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Efficient oligonucleotide probe selection for pan-genomic tiling arrays
(2009-09-16)
Background: Array comparative genomic hybridization is a fast and cost-effective method for detecting, genotyping, and comparing the genomic sequence of unknown bacterial isolates. This method, as with all microarray ...
High-coverage sequencing and annotated assemblies of the budgerigar genome
(Springer Nature, 2014-07-08)
Parrots belong to a group of behaviorally advanced vertebrates and have an advanced ability of vocal learning relative to other vocal-learning birds. They can imitate human speech, synchronize their body movements to a ...
Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A
(Springer Nature, 2008-05-01)
Xanthomonas oryzae pv. oryzae causes bacterial blight of rice (Oryza sativa L.), a major disease that constrains production of this staple crop in many parts of the world. We report here on the complete genome sequence of ...
Automated ensemble assembly and validation of microbial genomes
(Springer Nature, 2014-05-03)
The continued democratization of DNA sequencing has sparked a new wave of development of genome assembly and assembly validation methods. As individual research labs, rather than centralized centers, begin to sequence the ...
Probing the pan-genome of Listeria monocytogenes: new insights into intraspecific niche expansion and genomic diversification
(Springer Nature, 2010-09-16)
Bacterial pathogens often show significant intraspecific variations in ecological fitness, host preference and pathogenic potential to cause infectious disease. The species of Listeria monocytogenes, a facultative intracellular ...
Genome assembly forensics: finding the elusive mis-assembly
(Springer Nature, 2008-03-14)
We present the first collection of tools aimed at automated genome assembly validation. This work formalizes several mechanisms for detecting mis-assemblies, and describes their implementation in our automated validation ...
The rise of a digital immune system
(Springer Nature, 2012-07-12)
Driven by million-fold improvements in biotechnology, biology is increasingly shifting towards high-resolution, quantitative approaches to study the molecular dynamics of entire populations. One exciting application enabled ...