Strain-specific genome evolution in Trypanosoma cruzi, the agent of Chagas disease

Identification of a novel base J binding protein complex involved in RNA polymerase II transcription termination in trypanosomes

(2020) Rudo Kieft et al.   PLoS Genetics

A Genome Assembly of the Barley ‘Transformation Reference’ Cultivar Golden Promise

(2020) Miriam Schreiber et al.   G3-Genes Genomes Genetics

Improving Illumina assemblies with Hi‐C and long reads: An example with the North African dromedary

(2019) Jean P. Elbers et al.   Molecular Ecology Resources

Nanopore Sequencing Significantly Improves Genome Assembly of the Protozoan Parasite Trypanosoma cruzi

(2019) Florencia Díaz-Viraqué et al.   Genome Biology and Evolution

Regulation of gene expression in trypanosomatids: living with polycistronic transcription

(2019) Christine Clayton   Open Biology

A Highly Contiguous Reference Genome for Northern Bobwhite (Colinus virginianus)

(2019) Jessie F. Salter et al.   G3-Genes Genomes Genetics

Genomic assemblies of newly sequenced Trypanosoma cruzi strains reveal new genomic expansion and greater complexity

(2018) Francisco Callejas-Hernández et al.   Scientific Reports

Genome organization and DNA accessibility control antigenic variation in trypanosomes

(2018) Laura S. M. Müller et al.   NATURE

Complex DNA structures trigger copy number variation across the Plasmodium falciparum genome

(2018) Adam C Huckaby et al.   NUCLEIC ACIDS RESEARCH

Recombination-driven generation of the largest pathogen repository of antigen variants in the protozoan Trypanosoma cruzi

(2016) D. Brent Weatherly et al.   BMC GENOMICS

Chromosome-scale shotgun assembly using an in vitro method for long-range linkage

(2016) Nicholas H. Putnam et al.   GENOME RESEARCH

Companion: a web server for annotation and analysis of parasite genomes

(2016) Sascha Steinbiss et al.   NUCLEIC ACIDS RESEARCH

Base J and H3.V Regulate Transcriptional Termination in Trypanosoma brucei

(2016) Danae Schulz et al.   PLoS Genetics

Histone H3 Variant Regulates RNA Polymerase II Transcription Termination and Dual Strand Transcription of siRNA Loci in Trypanosoma brucei

(2016) David Reynolds et al.   PLoS Genetics

Masters of Disguise: Antigenic Variation and the VSG Coat in Trypanosoma brucei

(2016) Monica R. Mugnier et al.   PLoS Pathogens

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Chromosomal copy number variation reveals differential levels of genomic plasticity in distinct Trypanosoma cruzi strains

(2015) João Luís Reis-Cunha et al.   BMC GENOMICS

Evolution of Trypanosoma cruzi: clarifying hybridisations, mitochondrial introgressions and phylogenetic relationships between major lineages

(2015) Nicolás Tomasini et al.   MEMORIAS DO INSTITUTO OSWALDO CRUZ

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

Regulation of transcription termination by glucosylated hydroxymethyluracil, base J, in Leishmania major and Trypanosoma brucei

(2014) D. Reynolds et al.   NUCLEIC ACIDS RESEARCH

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

Comprehensive Proteomic Analysis of Trypanosoma cruzi Epimastigote Cell Surface Proteins by Two Complementary Methods

(2013) Rayner M. L. Queiroz et al.   JOURNAL OF PROTEOME RESEARCH

High-throughput genome scaffolding from in vivo DNA interaction frequency

(2013) Noam Kaplan et al.   NATURE BIOTECHNOLOGY

Genome assembly and haplotyping with Hi-C

(2013) Jan O Korbel et al.   NATURE BIOTECHNOLOGY

Interclonal Variations in the Molecular Karyotype of Trypanosoma cruzi: Chromosome Rearrangements in a Single Cell-Derived Clone of the G Strain

(2013) Fabio Mitsuo Lima et al.   PLoS One

Trypanosoma cruzi TcSMUG L-surface Mucins Promote Development and Infectivity in the Triatomine Vector Rhodnius prolixus

(2013) Marcelo S. Gonzalez et al.   PLoS Neglected Tropical Diseases

Web Apollo: a web-based genomic annotation editing platform

(2013) Eduardo Lee et al.   GENOME BIOLOGY

Glucosylated Hydroxymethyluracil, DNA Base J, Prevents Transcriptional Readthrough in Leishmania

(2012) Henri G.A.M. van Luenen et al.   CELL

Multigene Families in Trypanosoma cruzi and Their Role in Infectivity

(2012) Luis Miguel De Pablos et al.   INFECTION AND IMMUNITY

American Trypanosomiasis (Chagas Disease)

(2012) Anis Rassi et al.   INFECTIOUS DISEASE CLINICS OF NORTH AMERICA

MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity

(2012) Y. Wang et al.   NUCLEIC ACIDS RESEARCH

Mind the Gap: Upgrading Genomes with Pacific Biosciences RS Long-Read Sequencing Technology

(2012) Adam C. English et al.   PLoS One

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

Comparative Genomics Reveals Two Novel RNAi Factors in Trypanosoma brucei and Provides Insight into the Core Machinery

(2012) Rebecca L. Barnes et al.   PLoS Pathogens

Epigenetic Regulation of Polymerase II Transcription Initiation in Trypanosoma cruzi: Modulation of Nucleosome Abundance, Histone Modification, and Polymerase Occupancy by O-Linked Thymine DNA Glucosylation

(2011) Dilrukshi Ekanayake et al.   EUKARYOTIC CELL

The revised Trypanosoma cruzi subspecific nomenclature: Rationale, epidemiological relevance and research applications

(2011) Bianca Zingales et al.   INFECTION GENETICS AND EVOLUTION

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

(2011) F. Sievers et al.   Molecular Systems Biology

Genome Size, Karyotype Polymorphism and Chromosomal Evolution in Trypanosoma cruzi

(2011) Renata T. Souza et al.   PLoS One

Analyses of 32 Loci Clarify Phylogenetic Relationships among Trypanosoma cruzi Lineages and Support a Single Hybridization prior to Human Contact

(2011) Carlos A. Flores-López et al.   PLoS Neglected Tropical Diseases

Shotgun Sequencing Analysis of Trypanosoma cruzi I Sylvio X10/1 and Comparison with T. cruzi VI CL Brener

(2011) Oscar Franzén et al.   PLoS Neglected Tropical Diseases

Iterative Correction of Reference Nucleotides (iCORN) using second generation sequencing technology

(2010) Thomas D. Otto et al.   BIOINFORMATICS

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Two thymidine hydroxylases differentially regulate the formation of glucosylated DNA at regions flanking polymerase II polycistronic transcription units throughout the genome of Trypanosoma brucei

(2010) Laura J. Cliffe et al.   NUCLEIC ACIDS RESEARCH

Chromosome level assembly of the hybrid Trypanosoma cruzi genome

(2009) D Brent Weatherly et al.   BMC GENOMICS

Evaluation of high efficiency gene knockout strategies for Trypanosoma cruzi

(2009) Dan Xu et al.   BMC MICROBIOLOGY

Four histone variants mark the boundaries of polycistronic transcription units in Trypanosoma brucei

(2009) T. N. Siegel et al.   GENES & DEVELOPMENT

A new consensus for Trypanosoma cruzi intraspecific nomenclature: second revision meeting recommends TcI to TcVI

(2009) B Zingales et al.   MEMORIAS DO INSTITUTO OSWALDO CRUZ

GPIomics: global analysis of glycosylphosphatidylinositol-anchored molecules of Trypanosoma cruzi

(2009) Ernesto S Nakayasu et al.   Molecular Systems Biology

TriTrypDB: a functional genomic resource for the Trypanosomatidae

(2009) Martin Aslett et al.   NUCLEIC ACIDS RESEARCH

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE

TcSNP: a database of genetic variation in Trypanosoma cruzi

(2008) A. A. Ackermann et al.   NUCLEIC ACIDS RESEARCH

Telomeric Expression Sites Are Highly Conserved in Trypanosoma brucei

(2008) Christiane Hertz-Fowler et al.   PLoS One