Andrew Warren
A5016058860- Genomics and Phylogenetic Studies
- Bacteriophages and microbial interactions
- Aortic aneurysm repair treatments
- Cardiac, Anesthesia and Surgical Outcomes
- RNA and protein synthesis mechanisms
- Microbial Community Ecology and Physiology
- Machine Learning in Bioinformatics
- Chromosomal and Genetic Variations
- Aortic Disease and Treatment Approaches
- Molecular Biology Techniques and Applications
- Gut microbiota and health
- Microbial Metabolic Engineering and Bioproduction
- thermodynamics and calorimetric analyses
- Bacterial Identification and Susceptibility Testing
- Bioinformatics and Genomic Networks
- COVID-19 epidemiological studies
- Advanced Data Storage Technologies
- Monoclonal and Polyclonal Antibodies Research
- Protein purification and stability
- Biomedical Text Mining and Ontologies
- Cellular transport and secretion
- Protist diversity and phylogeny
- Gene expression and cancer classification
- Genetics, Bioinformatics, and Biomedical Research
- Machine Learning and Data Classification
Pacific Northwest University of Health Sciences
2023-2025
University of Washington
2023-2025
Biocom
2016-2024
University of Virginia
2019-2024
Brotman Baty Institute
2024
Swedish Medical Center
2024
University of Wollongong
2024
Illumina (United States)
2023
Deltares
2023
Virginia Tech
2007-2017
The Pathosystems Resource Integration Center (PATRIC) is the bacterial Bioinformatics (https://www.patricbrc.org). Recent changes to PATRIC include a redesign of web interface and some new services that provide users with platform takes them from raw reads an integrated analysis experience. redesigned allows researchers direct access tools data, emphasis has changed user-created genome-groups, detailed summaries views data have selected. Perhaps biggest change been enhanced capability for...
The Pathosystems Resource Integration Center (PATRIC) is the all-bacterial Bioinformatics (BRC) (http://www.patricbrc.org). A joint effort by two of original National Institute Allergy and Infectious Diseases-funded BRCs, PATRIC provides researchers with an online resource that stores integrates a variety data types [e.g. genomics, transcriptomics, protein–protein interactions (PPIs), three-dimensional protein structures sequence typing data] associated metadata. Datatypes are summarized for...
The PathoSystems Resource Integration Center (PATRIC) is the bacterial Bioinformatics funded by National Institute of Allergy and Infectious Diseases (https://www.patricbrc.org). PATRIC supports bioinformatic analyses all bacteria with a special emphasis on pathogens, offering rich comparative analysis environment that provides users access to over 250 000 uniformly annotated publicly available genomes curated metadata. offers web-based visualization tools, private workspace in which can...
Abstract The National Institute of Allergy and Infectious Diseases (NIAID) established the Bioinformatics Resource Center (BRC) program to assist researchers with analyzing growing body genome sequence other omics-related data. In this report, we describe merger PAThosystems Integration (PATRIC), Influenza Research Database (IRD) Virus Pathogen Analysis (ViPR) BRCs form Bacterial Viral (BV-BRC) https://www.bv-brc.org/. combined BV-BRC leverages functionality bacterial viral resources provide...
Abstract Evaluating metagenomic software is key for optimizing metagenome interpretation and focus of the Initiative Critical Assessment Metagenome Interpretation (CAMI). The CAMI II challenge engaged community to assess methods on realistic complex datasets with long- short-read sequences, created computationally from around 1,700 new known genomes, as well 600 plasmids viruses. Here we analyze 5,002 results by 76 program versions. Substantial improvements were seen in assembly, some due...
The Pathosystems Resource Integration Center (PATRIC, www.patricbrc.org) is designed to provide researchers with the tools and services that they need perform genomic other 'omic' data analyses. In response mounting concern over antimicrobial resistance (AMR), PATRIC team has been developing new help understand AMR its genetic determinants. To support comparative analyses, we have added phenotype 15 000 genomes in database, often assembling from reads public archives collecting their...
Diverse gene products including phytotoxins, pathogen-associated molecular patterns, and type III secreted effectors influence interactions between Pseudomonas syringae strains plants, with additional yet uncharacterized factors likely contributing as well. Of particular interest are those governing pathogen-host specificity. Comparative genomics of closely related pathogens different host specificity represents an excellent approach for identification genes to host-range determination. A...
Protein-coding gene detection in prokaryotic genomes is considered a much simpler problem than intron-containing eukaryotic genomes. However there have been reports that finder programs problems with small genes (either over-predicting or under-predicting). Therefore the question arises as to whether current genome annotations systematically missing, genes. We developed high-performance computing methodology investigate this problem. In we compare all ORFs larger equal 33 aa from...
ABSTRACT Global airline networks play a key role in the global importation of emerging infectious diseases. Detailed information on air traffic between international airports has been demonstrated to be useful retrospectively validating and prospectively predicting case emergence other countries. In this paper, we use well-established metric known as effective distance data from IATA quantify risk for different countries consequence direct China, compare it against arrival times first 24...
Antimicrobial resistance (AMR) is a major global health threat that affects millions of people each year. Funding agencies worldwide and the research community have expended considerable capital effort tracking evolution spread AMR by isolating sequencing bacterial strains performing antimicrobial susceptibility testing (AST). For last several years, we been capturing these efforts curating data from literature resources building set assembled genome sequences are paired with...
This paper describes an integrated, data-driven operational pipeline based on national agent-based models to support federal and state-level pandemic planning response. The consists of ( i) automatic semantic-aware scheduling method that coordinates jobs across two separate high performance computing systems; ii) a data collect, integrate organize county-level disaggregated for initialization post-simulation analysis; iii) digital twin social contact networks made up 288 Million individuals...
Research on cargomobilities has emphasised containerisation, algorithmic management, and the cost-driven calculus of logistics firms. Less visible is necessary human labour that coordinates in challenging environments—for example, those workers who manoeuvre ships at seaports. In response, we take to water learn how ports function as spaces everyday mobilities work. We follow a day working life marine pilots—a specialist, locally-based workforce board foreign-flagged dock them safely. Their...
Tumor development in glandular tissues is associated with structural alterations the hollow ducts and spherical structures that comprise such tissues. We describe a signaling axis involving sustained activation of GTP-binding protein, ARF6, provokes dramatic changes organization epithelial cysts, reminiscent tumorigenic phenotypes. In reconstituted basement membrane cultures renal enhanced ARF6 induces formation cell-filled multiple lumens disassembled cadherin-based cell-cell contacts. All...
We investigated the influence of genetic variants on atherosclerosis using whole exome sequencing in cases and controls from autopsy study "Pathobiological Determinants Atherosclerosis Youth (PDAY)". identified a PDAY case group with highest total amounts raised lesions (n = 359) for comparisons control no detectable 626). In addition to standard capture, we included genome-wide proximal promoter regions that contain sequences regulate gene expression. Our statistical analyses single variant...
Abstract Evaluating metagenomic software is key for optimizing metagenome interpretation and focus of the community-driven initiative Critical Assessment Metagenome Interpretation (CAMI). In its second challenge, CAMI engaged community to assess their methods on realistic complex datasets with long short reads, created from ∼1,700 novel known microbial genomes, as well ∼600 plasmids viruses. Altogether 5,002 results by 76 program versions were analyzed, representing a 22x increase in...