A5066623854- Genomics and Phylogenetic Studies
- Microbial Community Ecology and Physiology
- Bacterial Genetics and Biotechnology
- Gene Regulatory Network Analysis
- Microbial Metabolic Engineering and Bioproduction
- RNA and protein synthesis mechanisms
- CRISPR and Genetic Engineering
- Evolution and Genetic Dynamics
- Bacteriophages and microbial interactions
- Microbial Fuel Cells and Bioremediation
- Bioinformatics and Genomic Networks
- Wastewater Treatment and Nitrogen Removal
- Biofuel production and bioconversion
- Seismic Waves and Analysis
- Chromium effects and bioremediation
- Geophysical Methods and Applications
- Seismology and Earthquake Studies
- Gut microbiota and health
- Mine drainage and remediation techniques
- Genetics, Bioinformatics, and Biomedical Research
- Gene expression and cancer classification
- Fungal and yeast genetics research
- Radioactive element chemistry and processing
- Metabolomics and Mass Spectrometry Studies
- Viral Infectious Diseases and Gene Expression in Insects
Lawrence Berkeley National Laboratory
2016-2025
University of California, Berkeley
2016-2025
Genomics (United Kingdom)
2024
Montana State University
2023-2024
University of California System
2012-2024
Oak Ridge National Laboratory
2012-2024
University of Tennessee at Knoxville
2009-2024
Innovative Genomics Institute
2020-2023
Space Micro (United States)
2022
Energy Biosciences Institute
2012-2021
We recently described FastTree, a tool for inferring phylogenies alignments with up to hundreds of thousands sequences. Here, we describe improvements FastTree that improve its accuracy without sacrificing scalability.Where 1 used nearest-neighbor interchanges (NNIs) and the minimum-evolution criterion tree, 2 adds subtree-pruning-regrafting (SPRs) maximum-likelihood NNIs. uses heuristics restrict search better trees estimates rate evolution each site (the "CAT" approximation). Nevertheless,...
Gene families are growing rapidly, but standard methods for inferring phylogenies do not scale to alignments with over 10,000 sequences. We present FastTree, a method constructing large and estimating their reliability. Instead of storing distance matrix, FastTree stores sequence profiles internal nodes in the tree. uses these implement Neighbor-Joining heuristics quickly identify candidate joins. then nearest neighbor interchanges reduce length For an alignment N sequences, L sites,...
Abstract Motivation: Molecular biotechnology now makes it possible to build elaborate systems models, but the biology community needs information standards if models are be shared, evaluated and developed cooperatively. Results: We summarize Systems Biology Markup Language (SBML) Level 1, a free, open, XML-based format for representing biochemical reaction networks. SBML is software-independent language describing common research in many areas of computational biology, including cell...
In cellular regulatory networks, genetic activity is controlled by molecular signals that determine when and how often a given gene transcribed. genetically pathways, the protein product encoded one regulates expression of other genes. The time delay, after activation first promoter, to reach an effective level control next promoter depends on rate accumulation. We have analyzed chemical reactions controlling transcript initiation translation termination in single such “genetically coupled”...
Abstract Fluctuations in rates of gene expression can produce highly erratic time patterns protein production individual cells and wide diversity instantaneous concentrations across cell populations. When two independently produced regulatory proteins acting at low cellular competitively control a switch point pathway, stochastic variations their probabilistic pathway selection, so that an initially homogeneous population partitions into distinct phenotypic subpopulations. Many pathogenic...
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...
Abstract Unraveling the drivers controlling community assembly is a central issue in ecology. Although it generally accepted that selection, dispersal, diversification and drift are major processes, defining their relative importance very challenging. Here, we present framework to quantitatively infer mechanisms by phylogenetic bin-based null model analysis (iCAMP). iCAMP shows high accuracy (0.93–0.99), precision (0.80–0.94), sensitivity (0.82–0.94), specificity (0.95–0.98) on simulated...
Significance The study of ecological succession remains at the core ecology. Understanding trajectories and mechanisms controlling is crucial to predicting responses ecosystems environmental change projecting their future states. By definition, deterministic expected under homogeneous abiotic biotic starting conditions. This study, however, shows that groundwater microbial communities in response nutrient amendment primarily stochastic, but drivers biodiversity are dynamic rather than...
Biochemical dynamics are often determined by series of single molecule events such as gene expression and reactions involving protein concentrations at nanomolar concentrations. Molecular fluctuations, consequently, may be biological significance. For example, heterogeneity in clonal populations is believed to arise from molecular fluctuations expression. A realistic description, therefore, requires a probabilistic description the biochemical deterministic descriptions cannot capture...
DNA from low-biodiversity fracture water collected at 2.8-kilometer depth in a South African gold mine was sequenced and assembled into single, complete genome. This bacterium, Candidatus Desulforudis audaxviator, composes >99.9% of the microorganisms inhabiting fluid phase this particular fracture. Its genome indicates motile, sporulating, sulfate-reducing, chemoautotrophic thermophile that can fix its own nitrogen carbon by using machinery shared with archaea. audaxviator is capable an...
We demonstrate the efficacy of a genome-wide protocol in yeast that allows identification those gene products functionally interact with small molecules and result inhibition cellular proliferation. Here we present results from screening 10 diverse compounds 80 experiments against complete collection heterozygous deletion strains. These include anticancer antifungal agents, statins, alverine citrate, dyclonine. In several cases, identified previously known interactions; furthermore, each...
Transposon mutagenesis with next-generation sequencing (TnSeq) is a powerful approach to annotate gene function in bacteria, but existing protocols for TnSeq require laborious preparation of every sample before sequencing. Thus, the are not amenable throughput necessary identify phenotypes and functions majority genes diverse bacteria. Here, we present method, random bar code transposon-site (RB-TnSeq), which increases mutant fitness profiling by incorporating DNA codes into Tn5 mariner...
Since 2003, MicrobesOnline (http://www.microbesonline.org) has been providing a community resource for comparative and functional genome analysis. The portal includes over 1000 complete genomes of bacteria, archaea fungi thousands expression microarrays from diverse organisms ranging model such as Escherichia coli Saccharomyces cerevisiae to environmental microbes Desulfovibrio vulgaris Shewanella oneidensis. To assist in annotating genes reconstructing their evolutionary history, browser...
Standard biological parts, such as BioBricks™ provide the foundation for a new engineering discipline that enables design and construction of synthetic systems with variety applications in bioenergy, materials, therapeutics, environmental remediation. Although original assembly standard has found widespread use, it several shortcomings limit its range potential applications. In particular, system is not suitable protein fusions due to an unfavorable scar sequence encodes in-frame stop codon....
Article21 June 2018Open Access Transparent process Deciphering microbial interactions in synthetic human gut microbiome communities Ophelia S Venturelli Corresponding Author [email protected] orcid.org/0000-0003-2200-1963 Department of Biochemistry, University Wisconsin-Madison, Madison, WI, USA Search for more papers by this author Alex V Carr Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, Garth Fisher Ryan H Hsu...
The inability to predict heterologous gene expression levels precisely hinders our ability engineer biological systems. Using well-characterized regulatory elements offers a potential solution only if such behave predictably when combined. We synthesized 12,563 combinations of common promoters and ribosome binding sites simultaneously measured DNA, RNA, protein from the entire library. simple model, we found that RNA were within twofold expected 80% 64% time, respectively. large dataset...