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19 results on '"Kilianski, Andy"'

1. Reply to Lipeitch

Author

Kilianski, Andy, Nuzzo, Jennifer B., and Modjarrad, Kayvon

Published
2016

5. Comparative Characterization of the Sindbis Virus Proteome from Mammalian and Invertebrate Hosts Identifies nsP2 as a Component of the Virion and Sorting Nexin 5 as a Significant Host Factor for Alphavirus Replication

Author

Schuchman, Ryan, primary, Kilianski, Andy, additional, Piper, Amanda, additional, Vancini, Ricardo, additional, Ribeiro, José M. C., additional, Sprague, Thomas R., additional, Nasar, Farooq, additional, Boyd, Gabrielle, additional, Hernandez, Raquel, additional, and Glaros, Trevor, additional

Published
2018
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7. Pathosphere.org: pathogen detection and characterization through a web-based, open source informatics platform

Author

Kilianski, Andy, Yao, Shijie, Carcel, Patrick, Roth, Pierce, Schulte, Josh, Donarum, Greg B., Fochler, Ed T., Hill, Jessica M., Liem, Alvin T., Wiley, Michael R., Ladner, Jason T., Pfeffer, Bradley P., Elliot, Oliver T., Petrosov, Alexandra, Jima, Dereje D., Vallard, Tyghe G., Melendrez, Melanie C., Skowronski, Evan, Quan, Phenix-Lan, Lipkin, W. Ian, Gibbons, Henry S., Hirschberg, David L., Palacios, Gustavo F., and Rosenzweig, C. Nicole

Subjects
Identification, Pathogenic microorganisms, Medical records--Data processing, Medicine
Abstract

Background The detection of pathogens in complex sample backgrounds has been revolutionized by wide access to next-generation sequencing (NGS) platforms. However, analytical methods to support NGS platforms are not as uniformly available. Pathosphere (found at Pathosphere.org) is a cloud - based open - sourced community tool that allows for communication, collaboration and sharing of NGS analytical tools and data amongst scientists working in academia, industry and government. The architecture allows for users to upload data and run available bioinformatics pipelines without the need for onsite processing hardware or technical support. Results The pathogen detection capabilities hosted on Pathosphere were tested by analyzing pathogen-containing samples sequenced by NGS with both spiked human samples as well as human and zoonotic host backgrounds. Pathosphere analytical pipelines developed by Edgewood Chemical Biological Center (ECBC) identified spiked pathogens within a common sample analyzed by 454, Ion Torrent, and Illumina sequencing platforms. ECBC pipelines also correctly identified pathogens in human samples containing arenavirus in addition to animal samples containing flavivirus and coronavirus. These analytical methods were limited in the detection of sequences with limited homology to previous annotations within NCBI databases, such as parvovirus. Utilizing the pipeline-hosting adaptability of Pathosphere, the analytical suite was supplemented by analytical pipelines designed by the United States Army Medical Research Insititute of Infectious Diseases and Walter Reed Army Institute of Research (USAMRIID-WRAIR). These pipelines were implemented and detected parvovirus sequence in the sample that the ECBC iterative analysis previously failed to identify. Conclusions By accurately detecting pathogens in a variety of samples, this work demonstrates the utility of Pathosphere and provides a platform for utilizing, modifying and creating pipelines for a variety of NGS technologies developed to detect pathogens in complex sample backgrounds. These results serve as an exhibition for the existing pipelines and web-based interface of Pathosphere as well as the plug-in adaptability that allows for integration of newer NGS analytical software as it becomes available.

Published
2015
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10. Use of Unamplified RNA/cDNA–Hybrid Nanopore Sequencing for Rapid Detection and Characterization of RNA Viruses

Author

Kilianski, Andy, primary, Roth, Pierce A., additional, Liem, Alvin T., additional, Hill, Jessica M., additional, Willis, Kristen L., additional, Rossmaier, Rebecca D., additional, Marinich, Andrew V., additional, Maughan, Michele N., additional, Karavis, Mark A., additional, Kuhn, Jens H., additional, Honko, Anna N., additional, and Rosenzweig, C. Nicole, additional

Published
2016
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11. Pathosphere.org: pathogen detection and characterization through a web-based, open source informatics platform

Author

Kilianski, Andy, primary, Carcel, Patrick, additional, Yao, Shijie, additional, Roth, Pierce, additional, Schulte, Josh, additional, Donarum, Greg B., additional, Fochler, Ed T., additional, Hill, Jessica M., additional, Liem, Alvin T., additional, Wiley, Michael R., additional, Ladner, Jason T., additional, Pfeffer, Bradley P., additional, Elliot, Oliver, additional, Petrosov, Alexandra, additional, Jima, Dereje D., additional, Vallard, Tyghe G., additional, Melendrez, Melanie C., additional, Skowronski, Evan, additional, Quan, Phenix-Lan, additional, Lipkin, W. Ian, additional, Gibbons, Henry S., additional, Hirschberg, David L., additional, Palacios, Gustavo F., additional, and Rosenzweig, C. Nicole, additional

Published
2015
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19. The planning, execution, and evaluation of a mass prophylaxis full-scale exercise in cook county, IL.

Author

Kilianski A, O'Rourke AT, Carlson CL, Parikh SM, and Shipman-Amuwo F

Subjects
Bioterrorism, Emergency Responders education, Humans, Illinois, Inservice Training standards, Local Government, Disaster Planning, Influenza A Virus, H7N9 Subtype drug effects, Influenza, Human prevention & control, Inservice Training organization & administration, Mass Vaccination organization & administration, Program Evaluation
Abstract

Increasing threats of bioterrorism and the emergence of novel disease agents, including the recent international outbreaks of H7N9 influenza and MERS-CoV, have stressed the importance and highlighted the need for public health preparedness at local, regional, and national levels. To test plans that were developed for mass prophylaxis scenarios, in April 2013 the Cook Country Department of Public Health (CCDPH) and the Triple Community (TripCom) Medical Reserve Corps (MRC) executed a full-scale mass prophylaxis exercise in response to a simulated anthrax bioterrorism attack. The exercise took place over 2 days and included the TripCom Point-of-Dispensing (POD) Management Team, volunteers from the TripCom MRC, and neighboring public health departments and MRCs. Individuals from the community volunteered as actors during the exercise, while local municipal, police, and fire personnel coordinated their responses to create the most realistic simulation possible. The exercise was designed to test the capacity of TripCom and CCDPH to implement plans for organizing municipal staff and volunteers to efficiently distribute prophylaxis to the community. Based on results from POD clinic flow, accuracy of prophylaxis distribution, and observations from evaluators, the exercise was successful in demonstrating areas that were operationally efficient as well as identifying areas that can be improved on. These include improvements to the just-in-time training for POD staff, the health screening and consent forms handed out to patients, the physical setup of the POD, and the command structure and communication for the management of POD operations. This article demonstrates the need for full-scale exercises and identifies gaps in POD planning that can be integrated into future plans, exercises, and emergency response.

Published
2014
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