Integrating microRNA and mRNA expression profiling in Symbiodinium microadriaticum, a dinoflagellate symbiont of reef-building corals

Draft Assembly of the Symbiodinium minutum Nuclear Genome Reveals Dinoflagellate Gene Structure

(2013) Eiichi Shoguchi et al.   CURRENT BIOLOGY

Do miRNAs have a deep evolutionary history?

(2012) James E. Tarver et al.   BIOESSAYS

Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels

(2012) Marcel H. Schulz et al.   BIOINFORMATICS

Protein evolution in two co-occurring types of Symbiodinium: an exploration into the genetic basis of thermal tolerance in Symbiodinium clade D

(2012) Jason T Ladner et al.   BMC EVOLUTIONARY BIOLOGY

The Trypanosoma brucei CCCH zinc finger proteins ZC3H12 and ZC3H13

(2012) Benard Aswani Ouna et al.   MOLECULAR AND BIOCHEMICAL PARASITOLOGY

GenBank

(2012) Dennis A. Benson et al.   NUCLEIC ACIDS RESEARCH

Symbiodinium Transcriptomes: Genome Insights into the Dinoflagellate Symbionts of Reef-Building Corals

(2012) Till Bayer et al.   PLoS One

Transcriptional Response of Two Core Photosystem Genes in Symbiodinium spp. Exposed to Thermal Stress

(2012) Michael P. McGinley et al.   PLoS One

Quake: quality-aware detection and correction of sequencing errors

(2012) David R Kelley et al.   GENOME BIOLOGY

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers

(2011) Guillaume Marçais et al.   BIOINFORMATICS

Transcriptomic response of the red tide dinoflagellate, Karenia brevis, to nitrogen and phosphorus depletion and addition

(2011) Jeanine S Morey et al.   BMC GENOMICS

Functional implications of microRNAs in acute myeloid leukemia by integrating microRNA and messenger RNA expression profiling

(2011) Violaine Havelange et al.   CANCER

Identification of putative miRNAs from the deep-branching unicellular flagellates

(2011) Po-Jung Huang et al.   GENOMICS

Differential sensitivity of coral larvae to natural levels of ultraviolet radiation during the onset of larval competence

(2011) MANUEL ARANDA et al.   MOLECULAR ECOLOGY

The UniProt-GO Annotation database in 2011

(2011) E. C. Dimmer et al.   NUCLEIC ACIDS RESEARCH

miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades

(2011) Marc R. Friedländer et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database

(2011) M. Punta et al.   NUCLEIC ACIDS RESEARCH

A microRNA derived from an apparent canonical biogenesis pathway regulates variant surface protein gene expression in Giardia lamblia

(2011) A. A. Saraiya et al.   RNA

The emerging world of small silencing RNAs in protozoan parasites

(2011) Vanessa D. Atayde et al.   TRENDS IN PARASITOLOGY

UniProt Knowledgebase: a hub of integrated protein data

(2011) M. Magrane et al.   Database-The Journal of Biological Databases and Curation

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Eukaryotic cold shock domain proteins: highly versatile regulators of gene expression

(2010) Marija Mihailovich et al.   BIOESSAYS

Transcriptional Control of Gene Expression by MicroRNAs

(2010) Basel Khraiwesh et al.   CELL

Coral host transcriptomic states are correlated withSymbiodiniumgenotypes

(2010) M. K. DeSALVO et al.   MOLECULAR ECOLOGY

The Ectocarpus genome and the independent evolution of multicellularity in brown algae

(2010) J. Mark Cock et al.   NATURE

Cell signalling by microRNA165/6 directs gene dose-dependent root cell fate

(2010) Annelie Carlsbecker et al.   NATURE

miRBase: integrating microRNA annotation and deep-sequencing data

(2010) A. Kozomara et al.   NUCLEIC ACIDS RESEARCH

Threatened Corals Provide Underexplored Microbial Habitats

(2010) Shinichi Sunagawa et al.   PLoS One

Transcriptome Profiling of a Toxic Dinoflagellate Reveals a Gene-Rich Protist and a Potential Impact on Gene Expression Due to Bacterial Presence

(2010) Ahmed Moustafa et al.   PLoS One

Location-Specific Responses to Thermal Stress in Larvae of the Reef-Building Coral Montastraea faveolata

(2010) Nicholas R. Polato et al.   PLoS One

Spliced leader-based metatranscriptomic analyses lead to recognition of hidden genomic features in dinoflagellates

(2010) S. Lin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The origin and early evolution of eukaryotes in the light of phylogenomics

(2010) Eugene V Koonin   GENOME BIOLOGY

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Effects of temperature on gene expression in embryos of the coral Montastraea faveolata

(2009) Christian R Voolstra et al.   BMC GENOMICS

An Epigenetic Switch Involving NF-κB, Lin28, Let-7 MicroRNA, and IL6 Links Inflammation to Cell Transformation

(2009) Dimitrios Iliopoulos et al.   CELL

MicroRNAs: Target Recognition and Regulatory Functions

(2009) David P. Bartel   CELL

Origins and Mechanisms of miRNAs and siRNAs

(2009) Richard W. Carthew et al.   CELL

Identification of microRNA in the protist Trichomonas vaginalis

(2009) Wei-Chen Lin et al.   GENOMICS

Gene expression microarray analysis encompassing metamorphosis and the onset of calcification in the scleractinian coral Montastraea faveolata

(2009) Alejandro Reyes-Bermudez et al.   Marine Genomics

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

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

Structural insights into mechanisms of the small RNA methyltransferase HEN1

(2009) Ying Huang et al.   NATURE

Small silencing RNAs: an expanding universe

(2009) Megha Ghildiyal et al.   NATURE REVIEWS GENETICS

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Sorting of Small RNAs into Arabidopsis Argonaute Complexes Is Directed by the 5′ Terminal Nucleotide

(2008) Shijun Mi et al.   CELL

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

Differential gene expression during thermal stress and bleaching in the Caribbean coralMontastraea faveolata

(2008) M. K. DESALVO et al.   MOLECULAR ECOLOGY

Early origins and evolution of microRNAs and Piwi-interacting RNAs in animals

(2008) Andrew Grimson et al.   NATURE

Discovering microRNAs from deep sequencing data using miRDeep

(2008) Marc R Friedländer et al.   NATURE BIOTECHNOLOGY

MicroRNAs control de novo DNA methylation through regulation of transcriptional repressors in mouse embryonic stem cells

(2008) Lasse Sinkkonen et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

A mammalian microRNA cluster controls DNA methylation and telomere recombination via Rbl2-dependent regulation of DNA methyltransferases

(2008) Roberta Benetti et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

GOEAST: a web-based software toolkit for Gene Ontology enrichment analysis

(2008) Qi Zheng et al.   NUCLEIC ACIDS RESEARCH

Rapid determination of the damage to photosynthesis caused by salt and osmotic stresses using delayed fluorescence of chloroplasts

(2008) Lingrui Zhang et al.   PHOTOCHEMICAL & PHOTOBIOLOGICAL SCIENCES

Salt stress inhibits photosystems II and I in cyanobacteria

(2008) Suleyman I. Allakhverdiev et al.   PHOTOSYNTHESIS RESEARCH

Criteria for Annotation of Plant MicroRNAs

(2008) B. C. Meyers et al.   PLANT CELL