Items where Community is "CSHL labs > Stein lab"

Up a level
Export as [feed] Atom [feed] RSS 1.0 [feed] RSS 2.0
Group by: Item Type | No Grouping
Jump to: Paper | Book Section
Number of items at this level: 103.

Paper

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)

Thomas, C. G., Wang, W., Jovelin, R., Ghosh, R., Lomasko, T., Trinh, Q., Kruglyak, L., Stein, L. D., Cutter, A. D. (2015) Full-genome evolutionary histories of selfing, splitting, and selection in Caenorhabditis. Genome Research, 25 (5). pp. 667-678. ISSN 1088-9051

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

Haw, R., Hermjakob, H., D'Eustachio, P., Stein, L. D. (2011) Reactome pathway analysis to enrich biological discovery in proteomics data sets. Proteomics, 11 (18). pp. 3598-3613. ISSN 16159853 (ISSN)

Feng, X., Grossman, R., Stein, L. D. (2011) PeakRanger: A cloud-enabled peak caller for ChIP-seq data. Bmc Bioinformatics, 12. ISSN 1471-2105

Sawey, E. T., Chanrion, M., Cai, C., Wu, G., Zhang, J., Zender, L., Zhao, A., Busuttil, R. W., Yee, H., Stein, L. D., French, D. M., Finn, Richard S, Lowe, S. W., Powers, S. (2011) Identification of a Therapeutic Strategy Targeting Amplified FGF19 in Liver Cancer by Oncogenomic Screening. Cancer Cell, 19 (3). pp. 347-358. ISSN 1535-6108

Croft, D., O'Kelly, G., Wu, G., Haw, R., Gillespie, M., Matthews, L., Caudy, M., Garapati, P., Gopinath, G., Jassal, B., Jupe, S., Kataskaya, I., Mahajan, 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 Res, 39 (Suppl ). D691-7. ISSN 1362-4962 (Electronic) 0305-1048 (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.).

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)

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

Gill, N., SanMiguel, P., Dhillon, B. D. S., Abernathy, B., Kim, H., Stein, L. D., Ware, D. H., Wing, R., Jackson, S. A. (2010) Dynamic Oryza Genomes: Repetitive DNA Sequences as Genome Modeling Agents. Rice, 3 (4). pp. 251-269.

Roy, S., Ernst, J., Kharchenko, P. V., Kheradpour, P., Negre, N., Eaton, M. L., Landolin, J. M., Bristow, C. A., Ma, L. J., Lin, M. F., Washietl, S., Arshinoff, B. I., Ay, F., Meyer, P. E., Robine, N., Washington, N. L., Di Stefano, L., Berezikov, E., Brown, C. D., Candeias, R., Carlson, J. W., Carr, A., Jungreis, I., Marbach, D., Sealfon, R., Tolstorukov, M. Y., Will, S., Alekseyenko, A. A., Artieri, C., Booth, B. W., Brooks, A. N., Dai, Q., Davis, C. A., Duff, M. O., Feng, X., Gorchakov, A. A., Gu, T. T., Henikoff, J. G., Kapranov, P., Li, R. H., MacAlpine, H. K., Malone, J., Minoda, A., Nordman, J., Okamura, K., Perry, M., Powell, S. K., Riddle, N. C., Sakai, A., Samsonova, A., Sandler, J. E., Schwartz, Y. B., Sher, N., Spokony, R., Sturgill, D., van Baren, M., Wan, K. H., Yang, L., Yu, C., Feingold, E., Good, P., Guyer, M., Lowdon, R., Ahmad, K., Andrews, J., Berger, B., Brenner, S. E., Brent, M. R., Cherbas, L., Elgin, S. C. R., Gingeras, T. R., Grossman, R., Hoskins, R. A., Kaufman, T. C., Kent, W., Kuroda, M. I., Orr-Weaver, T., Perrimon, N., Pirrotta, V., Posakony, J. W., Ren, B., Russell, S., Cherbas, P., Graveley, B. R., Lewis, S., Micklem, G., Oliver, B., Park, P. J., Celniker, S. E., Henikoff, S., Karpen, G. H., Lai, E. C., MacAlpine, D. M., Stein, L. D., White, K. P., Kellis, M. (2010) Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE. Science, 330 (6012). pp. 1787-1797. ISSN 0036-8075

Gerstein, M. B., Lu, Z. J., Van Nostrand, E. L., Cheng, C., Arshinoff, B. I., Liu, T., Yip, K. Y., Robilotto, R., Rechtsteiner, A., Ikegami, K., Alves, P., Chateigner, A., Perry, M., Morris, M., Auerbach, R. K., Feng, X., Leng, J., Vielle, A., Niu, W., Rhrissorrakrai, K., Agarwal, A., Alexander, R. P., Barber, G., Brdlik, C. M., Brennan, J., Brouillet, J. J., Carr, A., Cheung, M. S., Clawson, H., Contrino, S., Dannenberg, L. O., Dernburg, A. F., Desai, A., Dick, L., Dose, A. C., Du, J. A., Egelhofer, T., Ercan, S., Euskirchen, G., Ewing, B., Feingold, E. A., Gassmann, R., Good, P. J., Green, P., Gullier, F., Gutwein, M., Guyer, M. S., Habegger, L., Han, T., Henikoff, J. G., Henz, S. R., Hinrichs, A., Holster, H., Hyman, T., Iniguez, A. L., Janette, J., Jensen, M., Kato, M., Kent, W. J., Kephart, E., Khivansara, V., Khurana, E., Kim, J. K., Kolasinska-Zwierz, P., Lai, E. C., Latorre, I., Leahey, A., Lewis, S., Lloyd, P., Lochovsky, L., Lowdon, R. F., Lubling, Y., Lyne, R., MacCoss, M., Mackowiak, S. D., Mangone, M., McKay, S. J., Mecenas, D., Merrihew, G., Miller, D. M., Muroyama, A., Murray, J. I., Ooi, S. L., Pham, H., Phippen, T., Preston, E. A., Rajewsky, N., Ratsch, G., Rosenbaum, H., Rozowsky, J., Rutherford, K., Ruzanov, P., Sarov, M., Sasidharan, R., Sboner, A., Scheid, P., Segal, E., Shin, H. J., Shou, C., Slack, F. J., Stein, L. D. (2010) Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project. Science, 330 (6012). pp. 1775-1787. ISSN 0036-8075

Wang, L., Stein, L. D. (2010) Localizing triplet periodicity in DNA and cDNA sequences. BMC Bioinformatics, 11. p. 550. ISSN 1471-2105 (Electronic) 1471-2105 (Linking)

Schreiber, S. L., Shamji, A. F., Clemons, P. A., Hon, C., Koehler, A. N., Munoz, B., Palmer, M., Stern, A. M., Wagner, B. K., Powers, S., Lowe, S. W., Guo, X., Krasnitz, A., Sawey, E. T., Sordella, R., Stein, L. D., Trotman, L. C., Califano, A., Dalla-Favera, R., Ferrando, A., Iavarone, A., Pasqualucci, L., Silva, J., Stockwell, B. R., Hahn, W. C., Chin, L., DePinho, R. A., Boehm, J. S., Gopal, S., Huang, A., Root, D. E., Weir, B. A., Gerhard, D. S., Zenklusen, J. C., Roth, M. G., White, M. A., Minna, J. D., MacMillan, J. B., Posner, B. A. (2010) Towards patient-based cancer therapeutics. Nature Biotechnology, 28 (9). pp. 904-906.

Wu, G. M., Feng, X., Stein, L. D. (2010) A human functional protein interaction network and its application to cancer data analysis. Genome Biology, 11 (5). ISSN 1474-760X

Negre, N., Brown, C. D., Shah, P. K., Kheradpour, P., Morrison, C. A., Henikoff, J. G., Feng, X., Ahmad, K., Russell, S., White, R. A. H., Stein, L. D., Henikoff, S., Kellis, M., White, K. P. (2010) A Comprehensive Map of Insulator Elements for the Drosophila Genome. Plos Genetics, 6 (1). ISSN 1553-7390

Cranston, K. A., Hurwitz, B. L., Sanderson, M. J., Ware, D. H., Wing, R. A., Stein, L. D. (2010) Phylogenomic analysis of BAC-end sequence libraries in Oryza (Poaceae). Systematic Botany, 35 (3). pp. 512-523.

Hurwitz, B. L., Kudrna, D., Yu, Y., Sebastian, A., Zuccolo, A., Jackson, S. A., Ware, D. H., Wing, R. A., Stein, L. D. (2010) Rice structural variation: A comparative analysis of structural variation between rice and three of its closest relatives in the genus Oryza. Plant Journal, 63 (6). pp. 990-1003.

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.

Liang, C., Mao, L., Ware, D. H., Stein, L. D. (2009) Evidence-based gene predictions in plant genomes. Genome Res, 19 (10). 1912-1923 .

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

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.

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. (2009) Strong association of socioeconomic status with genetic ancestry in Latinos: implications for admixture studies of type 2 diabetes. Diabetologia, 52 (8). 1528-1536 .

Prokopenko, I., Zeggini, E., Hanson, R. L., Mitchell, B. D., Rayner, N. W., Akan, P., Baier, L., Das, S. K., Elliott, K. S., Fu, M., Frayling, T. M., Groves, C. J., Gwilliam, R., Scott, L. J., Voight, B. F., Hattersley, A. T., Hu, C., Morris, A. D., Ng, M., Palmer, C. N. A., Tello-Ruiz, M., Vaxillaire, M., Wang, C. R., Stein, L. D., Chan, J., Jia, W. P., Froguel, P., Elbein, S. C., Deloukas, P., Bogardus, C., Shuldiner, A. R., McCarthy, M. I. (2009) Linkage Disequilibrium Mapping of the Replicated Type 2 Diabetes Linkage Signal on Chromosome 1q. Diabetes, 58 (7). pp. 1704-1709. ISSN 0012-1797

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. (2009) Unlocking the secrets of the genome. Nature, 459 (7249). pp. 927-30. ISSN 1476-4687 (Electronic)0028-0836 (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.

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.

Stein, L. D. (2008) Bioinformatics: alive and kicking. Genome Biology, 9 (12). p. 114. ISSN 1465-6906

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

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.

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.

Kim, H. R., Hurwitz, B. L., Yu, Y., Collura, K., Gill, N., SanMiguel, P., Mullikin, J. C., Maher, C., Nelson, W., Wissotski, M., Braidotti, M., Kudrna, D., Goigochia, J. L., Stein, L. D., Ware, D. H., Jackson, S., Soderlund, C., Wing, R. (2008) Construction, alignment and analysis of 12 framework physical maps that represent the 10 genome types of the genus Oryza. Genome Biology, 9 (2). R45. ISSN 1465-6906

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.

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.

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.

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.

Coghlan, A., Fiedler, T. J., McKay, S. J., Flicek, P., Harris, T. W., Blasiar, D., Stein, L. D. (2008) nGASP - the nematode genome annotation assessment project. Bmc Bioinformatics, 9 (1). p. 549.

Frazer, K. A., Ballinger, D. G., Cox, D. R., Hinds, D. A., Stuve, L. L., Gibbs, R. A., Belmont, J. W., Boudreau, A., Hardenbol, P., Leal, S. M., Pasternak, S., Wheeler, D. A., Willis, T. D., Yu, F. L., Yang, H. M., Zeng, C. Q., Gao, Y., Hu, H. R., Hu, W. T., Li, C. H., Lin, W., Liu, S. Q., Pan, H., Tang, X. L., Wang, J., Wang, W., Yu, J., Zhang, B., Zhang, Q. R., Zhao, H. B., Zhao, H., Zhou, J., Gabriel, S. B., Barry, R., Blumenstiel, B., Camargo, A., Defelice, M., Faggart, M., Goyette, M., Gupta, S., Moore, J., Nguyen, H., Onofrio, R. C., Parkin, M., Roy, J., Stahl, E., Winchester, E., Ziaugra, L., Altshuler, D., Shen, Y., Yao, Z. J., Huang, W., Chu, X., He, Y. G., Jin, L., Liu, Y. F., Shen, Y. Y., Sun, W. W., Wang, H. F., Wang, Y., Wang, Y., Xiong, X. Y., Xu, L., Waye, M. M. Y., Tsui, S. K. W., Wong, J. T. F., Galver, L. M., Fan, J. B., Gunderson, K., Murray, S. S., Oliphant, A. R., Chee, M. S., Montpetit, A., Chagnon, F., Ferretti, V., Leboeuf, M., Olivier, J. F., Phillips, M. S., Roumy, S., Sallee, C., Verner, A., Hudson, T. J., Kwok, P. Y., Cai, D. M., Koboldt, D. C., Miller, R. D., Pawlikowska, L., Taillon-Miller, P., Xiao, M., Tsui, L. C., Mak, W., Song, Y. Q., Tam, P. K. H., Nakamura, Y., Kawaguchi, T., Kitamoto, T., Morizono, T., Nagashima, A., Ohnishi, Y., Sekine, A. (2007) A second generation human haplotype map of over 3.1 million SNPs. Nature, 449 (7164). 851-U3. ISSN 0028-0836

Stein, L. D. (2007) X Window System survival guide. Curr Protoc Bioinformatics, Append. Appendix 1D.

Ilic, K., Kellogg, E. A., Jaiswal, P., Zapata, F., Stevens, P. F., Vincent, L. P., Avraham, S., Reiser, L., Pujar, A., Sachs, M. M., Whitman, N. T., McCouch, S. R., Schaeffer, M. L., Ware, D. H., Stein, L. D., Rhee, S. Y. (2007) The plant structure ontology, a unified vocabulary of anatomy and morphology of a flowering plant. Plant Physiology, 143 (2). pp. 587-599. ISSN 0032-0889

Stein, L. D. (2007) Unix survival guide. Curr Protoc Bioinformatics, Append. Appendix 1C.

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

Girard, L. R., Fiedler, T. J., Harris, T. W., Carvalho, F., Antoshechkin, I., Han, M., Sternberg, P.l W., Stein, L. D., Chalfie, M. (2007) WormBook: the online review of Caenorhabditis elegans biology. Nucleic Acids Res, 35 (Databa). D472-D475. ISSN 0305-1048

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

Chen, N., Mah, A., Blacque, O. E., Chu, J., Phgora, K., Bakhoum, M. W., Newbury, C. R. Hunt, Khattra, J., Chan, S. W., Go, A., Efimenko, E., Johnsen, R. C., Phirke, P., Swoboda, P., Marra, M., Moerman, D. G., Leroux, M. R., Baillie, D. L., Stein, L. D. (2006) Identification of ciliary and ciliopathy genes in Caenorhabditis elegans through comparative genomics. Genome Biology, 7 (12). R126. ISSN 1474-760X

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

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)

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)

Maher, C., Stein, L. D., Ware, D. (2006) Evolution of Arabidopsis microRNA families through duplication events. Genome Res, 16 (4). pp. 510-9. ISSN 1088-9051 (Print)

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)

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.

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

Thorisson, G. A., Smith, A. V., Krishnan, L., Stein, L. D. (2005) The International HapMap Project Web site. Genome Res, 15 (11). pp. 1592-3. ISSN 1088-9051 (Print)

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

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

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)

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)

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)

Pan, X., Li, Y., Stein, L. D. (2005) Site preferences of insertional mutagenesis agents in Arabidopsis. Plant Physiol, 137 (1). pp. 168-75. ISSN 0032-0889 (Print)

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)

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

Stein, L. D. (2004) Human genome: end of the beginning. Nature, 431 (7011). pp. 915-6. ISSN 1476-4687 (Electronic)

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

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)

Chen, N. (2004) Using RepeatMasker to identify repetitive elements in genomic sequences. Curr Protoc Bioinformatics, Chapte. Unit 4.10.

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)

Gibbs, R. A., Belmont, J. W., Hardenbol, P., Willis, T. D., Yu, F. L., Yang, H. M., Ch'ang, L. Y., Huang, W., Liu, B., Shen, Y., Tam, P. K. H., Tsui, L. C., Waye, M. M. Y., Wong, J. T. F., Zeng, C. Q., Zhang, Q. R., Chee, M. S., Galver, L. M., Kruglyak, S., Murray, S. S., Oliphant, A. R., Montpetit, A., Hudson, T. J., Chagnon, F., Ferretti, V., Leboeuf, M., Phillips, M. S., Verner, A., Kwok, P. Y., Duan, S. H., Lind, D. L., Miller, R. D., Rice, J. P., Saccone, N. L., Taillon-Miller, P., Xiao, M., Nakamura, Y., Sekine, A., Sorimachi, K., Tanaka, T., Tanaka, Y., Tsunoda, T., Yoshino, E., Bentley, D. R., Deloukas, P., Hunt, S., Powell, D., Altshuler, D., Gabriel, S. B., Qiu, R. Z., Ken, A., Dunston, G. M., Kato, K., Niikawa, N., Knoppers, B. M., Foster, M. W., Clayton, E. W., Wang, V. O., Watkin, J., Gibbs, R. A., Belmont, J. W., Sodergren, E., Weinstock, G. M., Wilson, R. K., Fulton, L. L., Rogers, J., Birren, B. W., Han, H., Wang, H. G., Godbout, M., Wallenburg, J. C., L'Archeveque, P., Bellemare, G., Todani, K., Fujita, T., Tanaka, S., Holden, A. L., Lai, E. H., Collins, F. S., Brooks, L. D., McEwen, J. E., Guyer, M. S., Jordan, E., Peterson, J. L., Spiegel, J., Sung, L. M., Zacharia, L. F., Kennedy, K., Dunn, M. G., Seabrook, R., Shillito, M., Skene, B., Stewart, J. G., Valle, D. L., Clayton, E. W., Jorde, L. B., Belmont, J. W., Chakravarti, A., Cho, M. K., Duster, T. (2003) The International HapMap Project. Nature, 426 (6968). pp. 789-796. ISSN 0028-0836

Stein, L. D., Bao, Z., Blasiar, D., Blumenthal, T., Brent, M. R., Chen, N., Chinwalla, A., Clarke, L., Clee, C., Coghlan, A., Coulson, A., D'Eustachio, P., Fitch, D. H., Fulton, L. A., Fulton, R. E., Griffiths-Jones, S., Harris, T. W., Hillier, L. W., Kamath, R., Kuwabara, P. E., Mardis, E. R., Marra, M. A., Miner, T. L., Minx, P., Mullikin, J. C., Plumb, R. W., Rogers, J., Schein, J. E., Sohrmann, M., Spieth, J., Stajich, J. E., Wei, C., Willey, D., Wilson, R. K., Durbin, R., Waterston, R. H. (2003) The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics. PLoS Biology, 1 (2). E45. ISSN 1544-9173

May, B. P., Liu, H., Vollbrecht, E., Senior, L., Rabinowicz, P. D., Roh, D., Pan, X. K., Stein, L., Freeling, M., Alexander, D., Martienssen, R. (2003) Maize-targeted mutagenesis: A knockout resource for maize. Proceedings of the National Academy of Sciences of the United States of America, 100 (20). pp. 11541-11546. ISSN 0027-8424

Matise, T. C., Sachidanandam, R., Clark, A. G., Kruglyak, L., Wijsman, E., Kakol, J., Buyske, S., Chui, B., Cohen, P., de Toma, C., Ehm, M., Glanowski, S., He, C. S., Heil, J., Markianos, K., McMullen, I., Pericak-Vance, M. A., Silbergleit, A., Stein, L., Wagner, M., Wilson, A. F., Winick, J. D., Winn-Deen, E. S., Yamashiro, C. T., Cann, H. M., Lai, E., Holden, A. L. (2003) A 3.9-centimorgan-resolution human single-nucleotide polymorphism linkage map and screening set. American Journal of Human Genetics, 73 (2). pp. 271-284. ISSN 0002-9297

Stein, L. (2003) Large scale sequencing. Current Protocols in Bioinformatics. Unit 11.01. ISSN 1934-340X (Electronic)1934-3396 (Linking)

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

Ware, D., Stein, L. (2003) Comparison of genes among cereals. Current Opinion in Plant Biology, 6 (2). pp. 121-7. ISSN 1369-5266

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

Thorisson, G. A., Stein, L. D. (2003) The SNP Consortium website: past, present and future. Nucleic Acids Research, 31 (1). pp. 124-127. ISSN 0305-1048

Harris, T. W., Lee, R., Schwarz, E., Bradnam, K., Lawson, D., Chen, W., Blasier, D., Kenny, E., Cunningham, F., Kishore, R., Chan, J., Muller, H. M., Petcherski, A., Thorisson, G., Day, A., Bieri, T., Rogers, A., Chen, C. K., Spieth, J., Sternberg, P., Durbin, R., Stein, L. D. (2003) WormBase: a cross-species database for comparative genomics. Nucleic Acids Research, 31 (1). pp. 133-137. ISSN 0305-1048

Yu, Y., Rambo, T., Currie, J., Saski, C., Kim, H. R., Collura, K., Thompson, S., Simmons, J., Yang, T. J., Nah, G., Patel, A. J., Thurmond, S., Henry, D., Oates, R., Palmer, M., Pries, G., Gibson, J., Anderson, H., Paradkar, M., Crane, L., Dale, J., Carver, M. B., Wood, T., Frisch, D., Engler, F., Soderlund, C., Palmer, L. E., Tetylman, L., Nascimento, L., de la Bastide, M., Spiegel, L., Ware, D., O'Shaughnessy, A., Dike, S., Dedhia, N., Preston, R., Huang, E., Ferraro, K., Kuit, K., Miller, B., Zutavern, T., Katzenberger, F., Muller, S., Balija, V., Martienssen, R. A., Stein, L., Minx, P., Johnson, D., Cordum, H., Mardis, E., Cheng, Z., Jiang, J., Wilson, R., McCombie, W. R., Wing, R. A., Yuan, Q., Ouyang, S., Liu, J., Jones, K. M., Gansberger, K., Moffat, K., Hill, J., Tsitrin, T., Overton, L., Bera, J., Kim, M., Jin, S., Tallon, L., Ciecko, A., Pai, G., van Aken, S., Utterback, T., Reidmuller, S., Bormann, J., Feldblyum, T., Hsiao, J., Zismann, V., Blunt, S., de Vazeilles, A., Shaffer, T., Koo, H., Suh, B., Yang, Q., Haas, B., Peterson, J., Pertea, M., Volfovsky, N., Wortman, J., White, O., Salzberg, S. L., Fraser, C. M., Robin Buell, C., Messing, J., Song, R., Fuks, G., Llaca, V., Kovchak, S., Young, S., Bowers, J. E., Paterson, A. H. (2003) In-depth view of structure, activity, and evolution of rice chromosome 10. Science, 300 (5625). pp. 1566-1569. ISSN 00368075 (ISSN)

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

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

Stajich, J. E., Block, D., Boulez, K., Brenner, S. E., Chervitz, S. A., Dagdigian, C., Fuellen, G., Gilbert, J. G., Korf, I., Lapp, H., Lehvaslaiho, H., Matsalla, C., Mungall, C. J., Osborne, B. I., Pocock, M. R., Schattner, P., Senger, M., Stein, L. D., Stupka, E., Wilkinson, M. D., Birney, E. (2002) The Bioperl toolkit: Perl modules for the life sciences. Genome Research, 12 (10). pp. 1611-8. ISSN 10889051 (ISSN)

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

Matise, T. C., Sachidanandam, R., Clark, A., Kruglyak, L., Wijsman, E., Chui, B., Cohen, P., de Toma, C., Ehm, M., Glanowski, S., He, C., Heil, J., McMullen, I., Stein, L., Wagner, M., Winick, J., Winn-Deen, E. S., Cann, H. M., Lai, E., Holden, H. L. (2002) A high-resolution human SNP linkage map. American Journal of Human Genetics, 71 (4). p. 206. ISSN 0002-9297

Stein, L. (2002) Creating a bioinformatics nation. Nature, 417 (6885). pp. 119-120. ISSN 0028-0836

Bruskiewich, R., Coe, E. H., Jaiswal, P., McCouch, S., Polacco, M., Stein, L., Vincent, L., Ware, D. (2002) The Plant Ontology (TM) Consortium and plant ontologies. Comparative and Functional Genomics, 3 (2). pp. 137-142. ISSN 1531-6912

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

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

Liu, H., Sachidanandam, R., Stein, L. (2001) Comparative genomics between rice and Arabidopsis shows scant collinearity in gene order. Genome Research, 11 (12). pp. 2020-2026. ISSN 1088-9051

Stein, L. (2001) Genome annotation: From sequence to biology. Nature Reviews Genetics, 2 (7). pp. 493-503. ISSN 1471-0056

Stein, L. D. (2001) Genetic analyses on DNA microarrays. Curr Protoc Hum Genet, Chapte. Unit 11 .01.

Sachidanandam, R., Weissman, D., Schmidt, S. C., Kakol, J. M., Stein, L. D., Marth, G., Sherry, S., Mullikin, J. C., Mortimore, B. J., Willey, D. L., Hunt, S. E., Cole, C. G., Coggill, P. C., Rice, C. M., Ning, Z., Rogers, J., Bentley, D. R., Kwok, P. Y., Mardis, E. R., Yeh, R. T., Schultz, B., Cook, L., Davenport, R., Dante, M., Fulton, L., Hillier, L., Waterston, R. H., McPherson, J. D., Gilman, B., Schaffner, S., Van Etten, W. J., Reich, D., Higgins, J., Daly, M. J., Blumenstiel, B., Baldwin, J., Stange-Thomann, N., Zody, M. C., Linton, L., Lander, E. S., Altshuler, D. (2001) A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature, 409 (6822). pp. 928-33.

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

Dowell, R. D., Jokerst, R. M., Day, A., Eddy, S. R., Stein, L. (2001) The distributed annotation system. BMC Bioinformatics, 2. p. 7.

Piano, F., Schetter, A. J., Mangone, M., Stein, L., Kemphues, K. J. (2000) RNAi analysis of genes expressed in the ovary of Caenorhabditis elegans. Current Biology, 10 (24). pp. 1619-1622. ISSN 0960-9822

Stein, L. D. (1999) Internet access to the C. elegans genome. Trends in Genetics, 15 (10). pp. 425-7. ISSN 0168-9525 (Print)

Nusbaum, C., Slonim, D. K., Harris, K. L., Birren, B. W., Steen, R. G., Stein, L. D., Miller, J., Dietrich, W. F., Nahf, R., Wang, V., Merport, O., Castle, A. B., Husain, Z., Farino, G., Gray, D., Anderson, M. O., Devine, R., Horton, L. T., Ye, W., Wu, X., Kouyoumjian, V., Zemsteva, I. S., Wu, Y., Collymore, A. J., Courtney, D. F., Tam, J., Cadman, M., Haynes, A. R., Heuston, C., Marsland, T., Southwell, A., Trickett, P., Strivens, M. A., Ross, M. T., Makalowski, W., Xu, Y., Boguski, M. S., Carter, N. P., Denny, P., Brown, S. D., Hudson, T. J., Lander, E. S. (1999) A YAC-based physical map of the mouse genome. Nature Genetics, 22 (4). pp. 388-93.

Rabinowicz, P. D., Schutz, K., Dedhia, N., Yordan, C., Parnell, L. D., Stein, L., McCombie, W. R., Martienssen, R. A. (1999) Differential methylation of genes and retrotransposons facilitates shotgun sequencing of the maize genome. Nature Genetics, 23 (3). pp. 305-308. ISSN 10614036 (ISSN)

Stein, L. D., Thierry-Mieg, J. (1998) Scriptable access to the Caenorhabditis elegans genome sequence and other ACEDB databases. Genome Research, 8 (12). pp. 1308-15. ISSN 1088-9051 (Print)

Wang, D. G., Fan, J. B., Siao, C. J., Berno, A., Young, P., Sapolsky, R., Ghandour, G., Perkins, N., Winchester, E., Spencer, J., Kruglyak, L., Stein, L., Hsie, L., Topaloglou, T., Hubbell, E., Robinson, E., Mittmann, M., Morris, M. S., Shen, N. P., Kilburn, D., Rioux, J., Nusbaum, C., Rozen, S., Hudson, T. J., Lipshutz, R., Chee, M., Lander, E. S. (1998) Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome. Science, 280 (5366). pp. 1077-1082. ISSN 0036-8075

Stein, L. D., Cartinhour, S., Thierry-Mieg, D., Thierry-Mieg, J. (1998) JADE: an approach for interconnecting bioinformatics databases. Gene, 209 (1-2). GC39-GC43.

Stein, L. D. (1998) Of mice and men: navigating public physical mapping databases. Methods of Biochemical Analysis, 39. pp. 268-98. ISSN 0076-6941 (Print)

Book Section

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)

Stein, L. D. (2001) Using Perl to facilitate biological analysis. In: Bioinformatics: a practical guide to the analysis of genes and proteins. Methods of Biochemical Analysis, 43 . Wiley, New York, pp. 413-49. ISBN 0076-6941 (Print)

This list was generated on Sat Dec 16 00:26:52 2017 EST.
CSHL HomeAbout CSHLResearchEducationNews & FeaturesCampus & Public EventsCareersGiving