MODELTEST: testing the model of DNA substitution. - David Posada; Keith A. Crandall (Bioinform., 1998)

TCS: Estimating Gene Genealogies. - Mark J. Clement; Quinn Snell; Peter Walker; David Posada; Keith A. Crandall (IPDPS, 2002)

TreeSAAP: Selection on Amino Acid Properties using phylogenetic trees. - Steve Woolley; Justin Johnson 002; Matthew J. Smith; Keith A. Crandall; David A. McClellan (Bioinform., 2003)

Jumpstarting phylogenetic analysis. - Jesse Mecham; Mark J. Clement; Quinn Snell; Todd Freestone; Kevin D. Seppi; Keith A. Crandall (Int. J. Bioinform. Res. Appl., 2006)

Phylogenetic search through partial tree mixing. - Kenneth Sundberg; Mark J. Clement; Quinn Snell; Dan Ventura; Michael Whiting; Keith A. Crandall (BMC Bioinform., 2012)

Clinical PathoScope: rapid alignment and filtration for accurate pathogen identification in clinical samples using unassembled sequencing data. - Allyson L. Byrd; Joseph F. Perez-Rogers; Solaiappan Manimaran; Eduardo Castro-Nallar; Ian Toma; Tim McCaffrey; Marc Siegel; Gary Benson; Keith A. Crandall; William Johnson (BMC Bioinform., 2014)

Using phylogenetically-informed annotation (PIA) to search for light-interacting genes in transcriptomes from non-model organisms. - Daniel I. Speiser; M. Sabrina Pankey; Alexander K. Zaharoff; Barbara A. Battelle; Heather D. Bracken-Grissom; Jesse W. Breinholt; Seth M. Bybee; Thomas W. Cronin; Anders Garm; Annie R. Lindgren; Nipam H. Patel; Megan L. Porter; et al. (BMC Bioinform., 2014)

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)

Telescope: Characterization of the retrotranscriptome by accurate estimation of transposable element expression. - Matthew L. Bendall; Miguel de Mulder; Luis Pedro Iñiguez; Aarón Lecanda-Sánchez; Marcos Pérez-Losada; Mario A. Ostrowski; R. Brad Jones; Lubbertus C. F. Mulder; Gustavo Reyes-Terán; Keith A. Crandall; Christopher E. Ormsby; Douglas F. Nixon (PLoS Comput. Biol., 2019)

ReQTL: identifying correlations between expressed SNVs and gene expression using RNA-sequencing data. - Liam F. Spurr; Nawaf Alomran; Pavlos Bousounis; Dacian Reece-Stremtan; N. M. Prashant; Hongyu Liu; Piotr Slowinski; Muzi Li; Qianqian Zhang; Justin Sein; Gabriel Asher; Keith A. Crandall; et al. (Bioinform., 2020)

COVID-19 biomarkers and their overlap with comorbidities in a disease biomarker data model. - Nikhita Gogate; Daniel Lyman; Amanda Bell; Edmund Cauley; Keith A. Crandall; Ashia Joseph; Robel Y. Kahsay; Darren A. Natale; Lynn M. Schriml; Sabyasach Sen; Raja Mazumder (Briefings Bioinform., 2021)

Omics community detection using multi-resolution clustering. - Ali Rahnavard; Suvo Chatterjee; Bahar Sayoldin; Keith A. Crandall; Fasil Tekola-Ayele; Himel Mallick (Bioinform., 2021)

Each patient is a research biorepository: informatics-enabled research on surplus clinical specimens via the living BioBank. - Alexander V. Alekseyenko; Bashir Hamidi; Trevor D. Faith; Keith A. Crandall; Jennifer G. Powers; Christopher Metts; James E. Madory; Steven L. Carroll; Jihad S. Obeid; Leslie A. Lenert (J. Am. Medical Informatics Assoc., 2021)

Synergies between centralized and federated approaches to data quality: a report from the national COVID cohort collaborative. - Emily R. Pfaff; Andrew T. Girvin; Davera Gabriel; Kristin Kostka; Michele Morris; Matvey B. Palchuk; Harold P. Lehmann; Benjamin R. C. Amor; Mark Bissell; Katie R. Bradwell; Sigfried Gold; Stephanie S. Hong; et al. (J. Am. Medical Informatics Assoc., 2022)