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Reactome, Mutation Surveyor, GeneMarker 1.5, GastroPlus, BioXM, GenePattern 2.0, Robert Merold, David Rubin, Ned Haubein


Downloads & Upgrades

Version 17 of the Reactome knowledgebase of biological processes in humans is available at New modules include signaling cascades mediated by TGF-beta, RIG-I, and Toll-like receptors 3 and 4; the conjugation phase of xenobiotic metabolism; aspects of the metabolism of lipoproteins; cell cycle regulation by the anaphase-promoting complex; and ATR activation in response to replication stress. Reactome now includes 1,828 curated human reactions and 1,369 annotated human proteins.

SoftGenetics has released an updated version of its Mutation Surveyor software that includes a new function for automated analysis of methylation sequence traces. The company claims that this feature makes Mutation Surveyor "the first software to automate the analysis of DNA sequence traces containing chemical modifications of DNA that can be inherited without changing the DNA sequence." A 30-day free trial of the software is available at

SoftGenetics has also released GeneMarker 1.5, which includes several enhanced size-calling algorithms for fragment-based genetic analysis. GeneMarker 1.5 also includes additional application functionalities for quantitative analysis using either the peak height or area; as well as a new automatic "dye" setting that offers "enhanced compatibility for use with all major electrophoresis systems," the company said.

Simulations Plus has released version 5.1 of its GastroPlus software for simulating oral absorption, pharmacokinetics, and pharmacodynamics. New features include a Units Converter that enables scientists to input their in vitro metabolism and transporter data in their own units and convert them into the units and scaling needed within GastroPlus, as well as expanded graphics and file output options.

Biomax Informatics has released the BioXM Knowledge Management Environment, a data-integration system that enables users to build biomedical networks from multiple data sources and then explore and mine them with a query builder.

The Broad Institute of MIT and Harvard has released GenePattern 2.0, an upgrade of its software tool for analyzing gene expression data. GenePattern enable researchers to perform custom data analyses and to record them for later playback. Version 2.0 includes components for analyzing proteomic data.

CuraGen subsidiary 454 Life Sciences has released version 1.02 of its Genome Sequencer 20 System, which includes several improvements, including new software algorithms to enable additional applications and a LIMS-enabled mode to help embed the system into lab infrastructures. The new software algorithms enable improved assembly and contigging and support sequencing of hundreds of thousands of short DNA fragments such as SAGE tags, miRNA, or chromatin immunoprecipitation fragments.


People in the News

Robert Merold has joined Cognia as president and CEO. David Rubin, who was formerly president and CEO, is now senior vice president of product management. Merold was previously the chief operating officer and a member of the board of directors of Proteome, which was acquired by Incyte Genomics in 2000. Prior to Proteome, Merold held a variety of management positions at IMS Health, Bristol-Myers Squibb Consumer Healthcare Products, and Proctor & Gamble. He also serves on the board of directors for Leadscope. Merold has been on Cognia's board of directors since 2002. He told BioInform that the company is in the process of seeking venture capital funding and needed someone with "more operational experience" at the helm.

The BioAnalytics Group has appointed Ned Haubein as senior scientist for its biological modeling, simulation, and analysis businesses. Haubein previously held software-development positions at Physiome Sciences and BioSoftware Systems.

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The Scan

Single-Cell Sequencing Points to Embryo Mosaicism

Mosaicism may affect preimplantation genetic tests for aneuploidy, a single-cell sequencing-based analysis of almost three dozen embryos in PLOS Genetics finds.

Rett Syndrome Mouse Model Study Points to RNA Editing Possibilities

Investigators targeted MECP2 in mutant mouse models of Rett syndrome, showing in PNAS that they could restore its expression and dial down symptoms.

Investigators Find Shared, Distinct Genetic Contributors to Childhood Hodgkin Lymphoma

An association study in JAMA Network Open uncovers risk variants within and beyond the human leukocyte antigen locus.

Transcriptomic, Epigenetic Study Appears to Explain Anti-Viral Effects of TB Vaccine

Researchers report in Science Advances on an interferon signature and long-term shifts in monocyte cell DNA methylation in Bacille Calmette-Guérin-vaccinated infant samples.