Publications by authors named "Daniel E Neafsey"

89Publications

Radiation with reticulation marks the origin of a major malaria vector.

Proc Natl Acad Sci U S A 2020 Dec 1;117(50):31583-31590. Epub 2020 Dec 1.

Department of Biological Sciences, University of Notre Dame, South Bend, IN 46556;

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December 2020

Identity-by-descent with uncertainty characterises connectivity of Plasmodium falciparum populations on the Colombian-Pacific coast.

PLoS Genet 2020 11 16;16(11):e1009101. Epub 2020 Nov 16.

Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA.

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November 2020

The Anopheles coluzzii microbiome and its interaction with the intracellular parasite Wolbachia.

Sci Rep 2020 08 14;10(1):13847. Epub 2020 Aug 14.

Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02144, USA.

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August 2020

Local emergence in Amazonia of C580Y mutants associated with artemisinin resistance.

Elife 2020 05 12;9. Epub 2020 May 12.

Laboratoire de parasitologie, Centre Nationale de Référence du Paludisme, World Health Organization Collaborating Center for surveillance of antimalarial drug resistance, Institut Pasteur de la Guyane, Cayenne, French Guiana.

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May 2020

Resolving the cause of recurrent Plasmodium vivax malaria probabilistically.

Nat Commun 2019 12 6;10(1):5595. Epub 2019 Dec 6.

Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand.

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December 2019

Detection of low-density Plasmodium falciparum infections using amplicon deep sequencing.

Malar J 2019 Jul 1;18(1):219. Epub 2019 Jul 1.

Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.

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July 2019

Estimating Relatedness Between Malaria Parasites.

Genetics 2019 08 17;212(4):1337-1351. Epub 2019 Jun 17.

Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115.

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August 2019

Mutations in actin-binding protein coronin confer reduced artemisinin susceptibility.

Proc Natl Acad Sci U S A 2018 12 12;115(50):12799-12804. Epub 2018 Nov 12.

Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115;

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December 2018

Probing sexual commitment at the single-cell level.

Wellcome Open Res 2018 17;3:70. Epub 2018 Oct 17.

Wellcome Centre for Molecular Parasitology, Institute of Infection, Immunity & Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK.

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October 2018

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

Malar J 2018 May 15;17(1):196. Epub 2018 May 15.

Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.

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May 2018

Quantifying connectivity between local Plasmodium falciparum malaria parasite populations using identity by descent.

PLoS Genet 2017 Oct 27;13(10):e1007065. Epub 2017 Oct 27.

Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America.

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October 2017

Malaria Genomics in the Era of Eradication.

Cold Spring Harb Perspect Med 2017 Aug 1;7(8). Epub 2017 Aug 1.

Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115.

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August 2017

Mosquito Vectors and the Globalization of Plasmodium falciparum Malaria.

Annu Rev Genet 2016 Nov 3;50:447-465. Epub 2016 Oct 3.

Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland 20852; email:

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November 2016

Genomic Dark Matter Illuminated: Anopheles Y Chromosomes.

Trends Parasitol 2016 08 2;32(8):585-587. Epub 2016 Jun 2.

Broad Institute of MIT and Harvard, Cambridge, MA, USA.

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August 2016

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

Proc Natl Acad Sci U S A 2016 May 17;113(22):6271-6. Epub 2016 May 17.

Laboratory of Malaria and Vector Research, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852;

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May 2016

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

BMC Genomics 2016 Mar 5;17:187. Epub 2016 Mar 5.

Genome Sequencing and Analysis Program, Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02142, USA.

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March 2016

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

Proc Natl Acad Sci U S A 2015 Sep 10;112(37):11672-7. Epub 2015 Aug 10.

Laboratoire de parasitologie, WHO Collaborating Center for Surveillance of Anti-Malarial Drug Resistance, Centre National de Référence du paludisme, Laboratoire associé pour la région Antilles-Guyane, Institut Pasteur de la Guyane, 97300 Cayenne, French Guiana;

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September 2015

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

Am J Trop Med Hyg 2015 Oct 6;93(4):801-9. Epub 2015 Jul 6.

Department of Medicine, Division of Infectious Diseases, University of California San Diego, La Jolla, California; Laboratorio ICEMR-Amazonia, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú; Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Perú; Antigen Discovery Inc., Irvine, California; Malaria Research Group, Broad Institute of MIT and Harvard University, Cambridge, Massachusetts; Seattle Biomed, Seattle, Washington; Department of Medicine, Division of Global Public Health, University of California San Diego, La Jolla, California; Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland

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October 2015

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

PLoS Negl Trop Dis 2015 Mar 17;9(3):e0003539. Epub 2015 Mar 17.

Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America; Broad Institute, Cambridge, Massachusetts, United States of America; Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America.

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March 2015

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

Authors:
Daniel E Neafsey Robert M Waterhouse Mohammad R Abai Sergey S Aganezov Max A Alekseyev James E Allen James Amon Bruno Arcà Peter Arensburger Gleb Artemov Lauren A Assour Hamidreza Basseri Aaron Berlin Bruce W Birren Stephanie A Blandin Andrew I Brockman Thomas R Burkot Austin Burt Clara S Chan Cedric Chauve Joanna C Chiu Mikkel Christensen Carlo Costantini Victoria L M Davidson Elena Deligianni Tania Dottorini Vicky Dritsou Stacey B Gabriel Wamdaogo M Guelbeogo Andrew B Hall Mira V Han Thaung Hlaing Daniel S T Hughes Adam M Jenkins Xiaofang Jiang Irwin Jungreis Evdoxia G Kakani Maryam Kamali Petri Kemppainen Ryan C Kennedy Ioannis K Kirmitzoglou Lizette L Koekemoer Njoroge Laban Nicholas Langridge Mara K N Lawniczak Manolis Lirakis Neil F Lobo Ernesto Lowy Robert M MacCallum Chunhong Mao Gareth Maslen Charles Mbogo Jenny McCarthy Kristin Michel Sara N Mitchell Wendy Moore Katherine A Murphy Anastasia N Naumenko Tony Nolan Eva M Novoa Samantha O'Loughlin Chioma Oringanje Mohammad A Oshaghi Nazzy Pakpour Philippos A Papathanos Ashley N Peery Michael Povelones Anil Prakash David P Price Ashok Rajaraman Lisa J Reimer David C Rinker Antonis Rokas Tanya L Russell N'Fale Sagnon Maria V Sharakhova Terrance Shea Felipe A Simão Frederic Simard Michel A Slotman Pradya Somboon Vladimir Stegniy Claudio J Struchiner Gregg W C Thomas Marta Tojo Pantelis Topalis José M C Tubio Maria F Unger John Vontas Catherine Walton Craig S Wilding Judith H Willis Yi-Chieh Wu Guiyun Yan Evgeny M Zdobnov Xiaofan Zhou Flaminia Catteruccia George K Christophides Frank H Collins Robert S Cornman Andrea Crisanti Martin J Donnelly Scott J Emrich Michael C Fontaine William Gelbart Matthew W Hahn Immo A Hansen Paul I Howell Fotis C Kafatos Manolis Kellis Daniel Lawson Christos Louis Shirley Luckhart Marc A T Muskavitch José M Ribeiro Michael A Riehle Igor V Sharakhov Zhijian Tu Laurence J Zwiebel Nora J Besansky

Science 2015 Jan 27;347(6217):1258522. Epub 2014 Nov 27.

Eck Institute for Global Health and Department of Biological Sciences, University of Notre Dame, 317 Galvin Life Sciences Building, Notre Dame, IN 46556, USA.

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January 2015

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

J Infect Dis 2015 Apr 7;211(8):1342-51. Epub 2014 Nov 7.

Laboratorio de Malaria, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía Institute de Medicina Tropical, Universidad Peruana Cayetano Heredia, Lima.

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April 2015

Genetic dissection of Anopheles gambiae gut epithelial responses to Serratia marcescens.

PLoS Pathog 2014 Mar 6;10(3):e1003897. Epub 2014 Mar 6.

Department of Life Sciences, Imperial College London, London, United Kingdom; The Cyprus Institute, Nicosia, Cyprus.

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March 2014

Malaria life cycle intensifies both natural selection and random genetic drift.

Proc Natl Acad Sci U S A 2013 Dec 20;110(50):20129-34. Epub 2013 Nov 20.

Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138.

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December 2013

VAR2CSA signatures of high Plasmodium falciparum parasitemia in the placenta.

PLoS One 2013 25;8(7):e69753. Epub 2013 Jul 25.

Barcelona Centre for International Health Research, CRESIB, Hospital Clínic-Universitat de Barcelona, Barcelona, Spain.

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March 2014

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

Authors:
Daniel E Neafsey

Nat Genet 2013 Jun;45(6):589-90

Broad Institute, Cambridge, Massachusetts, USA.

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June 2013

‘Big data’ from shrinking pathogen populations.

Authors:
Daniel E Neafsey

Mol Ecol 2013 Jan;22(2):271-2

Broad Institute, Cambridge, MA 02142, USA.

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January 2013

Harnessing genomics and genome biology to understand malaria biology.

Nat Rev Genet 2012 Apr 12;13(5):315-28. Epub 2012 Apr 12.

Department of Immunology and Infectious Disease, Harvard School of Public Health, 665 Huntington Avenue, Boston, Massachusetts 02115, USA.

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April 2012

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

Genome Biol 2011 18;12(3):303. Epub 2011 Mar 18.

Broad Institute, 7 Cambridge Center, Cambridge, MA 02142, USA.

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January 2012

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

Infect Genet Evol 2010 Mar 30;10(2):200-6. Epub 2009 Nov 30.

Laboratory of Bacteriology and Virology, Le Dantec Hospital, and Laboratory of Parasitology, Faculty of Medicine and Pharmacy, Cheikh Anta Diop University, Dakar BP 7325, Senegal.

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March 2010

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

Genome Res 2009 Nov 10;19(11):2021-7. Epub 2009 Sep 10.

Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, 08028 Barcelona, Spain.

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November 2009

Stepwise acquisition of pyrimethamine resistance in the malaria parasite.

Proc Natl Acad Sci U S A 2009 Jul 8;106(29):12025-30. Epub 2009 Jul 8.

Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.

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July 2009

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

Annu Rev Microbiol 2009 ;63:385-409

Department of Science and Engineering, Oregon Health & Science University, Beaverton, Oregon 97006, USA.

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October 2009

Cross-kingdom patterns of alternative splicing and splice recognition.

Genome Biol 2008 5;9(3):R50. Epub 2008 Mar 5.

The Broad Institute of MIT and Harvard, Cambridge Center, Cambridge, MA 02142, USA.

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June 2008

Mechanisms of intron gain and loss in Cryptococcus.

Genome Biol 2008 Jan 30;9(1):R24. Epub 2008 Jan 30.

Department of Plant and Microbial Biology, University of California at Berkeley, Berkeley, CA 94720, USA.

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January 2008

Complex selection on intron size in Cryptococcus neoformans.

Mol Biol Evol 2008 Feb 2;25(2):247-53. Epub 2008 Jan 2.

Microbial Analysis Group, Broad Institute of MIT and Harvard, Cambridge.

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February 2008

Positive selection for unpreferred codon usage in eukaryotic genomes.

BMC Evol Biol 2007 Jul 18;7:119. Epub 2007 Jul 18.

Microbial Analysis Group, Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA.

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July 2007

Dual modes of natural selection on upstream open reading frames.

Mol Biol Evol 2007 Aug 9;24(8):1744-51. Epub 2007 May 9.

Microbial Analysis Group, Broad Institute of MIT and Harvard, Cambridge, MA, USA.

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August 2007

Evolutionary conservation of UTR intron boundaries in Cryptococcus.

Mol Biol Evol 2007 May 20;24(5):1140-8. Epub 2007 Mar 20.

Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand.

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May 2007

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

Mol Biol Evol 2005 Jul 27;22(7):1621-6. Epub 2005 Apr 27.

Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.

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July 2005

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

Gene 2005 May 7;350(2):161-71. Epub 2005 Apr 7.

Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA.

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May 2005

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

Mol Biol Evol 2004 Dec 1;21(12):2310-8. Epub 2004 Sep 1.

Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA.

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December 2004

Genome size evolution in pufferfish: a comparative analysis of diodontid and tetraodontid pufferfish genomes.

Genome Res 2003 May;13(5):821-30

Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA.

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May 2003