Ryan Layer | University of Virginia Computer Science

Bioinformatics
- Combating subclonal evolution of resistant cancer phenotypes.
  
  Brady SW, McQuerry JA, Qiao Y, Piccolo SR, Shrestha G, Jenkins DF, Layer RM, Pedersen BS, Miller RH, Esch A, Selitsky SR, Parker JS, Anderson LA, Dalley BK, Factor RE, Reddy CB, Boltax JP, Li DY, Moos JP, Gray JW, Heiser LM, Buys SS, Cohen AL, Johnson WE, Quinlan AR, Marth G, Werner TL and Bild AH
  
  Nature Communications. 2017 Nov 1; 8:1231.
- Vcfanno: fast, flexible annotation of genetic variants
  
  Pedersen BS, Layer RM, and Quinlan AR
  
  Genome Biology. 2016 Jun 1; 17:118.
- Efficient genotype compression and analysis of large genetic-variation data sets
  
  Layer RM, Kindlon N, Karczewski KJ, ExAC, and Quinlan AR
  
  Nature Methods. 2015 Nov. doi:10.1038/nmeth.3654
- SpeedSeq: Ultra-fast personal genome analysis and interpretation
  
  Chiang C, Layer RM, Faust GG, Lindberg MR, Rose DB, Garrison EP, Marth GT, Quinlan AR, and Hall IM.
  
  Nature Methods. 2015 Aug; 12:966-68.
- Exploring Genetic Variation and Genotypes Among Millions of Genomes.
  
  The Biology of Genomes, Cold Spring Harbor Laboratory, NY, 2015 May
- A parallel algorithm for N-way interval set intersection
  
  Layer RM and Quinlan AR
  
  Proceedings of the IEEE. 2015 Oct; 10.1109/JPROC.2015.2461494
- MUNC: A lncRNA that induces the expression of pro-myogenic genes in skeletal myogenesis
  
  Mueller AC, Cichewicz MA, Dey BK, Layer R, Reon BJ, Gagan JR, and Dutta A
  
  Molecular and cellular biology. 2014 Nov. MCB.01079-14.
- Exploring Genetic Variation and Genotypes Among Millions of Genomes
  
  American Society of Human Genetics (ASHG), San Diego, CA, October 2014
- Scaling Genotype-based Genetic Variation Discovery to Millions of Genomes
  
  Genome Informatics, Cambridge, UK, November 2014
- LUMPY: A probabilistic framework for structural variant discovery.
  
  Layer RM, Chiang C, Quinlan AR, Hall IM
  
  Genome Biology. 2014 Jun 26; 15:R84.
- SpeedSeq: A 24-hour, open-source variant calling pipeline for clinical genome interpretation.
  
  Advances in Genome Biology and Technology (AGBT), Marco Island, FL, February 2014
- Regulation of several androgen-induced genes through the repression of the miR-99a/let-7c/miR-125b-2 miRNA cluster in prostate cancer cells
  
  Sun D, Layer RM, Mueller AC, Cichewicz MA, Negishi M, Paschal BM, Dutta A
  
  Oncogene. 2013 Mar 18.
- Breakpoint profiling of 64 cancer genomes reveals numerous complex rearrangements spawned by homology-independent mechanisms
  
  Malhotra A, Lindberg MR, Faust GG, Leibowitz ML, Clark RA, Layer RM, Quinlan AR, and Hall IM
  
  Genome Res. 2013 May; 23(5):762-76.
- Notch3 and Mef2c Are Mutually Antagonistic via Mkp1 and miR-1/206 in Differentiating Myoblasts
  
  Gagan J, Dey BK, Layer RM, Yan Z, Dutta A
  
  J. Biol. Chem. 2012 Nov 23; 287(48):40360-70.
- Binary Interval Search (BITS): A Scalable Algorithm for Counting Interval Intersections
  
  Layer RM, Skadron K, Robins, G Hall IM, Quinlan AR
  
  Bioinformatics. 2013 Jan 1; 29(1):1-7.
- Extrachromosomal MicroDNAs and Chromosomal Microdeletions in Normal Tissues
  
  Shibata Y, Kumar P, Layer RM, Willcox S, Gagan JR, Griffith JD, Dutta A
  
  Science. 2012 Apr 6; 336(6077):82-6.
- MICRORNA-378 targets the myogenic repressor MyoR during myoblast differentiation
  
  Gagan J, Dey BK, Layer RM, Yan A, Dutta A
  
  J. Biol. Chem. 2011 Jun 3; 286(22):19431-8.
- Nuclear Scaffold Attachment Sites within ENCODE Regions Associate with Actively Transcribed Genes
  
  Keaton MA, Taylor CM, Layer RM, Dutta A
  
  PLoS ONE. 2011 Mar 14; 6(3):e17912.
Security
- Coupled Petri Nets for Computer Network Risk Analysis
  
  Henry M, Layer RM, Zaret D
  
  International Journal of Critical Infrastructure Protection. 2010 July; 3(3):67-75.
- Evaluating the risk of cyber attacks on SCADA systems via Petri net analysis with application to hazardous liquid loading operations
  
  Henry M, Layer RM, Zaret D
  
  In Proceedings of the 2009 IEEE International Conference on Technologies for Homeland Security. IEEE Computer Society, Washington, DC, USA, 607-14.
Teaching
- Counting Squares - Assignment for middle school through CS1.
  
  Tychonievich L, Sherriff M, and Layer RM
  
  Nifty Assignments Panel, The 46st ACM Technical Symposium on Computer Science Education, Kansas City, KS, Mar 4-7, 2015.
- "Inform, Experience, Implement" Teaching an Intensive High School Summer Course
  
  Layer RM, Sherriff M, Tychonievich L
  
  In Proceedings of the 2012 IEEE Frontiers in Education Conference. IEEE Computer Society, Washington, DC, USA, 1-6.