Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM. - Charles J. Vaske; Stephen C. Benz; J. Zachary Sanborn; Dent Earl; Christopher Szeto; Jingchun Zhu; David Haussler; Joshua M. Stuart (Bioinform., 2010)

Cactus Graphs for Genome Comparisons. - Benedict Paten; Mark Diekhans; Dent Earl; John St. John; Jian Ma 004; Bernard B. Suh; David Haussler (J. Comput. Biol., 2011)

HAL: a hierarchical format for storing and analyzing multiple genome alignments. - Glenn Hickey; Benedict Paten; Dent Earl; Daniel R. Zerbino; David Haussler (Bioinform., 2013)

Building a Pangenome Reference for a Population. - Ngan Nguyen; Glenn Hickey; Daniel R. Zerbino; Brian J. Raney; Dent Earl; Joel Armstrong; David Haussler; Benedict Paten (RECOMB, 2014)

Evaluation And Application Of The Three A's Of Genomics: Assembly, Alignment, Annotation. - Dent Earl (2014)

Building a Pan-Genome Reference for a Population. - Ngan Nguyen; Glenn Hickey; Daniel R. Zerbino; Brian J. Raney; Dent Earl; Joel Armstrong; W. James Kent; David Haussler; Benedict Paten (J. Comput. Biol., 2015)