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High-quality draft assemblies of mammalian genomes from massively parallel sequence data.

• Sante Gnerre, Iain Maccallum, +17 authors David B. Jaffe
• Proceedings of the National Academy of Sciences…
• 2011

Massively parallel DNA sequencing technologies are revolutionizing genomics by making it possible to generate billions of relatively short (~100-base) sequence reads at very low cost. Whereas such… (More)

Evolution of genes and genomes on the Drosophila phylogeny

• Andrew G. Clark, Michael B. Eisen, +411 authors Iain Maccallum
• Nature
• 2007

Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome… (More)

ALLPATHS: de novo assembly of whole-genome shotgun microreads.

• Jonathan L. Butler, Iain Maccallum, +5 authors David B. Jaffe
• Genome research
• 2008

New DNA sequencing technologies deliver data at dramatically lower costs but demand new analytical methods to take full advantage of the very short reads that they produce. We provide an initial,… (More)

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

• Dent Earl, Keith Bradnam, +68 authors Benedict Paten
• Genome research
• 2011

Low-cost short read sequencing technology has revolutionized genomics, though it is only just becoming practical for the high-quality de novo assembly of a novel large genome. We describe the… (More)

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species

• Keith R Bradnam, Joseph Nathaniel Fass, +88 authors Ian F Korf
• GigaScience
• 2013

BACKGROUND The process of generating raw genome sequence data continues to become cheaper, faster, and more accurate. However, assembly of such data into high-quality, finished genome sequences… (More)

The genomic substrate for adaptive radiation in African cichlid fish

• David Brawand, Catherine E Wagner, +72 authors Federica di Palma
• Nature
• 2014

Cichlid fishes are famous for large, diverse and replicated adaptive radiations in the Great Lakes of East Africa. To understand the molecular mechanisms underlying cichlid phenotypic diversity, we… (More)

The African coelacanth genome provides insights into tetrapod evolution

• Chris T Amemiya, Jessica Alföldi, +88 authors Kerstin Lindblad-Toh
• 2013

Chris T. Amemiya*, Jessica Alföldi*, Alison P. Lee, Shaohua Fan, Hervé Philippe, Iain MacCallum, Ingo Braasch, Tereza Manousaki, Igor Schneider, Nicolas Rohner, Chris Organ, Domitille Chalopin,… (More)

ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads

• Iain Maccallum, Dariusz Przybylski, +11 authors David B. Jaffe
• Genome Biology
• 2009

We demonstrate that genome sequences approaching finished quality can be generated from short paired reads. Using 36 base (fragment) and 26 base (jumping) reads from five microbial genomes of varied… (More)

Comprehensive variation discovery in single human genomes

• Neil I. Weisenfeld, Shuangye Yin, +11 authors David B. Jaffe
• Nature Genetics
• 2014

Complete knowledge of the genetic variation in individual human genomes is a crucial foundation for understanding the etiology of disease. Genetic variation is typically characterized by sequencing… (More)

Finished bacterial genomes from shotgun sequence data.

• Filipe J. Ribeiro, Dariusz Przybylski, +12 authors David B. Jaffe
• Genome research
• 2012

Exceptionally accurate genome reference sequences have proven to be of great value to microbial researchers. Thus, to date, about 1800 bacterial genome assemblies have been "finished" at great… (More)

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