Vcfanno: fast, flexible annotation of genetic variants

por Pedersen, Brent S., Layer, Ryan M., Quinlan, Aaron R.
Publicado 2016

webGQT: A Shiny Server for Genotype Query Tools for Model-Based Variant Filtering

por Arumilli, Meharji, Layer, Ryan M., Hytönen, Marjo K., Lohi, Hannes
Publicado 2020

Nuclear Scaffold Attachment Sites within ENCODE Regions Associate with Actively Transcribed Genes

por Keaton, Mignon A., Taylor, Christopher M., Layer, Ryan M., Dutta, Anindya
Publicado 2011

LUMPY: a probabilistic framework for structural variant discovery

por Layer, Ryan M, Chiang, Colby, Quinlan, Aaron R, Hall, Ira M
Publicado 2014

Efficient genotype compression and analysis of large genetic variation datasets

por Layer, Ryan M., Kindlon, Neil, Karczewski, Konrad J., Quinlan, Aaron R.
Publicado 2015

Editorial: Genomic Colocalization and Enrichment Analyses

por Kanduri, Chakravarthi, Sandve, Geir Kjetil, Hovig, Eivind, De, Subhajyoti, Layer, Ryan M.
Publicado 2021

Searching thousands of genomes to classify somatic and novel structural variants using STIX

por Chowdhury, Murad, Pedersen, Brent S., Sedlazeck, Fritz J., Quinlan, Aaron R., Layer, Ryan M.
Publicado 2022

Author Correction: Searching thousands of genomes to classify somatic and novel structural variants using STIX

por Chowdhury, Murad, Pedersen, Brent S., Sedlazeck, Fritz J., Quinlan, Aaron R., Layer, Ryan M.
Publicado 2022

Regulatory sharing between estrogen receptor α bound enhancers

por Carleton, Julia B, Ginley-Hidinger, Matthew, Berrett, Kristofer C, Layer, Ryan M, Quinlan, Aaron R, Gertz, Jason
Publicado 2020

Samplot: a platform for structural variant visual validation and automated filtering

por Belyeu, Jonathan R., Chowdhury, Murad, Brown, Joseph, Pedersen, Brent S., Cormier, Michael J., Quinlan, Aaron R., Layer, Ryan M.
Publicado 2021

svtools: population-scale analysis of structural variation

por Larson, David E, Abel, Haley J, Chiang, Colby, Badve, Abhijit, Das, Indraniel, Eldred, James M, Layer, Ryan M, Hall, Ira M
Publicado 2019

Identification of High-Confidence Structural Variants in Domesticated Rainbow Trout Using Whole-Genome Sequencing

por Liu, Sixin, Gao, Guangtu, Layer, Ryan M., Thorgaard, Gary H., Wiens, Gregory D., Leeds, Timothy D., Martin, Kyle E., Palti, Yniv
Publicado 2021

Breakpoint profiling of 64 cancer genomes reveals numerous complex rearrangements spawned by homology-independent mechanisms

por Malhotra, Ankit, Lindberg, Michael, Faust, Gregory G., Leibowitz, Mitchell L., Clark, Royden A., Layer, Ryan M., Quinlan, Aaron R., Hall, Ira M.
Publicado 2013

SpeedSeq: Ultra-fast personal genome analysis and interpretation

por 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.
Publicado 2015

SV-plaudit: A cloud-based framework for manually curating thousands of structural variants

por 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
Publicado 2018

Coloc-stats: a unified web interface to perform colocalization analysis of genomic features

por Simovski, Boris, Kanduri, Chakravarthi, Gundersen, Sveinung, Titov, Dmytro, Domanska, Diana, Bock, Christoph, Bossini-Castillo, Lara, Chikina, Maria, Favorov, Alexander, Layer, Ryan M, Mironov, Andrey A, Quinlan, Aaron R, Sheffield, Nathan C, Trynka, Gosia, Sandve, Geir K
Publicado 2018

Whole-genome analysis for effective clinical diagnosis and gene discovery in early infantile epileptic encephalopathy

por 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.
Publicado 2018

Mapping and characterization of structural variation in 17,795 human genomes

por Abel, Haley J., Larson, David E., Regier, Allison A., Chiang, Colby, Das, Indraniel, Kanchi, Krishna L., Layer, Ryan M., Neale, Benjamin M., Salerno, William J., Reeves, Catherine, Buyske, Steven, Matise, Tara C., Muzny, Donna M., Zody, Michael C., Lander, Eric S., Dutcher, Susan K., Stitziel, Nathan O., Hall, Ira M.
Publicado 2020

The structural variation landscape in 492 Atlantic salmon genomes

por 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.
Publicado 2020

Combating subclonal evolution of resistant cancer phenotypes

por 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.
Publicado 2017