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Estimates of Positive Darwinian Selection Are Inflated by Errors in Sequencing, Annotation, and Alignment
(2009)Genome Biology and EvolutionPublished estimates of the proportion of positively selected genes (PSGs) in human vary over three orders of magnitude. In mammals, estimates of the proportion of PSGs cover an even wider range of values. We used 2,980 orthologous protein-coding genes from human, chimpanzee, macaque, dog, cow, rat, and mouse as well as an established phylogenetic topology to infer the fraction of PSGs in all seven terminal branches. The inferred fraction ...Journal Article -
Ambiguous Nucleotide Calls From Population-based Sequencing of HIV-1 are a Marker for Viral Diversity and the Age of Infection
(2011)Clinical Infectious DiseasesJournal Article -
As-rigid-as-possible mosaicking and serial section registration of large ssTEM datasets
(2010)BioinformaticsJournal Article -
Survey of branch support methods demonstrates accuracy, power, and robustness of fast likelihood-based approximation schemes
(2011)Systematic BiologyJournal Article -
Embedding of Cortical Representations by the Superficial Patch System
(2011)Cerebral CortexJournal Article -
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Nogo-a regulates neuralprecursor migration in the embryonic mouse cortex
(2010)Cerebral CortexJournal Article -
The what, where, how and why of gene ontology - a primer for bioinformaticians
(2011)Briefings in BioinformaticsWith high-throughput technologies providing vast amounts of data, it has become more important to provide systematic, quality annotations. The Gene Ontology (GO) project is the largest resource for cataloguing gene function. Nonetheless, its use is not yet ubiquitous and is still fraught with pitfalls. In this review, we provide a short primer to the GO for bioinformaticians. We summarize important aspects of the structure of the ontology, ...Journal Article -
Base-calling for next-generation sequencing platforms
(2011)Briefings in BioinformaticsNext-generation sequencing platforms are dramatically reducing the cost of DNA sequencing. With these technologies, bases are inferred from light intensity signals, a process commonly referred to as base-calling. Thus, understanding and improving the quality of sequence data generated using these approaches are of high interest. Recently, a number of papers have characterized the biases associated with base-calling and proposed methodological ...Journal Article -
A synthetic low-frequency mammalian oscillator
(2010)Nucleic Acids ResearchCircadian clocks have long been known to be essential for the maintenance of physiological and behavioral processes in a variety of organisms ranging from plants to humans. Dysfunctions that subvert gene expression of oscillatory circadian-clock components may result in severe pathologies, including tumors and metabolic disorders. While the underlying molecular mechanisms and dynamics of complex gene behavior are not fully understood, ...Journal Article