A5049471852- Computational Drug Discovery Methods
- Genomics and Phylogenetic Studies
- Nanoplatforms for cancer theranostics
- Microbial Metabolic Engineering and Bioproduction
- Landfill Environmental Impact Studies
- Gene expression and cancer classification
- Advanced Memory and Neural Computing
- Bioinformatics and Genomic Networks
- 2D Materials and Applications
- Machine Learning in Bioinformatics
- Machine Learning in Materials Science
- RNA and protein synthesis mechanisms
- Biofuel production and bioconversion
- Antibiotic Resistance in Bacteria
- Ferroelectric and Negative Capacitance Devices
- Nanocluster Synthesis and Applications
- Perovskite Materials and Applications
- Protein Structure and Dynamics
- Odor and Emission Control Technologies
- Molecular Biology Techniques and Applications
- Advanced Nanomaterials in Catalysis
- Cell Image Analysis Techniques
- Surgical Simulation and Training
- Photodynamic Therapy Research Studies
- Bacterial Identification and Susceptibility Testing
Argonne National Laboratory
2016-2025
Wenzhou Medical University
2019-2025
First Affiliated Hospital of Wenzhou Medical University
2019-2025
Huazhong University of Science and Technology
2012-2024
University of Chicago
2012-2024
Shanghai Jiao Tong University
2015-2024
Renji Hospital
2021-2024
The University of Texas MD Anderson Cancer Center
2023-2024
National Engineering Research Center for Nanotechnology
2024
Yiwu Science and Technology Research Institute
2022-2024
In 2004, the SEED (http://pubseed.theseed.org/) was created to provide consistent and accurate genome annotations across thousands of genomes as a platform for discovering developing de novo annotations. The is constantly updated integration genomic data with database, web front end, API server scripts. It used by many scientists predicting gene functions new pathways. addition being powerful database bioinformatics research, also houses subsystems (collections functionally related protein...
The RAST (Rapid Annotation using Subsystem Technology) annotation engine was built in 2008 to annotate bacterial and archaeal genomes. It works by offering a standard software pipeline for identifying genomic features (i.e., protein-encoding genes RNA) annotating their functions. Recently, order make more useful research tool keep pace with advancements bioinformatics, it has become desirable build version of that is both customizable extensible. In this paper, we describe the kit (RASTtk),...
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...
To the Editor: Over past two decades, scale and complexity of genomics technologies data have advanced from sequencing genomes a few organisms to generating metagenomes, genome variation, gene expression, metabolites, phenotype for thousands their communities.A major challenge in this data-rich age biology is integrating heterogeneous distributed into predictive models biological function, ranging single entire ecologies.The US Department Energy (DOE) has invested substantially efforts...
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 To tackle the issue of inferior cycle stability and rate capability for MnO anode materials in lithium ion batteries, a facile strategy is explored to prepare hybrid material consisting nanocrystals grown on conductive graphene nanosheets. The prepared MnO/graphene exhibits reversible capacity as high 2014.1 mAh g −1 after 150 discharge/charge cycles at 200 mA , excellent (625.8 3000 ), superior cyclability (843.3 even 400 2000 with only 0.01% loss per cycle). results suggest that...
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...
Low-cost short read sequencing technology has revolutionized genomics, though it is only just becoming practical for the high-quality de novo assembly of a novel large genome. We describe Assemblathon 1 competition, which aimed to comprehensively assess state art in methods when applied current technologies. In collaborative effort, teams were asked assemble simulated Illumina HiSeq data set an unknown, diploid A total 41 assemblies from 17 different groups received. Novel haplotype aware...
The emergence and spread of antimicrobial resistance (AMR) mechanisms in bacterial pathogens, coupled with the dwindling number effective antibiotics, has created a global health crisis. Being able to identify genetic AMR predict phenotypes pathogens prior culturing could inform clinical decision-making improve reaction time. At PATRIC ( http://patricbrc.org/ ), we have been collecting genomes metadata for several years. In order advance phenotype prediction identification genomic regions...
Antimicrobial resistant infections are a serious public health threat worldwide. Whole genome sequencing approaches to rapidly identify pathogens and predict antibiotic resistance phenotypes becoming more feasible may offer way reduce clinical test turnaround times compared conventional culture-based methods, in turn, improve patient outcomes. In this study, we use whole sequence data from 1668 isolates of Klebsiella pneumoniae develop XGBoost-based machine learning model that accurately...
The low efficiency of photodynamic therapy (PDT) is caused by tumor hypoxia and the adaptive immune resistance/evasion cells, while currently emerging checkpoint restores intrinsic capacities but can't directly attack cells. Methods: Herein we report an integrated nanoplatform that combines PDT with immunotherapy to enhance therapeutic effects simultaneously inhibit cells resistance/evasion. To achieve this, fabricated Mn@CaCO3/ICG nanoparticles loaded them PD-L1-targeting siRNA. Results:...
Abstract Convolutional neural networks (CNNs) have been successfully used in many applications where important information about data is embedded the order of features, such as speech and imaging. However, most tabular do not assume a spatial relationship between thus are unsuitable for modeling using CNNs. To meet this challenge, we develop novel algorithm, image generator (IGTD), to transform into images by assigning features pixel positions so that similar close each other image. The...
Abstract Second harmonic generation (SHG) as an essential nonlinear optical effect, has gradually shifted its research trend toward the integration and miniaturization of photonic optoelectronic on‐chip devices in recent years. 2D layered materials (2DLMs) open up a new paradigm optics due to their large second‐order susceptibility, atomically thin structure, perfect phase‐matching. However, 2DLMs are facing bottleneck weak SHG conversion efficiency limit caused by short light–matter...
The remarkable advance in sequencing technology and the rising interest medical environmental microbiology, biotechnology, synthetic biology resulted a deluge of published microbial genomes. Yet, genome annotation, comparison, modeling remain major bottleneck to translation sequence information into biological knowledge, hence computational analysis tools are continuously being developed for rapid annotation interpretation. Among earliest, most comprehensive resources prokaryotic analysis,...
ABSTRACT Klebsiella pneumoniae is a major human pathogen responsible for high morbidity and mortality rates. The emergence spread of strains resistant to multiple antimicrobial agents documented large nosocomial outbreaks are especially concerning. To develop new therapeutic strategies K. , it imperative understand the population genomic structure causing infections. address this knowledge gap, we sequenced genomes 1,777 extended-spectrum beta-lactamase-producing cultured from patients in...
Thin films of MoO2 nanoparticles and graphene sheets are created by layer-by-layer (LBL) assembly as binder-free anodes for lithium-ion batteries. Both anionic polyoxometalate clusters oxide nanosheets with oxygen functional groups on both basal planes edges assembled into LBL the aid a cationic polyelectrolyte. After subsequent thermal treatment in an Ar–H2 atmosphere, hybrid MoO2–graphene three-dimensionally interconnected nanopores formed, which comprise ultrafine homogeneously embedded...
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...
The National Cancer Institute drug pair screening effort against 60 well-characterized human tumor cell lines (NCI-60) presents an unprecedented resource for modeling combinational activity. We present a computational model predicting line response to subset of pairs in the NCI-ALMANAC database. Based on residual neural networks encoding features as well growth, our explains 94% variance. While best result is achieved with combination molecular feature types (gene expression, microRNA and...
A unique matrix metalloproteinase 2-targeted photosensitizer delivery platform was developed in this study for tumor-targeting imaging and photodynamic therapy. The model therapeutic agent chlorin e6 (Ce6) first covalently conjugated with 2-cleavable polypeptide then modified polyethylene glycol via a redox-responsive cleavable disulfide linker. resultant PEGylated Ce6 (PEG-SS-Ce6-MMP2) nanoparticles, which formed self-assembly, were observed to be monodisperse significantly stable aqueous...
Abstract Transfer learning, which transfers patterns learned on a source dataset to related target for constructing prediction models, has been shown effective in many applications. In this paper, we investigate whether transfer learning can be used improve the performance of anti-cancer drug response models. Previous studies focused building models predict tumor cells specific treatment. We more challenging task general that make predictions both new and drugs. Uniquely, power three...