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2014
Alzheimer's disease: early alterations in brain DNA methylation at ANK1, BIN1, RHBDF2 and other loci.De Jager, PL, Srivastava G., Lunnon K., Burgess J., Schalkwyk LC, Yu L., Eaton ML, Keenan BT, Ernst J., McCabe C., Tang A., Raj T., Replogle J., Brodeur W., Gabriel S., Chai HS, Younkin C., Younkin SG, Zou F., Szyf M., et al. Nature neuroscience, 2014/09/01, Volume 17, Issue 9, p.1156-1163, (2014) Read More / View Supplemental Materials
Abstract
Diverse patterns of genomic targeting by transcriptional regulators in Drosophila melanogaster.Slattery, M., Ma L., Spokony RF, Arthur RK, Kheradpour P., Kundaje A., Nègre N., Crofts A., Ptashkin R., Zieba J., Ostapenko A., Suchy S., Victorsen A., Jameel N., Grundstad AJ, Gao W., Moran JR, Rehm EJ, Grossman RL, Kellis M., et al. Genome research, 2014/07/01, Volume 24, Issue 7, p.1224-35, (2014) Read More / View Supplemental Materials
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Genetic association study of QT interval highlights role for calcium signaling pathways in myocardial repolarization.Arking, DE, Pulit SL, Crotti L., van der Harst P., Munroe PB, Koopmann TT, Sotoodehnia N., Rossin EJ, Morley M., Wang X., Johnson AD, Lundby A., Gudbjartsson DF, Noseworthy PA, Eijgelsheim M., Bradford Y., Tarasov KV, Dörr M., Müller-Nurasyid M., Lahtinen AM, et al. Nature genetics, 2014/06/22, (2014) Read More / View Supplemental Materials
Abstract
Pareto-optimal phylogenetic tree reconciliation.Libeskind-Hadas, R., Wu YC, Bansal MS, and Kellis M. Bioinformatics (Oxford, England), 2014/06/15, Volume 30, Issue 12, p.i87-i95, (2014) Read More / View Supplemental Materials
Abstract
Common genetic variants modulate pathogen-sensing responses in human dendritic cells.Lee, MN, Ye C., Villani AC, Raj T., Li W., Eisenhaure TM, Imboywa SH, Chipendo PI, Ran FA, Slowikowski K., Ward LD, Raddassi K., McCabe C., Lee MH, Frohlich IY, Hafler DA, Kellis M., Raychaudhuri S., Zhang F., Stranger BE, et al. Science (New York, N.Y.), 2014/03/07, Volume 343, Issue 6175, p.1246980, (2014) Read More / View Supplemental Materials
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2013
Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo.Rouskin, S., Zubradt M., Washietl S., Kellis M., and Weissman JS Nature, 2013/12/15, (2013) Read More / View Supplemental Materials
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Systematic discovery and characterization of regulatory motifs in ENCODE TF binding experiments.Kheradpour, P., and Kellis M. Nucleic acids research, 2013/12/13, (2013) Read More / View Supplemental Materials
Abstract
Network deconvolution as a general method to distinguish direct dependencies in networks.Feizi, S., Marbach D., Médard M., and Kellis M. Nature biotechnology, 2013/08/01, Volume 31, Issue 8, p.726-33, (2013) Read More / View Supplemental Materials
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Arboretum: Reconstruction and analysis of the evolutionary history of condition-specific transcriptional modules.Roy, S., Wapinski I., Pfiffner J., French C., Socha A., Konieczka J., Habib N., Kellis M., Thompson D., and Regev A. Genome research, 2013/06/01, Volume 23, Issue 6, p.1039-50, (2013) Read More / View Supplemental Materials
Abstract
The Genotype-Tissue Expression (GTEx) project.Lonsdale, J., Thomas J., Salvatore M., Phillips R., Lo E., Shad S., Hasz R., Walters G., Garcia F., Young N., Foster B., Moser M., Karasik E., Gillard B., Ramsey K., Sullivan S., Bridge J., Magazine H., Syron J., Fleming J., et al. Nature genetics, 2013/05/29, Volume 45, Issue 6, p.580-5, (2013) Read More / View Supplemental Materials
Evolutionary principles of modular gene regulation in yeasts.Thompson, DA, Roy S., Chan M., Styczynsky MP, Pfiffner J., French C., Socha A., Thielke A., Napolitano S., Muller P., Kellis M., Konieczka JH, Wapinski I., and Regev A. eLife, 2013/01/01, Volume 2, p.e00603, (2013) Read More / View Supplemental Materials
Abstract
2012
Disruption of a large intergenic noncoding RNA in subjects with neurodevelopmental disabilities.Talkowski, ME, Maussion G., Crapper L., Rosenfeld JA, Blumenthal I., Hanscom C., Chiang C., Lindgren A., Pereira S., Ruderfer D., Diallo AB, Lopez JP, Turecki G., Chen ES, Gigek C., Harris DJ, Lip V., An Y., Biagioli M., Macdonald ME, et al. American journal of human genetics, 2012/12/07, Volume 91, Issue 6, p.1128-34, (2012) Read More / View Supplemental Materials
Abstract
Integrative annotation of chromatin elements from ENCODE data.Hoffman, MM, Ernst J., Wilder SP, Kundaje A., Harris RS, Libbrecht M., Giardine B., Ellenbogen PM, Bilmes JA, Birney E., Hardison RC, Dunham I., Kellis M., and Noble WS Nucleic acids research, 2012/12/05, (2012) Read More / View Supplemental Materials
Abstract
Computational analysis of noncoding RNAs.Washietl, S., Will S., Hendrix DA, Goff LA, Rinn JL, Berger B., and Kellis M. Wiley interdisciplinary reviews. RNA, 2012/11/01, Volume 3, Issue 6, p.759-78, (2012) Read More / View Supplemental Materials
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Interpreting noncoding genetic variation in complex traits and human disease.Ward, LD, and Kellis M. Nature biotechnology, 2012/11/01, Volume 30, Issue 11, p.1095-106, (2012) Read More / View Supplemental Materials
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Wisdom of crowds for robust gene network inference.Marbach, D., Costello JC, Küffner R., Vega NM, Prill RJ, Camacho DM, Allison KR, The DREAM5 Consortium, Aderhold A., Allison KR, Bonneau R., Camacho DM, Chen Y., Collins JJ, Cordero F., Costello JC, Crane M., Dondelinger F., Drton M., Esposito R., et al. Nature methods, 2012/07/15, (2012) Read More / View Supplemental Materials
Abstract
Efficient algorithms for the reconciliation problem with gene duplication, horizontal transfer and loss.Bansal, MS, Alm EJ, and Kellis M. Bioinformatics (Oxford, England), 2012/06/15, Volume 28, Issue 12, p.i283-i291, (2012) Read More / View Supplemental Materials
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ChromHMM: automating chromatin-state discovery and characterization.Ernst, J., and Kellis M. Nature methods, 2012/02/28, Volume 9, Issue 3, p.215-6, (2012) Read More / View Supplemental Materials
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
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Unified modeling of gene duplication, loss, and coalescence using a locus tree.Rasmussen, MD, and Kellis M. Genome research, 2012/02/16, (2012) Read More / View Supplemental Materials
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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
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Sequences to systems.Kellis, M., and Rinn JL Genome biology, 2012/01/09, Volume 11, Issue 5, p.303, (2012) Read More / View Supplemental Materials
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HaploReg: a resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants.Ward, LD, and Kellis M. Nucleic acids research, 2012/01/01, Volume 40, Issue 1, p.D930-4, (2012) Read More / View Supplemental Materials
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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 1-44 of 44 Results