Complexity of Approximating Closest Substring Problems. - Patricia A. Evans; Andrew D. Smith (FCT, 2003)

Toward Optimal Motif Enumeration. - Patricia A. Evans; Andrew D. Smith (WADS, 2003)

A Transition Probability Model for Amino Acid Substitutions from Blocks. - Shalini Veerassamy; Andrew D. Smith; Elisabeth R. M. Tillier (J. Comput. Biol., 2003)

On the complexity of finding common approximate substrings. - Patricia A. Evans; Andrew D. Smith; Harold T. Wareham (Theor. Comput. Sci., 2003)

Mining ChIP-chip data for transcription factor and cofactor binding sites. - Andrew D. Smith; Pavel Sumazin; Debopriya Das; Michael Q. Zhang (ISMB (Supplement of Bioinformatics), 2005)

DWE: Discriminating Word Enumerator. - Pavel Sumazin; Gengxin Chen; Naoya Hata; Andrew D. Smith; Theresa Zhang; Michael Q. Zhang (Bioinform., 2005)

SIMPROT: Using an empirically determined indel distribution in simulations of protein evolution. - Andy Pang; Andrew D. Smith; Paulo A. S. Nuin; Elisabeth R. M. Tillier (BMC Bioinform., 2005)

Computational prediction of novel components of lung transcriptional networks. - M. Juanita Martinez; Andrew D. Smith; Bilan Li; Michael Q. Zhang; Kevin S. Harrod (Bioinform., 2007)

Statistical significance of cis-regulatory modules. - Dustin E. Schones; Andrew D. Smith; Michael Q. Zhang (BMC Bioinform., 2007)

Integrative bioinformatics analysis of transcriptional regulatory programs in breast cancer cells. - Atsushi Niida; Andrew D. Smith; Seiya Imoto; Shuichi Tsutsumi; Hiroyuki Aburatani; Michael Q. Zhang; Tetsu Akiyama (BMC Bioinform., 2008)

Using quality scores and longer reads improves accuracy of Solexa read mapping. - Andrew D. Smith; Zhenyu Xuan; Michael Q. Zhang (BMC Bioinform., 2008)

Updates to the RMAP short-read mapping software. - Andrew D. Smith; Wen-Yu Chung; Emily Hodges; Jude Kendall; Gregory J. Hannon; James Hicks; Zhenyu Xuan; Michael Q. Zhang (Bioinform., 2009)

Gene set-based module discovery in the breast cancer transcriptome. - Atsushi Niida; Andrew D. Smith; Seiya Imoto; Hiroyuki Aburatani; Michael Q. Zhang; Tetsu Akiyama (BMC Bioinform., 2009)

Challenges in Understanding Genome-Wide DNA Methylation. - Michael Q. Zhang; Andrew D. Smith (J. Comput. Sci. Technol., 2009)

Identifying dispersed epigenomic domains from ChIP-Seq data. - Qiang Song 003; Andrew D. Smith (Bioinform., 2011)

Multiple Sequence Assembly from Reads Alignable to a Common Reference Genome. - Qian Peng; Andrew D. Smith (IEEE ACM Trans. Comput. Biol. Bioinform., 2011)

Site identification in high-throughput RNA-protein interaction data. - Philip J. Uren; Emad Bahrami Samani; Suzanne C. Burns; Mei Qiao; Fedor V. Karginov; Emily Hodges; Gregory J. Hannon; Jeremy R. Sanford; Luiz O. F. Penalva; Andrew D. Smith (Bioinform., 2012)

MLML: consistent simultaneous estimates of DNA methylation and hydroxymethylation. - Jianghan Qu; Meng Zhou; Qiang Song 003; Elizabeth E. Hong; Andrew D. Smith (Bioinform., 2013)

A Geometric Interpretation for Local Alignment-Free Sequence Comparison. - Ehsan Behnam; Michael S. Waterman; Andrew D. Smith (J. Comput. Biol., 2013)

The Amordad database engine for metagenomics. - Ehsan Behnam; Andrew D. Smith (Bioinform., 2014)

Modeling genome coverage in single-cell sequencing. - Timothy Daley; Andrew D. Smith (Bioinform., 2014)

Using beta-binomial regression for high-precision differential methylation analysis in multifactor whole-genome bisulfite sequencing experiments. - Egor Dolzhenko; Andrew D. Smith (BMC Bioinform., 2014)

Applications of species accumulation curves in large-scale biological data analysis. - Chao Deng; Timothy Daley; Andrew D. Smith (Quant. Biol., 2015)

WALT: fast and accurate read mapping for bisulfite sequencing. - Haifeng Chen; Andrew D. Smith; Ting Chen (Bioinform., 2016)

Riborex: fast and flexible identification of differential translation from Ribo-seq data. - Wenzheng Li; Weili Wang; Philip J. Uren; Luiz O. F. Penalva; Andrew D. Smith (Bioinform., 2017)

A tool to visualize and analyze perfusion data: Development and application of the R package "CTP". - Seth T. Lirette; Andrew D. Smith; Inmaculada B. Aban (Comput. Methods Programs Biomed., 2018)

Accurate detection of short and long active ORFs using Ribo-seq data. - Saket Choudhary; Wenzheng Li; Andrew D. Smith (Bioinform., 2020)

Predicting the Number of Bases to Attain Sufficient Coverage in High-Throughput Sequencing Experiments. - Chao Deng; Timothy Daley; Peter Calabrese; Jie Ren 006; Andrew D. Smith (J. Comput. Biol., 2020)

Artificial Intelligence in Perioperative Medicine: A Proposed Common Language With Applications to FDA-Approved Devices. - Ryan L. Melvin; Matthew G. Broyles; Elizabeth W. Duggan; Sonia John; Andrew D. Smith; Dan E. Berkowitz (Frontiers Digit. Health, 2022)

On attainability of Kendall's tau matrices and concordance signatures. - Alexander J. McNeil; Johanna Neslehová; Andrew D. Smith (J. Multivar. Anal., 2022)

Counting Distinguishable RNA Secondary Structures. - Masaru Nakajima; Andrew D. Smith (J. Comput. Biol., 2023)

Pulmonary Surface Irregularity Score as a New Quantitative CT Marker for Idiopathic Pulmonary Fibrosis - a Pilot Study. - Asser M. Abou Elkassem; Rafah Mresh; Ahmed Farag; Steven Rothenberg; Seth T. Lirette; Andrew D. Smith; Tejaswini Kulkarni (J. Digit. Imaging, 2023)

Strengths-weaknesses-opportunities-threats analysis of artificial intelligence in anesthesiology and perioperative medicine. - Henry J. Paiste; Ryan Godwin; Andrew D. Smith; Dan E. Berkowitz; Ryan L. Melvin (Frontiers Digit. Health, 2024)