A5045072057- Genomics and Phylogenetic Studies
- Evolutionary Algorithms and Applications
- Neural Networks and Reservoir Computing
- Advanced Memory and Neural Computing
- Neural dynamics and brain function
- Bacteriophages and microbial interactions
- Microbial Community Ecology and Physiology
- Genomics and Chromatin Dynamics
- Antimicrobial Resistance in Staphylococcus
- Elevator Systems and Control
- Biochemical Analysis and Sensing Techniques
- RNA and protein synthesis mechanisms
- Bacterial Identification and Susceptibility Testing
- Single-cell and spatial transcriptomics
- Microbial infections and disease research
- Systemic Lupus Erythematosus Research
- Epigenetics and DNA Methylation
- Viral gastroenteritis research and epidemiology
- Cancer Genomics and Diagnostics
- RNA modifications and cancer
- Gene Regulatory Network Analysis
- Probiotics and Fermented Foods
- Chronic Lymphocytic Leukemia Research
- Neural Networks and Applications
- Olfactory and Sensory Function Studies
United States Food and Drug Administration
2013-2019
Food and Drug Administration
2018
Center for Devices and Radiological Health
2015-2018
University of Florida
2010-2012
Binghamton University
2007-2010
Abstract FDA proactively invests in tools to support innovation of emerging technologies, such as infectious disease next generation sequencing (ID-NGS). Here, we introduce FDA-ARGOS quality-controlled reference genomes a public database for diagnostic purposes and demonstrate its utility on the example two use cases. We provide quality control metrics genomic resource outline need genome gap filling domain. In first case, show more accurate microbial identification Enterococcus avium from...
The DNA base modification N6-methyladenine (m6A) is involved in many pathways related to the survival of bacteria and their interactions with hosts. Nanopore sequencing offers a new, portable method detect modifications. Here, we show that neural network can improve m6A detection at trained sequence contexts compared previously published methods using deviations between measured expected current values as each adenine travels through pore. model, implemented mCaller software package, be...
Abstract Many genomes are incorrectly identified at GenBank. We developed a plan to find and correct misidentified using genomic comparison statistics together with scaffold of reliably from type. A workshop was organized broad representation the bacterial taxonomic community review proposal, GenBank Microbial Genomic Taxonomy Workshop, Bethesda MD, May 12–13, 2015.
Staphylococcus aureus is a major human pathogen with well-characterized bacteriophage contributions to its virulence potential. Recently, we identified plasmidial and episomal prophages in S. strains using an extra-chromosomal DNA (exDNA) isolation sequencing approach, uncovering the phage ϕBU01, which was found encode important determinants. Here, expanded our of aureus, selecting 15 diverse clinical isolates known chromosomal sequences for exDNA next-generation sequencing. We uncovered...
Although the cellular organization of many primary sensory nuclei has been well characterized, questions remain about functional architecture first central relay for gustation, rostral nucleus solitary tract (NTS). Here we used electrophysiological data recorded from single cells in NTS to inform a network model taste processing. Previous studies showed that electrical stimulation chorda tympani (CT) nerve initiates two types inhibitory influences with different time courses separate groups...
ABSTRACT Infectious disease next generation sequencing (ID-NGS) diagnostics are on the cusp of revolutionizing clinical market. To facilitate this transition, FDA proactively invested in tools to support innovation emerging technologies. and collaborators established a publicly available database, dAtabase for Regulatory-Grade micrObial Sequences (FDA-ARGOS), as tool fill reference database gaps with quality-controlled genomes. This manuscript discusses quality control metrics proposed...
One of the black arts evolutionary computation is design effective fitness functions. For some tasks appropriate function easy to identify, but many times obvious approach induces unforeseen failures process discover genomes with desired properties. We present a series functions we have tried on task evolving spiking neural networks. The paradigm compare output spike trains produced by networks provided target trains. initial attempts failed dramatically, and subsequent versions revealed new...
We are interested in engineering smart machines that enable backtracking of emergent behaviors. Our SSNNS simulator consists hand-picked tools to explore spiking neural networks more depth with flexibility. is based on the Spike Response Model (SRM) capabilities for short and long term memory. A genetic algorithm, namely CHC, used independently generate such example systems produce patterns interest. Foundational work growing field has shown precise spike timing may be biologically plausible...
In this paper we survey the current state of art in spiking neural networks research and outline our approach to building smart machines. A thorough understanding history, open questions, limitations these can help community gain a better grip on new technology bridge missing gaps. It is necessary look at various aspects networks, such as different modeling approaches, encoding schemes, simulators learning techniques order efficiently make use networks. One paramount characteristic precise...
Interdisciplinary problem solving in computational biology requires a fundamental understanding of complex biological adaptive systems, from cellular to molecular level order tackle challenging problems such as neurodegenerative diseases. In this work we present description and an initial evaluation Spiking Neural Network-Genetic Algorithm (SNN-GA) system are developing for the prediction transcription factor binding sites (TFBS). The SNN-GA approach is based on modeling information...
Complex disorders are a class of diseases whose phenotypic variance is caused by the interplay multiple genetic and environmental factors. Analyzing complexity underlying architecture such traits may help develop more efficient diagnostic tests therapeutic protocols. Despite continuous advances in revealing basis many complex using genome-wide association studies (GWAS), major proportion their has remained unexplained, part because GWAS unable to reliably detect small individual risk...
The computational identification of regulatory elements in genomic DNA is key to understanding the infrastructure a cell. We present an innovative tool identify Transcription Factor Binding Sites (TFBSs) sequences. show that our Positional Pattern Detection able attain high sensitivity and specificity TFBS detection by capturing dependencies between nucleotide positions within TFBS, thereby elucidating complex interactions may be critical for activity.