• Bioinformatics
    • Pedersen BS, Layer RM, and Quinlan AR, Vcfanno: fast, flexible annotation of genetic variants. Genome Biology. 2016 Jun 1; 17:118.
    • Layer RM, Kindlon N, Karczewski KJ, ExAC, and Quinlan AR. Efficient genotype compression and analysis of large genetic-variation data sets. Nature Methods. 2015 Nov. doi:10.1038/nmeth.3654
    • Chiang C, Layer RM, Faust GG, Lindberg MR, Rose DB, Garrison EP, Marth GT, Quinlan AR, and Hall IM. SpeedSeq: Ultra-fast personal genome analysis and interpretation. 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
    • Layer RM and Quinlan AR. A parallel algorithm for N-way interval set intersection. Proceedings of the IEEE. 2015 Oct; 10.1109/JPROC.2015.2461494
    • Mueller AC, Cichewicz MA, Dey BK, Layer R, Reon BJ, Gagan JR, and Dutta A. MUNC: A lncRNA that induces the expression of pro-myogenic genes in skeletal myogenesis. 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
    • Layer RM, Chiang C, Quinlan AR, Hall IM, LUMPY: A probabilistic framework for structural variant discovery. 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
    • Sun D, Layer RM, Mueller AC, Cichewicz MA, Negishi M, Paschal BM, Dutta A, Regulation of several androgen-induced genes through the repression of the miR-99a/let-7c/miR-125b-2 miRNA cluster in prostate cancer cells. Oncogene. 2013 Mar 18.
    • Malhotra A, Lindberg MR, Faust GG, Leibowitz ML, Clark RA, Layer RM, Quinlan AR, and Hall IM, Breakpoint profiling of 64 cancer genomes reveals numerous complex rearrangements spawned by homology-independent mechanisms, Genome Res. 2013 May; 23(5):762-76.
    • Gagan J, Dey BK, Layer RM, Yan Z, Dutta A, Notch3 and Mef2c Are Mutually Antagonistic via Mkp1 and miR-1/206 in Differentiating Myoblasts , J. Biol. Chem. 2012 Nov 23; 287(48):40360-70.
    • Layer RM, Skadron K, Robins, G Hall IM, Quinlan AR, Binary Interval Search (BITS): A Scalable Algorithm for Counting Interval Intersections, Bioinformatics. 2013 Jan 1; 29(1):1-7.
    • Shibata Y, Kumar P, Layer RM, Willcox S, Gagan JR, Griffith JD, Dutta A, Extrachromosomal MicroDNAs and Chromosomal Microdeletions in Normal Tissues, Science. 2012 Apr 6; 336(6077):82-6.
    • Gagan J, Dey BK, Layer RM, Yan A, Dutta A, MICRORNA-378 targets the myogenic repressor MyoR during myoblast differentiation, J. Biol. Chem. 2011 Jun 3; 286(22):19431-8.
    • Keaton MA, Taylor CM, Layer RM, Dutta A, Nuclear Scaffold Attachment Sites within ENCODE Regions Associate with Actively Transcribed Genes, PLoS ONE. 2011 Mar 14; 6(3):e17912.
  • Security
    • Henry M, Layer RM, Zaret D, Coupled Petri Nets for Computer Network Risk Analysis, International Journal of Critical Infrastructure Protection. 2010 July; 3(3):67-75.
    • Henry M, Layer RM, Zaret D, Evaluating the risk of cyber attacks on SCADA systems via Petri net analysis with application to hazardous liquid loading operations, In Proceedings of the 2009 IEEE International Conference on Technologies for Homeland Security. IEEE Computer Society, Washington, DC, USA, 607-14.
  • Teaching
    • Tychonievich L, Sherriff M, and Layer RM. "Counting Squares - Assignment for middle school through CS1." Nifty Assignments Panel, The 46st ACM Technical Symposium on Computer Science Education, Kansas City, KS, Mar 4-7, 2015.
    • Layer RM, Sherriff M, Tychonievich L, "Inform, Experience, Implement" - Teaching an Intensive High School Summer Course, In Proceedings of the 2012 IEEE Frontiers in Education Conference. IEEE Computer Society, Washington, DC, USA, 1-6.