Strains used in whole organism Plasmodium falciparum vaccine trials differ in genome structure, sequence, and immunogenic potential

[1]  Zalak V. Shah,et al.  Optimization of parasite DNA enrichment approaches to generate whole genome sequencing data for Plasmodium falciparum from low parasitaemia samples , 2019, Malaria Journal.

[2]  M. Berriman,et al.  Progression of the canonical reference malaria parasite genome from 2002–2019 , 2019, Wellcome open research.

[3]  A. Sette,et al.  Comprehensive Review of Human Plasmodium falciparum-Specific CD8+ T Cell Epitopes , 2019, Front. Immunol..

[4]  Joana C. Silva,et al.  A Plasmodium berghei sporozoite-based vaccination platform against human malaria , 2018, npj Vaccines.

[5]  D. Conway,et al.  Long read assemblies of geographically dispersed Plasmodium falciparum isolates reveal highly structured subtelomeres , 2018, Wellcome open research.

[6]  Alex B. Miller,et al.  Author Correction: A human monoclonal antibody prevents malaria infection by targeting a new site of vulnerability on the parasite , 2018, Nature Medicine.

[7]  Julien Guizetti,et al.  A Specific PfEMP1 Is Expressed in P. falciparum Sporozoites and Plays a Role in Hepatocyte Infection , 2018, Cell reports.

[8]  A. Vaughan,et al.  A Plasmodium Parasite with Complete Late Liver Stage Arrest Protects against Preerythrocytic and Erythrocytic Stage Infection in Mice , 2018, Infection and Immunity.

[9]  S. Hoffman,et al.  A public antibody lineage that potently inhibits malaria infection by dual binding to the circumsporozoite protein , 2018, Nature Medicine.

[10]  Alex B. Miller,et al.  A human monoclonal antibody prevents malaria infection and defines a new site of vulnerability on Plasmodium falciparum circumsporozoite protein , 2018, Nature Medicine.

[11]  Daniel B. Roche,et al.  Functional analysis of Plasmodium falciparum subpopulations associated with artemisinin resistance in Cambodia , 2017, Malaria Journal.

[12]  M. Huynen,et al.  Modest heterologous protection after Plasmodium falciparum sporozoite immunization: a double-blind randomized controlled clinical trial , 2017, BMC Medicine.

[13]  Joana C. Silva,et al.  Association of a Novel Mutation in the Plasmodium falciparum Chloroquine Resistance Transporter With Decreased Piperaquine Sensitivity , 2017, The Journal of infectious diseases.

[14]  P. V. van Genderen,et al.  Infectivity of Plasmodium falciparum sporozoites determines emerging parasitemia in infected volunteers , 2017, Science Translational Medicine.

[15]  Jonathan J. Juliano,et al.  Partner-Drug Resistance and Population Substructuring of Artemisinin-Resistant Plasmodium falciparum in Cambodia , 2017, Genome biology and evolution.

[16]  D. Pratt,et al.  Role of controlled human malaria infection (CHMI) in malaria vaccine development: A U.S. food & drug administration (FDA) perspective. , 2017, Vaccine.

[17]  Erin E Gabriel,et al.  Safety and efficacy of PfSPZ Vaccine against Plasmodium falciparum via direct venous inoculation in healthy malaria-exposed adults in Mali: a randomised, double-blind phase 1 trial. , 2017, The Lancet. Infectious diseases.

[18]  Joana C. Silva,et al.  New var reconstruction algorithm exposes high var sequence diversity in a single geographic location in Mali , 2017, Genome Medicine.

[19]  Sumana Chakravarty,et al.  Sterile protection against human malaria by chemoattenuated PfSPZ vaccine , 2017, Nature.

[20]  Mario Roederer,et al.  Attenuated PfSPZ Vaccine induces strain-transcending T cells and durable protection against heterologous controlled human malaria infection , 2017, Proceedings of the National Academy of Sciences.

[21]  Samuel A. Assefa,et al.  Culture adaptation of malaria parasites selects for convergent loss-of-function mutants , 2017, Scientific Reports.

[22]  Sumana Chakravarty,et al.  Protection against Plasmodium falciparum malaria by PfSPZ Vaccine. , 2017, JCI insight.

[23]  Sergey Koren,et al.  Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation , 2016, bioRxiv.

[24]  François Nosten,et al.  Longitudinal genomic surveillance of Plasmodium falciparum malaria parasites reveals complex genomic architecture of emerging artemisinin resistance , 2017, Genome Biology.

[25]  Michael C. Schatz,et al.  Assemblytics: a web analytics tool for the detection of variants from an assembly , 2016, Bioinform..

[26]  R. Sinden,et al.  Routine in vitro culture of P. falciparum gametocytes to evaluate novel transmission-blocking interventions , 2016, Nature Protocols.

[27]  Mihir Kekre,et al.  Whole genome sequencing of Plasmodium falciparum from dried blood spots using selective whole genome amplification , 2016, Malaria Journal.

[28]  M. Schatz,et al.  Complete telomere-to-telomere de novo assembly of the Plasmodium falciparum genome through long-read (>11 kb), single molecule, real-time sequencing , 2016, DNA research : an international journal for rapid publication of reports on genes and genomes.

[29]  V. Nene,et al.  The biology of Theileria parva and control of East Coast fever - Current status and future trends. , 2016, Ticks and tick-borne diseases.

[30]  Mario Roederer,et al.  Protection against malaria at 1 year and immune correlates following PfSPZ vaccination , 2016, Nature Medicine.

[31]  M. Nielsen,et al.  NetMHCpan-3.0; improved prediction of binding to MHC class I molecules integrating information from multiple receptor and peptide length datasets , 2016, Genome Medicine.

[32]  Nicholas P. J. Day,et al.  Genomic epidemiology of artemisinin resistant malaria. , 2016, eLife.

[33]  E. Kamau,et al.  The Genotypic and Phenotypic Stability of Plasmodium falciparum Field Isolates in Continuous In Vitro Culture , 2016, PloS one.

[34]  Trevor Bedford,et al.  Genetic Diversity and Protective Efficacy of the RTS,S/AS01 Malaria Vaccine. , 2015, The New England journal of medicine.

[35]  Joana C. Silva,et al.  The genomes of three stocks comprising the most widely utilized live sporozoite Theileria parva vaccine exhibit very different degrees and patterns of sequence divergence , 2015, BMC Genomics.

[36]  D. Wirth,et al.  Adaptive evolution of malaria parasites in French Guiana: Reversal of chloroquine resistance by acquisition of a mutation in pfcrt , 2015, Proceedings of the National Academy of Sciences.

[37]  Jacqueline A. Keane,et al.  Circlator: automated circularization of genome assemblies using long sequencing reads , 2015, Genome Biology.

[38]  G. van Gemert,et al.  Heterologous Protection against Malaria after Immunization with Plasmodium falciparum Sporozoites , 2015, PloS one.

[39]  John C. Tan,et al.  Independent emergence of artemisinin resistance mutations among Plasmodium falciparum in Southeast Asia. , 2015, The Journal of infectious diseases.

[40]  Andrew R. Jones,et al.  Allele frequency net 2015 update: new features for HLA epitopes, KIR and disease and HLA adverse drug reaction associations , 2014, Nucleic Acids Res..

[41]  Christina A. Cuomo,et al.  Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement , 2014, PloS one.

[42]  A. Barry,et al.  Strategies for Designing and Monitoring Malaria Vaccines Targeting Diverse Antigens , 2014, Front. Immunol..

[43]  Samuel A. Assefa,et al.  A barcode of organellar genome polymorphisms identifies the geographic origin of Plasmodium falciparum strains , 2014, Nature Communications.

[44]  D. Kwiatkowski,et al.  A transcriptional switch underlies commitment to sexual development in human malaria parasites , 2014, Nature.

[45]  Mauricio O. Carneiro,et al.  From FastQ Data to High‐Confidence Variant Calls: The Genome Analysis Toolkit Best Practices Pipeline , 2013, Current protocols in bioinformatics.

[46]  Mario Roederer,et al.  Protection Against Malaria by Intravenous Immunization with a Nonreplicating Sporozoite Vaccine , 2013, Science.

[47]  Aaron A. Klammer,et al.  Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data , 2013, Nature Methods.

[48]  Gilean McVean,et al.  Multiple populations of artemisinin-resistant Plasmodium falciparum in Cambodia , 2013, Nature Genetics.

[49]  O. Doumbo,et al.  Molecular basis of allele-specific efficacy of a blood-stage malaria vaccine: vaccine development implications. , 2013, The Journal of infectious diseases.

[50]  S. Hoffman,et al.  NF135.C10: A New Plasmodium falciparum Clone for Controlled Human Malaria Infections , 2012, The Journal of infectious diseases.

[51]  S. Iwanaga,et al.  Identification of an AP2-family Protein That Is Critical for Malaria Liver Stage Development , 2012, PloS one.

[52]  John C. Tan,et al.  Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing , 2012, Nature.

[53]  Thomas S. Rask,et al.  Plasmodium falciparum erythrocyte membrane protein 1 domain cassettes 8 and 13 are associated with severe malaria in children , 2012, Proceedings of the National Academy of Sciences.

[54]  Sergey I. Nikolenko,et al.  SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing , 2012, J. Comput. Biol..

[55]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

[56]  F. Ayala,et al.  Multiple independent introductions of Plasmodium falciparum in South America , 2011, Proceedings of the National Academy of Sciences.

[57]  E. R. James,et al.  Live Attenuated Malaria Vaccine Designed to Protect Through Hepatic CD8+ T Cell Immunity , 2011, Science.

[58]  D. Higgins,et al.  Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega , 2011, Molecular systems biology.

[59]  Sean R. Eddy,et al.  Accelerated Profile HMM Searches , 2011, PLoS Comput. Biol..

[60]  O. Doumbo,et al.  A field trial to assess a blood-stage malaria vaccine. , 2011, The New England journal of medicine.

[61]  M. DePristo,et al.  A framework for variation discovery and genotyping using next-generation DNA sequencing data , 2011, Nature Genetics.

[62]  Thomas S. Rask,et al.  Plasmodium falciparum Erythrocyte Membrane Protein 1 Diversity in Seven Genomes – Divide and Conquer , 2010, PLoS Comput. Biol..

[63]  M. DePristo,et al.  The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. , 2010, Genome research.

[64]  May Ho,et al.  Plasmodium falciparum genome-wide scans for positive selection, recombination hot spots and resistance to antimalarial drugs , 2010, Nature Genetics.

[65]  Sumana Chakravarty,et al.  Development of a metabolically active, non-replicating sporozoite vaccine to prevent Plasmodium falciparum malaria , 2010, Human vaccines.

[66]  C. Plowe,et al.  Genetic diversity and malaria vaccine design, testing and efficacy: preventing and overcoming ‘vaccine resistant malaria’ , 2009, Parasite immunology.

[67]  David H. Alexander,et al.  Fast model-based estimation of ancestry in unrelated individuals. , 2009, Genome research.

[68]  C. Plowe.  The evolution of drug-resistant malaria. , 2009, Transactions of the Royal Society of Tropical Medicine and Hygiene.

[69]  M. Tanner,et al.  First generation leishmaniasis vaccines: a review of field efficacy trials. , 2008, Vaccine.

[70]  Joseph D. Smith,et al.  A family affair: var genes, PfEMP1 binding, and malaria disease. , 2006, Current opinion in microbiology.

[71]  Thomas D. Wu,et al.  GMAP: a genomic mapping and alignment program for mRNA and EST sequence , 2005, Bioinform..

[72]  G Thomson,et al.  Differentiation between African populations is evidenced by the diversity of alleles and haplotypes of HLA class I loci. , 2004, Tissue antigens.

[73]  Ruben Abagyan,et al.  Excess Polymorphisms in Genes for Membrane Proteins in Plasmodium falciparum , 2002, Science.

[74]  Jonathan E. Allen,et al.  Genome sequence of the human malaria parasite Plasmodium falciparum , 2002, Nature.

[75]  S. Meshnick,et al.  Epidemiology of drug-resistant malaria. , 2002, The Lancet. Infectious diseases.

[76]  S. Hoffman,et al.  The Complexity of Protective Immunity Against Liver-Stage Malaria1 2 , 2000, The Journal of Immunology.

[77]  S. Salzberg,et al.  Alignment of whole genomes. , 1999, Nucleic acids research.

[78]  R. Armijos,et al.  Field trial of a vaccine against New World cutaneous leishmaniasis in an at-risk child population: safety, immunogenicity, and efficacy during the first 12 months of follow-up. , 1998, The Journal of infectious diseases.

[79]  J. García-Pacheco,et al.  HLA class I and class II allele distribution in the Bubi population from the island of Bioko (Equatorial Guinea). , 1997, Tissue antigens.

[80]  D. Conway,et al.  Geographical distribution of a variant epitope of Pfs48/45, a Plasmodium falciparum transmission-blocking vaccine candidate. , 1996, Molecular and biochemical parasitology.

[81]  L. BenMohamed,et al.  Plasmodium falciparum liver stage antigen-1 is well conserved and contains potent B and T cell determinants. , 1994, Journal of immunology.

[82]  M. Good,et al.  CD8+ T cells (cytotoxic/suppressors) are required for protection in mice immunized with malaria sporozoites. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[83]  V. Nussenzweig,et al.  γ Interferon, CD8+ T cells and antibodies required for immunity to malaria sporozoites , 1987, Nature.

[84]  G. Langsley,et al.  A liver-stage-specific antigen of Plasmodium falciparum characterized by gene cloning , 1987, Nature.

[85]  T. Burkot,et al.  Genetic analysis of the human malaria parasite Plasmodium falciparum. , 1987, Science.

[86]  D. Bj,et al.  Tropical malaria contracted the natural way in the Netherlands , 1979 .

[87]  W. Trager,et al.  Human malaria parasites in continuous culture. , 1976, Science.