List of works by Daniel Neafsey

'Next-generation' sequencing becomes 'now-generation'.

scientific article published on 18 March 2011

A general SNP-based molecular barcode for Plasmodium falciparum identification and tracking

scientific article published on 29 October 2008

A genome-wide map of diversity in Plasmodium falciparum

scientific article published on 10 December 2006

A genomic and evolutionary approach reveals non-genetic drug resistance in malaria

scientific article (publication date: 2014)

Adaptive evolution of malaria parasites in French Guiana: Reversal of chloroquine resistance by acquisition of a mutation in pfcrt

scientific article

An epigenetic antimalarial resistance mechanism involving parasite genes linked to nutrient uptake

scientific article published on 28 May 2013

Application of genomics to field investigations of malaria by the international centers of excellence for malaria research

scientific article

Breakdown in the process of incipient speciation in Anopheles gambiae

scientific article published on 18 January 2013

COIL: a methodology for evaluating malarial complexity of infection using likelihood from single nucleotide polymorphism data

scientific article

Candidate-gene based GWAS identifies reproducible DNA markers for metabolic pyrethroid resistance from standing genetic variation in East African Anopheles gambiae

scientific article published on 13 February 2018

Chromerid genomes reveal the evolutionary path from photosynthetic algae to obligate intracellular parasites

scientific article

Comparative evolutionary genomics of human malaria parasites

scientific article published on 18 October 2008

Comparative genomic analyses of the human fungal pathogens Coccidioides and their relatives

scientific article

Complex selection on 5' splice sites in intron-rich organisms

scientific article published on 10 September 2009

Complex selection on intron size in Cryptococcus neoformans

scientific article published on 2 January 2008

Convergent loss of an anciently duplicated, functionally divergent RH2 opsin gene in the fugu and Tetraodon pufferfish lineages

scientific article

Cross-kingdom patterns of alternative splicing and splice recognition

scientific article (publication date: 2008)

De Novo Mutations Resolve Disease Transmission Pathways in Clonal Malaria.

scientific article

Development of a single nucleotide polymorphism barcode to genotype Plasmodium vivax infections

scientific article

Different regulatory mechanisms underlie similar transposable element profiles in pufferfish and fruitflies

scientific article published in September 2004

Diversity-oriented synthesis yields novel multistage antimalarial inhibitors

scientific article (publication date: 7 September 2016)

Dual modes of natural selection on upstream open reading frames.

scientific article published on 9 May 2007

Estimating Relatedness Between Malaria Parasites

scientific article published on 17 June 2019

Evaluation of DISCOVAR de novo using a mosquito sample for cost-effective short-read genome assembly

scientific article published on 5 March 2016

Evolution of noncoding and silent coding sites in the Plasmodium falciparum and Plasmodium reichenowi genomes.

scientific article published on 27 April 2005

Evolutionary conservation of UTR intron boundaries in Cryptococcus.

scientific article published on 20 March 2007

Evolutionary roles of upstream open reading frames in mediating gene regulation in fungi

scientific article published on January 2009

Genetic dissection of Anopheles gambiae gut epithelial responses to Serratia marcescens

scientific article

Genetic diversity and selection at the Plasmodium vivax apical membrane antigen-1 (PvAMA-1) locus in a Sri Lankan population

scientific article published on 22 January 2007

Genetic relatedness analysis reveals the cotransmission of genetically related Plasmodium falciparum parasites in Thiès, Senegal

scientific article published on 24 January 2017

Genetic surveillance detects both clonal and epidemic transmission of malaria following enhanced intervention in Senegal

scientific article

Genome Size Evolution in Pufferfish: A Comparative Analysis of Diodontid and Tetraodontid Pufferfish Genomes ⬇️

scientific article published on May 1, 2003

Genome sequencing sheds light on emerging drug resistance in malaria parasites.

scientific article published in June 2013

Genome-Scale Protein Microarray Comparison of Human Antibody Responses in Plasmodium vivax Relapse and Reinfection

scientific article

Genome-level determination of Plasmodium falciparum blood-stage targets of malarial clinical immunity in the Peruvian Amazon

scientific article

Genome-wide SNP genotyping highlights the role of natural selection in Plasmodium falciparum population divergence

scientific article published on 15 December 2008

Genomic Dark Matter Illuminated: Anopheles Y Chromosomes

scientific article published on 2 June 2016

Genomic architecture and introgression shape a butterfly radiation

scientific article published on 01 November 2019

Genomic sequencing of Plasmodium falciparum malaria parasites from Senegal reveals the demographic history of the population

scientific article

Harnessing genomics and genome biology to understand malaria biology

scientific article published on 12 April 2012

Host-mediated selection impacts the diversity of Plasmodium falciparum antigens within infections.

scientific article published on 11 April 2018

Human cerebral malaria and Plasmodium falciparum genotypes in Malawi

scientific article published on 7 February 2012

Hybrid selection for sequencing pathogen genomes from clinical samples

scientific article published on 11 August 2011

Identification and functional validation of the novel antimalarial resistance locus PF10_0355 in Plasmodium falciparum

scientific article

Immune characterization of Plasmodium falciparum parasites with a shared genetic signature in a region of decreasing transmission

scientific article

Improved Aedes aegypti mosquito reference genome assembly enables biological discovery and vector control

Improved reference genome of Aedes aegypti informs arbovirus vector control

scientific article published in Nature

Local emergence in Amazonia of Plasmodium falciparum k13 C580Y mutants associated with in vitro artemisinin resistance

scientific article published on 12 May 2020

Longitudinal genomic surveillance of Plasmodium falciparum malaria parasites reveals complex genomic architecture of emerging artemisinin resistance

scientific article (publication date: 28 April 2017)

Longitudinal genomic surveillance of Plasmodium falciparum malaria parasites reveals complex genomic architecture of emerging artemisinin resistance in western Thailand

scientific article published on 2 November 2016

Malaria Genomics in the Era of Eradication

scientific article published on 07 April 2017

Malaria life cycle intensifies both natural selection and random genetic drift

scientific article

Mapping malaria by combining parasite genomic and epidemiologic data

scholarly article by Amy Wesolowski et al published 18 October 2018 in BMC Medicine

Mechanisms of intron gain and loss in Cryptococcus

scientific article

Modeling malaria genomics reveals transmission decline and rebound in Senegal

scientific article published on 4 May 2015

Mosquito Vectors and the Globalization of Plasmodium falciparum Malaria

scientific article

Mosquito genomics. Extensive introgression in a malaria vector species complex revealed by phylogenomics

scientific article

Mosquito genomics. Highly evolvable malaria vectors: the genomes of 16 Anopheles mosquitoes

scientific article published on 27 November 2014

Natural diversity of the malaria vector Anopheles gambiae

scholarly article by Alistair Miles et al published 22 December 2016 in bioRxiv

Patterns of genomic differentiation between ecologically differentiated M and S forms of Anopheles gambiae in West and Central Africa

scientific article published on January 2012

Population genetic analysis of large sequence polymorphisms in Plasmodium falciparum blood-stage antigens

scientific article

Population genomic sequencing of Coccidioides fungi reveals recent hybridization and transposon control

scientific article

Population genomic structure and adaptation in the zoonotic malaria parasite Plasmodium knowlesi

scientific article

Population genomics of Plasmodium vivax in Panama to assess the risk of case importation on malaria elimination

scientific article published on 14 December 2020

Population genomics reveals the expansion of highly inbred Plasmodium vivax lineages in the main malaria hotspot of Brazil

scientific article published on 28 October 2020

Population genomics studies identify signatures of global dispersal and drug resistance in Plasmodium vivax

scientific article published on 27 June 2016

Positive selection for unpreferred codon usage in eukaryotic genomes

scientific article

Probing sexual commitment at the single-cell level

Quantitative Proteomic Profiling Reveals Novel Plasmodium falciparum Surface Antigens and Possible Vaccine Candidates

scientific article published on 21 November 2017

Radiation with reticulation marks the origin of a major malaria vector

scientific article published on 01 December 2020

Role of Plasmodium vivax Duffy-binding protein 1 in invasion of Duffy-null Africans ⬇️

scientific article published on 17 May 2016

SNP genotyping identifies new signatures of selection in a deep sample of West African Plasmodium falciparum malaria parasites

scientific article published on 11 June 2012

Sequence-based association and selection scans identify drug resistance loci in the Plasmodium falciparum malaria parasite

scientific article

Standardized metadata for human pathogen/vector genomic sequences

scientific article (publication date: 2014)

Stepwise acquisition of pyrimethamine resistance in the malaria parasite

scientific article published on 08 July 2009

THE REAL McCOIL: A method for the concurrent estimation of the complexity of infection and SNP allele frequency for malaria parasites.

scientific article

The evolution of the Anopheles 16 genomes project

scientific article published on 08 July 2013

The malaria parasite Plasmodium vivax exhibits greater genetic diversity than Plasmodium falciparum

scientific article

Transcriptional correlates of malaria in RTS,S/AS01-vaccinated African children: a matched case-control study

scientific article published on 21 January 2022

Transmission of molecularly undetectable circulating parasite clones leads to high infection complexity in mosquitoes post feeding.

scientific article published on 5 May 2018

VAR2CSA signatures of high Plasmodium falciparum parasitemia in the placenta

scientific article

hmmIBD: software to infer pairwise identity by descent between haploid genotypes.

scientific article published on 15 May 2018

‘Big data’ from shrinking pathogen populations

scientific article

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