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    22837 Publications
    3073 Total Profiles
    23 Edited Profiles

    Chandonia, John-Marc

    TitleCompl Biologist Res Sci/Engr
    SchoolLawrence Berkeley National Lab
    DepartmentPhysical Biosciences
    Address1 Cyclotron Road
    Berkeley CA 94720
    Phone510/292-9495

       Bibliographic 
       Publications
      Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can sign in to make corrections and additions, or contact us for help.
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      1. Fox NK, Brenner SE, Chandonia JM. The value of protein structure classification information-Surveying the scientific literature. Proteins. 2015 Nov; 83(11):2025-38.
        View in: PubMed
      2. Fox NK, Brenner SE, Chandonia JM. SCOPe: Structural Classification of Proteins--extended, integrating SCOP and ASTRAL data and classification of new structures. Nucleic Acids Res. 2014 Jan 1; 42(1):D304-9.
        View in: PubMed
      3. 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. High-throughput isolation and characterization of untagged membrane protein complexes: outer membrane complexes of Desulfovibrio vulgaris. J Proteome Res. 2012 Dec 7; 11(12):5720-35.
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      4. 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. Generalized schemes for high-throughput manipulation of the Desulfovibrio vulgaris genome. Appl Environ Microbiol. 2011 Nov; 77(21):7595-604.
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      5. 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. Towards a rigorous network of protein-protein interactions of the model sulfate reducer Desulfovibrio vulgaris Hildenborough. PLoS One. 2011; 6(6):e21470.
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      6. Huang YW, Arkin AP, Chandonia JM. WIST: toolkit for rapid, customized LIMS development. Bioinformatics. 2011 Feb 1; 27(3):437-8.
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      7. 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. Survey of large protein complexes in D. vulgaris reveals great structural diversity. Proc Natl Acad Sci U S A. 2009 Sep 29; 106(39):16580-5.
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      8. Kim SH, Shin DH, Kim R, Adams P, Chandonia JM. Structural genomics of minimal organisms: pipeline and results. Methods Mol Biol. 2008; 426:475-96.
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      9. Andreeva A, Howorth D, Chandonia JM, Brenner SE, Hubbard TJ, Chothia C, Murzin AG. Data growth and its impact on the SCOP database: new developments. Nucleic Acids Res. 2008 Jan; 36(Database issue):D419-25.
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      10. Shin DH, Hou J, Chandonia JM, Das D, Choi IG, Kim R, Kim SH. Structure-based inference of molecular functions of proteins of unknown function from Berkeley Structural Genomics Center. J Struct Funct Genomics. 2007 Sep; 8(2-3):99-105.
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      11. Lowery TJ, Pelton JG, Chandonia JM, Kim R, Yokota H, Wemmer DE. NMR structure of the N-terminal domain of the replication initiator protein DnaA. J Struct Funct Genomics. 2007 Mar; 8(1):11-7.
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      12. Chandonia JM. StrBioLib: a Java library for development of custom computational structural biology applications. Bioinformatics. 2007 Aug 1; 23(15):2018-20.
        View in: PubMed
      13. 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. The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families. PLoS Biol. 2007 Mar; 5(3):e16.
        View in: PubMed
      14. Chandonia JM, Kim SH. Structural proteomics of minimal organisms: conservation of protein fold usage and evolutionary implications. BMC Struct Biol. 2006; 6:7.
        View in: PubMed
      15. Chandonia JM, Kim SH, Brenner SE. Target selection and deselection at the Berkeley Structural Genomics Center. Proteins. 2006 Feb 1; 62(2):356-70.
        View in: PubMed
      16. Chandonia JM, Brenner SE. The impact of structural genomics: expectations and outcomes. Science. 2006 Jan 20; 311(5759):347-51.
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      17. Smith A, Chandonia JM, Brenner SE. ANDY: a general, fault-tolerant tool for database searching on computer clusters. Bioinformatics. 2006 Mar 1; 22(5):618-20.
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      18. Zhang Y, Chandonia JM, Ding C, Holbrook SR. Comparative mapping of sequence-based and structure-based protein domains. BMC Bioinformatics. 2005; 6:77.
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      19. Chandonia JM, Brenner SE. Implications of structural genomics target selection strategies: Pfam5000, whole genome, and random approaches. Proteins. 2005 Jan 1; 58(1):166-79.
        View in: PubMed
      20. 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. Structural genomics of minimal organisms and protein fold space. J Struct Funct Genomics. 2005; 6(2-3):63-70.
        View in: PubMed
      21. Chandonia JM, Brenner S. Update on the pfam5000 strategy for selection of structural genomics targets. Conf Proc IEEE Eng Med Biol Soc. 2005; 1:751-5.
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      22. Chandonia JM, Earnest TN, Brenner SE. Structural genomics and structural biology: compare and contrast. Genome Biol. 2004; 5(9):343.
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      23. Crooks GE, Hon G, Chandonia JM, Brenner SE. WebLogo: a sequence logo generator. Genome Res. 2004 Jun; 14(6):1188-90.
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      24. Chandonia JM, Hon G, Walker NS, Lo Conte L, Koehl P, Levitt M, Brenner SE. The ASTRAL Compendium in 2004. Nucleic Acids Res. 2004 Jan 1; 32(Database issue):D189-92.
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      25. Chandonia JM, Cohen FE. New local potential useful for genome annotation and 3D modeling. J Mol Biol. 2003 Sep 26; 332(4):835-50.
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      26. Chandonia JM, Walker NS, Lo Conte L, Koehl P, Levitt M, Brenner SE. ASTRAL compendium enhancements. Nucleic Acids Res. 2002 Jan 1; 30(1):260-3.
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      27. Chandonia JM, Karplus M. New methods for accurate prediction of protein secondary structure. Proteins. 1999 May 15; 35(3):293-306.
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      28. Schwartz HL, Chandonia JM, Kash SF, Kanaani J, Tunnell E, Domingo A, Cohen FE, Banga JP, Madec AM, Richter W, Baekkeskov S. High-resolution autoreactive epitope mapping and structural modeling of the 65 kDa form of human glutamic acid decarboxylase. J Mol Biol. 1999 Apr 16; 287(5):983-99.
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      29. Chandonia JM, Karplus M. The importance of larger data sets for protein secondary structure prediction with neural networks. Protein Sci. 1996 Apr; 5(4):768-74.
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      30. Chandonia JM, Karplus M. Neural networks for secondary structure and structural class predictions. Protein Sci. 1995 Feb; 4(2):275-85.
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