Publications

Journals

Mining Thousands of Genomes to Classify Somatic and Pathogenic Structural Variants
Layer RM, Sedlazeck FJ, Pedersen BS, Quinlan AR. bioRxiv. 2021 April 22.

Identification of High-Confidence Structural Variants in Domesticated Rainbow Trout Using Whole-Genome Sequencing
Liu S, Gao G, Layer RM, Thorgaard GH, Wiens GD, Leeds TD, Martin KE, and Palti Y. Frontiers in Genetics. 2021 Feburary 25. 12. 237.

The M1 aminopeptidase NPEPPS is a novel regulator of cisplatin sensitivity
Jones RT, Goodspeed A, Akbarzadeh MC, Scholtes M, Vekony H, Jean A, Tilton CB, Orman MV, Joshi M, Laajala TD, Javaid M, Clambey ET, Layer RM, Parker S, Mahmoudi T, Zuiverloon T, Theodorescu D, and Costello JC. bioRxiv. 2021 March 24.

The structural variation landscape in 492 Atlantic salmon genomes
Bertolotti AC, Layer RM, Gundappa MK, Gallagher MD, Pehlivanoglu E, Nome T, Robledo D, Kent MP, Røsæg LL, Holen MM, Mulugeta TD, Ashton TJ, Hindar K, Sægrov H, Florø-Larsen B, Erkinaro J, Primmer CR, Bernatchez L, Martin SAM, Johnston IA, Sandve SR, Lien S, and Macqueen DJ. Nature communications. 2020 October 14. 11. 5176.

Regulatory sharing between estrogen receptor α bound enhancers
Carleton JB, Ginley-Hidinger M, Berrett KC, Layer RM, Quinlan AR, and Gertz J. Nucleic acids research. 2020 July 09. 48(12). 6597-610.

Mapping and characterization of structural variation in 17,795 human genomes
Abel HJ, Larson DE, Regier AA, Chiang CC, Das I, Kanchi KL, Layer RM, Neale BM, Salerno WJ, Reeves C, Buyske S, Matise TC, Muzny DM, Zody MC, Lander ES, Dutcher SK, Stitziel NO, and Hall IM. Nature. 2020 May 27. 583. 83-9.

webGQT: A Shiny Server for Genotype Query Tools for Model-Based Variant Filtering
Arumilli M, Layer RM, Hytönen MK, and Lohi H. Frontiers in genetics. 2020 March 3.

Genomic Colocalization and Enrichment Analyses
Kanduri C, Sandve GK, Hovig E, De S, and Layer RM. Frontiers in Genetics. 2021 January 26.

Samplot: A platform for structural variant visual validation and automated filtering
Belyeu JR, Chowdhury M, Brown J, Pedersen BS, Cormier MJ, Quinlan AR, and Layer RM. bioRxiv. 2020 December 10.

Case Study: Using Facebook Data to Monitor Adherence to Stay-at-home Orders in Colorado and Utah
Layer RM, Fosdick B, Larremore DB, Bradshaw M, Doherty P. medRxiv. 2020 July 30.

svtools: population-scale analysis of structural variation
Larson DE, Abel HJ, Chiang C, Badve A, Das I, Eldred HM, Layer RM, and Hall IM. 2019 November 15. 35(22). 4782-87.

A map of constrained coding regions in the human genome
Havrilla JM, Pedersen BS, Layer RM, and Quinlan AR. Nature genetics. 2018 December 10. 51. 88-95.

Whole-genome analysis for effective clinical diagnosis and gene discovery in early infantile epileptic encephalopathy
Ostrander BEP, Butterfield RJ, Pedersen BS, Farrell AJ, Layer RM, Ward A, Miller C, DiSera T, Filloux FM, Candee MS, Newcomb T, Bonkowsky JL, Marth GT, and Quinlan AR. NPJ genomic medicine. 2018 August 13. 3(1). 1-10.

Coloc-stats: a unified web interface to perform colocalization analysis of genomic features
Simovski B, Kanduri C, Gundersen S, Titov D, Domanska D, Bock C, Bossini-Castillo L, Chikina M, Favorov A, Layer RM, Mironov AA, Quinlan AR, Sheffield NC, Trynka G, and Sandve GK. Nucleic acids research. 2018 July 2. 46(W1). 186-93.

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. Gigascience. 2018 May 31. 7(7).

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