Transcriptome assembly and differential gene expression of the invasive avian malaria parasite Plasmodium relictum in Hawaiʻi

Differential gene expression of Plasmodium homocircumflexum (lineage pCOLL4) across two experimentally infected passerine bird species

(2020) L. Garcia-Longoria et al.   GENOMICS

Genomic Advances in Avian Malaria Research

(2019) Elin Videvall   TRENDS IN PARASITOLOGY

Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

(2019) Daehwan Kim et al.   NATURE BIOTECHNOLOGY

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

(2018) Ulrike Böhme et al.   GENOME RESEARCH

Transcriptomic Studies of Malaria: a Paradigm for Investigation of Systemic Host-Pathogen Interactions

(2018) Hyun Jae Lee et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

De novo transcriptome assembly and preliminary analyses of two avian malaria parasites, Plasmodium delichoni and Plasmodium homocircumflexum

(2018) Joshua Weinberg et al.   GENOMICS

The transcriptome of the avian malaria parasite Plasmodium ashfordi displays host-specific gene expression

(2017) Elin Videvall et al.   MOLECULAR ECOLOGY

Characterization of P. vivax blood stage transcriptomes from field isolates reveals similarities among infections and complex gene isoforms

(2017) Adam Kim et al.   Scientific Reports

Plasmodium Helical Interspersed Subtelomeric (PHIST) Proteins, at the Center of Host Cell Remodeling

(2016) Jan D. Warncke et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Simulation-based comprehensive benchmarking of RNA-seq aligners

(2016) Giacomo Baruzzo et al.   NATURE METHODS

De novo assembly and transcriptome analysis of Plasmodium gallinaceum identifies the Rh5 interacting protein (ripr), and reveals a lack of EBL and RH gene family diversification

(2015) Elvin J Lauron et al.   MALARIA JOURNAL

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

(2014) S. Anders et al.   BIOINFORMATICS

Genomic resources for the endangered Hawaiian honeycreepers

(2014) Taylor Callicrate et al.   BMC GENOMICS

Experimental Evidence for Evolved Tolerance to Avian Malaria in a Wild Population of Low Elevation Hawai‘i ‘Amakihi (Hemignathus virens)

(2014) Carter T. Atkinson et al.   EcoHealth

A Plasmodium falciparum PHIST protein binds the virulence factor PfEMP1 and comigrates to knobs on the host cell surface

(2014) Alexander Oberli et al.   FASEB JOURNAL

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

Multilocus Resolution of Phylogeny and Timescale in the Extant Adaptive Radiation of Hawaiian Honeycreepers

(2011) Heather R.L. Lerner et al.   CURRENT BIOLOGY

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Introduced Avian Diseases, Climate Change, and the Future of Hawaiian Honeycreepers

(2009) Carter T. Atkinson et al.   JOURNAL OF AVIAN MEDICINE AND SURGERY

Dynamics of parasitemia of malaria parasites in a naturally and experimentally infected migratory songbird, the great reed warbler Acrocephalus arundinaceus

(2008) Pavel Zehtindjiev et al.   EXPERIMENTAL PARASITOLOGY

Comparative genomics of the neglected human malaria parasite Plasmodium vivax

(2008) Jane M. Carlton et al.   NATURE

PlasmoDB: a functional genomic database for malaria parasites

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