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  • Showing 1-23 of 23 Results
2012
Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay.Melnikov, A., Murugan A., Zhang X., Tesileanu T., Wang L., Rogov P., Feizi S., Gnirke A., Callan CG Jr, Kinney JB, Kellis M., Lander E. S., and Mikkelsen TS Nature biotechnology, 2012/02/26, Volume 30, Issue 3, p.271-7, (2012) Read More / View Supplemental Materials
Abstract
RNA folding with soft constraints: reconciliation of probing data and thermodynamic secondary structure prediction.Washietl, S., Hofacker IL, Stadler PF, and Kellis M. Nucleic acids research, 2012/01/28, (2012) Read More / View Supplemental Materials
Abstract
2011
Combinatorial patterning of chromatin regulators uncovered by genome-wide location analysis in human cells.Ram, O., Goren A., Amit I., Shoresh N., Yosef N., Ernst J., Kellis M., Gymrek M., Issner R., Coyne M., Durham T., Zhang X., Donaghey J., Epstein CB, Regev A., and Bernstein BE Cell, 2011/12/23, Volume 147, Issue 7, p.1628-39, (2011) Read More / View Supplemental Materials
Abstract
The changing face of genomics.Kellis, M. Genome biology, 2011/12/08, Volume 5, Issue 5, p.324, (2011) Read More / View Supplemental Materials
Large-scale discovery and validation of functional elements in the human genome.Bernstein, BE, and Kellis M. Genome biology, 2011/12/08, Volume 6, Issue 3, p.312, (2011) Read More / View Supplemental Materials
Abstract
Methods in comparative genomics: genome correspondence, gene identification and regulatory motif discovery.Kellis, M., Patterson N., Birren B., Berger B., and Lander E. S. Journal of computational biology : a journal of computational molecular cell biology, 2011/12/08, Volume 11, Issue 2-3, p.319-55, (2011) Read More / View Supplemental Materials
Abstract
A high-resolution map of human evolutionary constraint using 29 mammals.Lindblad-Toh, K., Garber M., Zuk O., Lin MF, Parker BJ, Washietl S., Kheradpour P., Ernst J., Jordan G., Mauceli E., Ward LD, Lowe CB, Holloway AK, Clamp M., Gnerre S., Alföldi J., Beal K., Chang J., Clawson H., Cuff J., et al. Nature, 2011/10/12, Volume 478, Issue 7370, p.476-82, (2011) Read More / View Supplemental Materials
Abstract
Mapping and analysis of chromatin state dynamics in nine human cell types.Ernst, J., Kheradpour P., Mikkelsen TS, Shoresh N., Ward LD, Epstein CB, Zhang X., Wang L., Issner R., Coyne M., Ku M., Durham T., Kellis M., and Bernstein BE Nature, 2011/05/05, Volume 473, Issue 7345, p.43-9, (2011) Read More / View Supplemental Materials
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2010
The NIH Roadmap Epigenomics Mapping Consortium.Bernstein, BE, Stamatoyannopoulos JA, Costello JF, Ren B., Milosavljevic A., Meissner A., Kellis M., Marra MA, Beaudet AL, Ecker JR, Farnham PJ, Hirst M., Lander E. S., Mikkelsen TS, and Thomson JA Nature biotechnology, 2010/10/01, Volume 28, Issue 10, p.1045-8, (2010) Read More / View Supplemental Materials
Abstract
2009
Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals.Guttman, M., Amit I., Garber M., French C., Lin MF, Feldser D., Huarte M., Zuk O., Carey BW, Cassady JP, Cabili MN, Jaenisch R., Mikkelsen TS, Jacks T., Hacohen N., Bernstein BE, Kellis M., Regev A., Rinn JL, and Lander E. S. Nature, 2009/03/12, Volume 458, Issue 7235, p.223-7, (2009) Read More / View Supplemental Materials
Abstract
2008
Performance and scalability of discriminative metrics for comparative gene identification in 12 Drosophila genomes.Lin, MF, Deoras AN, Rasmussen MD, and Kellis M. PLoS computational biology, 2008/04/18, Volume 4, Issue 4, p.e1000067, (2008) Read More / View Supplemental Materials
Abstract
A single Hox locus in Drosophila produces functional microRNAs from opposite DNA strands.Stark, A., Bushati N., Jan CH, Kheradpour P., Hodges E., Brennecke J., Bartel DP, Cohen SM, and Kellis M. Genes & development, 2008/01/01, Volume 22, Issue 1, p.8-13, (2008) Read More / View Supplemental Materials
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2007
Distinguishing protein-coding and noncoding genes in the human genome.Clamp, M., Fry B., Kamal M., Xie X., Cuff J., Lin MF, Kellis M., Lindblad-Toh K., and Lander E. S. Proceedings of the National Academy of Sciences of the United States of America, 2007/12/04, Volume 104, Issue 49, p.19428-33, (2007) Read More / View Supplemental Materials
Abstract
Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomes.Lin, MF, Carlson JW, Crosby MA, Matthews BB, Yu C., Park S., Wan KH, Schroeder AJ, Gramates LS, St Pierre SE, Roark M., Wiley KL Jr, Kulathinal RJ, Zhang P., Myrick KV, Antone JV, Celniker SE, Gelbart WM, and Kellis M. Genome research, 2007/12/01, Volume 17, Issue 12, p.1823-36, (2007) Read More / View Supplemental Materials
Abstract
Systematic discovery and characterization of fly microRNAs using 12 Drosophila genomes.Stark, A., Kheradpour P., Parts L., Brennecke J., Hodges E., Hannon GJ, and Kellis M. Genome research, 2007/12/01, Volume 17, Issue 12, p.1865-79, (2007) Read More / View Supplemental Materials
Abstract
Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures.Stark, A., Lin MF, Kheradpour P., Pedersen JS, Parts L., Carlson JW, Crosby MA, Rasmussen MD, Roy S., Deoras AN, Ruby JG, Brennecke J., curators Harvard FlyBase, Berkeley Drosophila Genome Project, Hodges E., Hinrichs AS, Caspi A., Paten B., Park SW, Han MV, et al. Nature, 2007/11/08, Volume 450, Issue 7167, p.219-32, (2007) Read More / View Supplemental Materials
Abstract
Evolution of genes and genomes on the Drosophila phylogeny.Drosophila 12 Genomes, Consortium, Clark AG, Eisen MB, Smith DR, Bergman CM, Oliver B., Markow TA, Kaufman TC, Kellis M., Gelbart W., Iyer VN, Pollard DA, Sackton TB, Larracuente AM, Singh ND, Abad JP, Abt DN, Adryan B., Aguade M., Akashi H., et al. Nature, 2007/11/08, Volume 450, Issue 7167, p.203-18, (2007) Read More / View Supplemental Materials
Abstract
Systematic discovery of regulatory motifs in conserved regions of the human genome, including thousands of CTCF insulator sites.Xie, X., Mikkelsen TS, Gnirke A., Lindblad-Toh K., Kellis M., and Lander E. S. Proceedings of the National Academy of Sciences of the United States of America, 2007/04/24, Volume 104, Issue 17, p.7145-50, (2007) Read More / View Supplemental Materials
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2005
Genome sequence, comparative analysis and haplotype structure of the domestic dog.Lindblad-Toh, K., Wade CM, Mikkelsen TS, Karlsson EK, Jaffe DB, Kamal M., Clamp M., Chang JL, Kulbokas EJ 3rd, Zody MC, Mauceli E., Xie X., Breen M., Wayne RK, Ostrander EA, Ponting CP, Galibert F., Smith DR, de Jong PJ, Kirkness E., et al. Nature, 2005/12/08, Volume 438, Issue 7069, p.803-19, (2005) Read More / View Supplemental Materials
Abstract
Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals.Xie, X., Lu J., Kulbokas E. J., Golub T. R., Mootha V., Lindblad-Toh K., Lander E. S., and Kellis M. Nature, 2005/03/17, Volume 434, Issue 7031, p.338-45, (2005) Read More / View Supplemental Materials
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2004
Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype.Jaillon, O., Aury JM, Brunet F., Petit JL, Stange-Thomann N., Mauceli E., Bouneau L., Fischer C., Ozouf-Costaz C., Bernot A., Nicaud S., Jaffe D., Fisher S., Lutfalla G., Dossat C., Segurens B., Dasilva C., Salanoubat M., Levy M., Boudet N., et al. Nature, 2004/10/21, Volume 431, Issue 7011, p.946-57, (2004) Read More / View Supplemental Materials
Abstract
Transcriptional regulatory code of a eukaryotic genome.Harbison, CT, Gordon DB, Lee TI, Rinaldi NJ, Macisaac KD, Danford TW, Hannett NM, Tagne JB, Reynolds DB, Yoo J., Jennings EG, Zeitlinger J., Pokholok DK, Kellis M., Rolfe PA, Takusagawa KT, Lander E. S., Gifford DK, Fraenkel E., and Young RA Nature, 2004/09/02, Volume 431, Issue 7004, p.99-104, (2004) Read More / View Supplemental Materials
Abstract
Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae.Kellis, M., Birren BW, and Lander E. S. Nature, 2004/04/08, Volume 428, Issue 6983, p.617-24, (2004) Read More / View Supplemental Materials
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  • Showing 1-23 of 23 Results