Items where Year is 2009

Paper

Antonescu, C. R., Yoshida, A., Guo, T., Chang, N. E., Zhang, L., Agaram, N. P., Qin, L. X., Brennan, M. F., Singer, S., Maki, R. G. (September 2009) KDR activating mutations in human angiosarcomas are sensitive to specific kinase inhibitors. Cancer Res, 69 (18). pp. 7175-9. ISSN 1538-7445 (Electronic)0008-5472 (Linking)

Aravin, A. A., van der Heijden, G. W., Castaneda, J., Vagin, V. V., Hannon, G. J., Bortvin, A. (December 2009) Cytoplasmic Compartmentalization of the Fetal piRNA Pathway in Mice. Plos Genetics, 5 (12). e1000764. ISSN 1553-7390

Asari, H., Zador, A. M. (August 2009) Long-Lasting Context Dependence Constrains Neural Encoding Models in Rodent Auditory Cortex. J Neurophysiol, 102 (5). pp. 2638-56.

Atwal, G. S., Kirchhoff, T., Bond, E. E., Montagna, M., Menin, C., Bertorelle, R., Scaini, M. C., Bartel, F., Böhnke, A., Pempe, C., Gradhand, E., Hauptmann, S., Offit, K., Levine, A. J., Bond, G. L. (June 2009) Altered tumor formation and evolutionary selection of genetic variants in the human MDM4 oncogene. Proc Natl Acad Sci U S A, 106 (25). pp. 10236-10241. ISSN 1091-6490 (Electronic)0027-8424 (Linking)

Bannard, O., Kraman, M., Fearon, D. T. (January 2009) Secondary replicative function of CD8+ T cells that had developed an effector phenotype. Science, 323 (5913). pp. 505-9. ISSN 1095-9203 (Electronic)0036-8075 (Linking)

Bayer, M., Nawy, T., Giglione, C., Galli, M., Meinnel, T., Lukowitz, W. (March 2009) Paternal Control of Embryonic Patterning in Arabidopsis thaliana. Science, 323 (5920). pp. 1485-1488. ISSN 0036-8075

Benita, Y., Kikuchi, H., Smith, A. D., Zhang, M. Q., Chung, D. C., Xavier, R. J. (August 2009) An integrative genomics approach identifies Hypoxia Inducible Factor-1 (HIF-1)-target genes that form the core response to hypoxia. Nucleic Acids Res, 37 (14). 4587–4602.

Benitez-Alfonso, Y., Cilia, M., Roman, A. S., Thomas, C., Maule, A., Hearn, S., Jackson, D. P. (March 2009) Control of Arabidopsis meristem development by thioredoxin-dependent regulation of intercellular transport. Proc Natl Acad Sci U S A, 106 (9). pp. 3615-3620. ISSN 0027-8424

Benitez-Alfonso, Y., Jackson, D. P. (July 2009) Redox homeostasis regulates plasmodesmal communication in Arabidopsis meristems. Plant Signaling and Behavior, 4 (7). pp. 655-659.

Bennett, Lori, Yang, Ming, Enikolopov, G. N., Iacovitti, Lorraine (June 2009) Circumventricular organs: A novel site of neural stem cells in the adult brain. Molecular and Cellular Neuroscience, 41 (3). pp. 337-347.

Birney, E., Hudson, T. J., Green, E. D., Gunter, C., Eddy, S., Rogers, J., Harris, J. R., Ehrlich, S. D., Apweiler, R., Austin, C. P., Berglund, L., Bobrow, M., Bountra, C., Brookes, A. J., Cambon-Thomsen, A., Carter, N. P., Chisholm, R. L., Contreras, J. L., Cooke, R. M., Crosby, W. L., Dewar, K., Durbin, R., Dyke, S. O., Ecker, J. R., El Emam, K., Feuk, L., Gabriel, S. B., Gallacher, J., Gelbart, W. M., Granell, A., Guarner, F., Hubbard, T., Jackson, S. A., Jennings, J. L., Joly, Y., Jones, S. M., Kaye, J., Kennedy, K. L., Knoppers, B. M., Kyrpides, N. C., Lowrance, W. W., Luo, J., MacKay, J. J., Martin-Rivera, L., McCombie, W. R., McPherson, J. D., Miller, L., Miller, W., Moerman, D., Mooser, V., Morton, C. C., Ostell, J. M., Ouellette, B. F., Parkhill, J., Raina, P. S., Rawlings, C., Scherer, S. E., Scherer, S. W., Schofield, P. N., Sensen, C. W., Stodden, V. C., Sussman, M. R., Tanaka, T., Thornton, J., Tsunoda, T., Valle, D., Vuorio, E. I., Walker, N. M., Wallace, S., Weinstock, G., Whitman, W. B., Worley, K. C., Wu, C., Wu, J., Yu, J. (September 2009) Prepublication data sharing. Nature, 461 (7261). pp. 168-70. ISSN 0028-0836

Blobel, G. A., Kadauke, S., Wang, E., Lau, A. W., Zuber, J., Chou, M. M., Vakoc, C. R. (December 2009) A Reconfigured Pattern of MLL Occupancy within Mitotic Chromatin Promotes Rapid Transcriptional Reactivation Following Mitotic Exit. Molecular Cell, 36 (6). pp. 970-983.

Blum, A. L., Li, W., Cressy, M., Dubnau, J. T. (August 2009) Short- and Long-Term Memory in Drosophila Require cAMP Signaling in Distinct Neuron Types. Current Biology, 19 (16). 1341-1350 . ISSN 0960-9822

Boersema, P. J., Taouatas, N., Altelaar, A. F. M., Gouw, J. W., Ross, P. L., Pappin, D. J., Heck, A. J. R., Mohammed, S. (April 2009) Straightforward and de Novo Peptide Sequencing by MALDI-MS/MS Using a Lys-N Metalloendopeptidase. Molecular & Cellular Proteomics, 8 (4). pp. 650-660. ISSN 1535-9476

Boettner, B., Van Aelst, L. (October 2009) Control of cell adhesion dynamics by Rap1 signaling. Curr Opin Cell Biol, 21 (5). 684-693 .

Bohland, Jason W, Wu, Caizhi, Barbas, Helen, Bokil, Hemant, Bota, Mihail, Breiter, Hans C, Cline, Hollis T, Doyle, John C, Freed, Peter J, Greenspan, Ralph J, Haber, Suzanne N, Hawrylycz, Michael, Herrera, Daniel G, Hilgetag, Claus C, Huang, Z Josh, Jones, Allan, Jones, Edward G, Karten, Harvey J, Kleinfeld, David, Kotter, Rolf, Lester, Henry A, Lin, John M, Mensh, Brett D, Mikula, Shawn, Panksepp, Jaak, Price, Joseph L, Safdieh, Joseph, Saper, Clifford B, Schiff, Nicholas D, Schmahmann, Jeremy D, Stillman, Bruce W, Svoboda, Karel, Swanson, Larry W, Toga, Arthur W, Essen, David C Van, Watson, James D, Mitra, Partha P (January 2009) A proposal for a coordinated effort for the determination of brainwide neuroanatomical connectivity in model organisms at a mesoscopic scale. PLoS Computational Biology. (Submitted)

Bohland, J. W., Bokil, H., Allen, C. B., Mitra, P. P. (September 2009) The brain atlas concordance problem: quantitative comparison of anatomical parcellations. PLoS ONE, 4 (9). e7200. ISSN 1932-6203 (Electronic)

Bohland, J. W., Wu, C., Barbas, H., Bokil, H., Bota, M., Breiter, H. C., Cline, H. T., Doyle, J. C., Freed, P. J., Greenspan, R. J., Haber, S. N., Hawrylycz, M., Herrera, D. G., Hilgetag, C. C., Huang, Z. J., Jones, A., Jones, E. G., Karten, H. J., Kleinfeld, D., Kotter, R., Lester, H. A., Lin, J. M., Mensh, B. D., Mikula, S., Panksepp, J., Price, J. L., Safdieh, J., Saper, C. B., Schiff, N. D., Schmahmann, J. D., Stillman, B. W., Svoboda, K., Swanson, L. W., Toga, A. W., Van Essen, D. C., Watson, J. D., Mitra, P. P. (March 2009) A proposal for a coordinated effort for the determination of brainwide neuroanatomical connectivity in model organisms at a mesoscopic scale. PLoS Computational Biology, 5 (3). e1000334. ISSN 1553734X

Bolduc, F. V., Tully, T. (January 2009) Fruit flies and intellectual disability. Fly, 3 (1). pp. 91-104. ISSN 1933-6934

Boles, M. K., Wilkinson, B. M., Maxwell, A., Lai, L., Mills, A. A., Nishijima, I., Salinger, A. P., Moskowitz, I., Hirschi, K. K., Liu, B., Bradley, A., Justice, M. J. (March 2009) A mouse chromosome 4 balancer ENU-mutagenesis screen isolates eleven lethal lines. BMC Genet, 10 (1). p. 12.

Bric, A., Miething, C., Bialucha, C. U., Scuoppo, C., Zender, L., Krasnitz, A., Xuan, Z., Zuber, J., Wigler, M. H., Hicks, J. B., McCombie, W. R., Hemann, M. T., Hannon, G. J., Powers, S., Lowe, S. W. (October 2009) Functional identification of tumor-suppressor genes through an in vivo RNA interference screen in a mouse lymphoma model. Cancer Cell, 16 (4). pp. 324-35. ISSN 1535-6108

Brooks, L., Strable, J., Zhang, X., Ohtsu, K., Zhou, R., Sarkar, A., Hargreaves, S., Elshire, R. J., Eudy, D., Pawlowska, T., Ware, D. H., Janick-Buckner, D., Buckner, B., Timmermans, M. C. P., Schnable, P. S., Nettleton, D., Scanlon, M. J. (May 2009) Microdissection of shoot meristem functional domains. PLoS Genet, 5 (5). e1000476.

Buckler, E. S., Holland, J. B., Bradbury, P. J., Acharya, C. B., Brown, P. J., Browne, C., Ersoz, E., Flint-Garcia, S., Garcia, A., Glaubitz, J. C., Goodman, M. M., Harjes, C., Guill, K., Kroon, D. E., Larsson, S., Lepak, N. K., Li, H., Mitchell, S. E., Pressoir, G., Peiffer, J. A., Rosas, M. O., Rocheford, T. R., Romay, M. C., Romero, S., Salvo, S., Sanchez Villeda, H., da Silva, H. S., Sun, Q., Tian, F., Upadyayula, N., Ware, D. H., Yates, H., Yu, J., Zhang, Z., Kresovich, S., McMullen, M. D. (August 2009) The genetic architecture of maize flowering time. Science, 325 (5941). pp. 714-8. ISSN 1095-9203 (Electronic)

Cai, J., Donaldson, A., Yang, M., German, M. S., Enikolopov, G. N., Iacovitti, L. (January 2009) The Role of Lmx1a in the Differentiation of Human Embryonic Stem Cells into Midbrain Dopamine Neurons in Culture and After Transplantation into a Parkinson's Disease Model. Stem Cells, 27 (1). pp. 220-229.

Castellano, L., Giamas, G., Jacob, J., Coombes, R. C., Lucchesi, W., Thiruchelvam, P., Barton, G., Jiao, L. R., Wait, R., Waxman, J., Hannon, G. J., Stebbing, J. (2009) The estrogen receptor-α-induced microRNA signature regulates itself and its transcriptional response. Proceedings of the National Academy of Sciences of the United States of America, 106 (37). pp. 15732-15737. ISSN 00278424 (ISSN)

Celniker, S. E., Dillon, L. A., Gerstein, M. B., Gunsalus, K. C., Henikoff, S., Karpen, G. H., Kellis, M., Lai, E. C., Lieb, J. D., MacAlpine, D. M., Micklem, G., Piano, F., Snyder, M., Stein, L. D., White, K. P., Waterston, R. H. (June 2009) Unlocking the secrets of the genome. Nature, 459 (7249). pp. 927-30. ISSN 1476-4687 (Electronic)0028-0836 (Linking)

Chakraborty, A. A., Tansey, W. P. (January 2009) Adenoviral E1A Function through Myc. Cancer Res, 69 (1). pp. 6-9.

Chakraborty, A. A. , Tansey, W. P. (June 2009) Inference of cell cycle-dependent proteolysis by laser scanning cytometry. Experimental Cell Research, 315 (10). pp. 1772-1778.

Chen, C. M., Chiu, S. L., Shen, W., Cline, H. T. (2009) Co-expression of Argonaute2 Enhances Short Hairpin RNA-induced RNA Interference in Xenopus CNS Neurons In Vivo. Frontiers in Neuroscience, 3. p. 63.

Chiang, H-C., Iijima, K., Hakker, I., Zhong, Y. (June 2009) Distinctive roles of different {beta}-amyloid 42 aggregates in modulation of synaptic functions. FASEB J., 23 (6). pp. 1969-1977.

Chitwood, D. H., Nogueira, F. T. S., Howell, M. D., Montgomery, T. A., Carrington, J. C., Timmermans, M. C. P. (March 2009) Pattern formation via small RNA mobility. Genes Dev, 23 (5). pp. 549-554. ISSN 0890-9369

Chou, S. T., Khandros, E., Bailey, L. C., Nichols, K. E., Vakoc, C. R., Yao, Y., Huang, Z., Crispino, J. D., Hardison, R. C., Blobel, G. A., Weiss, M. J. (July 2009) Graded repression of PU.1/Sfpi1 gene transcription by GATA factors regulates hematopoietic cell fate. Blood, 114 (5). pp. 983-994.

Chugh, R., Wathen, J. K., Maki, R. G., Benjamin, R. S., Patel, S. R., Meyers, P. A., Priebat, D. A., Reinke, D. K., Thomas, D. G., Keohan, M. L., Samuels, B. L., Baker, L. H. (July 2009) Phase II multicenter trial of imatinib in 10 histologic subtypes of sarcoma using a bayesian hierarchical statistical model. J Clin Oncol, 27 (19). pp. 3148-53. ISSN 1527-7755 (Electronic)0732-183X (Linking)

Church, Deanna M., Goodstadt, Leo, Hillier, LaDeana W., Zody, Michael C., Goldstein, Steve, She, Xinwe, Bult, Carol J., Agarwala, Richa, Cherry, Joshua L., DiCuccio, Michael, Hlavina, Wratko, Kapustin, Yuri, Meric, Peter, Maglott, Donna, Birtle, Zoë, Marques, Ana C., Graves, Tina, Zhou, Shiguo, Teague, Brian, Potamousis, Konstantinos, Churas, Christopher, Place, Michael, Herschleb, Jill, Runnheim, Ron, Forrest, Daniel, Amos-Landgraf, James, Schwartz, David C., Cheng, Ze, Lindblad-Toh, Kerstin, Eichler, Evan E., Ponting, Chris P., The Mouse Genome Sequencing, Consortium (May 2009) Lineage-Specific Biology Revealed by a Finished Genome Assembly of the Mouse. PLoS Biol, 7 (5). e1000112.

Cibrian-Jaramillo, A., Martienssen, R. A. (2009) Darwin's "Abominable Mystery": the role of RNA interference in the evolution of flowering plants. Cold Spring Harbor Symposia on Quantitative Biology, 74. pp. 267-273. ISSN 00917451 (ISSN)

Collins, G. A., Lipford, J. R., Deshaies, R. J., Tansey, W. P. (October 2009) Gal4 turnover and transcription activation. Nature, 461 (7265). E7-E7.

Cornman, R. S., Chen, Y. P., Schatz, M. C., Street, C., Zhao, Y., Desany, B., Egholm, M., Hutchison, S., Pettis, J. S., Lipkin, W. I., Evans, J. D. (2009) Genomic analyses of the microsporidian Nosema ceranae, an emergent pathogen of honey bees. PLoS Pathogens, 5 (6). ISSN 15537366 (ISSN)

Couvillion, M. T., Lee, S. R., Hogstad, B., Malone, C. D., Tonkin, L. A., Sachidanandam, R., Hannon, G. J., Collins, K. (2009) Sequence, biogenesis, and function of diverse small RNA classes bound to the Piwi family proteins of Tetrahymena thermophila. Genes and Development, 23 (17). pp. 2016-2032. ISSN 08909369 (ISSN)

Cranston, K. A., Hurwitz, B. L., Ware, D. H., Stein, L. D., Wing, R. A. (October 2009) Species Trees from Highly Incongruent Gene Trees in Rice. Systematic Biology, 58 (5). pp. 489-500. ISSN 1063-5157

Czech, B., Zhou, R., Erlich, Y., Brennecke, J., Binari, R., Villalta, C., Gordon, A., Perrimon, N., Hannon, G. J. (2009) Hierarchical Rules for Argonaute Loading in Drosophila. Molecular Cell, 36 (3). pp. 445-456. ISSN 10972765 (ISSN)

Daulny, A., Tansey, W. P. (April 2009) Damage control: DNA repair, transcription, and the ubiquitin-proteasome system. DNA Repair, 8 (4). pp. 444-448.

De Araújo, M. M., Bonnal, S., Hastings, M. L., Krainer, A. R., Valcárcel, J. (April 2009) Differential 3′ splice site recognition of SMN1 and SMN2 transcripts by U2AF and U2 snRNP. RNA, 15 (4). pp. 515-523.

Dematteo, R. P., Ballman, K. V., Antonescu, C. R., Maki, R. G., Pisters, P. W., Demetri, G. D., Blackstein, M. E., Blanke, C. D., von Mehren, M., Brennan, M. F., Patel, S., McCarter, M. D., Polikoff, J. A., Tan, B. R., Owzar, K., American College of Surgeons Oncology Group Intergroup Adjuvant, Gist Study Team (March 2009) Adjuvant imatinib mesylate after resection of localised, primary gastrointestinal stromal tumour: a randomised, double-blind, placebo-controlled trial. Lancet, 373 (9669). pp. 1097-104. ISSN 1474-547X (Electronic)0140-6736 (Linking)

Demetri, G. D., Heinrich, M. C., Fletcher, J. A., Fletcher, C. D., Van den Abbeele, A. D., Corless, C. L., Antonescu, C. R., George, S., Morgan, J. A., Chen, M. H., Bello, C. L., Huang, X., Cohen, D. P., Baum, C. M., Maki, R. G. (September 2009) Molecular target modulation, imaging, and clinical evaluation of gastrointestinal stromal tumor patients treated with sunitinib malate after imatinib failure. Clin Cancer Res, 15 (18). pp. 5902-9. ISSN 1078-0432 (Print)1078-0432 (Linking)

Deutsch, C. K., Malhotra, D., Krause, V., McCarthy, S. E., Krastoshevsky, O., Coleman, M., Francis, R. W., Bodkin, J. A., Boling, L., Cole, J., Gibbs, A., Johnson, F., Lerbinger, J., Mendell, N. R., Sebat, J., Levy, D. L. (March 2009) Rare Gene Copy Number Variations Are Associated with Specific Endophenotypes in Schizophrenia. Schizophrenia Bulletin, 35 (Suppl.). p. 117. ISSN 0586-7614

Ding, D., Zhang, L., Wang, H., Liu, Z., Zhang, Z., Zheng, Y. (January 2009) Differential expression of miRNAs in response to salt stress in maize roots. Ann Bot, 103 (1). pp. 29-38.

Doehlemann, G., van der Linde, K., Amann, D., Schwammbach, D., Hof, A., Mohanty, A., Jackson, D. P., Kahmann, R. (February 2009) Pep1, a Secreted Effector Protein of Ustilago maydis, Is Required for Successful Invasion of Plant Cells. Plos Pathogens, 5 (2). e1000290. ISSN 1553-7366

Dunn, M. P., Di Gregorio, A. (April 2009) The evolutionarily conserved leprecan gene: its regulation by Brachyury and its role in the developing Ciona notochord. Dev Biol, 328 (2). pp. 561-74. ISSN 0012-1606

Ellis, L., Bots, M., Lindemann, R. K., Bolden, J. E., Newbold, A., Cluse, L. A., Scott, C. L., Strasser, A., Atadja, P., Lowe, S. W., Johnstone, R. W. (July 2009) The histone deacetylase inhibitors LAQ824 and LBH589 do not require death receptor signaling or a functional apoptosome to mediate tumor cell death or therapeutic efficacy. Blood, 114 (2). pp. 380-393.

Engel, T. A., Helbig, B., Russell, D. F., Schimansky-Geier, L., Neiman, A. B. (August 2009) Coherent stochastic oscillations enhance signal detection in spiking neurons. Phys Rev E Stat Nonlin Soft Matter Phys, 80 (2 Pt 1). 021919. ISSN 1539-3755 (Print)1539-3755 (Linking)

Engel, Tatiana, Wang, Xiao-Jing (2009) Category learning and decision making: a cortical circuit model. Frontiers in Systems Neuroscience. p. 55. ISSN 1662-5137

Erlich, Yaniv, Gordon, Assaf, Brand, Michael, Hannon, Gregory J, Mitra, Partha P (September 2009) Compressed Genotyping. IEEE Transactions on Information Theory. (Submitted)

Erlich, Y., Chang, K., Gordon, A., Ronen, R., Navon, O., Rooks, M., Hannon, G. J. (2009) DNA Sudoku - Harnessing high-throughput sequencing for multiplexed specimen analysis. Genome Research, 19 (7). pp. 1243-1253. ISSN 10889051 (ISSN)

Evrin, C., Clarke, P., Zech, J., Lurz, R., Sun, J. C., Uhle, S., Li, H. L., Stillman, B., Speck, C. (December 2009) A double-hexameric MCM2-7 complex is loaded onto origin DNA during licensing of eukaryotic DNA replication. Proceedings of the National Academy of Sciences of the United States of America, 106 (48). pp. 20240-20245. ISSN 0027-8424

Ewald, R. C., Cline, H. T. (September 2009) Cloning and Phylogenetic Analysis of NMDA Receptor Subunits NR1, NR2A and NR2B in Xenopus laevis Tadpoles. Front Mol Neurosci, 2. p. 4.

Ezhkova, E., Pasolli, H. A., Parker, J. S., Stokes, N., Su, I. H., Hannon, G. J., Tarakhovsky, A., Fuchs, E. (March 2009) Ezh2 Orchestrates Gene Expression for the Stepwise Differentiation of Tissue-Specific Stem Cells. Cell, 136 (6). pp. 1122-1135. ISSN 0092-8674

Fabian, M. R., Mathonnet, G., Sundermeier, T., Mathys, H., Zipprich, J. T., Svitkin, Y. V., Rivas, F., Jinek, M., Wohlschlegel, J., Doudna, J. A., Chen, C. Y. A., Shyu, A. B., Yates Iii, J. R., Hannon, G. J., Filipowicz, W., Duchaine, T. F., Sonenberg, N. (2009) Mammalian miRNA RISC Recruits CAF1 and PABP to Affect PABP-Dependent Deadenylation. Molecular Cell, 35 (6). pp. 868-880. ISSN 10972765 (ISSN)

Fagegaltier, D., Bougé, A.-L., Berry, B., Poisot, É., Sismeiro, O., Coppée, J.-Y., Théodore, L., Voinnet, O., Antoniewski, C. (December 2009) The endogenous siRNA pathway is involved in heterochromatin formation in Drosophila. Proceedings of the National Academy of Sciences of the United States of America, 106 (50). pp. 21258-21263.

Feher, O., Wang, H., Saar, S., Mitra, P. P., Tchernichovski, O. (May 2009) De novo establishment of wild-type song culture in the zebra finch. Nature, 459 (7246). pp. 564-568. ISSN 0028-0836

Feigin, M. E., Muthuswamy, S. K. (October 2009) Polarity proteins regulate mammalian cell-cell junctions and cancer pathogenesis. Curr Opin Cell Biol, 21 (5). 694-700 .

Fejes-Toth, K., Sotirova, V., Sachidanandam, R., Assaf, G., Hannon, G. J., Kapranov, P., Foissac, S., Willingham, A. T., Duttagupta, R., Dumais, E., Gingeras, T. R. (February 2009) Post-transcriptional processing generates a diversity of 5'-modified long and short RNAs. Nature, 457 (7232). pp. 1028-1032. ISSN 0028-0836

Florez, J., Price, A., Campbell, D., Riba, L., Parra, M., Yu, F., Duque, C., Saxena, R., Gallego, N., Tello-Ruiz, M., Franco, L., Rodríguez-Torres, M., Villegas, A., Bedoya, G., Aguilar-Salinas, C., Tusié-Luna, M., Ruiz-Linares, A., Reich, D. (August 2009) Strong association of socioeconomic status with genetic ancestry in Latinos: implications for admixture studies of type 2 diabetes. Diabetologia, 52 (8). 1528-1536 .

Frenette, P. S., Mendez-Ferrer, S., Lucas-Alcaraz, D., Batista, M., Lira, S., Michurina, T. V., Enikolopov, G. N. (November 2009) The Hematopoietic Stem Cell Niche. Blood, 114 (22). p. 1586. ISSN 0006-4971

Fu, Y.-Y., Lin, C.-W., Enikolopov, G. N., Sibley, E., Chiang, A.-S., Tang, S.-C. (August 2009) Microtome-Free 3-Dimensional Confocal Imaging Method for Visualization of Mouse Intestine With Subcellular-Level Resolution. Gastroenterology, 137 (2). pp. 453-465.

Gao, X., Enikolopov, G. N., Chen, J. (October 2009) Moderate traumatic brain injury promotes proliferation of quiescent neural progenitors in the adult hippocampus. Experimental Neurology, 219 (2). pp. 516-523.

Garner, T. P., Williams, H. E., Gluszyk, K. I., Roe, S., Oldham, N. J., Stevens, M. F., Moses, J. E., Searle, M. S. (October 2009) Selectivity of small molecule ligands for parallel and anti-parallel DNA G-quadruplex structures. Org Biomol Chem, 7 (20). pp. 4194-200. ISSN 1477-0520

Gass, P., Henn, F. A. (July 2009) Is there a role for neurogenesis in depression? Biol Psychiatry, 66 (1). pp. 3-4. ISSN 0006-3223

George, S., Merriam, P., Maki, R. G., Van den Abbeele, A. D., Yap, J. T., Akhurst, T., Harmon, D. C., Bhuchar, G., O'Mara, M. M., D'Adamo, D. R., Morgan, J., Schwartz, G. K., Wagner, A. J., Butrynski, J. E., Demetri, G. D., Keohan, M. L. (July 2009) Multicenter phase II trial of sunitinib in the treatment of nongastrointestinal stromal tumor sarcomas. J Clin Oncol, 27 (19). pp. 3154-60. ISSN 1527-7755 (Electronic)0732-183X (Linking)

Gessler, D. D., Schiltz, G. S., May, G. D., Avraham, S., Town, C. D., Grant, D., Nelson, R. T. (September 2009) SSWAP: A Simple Semantic Web Architecture and Protocol for semantic web services. BMC Bioinformatics, 10. p. 309.

Ghafoori, A., Lee, C., Perez, B., Johnston, S., Rodrigues, R., Badea, C., Kim, Y., Lowe, S. W., Kirsch, D. G. (2009) In Vivo shRNA to Study the Molecular Mechanisms of Radiation Response of Primary Cancers in Mice. International Journal of Radiation Oncology Biology Physics, 75 (3). S171-S172. ISSN 0360-3016

Gholami, Sepideh, Jacobs, Charlotte D, Kapp, Daniel S, Parast, Layla M, Norton, Jeffrey A (2009) The value of surgery for retroperitoneal sarcoma. Sarcoma, 2009. p. 605840. ISSN 1357-714X

Gibby, K. A., McDonnell, K., Schmidt, M. O., Wellstein, A. (May 2009) A distinct role for secreted fibroblast growth factor-binding proteins in development. Proc Natl Acad Sci U S A, 106 (21). pp. 8585-8590.

Gillis, J., Pavlidis, P. (2009) A methodology for the analysis of differential coexpression across the human lifespan. BMC Bioinformatics, 10. p. 306. ISSN 14712105 (ISSN)

Gingeras, T. R. (September 2009) Implications of chimaeric non-co-linear transcripts. Nature, 461 (7261). pp. 206-11. ISSN 1476-4687 (Electronic)

Gingeras, T. R. (April 2009) Missing lincs in the transcriptome. Nature Biotechnology, 27 (4). pp. 346-347. ISSN 1087-0156

Godenschwege, T., Forde, R., Davis, C. P., Paul, A., Beckwith, K., Duttaroy, A. (September 2009) Mitochondrial superoxide radicals differentially affect muscle activity and neural function. Genetics, 183 (1). pp. 175-184.

Gold, J. S., Gonen, M., Gutierrez, A., Broto, J. M., Garcia-del-Muro, X., Smyrk, T. C., Maki, R. G., Singer, S., Brennan, M. F., Antonescu, C. R., Donohue, J. H., DeMatteo, R. P. (November 2009) Development and validation of a prognostic nomogram for recurrence-free survival after complete surgical resection of localised primary gastrointestinal stromal tumour: a retrospective analysis. Lancet Oncol, 10 (11). pp. 1045-52. ISSN 1474-5488 (Electronic)1470-2045 (Linking)

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Skirpan, A., Culler, A. H., Gallavotti, A., Jackson, D., Cohen, J. D., McSteen, P. (March 2009) BARREN INFLORESCENCE2 Interaction with ZmPIN1a Suggests a Role in Auxin Transport During Maize Inflorescence Development. Plant and Cell Physiology, 50 (3). pp. 652-657. ISSN 0032-0781

Slotkin, R. K., Vaughn, M., Borges, F., Tanurdzic, M., Becker, J. D., Feijo, J. A., Martienssen, R. A. (February 2009) Epigenetic reprogramming and small RNA silencing of transposable elements in pollen. Cell, 136 (3). pp. 461-72. ISSN 1097-4172 (Electronic)0092-8674 (Linking)

Smith, A. D., Chung, W. Y., Hodges, E., Kendall, Jude T., Hannon, G. J., Hicks, J. B., Xuan, Z., Zhang, M. Q. (November 2009) Updates to the RMAP short-read mapping software. Bioinformatics, 25 (21). pp. 2841-2842.

Song, Q., Sun, K., Shuai, Y. C., Lin, R., You, W., Wang, L., Zhong, Y. (July 2009) Suppressor of hairless is required for long-term memory formation in drosophila. Journal of Neurogenetics, 23 (4). pp. 405-411.

Soucy, E. R., Albeanu, D. F., Fantana, A. L., Murthy, V. N., Meister, M. (2009) Precision and diversity in an odor map on the olfactory bulb. Nature Neuroscience, 12 (2). pp. 210-220. ISSN 10976256 (ISSN)

Starr, T. K., Allaei, R., Silverstein, K. A. T., Staggs, R. A., Sarver, A. L., Bergemann, T. L., Gupta, M., O'Sullivan, M. G., Matise, I., Dupuy, A. J., Collier, L. S., Powers, S., Oberg, A. L., Asmann, Y. W., Thibodeau, S. N., Tessarollo, L., Copeland, N. G., Jenkins, N. A., Cormier, R. T., Largaespada, D. A. (March 2009) A Transposon-Based Genetic Screen in Mice Identifies Genes Altered in Colorectal Cancer. Science, 323 (5922). pp. 1747-1750. ISSN 0036-8075

Sunwoo, H., Dinger, M. E., Wilusz, J. E., Amaral, P. P., Mattick, J. S., Spector, D. L. (March 2009) MEN epsilon/beta nuclear-retained non-coding RNAs are up-regulated upon muscle differentiation and are essential components of paraspeckles. Genome Research, 19 (3). pp. 347-359. ISSN 10889051 (ISSN)

Tegay, D. H., Chan, K. K., Leung, L., Wang, C., Burkett, S., Stone, G., Stanyon, R., Toriello, H. V., Hatchwell, E. (March 2009) Toriello-Carey syndrome in a patient with a de novo balanced translocation [46,XY,t(2;14)(q33;q22)] interrupting SATB2. Clinical Genetics, 75 (3). pp. 259-264. ISSN 0009-9163

Temple, G., Gerhard, D. S., Rasooly, R., Feingold, E. A., Good, P. J., Robinson, C., Mandich, A., Derge, J. G., Lewis, J., Shoaf, D., Collins, F. S., Jang, W., Wagner, L., Shenmen, C. M., Misquitta, L., Schaefer, C. F., Buetow, K. H., Bonner, T. I., Yankie, L., Ward, M., Phan, L., Astashyn, A., Brown, G., Farrell, C., Hart, J., Landrum, M., Maidak, B. L., Murphy, M., Murphy, T., Rajput, B., Riddick, L., Webb, D., Weber, J., Wu, W., Pruitt, K. D., Maglott, D., Siepel, A., Brejova, B., Diekhans, M., Harte, R., Baertsch, R., Kent, J., Haussler, D., Brent, M., Langton, L., Comstock, C. L., Stevens, M., Wei, C., van Baren, M. J., Salehi-Ashtiani, K., Murray, R. R., Ghamsari, L., Mello, E., Lin, C., Pennacchio, C., Schreiber, K., Shapiro, N., Marsh, A., Pardes, E., Moore, T., Lebeau, A., Muratet, M., Simmons, B., Kloske, D., Sieja, S., Hudson, J., Sethupathy, P., Brownstein, M., Bhat, N., Lazar, J., Jacob, H., Gruber, C. E., Smith, M. R., McPherson, J., Garcia, A. M., Gunaratne, P. H., Wu, J., Muzny, D., Gibbs, R. A., Young, A. C., Bouffard, G. G., Blakesley, R. W., Mullikin, J., Green, E. D., Dickson, M. C., Rodriguez, A. C., Grimwood, J., Schmutz, J., Myers, R. M., Hirst, M., Zeng, T., Tse, K., Moksa, M., Deng, M., Ma, K., Mah, D., Pang, J., Taylor, G., Chuah, E., Deng, A. (December 2009) The completion of the Mammalian Gene Collection (MGC). Genome Research, 19 (12). pp. 2324-33. ISSN 1088-9051

Tessanne, K., Stroud, T., Long, C., Hannon, G. J., Sadeghieh, S., Hwang, E., Chen, S., Polejaeva, I., Westhusin, M. (2009) Development of Transgenic Livestock with Reduced Myostatin Expression Using Rna Interference. Reproduction Fertility and Development, 21 (1). p. 251. ISSN 1031-3613

Thomas, R., Rebbeck, C. A., Leroi, A. M., Burt, A., Breen, M. (October 2009) Extensive conservation of genomic imbalances in canine transmissible venereal tumors (CTVT) detected by microarray-based CGH analysis. Chromosome Research, 17 (7). pp. 927-934. ISSN 0967-3849

Tonks, N. K. (October 2009) Pseudophosphatases: grab and hold on. Cell, 139 (3). pp. 464-5.

Trapnell, C., Schatz, M. C. (2009) Optimizing data intensive GPGPU computations for DNA sequence alignment. Parallel Computing, 35 (8-9). pp. 429-440. ISSN 01678191 (ISSN)

Tripic, T., Deng, W., Cheng, Y., Zhang, Y., Vakoc, C. R., Gregory, G. D., Hardison, R. C., Blobel, G. A. (2009) SCL and associated proteins distinguish active from repressive GATA transcription factor complexes. Blood, 113 (10). pp. 2191-2201. ISSN 00064971 (ISSN)

Tsigankov, D. N., Koulakov, A. A. (November 2009) Optimal axonal and dendritic branching strategies during the development of neural circuitry. Front Neural Circuits, 3. p. 18. ISSN 1662-5110 (Electronic)

Uziel, T., Karginov, F. V., Xie, S. Q., Parker, J. S., Wang, Y. D., Gajjar, A., He, L., Ellison, D., Gilbertson, R. J., Hannon, G. J., Roussel, M. F. (February 2009) The miR-17 similar to 92 cluster collaborates with the Sonic Hedgehog pathway in medulloblastoma. Proceedings of the National Academy of Sciences of the United States of America, 106 (8). pp. 2812-2817. ISSN 0027-8424

Vagin, V. V., Hannon, G. J., Aravin, A. A. (2009) Arginine methylation as a molecular signature of the Piwi small RNA pathway. Cell Cycle, 8 (24). pp. 4003-4004. ISSN 15384101 (ISSN)

Vagin, V. V., Wohlschlegel, J., Qu, J., Jonsson, Z., Huang, X., Chuma, S., Girard, A., Sachidanandam, R., Hannon, G. J., Aravin, A. A. (2009) Proteomic analysis of murine Piwi proteins reveals a role for arginine methylation in specifying interaction with Tudor family members. Genes and Development, 23 (15). pp. 1749-1762. ISSN 08909369 (ISSN)

Vakoc, C. R., Blobel, G. A., Wen, Y.-Y., Gibbs, R. A., Johnstone, C. N., Rustgi, A. K. (March 2009) Low frequency of MLL3 mutations in colorectal carcinoma. Cancer Genetics and Cytogenetics, 189 (2). pp. 140-141. ISSN 0165-4608

Wais, M., Wu, C., Zahid, T., Sheppy, E., Gillis, J., del Campo, M., Wan, Q., Zhang, L. (2009) Repeated hypoxic episodes induce seizures and alter hippocampal network activities in mice. Neuroscience, 161 (2). pp. 599-613. ISSN 03064522 (ISSN)

Wang, L., Markley, J. L. (May 2009) Empirical correlation between protein backbone (15)N and (13)C secondary chemical shifts and its application to nitrogen chemical shift re-referencing. J Biomol NMR, 44 (2). p. 95. ISSN 1573-5001 (Electronic)

Wang, L., Uilecan, I. V., Assadi, A. H., Kozmik, C. A., Spalding, E. P. (April 2009) HYPOTrace: Image Analysis Software for Measuring Hypocotyl Growth and Shape Demonstrated on Arabidopsis Seedlings Undergoing Photomorphogenesis. Plant Physiol., 149 (4). pp. 1632-1637.

Wang, X., Xuan, Z., Zhao, X., Li, Y., Zhang, M. Q. (February 2009) High-resolution human core-promoter prediction with CoreBoost_HM. Genome Res, 19 (2). pp. 266-75.

Wang, Z, Wang, J, Chong, S, Lee, C (March 2009) Mining Potential Functionally Significant Polymorphisms at the ATP-Binding- Cassette Transporter Genes. Current Pharmacogenomics and Personalized Medicine: the international journal for expert reviews in pharmacogenomics, 7 (1). pp. 40-58. ISSN 1875-6921

Wang, Zihua, Sew, Pui-Hoon, Chong, Samuel S, Lee, Caroline GL (December 2009) Realtime exonuclease-mediated allelic discrimination (READ): a simple homogeneous genotyping assay for SNPs at the ABC gene loci. Pharmacogenomics, 10 (12). pp. 1995-2001. ISSN 1462-2416

Watson, J. D. (November 2009) Living with my personal genome. Personalized Medicine, 6 (6). p. 607. ISSN 1741-0541

Wee, Tse-Luen, Mau, Yi-Wen, Fang, Chia-Yi, Hsu, Hsiang-Ling, Han, Chau-Chung, Chang, Huan-Cheng (2009) Preparation and characterization of green fluorescent nanodiamonds for biological applications. Diamond and Related Materials, 18 (2-3). pp. 567-573. ISSN 0925-9635

Wei, F., Stein, J. C., Liang, C., Zhang, J., Fulton, R. S., Baucom, R. S., De Paoli, E., Zhou, S., Yang, L., Han, Y., Pasternak, S., Narechania, A., Zhang, L., Yeh, C. T., Ying, K., Nagel, D. H., Collura, K., Kudrna, D., Currie, J., Lin, J., Kim, H., Angelova, A., Scara, G., Wissotski, M., Golser, W., Courtney, L., Kruchowski, S., Graves, T. A., Rock, S. M., Adams, S., Fulton, L. A., Fronick, C., Courtney, W., Kramer, M., Spiegel, L., Nascimento, L., Kalyanaraman, A., Chaparro, C., Deragon, J. M., Miguel, P. S., Jiang, N., Wessler, S. R., Green, P. J., Yu, Y., Schwartz, D. C., Meyers, B. C., Bennetzen, J. L., Martienssen, R. A., McCombie, W. R., Aluru, S., Clifton, S. W., Schnable, P. S., Ware, D., Wilson, R. K., Wing, R. A. (November 2009) Detailed analysis of a contiguous 22-Mb region of the maize genome. PLoS genetics, 5 (11). e1000728. ISSN 1553-7404 (Electronic)1553-7390 (Linking)

Wei, F., Zhang, J., Zhou, S., He, R., Schaeffer, M., Collura, K., Kudrna, D., Faga, B. P., Wissotski, M., Golser, W., Rock, S. M., Graves, T. A., Fulton, R. S., Coe, E., Schnable, P. S., Schwartz, D. C., Ware, D. H., Clifton, S. W., Wilson, R. K., Wing, R. A. (November 2009) The physical and genetic framework of the maize b73 genome. PLoS Genet, 5 (11). e1000715. ISSN 1553-7404 (Electronic)

White, E., Lowe, S. W. (April 2009) Eating to exit: autophagy-enabled senescence revealed. Genes Dev, 23 (7). pp. 784-787. ISSN 0890-9369

Wilusz, J. E., Sunwoo, H., Spector, D. L. (July 2009) Long noncoding RNAs: functional surprises from the RNA world. Genes & Development, 23 (13). pp. 1494-1504. ISSN 0890-9369

Wood, L., Gray, N. W., Zhou, Z. L., Greenberg, M. E., Shepherd, G. M. G. (October 2009) Synaptic Circuit Abnormalities of Motor-Frontal Layer 2/3 Pyramidal Neurons in an RNA Interference Model of Methyl-CpG-Binding Protein 2 Deficiency. J Neurosci, 29 (40). pp. 12440-12448. ISSN 0270-6474

Wu, M. V., Manoli, D. S., Fraser, E. J., Coats, J. K., Tollkuhn, J., Honda, S., Harada, N., Shah, N. M. (October 2009) Estrogen masculinizes neural pathways and sex-specific behaviors. Cell, 139 (1). pp. 61-72. ISSN 1097-4172 (Electronic)0092-8674 (Linking)

Xu, M. Z., Yao, T. J., Lee, N. P. Y., Ng, I. O. L., Chan, Y. T., Zender, L., Lowe, S. W., Poon, R. T. P., Luk, J. M. (October 2009) Yes-Associated Protein Is an Independent Prognostic Marker in Hepatocellular Carcinoma. Cancer, 115 (19). pp. 4576-4585. ISSN 0008-543X

Xu, Q., Schlabach, M. R., Hannon, G. J., Elledge, S. J. (2009) Design of 240,000 orthogonal 25mer DNA barcode probes. Proceedings of the National Academy of Sciences of the United States of America, 106 (7). pp. 2289-2294. ISSN 00278424 (ISSN)

Xu, X. M., Wang, J., Benitez-Alfonso, Y., Jackson, D. P. (June 2009) Regulation of KNOTTED1 cell-to-cell trafficking by a chaperonin protein. Comparative Biochemistry and Physiology - Part A: Molecular & Integrative Physiology, 153 (2, Sup). S211.

Yazinski, Stephanie A, Westcott, Peter MK, Ong, Kelly, Pinkas, Jan, Peters, Rachel M, Weiss, Robert S (December 2009) Dual inactivation of Hus1 and p53 in the mouse mammary gland results in accumulation of damaged cells and impaired tissue regeneration. Proceedings of the National Academy of Sciences of the United States of America, 106 (50). pp. 21282-21287. ISSN 0027-8424

Yoon, S., Xuan, Z., Makarov, V., Ye, K., Sebat, J. (September 2009) Sensitive and accurate detection of copy number variants using read depth of coverage. Genome Res, 19. p. 9.

Youens-Clark, K., Faga, B. P., Yap, I. V., Stein, L. D., Ware, D. H. (November 2009) CMap 1.01: A comparative mapping application for the Internet. Bioinformatics, 25 (22). pp. 3040-3042.

Yu, S. R., Smirnova, J. B., Friedberg, E. C., Stillman, B., Akiyama, M., Owen-Hughes, T., Waters, R., Reed, S. H. (January 2009) ABF1-binding Sites Promote Efficient Global Genome Nucleotide Excision Repair. Journal of Biological Chemistry, 284 (2). pp. 966-973. ISSN 0021-9258

Zhang, L., Chia, J. M., Kumari, S., Stein, J. C., Liu, Z., Narechania, A., Maher, C. A., Guill, K., McMullen, M. D., Ware, D. H. (November 2009) A Genome-Wide Characterization of MicroRNA Genes in Maize. PLoS Genet, 5 (11). e1000716. ISSN 1553-7404 (Electronic)

Zhang, L., Hammell, M., Kudlow, B. A., Ambros, V., Han, M. (September 2009) Systematic analysis of dynamic miRNA-target interactions during C. elegans development. Development, 136 (18). pp. 3043-55. ISSN 0950-1991

Zhang, M. Q., Waterman, M. S., Zhang, X. (January 2009) The seventh Asia Pacific bioinformatics conference (APBC2009). BMC Bioinformatics, 10 (SUPPL.).

Zhang, N., Lyons, S., Lim, E., Lassota, P. (August 2009) A spontaneous acinar cell carcinoma model for monitoring progression of pancreatic lesions and response to treatment through noninvasive bioluminescence imaging. Clin Cancer Res, 15 (15). pp. 4915-24. ISSN 1078-0432 (Print)1078-0432 (Linking)

Zhang, X., Lian, Z., Padden, C., Gerstein, M. B., Rozowsky, J., Snyder, M., Gingeras, T. R., Kapranov, P., Weissman, S. M., Newburger, P. E. (March 2009) A myelopoiesis-associated regulatory intergenic noncoding RNA transcript within the human HOXA cluster. Blood, 113 (11). pp. 2526-34. ISSN 1528-0020 (Electronic)

Zhang, Y., Song, G., Vinar, T., Green, E. D., Siepel, A., Miller, W. (August 2009) Evolutionary history reconstruction for Mammalian complex gene clusters. J Comput Biol, 16 (8). pp. 1051-70. ISSN 1066-5277

Zhang, F., Moses, J. E. (April 2009) Benzyne click chemistry with in situ generated aromatic azides. Org Lett, 11 (7). pp. 1587-90. ISSN 1523-7052

Zhao, H., Zheng, X., Yuan, X., Wang, L., Wang, X., Zhong, Y., Xie, Z., Tully, T. (January 2009) ben Functions with Scamp during Synaptic Transmission and Long-Term Memory Formation in Drosophila. J Neurosci, 29 (2). pp. 414-424.

Zhao, R., Bodnar, M. S., Spector, D. L. (April 2009) Nuclear neighborhoods and gene expression. Current Opinion in Genetics & Development, 19 (2). pp. 172-179. ISSN 0959-437X

Zhong, H., Sia, G.-M., Sato, T. R., Gray, N. W., Mao, T., Khuchua, Z., Huganir, R. L., Svoboda, K. (May 2009) Subcellular Dynamics of Type II PKA in Neurons. Neuron, 62 (3). pp. 363-374.

Zhou, R., Czech, B., Brennecke, J., Sachidanandam, R., Wohlschlegel, J. A., Perrimon, N., Hannon, G. J. (2009) Processing of Drosophila endo-siRNAs depends on a specific Loquacious isoform. RNA, 15 (10). pp. 1886-1895. ISSN 13558382 (ISSN)

Zhou, S., Wei, F., Nguyen, J., Bechner, M., Potamousis, K., Goldstein, S., Pape, L., Mehan, M. R., Churas, C., Pasternak, S., Forrest, D. K., Wise, R., Ware, D. H., Wing, R. A., Waterman, M. S., Livny, M., Schwartz, D. C. (November 2009) A single molecule scaffold for the maize genome. PLoS Genet, 5 (11). e1000711. ISSN 1553-7404 (Electronic)

Zimin, A. V., Delcher, A. L., Florea, L., Kelley, D. R., Schatz, M. C., Puiu, D., Hanrahan, F., Pertea, G., Van Tassell, C. P., Sonstegard, T. S., Marçais, G., Roberts, M., Subramanian, P., Yorke, J. A., Salzberg, S. L. (2009) A whole-genome assembly of the domestic cow, Bos taurus. Genome Biology, 10 (4). ISSN 14747596 (ISSN)

Zink, M., Vollmayr, B., Gebicke-Haerter, P. J., Henn, F. A. (September 2009) Reduced expression of GABA transporter GAT3 in helpless rats, an animal model of depression. Neurochemical Research, 34 (9). pp. 1584-93. ISSN 0364-3190

Zito, K., Scheuss, V., Knott, G., Hill, T., Svoboda, K. (January 2009) Rapid Functional Maturation of Nascent Dendritic Spines. Neuron, 61 (2). pp. 247-258.

Zuber, J., Radtke, I., Pardee, T. S., Zhao, Z., Rappaport, A. R., Luo, W., McCurrach, M. E., Yang, M. M., Dolan, M. E., Kogan, S. C., Downing, J. R., Lowe, S. W. (April 2009) Mouse models of human AML accurately predict chemotherapy response. Genes Dev, 23 (7). pp. 877-89.

de Bivort, B. L., Guo, H.- F., Zhong, Y. (April 2009) Notch signaling is required for activity-dependent synaptic plasticity at the Drosophila neuromuscular junction. J Neurogenet, 23 (4). pp. 395-404. ISSN 1563-5260 (Electronic)

Book Section

Andresen, B. S., Krainer, A. R. (2009) When the genetic code is not enough: How sequence variations can affect pre-mRNA splicing and cause (complex) disease. In: Genetics of Complex Human Diseases: A Laboratory Manual. Cold Spring Harbor Laboratory Press, pp. 165-182. ISBN 9780879698836

Celaya, R. B., Pedmale, U. V., Liscum, E. (2009) Signaling in Plant Phototropism. In: Signaling in Plants. Springer Berlin Heidelberg, pp. 239-260. ISBN 9783540892281

Ewald, A., Werb, Z., Egeblad, M. (2009) Dynamic, Long-Term, In Vivo Imaging of Tumor-Stroma Interactions in Mouse Models of Breast Cancer Using Spinning-Disk Confocal Microscopy. In: Live Cell Imaging: A Laboratory Manual, Second Edition. Cold Spring Harbor Laboratory Press, New York, pp. 419-439. ISBN 9780879698935

Foster, Toshi M, Timmermans, Marja C. P. (2009) Axial Patterning of the Maize Leaf. In: Handbook of Maize: Its Biology. Springer New York, pp. 161-178. ISBN 978-0-387-79417-4

Jackson, D. P. (2009) Vegetative Shoot Meristem. In: Handbook of Maize: Its Biology. Springer, pp. 1-12. ISBN 978-0-387-79417-4

Stillman, B. (2009) Initiation of DNA replication. In: The Cell Division Cycle: Controlling when and where cells divide and differentiate, The Biomedical & Life Sciences Collection. Henry Stewart Talks Ltd, London.

Vinar, Tomas, Brejova, B., Song, Giltae, Siepel, Adam (2009) Reconstructing Histories of Complex Gene Clusters on a Phylogeny. In: Comparative Genomics. Lecture Notes in Computer Science, 5817 . Springer Berlin Heidelberg, pp. 150-163. ISBN 978-3-642-04743-5

Monograph

Stillman, Bruce (2009) Annual Report. Project Report. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY.

Conference or Workshop Item

Traina, TA, Theodoulou, M, Dugan, U, Feigin, K, Patil, S, Geneus, S, Godfrey, L, Norton, L, Hudis, C (2009) A novel capecitabine dosing schedule combined with bevacizumab is safe and active in patients with metastatic breast cancer: a phase II study. In: UNSPECIFIED.

Book

Navlakha, S., White, J., Nagarajan, N., Pop, M., Kingsford, C. (May 2009) Finding biologically accurate clusterings in hierarchical tree decompositions using the variation of information. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 5541 L . Springer, pp. 400-417. ISBN 03029743 (ISSN); 9783642020070 (ISBN)

Stewart, D., Stillman, B., Witkowski, J. (2009) Evolution: The Molecular Landscape. Cold Spring Harbor Laboratory Press.

Thesis

Chitwood, D. H. (2009) Patterning in Leaves via a Cascade of Small RNAs. PhD thesis, Cold Spring Harbor Laboratory.

John, K.A. (March 2009) Characterization of the role of DOCK7 in neuronal development. PhD thesis, Cold Spring Harbor Laboratory.

Wilusz, J. E. (March 2009) 3’ end processing of long nuclear-retained non-coding RNAs yields tRNA-like small RNAs. PhD thesis, Cold Spring Harbor Laboratory.

Patent

Michael Wigler (2009) Use of representations of DNA for genetic analysis. United States Patent 7531307. .

Video

Ewald, A. J., Werb, Z., Egeblad, M. (2009) Myeloid cells extravasate and infiltrate late carcinoma lesions. [Video]

Ewald, A. J., Werb, Z., Egeblad, M. (2009) c-fms+ myeloid cells migrate in response to wounding on the surface of a normal mammary gland. [Video]