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

Up a level
Export as [feed] Atom [feed] RSS 1.0 [feed] RSS 2.0
Group by: Authors | Item Type
Jump to: A | B | C | D | F | G | H | J | K | L | M | N | O | P | R | S | T | V | W | X | Y | Z
Number of items at this level: 76.

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. (January 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. (January 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. (November 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. (January 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. (October 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. (October 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. (January 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. (November 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. (January 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. (January 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. (March 1989) The REF52 protein database. Methods of database construction and analysis using the QUEST system and characterizations of protein patterns from proliferating and quiescent REF52 cells. J Biol Chem, 264 (9). pp. 5283-98. ISSN 0021-9258

Garrels, J. I., Franza, B. R., Chang, C., Latter, G. (December 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. (November 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. (September 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. (September 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 (November 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. (January 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. (January 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

Harper, L., Campbell, J., Cannon, E. K. S., Jung, S., Poelchau, M., Walls, R., Andorf, C., Arnaud, E., Berardini, T. Z., Birkett, C., Cannon, S., Carson, J., Condon, B., Cooper, L., Dunn, N., Elsik, C. G., Farmer, A., Ficklin, S. P., Grant, D., Grau, E., Herndon, N., Hu, Z. L., Humann, J., Jaiswal, P., Jonquet, C., Laporte, M. A., Larmande, P., Lazo, G., McCarthy, F., Menda, N., Mungall, C. J., Munoz-Torres, M. C., Naithani, S., Nelson, R., Nesdill, D., Park, C., Reecy, J., Reiser, L., Sanderson, L. A., Sen, T. Z., Staton, M., Subramaniam, S., Tello-Ruiz, M. K., Unda, V., Unni, D., Wang, L., Ware, D., Wegrzyn, J., Williams, J., Woodhouse, M., Yu, J., Main, D. (January 2018) AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture. Database (Oxford), 2018. ISSN 1758-0463

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. (January 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. Methods Mol Biol, 351. pp. 31-50. ISSN 1940-6029 (Electronic)1064-3745 (Linking)

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. (January 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. (January 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. (August 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. (January 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. (January 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. (November 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. (January 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. (January 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. (January 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. (October 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. (May 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. (May 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. (June 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. (June 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. (February 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. (April 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. (August 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. (January 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. (February 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. (January 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. (January 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. (December 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. (January 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. (April 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. (December 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. (January 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. (May 2003) Integrating biological databases. Nature Reviews Genetics, 4 (5). pp. 337-345. ISSN 1471-0056

Stein, L. D. (September 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. (October 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. (December 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. (June 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. (January 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. (December 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. (January 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. (November 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. (May 2007) SnapShot: Genetic mouse models of cancer. Cell, 129 (4). p. 838. ISSN 0092-8674

Zhang, C., Krainer, A. R., Zhang, M. Q. (October 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. (May 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. (June 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. (January 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. (February 2007) Boosting with stumps for predicting transcription start sites. Genome Biol, 8 (2). R17. ISSN 1465-6914 (Electronic)

This list was generated on Wed Jan 16 04:09:47 2019 EST.
CSHL HomeAbout CSHLResearchEducationNews & FeaturesCampus & Public EventsCareersGiving