Items where Subject is "bioinformatics > genomics and proteomics > databases > databases"

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Number of items at this level: 56.

A

Aloy, P., Gavin, A. C., Ideker, T., Walhout, M. (2010) SYSTEMS BIOLOGY: NETWORKS. In: Joint Cold Spring Harbor Laboratory/Wellcome Trust Conference on SYSTEMS BIOLOGY: NETWORKS, August 11–August 15, 2010, Wellcome Trust Conference Center, Hixton UK.

Arnaiz, Olivier, Cain, Scott, Cohen, Jean, Sperling, Linda (2007) ParameciumDB: a community resource that integrates the Paramecium tetraurelia genome sequence with genetic data. Nucleic Acids Res, 35. D439-D444. ISSN 0305-1048

B

Benfey, P., Carpenter, A., Waterston, W., Ohler, U. (2010) AUTOMATED IMAGING & HIGH-THROUGHPUT PHENOTYPING. In: 2010 meeting on Automated Imaging and high througput phenotyping, December 5–December 8, 2010, Cold Spring Harbor Laboratory.

Bieri, T., Blasiar, D., Ozersky, P., Antoshechkin, I., Bastiani, C., Canaran, P., Chan, J., Chen, N., Chen, W. J., Davis, P., Fiedler, T. J., Girard, L. R., Han, M., Harris, T. W., Kishore, R., Lee, R., McKay, S. J., Müller, H- M., Nakamura, C., Petcherski, A., Rangarajan, A., Rogers, A., Schindelman, G., Schwarz, E. M., Spooner, W., Tuli, M. A., Van Auken, K., Wang, D., Wang, X., Williams, G., Durbin, R., Stein, L. D., Sternberg, P. W., Spieth, J. (2007) WormBase: new content and better access. Nucleic Acids Res, 35 (Databa). D506-D510. ISSN 0305-1048

Boyle, B., Hopkins, N., Lu, Z. Y., Garay, J. A. R., Mozzherin, D., Rees, T., Matasci, N., Narro, M. L., Piel, W. H., McKay, S. J., Lowry, S., Freeland, C., Peet, R. K., Enquist, B. J. (2013) The taxonomic name resolution service: an online tool for automated standardization of plant names. BMC Bioinformatics, 14. ISSN 1471-2105

Brenner, E. D., Katari, M. S., Stevenson, D. W., Rudd, S. A., Douglas, A. W., Moss, W. N., Twigg, R. W., Runko, S. J., Stellari, G. M., McCombie, W. R., Coruzzi, G. M. (2005) EST analysis in Ginkgo biloba: an assessment of conserved developmental regulators and gymnosperm specific genes. BMC Genomics, 6. p. 143. ISSN 1471-2164

C

Canaran, P., Stein, L. D., Ware, D. H. (2006) Look-Align: an interactive web-based multiple sequence alignment viewer with polymorphism analysis support. Bioinformatics, 22 (7). pp. 885-6. ISSN 1367-4803 (Print)

Chen, N., Harris, T. W., Antoshechkin, I., Bastiani, C., Bieri, T., Blasiar, D., Bradnam, K., Canaran, P., Chan, J., Chen, C.-K., Chen, W. J., Cunningham, F., Davis, P., Kenny, E., Kishore, Ra.., Lawson, D., Lee, R., Muller, H. M., Nakamura, Ce., Pai, S., Ozersky, P., Petcherski, A., Rogers, An., Sabo, A., Schwarz, Er. M., Van Auken, K., Wang, Q., Durbin, R., Spieth, J., Sternberg, P. W., Stein, L. D. (2005) WormBase: a comprehensive data resource for Caenorhabditis biology and genomics. Nucleic Acids Res, 33 (Databa). D383-9. ISSN 1362-4962 (Electronic)

Chen, N., Pai, S., Zhao, Z., Mah, A., Newbury, R., Johnsen, R. C., Altun, Z., Moerman, D. G., Baillie, D. L., Stein, L. D. (2005) Identification of a nematode chemosensory gene family. Proc Natl Acad Sci U S A, 102 (1). pp. 146-51. ISSN 0027-8424 (Print)

Chen, N., Stein, L. D. (2006) Conservation and functional significance of gene topology in the genome of Caenorhabditis elegans. Genome Res, 16 (5). pp. 606-17. ISSN 1088-9051 (Print)

Cokol, M., Weinstein, Z. B., Yilancioglu, K., Tasan, M., Doak, A., Cansever, D., Mutlu, B., Li, S., Rodriguez-Esteban, R., Akhmedov, M., Guvenek, A., Cokol, M., Cetiner, S., Giaever, G., Iossifov, I., Nislow, C., Shoichet, B., Roth, F. P. (2014) Large-Scale Identification and Analysis of Suppressive Drug Interactions. Chemistry & Biology, 21 (4). pp. 541-551. ISSN 1074-5521

Croft, D., Mundo, A. F., Haw, R., Milacic, M., Weiser, J., Wu, G., Caudy, M., Garapati, P., Gillespie, M., Kamdar, M. R., Jassal, B., Jupe, S., Matthews, L., May, B., Palatnik, S., Rothfels, K., Shamovsky, V., Song, H., Williams, M., Birney, E., Hermjakob, H., Stein, L., D'Eustachio, P. (2014) The Reactome pathway knowledgebase. Nucleic Acids Research, 42 (Databa). D472-7. ISSN 0305-1048

Croft, D., O'Kelly, G., Wu, G., Haw, R., Gillespie, M., Matthews, L., Caudy, M., Garapati, P., Gopinath, G., Jassal, B., Jupe, S., Kalatskaya, I., MayMahajan, S., May, B., Ndegwa, N., Schmidt, E., Shamovsky, V., Yung, C., Birney, E., Hermjakob, H., D'Eustachio, P., Stein, L. D. (2011) Reactome: A database of reactions, pathways and biological processes. Nucleic Acids Research, 39 (SUPPL.).

D

Das, R., Dimitrova, N., Xuan, Z. Y., Rollins, R. A., Haghighi, F., Edwards, J. R., Ju, J. Y., Bestor, T. H., Zhang, M. Q. (2006) Computational prediction of methylation status in human genomic sequences. Proc Natl Acad Sci U S A, 103 (28). pp. 10713-6. ISSN 0027-8424 (Print)

Dong, D. L., Liu, R., Sherlock, R., Wigler, M. H., Nestler, H. P. (1999) Molecular forceps from combinatorial libraries prevent the farnesylation of Ras by binding to its carboxyl terminus. Chem Biol, 6 (3). pp. 133-41. ISSN 1074-5521 (Print)

d'Alencon, E., Negre, N., Stanojcic, S., Alassoeur, B., Gimenez, S., Leger, A., Abd-Alla, A., Juliant, S., Fournier, P. (2011) Characterization of a CENP-B homolog in the holocentric Lepidoptera Spodoptera frugiperda. Gene, 485 (2). pp. 91-101. ISSN 0378-1119

de la Bastide, M., McCombie, W. R. (2007) Assembling genomic DNA sequences with PHRAP. Current Protocols in Bioinformatics (Unit 1). ISSN 1934-340X (Electronic)1934-3396 (Linking)

E

Eilbeck, K., Lewis, S. E., Mungall, C. J., Yandell, M., Stein, L. D., Durbin, R., Ashburner, M. (2005) The Sequence Ontology: a tool for the unification of genome annotations. Genome Biology, 6 (5). ISSN 1465-6914

G

Guberman, J. M., Ai, J., Arnaiz, O., Baran, J., Blake, A., Baldock, R., Chelala, C., Croft, D., Cros, A., Cutts, R. J., Di Génova, A., Forbes, S., Fujisawa, T., Gadaleta, E., Goodstein, D. M., Gundem, G., Haggarty, B., Haider, S., Hall, M., Harris, T., Haw, R., Hu, S., Hubbard, S., Hsu, J., Iyer, V., Jones, P., Katayama, T., Kinsella, R., Kong, L., Lawson, D., Liang, Y., Lopez-Bigas, N., Luo, J., Lush, M., Mason, J., Moreews, F., Ndegwa, N., Oakley, D., Perez-Llamas, C., Primig, M., Rivkin, E., Rosanoff, S., Shepherd, R., Simon, R., Skarnes, B., Smedley, D., Sperling, L., Spooner, W., Stevenson, P., Stone, K., Teague, J., Wang, J., Whitty, B., Wong, D. T., Wong-Erasmus, M., Yao, L., Youens-Clark, K., Yung, C., Zhang, J., Kasprzyk, A. (2011) BioMart Central Portal: an open database network for the biological community. Database : the journal of biological databases and curation, 2011. ISSN 17580463 (ISSN)

H

Healy, J., Thomas, E. E., Schwartz, J. T., Wigler, M. H. (2003) Annotating large genomes with exact word matches. Genome Research, 13 (10). pp. 2306-2315. ISSN 1088-9051

J

Jiang, C., Xuan, Z. Y., Zhao, F., Zhang, M. Q. (2007) TRED: a transcriptional regulatory element database, new entries and other development. Nucleic Acids Res, 35 (Databa). D137-D140. ISSN 0305-1048

Joshi-Tope, G., Vastrik, I., Gopinath, G. R., Matthews, L., Schmidt, E., Gillespie, M., D'Eustachio, P., Jassal, B., Lewis, S., Wu, G., Birney, E., Stein, L. (2003) The genome knowledgebase: A resource for biologists and bioinformaticists. Cold Spring Harbor Symposia on Quantitative Biology, 68. pp. 237-243. ISSN 0091-7451

K

Kersey, P. J., Allen, J. E., Christensen, M., Davis, P., Falin, L. J., Grabmueller, C., Hughes, D. S., Humphrey, J., Kerhornou, A., Khobova, J., Langridge, N., McDowall, M. D., Maheswari, U., Maslen, G., Nuhn, M., Ong, C. K., Paulini, M., Pedro, H., Toneva, I., Tuli, M. A., Walts, B., Williams, G., Wilson, D., Youens-Clark, K., Monaco, M. K., Stein, J., Wei, X., Ware, D., Bolser, D. M., Howe, K. L., Kulesha, E., Lawson, D., Staines, D. M. (2014) Ensembl Genomes 2013: scaling up access to genome-wide data. Nucleic Acids Research, 42 (Databa). D546-52. ISSN 0305-1048

Kim, Y. C., Jung, Y. C., Xuan, Z., Dong, H., Zhang, M. Q., Wang, S. M. (2006) Pan-genome isolation of low abundance transcripts using SAGE tag. Febs Letters, 580 (28-29). pp. 6721-6729. ISSN 0014-5793

Kinney, J. B., Atwal, G. S. (2014) Equitability, mutual information, and the maximal information coefficient. Proceedings of the National Academy of Sciences of the United States of America, 111 (9). pp. 3354-9. ISSN 0027-8424

L

Latter, G. I., Boutell, T., Monardo, P. J., Kobayashi, R., Futcher, B., McLaughlin, C. S., Garrels, J. I. (1995) A Saccharomyces cerevisiae Internet protein resource now available. Electrophoresis, 16 (7). pp. 1170-4.

Lawrence, Carolyn J., Ware, Doreen (2008) Databases and data mining. In: Handbook of Maize: History and Practice of Genetics and Genomics. Springer Science + Business Media LLC, pp. 659-672. ISBN 978-0-387-77862-4

Liang, C., Jaiswal, P., Hebbard, C., Avraham, S., Buckler, E. S., Casstevens, T., Hurwitz, B. L., McCouch, S., Ni, J., Pujar, A., Ravenscroft, D., Ren, L., Spooner, W., Tecle, I., Thomason, J., Tung, C. W., Wei, X., Yap, I., Youens-Clark, K., Ware, D. H., Stein, L. D. (2008) Gramene: a growing plant comparative genomics resource. Nucleic Acids Res, 36 (Databa). D947-53.

Liu-Sullivan, N., Zhang, J., Bakleh, A., Marchica, J., Li, J., Siolas, D., Laquerre, S., Degenhardt, Y. Y., Wooster, R., Chang, K., Hannon, G. J., Powers, S. (2011) Pooled shRNA screen for sensitizers to inhibition of the mitotic regulator polo-like kinase (PLK1). Oncotarget, 2 (12). pp. 1254-64. ISSN 1949-2553 (Electronic) 1949-2553 (Linking)

M

Matthews, L., Gopinath, G., Gillespie, M., Caudy, M., Croft, D., de Bono, B., Garapati, P., Hemish, J., Hermjakob, H., Jassal, B., Kanapin, A., Lewis, S., Mahajan, S., May, B., Schmidt, E., Vastrik, I., Wu, G., Birney, E., Stein, L. D., D'Eustachio, P. (2009) Reactome knowledgebase of human biological pathways and processes. Nucleic Acids Res, 37. D619-22.

Monaco, M. K., Stein, J., Naithani, S., Wei, S., Dharmawardhana, P., Kumari, S., Amarasinghe, V., Youens-Clark, K., Thomason, J., Preece, J., Pasternak, S., Olson, A., Jiao, Y., Lu, Z., Bolser, D., Kerhornou, A., Staines, D., Walts, B., Wu, G., D'Eustachio, P., Haw, R., Croft, D., Kersey, P. J., Stein, L., Jaiswal, P., Ware, D. (2014) Gramene 2013: comparative plant genomics resources. Nucleic Acids Research, 42 (Databa). D1193-9. ISSN 0305-1048

Myers, R. M., Stamatoyannopoulos, J., Snyder, M., Dunham, I., Hardison, R. C., Bernstein, B. E., Gingeras, T. R., Kent, W. J., Birney, E., Wold, B., Crawford, G. E., Epstein, C. B., Shoresh, N., Ernst, J., Mikkelsen, T. S., Kheradpour, P., Zhang, X. L., Wang, L., Issner, R., Coyne, M. J., Durham, T., Ku, M. C., Truong, T., Ward, L. D., Altshuler, R. C., Lin, M. F., Kellis, M., Davis, C. A., Kapranov, P., Dobin, A., Zaleski, C., Schlesinger, F., Batut, P., Chakrabortty, S., Jha, S., Lin, W., Drenkow, J., Wang, H. E., Bell, K. G., Gao, H., Bell, I., Dumais, E., Dumais, J., Antonarakis, S. E., Ucla, C., Borel, C., Guigo, R., Djebali, S., Lagarde, J., Kingswood, C., Ribeca, P., Sammeth, M., Alioto, T., Merkel, A., Tilgner, H., Carninci, P., Hayashizaki, Y., Lassmann, T., Takahashi, H., Abdelhamid, R. F., Hannon, G., Fejes-Toth, K., Preall, J., Gordon, A., Sotirova, V., Reymond, A., Howald, C., Graison, E. A. Y., Chrast, J., Ruan, Y. J., Ruan, X. A., Shahab, A., Poh, W. T., Wei, C. L., Furey, T. S., Boyle, A. P., Sheffield, N. C., Song, L. Y., Shibata, Y., Vales, T., Winter, D., Zhang, Z. C., London, D., Wang, T. Y., Keefe, D., Iyer, V. R., Lee, B. K., McDaniell, R. M., Liu, Z., Battenhouse, A., Bhinge, A. A., Lieb, J. D., Grasfeder, L. L., Showers, K. A., Giresi, P. G., Kim, S. K. C., Shestak, C., Pauli, F., Reddy, T. E., Gertz, J. (2011) A User's Guide to the Encyclopedia of DNA Elements (ENCODE). Plos Biology, 9 (4). ISSN 1544-9173

N

Ng, L., Bernard, A., Lau, C., Overly, C. C., Dong, H.-W., Kuan, C., Pathak, S., Sunkin, S. M., Dang, C., Bohland, J. W., Bokil, H. S., Mitra, P. P., Puelles, L., Hohmann, J., Anderson, D. J., Lein, E. S., Jones, A. R., Hawrylycz, M. (2009) An anatomic gene expression atlas of the adult mouse brain. Nat Neurosci, 12 (3). pp. 356-362. ISSN 1097-6256

Ni, J., Pujar, A., Youens-Clark, K., Yap, I. V., Jaiswal, P., Tecle, I., Tung, C.-W., Ren, L. , Spooner, W., Wei, X, Avraham, S, Ware, D. H., Stein, L. D., McCouch, S. (2009) Gramene QTL database: development, content and applications. Database, 2009. bap005.

O

O'Connor, B. D., Day, A., Cain, S., Arnaiz, O., Sperling, L., Stein, L. D. (2008) GMODWeb: a web framework for the generic model organism database. Genome Biol, 9 (6). R102.

Ohlmeyer, M. H. J., Swanson, R. N., Dillard, L. W., Reader, J. C., Asouline, G., Kobayashi, R., Wigler, M. H., Still, W. C. (1993) Complex synthetic chemical libraries indexed with molecular tags. Proceedings of the National Academy of Sciences of the United States of America, 90 (23). pp. 10922-10926. ISSN 0027-8424

Olson, A., Sheth, N., Lee, J., Hannon, G. J., Sachidanandam, R. (2005) Rnai codex - a comprehensive RNAi resource. Briefings in Bioinformatics, 6 (1). pp. 104-106. ISSN 1467-5463

Olson, A., Sheth, N., Lee, J. S., Hannon, G. J., Sachidanandam, R. (2006) RNAi Codex: a portal/database for short-hairpin RNA (shRNA) gene-silencing constructs. Nucleic Acids Res, 34 (Databa). D153-7. ISSN 1362-4962 (Electronic)

Olson, A. J., Tully, T., Sachidanandam, R. (2005) GeneSeer: a sage for gene names and genomic resources. BMC Genomics, 6 (1). p. 134. ISSN 1471-2164 (Electronic)

P

Pan, X. K., Stein, L. D., Brendel, V. (2005) SynBrowse: a synteny browser for comparative sequence analysis. Bioinformatics, 21 (17). pp. 3461-3468. ISSN 1367-4803

Pujar, An., Jaiswal, P., Kellogg, E. A., Ilic, K., Vincent, L., Avraham, Sh., Stevens, P., Zapata, F., Reiser, L., Rhee, S. Y., Sachs, M. M., Schaeffer, M., Stein, L. D., Ware, D. H., McCouch, S. (2006) Whole-plant growth stage ontology for angiosperms and its application in plant biology. Plant Physiology, 142 (2). pp. 414-428. ISSN 00320889

R

Roberts, R. J. (1989) Benefits of Databases. Nature, 342 (6246). p. 114. ISSN 0028-0836

Rogers, A., Antoshechkin, I., Bieri, T., Blasiar, D., Bastiani, C., Canaran, P., Chan, J., Chen, W. J., Davis, P., Fernandes, J., Fiedler, T. J., Han, M. , Harris, T. , Kishore, R., Lee, R., McKay, S. J., Muller, H. M., Nakamura, C., Ozersky, P., Petcherski, A., Schindelman, G., Schwarz, E. M., Spooner, W., Tuli, M. A., Auken, K. V., Wang, D., Wang, X., Williams, G., Yook, K., Durbin, R., Stein, L. D., Spieth, J., Sternberg, P. W. (2008) WormBase 2007. Nucl. Acids Res., 36 (Databa). D612-7.

S

Schmidt, C. J., Romanov, M., Ryder, O., Magrini, V., Hickenbotham, M., Glasscock, J., McGrath, S., Mardis, E., Stein, L. D. (2008) Gallus GBrowse: a unified genomic database for the chicken. Nucleic Acids Res, 36 (Databa). D719-23.

Schwarz, E. M., Antoshechkin, I., Bastiani, C., Bieri, T., Blasiar, D., Canaran, P., Chan, J., Chen, N., Chen, W. J., Davis, P., Fiedler, T. J., Girard, L., Harris, T. W., Kenny, E. E., Kishore, R., Lawson, D., Lee, R., Muller, H. M., Nakamura, C., Ozersky, P., Petcherski, A., Rogers, A., Spooner, W., Tuli, M. A., Van Auken, K., Wang, D., Durbin, R., Spieth, J., Stein, L. D., Sternberg, P. W. (2006) WormBase: better software, richer content. Nucl. Acids Res., 34 (suppl_). D475-478.

Sheth, N., Roca, X., Hastings, M. L., Roeder, T., Krainer, A. R., Sachidanandam, R. (2006) Comprehensive splice-site analysis using comparative genomics. Nucleic Acids Res, 34 (14). pp. 3955-3967. ISSN 1362-4962 (Electronic)

Smith, A. D., Sumazin, P., Zhang, M. Q. (2007) Tissue-specific regulatory elements in mammalian promoters. Molecular Systems Biology, 3. ISSN 1744-4292

Smith, P. J., Zhang, C., Wang, J., Chew, S. L., Zhang, M. Q., Krainer, A. R. (2006) An increased specificity score matrix for the prediction of SF2/ASF-specific exonic splicing enhancers. Hum Mol Genet, 15 (16). pp. 2490-508. ISSN 0964-6906 (Print)

Stein, L. D. (2008) Towards a cyberinfrastructure for the biological sciences: progress, visions and challenges. Nat Rev Genet, 9 (9). pp. 678-688.

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

Sumazin, P., Chen, G., Hata, N., Smith, A. D., Zhang, T., Zhang, M. Q. (2005) DWE: discriminating word enumerator. Bioinformatics, 21 (1). pp. 31-8. ISSN 1367-4803 (Print)

W

Wang, J., Smith, P. J., Krainer, A. R., Zhang, M. Q. (2005) Distribution of SR protein exonic splicing enhancer motifs in human protein-coding genes. Nucleic Acids Res, 33 (16). pp. 5053-62. ISSN 1362-4962 (Electronic)

Y

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

Z

Zhang, M. Q. (2005) Using CorePromoter to find human core promoters. Curr Protoc Bioinformatics, Chapte. Unit 2.9. ISSN 1934-340X (Electronic)

Zhao, F., Xuan, Z., Liu, L., Zhang, M. Q. (2005) TRED: a Transcriptional Regulatory Element Database and a platform for in silico gene regulation studies. Nucleic Acids Res, 33 (Databa). D103-107. ISSN 1362-4962 (Electronic)

Zheng, D., Frankish, A., Baertsch, R., Kapranov, P., Reymond, A., Siew, W. C., Lu, Y., Denoeud, F., Antonarakis, S. E., Snyder, M., Ruan, Y., Wei, C. L., Gingeras, T. R., Guigó, R., Harrow, J., Gerstein, M. B. (2007) Pseudogenes in the ENCODE regions: Consensus annotation, analysis of transcription, and evolution. Genome Research, 17 (6). pp. 839-851. ISSN 10889051 (ISSN)

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