Search Results - "Layer, Ryan M"

LUMPY: a probabilistic framework for structural variant discovery by Layer, Ryan M, Chiang, Colby, Quinlan, Aaron R, Hall, Ira M

“…Comprehensive discovery of structural variation (SV) from whole genome sequencing data requires multiple detection signals including read-pair, split-read,…”
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A map of constrained coding regions in the human genome by Havrilla, James M., Pedersen, Brent S., Layer, Ryan M., Quinlan, Aaron R.

“…Deep catalogs of genetic variation from thousands of humans enable the detection of intraspecies constraint by identifying coding regions with a scarcity of…”
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SpeedSeq: ultra-fast personal genome analysis and interpretation by Chiang, Colby, Layer, Ryan M, Faust, Gregory G, Lindberg, Michael R, Rose, David B, Garrison, Erik P, Marth, Gabor T, Quinlan, Aaron R, Hall, Ira M

“…SpeedSeq is an open-source software suite offering very fast, accurate and comprehensive analysis of single-nucleotide and structural variants from whole…”
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GIGGLE: a search engine for large-scale integrated genome analysis by Layer, Ryan M, Pedersen, Brent S, DiSera, Tonya, Marth, Gabor T, Gertz, Jason, Quinlan, Aaron R

“…GIGGLE is a genome interval search engine that enables extremely fast queries of genome features from thousands of genome annotation sets. GIGGLE is a genomics…”
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Samplot: a platform for structural variant visual validation and automated filtering by Belyeu, Jonathan R, Chowdhury, Murad, Brown, Joseph, Pedersen, Brent S, Cormier, Michael J, Quinlan, Aaron R, Layer, Ryan M

“…Visual validation is an important step to minimize false-positive predictions from structural variant (SV) detection. We present Samplot, a tool for creating…”
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The structural variation landscape in 492 Atlantic salmon genomes by Bertolotti, Alicia C., Layer, Ryan M., Gundappa, Manu Kumar, Gallagher, Michael D., Pehlivanoglu, Ege, Nome, Torfinn, Robledo, Diego, Kent, Matthew P., Røsæg, Line L., Holen, Matilde M., Mulugeta, Teshome D., Ashton, Thomas J., Hindar, Kjetil, Sægrov, Harald, Florø-Larsen, Bjørn, Erkinaro, Jaakko, Primmer, Craig R., Bernatchez, Louis, Martin, Samuel A. M., Johnston, Ian A., Sandve, Simen R., Lien, Sigbjørn, Macqueen, Daniel J.

“…Structural variants (SVs) are a major source of genetic and phenotypic variation, but remain challenging to accurately type and are hence poorly characterized…”
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Combating subclonal evolution of resistant cancer phenotypes by Brady, Samuel W., McQuerry, Jasmine A., Qiao, Yi, Piccolo, Stephen R., Shrestha, Gajendra, Jenkins, David F., Layer, Ryan M., Pedersen, Brent S., Miller, Ryan H., Esch, Amanda, Selitsky, Sara R., Parker, Joel S., Anderson, Layla A., Dalley, Brian K., Factor, Rachel E., Reddy, Chakravarthy B., Boltax, Jonathan P., Li, Dean Y., Moos, Philip J., Gray, Joe W., Heiser, Laura M., Buys, Saundra S., Cohen, Adam L., Johnson, W. Evan, Quinlan, Aaron R., Marth, Gabor, Werner, Theresa L., Bild, Andrea H.

“…Metastatic breast cancer remains challenging to treat, and most patients ultimately progress on therapy. This acquired drug resistance is largely due to…”
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Breakpoint profiling of 64 cancer genomes reveals numerous complex rearrangements spawned by homology-independent mechanisms by Malhotra, Ankit, Lindberg, Michael, Faust, Gregory G, Leibowitz, Mitchell L, Clark, Royden A, Layer, Ryan M, Quinlan, Aaron R, Hall, Ira M

“…Tumor genomes are generally thought to evolve through a gradual accumulation of mutations, but the observation that extraordinarily complex rearrangements can…”
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Embracing firefly flash pattern variability with data-driven species classification by Martin, Owen, Nguyen, Chantal, Sarfati, Raphael, Chowdhury, Murad, Iuzzolino, Michael L., Nguyen, Dieu My T., Layer, Ryan M., Peleg, Orit

“…Many nocturnally active fireflies use precisely timed bioluminescent patterns to identify mates, making them especially vulnerable to light pollution. As…”
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Editorial: Genomic Colocalization and Enrichment Analyses by Kanduri, Chakravarthi, Sandve, Geir Kjetil, Hovig, Eivind, De, Subhajyoti, Layer, Ryan M

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webGQT: A Shiny Server for Genotype Query Tools for Model-Based Variant Filtering by Arumilli, Meharji, Layer, Ryan M, Hytönen, Marjo K, Lohi, Hannes

“…Genotype Query Tools (GQT) were developed to discover disease-causing variations from billions of genotypes and millions of genomes, processes data at…”
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Identification of High-Confidence Structural Variants in Domesticated Rainbow Trout Using Whole-Genome Sequencing by Liu, Sixin, Gao, Guangtu, Layer, Ryan M, Thorgaard, Gary H, Wiens, Gregory D, Leeds, Timothy D, Martin, Kyle E, Palti, Yniv

“…Genomic structural variants (SVs) are a major source of genetic and phenotypic variation but have not been investigated systematically in rainbow trout ( ), an…”
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Whole-genome analysis for effective clinical diagnosis and gene discovery in early infantile epileptic encephalopathy by Ostrander, Betsy E. P., Butterfield, Russell J., Pedersen, Brent S., Farrell, Andrew J., Layer, Ryan M., Ward, Alistair, Miller, Chase, DiSera, Tonya, Filloux, Francis M., Candee, Meghan S., Newcomb, Tara, Bonkowsky, Joshua L., Marth, Gabor T., Quinlan, Aaron R.

“…Early infantile epileptic encephalopathy (EIEE) is a devastating epilepsy syndrome with onset in the first months of life. Although mutations in more than 50…”
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SV-plaudit: A cloud-based framework for manually curating thousands of structural variants by Belyeu, Jonathan R, Nicholas, Thomas J, Pedersen, Brent S, Sasani, Thomas A, Havrilla, James M, Kravitz, Stephanie N, Conway, Megan E, Lohman, Brian K, Quinlan, Aaron R, Layer, Ryan M

“…SV-plaudit is a framework for rapidly curating structural variant (SV) predictions. For each SV, we generate an image that visualizes the coverage and…”
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Vcfanno: fast, flexible annotation of genetic variants by Pedersen, Brent S, Layer, Ryan M, Quinlan, Aaron R

“…The integration of genome annotations is critical to the identification of genetic variants that are relevant to studies of disease or other traits. However,…”
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Nuclear scaffold attachment sites within ENCODE regions associate with actively transcribed genes by Keaton, Mignon A, Taylor, Christopher M, Layer, Ryan M, Dutta, Anindya

“…The human genome must be packaged and organized in a functional manner for the regulation of DNA replication and transcription. The nuclear scaffold/matrix,…”
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Publisher Correction: Combating subclonal evolution of resistant cancer phenotypes by Brady, Samuel W., McQuerry, Jasmine A., Qiao, Yi, Piccolo, Stephen R., Shrestha, Gajendra, Jenkins, David F., Layer, Ryan M., Pedersen, Brent S., Miller, Ryan H., Esch, Amanda, Selitsky, Sara R., Parker, Joel S., Anderson, Layla A., Dalley, Brian K., Factor, Rachel E., Reddy, Chakravarthy B., Boltax, Jonathan P., Li, Dean Y., Moos, Philip J., Gray, Joe W., Heiser, Laura M., Buys, Saundra S., Cohen, Adam L., Johnson, W. Evan, Quinlan, Aaron R., Marth, Gabor, Werner, Theresa L., Bild, Andrea H.

“…The originally published version of this Article contained an error in Figure 4. In panel a, grey boxes surrounding the subclones associated with patients #2…”
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An analytical framework for whole-genome sequence association studies and its implications for autism spectrum disorder by Werling, Donna M., Brand, Harrison, An, Joon-Yong, Stone, Matthew R., Zhu, Lingxue, Glessner, Joseph T., Collins, Ryan L., Dong, Shan, Layer, Ryan M., Markenscoff-Papadimitriou, Eirene, Farrell, Andrew, Schwartz, Grace B., Wang, Harold Z., Currall, Benjamin B., Zhao, Xuefang, Dea, Jeanselle, Duhn, Clif, Erdman, Carolyn A., Gilson, Michael C., Yadav, Rachita, Handsaker, Robert E., Kashin, Seva, Klei, Lambertus, Mandell, Jeffrey D., Nowakowski, Tomasz J., Liu, Yuwen, Pochareddy, Sirisha, Smith, Louw, Walker, Michael F., Waterman, Matthew J., He, Xin, Kriegstein, Arnold R., Rubenstein, John L., Sestan, Nenad, McCarroll, Steven A., Neale, Benjamin M., Coon, Hilary, Willsey, A. Jeremy, Buxbaum, Joseph D., Daly, Mark J., State, Matthew W., Quinlan, Aaron R., Marth, Gabor T., Roeder, Kathryn, Devlin, Bernie, Talkowski, Michael E., Sanders, Stephan J.

“…Genomic association studies of common or rare protein-coding variation have established robust statistical approaches to account for multiple testing. Here we…”
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Efficient genotype compression and analysis of large genetic-variation data sets by Layer, Ryan M, Kindlon, Neil, Karczewski, Konrad J, Quinlan, Aaron R

“…Genotype Query Tools allows fast individual-centric indexing and mining of large variant data sets. Genotype Query Tools (GQT) is an indexing strategy that…”
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svtools: population-scale analysis of structural variation by Larson, David E, Abel, Haley J, Chiang, Colby, Badve, Abhijit, Das, Indraniel, Eldred, James M, Layer, Ryan M, Hall, Ira M

“…Abstract Summary Large-scale human genetics studies are now employing whole genome sequencing with the goal of conducting comprehensive trait mapping analyses…”
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