Search Results - "Alexis, Maria S"

RNA Sequence Context Effects Measured In Vitro Predict In Vivo Protein Binding and Regulation by Taliaferro, J. Matthew, Lambert, Nicole J., Sudmant, Peter H., Dominguez, Daniel, Merkin, Jason J., Alexis, Maria S., Bazile, Cassandra A., Burge, Christopher B.

“…Many RNA binding proteins (RBPs) bind specific RNA sequence motifs, but only a small fraction (∼15%–40%) of RBP motif occurrences are occupied in vivo. To…”
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Understanding species-specific and conserved RNA-protein interactions in vivo and in vitro by Harris, Sarah E., Alexis, Maria S., Giri, Gilbert, Cavazos, Francisco F., Hu, Yue, Murn, Jernej, Aleman, Maria M., Burge, Christopher B., Dominguez, Daniel

“…While evolution is often considered from a DNA- and protein-centric view, RNA-based regulation can also impact gene expression and protein sequences. Here we…”
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Extensive conservation of ancient microsynteny across metazoans due to cis-regulatory constraints by Irimia, Manuel, Tena, Juan J, Alexis, Maria S, Fernandez-Miñan, Ana, Maeso, Ignacio, Bogdanovic, Ozren, de la Calle-Mustienes, Elisa, Roy, Scott W, Gómez-Skarmeta, José L, Fraser, Hunter B

“…The order of genes in eukaryotic genomes has generally been assumed to be neutral, since gene order is largely scrambled over evolutionary time. Only a handful…”
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Origins and Impacts of New Mammalian Exons by Merkin, Jason J., Chen, Ping, Alexis, Maria S., Hautaniemi, Sampsa K., Burge, Christopher B.

“…Mammalian genes are composed of exons, but the evolutionary origins and functions of new internal exons are poorly understood. Here, we analyzed patterns of…”
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Sequence, Structure, and Context Preferences of Human RNA Binding Proteins by Dominguez, Daniel, Freese, Peter, Alexis, Maria S., Su, Amanda, Hochman, Myles, Palden, Tsultrim, Bazile, Cassandra, Lambert, Nicole J., Van Nostrand, Eric L., Pratt, Gabriel A., Yeo, Gene W., Graveley, Brenton R., Burge, Christopher B.

“…RNA binding proteins (RBPs) orchestrate the production, processing, and function of mRNAs. Here, we present the affinity landscapes of 78 human RBPs using an…”
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Meta-analysis of RNA-seq expression data across species, tissues and studies by Sudmant, Peter H, Alexis, Maria S, Burge, Christopher B

“…Differences in gene expression drive phenotypic differences between species, yet major organs and tissues generally have conserved gene expression programs…”
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Acidification of Tumor at Stromal Boundaries Drives Transcriptome Alterations Associated with Aggressive Phenotypes by Rohani, Nazanin, Hao, Liangliang, Alexis, Maria S, Joughin, Brian A, Krismer, Konstantin, Moufarrej, Mira N, Soltis, Anthony R, Lauffenburger, Douglas A, Yaffe, Michael B, Burge, Christopher B, Bhatia, Sangeeta N, Gertler, Frank B

“…Acidosis is a fundamental feature of the tumor microenvironment, which directly regulates tumor cell invasion by affecting immune cell function, clonal cell…”
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