Graduate MCO

Student Publications

2014 Publications

63 Publications listed for 2014

  1. Lorenzo, DN, Badea, A, Davis, J, Hostettler, J, He, J, Zhong, G, Zhuang, X, and Bennett, V. (2014) A PIK3C3-ankyrin-B-dynactin pathway promotes axonal growth and multiorganelle transport. J. Cell Biol., 207(6):735-52. PMID: 25533844 PMC4274267
    Xiaowei Zhuang Lab (CCB)
  2. Nannas, NJ, O’Toole, ET, Winey, M, and Murray, AW. (2014) Chromosomal attachments set length and microtubule number in the Saccharomyces cerevisiae mitotic spindle. Mol. Biol. Cell, 25(25):4034-4048. PMID: 25318669
    Andrew Murray Lab (MCB)
  3. Konermann, S, Brigham, MD, Trevino, AE, Joung, J, Abudayyeh, OO, Barcena, C, Hsu, PD, Habib, N, Gootenberg, JS, Nishimasu, H, Nureki, O, and Zhang, F. (2014) Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex. Nature, . PMID: 25494202
    Feng Zhang Lab (BROAD)
    Xiaowei Zhuang Lab (CCB)
  4. Deshpande, AJ, Deshpande, A, Sinha, AU, Chen, L, Chang, J, Cihan, A, Fazio, M, Chen, CW, Zhu, N, Koche, R, Dzhekieva, L, Ibáñez, G, Dias, S, Banka, D, Krivtsov, A, Luo, M, Roeder, RG, Bradner, JE, Bernt, KM, and Armstrong, SA. (2014) AF10 Regulates Progressive H3K79 Methylation and HOX Gene Expression in Diverse AML Subtypes. Cancer Cell, 26(6):896-908. PMID: 25464900
    Scott Armstrong Lab (HSCI)
  5. Leiman, SA, Arboleda, LC, Spina, JS, and McLoon, AL. (2014) SinR is a mutational target for fine-tuning biofilm formation in laboratory-evolved strains of Bacillus subtilis. BMC Microbiol., 14(1):301. PMID: 25433524 PMC4258274
    Richard Losick Lab (MCB)
  6. Sysoeva, TA, Bane, LB, Xiao, DY, Bose, B, Chilton, SS, Gaudet, R, and Burton, BM. (2014) Structural characterization of the late competence protein ComFB from Bacillus subtilis. Biosci. Rep., . PMID: 25423369
    Rachelle Gaudet Lab (MCB)
    Briana Burton Lab (MCB)
  7. Meissner, TB, Mandal, PK, Ferreira, LM, Rossi, DJ, and Cowan, CA. (2014) Genome editing for human gene therapy. Meth. Enzymol., 546:273-95. PMID: 25398345
    Chad Cowan Lab (SCRB)
    Jack Strominger Lab (MCB)
  8. Pattanayak, V, Guilinger, JP, and Liu, DR. (2014) Determining the Specificities of TALENs, Cas9, and Other Genome-Editing Enzymes. Meth. Enzymol., 546:47-78. PMID: 25398335
    David Liu Lab (CCB)
  9. Mandal, PK, Ferreira, LM, Collins, R, Meissner, TB, Boutwell, CL, Friesen, M, Vrbanac, V, Garrison, BS, Stortchevoi, A, Bryder, D, Musunuru, K, Brand, H, Tager, AM, Allen, TM, Talkowski, ME, Rossi, DJ, and Cowan, CA. (2014) Efficient ablation of genes in human hematopoietic stem and effector cells using CRISPR/Cas9. Cell Stem Cell, 15(5):643-52. PMID: 25517468 PMC4269831
    Chad Cowan Lab (SCRB)
    Jack Strominger Lab (MCB)
  10. Zuris, JA, Thompson, DB, Shu, Y, Guilinger, JP, Bessen, JL, Hu, JH, Maeder, ML, Joung, JK, Chen, ZY, and Liu, DR. (2014) Cationic lipid-mediated delivery of proteins enables efficient protein-based genome editing in vitro and in vivo. Nat. Biotechnol., . PMID: 25357182
    David Liu Lab (CCB)
  11. Huberman, LB, and Murray, AW. (2014) A model for cell wall dissolution in mating yeast cells: polarized secretion and restricted diffusion of cell wall remodeling enzymes induces local dissolution. PLoS ONE, 9(10):e109780. PMID: 25329559 PMC4199604
    Andrew Murray Lab (MCB)
  12. Budin, I, Prwyes, N, Zhang, N, and Szostak, JW. (2014) Chain-length heterogeneity allows for the assembly of fatty acid vesicles in dilute solutions. Biophys. J., 107(7):1582-90. PMID: 25296310 PMC4190651
    Jack Szostak Lab (HMS GENETICS)
  13. Johnson, LM, Barrick, S, Hager, MV, McFedries, A, Homan, EA, Rabaglia, ME, Keller, MP, Attie, AD, Saghatelian, A, Bisello, A, and Gellman, SH. (2014) A potent α/β-peptide analogue of GLP-1 with prolonged action in vivo. J. Am. Chem. Soc., 136(37):12848-51. PMID: 25191938 PMC4183665
    Alan Saghatelian Lab (CCB)
  14. Miller, SB, Yildiz, FZ, Lo, JA, Wang, B, and D’Souza, VM. (2014) A structure-based mechanism for tRNA and retroviral RNA remodelling during primer annealing. Nature, . PMID: 25209668
    Victoria D’Souza Lab (MCB)
  15. Foulston, L, Elsholz, AK, DeFrancesco, AS, and Losick, R. (2014) The Extracellular Matrix of Staphylococcus aureus Biofilms Comprises Cytoplasmic Proteins That Associate with the Cell Surface in Response to Decreasing pH. MBio, 5(5). PMID: 25182325
    Richard Losick Lab (MCB)
  16. Hilinski, GJ, Kim, YW, Hong, J, Kutchukian, PS, Crenshaw, CM, Berkovitch, SS, Chang, A, Ham, S, and Verdine, GL. (2014) Stitched α-Helical Peptides via Bis Ring-Closing Metathesis. J. Am. Chem. Soc., 136(35):12314-22. PMID: 25105213
    Gregory Verdine Lab (SCRB)
  17. Zhong, G, He, J, Zhou, R, Lorenzo, D, Babcock, HP, Bennett, V, and Zhuang, X. (2014) Developmental mechanism of the periodic membrane skeleton in axons. Elife, 3. PMID: 25535840
    Xiaowei Zhuang Lab (CCB)
  18. Ashrafi, G, Schlehe, JS, LaVoie, MJ, and Schwarz, TL. (2014) Mitophagy of damaged mitochondria occurs locally in distal neuronal axons and requires PINK1 and Parkin. J. Cell Biol., 206(5):655-70. PMID: 25154397 PMC4151150
    Thomas Schwarz Lab (HMS)
  19. Wang, F, Chan, C, Weir, NR, and Denic, V. (2014) The Get1/2 transmembrane complex is an endoplasmic-reticulum membrane protein insertase. Nature, 512(7515):441-4. PMID: 25043001
    Vlad Denic Lab (MCB)
  20. Yuan, AH, Garrity, SJ, Nako, E, and Hochschild, A. (2014) Prion propagation can occur in a prokaryote and requires the ClpB chaperone. Elife, 3:e02949. PMID: 25122461
    Ann Hochschild Lab (HMS MICROBIO)
  21. Slenn, TJ, Morris, B, Havens, CG, Freeman, RM, Takahashi, TS, and Walter, JC. (2014) Thymine DNA Glycosylase Is a CRL4Cdt2 Substrate. J. Biol. Chem., 289(33):23043-55. PMID: 24947512PMC4132803
    Johannes Walter Lab (HMS)
  22. Nannas, NJ, and Murray, AW. (2014) Tethering sister centromeres to each other suggests the spindle checkpoint detects stretch within the kinetochore. PLoS Genet., 10(8):e1004492. PMID: 25101645PMC4125069
    Andrew Murray Lab (MCB)
  23. Lebar, MD, May, JM, Meeske, AJ, Leiman, SA, Lupoli, TJ, Tsukamoto, H, Losick, R, Rudner, DZ, Walker, S, and Kahne, D. (2014) Reconstitution of peptidoglycan cross-linking leads to improved fluorescent probes of cell wall synthesis. J. Am. Chem. Soc., 136(31):10874-7. PMID: 25036369PMC4132960
    Richard Losick Lab (MCB)
    Daniel Kahne Lab (CCB)
  24. Smith, ZD, Chan, MM, Humm, KC, Karnik, R, Mekhoubad, S, Regev, A,Eggan, K, and Meissner, A. (2014) DNA methylation dynamics of the human preimplantation embryo. Nature, 511(7511):611-5. PMID: 25079558
    Kevin Eggan Lab (SCRB)
    Alex Meissner Lab (SCRB)
  25. Chong, S, Chen, C, Ge, H, and Xie, XS. (2014) Mechanism of transcriptional bursting in bacteria. Cell, 158(2):314-26. PMID: 25036631 PMC4105854
    X. Sunney Xie Lab (CCB)
  26. Schwartz, S, Mumbach, MR, Jovanovic, M, Wang, T, Maciag, K, Bushkin, GG, Mertins, P, Ter-Ovanesyan, D, Habib, N, Cacchiarelli, D, Sanjana, NE, Freinkman, E, Pacold, ME, Satija, R, Mikkelsen, TS, Hacohen, N, Zhang, F, Carr, SA, Lander, ES, and Regev, A. (2014) Perturbation of m6A writers reveals two distinct classes of mRNA methylation at internal and 5′ sites. Cell Rep, 8(1):284-96. PMID: 24981863PMC4142486
    George Church Lab (HMS GENETICS)
  27. Harris, G, Shen, Y, Ha, H, Donato, A, Wallis, S, Zhang, X, and Zhang, Y. (2014) Dissecting the signaling mechanisms underlying recognition and preference of food odors. J. Neurosci., 34(28):9389-403. PMID: 25009271 PMC4087214
    Yun Zhang Lab (OEB)

  28. Besprozvannaya, M, and Burton, BM. (2014) Do the same traffic rules apply? Directional chromosome segregation by SpoIIIE and FtsK. Mol. Microbiol., 93(4):599-608. PMID: 25040776
    Briana Burton Lab (MCB)
  29. Maianti, JP, McFedries, A, Foda, ZH,Kleiner, RE, Du, XQ, Leissring, MA, Tang, WJ, Charron, MJ, Seeliger, MA,Saghatelian, A, and Liu, DR. (2014) Anti-diabetic activity of insulin-degrading enzyme inhibitors mediated by multiple hormones. Nature, 511(7507):94-8. PMID:24847884 PMC4142213
    David Liu Lab (CCB)
    Alan Saghatelian Lab (CCB)
  30. Shiu, PK, Zhuang, JJ, and Hunter, CP. (2014) Assays for direct and indirect effects of C. elegans endo-siRNAs. Methods Mol. Biol., 1173:71-87. PMID: 24920361
    Craig Hunter Lab (MCB)
  31. Kiskinis, E, Sandoe, J, Williams, LA,Boulting, GL, Moccia, R, Wainger, BJ, Han, S, Peng, T, Thams, S, Mikkilineni, S, Mellin, C, Merkle, FT, Davis-Dusenbery, BN, Ziller, M, Oakley, D, Ichida, J, Di Costanzo, S, Atwater, N, Maeder, ML, Goodwin, MJ, Nemesh, J, Handsaker, RE, Paull, D, Noggle, S, McCarroll, SA, Joung, JK, Woolf, CJ, Brown, RH, and Eggan, K. (2014) Pathways disrupted in human ALS motor neurons identified through genetic correction of mutant SOD1. Cell Stem Cell, 14(6):781-95. PMID: 24704492
    Kevin Eggan Lab (SCRB)
  32. Hsu, PD, Lander, ES, and Zhang, F. (2014) Development and applications of CRISPR-Cas9 for genome engineering. Cell, 157(6):1262-78. PMID: 24906146
    Feng Zhang Lab (BROAD)
    Xiaowei Zhuang Lab (CCB)
  33. Gagnon, JA, Valen, E, Thyme, SB, Huang, P, Ahkmetova, L, Pauli, A, Montague, TG, Zimmerman, S, Richter, C, and Schier, AF. (2014) Efficient mutagenesis by Cas9 protein-mediated oligonucleotide insertion and large-scale assessment of single-guide RNAs. PLoS ONE, 9(5):e98186. PMID:24873830 PMC4038517
    Alex Schier Lab (MCB)
  34. Montague, TG, Cruz, JM, Gagnon, JA, Church, GM, and Valen, E. (2014) CHOPCHOP: a CRISPR/Cas9 and TALEN web tool for genome editing. Nucleic Acids Res., 42(Web Server issue):W401-7. PMID:24861617
    Alex Schier Lab (MCB)
  35. McDonald, RI, Guilinger, JP, Mukherji, S, Curtis, EA, Lee, WI, and Liu, DR. (2014) Electrophilic activity-based RNA probes reveal a self-alkylating RNA for RNA labeling. Nat. Chem. Biol., 10(12):1049-54. PMID: 25306441 PMC4232462
    David Liu Lab (CCB)
  36. Saar, BG, Freudiger, CW, Xu, X, Huttner, A, Kesari, S, Young, G, and Xie, XS. (2014) Coherent Raman tissue imaging in the brain. Cold Spring Harb Protoc, 2014(5). PMID: 24786507
    X. Sunney Xie Lab (CCB)
  37. Besprozvannaya, M, Pivorunas, VL, and Burton, BM. (2014) Mechanistic study of classical translocation-dead SpoIIIE36 reveals the functional importance of the hinge within the SpoIIIE motor. J. Bacteriol., 196(13):2481-90. PMID:24769697 PMC4054170
    Briana Burton Lab (MCB)
  38. Choudhary, A, Hu He, K, Mertins, P, Udeshi, ND, Dančík, V, Fomina-Yadlin, D, Kubicek, S, Clemons, PA, Schreiber, SL, Carr, SA, and Wagner, BK. (2014) Quantitative-proteomic comparison of alpha and Beta cells to uncover novel targets for lineage reprogramming. PLoS ONE, 9(4):e95194. PMID: 24759943PMC3997365
    Stuart Schreiber Lab (CCB)
  39. Yang, H, Vallandingham, J, Shiu, P, Li, H,Hunter, CP, and Mak, HY. (2014) The DEAD box helicase RDE-12 promotes amplification of RNAi in cytoplasmic foci in C. elegans. Curr. Biol., 24(8):832-8. PMID:24684930
    Craig Hunter Lab (MCB)
  40. Wainger, BJ, Kiskinis, E, Mellin, C, Wiskow, O, Han, SS, Sandoe, J, Perez, NP, Williams, LA, Lee, S, Boulting, G, Berry, JD, Brown, RH, Cudkowicz, ME, Bean, BP,Eggan, K, and Woolf, CJ. (2014) Intrinsic membrane hyperexcitability of amyotrophic lateral sclerosis patient-derived motor neurons. Cell Rep, 7(1):1-11. PMID:24703839 PMC4023477
    Kevin Eggan Lab (SCRB)
  41. McElroy, KA, Kang, H, and Kuroda, MI. (2014) Are we there yet? Initial targeting of the Male-Specific Lethal and Polycomb group chromatin complexes in Drosophila. Open Biol, 4:140006. PMID: 24671948PMC3971409
    Mitzi Kuroda Lab (HMS GENETICS)
  42. Chen, X, and Engert, F. (2014) Navigational strategies underlying phototaxis in larval zebrafish. Front Syst Neurosci, 8:39. PMID: 24723859PMC3971168
    Florian Engert Lab (MCB)
  43. Donoughe, S, Nakamura, T, Ewen-Campen, B, Green, DA, Henderson, L, andExtavour, CG. (2014) BMP signaling is required for the generation of primordial germ cells in an insect. Proc. Natl. Acad. Sci. U.S.A., 111(11):4133-8. PMID: 24591634PMC3964053
    Cassandra Extavour Lab (OEB)
  44. Galonska, C, Smith, ZD, and Meissner, A. (2014) In Vivo and in vitro dynamics of undifferentiated embryonic cell transcription factor 1. Stem Cell Reports, 2(3):245-52. PMID: 24672748PMC3964277
    Alex Meissner Lab (SCRB)
  45. Lee, MN, Ye, C, Villani, AC, Raj, T, Li, W, Eisenhaure, TM, Imboywa, SH, Chipendo, PI, Ran, FA, Slowikowski, K, Ward, LD, Raddassi, K, McCabe, C, Lee, MH, Frohlich, IY, Hafler, DA, Kellis, M, Raychaudhuri, S,Zhang, F, Stranger, BE, Benoist, CO, De Jager, PL, Regev, A, and Hacohen, N. (2014) Common genetic variants modulate pathogen-sensing responses in human dendritic cells. Science, 343(6175):1246980. PMID: 24604203 PMC4124741
    Feng Zhang Lab (BROAD)
  46. Lone, AM, Leidl, M, McFedries, AK, Horner, JW, Creemers, J, and Saghatelian, A. (2014) Deletion of PREPl causes growth impairment and hypotonia in mice. PLoS ONE, 9(2):e89160. PMID: 24586561PMC3938459
    Alan Saghatelian Lab (CCB)
  47. Guilinger, JP, Thompson, DB, and Liu, DR. (2014) Fusion of catalytically inactive Cas9 to FokI nuclease improves the specificity of genome modification. Nat. Biotechnol., 32(6):577-82. PMID: 24770324
    David Liu Lab (CCB)
  48. Pyzocha, NK, Ran, FA, Hsu, PD, andZhang, F. (2014) RNA-Guided Genome Editing of Mammalian Cells. Methods Mol. Biol., 1114:269-77. PMID: 24557909
    Xiaowei Zhuang Lab (CCB)
    Feng Zhang Lab (BROAD)
  49. Rebets, Y, Lupoli, T, Qiao, Y, Schirner, K, Villet, R, Hooper, D, Kahne, D, and Walker, S. (2014) Moenomycin resistance mutations in Staphylococcus aureus reduce peptidoglycan chain length and cause aberrant cell division. ACS Chem. Biol., 9(2):459-67. PMID: 24255971PMC3944067
    Daniel Kahne Lab (CCB)
  50. Luo, L, Cook, N, Venkatachalam, V, Martinez-Velazquez, LA, Zhang, X, Calvo, AC, Hawk, J, Macinnis, BL, Frank, M, Ng, JH, Klein, M, Gershow, M, Hammarlund, M, Goodman, MB, Colón-Ramos, DA,Zhang, Y, and Samuel, AD. (2014) Bidirectional thermotaxis in Caenorhabditis elegans is mediated by distinct sensorimotor strategies driven by the AFD thermosensory neurons. Proc. Natl. Acad. Sci. U.S.A., 111(7):2776-81. PMID:24550307
    Yun Zhang Lab (OEB)
  51. Guilinger, JP, Pattanayak, V, Reyon, D, Tsai, SQ, Sander, JD, Joung, JK, and Liu, DR. (2014) Broad specificity profiling of TALENs results in engineered nucleases with improved DNA-cleavage specificity. Nat. Methods, . PMID: 24531420
    David Liu Lab (CCB)
  52. Tucker, AT, Bobay, BG, Banse, AV, Olson, AL, Soderblom, EJ, Arthur Moseley, M, Thompson, RJ, Varney, KM, Losick, R, and Cavanagh, J. (2014) A DNA mimic: The structure and mechanism of action for the anti-repressor protein AbbA. J. Mol. Biol., . PMID: 24534728
    Richard Losick Lab (MCB)
  53. Pauli, A, Norris, ML, Valen, E, Chew, GL, Gagnon, JA, Zimmerman, S, Mitchell, A, Ma, J, Dubrulle, J, Reyon, D, Tsai, SQ, Joung, JK, Saghatelian, A, and Schier, AF. (2014) Toddler: an embryonic signal that promotes cell movement via Apelin receptors. Science, 343(6172):1248636. PMID: 24407481
    Alex Schier Lab (MCB)
    Alan Saghatelian Lab (CCB)
  54. Nishimasu, H, Ran, FA, Hsu, PD, Konermann, S, Shehata, SI, Dohmae, N, Ishitani, R, Zhang, F, and Nureki, O. (2014) Crystal Structure of Cas9 in Complex with Guide RNA and Target DNA. Cell, . PMID:24529477
    Feng Zhang Lab (BROAD)
    Xiaowei Zhuang Lab (CCB)
  55. Avalos, AM, Bilate, AM, Witte, MD, Tai, AK,He, J, Frushicheva, MP, Thill, PD, Meyer-Wentrup, F, Theile, CS, Chakraborty, AK,Zhuang, X, and Ploegh, HL. (2014) Monovalent engagement of the BCR activates ovalbumin-specific transnuclear B cells. J. Exp. Med., 211(2):365-79. PMID:24493799 PMC3920557
    Xiaowei Zhuang Lab (CCB)
  56. Mirkin, EV, Chang, FS, and Kleckner, N. (2014) Protein-mediated chromosome pairing of repetitive arrays. J. Mol. Biol., 426(3):550-7. PMID: 24211468PMC3898463
    Nancy Kleckner Lab (MCB)
  57. Green, DA, and Extavour, CG. (2014) Insulin signalling underlies both plasticity and divergence of a reproductive trait in Drosophila. Proc. Biol. Sci., 281(1779):20132673. PMID: 24500165
    Cassandra Extavour Lab (OEB)
  58. Wu, X, Scott, DA, Kriz, AJ, Chiu, AC, Hsu, PD, Dadon, DB, Cheng, AW, Trevino, AE, Konermann, S, Chen, S, Jaenisch, R, Zhang, F, and Sharp, PA. (2014) Genome-wide binding of the CRISPR endonuclease Cas9 in mammalian cells. Nat. Biotechnol., 32(7):670-6. PMID: 24752079PMC4145672
    Feng Zhang Lab (BROAD)
    Xiaowei Zhuang Lab (CCB)
  59. Freudiger, CW, Yang, W, Holtom, GR, Peyghambarian, N, Xie, XS, and Kieu, KQ. (2014) Stimulated Raman Scattering Microscopy with a Robust Fibre Laser Source. Nat Photonics, 8(2):153-159. PMID:25313312 PMC4193905
    X. Sunney Xie Lab (CCB)
  60. Lupoli, TJ, Lebar, MD, Markovski, M, Bernhardt, T, Kahne, D, and Walker, S. (2014) Lipoprotein activators stimulate Escherichia coli penicillin-binding proteins by different mechanisms. J. Am. Chem. Soc., 136(1):52-5. PMID: 24341982PMC3961711
    Daniel Kahne Lab (CCB)
  61. Zhang, X, Zhu, Y, Chen, X, Zhang, Y,Zhang, Y, Jia, Y, Wang, H, Liu, Y, and Xiao, L. (2014) Baicalein ameliorates inflammatory-related apoptotic and catabolic phenotypes in human chondrocytes. Int. Immunopharmacol., 21(2):301-8. PMID: 24859058
    Yun Zhang Lab (OEB)
  62. Hacisuleyman, E, Goff, LA, Trapnell, C, Williams, A, Henao-Mejia, J, Sun, L, McClanahan, P, Hendrickson, DG, Sauvageau, M, Kelley, DR, Morse, M, Engreitz, J, Lander, ES, Guttman, M, Lodish, HF, Flavell, R, Raj, A, and Rinn, JL. (2014) Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre. Nat. Struct. Mol. Biol., 21(2):198-206. PMID:24463464
    John Rinn Lab (SCRB)
  63. Ichida, JK, TCW, J, T C W, J, Williams, LA, Carter, AC, Shi, Y, Moura, MT, Ziller, M, Singh, S, Amabile, G, Bock, C, Umezawa, A, Rubin, LL, Bradner, JE, Akutsu, H, Meissner, A, and Eggan, K. (2014) Notch inhibition allows oncogene-independent generation of iPS cells. Nat. Chem. Biol., 10(8):632-9. PMID: 24952596 PMC4310751
    Kevin Eggan Lab (SCRB)