Items where Subject is "bioinformatics > genomics and proteomics > alignment > sequence alignment"

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Number of items at this level: 40.

A

Albert, F. W., Hodges, E., Jensen, J. D., Besnier, F., Xuan, Z. Y., Rooks, M., Bhattacharjee, A., Brizuela, L., Good, J. M., Green, R. E., Burbano, H. A., Plyusnina, I. Z., Trut, L., Andersson, L., Schoneberg, T., Carlborg, O., Hannon, G. J., Paabo, S. (2011) Targeted resequencing of a genomic region influencing tameness and aggression reveals multiple signals of positive selection. Heredity, 107 (3). pp. 205-214. ISSN 0018-067X

Alestrom, P., Stenlund, A., Li, P., Bellett, A., Pettersson, U. (1982) Sequence homology between avian and human adenoviruses. J Virol, 42 (1). pp. 306-10. ISSN 0022-538X (Print)0022-538X (Linking)

Alestrom, P., Stenlund, A., Li, P., Pettersson, U. (1982) A common sequence in the inverted terminal repetitions of human and avian adenoviruses. Gene, 18 (2). pp. 193-7. ISSN 0378-1119 (Print)0378-1119 (Linking)

B

Bevan, M., Bancroft, I., Mewes, H. W., Martienssen, R., McCombie, R. (1999) Clearing a path through the jungle: Progress in Arabidopsis genomics. Bioessays, 21 (2). pp. 110-120. ISSN 02659247 (ISSN)

Birol, I., Champ, M., Cant, J. (2010) GENOME INFORMATICS. In: Joint Cold Spring Harbor Laboratory/Wellcome Trust Conference on GENOME INFORMATICS, September 15–September 19, 2010, Wellcome Conference Center.

Bogdanove, A. J., Koebnik, R., Lu, H., Furutani, A., Angiuoli, S. V., Patil, P. B., Van Sluys, M. A., Ryan, R. P., Meyer, D. F., Han, S. W., Aparna, G., Rajaram, M., Delcher, A. L., Phillippy, A. M., Puiu, D., Schatz, M. C., Shumway, M., Sommer, D. D., Trapnell, C., Benahmed, F., Dimitrov, G., Madupu, R., Radune, D., Sullivan, S., Jha, G., Ishihara, H., Lee, S. W., Pandey, A., Sharma, V., Sriariyanun, M., Szurek, B., Vera-Cruz, C. M., Dorman, K. S., Ronald, P. C., Verdier, V., Dow, J. M., Sonti, R. V., Tsuge, S., Brendel, V. P., Rabinowicz, P. D., Leach, J. E., White, F. F., Salzberg, S. L. (2011) Two new complete genome sequences offer insight into host and tissue specificity of plant pathogenic Xanthomonas spp. Journal of Bacteriology, 193 (19). pp. 5450-5464. ISSN 00219193 (ISSN)

C

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

Capra, J. A., Hubisz, M. J., Kostka, D., Pollard, K. S., Siepel, A. (2013) A model-based analysis of GC-biased gene conversion in the human and chimpanzee genomes. PLoS Genetics, 9 (8). e1003684. ISSN 15537390 (ISSN)

Church, D. M., Schneider, V. A., Steinberg, K. M., Schatz, M. C., Quinlan, A. R., Chin, C. S., Kitts, P. A., Aken, B., Marth, G. T., Hoffman, M. M., Herrero, J., Mendoza, M. L. Z., Durbin, R., Flicek, P. (2015) Extending reference assembly models. Genome Biology, 16. Article no. 13. ISSN 1465-6906

D

Djebali, S., Kapranov, P., Foissac, S., Lagarde, J., Reymond, A., Ucla, C., Wyss, C., Drenkow, J., Dumais, E., Murray, R. R., Lin, C., Szeto, D., Denoeud, F., Calvo, M., Frankish, A., Harrow, J., Makrythanasis, P., Vidal, M., Salehi-Ashtiani, K., Antonarakis, S. E., Gingeras, T. R., Guigo, R. (2008) Efficient targeted transcript discovery via array-based normalization of RACE libraries. Nature Methods, 5 (7). pp. 629-35. ISSN 15487091 (ISSN)

Dobin, A., Davis, C. A., Schlesinger, F., Drenkow, J., Zaleski, C., Jha, S., Batut, P., Chaisson, M., Gingeras, T. R. (2013) STAR: ultrafast universal RNA-seq aligner. Bioinformatics, 29 (1). pp. 15-21. ISSN 1367-4803

Dobin, A., Gingeras, T. R. (2016) Optimizing RNA-Seq Mapping with STAR. Methods Mol Biol, 1415. pp. 245-262. ISSN 1940-6029 (Electronic)1064-3745 (Linking)

F

Farrar, J. E., Nater, M., Caywood, E., McDevitt, M. A., Kowalski, J., Takemoto, C. M., Talbot, C. C., Meltzer, P., Esposito, D., Beggs, A. H., Schneider, H. E., Grabowska, A., Ball, S. E., Niewiadomska, E., Sieff, C. A., Vlachos, A., Atsidaftos, E., Ellis, S. R., Lipton, J. M., Gazda, H. T., Areci, R. J. (2008) Abnormalities of the large ribosomal subunit protein, Rp135a, in Diamond-Blackfan anemia. Blood, 112 (5). pp. 1582-1592. ISSN 0006-4971

G

Gallavotti, A., Barazesh, S., Malcomber, S., Hall, D., Jackson, D. P., Schmidt, R. J., McSteen, P. (2008) sparse inflorescence1 encodes a monocot-specific YUCCA-like gene required for vegetative and reproductive development in maize. Proceedings of the National Academy of Sciences of the United States of America, 105 (39). pp. 15196-201. ISSN 0027-8424

Green, S. R., Manche, L., Mathews, M. B. (1995) Two functionally distinct RNA-binding motifs in the regulatory domain of the protein kinase DAI. Mol Cell Biol, 15 (1). pp. 358-64. ISSN 0270-7306 (Print)

Gronau, I., Hubisz, M. J., Gulko, B., Danko, C. G., Siepel, A. (2011) Bayesian inference of ancient human demography from individual genome sequences. Nat Genet, 43 (10). pp. 1031-4. ISSN 1061-4036

H

Hinkley, C. S., Blasco, M. A., Funk, W. D., Feng, J., Villeponteau, B., Greider, C. W., Herr, W. (1998) The mouse telomerase RNA 5"-end lies just upstream of the telomerase template sequence. Nucleic Acids Research, 26 (2). pp. 532-6. ISSN 0305-1048

K

Kosiol, C., Vinar, T., da Fonseca, R. R., Hubisz, M. J., Bustamante, C. D., Nielsen, R., Siepel, A. (2008) Patterns of positive selection in six Mammalian genomes. Plos Genetics, 4 (8). e1000144. ISSN 1553-7390

Kostka, D., Hubisz, M. J., Siepel, A., Pollard, K. S. (2012) The role of GC-biased gene conversion in shaping the fastest evolving regions of the human genome. Mol Biol Evol, 29 (3). pp. 1047-57. ISSN 0737-4038

L

Langmead, B., Schatz, M. C., Lin, J., Pop, M., Salzberg, S. L. (2009) Searching for SNPs with cloud computing. Genome Biology, 10 (11). ISSN 14747596 (ISSN)

M

Ma, Y., Mathews, M. B. (1996) Structure, function, and evolution of adenovirus-associated RNA: a phylogenetic approach. Journal of Virology, 70 (8). pp. 5083-99. ISSN 0022-538X

Margulies, E. H., Cooper, G. M., Asimenos, G., Thomas, D. J., Dewey, C. N., Siepel, A., Birney, E., Keefe, D., Schwartz, A. S., Hou, M., Taylor, J., Nikolaev, S., Montoya-Burgos, J. I., Loytynoja, A., Whelan, S., Pardi, F., Massingham, T., Brown, J. B., Bickel, P., Holmes, I., Mullikin, J. C., Ureta-Vidal, A., Paten, B., Stone, E. A., Rosenbloom, K. R., Kent, W. J., Bouffard, G. G., Guan, X., Hansen, N. F., Idol, J. R., Maduro, V. V., Maskeri, B., McDowell, J. C., Park, M., Thomas, P. J., Young, A. C., Blakesley, R. W., Muzny, D. M., Sodergren, E., Wheeler, D. A., Worley, K. C., Jiang, H., Weinstock, G. M., Gibbs, R. A., Graves, T., Fulton, R., Mardis, E. R., Wilson, R. K., Clamp, M., Cuff, J., Gnerre, S., Jaffe, D. B., Chang, J. L., Lindblad-Toh, K., Lander, E. S., Hinrichs, A., Trumbower, H., Clawson, H., Zweig, A., Kuhn, R. M., Barber, G., Harte, R., Karolchik, D., Field, M. A., Moore, R. A., Matthewson, C. A., Schein, J. E., Marra, M. A., Antonarakis, S. E., Batzoglou, S., Goldman, N., Hardison, R., Haussler, D., Miller, W., Pachter, L., Green, E. D., Sidow, A. (2007) Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. Genome Research, 17 (6). pp. 760-74. ISSN 1088-9051

Menon, R. K., Bhat, G. P., Schatz, M. C. (2011) Rapid parallel genome indexing with MapReduce. 2nd International Workshop on MapReduce and Its Applications, MapReduce'11, Co-located with 20th International ACM Symposium on High-Performance Parallel and Distributed Computing, HPDC 2011 . ACM, pp. 51-58. ISBN 9781450307000 (ISBN)

Miller, W., Rosenbloom, K., Hardison, R. C., Hou, M., Taylor, J., Raney, B., Burhans, R., King, D. C., Baertsch, R., Blankenberg, D., Kosakovsky Pond, S. L., Nekrutenko, A., Giardine, B., Harris, R. S., Tyekucheva, S., Diekhans, M., Pringle, T. H., Murphy, W. J., Lesk, A., Weinstock, G. M., Lindblad-Toh, K., Gibbs, R. A., Lander, E. S., Siepel, A., Haussler, D., Kent, W. J. (2007) 28-way vertebrate alignment and conservation track in the UCSC Genome Browser. Genome Research, 17 (12). pp. 1797-808. ISSN 1088-9051

N

Nene, V., Wortman, J. R., Lawson, D., Haas, B., Kodira, C., Tu, Z., Loftus, B., Xi, Z., Megy, K., Grabherr, M., Ren, Q., Zdobnov, E. M., Lobo, N. F., Campbell, K. S., Brown, S. E., Bonaldo, M. F., Zhu, J., Sinkins, S. P., Hogenkamp, D. G., Amedeo, P., Arensburger, P., Atkinson, P. W., Bidwell, S., Biedler, J., Birney, E., Bruggner, R. V., Costas, J., Coy, M. R., Crabtree, J., Crawford, M., DeBruyn, B., DeCaprio, D., Eiglmeier, K., Eisenstadt, E., El-Dorry, H., Gelbart, W. M., Gomes, S. L., Hammond, M., Hannick, L. I., Hogan, J. R., Holmes, M. H., Jaffe, D., Johnston, J. S., Kennedy, R. C., Koo, H., Kravitz, S., Kriventseva, E. V., Kulp, D., LaButti, K., Lee, E., Li, S., Lovin, D. D., Mao, C., Mauceli, E., Menck, C. F. M., Miller, J. R., Montgomery, P., Mori, A., Nascimento, A. L., Naveira, H. F., Nusbaum, C., O'Leary, S., Orvis, J., Pertea, M., Quesneville, H., Reidenbach, K. R., Rogers, Y. H., Roth, C. W., Schneider, J. R., Schatz, M., Shumway, M., Stanke, M., Stinson, E. O., Tubio, J. M. C., VanZee, J. P., Verjovski-Almeida, S., Werner, D., White, O., Wyder, S., Zeng, Q., Zhao, Q., Zhao, Y., Hill, C. A., Raikhel, A. S., Soares, M. B., Knudson, D. L., Lee, N. H., Galagan, J., Salzberg, S. L., Paulsen, I. T., Dimopoulos, G., Collins, F. H., Birren, B., Fraser-Liggett, C. M., Severson, D. W. (2007) Genome sequence of Aedes aegypti, a major arbovirus vector. Science, 316 (5832). pp. 1718-1723. ISSN 00368075 (ISSN)

Neuwald, A. F. (2003) Evolutionary clues to DNA polymerase III beta clamp structural mechanisms. Nucleic Acids Research, 31 (15). pp. 4503-4516. ISSN 0305-1048

Neuwald, A. F., Aravind, L., Spouge, J. L., Koonin, E. V. (1999) AAA+: A class of chaperone-like ATPases associated with the assembly, operation, and disassembly of protein complexes. Genome Research, 9 (1). pp. 27-43. ISSN 1088-9051 (Print)

O

O'Gara, M., McCloy, K., Malone, T., Cheng, X. (1995) Structure-based sequence alignment of three AdoMet-dependent DNA methyltransferases. Gene, 157 (1-2). pp. 135-8. ISSN 0378-1119 (Print)

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. (2010) Detection of nonneutral substitution rates on mammalian phylogenies. Genome Res, 20 (1). pp. 110-21. ISSN 1088-9051

R

Rasmussen, M. D., Hubisz, M. J., Gronau, I., Siepel, A. (2014) Genome-wide inference of ancestral recombination graphs. PLoS Genetics, 10 (5). e1004342. ISSN 15537390 (ISSN)

S

Salzberg, S. L., Phillippy, A. M., Zimin, A., Puiu, D., Magoc, T., Koren, S., Treangen, T. J., Schatz, M. C., Delcher, A. L., Roberts, M., Marcais, G., Pop, M., Yorke, J. A. (2012) GAGE: A critical evaluation of genome assemblies and assembly algorithms. Genome Res, 22 (3). pp. 557-67. ISSN 1549-5469 (Electronic)1088-9051 (Linking)

Schatz, M. C., Trapnell, C., Delcher, A. L., Varshney, A. (2007) High-throughput sequence alignment using Graphics Processing Units. Bmc Bioinformatics, 8. ISSN 14712105 (ISSN)

Siepel, A., Haussler, D. (2004) Phylogenetic estimation of context-dependent substitution rates by maximum likelihood. Mol Biol Evol, 21 (3). pp. 468-88. ISSN 0737-4038 (Print)0737-4038

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

T

Trapnell, C., Schatz, M. C. (2009) Optimizing data intensive GPGPU computations for DNA sequence alignment. Parallel Computing, 35 (8-9). pp. 429-440. ISSN 01678191 (ISSN)

W

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)

Wong, M. W., Henry, R. W., Ma, B., Kobayashi, R., Klages, N., Matthias, P., Strubin, M., Hernandez, N. (1998) The large subunit of basal transcription factor SNAPc is a Myb domain protein that interacts with Oct-1. Molecular and Cellular Biology, 18 (1). pp. 368-77. ISSN 0270-7306 (Print)

Z

Zhang, M. Q. (2000) Discriminant analysis and its application in DNA sequence motif recognition. Brief Bioinform, 1 (4). pp. 331-42. ISSN 1467-5463 (Print)

Zhang, M. Q., Marr, T. G. (1995) Alignment of molecular sequences seen as random path analysis. Journal of Theoretical Biology, 174 (2). pp. 119-29. ISSN 0022-5193 (Print)

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