Transcriptome analysis illuminates the nature of the intracellular interaction in a vertebrate-algal symbiosis

Transcriptional characterization of Vibrio fischeri during colonization of juvenile Euprymna scolopes

(2017) Luke R. Thompson et al.   ENVIRONMENTAL MICROBIOLOGY

Olfactomedin 4 expression and functions in innate immunity, inflammation, and cancer

(2016) Wenli Liu et al.   CANCER AND METASTASIS REVIEWS

The transcriptomic response of the coralAcropora digitiferato a competentSymbiodiniumstrain: the symbiosome as an arrested early phagosome

(2016) A. R. Mohamed et al.   MOLECULAR ECOLOGY

Dual RNA-seq unveils noncoding RNA functions in host–pathogen interactions

(2016) Alexander J. Westermann et al.   NATURE

Transcriptome-based global analysis of gene expression in response to carbon dioxide deprivation in the green algae Chlorella pyrenoidosa

(2016) Jianhua Fan et al.   Algal Research-Biomass Biofuels and Bioproducts

Ambivalent Outcomes of Cell Apoptosis: A Barrier or Blessing in Malaria Progression

(2016) Parik Kakani et al.   Frontiers in Microbiology

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Apical Invasion of Intestinal Epithelial Cells by Salmonella typhimurium Requires Villin to Remodel the Brush Border Actin Cytoskeleton

(2015) Nouara Lhocine et al.   Cell Host & Microbe

Toll-like receptor signaling in parasitic infections

(2015) Dalia S Ashour   Expert Review of Clinical Immunology

Comparative Genomics of a Bacterivorous Green Alga Reveals Evolutionary Causalities and Consequences of Phago-Mixotrophic Mode of Nutrition

(2015) John A. Burns et al.   Genome Biology and Evolution

Impact of three Illumina library construction methods on GC bias and HLA genotype calling

(2015) James H. Lan et al.   HUMAN IMMUNOLOGY

The VGF-derived peptide TLQP-62 modulates insulin secretion and glucose homeostasis

(2015) P. Petrocchi-Passeri et al.   JOURNAL OF MOLECULAR ENDOCRINOLOGY

Algae after dark: mechanisms to cope with anoxic/hypoxic conditions

(2015) Wenqiang Yang et al.   PLANT JOURNAL

Induction of Photosynthetic Carbon Fixation in Anoxia Relies on Hydrogenase Activity and Proton-Gradient Regulation-Like1-Mediated Cyclic Electron Flow inChlamydomonas reinhardtii

(2015) Damien Godaux et al.   PLANT PHYSIOLOGY

The Symbiodinium kawagutii genome illuminates dinoflagellate gene expression and coral symbiosis

(2015) S. Lin et al.   SCIENCE

Malaria parasites target the hepatocyte receptor EphA2 for successful host infection

(2015) A. Kaushansky et al.   SCIENCE

Oxidative Stress Control by Apicomplexan Parasites

(2015) Soraya S. Bosch et al.   Biomed Research International

Initial characterization of the large genome of the salamander Ambystoma mexicanum using shotgun and laser capture chromosome sequencing

(2015) Melissa C. Keinath et al.   Scientific Reports

The Importance of Microbes in Animal Development: Lessons from the Squid-Vibrio Symbiosis

(2014) Margaret J. McFall-Ngai   Annual Review of Microbiology

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Conservation and divergence in the frog immunome: pyrosequencing and de novo assembly of immune tissue transcriptomes

(2014) Anna E. Savage et al.   GENE

Bacteria in the Vaginal Microbiome Alter the Innate Immune Response and Barrier Properties of the Human Vaginal Epithelia in a Species-Specific Manner

(2014) Sylvie Y. Doerflinger et al.   JOURNAL OF INFECTIOUS DISEASES

Are Niemann-Pick type C proteins key players in cnidarian-dinoflagellate endosymbioses?

(2014) Vincent Dani et al.   MOLECULAR ECOLOGY

Variation in RNA-Seq Transcriptome Profiles of Peripheral Whole Blood from Healthy Individuals with and without Globin Depletion

(2014) Heesun Shin et al.   PLoS One

PASTEC: An Automatic Transposable Element Classification Tool

(2014) Claire Hoede et al.   PLoS One

Phylogenetic Analysis of Algal Symbionts Associated with Four North American Amphibian Egg Masses

(2014) Eunsoo Kim et al.   PLoS One

New Candidate Biomarkers in the Female Genital Tract to Evaluate Microbicide Toxicity

(2014) Scott Fields et al.   PLoS One

The roles of oxygen and ammonia in the symbiotic relationship between the spotted salamander Ambystoma maculatum and the green alga Oophila amblystomatis during embryonic development

(2014) Daniel P. Small et al.   SYMBIOSIS

Fighting a Losing Battle: Vigorous Immune Response Countered by Pathogen Suppression of Host Defenses in the Chytridiomycosis-Susceptible Frog Atelopus zeteki

(2014) Amy R. Ellison et al.   G3-Genes Genomes Genetics

De novo transcriptomic analysis of hydrogen production in the green alga Chlamydomonas moewusii through RNA-Seq

(2013) Shihui Yang et al.   Biotechnology for Biofuels

De novo transcriptome sequencing of axolotl blastema for identification of differentially expressed genes during limb regeneration

(2013) Cheng-Han Wu et al.   BMC GENOMICS

Loss of Cytochrome c Oxidase Promotes RAS-Dependent ROS Production from the ER Resident NADPH Oxidase, Yno1p, in Yeast

(2013) Jane E. Leadsham et al.   Cell Metabolism

Hypoxia promotes liver-stage malaria infection in primary human hepatocytes in vitro

(2013) S. Ng et al.   Disease Models & Mechanisms

Steap4 Plays a Critical Role in Osteoclastogenesisin Vitroby Regulating Cellular Iron/Reactive Oxygen Species (ROS) Levels and cAMP Response Element-binding Protein (CREB) Activation

(2013) Jian Zhou et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The role of short-chain fatty acids in the interplay between diet, gut microbiota, and host energy metabolism

(2013) Gijs den Besten et al.   JOURNAL OF LIPID RESEARCH

Analysis of the Human Tissue-specific Expression by Genome-wide Integration of Transcriptomics and Antibody-based Proteomics

(2013) Linn Fagerberg et al.   MOLECULAR & CELLULAR PROTEOMICS

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

Increased photosystem II stability promotes H2 production in sulfur-deprived Chlamydomonas reinhardtii

(2013) A. Volgusheva et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Extensive Differences in Gene Expression Between Symbiotic and Aposymbiotic Cnidarians

(2013) Erik M. Lehnert et al.   G3-Genes Genomes Genetics

Comparative RNA-seq Analysis in the Unsequenced Axolotl: The Oncogene Burst Highlights Early Gene Expression in the Blastema

(2013) Ron Stewart et al.   PLoS Computational Biology

Fermentation metabolism and its evolution in algae

(2013) Claudia Catalanotti et al.   Frontiers in Plant Science

Removing technical variability in RNA-seq data using conditional quantile normalization

(2012) K. D. Hansen et al.   BIOSTATISTICS

Gemi: PCR Primers Prediction from Multiple Alignments

(2012) Haitham Sobhy et al.   COMPARATIVE AND FUNCTIONAL GENOMICS

Emerging roles for TNIP1 in regulating post-receptor signaling

(2012) Vincent P. Ramirez et al.   CYTOKINE & GROWTH FACTOR REVIEWS

Regulation of cnidarian–dinoflagellate mutualisms: Evidence that activation of a host TGFβ innate immune pathway promotes tolerance of the symbiont

(2012) Olivier Detournay et al.   DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY

Validation of housekeeping genes for gene expression studies in an ice alga Chlamydomonas during freezing acclimation

(2012) Chenlin Liu et al.   EXTREMOPHILES

High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression

(2012) P. Batut et al.   GENOME RESEARCH

Intracapsular algae provide fixed carbon to developing embryos of the salamander Ambystoma maculatum

(2012) E. R. Graham et al.   JOURNAL OF EXPERIMENTAL BIOLOGY

Evidence that glucose is the major transferred metabolite in dinoflagellate-cnidarian symbiosis

(2012) M. S. Burriesci et al.   JOURNAL OF EXPERIMENTAL BIOLOGY

Cell Biology of Cnidarian-Dinoflagellate Symbiosis

(2012) S. K. Davy et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Dual RNA-seq of pathogen and host

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

Primer3—new capabilities and interfaces

(2012) Andreas Untergasser et al.   NUCLEIC ACIDS RESEARCH

Effects of Gut Microbes on Nutrient Absorption and Energy Regulation

(2012) Rosa Krajmalnik-Brown et al.   NUTRITION IN CLINICAL PRACTICE

Bcl-2 family member Bcl-G is not a proapoptotic protein

(2012) M Giam et al.   Cell Death & Disease

An Interspecies Regulatory Network Inferred from Simultaneous RNA-seq of Candida albicans Invading Innate Immune Cells

(2012) Lanay Tierney et al.   Frontiers in Microbiology

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

(2011) Bo Li et al.   BMC BIOINFORMATICS

Olfactomedin-4 is a glycoprotein secreted into mucus in active IBD

(2011) Michael Gersemann et al.   Journal of Crohns & Colitis

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Host-mediated regulation of superinfection in malaria

(2011) Silvia Portugal et al.   NATURE MEDICINE

HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment

(2011) Michael Remmert et al.   NATURE METHODS

Remodeling of the Metabolome during Early Frog Development

(2011) Livia Vastag et al.   PLoS One

REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms

(2011) Fran Supek et al.   PLoS One

Intracellular invasion of green algae in a salamander host

(2011) R. Kerney et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Toll-Like Receptor 2 Pathway Establishes Colonization by a Commensal of the Human Microbiota

(2011) J. L. Round et al.   SCIENCE

Primary Involvement of NADPH Oxidase 4 in Hypoxia-Induced Generation of Reactive Oxygen Species in Adipose-Derived Stem Cells

(2011) Ji Hye Kim et al.   STEM CELLS AND DEVELOPMENT

Dual oxidase in the intestinal epithelium of zebrafish larvae has anti-bacterial properties

(2010) Maria Vega Flores et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Calcification in bleached and unbleached Montastraea faveolata: evaluating the role of oxygen and glycerol

(2010) M. F. Colombo-Pallotta et al.   CORAL REEFS

Lipid hydrolizing enzymes in virulence:Mycobacterium tuberculosisas a model system

(2010) Gurdyal Singh et al.   CRITICAL REVIEWS IN MICROBIOLOGY

Tilapia hepcidin (TH)2-3 as a transgene in transgenic fish enhances resistance to Vibrio vulnificus infection and causes variations in immune-related genes after infection by different bacterial species

(2010) Jung-Chen Hsieh et al.   FISH & SHELLFISH IMMUNOLOGY

Colorectal carcinoma cells—Regulation of survival and growth by SGK1

(2010) Florian Lang et al.   INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY

Central carbon metabolism of Plasmodium parasites

(2010) Kellen L. Olszewski et al.   MOLECULAR AND BIOCHEMICAL PARASITOLOGY

The developmental transcriptome of Drosophila melanogaster

(2010) Brenton R. Graveley et al.   NATURE

Multiple facets of anoxic metabolism and hydrogen production in the unicellular green alga Chlamydomonas reinhardtii

(2010) Arthur R. Grossman et al.   NEW PHYTOLOGIST

RNA-Seq Analysis of Sulfur-DeprivedChlamydomonasCells Reveals Aspects of Acclimation Critical for Cell Survival

(2010) David González-Ballester et al.   PLANT CELL

Olfactomedin 4 down-regulates innate immunity against Helicobacter pylori infection

(2010) W. Liu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcriptional patterns in both host and bacterium underlie a daily rhythm of anatomical and metabolic change in a beneficial symbiosis

(2010) A. M. Wier et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A scaling normalization method for differential expression analysis of RNA-seq data

(2010) Mark D Robinson et al.   GENOME BIOLOGY

ABINs: A20 binding inhibitors of NF-κB and apoptosis signaling

(2009) Lynn Verstrepen et al.   BIOCHEMICAL PHARMACOLOGY

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Study of hydrogen production by three strains of Chlorella isolated from the soil in the Algerian Sahara

(2009) Samira Chader et al.   INTERNATIONAL JOURNAL OF HYDROGEN ENERGY

SeaView Version 4: A Multiplatform Graphical User Interface for Sequence Alignment and Phylogenetic Tree Building

(2009) M. Gouy et al.   MOLECULAR BIOLOGY AND EVOLUTION

The host transcriptome remains unaltered during the establishment of coral-algal symbioses

(2009) CHRISTIAN R. VOOLSTRA et al.   MOLECULAR ECOLOGY

Amplification efficiency: linking baseline and bias in the analysis of quantitative PCR data

(2009) J. M. Ruijter et al.   NUCLEIC ACIDS RESEARCH

Genome-Wide Transcriptional Response of Silurana (Xenopus) tropicalis to Infection with the Deadly Chytrid Fungus

(2009) Erica Bree Rosenblum et al.   PLoS One

Transcriptome for Photobiological Hydrogen Production Induced by Sulfur Deprivation in the Green AlgaChlamydomonas reinhardtii

(2008) Anh Vu Nguyen et al.   EUKARYOTIC CELL

Insulin sensitivity: modulation by nutrients and inflammation

(2008) Simon Schenk et al.   JOURNAL OF CLINICAL INVESTIGATION

Saprolegniaceae identified on amphibian eggs throughout the Pacific Northwest, USA, by internal transcribed spacer sequences and phylogenetic analysis

(2008) J. E. Petrisko et al.   MYCOLOGIA

Worlds within worlds: evolution of the vertebrate gut microbiota

(2008) Ruth E. Ley et al.   NATURE REVIEWS MICROBIOLOGY

IDT SciTools: a suite for analysis and design of nucleic acid oligomers

(2008) R. Owczarzy et al.   NUCLEIC ACIDS RESEARCH

MUC1 Mucin Is a Negative Regulator of Toll-Like Receptor Signaling

(2007) Keiko Ueno et al.   AMERICAN JOURNAL OF RESPIRATORY CELL AND MOLECULAR BIOLOGY