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Genome variation and meiotic recombination in Plasmodium falciparum : insights from deep sequencing of genetic crosses

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Current Protocols in Bioinformatics

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Variable Numbers of Tandem Repeats in Plasmodium falciparum Genes

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Regulating double-stranded DNA break repair towards crossover or non-crossover during mammalian meiosis

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Mechanism and control of recombination in fungi

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Mutagenesis and comutagenesis by lead compounds

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An RFLP map of the Plasmodium falciparum genome, recombination rates and favored linkage groups in a genetic cross

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Proof of intragenic recombination in Plasmodium falciparum

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Erythrocyte Binding Protein PfRH5 Polymorphisms Determine Species-Specific Pathways of Plasmodium falciparum Invasion

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Distribution of meiotic recombination events: talking to your neighbors

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Analysis of malaria parasite phenotypes using experimental genetic crosses of Plasmodium falciparum

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Gene copy number and malaria biology

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Estimating genotyping error rates from Mendelian errors in SNP array genotypes and their impact on inference

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Sequence diversity and evolution of the malaria vaccine candidate merozoite surface protein-1 (MSP-1) of Plasmodium falciparum

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Chloroquine resistance not linked to mdr-like genes in a Plasmodium falciparum cross

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Frequent ectopic recombination of virulence factor genes in telomeric chromosome clusters of P. falciparum

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Genome sequence of the human malaria parasite Plasmodium falciparum

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High-resolution mapping of meiotic crossovers and non-crossovers in yeast

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Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing

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A molecular marker of artemisinin-resistant Plasmodium falciparum malaria

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De novo assembly and genotyping of variants using colored de Bruijn graphs

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Multiple populations of artemisinin-resistant Plasmodium falciparum in Cambodia

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A framework for variation discovery and genotyping using next-generation DNA sequencing data

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Intense and highly localized gene conversion activity in human meiotic crossover hot spots

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Genome variation and evolution of the malaria parasite Plasmodium falciparum

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Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes

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Plasmodium falciparum genetic crosses in a humanized mouse model

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Genetic linkage and association analyses for trait mapping in Plasmodium falciparum

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The role of replicates for error mitigation in next-generation sequencing

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Evolution of allelic dimorphism in malarial surface antigens

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Microsatellites: genomic distribution, putative functions and mutational mechanisms: a review

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Spread of Artemisinin Resistance in Plasmodium falciparum Malaria

inferredcites →https://doi.org/10.1073/pnas.88.8.3382openalex-snapshot

Genetic mapping of the chloroquine-resistance locus on Plasmodium falciparum chromosome 7.

inferredcites →https://doi.org/10.1073/pnas.91.3.1143openalex-snapshot

Selection for mefloquine resistance in Plasmodium falciparum is linked to amplification of the pfmdr1 gene and cross-resistance to halofantrine and quinine.

inferredcites →https://doi.org/10.1093/bioinformatics/btp324openalex-snapshot

Fast and accurate short read alignment with Burrows–Wheeler transform

inferredcites →https://doi.org/10.1093/gbe/evr045openalex-snapshot

Increased Polymorphism Near Low-Complexity Sequences across the Genomes of Plasmodium falciparum Isolates

inferredcites →https://doi.org/10.1093/genetics/137.4.1019openalex-snapshot

Meiotic gene conversion tract length distribution within the rosy locus of Drosophila melanogaster.

inferredcites →https://doi.org/10.1093/molbev/msl185openalex-snapshot

Recurrent Gene Amplification and Soft Selective Sweeps during Evolution of Multidrug Resistance in Malaria Parasites

inferredcites →https://doi.org/10.1093/molbev/msp063openalex-snapshot

Variation in the Ratio of Nucleotide Substitution and Indel Rates across Genomes in Mammals and Bacteria

inferredcites →https://doi.org/10.1093/molbev/msq108openalex-snapshot

Low-Complexity Regions in Plasmodium falciparum: Missing Links in the Evolution of an Extreme Genome

inferredcites →https://doi.org/10.1098/rspb.2012.1108openalex-snapshot

Gene duplication as a mechanism of genomic adaptation to a changing environment

inferredcites →https://doi.org/10.1099/vir.0.82402-0openalex-snapshot

Recombination and gene duplication in the evolutionary diversification of P1 proteins in the family Potyviridae

inferredcites →https://doi.org/10.1101/gr.093443.109openalex-snapshot

LookSeq: A browser-based viewer for deep sequencing data

inferredcites →https://doi.org/10.1101/gr.103663.109openalex-snapshot

Copy number variation, chromosome rearrangement, and their association with recombination during avian evolution

inferredcites →https://doi.org/10.1101/gr.107524.110openalex-snapshot

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

inferredcites →https://doi.org/10.1101/gr.148718.112openalex-snapshot

The origin, evolution, and functional impact of short insertion–deletion variants identified in 179 human genomes

inferredcites →https://doi.org/10.1111/cmi.12162openalex-snapshot

Epigenetic switches in clag3 genes mediate blasticidin S resistance in malaria parasites

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Encoded errors: mutations and rearrangements mediated by misalignment at repetitive DNA sequences

inferredcites →https://doi.org/10.1111/mmi.12162openalex-snapshot

Direct evidence for the adaptive role of copy number variation on antifolate susceptibility in P lasmodium falciparum

inferredcites →https://doi.org/10.1111/mmi.12349openalex-snapshot

The interplay between drug resistance and fitness in malaria parasites

inferredcites →https://doi.org/10.1111/mmi.12505openalex-snapshot

Structural polymorphism in the promoter of pfmrp2 confers P lasmodium falciparum tolerance to quinoline drugs

inferredcites →https://doi.org/10.1126/science.1117196openalex-snapshot

A Fine-Scale Map of Recombination Rates and Hotspots Across the Human Genome

inferredcites →https://doi.org/10.1126/science.286.5443.1351openalex-snapshot

A Genetic Map and Recombination Parameters of the Human Malaria Parasite Plasmodium falciparum

inferredcites →https://doi.org/10.1126/science.3299700openalex-snapshot

Genetic Analysis of the Human Malaria Parasite Plasmodium falciparum

inferredcites →https://doi.org/10.1186/1471-2164-12-116openalex-snapshot

High-throughput 454 resequencing for allele discovery and recombination mapping in Plasmodium falciparum

inferredcites →https://doi.org/10.1186/1471-2164-12-457openalex-snapshot

The landscape of inherited and de novo copy number variants in a plasmodium falciparum genetic cross

inferredcites →https://doi.org/10.1186/1471-2164-14-128openalex-snapshot

A Poisson hierarchical modelling approach to detecting copy number variation in sequence coverage data

inferredcites →https://doi.org/10.1186/gb-2008-9-12-r178openalex-snapshot

Core promoters are predicted by their distinct physicochemical properties in the genome of Plasmodium falciparum

inferredcites →https://doi.org/10.1186/gb-2011-12-4-r33openalex-snapshot

High recombination rates and hotspots in a Plasmodium falciparum genetic cross

inferredcites →https://doi.org/10.1186/gb-2013-14-9-r97openalex-snapshot

Assembly of a phased diploid Candida albicansgenome facilitates allele-specific measurements and provides a simple model for repeat and indel structure

inferredcites →https://doi.org/10.1186/s13073-014-0089-zopenalex-snapshot

Reducing INDEL calling errors in whole genome and exome sequencing data

inferredcites →https://doi.org/10.1242/jcs.074427openalex-snapshot

The choice in meiosis – defining the factors that influence crossover or non-crossover formation

inferredcites →https://doi.org/10.1371/journal.pbio.0060238openalex-snapshot

Regulatory Hotspots in the Malaria Parasite Genome Dictate Transcriptional Variation

inferredcites →https://doi.org/10.1371/journal.pgen.1000243openalex-snapshot

Adaptive Copy Number Evolution in Malaria Parasites

inferredcites →https://doi.org/10.1371/journal.pgen.1003293openalex-snapshot

Mitotic Evolution of Plasmodium falciparum Shows a Stable Core Genome but Recombination in Antigen Families

inferredcites →https://doi.org/10.1371/journal.pgen.1004812openalex-snapshot

Generation of Antigenic Diversity in Plasmodium falciparum by Structured Rearrangement of Var Genes During Mitosis

inferredcites →https://doi.org/10.1371/journal.ppat.0020057openalex-snapshot

A Systematic Map of Genetic Variation in Plasmodium falciparum

inferredcites →https://doi.org/10.1371/journal.ppat.1000195openalex-snapshot

Proteomic Profiling of Plasmodium Sporozoite Maturation Identifies New Proteins Essential for Parasite Development and Infectivity

inferredcites →https://doi.org/10.1371/journal.ppat.1000569openalex-snapshot

Plasmodium falciparum Heterochromatin Protein 1 Marks Genomic Loci Linked to Phenotypic Variation of Exported Virulence Factors

inferredcites →https://doi.org/10.1371/journal.ppat.1003488openalex-snapshot

Asparagine Repeats in Plasmodium falciparum Proteins: Good for Nothing?

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1007/978-3-319-43681-4_18openalex-snapshot

A Natural Encoding of Genetic Variation in a Burrows-Wheeler Transform to Enable Mapping and Genome Inference

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Non-human primate malaria parasites: out of the forest and into the laboratory

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Genomic analysis of local variation and recent evolution in Plasmodium vivax

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Genomics reveals heterogeneous Plasmodium falciparum transmission and selection signals in Zambia

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A GPU-accelerated compute framework for pathogen genomic variant identification to aid genomic epidemiology of infectious disease: a malaria case study

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Population Genomic Evidence of Adaptive Response during the Invasion History of Plasmodium falciparum in the Americas

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Detection of simple and complex de novo mutations without, with, or with multiple reference sequences

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Modeling the genetic relatedness of Plasmodium falciparum parasites following meiotic recombination and cotransmission

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