Items where Subject is "bioinformatics > genomics and proteomics > Mapping and Rendering > Sequence Rendering"

Up a level
Export as [feed] Atom [feed] RSS 1.0 [feed] RSS 2.0
Group by: Authors | Item Type
Jump to: A | B | C | D | E | F | G | H | J | K | L | M | N | P | R | S | T | V | W | X | Y
Number of items at this level: 73.

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

Amid, C., Frankish, A., Aken, B., Ezkurdia, I., Kokocinsk, F., Gilbert, J., White, S., Carninci, P., Gingeras, T. R., Guigo, R., Searle, S., Tress, M. L., Harrow, J., Hubbard, T. (2010) From identification to validation to gene count. Genome Biology, 11 (Suppl ). ISSN 1474-760X

Ammiraju, J. S. S., Song, X., Luo, M., Sisneros, N., Angelova, A., Kudrna, D., Kim, H., Yu, Y., Goicoechea, J. L., Lorieux, M., Kurata, N., Brar, D., Ware, D. H., Jackson, S., Wing, R. A. (2010) The Oryza BAC resource: A genus-wide and genome scale tool for exploring rice genome evolution and leveraging useful genetic diversity from wild relatives. Breeding Science, 60 (5). pp. 536-543. ISSN 13447610 (ISSN)

Andersen, J. N., Del Vecchio, R. L., Kannan, N., Gergel, J., Neuwald, A. F., Tonks, N.K. (2005) Computational analysis of protein tyrosine phosphatases: practical guide to bioinformatics and data resources. Methods, 35 (1). pp. 90-114. ISSN 1046-2023 (Print)

Aravin, A. A., Gaidatzis, D., Pfeffer, S., Lagos-Quintana, M., Landgraf, P., Iovino, N., Morris, P., Brownstein, M. J., Kuramochi-Miyagawa, S., Nakano, T., Chien, M. C., Russo, J. J., Ju, J. Y., Sheridan, R., Sander, C., Zavolan, M. , Tuschl, T. (2006) A novel class of small RNAs bind to MILI protein in mouse testes. Nature, 442 (7099). pp. 203-7. ISSN 1476-4687 (Electronic)

Argout, X., Salse, J., Aury, J. M., Guiltinan, M. J., Droc, G., Gouzy, J., Allegre, M., Chaparro, C., Legavre, T., Maximova, S. N., Abrouk, M., Murat, F., Fouet, O., Poulain, J., Ruiz, M., Roguet, Y., Rodier-Goud, M., Barbosa-Neto, J. F., Sabot, F., Kudrna, D., Ammiraju, J. S. S., Schuster, S. C., Carlson, J. E., Sallet, E., Schiex, T., Dievart, A., Kramer, M. R., Gelley, L., Shi, Z., Bérard, A., Viot, C., Boccara, M., Risterucci, A. M., Guignon, V., Sabau, X., Axtell, M. J., Ma, Z., Zhang, Y, Brown, S., Bourge, M., Golser, W., Song, X., Clement, D., Rivallan, R., Tahi, M., Akaza, J. M., Pitollat, B., Gramacho, K., D'Hont, A., Brunel, D., Infante, D., Kebe, I., Costet, P., Wing, R., McCombie, W. R., Guiderdoni, E., Quetier, F., Panaud, O., Wincker, P., Bocs, S., Lanaud, C. (2011) The genome of Theobroma cacao. Nature Genetics, 43 (2). pp. 101-108. ISSN 10614036

Arnaiz, Olivier, Cain, Scott, Cohen, Jean, Sperling, Linda (2007) ParameciumDB: a community resource that integrates the Paramecium tetraurelia genome sequence with genetic data. Nucleic Acids Res, 35. D439-D444. ISSN 0305-1048

B

Barker, D., McCoy, M., Weinberg, R., Goldfarb, M., Wigler, M. H., Burt, R., Gardner, E., White, R. (1983) A test of the role of two oncogenes in inherited predisposition to colon cancer. Mol Biol Med, 1 (2). pp. 199-206. ISSN 0735-1313 (Print)

Berezikov, E., Robine, N., Samsonova, A., Westholm, J. O., Naqvi, A., Hung, J. H., Okamura, K., Dai, Q., Bortolamiol-Becet, D., Martin, R., Zhao, Y. J., Zamore, P. D., Hannon, G. J., Marra, M. A., Weng, Z. P., Perrimon, N., Lai, E. C. (2011) Deep annotation of Drosophila melanogaster microRNAs yields insights into their processing, modification, and emergence. Genome Research, 21 (2). pp. 203-215. ISSN 1088-9051

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

Burbano, H. A., Hodges, E., Green, R. E., Briggs, A. W., Krause, J., Meyer, M., Good, J. M., Maricic, T., Johnson, P. L. F., Xuan, Z. Y., Rooks, M., Bhattacharjee, A., Brizuela, L., Albert, F. W., De La Rasilla, M., Fortea, J., Rosas, A., Lachmann, M., Hannon, G. J., Paabo, S. (2010) Targeted investigation of the neandertal genome by array-based sequence capture. Science, 328 (5979). pp. 723-725.

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)

Cibrian-Jaramillo, A., De la Torre-Barcena, J. E., Lee, E. K., Katari, M. S., Little, D. P., Stevenson, D. W., Martienssen, R. A., Coruzzi, G. M., DeSalle, R. (2010) Using Phylogenomic Patterns and Gene Ontology to Identify Proteins of Importance in Plant Evolution. Genome Biology and Evolution, 2. pp. 225-239. ISSN 1759-6653

Cornman, R. S., Chen, Y. P., Schatz, M. C., Street, C., Zhao, Y., Desany, B., Egholm, M., Hutchison, S., Pettis, J. S., Lipkin, W. I., Evans, J. D. (2009) Genomic analyses of the microsporidian Nosema ceranae, an emergent pathogen of honey bees. PLoS Pathogens, 5 (6). ISSN 15537366 (ISSN)

Cornman, S. R., Schatz, M. C., Johnston, S. J., Chen, Y., Pettis, J., Hunt, G., Bourgeois, L., Elsik, C., Anderson, D., Grozinger, C. M., Evans, J. D. (2010) Genomic survey of the ectoparasitic mite Varroa destructor, a major pest of the honey bee Apis mellifera. BMC Genomics, 11 (1). ISSN 14712164 (ISSN)

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.

D

Dalloul, R. A., Long, J. A., Zimin, A. V., Aslam, L., Beal, K., Blomberg, L. A., Bouffard, P., Burt, D. W., Crasta, O., Crooijmans, R. P. M. A., Cooper, K., Coulombe, R. A., De, S., Delany, M. E., Dodgson, J. B., Dong, J. J., Evans, C., Frederickson, K. M., Flicek, P., Florea, L., Folkerts, O., Groenen, M. A. M., Harkins, T. T., Herrero, J., Hoffmann, S., Megens, H. J., Jiang, A., de Jong, P., Kaiser, P., Kim, H., Kim, K. W., Kim, S., Langenberger, D., Lee, M. K., Lee, T., Mane, S., Marcais, G., Marz, M., McElroy, A. P., Modise, T., Nefedov, M., Notredame, C., Paton, I. R., Payne, W. S., Pertea, G., Prickett, D., Puiu, D., Qioa, D., Raineri, E., Ruffier, M., Salzberg, S. L., Schatz, M. C., Scheuring, C., Schmidt, C. J., Schroeder, S., Searle, S. M. J., Smith, E. J., Smith, J., Sonstegard, T. S., Stadler, P. F., Tafer, H., Tu, Z., van Tassell, C. P., Vilella, A. J., Williams, K. P., Yorke, J. A., Zhang, L., Zhang, H. B., Zhang, X., Zhang, Y., Reed, K. M. (2010) Multi-platform next-generation sequencing of the domestic Turkey (Meleagris gallopavo): Genome assembly and analysis. PLoS Biology, 8 (9). ISSN 1544-9173

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)

Eichler, E. E., Nickerson, D. A., Altshuler, D., Bowcock, A. M., Brooks, L. D., Carter, N. P., Church, D. M., Felsenfeld, A., Guyer, M., Lee, C., Lupski, J. R., Mullikin, J. C., Pritchard, J. K., Sebat, J., Sherry, S. T., Smith, D., Valle, D., Waterston, R. H. (2007) Completing the map of human genetic variation. Nature, 447 (7141). pp. 161-165. ISSN 0028-0836

Erlich, Y., Edvardson, S., Hodges, E., Zenvirt, S., Thekkat, P., Shaag, A., Dor, T., Hannon, G. J., Elpeleg, O. (2011) Exome sequencing and disease-network analysis of a single family implicate a mutation in KIF1A in hereditary spastic paraparesis. Genome Research, 21 (5). pp. 658-664. ISSN 1088-9051

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.

F

Fan, S., Zhang, M. Q., Zhang, X. (2008) Histone methylation marks play important roles in predicting the methylation status of CpG islands. Biochemical and Biophysical Research Communications, 374 (3). pp. 559-564. ISSN 0006291X

Fang, F., Fan, S., Zhang, X., Zhang, M. Q. (2006) Predicting methylation status of CpG islands in the human brain. Bioinformatics, 22 (18). pp. 2204-2209. ISSN 13674803

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

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

Henderson, S. C., Spector, D. L. (1992) Nonrandom Arrangement of DNA-Sequences in Diploid Human-Cells. Molecular Biology of the Cell, 3 (Suppl). A137-A137. ISSN 1059-1524

Hill, B. T., Skowronski, J. (2005) Human N-myristoyltransferases form stable complexes with lentiviral nef and other viral and cellular substrate proteins. J Virol, 79 (2). pp. 1133-41. ISSN 0022-538X (Print)

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., Smith, A. D., Kendall, J. T., Xuan, Z., Ravi, K., Rooks, M., Zhang, M. Q., Ye, K., Bhattacharjee, A., Brizuela, L., McCombie, W. R., Wigler, M. H., Hannon, G. J., Hicks, J. B. (2009) High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing. Genome Research, 19 (9). pp. 1593-1605. ISSN 1088-9051

J

Jackson, D. P., Culianez-Macia, F., Prescott, A. G., Roberts, K., Martin, C. (1991) Expression patterns of myb genes from Antirrhinum flowers. Plant Cell, 3 (2). pp. 115-125. ISSN 1040-4651 (Print)1040-4651 (Linking)

K

Kampa, D., Cheng, J., Kapranov, P., Yamanaka, M., Brubaker, S., Cawley, S., Drenkow, J., Piccolboni, A., Bekiranov, S., Helt, G., Tammana, H., Gingeras, T. R. (2004) Novel RNAs identified from a in-depth analysis of the transcriptome of human chromosomes 21 and 22. Genome Research, 14 (3). pp. 331-342. ISSN 10889051 (ISSN)

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

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)

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

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)

Long, D. D., Grosse, I., Marx, K. A. (2004) Coding and non-coding DNA thermal stability differences in eukaryotes studied by melting simulation, base shuffling and DNA nearest neighbor frequency analysis. Biophysical Chemistry, 110 (1-2). pp. 25-38. ISSN 0301-4622

M

Martienssen, R. A. (2004) Crop Plant Genome sequence: What is it good for? Crop Science, 44 (6). pp. 1898-1899. ISSN 0011-183X

Matsumoto, T., Wu, J. Z., Kanamori, H., Katayose, Y., Fujisawa, M., Namiki, N., Mizuno, H., Yamamoto, K., Antonio, B. A., Baba, T., Sakata, K., Nagamura, Y., Aoki, H., Arikawa, K., Arita, K., Bito, T., Chiden, Y., Fujitsuka, N., Fukunaka, R., Hamada, M., Harada, C., Hayashi, A., Hijishita, S., Honda, M., Hosokawa, S., Ichikawa, Y., Idonuma, A., Iijima, M., Ikeda, M., Ikeno, M., Ito, K., Ito, S., Ito, T., Ito, Y., Ito, Y., Iwabuchi, A., Kamiya, K., Karasawa, W., Kurita, K., Katagiri, S., Kikuta, A., Kobayashi, H., Kobayashi, N., Machita, K., Maehara, T., Masukawa, M., Mizubayashi, T., Mukai, Y., Nagasaki, H., Nagata, Y., Naito, S., Nakashima, M., Nakama, Y., Nakamichi, Y., Nakamura, M., Meguro, A., Negishi, M., Ohta, I., Ohta, T., Okamoto, M., Ono, N., Saji, S., Sakaguchi, M., Sakai, K., Shibata, M., Shimokawa, T., Song, J. Y., Takazaki, Y., Terasawa, K., Tsugane, M., Tsuji, K., Ueda, S., Waki, K., Yamagata, H., Yamamoto, M., Yamamoto, S., Yamane, H., Yoshiki, S., Yoshihara, R., Yukawa, K., Zhong, H. S., Yano, M., Sasaki, T., Yuan, Q. P., Shu, O. T., Liu, J., Jones, K. M., Gansberger, K., Moffat, K., Hill, J., Bera, J., Fadrosh, D., Jin, S. H., Johri, S., Kim, M., Overton, L., Reardon, M., Tsitrin, T., Vuong, H., Weaver, B. (2005) The map-based sequence of the rice genome. Nature, 436 (7052). pp. 793-800. ISSN 0028-0836

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)

Murchison, E. P., Kheradpour, P., Sachidanandam, R., Smith, C., Hodges, E., Xuan, Z., Kellis, M., Grutzner, F., Stark, A., Hannon, G. J. (2008) Conservation of small RNA pathways in platypus. Genome Research, 18 (6). pp. 995-1004. ISSN 1088-9051

Murchison, E. P., Tovar, C., Hsu, A., Bender, H. S., Kheradpour, P., Rebbeck, C. A., Obendorf, D., Conlan, C., Bahlo, M., Blizzard, C. A., Pyecroft, S., Kreiss, A., Kellis, M., Stark, A., Harkins, T. T., Marshall Graves, J. A., Woods, G. M., Hannon, G. J., Papenfuss, A. T. (2010) The Tasmanian devil transcriptome reveals Schwann cell origins of a clonally transmissible cancer. Science, 327 (5961). pp. 84-7. ISSN 1095-9203 (Electronic) 1095-9203 (Linking)

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

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

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

Plessy, C., Bertin, N., Takahashi, H., Simone, R., Salimullah, Md, Lassmann, T., Vitezic, M., Severin, J., Olivarius, S., Lazarevic, D., Hornig, N., Orlando, V., Bell, I., Gao, H., Dumais, J., Kapranov, P., Wang, H., Davis, C. A., Gingeras, T. R., Kawai, J., Daub, C. O., Hayashizaki, Y., Gustincich, S., Carninci, P. (2010) Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan. Nature Methods, 7 (7). pp. 528-34. ISSN 15487091 (ISSN)

Powers, S., Kataoka, T., Fasano, O., Goldfarb, M., Strathern, J., Broach, J., Wigler, M. H. (1984) Genes in Saccharomyces cerevisiae encoding proteins with domains homologous to the mammalian ras proteins. Cell, 36 (3). pp. 607-612.

R

Rasko, T., Der, A., Klement, E., Slaska-Kiss, K., Posfai, E., Medzihradszky, K. F., Marshak, D. R., Roberts, R. J. , Kiss, A. (2010) BspRI restriction endonuclease: cloning, expression in Escherichia coli and sequential cleavage mechanism. Nucleic Acids Res. ISSN 1362-4962 (Electronic) 0305-1048 (Linking)

Russnes, H. G., Vollan, H. K. M., Lingjærde, O. C., Krasnitz, A., Lundin, P., Naume, B., Sørlie, T., Borgen, E., Rye, I. H., Langerød, A., Chin, S. F., Teschendorff, A. E., Stephens, P. J., Månér, S., Schlichting, E., Baumbusch, L. O., Kåresen, R., Stratton, M. P., Wigler, M. H., Caldas, C., Zetterberg, A., Hicks, J. B., Børresen-Dale, A. L. (2010) Genomic architecture characterizes tumor progression paths and fate in breast cancer patients. Science Translational Medicine, 2 (38).

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.

Speck, C., Stillman, B. (2007) Cdc6 ATPase activity regulates ORC center dot Cdc6 stability and the selection of specific DNA sequences as origins of DNA replication. Journal of Biological Chemistry, 282 (16). pp. 11705-11714. ISSN 0021-9258

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

T

Tian, G. W., Mohanty, A., Chary, S. N., Li, S. J., Paap, B., Drakakaki, G., Kopec, C. D., Li, J. X., Ehrhardt, D., Jackson, D., Rhee, S. Y., Raikhel, N. V., Citovsky, V. (2004) High-throughput fluorescent tagging of full-length arabidopsis gene products in planta. Plant Physiology, 135 (1). pp. 25-38. ISSN 0032-0889

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., Penmetsa, R. V., Dutta, S., Kulwal, P. L., Saxena, R. K., Datta, S., Sharma, T. R., Rosen, B., Carrasquilla-Garcia, N., Farmer, A. D., Dubey, A., Saxena, K. B., Gao, J., Fakrudin, B., Singh, M. N., Singh, B. P., Wanjari, K. B., Yuan, M., Srivastava, R. K., Kilian, A., Upadhyaya, H. D., Mallikarjuna, N., Town, C. D., Bruening, G. E., He, G., May, G. D., McCombie, W. R., Jackson, S. A., Singh, N. K., Cook, D. R. (2010) Pigeonpea genomics initiative (PGI): An international effort to improve crop productivity of pigeonpea (Cajanus cajan L.). Molecular Breeding, 26 (3). pp. 393-408.

W

Wang, S. M., Zhang, M. Q. (2010) Transcriptome Study for Early Hematopoiesis-Achievement, Challenge and New Opportunity. Journal of Cellular Physiology, 223 (3). pp. 549-552. ISSN 0021-9541

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)

Wines, M. E., Lee, L., Katari, M. S., Zhang, L., DeRossi, C., Shi, Y., Perkins, S., Feldman, M., McCombie, W. Richard, Holdener, B. C. (2001) Identification of mesoderm development (mesd) candidate genes by comparative mapping and genome sequence analysis. Genomics, 72 (1). pp. 88-98. ISSN 08887543 (ISSN)

Woolcock, B., Kazianis, S., Lucito, R., Walter, R. B., Kallman, K. D., Morizot, D. C., Vielkind, J. R. (2006) Allele-specific marker generation and linkage mapping on the Xiphophorus sex chromosomes. Zebrafish, 3 (1). pp. 23-37. ISSN 15458547

X

Xu, H. P., Yanak, B. L., Wigler, M. H., Gorin, M. B. (1996) New polymorphic markers in the vicinity of the pearl locus on mouse chromosome 13. Mamm Genome, 7 (1). pp. 16-9. ISSN 0938-8990 (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)

This list was generated on Wed Aug 23 19:28:31 2017 EDT.
CSHL HomeAbout CSHLResearchEducationNews & FeaturesCampus & Public EventsCareersGiving