The Celera Discovery SystemTM. - Anthony R. Kerlavage; Vivien Bonazzi; Matteo di Tommaso; Charles Lawrence; Peter Li; Frank Mayberry; Richard J. Mural; Marc Nodell; Mark Yandell; Jinghui Zhang; Paul D. Thomas (Nucleic Acids Res., 2002)

BLAST - an essential guide to the basic local alignment search tool. - Ian Korf; Mark Yandell; Joseph A. Bedell (O'Reilly, 2003)

Identification of key concepts in biomedical literature using a modified Markov heuristic. - William H. Majoros; G. M. Subramanian; Mark Yandell (Bioinform., 2003)

Large-Scale Trends in the Evolution of Gene Structures within 11 Animal Genomes. - Mark Yandell; Chris Mungall; Chris Smith; Simon Prochnik; Joshua S. Kaminker; George Hartzell; Suzanna Lewis; Gerald M. Rubin (PLoS Comput. Biol., 2006)

Genome-Wide Analysis of Human Disease Alleles Reveals That Their Locations Are Correlated in Paralogous Proteins. - Mark Yandell; Barry Moore; Fidel Salas; Chris Mungall; Andrew MacBride; Charles White; Martin G. Reese (PLoS Comput. Biol., 2008)

Quantitative measures for the management and comparison of annotated genomes. - Karen Eilbeck; Barry Moore; Carson Holt; Mark Yandell (BMC Bioinform., 2009)

MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects. - Carson Holt; Mark Yandell (BMC Bioinform., 2011)

ImagePlane: An Automated Image Analysis Pipeline for High-Throughput Screens Using the Planarian Schmidtea mediterranea. - Steven Flygare; Michael Campbell; Robert Mars Ross; Barry Moore; Mark Yandell (J. Comput. Biol., 2013)

Wham: Identifying Structural Variants of Biological Consequence. - Zev N. Kronenberg; Edward J. Osborne; Kelsey R. Cone; Brett J. Kennedy; Eric T. Domyan; Michael D. Shapiro; Nels C. Elde; Mark Yandell (PLoS Comput. Biol., 2015)

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)

Predicting gene structure changes resulting from genetic variants via exon definition features. - William H. Majoros; Carson Holt; Michael Campbell; Doreen Ware; Mark Yandell; Timothy E. Reddy (Bioinform., 2018)

The VAAST Variant Prioritizer (VVP): ultrafast, easy to use whole genome variant prioritization tool. - Steven Flygare; Edgar Javier Hernandez; Lon Phan; Barry Moore; Man Li; Anthony Fejes; Hao Hu; Karen Eilbeck; Chad D. Huff; Lynn Jorde; Martin G. Reese; Mark Yandell (BMC Bioinform., 2018)

A Poisson binomial-based statistical testing framework for comorbidity discovery across electronic health record datasets. - Gordon Lemmon; Sergiusz Wesolowski; Alex Henrie; Martin Tristani-Firouzi; Mark Yandell (Nat. Comput. Sci., 2021)

A machine learning decision support tool optimizes WGS utilization in a neonatal intensive care unit. - Edwin F. Juarez; Bennet Peterson; Erica Sanford Kobayashi; Sheldon Gilmer; Laura E. Tobin; Brandan Schultz; Jerica Lenberg; Jeanne Carroll; Shiyu Bai-Tong; Nathaly M. Sweeney; Curtis Beebe; Lawrence Stewart; et al. (npj Digit. Medicine, 2025)