qTeller: a tool for comparative multi-genomic gene expression analysis

Motivation: Over the last decade, RNA-Seq whole-genome sequencing has become a widely used method for measuring and understanding transcriptome-level changes in gene expression. Since RNA-Seq is relatively inexpensive, it can be used on multiple genomes to evaluate gene expression across many different conditions, tissues and cell types. Although many tools exist to map and compare RNA-Seq at the genomics level, few web-based tools are dedicated to making data generated for individual genomic analysis accessible and reusable at a gene-level scale for comparative analysis between genes, across different genomes and meta-analyses. Results: To address this challenge, we revamped the comparative gene expression tool qTeller to take advantage of the growing number of public RNA-Seq datasets. qTeller allows users to evaluate gene expression data in a defined genomic interval and also perform two-gene comparisons across multiple user-chosen tissues. Though previously unpublished, qTeller has been cited extensively in the scientific literature, demonstrating its importance to researchers. Our new version of qTeller now supports multiple genomes for intergenomic comparisons, and includes capabilities for both mRNA and protein abundance datasets. Other new features include support for additional data formats, modernized interface and back-end database and an optimized framework for adoption by other organisms’ databases. Availability and implementation: The source code for qTeller is open-source and available through GitHub (https:// github.com/Maize-Genetics-and-Genomics-Database/qTeller). A maize instance of qTeller is available at the Maize Genetics and Genomics database (MaizeGDB) (https://qteller.maizegdb.org/), where we have mapped over 200 unique datasets from GenBank across 27 maize genomes

PedigreeNet: A Web-based Pedigree Viewer for Biological Databases

MotivationPlant breeding aims to improve current germplasm that can tolerate a wide range of biotic and abiotic stresses. To accomplish this goal, breeders rely on developing a deeper understanding of genetic makeup and relationships between plant varieties to make informed plant selections. Although rapid advances in genotyping technology generated a large amount of data for breeders, tools that facilitate pedigree analysis and visualization are scant, leaving breeders to use classical, but inherently limited, hierarchical pedigree diagrams for a handful of plant varieties. To answer this need, we developed a simple web-based tool that can be easily implemented at biological databases, called PedigreeNet, to create and visualize customizable pedigree relationships in a network context, displaying pre- and user-uploaded data.ResultsAs a proof-of-concept, we implemented PedigreeNet at the maize model organism database, MaizeGDB. The PedigreeNet viewer at MaizeGDB has a dynamically-generated pedigree network of 4706 maize lines and 5487 relationships that are currently available as both a stand-alone web-based tool and integrated directly on the MaizeGDB Stock Pages. The tool allows the user to apply a number of filters, select or upload their own breeding relationships, center a pedigree network on a plant variety, identify the common ancestor between two varieties, and display the shortest path(s) between two varieties on the pedigree network. The PedigreeNet code layer is written as a JavaScript wrapper around Cytoscape Web. PedigreeNet fills a great need for breeders to have access to an online tool to represent and visually customize pedigree relationships.Availability and implementationPedigreeNet is accessible at https://www.maizegdb.org/breeders_toolbox. The open source code is publically and freely available at GitHub: https://github.com/Maize-Genetics-and-Genomics-Database/PedigreeNet.Supplementary informationSupplementary data are available at Bioinformatics online

SNPversity: a web-based tool for visualizing diversity

https://www.maizegdb.org/snpversity

Surveying the Maize community for their diversity and pedigree visualization needs to prioritize tool development and curation

The Maize Genetics and Genomics Database (MaizeGDB) team prepared a survey to identify breeders’ needs for visualizing pedigrees, diversity data and haplotypes in order to prioritize tool development and curation efforts at MaizeGDB. The survey was distributed to the maize research community on behalf of the Maize Genetics Executive Committee in Summer 2015. The survey garnered 48 responses from maize researchers, of which more than half were self-identified as breeders. The survey showed that the maize researchers considered their top priorities for visualization as: (i) displaying single nucleotide polymorphisms in a given region for a given list of lines, (ii) showing haplotypes for a given list of lines and (iii) presenting pedigree relationships visually. The survey also asked which populations would be most useful to display. The following two populations were on top of the list: (i) 3000 publicly available maize inbred lines used in Romay et al. (Comprehensive genotyping of the USA national maize inbred seed bank. Genome Biol, 2013;14:R55) and (ii) maize lines with expired Plant Variety Protection Act (ex-PVP) certificates. Driven by this strong stakeholder input, MaizeGDB staff are currently working in four areas to improve its interface and web-based tools: (i) presenting immediate progenies of currently available stocks at the MaizeGDB Stock pages, (ii) displaying the most recent ex-PVP lines described in the Germplasm Resources Information Network (GRIN) on the MaizeGDB Stock pages, (iii) developing network views of pedigree relationships and (iv) visualizing genotypes from SNP-based diversity datasets. These survey results can help other biological databases to direct their efforts according to user preferences as they serve similar types of data sets for their communities. https://www.maizegdb.org

Psychological Science and Innovative Strategies for Informing Health Care Redesign: A Policy Brief

Recent health care legislation and shifting health care financing strategies are transforming health and behavioral health (a broad term referring to mental health, substance use, and health behavior) care in the United States. Advances in knowledge regarding effective treatment and services coupled with incentives for innovation in health and behavioral health care delivery systems make this a unique time for mobilizing our science to enhance the success of health and behavioral health care redesign. To optimize the potential of our current health care environment, a team was formed composed of leaders from the Societies of Clinical Child & Adolescent Psychology, Pediatric Psychology, and Child and Family Policy and Practice (Divisions 53, 54, and 37 of the American Psychological Association). This team was charged with reviewing the scientific and policy literature with a focus on five major issues: (a) improving access to care and reducing health disparities, (b) integrating behavioral health care within primary care, (c) preventive services, (d) enhancing quality and outcomes of care, and (e) training and workforce development. The products of that work are summarized here, including recommendations for future research, clinical, training, and policy directions. We conclude that the current emphasis on accountable care and evaluation of the outcomes of care offer numerous opportunities for psychologists to integrate science and practice for the benefit of our children, families, and nation. The dramatic changes that are occurring in psychological and behavioral health care services and payment systems also require evolution in our practice and training models

Psychological Science and Innovative Strategies for Informing Health Care Redesign: A Policy Brief

Recent health care legislation and shifting health care financing strategies are transforming health and behavioral health (a broad term referring to mental health, substance use, and health behavior) care in the United States. Advances in knowledge regarding effective treatment and services coupled with incentives for innovation in health and behavioral health care delivery systems make this a unique time for mobilizing our science to enhance the success of health and behavioral health care redesign. To optimize the potential of our current health care environment, a team was formed composed of leaders from the Societies of Clinical Child & Adolescent Psychology, Pediatric Psychology, and Child and Family Policy and Practice (Divisions 53, 54, and 37 of the American Psychological Association). This team was charged with reviewing the scientific and policy literature with a focus on five major issues: (a) improving access to care and reducing health disparities, (b) integrating behavioral health care within primary care, (c) preventive services, (d) enhancing quality and outcomes of care, and (e) training and workforce development. The products of that work are summarized here, including recommendations for future research, clinical, training, and policy directions. We conclude that the current emphasis on accountable care and evaluation of the outcomes of care offer numerous opportunities for psychologists to integrate science and practice for the benefit of our children, families, and nation. The dramatic changes that are occurring in psychological and behavioral health care services and payment systems also require evolution in our practice and training models

SNPversity: a web-based tool for visualizing diversity

https://www.maizegdb.org/snpversity