Dylan Chivian
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Explore the profile of Dylan Chivian including associated specialties, affiliations and a list of published articles.
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33
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3375
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Recent Articles
11.
Chen Z, Friedland G, Pereira J, Reveco S, Chan R, Park J, et al.
J Biol Chem
. 2012 May;
287(30):25335-43.
PMID: 22645145
Enzymes are traditionally viewed as having exquisite substrate specificity; however, recent evidence supports the notion that many enzymes have evolved activities against a range of substrates. The diversity of activities...
12.
DeAngelis K, Dhaeseleer P, Chivian D, Fortney J, Khudyakov J, Simmons B, et al.
Stand Genomic Sci
. 2011 Dec;
5(1):69-85.
PMID: 22180812
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...
13.
Ma S, Garcia D, Redding-Johanson A, Friedland G, Chan R, Batth T, et al.
Metab Eng
. 2011 Aug;
13(5):588-97.
PMID: 21810477
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...
14.
Bates J, Chivian D, Arkin A
Nucleic Acids Res
. 2011 Jun;
39(Web Server issue):W400-5.
PMID: 21624891
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...
15.
Dehal P, Joachimiak M, Price M, Bates J, Baumohl J, Chivian D, et al.
Nucleic Acids Res
. 2009 Nov;
38(Database issue):D396-400.
PMID: 19906701
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...
16.
Walker C, Stolyar S, Chivian D, Pinel N, Gabster J, Dehal P, et al.
Environ Microbiol
. 2009 Sep;
11(9):2244-52.
PMID: 19737303
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...
17.
Chivian D, Brodie E, Alm E, Culley D, Dehal P, DeSantis T, et al.
Science
. 2008 Oct;
322(5899):275-8.
PMID: 18845759
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...
18.
Das R, Qian B, Raman S, Vernon R, Thompson J, Bradley P, et al.
Proteins
. 2007 Sep;
69 Suppl 8:118-28.
PMID: 17894356
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...
19.
Tress M, Cheng J, Baldi P, Joo K, Lee J, Seo J, et al.
Proteins
. 2007 Aug;
69 Suppl 8:137-51.
PMID: 17680686
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...
20.
Haft R, Gachelet E, Nguyen T, Toussaint L, Chivian D, Traxler B
J Bacteriol
. 2007 Jul;
189(18):6626-34.
PMID: 17631633
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...