Ryan Layer
Ryan Layer
Verified email at colorado.edu - Homepage
TitleCited byYear
LUMPY: a probabilistic framework for structural variant discovery
RM Layer, C Chiang, AR Quinlan, IM Hall
Genome biology 15 (6), R84, 2014
SpeedSeq: ultra-fast personal genome analysis and interpretation
C Chiang, RM Layer, GG Faust, MR Lindberg, DB Rose, EP Garrison, ...
Nature methods 12 (10), 966, 2015
Breakpoint profiling of 64 cancer genomes reveals numerous complex rearrangements spawned by homology-independent mechanisms
A Malhotra, M Lindberg, GG Faust, ML Leibowitz, RA Clark, RM Layer, ...
Genome research 23 (5), 762-776, 2013
MicroRNA-378 targets the myogenic repressor MyoR during myoblast differentiation
J Gagan, BK Dey, R Layer, Z Yan, A Dutta
Journal of Biological Chemistry 286 (22), 19431-19438, 2011
Extrachromosomal microDNAs and chromosomal microdeletions in normal tissues
Y Shibata, P Kumar, R Layer, S Willcox, JR Gagan, JD Griffith, A Dutta
Science 336 (6077), 82-86, 2012
Regulation of several androgen-induced genes through the repression of the miR-99a/let-7c/miR-125b-2 miRNA cluster in prostate cancer cells
D Sun, R Layer, AC Mueller, MA Cichewicz, M Negishi, BM Paschal, ...
Oncogene 33 (11), 1448, 2014
Notch3 and Mef2c proteins are mutually antagonistic via Mkp1 protein and miR-1/206 microRNAs in differentiating myoblasts
J Gagan, BK Dey, R Layer, Z Yan, A Dutta
Journal of Biological Chemistry 287 (48), 40360-40370, 2012
MUNC, a long noncoding RNA that facilitates the function of MyoD in skeletal myogenesis
AC Mueller, MA Cichewicz, BK Dey, R Layer, BJ Reon, JR Gagan, A Dutta
Molecular and cellular biology 35 (3), 498-513, 2015
An analytical framework for whole-genome sequence association studies and its implications for autism spectrum disorder
DM Werling, H Brand, JY An, MR Stone, L Zhu, JT Glessner, RL Collins, ...
Nature genetics 50 (5), 727, 2018
Nifty assignments
N Parlante, J Zelenski, M Craig, J DeNero, M Guzdial, DJ Malan, ...
Proceeding of the 44th ACM technical symposium on Computer science education …, 2013
Vcfanno: fast, flexible annotation of genetic variants
BS Pedersen, RM Layer, AR Quinlan
Genome biology 17 (1), 118, 2016
Efficient genotype compression and analysis of large genetic-variation data sets
RM Layer, N Kindlon, KJ Karczewski, AR Quinlan, ...
Nature methods 13 (1), 63, 2016
Binary Interval Search: a scalable algorithm for counting interval intersections
RM Layer, K Skadron, G Robins, IM Hall, AR Quinlan
Bioinformatics 29 (1), 1-7, 2012
Nuclear scaffold attachment sites within ENCODE regions associate with actively transcribed genes
MA Keaton, CM Taylor, RM Layer, A Dutta
PLoS One 6 (3), e17912, 2011
Evaluating the risk of cyber attacks on SCADA systems via Petri net analysis with application to hazardous liquid loading operations
MH Henry, RM Layer, KZ Snow, DR Zaret
2009 IEEE Conference on Technologies for Homeland Security, 607-614, 2009
Coupled Petri nets for computer network risk analysis
MH Henry, RM Layer, DR Zaret
International Journal of Critical Infrastructure Protection 3 (2), 67-75, 2010
Combating subclonal evolution of resistant cancer phenotypes
SW Brady, JA McQuerry, Y Qiao, SR Piccolo, G Shrestha, DF Jenkins, ...
Nature Communications 8 (1), 1231, 2017
A map of constrained coding regions in the human genome
JM Havrilla, BS Pedersen, RM Layer, AR Quinlan
Nat Genet 51 (1), 88-95, 2019
Limited contribution of rare, noncoding variation to autism spectrum disorder from sequencing of 2,076 genomes in quartet families
DM Werling, H Brand, JY An, MR Stone, JT Glessner, L Zhu, RL Collins, ...
BioRxiv, 127043, 2017
GIGGLE: a search engine for large-scale integrated genome analysis
RM Layer, BS Pedersen, T DiSera, GT Marth, J Gertz, AR Quinlan
Nature methods 15 (2), 123, 2018
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