Epigenetic regulation of Plasmodium falciparum clonally variant gene expression during development in Anopheles gambiae

Epigenetics, cellular memory and gene regulation

(2016) Steven Henikoff et al.   CURRENT BIOLOGY

Landscape and Dynamics of Transcription Initiation in the Malaria Parasite Plasmodium falciparum

(2016) Sophie H. Adjalley et al.   Cell Reports

Mosquito Passage Dramatically Changes var Gene Expression in Controlled Human Plasmodium falciparum Infections

(2016) Anna Bachmann et al.   PLoS Pathogens

Comparison of genomic signatures of selection on Plasmodium falciparum between different regions of a country with high malaria endemicity

(2015) Craig W. Duffy et al.   BMC GENOMICS

Experimental study of the relationship between Plasmodium gametocyte density and infection success in mosquitoes; implications for the evaluation of malaria transmission-reducing interventions

(2015) Dari F. Da et al.   EXPERIMENTAL PARASITOLOGY

The kdr-bearing haplotype and susceptibility to Plasmodium falciparum in Anopheles gambiae: genetic correlation and functional testing

(2015) Christian Mitri et al.   MALARIA JOURNAL

Histone exchange, chromatin structure and the regulation of transcription

(2015) Swaminathan Venkatesh et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

The nucleosome landscape ofPlasmodium falciparumreveals chromatin architecture and dynamics of regulatory sequences

(2015) Philip Reiner Kensche et al.   NUCLEIC ACIDS RESEARCH

The MEME Suite

(2015) Timothy L. Bailey et al.   NUCLEIC ACIDS RESEARCH

Antisense long noncoding RNAs regulatevargene activation in the malaria parasitePlasmodium falciparum

(2015) Inbar Amit-Avraham et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Antibiotics in ingested human blood affect the mosquito microbiota and capacity to transmit malaria

(2015) Mathilde Gendrin et al.   Nature Communications

Genome-Wide Identification of the Target Genes of AP2-O, a Plasmodium AP2-Family Transcription Factor

(2015) Izumi Kaneko et al.   PLoS Pathogens

Mosquitoes Reset Malaria Parasites

(2015) Philip J. Spence et al.   PLoS Pathogens

Multiple dimensions of epigenetic gene regulation in the malaria parasite Plasmodium falciparum

(2014) Ferhat Ay et al.   BIOESSAYS

ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases

(2014) Li Shen et al.   BMC GENOMICS

A Plasmodium falciparum Histone Deacetylase Regulates Antigenic Variation and Gametocyte Conversion

(2014) Bradley I. Coleman et al.   Cell Host & Microbe

Characterization ofPlasmodiumdevelopmental transcriptomes inAnopheles gambiaemidgut reveals novel regulators of malaria transmission

(2014) Karolina A. Akinosoglou et al.   CELLULAR MICROBIOLOGY

A heavy legacy: offspring of malaria-infected mosquitoes show reduced disease resistance

(2014) Amélie Vantaux et al.   MALARIA JOURNAL

A cascade of DNA-binding proteins for sexual commitment and development in Plasmodium

(2014) Abhinav Sinha et al.   NATURE

Exonuclease-mediated degradation of nascent RNA silences genes linked to severe malaria

(2014) Qingfeng Zhang et al.   NATURE

A transcriptional switch underlies commitment to sexual development in malaria parasites

(2014) Björn F. C. Kafsack et al.   NATURE

deepTools: a flexible platform for exploring deep-sequencing data

(2014) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Insecticide exposure impacts vector-parasite interactions in insecticide-resistant malaria vectors

(2014) H. Alout et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Global target mRNA specification and regulation by the RNA-binding protein ZFP36

(2014) Neelanjan Mukherjee et al.   GENOME BIOLOGY

Multiplexed Illumina sequencing libraries from picogram quantities of DNA

(2013) Sarah K Bowman et al.   BMC GENOMICS

Epigenetic regulation of the Plasmodium falciparum genome

(2013) M. F. Duffy et al.   Briefings in Functional Genomics

Perturbations ofPlasmodium Puf2 expression and RNA-seq of Puf2-deficient sporozoites reveal a critical role in maintaining RNA homeostasis and parasite transmissibility

(2013) Scott E. Lindner et al.   CELLULAR MICROBIOLOGY

Mosquito transmission, growth phenotypes and the virulence of malaria parasites

(2013) Laura C Pollitt et al.   MALARIA JOURNAL

Vector transmission regulates immune control of Plasmodium virulence

(2013) Philip J. Spence et al.   NATURE

Anopheles coluzzii and Anopheles amharicus, new members of the Anopheles gambiae complex

(2013) MAUREEN COETZEE et al.   ZOOTAXA

Correction: The Neonatal Fc Receptor (FcRn) Enhances Human Immunodeficiency Virus Type 1 (HIV-1) Transcytosis across Epithelial Cells

(2013) Sandeep Gupta et al.   PLoS Pathogens

Optimizing illumina next-generation sequencing library preparation for extremely at-biased genomes

(2012) Samuel O Oyola et al.   BMC GENOMICS

PfSET10, a Plasmodium falciparum Methyltransferase, Maintains the Active var Gene in a Poised State during Parasite Division

(2012) Jennifer C. Volz et al.   Cell Host & Microbe

Transcriptional variation in the malaria parasite Plasmodium falciparum

(2012) N. Rovira-Graells et al.   GENOME RESEARCH

Detecting differential usage of exons from RNA-seq data

(2012) S. Anders et al.   GENOME RESEARCH

Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing

(2012) Magnus Manske et al.   NATURE

Identifying ChIP-seq enrichment using MACS

(2012) Jianxing Feng et al.   Nature Protocols

Predicting the effects of frameshifting indels

(2012) Jing Hu et al.   GENOME BIOLOGY

Positive Selection of Plasmodium falciparum Parasites With Multiple var2csa-Type PfEMP1 Genes During the Course of Infection in Pregnant Women

(2011) Adam F. Sander et al.   JOURNAL OF INFECTIOUS DISEASES

Heterochromatin formation in bistable chromatin domains controls the epigenetic repression of clonally variant Plasmodium falciparum genes linked to erythrocyte invasion

(2011) Valerie M. Crowley et al.   MOLECULAR MICROBIOLOGY

Histone H3 lysine 9 trimethylation and HP1γ favor inclusion of alternative exons

(2011) Violaine Saint-André et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

RNA-Seq analysis of splicing in Plasmodium falciparum uncovers new splice junctions, alternative splicing and splicing of antisense transcripts

(2011) K. Sorber et al.   NUCLEIC ACIDS RESEARCH

Malaria antifolate resistance with contrasting Plasmodium falciparum dihydrofolate reductase (DHFR) polymorphisms in humans and Anopheles mosquitoes

(2011) S. Mharakurwa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Histone modification: cause or cog?

(2011) Steven Henikoff et al.   TRENDS IN GENETICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

SOPRA: Scaffolding algorithm for paired reads via statistical optimization

(2010) Adel Dayarian et al.   BMC BIOINFORMATICS

The Apicomplexan AP2 family: Integral factors regulating Plasmodium development

(2010) Heather J. Painter et al.   MOLECULAR AND BIOCHEMICAL PARASITOLOGY

Identification and Genome-Wide Prediction of DNA Binding Specificities for the ApiAP2 Family of Regulators from the Malaria Parasite

(2010) Tracey L. Campbell et al.   PLoS Pathogens

H2A.Z Demarcates Intergenic Regions of the Plasmodium falciparum Epigenome That Are Dynamically Marked by H3K9ac and H3K4me3

(2010) Richárd Bártfai et al.   PLoS Pathogens

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Genome-wide Analysis of Heterochromatin Associates Clonally Variant Gene Regulation with Perinuclear Repressive Centers in Malaria Parasites

(2009) Jose-Juan Lopez-Rubio et al.   Cell Host & Microbe

Plasmodium falciparum genotypes diversity in symptomatic malaria of children living in an urban and a rural setting in Burkina Faso

(2009) Issiaka Soulama et al.   MALARIA JOURNAL

Identification of a transcription factor in the mosquito-invasive stage of malaria parasites

(2009) Masao Yuda et al.   MOLECULAR MICROBIOLOGY

Transcription factor AP2-Sp and its target genes in malarial sporozoites

(2009) Masao Yuda et al.   MOLECULAR MICROBIOLOGY

Dynamic histone H3 epigenome marking during the intraerythrocytic cycle of Plasmodium falciparum

(2009) A. M. Salcedo-Amaya et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2009) Christian Flueck et al.   PLoS Pathogens

Studying alternative splicing regulatory networks through partial correlation analysis

(2009) Liang Chen et al.   GENOME BIOLOGY

Antigenic Variation in Plasmodium falciparum

(2008) Artur Scherf et al.   Annual Review of Microbiology

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

Distinct Malaria Parasite Sporozoites Reveal Transcriptional Changes That Cause Differential Tissue Infection Competence in the Mosquito Vector and Mammalian Host

(2008) S. A. Mikolajczak et al.   MOLECULAR AND CELLULAR BIOLOGY

Specific DNA-binding by Apicomplexan AP2 transcription factors

(2008) E. K. De Silva et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Chromatin associated sense and antisense noncoding RNAs are transcribed from the var gene family of virulence genes of the malaria parasite Plasmodium falciparum

(2008) C. Epp et al.   RNA

Switching Plasmodium falciparum genes on and off for erythrocyte invasion

(2008) Alfred Cortés   TRENDS IN PARASITOLOGY

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

(2008) Edwin Lasonder et al.   PLoS Pathogens