DNA-binding protein PfAP2-P regulates parasite pathogenesis during malaria parasite blood stages

Genome-wide landscape of ApiAP2 transcription factors reveals a heterochromatin-associated regulatory network during Plasmodium falciparum blood-stage development

(2022) Xiaomin Shang et al.   NUCLEIC ACIDS RESEARCH

Novel insights from the Plasmodium falciparum sporozoite-specific proteome by probabilistic integration of 26 studies

(2021) Lisette Meerstein-Kessel et al.   PLoS Computational Biology

Integrated analysis of multimodal single-cell data

(2021) Yuhan Hao et al.   CELL

A single-cell atlas of Plasmodium falciparum transmission through the mosquito

(2021) Eliana Real et al.   Nature Communications

A heat-shock response regulated by the PfAP2-HS transcription factor protects human malaria parasites from febrile temperatures

(2021) Elisabet Tintó-Font et al.   Nature Microbiology

Real-time dynamics of Plasmodium NDC80 reveals unusual modes of chromosome segregation during parasite proliferation

(2020) Mohammad Zeeshan et al.   JOURNAL OF CELL SCIENCE

Dissecting the role of PfAP2-G in malaria gametocytogenesis

(2020) Gabrielle A. Josling et al.   Nature Communications

Malaria parasites regulate intra-erythrocytic development duration via serpentine receptor 10 to coordinate with host rhythms

(2020) Amit K. Subudhi et al.   Nature Communications

Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage

(2019) Dvir Aran et al.   NATURE IMMUNOLOGY

CHETAH: a selective, hierarchical cell type identification method for single-cell RNA sequencing

(2019) Jurrian K de Kanter et al.   NUCLEIC ACIDS RESEARCH

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

(2019) Virginia M. Howick et al.   SCIENCE

Identification of essential exportedPlasmodium falciparumprotein kinases in malaria‐infected red blood cells

(2019) Ghizal Siddiqui et al.   BRITISH JOURNAL OF HAEMATOLOGY

Comparative Heterochromatin Profiling Reveals Conserved and Unique Epigenome Signatures Linked to Adaptation and Development of Malaria Parasites

(2018) Sabine A. Fraschka et al.   Cell Host & Microbe

Chromatin Accessibility-Based Characterization of the Gene Regulatory Network Underlying Plasmodium falciparum Blood-Stage Development

(2018) Christa Geeke Toenhake et al.   Cell Host & Microbe

Uncovering the essential genes of the human malaria parasitePlasmodium falciparumby saturation mutagenesis

(2018) Min Zhang et al.   SCIENCE

A Specific PfEMP1 Is Expressed in P. falciparum Sporozoites and Plays a Role in Hepatocyte Infection

(2018) Gigliola Zanghì et al.   Cell Reports

A protease cascade regulates release of the human malaria parasite Plasmodium falciparum from host red blood cells

(2018) James A. Thomas et al.   Nature Microbiology

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

(2017) Asaf Poran et al.   NATURE

UCSF ChimeraX: Meeting modern challenges in visualization and analysis

(2017) Thomas D. Goddard et al.   PROTEIN SCIENCE

Generating conditional gene knockouts in Plasmodium – a toolkit to produce stable DiCre recombinase-expressing parasite lines using CRISPR/Cas9

(2017) Ellen Knuepfer et al.   Scientific Reports

Molecular Signaling Involved in Entry and Exit of Malaria Parasites from Host Erythrocytes

(2017) Shailja Singh et al.   Cold Spring Harbor Perspectives in Medicine

Malaria Epigenetics

(2017) Alfred Cortés et al.   Cold Spring Harbor Perspectives in Medicine

Cyclic nucleotide signalling in malaria parasites

(2017) David A. Baker et al.   Open Biology

A versatile strategy for rapid conditional genome engineering using loxP sites in a small synthetic intron in Plasmodium falciparum

(2016) Matthew L. Jones et al.   Scientific Reports

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

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

Profiling the Essential Nature of Lipid Metabolism in Asexual Blood and Gametocyte Stages of Plasmodium falciparum

(2015) Sonia Gulati et al.   Cell Host & Microbe

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

Sexual development in Plasmodium parasites: knowing when it's time to commit

(2015) Gabrielle A. Josling et al.   NATURE REVIEWS MICROBIOLOGY

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

A statistical approach for inferring the 3D structure of the genome

(2014) N. Varoquaux et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

(2014) Suhas S.P. Rao et al.   CELL

Surface antigens of Plasmodium falciparum-infected erythrocytes as immune targets and malaria vaccine candidates

(2014) Jo-Anne Chan et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

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

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

PfSETvs methylation of histone H3K36 represses virulence genes in Plasmodium falciparum

(2013) Lubin Jiang et al.   NATURE

Malaria Parasite cGMP-dependent Protein Kinase Regulates Blood Stage Merozoite Secretory Organelle Discharge and Egress

(2013) Christine R. Collins et al.   PLoS Pathogens

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation

(2012) Davis J. McCarthy et al.   NUCLEIC ACIDS RESEARCH

Identification of an AP2-family Protein That Is Critical for Malaria Liver Stage Development

(2012) Shiroh Iwanaga et al.   PLoS One

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

DREME: motif discovery in transcription factor ChIP-seq data

(2011) Timothy L. Bailey   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Intravenous immunoglobulin in the treatment of paediatric cerebral malaria

(2010) T. E. TAYLOR et al.   CLINICAL AND EXPERIMENTAL IMMUNOLOGY

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

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

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

Plasmodium falciparum heterochromatin protein 1 binds to tri-methylated histone 3 lysine 9 and is linked to mutually exclusive expression of var genes

(2009) K. Perez-Toledo et al.   NUCLEIC ACIDS RESEARCH

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

(2009) Christian Flueck et al.   PLoS Pathogens

Antigenic Variation in Plasmodium falciparum

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

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY