Search Results - "Araya, Carlos L."

Deep mutational scanning: assessing protein function on a massive scale by Araya, Carlos L, Fowler, Douglas M

“…Analysis of protein mutants is an effective means to understand their function. Protein display is an approach that allows large numbers of mutants of a…”
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Sushi.R: flexible, quantitative and integrative genomic visualizations for publication-quality multi-panel figures by Phanstiel, Douglas H, Boyle, Alan P, Araya, Carlos L, Snyder, Michael P

“…Interpretation and communication of genomic data require flexible and quantitative tools to analyze and visualize diverse data types, and yet, a comprehensive…”
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Genome-scale measurement of off-target activity using Cas9 toxicity in high-throughput screens by Morgens, David W., Wainberg, Michael, Boyle, Evan A., Ursu, Oana, Araya, Carlos L., Tsui, C. Kimberly, Haney, Michael S., Hess, Gaelen T., Han, Kyuho, Jeng, Edwin E., Li, Amy, Snyder, Michael P., Greenleaf, William J., Kundaje, Anshul, Bassik, Michael C.

“…CRISPR-Cas9 screens are powerful tools for high-throughput interrogation of genome function, but can be confounded by nuclease-induced toxicity at both on- and…”
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fundamental protein property, thermodynamic stability, revealed solely from large-scale measurements of protein function by Araya, Carlos L, Fowler, Douglas M, Chen, Wentao, Muniez, Ike, Kelly, Jeffery W, Fields, Stanley

“…The ability of a protein to carry out a given function results from fundamental physicochemical properties that include the protein’s structure, mechanism of…”
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Quantitative analysis of RNA-protein interactions on a massively parallel array reveals biophysical and evolutionary landscapes by Buenrostro, Jason D, Araya, Carlos L, Chircus, Lauren M, Layton, Curtis J, Chang, Howard Y, Snyder, Michael P, Greenleaf, William J

“…Repurposing a DNA sequencing instrument for high-throughput analysis of RNA-protein interactions enables detailed analysis of sequence-function relationships…”
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High-resolution mapping of protein sequence-function relationships by Fields, Stanley, Fowler, Douglas M, Araya, Carlos L, Fleishman, Sarel J, Kellogg, Elizabeth H, Stephany, Jason J, Baker, David

“…The combination of protein display, moderate selection for protein activity and high-throughput DNA sequencing can be applied to hundreds of thousands of…”
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Enrich: software for analysis of protein function by enrichment and depletion of variants by Fowler, Douglas M., Araya, Carlos L., Gerard, Wayne, Fields, Stanley

“…Measuring the consequences of mutation in proteins is critical to understanding their function. These measurements are essential in such applications as…”
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Identification of significantly mutated regions across cancer types highlights a rich landscape of functional molecular alterations by Araya, Carlos L, Cenik, Can, Reuter, Jason A, Kiss, Gert, Pande, Vijay S, Snyder, Michael P, Greenleaf, William J

“…William Greenleaf, Michael Snyder, Carlos Araya and colleagues use density-based clustering methods on ~4,700 exomes from 21 tumor types to detect…”
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Whole-genome sequencing of a laboratory-evolved yeast strain by Araya, Carlos L, Payen, Celia, Dunham, Maitreya J, Fields, Stanley

“…Experimental evolution of microbial populations provides a unique opportunity to study evolutionary adaptation in response to controlled selective pressures…”
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AceTree: a tool for visual analysis of Caenorhabditis elegans embryogenesis by Boyle, Thomas J, Bao, Zhirong, Murray, John I, Araya, Carlos L, Waterston, Robert H

“…The invariant lineage of the nematode Caenorhabditis elegans has potential as a powerful tool for the description of mutant phenotypes and gene expression…”
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Integrative analysis of RNA, translation, and protein levels reveals distinct regulatory variation across humans by Cenik, Can, Cenik, Elif Sarinay, Byeon, Gun W, Grubert, Fabian, Candille, Sophie I, Spacek, Damek, Alsallakh, Bilal, Tilgner, Hagen, Araya, Carlos L, Tang, Hua, Ricci, Emiliano, Snyder, Michael P

“…Elucidating the consequences of genetic differences between humans is essential for understanding phenotypic diversity and personalized medicine. Although…”
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Regulatory analysis of the C. elegans genome with spatiotemporal resolution by Araya, Carlos L., Kawli, Trupti, Kundaje, Anshul, Jiang, Lixia, Wu, Beijing, Vafeados, Dionne, Terrell, Robert, Weissdepp, Peter, Gevirtzman, Louis, Mace, Daniel, Niu, Wei, Boyle, Alan P., Xie, Dan, Ma, Lijia, Murray, John I., Reinke, Valerie, Waterston, Robert H., Snyder, Michael

“…Discovering the structure and dynamics of transcriptional regulatory events in the genome with cellular and temporal resolution is crucial to understanding the…”
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Scalable approaches for generating, validating and incorporating data from high-throughput functional assays to improve clinical variant classification by Padigepati, Samskruthi Reddy, Stafford, David A., Tan, Christopher A., Silvis, Melanie R., Jamieson, Kirsty, Keyser, Andrew, Nunez, Paola Alejandra Correa, Nicoludis, John M., Manders, Toby, Fresard, Laure, Kobayashi, Yuya, Araya, Carlos L., Aradhya, Swaroop, Johnson, Britt, Nykamp, Keith, Reuter, Jason A.

“…As the adoption and scope of genetic testing continue to expand, interpreting the clinical significance of DNA sequence variants at scale remains a formidable…”
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Comparative analysis of regulatory information and circuits across distant species by Boyle, Alan P., Araya, Carlos L., Brdlik, Cathleen, Cayting, Philip, Cheng, Chao, Cheng, Yong, Gardner, Kathryn, Hillier, LaDeana W., Janette, Judith, Jiang, Lixia, Kasper, Dionna, Kawli, Trupti, Kheradpour, Pouya, Kundaje, Anshul, Li, Jingyi Jessica, Ma, Lijia, Niu, Wei, Rehm, E. Jay, Rozowsky, Joel, Slattery, Matthew, Spokony, Rebecca, Terrell, Robert, Vafeados, Dionne, Wang, Daifeng, Weisdepp, Peter, Wu, Yi-Chieh, Xie, Dan, Yan, Koon-Kiu, Feingold, Elise A., Good, Peter J., Pazin, Michael J., Huang, Haiyan, Bickel, Peter J., Brenner, Steven E., Reinke, Valerie, Waterston, Robert H., Gerstein, Mark, White, Kevin P., Kellis, Manolis, Snyder, Michael

“…A map of genome-wide binding locations of 165 human, 93 worm and 52 fly transcription-regulatory factors (almost 50% presented for the first time) from diverse…”
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Genome-Wide Analysis of Nascent Transcription in Saccharomyces cerevisiae by McKinlay, Anastasia, Araya, Carlos L, Fields, Stanley

“…The assessment of transcriptional regulation requires a genome-wide survey of active RNA polymerases. Thus, we combined the nuclear run-on assay, which labels…”
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Developing large-scale molecular stability engines for clinical variant interpretation by Nicoludis, John M., Ptacek, Gabor F., Morin-Leisk, Jeanne, Colavin, Alexandre, Araya, Carlos L.

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Direct, High-Throughput Measurement of Quantitative RNA Affinity Landscapes by Buenrostro, Jason D., Chircus, Lauren, Araya, Carlos L., Layton, Curtis, Greenleaf, William J.

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Correction: Corrigendum: Regulatory analysis of the C. elegans genome with spatiotemporal resolution by Araya, Carlos L., Kawli, Trupti, Kundaje, Anshul, Jiang, Lixia, Wu, Beijing, Vafeados, Dionne, Terrell, Robert, Weissdepp, Peter, Gevirtzman, Louis, Mace, Daniel, Niu, Wei, Boyle, Alan P., Xie, Dan, Ma, Lijia, Murray, John I., Reinke, Valerie, Waterston, Robert H., Snyder, Michael

“…Nature 512, 400–405 (2014); doi:10.1038/nature13497 In this Article, when processing C. elegans ChIP-seq libraries, the gene label ZK337.2 (KLU-1, a C2H2…”
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Corrigendum: Regulatory analysis of the C. elegans genome with spatiotemporal resolution by Araya, Carlos L, Kawli, Trupti, Kundaje, Anshul, Jiang, Lixia, Wu, Beijing, Vafeados, Dionne, Terrell, Robert, Weissdepp, Peter, Gevirtzman, Louis, Mace, Daniel, Niu, Wei, Boyle, Alan P, Xie, Dan, Ma, Lijia, Murray, John I, Reinke, Valerie, Waterston, Robert H, Snyder, Michael

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Erratum: Corrigendum: Regulatory analysis of the C. elegans genome with spatiotemporal resolution by Araya, Carlos L., Kawli, Trupti, Kundaje, Anshul, Jiang, Lixia, Wu, Beijing, Vafeados, Dionne, Terrell, Robert, Weissdepp, Peter, Gevirtzman, Louis, Mace, Daniel, Niu, Wei, Boyle, Alan P., Xie, Dan, Ma, Lijia, Murray, John I., Reinke, Valerie, Waterston, Robert H., Snyder, Michael

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