Data Management, Analysis, and Resources Dissemination Core summary The Broad Institute?s Genomic Center for Infectious Disease (GCID) will continue to apply its deep experience in large-scale genomic analysis to study the virulence, transmission, and drug sensitivity of pathogens as well as their critical interactions with hosts, vectors and other microbes. Achieving this will require combining data sets from diverse technologies with bioinformatics capabilities and computational analyses. The Broad GCID will draw on its expertise building and maintaining efficient computational processes and computational infrastructure to create a robust Data Management, Analysis, and Resources Dissemination Core. The Core will support our Research Projects with high-throughput sample tracking, metadata and data management, large-scale analysis, development of novel computational methods, and the rapid release of high quality data and associated resources. Our Data Core will harness the extensive technological capabilities of the Broad Institute and the vast experience of our personnel in genomic research to serve the ambitious goals of our Research Projects. The Core will also maintain a program of ongoing method development tied to innovations in the Technology Core and the goals of the Research Projects; these include methods for strain analysis in metagenomic samples, improved quality control analysis of sequence data, updating assembly methods to use long read- and hybrid-data, customized 10x Genomics data applications, analysis of horizontally transferred sequences, methods for Tn-Seq analysis, and training and evaluating new methods for variant calling. These methods are cross-cutting across our Research Projects and will be widely applicable to genomic infectious disease research. In addition to releasing data to public repositories, the Data Core will continue to move pipelines, processes, and data sets to the cloud, to accelerate the infectious research community?s access to our data and tools and enable others to reproduce our analyses.
| Rhodes, Johanna; Abdolrasouli, Alireza; Farrer, Rhys A et al. (2018) Genomic epidemiology of the UK outbreak of the emerging human fungal pathogen Candida auris. Emerg Microbes Infect 7:43 |
| Sephton-Clark, Poppy C S; Muñoz, Jose F; Ballou, Elizabeth R et al. (2018) Pathways of Pathogenicity: Transcriptional Stages of Germination in the Fatal Fungal Pathogen Rhizopus delemar. mSphere 3: |
| Ene, Iuliana V; Farrer, Rhys A; Hirakawa, Matthew P et al. (2018) Global analysis of mutations driving microevolution of a heterozygous diploid fungal pathogen. Proc Natl Acad Sci U S A 115:E8688-E8697 |
| Siddle, Katherine J; Eromon, Philomena; Barnes, Kayla G et al. (2018) Genomic Analysis of Lassa Virus during an Increase in Cases in Nigeria in 2018. N Engl J Med 379:1745-1753 |
| Brennan-Krohn, Thea; Pironti, Alejandro; Kirby, James E (2018) Synergistic Activity of Colistin-Containing Combinations against Colistin-Resistant Enterobacteriaceae. Antimicrob Agents Chemother 62: |
| Messina, Julia A; Wolfe, Cameron R; Hemmersbach-Miller, Marion et al. (2018) Genomic characterization of recurrent mold infections in thoracic transplant recipients. Transpl Infect Dis 20:e12935 |
| Schaffner, Stephen F; Taylor, Aimee R; Wong, Wesley et al. (2018) hmmIBD: software to infer pairwise identity by descent between haploid genotypes. Malar J 17:196 |
| Farrer, Rhys A; Ford, Christopher B; Rhodes, Johanna et al. (2018) Transcriptional Heterogeneity of Cryptococcus gattii VGII Compared with Non-VGII Lineages Underpins Key Pathogenicity Pathways. mSphere 3: |
| Myhrvold, Cameron; Freije, Catherine A; Gootenberg, Jonathan S et al. (2018) Field-deployable viral diagnostics using CRISPR-Cas13. Science 360:444-448 |
| Cuomo, Christina A; Rhodes, Johanna; Desjardins, Christopher A (2018) Advances in Cryptococcus genomics: insights into the evolution of pathogenesis. Mem Inst Oswaldo Cruz 113:e170473 |
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