Publications by authors named "Ryan Layer"

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Rapid, Reliable, and Interpretable Copy Number Variant Curation Visualizations for Diagnostic Settings with SeeNV.
Michael S Bradshaw, Jishnu Raychaudhuri, Lachlan Murphy, Rebecca Barnard, Taylor Firman, Ryan M Layer

J Mol Diagn· May 2025

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STABIX: Summary statistic-based GWAS indexing and compression.
Kristen Schneider, Simon Walker, Chris Gignoux, Ryan Layer

Bioinformatics· May 2025

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Biologically inspired graphs to explore massive genetic datasets.
Ryan M Layer

Nat Comput Sci· February 2025

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Hypothesis generation for rare and undiagnosed diseases through clustering and classifying time-versioned biological ontologies.
Michael S Bradshaw, Connor Gibbs, Skylar Martin, Taylor Firman, Alisa Gaskell, Ryan Layer

PLoS One· December 2024

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GenoSiS: A Biobank-Scale Genotype Similarity Search Architecture for Creating Dynamic Patient-Match Cohorts.
Kristen Schneider, Murad Chowdhury, Mariano Tepper, Jawad Khan, , Ryan Layer

bioRxiv· November 2024

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Implications of noncoding regulatory functions in the development of insulinomas.
Mireia Ramos-Rodríguez, Marc Subirana-Granés, Richard Norris, Valeria Sordi, Ángel Fernández, Ryan Layer

Cell Genom· August 2024

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NPEPPS Is a Druggable Driver of Platinum Resistance.
Robert T Jones, Mathijs Scholtes, Andrew Goodspeed, Maryam Akbarzadeh, Saswat Mohapatra, Ryan Layer

Cancer Res· May 2024

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Calling Structural Variants with Confidence from Short-Read Data in Wild Bird Populations.
Gabriel David, Alicia Bertolotti, Ryan Layer, Douglas Scofield, Alexander Hayward

Genome Biol Evol· April 2024

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

Sci Rep· February 2024

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Author Correction: Searching thousands of genomes to classify somatic and novel structural variants using STIX.
Murad Chowdhury, Brent S Pedersen, Fritz J Sedlazeck, Aaron R Quinlan, Ryan M Layer

Nat Methods· June 2022

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RAREsim: A simulation method for very rare genetic variants.
Megan Null, Josée Dupuis, Pezhman Sheinidashtegol, Ryan M Layer, Christopher R Gignoux

Am J Hum Genet· April 2022

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A complete reference genome improves analysis of human genetic variation.
Sergey Aganezov, Stephanie M Yan, Daniela C Soto, Melanie Kirsche, Samantha Zarate, Ryan Layer

Science· April 2022

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Searching thousands of genomes to classify somatic and novel structural variants using STIX.
Murad Chowdhury, Brent S Pedersen, Fritz J Sedlazeck, Aaron R Quinlan, Ryan M Layer

Nat Methods· April 2022

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

Genome Biol· May 2021

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Identification of High-Confidence Structural Variants in Domesticated Rainbow Trout Using Whole-Genome Sequencing.
Sixin Liu, Guangtu Gao, Ryan M Layer, Gary H Thorgaard, Gregory D Wiens

Front Genet· February 2021

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

Front Genet· January 2021

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The structural variation landscape in 492 Atlantic salmon genomes.
Alicia C Bertolotti, Ryan M Layer, Manu Kumar Gundappa, Michael D Gallagher, Ege Pehlivanoglu

Nat Commun· October 2020

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Mapping and characterization of structural variation in 17,795 human genomes.
Haley J Abel, David E Larson, Allison A Regier, Colby Chiang, Indraniel Das, Ryan M Layer

Nature· July 2020

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Regulatory sharing between estrogen receptor α bound enhancers.
Julia B Carleton, Matthew Ginley-Hidinger, Kristofer C Berrett, Ryan M Layer, Aaron R Quinlan

Nucleic Acids Res· July 2020

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

Front Genet· March 2020

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

Bioinformatics· November 2019

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

Nat Genet· January 2019

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Whole-genome analysis for effective clinical diagnosis and gene discovery in early infantile epileptic encephalopathy.
Betsy E P Ostrander, Russell J Butterfield, Brent S Pedersen, Andrew J Farrell, Ryan M Layer

NPJ Genom Med· August 2018

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SV-plaudit: A cloud-based framework for manually curating thousands of structural variants.
Jonathan R Belyeu, Thomas J Nicholas, Brent S Pedersen, Thomas A Sasani, James M Havrilla, Ryan M Layer

Gigascience· July 2018

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Coloc-stats: a unified web interface to perform colocalization analysis of genomic features.
Boris Simovski, Chakravarthi Kanduri, Sveinung Gundersen, Dmytro Titov, Diana Domanska, Ryan M Layer

Nucleic Acids Res· July 2018

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