Prominent role of the Ig-like V domain in trans-interactions of nectins. Nectin3 and nectin 4 bind to the predicted C-C'-C"-D beta-strands of the nectin1 V domain.

Nectins form a family of integral molecules that belong to the immunoglobulin superfamily. Their ectodomain is made of three Ig-like domains (V, C, C). This family comprises at least five members, namely nectin1, -2, -3, -4, and poliovirus receptor (PVR), that are involved in different physiological and pathological processes. (i) Nectins are adhesion molecules localized at adherens junctions in epithelial cells. (ii) Some nectins act as poliovirus or alpha-herpesvirus receptors (nectin1). (iii) Nectin1 mutations are involved in orofacial developmental abnormalities in humans. Adhesion properties of nectins are mediated by Ca(2+)-independent homophilic and heterophilic processes through ectodomain trans-interactions. We have described a nectin trans-hetero-interaction network: nectin3 binds to nectin1, nectin2, and PVR; nectin1 also binds to nectin4. In the present study we compared the affinities of the different trans-interactions mediated by nectin1. We found that the K(D) of nectin1/nectin3 and nectin1/nectin4 interactions is 1 and 100 nm, respectively, whereas the K(D) of the nectin1-mediated homophilic interaction is 1 microm. We show that nectin1/nectin3 and nectin1/nectin4 trans-hetero-interactions were mediated through trans V to V domain interactions, whereas C domains contributed to increase the affinity of the interaction. Nectin3 and nectin4 share a common binding region in the nectin1 V domain: (i) nectin3 strongly competed with nectin4 binding, (ii) nectin3 and nectin4 binding to nectin1 was reduced by a number of monoclonal antibodies directed against the nectin1 V domain, and (iii) the glycoprotein D of herpes simplex virus-1 that binds to the V domain of nectin1 reduced nectin3 and nectin4 binding. Finally, using chimeric nectin1/PVR receptors where PVR V domain beta-strands were substituted with the corresponding regions of nectin1, the nectin3 and nectin4 minimal binding region on nectin1 V domain was mapped to the C-C'-C"-D beta-strands

Savant Genome Browser 2: visualization and analysis for population-scale genomics

High-throughput sequencing (HTS) technologies are providing an unprecedented capacity for data generation, and there is a corresponding need for efficient data exploration and analysis capabilities. Although most existing tools for HTS data analysis are developed for either automated (e.g. genotyping) or visualization (e.g. genome browsing) purposes, such tools are most powerful when combined. For example, integration of visualization and computation allows users to iteratively refine their analyses by updating computational parameters within the visual framework in real-time. Here we introduce the second version of the Savant Genome Browser, a standalone program for visual and computational analysis of HTS data. Savant substantially improves upon its predecessor and existing tools by introducing innovative visualization modes and navigation interfaces for several genomic datatypes, and synergizing visual and automated analyses in a way that is powerful yet easy even for non-expert users. We also present a number of plugins that were developed by the Savant Community, which demonstrate the power of integrating visual and automated analyses using Savant. The Savant Genome Browser is freely available (open source) at www.savantbrowser.co

International federation of genomic medicine databases using GA4GH standards

We promote a shared vision and guide for how and when to federate genomic and health-related data sharing, enabling connections and insights across independent, secure databases. The GA4GH encourages a federated approach wherein data providers have the mandate and resources to share, but where data cannot move for legal or technical reasons. We recommend a federated approach to connect national genomics initiatives into a global network and precision medicine resource

SHRiMP: Accurate Mapping of Short Color-space Reads

The development of Next Generation Sequencing technologies, capable of sequencing hundreds of millions of short reads (25–70 bp each) in a single run, is opening the door to population genomic studies of non-model species. In this paper we present SHRiMP - the SHort Read Mapping Package: a set of algorithms and methods to map short reads to a genome, even in the presence of a large amount of polymorphism. Our method is based upon a fast read mapping technique, separate thorough alignment methods for regular letter-space as well as AB SOLiD (color-space) reads, and a statistical model for false positive hits. We use SHRiMP to map reads from a newly sequenced Ciona savignyi individual to the reference genome. We demonstrate that SHRiMP can accurately map reads to this highly polymorphic genome, while confirming high heterozygosity of C. savignyi in this second individual. SHRiMP is freely available at http://compbio.cs.toronto.edu/shrimp

GA4GH: International policies and standards for data sharing across genomic research and healthcare.

The Global Alliance for Genomics and Health (GA4GH) aims to accelerate biomedical advances by enabling the responsible sharing of clinical and genomic data through both harmonized data aggregation and federated approaches. The decreasing cost of genomic sequencing (along with other genome-wide molecular assays) and increasing evidence of its clinical utility will soon drive the generation of sequence data from tens of millions of humans, with increasing levels of diversity. In this perspective, we present the GA4GH strategies for addressing the major challenges of this data revolution. We describe the GA4GH organization, which is fueled by the development efforts of eight Work Streams and informed by the needs of 24 Driver Projects and other key stakeholders. We present the GA4GH suite of secure, interoperable technical standards and policy frameworks and review the current status of standards, their relevance to key domains of research and clinical care, and future plans of GA4GH. Broad international participation in building, adopting, and deploying GA4GH standards and frameworks will catalyze an unprecedented effort in data sharing that will be critical to advancing genomic medicine and ensuring that all populations can access its benefits

System for Interpretation of Personal Genomes

Genomics is undergoing a revolution sparked by higher throughput and cost effective DNA sequencing technologies. Sequencing has become a ubiquitous tool with varied inputs, scopes, techniques, technologies, and purposes. There is potential for the development of software systems that assist in translating raw sequence data into actionable information that helps improve disease assessment, detection, and treatment so that individuals who are or may be affected by genetic conditions are treated with an unprecedented level of precision and predictiveness. This new kind of medicine informed by personal genomic interpretation promises to have immense medical and economic benefits. Despite the capacity of new sequencing technologies to generate huge volumes of raw sequence data, it remains a substantial informatics challenge to efficiently analyze it. HTS technologies produce data at a rate that exceeds Moore's Law, creating enormous technical and usability issues. Freely available tools that are both powerful enough to be efficient and user-friendly enough to be used by genomic researchers without informatics expertise are scarce. Notwithstanding a few exceptions, users are often forced to choose between powerful, specialized software that needs to be run on the command-line or alternatives that are less specialized but are graphical and user-friendly. This thesis presents two software platforms that combine techniques from various domains of computer science, most notably data structures, databases, algorithm design, data visualization, user interface design, and user experience design, that together form a highly integrated system for interpretation of personal genomes that is both powerful and easy to use.Ph.D

Approximating the location of integrand discontinuities for penumbral illumination computation with area light sources

Abstract. The problem of computing soft shadows with area light sources has received considerable attention in computer graphics. In part, this is a difficult problem because the integral that defines the radiance at a point must take into account the visibility function. Most of the solutions proposed have been limited to polygonal environments, and require a full visibility determination preprocessing step. The result is typically a partitioning of the environment into regions that have a similar view of the light source. We propose a new approach that can be successfully applied to arbitrary environments. The approach is based on the observation that, in the presence of occluders, the primary difficulty in computing the integral that defines the contribution of an area light source, is that of determining the visible domain of the integrand. We extend a recent shadow algorithm for linear light sources in order to calculate a polygonal approximation to this visible domain. We demonstrate for an important class of shadowing problems, and in particular, for convex occluders, that the shape of the visible domain only needs to be roughly approximated by a polygonal boundary. We then use this boundary to subdivide an area light source into a small number of triangles that can be integrated efficiently using either a deterministic solution, or a low degree numerical cubature