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A Pattern-Based Method for the Identification of MicroRNA Binding Sites and Their Corresponding Heteroduplexes
We present rna22, a method for identifying microRNA binding sites and their corresponding heteroduplexes. Rna22 does not rely upon cross-species conservation, is resilient to noise, and, unlikeExpand
Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite
A metagenomic analysis of the bacterial community resident in the hindgut paunch of a wood-feeding ‘higher’ Nasutitermes species shows the presence of a large, diverse set of bacterial genes for cellulose and xylan hydrolysis, the first system-wide gene analysis of a microbial community specialized towards plant lignocellulose degradation. Expand
The Draft Genome of Ciona intestinalis: Insights into Chordate and Vertebrate Origins
A draft of the protein-coding portion of the genome of the most studied ascidian, Ciona intestinalis, is generated, suggesting that ascidians contain the basic ancestral complement of genes involved in cell signaling and development. Expand
Dynamic changes in the human methylome during differentiation.
A whole-genome comparative view of DNA methylation using bisulfite sequencing of three cultured cell types representing progressive stages of differentiation highlights the value of high-resolution methylation maps, in conjunction with other systems-level analyses, for investigation of previously undetectable developmental regulatory mechanisms. Expand
Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communities
A metagenomic analysis of two lab-scale EBPR sludges dominated by the uncultured bacterium, “Candidatus Accumulibacter phosphatis,” sheds light on several controversies in EBPR metabolic models and provides hypotheses explaining the dominance of A. phosphatis. Expand
Accurate phylogenetic classification of variable-length DNA fragments
PhyloPythia is presented, a composition-based classifier that combines higher-level generic clades from a set of 340 completed genomes with sample-derived population models and allows the accurate classification of most sequence fragments across all considered taxonomic ranks, even for unknown organisms. Expand
The Expression of MicroRNA miR-107 Decreases Early in Alzheimer's Disease and May Accelerate Disease Progression through Regulation of β-Site Amyloid Precursor Protein-Cleaving Enzyme 1
Together, the coordinated application of miRNA profiling, Affymetrix microarrays, new bioinformatics predictions, in situ hybridization, and biochemical validation indicate that miR-107 may be involved in accelerated disease progression through regulation of BACE1. Expand
Coding-Independent Regulation of the Tumor Suppressor PTEN by Competing Endogenous mRNAs
This study identified and validated endogenous protein-coding transcripts that regulate PTEN, antagonize PI3K/AKT signaling, and possess growth- and tumor-suppressive properties and presents a road map for the prediction and validation of ceRNA activity and networks and thus imparts a trans-regulatory function to protein- coding mRNAs. Expand
Combinatorial pattern discovery in biological sequences: The TEIRESIAS algorithm [published erratum appears in Bioinformatics 1998;14(2): 229]
A new algorithm for the discovery of rigid patterns (motifs) in biological sequences that is combinatorial in nature and able to produce all patterns that appear in at least a (user-defined) minimum number of sequences, yet it manages to be very efficient by avoiding the enumeration of the entire pattern space. Expand
MicroRNAs to Nanog, Oct4 and Sox2 coding regions modulate embryonic stem cell differentiation
The findings demonstrate the abundance of CDS-located miRNA targets, some of which can be species-specific, and support an augmented model whereby animal miRNAs exercise their control on mRNAs through targets that can reside beyond the 3′ untranslated region. Expand