A5089401594- Viral gastroenteritis research and epidemiology
- Animal Virus Infections Studies
- CRISPR and Genetic Engineering
- RNA and protein synthesis mechanisms
- Viral Infections and Immunology Research
- Advanced biosensing and bioanalysis techniques
- Virus-based gene therapy research
- Evolution and Genetic Dynamics
- Genomics and Rare Diseases
- RNA modifications and cancer
- Plant Virus Research Studies
- Herpesvirus Infections and Treatments
- Bacteriophages and microbial interactions
- Distributed systems and fault tolerance
- Respiratory viral infections research
- Video Surveillance and Tracking Methods
- Poxvirus research and outbreaks
- Innovative Microfluidic and Catalytic Techniques Innovation
- Vector-Borne Animal Diseases
- Bioinformatics and Genomic Networks
- Enzyme Structure and Function
- Protein Structure and Dynamics
- Virology and Viral Diseases
- Epilepsy research and treatment
- Traffic and Road Safety
Western Regional Research Center
2011-2024
The University of Texas at Austin
2023-2024
Hamad bin Khalifa University
2023
Broad Institute
2018-2022
Harvard University
2018-2021
Massachusetts Institute of Technology
2020-2021
Center for Systems Biology
2018
United States Department of Agriculture
2010-2017
Agricultural Research Service
2011-2017
The great majority of globally circulating pathogens go undetected, undermining patient care and hindering outbreak preparedness response. To enable routine surveillance comprehensive diagnostic applications, there is a need for detection technologies that can scale to test many samples
Engineering stabilized proteins is a fundamental challenge in the development of industrial and pharmaceutical biotechnologies. We present Stability Oracle: structure-based graph-transformer framework that achieves SOTA performance on accurately identifying thermodynamically stabilizing mutations. Our introduces several innovations to overcome well-known challenges data scarcity bias, generalization, computation time, such as: Thermodynamic Permutations for augmentation, structural amino...
Design of nucleic acid-based viral diagnostics typically follows heuristic rules and, to contend with variation, focuses on a genome's conserved regions. A design process could, instead, directly optimize diagnostic effectiveness using learned model sensitivity for targets and their variants. Toward that goal, we screen 19,209 diagnostic-target pairs, concentrated CRISPR-based diagnostics, train deep neural network accurately predict readout. We join this combinatorial optimization maximize...
To characterize the specificity and effect of pH ionic strength on kinetics virus binding to histo-blood group antigens (HBGA)-conjugated magnetic beads.HBGAs from porcine gastric mucin (PGM) have been conjugated beads (PGM-MB) for concentration NoV. A GII.4 was used detailed study a panel genogroup I (GI) NoVs, II (GII) NoVs recombinant (rNoVs) were efficiency assays. We determined that NoV can be captured after 15min incubation with PGM-MB, recovery is decreased extended times. rNoV as...
Abstract Stabilizing proteins is a fundamental challenge in protein engineering and almost always prerequisite for the development of industrial pharmaceutical biotechnologies. Here we present Stability Oracle: structure-based graph-transformer framework that achieves state-of-the-art performance on predicting effect point mutation protein’s thermodynamic stability (ΔΔG). A strength our model its ability to identify stabilizing mutations, which often make up small fraction mutational...
Bacterial pathogens and human norovirus (HuNoV) are major cause for acute gastroenteritis caused by contaminated food water. Public waterways can become from a variety of sources flood after heavy rain events, leading to pathogen contamination produce fields. We initiated survey several public watersheds in leafy green production region the Central California Coast determine prevalence HuNoV as well bacterial pathogens. Moore swabs were used collect environmental samples bi-monthly at over...
Water is an important route for human norovirus (HuNoV) transmission. Using magnetic beads conjugated with blood group-like antigens (HuNoV receptors), we developed a simple and rapid receptor-binding capture sequestration (RBCMS) method compared it to the existing negatively charged membrane absorption/elution (NCMAE) concentrating HuNoV from sewage effluent. RBCMS required 6-fold-less sample volume than NCMAE also resulted in significantly higher yield of HuNoV. The concentrations...
Human noroviruses (HuNoVs) are the major cause of epidemic nonbacterial gastroenteritis. Although quantitative (real-time) reverse transcription-PCR (qRT-PCR) is widely used for detecting HuNoVs, it only detects presence viral RNA and does not indicate infectivity. blood group antigens (HBGAs) have been identified as receptors/co-receptors both HuNoVs Tulane virus (TV) crucial infection. We propose that infectivity can be evaluated with a molecular assay based on receptor-captured viruses....
Histo-blood group antigens (HBGAs) are considered as receptors/co-receptors for human norovirus (HuNoV). It has been reported that binding of HuNoV-derived virus-like particles (VLPs) to HBGA-like molecules-expressing bacteria increased the stability VLPs heat-denaturation (HD). In this study, we tested HBGA-like-binding-conveyed protection against HD on viral replication using Tulane virus (TV) and Escherichia coli O86:H2 (O86:H2), with E. K-12 (K-12) used a control. Expression HBGA type B...
Abstract Diagnostics, particularly for rapidly evolving viruses, stand to benefit from a principled, measurement-driven design that harnesses machine learning and vast genomic data—yet the capability such has not been previously built. Here, we develop extensively validate an approach designing viral diagnostics applies learned model within combinatorial optimization framework. Concentrating on CRISPR-based diagnostics, screen library of 19,209 diagnostic–target pairs train deep neural...
3’ untranslated region (3’UTR) variants are strongly associated with human traits and diseases, yet few have been causally identified. We developed the Massively Parallel Reporter Assay for 3’UTRs (MPRAu) to sensitively assay 12,173 3’UTR variants. applied MPRAu six cell lines, focusing on genetic genome-wide association studies (GWAS) evolutionary adaptation. expands our understanding of function, suggesting that low-complexity sequences predominately explain regulatory activity. adapt...
Oracle networks feeding off-chain information to a blockchain are required solve distributed agreement problem since these receive from multiple sources and at different times. We make key observation that in most cases, the value obtained by network nodes close proximity. define notion of distance leverage availability or state machine replication (SMR) service this with an honest simple majority instead conventional requirement super nodes. Values being proximity, therefore, forming...
Abstract 3’ untranslated region (3’UTR) variants are strongly associated with human traits and diseases, yet few have been causally identified. We developed the Massively Parallel Reporter Assay for 3’UTRs (MPRAu) to sensitively assay 12,173 3’UTR variants. applied MPRAu six cell lines, focusing on genetic genome-wide association studies (GWAS) evolutionary adaptation. expands our understanding of function, suggesting that low-complexity sequences predominately explain regulatory activity....
Abstract Metagenomic sequencing has the potential to transform microbial detection and characterization, but new tools are needed improve its sensitivity. We developed CATCH (Compact Aggregation of Targets for Comprehensive Hybridization), a computational method enhance nucleic acid capture enrichment diverse taxa. designs compact probe sets that achieve full coverage known sequence diversity scale well with this diversity. To illustrate applications CATCH, we focused on capturing viral...
Oracle networks feeding off-chain information to a blockchain are required solve distributed agreement problem since these receive from multiple sources and at different times. We make key observation that in most cases, the value obtained by oracle network nodes close proximity. define notion of distance leverage availability state machine replication (SMR) service this with an honest simple majority instead conventional requirement super nodes. Values being proximity, therefore, forming...