The Malaria Cell Atlas: Single parasite transcriptomes across the complete Plasmodium life cycle

DoubletFinder: Doublet Detection in Single-Cell RNA Sequencing Data Using Artificial Nearest Neighbors

(2019) Christopher S. McGinnis et al.   Cell Systems

Complete avian malaria parasite genomes reveal features associated with lineage-specific evolution in birds and mammals

(2018) Ulrike Böhme et al.   GENOME RESEARCH

Integrating single-cell transcriptomic data across different conditions, technologies, and species

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

scmap: projection of single-cell RNA-seq data across data sets

(2018) Vladimir Yu Kiselev et al.   NATURE METHODS

Cell type transcriptome atlas for the planarianSchmidtea mediterranea

(2018) Christopher T. Fincher et al.   SCIENCE

Integrated pathogen load and dual transcriptome analysis of systemic host-pathogen interactions in severe malaria

(2018) Hyun Jae Lee et al.   Science Translational Medicine

A comprehensive evaluation of module detection methods for gene expression data

(2018) Wouter Saelens et al.   Nature Communications

Genome-wide real-time in vivo transcriptional dynamics during Plasmodium falciparum blood-stage development

(2018) Heather J. Painter et al.   Nature Communications

Single-cell RNA-seq reveals hidden transcriptional variation in malaria parasites

(2018) Adam J Reid et al.   eLife

RNA velocity of single cells

(2018) Gioele La Manno et al.   NATURE

M3Drop: dropout-based feature selection for scRNASeq

(2018) Tallulah S Andrews et al.   BIOINFORMATICS

Single-cell RNA sequencing reveals a signature of sexual commitment in malaria parasites

(2017) Asaf Poran et al.   NATURE

SC3: consensus clustering of single-cell RNA-seq data

(2017) Vladimir Yu Kiselev et al.   NATURE METHODS

Massively parallel digital transcriptional profiling of single cells

(2017) Grace X. Y. Zheng et al.   Nature Communications

A novel genetic technique in Plasmodium berghei allows liver stage analysis of genes required for mosquito stage development and demonstrates that de novo heme synthesis is essential for liver stage development in the malaria parasite

(2017) Upeksha L. Rathnapala et al.   PLoS Pathogens

Antibody-independent mechanisms regulate the establishment of chronic Plasmodium infection

(2017) Thibaut Brugat et al.   Nature Microbiology

A Single-Cell Transcriptomic Map of the Human and Mouse Pancreas Reveals Inter- and Intra-cell Population Structure

(2016) Maayan Baron et al.   Cell Systems

Integrated analysis of the Plasmodium species transcriptome

(2016) Regina Hoo et al.   EBioMedicine

A Genome-Scale Vector Resource Enables High-Throughput Reverse Genetic Screening in a Malaria Parasite

(2015) Ana Rita Gomes et al.   Cell Host & Microbe

Processing of Plasmodium falciparum Merozoite Surface Protein MSP1 Activates a Spectrin-Binding Function Enabling Parasite Egress from RBCs

(2015) Sujaan Das et al.   Cell Host & Microbe

Plasmodium knowlesi gene expression differs in ex vivo compared to in vitro blood-stage cultures

(2015) Stacey A Lapp et al.   MALARIA JOURNAL

The Technology and Biology of Single-Cell RNA Sequencing

(2015) Aleksandra A. Kolodziejczyk et al.   MOLECULAR CELL

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

Plasmodium P-Type Cyclin CYC3 Modulates Endomitotic Growth during Oocyst Development in Mosquitoes

(2015) Magali Roques et al.   PLoS Pathogens

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

(2015) Izumi Kaneko et al.   PLoS Pathogens

A Plasmodium Phospholipase Is Involved in Disruption of the Liver Stage Parasitophorous Vacuole Membrane

(2015) Paul-Christian Burda et al.   PLoS Pathogens

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

A comprehensive evaluation of rodent malaria parasite genomes and gene expression

(2014) Thomas D Otto et al.   BMC BIOLOGY

Genetic crosses and complementation reveal essential functions for thePlasmodiumstage-specific actin2 in sporogonic development

(2014) Maria Andreadaki et al.   CELLULAR MICROBIOLOGY

In Vitro Alterations Do Not Reflect a Requirement for Host Cell Cycle Progression during Plasmodium Liver Stage Infection

(2014) Kirsten K. Hanson et al.   EUKARYOTIC CELL

Proteomic analysis of the Plasmodium male gamete reveals the key role for glycolysis in flagellar motility

(2014) Arthur M Talman et al.   MALARIA JOURNAL

The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

ForceAtlas2, a Continuous Graph Layout Algorithm for Handy Network Visualization Designed for the Gephi Software

(2014) Mathieu Jacomy et al.   PLoS One

Silence, activate, poise and switch! Mechanisms of antigenic variation inPlasmodium falciparum

(2013) Julien Guizetti et al.   CELLULAR MICROBIOLOGY

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Transcriptional variation in the malaria parasite Plasmodium falciparum

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

Adaptation of the genetically tractable malaria pathogen Plasmodium knowlesi to continuous culture in human erythrocytes

(2012) R. W. Moon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Coordinating genome expression with cell size

(2012) Samuel Marguerat et al.   TRENDS IN GENETICS

Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data

(2011) T. Carver et al.   BIOINFORMATICS

DREME: motif discovery in transcription factor ChIP-seq data

(2011) Timothy L. Bailey   BIOINFORMATICS

Directional gene expression and antisense transcripts in sexual and asexual stages of Plasmodium falciparum

(2011) María J López-Barragán et al.   BMC GENOMICS

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

NWChem: A comprehensive and scalable open-source solution for large scale molecular simulations

(2010) M. Valiev et al.   COMPUTER PHYSICS COMMUNICATIONS

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

A scaling normalization method for differential expression analysis of RNA-seq data

(2010) Mark D Robinson et al.   GENOME BIOLOGY

Egress ofPlasmodium bergheigametes from their host erythrocyte is mediated by the MDV-1/PEG3 protein

(2009) Marta Ponzi et al.   CELLULAR MICROBIOLOGY

LISP1 is important for the egress ofPlasmodium bergheiparasites from liver cells

(2009) Tomoko Ishino et al.   CELLULAR MICROBIOLOGY

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

(2009) Iwanka Kozarewa et al.   NATURE METHODS

In silico discovery of transcription regulatory elements in Plasmodium falciparum

(2008) Jason A Young et al.   BMC GENOMICS

The conserved plant sterility gene HAP2 functions after attachment of fusogenic membranes in Chlamydomonas and Plasmodium gametes

(2008) Y. Liu et al.   GENES & DEVELOPMENT

PlasmoDB: a functional genomic database for malaria parasites

(2008) C. Aurrecoechea et al.   NUCLEIC ACIDS RESEARCH