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2010

Improved hidden Markov models for molecular motors, part 2: Extensions and application to experimental data

Syed, S., Müllner, F. E., Selvin, P. R. & Sigworth, F. J., Dec 1 2010, In : Biophysical journal. 99, 11, p. 3696-3703 8 p.

Research output: Contribution to journalArticle

Insights into interphase large-scale chromatin structure from analysis of engineered chromosome regions

Belmont, A. S., Hu, Y., Sinclair, P. B., Wu, W., Bian, Q. & Kireev, I., Dec 1 2010, In : Cold Spring Harbor symposia on quantitative biology. 75, p. 453-460 8 p.

Research output: Contribution to journalArticle

Integrated biochemical and mechanical signals regulate multifaceted human embryonic stem cell functions

Li, D., Zhou, J., Wang, L., Shin, M. E., Su, P., Lei, X., Kuang, H., Guo, W., Yang, H., Cheng, L., Tanaka, T. S., Leckband, D. E., Reynolds, A. B., Duan, E. & Wang, F., Nov 1 2010, In : Journal of Cell Biology. 191, 3, p. 631-644 14 p.

Research output: Contribution to journalArticle

Lineage-specific transcription factors and the evolution of gene regulatory networks

Nowick, K. & Stubbs, L., Jan 16 2010, In : Briefings in Functional Genomics and Proteomics. 9, 1, p. 65-78 14 p., elp056.

Research output: Contribution to journalArticle

Mammalian target of rapamycin regulates miRNA-1 and follistatin in skeletal myogenesis

Sun, Y., Ge, Y., Drnevich, J., Zhao, Y., Band, M. & Chen, J., Jun 28 2010, In : Journal of Cell Biology. 189, 7, p. 1157-1169 13 p.

Research output: Contribution to journalArticle

Material properties of the cell dictate stress-induced spreading and differentiation in embryonic stemcells

Chowdhury, F., Na, S., Li, D., Poh, Y. C., Tanaka, T. S., Wang, F. & Wang, N., Jan 2010, In : Nature Materials. 9, 1, p. 82-88 7 p.

Research output: Contribution to journalArticle

Mechanical force affects expression of an in vitro metastasis-like phenotype in HCT-8 cells

Tang, X., Kuhlenschmidt, T. B., Zhou, J., Bell, P., Wang, F., Kuhlenschmidt, M. S. & Saif, T. A., Oct 20 2010, In : Biophysical journal. 99, 8, p. 2460-2469 10 p.

Research output: Contribution to journalArticle

Novel domains in the hnRNP G/RBMX protein with distinct roles in RNA binding and targeting nascent transcripts

Kanhoush, R., Beenders, B., Perrin, C., Moreau, J., Bellini, M. & Penrad-Mobayed, M., Jan 1 2010, In : Nucleus. 1, 1, p. 109-122 14 p.

Research output: Contribution to journalArticle

Nuclear organization and dynamics of 7SK RNA in regulating gene expression

Prasanth, K. V., Camiolo, M., Chan, G., Tripathi, V., Denis, L., Nakamura, T., Hübner, M. R. & Spector, D. L., Dec 1 2010, In : Molecular biology of the cell. 21, 23, p. 4184-4196 13 p.

Research output: Contribution to journalArticle

Peptides from purified soybean β-conglycinin inhibit fatty acid synthase by interaction with the thioesterase catalytic domain

Martinez-Villaluenga, C., Rupasinghe, S. G., Schuler, M. A. & Gonzalez De Mejia, E., Mar 1 2010, In : FEBS Journal. 277, 6, p. 1481-1493 13 p.

Research output: Contribution to journalArticle

Polypurine-repeat-containing RNAs: A novel class of long non-coding RNA in mammalian cells

Zheng, R., Shen, Z., Tripathi, V., Xuan, Z., Freier, S. M., Bennett, C. F., Prasanth, S. G. & Prasanth, K. V., Nov 1 2010, In : Journal of cell science. 123, 21, p. 3734-3744 11 p.

Research output: Contribution to journalArticle

Quantitative analysis of actin turnover in listeria comet tails: Evidence for catastrophic filament turnover

Kueh, H. Y., Brieher, W. M. & Mitchison, T. J., Oct 6 2010, In : Biophysical journal. 99, 7, p. 2153-2162 10 p.

Research output: Contribution to journalArticle

Rapid sequence and expression divergence suggest selection for novel function in primate-specific KRAB-ZNF genes

Nowick, K., Hamilton, A. T., Zhang, H. & Stubbs, L., Nov 1 2010, In : Molecular biology and evolution. 27, 11, p. 2606-2617 12 p.

Research output: Contribution to journalArticle

Regulation of inhibitory synapses by presynaptic D4 dopamine receptors in thalamus

Govindaiah, G., Wang, T., Gillette, M. U., Crandall, S. R. & Cox, C. L., Nov 1 2010, In : Journal of neurophysiology. 104, 5, p. 2757-2765 9 p.

Research output: Contribution to journalArticle

Slowing Bacterial Translation Speed Enhances Eukaryotic Protein Folding Efficiency

Siller, E., DeZwaan, D. C., Anderson, J. F., Freeman, B. C. & Barral, J. M., Jan 1 2010, In : Journal of Molecular Biology. 396, 5, p. 1310-1318 9 p.

Research output: Contribution to journalArticle

Spatiotemporal organization, regulation, and functions of tractions during neutrophil chemotaxis

Shin, M. E., He, Y., Li, D., Na, S., Chowdhury, F., Poh, Y. C., Collin, O., Su, P., De Lanerolle, P., Schwartz, M. A., Wang, N. & Wang, F., Oct 28 2010, In : Blood. 116, 17, p. 3297-3310 14 p.

Research output: Contribution to journalArticle

The G-protein-coupled receptor, GPR84, is important for eye development in Xenopus laevis

Perry, K. J., Johnson, V. R., Malloch, E. L., Fukui, L., Wever, J., Thomas, A. G., Hamilton, P. W. & Henry, J. J., Nov 1 2010, In : Developmental Dynamics. 239, 11, p. 3024-3037 14 p.

Research output: Contribution to journalArticle

The nuclear-retained noncoding RNA MALAT1 regulates alternative splicing by modulating SR splicing factor phosphorylation

Tripathi, V., Ellis, J. D., Shen, Z., Song, D. Y., Pan, Q., Watt, A. T., Freier, S. M., Bennett, C. F., Sharma, A., Bubulya, P. A., Blencowe, B. J., Prasanth, S. G. & Prasanth, K. V., Sep 1 2010, In : Molecular cell. 39, 6, p. 925-938 14 p.

Research output: Contribution to journalArticle

The slipper snail, Crepidula: An emerging lophotrochozoan model system

Henry, J. J., Collin, R. & Perry, K. J., Jun 1 2010, In : Biological Bulletin. 218, 3, p. 211-229 19 p.

Research output: Contribution to journalArticle

Topography and refractometry of nanostructures using spatial light interference microscopy

Wang, Z., Chun, I. S., Li, X., Ong, Z. Y., Pop, E., Millet, L., Gillette, M. & Popescu, G., Jan 15 2010, In : Optics Letters. 35, 2, p. 208-210 3 p.

Research output: Contribution to journalArticle

β-catenin and early development in the Gastropod, Crepidula fornicata

Henry, J. Q., Perry, K. J. & Martindale, M. Q., Nov 1 2010, In : Integrative and comparative biology. 50, 5, p. 707-719 13 p.

Research output: Contribution to journalArticle

2009

A MicroRNA Imparts Robustness against Environmental Fluctuation during Development

Li, X., Cassidy, J. J., Reinke, C. A., Fischboeck, S. & Carthew, R. W., Apr 17 2009, In : Cell. 137, 2, p. 273-282 10 p.

Research output: Contribution to journalArticle

Comparative toxicity of mycotoxins to navel orangeworm (Amyelois transitella) and corn earworm (Helicoverpa zea)

Niu, G., Siegel, J., Schuler, M. A. & Berenbaum, M. R., Aug 14 2009, In : Journal of Chemical Ecology. 35, 8, p. 951-957 7 p.

Research output: Contribution to journalArticle

Complexity in transcription control at the activation domain-Mediator interface

Balamotis, M. A., Pennella, M. A., Stevens, J. L., Wasylyk, B., Belmont, A. S. & Berk, A. J., May 5 2009, In : Science Signaling. 2, 69, p. ra20

Research output: Contribution to journalArticle

Cytochrome P450 monooxygenases as reporters for circadian-regulated pathways

Pan, Y., Michael, T. P., Hudson, M. E., Kay, S. A., Chory, J. & Schuler, M. A., Jun 1 2009, In : Plant physiology. 150, 2, p. 858-878 21 p.

Research output: Contribution to journalArticle

Domains of heterochromatin protein 1 required for Drosophila melanogaster heterochromatin spreading

Hines, K. A., Cryderman, D. E., Flannery, K. M., Hongbo, Y., Vitalini, M. W., Hazelrigg, T., Mizzen, C. A. & Wallrath, L. L., Aug 2009, In : Genetics. 182, 4, p. 967-977 11 p.

Research output: Contribution to journalArticle

Ecological significance of induction of broad-substrate cytochrome p450s by natural and synthetic inducers in Helicoverpa Zea

Wen, Z., Zeng, R. S., Niu, G., Berenbaum, M. R. & Schuler, M. A., Feb 1 2009, In : Journal of Chemical Ecology. 35, 2, p. 183-189 7 p.

Research output: Contribution to journalArticle

Electrochemical cues regulate assembly of the Frizzled/Dishevelled complex at the plasma membrane during planar epithelial polarization

Simons, M., Gault, W. J., Gotthardt, D., Rohatgi, R., Klein, T. J., Shao, Y., Lee, H. J., Wu, A. L., Fang, Y., Satlin, L. M., Dow, J. T., Chen, J., Zheng, J., Boutros, M. & Mlodzik, M., Feb 24 2009, In : Nature Cell Biology. 11, 3, p. 286-294 9 p.

Research output: Contribution to journalArticle

Enhanced toxicity and induction of cytochrome P450s suggest a cost of "eavesdropping" in a multitrophic interaction

Zeng, R. S., Wen, Z., Niu, G., Schuler, M. A. & Berenbaum, M. R., May 1 2009, In : Journal of Chemical Ecology. 35, 5, p. 526-532 7 p.

Research output: Contribution to journalArticle

FIONA on Caenorhabditis elegans

Kural, C., Nonet, M. L. & Selvin, P. R., Jun 9 2009, In : Biochemistry. 48, 22, p. 4663-4665 3 p.

Research output: Contribution to journalArticle

Fragile X Mental Retardation Protein FMRP binds mRNAs in the nucleus

Kim, M., Bellini, M. & Ceman, S., Jan 2009, In : Molecular and cellular biology. 29, 1, p. 214-228 15 p.

Research output: Contribution to journalArticle

Gene expression profiles of lens regeneration and development in Xenopus laevis

Malloch, E. L., Perry, K. J., Fukui, L., Johnson, V. R., Wever, J., Beck, C. W., King, M. W. & Henry, J. J., Sep 21 2009, In : Developmental Dynamics. 238, 9, p. 2340-2356 17 p.

Research output: Contribution to journalArticle

Histone acetyltransferase Hbo1: Catalytic activity, cellular abundance, and links to primary cancers

Iizuka, M., Takahashi, Y., Mizzen, C. A., Cook, R. G., Fujita, M., Allis, C. D., Frierson, H. F., Fukusato, T. & Smith, M. M., May 1 2009, In : Gene. 436, 1-2, p. 108-114 7 p.

Research output: Contribution to journalArticle

Large-scale chromatin structure of inducible genes: Transcription on a condensed, linear template

Hu, Y., Kireev, I., Plutz, M., Ashourian, N. & Belmont, A. S., Apr 6 2009, In : Journal of Cell Biology. 185, 1, p. 87-100 14 p.

Research output: Contribution to journalArticle

Lineage-specific biology revealed by a finished genome assembly of the mouse

Church, D. M., Goodstadt, L., Hillier, L. W., Zody, M. C., Goldstein, S., She, X., Bult, C. J., Agarwala, R., Cherry, J. L., DiCuccio, M., Hlavina, W., Kapustin, Y., Meric, P., Maglott, D., Birtle, Z., Marques, A. C., Graves, T., Zhou, S., Teague, B., Potamousis, K. & 155 others, Churas, C., Place, M., Herschleb, J., Runnheim, R., Forrest, D., Amos-Landgraf, J., Schwartz, D. C., Cheng, Z., Lindblad-Toh, K., Eichler, E. E., Ponting, C. P., Muzny, D. M., Dugan-Rocha, S., Ding, Y., Scherer, S. E., Buhay, C. J., Cree, A., Hernandez, J., Holder, M., Hume, J., Jackson, L. R., Kovar, C., Lee, S. L., Lewis, L. R., Metzker, M. L., Narareth, L. V., Sabo, A., Sodergren, E., Gibbs, R. A., FitzGerald, M., Cook, A., Jaffe, D. B., Garber, M., Zimmer, A. R., Pirun, M., Russell, L., Sharpe, T., Chaturvedi, M. K. K., Wilkinson, J., LaButti, K., Yang, X., Bessette, D., Allen, N. R., Nguyen, C., Nguyen, T., Dunbar, C., Lubonja, R., Matthews, C., Liu, X., Benamara, M., Negash, T., Lokyitsang, T., Decktor, K., Piqani, B., Munson, G., Tenzin, P., Stone, S., Macdonald, P., Arachchi, H., Abouelleil, A., Lui, A., Priest, M., Gearin, G., Brown, A., Aftuck, L., Shea, T., Sykes, S., Berlin, A., Chu, J., Dooley, K., Hagopian, D., Hall, J., Hafez, N., Smith, C. L., Olandt, P., Miller, K., Ventkataraman, V., Rachupka, A., Dorris, L., Ayotte, L., Mabbitt, R., Erickson, J., Horn, A., An, P., Naylor, J. W., Settipalli, S., Lander, E. S., Wilson, R. K., Graves, T. A., Fulton, R. S., Rock, S. M., Chinwalla, A. T., Bernard, K., Courtney, L. P., Fronick, C., Fulton, L. L., O'Laughlin, M., Kremitzki, C. L., Minx, P. J., Nelson, J. O., Schatzkamer, K. L., Strong, C., Wollam, A. M., Weinstock, G. M., Yang, S. P., Rogers, J., Grafham, D., Humphray, S., Nicholson, C., Bird, C., Brown, A. J., Burton, J., Clee, C., Hunt, A., Jones, M. C., Lloyd, C., Matthews, L., Mclaren, K., Mclaren, S., McLay, K., Palmer, S. A., Plumb, R., Shownkeen, R., Sims, S., Quail, M. A., Whitehead, S. L., Willey, D. L., Deschamps, S., Kenton, S., Song, L., Do, T., Roe, B., Bouffard, G. G., Blakesley, R. W., Green, E. D., Kucherlapati, R., Grills, G., Li, L., Montgomery, K. T., Kramer, M., Speigel, L., McCombie, W. R., Lucas, S., Terry, A., Gordon, L., Stubbs, L., Denny, P., Brown, S. D. M., Mallon, A. M., Campbell, R. D., Botherby, M. R. M., Jackson, I. J., Rubenfield, M. J., Rogosin, A. M. & Smith, D. R., May 2009, In : PLoS biology. 7, 5, e1000112.

Research output: Contribution to journalArticle

Mitotic chromosome structure: Reproducibility of folding and symmetry between sister chromatids

Strukov, Y. G. & Belmont, A. S., Feb 18 2009, In : Biophysical journal. 96, 4, p. 1617-1628 12 p.

Research output: Contribution to journalArticle

mTOR regulates skeletal muscle regeneration in vivo through kinase-dependent and kinase-independent mechanisms

Ge, Y., Wu, A. L., Warnes, C., Liu, J., Zhang, C., Kawasome, H., Terada, N., Boppart, M. D., Schoenherr, C. J. & Chen, J., Dec 1 2009, In : American Journal of Physiology - Cell Physiology. 297, 6, p. C1434-C1444

Research output: Contribution to journalArticle

mTOR supports long-term self-renewal and suppresses mesoderm and endoderm activities of human embryonic stem cells

Zhou, J., Su, P., Wang, L., Chen, J., Zimmermann, M., Genbacev, O., Afonja, O., Horne, M. C., Tanaka, T., Duan, E., Fisher, S. J., Liao, J., Chen, J. & Wang, F., May 12 2009, In : Proceedings of the National Academy of Sciences of the United States of America. 106, 19, p. 7840-7845 6 p.

Research output: Contribution to journalArticle

Myosin VI Dimerization Triggers an Unfolding of a Three-Helix Bundle in Order to Extend Its Reach

Mukherjea, M., Llinas, P., Kim, H. J., Travaglia, M., Safer, D., Ménétrey, J., Franzini-Armstrong, C., Selvin, P. R., Houdusse, A. & Sweeney, H. L., Aug 14 2009, In : Molecular cell. 35, 3, p. 305-315 11 p.

Research output: Contribution to journalArticle

Myosin VI undergoes a 180° power stroke implying an uncoupling of the front lever arm

Reifenberger, J. G., Toprak, E., Kim, H. J., Safer, D., Sweeney, H. L. & Selvin, P. R., Dec 4 2009, In : Proceedings of the National Academy of Sciences of the United States of America. 106, 43, p. 18255-18260 6 p.

Research output: Contribution to journalArticle

Orc1 controls centriole and centrosome copy number in human cells

Hemerly, A. S., Prasanth, S. G., Siddiqui, K. & Stillman, B., Feb 6 2009, In : Science. 323, 5915, p. 789-793 5 p.

Research output: Contribution to journalArticle

Phosphorylation of FMRP inhibits association with Dicer

Cheever, A. & Ceman, S., Mar 1 2009, In : RNA. 15, 3, p. 362-366 5 p.

Research output: Contribution to journalArticle

Quercetin-metabolizing CYP6AS enzymes of the pollinator Apis mellifera (Hymenoptera: Apidae)

Mao, W., Rupasinghe, S. G., Johnson, R. M., Zangerl, A. R., Schuler, M. A. & Berenbaum, M. R., Dec 2009, In : Comparative Biochemistry and Physiology - B Biochemistry and Molecular Biology. 154, 4, p. 427-434 8 p.

Research output: Contribution to journalArticle

Regenerative Growth in Drosophila Imaginal Discs Is Regulated by Wingless and Myc

Smith-Bolton, R. K., Worley, M. I., Kanda, H. & Hariharan, I. K., Jun 16 2009, In : Developmental cell. 16, 6, p. 797-809 13 p.

Research output: Contribution to journalArticle

Signal transducer and activator of transcription 3 (STAT3) mediates amino acid inhibition of insulin ignaling through serine 727 phosphorylation

Kim, J. H., Yoon, M. S. & Chen, J., Dec 18 2009, In : Journal of Biological Chemistry. 284, 51, p. 35425-35432 8 p.

Research output: Contribution to journalArticle

Silencing by small RNAs is linked to endosomal trafficking

Lee, Y. S., Pressman, S., Andress, A. P., Kim, K., White, J. L., Cassidy, J. J., Li, X., Lubell, K., Lim, D. H., Cho, I. S., Nakahara, K., Preall, J. B., Bellare, P., Sontheimer, E. J. & Carthew, R. W., Aug 17 2009, In : Nature Cell Biology. 11, 9, p. 1150-1156 7 p.

Research output: Contribution to journalArticle

Temporally restricted role of retinal PACAP: Integration of the phase-advancing light signal to the SCN

Beaulé, C., Mitchell, J. W., Lindberg, P. T., Damadzic, R., Eiden, L. E. & Gillette, M. U., Apr 1 2009, In : Journal of biological rhythms. 24, 2, p. 126-134 9 p.

Research output: Contribution to journalArticle