A5075454403- Microbial Metabolic Engineering and Bioproduction
- Bioinformatics and Genomic Networks
- Gene Regulatory Network Analysis
- Metabolomics and Mass Spectrometry Studies
- Biofuel production and bioconversion
- Acute Ischemic Stroke Management
- Neurosurgical Procedures and Complications
- Intracerebral and Subarachnoid Hemorrhage Research
- Bacterial Genetics and Biotechnology
- RNA and protein synthesis mechanisms
- Enzyme Catalysis and Immobilization
- Stroke Rehabilitation and Recovery
- Viral Infectious Diseases and Gene Expression in Insects
- Theoretical and Computational Physics
- Traumatic Brain Injury and Neurovascular Disturbances
- Electronic Health Records Systems
- Reservoir Engineering and Simulation Methods
- Evolution and Genetic Dynamics
- Conducting polymers and applications
- Advanced Control Systems Optimization
- Enzyme Structure and Function
- Biomedical Text Mining and Ontologies
- Digital Image Processing Techniques
- Machine Learning in Healthcare
- Epilepsy research and treatment
United Nations Economic and Social Commission for Asia and the Pacific
2021-2024
University of California, San Diego
2014-2023
La Jolla Bioengineering Institute
2018-2023
Amyris (United States)
2023
Sunshine Coast University Hospital
2023
Johns Hopkins Medicine
2021
Johns Hopkins University
2019-2021
Cornell University
2019-2020
Weill Cornell Medicine
2019-2020
New York University
2020
Genome-scale metabolic models are mathematically-structured knowledge bases that can be used to predict pathway usage and growth phenotypes. Furthermore, they generate test hypotheses when integrated with experimental data. To maximize the value of these models, centralized repositories high-quality must established, adhere established standards model components linked relevant databases. Tools for visualization further enhance their utility. meet needs, we present BiGG Models...
Escher is a web application for visualizing data on biological pathways. Three key features make uniquely effective tool pathway visualization. First, users can rapidly design new maps. provides suggestions based user and genome-scale models, so draw pathways in semi-automated way. Second, visualize related to genes or proteins the associated reactions pathways, using rules that define which enzymes catalyze each reaction. Thus, identify trends common genomic types (e.g. RNA-Seq, proteomics,...
Cortical neural prostheses require chronically implanted small-area microelectrode arrays that simultaneously record and stimulate activity. It is necessary to develop new materials with low interface impedance large charge transfer capacity for this application we explore the use of conducting polymer poly(3,4-ethylenedioxythiophene) (PEDOT) same. We subjected PEDOT coated electrodes voltage cycling between -0.6 0.8 V, 24 h continuous biphasic stimulation at 3 mC/cm <sup...
Abstract The BiGG Models knowledge base (http://bigg.ucsd.edu) is a centralized repository for high-quality genome-scale metabolic models. For the past 12 years, website has allowed users to browse and search Within this update, we detail new content features in repository, continuing original effort connect each model genome annotations external databases as well standardization of reactions metabolites. We describe addition 31 models that expand portion phylogenetic tree covered by Models....
Underlying cellular responses is a transcriptional regulatory network (TRN) that modulates gene expression. A useful description of the TRN would decompose transcriptome into targeted effects individual regulators. Here, we apply unsupervised machine learning to diverse compendium over 250 high-quality Escherichia coli RNA-seq datasets identify 92 statistically independent signals modulate expression specific sets. We show 61 these transcriptomic represent currently characterized...
Abstract Poly(3,4-ethylene dioxythiophene) (PEDOT) is a chemically stable, conjugated polymer that of considerable interest for variety applications including coatings interfacing electronic biomedical devices with living tissue. Here, we describe recent work from our laboratory and elsewhere to investigate the morphology PEDOT in solid state. We discuss importance oxidative chemical electrochemical polymerization, as well critical role counterion used during synthesis film deposition. have...
Genome-scale models of metabolism and macromolecular expression (ME-models) explicitly compute the optimal proteome composition a growing cell. ME-models expand upon well-established genome-scale (M-models), they enable new fundamental understanding cellular growth. have increased predictive capabilities accuracy due to their inclusion biosynthetic costs for machinery life, but come with significant increase in model size complexity. This challenge results which are both difficult...
Experimental studies of Escherichia coli K-12 MG1655 often implicate poorly annotated genes in cellular phenotypes. However, we lack a systematic understanding these genes. How many are there? What information is available for them? And what features do they share that could explain the gap our understanding? Efforts to build predictive, whole-cell models E. inevitably face this knowledge gap. We approached questions systematically by assembling annotations from bases EcoCyc, EcoGene,...
Genome-scale metabolic models (GEMs) are mathematically structured knowledge bases of metabolism that provide phenotypic predictions from genomic information. GEM-guided growth phenotypes rely on the accurate definition a biomass objective function (BOF) is designed to include key cellular components such as major macromolecules (DNA, RNA, proteins), lipids, coenzymes, inorganic ions and species-specific components. Despite its importance, no standardized computational platform currently...
Report8 April 2019Open Access Transparent process Enzyme promiscuity shapes adaptation to novel growth substrates Gabriela I Guzmán Department of Bioengineering, University California, San Diego, La Jolla, CA, USA Search for more papers by this author Troy E Sandberg orcid.org/0000-0003-3240-3659 Ryan A LaCroix Ákos Nyerges orcid.org/0000-0002-1581-490X Synthetic and Systems Biology Unit, Institute Biochemistry, Biological Research Centre the Hungarian Academy Sciences, Szeged, Hungary...
Gene replacement and pre-mRNA splicing modifier therapies represent breakthrough gene targeting treatments for the neuromuscular disease spinal muscular atrophy (SMA), but mechanisms underlying variable efficacy of treatment are incompletely understood. Our examination severe infantile onset human SMA tissues obtained at expedited autopsy revealed persistence developmentally immature motor neuron axons, many which actively degenerating. We identified similar features in a mouse model SMA,...
Abstract Several studies have shown that neither the formal representation nor functional requirements of genome-scale metabolic models (GEMs) are precisely defined. Without a consistent standard, comparability, reproducibility, and interoperability across groups software tools cannot be guaranteed. Here, we present memote ( https://github.com/opencobra/memote ) an open-source containing community-maintained, standardized set me tabolic mo del te sts. The tests cover range aspects from...
The advent of model-enabled workflows in systems biology allows for the integration experimental data types with genome-scale models to discover new features biology. This work demonstrates such a workflow, aimed at establishing metabolomics platform applied study differences metabolomes between anaerobic and aerobic growth Escherichia coli. Constraint-based modeling was utilized deduce target list compounds downstream method development. An analytical methodology developed tailored compound...
Flux balance analysis (FBA) is a widely-used method for analyzing metabolic networks. However, most existing tools that implement FBA require downloading software and writing code. Furthermore, generates predictions networks with thousands of components, so meaningful changes in solutions can be difficult to identify. These challenges make it beginners learn how works. To meet this need, we present Escher-FBA, web application interactive simulations within pathway visualization. Escher-FBA...
To estimate the risk of intracerebral hemorrhage (ICH) recurrence in a large, diverse, US-based population and to identify racial/ethnic socioeconomic subgroups at higher risk.We performed longitudinal analysis prospectively collected claims data from all hospitalizations nonfederal California hospitals between 2005 2011. We used validated diagnosis codes nontraumatic ICH our primary outcome recurrent ICH. residents who survived discharge were included. log-rank tests for unadjusted analyses...
Growth rate and yield are fundamental features of microbial growth. However, we lack a mechanistic quantitative understanding the rate-yield relationship. Studies pairing computational predictions with experiments have shown importance maintenance energy proteome allocation in explaining tradeoffs overflow metabolism. Recently, adaptive evolution Escherichia coli reveal phenotypic diversity beyond what has been explained using simple models growth versus yield. Here, identify two-dimensional...