Recent Broad Publications

Hopping between Differentiation States in Lung Adenocarcinoma.
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Programmable repression and activation of bacterial gene expression using an engineered CRISPR-Cas system.
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The Genome of Anopheles darlingi, the main neotropical malaria vector.
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ATHLATES: accurate typing of human leukocyte antigen through exome sequencing.
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Integrated proteomic analysis of post-translational modifications by serial enrichment.
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Scientific Publications

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Filters: Author is Pachter, L [Clear All Filters]

2012

Differential analysis of gene regulation at transcript resolution with RNA-seq.Trapnell, C., Hendrickson DG, Sauvageau M., Goff L., Rinn JL, and Pachter L. Nature biotechnology, 2012/12/09, Volume 31, Issue 1, p.46-53, (2012) Read More / View Supplemental Materials

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks.Trapnell, C., Roberts A., Goff L., Pertea G., Kim D., Kelley DR, Pimentel H., Salzberg SL, Rinn JL, and Pachter L. Nature protocols, 2012/03/01, Volume 7, Issue 3, p.562-78, (2012) Read More / View Supplemental Materials

2007

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

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

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.ENCODE Project, Consortium, Birney E., Stamatoyannopoulos JA, Dutta A., Guigó R., Gingeras TR, Margulies EH, Weng Z., Snyder M., Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S., Koch CM, Asthana S., Malhotra A., Adzhubei I., Greenbaum JA, Andrews RM, et al. Nature, 2007/06/14, Volume 447, Issue 7146, p.799-816, (2007) Read More / View Supplemental Materials

Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome.Margulies, EH, Cooper GM, Asimenos G., Thomas DJ, Dewey CN, Siepel A., Birney E., Keefe D., Schwartz AS, Hou M., Taylor J., Nikolaev S., Montoya-Burgos JI, Löytynoja A., Whelan S., Pardi F., Massingham T., Brown JB, Bickel P., Holmes I., et al. Genome research, 2007/06/01, Volume 17, Issue 6, p.760-74, (2007) Read More / View Supplemental Materials