Daniel E Neafsey

Summary

Publications

  1. pmc The evolution of the Anopheles 16 genomes project
    Daniel E Neafsey
    Broad Institute, Cambridge, Massachusetts 02142, USA
    G3 (Bethesda) 3:1191-4. 2013
  2. 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
  3. ncbi request reprint ‘Big data’ from shrinking pathogen populations
    Daniel E Neafsey
    Broad Institute, Cambridge, MA 02142, USA
    Mol Ecol 22:271-2. 2013
  4. pmc Human cerebral malaria and Plasmodium falciparum genotypes in Malawi
    Danny A Milner
    Department of Pathology, Brigham and Women s Hospital, 75 Francis Street, Amory 3, Boston, MA 02115, USA
    Malar J 11:35. 2012
  5. pmc 'Next-generation' sequencing becomes 'now-generation'
    Daniel E Neafsey
    Broad Institute, 7 Cambridge Center, Cambridge, MA 02142, USA
    Genome Biol 12:303. 2011
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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

Collaborators

Detail Information

Publications20

  1. pmc The evolution of the Anopheles 16 genomes project
    Daniel E Neafsey
    Broad Institute, Cambridge, Massachusetts 02142, USA
    G3 (Bethesda) 3:1191-4. 2013
    ....
  2. 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...
  3. 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...
  4. pmc Human cerebral malaria and Plasmodium falciparum genotypes in Malawi
    Danny A Milner
    Department of Pathology, Brigham and Women s Hospital, 75 Francis Street, Amory 3, Boston, MA 02115, USA
    Malar J 11:35. 2012
    ..A Taqman 24 Single Nucleotide Polymorphisms (SNP) molecular barcode assay was developed for use in laboratory parasites which estimates genotype number and identifies the predominant genotype...
  5. 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...
  6. 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...
  7. 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
    ....
  8. 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...
  9. 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...
  10. 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...
  11. 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
    ....
  12. 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...
  13. 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...
  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 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...
  16. 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...
  17. 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...
  18. 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
    ....
  19. 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...
  20. 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...