Items where Subject is "genome annotation"

A

Ahn, J., Won, T. W., Zia, A., Reutter, H., Kaplan, D. E., Sparks, R., Gruen, J. R. (November 2001) Peaks of linkage are localized by a BAC/PAC contig of the 6p reading disability locus. Genomics, 78 (1-2). pp. 19-29. ISSN 0888-7543

Alonge, M., Wang, X., Benoit, M., Soyk, S., Pereira, L., Zhang, L., Suresh, H., Ramakrishnan, S., Maumus, F., Ciren, D., Levy, Y., Harel, T. H., Shalev-Schlosser, G., Amsellem, Z., Razifard, H., Caicedo, A. L., Tieman, D. M., Klee, H., Kirsche, M., Aganezov, S., Ranallo-Benavidez, T. R., Lemmon, Z. H., Kim, J., Robitaille, G., Kramer, M., Goodwin, S., McCombie, W. R., Hutton, S., Van Eck, J., Gillis, J., Eshed, Y., Sedlazeck, F. J., van der Knaap, E., Schatz, M. C., Lippman, Z. B. (July 2020) Major Impacts of Widespread Structural Variation on Gene Expression and Crop Improvement in Tomato. Cell, 182 (1). 145-161.e23. ISSN 0092-8674 (Print)0092-8674

Amaral, Paulo, Carbonell-Sala, Silvia, De La Vega, Francisco M, Faial, Tiago, Frankish, Adam, Gingeras, Thomas, Guigo, Roderic, Harrow, Jennifer L, Hatzigeorgiou, Artemis G, Johnson, Rory, Murphy, Terence D, Pertea, Mihaela, Pruitt, Kim D, Pujar, Shashikant, Takahashi, Hazuki, Ulitsky, Igor, Varabyou, Ales, Wells, Christine A, Yandell, Mark, Carninci, Piero, Salzberg, Steven L (October 2023) The status of the human gene catalogue. Nature, 622 (7981). pp. 41-47. ISSN 0028-0836

Amaral, Paulo, Carbonell-Sala, Silvia, De La Vega, Francisco M, Faial, Tiago, Frankish, Adam, Gingeras, Thomas, Guigo, Roderic, Harrow, Jennifer L, Hatzigeorgiou, Artemis G, Johnson, Rory, Murphy, Terence D, Pertea, Mihaela, Pruitt, Kim D, Pujar, Shashikant, Takahashi, Hazuki, Ulitsky, Igor, Varabyou, Ales, Wells, Christine A, Yandell, Mark, Carninci, Piero, Salzberg, Steven L (March 2023) The status of the human gene catalogue. (Submitted)

Andrews, Peter A., Iossifov, Ivan, Kendall, Jude, Marks, Steven, Muthuswamy, Lakshmi, Wang, Zihua, Levy, Dan, Wigler, Michael (September 2016) MUMdex: MUM-based structural variation detection. bioRxiv. 078261.

B

Benoit, Matthias, Drost, Hajk-Georg (April 2021) A Predictive Approach to Infer the Activity and Natural Variation of Retrotransposon Families in Plants. Methods in Molecular Biology, 2250. pp. 1-14. ISSN 1064-3745

Bradnam, K. R., Fass, J. N., Alexandrov, A., Baranay, P., Bechner, M., Birol, I., Boisvert, S., Chapman, J. A., Chapuis, G., Chikhi, R., Chitsaz, H., Chou, W. C., Corbeil, J., Del Fabbro, C., Docking, T. R., Durbin, R., Earl, D., Emrich, S., Fedotov, P., Fonseca, N. A., Ganapathy, G., Gibbs, R. A., Gnerre, S., Godzaridis, E., Goldstein, S., Haimel, M., Hall, G., Haussler, D., Hiatt, J. B., Ho, I. Y., Howard, J., Hunt, M., Jackman, S. D., Jaffe, D. B., Jarvis, E. D., Jiang, H., Kazakov, S., Kersey, P. J., Kitzman, J. O., Knight, J. R., Koren, S., Lam, T. W., Lavenier, D., Laviolette, F., Li, Y., Li, Z., Liu, B., Liu, Y., Luo, R., Maccallum, I., Macmanes, M. D., Maillet, N., Melnikov, S., Naquin, D., Ning, Z., Otto, T. D., Paten, B., Paulo, O. S., Phillippy, A. M., Pina-Martins, F., Place, M., Przybylski, D., Qin, X., Qu, C., Ribeiro, F. J., Richards, S., Rokhsar, D. S., Ruby, J. G., Scalabrin, S., Schatz, M. C., Schwartz, D. C., Sergushichev, A., Sharpe, T., Shaw, T. I., Shendure, J., Shi, Y., Simpson, J. T., Song, H., Tsarev, F., Vezzi, F., Vicedomini, R., Vieira, B. M., Wang, J., Worley, K. C., Yin, S., Yiu, S. M., Yuan, J., Zhang, G., Zhang, H., Zhou, S., Korf, I. F. (2013) Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. Gigascience, 2 (1). p. 10. ISSN 2047-217x

C

Campbell, M. S., Law, M., Holt, C., Stein, J. C., Moghe, G. D., Hufnagel, D. E., Lei, J., Achawanantakun, R., Jiao, D., Lawrence, C. J., Ware, D., Shiu, S. H., Childs, K. L., Sun, Y., Jiang, N., Yandell, M. (February 2014) MAKER-P: A Tool Kit for the Rapid Creation, Management, and Quality Control of Plant Genome Annotations. Plant Physiol, 164 (2). pp. 513-24. ISSN 0032-0889

D

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

Dunham, I., Kundaje, A., Aldred, S. F., Collins, P. J., Davis, C., Doyle, F., Epstein, C. B., Frietze, S., Harrow, J., Kaul, R., Khatun, J., Lajoie, B. R., Landt, S. G., Lee, B. K., Pauli, F., Rosenbloom, K. R., Sabo, P., Safi, A., Sanyal, A., Shoresh, N., Simon, J. M., Song, L., Trinklein, N. D., Altshuler, R. C., Birney, E., Brown, J. B., Cheng, C., Djebali, S., Dong, X. J., Ernst, J., Furey, T. S., Gerstein, M., Giardine, B., Greven, M., Hardison, R. C., Harris, R. S., Herrero, J., Hoffman, M. M., Iyer, S., Kellis, M., Kheradpour, P., Lassmann, T., Li, Q. H., Lin, X., Marinov, G. K., Merkel, A., Mortazavi, A., Parker, S. C. J., Reddy, T. E., Rozowsky, J., Schlesinger, F., Thurman, R. E., Wang, J., Ward, L. D., Whitfield, T. W., Wilder, S. P., Wu, W., Xi, H. L. S., Yip, K. Y., Zhuang, J. L., Bernstein, B. E., Green, E. D., Gunter, C., Snyder, M., Pazin, M. J., Lowdon, R. F., Dillon, L. A. L., Adams, L. B., Kelly, C. J., Zhang, J., Wexler, J. R., Good, P. J., Feingold, E. A., Crawford, G. E., Dekker, J., Elnitski, L., Farnham, P. J., Giddings, M. C., Gingeras, T. R., Guigo, R., Hubbard, T. J., Kent, W. J., Lieb, J. D., Margulies, E. H., Myers, R. M., Stamatoyannopoulos, J. A., Tenenbaum, S. A., Weng, Z. P., White, K. P., Wold, B., Yu, Y., Wrobel, J., Risk, B. A., Gunawardena, H. P., Kuiper, H. C., Maier, C. W., Xie, L., Chen, X., Mikkelsen, T. S., Gillespie, S. (September 2012) An integrated encyclopedia of DNA elements in the human genome. Nature, 489 (7414). pp. 57-74. ISSN 0028-0836

G

Ganapathy, G., Howard, J. T., Ward, J. M., Li, J., Li, B., Li, Y., Xiong, Y., Zhang, Y., Zhou, S., Schwartz, D. C., Schatz, M., Aboukhalil, R., Fedrigo, O., Bukovnik, L., Wang, T., Wray, G., Rasolonjatovo, I., Winer, R., Knight, J. R., Koren, S., Warren, W. C., Zhang, G., Phillippy, A. M., Jarvis, E. D. (July 2014) High-coverage sequencing and annotated assemblies of the budgerigar genome. Gigascience, 3. p. 11. ISSN 2047-217x

Gillis, J., Pavlidis, P. (February 2013) Assessing identity, redundancy and confounds in Gene Ontology annotations over time. Bioinformatics, 29 (4). pp. 476-82. ISSN 1367-4811 (Electronic)1367-4803 (Linking)

H

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

Hufford, Matthew B, Seetharam, Arun S, Woodhouse, Margaret R, Chougule, Kapeel M, Ou, Shujun, Liu, Jianing, Ricci, William A, Guo, Tingting, Olson, Andrew, Qiu, Yinjie, Della Coletta, Rafael, Tittes, Silas, Hudson, Asher I, Marand, Alexandre P, Wei, Sharon, Lu, Zhenyuan, Wang, Bo, Tello-Ruiz, Marcela K, Piri, Rebecca D, Wang, Na, Kim, Dong Won, Zeng, Yibing, O'Connor, Christine H, Li, Xianran, Gilbert, Amanda M, Baggs, Erin, Krasileva, Ksenia V, Portwood, John L, Cannon, Ethalinda KS, Andorf, Carson M, Manchanda, Nancy, Snodgrass, Samantha J, Hufnagel, David E, Jiang, Qiuhan, Pedersen, Sarah, Syring, Michael L, Kudrna, David A, Llaca, Victor, Fengler, Kevin, Schmitz, Robert J, Ross-Ibarra, Jeffrey, Yu, Jianming, Gent, Jonathan I, Hirsch, Candice N, Ware, Doreen, Dawe, R Kelly (August 2021) De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes. Science, 373 (6555). pp. 655-662. ISSN 0036-8075

Hulse-Kemp, Amanda M, Bostan, Hamed, Chen, Shiyu, Ashrafi, Hamid, Stoffel, Kevin, Sanseverino, Walter, Li, Linzhou, Cheng, Shifeng, Schatz, Michael C, Garvin, Tyler, du Toit, Lindsey J, Tseng, Elizabeth, Chin, Jason, Iorizzo, Massimo, Van Deynze, Allen (June 2021) An anchored chromosome-scale genome assembly of spinach improves annotation and reveals extensive gene rearrangements in euasterids. The Plant Genome. e20101. ISSN 1940-3372

I

Itoh, T., Tanaka, T., Barrero, R. A., Yamasaki, C., Fujii, Y., Hilton, P. B., Antonio, B. A., Aono, H., Apweiler, R., Bruskiewich, R., Bureau, T., Burr, F., De Oliveira, A. C., Fuks, G., Habara, T., Haberer, G., Han, B., Harada, E., Hiraki, A. T., Hirochika, H., Hoen, D., Hokari, H., Hosokawa, S., Hsing, Y. I., Ikawa, H., Ikeo, K., Imanishi, T., Ito, Y., Jaiswal, P., Kanno, M., Kawahara, Y., Kawamura, T., Kawashima, H., Khurana, J. P., Kikuchi, S., Komatsu, S., Koyanagi, K. O., Kubooka, H., Lieberherr, D., Lin, Y. C., Lonsdale, D., Matsumoto, T., Matsuya, A., McCombie, W. R., Messing, J., Miyao, A., Mulder, N., Nagamura, Y., Nam, J., Namiki, N., Numa, H., Nurimoto, S., O'Donovan, C., Ohyanagi, H., Okido, T., Oota, S., Osato, N., Palmer, L. E., Quetier, F., Raghuvanshi, S., Saichi, N., Sakai, H., Sakai, Y., Sakata, K., Sakurai, T., Sato, F., Sato, Y., Schoof, H., Seki, M., Shibata, M., Shimizu, Y., Shinozaki, K., Shinso, Y., Singh, N. K., Smith-White, B., Takeda, J. I., Tanino, M., Tatusova, T., Thongjuea, S., Todokoro, F., Tsugane, M., Tyagi, A. K., Vanavichit, A., Wang, A., Wing, R. A., Yamaguchi, K., Yamamoto, M., Yamamoto, N., Yu, Y., Zhang, H., Zhao, Q., Higo, K., Burr, B., Gojobori, T., Sasaki, T. (2007) Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana: The Rice Annotation Project. Genome Research, 17 (2). pp. 175-183. ISSN 10889051 (ISSN)

K

Klessig, D. F., Wigler, M. H., Grodzicker, T. (1980) Construction of Co Transformation of Human Cell Lines Which Express Segments of the Adenovirus Genome. Journal of Supramolecular Structure, 9 (SUPPL.). p. 256.

L

Law, M., Childs, K. L., Campbell, M. S., Stein, J. C., Holt, C., Panchy, N., Lei, J., Jao, D., Andorf, C. M., Lawrence, C. J., Ware, D., Shiu, S. H., Sun, Y., Jiang, N., Yandell, M. (November 2014) Automated update, revision and quality control of the Zea mays genome annotations using MAKER-P improves the B73 RefGen_v3 gene models and identifies new genes. Plant Physiology. ISSN 0032-0889

Law, M., Childs, K. L., Campbell, M. S., Stein, J. C., Olson, A. J., Holt, C., Panchy, N., Lei, J., Jiao, D., Andorf, C. M., Lawrence, C. J., Ware, D., Shiu, S. H., Sun, Y., Jiang, N., Yandell, M. (January 2015) Automated Update, Revision, and Quality Control of the Maize Genome Annotations Using MAKER-P Improves the B73 RefGen_v3 Gene Models and Identifies New Genes. Plant Physiol, 167 (1). pp. 25-39. ISSN 0032-0889

Lisitsyn, N., Lisitsyn, N., Wigler, M. H. (February 1993) Cloning the differences between two complex genomes. Science, 259 (5097). pp. 946-51. ISSN 0036-8075 (Print)

O

Olson, A., Klein, R. R., Dugas, D. V., Lu, Z. Y., Regulski, M., Klein, P. E., Ware, D. (July 2014) Expanding and Vetting Sorghum bicolor Gene Annotations through Transcriptome and Methylome Sequencing. Plant Genome, 7 (2). p. 20. ISSN 1940-3372

Ou, S., Su, W., Liao, Y., Chougule, K., Agda, J. R. A., Hellinga, A. J., Lugo, C. S. B., Elliott, T. A., Ware, D., Peterson, T., Jiang, N., Hirsch, C. N., Hufford, M. B. (December 2019) Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline. Genome Biol, 20 (1). p. 275. ISSN 1474-7596 (Public Dataset)

P

Palmer, L. E., McCombie, W. R. (2002) On the importance of being finished. Genome Biology, 3 (10). 2010.1-2010.4. ISSN 14656906 (ISSN)

Pollard, K. S., Hubisz, M. J., Rosenbloom, K. R., Siepel, A. (January 2010) Detection of nonneutral substitution rates on mammalian phylogenies. Genome Res, 20 (1). pp. 110-21. ISSN 1088-9051

R

Rozowsky, Joel, Drenkow, Jorg, Yang, Yucheng, Gursoy, Gamze, Galeev, Timur, Borsari, Beatrice, Epstein, Charles, Xiong, Kun, Xu, Jinrui, Gao, Jiahao, Yu, Keyang, Berthel, Ana, Chen, Zhanlin, Navarro, Fabio, Liu, Jason, Sun, Maxwell, Wright, James, Chang, Justin, Cameron, Christopher, Shoresh, Noam, Gaskell, Elizabeth, Adrian, Jessika, Aganezov, Sergey, Balderrama-Gutierrez, Gabriela, Banskota, Samridhi, Corona, Guillermo, Chee, Sora, Chhetri, Surya, Martins, Gabriel, Danyko, Cassidy, Davis, Carrie, Farid, Daniel, Farrell, Nina, Gabdank, Idan, Gofin, Yoel, Gorkin, David, Gu, Mengting, Hecht, Vivian, Hitz, Benjamin, Issner, Robbyn, Kirsche, Melanie, Kong, Xiangmeng, Lam, Bonita, Li, Shantao, Li, Bian, Li, Tianxiao, Li, Xiqi, Lin, Khine, Luo, Ruibang, Mackiewicz, Mark, Moore, Jill, Mudge, Jonathan, Nelson, Nicholas, Nusbaum, Chad, Popov, Ioann, Pratt, Henry, Qiu, Yunjiang, Ramakrishnan, Srividya, Raymond, Joe, Salichos, Leonidas, Scavelli, Alexandra, Schreiber, Jacob, Sedlazeck, Fritz, See, Lei, Sherman, Rachel, Shi, Xu, Shi, Minyi, Sloan, Cricket, Strattan, Seth, Tan, Zhen, Tanaka, Forrest, Vlasova, Anna, Wang, Jun, Werner, Jonathan, Williams, Brian, Xu, Min, Yan, Chengfei, Yu, Lu, Zaleski, Christopher, Zhang, Jing, Cherry, Michael, Mendenhall, Eric, Noble, William, Weng, Zhiping, Levine, Morgan, Dobin, Alexander, Wold, Barbara, Mortazavi, Ali, Ren, Bing, Gillis, Jesse, Myers, Richard, Snyder, Michael, Choudhary, Jyoti, Milosavljevic, Aleksandar, Schatz, Michael, Guigo, Roderic, Bernstein, Bradley, Gingeras, Thomas, Gerstein, Mark (April 2021) Multi-tissue integrative analysis of personal epigenomes. bioRxiv. (Unpublished)

S

Saw, J. H. W., Schatz, M., Brown, M. V., Kunkel, D. D., Foster, J. S., Shick, H., Christensen, S., Hou, S., Wan, X., Donachie, S. P. (October 2013) Cultivation and Complete Genome Sequencing of Gloeobacter kilaueensis sp. nov., from a Lava Cave in Kīlauea Caldera, Hawai'i. PLoS ONE, 8 (10). ISSN 19326203 (ISSN)

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

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

Sun, S., Zhou, Y., Chen, J., Shi, J., Zhao, H., Zhao, H., Song, W., Zhang, M., Cui, Y., Dong, X., Liu, H., Ma, X., Jiao, Y., Wang, B., Wei, X., Stein, J. C., Glaubitz, J. C., Lu, F., Yu, G., Liang, C., Fengler, K., Li, B., Rafalski, A., Schnable, P. S., Ware, D. H., Buckler, E. S., Lai, J. (July 2018) Extensive intraspecific gene order and gene structural variations between Mo17 and other maize genomes. Nat Genet, 50 (9). pp. 1289-1295. ISSN 1061-4036

W

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