Items where Subject is "bioinformatics > genomics and proteomics > annotation > map annotation"

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Number of items at this level: 54.

A

Amid, C., Frankish, A., Aken, B., Ezkurdia, I., Kokocinsk, F., Gilbert, J., White, S., Carninci, P., Gingeras, T. R., Guigo, R., Searle, S., Tress, M. L., Harrow, J., Hubbard, T. (2010) From identification to validation to gene count. Genome Biology, 11 (Suppl ). ISSN 1474-760X

Aravin, A. A., Gaidatzis, D., Pfeffer, S., Lagos-Quintana, M., Landgraf, P., Iovino, N., Morris, P., Brownstein, M. J., Kuramochi-Miyagawa, S., Nakano, T., Chien, M. C., Russo, J. J., Ju, J. Y., Sheridan, R., Sander, C., Zavolan, M. , Tuschl, T. (2006) A novel class of small RNAs bind to MILI protein in mouse testes. Nature, 442 (7099). pp. 203-7. ISSN 1476-4687 (Electronic)

B

Bohland, J. W., Bokil, H., Allen, C. B., Mitra, P. P. (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. (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

C

Cawley, S., Bekiranov, S., Ng, H. H., Kapranov, P., Sekinger, E. A., Kampa, D., Piccolboni, A., Sementchenko, V., Cheng, J., Williams, A. J., Wheeler, R., Wong, B., Drenkow, J., Yamanaka, M., Patel, S., Brubaker, S., Tammana, H., Helt, G., Struhl, K., Gingeras, T. R. (2004) Unbiased Mapping of Transcription Factor Binding Sites along Human Chromosomes 21 and 22 Points to Widespread Regulation of Noncoding RNAs. Cell, 116 (4). pp. 499-509. ISSN 0092-8674

Coghlan, A., Eichler, E. E., Oliver, S. G., Paterson, A. H., Stein, L. D. (2005) Chromosome evolution in eukaryotes: a multi-kingdom perspective. Trends in Genetics, 21 (12). pp. 673-682. ISSN 0168-9525

Colicelli, J., Field, J., Ballester, R., Chester, N., Young, D., Wigler, M. H. (1990) Mutational mapping of RAS-responsive domains of the Saccharomyces cerevisiae adenylyl cyclase. Molecular & Cellular Biology, 10 (6). pp. 2539-43. ISSN 0270-7306

D

Dalloul, R. A., Long, J. A., Zimin, A. V., Aslam, L., Beal, K., Blomberg, L. A., Bouffard, P., Burt, D. W., Crasta, O., Crooijmans, R. P. M. A., Cooper, K., Coulombe, R. A., De, S., Delany, M. E., Dodgson, J. B., Dong, J. J., Evans, C., Frederickson, K. M., Flicek, P., Florea, L., Folkerts, O., Groenen, M. A. M., Harkins, T. T., Herrero, J., Hoffmann, S., Megens, H. J., Jiang, A., de Jong, P., Kaiser, P., Kim, H., Kim, K. W., Kim, S., Langenberger, D., Lee, M. K., Lee, T., Mane, S., Marcais, G., Marz, M., McElroy, A. P., Modise, T., Nefedov, M., Notredame, C., Paton, I. R., Payne, W. S., Pertea, G., Prickett, D., Puiu, D., Qioa, D., Raineri, E., Ruffier, M., Salzberg, S. L., Schatz, M. C., Scheuring, C., Schmidt, C. J., Schroeder, S., Searle, S. M. J., Smith, E. J., Smith, J., Sonstegard, T. S., Stadler, P. F., Tafer, H., Tu, Z., van Tassell, C. P., Vilella, A. J., Williams, K. P., Yorke, J. A., Zhang, L., Zhang, H. B., Zhang, X., Zhang, Y., Reed, K. M. (2010) Multi-platform next-generation sequencing of the domestic Turkey (Meleagris gallopavo): Genome assembly and analysis. PLoS Biology, 8 (9). ISSN 1544-9173

Denoeud, F., Kapranov, P., Ucla, C., Frankish, A., Castelo, R., Drenkow, J., Lagarde, J., Alioto, T., Manzano, C., Chrast, J., Dike, S., Wyss, C., Henrichsen, C. N., Holroyd, N., Dickson, M. C., Taylor, R., Hance, Z., Foissac, S., Myers, R. M., Rogers, J., Hubbard, T., Harrow, J., Guigó, R., Gingeras, T. R., Antonarakis, S. E., Reymond, A. (2007) Prominent use of distal 5′ transcription start sites and discovery of a large number of additional exons in ENCODE regions. Genome Research, 17 (6). pp. 746-759. ISSN 10889051 (ISSN)

G

Gao, M. Q., Li, G. Y., McCombie, W. R., Quiros, C. F. (2005) Comparative analysis of a transposon-rich Brassica oleracea BAC clone with its corresponding sequence in A-thaliana. Theoretical and Applied Genetics, 111 (5). pp. 949-955. ISSN 0040-5752

H

Hamaguchi, M., O'Connor, E. A., Chen, T., Parnell, L., McCombie, R. W., Wigler, M. H. (1998) Rapid isolation of cDNA by hybridization. Proceedings of the National Academy of Sciences of the United States of America, 95 (7). pp. 3764-9. ISSN 0027-8424

He, L., Hannon, G. J. (2004) MicroRNAs: Small RNAs with a big role in gene regulation. Nature Reviews Genetics, 5 (8). pp. 522-532. ISSN 1471-0056

Hodges, E., Smith, A. D., Kendall, J. T., Xuan, Z., Ravi, K., Rooks, M., Zhang, M. Q., Ye, K., Bhattacharjee, A., Brizuela, L., McCombie, W. R., Wigler, M. H., Hannon, G. J., Hicks, J. B. (2009) High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing. Genome Research, 19 (9). pp. 1593-1605. ISSN 1088-9051

I

Iossifov, I., Zheng, T., Baron, M., Gilliam, T. C., Rzhetsky, A. (2008) Genetic-linkage mapping of complex hereditary disorders to a whole-genome molecular-interaction network. Genome Res, 18 (7). pp. 1150-62. ISSN 1088-9051 (Print)1088-9051 (Linking)

J

Jenik, P. D., Gillmor, C. S., Lukowitz, W. (2007) Embryonic patterning in Arabidopsis thaliana. Annu Rev Cell Dev Biol, 23. pp. 207-236. ISSN 1081-0706 (Print)

K

Kampa, D., Kapranov, P., Cawley, S., Bekiranov, S., Ng, H. H., Sekinger, E. A., Piccolboni, A., Sementchenko, V., Cheng, J., Drenkow, J., Yamanaka, M., Patel, S., Brubaker, S., Tammana, H., Narayanan, B., Helt, G., Struhl, K., Gingeras, T. R. (2003) Global mapping of functionally-important and regulatory regions on human chromosomes 21 and 22 reveal novel regulatory networks in the human genome. American Journal of Human Genetics, 73 (5). p. 185. ISSN 0002-9297

Kapranov, P., Cawley, S. E., Drenkow, J., Bekiranov, S., Strausberg, R. L., Fodor, S. P. A., Gingeras, T. R. (2002) Large-scale transcriptional activity in chromosomes 21 and 22. Science, 296 (5569). pp. 916-919. ISSN 00368075 (ISSN)

Kapranov, P., Cheng, J., Dike, S., Nix, D. A., Duttagupta, R., Willingham, A. T., Stadler, P. F., Hertel, J., Hackermüller, J., Hofacker, I. L., Bell, I., Cheung, E., Drenkow, J., Dumais, E., Patel, S., Helt, G., Ganesh, M., Ghosh, S., Piccolboni, A., Sementchenko, V., Tammana, H., Gingeras, T. R. (2007) RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science, 316 (5830). pp. 1484-1488. ISSN 00368075 (ISSN)

Kendall, J. T., Liu, Q. A., Bakleh, A., Krasnitz, A., Nguyen, K. C. Q., Lakshmi, B., Gerald, W., Powers, S., Mu, D. (2007) Oncogenic cooperation and coamplification of developmental transcription factor genes in lung cancer. Proc Natl Acad Sci U S A, 104 (42). pp. 16663-16668. ISSN 0027-8424 (Print)

Kepecs, A., Raghavachari, S. (2007) Gating information by two-state membrane potential fluctuations. J Neurophysiol, 97 (4). pp. 3015-23. ISSN 0022-3077 (Print)

Klejman, M. P., Zhao, X. M., van Schaik, F. M. A., Herr, W., Timmers, H. T. M. (2005) Mutational analysis of BTAF1-TBP interaction: BTAF1 can rescue DNA-binding defective TBP mutants. Nucleic Acids Research, 33 (17). pp. 5426-5436. ISSN 0305-1048

Koulakov, A. A., Tsigankov, D. N. (2004) A stochastic model for retinocollicular map development. BMC Neurosci, 5. p. 30. ISSN 1471-2202 (Electronic)

Krapivsky, P. L., Ben-Naim, E., Grosse, I. R. (2004) Stable distributions in stochastic fragmentation. Journal of Physics a-Mathematical and General, 37 (8). pp. 2863-2880. ISSN 0305-4470

L

Landgraf, P., Rusu, M., Sheridan, R., Sewer, A., Iovino, N., Aravin, A. A., Pfeffer, S., Rice, A., Kamphorst, A. O., Landthaler, M., Lin, C., Socci, N. D., Hermida, L., Fulci, V., Chiaretti, S., Foa, R., Schliwka, J., Fuchs, U., Novosel, A., Muller, R. U., Schermer, B., Bissels, U., Inman, J., Phan, Q., Chien, M. C., Weir, D. B., Choksi, R., De Vita, G., Frezzetti, D., Trompeter, H. I., Hornung, V., Teng, G., Hartmann, G., Palkovits, M., Di Lauro, R., Wernet, P., Macino, G., Rogler, C. E., Nagle, J. W., Ju, J. Y., Papavasiliou, F. N., Benzing, T., Lichter, P., Tam, W., Brownstein, M. J., Bosio, A., Borkhardt, A., Russo, J. J., Sander, C., Zavolan, M., Tuschl, T. (2007) A mammalian microRNA expression atlas based on small RNA library sequencing. Cell, 129 (7). pp. 1401-1414. ISSN 0092-8674

Li, G., Ruan, X. A., Auerbach, R. K., Sandhu, K. S., Zheng, M., Wang, P. C., Poh, H. M., Goh, Y., Lim, J., Zhang, J., Sim, H. S., Peh, S. Q., Mulawadi, F. H., Ong, C. T., Orlov, Y. L., Hong, S., Zhang, Z., Landt, S. G., Raha, D., Euskirchen, G., Wei, C-L., Ge, W., Wang, H., Davis, C. A., Fisher-Aylor, K. I., Mortazavi, A., Gerstein, M., Gingeras, T. R., Wold, B., Sun, Yi, Fullwood, M. J., Cheung, E., Liu, E., Sung, W.-K., Snyder, M., Ruan, Y. (2012) Extensive Promoter-Centered Chromatin Interactions Provide a Topological Basis for Transcription Regulation. Cell, 148 (1–2). pp. 84-98. ISSN 0092-8674

Lin, H. H., Lin, C. Y., Chiang, A. S. (2007) Internal representations of smell in the Drosophila brain. Journal of Biomedical Science, 14 (4). pp. 453-459. ISSN 1021-7770

Lin, J., Schatz, M. C. (2010) Design patterns for efficient graph algorithms in MapReduce. 8th Workshop on Mining and Learning with Graphs, MLG'10 . MLG, pp. 78-85. ISBN 9781450302142 (ISBN)

Lisitsyn, N. A., Segre, J. A., Kusumi, K., Lisitsyn, N. M., Nadeau, J. H., Frankel, W. N., Wigler, M. H., Lander, E. S. (1994) Direct isolation of polymorphic markers linked to a trait by genetically directed representational difference analysis. Nat Genet, 6 (1). pp. 57-63. ISSN 1061-4036 (Print)

Luna, R., Hernandez, A., Brody, C. D., Romo, R. (2005) Neural codes for perceptual discrimination in primary somatosensory cortex. Nature Neuroscience, 8 (9). pp. 1210-1219. ISSN 1097-6256

M

Machens, C. K., Romo, R., Brody, C. D. (2005) Flexible control of mutual inhibition: a neural model of two-interval discrimination. Science, 307 (5712). pp. 1121-4. ISSN 1095-9203 (Electronic)

Martienssen, R. A., Zaratiegui, M., Goto, D. B. (2005) RNA interference and heterochromatin in the fission yeast Schizosaccharomyces pombe. Trends Genet, 21 (8). pp. 450-6. ISSN 0168-9525 (Print)

Matsumoto, T., Wu, J. Z., Kanamori, H., Katayose, Y., Fujisawa, M., Namiki, N., Mizuno, H., Yamamoto, K., Antonio, B. A., Baba, T., Sakata, K., Nagamura, Y., Aoki, H., Arikawa, K., Arita, K., Bito, T., Chiden, Y., Fujitsuka, N., Fukunaka, R., Hamada, M., Harada, C., Hayashi, A., Hijishita, S., Honda, M., Hosokawa, S., Ichikawa, Y., Idonuma, A., Iijima, M., Ikeda, M., Ikeno, M., Ito, K., Ito, S., Ito, T., Ito, Y., Ito, Y., Iwabuchi, A., Kamiya, K., Karasawa, W., Kurita, K., Katagiri, S., Kikuta, A., Kobayashi, H., Kobayashi, N., Machita, K., Maehara, T., Masukawa, M., Mizubayashi, T., Mukai, Y., Nagasaki, H., Nagata, Y., Naito, S., Nakashima, M., Nakama, Y., Nakamichi, Y., Nakamura, M., Meguro, A., Negishi, M., Ohta, I., Ohta, T., Okamoto, M., Ono, N., Saji, S., Sakaguchi, M., Sakai, K., Shibata, M., Shimokawa, T., Song, J. Y., Takazaki, Y., Terasawa, K., Tsugane, M., Tsuji, K., Ueda, S., Waki, K., Yamagata, H., Yamamoto, M., Yamamoto, S., Yamane, H., Yoshiki, S., Yoshihara, R., Yukawa, K., Zhong, H. S., Yano, M., Sasaki, T., Yuan, Q. P., Shu, O. T., Liu, J., Jones, K. M., Gansberger, K., Moffat, K., Hill, J., Bera, J., Fadrosh, D., Jin, S. H., Johri, S., Kim, M., Overton, L., Reardon, M., Tsitrin, T., Vuong, H., Weaver, B. (2005) The map-based sequence of the rice genome. Nature, 436 (7052). pp. 793-800. ISSN 0028-0836

McKay, S. J., Vergara, I. A., Stajich, J. E. (2010) Using the Generic Synteny Browser (GBrowse_syn). Curr Protoc Bioinformatics, Chapte. Unit 9 12. ISSN 1934-340X (Electronic) 1934-3396 (Linking)

Meyers, D. A., Antonarakis, S. E., Fearon, E. R., Mallonee, R. L., Waber, P. G., Phillips, J. A., Kazazian, H. H., Levine, M., Kronenberg, H. M., Wigler, M. H., Ullrich, A. (1984) Use of DNA Polymorphisms to Establish the Linkage Map of the Pth, Beta-Globin, C-Ha-Ras-1, and Insulin Loci on 11p. Cytogenetics and Cell Genetics, 37 (1-4). pp. 540-541. ISSN 0301-0171

Miller, R. D., Phillips, M. S., Jo, I., Donaldson, M. A., Studebaker, J. F., Addleman, N., Alfisi, S. V., Ankener, W. M., Bhatti, H. A., Callahan, C. E., Carey, B. J., Conley, C. L., Cyr, J. M., Derohannessian, V., Donaldson, R. A., Elosua, C., Ford, S. E., Forman, A. M., Gelfand, C. A., Grecco, N. M., Gutendorf, S. M., Hock, C. R., Hozza, M. J., Hur, S., In, S. M., Jackson, D. L., Jo, S. A., Jung, S. C., Kim, S., Kimm, K., Kloss, E. F., Koboldt, D. C., Kuebler, J. M., Kuo, F. S., Lathrop, J. A., Lee, J. K., Leis, K. L., Livingston, S. A., Lovins, E. G., Lundy, M. L., Maggan, S., Minton, M., Mockler, M. A., Morris, D. W., Nachtman, E. P., Oh, B., Park, C., Park, C. W., Pavelka, N., Perkins, A. B., Restine, S. L., Sachidanandam, R., Reinhart, A. J., Scott, K. E., Restine, S. L., Sachidanandam, R., Reinhart, A. J., Scott, K. E., Shah, G. J., Tate, J. M., Varde, S. A., Walters, A., White, J. R., Yoo, Y. K., Lee, J. E., Boyce-Jacino, M. T., Kwok, P. Y. (2005) High-density single-nucleotide polymorphism maps of the human genome. Genomics, 86 (2). pp. 117-126. ISSN 0888-7543

Miyamichi, K., Amat, F., Moussavi, F., Wang, C., Wickersham, I., Wall, N. R., Taniguchi, H., Tasic, B., Huang, Z. J., He, Z., Callaway, E. M., Horowitz, M. A., Luo, L. (2010) Cortical representations of olfactory input by trans-synaptic tracing. Nature, 472 (7342). pp. 191-196. ISSN 0028-0836

Mizuno, H., Atwal, G. S., Wang, H., Levine, A. J., Vazquez, A. (2010) Fine-scale detection of population-specific linkage disequilibrium using haplotype entropy in the human genome. BMC Genet, 11. p. 27. ISSN 1471-2156 (Electronic) 1471-2156 (Linking)

N

Newey, S. E., Velamoor, V., Govek, E.-E., Van Aelst, L. (2005) Rho GTPases, dendritic structure, and mental retardation. J Neurobiol, 64 (1). pp. 58-74. ISSN 0022-3034 (Print)

R

Rabin, M., Birnbaum, D., Young, D., Birchmeier, C., Wigler, M. H., Ruddle, F. H. (1987) Human ROS1 and MAS1 oncogenes located in regions of chromosome 6 associated with tumor-specific rearrangements. Oncogene Res, 1 (2). pp. 169-78. ISSN 0890-6467 (Print)

Rada-Iglesias, A., Ameur, A., Kapranov, P., Enroth, S., Komorowski, J., Gingeras, T. R., Wadelius, C. (2008) Whole-genome maps of USF1 and USF2 binding and histone H3 acetylation reveal new aspects of promoter structure and candidate genes for common human disorders. Genome Research, 18 (3). pp. 380-92. ISSN 10889051 (ISSN)

Ramani, A. K., Nelson, A. C., Kapranov, P., Bell, I., Gingeras, T. R., Fraser, A. G. (2009) High resolution transcriptome maps for wild-type and nonsense-mediated decay-defective Caenorhabditis elegans. Genome Biology, 10 (9). R101. ISSN 1474-7596

Ruthazer, E. S., Cline, H. T. (2004) Insights into activity-dependent map formation from the retinotectal system: a middle-of-the-brain perspective. J Neurobiol, 59 (1). pp. 134-46. ISSN 0022-3034 (Print)

S

Sato, T. R., Gray, N. W., Mainen, Z. F., Svoboda, K. (2007) The Functional Microarchitecture of the Mouse Barrel Cortex. PLoS Biology, 5 (7). e189.

Shepherd, G. M., Svoboda, K. (2005) Laminar and columnar organization of ascending excitatory projections to layer 2/3 pyramidal neurons in rat barrel cortex. J Neurosci, 25 (24). pp. 5670-9. ISSN 0270-6474

Stein, L. D. (2004) Using the Reactome database. Curr Protoc Bioinformatics, Chapte. Unit 8.7.

T

Tsigankov, D. N., Koulakov, A. A. (2006) A unifying model for activity-dependent and activity-independent mechanisms predicts complete structure of topographic maps in ephrin-A deficient mice. J Comput Neurosci, 21 (1). pp. 101-14. ISSN 0929-5313 (Print)

U

Uchida, N., Kepecs, A., Mainen, Z. F. (2006) Seeing at a glance, smelling in a whiff: rapid forms of perceptual decision making. Nature Reviews Neuroscience, 7 (6). pp. 485-91. ISSN 1471-0048

V

Varshney, R. K., Penmetsa, R. V., Dutta, S., Kulwal, P. L., Saxena, R. K., Datta, S., Sharma, T. R., Rosen, B., Carrasquilla-Garcia, N., Farmer, A. D., Dubey, A., Saxena, K. B., Gao, J., Fakrudin, B., Singh, M. N., Singh, B. P., Wanjari, K. B., Yuan, M., Srivastava, R. K., Kilian, A., Upadhyaya, H. D., Mallikarjuna, N., Town, C. D., Bruening, G. E., He, G., May, G. D., McCombie, W. R., Jackson, S. A., Singh, N. K., Cook, D. R. (2010) Pigeonpea genomics initiative (PGI): An international effort to improve crop productivity of pigeonpea (Cajanus cajan L.). Molecular Breeding, 26 (3). pp. 393-408.

W

Walhout, A. J., Sordella, R., Lu, X., Hartley, J. L., Temple, G. F., Brasch, M. A., Thierry-Mieg, N., Vidal, M. (2000) Protein interaction mapping in C. elegans using proteins involved in vulval development. Science, 287 (5450). pp. 116-22. ISSN 0036-8075 (Print)

Whipple, C. J., Hall, D. H., DeBlasio, S. L., Taguchi-Shiobara, F., Schmidt, R. J., Jackson, D. P. (2010) A Conserved Mechanism of Bract Suppression in the Grass Family. Plant Cell. ISSN 1532-298X (Electronic) 1040-4651 (Linking)

Willingham, A. T., Dike, S., Cheng, J., Manak, J. R., Bell, I., Cheung, E., Drenkow, J., Dumais, E., Duttagupta, R., Ganesh, M., Ghosh, S., Helt, G., Nix, D., Piccolboni, A., Sementchenko, V., Tammana, H., Kapranov, P., Gingeras, T. R. (2006) Transcriptional landscape of the human and fly genomes: Nonlinear and multifunctional modular model of transcriptomes. Cold Spring Harbor Symposia on Quantitative Biology, 71. pp. 101-110. ISSN 00917451 (ISSN)

Wing, R. A., Ammiraju, J. S. S., Luo, M. Z. X., Kim, H., Yu, Y. S., Kudrna, D., Goicoechea, J. L., Wang, W. M., Nelson, W., Rao, K., Brar, D., Mackill, D. J., Han, B., Soderlund, C., Stein, L., SanMiguel, P., Jackson, S. (2005) The Oryza Map Alignment Project: The golden path to unlocking the genetic potential of wild rice species. Plant Molecular Biology, 59 (1). pp. 53-62. ISSN 0167-4412

Wu, J., Anczukow, O., Krainer, A. R., Zhang, M. Q., Zhang, C. (2013) OLego: fast and sensitive mapping of spliced mRNA-Seq reads using small seeds. Nucleic Acids Research, 41 (10). pp. 5149-5163. ISSN 03051048 (ISSN)

Z

Zador, A. M., Agmon-Snir, H., Segev, I. (1995) The morphoelectrotonic transform: A graphical approach to dendritic function. Journal of Neuroscience, 15 (3 I). pp. 1669-1682. ISSN 02706474 (ISSN)

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