Comparative Life Cycle Transcriptomics Revises Leishmania mexicana Genome Annotation and Links a Chromosome Duplication with Parasitism of Vertebrates

Phytomonas: Trypanosomatids Adapted to Plant Environments

(2015) Eleanor Jaskowska et al.   PLoS Pathogens

Small Proteins Can No Longer Be Ignored

(2014) Gisela Storz et al.   Annual Review of Biochemistry

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

On the extent and role of the small proteome in the parasitic eukaryote Trypanosoma brucei

(2014) Megan Ericson et al.   BMC BIOLOGY

SLaP mapper: A webserver for identifying and quantifying spliced-leader addition and polyadenylation site usage in kinetoplastid genomes

(2014) Michael Fiebig et al.   MOLECULAR AND BIOCHEMICAL PARASITOLOGY

Networks of gene expression regulation in Trypanosoma brucei

(2014) C.E. Clayton   MOLECULAR AND BIOCHEMICAL PARASITOLOGY

Emerging evidence for functional peptides encoded by short open reading frames

(2014) Shea J. Andrews et al.   NATURE REVIEWS GENETICS

The Streamlined Genome of Phytomonas spp. Relative to Human Pathogenic Kinetoplastids Reveals a Parasite Tailored for Plants

(2014) Betina M. Porcel et al.   PLoS Genetics

Metabolic Reprogramming during Purine Stress in the Protozoan Pathogen Leishmania donovani

(2014) Jessica L. Martin et al.   PLoS Pathogens

The transcriptome of Leishmania major in the axenic promastigote stage: transcript annotation and relative expression levels by RNA-seq

(2013) Alberto Rastrojo et al.   BMC GENOMICS

Iron uptake controls the generation ofLeishmaniainfective forms through regulation of ROS levels

(2013) Bidyottam Mittra et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Adaptin evolution in kinetoplastids and emergence of the variant surface glycoprotein coat in African trypanosomatids

(2013) Paul T. Manna et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Conserved Regulation of Cardiac Calcium Uptake by Peptides Encoded in Small Open Reading Frames

(2013) E. G. Magny et al.   SCIENCE

Detailed interrogation of trypanosome cell biology via differential organelle staining and automated image analysis

(2012) Richard J Wheeler et al.   BMC BIOLOGY

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

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

Disability-adjusted life years (DALYs) for 291 diseases and injuries in 21 regions, 1990–2010: a systematic analysis for the Global Burden of Disease Study 2010

(2012) Christopher J L Murray et al.   LANCET

Dual RNA-seq of pathogen and host

(2012) Alexander J. Westermann et al.   NATURE REVIEWS MICROBIOLOGY

Leishmaniasis Worldwide and Global Estimates of Its Incidence

(2012) Jorge Alvar et al.   PLoS One

Adaptive mechanisms in pathogens: universal aneuploidy in Leishmania

(2012) An Mannaert et al.   TRENDS IN PARASITOLOGY

Genome organization is a major component of gene expression control in response to stress and during the cell division cycle in trypanosomes

(2012) S. Kelly et al.   Open Biology

Transcriptome Patterns from Primary Cutaneous Leishmania braziliensis Infections Associate with Eventual Development of Mucosal Disease in Humans

(2012) Ana Claudia Maretti-Mira et al.   PLoS Neglected Tropical Diseases

Impact of Leishmania metalloprotease GP63 on macrophage signaling

(2012) Amandine Isnard et al.   Frontiers in Cellular and Infection Microbiology

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Quantitative proteome profiling informs on phenotypic traits that adapt Leishmania donovani for axenic and intracellular proliferation

(2011) Pascale Pescher et al.   CELLULAR MICROBIOLOGY

An expanding universe of small proteins

(2011) Errett C Hobbs et al.   CURRENT OPINION IN MICROBIOLOGY

Small Open Reading Frames: Current Prediction Techniques and Future Prospect

(2011) Haoyu Cheng et al.   CURRENT PROTEIN & PEPTIDE SCIENCE

Chromosome and gene copy number variation allow major structural change between species and strains of Leishmania

(2011) M. B. Rogers et al.   GENOME RESEARCH

Whole genome sequencing of multiple Leishmania donovani clinical isolates provides insights into population structure and mechanisms of drug resistance

(2011) T. Downing et al.   GENOME RESEARCH

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

Dual targeting of isoleucyl-tRNA synthetase in Trypanosoma brucei is mediated through alternative trans-splicing

(2011) Jochen Rettig et al.   NUCLEIC ACIDS RESEARCH

Comparative evaluation of label-free SINQ normalized spectral index quantitation in the central proteomics facilities pipeline

(2011) David C. Trudgian et al.   PROTEOMICS

Optimization of parameters for coverage of low molecular weight proteins

(2010) Stephan A. Müller et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

Metabolic Pathways Required for the Intracellular Survival of Leishmania

(2010) Malcolm J. McConville et al.   Annual Review of Microbiology

CPFP: a central proteomics facilities pipeline

(2010) D. C. Trudgian et al.   BIOINFORMATICS

Beyond 9+0: noncanonical axoneme structures characterize sensory cilia from protists to humans

(2010) Eva Gluenz et al.   FASEB JOURNAL

Multiple levels of gene regulation mediate differentiation of the intracellular pathogen Leishmania

(2010) T. Lahav et al.   FASEB JOURNAL

The Drosophila melanogaster transcriptome by paired-end RNA sequencing

(2010) B. Daines et al.   GENOME RESEARCH

Transcriptomics throughout the life cycle of Leishmania infantum: High down-regulation rate in the amastigote stage

(2010) Pedro J. Alcolea et al.   INTERNATIONAL JOURNAL FOR PARASITOLOGY

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

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

The primary transcriptome of the major human pathogen Helicobacter pylori

(2010) Cynthia M. Sharma et al.   NATURE

Genome-wide analysis of mRNA abundance in two life-cycle stages of Trypanosoma brucei and identification of splicing and polyadenylation sites

(2010) Tim Nicolai Siegel et al.   NUCLEIC ACIDS RESEARCH

The Transcriptome of the Human Pathogen Trypanosoma brucei at Single-Nucleotide Resolution

(2010) Nikolay G. Kolev et al.   PLoS Pathogens

Spliced Leader Trapping Reveals Widespread Alternative Splicing Patterns in the Highly Dynamic Transcriptome of Trypanosoma brucei

(2010) Daniel Nilsson et al.   PLoS Pathogens

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

(2010) Matthew D Young et al.   GENOME BIOLOGY

Paracrine signaling in a bacterium

(2009) D. Lopez et al.   GENES & DEVELOPMENT

Whole-genome comparative RNA expression profiling of axenic and intracellular amastigote forms of Leishmania infantum

(2009) Annie Rochette et al.   MOLECULAR AND BIOCHEMICAL PARASITOLOGY

Gel free analysis of the proteome of intracellular Leishmania mexicana

(2009) Daniel Paape et al.   MOLECULAR AND BIOCHEMICAL PARASITOLOGY

Upstream open reading frames cause widespread reduction of protein expression and are polymorphic among humans

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

Preferential translation of Hsp83 in Leishmania requires a thermosensitive polypyrimidine-rich element in the 3' UTR and involves scanning of the 5' UTR

(2009) M. David et al.   RNA

Kinetoplastids: related protozoan pathogens, different diseases

(2008) Ken Stuart et al.   JOURNAL OF CLINICAL INVESTIGATION

Robust Prediction of the MASCOT Score for an Improved Quality Assessment in Mass Spectrometric Proteomics

(2008) Thomas Koenig et al.   JOURNAL OF PROTEOME RESEARCH

Transgenic, FluorescentLeishmania mexicanaAllow Direct Analysis of the Proteome of Intracellular Amastigotes

(2008) Daniel Paape et al.   MOLECULAR & CELLULAR PROTEOMICS

Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution

(2008) Brian T. Wilhelm et al.   NATURE

Deadenylation-independent stage-specific mRNA degradation in Leishmania

(2008) Simon Haile et al.   NUCLEIC ACIDS RESEARCH

Coordinate regulation of a family of promastigote-enriched mRNAs by the 3′UTR PRE element in Leishmania mexicana

(2007) Timothy R. Holzer et al.   MOLECULAR AND BIOCHEMICAL PARASITOLOGY