Invited Keynote Talk: Haplotype Sharing for Genome-Wide Case-Control Association Studies. - Andrew S. Allen (ISBRA, 2008)

SVA: software for annotating and visualizing sequenced human genomes. - Dongliang Ge; Elizabeth K. Ruzzo; Kevin V. Shianna; Min He; Kimberly Pelak; Erin L. Heinzen; Anna C. Need; Elizabeth T. Cirulli; Jessica M. Maia; Samuel P. Dickson; Mingfu Zhu; Abanish Singh; et al. (Bioinform., 2011)

Leveraging Prior Information to Detect Causal Variants via Multi-Variant Regression. - Nanye Long; Samuel P. Dickson; Jessica M. Maia; Hee Shin Kim; Qianqian Zhu; Andrew S. Allen (PLoS Comput. Biol., 2013)

Ruratae: a physics-based audio engine. - Andrew S. Allen (2014)

Exploiting expression patterns across multiple tissues to map expression quantitative trait loci. - Chaitanya R. Acharya; Janice M. McCarthy; Kouros Owzar; Andrew S. Allen (BMC Bioinform., 2016)

Quantifying the Impact of Non-coding Variants on Transcription Factor-DNA Binding. - Jingkang Zhao; Dongshunyi Li; Jungkyun Seo; Andrew S. Allen; Raluca Gordân (RECOMB, 2017)

High-throughput interpretation of gene structure changes in human and nonhuman resequencing data, using ACE. - William H. Majoros; Michael Campbell; Carson Holt; Erin K. DeNardo; Doreen Ware; Andrew S. Allen; Mark Yandell; Timothy E. Reddy (Bioinform., 2017)

Mapping eQTL by leveraging multiple tissues and DNA methylation. - Chaitanya R. Acharya; Kouros Owzar; Andrew S. Allen (BMC Bioinform., 2017)

bcSeq: an R package for fast sequence mapping in high-throughput shRNA and CRISPR screens. - Jiaxing Lin; Jeremy Gresham; Tongrong Wang; So Young Kim; James Alvarez; Jeffrey S. Damrauer; Scott Floyd; Joshua A. Granek; Andrew S. Allen; Cliburn Chan; Jichun Xie; Kouros Owzar (Bioinform., 2018)

meaRtools: An R package for the analysis of neuronal networks recorded on microelectrode arrays. - Sahar Gelfman; Quanli Wang; Yi-Fan Lu; Diana Hall; Christopher D. Bostick; Ryan Dhindsa; Matt Halvorsen; K. Melodi McSweeney; Ellese Cotterill; Tom Edinburgh; Michael A. Beaumont; Wayne N. Frankel; et al. (PLoS Comput. Biol., 2018)

Efficient estimation of grouped survival models. - Zhiguo Li; Jiaxing Lin; Alexander B. Sibley; Tracy Truong; Katherina C. Chua; Yu Jiang; Janice M. McCarthy; Deanna L. Kroetz; Andrew S. Allen; Kouros Owzar (BMC Bioinform., 2019)

Bayesian estimation of genetic regulatory effects in high-throughput reporter assays. - William H. Majoros; Young-Sook Kim; Alejandro Barrera; Fan Li; Xingyan Wang; Sarah J. Cunningham; Graham D. Johnson; Cong Guo; William L. Lowe; Denise M. Scholtens; M. Geoffrey Hayes; Timothy E. Reddy; et al. (Bioinform., 2020)

A Bayesian hierarchical model to estimate DNA methylation conservation in colorectal tumors. - Kevin A. Murgas; Yanlin Ma; Lidea K. Shahidi; Sayan Mukherjee 001; Andrew S. Allen; Darryl Shibata; Marc D. Ryser (Bioinform., 2021)

Focused goodness of fit tests for gene set analyses. - Mengqi Zhang; Sahar Gelfman; Cristiane Araujo Martins Moreno; Janice M. McCarthy; Matthew B. Harms; David B. Goldstein; Andrew S. Allen (Briefings Bioinform., 2022)