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1

Comparative evolutionary genomics of human malaria parasites

Jane M. Carlton, Ananias A. Escalante, Daniel Neafsey, Sarah K. Volkman

Journal:

Trends in Parasitology

Year:

2008

Language:

english

File:

PDF, 211 KB

english, 2008

2

Mosquito Vectors and the Globalization of Plasmodium falciparum Malaria

Molina-Cruz, Alvaro, Zilversmit, Martine M., Neafsey, Daniel E., Hartl, Daniel L., Barillas-Mury, Carolina

Journal:

Annual Review of Genetics

Year:

2016

Language:

english

File:

PDF, 1.02 MB

english, 2016

3

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

Weetman, David, Wilding, Craig S., Neafsey, Daniel E., Müller, Pie, Ochomo, Eric, Isaacs, Alison T., Steen, Keith, Rippon, Emily J., Morgan, John C., Mawejje, Henry D., Rigden, Daniel J., Okedi, Loyce

Journal:

Scientific Reports

Year:

2018

Language:

english

File:

PDF, 1.33 MB

english, 2018

4

Genomic architecture and introgression shape a butterfly radiation

Edelman, Nathaniel B., Frandsen, Paul B., Miyagi, Michael, Clavijo, Bernardo, Davey, John, Dikow, Rebecca B., García-Accinelli, Gonzalo, Van Belleghem, Steven M., Patterson, Nick, Neafsey, Daniel E.,

Journal:

Year:

2019

Language:

english

File:

PDF, 789 KB

english, 2019

5

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

Ambroise D. Ahouidi, Amy K. Bei, Daniel E. Neafsey, Ousmane Sarr, Sarah Volkman, Dan Milner, Janet Cox-Singh, Marcelo U. Ferreira, Omar Ndir, Zul Premji, Souleymane Mboup, Manoj T. Duraisingh

Journal:

Infection, Genetics and Evolution

Year:

2010

Language:

english

File:

PDF, 279 KB

english, 2010

6

A genome-wide map of diversity in Plasmodium falciparum

Volkman, Sarah K, Sabeti, Pardis C, DeCaprio, David, Neafsey, Daniel E, Schaffner, Stephen F, Milner, Danny A, Daily, Johanna P, Sarr, Ousmane, Ndiaye, Daouda, Ndir, Omar

Journal:

Nature Genetics

Year:

2006

Language:

english

File:

PDF, 363 KB

english, 2006

7

Binge Ethanol-Induced Brain Damage in Rats: Effect of Inhibitors of Nitric Oxide Synthase

Jian-Yun Zou, Daniel B. Martinez, Edward J. Neafsey, Michael A. Collins

Journal:

Alcoholism: Clinical and Experimental Research

Year:

1996

Language:

english

File:

PDF, 1.12 MB

english, 1996

8

Positive selection for unpreferred codon usage in eukaryotic genomes

Daniel E Neafsey, James E Galagan

Journal:

BMC Evolutionary Biology

Year:

2007

Language:

english

File:

PDF, 321 KB

english, 2007

9

Human cerebral malaria andPlasmodium falciparumgenotypes in Malawi

Danny A Milner, Jimmy Vareta, Clarissa Valim, Jacqui Montgomery, Rachel F Daniels, Sarah K Volkman, Daniel E Neafsey, Daniel J Park, Stephen F Schaffner, Nira C Mahesh, Kayla G Barnes, David M Rosen,

Journal:

Malaria Journal

Year:

2012

Language:

english

File:

PDF, 360 KB

english, 2012

10

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

Sarah K. Volkman, Daouda Ndiaye, Mahamadou Diakite, Ousmane A. Koita, Davis Nwakanma, Rachel F. Daniels, Daniel J. Park, Daniel E. Neafsey, Marc A.T. Muskavitch, Donald J. Krogstad, Pardis C. Sabeti,

Journal:

Year:

2012

Language:

english

File:

PDF, 460 KB

english, 2012

11

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

Daniel E. Neafsey, Daniel L. Hartl

Journal:

Year:

2005

Language:

english

File:

PDF, 389 KB

english, 2005

12

Erratum to “Convergent loss of an anciently duplicated, functionally divergent RH2 opsin gene in the fugu and Tetraodon pufferfish lineages” [Gene 350 (2005) 161–171]

Daniel E. Neafsey, Daniel L. Hartl

Journal:

Year:

2006

Language:

english

File:

PDF, 51 KB

english, 2006

13

‘Big data’ from shrinking pathogen populations

Neafsey, Daniel E.

Journal:

Molecular Ecology

Year:

2013

Language:

english

File:

PDF, 343 KB

english, 2013

14

Evolutionary Roles of Upstream Open Reading Frames in Mediating Gene Regulation in Fungi

Hood, Heather M., Neafsey, Daniel E., Galagan, James, Sachs, Matthew S.

Journal:

Annual Review of Microbiology

Year:

2009

Language:

english

File:

PDF, 3.18 MB

english, 2009

15

Harnessing genomics and genome biology to understand malaria biology

Volkman, Sarah K., Neafsey, Daniel E., Schaffner, Stephen F., Park, Daniel J., Wirth, Dyann F.

Journal:

Nature Reviews Genetics

Year:

2012

Language:

english

File:

PDF, 1.25 MB

english, 2012

16

Genome sequencing sheds light on emerging drug resistance in malaria parasites

Neafsey, Daniel E

Journal:

Nature Genetics

Year:

2013

Language:

english

File:

PDF, 131 KB

english, 2013

17

Genome-wide SNP genotyping highlights the role of natural selection inPlasmodium falciparumpopulation divergence

Daniel E Neafsey, Stephen F Schaffner, Sarah K Volkman, Daniel Park…

Journal:

Year:

2008

Language:

english

File:

PDF, 673 KB

english, 2008

18

Cross-kingdom patterns of alternative splicing and splice recognition

Abigail M McGuire, Matthew D Pearson, Daniel E Neafsey, James E Galagan

Journal:

Year:

2008

Language:

english

File:

PDF, 515 KB

english, 2008

19

Mechanisms of intron gain and loss inCryptococcus

Thomas J Sharpton, Daniel E Neafsey, James E Galagan, John W Taylor

Journal:

Year:

2008

Language:

english

File:

PDF, 639 KB

english, 2008

20

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

Neafsey, Daniel E, Galinsky, Kevin, Jiang, Rays H Y, Young, Lauren, Sykes, Sean M, Saif, Sakina, Gujja, Sharvari, Goldberg, Jonathan M, Young, Sarah, Zeng, Qiandong, Chapman, Sinéad B, Dash, Aditya P,

Journal:

Nature Genetics

Year:

2012

Language:

english

File:

PDF, 551 KB

english, 2012

21

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

Daniel E Neafsey,Brian J Haas

Journal:

Year:

2011

Language:

english

File:

PDF, 240 KB

english, 2011

22

Immune Characterization of Plasmodium falciparum Parasites with a Shared Genetic Signature in a Region of Decreasing Transmission

Bei, Amy K., Diouf, Ababacar, Miura, Kazutoyo, Larremore, Daniel B., Ribacke, Ulf, Tullo, Gregory, Moss, Eli L., Neafsey, Daniel E., Daniels, Rachel F., Zeituni, Amir E., Nosamiefan, Iguosadolo, Volkm

Journal:

Infection and Immunity

Year:

2015

Language:

english

File:

PDF, 1.06 MB

english, 2015

23

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

Herman, Jonathan D, Rice, Daniel P, Ribacke, Ulf, Silterra, Jacob, Deik, Amy A, Moss, Eli L, Broadbent, Kate M, Neafsey, Daniel E, Desai, Michael M, Clish, Clary B, Mazitschek, Ralph, Wirth, Dyann F

Journal:

Year:

2014

Language:

english

File:

PDF, 2.37 MB

english, 2014

24

Metabolic QTL Analysis Links Chloroquine Resistance in Plasmodium falciparum to Impaired Hemoglobin Catabolism

Lewis, Ian A., Wacker, Mark, Olszewski, Kellen L., Cobbold, Simon A., Baska, Katelynn S., Tan, Asako, Ferdig, Michael T., Llinás, Manuel, Neafsey, Daniel E.

Journal:

Year:

2014

Language:

english

File:

PDF, 1005 KB

english, 2014

25

Identification and Functional Validation of the Novel Antimalarial Resistance Locus PF10_0355 in Plasmodium falciparum

Van Tyne, Daria, Park, Daniel J., Schaffner, Stephen F., Neafsey, Daniel E., Angelino, Elaine, Cortese, Joseph F., Barnes, Kayla G., Rosen, David M., Lukens, Amanda K., Daniels, Rachel F., Milner, Dan

Journal:

Year:

2011

Language:

english

File:

PDF, 1.12 MB

english, 2011

26

Genetic Dissection of Anopheles gambiae Gut Epithelial Responses to Serratia marcescens

Stathopoulos, Stavros, Neafsey, Daniel E., Lawniczak, Mara K. N., Muskavitch, Marc A. T., Christophides, George K., Schneider, David S.

Journal:

Year:

2014

Language:

english

File:

PDF, 1.63 MB

english, 2014

27

Genetic Diversity and Protective Efficacy of the RTS,S/AS01 Malaria Vaccine

Neafsey, Daniel E., Juraska, Michal, Bedford, Trevor, Benkeser, David, Valim, Clarissa, Griggs, Allison, Lievens, Marc, Abdulla, Salim, Adjei, Samuel, Agbenyega, Tsiri, Agnandji, Selidji T., Aide, Ped

Journal:

New England Journal of Medicine

Year:

2015

Language:

english

File:

PDF, 1.13 MB

english, 2015

28

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

Assefa, Samuel, Lim, Caeul, Preston, Mark D., Duffy, Craig W., Nair, Mridul B., Adroub, Sabir A., Kadir, Khamisah A., Goldberg, Jonathan M., Neafsey, Daniel E., Divis, Paul, Clark, Taane G., Duraising

Journal:

Proceedings of the National Academy of Sciences

Year:

2015

Language:

english

File:

PDF, 1.40 MB

english, 2015

29

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

Gunalan, Karthigayan, Lo, Eugenia, Hostetler, Jessica B., Yewhalaw, Delenasaw, Mu, Jianbing, Neafsey, Daniel E., Yan, Guiyun, Miller, Louis H.

Journal:

Proceedings of the National Academy of Sciences

Year:

2016

Language:

english

File:

PDF, 1.36 MB

english, 2016

30

Genotyping malaria parasites to understand malaria transmission

Volkman, S.K., Daniels, R., Chang, H., Park, D.C., Neafsey, D.E., Schaffner, S.F., Lukens, A.K., Mboup, S., Sabeti, P.C., Wirth, D.F., Hartl, D.L.

Journal:

Annals of Global Health

Year:

2015

Language:

english

File:

PDF, 85 KB

english, 2015

31

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

Love, R. Rebecca, Weisenfeld, Neil I., Jaffe, David B., Besansky, Nora J., Neafsey, Daniel E.

Journal:

Year:

2016

Language:

english

File:

PDF, 2.95 MB

english, 2016

32

Genomic Dark Matter Illuminated: Anopheles Y Chromosomes

Redmond, Seth N., Neafsey, Daniel E.

Journal:

Trends in Parasitology

Year:

2016

Language:

english

File:

PDF, 409 KB

english, 2016

33

Malaria Genomics in the Era of Eradication

Neafsey, Daniel E., Volkman, Sarah K.

Journal:

Cold Spring Harbor Perspectives in Medicine

Year:

2017

Language:

english

File:

PDF, 632 KB

english, 2017

34

De Novo Mutations Resolve Disease Transmission Pathways in Clonal Malaria

Redmond, Seth N, MacInnis, Bronwyn M, Bopp, Selina, Bei, Amy K, Ndiaye, Daouda, Hartl, Daniel L, Wirth, Dyann F, Volkman, Sarah K, Neafsey, Daniel E, Falush, Daniel

Journal:

Molecular Biology and Evolution

Year:

2018

Language:

english

File:

PDF, 464 KB

english, 2018

35

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

Chang, Hsiao-Han, Worby, Colin J., Yeka, Adoke, Nankabirwa, Joaniter, Kamya, Moses R., Staedke, Sarah G., Dorsey, Grant, Murphy, Maxwell, Neafsey, Daniel E., Jeffreys, Anna E., Hubbart, Christina, Roc

Journal:

PLoS Computational Biology

Year:

2017

Language:

english

File:

PDF, 2.87 MB

english, 2017

36

Genetic Surveillance Detects Both Clonal and Epidemic Transmission of Malaria following Enhanced Intervention in Senegal

Daniels, Rachel, Chang, Hsiao-Han, Séne, Papa Diogoye, Park, Danny C., Neafsey, Daniel E., Schaffner, Stephen F., Hamilton, Elizabeth J., Lukens, Amanda K., Van Tyne, Daria, Mboup, Souleymane, Sabeti,

Journal:

Year:

2013

Language:

english

File:

PDF, 351 KB

english, 2013

37

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

Schaffner, Stephen F., Taylor, Aimee R., Wong, Wesley, Wirth, Dyann F., Neafsey, Daniel E.

Journal:

Malaria Journal

Year:

2018

Language:

english

File:

PDF, 1018 KB

english, 2018

38

Mapping malaria by combining parasite genomic and epidemiologic data

Wesolowski, Amy, Taylor, Aimee R, Chang, Hsiao-Han, Verity, Robert, Tessema, Sofonias, Bailey, Jeffrey A, Alex Perkins, T, Neafsey, Daniel E, Greenhouse, Bryan, Buckee, Caroline O

Journal:

Year:

2018

Language:

english

File:

PDF, 793 KB

english, 2018

39

Mutations in Plasmodium falciparum actin-binding protein coronin confer reduced artemisinin susceptibility

Demas, Allison R., Sharma, Aabha I., Wong, Wesley, Early, Angela M., Redmond, Seth, Bopp, Selina, Neafsey, Daniel E., Volkman, Sarah K., Hartl, Daniel L., Wirth, Dyann F.

Journal:

Proceedings of the National Academy of Sciences

Year:

2018

Language:

english

File:

PDF, 808 KB

english, 2018

40

Correction to: Mapping malaria by combining parasite genomic and epidemiologic data

Wesolowski, Amy, Taylor, Aimee R., Chang, Hsiao-Han, Verity, Robert, Tessema, Sofonias, Bailey, Jeffrey A., Alex Perkins, T., Neafsey, Daniel E., Greenhouse, Bryan, Buckee, Caroline O.

Journal:

Year:

2018

Language:

english

File:

PDF, 230 KB

english, 2018

41

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

Early, Angela M., Daniels, Rachel F., Farrell, Timothy M., Grimsby, Jonna, Volkman, Sarah K., Wirth, Dyann F., MacInnis, Bronwyn L., Neafsey, Daniel E.

Journal:

Malaria Journal

Year:

2019

Language:

english

File:

PDF, 1.70 MB

english, 2019

42

Resolving the cause of recurrent Plasmodium vivax malaria probabilistically

Taylor, Aimee R., Watson, James A., Chu, Cindy S., Puaprasert, Kanokpich, Duanguppama, Jureeporn, Day, Nicholas P. J., Nosten, Francois, Neafsey, Daniel E., Buckee, Caroline O., Imwong, Mallika, White

Journal:

Nature Communications

Year:

2019

File:

PDF, 1.02 MB

2019

43

Linked-read sequencing identifies abundant microinversions and introgression in the arboviral vector Aedes aegypti

Redmond, Seth N., Sharma, Atashi, Sharakhov, Igor, Tu, Zhijian, Sharakhova, Maria, Neafsey, Daniel E.

Journal:

Year:

2020

Language:

english

File:

PDF, 1.86 MB

english, 2020

44

Amplicon deep sequencing of kelch13 in Plasmodium falciparum isolates from Senegal

Gaye, Amy, Sy, Mouhamad, Ndiaye, Tolla, Siddle, Katherine J., Park, Daniel J., Deme, Awa B., Mbaye, Aminata, Dieye, Baba, Ndiaye, Yaye Die, Neafsey, Daniel E., Early, Angela, Farrell, Timothy, Yade, M

Journal:

Malaria Journal

Year:

2020

File:

PDF, 1.48 MB

2020

45

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

Straub, Timothy J., Shaw, W. Robert, Marcenac, Perrine, Sawadogo, Simon P., DabirÃ©, Roch K., DiabatÃ©, Abdoulaye, Catteruccia, Flaminia, Neafsey, Daniel E.

Journal:

Scientific Reports

Year:

2020

File:

PDF, 1.94 MB

2020

46

Use of a Plasmodium vivax genetic barcode for genomic surveillance and parasite tracking in Sri Lanka

Dewasurendra, Rajika L., Baniecki, Mary Lynn, Schaffner, Stephen, Siriwardena, Yamuna, Moon, Jade, Doshi, R., Gunawardena, Sharmini, Daniels, Rachel F., Neafsey, Daniel, Volkman, Sarah, Chandrasekhara

Journal:

Malaria Journal

Year:

2020

File:

PDF, 1.24 MB

2020

47

A population genomic unveiling of a new cryptic mosquito taxon within the malariaâtransmitting Anopheles gambiae complex

Tennessen, Jacob A., Ingham, Victoria A., ToÃ©, KobiÃ© Hyacinthe, GuelbÃ©ogo, Wamdaogo Moussa, Sagnon, NâFalÃ©, Kuzma, Rebecca, Ranson, Hilary, Neafsey, Daniel E.

Journal:

Molecular Ecology

Year:

2020

File:

PDF, 8.05 MB

2020