The UCSC Genome Browser database: 2015 update

Kate R. Rosenbloom, Joel Armstrong, Galt P Barber, +26

Nucleic Acids Research

BiologyBiological DatabaseBioinformatics DatabaseNext-generation SequencingGenetics +10

Assemblathon 1: A competitive assessment of de novo short read assembly methods

Dent Earl, Keith Bradnam, John St. John, +68

Genome Research

An evolutionary arms race between KRAB zinc-finger genes ZNF91/93 and SVA/L1 retrotransposons

Frank M. J. Jacobs, David Greenberg, Ngan Nguyen, +6

Nature

BiologySva/l1 RetrotransposonsNatural SciencesGeneticsEvolutionary Biology +8

Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser

Brian J. Raney, Timothy R. Dreszer, Galt P Barber, +8

Bioinformatics

Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs

Richard E. Green, Edward L. Braun, Joel Armstrong, +52

Science

BiologyPhylogeneticsMolecular EcologyDraft GenomesComparative Genomics +13

Cactus: Algorithms for genome multiple sequence alignment

Benedict Paten, Dent Earl, Ngan Nguyen, +3

Genome Research

Alignathon: a competitive assessment of whole-genome alignment methods

Dent Earl, Ngan Nguyen, Glenn Hickey, +22

Genome Research

Comparative GenomicsGeneticsGenomicsSequence AlignmentPhylogenetics +18

Comparative proteogenomics: Combining mass spectrometry and comparative genomics to analyze multiple genomes

Nitin Gupta, Jamal Benhamida, Vipul Bhargava, +12

Genome Research

Building a Pan-Genome Reference for a Population

Ngan Nguyen, Glenn Hickey, Daniel R. Zerbino, +6

Journal of Computational Biology

GeneticsCactus SoftwareGenomicsSequence AlignmentMolecular Ecology +18

Comparative assembly hubs: Web-accessible browsers for comparative genomics

Ngan Nguyen, Glenn Hickey, Brian J. Raney, +7

Bioinformatics