MicroRNAs (miRNAs), which play critical roles in gene regulatory networks, have emerged as promising diagnostic and prognostic biomarkers for human cancer. In particular, circulating miRNAs that are secreted into circulation exist in remarkably stable forms, and have enormous potential to be leveraged as non-invasive biomarkers for early cancer detection. Novel and user-friendly tools are desperately needed to facilitate data mining of the vast amount of miRNA expression data from The Cancer Genome Atlas (TCGA) and large-scale circulating miRNA profiling studies. To fill this void, we developed CancerMIRNome, a comprehensive database for the interactive analysis and visualization of miRNA expression profiles based on 10 554 samples from 33 TCGA projects and 28 633 samples from 40 public circulating miRNome datasets. A series of cutting-edge bioinformatics tools and machine learning algorithms have been packaged in CancerMIRNome, allowing for the pan-cancer analysis of a miRNA of interest across multiple cancer types and the comprehensive analysis of miRNome profiles to identify dysregulated miRNAs and develop diagnostic or prognostic signatures. The data analysis and visualization modules will greatly facilitate the exploit of the valuable resources and promote translational application of miRNA biomarkers in cancer. The CancerMIRNome database is publicly available at http://bioinfo.jialab-ucr.org/CancerMIRNome.

Premise: The measurement of leaf morphometric parameters from digital images can be time-consuming or restrictive when using digital image analysis softwares. The Multiple Leaf Sample Extraction System (MuLES) is a new tool that enables highthroughput leaf shape analysis with minimal user input or prerequisites, such as coding knowledge or image modification. Methods and Results: MuLES uses contrasting pixel color values to distinguish between leaf objects and their background area, eliminating the need for color threshold-based methods or color correction cards typically required in other software methods. The leaf morphometric parameters measured by this software, especially leaf aspect ratio, were able to distinguish between large populations of different accessions for the same species in a high-throughput manner.Conclusions: MuLES provides a simple method for the rapid measurement of leaf morphometric parameters in large plant populations from digital images and demonstrates the ability of leaf aspect ratio to distinguish between closely related plant types.

MicroRNAs (miRNAs), which play critical roles in gene regulatory networks, have emerged as promising biomarkers for a variety of human diseases, including cancer. In particular, circulating miRNAs that are secreted into circulation exist in remarkably stable forms, and have enormous potential to be leveraged as non-invasive diagnostic biomarkers for early cancer detection. The vast amount of miRNA expression data from tens of thousands of samples in various types of cancers generated by The Cancer Genome Atlas (TCGA) and circulating miRNA data produced by many large-scale circulating miRNA profiling studies provide extraordinary opportunities for the discovery and validation of miRNA signatures in cancer. Novel and user-friendly tools are desperately needed to facilitate the data mining of such valuable cancer miRNome datasets. To fill this void, we developed CancerMIRNome, a web server for interactive analysis and visualization of cancer miRNome data based on TCGA and public circulating miRNome datasets. A series of cutting-edge bioinformatics tools and functions have been packaged in CancerMIRNome, allowing for a pan-cancer analysis of a miRNA of interest across multiple cancer types and a comprehensive analysis of cancer miRNome at the dataset level. The CancerMIRNome web server is freely available at http://bioinfo.jialab-ucr.org/CancerMIRNome.

Our recent algorithm, Hapi, infers chromosome-scale haplotypes using genomic data of a small number of single gametes. Its advanced version, IIIandMe, is proposed here to achieve comparable phasing accuracy with as few as three gametes, pushing the analysis to its limit. The new method is validated with simulation and a citrus gamete dataset. The rapid advances in genotyping technologies promise a broad application of IIIandMe in disclosing important genetic information.