Complex selection on 5' splice sites in intron-rich organisms (2009)
Irimia, Manuel, Roy, Scott William, Neafsey, Daniel E., Abril, Josep F., Garcia-Fernandez, Jordi, Koonin, Eugene V.
In contrast to the typically streamlined genomes of prokaryotes, many eukaryotic genomes are riddled with long intergenic regions, spliceosomal introns, and repetitive elements. What explains the...
Neafsey, Daniel E, Schaffner, Stephen F, Volkman, Sarah K, Park, Daniel, Montgomery, Philip, Milner, Danny A, ...
Abstract Background The malaria parasite Plasmodium falciparum exhibits abundant genetic diversity, and this diversity is key to its success as a pathogen. Previous efforts to study genetic diversity...
A general SNP-based molecular barcode for Plasmodium falciparumidentification and tracking (2008)
Daniels, Rachel, Volkman, Sarah K, Milner, Danny A, Mahesh, Nira, Neafsey, Daniel E, Park, Daniel J, ...
Abstract Background Single nucleotide polymorphism (SNP) genotyping provides the means to develop a practical, rapid, inexpensive assay that will uniquely identify any Plasmodium falciparum parasite...
A general SNP-based molecular barcode for Plasmodium falciparum identification and tracking (2008)
Daniels, Rachel, Volkman, Sarah K., Milner, Danny A., Mahesh, Nira, Neafsey, Daniel E., Park, Daniel J., ...
Background: Single nucleotide polymorphism (SNP) genotyping provides the means to develop a practical, rapid, inexpensive assay that will uniquely identify any Plasmodium falciparum parasite using a...
Cross-kingdom patterns of alternative splicing and splice recognition (2008)
McGuire, Abigail M, Pearson, Matthew D, Neafsey, Daniel E, Galagan, James E
Abstract Background Variations in transcript splicing can reveal how eukaryotes recognize intronic splice sites. Retained introns (RIs) commonly appear when the intron definition (ID) mechanism of...
Mechanisms of intron gain and loss in Cryptococcus (2008)
Sharpton, Thomas J, Neafsey, Daniel E, Galagan, James E, Taylor, John W
Abstract Background Genome comparisons across deep phylogenetic divergences have revealed that spliceosomal intron gain and loss are common evolutionary events. However, because of the deep...
Complex Selection on Intron Size in Cryptococcus neoformans (2008)
Hughes, Stephanie S., Buckley, Cedric O., Neafsey, Daniel E.
We conducted a genome-wide analysis of the roles of mutation and selection in sculpting intron size in the fungal pathogen Cryptococcus neoformans. We find that deletion rate is positively associated...
Dual Modes of Natural Selection on Upstream Open Reading Frames (2007)
Neafsey, Daniel E., Galagan, James E.
Upstream open reading frames (uORFs) are common features of eukaryotic genes, occurring in 10%–25% of 5′ leader sequences. Upstream ORFs that have been subjected to experimental analysis have...
Positive selection for unpreferred codon usage in eukaryotic genomes (2007)
Neafsey, Daniel E, Galagan, James E
Abstract Background Natural selection has traditionally been understood as a force responsible for pushing genes to states of higher translational efficiency, whereas lower translational efficiency...
Evolutionary Conservation of UTR Intron Boundaries in Cryptococcus (2007)
Roy, Scott William, Penny, David, Neafsey, Daniel E.
Despite significant progress, the general functional and evolutionary significance of the untranslated regions (UTRs) of eukaryotic transcripts remain mysterious. Particularly mysterious is the...
Gunasekera, Anusha M., Wickramarachchi, Thilan, Neafsey, Daniel E., Ganguli, Ishani, Perera, Lakshman, Premaratne, Prasad H., ...
Plasmodium vivax apical membrane antigen 1 (PvAMA-1) is an important malaria vaccine candidate. We present the first comprehensive analysis of nucleotide diversity across the entire PvAMA-1 gene...
Evolutionary Conservation of UTR Intron Boundaries in Cryptococcus (2007)
Roy, Scott William, Penny, David, Neafsey, Daniel E.
Despite significance progress, the general functional and evolutionary significance of the untranslated regions (UTRs) of eukaryotic transcripts remains mysterious. Particularly mysterious is the...
Neafsey, Daniel E., Hartl, Daniel L., Berriman, Matt
We compared levels of sequence divergence between fourfold synonymous coding sites and noncoding sites from the intergenic and intronic regions of the Plasmodium falciparum and Plasmodium reichenowi...
Neafsey, Daniel E., Hartl, Daniel L., Berriman, Matt
We compared levels of sequence divergence between fourfold synonymous coding sites and noncoding sites from the intergenic and intronic regions of the Plasmodium falciparum and Plasmodium reichenowi...
Neafsey, Daniel E., Hartl, Daniel L., Berriman, Matt
We compared levels of sequence divergence between fourfold synonymous coding sites and noncoding sites from the intergenic and intronic regions of the Plasmodium falciparum and Plasmodium reichenowi...
Neafsey, Daniel E., Blumenstiel, Justin P., Hartl, Daniel L.
Comparative analysis of recently sequenced eukaryotic genomes has uncovered extensive variation in transposable element (TE) abundance, diversity, and distribution. The TE profile in the sequenced...
Neafsey, Daniel E., Blumenstiel, Justin P., Hartl, Daniel L.
Comparative analysis of recently sequenced eukaryotic genomes has uncovered extensive variation in transposable element (TE) abundance, diversity, and distribution. The TE profile in the sequenced...
Neafsey, Daniel E., Blumenstiel, Justin P., Hartl, Daniel L.
Comparative analysis of recently sequenced eukaryotic genomes has uncovered extensive variation in transposable element (TE) abundance, diversity, and distribution. The TE profile in the sequenced...
Neafsey, Daniel E., Palumbi, Stephen R.
Smooth pufferfish of the family Tetraodontidae have the smallest vertebrate genomes yet measured. They have a haploid genome size of ∼400 million bp (Mb), which is almost eight times smaller than...
Neafsey, Daniel E., Palumbi, Stephen R.
Smooth pufferfish of the family Tetraodontidae have the smallest vertebrate genomes yet measured. They have a haploid genome size of ∼400 million bp (Mb), which is almost eight times smaller than...
Neafsey, Daniel E., Palumbi, Stephen R.
Smooth pufferfish of the family Tetraodontidae have the smallest vertebrate genomes yet measured. They have a haploid genome size of ∼400 million bp (Mb), which is almost eight times smaller than...
Mechanisms of intron gain and loss in Cryptococcus
Sharpton, Thomas J, Neafsey, Daniel E, Galagan, James E, Taylor, John W
Comparison of five relatively closely related yeast Cryptococcus genomes suggests that recombination causes internal intron loss and that DNA repeat expansion can create new introns in a population.
Cross-kingdom patterns of alternative splicing and splice recognition
McGuire, Abigail M, Pearson, Matthew D, Neafsey, Daniel E, Galagan, James E
A comprehensive survey of alternate splicing across 42 eukaryotes so as to gain insight into how spliceosomal introns are recognized.
A general SNP-based molecular barcode for Plasmodium falciparum identification and tracking
Daniels, Rachel, Volkman, Sarah K, Milner, Danny A, Mahesh, Nira, Neafsey, Daniel E, Park, Daniel J, ...
Neafsey, Daniel E, Schaffner, Stephen F, Volkman, Sarah K, Park, Daniel, Montgomery, Philip, Milner, Danny A, ...
An array-based SNP genotyping platform for Plasmodium falciparum is reported together with an analysis of SNP diversity in global population samples.
Comparative genomic analyses of the human fungal pathogens Coccidioides and their relatives
Sharpton, Thomas J., Stajich, Jason E., Rounsley, Steven D., Gardner, Malcolm J., Wortman, Jennifer R., Jordar, Vinita S., ...
While most Ascomycetes tend to associate principally with plants, the dimorphic fungi Coccidioides immitis and Coccidioides posadasii are primary pathogens of immunocompetent mammals, including...