A systems-level gene regulatory network model for Plasmodium falciparum

A Kelch13-defined endocytosis pathway mediates artemisinin resistance in malaria parasites

(2020) Jakob Birnbaum et al.   SCIENCE

Plasmodium falciparum Artemisinin Resistance: The Effect of Heme, Protein Damage, and Parasite Cell Stress Response

(2020) Melissa R. Rosenthal et al.   ACS Infectious Diseases

Elucidating Mechanisms of Drug-Resistant Plasmodium falciparum

(2019) Leila S. Ross et al.   Cell Host & Microbe

Epigenetic Variation and Regulation in Malaria Parasites

(2018) Manoj T. Duraisingh et al.   Annual Review of Microbiology

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

(2018) Gigliola Zanghì et al.   Cell Reports

Topological and statistical analyses of gene regulatory networks reveal unifying yet quantitatively different emergent properties

(2018) Wilberforce Zachary Ouma et al.   PLoS Computational Biology

Exploring parasite heterogeneity using single-cell RNA-seq reveals a gene signature among sexual stage Plasmodium falciparum parasites

(2018) Mtakai Ngara et al.   EXPERIMENTAL CELL RESEARCH

The Gene Ontology Resource: 20 years and still GOing strong

(2018)   NUCLEIC ACIDS RESEARCH

The Pfam protein families database in 2019

(2018) Sara El-Gebali et al.   NUCLEIC ACIDS RESEARCH

Variant surface antigens of Plasmodium falciparum and their roles in severe malaria

(2017) Mats Wahlgren et al.   NATURE REVIEWS MICROBIOLOGY

20 years of the SMART protein domain annotation resource

(2017) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Systematic CRISPR-Cas9-Mediated Modifications of Plasmodium yoelii ApiAP2 Genes Reveal Functional Insights into Parasite Development

(2017) Cui Zhang et al.   mBio

Understanding transcriptional regulatory networks using computational models

(2016) Bing He et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Integrated transcriptomic and proteomic analyses ofP. falciparumgametocytes: molecular insight into sex-specific processes and translational repression

(2016) Edwin Lasonder et al.   NUCLEIC ACIDS RESEARCH

Malaria Parasite Metabolic Pathways (MPMP) Upgraded with Targeted Chemical Compounds

(2016) Hagai Ginsburg et al.   TRENDS IN PARASITOLOGY

Network analysis identifies Rv0324 and Rv0880 as regulators of bedaquiline tolerance in Mycobacterium tuberculosis

(2016) Eliza J. R. Peterson et al.   Nature Microbiology

Bicluster Sampled Coherence Metric (BSCM) provides an accurate environmental context for phenotype predictions

(2015) Samuel A Danziger et al.   BMC Systems Biology

A molecular mechanism of artemisinin resistance in Plasmodium falciparum malaria

(2015) Alassane Mbengue et al.   NATURE

cMonkey2: Automated, systematic, integrated detection of co-regulated gene modules for any organism

(2015) David J. Reiss et al.   NUCLEIC ACIDS RESEARCH

circlize implements and enhances circular visualization in R

(2014) Zuguang Gu et al.   BIOINFORMATICS

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

A Plasmodium falciparum Histone Deacetylase Regulates Antigenic Variation and Gametocyte Conversion

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

A system-level model for the microbial regulatory genome

(2014) A. N. Brooks et al.   Molecular Systems Biology

A transcriptional switch underlies commitment to sexual development in malaria parasites

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

A high-resolution network model for global gene regulation in Mycobacterium tuberculosis

(2014) Eliza J.R. Peterson et al.   NUCLEIC ACIDS RESEARCH

UniProt: a hub for protein information

(2014)   NUCLEIC ACIDS RESEARCH

K13-propeller mutations confer artemisinin resistance in Plasmodium falciparum clinical isolates

(2014) J. Straimer et al.   SCIENCE

Population transcriptomics of human malaria parasites reveals the mechanism of artemisinin resistance

(2014) S. Mok et al.   SCIENCE

Genome-wide regulatory dynamics of translation in the Plasmodium falciparum asexual blood stages

(2014) Florence Caro et al.   eLife

Robust data-driven incorporation of prior knowledge into the inference of dynamic regulatory networks

(2013) Alex Greenfield et al.   BIOINFORMATICS

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

A molecular marker of artemisinin-resistant Plasmodium falciparum malaria

(2013) Frédéric Ariey et al.   NATURE

Molecular mechanisms of system responses to novel stimuli are predictable from public data

(2013) Samuel A. Danziger et al.   NUCLEIC ACIDS RESEARCH

Transcriptional variation in the malaria parasite Plasmodium falciparum

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

Mechanisms ofin vitroresistance to dihydroartemisinin inPlasmodium falciparum

(2012) Long Cui et al.   MOLECULAR MICROBIOLOGY

Dominating scale-free networks with variable scaling exponent: heterogeneous networks are not difficult to control

(2012) Jose C Nacher et al.   NEW JOURNAL OF PHYSICS

Transcriptional Profiling of Plasmodium falciparum Parasites from Patients with Severe Malaria Identifies Distinct Low vs. High Parasitemic Clusters

(2012) Danny A. Milner et al.   PLoS One

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

(2012) Shiroh Iwanaga et al.   PLoS One

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

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

The Puf-Family RNA-Binding Protein Puf2 Controls Sporozoite Conversion to Liver Stages in the Malaria Parasite

(2011) Katja Müller et al.   PLoS One

Transition of Plasmodium Sporozoites into Liver Stage-Like Forms Is Regulated by the RNA Binding Protein Pumilio

(2011) Carina S. S. Gomes-Santos et al.   PLoS Pathogens

In silico and biological survey of transcription-associated proteins implicated in the transcriptional machinery during the erythrocytic development of Plasmodium falciparum

(2010) Emmanuel Bischoff et al.   BMC GENOMICS

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

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

PlasmoDB: a functional genomic database for malaria parasites

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

Comparative genomics of transcription factors and chromatin proteins in parasitic protists and other eukaryotes

(2007) Lakshminarayan M. Iyer et al.   INTERNATIONAL JOURNAL FOR PARASITOLOGY