Genomes and Genes
Daniel E Neafsey
Affiliation: Massachusetts Institute of Technology
- Complex selection on intron size in Cryptococcus neoformansStephanie S Hughes
Microbial Analysis Group, Broad Institute of MIT and Harvard, Cambridge
Mol Biol Evol 25:247-53. 2008....
- Mechanisms of intron gain and loss in CryptococcusThomas J Sharpton
Department of Plant and Microbial Biology, University of California at Berkeley, Berkeley, CA 94720, USA
Genome Biol 9:R24. 2008..To ascertain mechanisms of intron gain and loss, we compared five relatively closely related genomes from the yeast Cryptococcus...
- Convergent loss of an anciently duplicated, functionally divergent RH2 opsin gene in the fugu and Tetraodon pufferfish lineagesDaniel E Neafsey
Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
Gene 350:161-71. 2005..Interspecific comparison of the remaining fugu RH2-2 coding sequence paradoxically indicates that the gene was under strong purifying selection until the truncation occurred...
- Evolution of noncoding and silent coding sites in the Plasmodium falciparum and Plasmodium reichenowi genomesDaniel E Neafsey
Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
Mol Biol Evol 22:1621-6. 2005..Divergence rates of different classes of silent sites in these Plasmodium genomes are determined by a combination of mutational and selective pressures...
- Dual modes of natural selection on upstream open reading framesDaniel E Neafsey
Microbial Analysis Group, Broad Institute of MIT and Harvard, Cambridge, MA, USA
Mol Biol Evol 24:1744-51. 2007..Our analysis suggests that uORFs are an important and underappreciated mechanism of post-transcriptional gene regulation in eukaryotes...
- Positive selection for unpreferred codon usage in eukaryotic genomesDaniel E Neafsey
Microbial Analysis Group, Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
BMC Evol Biol 7:119. 2007....
- Genome-wide SNP genotyping highlights the role of natural selection in Plasmodium falciparum population divergenceDaniel E Neafsey
Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
Genome Biol 9:R171. 2008..To that end, we have developed a high throughput single nucleotide polymorphism (SNP) genotyping platform for P. falciparum...
- Malaria life cycle intensifies both natural selection and random genetic driftHsiao Han Chang
Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138
Proc Natl Acad Sci U S A 110:20129-34. 2013..These results highlight the importance of considering the malaria life cycle when applying existing population genetic tools based on the WF model. The same caveat applies to other species with similarly complex life cycles. ..
- A general SNP-based molecular barcode for Plasmodium falciparum identification and trackingRachel Daniels
Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
Malar J 7:223. 2008....
- Genomic sequencing of Plasmodium falciparum malaria parasites from Senegal reveals the demographic history of the populationHsiao Han Chang
Department of Organismic and Evolutionary Biology, Harvard University
Mol Biol Evol 29:3427-39. 2012....
- Sequence-based association and selection scans identify drug resistance loci in the Plasmodium falciparum malaria parasiteDaniel J Park
Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
Proc Natl Acad Sci U S A 109:13052-7. 2012..falciparum...
- Population genomic sequencing of Coccidioides fungi reveals recent hybridization and transposon controlDaniel E Neafsey
Broad Institute, Cambridge, Massachusetts 02142, USA
Genome Res 20:938-46. 2010..This study highlights the importance of population genomic data for detecting subtle but potentially important phenomena such as introgression...
- Different regulatory mechanisms underlie similar transposable element profiles in pufferfish and fruitfliesDaniel E Neafsey
Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
Mol Biol Evol 21:2310-8. 2004..Inference of regulatory processes governing TE profiles should take into account factors such as effective population size, incidence of inbreeding/outcrossing, and other species-specific traits...
- Genetic relatedness analysis reveals the cotransmission of genetically related Plasmodium falciparum parasites in Thiès, SenegalWesley Wong
Department of Immunology and Infectious Diseases, Harvard T H Chan School of Public Health, Boston, MA, 02115, USA
Genome Med 9:5. 2017..Current epidemiology models simulate polygenomic infections via superinfection (multiple mosquito bites), despite growing evidence that cotransmission (a single mosquito bite) may contribute to polygenomic infections...
- Cross-kingdom patterns of alternative splicing and splice recognitionAbigail M McGuire
The Broad Institute of MIT and Harvard, Cambridge Center, Cambridge, MA 02142, USA
Genome Biol 9:R50. 2008..We have performed a comprehensive survey of alternative splicing across 42 eukaryotes to gain insight into how spliceosomal introns are recognized...
- The malaria parasite Plasmodium vivax exhibits greater genetic diversity than Plasmodium falciparumDaniel E Neafsey
Broad Institute, Cambridge, Massachusetts, USA
Nat Genet 44:1046-50. 2012..vivax. These findings warrant a deeper survey of variation in P. vivax to equip disease interventions targeting the distinctive biology of this neglected but major pathogen...
- Stepwise acquisition of pyrimethamine resistance in the malaria parasiteElena R Lozovsky
Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
Proc Natl Acad Sci U S A 106:12025-30. 2009..Our results also suggest an explanation for why I164L is detected in Southeast Asia and South America, but not at significant frequencies in Africa...
- Genome size evolution in pufferfish: a comparative analysis of diodontid and tetraodontid pufferfish genomesDaniel E Neafsey
Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
Genome Res 13:821-30. 2003..We comment on the role that large insertions may play in the evolution of genome size in these two groups...
- COIL: a methodology for evaluating malarial complexity of infection using likelihood from single nucleotide polymorphism dataKevin Galinsky
Department of Biostatistics, Harvard School of Public Health, Boston, MA, 02115, USA
Malar J 14:4. 2015..This manuscript describes a method for estimating COI using likelihood, called COIL, from a panel of bi-allelic genotyping assays...
- Genetic diversity and selection at the Plasmodium vivax apical membrane antigen-1 (PvAMA-1) locus in a Sri Lankan populationAnusha M Gunasekera
Department of Immunology and Infectious Diseases, Harvard School of Public Health, Harvard University, USA
Mol Biol Evol 24:939-47. 2007..Regions of this surface that show constrained variability may prove to be promising vaccine targets...
- Modeling malaria genomics reveals transmission decline and rebound in SenegalRachel F Daniels
Departments of Immunology and Infectious Diseases and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138
Proc Natl Acad Sci U S A 112:7067-72. 2015..The results also suggest that genomics combined with epidemiological modeling may afford prompt, continuous, and cost-effective tracking of progress toward malaria elimination. ..
- The evolution of the Anopheles 16 genomes projectDaniel E Neafsey
Broad Institute, Cambridge, Massachusetts 02142, USA
G3 (Bethesda) 3:1191-4. 2013....
- ‘Big data’ from shrinking pathogen populationsDaniel E Neafsey
Broad Institute, Cambridge, MA 02142, USA
Mol Ecol 22:271-2. 2013..The interpretation of such data will require close consideration of biological context, however, at both the species and the population level...
- Application of genomics to field investigations of malaria by the international centers of excellence for malaria researchSarah K Volkman
Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA 02115, USA
Acta Trop 121:324-32. 2012....
- Genome sequencing sheds light on emerging drug resistance in malaria parasitesDaniel E Neafsey
Broad Institute, Cambridge, Massachusetts, USA
Nat Genet 45:589-90. 2013..Whole-genome sequencing offers a chance to better understand and perhaps undermine the parasite's evolutionary response to this drug...
- Hybrid selection for sequencing pathogen genomes from clinical samplesAlexandre Melnikov
Genome Sequencing and Analysis Program, Broad Institute, Cambridge, MA 02142, USA
Genome Biol 12:R73. 2011..This approach will enable efficient genome sequencing of pathogens from clinical samples, as well as sequencing of endosymbiotic organisms such as Wolbachia that live inside diverse metazoan phyla...
- 'Next-generation' sequencing becomes 'now-generation'Daniel E Neafsey
Broad Institute, 7 Cambridge Center, Cambridge, MA 02142, USA
Genome Biol 12:303. 2011..A report on the Advances in Genome Biology & Technology conference, Marco Island, USA, 2-5 February 2011...
- Evolutionary conservation of UTR intron boundaries in CryptococcusScott William Roy
Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand
Mol Biol Evol 24:1140-8. 2007..These results focus attention on the functional roles of eukaryotic UTRs and deepen the mystery of UTR intron splicing...
- A genome-wide map of diversity in Plasmodium falciparumSarah K Volkman
Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts 02115, USA
Nat Genet 39:113-9. 2007..We provide an initial map of genetic diversity in P. falciparum and demonstrate its potential utility in identifying genes subject to recent natural selection and in understanding the population genetics of this parasite...