Stony Brook University

About: Stony Brook University is a education organization based out in Stony Brook, New York, United States. It is known for research contribution in the topics: Population & Poison control. The organization has 32534 authors who have published 68218 publications receiving 3035131 citations. The organization is also known as: State University of New York at Stony Brook & SUNY Stony Brook.

Molecular genetic bases of Salmonella entry into host cells

Abstract: Salmonella spp. can enter into non-phagocytic cells, a property that is essential for their pathogenicity. Recently, considerable progress has been made in the understanding of the molecular genetic bases of this process. It is now evident that Salmonella entry functions are largely encoded on a 35-40 kb region of the Salmonella chromosome located at centisome 63. The majority of the loci in this region encode components of a type III or contact-dependent secretion system homologous to those described in a variety of animal and plant-pathogenic bacteria as well as a number of proteins that require this system for their export to the extracellular environment. A somewhat unexpected finding has been the remarkable homology between the Salmonella and Shigella proteins that mediate the entry of these organisms into cultured epithelial cells.

Low concordance of multiple variant-calling pipelines: practical implications for exome and genome sequencing

Abstract: Background: To facilitate the clinical implementation of genomic medicine by next-generation sequencing, it will be critically important to obtain accurate and consistent variant calls on personal genomes. Multiple software tools for variant calling are available, but it is unclear how comparable these tools are or what their relative merits in real-world scenarios might be. Methods: We sequenced 15 exomes from four families using commercial kits (Illumina HiSeq 2000 platform and Agilent SureSelect version 2 capture kit), with approximately 120X mean coverage. We analyzed the raw data using near-default parameters with five different alignment and variant-calling pipelines (SOAP, BWA-GATK, BWA-SNVer, GNUMAP, and BWA-SAMtools). We additionally sequenced a single whole genome using the sequencing and analysis pipeline from Complete Genomics (CG), with 95% of the exome region being covered by 20 or more reads per base. Finally, we validated 919 single-nucleotide variations (SNVs) and 841 insertions and deletions (indels), including similar fractions of GATK-only, SOAP-only, and shared calls, on the MiSeq platform by amplicon sequencing with approximately 5000X mean coverage. Results: SNV concordance between five Illumina pipelines across all 15 exomes was 57.4%, while 0.5 to 5.1% of variants were called as unique to each pipeline. Indel concordance was only 26.8% between three indel-calling pipelines, even after left-normalizing and intervalizing genomic coordinates by 20 base pairs. There were 11% of CG variants falling within targeted regions in exome sequencing that were not called by any of the Illumina-based exome analysis pipelines. Based on targeted amplicon sequencing on the MiSeq platform, 97.1%, 60.2%, and 99.1% of the GATK-only, SOAP-only and shared SNVs could be validated, but only 54.0%, 44.6%, and 78.1% of the GATKonly, SOAP-only and shared indels could be validated. Additionally, our analysis of two families (one with four individuals and the other with seven), demonstrated additional accuracy gained in variant discovery by having access to genetic data from a multi-generational family. Conclusions: Our results suggest that more caution should be exercised in genomic medicine settings when analyzing individual genomes, including interpreting positive and negative findings with scrutiny, especially for indels. We advocate for renewed collection and sequencing of multi-generational families to increase the overall accuracy of whole genomes.

Fused-layer CNN accelerators

Abstract: Deep convolutional neural networks (CNNs) are rapidly becoming the dominant approach to computer vision and a major component of many other pervasive machine learning tasks, such as speech recognition, natural language processing, and fraud detection. As a result, accelerators for efficiently evaluating CNNs are rapidly growing in popularity. The conventional approaches to designing such CNN accelerators is to focus on creating accelerators to iteratively process the CNN layers. However, by processing each layer to completion, the accelerator designs must use off-chip memory to store intermediate data between layers, because the intermediate data are too large to fit on chip. In this work, we observe that a previously unexplored dimension exists in the design space of CNN accelerators that focuses on the dataflow across convolutional layers. We find that we are able to fuse the processing of multiple CNN layers by modifying the order in which the input data are brought on chip, enabling caching of intermediate data between the evaluation of adjacent CNN layers. We demonstrate the effectiveness of our approach by constructing a fused-layer CNN accelerator for the first five convolutional layers of the VGGNet-E network and comparing it to the state-of-the-art accelerator implemented on a Xilinx Virtex-7 FPGA. We find that, by using 362KB of on-chip storage, our fused-layer accelerator minimizes off-chip feature map data transfer, reducing the total transfer by 95%, from 77MB down to 3.6MB per image.