Items where Subject is "sequence alignment"

Paper

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. (September 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. (April 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. (May 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)

Alonge, M., Soyk, S., Ramakrishnan, S., Wang, X., Goodwin, S., Sedlazeck, F. J., Lippman, Z. B., Schatz, M. C. (October 2019) RaGOO: fast and accurate reference-guided scaffolding of draft genomes. Genome Biol, 20 (1). p. 224. ISSN 1474-7596 (Public Dataset)

Ballouz, S., Dobin, A., Gingeras, T. R., Gillis, J. (May 2018) The fractured landscape of RNA-seq alignment: the default in our STARs. Nucleic Acids Res. ISSN 0305-1048

Baumruker, T., Sturm, R., Herr, W. (November 1988) OBP100 binds remarkably degenerate octamer motifs through specific interactions with flanking sequences. Genes Dev, 2 (11). pp. 1400-13. ISSN 0890-9369

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)

Bhattacharya, Nicholas, Thomas, Neil, Rao, Roshan, Dauparas, Justas, Koo, Peter K, Baker, David, Song, Yun S, Ovchinnikov, Sergey (2022) Interpreting Potts and Transformer Protein Models Through the Lens of Simplified Attention. Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, 27. pp. 34-45. ISSN 2335-6936

Biederstedt, E., Oliver, J. C., Hansen, N. F., Jajoo, A., Dunn, N., Olson, A., Busby, B., Dilthey, A. T. (September 2018) NovoGraph: Human genome graph construction from multiple long-read de novo assemblies. F1000Res, 7. p. 1391. ISSN 2046-1402

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)

Canaran, P., Stein, L. D., Ware, D. H. (April 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. (January 2015) Extending reference assembly models. Genome Biology, 16. Article no. 13. ISSN 1465-6906

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) (Public Dataset)

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

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

Dobin, Alexander, Gingeras, Thomas (November 2013) Comment on TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions by Kim et al. BioRxiv. (Unpublished)

Efstratiadis, A., Maniatis, T., Kafatos, F. C. (1977) Primary Structure of Rabbit Beta-Globin Messenger-Rna as Determined from Cloned DNA. Cell, 10 (4). pp. 571-585.

Evans, R. M., Parkin, A., Roessler, M. M., Murphy, B. J., Adamson, H., Lukey, M. J., Sargent, F., Volbeda, A., Fontecilla-Camps, J. C., Armstrong, F. A. (February 2013) Principles of sustained enzymatic hydrogen oxidation in the presence of oxygen--the crucial influence of high potential Fe-S clusters in the electron relay of [NiFe]-hydrogenases. J Am Chem Soc, 135 (7). pp. 2694-707. ISSN 1520-5126

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. (September 2008) Abnormalities of the large ribosomal subunit protein, Rp135a, in Diamond-Blackfan anemia. Blood, 112 (5). pp. 1582-1592. ISSN 0006-4971

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. (January 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. (October 2011) Bayesian inference of ancient human demography from individual genome sequences. Nat Genet, 43 (10). pp. 1031-4. ISSN 1061-4036

Hinkley, C. S., Blasco, M. A., Funk, W. D., Feng, J., Villeponteau, B., Greider, C. W., Herr, W. (January 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

Katt, W. P., Lukey, M. J., Cerione, R. A. (January 2017) A tale of two glutaminases: homologous enzymes with distinct roles in tumorigenesis. Future Med Chem, 9 (2). pp. 223-243. ISSN 1756-8927

Kirsche, Melanie, Das, Arun, Schatz, Michael C (May 2021) Sapling: accelerating suffix array queries with learned data models. Bioinformatics, 37 (6). pp. 744-749. ISSN 1367-4803

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. (March 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

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)

Lukey, M. J., Roessler, M. M., Parkin, A., Evans, R. M., Davies, R. A., Lenz, O., Friedrich, B., Sargent, F., Armstrong, F. A. (October 2011) Oxygen-tolerant [NiFe]-hydrogenases: the individual and collective importance of supernumerary cysteines at the proximal Fe-S cluster. J Am Chem Soc, 133 (42). pp. 16881-92. ISSN 1520-5126

Ma, Y., Mathews, M. B. (August 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. (June 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. MapReduce '11 Proceedings of the second international workshop on MapReduce and its applications . pp. 51-58.

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. (December 2007) 28-way vertebrate alignment and conservation track in the UCSC Genome Browser. Genome Research, 17 (12). pp. 1797-808. ISSN 1088-9051

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

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

Petti, Samantha, Bhattacharya, Nicholas, Rao, Roshan, Dauparas, Justas, Thomas, Neil, Zhou, Juannan, Rush, Alexander M, Koo, Peter, Ovchinnikov, Sergey (November 2022) End-to-end learning of multiple sequence alignments with differentiable Smith-Waterman. Bioinformatics. ISSN 1367-4803

Petti, Samantha, Bhattacharya, Nicholas, Rao, Roshan, Dauparas, Justas, Thomas, Neil, Zhou, Juannan, Rush, Alexander M, Koo, Peter K, Ovchinnikov, Sergey (October 2021) End-to-end learning of multiple sequence alignments with differentiable Smith-Waterman. BioRxiv. (Unpublished)

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

Posfai, J., Bhagwat, A. S., Roberts, R. J. (December 1988) Sequence Motifs Specific for Cytosine Methyltransferases. Gene, 74 (1). pp. 262-266. ISSN 0378-1119

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)

Rollauer, S. E., Tarry, M. J., Graham, J. E., Jaaskelainen, M., Jager, F., Johnson, S., Krehenbrink, M., Liu, S. M., Lukey, M. J., Marcoux, J., McDowell, M. A., Rodriguez, F., Roversi, P., Stansfeld, P. J., Robinson, C. V., Sansom, M. S., Palmer, T., Hogbom, M., Berks, B. C., Lea, S. M. (December 2012) Structure of the TatC core of the twin-arginine protein transport system. Nature, 492 (7428). pp. 210-4. ISSN 1476-4687 (Public Dataset)

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

Tareen, A., Kinney, J. B. (December 2019) Logomaker: beautiful sequence logos in Python. Bioinformatics. ISSN 1367-4803 (Public Dataset)

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)

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

White, J. R., Navlakha, S., Nagarajan, N., Ghodsi, M. R., Kingsford, C., Pop, M. (March 2010) Alignment and clustering of phylogenetic markers--implications for microbial diversity studies. BMC Bioinformatics, 11 (3). p. 152. ISSN 1471-2105

Wilkie, N. M., Cortini, R. (1976) Sequence Arrangement in Herpes-Simplex Virus Type One DNA - Identification of Terminal Fragments in Restriction Endonuclease Digests and Evidence for Inversions in Redundant and Unique Sequences. Journal of Virology, 20 (1). pp. 211-221.

Wong, M. W., Henry, R. W., Ma, B., Kobayashi, R., Klages, N., Matthias, P., Strubin, M., Hernandez, N. (January 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)

Wu, Yaoyao, Johnson, Lynn, Song, Baoxing, Romay, Cinta, Stitzer, Michelle, Siepel, Adam, Buckler, Edward, Scheben, Armin (June 2021) A multiple genome alignment workflow shows the impact of repeat masking and parameter tuning on alignment of functional regions in plants. BioRxiv. (Unpublished)

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

Conference or Workshop Item

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