Kerfuffle: a web tool for multi-species gene colocalization analysis

The evolutionary pressures that underlie the large-scale functional organization of the genome are not well understood in eukaryotes. Recent evidence suggests that functionally similar genes may colocalize (cluster) in the eukaryotic genome, suggesting the role of chromatin-level gene regulation in shaping the physical distribution of coordinated genes. However, few of the bioinformatic tools currently available allow for a systematic study of gene colocalization across several, evolutionarily distant species. Kerfuffle is a web tool designed to help discover, visualize, and quantify the physical organization of genomes by identifying significant gene colocalization and conservation across the assembled genomes of available species (currently up to 47, from humans to worms). Kerfuffle only requires the user to specify a list of human genes and the names of other species of interest. Without further input from the user, the software queries the e!Ensembl BioMart server to obtain positional information and discovers homology relations in all genes and species specified. Using this information, Kerfuffle performs a multi-species clustering analysis, presents downloadable lists of clustered genes, performs Monte Carlo statistical significance calculations, estimates how conserved gene clusters are across species, plots histograms and interactive graphs, allows users to save their queries, and generates a downloadable visualization of the clusters using the Circos software. These analyses may be used to further explore the functional roles of gene clusters by interrogating the enriched molecular pathways associated with each cluster.Comment: BMC Bioinformatics, In pres

A MOSAIC of methods: Improving ortholog detection through integration of algorithmic diversity

Ortholog detection (OD) is a critical step for comparative genomic analysis of protein-coding sequences. In this paper, we begin with a comprehensive comparison of four popular, methodologically diverse OD methods: MultiParanoid, Blat, Multiz, and OMA. In head-to-head comparisons, these methods are shown to significantly outperform one another 12-30% of the time. This high complementarity motivates the presentation of the first tool for integrating methodologically diverse OD methods. We term this program MOSAIC, or Multiple Orthologous Sequence Analysis and Integration by Cluster optimization. Relative to component and competing methods, we demonstrate that MOSAIC more than quintuples the number of alignments for which all species are present, while simultaneously maintaining or improving functional-, phylogenetic-, and sequence identity-based measures of ortholog quality. Further, we demonstrate that this improvement in alignment quality yields 40-280% more confidently aligned sites. Combined, these factors translate to higher estimated levels of overall conservation, while at the same time allowing for the detection of up to 180% more positively selected sites. MOSAIC is available as python package. MOSAIC alignments, source code, and full documentation are available at http://pythonhosted.org/bio-MOSAIC

Systematizing Genome Privacy Research: A Privacy-Enhancing Technologies Perspective

Rapid advances in human genomics are enabling researchers to gain a better understanding of the role of the genome in our health and well-being, stimulating hope for more effective and cost efficient healthcare. However, this also prompts a number of security and privacy concerns stemming from the distinctive characteristics of genomic data. To address them, a new research community has emerged and produced a large number of publications and initiatives. In this paper, we rely on a structured methodology to contextualize and provide a critical analysis of the current knowledge on privacy-enhancing technologies used for testing, storing, and sharing genomic data, using a representative sample of the work published in the past decade. We identify and discuss limitations, technical challenges, and issues faced by the community, focusing in particular on those that are inherently tied to the nature of the problem and are harder for the community alone to address. Finally, we report on the importance and difficulty of the identified challenges based on an online survey of genome data privacy expertsComment: To appear in the Proceedings on Privacy Enhancing Technologies (PoPETs), Vol. 2019, Issue

Academic digital libraries of the future : an environment scan

Libraries are attempting to face a future in which almost every fixed point has disappeared. Users are changing; content is changing; research is taking new forms. Indeed the very need for libraries is being questioned in some quarters. This paper explores the nature of the changes and challenges facing higher education libraries and suggests key areas of strength and core activities which should be exploited to secure their future

Genome of Drosophila suzukii, the spotted wing drosophila.

Drosophila suzukii Matsumura (spotted wing drosophila) has recently become a serious pest of a wide variety of fruit crops in the United States as well as in Europe, leading to substantial yearly crop losses. To enable basic and applied research of this important pest, we sequenced the D. suzukii genome to obtain a high-quality reference sequence. Here, we discuss the basic properties of the genome and transcriptome and describe patterns of genome evolution in D. suzukii and its close relatives. Our analyses and genome annotations are presented in a web portal, SpottedWingFlyBase, to facilitate public access