Graduate MCO

Student Publications

2015 Publications

31 publications listed for 2015

  1. Kain, JS, Zhang, S, Akhund-Zade, J, Samuel, AD, Klein, M, and de, BL. (2015) Variability in thermal and phototactic preferences in Drosophila may reflect an adaptive bet-hedging strategy. Evolution, 69(12):3171-85.
    http://www.ncbi.nlm.nih.gov/pubmed/26531165
  2. Dengler, V, Foulston, L, DeFrancesco, AS, and Losick, R. (2015) An Electrostatic Net Model for the Role of Extracellular DNA in Biofilm Formation by Staphylococcus aureus. J Bacteriol, 197(24):3779-87.
    http://www.ncbi.nlm.nih.gov/pubmed/26416831
  3. Ye, Z, Mostajo-Radji, MA, Brown, JR, Rouaux, C, Tomassy, GS, Hensch, TK, and Arlotta, P. (2015) Instructing Perisomatic Inhibition by Direct Lineage Reprogramming of Neocortical Projection Neurons. Neuron, 88(3):475-83.
    http://www.ncbi.nlm.nih.gov/pubmed/26539889
  4. Brewster, MS, and Gaudet, R. (2015) How the TRPA1 receptor transmits painful stimuli: Inner workings revealed by electron cryomicroscopy. Bioessays, 37(11):1184-92.
    http://www.ncbi.nlm.nih.gov/pubmed/26387779
  5. Randlett, O, Wee, CL, Naumann, EA, Nnaemeka, O, Schoppik, D, Fitzgerald, JE, Portugues, R, Lacoste, AM, Riegler, C, Engert, F, and Schier, AF. (2015) Whole-brain activity mapping onto a zebrafish brain atlas. Nat Methods, 12(11):1039-46.
    http://www.ncbi.nlm.nih.gov/pubmed/26778924
  6. Kiani, S, Chavez, A, Tuttle, M, Hall, RN, Chari, R, Ter-Ovanesyan, D, Qian, J, Pruitt, BW, Beal, J, Vora, S, Buchthal, J, Kowal, EJ, Ebrahimkhani, MR, Collins, JJ, Weiss, R, and Church, G. (2015) Cas9 gRNA engineering for genome editing, activation and repression. Nat Methods, 12(11):1051-4.
    http://www.ncbi.nlm.nih.gov/pubmed/26344044
  7. Pauli, A, Montague, TG, Lennox, KA, Behlke, MA, and Schier, AF. (2015) Antisense Oligonucleotide-Mediated Transcript Knockdown in Zebrafish. PLoS One, 10(10):e0139504.
    http://www.ncbi.nlm.nih.gov/pubmed/26436892
  8. Hubbard, BP, Badran, AH, Zuris, JA, Guilinger, JP, Davis, KM, Chen, L, Tsai, SQ, Sander, JD, Joung, JK, and Liu, DR. (2015) Continuous directed evolution of DNA-binding proteins to improve TALEN specificity. Nat Methods, 12(10):939-42.
    http://www.ncbi.nlm.nih.gov/pubmed/26258293
  9. Menegas, W, Bergan, JF, Ogawa, SK, Isogai, Y, Umadevi, K, Osten, P, Uchida, N, and Watabe-Uchida, M. (2015) Dopamine neurons projecting to the posterior striatum form an anatomically distinct subclass. Elife, 4:e10032.
    http://www.ncbi.nlm.nih.gov/pubmed/26322384
  10. Kuo, SY, Castoreno, AB, Aldrich, LN, Lassen, KG, Goel, G, Dank, V, Kuballa, P, Latorre, I, Conway, KL, Sarkar, S, Maetzel, D, Jaenisch, R, Clemons, PA, Schreiber, SL, Shamji, AF, and Xavier, RJ. (2015) Small-molecule enhancers of autophagy modulate cellular disease phenotypes suggested by human genetics. Proc Natl Acad Sci U S A, 112(31):E4281-7.
    http://www.ncbi.nlm.nih.gov/pubmed/26195741
  11. Eun, YJ, Kapoor, M, Hussain, S, and Garner, EC. (2015) Bacterial Filament Systems: Toward Understanding Their Emergent Behavior and Cellular Functions. J Biol Chem, 290(28):17181-9.
    http://www.ncbi.nlm.nih.gov/pubmed/25957405
  12. Perez, JD, Rubinstein, ND, Fernandez, DE, Santoro, SW, Needleman, LA, Ho-Shing, O, Choi, JJ, Zirlinger, M, Chen, SK, Liu, JS, and Dulac, C. (2015) Quantitative and functional interrogation of parent-of-origin allelic expression biases in the brain. Elife, 4:e07860.
    http://www.ncbi.nlm.nih.gov/pubmed/26140685
  13. Bhullar, BA, Morris, ZS, Sefton, EM, Tok, A, Tokita, M, Namkoong, B, Camacho, J, Burnham, DA, and Abzhanov, A. (2015) A molecular mechanism for the origin of a key evolutionary innovation, the bird beak and palate, revealed by an integrative approach to major transitions in vertebrate history. Evolution, 69(7):1665-77.
    http://www.ncbi.nlm.nih.gov/pubmed/25964090
  14. Begun, J, Lassen, KG, Jijon, HB, Baxt, LA, Goel, G, Heath, RJ, Ng, A, Tam, JM, Kuo, SY, Villablanca, EJ, Fagbami, L, Oosting, M, Kumar, V, Schenone, M, Carr, SA, Joosten, LA, Vyas, JM, Daly, MJ, Netea, MG, Brown, GD, Wijmenga, C, and Xavier, RJ. (2015) Integrated Genomics of Crohn’s Disease Risk Variant Identifies a Role for CLEC12A in Antibacterial Autophagy. Cell Rep, 11(12):1905-18.
    http://www.ncbi.nlm.nih.gov/pubmed/26095365
  15. Cardarelli, L, Saak, C, and Gibbs, KA. (2015) Two Proteins Form a Heteromeric Bacterial Self-Recognition Complex in Which Variable Subdomains Determine Allele-Restricted Binding. MBio, 6(3):e00251.
    http://www.ncbi.nlm.nih.gov/pubmed/26060269
  16. Vincent, BJ, Scholes, C, Staller, MV, Wunderlich, Z, Estrada, J, Park, J, Bragdon, MD, Lopez, F, Biette, KM, and DePace, AH. (2015) Yearly planning meetings: individualized development plans aren’t just more paperwork. Mol Cell, 58(5):718-21.
    http://www.ncbi.nlm.nih.gov/pubmed/26046646
  17. Lacoste, AM, Schoppik, D, Robson, DN, Haesemeyer, M, Portugues, R, Li, JM, Randlett, O, Wee, CL, Engert, F, and Schier, AF. (2015) A convergent and essential interneuron pathway for Mauthner-cell-mediated escapes. Curr Biol, 25(11):1526-34.
    http://www.ncbi.nlm.nih.gov/pubmed/25959971
  18. Kang, H, McElroy, KA, Jung, YL, Alekseyenko, AA, Zee, BM, Park, PJ, and Kuroda, MI. (2015) Sex comb on midleg (Scm) is a functional link between PcG-repressive complexes in Drosophila. Genes Dev, 29(11):1136-50.
    http://www.ncbi.nlm.nih.gov/pubmed/26063573
  19. Ayroles, JF, Buchanan, SM, O’Leary, C, Skutt-Kakaria, K, Grenier, JK, Clark, AG, Hartl, DL, and de, BL. (2015) Behavioral idiosyncrasy reveals genetic control of phenotypic variability. Proc Natl Acad Sci U S A, 112(21):6706-11.
    http://www.ncbi.nlm.nih.gov/pubmed/25953335
  20. Aldrich, LN, Kuo, SY, Castoreno, AB, Goel, G, Kuballa, P, Rees, MG, Seashore-Ludlow, BA, Cheah, JH, Latorre, IJ, Schreiber, SL, Shamji, AF, and Xavier, RJ. (2015) Discovery of a Small-Molecule Probe for V-ATPase Function. J Am Chem Soc, 137(16):5563-8.
    http://www.ncbi.nlm.nih.gov/pubmed/25860544
  21. Dubrulle, J, Jordan, BM, Akhmetova, L, Farrell, JA, Kim, SH, Solnica-Krezel, L, and Schier, AF. (2015) Response to Nodal morphogen gradient is determined by the kinetics of target gene induction. Elife, 4.
    http://www.ncbi.nlm.nih.gov/pubmed/25869585
  22. Chavez, A, Scheiman, J, Vora, S, Pruitt, BW, Tuttle, M, P, E, Lin, S, Kiani, S, Guzman, CD, Wiegand, DJ, Ter-Ovanesyan, D, Braff, JL, Davidsohn, N, Housden, BE, Perrimon, N, Weiss, R, Aach, J, Collins, JJ, and Church, GM. (2015) Highly efficient Cas9-mediated transcriptional programming. Nat Methods, 12(4):326-8.
    http://www.ncbi.nlm.nih.gov/pubmed/25730490
  23. Sysoeva, TA, Bane, LB, Xiao, DY, Bose, B, Chilton, SS, Gaudet, R, and Burton, BM. (2015) Structural characterization of the late competence protein ComFB from Bacillus subtilis. Biosci Rep, 35(2).
    http://www.ncbi.nlm.nih.gov/pubmed/25423369
  24. Cohen, JY, Amoroso, MW, and Uchida, N. (2015) Serotonergic neurons signal reward and punishment on multiple timescales. Elife, 4.
    http://www.ncbi.nlm.nih.gov/pubmed/25714923
  25. Ceccaldi, R, Liu, JC, Amunugama, R, Hajdu, I, Primack, B, Petalcorin, MI, O’Connor, KW, Konstantinopoulos, PA, Elledge, SJ, Boulton, SJ, Yusufzai, T, and D’Andrea, AD. (2015) Homologous-recombination-deficient tumours are dependent on Pol-mediated repair. Nature, 518(7538):258-62.
    http://www.ncbi.nlm.nih.gov/pubmed/25642963
  26. 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. (2015) Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex. Nature, 517(7536):583-8.
    http://www.ncbi.nlm.nih.gov/pubmed/25494202
  27. Rogers, KW, Blssle, A, Schier, AF, and Mller, P. (2015) Measuring protein stability in living zebrafish embryos using fluorescence decay after photoconversion (FDAP). J Vis Exp, (95):52266.
    http://www.ncbi.nlm.nih.gov/pubmed/25650549
  28. Alekseyenko, AA, McElroy, KA, Kang, H, Zee, BM, Kharchenko, PV, and Kuroda, MI. (2015) BioTAP-XL: Cross-linking/Tandem Affinity Purification to Study DNA Targets, RNA, and Protein Components of Chromatin-Associated Complexes. Curr Protoc Mol Biol, 109:21.30.1-32.
    http://www.ncbi.nlm.nih.gov/pubmed/25559106
  29. Liu, JC, Ferreira, CG, and Yusufzai, T. (2015) Human CHD2 is a chromatin assembly ATPase regulated by its chromo- and DNA-binding domains. J Biol Chem, 290(1):25-34.
    http://www.ncbi.nlm.nih.gov/pubmed/25384982
  30. Ashrafi, G, and Schwarz, TL. (2015) PINK1- and PARK2-mediated local mitophagy in distal neuronal axons. Autophagy, 11(1):187-9.
    http://www.ncbi.nlm.nih.gov/pubmed/25607607
  31. Zuris, JA, Thompson, DB, Shu, Y, Guilinger, JP, Bessen, JL, Hu, JH, Maeder, ML, Joung, JK, Chen, ZY, and Liu, DR. (2015) Cationic lipid-mediated delivery of proteins enables efficient protein-based genome editing in vitro and in vivo. Nat Biotechnol, 33(1):73-80.
    http://www.ncbi.nlm.nih.gov/pubmed/25357182