Skip to main content
Premium Trial:

Request an Annual Quote

New Genomic Knowledgebase Combines Data From 30 Consortia

A University of Michigan team presents its new Genomic Knowledgebase (GenomicKB) in Nucleic Acids Research this week. This graph database combines data from 30 consortia, including from ENCODE, GENCODE, Genotype-Tissue Expression project, and NCBI dbVar, and encompasses 347 million nodes, 1.36 billion edges and 3.9 billion node/edge properties. GenomicKB further has a web-based portal where scientists may submit intuitive graph-based inquiries, such as: find "two genes which are both related to signal transduction, located on the same chromosome, and form ligand-receptor pairs," according to the developers. "With this portal, GenomicKB is capable of answering human genomics-related questions and conducting multi-modal analysis with a coding-free and interactive queries," the Michigan team adds. "Therefore, we expect that GenomicKB can attract researchers with diverse backgrounds and promote open science in genomic research."

The Scan

Machine Learning Helps ID Molecular Mechanisms of Pancreatic Islet Beta Cell Subtypes in Type 2 Diabetes

The approach helps overcome limitations of previous studies that had investigated the molecular mechanisms of pancreatic islet beta cells, the authors write in their Nature Genetics paper.

Culture-Based Methods, Shotgun Sequencing Reveal Transmission of Bifidobacterium Strains From Mothers to Infants

In a Nature Communications study, culture-based approaches along with shotgun sequencing give a better picture of the microbial strains transmitted from mothers to infants.

Microbial Communities Can Help Trees Adapt to Changing Climates

Tree seedlings that were inoculated with microbes from dry, warm, or cold sites could better survive drought, heat, and cold stress, according to a study in Science.

A Combination of Genetics and Environment Causes Cleft Lip

In a study published in Nature Communications, researchers investigate what combination of genetic and environmental factors come into play to cause cleft lip/palate.