Metabolic and molecular modelling of zebrafish gut biome to unravel antimicrobial peptides through metagenomics

Putative Antimicrobial Peptides in Fish: Using Zebrafish as a Representative

(2020) Xiyang Chen et al.   PROTEIN AND PEPTIDE LETTERS

Evaluating metagenomics tools for genome binning with real metagenomic datasets and CAMI datasets

(2020) Yi Yue et al.   BMC BIOINFORMATICS

Macrel: antimicrobial peptide screening in genomes and metagenomes

(2020) Célio Dias Santos-Júnior et al.   PeerJ

Shotgun metagenomics offers novel insights into taxonomic compositions, metabolic pathways and antibiotic resistance genes in fish gut microbiome

(2019) Anuj Tyagi et al.   ARCHIVES OF MICROBIOLOGY

The Gut Microbiome in Inflammatory Bowel Disease

(2019) Natalie C. Knox et al.   AMERICAN JOURNAL OF GASTROENTEROLOGY

Simple animal models for microbiome research

(2019) Angela E. Douglas   NATURE REVIEWS MICROBIOLOGY

Antimicrobial Peptide Designing and Optimization Employing Large-Scale Flexibility Analysis of Protein-Peptide Fragments

(2019) Neeraj Kumar et al.   ACS Omega

Dissection of the antimicrobial and hemolytic activity of Cap18: Generation of Cap18 derivatives with enhanced specificity

(2018) Anna Ebbensgaard et al.   PLoS One

The Gut Microbiota of Marine Fish

(2018) Sian Egerton et al.   Frontiers in Microbiology

Antimicrobial Peptides: Interaction With Model and Biological Membranes and Synergism With Chemical Antibiotics

(2018) Axel Hollmann et al.   Frontiers in Chemistry

A Dynamic Overview of Antimicrobial Peptides and Their Complexes

(2018) Viviane Silva de Paula et al.   MOLECULES

Phylogenetic barriers to horizontal transfer of antimicrobial peptide resistance genes in the human gut microbiota

(2018) Bálint Kintses et al.   Nature Microbiology

Metagenomics analysis of gut microbiota and immune modulation in zebrafish ( Danio rerio ) fed chitosan silver nanocomposites

(2017) R.M.C. Udayangani et al.   FISH & SHELLFISH IMMUNOLOGY

Unraveling the Microbial Interactions and Metabolic Potentials in Pre- and Post-treated Sludge from a Wastewater Treatment Plant Using Metagenomic Studies

(2017) Chandni Sidhu et al.   Frontiers in Microbiology

The association of aberrant folylpolyglutamate synthetase splicing with ex vivo methotrexate resistance and clinical outcome in childhood acute lymphoblastic leukemia

(2016) A. Wojtuszkiewicz et al.   HAEMATOLOGICA

Fast and sensitive taxonomic classification for metagenomics with Kaiju

(2016) Peter Menzel et al.   Nature Communications

Characterization of the Gut Microbiome Using 16S or Shotgun Metagenomics

(2016) Juan Jovel et al.   Frontiers in Microbiology

The association of aberrant folylpolyglutamate synthetase splicing with ex vivo methotrexate resistance and clinical outcome in childhood acute lymphoblastic leukemia

(2016) A. Wojtuszkiewicz et al.   HAEMATOLOGICA

Contribution of Amphipathicity and Hydrophobicity to the Antimicrobial Activity and Cytotoxicity of β-Hairpin Peptides

(2016) Ingrid A. Edwards et al.   ACS Infectious Diseases

Docking and molecular dynamics simulations of the ternary complex nisin 2 :lipid II

(2016) Sam Mulholland et al.   Scientific Reports

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

(2015) Dinghua Li et al.   BIOINFORMATICS

Virulence-Associated Enzymes of Cryptococcus neoformans

(2015) Fausto Almeida et al.   EUKARYOTIC CELL

Counteraction of antibiotic production and degradation stabilizes microbial communities

(2015) Eric D. Kelsic et al.   NATURE

DBAASP v.2: an enhanced database of structure and antimicrobial/cytotoxic activity of natural and synthetic peptides

(2015) Malak Pirtskhalava et al.   NUCLEIC ACIDS RESEARCH

Socially mediated induction and suppression of antibiosis during bacterial coexistence

(2015) Monica I. Abrudan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fully Blind Peptide-Protein Docking with pepATTRACT

(2015) Christina E.M. Schindler et al.   STRUCTURE

In vitro properties of designed antimicrobial peptides that exhibit potent antipneumococcal activity and produces synergism in combination with penicillin

(2015) Cheng-Foh Le et al.   Scientific Reports

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

The vitamin B12 analog cobinamide is an effective hydrogen sulfide antidote in a lethal rabbit model

(2014) M. Brenner et al.   CLINICAL TOXICOLOGY

Improved PEP-FOLD Approach for Peptide and Miniprotein Structure Prediction

(2014) Yimin Shen et al.   Journal of Chemical Theory and Computation

Klebsiella pneumoniae Peptidoglycan-Associated Lipoprotein and Murein Lipoprotein Contribute to Serum Resistance, Antiphagocytosis, and Proinflammatory Cytokine Stimulation

(2013) P.-F. Hsieh et al.   JOURNAL OF INFECTIOUS DISEASES

The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)

(2013) Ross Overbeek et al.   NUCLEIC ACIDS RESEARCH

Software applications for flux balance analysis

(2012) M. Lakshmanan et al.   BRIEFINGS IN BIOINFORMATICS

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

Side-chain hydrophobicity scale derived from transmembrane protein folding into lipid bilayers

(2011) C. P. Moon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-throughput generation, optimization and analysis of genome-scale metabolic models

(2010) Christopher S Henry et al.   NATURE BIOTECHNOLOGY

Stearic acid-induced cardiac lipotoxicity is independent of cellular lipid and is mitigated by the fatty acids oleic and capric acid but not by the PPAR agonist troglitazone

(2009) Simon W. Rabkin et al.   EXPERIMENTAL PHYSIOLOGY