Dylan Chivian

Dylan Chivian
Lawrence Berkeley National Laboratory | LBL · Physical Biosciences Division

PhD

About

59
Publications
11,827
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6,582
Citations
Citations since 2017
7 Research Items
2964 Citations
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20172018201920202021202220230200400600
20172018201920202021202220230200400600

Publications

Publications (59)
Article
DNA from low-biodiversity fracture water collected at 2.8-kilometer depth in a South African gold mine was sequenced and assembled into a single, complete genome. This bacterium, Candidatus Desulforudis audaxviator, composes >99.9% of the microorganisms inhabiting the fluid phase of this particular fracture. Its genome indicates a motile, sporulati...
Article
Full-text available
The metaMicrobesOnline database (freely available at http://meta.MicrobesOnline.org) offers phylogenetic analysis of genes from microbial genomes and metagenomes. Gene trees are constructed for canonical gene families such as COG and Pfam. Such gene trees allow for rapid homologue analysis and subfamily comparison of genes from multiple metagenomes...
Article
Rosetta ab initio protein structure predictions in CASP4 were considerably more consistent and more accurate than previous ab initio structure predictions. Large segments were correctly predicted (>50 residues superimposed within an RMSD of 6.5 A) for 16 of the 21 domains under 300 residues for which models were submitted. Models with the global fo...
Article
Uncultivated Bacteria and Archaea account for the vast majority of species on Earth, but obtaining their genomes directly from the environment, using shotgun sequencing, has only become possible recently. To realize the hope of capturing Earth’s microbial genetic complement and to facilitate the investigation of the functional roles of specific lin...
Article
Full-text available
The reconstruction of bacterial and archaeal genomes from shotgun metagenomes has enabled insights into the ecology and evolution of environmental and host-associated microbiomes. Here we applied this approach to >10,000 metagenomes collected from diverse habitats covering all of Earth’s continents and oceans, including metagenomes from human and a...
Article
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A Correction to this paper has been published: https://doi.org/10.1038/s41587-021-00898-4.
Article
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An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Preprint
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The U.S. Department of Energy Systems Biology Knowledgebase (KBase) is an open-source software and data platform designed to meet the grand challenge of systems biology — predicting and designing biological function from the biomolecular (small scale) to the ecological (large scale). KBase is available for anyone to use, and enables researchers to...
Conference Paper
Full-text available
Project Goals: The extrachromosomal plasmid DNA project is one of the discovery projects funded by ENIGMA. It is a short term, high impact, investigatory effort to study the plasmid populations of the ENIGMA wells. The goal of this project is to exclusively explore the prevalence of plasmid DNA in these communities. Additionally, the project aims a...
Conference Paper
Full-text available
The Oak Ridge Field Research Center, in Oak Ridge, TN, has contaminated and uncontaminated areas/wells where research can be conducted on the microbial communities present in the groundwater and sediment. Plasmids host and distribute non-essential genes, independent of the host’s chromosome, thereby benefitting the host bacteria in certain specific...
Article
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A major fraction of Earth's prokaryotic biomass dwells in the deep subsurface, where cellular abundances per volume of sample are lower, metabolism is slower, and generation times are longer than those in surface terrestrial and marine environments. How these conditions impact biotic interactions and evolutionary processes is largely unknown. Here...
Article
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Desulfovibrio carbinoliphilus subsp. oakridgensis FW-101-2B is an anaerobic, organic acid/alcohol-oxidizing, sulfate-reducing δ-proteobacterium. FW-101-2B was isolated from contaminated groundwater at The Field Research Center at Oak Ridge National Lab after in situ stimulation for heavy metal-reducing conditions. The genome will help elucidate the...
Article
Harnessing the biotechnological potential of the large number of proteins available in sequence databases requires scalable methods for functional characterization. Here we propose a workflow to address this challenge by combining phylogenomic guided DNA synthesis with high-throughput Mass Spectrometry, and applied it to the systematic characteriza...
Article
Full-text available
Tropical forest soils decompose litter rapidly with frequent episodes of anoxia, making it likely that bacteria using alternate terminal electron acceptors (TEAs) such as iron play a large role in supporting decomposition under these conditions. The prevalence of many types of metabolism in litter deconstruction makes these soils useful templates f...
Article
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Microbial engineering strategies that elicit global metabolic perturbations have the capacity to increase organism robustness for targeted metabolite production. In particular, perturbations to regulators of cellular systems that impact glycolysis and amino acid production while simultaneously decreasing fermentation by-products such as acetate and...
Article
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Background: Glycoside hydrolase family 5 (GH5) comprises enzymes with a wide range of activities critical for the deconstruction of lignocellulose. Results: Concurrent glucan and mannan specificity in over 70 members of GH5 can be ascribed to a conserved active site motif. Conclusion: Single domain multispecific hydrolases are widely prevalent. Sig...
Article
Full-text available
In an effort to discover anaerobic bacteria capable of lignin degradation, we isolated "Enterobacter lignolyticus" SCF1 on minimal media with alkali lignin as the sole source of carbon. This organism was isolated anaerobically from tropical forest soils collected from the Short Cloud Forest site in the El Yunque National Forest in Puerto Rico, USA,...
Article
Expression of foreign pathways often results in suboptimal performance due to unintended factors such as introduction of toxic metabolites, cofactor imbalances or poor expression of pathway components. In this study we report a 120% improvement in the production of the isoprenoid-derived sesquiterpene, amorphadiene, produced by an engineered strain...
Article
Full-text available
The Genome-Linked Application for Metabolic Maps (GLAMM) is a unified web interface for visualizing metabolic networks, reconstructing metabolic networks from annotated genome data, visualizing experimental data in the context of metabolic networks and investigating the construction of novel, transgenic pathways. This simple, user-friendly interfac...
Article
Full-text available
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 and fungi and thousands of expression microarrays from diverse organisms ranging from model organisms such as Escherichia coli and Sacc...
Article
The genome of Desulfovibrio vulgaris strain DePue, a sulfate-reducing Deltaproteobacterium isolated from heavy metal-impacted lake sediment, was completely sequenced and compared with the type strain D. vulgaris Hildenborough. The two genomes share a high degree of relatedness and synteny, but harbour distinct prophage and signatures of past phage...
Conference Paper
Microorganisms are a promising source of novel carbohydrate-active enzymes (cellulases, hemicellulases, and lignases) since they are primarily responsible for plant biomass degradation in nature. However, most carbohydrate-active enzymes used by industry come from only a few model organisms. To identify new lignocellulolytic enzymes we shotgun sequ...
Conference Paper
Full-text available
Microorganisms are a promising source of novel carbohydrate-active enzymes (cellulases, hemicellulases, and lignases) since they are primarily responsible for plant biomass degradation in nature. However, most carbohydrate-active enzymes used by industry come from only a few model organisms. To identify new lignocellulolytic enzymes we shotgun sequ...
Article
Full-text available
Type IV secretory systems are a group of bacterial transporters responsible for the transport of proteins and nucleic acids directly into recipient cells. Such systems play key roles in the virulence of some pathogenic organisms and in conjugation-mediated horizontal gene transfer. Many type IV systems require conserved “coupling proteins,” transme...
Article
Full-text available
Author Summary The three-dimensional structure of a protein can reveal much about that protein's evolutionary relationships and functions. Such information about all the proteins in an organism—the proteome—would offer a more global view of these relationships, but solving each structure individually would be a formidable task. In this study, we h...
Data
Full-text available
Complete Listing of Domain Predictions for All ORFs in Yeast All 14,934 domains predicted from the 6,238 sequences are presented in detail. (4.7 MB PDF)
Data
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Protein Structure Predictions with PMCM ≥ 0.8 The most confident predictions using the MCM are listed. (133 KB PDF)
Data
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Protein Structure Prediction with P(SF|D,GO) ≥ 0.8 The most confident predictions using the GO-integration strategy are listed. (77 KB PDF)
Data
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Benchmark Results Best predicted structure—the best predicted structure by RMS among the 1,000 created; Top5 is the cluster center from the five largest clusters; Best Match—the best domain match from all 30 cluster centers. (476 KB PDF)
Conference Paper
A more complete picture of life on Earth, and even life in the Earth, has recently become possible through the application of environmental genomics. We have obtained the complete genome sequence of a new genus of the Firmicutes, the uncultivated sulfate reducing bacterium Desulforudis audaxviator, by filtering fracture water from a borehole at 2.8...
Article
We describe predictions made using the Rosetta structure prediction methodology for both template-based modeling and free modeling categories in the Seventh Critical Assessment of Techniques for Protein Structure Prediction. For the first time, aggressive sampling and all-atom refinement could be carried out for the majority of targets, an advance...
Article
This paper details the assessment process and evaluation results for the Critical Assessment of Protein Structure Prediction (CASP7) domain prediction category. Domain predictions were assessed using the Normalized Domain Overlap score introduced in CASP6 and the accuracy of prediction of domain break points. The results of the analysis clearly dem...
Article
The utilization of natural microbial diversity in biotechnology is hindered by our inability to culture the vast majority of microorganisms and the observation that laboratory engineered bacteria rarely function in the wild. It is now clear that an understanding of the community structure, function and evolution of bacteria in their natural environ...
Article
We have developed a method that combines the ROSETTA de novo protein folding and refinement protocol with distance constraints derived from homologous structures to build homology models that are frequently more accurate than their templates. We test this method by building complete-chain models for a benchmark set of 22 proteins, each with 1 or 2...
Article
Full-text available
The accuracy of a homology model based on the structure of a distant relative or other topologically equivalent protein is primarily limited by the quality of the alignment. Here we describe a systematic approach for sequence-to-structure alignment, called ‘K*Sync’, in which alignments are generated by dynamic programming using a scoring function t...
Conference Paper
The deep subsurface planktonic community found at depths greater than 1.5 km across central South Africa is dominated by a species of Firmicutes that has never been successfully cultivated. A metagenome was assembled from DNA obtained from fracture water emanating from a borehole at 2.8 kilometers depth in a South African Gold mine. The draft assem...
Conference Paper
A metagenome was assembled from DNA obtained from fracture water emanating from a borehole at 2.8 kilometers depth in a South African Au mine. Prior analyses of SSU rRNA and dsrAB gene clone libraries indicated that the planktonic Community was dominated by a species of Firmicutes that has only been detected at depths greater than 1.5 km across cen...
Article
We describe Rosetta predictions in the Sixth Community-Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction (CASP), focusing on the free modeling category. Methods developed since CASP5 are described, and their application to selected targets is discussed. Highlights include improved performance on larger protei...
Article
The Robetta server and revised automatic protocols were used to predict structures for CASP6 targets. Robetta is a publicly available protein structure prediction server (http://robetta.bakerlab.org/ that uses the Rosetta de novo and homology modeling structure prediction methods. We incorporated some of the lessons learned in the CASP5 experiment...
Article
Domain boundary prediction is an important step in both experimental and computational protein structure characterization. We have developed two fully automated domain parsing methods: the first, Ginzu, which we have described previously, utilizes information from homologous sequences and structures, while the second, RosettaDOM, which has not been...
Article
The Robetta server (http://robetta.bakerlab.org) provides automated tools for protein structure prediction and analysis. For structure prediction, sequences submitted to the server are parsed into putative domains and structural models are generated using either comparative modeling or de novo structure prediction methods. If a confident match to a...
Article
A major limitation of current comparative modeling methods is the accuracy with which regions that are structurally divergent from homologues of known structure can be modeled. Because structural differences between homologous proteins are responsible for variations in protein function and specificity, the ability to model these differences has imp...
Article
Representations of the Polypeptide ChainPotential FunctionsSearch Methods ApplicationsFuture WorkFurther ReadingReferences
Article
Robetta is a fully automated protein structure prediction server that uses the Rosetta fragment-insertion method. It combines template-based and de novo structure prediction methods in an attempt to produce high quality models that cover every residue of a submitted sequence. The first step in the procedure is the automatic detection of the locatio...
Article
We describe predictions of the structures of CASP5 targets using Rosetta. The Rosetta fragment insertion protocol was used to generate models for entire target domains without detectable sequence similarity to a protein of known structure and to build long loop insertions (and N-and C-terminal extensions) in cases where a structural template was av...
Article
We use the Rosetta de novo structure prediction method to produce three-dimensional structure models for all Pfam-A sequence families with average length under 150 residues and no link to any protein of known structure. To estimate the reliability of the predictions, the method was calibrated on 131 proteins of known structure. For approximately 60...
Article
Rosetta ab initio protein structure predictions in CASP4 were considerably more consistent and more accurate than previous ab initio structure predictions. Large segments were correctly predicted (>50 residues superimposed within an RMSD of 6.5 Å) for 16 of the 21 domains under 300 residues for which models were submitted. Models with the global fo...
Article
Full-text available
We describe predictions made using the Rosetta structure prediction methodology for both template- based modeling and free modeling categories in the Seventh Critical Assessment of Techniques for Pro- tein Structure Prediction. For the first time, aggressive sampling and all-atom refinement could be car- ried out for the majority of targets, an adv...
Article
Thesis (Ph. D.)--University of Washington, 2005. The primary sequence of a protein encodes the three-dimensional shape that it will adopt, allowing one to attempt to predict the structure of a protein based oil its sequence. However, the reverse is not true: many different sequences will fold into the same topology. Nature takes advantage of this f...

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