Molecular profiling reveals features of clinical immunity and immunosuppression in asymptomatic P. falciparum malaria

High-dimensional mass cytometry identifies T cell and B cell signatures predicting reduced risk of Plasmodium vivax malaria

(2021) Lisa J. Ioannidis et al.   JCI Insight

NR1D1 modulates synovial inflammation and bone destruction in rheumatoid arthritis

(2020) Hui Liu et al.   Cell Death & Disease

IgM+ memory B cells induced in response to Plasmodium berghei adopt a germinal centre B cell phenotype during secondary infection

(2020) Halina M. Pietrzak et al.   PARASITOLOGY

Interleukin-13 drives metabolic conditioning of muscle to endurance exercise

(2020) Nelson H. Knudsen et al.   SCIENCE

Increased circulation time of Plasmodium falciparum underlies persistent asymptomatic infection in the dry season

(2020) Carolina M. Andrade et al.   NATURE MEDICINE

The blood transcriptome of childhood malaria

(2019) Angelica B.W. Boldt et al.   EBioMedicine

The R package Rsubread is easier, faster, cheaper and better for alignment and quantification of RNA sequencing reads

(2019) Yang Liao et al.   NUCLEIC ACIDS RESEARCH

Repeated clinical malaria episodes are associated with modification of the immune system in children

(2019) Yaw Bediako et al.   BMC Medicine

Safety and Differential Antibody and T-Cell Responses to Plasmodium falciparum Sporozoite Vaccine by Age in Tanzanian Adults, Adolescents, Children, and Infants

(2019) Said A. Jongo et al.   AMERICAN JOURNAL OF TROPICAL MEDICINE AND HYGIENE

A Molecular Signature in Blood Reveals a Role for p53 in Regulating Malaria-Induced Inflammation

(2019) Tuan M. Tran et al.   IMMUNITY

The nuclear receptor REV-ERBα modulates Th17 cell-mediated autoimmune disease

(2019) Christina Chang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

IgM in human immunity to Plasmodium falciparum malaria

(2019) M. J. Boyle et al.   Science Advances

Transcription Factor T-bet in B Cells Modulates Germinal Center Polarization and Antibody Affinity Maturation in Response to Malaria

(2019) Ann Ly et al.   Cell Reports

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

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

Prevalence of asymptomatic Plasmodium infections with sub-microscopic parasite densities in the northwestern border of Thailand: a potential threat to malaria elimination

(2018) Jetsumon Sattabongkot et al.   MALARIA JOURNAL

dtangle: accurate and robust cell type deconvolution

(2018) Gregory J Hunt et al.   BIOINFORMATICS

Haemopedia RNA-seq: a database of gene expression during haematopoiesis in mice and humans

(2018) Jarny Choi et al.   NUCLEIC ACIDS RESEARCH

Egr2 and 3 Inhibit T-bet–Mediated IFN-γ Production in T Cells

(2017) Randeep Singh et al.   JOURNAL OF IMMUNOLOGY

Safety and efficacy of PfSPZ Vaccine against Plasmodium falciparum via direct venous inoculation in healthy malaria-exposed adults in Mali: a randomised, double-blind phase 1 trial

(2017) Mahamadou S Sissoko et al.   LANCET INFECTIOUS DISEASES

Regulatory T cells impede acute and long-term immunity to blood-stage malaria through CTLA-4

(2017) Samarchith P Kurup et al.   NATURE MEDICINE

Accurate immune repertoire sequencing reveals malaria infection driven antibody lineage diversification in young children

(2017) Ben S. Wendel et al.   Nature Communications

Malaria-induced interferon-γ drives the expansion of Tbethi atypical memory B cells

(2017) Nyamekye Obeng-Adjei et al.   PLoS Pathogens

Major transcriptional changes observed in the Fulani, an ethnic group less susceptible to malaria

(2017) Jaclyn E Quin et al.   eLife

Immune Modulation of the T Cell Response in Asthma through Wnt10b

(2016) Jordis Trischler et al.   AMERICAN JOURNAL OF RESPIRATORY CELL AND MOLECULAR BIOLOGY

Robust hyperparameter estimation protects against hypervariable genes and improves power to detect differential expression

(2016) Belinda Phipson et al.   Annals of Applied Statistics

Treatment of Chronic Asymptomatic Plasmodium falciparum Infection Does Not Increase the Risk of Clinical Malaria Upon Reinfection

(2016) Silvia Portugal et al.   CLINICAL INFECTIOUS DISEASES

Somatically Hypermutated Plasmodium-Specific IgM+ Memory B Cells Are Rapid, Plastic, Early Responders upon Malaria Rechallenge

(2016) Akshay T. Krishnamurty et al.   IMMUNITY

IRF2BP2 transcriptional repressor restrains naive CD4 T cell activation and clonal expansion induced by TCR triggering

(2016) Cristiane Sécca et al.   JOURNAL OF LEUKOCYTE BIOLOGY

Surface expression of inhibitory (CTLA-4) and stimulatory (OX40) receptors by CD4+ regulatory T cell subsets circulating in human malaria

(2016) Raquel M. Gonçalves-Lopes et al.   MICROBES AND INFECTION

Protection against malaria at 1 year and immune correlates following PfSPZ vaccination

(2016) Andrew S Ishizuka et al.   NATURE MEDICINE

Severe Malaria Infections Impair Germinal Center Responses by Inhibiting T Follicular Helper Cell Differentiation

(2016) Victoria Ryg-Cornejo et al.   Cell Reports

“Asymptomatic” Malaria: A Chronic and Debilitating Infection That Should Be Treated

(2016) Ingrid Chen et al.   PLOS MEDICINE

Acute Malaria Induces PD1+CTLA4+ Effector T Cells with Cell-Extrinsic Suppressor Function

(2016) Maria Sophia Mackroth et al.   PLoS Pathogens

Transcriptomic evidence for modulation of host inflammatory responses during febrile Plasmodium falciparum malaria

(2016) Tuan M. Tran et al.   Scientific Reports

FlowSOM: Using self-organizing maps for visualization and interpretation of cytometry data

(2015) Sofie Van Gassen et al.   CYTOMETRY PART A

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

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

Functional capacities of human IgM memory B cells in early inflammatory responses and secondary germinal center reactions

(2015) Marc Seifert et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Circulating Th1-Cell-type Tfh Cells that Exhibit Impaired B Cell Help Are Preferentially Activated during Acute Malaria in Children

(2015) Nyamekye Obeng-Adjei et al.   Cell Reports

Genetic Resistance to Malaria Is Associated With Greater Enhancement of Immunoglobulin (Ig)M Than IgG Responses to a Broad Array ofPlasmodium falciparumAntigens

(2015) Charles Arama et al.   Open Forum Infectious Diseases

Impact of Malaria Control on Mortality and Anemia among Tanzanian Children Less than Five Years of Age, 1999–2010

(2015) Paul Smithson et al.   PLoS One

circlize implements and enhances circular visualization in R

(2014) Zuguang Gu et al.   BIOINFORMATICS

T Follicular Helper Cell Differentiation, Function, and Roles in Disease

(2014) Shane Crotty   IMMUNITY

Automated identification of stratifying signatures in cellular subpopulations

(2014) Robert V. Bruggner et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Co-infection of Long-Term Carriers of Plasmodium falciparum with Schistosoma haematobium Enhances Protection from Febrile Malaria: A Prospective Cohort Study in Mali

(2014) Safiatou Doumbo et al.   PLoS Neglected Tropical Diseases

voom: precision weights unlock linear model analysis tools for RNA-seq read counts

(2014) Charity W Law et al.   GENOME BIOLOGY

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

(2013) Y. Liao et al.   BIOINFORMATICS

Normalization of mass cytometry data with bead standards

(2013) Rachel Finck et al.   CYTOMETRY PART A

CXCL4 and CXCL10 Predict Risk of Fatal Cerebral Malaria

(2013) Nana O. Wilson et al.   DISEASE MARKERS

viSNE enables visualization of high dimensional single-cell data and reveals phenotypic heterogeneity of leukemia

(2013) El-ad David Amir et al.   NATURE BIOTECHNOLOGY

Molecular signatures of antibody responses derived from a systems biology study of five human vaccines

(2013) Shuzhao Li et al.   NATURE IMMUNOLOGY

The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote

(2013) Yang Liao et al.   NUCLEIC ACIDS RESEARCH

Opsonising Antibodies to P. falciparum Merozoites Associated with Immunity to Clinical Malaria

(2013) Danika L. Hill et al.   PLoS One

The CTLA-4 and PD-1/PD-L1 Inhibitory Pathways Independently Regulate Host Resistance to Plasmodium-induced Acute Immune Pathology

(2012) Julius Clemence R. Hafalla et al.   PLoS Pathogens

CD4+ Natural Regulatory T Cells Prevent Experimental Cerebral Malaria via CTLA-4 When Expanded In Vivo

(2010) Ashraful Haque et al.   PLoS Pathogens

The Plasmodium falciparum-Specific Human Memory B Cell Compartment Expands Gradually with Repeated Malaria Infections

(2010) Greta E. Weiss et al.   PLoS Pathogens

Gene ontology analysis for RNA-seq: accounting for selection bias

(2010) Matthew D Young et al.   GENOME BIOLOGY

Changes in malaria indices between 1999 and 2007 in The Gambia: a retrospective analysis

(2008) Serign J Ceesay et al.   LANCET

Malaria morbidity in Papua Indonesia, an area with multidrug resistant Plasmodium vivax and Plasmodium falciparum

(2008) Muhammad Karyana et al.   MALARIA JOURNAL