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Items: 38

1.

Large Circular Plasmids from Groundwater Plasmidomes Span Multiple Incompatibility Groups and Are Enriched in Multimetal Resistance Genes.

Kothari A, Wu YW, Chandonia JM, Charrier M, Rajeev L, Rocha AM, Joyner DC, Hazen TC, Singer SW, Mukhopadhyay A.

MBio. 2019 Feb 26;10(1). pii: e02899-18. doi: 10.1128/mBio.02899-18.

2.

SCOPe: classification of large macromolecular structures in the structural classification of proteins-extended database.

Chandonia JM, Fox NK, Brenner SE.

Nucleic Acids Res. 2019 Jan 8;47(D1):D475-D481. doi: 10.1093/nar/gky1134.

3.

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.

Nat Biotechnol. 2018 Jul 6;36(7):566-569. doi: 10.1038/nbt.4163. No abstract available.

4.

Lessons from the CAGI-4 Hopkins clinical panel challenge.

Chandonia JM, Adhikari A, Carraro M, Chhibber A, Cutting GR, Fu Y, Gasparini A, Jones DT, Kramer A, Kundu K, Lam HYK, Leonardi E, Moult J, Pal LR, Searls DB, Shah S, Sunyaev S, Tosatto SCE, Yin Y, Buckley BA.

Hum Mutat. 2017 Sep;38(9):1155-1168. doi: 10.1002/humu.23225. Epub 2017 Jun 12.

5.

Temporal Dynamics of In-Field Bioreactor Populations Reflect the Groundwater System and Respond Predictably to Perturbation.

King AJ, Preheim SP, Bailey KL, Robeson MS 2nd, Roy Chowdhury T, Crable BR, Hurt RA Jr, Mehlhorn T, Lowe KA, Phelps TJ, Palumbo AV, Brandt CC, Brown SD, Podar M, Zhang P, Lancaster WA, Poole F, Watson DB, W Fields M, Chandonia JM, Alm EJ, Zhou J, Adams MW, Hazen TC, Arkin AP, Elias DA.

Environ Sci Technol. 2017 Mar 7;51(5):2879-2889. doi: 10.1021/acs.est.6b04751. Epub 2017 Feb 10.

6.

SCOPe: Manual Curation and Artifact Removal in the Structural Classification of Proteins - extended Database.

Chandonia JM, Fox NK, Brenner SE.

J Mol Biol. 2017 Feb 3;429(3):348-355. doi: 10.1016/j.jmb.2016.11.023. Epub 2016 Nov 30.

7.

Quantitative Tagless Copurification: A Method to Validate and Identify Protein-Protein Interactions.

Shatsky M, Dong M, Liu H, Yang LL, Choi M, Singer ME, Geller JT, Fisher SJ, Hall SC, Hazen TC, Brenner SE, Butland G, Jin J, Witkowska HE, Chandonia JM, Biggin MD.

Mol Cell Proteomics. 2016 Jun;15(6):2186-202. doi: 10.1074/mcp.M115.057117. Epub 2016 Apr 20.

8.

Bacterial Interactomes: Interacting Protein Partners Share Similar Function and Are Validated in Independent Assays More Frequently Than Previously Reported.

Shatsky M, Allen S, Gold BL, Liu NL, Juba TR, Reveco SA, Elias DA, Prathapam R, He J, Yang W, Szakal ED, Liu H, Singer ME, Geller JT, Lam BR, Saini A, Trotter VV, Hall SC, Fisher SJ, Brenner SE, Chhabra SR, Hazen TC, Wall JD, Witkowska HE, Biggin MD, Chandonia JM, Butland G.

Mol Cell Proteomics. 2016 May;15(5):1539-55. doi: 10.1074/mcp.M115.054692. Epub 2016 Feb 12.

9.

The value of protein structure classification information-Surveying the scientific literature.

Fox NK, Brenner SE, Chandonia JM.

Proteins. 2015 Nov;83(11):2025-38. doi: 10.1002/prot.24915. Epub 2015 Sep 19.

10.

SCOPe: Structural Classification of Proteins--extended, integrating SCOP and ASTRAL data and classification of new structures.

Fox NK, Brenner SE, Chandonia JM.

Nucleic Acids Res. 2014 Jan;42(Database issue):D304-9. doi: 10.1093/nar/gkt1240. Epub 2013 Dec 3.

11.

High-throughput isolation and characterization of untagged membrane protein complexes: outer membrane complexes of Desulfovibrio vulgaris.

Walian PJ, Allen S, Shatsky M, Zeng L, Szakal ED, Liu H, Hall SC, Fisher SJ, Lam BR, Singer ME, Geller JT, Brenner SE, Chandonia JM, Hazen TC, Witkowska HE, Biggin MD, Jap BK.

J Proteome Res. 2012 Dec 7;11(12):5720-35. doi: 10.1021/pr300548d. Epub 2012 Oct 25.

12.

Generalized schemes for high-throughput manipulation of the Desulfovibrio vulgaris genome.

Chhabra SR, Butland G, Elias DA, Chandonia JM, Fok OY, Juba TR, Gorur A, Allen S, Leung CM, Keller KL, Reveco S, Zane GM, Semkiw E, Prathapam R, Gold B, Singer M, Ouellet M, Szakal ED, Jorgens D, Price MN, Witkowska HE, Beller HR, Arkin AP, Hazen TC, Biggin MD, Auer M, Wall JD, Keasling JD.

Appl Environ Microbiol. 2011 Nov;77(21):7595-604. doi: 10.1128/AEM.05495-11. Epub 2011 Sep 9.

13.

Towards a rigorous network of protein-protein interactions of the model sulfate reducer Desulfovibrio vulgaris Hildenborough.

Chhabra SR, Joachimiak MP, Petzold CJ, Zane GM, Price MN, Reveco SA, Fok V, Johanson AR, Batth TS, Singer M, Chandonia JM, Joyner D, Hazen TC, Arkin AP, Wall JD, Singh AK, Keasling JD.

PLoS One. 2011;6(6):e21470. doi: 10.1371/journal.pone.0021470. Epub 2011 Jun 28.

14.

WIST: toolkit for rapid, customized LIMS development.

Huang YW, Arkin AP, Chandonia JM.

Bioinformatics. 2011 Feb 1;27(3):437-8. doi: 10.1093/bioinformatics/btq676. Epub 2011 Jan 21.

15.

Survey of large protein complexes in D. vulgaris reveals great structural diversity.

Han BG, Dong M, Liu H, Camp L, Geller J, Singer M, Hazen TC, Choi M, Witkowska HE, Ball DA, Typke D, Downing KH, Shatsky M, Brenner SE, Chandonia JM, Biggin MD, Glaeser RM.

Proc Natl Acad Sci U S A. 2009 Sep 29;106(39):16580-5. doi: 10.1073/pnas.0813068106. Epub 2009 Sep 11.

16.

Structural genomics of minimal organisms: pipeline and results.

Kim SH, Shin DH, Kim R, Adams P, Chandonia JM.

Methods Mol Biol. 2008;426:475-96. doi: 10.1007/978-1-60327-058-8_32.

PMID:
18542885
17.

Data growth and its impact on the SCOP database: new developments.

Andreeva A, Howorth D, Chandonia JM, Brenner SE, Hubbard TJ, Chothia C, Murzin AG.

Nucleic Acids Res. 2008 Jan;36(Database issue):D419-25. Epub 2007 Nov 13.

18.

Structure-based inference of molecular functions of proteins of unknown function from Berkeley Structural Genomics Center.

Shin DH, Hou J, Chandonia JM, Das D, Choi IG, Kim R, Kim SH.

J Struct Funct Genomics. 2007 Sep;8(2-3):99-105. Epub 2007 Sep 2. Review.

PMID:
17764033
19.

NMR structure of the N-terminal domain of the replication initiator protein DnaA.

Lowery TJ, Pelton JG, Chandonia JM, Kim R, Yokota H, Wemmer DE.

J Struct Funct Genomics. 2007 Mar;8(1):11-7. Epub 2007 Aug 7.

PMID:
17680349
20.

StrBioLib: a Java library for development of custom computational structural biology applications.

Chandonia JM.

Bioinformatics. 2007 Aug 1;23(15):2018-20. Epub 2007 May 30.

21.

The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families.

Yooseph S, Sutton G, Rusch DB, Halpern AL, Williamson SJ, Remington K, Eisen JA, Heidelberg KB, Manning G, Li W, Jaroszewski L, Cieplak P, Miller CS, Li H, Mashiyama ST, Joachimiak MP, van Belle C, Chandonia JM, Soergel DA, Zhai Y, Natarajan K, Lee S, Raphael BJ, Bafna V, Friedman R, Brenner SE, Godzik A, Eisenberg D, Dixon JE, Taylor SS, Strausberg RL, Frazier M, Venter JC.

PLoS Biol. 2007 Mar;5(3):e16.

22.

Update on the pfam5000 strategy for selection of structural genomics targets.

Chandonia JM, Brenner S.

Conf Proc IEEE Eng Med Biol Soc. 2005;1:751-5.

PMID:
17282292
24.

The impact of structural genomics: expectations and outcomes.

Chandonia JM, Brenner SE.

Science. 2006 Jan 20;311(5759):347-51. Review.

PMID:
16424331
25.

ANDY: a general, fault-tolerant tool for database searching on computer clusters.

Smith A, Chandonia JM, Brenner SE.

Bioinformatics. 2006 Mar 1;22(5):618-20. Epub 2006 Jan 5.

PMID:
16397008
26.

Target selection and deselection at the Berkeley Structural Genomics Center.

Chandonia JM, Kim SH, Brenner SE.

Proteins. 2006 Feb 1;62(2):356-70.

PMID:
16276528
27.

Structural genomics of minimal organisms and protein fold space.

Kim SH, Shin DH, Liu J, Oganesyan V, Chen S, Xu QS, Kim JS, Das D, Schulze-Gahmen U, Holbrook SR, Holbrook EL, Martinez BA, Oganesyan N, DeGiovanni A, Lou Y, Henriquez M, Huang C, Jancarik J, Pufan R, Choi IG, Chandonia JM, Hou J, Gold B, Yokota H, Brenner SE, Adams PD, Kim R.

J Struct Funct Genomics. 2005;6(2-3):63-70.

PMID:
16211501
28.

Comparative mapping of sequence-based and structure-based protein domains.

Zhang Y, Chandonia JM, Ding C, Holbrook SR.

BMC Bioinformatics. 2005 Mar 25;6:77.

29.
30.

Structural genomics and structural biology: compare and contrast.

Chandonia JM, Earnest TN, Brenner SE.

Genome Biol. 2004;5(9):343. Epub 2004 Aug 25. No abstract available.

31.

WebLogo: a sequence logo generator.

Crooks GE, Hon G, Chandonia JM, Brenner SE.

Genome Res. 2004 Jun;14(6):1188-90.

32.

The ASTRAL Compendium in 2004.

Chandonia JM, Hon G, Walker NS, Lo Conte L, Koehl P, Levitt M, Brenner SE.

Nucleic Acids Res. 2004 Jan 1;32(Database issue):D189-92.

33.

New local potential useful for genome annotation and 3D modeling.

Chandonia JM, Cohen FE.

J Mol Biol. 2003 Sep 26;332(4):835-50.

PMID:
12972255
34.

ASTRAL compendium enhancements.

Chandonia JM, Walker NS, Lo Conte L, Koehl P, Levitt M, Brenner SE.

Nucleic Acids Res. 2002 Jan 1;30(1):260-3.

35.

New methods for accurate prediction of protein secondary structure.

Chandonia JM, Karplus M.

Proteins. 1999 May 15;35(3):293-306.

PMID:
10328264
36.

High-resolution autoreactive epitope mapping and structural modeling of the 65 kDa form of human glutamic acid decarboxylase.

Schwartz HL, Chandonia JM, Kash SF, Kanaani J, Tunnell E, Domingo A, Cohen FE, Banga JP, Madec AM, Richter W, Baekkeskov S.

J Mol Biol. 1999 Apr 16;287(5):983-99.

PMID:
10222205
37.
38.

Neural networks for secondary structure and structural class predictions.

Chandonia JM, Karplus M.

Protein Sci. 1995 Feb;4(2):275-85.

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