(Q24633552)

English

Whole genome sequencing of multiple Leishmania donovani clinical isolates provides insights into population structure and mechanisms of drug resistance

scientific article

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scholarly article

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Whole genome sequencing of multiple Leishmania donovani clinical isolates provides insights into population structure and mechanisms of drug resistance (English)

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multiple drug resistance

1 reference

based on heuristic

inferred from title

population structure

1 reference

based on heuristic

inferred from title

Leishmania donovani

object named as

Leishmania donovani

1 reference

based on heuristic

inferred from title

Matthew Berriman

20

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Manu Vanaerschot

17

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Saskia Decuypere

3

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13

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Christiane Hertz-Fowler

18

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object named as

Hideo Imamura

2

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James A. Cotton

object named as

James A Cotton

6

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Jeremy C. Mottram

object named as

Jeremy C Mottram

10

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16

object named as

Shyam Sundar

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author name string

Tim Downing

1

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Taane G Clark

4

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Graham H Coombs

5

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James D Hilley

7

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Simonne de Doncker

8

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Ilse Maes

9

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Mike A Quail

11

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Suman Rijal

12

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Gabriele Schönian

14

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Olivia Stark

15

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Jean-Claude Dujardin

19

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language of work or name

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publication date

December 2011

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Genome Research

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21

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2143-56

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12

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"Everything you always wanted to know about sex (but were afraid to ask)" in Leishmania after two decades of laboratory and field analyses

1 reference

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The evolution of amastin surface glycoproteins in trypanosomatid parasites

1 reference

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Quantitative prediction of molecular clock and ka/ks at short timescales

1 reference

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7 April 2017

Mechanisms of change in gene copy number

1 reference

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7 April 2017

Fast statistical alignment

1 reference

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7 April 2017

Comparative genomic analysis of three Leishmania species that cause diverse human disease

1 reference

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7 April 2017

Evolutionary and geographical history of the Leishmania donovani complex with a revision of current taxonomy

1 reference

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7 April 2017

The genome of the kinetoplastid parasite, Leishmania major

1 reference

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A2 gene of Old World cutaneous Leishmania is a single highly conserved functional gene

1 reference

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7 April 2017

Versatile and open software for comparing large genomes

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7 April 2017

BLAT—The BLAST-Like Alignment Tool

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7 April 2017

Formation of extrachromosomal circular amplicons with direct or inverted duplications in drug-resistant Leishmania tarentolae

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Statistical method for testing the neutral mutation hypothesis by DNA polymorphism

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Fundamental concepts in genetics: Effective population size and patterns of molecular evolution and variation

1 reference

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Basic local alignment search tool

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The Sequence Alignment/Map format and SAMtools

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7 April 2017

PAML 4: phylogenetic analysis by maximum likelihood

1 reference

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TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing

1 reference

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7 April 2017

Artemis: sequence visualization and annotation

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7 April 2017

Median-joining networks for inferring intraspecific phylogenies

1 reference

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7 April 2017

PAML: a program package for phylogenetic analysis by maximum likelihood

1 reference

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7 April 2017

Prediction of complete gene structures in human genomic DNA

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Identification of common molecular subsequences

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7 April 2017

Metabolomics to unveil and understand phenotypic diversity between pathogen populations

1 reference

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7 April 2017

Long- and short-term selective forces on malaria parasite genomes

1 reference

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7 April 2017

Linking in vitro and in vivo survival of clinical Leishmania donovani strains

1 reference

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7 April 2017

The neutral theory of molecular evolution in the genomic era

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Genetics in geographically structured populations: defining, estimating and interpreting F(ST)

1 reference

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7 April 2017

KaKs_Calculator: calculating Ka and Ks through model selection and model averaging

1 reference

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7 April 2017

Dual action of antimonial drugs on thiol redox metabolism in the human pathogen Leishmania donovani

1 reference

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7 April 2017

Genomic mapping by fingerprinting random clones: a mathematical analysis

1 reference

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Adaptive protein evolution at the Adh locus in Drosophila

1 reference

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7 April 2017

On the number of segregating sites in genetical models without recombination

1 reference

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7 April 2017

Positive selection at the protein network periphery: Evaluation in terms of structural constraints and cellular context

1 reference

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7 April 2017

A greedy algorithm for aligning DNA sequences

1 reference

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7 April 2017

Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection

1 reference

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7 April 2017

Evolutionary relationship of DNA sequences in finite populations

1 reference

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7 April 2017

The genetical structure of populations

1 reference

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7 April 2017

ACT: the Artemis Comparison Tool

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7 April 2017

SSAHA: a fast search method for large DNA databases

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7 April 2017

Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene

1 reference

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7 April 2017

Chromosome and gene copy number variation allow major structural change between species and strains of Leishmania

1 reference

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27 September 2017

Inference of population structure of Leishmania donovani strains isolated from different Ethiopian visceral leishmaniasis endemic areas

1 reference

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27 September 2017

Recent and recurrent selective sweeps of the antiviral RNAi gene Argonaute-2 in three species of Drosophila

1 reference

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27 September 2017

Shifts in the intensity of purifying selection: an analysis of genome-wide polymorphism data from two closely related yeast species

1 reference

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27 September 2017

Comparison of gene expression patterns among Leishmania braziliensis clinical isolates showing a different in vitro susceptibility to pentavalent antimony

1 reference

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27 September 2017

The population genetics of antibiotic resistance: integrating molecular mechanisms and treatment contexts.

1 reference

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27 September 2017

Improving draft assemblies by iterative mapping and assembly of short reads to eliminate gaps

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27 September 2017

High quality SNP calling using Illumina data at shallow coverage.

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27 September 2017

Development and evaluation of different PCR-based typing methods for discrimination of Leishmania donovani isolates from Nepal

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Temperature increase prevails over acidification in gene expression modulation of amastigote differentiation in Leishmania infantum

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27 September 2017

Estimation of allele frequencies from high-coverage genome-sequencing projects

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27 September 2017

Protein evolution on a human signaling network

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27 September 2017

Gene expression modulation is associated with gene amplification, supernumerary chromosomes and chromosome loss in antimony-resistant Leishmania infantum.

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27 September 2017

Structure, dynamics and function of Leishmania genome: resolving the puzzle of infection, genetics and evolution?

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27 September 2017

In vitro susceptibility of field isolates of Leishmania donovani to Miltefosine and amphotericin B: correlation with sodium antimony gluconate susceptibility and implications for treatment in areas of endemicity

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Population genetic inference from resequencing data

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27 September 2017

Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database

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Assessing the feasibility of GS FLX Pyrosequencing for sequencing the Atlantic salmon genome

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27 September 2017

Multiple origins of resistance-conferring mutations in Plasmodium vivax dihydrofolate reductase

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27 September 2017

Roles of trypanothione S-transferase and tryparedoxin peroxidase in resistance to antimonials

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27 September 2017

Increased levels of thiols protect antimony unresponsive Leishmania donovani field isolates against reactive oxygen species generated by trivalent antimony

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27 September 2017

Major changes in our DNA lead to major changes in our thinking

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27 September 2017

Leishmania MAP kinases--familiar proteins in an unusual context

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27 September 2017

Proteophosphoglycan is differentially expressed in sodium stibogluconate-sensitive and resistant Indian clinical isolates of Leishmania donovani

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27 September 2017

Adaptive evolution in humans revealed by the negative correlation between the polymorphism and fixation phases of evolution

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27 September 2017

Differential gene expression analysis in antimony-unresponsive Indian kala azar (visceral leishmaniasis) clinical isolates by DNA microarray.

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27 September 2017

Epidemiological dynamics of antimonial resistance in Leishmania donovani: genotyping reveals a polyclonal population structure among naturally-resistant clinical isolates from Nepal

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27 September 2017

The evolution and diversity of kinetoplastid flagellates.

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27 September 2017

Gene expression analysis of the mechanism of natural Sb(V) resistance in Leishmania donovani isolates from Nepal

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27 September 2017

MAVID: constrained ancestral alignment of multiple sequences

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27 September 2017

Inference of selection from multiple species alignments

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27 September 2017

Adaptive protein evolution in Drosophila

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27 September 2017

How to succeed in parasitic life without sex? Asking Leishmania

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27 September 2017

Leishmania infection and virulence

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27 September 2017

Statistical tests of selective neutrality in the age of genomics

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27 September 2017

Point mutations in a nucleoside transporter gene from Leishmania donovani confer drug resistance and alter substrate selectivity

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27 September 2017

High-throughput development and characterization of a genomewide collection of gene-based single nucleotide polymorphism markers by chip-based matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

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27 September 2017

The molecular evolution of Trypanosomatidae

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27 September 2017

The unusual gene organization of Leishmania major chromosome 1 may reflect novel transcription processes

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27 September 2017

Size-polymorphism of mini-exon gene-bearing chromosomes among natural populations of Leishmania, subgenus Viannia.

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27 September 2017

Leishmania major Friedlin chromosome 1 has an unusual distribution of protein-coding genes

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27 September 2017

Gene amplification in Leishmania tarentolae selected for resistance to sodium stibogluconate.

1 reference

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27 September 2017

Relation between variation in copy number of ribosomal RNA encoding genes and size of harbouring chromosomes in Leishmania of subgenus Viannia.

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27 September 2017

Plasticity in chromosome number and testing of essential genes in Leishmania by targeting

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27 September 2017

Resistance of leishmanial phosphatases to inactivation by oxygen metabolites

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27 September 2017

RATT: Rapid Annotation Transfer Tool

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30 May 2018

Iterative Correction of Reference Nucleotides (iCORN) using second generation sequencing technology

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30 May 2018

Elevated levels of tryparedoxin peroxidase in antimony unresponsive Leishmania donovani field isolates

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3227103

30 May 2018

ABACAS: algorithm-based automatic contiguation of assembled sequences

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30 May 2018

Characterization of an ABCG-like transporter from the protozoan parasite Leishmania with a role in drug resistance and transbilayer lipid movement

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3227103

30 May 2018

Modulation of gene expression in drug resistant Leishmania is associated with gene amplification, gene deletion and chromosome aneuploidy.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3227103

30 May 2018

A comparative study of type I and type II tryparedoxin peroxidases in Leishmania major

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3227103

30 May 2018

Comparison of the A2 gene locus in Leishmania donovani and Leishmania major and its control over cutaneous infection.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3227103

30 May 2018

Changing effective population size and the McDonald-Kreitman test

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3227103

30 May 2018

A2rel: a constitutively expressed Leishmania gene linked to an amastigote-stage-specific gene

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3227103

30 May 2018

Ranking procedures for arbitrarily restricted observation.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3227103

30 May 2018

Detection of extrachromosomal circular DNA sequences from tumor cells by an alkaline lysis, Alu-polymerase chain reaction technique

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3227103

30 May 2018

Estimation of the neutrality index.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3227103

28 November 2018

Epidemiology of Leishmania donovani infection in high-transmission foci in Nepal

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3227103

28 November 2018

Overexpression of histone H2A modulates drug susceptibility in Leishmania parasites

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3227103

28 November 2018

Assessing aquaglyceroporin gene status and expression profile in antimony-susceptible and -resistant clinical isolates of Leishmania donovani from India

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3227103

28 November 2018

Role of a differentially expressed cAMP phosphodiesterase in regulating the induction of resistance against oxidative damage in Leishmania donovani.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3227103

28 November 2018

Intracellular localization of the ABCC proteins of Leishmania and their role in resistance to antimonials

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3227103

28 November 2018

Quantification of adaptive evolution of genes expressed in avian brain and the population size effect on the efficacy of selection.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3227103

28 November 2018

Multilocus microsatellite typing (MLMT) reveals genetic homogeneity of Leishmania donovani strains in the Indian subcontinent.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3227103

28 November 2018

A Leishmania infantum cytosolic tryparedoxin activates B cells to secrete interleukin-10 and specific immunoglobulin

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3227103

28 November 2018

Aligning multiple whole genomes with Mercator and MAVID.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3227103

28 November 2018

Dynamic evolution of the innate immune system in Drosophila.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3227103

28 November 2018

Gene expression profiling of Leishmania (Leishmania) donovani: overcoming technical variation and exploiting biological variation.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3227103

28 November 2018

Antimonial treatment of visceral leishmaniasis: are current in vitro susceptibility assays adequate for prognosis of in vivo therapy outcome?

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3227103

28 November 2018

From genome to vaccines for leishmaniasis: Screening 100 novel vaccine candidates against murine Leishmania major infection

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3227103

28 November 2018

Two linked genes of Leishmania infantum encode tryparedoxins localised to cytosol and mitochondrion.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3227103

28 November 2018

Antigen genes for molecular epidemiology of leishmaniasis: polymorphism of cysteine proteinase B and surface metalloprotease glycoprotein 63 in the Leishmania donovani complex

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3227103

28 November 2018

Characterization of the A2-A2rel gene cluster in Leishmania donovani: involvement of A2 in visceralization during infection.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3227103

28 November 2018

A new developmentally regulated gene family in Leishmania amastigotes encoding a homolog of amastin surface proteins.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3227103

28 November 2018

Leishmania: amastigotes synthesize conserved secretory acid phosphatases during human infection.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3227103

28 November 2018

Antigenic variation in syringe passaged populations of Trypanosoma (Trypanozoon) brucei. 1. Rationalization of the experimental approach

1 reference

https://pubmed.ncbi.nlm.nih.gov/22038251

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

IL-10 from regulatory T cells determines vaccine efficacy in murine Leishmania major infection

1 reference

https://pubmed.ncbi.nlm.nih.gov/22038251

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

FISH analysis reveals aneuploidy and continual generation of chromosomal mosaicism in Leishmania major

1 reference

https://pubmed.ncbi.nlm.nih.gov/22038251

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Who believes in whole-genome scans for selection?

1 reference

https://pubmed.ncbi.nlm.nih.gov/22038251

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1101/GR.123430.111

1 reference

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

OpenCitations bibliographic resource ID

1 reference

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

1 reference

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

1 reference

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

ResearchGate publication ID

0 references

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