PATRICBRC
@PATRICBRC
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PATRIC, the NIAID-funded Bioinformatics Resource Center by University of Chicago, provides multi-omics data and analysis tools for bacterial pathogens.
Chicago, IL
Joined January 2011
New paper by Sanad et al. says "WGS, using PATRIC software to detect the virulence genes, revealed that 18 isolates had very similar virulence factor profiles, such as sopAD2, fimYD, pagOD, sitA, iroB, pipABCD, and sspA." https://t.co/aToUAGzTlz
#mdpipathogens via @Pathogens_MDPI
mdpi.com
Salmonella is estimated to cause over a million infections and ~400 deaths annually in the U.S. Salmonella enterica serotype Javiana strains (n = 409) that predominantly originated from the State of...
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" Nine highest-confidence SNPs were within “specialty genes” (a PATRIC-defined category of essential genes, virulence factors, AMR-associated genes, and others) in the functionally annotated genome available on PATRIC." https://t.co/lyb28C16De
#mdpipathogens via @Pathogens_MDPI
mdpi.com
Mycobacterium tuberculosis variant bovis (MBO) has one of the widest known mammalian host ranges, including humans.
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New paper by Gupta et al. used data from PATRIC/BV-BRc in their analysis. https://t.co/qDYWA0NJoM
pubmed.ncbi.nlm.nih.gov
Bacteria can exceptionally evolve and develop pathogenic features making it crucial to determine novel pathogenic proteins for specific therapeutic interventions. Therefore, we have developed a...
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"The bacterial training dataset was obtained by identifying 25 Mycobacterium genomes in the PATRIC dataset (designated as being either ‘representative’ or from RefSeq) that are prophage free, as determined using PHASTER and careful manual inspection." https://t.co/38PfeswRhz
academic.oup.com
Abstract. Advances in genome sequencing have produced hundreds of thousands of bacterial genome sequences, many of which have integrated prophages derived
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New paper by Zhang et al. says "...we performed a study based on screening and analyzing ST11 CRKP genomic data sourced from the Pathosystems Resource Integration Center (PATRIC) database between 2011 to 2020." https://t.co/O6WrTLq9wZ
#mdpigenes via @Genes_MDPI
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Recent paper by Benzerara et al. sayd "The search of homologous genes shared by C. fritschii PCC 6912 and PCC 9212 genomes was achieved based on unidirectional BLASTp best hits as implemented in the PATRIC proteome comparison tool." https://t.co/OEvJvvA1Vp
academic.oup.com
Abstract. Cyanobacteria have massively contributed to carbonate deposition over the geological history. They are traditionally thought to biomineralize CaC
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Recent paper by Czmil et al. says "Another tool we tested was Patric. This platform provides bioinformatics analyses of all bacteria, with special focus on pathogens. It supports hybrid genome assembly in the formula of short + long reads." https://t.co/qNnF7CNsfq via @PeerJLife
peerj.com
Background Next Generation Sequencing (NGS) techniques dominate today’s landscape of genetics and genomics research. Though Illumina still dominates worldwide sequencing, Oxford Nanopore is one of...
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Recent paper by Luo et al. mentions the data availble in PATRIC, now known as BV-BRC. https://t.co/IL23UafnTn
frontiersin.org
The gut microbiota is gaining increasing attention, and the concept of the "gut-liver axis" is gradually being recognized. Leaky gut resulting from injury an...
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Recent paper by Guard says "The PathoSystems Resource Integration Center (PATRIC) is a genomics-centric relational database and bioinformatics resource designed to assist scientists in infectious disease research." https://t.co/ShogBfOknq
#mdpipathogens via @Pathogens_MDPI
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Recent paper by Igbinosa et al. used PATRIC's Annotation Service in their analysis. https://t.co/EBBQxhaKy6
journals.asm.org
Five Staphylococcus saprophyticus strains were isolated from the fermented milk product nono in Nigeria and were sequenced using an Illumina MiSeq platform. The genome sizes ranged from 2.53 to 2.60...
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Recent paper by Tehan et. al used the FastOrtho script in their analysis, which was developed by the PATRIC team. https://t.co/ybKIAQrznh
pubs.acs.org
The genome of entomopathogenic fungus Tolypocladium inflatum Gams encodes 43 putative biosynthetic gene clusters for specialized metabolites, although genotype–phenotype linkages have been reported...
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Recent paper by Moynihan et al. used PATRIC's Proteome Comparison service to analyze their data. Great figure of this data! https://t.co/uGzeW6yUyj
pubs.acs.org
Antibiotic resistance has grown significantly in the last three decades, while research and development of new antibiotic classes has languished. Therefore, new chemical frameworks for the control of...
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Recent paper by Arrieta-Ortiz et al. says "Genes can be explored in the context of genome annotations, expression profiles, regulatory and metabolic membership, and other functional genomic information across databases including COG, Uniprot, and PATRIC." https://t.co/vMmx2OrBCn
cell.com
C. difficile is one of the leading causes of hospital-acquired infections. Arrieta-Ortiz et al. report three predictive models (with extensive validations) for dissecting interplay of regulation and...
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New paper by Usyk et al. assembled and annotated their genomes in PATRIC, now known as BV-BRC. https://t.co/tJRe24z7zm
pmc.ncbi.nlm.nih.gov
Immune checkpoint blockade (ICB) shows lasting benefits in advanced melanoma; however, not all patients respond to this treatment and many develop potentially life-threatening immune-related adverse...
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Recent paper by O'Neill et al. says "The S. felis C4 genome was annotated using the RAST tool kit via the Pathosystems Resource Integration Center (PATRIC) database."
elifesciences.org
The discovery and development of a feline skin commensal bacterium for bacteriotherapy against skin disease, that could benefit patients due to established low cytotoxicity, broad-spectrum antimicr...
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Using Genome Sequence Data to Predict SARS-CoV-2 Detection Cycle Threshold Values
medrxiv.org
The continuing emergence of SARS-CoV-2 variants of concern (VOCs) presents a serious public health threat, exacerbating the effects of the COVID19 pandemic. Although millions of genomes have been...
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Recent paper by Kang et al. says "To identify T3SS effectors (T3SEs), we used the predicted genes for each of the six strains from Patric 3.6 as queries for BLAST searches..." https://t.co/gfFrNxxG7J
#mdpimicroorganisms via @Micro_MDPI
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Recent paper by Hutchins et al. says "To identify the lineage of QI0054 and QI0055, we retrieved 260 high-quality genomes covering the five major L. monocytogenes lineages from the Patric database." https://t.co/JTKuz8uUOj
pmc.ncbi.nlm.nih.gov
Listeria monocytogenes is a rare cause of prosthetic joint infections (PJI). In this study, we describe a case of recurrent L. monocytogenes infections, 39 months apart, following debridement and...
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Recent paper by Her et al. says "To identify gene clusters associated with resistance, we compared presence/absence patterns of the gene clusters against resistant phenotype annotations (provided by and downloaded from PATRIC database)." https://t.co/VOGZFqSsEg
pmc.ncbi.nlm.nih.gov
Discerning genes crucial to antimicrobial resistance (AMR) mechanisms is becoming more and more important to accurately and swiftly identify AMR pathogenic strains. Pangenome-wide association studies...
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Recent paper by Shrestha et al. describe the taxonomic classification of their data in PATRIC, now known as BV-BRC.
pmc.ncbi.nlm.nih.gov
The ubiquitously present gram-negative bacteria Pantoea agglomerans is not a commonly known human pathogen. Recently, increasing recognition of the species as a human pathogen has led to controversy...
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