A5044587877- Microbial Metabolic Engineering and Bioproduction
- Biofuel production and bioconversion
- Enzyme Catalysis and Immobilization
- Bioinformatics and Genomic Networks
- Microbial Community Ecology and Physiology
- Gut microbiota and health
- Environmental DNA in Biodiversity Studies
- RNA and protein synthesis mechanisms
- Wastewater Treatment and Nitrogen Removal
- Slime Mold and Myxomycetes Research
- Protein Structure and Dynamics
- Hydrology and Watershed Management Studies
- Gene expression and cancer classification
- Plant biochemistry and biosynthesis
- Enzyme Structure and Function
- Scientific Computing and Data Management
- Metabolomics and Mass Spectrometry Studies
- Diet and metabolism studies
- Gene Regulatory Network Analysis
- Computational Drug Discovery Methods
- Animal Genetics and Reproduction
- Genomics and Phylogenetic Studies
Argonne National Laboratory
2018-2024
University of Chicago
2021
University of Minho
2014-2019
Abstract For over 10 years, ModelSEED has been a primary resource for the construction of draft genome-scale metabolic models based on annotated microbial or plant genomes. Now being released, biochemistry database serves as foundation biochemical data underlying and KBase. The embodies several properties that, taken together, distinguish it from other published resources by: (i) including compartmentalization, transport reactions, charged molecules proton balancing reactions; (ii)...
The importance and rate of development genome-scale metabolic models have been growing for the last few years, increasing demand software solutions that automate several steps this process. However, since TRIAGE's release, automatic integration transport reactions into has stalled.Here, we present Transport Systems Tracker (TranSyT). Unlike other systems annotation software, TranSyT does not rely on manual curation to expand its internal database, which is derived from highly curated records...
Abstract Since the release of ModelSEED in 2010, systems biology research community has used genome-scale metabolic model reconstruction pipeline to build over 200,000 draft reconstructions that support hundreds publications. Here we describe first comprehensive update this tool, with new features such as (i) a dramatically improved representation energy metabolism, which ensures models produce accurate amounts ATP per mol nutrient consumed; (ii) template for Archaea reconstruction; and...
Predicting elemental cycles and maintaining water quality under increasing anthropogenic influence requires understanding the spatial drivers of river microbiomes. However, unifying microbial processes governing biogeochemistry are hindered by a lack genome-resolved functional insights sampling across multiple rivers. Here we employed community science effort to accelerate sampling, sequencing, analyses microbiomes create Genome Resolved Open Watersheds database (GROWdb). This resource...
Abstract Background One of the European Union directives indicates that 10% all fuels must be bio-synthesized by 2020. In this regard, biobutanol—natively produced clostridial strains—poses as a promising alternative biofuel. possible approach to overcome difficulties industrial exploration native producers is expression more suitable pathways in robust microorganisms such Escherichia coli . The enumeration novel powerful tool, allowing identify non-obvious combinations enzymes produce...
Predicting elemental cycles and maintaining water quality under increasing anthropogenic influence requires knowledge of the spatial drivers river microbiomes. However, understanding core microbial processes governing biogeochemistry is hindered by a lack genome-resolved functional insights sampling across multiple rivers. Here we used community science effort to accelerate sampling, sequencing analyses microbiomes create Genome Resolved Open Watersheds database (GROWdb). GROWdb profiles...
ABSTRACT For over ten years, ModelSEED has been a primary resource for the construction of draft genome-scale metabolic models based on annotated microbial or plant genomes. Now being released, biochemistry database serves as foundation biochemical data underlying and KBase. The embodies several properties that, taken together, distinguish it from other published resources by: (i) including compartmentalization, transport reactions, charged molecules proton balancing reactions;; (ii)...
An amendment to this paper has been published and can be accessed via a link at the top of paper.
A better understanding of the genetic and metabolic mechanisms that confer stress resistance tolerance in plants is key to engineering new crops through advanced breeding technologies. This requires a systems biology approach builds on genome-wide regulation gene expression, plant metabolism, physiology growth. In this study, we examine response drought Sorghum, as leverage tools for transcriptomics modeling have implemented at U.S. Department Energy Systems Biology Knowledgebase (KBase)....
Metabolism has been a major field of study in the last years, mainly due to its importance understanding cell physiology and certain disease phenotypes deregulation. Genome-scale metabolic models (GSMMs) have established as important tools help achieve better human metabolism. Towards this aim, advances systems biology bioinformatics allowed reconstruction several GSMMs, although some limitations challenges remain, such lack external identifiers for both metabolites reactions. A pipeline was...
ABSTRACT The importance and rate of development genome-scale metabolic models have been growing for the last years, increasing demand software solutions that automate several steps this process. However, since TRIAGE’s release, automatic integration transport reactions into has stalled. Here we present Transport Systems Tracker ( TranSyT ), next iteration TRIAGE. Unlike its predecessor, does not rely on manual curation to expand internal database, derived from highly-curated records...
ABSTRACT Anthropogenic perturbations to the nitrogen cycle, primarily through use of synthetic fertilizers, is driving an unprecedented increase in emission nitrous oxide (N 2 O), a potent greenhouse gas and ozone depleting substance, causing urgency identifying sources sinks N O. Microbial denitrification primary contributor biotic production O anoxic regions soil, marine systems, wastewater treatment facilities. Here, comprehensive genome analysis, we show that pathway partitioning...