LUMPY: a probabilistic framework for structural variant discovery von Layer, Ryan M, Chiang, Colby, Quinlan, Aaron R, Hall, Ira M

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A map of constrained coding regions in the human genome von Havrilla, James M., Pedersen, Brent S., Layer, Ryan M., Quinlan, Aaron R.

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SpeedSeq: ultra-fast personal genome analysis and interpretation von Chiang, Colby, Layer, Ryan M, Faust, Gregory G, Lindberg, Michael R, Rose, David B, Garrison, Erik P, Marth, Gabor T, Quinlan, Aaron R, Hall, Ira M

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GIGGLE: a search engine for large-scale integrated genome analysis von Layer, Ryan M, Pedersen, Brent S, DiSera, Tonya, Marth, Gabor T, Gertz, Jason, Quinlan, Aaron R

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Breakpoint profiling of 64 cancer genomes reveals numerous complex rearrangements spawned by homology-independent mechanisms von Malhotra, Ankit, Lindberg, Michael, Faust, Gregory G, Leibowitz, Mitchell L, Clark, Royden A, Layer, Ryan M, Quinlan, Aaron R, Hall, Ira M

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Samplot: a platform for structural variant visual validation and automated filtering von Belyeu, Jonathan R., Chowdhury, Murad, Brown, Joseph, Pedersen, Brent S., Cormier, Michael J., Quinlan, Aaron R., Layer, Ryan M.

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Organic substrate diffusibility governs microbial community composition, nutrient removal performance and kinetics of granulation of aerobic granular sludge von Layer, M, Adler, A, Reynaert, E, Hernandez, A, Pagni, M, Morgenroth, E, Holliger, C, Derlon, N

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The structural variation landscape in 492 Atlantic salmon genomes von Bertolotti, Alicia C., Layer, Ryan M., Gundappa, Manu Kumar, Gallagher, Michael D., Pehlivanoglu, Ege, Nome, Torfinn, Robledo, Diego, Kent, Matthew P., Røsæg, Line L., Holen, Matilde M., Mulugeta, Teshome D., Ashton, Thomas J., Hindar, Kjetil, Sægrov, Harald, Florø-Larsen, Bjørn, Erkinaro, Jaakko, Primmer, Craig R., Bernatchez, Louis, Martin, Samuel A. M., Johnston, Ian A., Sandve, Simen R., Lien, Sigbjørn, Macqueen, Daniel J.

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Combating subclonal evolution of resistant cancer phenotypes von Brady, Samuel W., McQuerry, Jasmine A., Qiao, Yi, Piccolo, Stephen R., Shrestha, Gajendra, Jenkins, David F., Layer, Ryan M., Pedersen, Brent S., Miller, Ryan H., Esch, Amanda, Selitsky, Sara R., Parker, Joel S., Anderson, Layla A., Dalley, Brian K., Factor, Rachel E., Reddy, Chakravarthy B., Boltax, Jonathan P., Li, Dean Y., Moos, Philip J., Gray, Joe W., Heiser, Laura M., Buys, Saundra S., Cohen, Adam L., Johnson, W. Evan, Quinlan, Aaron R., Marth, Gabor, Werner, Theresa L., Bild, Andrea H.

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Embracing firefly flash pattern variability with data-driven species classification von Martin, Owen, Nguyen, Chantal, Sarfati, Raphael, Chowdhury, Murad, Iuzzolino, Michael L., Nguyen, Dieu My T., Layer, Ryan M., Peleg, Orit

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An analytical framework for whole-genome sequence association studies and its implications for autism spectrum disorder von Werling, Donna M., Brand, Harrison, An, Joon-Yong, Stone, Matthew R., Zhu, Lingxue, Glessner, Joseph T., Collins, Ryan L., Dong, Shan, Layer, Ryan M., Markenscoff-Papadimitriou, Eirene, Farrell, Andrew, Schwartz, Grace B., Wang, Harold Z., Currall, Benjamin B., Zhao, Xuefang, Dea, Jeanselle, Duhn, Clif, Erdman, Carolyn A., Gilson, Michael C., Yadav, Rachita, Handsaker, Robert E., Kashin, Seva, Klei, Lambertus, Mandell, Jeffrey D., Nowakowski, Tomasz J., Liu, Yuwen, Pochareddy, Sirisha, Smith, Louw, Walker, Michael F., Waterman, Matthew J., He, Xin, Kriegstein, Arnold R., Rubenstein, John L., Sestan, Nenad, McCarroll, Steven A., Neale, Benjamin M., Coon, Hilary, Willsey, A. Jeremy, Buxbaum, Joseph D., Daly, Mark J., State, Matthew W., Quinlan, Aaron R., Marth, Gabor T., Roeder, Kathryn, Devlin, Bernie, Talkowski, Michael E., Sanders, Stephan J.

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Editorial: Genomic Colocalization and Enrichment Analyses von Kanduri, Chakravarthi, Sandve, Geir Kjetil, Hovig, Eivind, De, Subhajyoti, Layer, Ryan M.

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webGQT: A Shiny Server for Genotype Query Tools for Model-Based Variant Filtering von Arumilli, Meharji, Layer, Ryan M., Hytonen, Marjo K., Lohi, Hannes

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Whole-genome analysis for effective clinical diagnosis and gene discovery in early infantile epileptic encephalopathy von Ostrander, Betsy E. P., Butterfield, Russell J., Pedersen, Brent S., Farrell, Andrew J., Layer, Ryan M., Ward, Alistair, Miller, Chase, DiSera, Tonya, Filloux, Francis M., Candee, Meghan S., Newcomb, Tara, Bonkowsky, Joshua L., Marth, Gabor T., Quinlan, Aaron R.

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Identification of High-Confidence Structural Variants in Domesticated Rainbow Trout Using Whole-Genome Sequencing von Liu, Sixin, Gao, Guangtu, Layer, Ryan M., Thorgaard, Gary H., Wiens, Gregory D., Leeds, Timothy D., Martin, Kyle E., Palti, Yniv

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Particulate substrate retention in plug-flow and fully-mixed conditions during operation of aerobic granular sludge systems von Layer, M., Bock, K., Ranzinger, F., Horn, H., Morgenroth, E., Derlon, N.

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Vcfanno: fast, flexible annotation of genetic variants von Pedersen, Brent S, Layer, Ryan M, Quinlan, Aaron R

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SV-plaudit: A cloud-based framework for manually curating thousands of structural variants von Belyeu, Jonathan R, Nicholas, Thomas J, Pedersen, Brent S, Sasani, Thomas A, Havrilla, James M, Kravitz, Stephanie N, Conway, Megan E, Lohman, Brian K, Quinlan, Aaron R, Layer, Ryan M

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Nuclear scaffold attachment sites within ENCODE regions associate with actively transcribed genes von Keaton, Mignon A, Taylor, Christopher M, Layer, Ryan M, Dutta, Anindya

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svtools: population-scale analysis of structural variation von Larson, David E, Abel, Haley J, Chiang, Colby, Badve, Abhijit, Das, Indraniel, Eldred, James M, Layer, Ryan M, Hall, Ira M

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