Daniel E Neafsey

Summary

Affiliation: Massachusetts Institute of Technology
Country: USA

Publications

  1. doi request reprint Complex selection on intron size in Cryptococcus neoformans
    Stephanie S Hughes
    Microbial Analysis Group, Broad Institute of MIT and Harvard, Cambridge
    Mol Biol Evol 25:247-53. 2008
  2. pmc Mechanisms of intron gain and loss in Cryptococcus
    Thomas J Sharpton
    Department of Plant and Microbial Biology, University of California at Berkeley, Berkeley, CA 94720, USA
    Genome Biol 9:R24. 2008
  3. pmc Genome-wide SNP genotyping highlights the role of natural selection in Plasmodium falciparum population divergence
    Daniel E Neafsey
    Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
    Genome Biol 9:R171. 2008
  4. ncbi request reprint Convergent loss of an anciently duplicated, functionally divergent RH2 opsin gene in the fugu and Tetraodon pufferfish lineages
    Daniel E Neafsey
    Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
    Gene 350:161-71. 2005
  5. ncbi request reprint Evolution of noncoding and silent coding sites in the Plasmodium falciparum and Plasmodium reichenowi genomes
    Daniel E Neafsey
    Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
    Mol Biol Evol 22:1621-6. 2005
  6. pmc Positive selection for unpreferred codon usage in eukaryotic genomes
    Daniel E Neafsey
    Microbial Analysis Group, Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
    BMC Evol Biol 7:119. 2007
  7. ncbi request reprint Dual modes of natural selection on upstream open reading frames
    Daniel E Neafsey
    Microbial Analysis Group, Broad Institute of MIT and Harvard, Cambridge, MA, USA
    Mol Biol Evol 24:1744-51. 2007
  8. pmc Malaria life cycle intensifies both natural selection and random genetic drift
    Hsiao Han Chang
    Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138
    Proc Natl Acad Sci U S A 110:20129-34. 2013
  9. pmc A general SNP-based molecular barcode for Plasmodium falciparum identification and tracking
    Rachel Daniels
    Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
    Malar J 7:223. 2008
  10. pmc Genomic sequencing of Plasmodium falciparum malaria parasites from Senegal reveals the demographic history of the population
    Hsiao Han Chang
    Department of Organismic and Evolutionary Biology, Harvard University
    Mol Biol Evol 29:3427-39. 2012

Collaborators

Detail Information

Publications26

  1. doi request reprint Complex selection on intron size in Cryptococcus neoformans
    Stephanie S Hughes
    Microbial Analysis Group, Broad Institute of MIT and Harvard, Cambridge
    Mol Biol Evol 25:247-53. 2008
    ....
  2. pmc Mechanisms of intron gain and loss in Cryptococcus
    Thomas 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...
  3. pmc Genome-wide SNP genotyping highlights the role of natural selection in Plasmodium falciparum population divergence
    Daniel 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...
  4. ncbi request reprint Convergent loss of an anciently duplicated, functionally divergent RH2 opsin gene in the fugu and Tetraodon pufferfish lineages
    Daniel 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...
  5. ncbi request reprint Evolution of noncoding and silent coding sites in the Plasmodium falciparum and Plasmodium reichenowi genomes
    Daniel 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...
  6. pmc Positive selection for unpreferred codon usage in eukaryotic genomes
    Daniel E Neafsey
    Microbial Analysis Group, Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
    BMC Evol Biol 7:119. 2007
    ....
  7. ncbi request reprint Dual modes of natural selection on upstream open reading frames
    Daniel 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...
  8. pmc Malaria life cycle intensifies both natural selection and random genetic drift
    Hsiao 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. ..
  9. pmc A general SNP-based molecular barcode for Plasmodium falciparum identification and tracking
    Rachel Daniels
    Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
    Malar J 7:223. 2008
    ....
  10. pmc Genomic sequencing of Plasmodium falciparum malaria parasites from Senegal reveals the demographic history of the population
    Hsiao Han Chang
    Department of Organismic and Evolutionary Biology, Harvard University
    Mol Biol Evol 29:3427-39. 2012
    ....
  11. pmc Sequence-based association and selection scans identify drug resistance loci in the Plasmodium falciparum malaria parasite
    Daniel J Park
    Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
    Proc Natl Acad Sci U S A 109:13052-7. 2012
    ..falciparum...
  12. pmc Population genomic sequencing of Coccidioides fungi reveals recent hybridization and transposon control
    Daniel 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...
  13. ncbi request reprint Different regulatory mechanisms underlie similar transposable element profiles in pufferfish and fruitflies
    Daniel 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...
  14. pmc Cross-kingdom patterns of alternative splicing and splice recognition
    Abigail 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...
  15. pmc The malaria parasite Plasmodium vivax exhibits greater genetic diversity than Plasmodium falciparum
    Daniel 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...
  16. pmc Genome size evolution in pufferfish: a comparative analysis of diodontid and tetraodontid pufferfish genomes
    Daniel 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...
  17. pmc Stepwise acquisition of pyrimethamine resistance in the malaria parasite
    Elena 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...
  18. ncbi request reprint Genetic diversity and selection at the Plasmodium vivax apical membrane antigen-1 (PvAMA-1) locus in a Sri Lankan population
    Anusha 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...
  19. pmc The evolution of the Anopheles 16 genomes project
    Daniel E Neafsey
    Broad Institute, Cambridge, Massachusetts 02142, USA
    G3 (Bethesda) 3:1191-4. 2013
    ....
  20. ncbi request reprint ‘Big data’ from shrinking pathogen populations
    Daniel 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...
  21. pmc Application of genomics to field investigations of malaria by the international centers of excellence for malaria research
    Sarah K Volkman
    Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA 02115, USA
    Acta Trop 121:324-32. 2012
    ....
  22. doi request reprint Genome sequencing sheds light on emerging drug resistance in malaria parasites
    Daniel 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...
  23. pmc Hybrid selection for sequencing pathogen genomes from clinical samples
    Alexandre 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...
  24. pmc '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...
  25. ncbi request reprint Evolutionary conservation of UTR intron boundaries in Cryptococcus
    Scott 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...
  26. ncbi request reprint A genome-wide map of diversity in Plasmodium falciparum
    Sarah 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...