High-quality reference genome of Fasciola gigantica: Insights into the genomic signatures of transposon-mediated evolution and specific parasitic adaption in tropical regions

Identifying and removing haplotypic duplication in primary genome assemblies

(2020) Dengfeng Guan et al.   BIOINFORMATICS

Understanding divergent domestication traits from the whole-genome sequencing of swamp and river buffalo populations

(2020) Xier Luo et al.   National Science Review

RepeatModeler2 for automated genomic discovery of transposable element families

(2020) Jullien M. Flynn et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Draft Genome of the Liver Fluke Fasciola gigantica

(2020) Tripti Pandey et al.   ACS Omega

Measuring and interpreting transposable element expression

(2020) Sophie Lanciano et al.   NATURE REVIEWS GENETICS

Surface molecules of extracellular vesicles secreted by the helminth pathogen Fasciola hepatica direct their internalisation by host cells

(2019) Eduardo de la Torre-Escudero et al.   PLoS Neglected Tropical Diseases

Global serum proteomic changes in water buffaloes infected with Fasciola gigantica

(2019) Fu-Kai Zhang et al.   Parasites & Vectors

Adaptive Radiation of the Flukes of the Family Fasciolidae Inferred from Genome-Wide Comparisons of Key Species

(2019) Young-Jun Choi et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2019) Daehwan Kim et al.   NATURE BIOTECHNOLOGY

Complex and dynamic transcriptional changes allow the helminth Fasciola gigantica to adjust to its intermediate snail and definitive mammalian hosts

(2019) Xiao-Xuan Zhang et al.   BMC GENOMICS

Generation of oxidative stress and induction of apoptotic like events in curcumin and thymoquinone treated adult Fasciola gigantica worms

(2019) Abdur Rehman et al.   EXPERIMENTAL PARASITOLOGY

Versatile genome assembly evaluation with QUAST-LG

(2018) Alla Mikheenko et al.   BIOINFORMATICS

Inter-Species/Host-Parasite Protein Interaction Predictions Reviewed

(2018) Jumoke Soyemi et al.   Current Bioinformatics

The genome of tapeworm Taenia multiceps sheds light on understanding parasitic mechanism and control of coenurosis disease

(2018) Wenhui Li et al.   DNA RESEARCH

Environmental changes during the Cretaceous-Paleogene mass extinction and Paleocene-Eocene Thermal Maximum: Implications for the Anthropocene

(2018) Gerta Keller et al.   GONDWANA RESEARCH

Advances in Fasciola hepatica research using ‘omics’ technologies

(2018) Krystyna Cwiklinski et al.   INTERNATIONAL JOURNAL FOR PARASITOLOGY

Piercing the dark matter: bioinformatics of long-range sequencing and mapping

(2018) Fritz J. Sedlazeck et al.   NATURE REVIEWS GENETICS

Biogenesis and function of ESCRT-dependent extracellular vesicles

(2018) Thomas Juan et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

De novo genome and transcriptome analyses provide insights into the biology of the trematode human parasite Fasciolopsis buski

(2018) Devendra Kumar Biswal et al.   PLoS One

Cytoscape StringApp: Network Analysis and Visualization of Proteomics Data

(2018) Nadezhda T. Doncheva et al.   JOURNAL OF PROTEOME RESEARCH

Canu: scalable and accurate long-read assembly via adaptivek-mer weighting and repeat separation

(2017) Sergey Koren et al.   GENOME RESEARCH

BUSCO Applications from Quality Assessments to Gene Prediction and Phylogenomics

(2017) Robert M Waterhouse et al.   MOLECULAR BIOLOGY AND EVOLUTION

Transcriptomic responses of water buffalo liver to infection with the digenetic fluke Fasciola gigantica

(2017) Fu-Kai Zhang et al.   Parasites & Vectors

Genomes of Fasciola hepatica from the Americas Reveal Colonization with Neorickettsia Endobacteria Related to the Agents of Potomac Horse and Human Sennetsu Fevers

(2017) Samantha N. McNulty et al.   PLoS Genetics

Cytosolic superoxide dismutase can provide protection against Fasciola gigantica

(2016) Wipaphorn Jaikua et al.   ACTA TROPICA

Protein disulfide isomerase mediates glutathione depletion-induced cytotoxicity

(2016) Kazushi Okada et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Aquaporin modulators: a patent review (2010–2015)

(2016) Graça Soveral et al.   EXPERT OPINION ON THERAPEUTIC PATENTS

BlastKOALA and GhostKOALA: KEGG Tools for Functional Characterization of Genome and Metagenome Sequences

(2016) Minoru Kanehisa et al.   JOURNAL OF MOLECULAR BIOLOGY

Exploring the gating mechanisms of aquaporin-3: new clues for the design of inhibitors?

(2016) A. de Almeida et al.   Molecular BioSystems

Regulatory activities of transposable elements: from conflicts to benefits

(2016) Edward B. Chuong et al.   NATURE REVIEWS GENETICS

UniProt: the universal protein knowledgebase

(2016)   NUCLEIC ACIDS RESEARCH

Current Threat of Triclabendazole Resistance in Fasciola hepatica

(2016) Jane M. Kelley et al.   TRENDS IN PARASITOLOGY

Actin and Actin-Binding Proteins

(2016) Thomas D. Pollard   Cold Spring Harbor Perspectives in Biology

Across intra-mammalian stages of the liver f luke Fasciola hepatica: a proteomic study

(2016) Lucía Sánchez Di Maggio et al.   Scientific Reports

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

Assembling large genomes with single-molecule sequencing and locality-sensitive hashing

(2015) Konstantin Berlin et al.   NATURE BIOTECHNOLOGY

p24 family proteins: key players in the regulation of trafficking along the secretory pathway

(2015) Noelia Pastor-Cantizano et al.   PROTOPLASMA

The Fasciola hepatica genome: gene duplication and polymorphism reveals adaptation to the host environment and the capacity for rapid evolution

(2015) Krystyna Cwiklinski et al.   GENOME BIOLOGY

Comprehensive comparison of large-scale tissue expression datasets

(2015) Alberto Santos et al.   PeerJ

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

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

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

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

Estimating Gene Gain and Loss Rates in the Presence of Error in Genome Assembly and Annotation Using CAFE 3

(2013) Mira V. Han et al.   MOLECULAR BIOLOGY AND EVOLUTION

Coupled transport of Arabidopsis p24 proteins at the ER–Golgi interface

(2012) Juan Carlos Montesinos et al.   JOURNAL OF EXPERIMENTAL BOTANY

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

(2012) Guangchuang Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

Real-Time Evolution of New Genes by Innovation, Amplification, and Divergence

(2012) J. Nasvall et al.   SCIENCE

Actin Structure and Function

(2011) Roberto Dominguez et al.   Annual Review of Biophysics

MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects

(2011) Carson Holt et al.   BMC BIOINFORMATICS

Regulation of chromatin by histone modifications

(2011) Andrew J Bannister et al.   CELL RESEARCH

Molecular and immunological characterization of Fasciola antigens recognized by the MM3 monoclonal antibody

(2011) L. Muiño et al.   MOLECULAR AND BIOCHEMICAL PARASITOLOGY

Transposon-mediated rewiring of gene regulatory networks contributed to the evolution of pregnancy in mammals

(2011) Vincent J Lynch et al.   NATURE GENETICS

SignalP 4.0: discriminating signal peptides from transmembrane regions

(2011) Thomas Nordahl Petersen et al.   NATURE METHODS

Estimating the timing of early eukaryotic diversification with multigene molecular clocks

(2011) L. W. Parfrey et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The draft genome of the carcinogenic human liver fluke Clonorchis sinensis

(2011) Xiaoyun Wang et al.   GENOME BIOLOGY

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

Functional analysis of novel aquaporins from Fasciola gigantica

(2010) Amornrat Geadkaew et al.   MOLECULAR AND BIOCHEMICAL PARASITOLOGY

Monomethylation of Histone H4-Lysine 20 Is Involved in Chromosome Structure and Stability and Is Essential for Mouse Development

(2009) H. Oda et al.   MOLECULAR AND CELLULAR BIOLOGY

The genome of the blood fluke Schistosoma mansoni

(2009) Matthew Berriman et al.   NATURE

STRING 8--a global view on proteins and their functional interactions in 630 organisms

(2008) L. J. Jensen et al.   NUCLEIC ACIDS RESEARCH

Human fascioliasis and the presence of hybrid/introgressed forms of Fasciola hepatica and Fasciola gigantica in Vietnam

(2007) Thanh Hoa Le et al.   INTERNATIONAL JOURNAL FOR PARASITOLOGY