Refining the transcriptome of the human malaria parasite Plasmodium falciparum using amplification-free RNA-seq

ApiAP2 Transcription Factors in Apicomplexan Parasites

(2019) Myriam Jeninga et al.   Pathogens

Transcriptome profiling reveals functional variation in Plasmodium falciparum parasites from controlled human malaria infection studies

(2019) Regina Hoo et al.   EBioMedicine

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

Characterization of the accessible genome in the human malaria parasite Plasmodium falciparum

(2018) José Luis Ruiz et al.   NUCLEIC ACIDS RESEARCH

GDV1 induces sexual commitment of malaria parasites by antagonizing HP1-dependent gene silencing

(2018) Michael Filarsky et al.   SCIENCE

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

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

The Plasmodium falciparum transcriptome in severe malaria reveals altered expression of genes involved in important processes including surface antigen–encoding var genes

(2018) Gerry Q. Tonkin-Hill et al.   PLOS BIOLOGY

Global genetic diversity of var2csa in Plasmodium falciparum with implications for malaria in pregnancy and vaccine development

(2018) Ernest Diez Benavente et al.   Scientific Reports

A forward genetic screen reveals a primary role for Plasmodium falciparum Reticulocyte Binding Protein Homologue 2a and 2b in determining alternative erythrocyte invasion pathways

(2018) Susana Campino et al.   PLoS Pathogens

A new method for sequencing the hypervariable Plasmodium falciparum gene var2csa from clinical samples

(2017) Antoine Dara et al.   MALARIA JOURNAL

Functional 5′ UTR mRNA structures in eukaryotic translation regulation and how to find them

(2017) Kathrin Leppek et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Complete telomere-to-telomerede novoassembly of thePlasmodium falciparumgenome through long-read (>11 kb), single molecule, real-time sequencing

(2016) Shruthi Sridhar Vembar et al.   DNA RESEARCH

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

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

The impact of amplification on differential expression analyses by RNA-seq

(2016) Swati Parekh et al.   Scientific Reports

Strand-specific RNA sequencing in Plasmodium falciparum malaria identifies developmentally regulated long non-coding RNA and circular RNA

(2015) Kate M Broadbent et al.   BMC GENOMICS

A bioinformatic survey of RNA-binding proteins in Plasmodium

(2015) BP Niranjan Reddy et al.   BMC GENOMICS

A Plasmodium Falciparum Bromodomain Protein Regulates Invasion Gene Expression

(2015) Gabrielle A. Josling et al.   Cell Host & Microbe

Unmasking alternative splicing inside protein-coding exons defines exitrons and their role in proteome plasticity

(2015) Yamile Marquez et al.   GENOME RESEARCH

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

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

CAGEr: precise TSS data retrieval and high-resolution promoterome mining for integrative analyses

(2015) Vanja Haberle et al.   NUCLEIC ACIDS RESEARCH

DNA-encoded nucleosome occupancy is associated with transcription levels in the human malaria parasite Plasmodium falciparum

(2014) Evelien M Bunnik et al.   BMC GENOMICS

Strand-specific RNA-Seq reveals widespread and developmentally regulated transcription of natural antisense transcripts in Plasmodium falciparum

(2014) T Siegel et al.   BMC GENOMICS

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

(2014) Abhinav Sinha et al.   NATURE

A transcriptional switch underlies commitment to sexual development in malaria parasites

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

Full-length RNA-seq from single cells using Smart-seq2

(2014) Simone Picelli et al.   Nature Protocols

Differences in Gene Transcriptomic Pattern of Plasmodium falciparum in Children with Cerebral Malaria and Asymptomatic Carriers

(2014) Talleh Almelli et al.   PLoS One

3′ Untranslated Regions Mediate Transcriptional Interference between Convergent Genes Both Locally and Ectopically in Saccharomyces cerevisiae

(2014) Luwen Wang et al.   PLoS Genetics

Dynamic regulation of the transcription initiation landscape at single nucleotide resolution during vertebrate embryogenesis

(2013) Chirag Nepal et al.   GENOME RESEARCH

H2A.Z/H2B.Z double-variant nucleosomes inhabit the AT-rich promoter regions of thePlasmodium falciparumgenome

(2013) Wieteke A. M. Hoeijmakers et al.   MOLECULAR MICROBIOLOGY

PfSETvs methylation of histone H3K36 represses virulence genes in Plasmodium falciparum

(2013) Lubin Jiang et al.   NATURE

Smart-seq2 for sensitive full-length transcriptome profiling in single cells

(2013) Simone Picelli et al.   NATURE METHODS

Sequence features of yeast and human core promoters that are predictive of maximal promoter activity

(2013) Shai Lubliner et al.   NUCLEIC ACIDS RESEARCH

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

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

(2012) Samuel O Oyola et al.   BMC GENOMICS

BamView: visualizing and interpretation of next-generation sequencing read alignments

(2012) T. Carver et al.   BRIEFINGS IN BIOINFORMATICS

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

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

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

NSR-seq transcriptional profiling enables identification of a gene signature of Plasmodium falciparum parasites infecting children

(2011) Marissa Vignali et al.   JOURNAL OF CLINICAL INVESTIGATION

Optimal enzymes for amplifying sequencing libraries

(2011) Michael A Quail et al.   NATURE METHODS

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

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

The Apicomplexan AP2 family: Integral factors regulating Plasmodium development

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

New insights into the blood-stage transcriptome ofPlasmodium falciparumusing RNA-Seq

(2010) Thomas D. Otto et al.   MOLECULAR MICROBIOLOGY

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

Bidirectional promoters generate pervasive transcription in yeast

(2009) Zhenyu Xu et al.   NATURE

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

(2009) Iwanka Kozarewa et al.   NATURE METHODS

Statistical estimation of cell-cycle progression and lineage commitment in Plasmodium falciparum reveals a homogeneous pattern of transcription in ex vivo culture

(2009) J. E. Lemieux et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

PlasmoDB: a functional genomic database for malaria parasites

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

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

Divergent Transcription from Active Promoters

(2008) Amy C. Seila et al.   SCIENCE

Nascent RNA Sequencing Reveals Widespread Pausing and Divergent Initiation at Human Promoters

(2008) Leighton J. Core et al.   SCIENCE