Journals

SV-plaudit: A cloud-based framework for manually curating thousands of structural variants
Belyeu JR, Nicholas TJ, Pedersen BS, Sasani TA, Havrilla JM, Kravitz SN, Conway ME, Lohman BK, Quinlan AR, and Layer RM. biorxiv. 2018 February 14.

GIGGLE: a search engine for large-scale integrated genome analysis
Layer RM, Pedersen BS, DiSera T, Marth GT, Gertz J, and Quinlan AR. Nature Methods. Published online: 2018 January 08

An analytical framework for whole genome sequence data and its implications for autism spectrum disorder
Werling DM, Brand H, An JY, Stone MR, Glessner JT, Zhe L, Collins RL, Dong S, Layer RM, Markenscoff-Papadimitriou EC, Farrell A, Schwartz GB, Currall BB, Dea JD, Docherty AR, Duhn C, Erdman C, Gilson M, Handsaker RE, Kashin S, Klei L, Mandell JD, Nowakowski TJ, Liu Y, Pochareddy S, Smith L, Wang HZ, Waterman MJ, He X, Kriegstein AR, Rubenstein JL, Sestan N, McCarroll SA, Neale BM, Coon HC, Willsey AJ, Buxbaum JD, Daly MJ, State MW, Quinlan AR, Marth G, Roeder K, Devlin B, Talkowski ME, and Sanders SJ. Nature Genetics. In press.

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 PJ, Gray JW, Heiser LM, Buys SS, Cohen AL, Johnson WE, Quinlan AR, Marth G, Werner TL, and Bild AH. Nature communications. 2017 November 1; 8:1231

Vcfanno: fast, flexible annotation of genetic variants
Pedersen BS, Layer RM, and Quinlan AR. Genome Biology. 2016 June 1; 17:118

Efficient genotype compression and analysis of large genetic-variation data sets
Layer RM, Kindlon N, Karczewski JK, and Quinlan AR. Nature Methods. 2015 November 9; 13:63-5.

SpeedSeq: Ultra-fast personal genome analysis and interpretation
Layer RM and Quinlan AR. A parallel algorithm for N-way interval set intersection. Chiang C, Layer RM, Faust GG, Lindberg MR, Rose DB, Garrison EP, Marth GT, Quinlan AR, and Hall IM. Nature Methods. 2015 August 10; 12:966-8

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 November 17; MCB. 01079-14.

LUMPY: A probabilistic framework for structural variant discovery
Layer RM, Chiang C, Quinlan AR, and Hall IM.  Genome Biology. 2014 June 26; 15:R84.

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, and Dutta A.  Oncogene. 2013 March 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 November 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 January 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 April 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 June 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 March 14; 6(3):e17912.

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.

Conference Proceedings

“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. 

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.

Meetings

STIX: A scalable index for mining large whole-genome sequence cohorts for reliable structural variant population allele frequency estimates
Genome Informatics, Cold Spring Harbor Laboratory, NY, November 2017

STIX: A scalable index for mining large whole-genome sequence cohorts for reliable structural variant population allele frequency estimates
American Society of Human Genetics (ASHG), Orlando, FL, October 2017

GIGGLE: a scalable and fast search engine for large-scale multi-omics data integration
Genome Informatics, Wellcome Genome Campus, UK, September 2016

Exploring Genetic Variation and Genotypes Among Millions of Genomes
Festival of Genomics, San Francisco, CA, November 2015

Exploring Genetic Variation and Genotypes Among Millions of Genomes
The Biology of Genomes, Cold Spring Harbor Laboratory, NY, May 2015

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

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

Book Chapters

Henry MH, Zaret DR, Carr JR, Gordon JD, Layer RM. Cyber-security of SCADA and Other Industrial Control Systems. Cyber Risk in Industrial Control Systems. 133-66. Springer International Publishing, 2016.

Technical Reports

Kreuter B, Layer RM, McDaniel M, Robins G, and Skadron K. Accelerating Genomic Analyses with Parallel Sliding Windows. University of Virginia, Department of Computer Science Technical Report # CS-2009-14, October 2010.

Patents

Layer RM and Quinlan AR. System, Method, and Computer Readable Medium for Rapid DNA Identification. US Patent 20,160,132,640, 2016