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This week, Pacific Biosciences released a software tool for its single-molecule, real-time sequencer that detects DNA base modifications associated with epigenetic regulation and DNA damage during the sequencing process.

According to the company, the new analysis tool enables users to detect and visualize these modifications. It works by measuring the rate of DNA base incorporation during the sequencing process. Researchers can also use the tool to re-analyze existing data to detect methylation and other base modifications.


Accelrys has released Discovery Studio 3.5, the latest version of its modeling and simulation software for small- and large-molecule life sciences research and development.

The release includes a validated ligand-profiling database for drug repurposing studies; tools to assess the development potential of putative biologics; updated scientific collections which enable organizations to build, deploy, analyze, and report on complex scientific data types using Accelrys Enterprise platform; and other new features.


Velvet 1.2.07 is now available.

This release includes a new file format option, an updated version of MetaVelvet, and several bug fixes.


The National Center for Biotechnology Information has released GenBank 190.0 via ftp.

Uncompressed 190.0 flatfiles require roughly 553 gigabytes for sequence files only; or 595 gigabytes to include the short directory, index, and text files. The ASN.1 data requires approximately 454 gigabytes.


This week, the genome browser team at the University of California, Santa Cruz released new browsers for the Western painted turtle and the lesser hedgehog tenrec, as well as updated assemblies for the cow, rat, and chicken.


Definiens, a provider of image analysis and data mining solutions for quantitative digital pathology, has released version 2 of its Image Miner software.

The new release provides researchers with the ability to investigate trends and patterns in large data sets as well as view analysis details in single images. It also links readouts and underlying images; supports predictive modeling by correlating image analysis results with data from sources like patient outcome data; and provides interactive plots and data tables for real-time feedback on study trends, among other features.


The Scan

Cell Atlas of Human Lung Development Gives View of Developing Airway

Researchers have generated a cell atlas of human lung development, which they report in Cell.

Study Finds Costs of Genome Sequencing May Limit Utility in Routine Care

Researchers report in the European Journal of Human Genetics that genome sequencing for rare disease diagnoses currently has similar benefits as less expensive exome analysis.

Study Suggests Nursing Mother's Diet Can Impact Offspring's Gut Microbiome

A new Cell Host and Microbe paper finds that mice whose mothers were fed a low-fiber diet during nursing experience lasting microbiota dysbiosis and increased obesity.

Study Links Genetic Risk for ADHD With Alzheimer's Disease

A higher polygenic risk score for attention-deficit/hyperactivity disorder is also linked to cognitive decline and Alzheimer's disease, a new study in Molecular Psychiatry finds.