Experimental demonstration and pan-structurome prediction of climate-associated riboSNitches in Arabidopsis.

Background: Genome-wide association studies (GWAS) aim to correlate phenotypic changes with genotypic variation. Upon transcription, single nucleotide variants (SNVs) may alter mRNA structure, with potential impacts on transcript stability, macromolecular interactions, and translation. However, plant genomes have not been assessed for the presence of these structure-altering polymorphisms or "riboSNitches.

Ranked choice voting for representative transcripts with TRaCE.

Summary: Genome sequencing projects annotate protein-coding gene models with multiple transcripts, aiming to represent all of the available transcript evidence. However, downstream analyses often operate on only one representative transcript per gene locus, sometimes known as the canonical transcript. To choose canonical transcripts, Transcript Ranking and Canonical Election (TRaCE) holds an 'election' in which a set of RNA-seq samples rank transcripts by annotation edit distance.

Thoraco-Abdominal Abnormalities in Bardet-Biedl Syndrome: Situs Inversus and Heterotaxy.

Objectives: To characterize the diversity and prevalence of thoraco-abdominal abnormalities in Bardet-Biedl syndrome (BBS), a model ciliopathy for understanding the role of cilia in human health.

Study Design: The Clinical Registry Investigating BBS, a worldwide registry exploring the phenotype and natural history of BBS, was used to conduct the study. Protected health information was obtained by subject or family interview and Health Insurance Portability and Accountability Act-approved release of data including imaging studies and genetic testing.

Versatile synthesis and rational design of caged morpholinos.

Embryogenesis is regulated by genetic programs that are dynamically executed in a stereotypic manner, and deciphering these molecular mechanisms requires the ability to control embryonic gene function with similar spatial and temporal precision. Chemical technologies can enable such genetic manipulations, as exemplified by the use of caged morpholino (cMO) oligonucleotides to inactivate genes in zebrafish and other optically transparent organisms with spatiotemporal control. Here we report optimized methods for the design and synthesis of hairpin cMOs incorporating a dimethoxynitrobenzyl (DMNB)-based bifunctional linker that permits cMO assembly in only three steps from commercially available reagents.

Features of 5'-splice-site efficiency derived from disease-causing mutations and comparative genomics.

Many human diseases, including Fanconi anemia, hemophilia B, neurofibromatosis, and phenylketonuria, can be caused by 5'-splice-site (5'ss) mutations that are not predicted to disrupt splicing, according to position weight matrices. By using comparative genomics, we identify pairwise dependencies between 5'ss nucleotides as a conserved feature of the entire set of 5'ss. These dependencies are also conserved in human-mouse pairs of orthologous 5'ss.

Lightweight genome viewer: portable software for browsing genomics data in its chromosomal context.

Background: Lightweight genome viewer (lwgv) is a web-based tool for visualization of sequence annotations in their chromosomal context. It performs most of the functions of larger genome browsers, while relying on standard flat-file formats and bypassing the database needs of most visualization tools. Visualization as an aide to discovery requires display of novel data in conjunction with static annotations in their chromosomal context.

GeneSeer: a sage for gene names and genomic resources.

Background: Independent identification of genes in different organisms and assays has led to a multitude of names for each gene. This balkanization makes it difficult to use gene names to locate genomic resources, homologs in other species and relevant publications.

Methods: We solve the naming problem by collecting data from a variety of sources and building a name-translation database.