CAFE: a computational tool for the study of gene family evolution. - Tijl De Bie; Nello Cristianini; Jeffery P. Demuth; Matthew W. Hahn (Bioinform., 2006)

Introduction to computational genomics - a case studies approach. - Nello Cristianini; Matthew W. Hahn (Cambridge University Press, 2007)

Gain and loss of phosphorylation sites in human cancer. - Predrag Radivojac; Peter H. Baenziger; Maricel G. Kann; Matthew E. Mort; Matthew W. Hahn; Sean D. Mooney (ECCB, 2008)

Limitations of Pseudogenes in Identifying Gene Losses. - James C. Costello; Mira V. Han; Matthew W. Hahn (RECOMB-CG, 2008)

Identifying Parent-Daughter Relationships Among Duplicated Genes. - Mira V. Han; Matthew W. Hahn (Pacific Symposium on Biocomputing, 2009)

All Human-Specific Gene Losses Are Present in the Genome as Pseudogenes. - Daniel R. Schrider; James C. Costello; Matthew W. Hahn (J. Comput. Biol., 2009)

Testing the Ortholog Conjecture with Comparative Functional Genomic Data from Mammals. - Nathan L. Nehrt; Wyatt T. Clark; Predrag Radivojac; Matthew W. Hahn (PLoS Comput. Biol., 2011)

Detecting Highly Differentiated Copy-Number Variants from Pooled Population Sequencing. - Daniel R. Schrider; David J. Begun; Matthew W. Hahn (Pacific Symposium on Biocomputing, 2013)

Extensive Error in the Number of Genes Inferred from Draft Genome Assemblies. - James F. Denton; Jose Lugo-Martinez; Abraham E. Tucker; Daniel R. Schrider; Wesley C. Warren; Matthew W. Hahn (PLoS Comput. Biol., 2014)

Session Introduction. - Yana Bromberg; Matthew W. Hahn; Predrag Radivojac (PSB, 2017)

Proteomic Evidence for In-Frame and Out-of-Frame Alternatively Spliced Isoforms in Human and Mouse. - Rodrigo F. Ramalho; Sujun Li; Predrag Radivojac; Matthew W. Hahn (IEEE ACM Trans. Comput. Biol. Bioinform., 2018)

A new class of metrics for learning on real-valued and structured data. - Ruiyu Yang; Yuxiang Jiang; Scott Mathews; Elizabeth A. Housworth; Matthew W. Hahn; Predrag Radivojac (Data Min. Knowl. Discov., 2019)

The ortholog conjecture revisited: the value of orthologs and paralogs in function prediction. - Moses Stamboulian; Rafael F. Guerrero; Matthew W. Hahn; Predrag Radivojac (Bioinform., 2020)

CAFE 5 models variation in evolutionary rates among gene families. - Fábio K. Mendes; Dan Vanderpool; Ben Fulton; Matthew W. Hahn (Bioinform., 2021)

Updated site concordance factors minimize effects of homoplasy and taxon sampling. - Yu K. Mo; Robert Lanfear; Matthew W. Hahn; Bui Quang Minh (Bioinform., 2023)

Phylogenetic inference using generative adversarial networks. - Megan L. Smith; Matthew W. Hahn (Bioinform., 2023)