Search Results - "Boyle, Evan A."

An Expanded View of Complex Traits: From Polygenic to Omnigenic by Boyle, Evan A., Li, Yang I., Pritchard, Jonathan K.

“…A central goal of genetics is to understand the links between genetic variation and disease. Intuitively, one might expect disease-causing variants to cluster…”
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Detection of human adaptation during the past 2000 years by Field, Yair, Boyle, Evan A, Telis, Natalie, Gao, Ziyue, Gaulton, Kyle J., Golan, David, Yengo, Loic, Rocheleau, Ghislain, Froguel, Philippe, McCarthy, Mark I., Pritchard, Jonathan K.

“…Detection of recent natural selection is a challenging problem in population genetics. Here we introduce the singleton density score (SDS), a method to infer…”
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Saturation editing of genomic regions by multiplex homology-directed repair by Findlay, Gregory M., Boyle, Evan A., Hause, Ronald J., Klein, Jason C., Shendure, Jay

“…The authors perform saturation mutagenesis of genomic regions in their native endogenous chromosomal context by using CRISPR/Cas9 RNA-guided cleavage and…”
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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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High‐resolution mapping of cancer cell networks using co‐functional interactions by Boyle, Evan A, Pritchard, Jonathan K, Greenleaf, William J

“…Powerful new technologies for perturbing genetic elements have recently expanded the study of genetic interactions in model systems ranging from yeast to human…”
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Enhancer connectome in primary human cells identifies target genes of disease-associated DNA elements by Mumbach, Maxwell R, Satpathy, Ansuman T, Boyle, Evan A, Dai, Chao, Gowen, Benjamin G, Cho, Seung Woo, Nguyen, Michelle L, Rubin, Adam J, Granja, Jeffrey M, Kazane, Katelynn R, Wei, Yuning, Nguyen, Trieu, Greenside, Peyton G, Corces, M Ryan, Tycko, Josh, Simeonov, Dimitre R, Suliman, Nabeela, Li, Rui, Xu, Jin, Flynn, Ryan A, Kundaje, Anshul, Khavari, Paul A, Marson, Alexander, Corn, Jacob E, Quertermous, Thomas, Greenleaf, William J, Chang, Howard Y

“…High-resolution contact maps of active enhancers and target genes generated by H3K27ac HiChIP in primary human cells provide rational guides to link noncoding…”
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MIPgen: optimized modeling and design of molecular inversion probes for targeted resequencing by Boyle, Evan A, O'Roak, Brian J, Martin, Beth K, Kumar, Akash, Shendure, Jay

“…Molecular inversion probes (MIPs) enable cost-effective multiplex targeted gene resequencing in large cohorts. However, the design of individual MIPs is a…”
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High-throughput biochemical profiling reveals sequence determinants of dCas9 off-target binding and unbinding by Boyle, Evan A., Andreasson, Johan O. L., Chircus, Lauren M., Sternberg, Samuel H., Wu, Michelle J., Guegler, Chantal K., Doudna, Jennifer A., Greenleaf, William J.

“…The bacterial adaptive immune system CRISPR–Cas9 has been appropriated as a versatile tool for editing genomes, controlling gene expression, and visualizing…”
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Mammalian target of rapamycin pathway mutations cause hemimegalencephaly and focal cortical dysplasia by D'Gama, Alissa M., Geng, Ying, Couto, Javier A., Martin, Beth, Boyle, Evan A., LaCoursiere, Christopher M., Hossain, Amer, Hatem, Nicole E., Barry, Brenda J., Kwiatkowski, David J., Vinters, Harry V., Barkovich, A. James, Shendure, Jay, Mathern, Gary W., Walsh, Christopher A., Poduri, Annapurna

“…Focal malformations of cortical development, including focal cortical dysplasia (FCD) and hemimegalencephaly (HME), are important causes of intractable…”
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Expanded palette of RNA base editors for comprehensive RBP-RNA interactome studies by Medina-Munoz, Hugo C., Kofman, Eric, Jagannatha, Pratibha, Boyle, Evan A., Yu, Tao, Jones, Krysten L., Mueller, Jasmine R., Lykins, Grace D., Doudna, Andrew T., Park, Samuel S., Blue, Steven M., Ranzau, Brodie L., Kohli, Rahul M., Komor, Alexis C., Yeo, Gene W.

“…RNA binding proteins (RBPs) are key regulators of RNA processing and cellular function. Technologies to discover RNA targets of RBPs such as TRIBE (targets of…”
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Junior scientists spotlight social bonds in seminars for diversity, equity, and inclusion in STEM by Boyle, Evan A, Goldberg, Gabriela, Schmok, Jonathan C, Burgado, Jillybeth, Izidro Layng, Fabiana, Grunwald, Hannah A, Balotin, Kylie M, Cuoco, Michael S, Chang, Keng-Chi, Ecklu-Mensah, Gertrude, Arakaki, Aleena K S, Ahmed, Noorsher, Garcia Arceo, Ximena, Jagannatha, Pratibha, Pekar, Jonathan, Iyer, Mallika, Yeo, Gene W

“…Disparities for women and minorities in science, technology, engineering, and math (STEM) careers have continued even amidst mounting evidence for the superior…”
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Deep sequencing of multiple regions of glial tumors reveals spatial heterogeneity for mutations in clinically relevant genes by Kumar, Akash, Boyle, Evan A, Tokita, Mari, Mikheev, Andrei M, Sanger, Michelle C, Girard, Emily, Silber, John R, Gonzalez-Cuyar, Luis F, Hiatt, Joseph B, Adey, Andrew, Lee, Choli, Kitzman, Jacob O, Born, Donald E, Silbergeld, Daniel L, Olson, James M, Rostomily, Robert C, Shendure, Jay

“…The extent of intratumoral mutational heterogeneity remains unclear in gliomas, the most common primary brain tumors, especially with respect to point…”
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Protocol to process crosslinking and immunoprecipitation data into annotated binding sites by Xu, Shuhao, Nguyen, Grady G., Naritomi, Jack T., Kopalle, Hema M., Yee, Brian A., Rothamel, Katherine L., Boyle, Evan A., Yeo, Gene W.

“…Here, we present a protocol for using Skipper, a pipeline designed to process crosslinking and immunoprecipitation (CLIP) data into annotated binding sites. We…”
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A germline homozygous mutation in the base-excision repair gene NTHL1 causes adenomatous polyposis and colorectal cancer by Weren, Robbert D A, Ligtenberg, Marjolijn J L, Kets, C Marleen, de Voer, Richarda M, Verwiel, Eugène T P, Spruijt, Liesbeth, van Zelst-Stams, Wendy A G, Jongmans, Marjolijn C, Gilissen, Christian, Hehir-Kwa, Jayne Y, Hoischen, Alexander, Shendure, Jay, Boyle, Evan A, Kamping, Eveline J, Nagtegaal, Iris D, Tops, Bastiaan B J, Nagengast, Fokko M, Geurts van Kessel, Ad, van Krieken, J Han J M, Kuiper, Roland P, Hoogerbrugge, Nicoline

“…Roland Kuiper and colleagues identify a homozygous germline nonsense mutation in the base-excision repair gene NTHL1 in three families with recessive…”
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Large-scale evaluation of the ability of RNA-binding proteins to activate exon inclusion by Schmok, Jonathan C., Jain, Manya, Street, Lena A., Tankka, Alex T., Schafer, Danielle, Her, Hsuan-Lin, Elmsaouri, Sara, Gosztyla, Maya L., Boyle, Evan A., Jagannatha, Pratibha, Luo, En-Ching, Kwon, Ester J., Jovanovic, Marko, Yeo, Gene W.

“…RNA-binding proteins (RBPs) modulate alternative splicing outcomes to determine isoform expression and cellular survival. To identify RBPs that directly drive…”
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Author Correction: Large-scale evaluation of the ability of RNA-binding proteins to activate exon inclusion by Schmok, Jonathan C., Jain, Manya, Street, Lena A., Tankka, Alex T., Schafer, Danielle, Her, Hsuan-Lin, Elmsaouri, Sara, Gosztyla, Maya L., Boyle, Evan A., Jagannatha, Pratibha, Luo, En-Ching, Kwon, Ester J., Jovanovic, Marko, Yeo, Gene W.

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Deactivated CRISPR Associated Protein 9 for Minor-Allele Enrichment in Cell-Free DNA by Aalipour, Amin, Dudley, Jonathan C, Park, Seung-Min, Murty, Surya, Chabon, Jacob J, Boyle, Evan A, Diehn, Maximilian, Gambhir, Sanjiv S

“…Cell-free DNA (cfDNA) diagnostics are emerging as a new paradigm of disease monitoring and therapy management. The clinical utility of these diagnostics is…”
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KIAA0586 is Mutated in Joubert Syndrome by Bachmann-Gagescu, Ruxandra, Phelps, Ian G., Dempsey, Jennifer C., Sharma, Vivek A., Ishak, Gisele E., Boyle, Evan A., Wilson, Meredith, Marques Lourenço, Charles, Arslan, Mutluay, Shendure, Jay, Doherty, Dan

“…ABSTRACT Joubert syndrome (JS) is a recessive neurodevelopmental disorder characterized by a distinctive mid‐hindbrain malformation. JS is part of a group of…”
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Mudskipper detects combinatorial RNA binding protein interactions in multiplexed CLIP data by Her, Hsuanlin, Rothamel, Katherine L., Nguyen, Grady G., Boyle, Evan A., Yeo, Gene W.

“…The uncovering of protein-RNA interactions enables a deeper understanding of RNA processing. Recent multiplexed crosslinking and immunoprecipitation (CLIP)…”
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Skipper analysis of eCLIP datasets enables sensitive detection of constrained translation factor binding sites by Boyle, Evan A., Her, Hsuan-Lin, Mueller, Jasmine R., Naritomi, Jack T., Nguyen, Grady G., Yeo, Gene W.

“…Technology for crosslinking and immunoprecipitation (CLIP) followed by sequencing (CLIP-seq) has identified the transcriptomic targets of hundreds of…”
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