  7. Zhu, TF, Budin, I, and Szostak, JW. (2013) Preparation of fatty acid micelles. Meth. Enzymol., 533:283-8. PMID: 24182934
    Jack Szostak Lab (HMS GENETICS)
  8. Zhu, TF, Budin, I, and Szostak, JW. (2013) Vesicle extrusion through polycarbonate track-etched membranes using a hand-held mini-extruder. Meth. Enzymol., 533:275-82. PMID: 24182933
    Jack Szostak Lab (HMS GENETICS)
  9. Zhu, TF, Budin, I, and Szostak, JW. (2013) Preparation of fatty acid or phospholipid vesicles by thin-film rehydration. Meth. Enzymol., 533:267-74. PMID: 24182932
    Jack Szostak Lab (HMS GENETICS)
  10. Ran, FA, Hsu, PD, Wright, J, Agarwala, V, Scott, DA, and Zhang, F. (2013) Genome engineering using the CRISPR-Cas9 system. Nat Protoc, 8(11):2281-308. PMID:24157548
    Feng Zhang Lab (BROAD)
    Xiaowei Zhuang Lab (CCB)
  11. Yilmaz, M, and Meister, M. (2013) Rapid innate defensive responses of mice to looming visual stimuli. Curr. Biol., 23(20):2011-5. PMID: 24120636PMC3809337
    Markus Meister Lab (MCB)
  12. Huberman, LB, and Murray, AW. (2013) Genetically engineered transvestites reveal novel mating genes in budding yeast. Genetics, 195(4):1277-90. PMID: 24121774PMC3832273
    Andrew Murray Lab (MCB)
  13. Murphy, CM, and Michael, WM. (2013) Control of DNA replication by the nucleus/cytoplasm ratio in Xenopus. J. Biol. Chem., 288(41):29382-93. PMID:23986447 PMC3795239
    Matthew Michael Lab (MCB)
  14. He, J, Sun, E, Bujny, MV, Kim, D, Davidson, MW, and Zhuang, X. (2013) Dual function of CD81 in influenza virus uncoating and budding. PLoS Pathog., 9(10):e1003701. PMID: 24130495PMC3795033
    Xiaowei Zhuang Lab (CCB)
  15. Doksani, Y, Wu, JY, de Lange, T, andZhuang, X. (2013) Super-resolution fluorescence imaging of telomeres reveals TRF2-dependent T-loop formation. Cell, 155(2):345-56. PMID: 24120135
    Xiaowei Zhuang Lab (CCB)
  16. Besprozvannaya, M, Pivorunas, VL, Feldman, Z, and Burton, BM. (2013) SpoIIIE Protein Achieves Directional DNA Translocation through Allosteric Regulation of ATPase Activity by an Accessory Domain. J. Biol. Chem., 288(40):28962-28974. PMID: 23974211 PMC3789994
    Briana Burton Lab (MCB)
  17. Leiman, SA, May, JM, Lebar, MD, Kahne, D, Kolter, R, and Losick, R. (2013) D-amino acids indirectly inhibit biofilm formation in Bacillus subtilis by interfering with protein synthesis. J. Bacteriol., 195(23):5391-5. PMID: 24097941 PMC3837952
    Richard Losick Lab (MCB)
  18. Mirkin, EV, Chang, FS, and Kleckner, N. (2013) Dynamic trans interactions in yeast chromosomes. PLoS ONE, 8(9):e75895. PMID: 24098740 PMC3786970
    Alex Schier Lab (MCB)
    Nancy Kleckner Lab (MCB)
  19. Nguyen, VQ, Ranjan, A, Stengel, F, Wei, D, Aebersold, R, Wu, C, and Leschziner, AE. (2013) Molecular Architecture of the ATP-Dependent Chromatin-Remodeling Complex SWR1. Cell, 154(6):1220-31. PMID: 24034246
    Andres Leschziner Lab (MCB)
  20. Ran, FA, Hsu, PD, Lin, CY, Gootenberg, JS, Konermann, S, Trevino, AE, Scott, DA, Inoue, A, Matoba, S, Zhang, Y, and Zhang, F. (2013) Double Nicking by RNA-Guided CRISPR Cas9 for Enhanced Genome Editing Specificity. Cell, 154(6):1380-9. PMID: 23992846
    Feng Zhang Lab (BROAD)
    Xiaowei Zhuang Lab (CCB)
  21. Maeder, ML, Angstman, JF, Richardson, ME, Linder, SJ, Cascio, VM, Tsai, SQ, Ho, QH, Sander, JD, Reyon, D, Bernstein, BE, Costello, JF, Wilkinson, MF, and Joung, JK. (2013) Targeted DNA demethylation and activation of endogenous genes using programmable TALE-TET1 fusion proteins. Nat. Biotechnol., 31(12):1137-42. PMID:24108092 PMC3858462
    Keith Joung Lab (MGH)
  22. Lienert, F, Torella, JP, Chen, JH, Norsworthy, M, Richardson, RR, andSilver, PA. (2013) Two- and three-input TALE-based AND logic computation in embryonic stem cells. Nucleic Acids Res., 41(21):9967-75. PMID: 23982518PMC3834826
    Pamela Silver Lab (HMS SYSBIO)
  23. Konermann, S, Brigham, MD, Trevino, AE,Hsu, PD, Heidenreich, M, Cong, L, Platt, RJ, Scott, DA, Church, GM, and Zhang, F. (2013) Optical control of mammalian endogenous transcription and epigenetic states. Nature, 500(7463):472-6. PMID:23877069
    Xiaowei Zhuang Lab (CCB)
    Feng Zhang Lab (BROAD)
  24. Sander, JD, Ramirez, CL, Linder, SJ,Pattanayak, V, Shoresh, N, Ku, M, Foden, JA, Reyon, D, Bernstein, BE, Liu, DR, and Joung, JK. (2013) In silico abstraction of zinc finger nuclease cleavage profiles reveals an expanded landscape of off-target sites. Nucleic Acids Res., 41(19):e181. PMID: 23945932 PMC3799455
    David Liu Lab (CCB)
  25. Chiu, IM, Morimoto, ET, Goodarzi, H, Liao, JT, O’Keeffe, S, Phatnani, HP, Muratet, M, Carroll, MC, Levy, S, Tavazoie, S, Myers, RM, and Maniatis, T. (2013) A neurodegeneration-specific gene-expression signature of acutely isolated microglia from an amyotrophic lateral sclerosis mouse model. Cell Rep, 4(2):385-401. PMID:23850290
    Tom Maniatis Lab (MCB)
  26. Mitchell, AJ, Lone, AM, Tinoco, AD, andSaghatelian, A. (2013) Proteolysis controls endogenous substance P levels. PLoS ONE, 8(7):e68638. PMID: 23894327PMC3716696
    Alan Saghatelian Lab (CCB)
  27. Yuan, Y, Tang, AJ, Castoreno, AB, Kuo, SY, Wang, Q, Kuballa, P, Xavier, R, Shamji, AF, Schreiber, SL, and Wagner, BK. (2013) Gossypol and an HMT G9a inhibitor act in synergy to induce cell death in pancreatic cancer cells. Cell Death Dis, 4:e690. PMID:23807219 PMC3702302
    Stuart Schreiber Lab (CCB)
  28. Gleason, EJ, and Kramer, EM. (2013) Conserved roles for Polycomb Repressive Complex 2 in the regulation of lateral organ development in Aquilegia x coerulea ‘Origami’. BMC Plant Biol., 13:185. PMID:24256402 PMC3840678
    Elena Kramer Lab (OEB)
  29. Rodrigues, AR, and Tabin, CJ. (2013) Developmental biology. Deserts and waves in gene expression. Science, 340(6137):1181-2. PMID: 23744937
    Cliff Tabin Lab (HMS GENETICS)
  30. Dickinson, BC, Leconte, AM, Allen, B,Esvelt, KM, and Liu, DR. (2013) Experimental interrogation of the path dependence and stochasticity of protein evolution using phage-assisted continuous evolution. Proc. Natl. Acad. Sci. U.S.A., 110(22):9007-12. PMID: 23674678PMC3670371
    David Liu Lab (CCB)
  31. McFedries, A, Schwaid, A, andSaghatelian, A. (2013) Methods for the elucidation of protein-small molecule interactions. Chem. Biol., 20(5):667-73. PMID: 23706633
    Alan Saghatelian Lab (CCB)
  32. Chew, GL, Pauli, A, Rinn, JL, Regev, A,Schier, AF, and Valen, E. (2013) Ribosome profiling reveals resemblance between long non-coding RNAs and 5′ leaders of coding RNAs. Development, 140(13):2828-34. PMID: 23698349 PMC3678345
    Alex Schier Lab (MCB)
  33. Ferreira, LM, and Mostajo-Radji, MA. (2013) How induced pluripotent stem cells are redefining personalized medicine. Gene, 520(1):1-6. PMID: 23470844
    Chad Cowan Lab (SCRB)
    Jack Strominger Lab (MCB)
    Paola Arlotta Lab (SCRB)
  34. López-Sagaseta, J, Dulberger, CL, Crooks, JE, Parks, CD, Luoma, AM, McFedries, A, Van Rhijn, I, Saghatelian, A, and Adams, EJ. (2013) The molecular basis for Mucosal-Associated Invariant T cell recognition of MR1 proteins. Proc. Natl. Acad. Sci. U.S.A., 110(19):E1771-8. PMID: 23613577PMC3651419
    Alan Saghatelian Lab (CCB)
  35. Cederquist, GY, Azim, E, Shnider, SJ, Padmanabhan, H, and Macklis, JD. (2013) Lmo4 establishes rostral motor cortex projection neuron subtype diversity. J. Neurosci., 33(15):6321-32. PMID: 23575831PMC3698850
    Jeffrey Macklis Lab (SCRB)
  36. Sung, RJ, Zhang, M, Qi, Y, and Verdine, GL. (2013) Structural and Biochemical Analysis of DNA Helix Invasion by the Bacterial 8-Oxoguanine DNA Glycosylase MutM. J. Biol. Chem., 288(14):10012-23. PMID: 23404556
    Gregory Verdine Lab (SCRB)
  37. Hsu, PD, Scott, DA, Weinstein, JA, Ran, FA, Konermann, S, Agarwala, V, Li, Y, Fine, EJ, Wu, X, Shalem, O, Cradick, TJ, Marraffini, LA, Bao, G, and Zhang, F. (2013) DNA targeting specificity of RNA-guided Cas9 nucleases. Nat. Biotechnol., 31(9):827-32. PMID: 23873081
    Feng Zhang Lab (BROAD)
    Xiaowei Zhuang Lab (CCB)
  38. Pattanayak, V, Lin, S, Guilinger, JP, Ma, E, Doudna, JA, and Liu, DR. (2013) High-throughput profiling of off-target DNA cleavage reveals RNA-programmed Cas9 nuclease specificity. Nat. Biotechnol., 31(9):839-43. PMID: 23934178PMC3782611
    David Liu Lab (CCB)
  39. Kaushansky, A, Ye, AS, Austin, LS, Mikolajczak, SA, Vaughan, AM, Camargo, N, Metzger, PG, Douglass, AN, Macbeath, G, and Kappe, SH. (2013) Suppression of Host p53 Is Critical for Plasmodium Liver-Stage Infection. Cell Rep, 3(3):630-7. PMID: 23478020
    Gavin MacBeath Lab (HMS SYSBIO)
  40. Frank, KL, Rogers, DR, Olins, HC, Vidoudez, C, and Girguis, PR. (2013) Characterizing the distribution and rates of microbial sulfate reduction at Middle Valley hydrothermal vents. ISME J, . PMID:23535916
    Peter Girguis Lab (OEB)
  41. Müller, P, Rogers, KW, Yu, SR, Brand, M, and Schier, AF. (2013) Morphogen transport. Development, 140(8):1621-38. PMID: 23533171
    Alex Schier Lab (MCB)
  42. Larabi, A, Devos, JM, Ng, SL, Nanao, MH, Round, A, Maniatis, T, and Panne, D. (2013) Crystal Structure and Mechanism of Activation of TANK-Binding Kinase 1. Cell Rep, 3(3):734-46. PMID: 23453971
    Tom Maniatis Lab (MCB)
  43. Deshpande, AJ, Chen, L, Fazio, M, Sinha, AU, Bernt, KM, Banka, D, Dias, S, Chang, J, Olhava, EJ, Daigle, SR, Richon, VM, Pollock, RM, and Armstrong, SA. (2013) Leukemic transformation by the MLL-AF6 fusion oncogene requires the H3K79 methyltransferase Dot1l. Blood, 121(13):2533-41. PMID: 23361907PMC3612861
    Scott Armstrong Lab (HSCI)
  44. Lebar, MD, Lupoli, TJ, Tsukamoto, H, May, JM, Walker, S, and Kahne, D. (2013) Forming cross-linked peptidoglycan from synthetic gram-negative Lipid II. J. Am. Chem. Soc., 135(12):4632-5. PMID:23480167 PMC3658469
    Daniel Kahne Lab (CCB)
  45. Zhang, X, Peterson, KA, Liu, XS,McMahon, AP, and Ohba, S. (2013) Gene Regulatory Networks Mediating Canonical Wnt Signal Directed Control of Pluripotency and Differentiation in Embryo Stem Cells. Stem Cells, . PMID: 23505158
    Andrew McMahon Lab (MCB)
  46. Zhuang, JJ, Banse, SA, and Hunter, CP. (2013) The nuclear argonaute NRDE-3 contributes to transitive RNAi in Caenorhabditis elegans. Genetics, 194(1):117-31. PMID: 23457236PMC3632460
    Craig Hunter Lab (MCB)
  47. Sandoe, J, and Eggan, K. (2013) Opportunities and challenges of pluripotent stem cell neurodegenerative disease models. Nat. Neurosci., 16(7):780-9. PMID:23799470
    Kevin Eggan Lab (SCRB)
  48. Cong, L, Ran, FA, Cox, D, Lin, S, Barretto, R, Habib, N, Hsu, PD, Wu, X, Jiang, W, Marraffini, LA, and Zhang, F. (2013) Multiplex genome engineering using CRISPR/Cas systems. Science, 339(6121):819-23. PMID: 23287718
    Feng Zhang Lab (BROAD)
    Xiaowei Zhuang Lab (CCB)
  49. Sun, L, Goff, LA, Trapnell, C, Alexander, R, Lo, KA, Hacisuleyman, E, Sauvageau, M, Tazon-Vega, B, Kelley, DR, Hendrickson, DG, Yuan, B, Kellis, M, Lodish, HF, andRinn, JL. (2013) Long noncoding RNAs regulate adipogenesis. Proc. Natl. Acad. Sci. U.S.A., . PMID: 23401553
    John Rinn Lab (SCRB)
  50. Wang, S, Bates, J, Li, X, Schanz, S, Chandler-Militello, D, Levine, C,Maherali, N, Studer, L, Hochedlinger, K, Windrem, M, and Goldman, SA. (2013) Human iPSC-derived oligodendrocyte progenitor cells can myelinate and rescue a mouse model of congenital hypomyelination. Cell Stem Cell, 12(2):252-64. PMID: 23395447 PMC3700553
    Konrad Hochedlinger Lab (HSCI)
  51. Chen, AE, Borowiak, M, Sherwood, RI, Kweudjeu, A, and Melton, DA. (2013) Functional evaluation of ES cell-derived endodermal populations reveals differences between Nodal and Activin A-guided differentiation. Development, 140(3):675-86. PMID: 23293299 PMC3561793
    Doug Melton Lab (SCRB)
  52. Koytiger, G, Kaushansky, A, Gordus, A, Rush, J, Sorger, PK, and MacBeath, G. (2013) Phosphotyrosine signaling proteins that drive oncogenesis tend to be highly interconnected. Mol. Cell Proteomics, 12(5):1204-13. PMID: 23358503PMC3650332
    Gavin MacBeath Lab (HMS SYSBIO)
  53. Fu, D, Holtom, G, Freudiger, C, Zhang, X, and Xie, XS. (2013) Hyperspectral Imaging with Stimulated Raman Scattering by Chirped Femtosecond Lasers. J Phys Chem B, . PMID: 23256635
    X. Sunney Xie Lab (CCB)
  54. Qin, Y, Zhang, X, and Zhang, Y. (2013) A neuronal signaling pathway of CaMKII and Gqα regulates experience-dependent transcription of tph-1. J. Neurosci., 33(3):925-35. PMID: 23325232PMC3711619
    Yun Zhang Lab (OEB)
  55. Kong, L, Ji, M, Holtom, GR, Fu, D,Freudiger, CW, and Xie, XS. (2013) Multicolor stimulated Raman scattering microscopy with a rapidly tunable optical parametric oscillator. Opt Lett, 38(2):145-7. PMID: 23454943 PMC3588591
    X. Sunney Xie Lab (CCB)
  56. Tabansky, I, Lenarcic, A, Draft, RW, Loulier, K, Keskin, DB, Rosains, J, Rivera-Feliciano, J, Lichtman, JW, Livet, J, Stern, JN, Sanes, JR, and Eggan, K. (2013) Developmental bias in cleavage-stage mouse blastomeres. Curr. Biol., 23(1):21-31. PMID: 23177476 PMC3543519
    Kevin Eggan Lab (SCRB)
    Jeff Lichtman Lab (MCB)
  57. Datta, S. S., & Weitz, D. A. (2013). Drainage in a model stratified porous medium. EPL (Europhysics Letters), 101(1), 14002. doi:10.1209/0295-5075/101/14002
    David Weitz Lab (SEAS)
  58. Krummel, AT, Datta, SS., Münster, S., &Weitz, DA. (2013). Visualizing multiphase flow and trapped fluid configurations in a model three-dimensional porous medium. AIChE Journal, 59(3), 1022–1029. doi:10.1002/aic.14005
    David Weitz Lab (SEAS)
  59. Vlassakis, J, Feinstein, E, Yang, D, Tilloy, A, Weiller, D, Kates-Harbeck, J, Coljee, V,Prentiss, M. 2013. Tension on dsDNA bound to ssDNA-RecA filaments may play an important role in driving efficient and accurate homology recognition and strand exchange. Physical Review E 87 (3), 032702.
    Mara Prentiss Lab (PHYSICS)
  60. Sun, E, He, J, and Zhuang, X. (2013) Dissecting the role of COPI complexes in influenza virus infection. J. Virol., 87(5):2673-85. PMID: 23255804PMC3571408
    Xiaowei Zhuang Lab (CCB)
  61. Sun, E, He, J, and Zhuang, X. (2013) Live cell imaging of viral entry. Curr Opin Virol, 3(1):34-43. PMID: 23395264 PMC3587724
    Xiaowei Zhuang Lab (CCB)
  62. Lone, AM, Kim, YG, and Saghatelian, A. (2013) Peptidomics methods for the identification of peptidase-substrate interactions. Curr Opin Chem Biol, 17(1):83-9. PMID: 23332665 PMC3594040
    Alan Saghatelian Lab (CCB)
  63. Olins, HC, Rogers, DR, Frank, KL, Vidoudez, C, and Girguis, PR. (2013) Assessing the influence of physical, geochemical and biological factors on anaerobic microbial primary productivity within hydrothermal vent chimneys. Geobiology, 11(3):279-93. PMID: 23551687
    Peter Girguis Lab (OEB)
  64. Maeder, ML, Linder, SJ, Reyon, D,Angstman, JF, Fu, Y, Sander, JD, andJoung, JK. (2013) Robust, synergistic regulation of human gene expression using TALE activators. Nat. Methods, 10(3):243-5. PMID: 23396285 PMC3584229
    Keith Joung Lab (MGH)
  65. Gebhardt, JC, Suter, DM, Roy, R, Zhao, ZW, Chapman, AR, Basu, S, Maniatis, T, andXie, XS. (2013) Single-molecule imaging of transcription factor binding to DNA in live mammalian cells. Nat. Methods, 10(5):421-6. PMID: 23524394 PMC3664538
    Tom Maniatis Lab (MCB)
    X. Sunney Xie Lab (CCB)
  66. Pardo-Martin, C, Allalou, A, Medina, J, Eimon, PM, Wählby, C, and Fatih Yanik, M. (2013) High-throughput hyperdimensional vertebrate phenotyping. Nat Commun, 4:1467. PMID: 23403568 PMC3573763
    Mehmet Fatih Yanik Lab (MIT-NEURO)
  67. Ashrafi, G, and Schwarz, TL. (2013) The pathways of mitophagy for quality control and clearance of mitochondria. Cell Death Differ., 20(1):31-42. PMID: 22743996PMC3524633
    Thomas Schwarz Lab (HMS)
  68. Slavoff, SA, Mitchell, AJ, Schwaid, AG, Cabili, MN, Ma, J, Levin, JZ, Karger, AD, Budnik, BA, Rinn, JL, and Saghatelian, A. (2013) Peptidomic discovery of short open reading frame-encoded peptides in human cells. Nat. Chem. Biol., 9(1):59-64. PMID:23160002
    Alan Saghatelian Lab (CCB)