Earl, Dent

Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM

Vaske, C. J., Benz, S. C., Sanborn, J. Z., Earl, D., Szeto, C., Zhu, J., Haussler, D., & Stuart, J. M. (2010) · Bioinformatics

Bioinformatics and Genomic NetworksCancer Genomics and Diagnostics

Cited by 786

Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs

Green, R. E., Braun, E. L., Armstrong, J., Earl, D., Nguyen, N., Hickey, G., Vandewege, M. W., St. John, J. A., Capella-Gutiérrez, S., Castoe, T. A., et al. (2014) · Science

Genomics and Phylogenetic StudiesChromosomal and Genetic Variations

Cited by 359

HAL: a hierarchical format for storing and analyzing multiple genome alignments

Hickey, G., Paten, B., Earl, D., Zerbino, D., & Haussler, D. (2013) · Bioinformatics

Genomics and Phylogenetic StudiesGenome Rearrangement Algorithms

Cited by 272

Sixteen diverse laboratory mouse reference genomes define strain-specific haplotypes and novel functional loci

Lilue, J., Doran, A. G., Fiddes, I. T., Abrudan, M., Armstrong, J., Bennett, R., Chow, W., Collins, J., Collins, S., Czechanski, A., et al. (2018) · Nature Genetics

Genomics and Phylogenetic StudiesChromosomal and Genetic Variations

Cited by 267

Cactus: Algorithms for genome multiple sequence alignment

Paten, B., Earl, D., Nguyen, N., Diekhans, M., Zerbino, D., & Haussler, D. (2011) · Genome Research

Genomics and Phylogenetic StudiesGenome Rearrangement Algorithms

Cited by 243

Comparative Annotation Toolkit (CAT)—simultaneous clade and personal genome annotation

Fiddes, I. T., Armstrong, J., Diekhans, M., Nachtweide, S., Kronenberg, Z. N., Underwood, J. G., Gordon, D., Earl, D., Keane, T., Eichler, E. E., et al. (2018) · Genome Research

Genomics and Phylogenetic StudiesChromosomal and Genetic Variations

Cited by 120

Alignathon: a competitive assessment of whole-genome alignment methods

Earl, D., Nguyen, N., Hickey, G., Harris, R. S., Fitzgerald, S., Beal, K., Seledtsov, I., Molodtsov, V., Raney, B. J., Clawson, H., et al. (2014) · Genome Research

Genomics and Phylogenetic StudiesGenome Rearrangement Algorithms

Cited by 113

Cactus Graphs for Genome Comparisons

Paten, B., Diekhans, M., Earl, D., John, J. S., Ma, J., Suh, B., & Haussler, D. (2011) · Journal of Computational Biology

Genome Rearrangement AlgorithmsGenomics and Phylogenetic Studies

Cited by 102