4.8 Article

Transcriptome, proteome and draft genome of Euglena gracilis

Related references

Note: Only part of the references are listed.
Article Biochemistry & Molecular Biology

The Pfam protein families database in 2019

Sara El-Gebali et al.

NUCLEIC ACIDS RESEARCH (2019)

Article Biochemistry & Molecular Biology

Secondary Plastids of Euglenids and Chlorarachniophytes Function with a Mix of Genes of Red and Green Algal Ancestry

Rafael I. Ponce-Toledo et al.

MOLECULAR BIOLOGY AND EVOLUTION (2018)

Article Biochemistry & Molecular Biology

KEGG: new perspectives on genomes, pathways, diseases and drugs

Minoru Kanehisa et al.

NUCLEIC ACIDS RESEARCH (2017)

Article Cell Biology

Evolution of the endomembrane systems of trypanosomatids - conservation and specialisation

Divya Venkatesh et al.

JOURNAL OF CELL SCIENCE (2017)

Article Biochemical Research Methods

Salmon provides fast and bias-aware quantification of transcript expression

Rob Patro et al.

NATURE METHODS (2017)

Article Biochemical Research Methods

GenomeScope: fast reference-free genome profiling from short reads

Gregory W. Vurture et al.

BIOINFORMATICS (2017)

Article Biochemistry & Molecular Biology

Peeping at TOMs-Diverse Entry Gates to Mitochondria Provide Insights into the Evolution of Eukaryotes

Jan Mani et al.

MOLECULAR BIOLOGY AND EVOLUTION (2016)

Article Evolutionary Biology

Intermediate introns in nuclear genes of euglenids - are they a distinct type?

Rafal Milanowski et al.

BMC EVOLUTIONARY BIOLOGY (2016)

Article Biochemistry & Molecular Biology

Kinetoplastid Phylogenomics Reveals the Evolutionary Innovations Associated with the Origins of Parasitism

Andrew P. Jackson et al.

CURRENT BIOLOGY (2016)

Article Biochemistry & Molecular Biology

Extreme Diversity of Diplonemid Eukaryotes in the Ocean

Olga Flegontova et al.

CURRENT BIOLOGY (2016)

Review Microbiology

Exploiting the Achilles' heel of membrane trafficking in trypanosomes

Martin Zoltner et al.

CURRENT OPINION IN MICROBIOLOGY (2016)

Article Evolutionary Biology

Ancient Eukaryotic Origin and Evolutionary Plasticity of Nuclear Lamina

Ludek Koreny et al.

GENOME BIOLOGY AND EVOLUTION (2016)

Article Biochemistry & Molecular Biology

Gene family phylogeny and the evolution of parasite cell surfaces

Andrew P. Jackson

MOLECULAR AND BIOCHEMICAL PARASITOLOGY (2016)

Article Biochemical Research Methods

The Perseus computational platform for comprehensive analysis of (prote)omics data

Stefka Tyanova et al.

NATURE METHODS (2016)

Article Biochemistry & Molecular Biology

Interactome Mapping Reveals the Evolutionary History of the Nuclear Pore Complex

Samson O. Obado et al.

PLOS BIOLOGY (2016)

Article Multidisciplinary Sciences

Conservation and divergence within the clathrin interactome of Trypanosoma cruzi

Ligia Cristina Kalb et al.

SCIENTIFIC REPORTS (2016)

Article Evolutionary Biology

Unexpectedly Streamlined Mitochondrial Genome of the Euglenozoan Euglena gracilis

Eva Dobakova et al.

GENOME BIOLOGY AND EVOLUTION (2015)

Review Biochemistry & Molecular Biology

Effect of Metals, Metalloids and Metallic Nanoparticles on Microalgae Growth and Industrial Product Biosynthesis: A Review

Krystian Miazek et al.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2015)

Article Biochemical Research Methods

Architecture of a Host-Parasite Interface: Complex Targeting Mechanisms Revealed Through Proteomics

Catarina Gadelha et al.

MOLECULAR & CELLULAR PROTEOMICS (2015)

Article Biochemistry & Molecular Biology

Identification of protein coding regions in RNA transcripts

Shiyuyun Tang et al.

NUCLEIC ACIDS RESEARCH (2015)

Review Microbiology

RNA-binding proteins involved in post-transcriptional regulation in bacteria

Elke Van Assche et al.

FRONTIERS IN MICROBIOLOGY (2015)

Review Biodiversity Conservation

Concepts for biocontrol in marine environments: is there a way forward?

Javier Atalah et al.

MANAGEMENT OF BIOLOGICAL INVASIONS (2015)

Article Biochemical Research Methods

Trimmomatic: a flexible trimmer for Illumina sequence data

Anthony M. Bolger et al.

BIOINFORMATICS (2014)

Article Biochemical Research Methods

InterProScan 5: genome-scale protein function classification

Philip Jones et al.

BIOINFORMATICS (2014)

Article Biochemical Research Methods

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

Alexandros Stamatakis

BIOINFORMATICS (2014)

Article Biochemistry & Molecular Biology

Discovery of Unconventional Kinetochores in Kinetoplastids

Bungo Akiyoshi et al.

Article Biochemistry & Molecular Biology

Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads

Rei Kajitani et al.

GENOME RESEARCH (2014)

Article Biochemical Research Methods

High-Confidence Glycosome Proteome for Procyclic Form Trypanosoma brucei by Epitope-Tag Organelle Enrichment and SILAC Proteomics

Maria Lucia S. Guether et al.

JOURNAL OF PROTEOME RESEARCH (2014)

Review Biochemistry & Molecular Biology

Evolution of parasitism in kinetoplastid flagellates

Julius Lukes et al.

MOLECULAR AND BIOCHEMICAL PARASITOLOGY (2014)

Article Biochemistry & Molecular Biology

Distribution of Conventional and Nonconventional Introns in Tubulin (α and β) Genes of Euglenids

Rafal Milanowski et al.

MOLECULAR BIOLOGY AND EVOLUTION (2014)

Review Microbiology

Motility and more: the flagellum of Trypanosoma brucei

Gerasimos Langousis et al.

NATURE REVIEWS MICROBIOLOGY (2014)

Article Biotechnology & Applied Microbiology

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

Michael I. Love et al.

GENOME BIOLOGY (2014)

Article Biotechnology & Applied Microbiology

BayesHammer: Bayesian clustering for error correction in single-cell sequencing

Sergey I. Nikolenko et al.

BMC GENOMICS (2013)

Article Biotechnology & Applied Microbiology

Assessing De Novo transcriptome assembly metrics for consistency and utility

Shawn T. O'Neil et al.

BMC GENOMICS (2013)

Article Biochemistry & Molecular Biology

Paratrypanosoma Is a Novel Early-Branching Trypanosomatid

Pavel Flegontov et al.

CURRENT BIOLOGY (2013)

Article Biotechnology & Applied Microbiology

Euglena sp as a suitable source of lipids for potential use as biofuel and sustainable wastewater treatment

Durga Madhab Mahapatra et al.

JOURNAL OF APPLIED PHYCOLOGY (2013)

Article Biochemistry & Molecular Biology

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

Kazutaka Katoh et al.

MOLECULAR BIOLOGY AND EVOLUTION (2013)

Review Plant Sciences

Light Detection and Signal Transduction in the BLUF Photoreceptors

Shinji Masuda

PLANT AND CELL PHYSIOLOGY (2013)

Article Biochemical Research Methods

CD-HIT: accelerated for clustering the next-generation sequencing data

Limin Fu et al.

BIOINFORMATICS (2012)

Article Biochemical Research Methods

SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data

Evguenia Kopylova et al.

BIOINFORMATICS (2012)

Letter Biochemistry & Molecular Biology

Tom40 is likely common to all mitochondria Response

Mascha Pusnik et al.

CURRENT BIOLOGY (2012)

Letter Biochemistry & Molecular Biology

Tom40 is likely common to all mitochondria

Vojtech Zarsky et al.

CURRENT BIOLOGY (2012)

Article Microbiology

Morphology of the Trypanosome Bilobe, a Novel Cytoskeletal Structure

Heather J. Esson et al.

EUKARYOTIC CELL (2012)

Article Biochemistry & Molecular Biology

Efficient de novo assembly of large genomes using compressed data structures

Jared T. Simpson et al.

GENOME RESEARCH (2012)

Article Microbiology

The Revised Classification of Eukaryotes

Sina M. Adl et al.

JOURNAL OF EUKARYOTIC MICROBIOLOGY (2012)

Article Multidisciplinary Sciences

Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs

Bruce A. Curtis et al.

NATURE (2012)

Article Biochemical Research Methods

Fast gapped-read alignment with Bowtie 2

Ben Langmead et al.

NATURE METHODS (2012)

Review Genetics & Heredity

Insights into the regulation of protein abundance from proteomic and transcriptomic analyses

Christine Vogel et al.

NATURE REVIEWS GENETICS (2012)

Article Multidisciplinary Sciences

Adenylate Cyclases of Trypanosoma brucei Inhibit the Innate Immune Response of the Host

Didier Salmon et al.

SCIENCE (2012)

Review Plant Sciences

UV-B photoreceptor-mediated signalling in plants

Marc Heijde et al.

TRENDS IN PLANT SCIENCE (2012)

Review Plant Sciences

AT_CHLORO: a chloroplast protein database dedicated to sub-plastidial localization

Christophe Bruley et al.

FRONTIERS IN PLANT SCIENCE (2012)

Article Biochemical Research Methods

Scaffolding pre-assembled contigs using SSPACE

Marten Boetzer et al.

BIOINFORMATICS (2011)

Article Evolutionary Biology

Eukaryote-to-eukaryote gene transfer gives rise to genome mosaicism in euglenids

Shinichiro Maruyama et al.

BMC EVOLUTIONARY BIOLOGY (2011)

Article Biochemistry & Molecular Biology

Mitochondrial Preprotein Translocase of Trypanosomatids Has a Bacterial Origin

Mascha Pusnik et al.

CURRENT BIOLOGY (2011)

Letter Biochemical Research Methods

SignalP 4.0: discriminating signal peptides from transmembrane regions

Thomas Nordahl Petersen et al.

NATURE METHODS (2011)

Article Biochemistry & Molecular Biology

The resistance of DMC1 D-loops to dissociation may account for the DMC1 requirement in meiosis

Dmitry V. Bugreev et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2011)

Article Biochemistry & Molecular Biology

KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases

Chen Xie et al.

NUCLEIC ACIDS RESEARCH (2011)

Article Multidisciplinary Sciences

High-quality draft assemblies of mammalian genomes from massively parallel sequence data

Sante Gnerre et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)

Article Biochemical Research Methods

BEDTools: a flexible suite of utilities for comparing genomic features

Aaron R. Quinlan et al.

BIOINFORMATICS (2010)

Article Biochemical Research Methods

TreeGraph 2: Combining and visualizing evidence from different phylogenetic analyses

Ben C. Stoever et al.

BMC BIOINFORMATICS (2010)

Article Biochemistry & Molecular Biology

The Genome of Naegleria gruberi Illuminates Early Eukaryotic Versatility

Lillian K. Fritz-Laylin et al.

Article Biochemistry & Molecular Biology

Comprehensive Analysis of HAMP Domains: Implications for Transmembrane Signal Transduction

Stanislaw Dunin-Horkawicz et al.

JOURNAL OF MOLECULAR BIOLOGY (2010)

Article Biochemistry & Molecular Biology

TriTrypDB: a functional genomic resource for the Trypanosomatidae

Martin Aslett et al.

NUCLEIC ACIDS RESEARCH (2010)

Article Multidisciplinary Sciences

FastTree 2-Approximately Maximum-Likelihood Trees for Large Alignments

Morgan N. Price et al.

PLOS ONE (2010)

Article Biochemical Research Methods

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

Salvador Capella-Gutierrez et al.

BIOINFORMATICS (2009)

Article Biotechnology & Applied Microbiology

Insights into the genome sequence of a free-living Kinetoplastid: Bodo saltans (Kinetoplastida: Euglenozoa)

Andrew P. Jackson et al.

BMC GENOMICS (2008)

Article Biology

The origin of plastids

C. J. Howe et al.

PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2008)

Article Biochemical Research Methods

Clustal W and clustal X version 2.0

M. A. Larkin et al.

BIOINFORMATICS (2007)

Review Engineering, Environmental

Molecular mechanisms of resistance to heavy metals in the protist Euglena gracilis

Jose S. Rodriguez-Zavala et al.

JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH PART A-TOXIC/HAZARDOUS SUBSTANCES & ENVIRONMENTAL ENGINEERING (2007)

Article Biochemistry & Molecular Biology

KAAS: an automatic genome annotation and pathway reconstruction server

Yuki Moriya et al.

NUCLEIC ACIDS RESEARCH (2007)

Article Biochemical Research Methods

CEGMA: a pipeline to accurately annotate core genes in eukaryotic genornes

Genis Parra et al.

BIOINFORMATICS (2007)

Review Biochemical Research Methods

Locating proteins in the cell using TargetP, SignalP and related tools

Olof Emanuelsson et al.

NATURE PROTOCOLS (2007)

Article Engineering, Aerospace

Gravitaxis of Euglena gracilis depends only partially on passive buoyancy

Peter R. Richter et al.

ADVANCES IN SPACE RESEARCH (2007)

Article Biotechnology & Applied Microbiology

Evolution of Tubulin Gene Arrays in Trypanosomatid parasites:: genomic restructuring in Leishmania

Andrew P. Jackson et al.

BMC GENOMICS (2006)

Article Multidisciplinary Sciences

The genome of the African trypanosome Trypanosoma brucei

M Berriman et al.

SCIENCE (2005)

Article Biochemical Research Methods

Automated generation of heuristics for biological sequence comparison

GS Slater et al.

BMC BIOINFORMATICS (2005)

Article Biochemistry & Molecular Biology

PrediSi:: prediction of signal peptides and their cleavage positions

K Hiller et al.

NUCLEIC ACIDS RESEARCH (2004)

Review Microbiology

Kinetoplast DNA network:: Evolution of an improbable structure

J Lukes et al.

EUKARYOTIC CELL (2002)

Review Plant Sciences

Primary and secondary endosymbiosis and the origin of plastids

GI McFadden

JOURNAL OF PHYCOLOGY (2001)

Article Biochemical Research Methods

MRBAYES: Bayesian inference of phylogenetic trees

JP Huelsenbeck et al.

BIOINFORMATICS (2001)

Article Biochemistry & Molecular Biology

Analysis of Euglena gracilis alpha-, beta- and gamma-tubulin genes:: introns and pre-mRNA maturation

J Canaday et al.

MOLECULAR GENETICS AND GENOMICS (2001)

Article Biochemistry & Molecular Biology

Cache -: a signaling domain common to animal Ca2+ channel subunits and a class of prokaryotic chemotaxis receptors

V Anantharaman et al.

TRENDS IN BIOCHEMICAL SCIENCES (2000)

Article Biochemistry & Molecular Biology

The photoreceptor protein of Euglena gracilis

L Barsanti et al.

FEBS LETTERS (2000)

Article Biochemistry & Molecular Biology

Base J originally found in kinetoplastida is also a minor constituent of nuclear DNA of Euglena gracilis

D Dooijes et al.

NUCLEIC ACIDS RESEARCH (2000)

Article Biochemistry & Molecular Biology

A new twist in trypanosome RNA metabolism:: cis-splicing of pre-mRNA

G Mair et al.