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

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Number of items at this level: 74.

A

Avraham, S., Tung, C. W., Ilic, K., Jaiswal, P., Kellogg, E. A., McCouch, S., Pujar, A., Reiser, L., Rhee, S. Y., Sachs, M. M., Schaeffer, M., Stein, L. D., Stevens, P., Vincent, L., Zapata, F., Ware, D. H. (2008) The Plant Ontology Database: a community resource for plant structure and developmental stages controlled vocabulary and annotations. Nucleic Acids Res, 36 (Databa). D449-54.

B

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

Boutell, T., Garrels, J. I., Franza, B. R., Monardo, P. J., Latter, G. I. (1994) REF52 on Global Gel Navigator: an internet-accessible two-dimensional gel electrophoresis database. Electrophoresis, 15 (11). pp. 1487-90.

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

C

Canaran, P., Buckler, E. S., Glaubitz, J. C., Stein, L. D., Sun, Q., Zhao, W., Ware, D. H. (2008) Panzea: an update on new content and features. Nucleic Acids Res, 36 (Databa). D1041-3.

Chen, N., Lawson, D., Bradnam, K., Harris, T. W., Stein, L. D. (2004) WormBase as an integrated platform for the C. elegans ORFeome. Genome Res, 14 (10B). pp. 2155-61. ISSN 1088-9051 (Print)

Cokol, M., Iossifov, I., Weinreb, C., Rzhetsky, A. (2005) Emergent behavior of growing knowledge about molecular interactions. Nat Biotechnol, 23 (10). pp. 1243-7. ISSN 1087-0156 (Print)1087-0156 (Linking)

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

Davuluri, R. V., Suzuki, Y., Sugano, S., Zhang, M. Q. (2000) CART classification of human 5 ' UTR sequences. Genome Research, 10 (11). pp. 1807-1816. ISSN 1088-9051

de la Cruz, N., Bromberg, S., Pasko, D., Shimoyama, M., Twigger, S., Chen, J. L., Chen, C. F., Fan, C., Foote, C., Gopinath, G. R., Harris, G., Hughes, A., Ji, Y., Jin, W. H., Li, D. W., Mathis, J., Nenasheva, N., Nie, J., Nigam, R., Petri, V., Reilly, D., Wang, W. Y., Wu, W. H., Zuniga-Meyer, A., Zhao, L., Kwitek, A., Tonellato, P., Jacob, H. (2005) The Rat Genome Database (RGD): developments towards a phenome database. Nucleic Acids Research, 33. D485-D491. ISSN 0305-1048

F

Fabregat, A., Sidiropoulos, K., Garapati, P., Gillespie, M., Hausmann, K., Haw, R., Jassal, B., Jupe, S., Korninger, F., McKay, S., Matthews, L., May, B., Milacic, M., Rothfels, K., Shamovsky, V., Webber, M., Weiser, J., Williams, M., Wu, G., Stein, L., Hermjakob, H., D'Eustachio, P. (2016) The Reactome pathway Knowledgebase. Nucleic Acids Res, 44 (D1). D481-487. ISSN 1362-4962 (Electronic)0305-1048 (Linking)

G

Garrels, J. I., Franza, B. R., Chang, C., Latter, G. (1990) Quantitative exploration of the REF52 protein database: cluster analysis reveals the major protein expression profiles in responses to growth regulation, serum stimulation, and viral transformation. Electrophoresis, 11 (12). pp. 1114-30. ISSN 0173-0835 (Print)0173-0835 (Linking)

Garrels, J. I., Futcher, B., Kobayashi, R., Latter, G. I., Schwender, B., Volpe, T., Warner, J. R., McLaughlin, C. S. (1994) Protein identifications for a Saccharomyces cerevisiae protein database. Electrophoresis, 15 (11). pp. 1466-86.

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

Goff, S. A, Vaughn, M., McKay, S., Lyons, E., Stapleton, A. E, Gessler, D. , Matasci, N., Wang, L., Hanlon, M., Lenards, A., Muir, A., Merchant, N., Lowry, S., Mock, S., Helmke, M., Kubach, A., Narro, M., Hopkins, N., Micklos, D., Hilgert, U., Gonzales, M, Jordan, C., Skidmore, E., Dooley, R., Cazes, J., McLay, R., Lu, Z., Pasternak, S., Koesterke, L., Piel, W. H., Grene, R., Noutsos, C., Gendler, K., Feng, X., Tang, C., Lent, M., Kim, S. J., Kvilekval, K., Manjunath, B.S., Tannen, V., Stamatakis, A., Sanderson, M. J., Welch, S. M., Cranston, K. , Soltis, P. , Soltis, D., O'Meara, B., Ane, C., Brutnell, T., Kleibenstein, D. J., White, J. W., Leebens-Mack, J., Donoghue, M. J., Spalding, E. P., Vision, T. J., Myers, C. R., Lowenthal, D., Enquist, B. J., Boyle, B., Akoglu, A., Andrews, G., Ram, S., Ware, D., Stein, L., Stanzione, D. (2011) The iPlant Collaborative: Cyberinfrastructure for Plant Biology. Frontiers in Plant Science, 2. ISSN 1664-462X

Goodman, L. (1997) More BLAST for the buck. Genome Research, 7 (9). pp. 858-9. ISSN 1088-9051

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)

Gupta, Parul, Naithani, Sushma, Tello-Ruiz, Marcela Karey, Chougule, Kapeel, D’Eustachio, Peter, Fabregat, Antonio, Jiao, Yinping, Keays, Maria, Lee, Young Koung, Kumari, Sunita, Mulvaney, Joseph, Olson, Andrew, Preece, Justin, Stein, Joshua, Wei, Sharon, Weiser, Joel, Huerta, Laura, Petryszak, Robert, Kersey, Paul, Stein, Lincoln D., Ware, Doreen, Jaiswal, Pankaj (2016) Gramene Database: Navigating Plant Comparative Genomics Resources. Current Plant Biology, 7-8. pp. 10-15. ISSN 2214-6628

H

Harger, C., Skupski, M., Allen, E., Clark, C., Crowley, D., Dickinson, E., Easley, D., Espinosa-Lujan, A., Farmer, A., Fields, C., Flores, L., Harris, L., Keen, G., Manning, M., McLeod, M., O'Neill, J., Pumilia, M., Reinert, R., Rider, D., Rohrlich, J., Romero, Y., Schwertfeger, J., Seluja, G., Siepel, A., Schad, P. A. (1997) The Genome Sequence DataBase version 1.0 (GSDB): from low pass sequences to complete genomes. Nucleic Acids Res, 25 (1). pp. 18-23. ISSN 0305-1048 (Print)0305-1048

Harger, C., Skupski, M., Bingham, J., Farmer, A., Hoisie, S., Hraber, P., Kiphart, D., Krakowski, L., McLeod, M., Schwertfeger, J., Seluja, G., Siepel, A., Singh, G., Stamper, D., Steadman, P., Thayer, N., Thompson, R., Wargo, P., Waugh, M., Zhuang, J. J., Schad, P. A. (1998) The Genome Sequence DataBase (GSDB): improving data quality and data access. Nucleic Acids Res, 26 (1). pp. 21-6. ISSN 0305-1048 (Print)0305-1048

Harris, T. W., Chen, N., Cunningham, F., Tello-Ruiz, M., Antoshechkin, I., Bastiani, C., Bieri, T., Blasiar, D., Bradnam, K., Chan, J., Chen, C. K., Chen, W. J., Davis, P., Kenny, E., Kishore, R., Lawson, D., Lee, R., Muller, H. M., Nakamura, C., Ozersky, P., Petcherski, A., Rogers, A., Sabo, A., Schwarz, E. M., Van Auken, K., Wang, Q., Durbin, R., Spieth, J., Sternberg, P. W., Stein, L. D. (2004) WormBase: a multi-species resource for nematode biology and genomics. Nucleic Acids Res, 32 (Databa). D411-7. ISSN 1362-4962 (Electronic)

Harris, T. W., Stein, L. D. (2006) WormBase: methods for data mining and comparative genomics. In: C. elegans: methods and applications. Methods Mol Biol, 351 . Humana Press, Totowa, NJ, pp. 31-50. ISBN 1064-3745 (Print)

Haw, R. A., Croft, D., Yung, C. K., Ndegwa, N., D'Eustachio, P., Hermjakob, H., Stein, L. D. (2011) The Reactome BioMart. Database : the journal of biological databases and curation, 2011. ISSN 17580463 (ISSN)

Hinrichs, A. S., Karolchik, D., Baertsch, R., Barber, G. P., Bejerano, G., Clawson, H., Diekhans, M., Furey, T. S., Harte, R. A., Hsu, F., Hillman-Jackson, J., Kuhn, R. M., Pedersen, J. S., Pohl, A., Raney, B. J., Rosenbloom, K. R., Siepel, A., Smith, K. E., Sugnet, C. W., Sultan-Qurraie, A., Thomas, D. J., Trumbower, H., Weber, R. J., Weirauch, M., Zweig, A. S., Haussler, D., Kent, W. J. (2006) The UCSC Genome Browser Database: update 2006. Nucleic Acids Res, 34 (Databa). D590-8. ISSN 0305-1048

Hubisz, M. J., Pollard, K. S., Siepel, A. (2011) PHAST and RPHAST: phylogenetic analysis with space/time models. Brief Bioinform, 12 (1). pp. 41-51. ISSN 1467-5463

J

Jaiswal, P., Avraham, S., Ilic, K., Kellogg, E. A., McCouch, S., Pujar, A., Reiser, L., Rhee, S. Y., Sachs, M. M., Schaeffer, M., Stein, L., Stevens, P., Vincent, L. D., Ware, D. H., Zapata, F. (2005) Plant Ontology (PO): a Controlled Vocabulary of Plant Structures and Growth Stages. Comp Funct Genomics, 6 (7-8). pp. 388-97. ISSN 1531-6912 (Print)

Jojic, V., Jojic, N., Meek, C., Geiger, D., Siepel, A., Haussler, D., Heckerman, D. (2004) Efficient approximations for learning phylogenetic HMM models from data. Bioinformatics, 20 Sup. i161-8. ISSN 1367-4803

Joshi-Tope, G., Gillespie, M., Vastrik, I., D'Eustachio, P., Schmidt, E., de Bono, B., Jassal, B., Gopinath, G. R., Wu, G. R., Matthews, L., Lewis, S., Birney, E., Stein, L. D. (2005) Reactome: a knowledgebase of biological pathways. Nucleic Acids Res, 33 (Databa). D428-32. ISSN 1362-4962 (Electronic)

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

Kohler, S., Vasilevsky, N. A., Engelstad, M., Foster, E., McMurry, J., Ayme, S., Baynam, G., Bello, S. M., Boerkoel, C. F., Boycott, K. M., Brudno, M., Buske, O. J., Chinnery, P. F., Cipriani, V., Connell, L. E., Dawkins, H. J., DeMare, L. E., Devereau, A. D., de Vries, B. B., Firth, H. V., Freson, K., Greene, D., Hamosh, A., Helbig, I., Hum, C., Jahn, J. A., James, R., Krause, R., Laulederkind, S. J., Lochmuller, H., Lyon, G. J., Ogishima, S., Olry, A., Ouwehand, W. H., Pontikos, N., Rath, A., Schaefer, F., Scott, R. H., Segal, M., Sergouniotis, P. I., Sever, R., Smith, C. L., Straub, V., Thompson, R., Turner, C., Turro, E., Veltman, M. W., Vulliamy, T., Yu, J., von Ziegenweidt, J., Zankl, A., Zuchner, S., Zemojtel, T., Jacobsen, J. O., Groza, T., Smedley, D., Mungall, C. J., Haendel, M., Robinson, P. N. (2016) The Human Phenotype Ontology in 2017. Nucleic Acids Res, 45 (D1). D865-D876. ISSN 1362-4962 (Electronic)0305-1048 (Linking)

Krauthammer, M., Kra, P., Iossifov, I., Gomez, S. M., Hripcsak, G., Hatzivassiloglou, V., Friedman, C., Rzhetsky, A. (2002) Of truth and pathways: chasing bits of information through myriads of articles. Bioinformatics, 18 Sup. S249-57. ISSN 1367-4803 (Print)1367-4803 (Linking)

Krishnakumar, V., Choi, Y., Beck, E., Wu, Q., Luo, A., Sylvester, A., Jackson, D., Chan, A. P. (2015) A Maize Database Resource that Captures Tissue-Specific and Subcellular-Localized Gene Expression, via Fluorescent Tags and Confocal Imaging. (Maize Cell Genomics Database). Plant & cell physiology, 56 (1). e12. ISSN 0032-0781

Kuhn, R. M., Karolchik, D., Zweig, A. S., Trumbower, H., Thomas, D. J., Thakkapallayil, A., Sugnet, C. W., Stanke, M., Smith, K. E., Siepel, A., Rosenbloom, K. R., Rhead, B., Raney, B. J., Pohl, A., Pedersen, J. S., Hsu, F., Hinrichs, A. S., Harte, R. A., Diekhans, M., Clawson, H., Bejerano, G., Barber, G. P., Baertsch, R., Haussler, D., Kent, W. J. (2007) The UCSC genome browser database: update 2007. Nucleic Acids Res, 35 (Databa). D668-73. ISSN 0305-1048

L

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

Li, J., Zhang, M. Q., Zhang, X. (2006) A new method for detecting human recombination hotspots and its applications to the HapMap ENCODE data. American Journal of Human Genetics, 79 (4). pp. 628-639. ISSN 00029297

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.

M

Marr, T. (1990) Technical Issues Associated with Building a National Genome Database. Abstracts of Papers American Chemical Society, 200 (1-2). ANYL 71.

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.

N

Naithani, S., Preece, J., D'Eustachio, P., Gupta, P., Amarasinghe, V., Dharmawardhana, P. D., Wu, G., Fabregat, A., Elser, J. L., Weiser, J., Keays, M., Fuentes, A. M., Petryszak, R., Stein, L. D., Ware, D., Jaiswal, P. (2016) Plant Reactome: a resource for plant pathways and comparative analysis. Nucleic Acids Res, 45 (D1). D1029-D1039. ISSN 1362-4962 (Electronic)0305-1048 (Linking)

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.

Noutsos, C., Perera, A. M., Nikolau, B. J., Seaver, S. M., Ware, D. H. (2015) Metabolomic Profiling of the Nectars of Aquilegia pubescens and A. Canadensis. PLoS One, 10 (5). e0124501. ISSN 1932-6203 (Electronic)1932-6203 (Linking)

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.

Oliver, S. L., Lenards, A. J., Barthelson, R. A., Merchant, N., McKay, S. J. (2013) Using the iplant collaborative discovery environment. Current protocols in bioinformatics (SUPPL.). 1.22. ISSN 19343396 (ISSN)

P

Pan, X. K., Liu, H., Clarke, J., Jones, J., Bevan, M., Stein, L. (2003) ATIDB: Arabidopsis thaliana insertion database. Nucleic Acids Research, 31 (4). pp. 1245-1251. ISSN 0305-1048

Popescu, G. V., Noutsos, C., Popescu, S. C. (2016) Big Data in Plant Science: Resources and Data Mining Tools for Plant Genomics and Proteomics. Methods Mol Biol, 1415. pp. 533-547. ISSN 1940-6029 (Electronic)1064-3745 (Linking)

R

Rodriguez-Esteban, R., Iossifov, I. (2009) Figure mining for biomedical research. Bioinformatics, 25 (16). pp. 2082-2084.

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.

Rzhetsky, A., Iossifov, I., Koike, T., Krauthammer, M., Kra, P., Morris, M., Yu, H., Duboue, P. A., Weng, W., Wilbur, W. J., Hatzivassiloglou, V., Friedman, C. (2004) GeneWays: a system for extracting, analyzing, visualizing, and integrating molecular pathway data. J Biomed Inform, 37 (1). pp. 43-53. ISSN 1532-0464 (Print)1532-0464 (Linking)

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.

Siepel, A., Farmer, A., Tolopko, A., Zhuang, M., Mendes, P., Beavis, W., Sobral, B. (2001) ISYS: a decentralized, component-based approach to the integration of heterogeneous bioinformatics resources. Bioinformatics, 17 (1). pp. 83-94. ISSN 1367-4803 (Print)1367-4803

Simpson, R. J., Tsugita, A., Celis, J. E., Garrels, J. I., Mewes, H. W. (1992) Workshop on 2-Dimensional Gel Protein Databases. Electrophoresis, 13 (12). pp. 1055-1061. ISSN 0173-0835

Skupski, M. P., Booker, M., Farmer, A., Harpold, M., Huang, W., Inman, J., Kiphart, D., Kodira, C., Root, S., Schilkey, F., Schwertfeger, J., Siepel, A., Stamper, D., Thayer, N., Thompson, R., Wortman, J., Zhuang, J. J., Harger, C. (1999) The Genome Sequence DataBase: towards an integrated functional genomics resource. Nucleic Acids Research, 27 (1). pp. 35-8. ISSN 0305-1048

Smedley, D., Haider, S., Durinck, S., Pandini, L., Provero, P., Allen, J., Arnaiz, O., Awedh, M. H., Baldock, R., Barbiera, G., Bardou, P., Beck, T., Blake, A., Bonierbale, M., Brookes, A. J., Bucci, G., Buetti, I., Burge, S., Cabau, C., Carlson, J. W., Chelala, C., Chrysostomou, C., Cittaro, D., Collin, O., Cordova, R., Cutts, R. J., Dassi, E., Genova, A. D., Djari, A., Esposito, A., Estrella, H., Eyras, E., Fernandez-Banet, J., Forbes, S., Free, R. C., Fujisawa, T., Gadaleta, E., Garcia-Manteiga, J. M., Goodstein, D., Gray, K., Guerra-Assuncao, J. A., Haggarty, B., Han, D. J., Han, B. W., Harris, T., Harshbarger, J., Hastings, R. K., Hayes, R. D., Hoede, C., Hu, S., Hu, Z. L., Hutchins, L., Kan, Z., Kawaji, H., Keliet, A., Kerhornou, A., Kim, S., Kinsella, R., Klopp, C., Kong, L., Lawson, D., Lazarevic, D., Lee, J. H., Letellier, T., Li, C. Y., Lio, P., Liu, C. J., Luo, J., Maass, A., Mariette, J., Maurel, T., Merella, S., Mohamed, A. M., Moreews, F., Nabihoudine, I., Ndegwa, N., Noirot, C., Perez-Llamas, C., Primig, M., Quattrone, A., Quesneville, H., Rambaldi, D., Reecy, J., Riba, M., Rosanoff, S., Saddiq, A. A., Salas, E., Sallou, O., Shepherd, R., Simon, R., Sperling, L., Spooner, W., Staines, D. M., Steinbach, D., Stone, K., Stupka, E., Teague, J. W., Dayem Ullah, A. Z., Wang, J., Ware, D. (2015) The BioMart community portal: an innovative alternative to large, centralized data repositories. Nucleic Acids Res, 43 (W1). W589-W598. ISSN 1362-4962 (Electronic)0305-1048 (Linking)

Stamm, S., Zhu, J., Nakai, K., Stoilov, P., Stoss, O., Zhang, M. Q. (2000) An alternative-exon database and its statistical analysis. DNA and Cell Biology, 19 (12). pp. 739-756. ISSN 1044-5498

Stein, L. (2002) Creating databases for biological information: an introduction. Current protocols in bioinformatics, Chapte. Unit 9.1.

Stein, L., Sternberg, P., Durbin, R., Thierry-Mieg, J., Spieth, J. (2001) WormBase: network access to the genome and biology of Caenorhabditis elegans. Nucleic Acids Research, 29 (1). pp. 82-86. ISSN 0305-1048

Stein, L. D. (2003) Integrating biological databases. Nature Reviews Genetics, 4 (5). pp. 337-345. ISSN 1471-0056

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., Mungall, C., Shu, S. Q., Caudy, M., Mangone, M., Day, A., Nickerson, E., Stajich, J. E., Harris, T. W., Arva, A., Lewis, S. (2002) The Generic Genome Browser: A building block for a model organism system database. Genome Research, 12 (10). pp. 1599-1610. ISSN 1088-9051

T

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. (2009) The completion of the Mammalian Gene Collection (MGC). Genome Research, 19 (12). pp. 2324-33. ISSN 1088-9051

Tsesmetzis, N., Couchman, M., Higgins, J., Smith, A., Doonan, J. H., Seifert, G. J., Schmidt, E. E., Vastrik, I., Birney, E., Wu, G., D'Eustachio, P., Stein, L. D., Morris, R. J., Bevan, M. W., Walsh, S. V. (2008) Arabidopsis Reactome: A Foundation Knowledgebase for Plant Systems Biology. Plant Cell, 20 (6). pp. 1426-36.

V

Vastrik, I., D'Eustachio, P., Schmidt, E., Joshi-Tope, G., Gopinath, G., Croft, D., de Bono, B., Gillespie, M., Jassal, B., Lewis, S., Matthews, L., Wu, G., Birney, E., Stein, L. D. (2007) Reactome: a knowledge base of biologic pathways and processes. Genome Biol, 8 (3). R39. ISSN 1474-760X

W

Ware, D., Jaiswal, P., Ni, J. J., Pan, X. K., Chang, K., Clark, K., Teytelman, L., Schmidt, S., Zhao, W., Cartinhour, S., McCouch, S., Stein, L. (2002) Gramene: a resource for comparative grass genomics. Nucleic Acids Research, 30 (1). pp. 103-105. ISSN 0305-1048

Ware, D. H. (2007) Gramene. Methods Mol Biol, 406. pp. 315-329. ISSN 1064-3745 (Print)

Ware, D. H., Jaiswal, P. J., Ni, J. J., Yap, I., Pan, X. K., Clark, K. Y., Teytelman, L., Schmidt, S. C., Zhao, W., Chang, K., Cartinhour, S., Stein, L. D., McCouch, S. R. (2002) Gramene, a tool for grass Genomics. Plant Physiology, 130 (4). pp. 1606-1613. ISSN 0032-0889

X

Xuan, Z. Y., Zhao, F., Wang, J., Chen, G., Zhang, M. Q. (2005) Genome-wide promoter extraction and analysis in human, mouse, and rat. Genome Biology, 6 (8). R72. ISSN 1465-6906

Y

Youens-Clark, K., Buckler, E., Casstevens, T., Chen, C., DeClerck, G., Derwent, P., Dharmawardhana, P., Jaiswal, P., Kersey, P., Karthikeyan, A. S., Lu, J., McCouch, S. R., Ren, L., Spooner, W., Stein, J. C., Thomason, J., Wei, S., Ware, D. H. (2011) Gramene database in 2010: Updates and extensions. Nucleic Acids Research, 39 (SUPPL.).

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

Zender, L., Zuber, J., Lowe, S. W. (2007) SnapShot: Genetic mouse models of cancer. Cell, 129 (4). p. 838. ISSN 0092-8674

Zhang, C., Krainer, A. R., Zhang, M. Q. (2007) Evolutionary impact of limited splicing fidelity in mammalian genes. Trends Genet, 23 (10). pp. 484-488. ISSN 0168-9525 (Print)

Zhang, M. Q., Marr, T. G. (1994) Fission yeast gene structure and recognition. Nucleic Acids Res, 22 (9). pp. 1750-9. ISSN 0305-1048 (Print)

Zhang, X., Madi, S., Borsuk, L., Nettleton, D., Elshire, R. J., Buckner, B., Janick-Buckner, D., Beck, J., Timmermans, M. C. P., Schnable, P. S., Scanlon, M. J. (2007) Laser microdissection of narrow sheath mutant maize uncovers novel gene expression in the shoot apical meristem. Plos Genetics, 3 (6). pp. 1040-1052. ISSN 1553-7390

Zhao, W., Canaran, P., Jurkuta, R., Fulton, T., Glaubitz, J., Buckler, E., Doebley, J., Gaut, B., Goodman, M., Holland, J., Kresovich, S., McMullen, M., Stein, L. D., Ware, D. (2006) Panzea: a database and resource for molecular and functional diversity in the maize genome. Nucleic Acids Res, 34 (Databa). D752-7. ISSN 1362-4962 (Electronic)

Zhao, Xi., Xuan, Z. Y., Zhang, M. Q. (2007) Boosting with stumps for predicting transcription start sites. Genome Biol, 8 (2). R17. ISSN 1465-6914 (Electronic)

This list was generated on Wed Apr 26 22:22:08 2017 EDT.
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