Daniel E Neafsey

Daniel E Neafsey

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Daniel E Neafsey

Publications by authors named "Daniel E Neafsey"

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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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http://dx.doi.org/10.1534/genetics.119.302120DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6707449PMC
August 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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http://dx.doi.org/10.1186/s12936-019-2856-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6604269PMC
July 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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http://www.pnas.org/lookup/doi/10.1073/pnas.1812317115
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http://dx.doi.org/10.1073/pnas.1812317115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6294886PMC
December 2018

Improved reference genome of Aedes aegypti informs arbovirus vector control.

Nature 2018 11 14;563(7732):501-507. Epub 2018 Nov 14.

Laboratory of Neurogenetics and Behavior, The Rockefeller University, New York, NY, USA.

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http://www.nature.com/articles/s41586-018-0692-z
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http://dx.doi.org/10.1038/s41586-018-0692-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6421076PMC
November 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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http://dx.doi.org/10.12688/wellcomeopenres.14645.4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6143928.4PMC
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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https://malariajournal.biomedcentral.com/articles/10.1186/s1
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http://dx.doi.org/10.1186/s12936-018-2349-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5952413PMC
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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http://dx.doi.org/10.1371/journal.pgen.1007065DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5678785PMC
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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http://dx.doi.org/10.1101/cshperspect.a025544DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5538406PMC
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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http://dx.doi.org/10.1146/annurev-genet-120215-035211DOI Listing
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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http://dx.doi.org/10.1016/j.pt.2016.05.008DOI Listing
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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http://dx.doi.org/10.1073/pnas.1606113113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4896682PMC
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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http://dx.doi.org/10.1186/s12864-016-2531-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4779211PMC
March 2016

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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http://dx.doi.org/10.4269/ajtmh.15-0232DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4596603PMC
October 2015

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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http://www.pnas.org/lookup/doi/10.1073/pnas.1507142112
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http://dx.doi.org/10.1073/pnas.1507142112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4577156PMC
September 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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http://dx.doi.org/10.1093/infdis/jiu614DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4402338PMC
April 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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http://dx.doi.org/10.1371/journal.pntd.0003539DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4362761PMC
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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http://dx.doi.org/10.1126/science.1258522DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4380271PMC
January 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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http://dx.doi.org/10.1371/journal.ppat.1003897DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3946313PMC
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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http://dx.doi.org/10.1073/pnas.1319857110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3864301PMC
December 2013

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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http://dx.doi.org/10.1038/ng.2648DOI Listing
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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http://dx.doi.org/10.1111/mec.12175DOI Listing
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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http://dx.doi.org/10.1038/nrg3187DOI Listing
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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http://dx.doi.org/10.1186/gb-2011-12-3-303DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3129669PMC
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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https://linkinghub.elsevier.com/retrieve/pii/S15671348090026
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http://dx.doi.org/10.1016/j.meegid.2009.11.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2829370PMC
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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http://dx.doi.org/10.1101/gr.089276.108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2775602PMC
November 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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http://dx.doi.org/10.1146/annurev.micro.62.081307.162835DOI Listing
October 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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http://dx.doi.org/10.1073/pnas.0905922106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2715478PMC
July 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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http://dx.doi.org/10.1186/gb-2008-9-3-r50DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2397502PMC
June 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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http://dx.doi.org/10.1093/molbev/msm220DOI Listing
February 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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http://genomebiology.biomedcentral.com/articles/10.1186/gb-2
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http://dx.doi.org/10.1186/gb-2008-9-1-r24DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2395259PMC
January 2008

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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https://academic.oup.com/mbe/article-lookup/doi/10.1093/molb
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http://dx.doi.org/10.1093/molbev/msm093DOI Listing
August 2007

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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http://dx.doi.org/10.1186/1471-2148-7-119DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1936986PMC
July 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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http://dx.doi.org/10.1093/molbev/msm045DOI Listing
May 2007

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

Mol Biol Evol 2007 Apr 22;24(4):939-47. Epub 2007 Jan 22.

Department of Immunology and Infectious Diseases, Harvard School of Public Health, Harvard University, USA.

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http://dx.doi.org/10.1093/molbev/msm013DOI Listing
April 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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http://dx.doi.org/10.1093/molbev/msi154DOI Listing
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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http://dx.doi.org/10.1016/j.gene.2005.02.011DOI Listing
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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https://academic.oup.com/mbe/article-lookup/doi/10.1093/molb
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http://dx.doi.org/10.1093/molbev/msh243DOI Listing
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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http://dx.doi.org/10.1101/gr.841703DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC430906PMC
May 2003