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Metagenome-assembled genome extraction and analysis from microbiomes using KBase.
Nat Protoc. 2023 Jan;18(1):208-238. doi: 10.1038/s41596-022-00747-x. Epub 2022 Nov 14.
Nat Protoc. 2023.
PMID: 36376589
Review.
Publisher Correction: Metagenome-assembled genome extraction and analysis from microbiomes using KBase.
Chivian D, Jungbluth SP, Dehal PS, Wood-Charlson EM, Canon RS, Allen BH, Clark MM, Gu T, Land ML, Price GA, Riehl WJ, Sneddon MW, Sutormin R, Zhang Q, Cottingham RW, Henry CS, Arkin AP.
Chivian D, et al. Among authors: riehl wj.
Nat Protoc. 2023 Feb;18(2):658. doi: 10.1038/s41596-022-00794-4.
Nat Protoc. 2023.
PMID: 36451056
No abstract available.
Item in Clipboard
A bacterial sensor taxonomy across earth ecosystems for machine learning applications.
Park H, Joachimiak MP, Jungbluth SP, Yang Z, Riehl WJ, Canon RS, Arkin AP, Dehal PS.
Park H, et al. Among authors: riehl wj.
mSystems. 2024 Jan 23;9(1):e0002623. doi: 10.1128/msystems.00026-23. Epub 2023 Dec 11.
mSystems. 2024.
PMID: 38078749
Free PMC article.
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A metabolic modeling platform for the computation of microbial ecosystems in time and space (COMETS).
Dukovski I, Bajić D, Chacón JM, Quintin M, Vila JCC, Sulheim S, Pacheco AR, Bernstein DB, Riehl WJ, Korolev KS, Sanchez A, Harcombe WR, Segrè D.
Dukovski I, et al. Among authors: riehl wj.
Nat Protoc. 2021 Nov;16(11):5030-5082. doi: 10.1038/s41596-021-00593-3. Epub 2021 Oct 11.
Nat Protoc. 2021.
PMID: 34635859
Free PMC article.
Review.
Item in Clipboard
KBase: The United States Department of Energy Systems Biology Knowledgebase.
Arkin AP, Cottingham RW, Henry CS, Harris NL, Stevens RL, Maslov S, Dehal P, Ware D, Perez F, Canon S, Sneddon MW, Henderson ML, Riehl WJ, Murphy-Olson D, Chan SY, Kamimura RT, Kumari S, Drake MM, Brettin TS, Glass EM, Chivian D, Gunter D, Weston DJ, Allen BH, Baumohl J, Best AA, Bowen B, Brenner SE, Bun CC, Chandonia JM, Chia JM, Colasanti R, Conrad N, Davis JJ, Davison BH, DeJongh M, Devoid S, Dietrich E, Dubchak I, Edirisinghe JN, Fang G, Faria JP, Frybarger PM, Gerlach W, Gerstein M, Greiner A, Gurtowski J, Haun HL, He F, Jain R, Joachimiak MP, Keegan KP, Kondo S, Kumar V, Land ML, Meyer F, Mills M, Novichkov PS, Oh T, Olsen GJ, Olson R, Parrello B, Pasternak S, Pearson E, Poon SS, Price GA, Ramakrishnan S, Ranjan P, Ronald PC, Schatz MC, Seaver SMD, Shukla M, Sutormin RA, Syed MH, Thomason J, Tintle NL, Wang D, Xia F, Yoo H, Yoo S, Yu D.
Arkin AP, et al. Among authors: riehl wj.
Nat Biotechnol. 2018 Jul 6;36(7):566-569. doi: 10.1038/nbt.4163.
Nat Biotechnol. 2018.
PMID: 29979655
Free PMC article.
No abstract available.
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Metabolic resource allocation in individual microbes determines ecosystem interactions and spatial dynamics.
Harcombe WR, Riehl WJ, Dukovski I, Granger BR, Betts A, Lang AH, Bonilla G, Kar A, Leiby N, Mehta P, Marx CJ, Segrè D.
Harcombe WR, et al. Among authors: riehl wj.
Cell Rep. 2014 May 22;7(4):1104-15. doi: 10.1016/j.celrep.2014.03.070. Epub 2014 May 1.
Cell Rep. 2014.
PMID: 24794435
Free PMC article.
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Signatures of arithmetic simplicity in metabolic network architecture.
Riehl WJ, Krapivsky PL, Redner S, Segrè D.
Riehl WJ, et al.
PLoS Comput Biol. 2010 Apr 1;6(4):e1000725. doi: 10.1371/journal.pcbi.1000725.
PLoS Comput Biol. 2010.
PMID: 20369010
Free PMC article.
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Optimal metabolic regulation using a constraint-based model.
Riehl WJ, Segrè D.
Riehl WJ, et al.
Genome Inform. 2008;20:159-70. doi: 10.1142/9781848163003_0014.
Genome Inform. 2008.
PMID: 19425131
Free PMC article.
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