Items where Subject is "bioinformatics > genomics and proteomics > analysis and processing > Sequence Data Processing"

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Number of items at this level: 50.

B

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.

Blankenberg, D., Gordon, A., Von Kuster, G., Coraor, N., Taylor, J., Nekrutenko, A. (2010) Manipulation of FASTQ data with Galaxy. Bioinformatics, 26 (14). pp. 1783-1785. ISSN 1367-4803

Brenner, E. D., Stevenson, D. W., McCombie, R. W., Katari, M. S., Rudd, S. A., Mayer, K. F., Palenchar, P. M., Runko, S. J., Twigg, R. W., Dai, G., Martienssen, R. A., Benfey, P. N., Coruzzi, G. M. (2003) Expressed sequence tag analysis in Cycas, the most primitive living seed plant. Genome Biology, 4 (12). R78. ISSN 1474-7596

C

Cabal, R., Khanin, R., Viali, A., Socci, N., Lucito, R., Olshen, A., Zhang, J., Gerald, W., Powers, S., Ladanyi, M. (2011) Testing and Validating High Throughput Genomic Analysis of FFPE Samples: Systematic Gene Expression Differences between Matched Frozen and FFPE Samples Due to Rapid mRNA Degradation Signals. Modern Pathology, 24. p. 1875. ISSN 0893-3952

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)

Celniker, S., Clark, A., Ponting, C., Weinstock, G. (2010) THE BIOLOGY OF GENOMES. In: 2010 meeting of THE BIOLOGY OF GENOMES, May 11–May 15, 2010, Cold Spring Harbor Laboratory.

Chia, J. M., Ware, D. H. (2011) Sequencing for the cream of the crop. Nature Biotechnology, 29 (2). pp. 138-9. ISSN 1546-1696 (Electronic) 1087-0156 (Linking)

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

Dimitrova, Nevenka , Atwal, Gurinder Singh “Mickey”, Vikalo, Haris, Yoon, Byung-Jun (2010) 9th IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS). In: 9th IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS), November 10–November 12, 2010, Cold Spring Harbor.

de la Bastide, M., McCombie, W. R. (2007) Assembling genomic DNA sequences with PHRAP. Current Protocols in Bioinformatics (Unit 1). ISSN 1934-340X (Electronic)1934-3396 (Linking)

E

Earl, D., Bradnam, K., St. John, J., Darling, A., Lin, D., Fass, J., Yu, H. O. K., Buffalo, V., Zerbino, D. R., Diekhans, M., Nguyen, N., Ariyaratne, P. N., Sung, W. K., Ning, Z., Haimel, M., Simpson, J. T., Fonseca, N. A., Birol, I., Docking, T. R., Ho, I. Y., Rokhsar, D. S., Chikhi, R., Lavenier, D., Chapuis, G., Naquin, D., Maillet, N., Schatz, M. C., Kelley, D. R., Phillippy, A. M., Koren, S., Yang, S. P., Wu, W., Chou, W. C., Srivastava, A., Shaw, T. I., Ruby, J. G., Skewes-Cox, P., Betegon, M., Dimon, M. T., Solovyev, V., Seledtsov, I., Kosarev, P., Vorobyev, D., Ramirez-Gonzalez, R., Leggett, R., MacLean, D., Xia, F., Luo, R., Li, Z., Xie, Y., Liu, B., Gnerre, S., MacCallum, I., Przybylski, D., Ribeiro, F. J., Sharpe, T., Hall, G., Kersey, P. J., Durbin, R., Jackman, S. D., Chapman, J. A., Huang, X., DeRisi, J. L., Caccamo, M., Li, Y., Jaffe, D. B., Green, R. E., Haussler, D., Korf, I., Paten, B. (2011) Assemblathon 1: A competitive assessment of de novo short read assembly methods. Genome Research, 21 (12). pp. 2224-2241. ISSN 10889051 (ISSN)

Erlich, Y., Gordon, A., Brand, M., Hannon, G. J., Mitra, P. P. (2010) Compressed genotyping. IEEE Transactions on Information Theory, 56 (2). pp. 706-723.

Erlich, Y., Mitra, P. P., Delabastide, M., McCombie, W. R., Hannon, G. J. (2008) Alta-Cyclic: a self-optimizing base caller for next-generation sequencing. Nature Methods, 5 (8). 679 - 682.

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

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

G

Gao, M. Q., Li, G. Y., McCombie, W. R., Quiros, C. F. (2005) Comparative analysis of a transposon-rich Brassica oleracea BAC clone with its corresponding sequence in A-thaliana. Theoretical and Applied Genetics, 111 (5). pp. 949-955. ISSN 0040-5752

Grosse, I., Bernaola-Galvan, P., Carpena, P., Roman-Roldan, R., Oliver, J., Stanley, H. E. (2002) Analysis of symbolic sequences using the Jensen-Shannon divergence. Physical Review E, 65 (4). ISSN 1063-651X

Gymrek, M., Erlich, Y. (2011) Using DNA sequencers as stethoscopes. Genome Med, 3 (11). p. 73. ISSN 1756-994X (Electronic)

H

Hass-Jacobus, B. L., Futrell-Griggs, M., Abernathy, B., Westerman, R., Goicoechea, J. L., Stein, J., Klein, P., Hurwitz, B., Zhou, B., Rakhshan, F., Sanyal, A., Gill, N., Lin, J. Y., Walling, J. G., Luo, M. Z., Ammiraju, J. S. S., Kudrna, D., Kim, H. R., Ware, D., Wing, Rod A., San Miguel, P., Jackson, S. A. (2006) Integration of hybridization-based markers (overgos) into physical maps for comparative and evolutionary explorations in the genus Oryza and in Sorghum. BMC Genomics, 7. p. 199. ISSN 14712164

Hodges, E., Rooks, M., Xuan, Z., Bhattacharjee, A., Gordon, D. B., Brizuela, L., McCombie, W. R., Hannon, G. J. (2009) Hybrid selection of discrete genomic intervals on custom-designed microarrays for massively parallel sequencing. Nature Protocols, 4 (6). pp. 960-974. ISSN 1754-2189

Hodges, E., Xuan, Z. Y., Balija, V., Kramer, M. R., Molla, M. N., Smith, S. W., Middle, C. M., Rodesch, M. J., Albert, T. J., Hannon, G. J., McCombie, W. R. (2007) Genome-wide in situ exon capture for selective resequencing. Nature Genetics, 39 (12). pp. 1522-7. ISSN 1061-4036

Holste, D., Grosse, I., Herzel, H. (2001) Statistical analysis of the DNA sequence of human chromosome 22. Physical Review E, 6404 (4). ISSN 1063-651X

K

Kingsford, C., Schatz, M. C., Pop, M. (2010) Assembly complexity of prokaryotic genomes using short reads. BMC Bioinformatics, 11. ISSN 14712105 (ISSN)

Kinney, J. B., Murugan, A., Callan, C. G., Cox, E. C. (2010) Using deep sequencing to characterize the biophysical mechanism of a transcriptional regulatory sequence. Proceedings of the National Academy of Sciences of the United States of America, 107 (20). pp. 9158-9163. ISSN 0027-8424

Kundeti, V. K., Rajasekaran, S., Dinh, H., Vaughn, M. W., Thapar, V. (2010) Efficient parallel and out of core algorithms for constructing large bi-directed de Bruijn graphs. BMC Bioinformatics, 11. Artical number 560.

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)

Li, W. T., Bernaola-Galvan, P., Haghighi, F., Grosse, I. (2002) Applications of recursive segmentation to the analysis of DNA sequences. Computers & Chemistry, 26 (5). pp. 491-510. ISSN 0097-8485

Liu-Sullivan, N., Zhang, J., Bakleh, A., Marchica, J., Li, J., Siolas, D., Laquerre, S., Degenhardt, Y. Y., Wooster, R., Chang, K., Hannon, G. J., Powers, S. (2011) Pooled shRNA screen for sensitizers to inhibition of the mitotic regulator polo-like kinase (PLK1). Oncotarget, 2 (12). pp. 1254-64. ISSN 1949-2553 (Electronic) 1949-2553 (Linking)

Lyon, Gholson J. (2012) Software Considerations for Processing, Analyzing and Interpreting Exome & Genome Sequence Data in Clinical Settings. In: World Genome Data Analysis Summit: Pre Conference Workshop, Nov 27th 2012, San Francisco. (Unpublished)

M

Machida, M., Yamazaki, S., Kunihiro, S., Tanaka, T., Kushida, N., Jinno, K., Haikawa, Y., Yamazaki, J., Yamamoto, S., Sekine, M., Oguchi, A., Nagai, Y., Sakai, M., Aoki, K., Ogura, K., Kudoh, Y., Kikuchi, H., Zhang, M. Q., Yanagida, M. (2000) A 38 kb segment containing the cdc2 gene from the left arm of fission yeast chromosome II: sequence analysis and characterization of the genomic DNA and cDNAs encoded on the segment. Yeast, 16 (1). pp. 71-80. ISSN 0749-503X

Martin-Gallardo, A., Marchuk, D. A., Gocayne, J., Kerlavage, A. R., McCombie, W. R., Venter, J. C., Collins, F. S., Wallace, M. R. (1992) Sequencing and analysis of genomic fragments from the NF1 locus. DNA sequence : The journal of DNA sequencing and mapping, 3 (4). pp. 237-243. ISSN 10425179 (ISSN)

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)

Myles, S., Chia, J. M., Hurwitz, B. L., Simon, C., Zhong, G. Y., Buckler, E., Ware, D. H. (2010) Rapid Genomic Characterization of the Genus Vitis. PLoS ONE, 5 (1). ISSN 1932-6203

N

Navin, N. E., Kendall, J. T., Troge, J. E., Andrews, P., Rodgers,  L., McIndoo, J., Cook, K., Stepansky,  A., Levy, D., Esposito, D., Muthuswamy, L., Krasnitz, A., McCombie, W. R., Hicks, J. B., Wigler, M. H. (2011) Tumour evolution inferred by single-cell sequencing. Nature, 472 (7341). pp. 90-94. ISSN 00280836 (ISSN)

Neuwald, A. F., Liu, J. S. (2004) Gapped alignment of protein sequence motifs through Monte Carlo optimization of a hidden Markov model. BMC Bioinformatics, 5. p. 157. ISSN 1471-2105 (Electronic)

Neuwald, A. F. (2006) Bayesian shadows of molecular mechanisms cast in the light of evolution. Trends Biochem Sci, 31 (7). pp. 374-82. ISSN 0968-0004 (Print)

P

Palmer, L. E., O'Shaughnessy, A. L., Preston, R. R., Santos, L., Balija, V. S., Nascimento, L. U., Zutavern, T. L., Henthorn, P. S., Hannon, G. J., McCombie, W. R. (2003) A Survey of Canine Expressed Sequence Tags and a Display of Their Annotations Through a Flexible Web-Based Interface. Journal of Heredity, 94 (1). pp. 15-22. ISSN 00221503 (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. (2010) The missing graphical user interface for genomics. Genome Biology, 11 (8). p. 128. ISSN 14656914 (ISSN)

Schatz, M. C., Delcher, A. L., Salzberg, S. L. (2010) Assembly of large genomes using second-generation sequencing. Genome Research, 20 (9). pp. 1165-1173. ISSN 10889051 (ISSN)

Schatz, M. C., Langmead, B., Salzberg, S. L. (2010) Cloud computing and the DNA data race. Nature Biotechnology, 28 (7). pp. 691-693.

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

T

The Tomato Genome Consortium, (2012) The tomato genome sequence provides insights into fleshy fruit evolution. Nature, 485 (7400). pp. 635-41. ISSN 1476-4687 (Electronic)0028-0836 (Linking)

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)

V

Varshney, R. K., Chen, W. B., Li, Y. P., Bharti, A. K., Saxena, R. K., Schlueter, J. A., Donoghue, M. T. A., Azam, S., Fan, G. Y., Whaley, A. M., Farmer, A. D., Sheridan, J., Iwata, A., Tuteja, R., Penmetsa, R. V., Wu, W., Upadhyaya, H. D., Yang, S. P., Shah, T., Saxena, K. B., Michael, T., McCombie, W. R., Yang, B. C., Zhang, G. Y., Yang, H. M., Wang, J., Spillane, C., Cook, D. R., May, G. D., Xu, X., Jackson, S. A. (2012) Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers. Nature Biotechnology, 30 (1). 83-U128. ISSN 1087-0156

Venter, J. C., Adams, M. D., Martin-Gallardo, A., McCombie, W. R., Fields, C. (1992) Genome sequence analysis: Scientific objectives and practical strategies. Trends in Biotechnology, 10 (1-2). pp. 8-11. ISSN 01679430 (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)

West, J., Healy, J., Wigler, M. H., Casey, W., Mishra, B. (2006) Validation of S. Pombe sequence assembly by microarray hybridization. J Comput Biol, 13 (1). pp. 1-20. ISSN 1066-5277 (Print)

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. (2011) Gramene database in 2010: updates and extensions. Nucleic Acids Res, 39. D1085-D1094. ISSN 1362-4962 (Electronic) 0305-1048 (Linking)

Z

Zwickl, D. J., Stein, J. C., Wing, R. A., Ware, D., Sanderson, M. J. (2014) Disentangling methodological and biological sources of gene tree discordance on Oryza (Poaceae) chromosome 3. Systematic Biology, 63 (5). pp. 645-659. ISSN 1076836X (ISSN)

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