Graduate MCO

Student Publications

2016 Publications

27 publications listed for 2016

  1. Lessing, D, Dial, TO, Wei, C, Payer, B, Carrette, LL, Kesner, B, Szanto, A, Jadhav, A, Maloney, DJ, Simeonov, A, Theriault, J, Hasaka, T, Bedalov, A, Bartolomei, MS, and Lee, JT. (2016) A high-throughput small molecule screen identifies synergism between DNA methylation and Aurora kinase pathways for X reactivation. Proc Natl Acad Sci U S A, 113(50):14366-14371.
    http://www.ncbi.nlm.nih.gov/pubmed/28182563
  2. Bozzi, AT, Bane, LB, Weihofen, WA, Singharoy, A, Guillen, ER, Ploegh, HL, Schulten, K, and Gaudet, R. (2016) Crystal Structure and Conformational Change Mechanism of a Bacterial Nramp-Family Divalent Metal Transporter. Structure, 24(12):2102-2114.
    http://www.ncbi.nlm.nih.gov/pubmed/27839948
  3. Saak, CC, and Gibbs, KA. (2016) The Self-Identity Protein IdsD Is Communicated between Cells in Swarming Proteus mirabilis Colonies. J Bacteriol, 198(24):3278-3286.
    http://www.ncbi.nlm.nih.gov/pubmed/27672195
  4. Tian, F, Yang, W, Mordes, DA, Wang, JY, Salameh, JS, Mok, J, Chew, J, Sharma, A, Leno-Duran, E, Suzuki-Uematsu, S, Suzuki, N, Han, SS, Lu, FK, Ji, M, Zhang, R, Liu, Y, Strominger, J, Shneider, NA, Petrucelli, L, Xie, XS, and Eggan, K. (2016) Monitoring peripheral nerve degeneration in ALS by label-free stimulated Raman scattering imaging. Nat Commun, 7:13283.
    http://www.ncbi.nlm.nih.gov/pubmed/27796305
  5. Chew, WL, Tabebordbar, M, Cheng, JK, Mali, P, Wu, EY, Ng, AH, Zhu, K, Wagers, AJ, and Church, GM. (2016) A multifunctional AAV-CRISPR-Cas9 and its host response. Nat Methods, 13(10):868-74.
    http://www.ncbi.nlm.nih.gov/pubmed/27595405
  6. Cho, H, Wivagg, CN, Kapoor, M, Barry, Z, Rohs, PD, Suh, H, Marto, JA, Garner, EC, and Bernhardt, TG. (2016) Bacterial cell wall biogenesis is mediated by SEDS and PBP polymerase families functioning semi-autonomously. Nat Microbiol, :16172.
    http://www.ncbi.nlm.nih.gov/pubmed/27643381
  7. Bozzi, AT, Bane, LB, Weihofen, WA, McCabe, AL, Singharoy, A, Chipot, CJ, Schulten, K, and Gaudet, R. (2016) Conserved methionine dictates substrate preference in Nramp-family divalent metal transporters. Proc Natl Acad Sci U S A, 113(37):10310-5.
    http://www.ncbi.nlm.nih.gov/pubmed/27573840
  8. Douglas, SM, Chubiz, LM, Harcombe, WR, Ytreberg, FM, and Marx, CJ. (2016) Parallel Mutations Result in a Wide Range of Cooperation and Community Consequences in a Two-Species Bacterial Consortium. PLoS One, 11(9):e0161837.
    http://www.ncbi.nlm.nih.gov/pubmed/27617746
  9. Wang, S, Su, JH, Beliveau, BJ, Bintu, B, Moffitt, JR, Wu, CT, and Zhuang, X. (2016) Spatial organization of chromatin domains and compartments in single chromosomes. Science, 353(6299):598-602.
    http://www.ncbi.nlm.nih.gov/pubmed/27445307
  10. Lee, J, Xue, M, Wzorek, JS, Wu, T, Grabowicz, M, Gronenberg, LS, Sutterlin, HA, Davis, RM, Ruiz, N, Silhavy, TJ, and Kahne, DE. (2016) Characterization of a stalled complex on the -barrel assembly machine. Proc Natl Acad Sci U S A, 113(31):8717-22.
    http://www.ncbi.nlm.nih.gov/pubmed/27439868
  11. Wahl, ME, and Murray, AW. (2016) Multicellularity makes somatic differentiation evolutionarily stable. Proc Natl Acad Sci U S A, 113(30):8362-7.
    http://www.ncbi.nlm.nih.gov/pubmed/27402737
  12. Perez, JD, Rubinstein, ND, and Dulac, C. (2016) New Perspectives on Genomic Imprinting, an Essential and Multifaceted Mode of Epigenetic Control in the Developing and Adult Brain. Annu Rev Neurosci, 39:347-84.
    http://www.ncbi.nlm.nih.gov/pubmed/27145912
  13. Chavez, A, Tuttle, M, Pruitt, BW, Ewen-Campen, B, Chari, R, Ter-Ovanesyan, D, Haque, SJ, Cecchi, RJ, Kowal, EJK, Buchthal, J, Housden, BE, Perrimon, N, Collins, JJ, and Church, G. (2016) Comparison of Cas9 activators in multiple species. Nat Methods, 13(7):563-567.
    http://www.ncbi.nlm.nih.gov/pubmed/27214048
  14. Lassen, KG, McKenzie, CI, Mari, M, Murano, T, Begun, J, Baxt, LA, Goel, G, Villablanca, EJ, Kuo, SY, Huang, H, Macia, L, Bhan, AK, Batten, M, Daly, MJ, Reggiori, F, Mackay, CR, and Xavier, RJ. (2016) Genetic Coding Variant in GPR65 Alters Lysosomal pH and Links Lysosomal Dysfunction with Colitis Risk. Immunity, 44(6):1392-405.
    http://www.ncbi.nlm.nih.gov/pubmed/27287411
  15. Lavrentovich, MO, Wahl, ME, Nelson, DR, and Murray, AW. (2016) Spatially Constrained Growth Enhances Conversional Meltdown. Biophys J, 110(12):2800-2808.
    http://www.ncbi.nlm.nih.gov/pubmed/27332138
  16. Fame, RM, MacDonald, JL, Dunwoodie, SL, Takahashi, E, and Macklis, JD. (2016) Cited2 Regulates Neocortical Layer II/III Generation and Somatosensory Callosal Projection Neuron Development and Connectivity. J Neurosci, 36(24):6403-19.
    http://www.ncbi.nlm.nih.gov/pubmed/27307230
  17. Wang, S, Su, JH, Zhang, F, and Zhuang, X. (2016) An RNA-aptamer-based two-color CRISPR labeling system. Sci Rep, 6:26857.
    http://www.ncbi.nlm.nih.gov/pubmed/27229896
  18. Chew, GL, Pauli, A, and Schier, AF. (2016) Conservation of uORF repressiveness and sequence features in mouse, human and zebrafish. Nat Commun, 7:11663.
    http://www.ncbi.nlm.nih.gov/pubmed/27216465
  19. Ferreira, LM, Meissner, TB, Mikkelsen, TS, Mallard, W, O’Donnell, CW, Tilburgs, T, Gomes, HA, Camahort, R, Sherwood, RI, Gifford, DK, Rinn, JL, Cowan, CA, and Strominger, JL. (2016) A distant trophoblast-specific enhancer controls HLA-G expression at the maternal-fetal interface. Proc Natl Acad Sci U S A, 113(19):5364-9.
    http://www.ncbi.nlm.nih.gov/pubmed/27078102
  20. Hacisuleyman, E, Shukla, CJ, Weiner, CL, and Rinn, JL. (2016) Function and evolution of local repeats in the Firre locus. Nat Commun, 7:11021.
    http://www.ncbi.nlm.nih.gov/pubmed/27009974
  21. Estrada, J, Ruiz-Herrero, T, Scholes, C, Wunderlich, Z, and DePace, AH. (2016) SiteOut: An Online Tool to Design Binding Site-Free DNA Sequences. PLoS One, 11(3):e0151740.
    http://www.ncbi.nlm.nih.gov/pubmed/26987123
  22. Zee, BM, Alekseyenko, AA, McElroy, KA, and Kuroda, MI. (2016) Streamlined discovery of cross-linked chromatin complexes and associated histone modifications by mass spectrometry. Proc Natl Acad Sci U S A, 113(7):1784-9.
    http://www.ncbi.nlm.nih.gov/pubmed/26831069
  23. Cabeen, MT, Leiman, SA, and Losick, R. (2016) Colony-morphology screening uncovers a role for the Pseudomonas aeruginosa nitrogen-related phosphotransferase system in biofilm formation. Mol Microbiol, 99(3):557-70.
    http://www.ncbi.nlm.nih.gov/pubmed/26483285
  24. Namkoong, B, Gven, S, Ramesan, S, Liaudanskaya, V, Abzhanov, A, and Demirci, U. (2016) Recapitulating cranial osteogenesis with neural crest cells in 3-D microenvironments. Acta Biomater, 31:301-311.
    http://www.ncbi.nlm.nih.gov/pubmed/26675129
  25. Tabebordbar, M, Zhu, K, Cheng, JKW, Chew, WL, Widrick, JJ, Yan, WX, Maesner, C, Wu, EY, Xiao, R, Ran, FA, Cong, L, Zhang, F, Vandenberghe, LH, Church, GM, and Wagers, AJ. (2016) In vivo gene editing in dystrophic mouse muscle and muscle stem cells. Science, 351(6271):407-411.
    http://www.ncbi.nlm.nih.gov/pubmed/26721686
  26. DeLoughery, A, Dengler, V, Chai, Y, and Losick, R. (2016) Biofilm formation by Bacillus subtilis requires an endoribonuclease-containing multisubunit complex that controls mRNA levels for the matrix gene repressor SinR. Mol Microbiol, 99(2):425-37.
    http://www.ncbi.nlm.nih.gov/pubmed/26434553
  27. Thomsen, ER, Mich, JK, Yao, Z, Hodge, RD, Doyle, AM, Jang, S, Shehata, SI, Nelson, AM, Shapovalova, NV, Levi, BP, and Ramanathan, S. (2016) Fixed single-cell transcriptomic characterization of human radial glial diversity. Nat Methods, 13(1):87-93.
    http://www.ncbi.nlm.nih.gov/pubmed/26524239