Development of a physical geometric phantom for deformable image registration credentialing of radiotherapy centers for a clinical trial.

Purpose: This study aimed to develop a physical geometric phantom for the deformable image registration (DIR) credentialing of radiotherapy centers for a clinical trial and tested the feasibility of the proposed phantom at multiple domestic and international institutions.

Methods And Materials: The phantom reproduced tumor shrinkage, rectum shape change, and body shrinkage using several physical phantoms with custom inserts. We tested the feasibility of the proposed phantom using 5 DIR patterns at 17 domestic and 2 international institutions (21 datasets).

Identification of differentially expressed microRNAs in human hepatocellular adenoma associated with type I glycogen storage disease: a potential utility as biomarkers.

Background: It is known that malignant transformation to hepatocellular carcinoma (HCC) occurs at a higher frequency in hepatocellular adenoma (HCA) from type I glycogen storage disease (GSD I) compared to HCA from other etiologies. In this study, we aimed to identify differentially expressed miRNAs in GSD Ia HCA as candidates that could serve as putative biomarkers for detection of GSD Ia HCA and/or risk assessment of malignant transformation.

Methods: Utilizing massively parallel sequencing, the miRNA profiling was performed for paired adenomas and normal liver tissues from seven GSD Ia patients.

LISE: a server using ligand-interacting and site-enriched protein triangles for prediction of ligand-binding sites.

LISE is a web server for a novel method for predicting small molecule binding sites on proteins. It differs from a number of servers currently available for such predictions in two aspects. First, rather than relying on knowledge of similar protein structures, identification of surface cavities or estimation of binding energy, LISE computes a score by counting geometric motifs extracted from sub-structures of interaction networks connecting protein and ligand atoms.

VarioWatch: providing large-scale and comprehensive annotations on human genomic variants in the next generation sequencing era.

VarioWatch (http://genepipe.ncgm.sinica.

Functional analysis of novel SNPs and mutations in human and mouse genomes.

Background: With the flood of information generated by the new generation of sequencing technologies, more efficient bioinformatics tools are needed for in-depth impact analysis of novel genomic variations. FANS (Functional Analysis of Novel SNPs) was developed to streamline comprehensive but tedious functional analysis steps into a few clicks and to offer a carefully designed presentation of results so researchers can focus more on thinking instead of typing and calculating.

Results: FANS http://fans.

GenoWatch: a disease gene mining browser for association study.

A human gene association study often involves several genomic markers such as single nucleotide polymorphisms (SNPs) or short tandem repeat polymorphisms, and many statistically significant markers may be identified during the study. GenoWatch can efficiently extract up-to-date information about multiple markers and their associated genes in batch mode from many relevant biological databases in real-time. The comprehensive gene information retrieved includes gene ontology, function, pathway, disease, related articles in PubMed and so on.

PrimerZ: streamlined primer design for promoters, exons and human SNPs.

PrimerZ (http://genepipe.ngc.sinica.

FASTSNP: an always up-to-date and extendable service for SNP function analysis and prioritization.

Single nucleotide polymorphism (SNP) prioritization based on the phenotypic risk is essential for association studies. Assessment of the risk requires access to a variety of heterogeneous biological databases and analytical tools. FASTSNP (function analysis and selection tool for single nucleotide polymorphisms) is a web server that allows users to efficiently identify and prioritize high-risk SNPs according to their phenotypic risks and putative functional effects.