Graduate MCO

Student Publications

2018 Publications

36 publications listed for 2018

  1. Masis, J, Mankus, D, Wolff, SBE, Guitchounts, G, Joesch, M, and Cox, DD. (2018) A Micro-CT-based Method for Characterizing Lesions and Locating Electrodes in Small Animal Brains. J Vis Exp, (141).
    http://www.ncbi.nlm.nih.gov/pubmed/30474629
  2. Moffitt, JR, Bambah-Mukku, D, Eichhorn, SW, Vaughn, E, Shekhar, K, Perez, JD, Rubinstein, ND, Hao, J, Regev, A, Dulac, C, and Zhuang, X. (2018) Molecular, spatial and functional single-cell profiling of the hypothalamic preoptic region. Science, .
    http://www.ncbi.nlm.nih.gov/pubmed/30385464
  3. Jordi, J, Guggiana-Nilo, D, Bolton, AD, Prabha, S, Ballotti, K, Herrera, K, Rennekamp, AJ, Peterson, RT, Lutz, TA, and Engert, F. (2018) High-throughput screening for selective appetite modulators: A multibehavioral and translational drug discovery strategy. Sci Adv, 4(10):eaav1966.
    http://www.ncbi.nlm.nih.gov/pubmed/30402545
  4. Bintu, B, Mateo, LJ, Su, JH, Sinnott-Armstrong, NA, Parker, M, Kinrot, S, Yamaya, K, Boettiger, AN, and Zhuang, X. (2018) Super-resolution chromatin tracing reveals domains and cooperative interactions in single cells. Science, 362(6413).
    http://www.ncbi.nlm.nih.gov/pubmed/30361340
  5. Rohs, PDA, Buss, J, Sim, SI, Squyres, GR, Srisuknimit, V, Smith, M, Cho, H, Sjodt, M, Kruse, AC, Garner, EC, Walker, S, Kahne, DE, and Bernhardt, TG. (2018) A central role for PBP2 in the activation of peptidoglycan polymerization by the bacterial cell elongation machinery. PLoS Genet, 14(10):e1007726.
    http://www.ncbi.nlm.nih.gov/pubmed/30335755
  6. Pham, VV, Salguero, C, Khan, SN, Meagher, JL, Brown, WC, Humbert, N, de, H, Smith, JL, and D’Souza, VM. (2018) HIV-1 Tat interactions with cellular 7SK and viral TAR RNAs identifies dual structural mimicry. Nat Commun, 9(1):4266.
    http://www.ncbi.nlm.nih.gov/pubmed/30323330
  7. Kim, S, Kerns, SJ, Ziesack, M, Bry, L, Gerber, GK, Way, JC, and Silver, PA. (2018) Quorum Sensing Can Be Repurposed To Promote Information Transfer between Bacteria in the Mammalian Gut. ACS Synth Biol, 7(9):2270-2281.
    http://www.ncbi.nlm.nih.gov/pubmed/30125499
  8. Spady, ES, Wyche, TP, Rollins, NJ, Clardy, J, Way, JC, and Silver, PA. (2018) Mammalian Cells Engineered To Produce New Steroids. Chembiochem, 19(17):1827-1833.
    http://www.ncbi.nlm.nih.gov/pubmed/29931794
  9. Menegas, W, Akiti, K, Amo, R, Uchida, N, and Watabe-Uchida, M. (2018) Dopamine neurons projecting to the posterior striatum reinforce avoidance of threatening stimuli. Nat Neurosci, .
    http://www.ncbi.nlm.nih.gov/pubmed/30177795
  10. Little, K, Tipping, MJ, and Gibbs, KA. (2018) Swarmer Cell Development of the Bacterium Proteus mirabilis Requires the Conserved Enterobacterial Common Antigen Biosynthesis Gene rffG. J Bacteriol, 200(18).
    http://www.ncbi.nlm.nih.gov/pubmed/29967121
  11. Mutlu, B, Chen, HM, Moresco, JJ, Orelo, BD, Yang, B, Gaspar, JM, Keppler-Ross, S, Yates, 3rd, Hall, DH, Maine, EM, and Mango, SE. (2018) Regulated nuclear accumulation of a histone methyltransferase times the onset of heterochromatin formation in C. elegans embryos. Sci Adv, 4(8):eaat6224.
    http://www.ncbi.nlm.nih.gov/pubmed/30140741
  12. Gehrke, JM, Cervantes, O, Clement, MK, Wu, Y, Zeng, J, Bauer, DE, Pinello, L, and Joung, JK. (2018) An APOBEC3A-Cas9 base editor with minimized bystander and off-target activities. Nat Biotechnol, .
    http://www.ncbi.nlm.nih.gov/pubmed/30059493
  13. Darnell, AM, Subramaniam, AR, and O’Shea, EK. (2018) Translational Control through Differential Ribosome Pausing during Amino Acid Limitation in Mammalian Cells. Mol Cell, 71(2):229-243.e11.
    http://www.ncbi.nlm.nih.gov/pubmed/30029003
  14. Bisson-Filho, AW, Zheng, J, and Garner, E. (2018) Archaeal imaging: leading the hunt for new discoveries. Mol Biol Cell, 29(13):1675-1681.
    http://www.ncbi.nlm.nih.gov/pubmed/30001185
  15. Zak, JD, Grimaud, J, Li, RC, Lin, CC, and Murthy, VN. (2018) Calcium-activated chloride channels clamp odor-evoked spike activity in olfactory receptor neurons. Sci Rep, 8(1):10600.
    http://www.ncbi.nlm.nih.gov/pubmed/30006552
  16. Zhang, Y, Burberry, A, Wang, JY, Sandoe, J, Ghosh, S, Udeshi, ND, Svinkina, T, Mordes, DA, Mok, J, Charlton, M, Li, QZ, Carr, SA, and Eggan, K. (2018) The C9orf72-interacting protein Smcr8 is a negative regulator of autoimmunity and lysosomal exocytosis. Genes Dev, 32(13-14):929-943.
    http://www.ncbi.nlm.nih.gov/pubmed/29950492
  17. Hong, G, Fu, TM, Qiao, M, Viveros, RD, Yang, X, Zhou, T, Lee, JM, Park, HG, Sanes, JR, and Lieber, CM. (2018) A method for single-neuron chronic recording from the retina in awake mice. Science, 360(6396):1447-1451.
    http://www.ncbi.nlm.nih.gov/pubmed/29954976
  18. Zhang, G, Baidin, V, Pahil, KS, Moison, E, Tomasek, D, Ramadoss, NS, Chatterjee, AK, McNamara, CW, Young, TS, Schultz, PG, Meredith, TC, and Kahne, D. (2018) Cell-based screen for discovering lipopolysaccharide biogenesis inhibitors. Proc Natl Acad Sci U S A, 115(26):6834-6839.
    http://www.ncbi.nlm.nih.gov/pubmed/29735709
  19. Zepeda Rivera, MA, Saak, CC, and Gibbs, KA. (2018) A Proposed Chaperone of the Bacterial Type VI Secretion System Functions To Constrain a Self-Identity Protein. J Bacteriol, 200(14).
    http://www.ncbi.nlm.nih.gov/pubmed/29555703
  20. Farrell, JA, Wang, Y, Riesenfeld, SJ, Shekhar, K, Regev, A, and Schier, AF. (2018) Single-cell reconstruction of developmental trajectories during zebrafish embryogenesis. Science, 360(6392).
    http://www.ncbi.nlm.nih.gov/pubmed/29700225
  21. Grimaud, J, and Murthy, VN. (2018) How to Monitor the Breathing of Laboratory Rodents: A Review of the Current Methods. J Neurophysiol, .
    http://www.ncbi.nlm.nih.gov/pubmed/29790839
  22. Chittim, CL, Irwin, SM, and Balskus, EP. (2018) Deciphering Human Gut Microbiota-Nutrient Interactions: A Role for Biochemistry. Biochemistry, 57(18):2567-2577.
    http://www.ncbi.nlm.nih.gov/pubmed/29669199
  23. Ziesack, M, Rollins, N, Shah, A, Dusel, B, Webster, G, Silver, PA, and Way, JC. (2018) Chimeric Fatty Acyl-Acyl Carrier Protein Thioesterases Provide Mechanistic Insight into Enzyme Specificity and Expression. Appl Environ Microbiol, 84(10).
    http://www.ncbi.nlm.nih.gov/pubmed/29549102
  24. Maini Rekdal V, and Balskus, EP. (2018) Gut Microbiota: Rational Manipulation of Gut Bacterial Metalloenzymes Provides Insights into Dysbiosis and Inflammation. Biochemistry, 57(16):2291-2293.
    http://www.ncbi.nlm.nih.gov/pubmed/29633827
  25. Barutcu, AR, Maass, PG, Lewandowski, JP, Weiner, CL, and Rinn, JL. (2018) A TAD boundary is preserved upon deletion of the CTCF-rich Firre locus. Nat Commun, 9(1):1444.
    http://www.ncbi.nlm.nih.gov/pubmed/29654311
  26. Kohl, J, Babayan, BM, Rubinstein, ND, Autry, AE, Marin-Rodriguez, B, Kapoor, V, Miyamishi, K, Zweifel, LS, Luo, L, Uchida, N, and Dulac, C. (2018) Functional circuit architecture underlying parental behaviour. Nature, 556(7701):326-331.
    http://www.ncbi.nlm.nih.gov/pubmed/29643503
  27. Masis, J, Mankus, D, Wolff, SBE, Guitchounts, G, Joesch, M, and Cox, DD. (2018) A micro-CT-based method for quantitative brain lesion characterization and electrode localization. Sci Rep, 8(1):5184.
    http://www.ncbi.nlm.nih.gov/pubmed/29581439
  28. Maass, PG, Barutcu, AR, Weiner, CL, and Rinn, JL. (2018) Inter-chromosomal Contact Properties in Live-Cell Imaging and in Hi-C. Mol Cell, 69(6):1039-1045.e3.
    http://www.ncbi.nlm.nih.gov/pubmed/29526697
  29. Lee, J, Sutterlin, HA, Wzorek, JS, Mandler, MD, Hagan, CL, Grabowicz, M, Tomasek, D, May, MD, Hart, EM, Silhavy, TJ, and Kahne, D. (2018) Substrate binding to BamD triggers a conformational change in BamA to control membrane insertion. Proc Natl Acad Sci U S A, 115(10):2359-2364.
    http://www.ncbi.nlm.nih.gov/pubmed/29463713
  30. McGee, JH, Shim, SY, Lee, SJ, Swanson, PK, Jiang, SY, Durney, MA, and Verdine, GL. (2018) Exceptionally high-affinity Ras binders that remodel its effector domain. J Biol Chem, 293(9):3265-3280.
    http://www.ncbi.nlm.nih.gov/pubmed/29282294
  31. Hussain, S, Wivagg, CN, Szwedziak, P, Wong, F, Schaefer, K, Izor, T, Renner, LD, Holmes, MJ, Sun, Y, Bisson-Filho, AW, Walker, S, Amir, A, Lwe, J, and Garner, EC. (2018) MreB filaments align along greatest principal membrane curvature to orient cell wall synthesis. Elife, 7.
    http://www.ncbi.nlm.nih.gov/pubmed/29469806
  32. Galonska, C, Charlton, J, Mattei, AL, Donaghey, J, Clement, K, Gu, H, Mohammad, AW, Stamenova, EK, Cacchiarelli, D, Klages, S, Timmermann, B, Cantz, T, Schler, HR, Gnirke, A, Ziller, MJ, and Meissner, A. (2018) Genome-wide tracking of dCas9-methyltransferase footprints. Nat Commun, 9(1):597.
    http://www.ncbi.nlm.nih.gov/pubmed/29426832
  33. Maass, PG, Barutcu, AR, Shechner, DM, Weiner, CL, Mel, M, and Rinn, JL. (2018) Spatiotemporal allele organization by allele-specific CRISPR live-cell imaging (SNP-CLING). Nat Struct Mol Biol, 25(2):176-184.
    http://www.ncbi.nlm.nih.gov/pubmed/29343869
  34. Kunjapur, AM, Stork, DA, Kuru, E, Vargas-Rodriguez, O, Landon, M, Sll, D, and Church, GM. (2018) Engineering posttranslational proofreading to discriminate nonstandard amino acids. Proc Natl Acad Sci U S A, 115(3):619-624.
    http://www.ncbi.nlm.nih.gov/pubmed/29301968
  35. Ziarek, JJ, Baptista, D, and Wagner, G. (2018) Recent developments in solution nuclear magnetic resonance (NMR)-based molecular biology. J Mol Med (Berl), 96(1):1-8.
    http://www.ncbi.nlm.nih.gov/pubmed/28643003
  36. Balleza, E, Kim, JM, and Cluzel, P. (2018) Systematic characterization of maturation time of fluorescent proteins in living cells. Nat Methods, 15(1):47-51.
    http://www.ncbi.nlm.nih.gov/pubmed/29320486