Application of a MAX-CUT Heuristic to the Contig Orientation Problem in Genome Assembly. - Paul M. Bodily; Mark J. Clement; Quinn Snell; Jared C. Price; Stanley Fujimoto; Nozomu Okuda (BCB, 2013)

Haplotype-centered mapping for improved alignments and genetic association studies. - Paul M. Bodily; Mark J. Clement; Quinn Snell; M. Stanley Fujimoto; Perry G. Ridge (BCB, 2014)

A structured approach to ensemble learning for Alzheimer's disease prediction. - Matthew Seeley; Mark J. Clement; Christophe G. Giraud-Carrier; Quinn Snell; Paul M. Bodily; Stanley Fujimoto (BCB, 2014)

Effects of error-correction of heterozygous next-generation sequencing data. - M. Stanley Fujimoto; Paul M. Bodily; Nozomu Okuda; Mark J. Clement; Quinn Snell (BMC Bioinform., 2014)

Heterozygous genome assembly via binary classification of homologous sequence. - Paul M. Bodily; M. Stanley Fujimoto; Cameron Ortega; Nozomu Okuda; Jared C. Price; Mark J. Clement; Quinn Snell (BMC Bioinform., 2015)

ScaffoldScaffolder: solving contig orientation via bidirected to directed graph reduction. - Paul M. Bodily; M. Stanley Fujimoto; Quinn Snell; Dan Ventura; Mark J. Clement (Bioinform., 2016)

A novel approach for multi-SNP GWAS and its application in Alzheimer's disease. - Paul M. Bodily; M. Stanley Fujimoto; Justin T. Page; Mark J. Clement; Mark T. W. Ebbert; Perry G. Ridge (BMC Bioinform., 2016)

Detecting false positive sequence homology: a machine learning approach. - M. Stanley Fujimoto; Anton Suvorov; Nicholas O. Jensen; Mark J. Clement; Seth M. Bybee (BMC Bioinform., 2016)

Modeling Global and local Codon Bias with Deep Language Models. - Masaki Stanley Fujimoto; Paul M. Bodily; Cole A. Lyman; Andrew J. Jacobsen; Quinn Snell; Mark J. Clement (BIBE, 2017)

Genome Polymorphism Detection Through Relaxed de Bruijn Graph Construction. - M. Stanley Fujimoto; Cole A. Lyman; Anton Suvorov; Paul M. Bodily; Quinn Snell; Keith A. Crandall; Seth M. Bybee; Mark J. Clement (BIBE, 2017)

Whole Genome Phylogenetic Tree Reconstruction Using Colored de Bruijn Graphs. - Cole A. Lyman; M. Stanley Fujimoto; Anton Suvorov; Paul M. Bodily; Quinn Snell; Keith A. Crandall; Seth M. Bybee; Mark J. Clement (BIBE, 2017)

The OGCleaner: filtering false-positive homology clusters. - M. Stanley Fujimoto; Anton Suvorov; Nicholas O. Jensen; Mark J. Clement; Quinn Snell; Seth M. Bybee (Bioinform., 2017)

The PepSeq Pipeline: Software for Antimicrobial Motif Discovery in Randomly-Generated Peptide Libraries. - Tanner D. Jensen; Kristi A. Bresciano; Emma Dallon; M. Stanley Fujimoto; Cole A. Lyman; Enoch Stewart; Joel Griffitts; Mark J. Clement (BCB, 2018)

Kcollections: A Fast and Efficient Library for K-mers. - M. Stanley Fujimoto; Cole A. Lyman; Mark J. Clement (IPDPS Workshops, 2020)

BART for Post-Correction of OCR Newspaper Text. - Elizabeth Soper; Stanley Fujimoto; Yen-Yun Yu (W-NUT, 2021)

Active Transfer Learning for Handwriting Recognition. - Eric Burdett; Stanley Fujimoto; Timothy Brown; Ammon Shurtz; Daniel Segrera; Lawry Sorenson; Mark J. Clement; Joseph Price (ICFHR, 2022)