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    Chandonia, John-Marc

    TitleCompl Biologist Res Sci/Engr
    SchoolLawrence Berkeley National Lab
    DepartmentEnviron Genomics & Systems Bio
    Address1 Cyclotron Road
    Berkeley CA 94720
    Phone510/292-9495
    vCardDownload vCard

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      Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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      1. Chandonia J, 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. Lessons from the CAGI-4 Hopkins clinical panel challenge. Hum Mutat. 2017 Sep; 38(9):1155-1168. PMID: 28397312.
        View in: PubMed
      2. King AJ, Preheim SP, Bailey KL, Robeson MS, Roy Chowdhury T, Crable BR, Hurt RA, 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 J, Alm EJ, Zhou J, Adams MW, Hazen TC, Arkin AP, Elias DA. Temporal Dynamics of In-Field Bioreactor Populations Reflect the Groundwater System and Respond Predictably to Perturbation. Environ Sci Technol. 2017 Mar 07; 51(5):2879-2889. PMID: 28112946.
        View in: PubMed
      3. 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 J, Biggin MD. Quantitative Tagless Copurification: A Method to Validate and Identify Protein-Protein Interactions. Mol Cell Proteomics. 2016 Jun; 15(6):2186-202. PMID: 27099342.
        View in: PubMed
      4. 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 J, Butland G. Bacterial Interactomes: Interacting Protein Partners Share Similar Function and Are Validated in Independent Assays More Frequently Than Previously Reported. Mol Cell Proteomics. 2016 May; 15(5):1539-55. PMID: 26873250; PMCID: PMC4858938 [Available on 05/01/17].
      5. Fox NK, Brenner SE, Chandonia J. The value of protein structure classification information-Surveying the scientific literature. Proteins. 2015 Nov; 83(11):2025-38. PMID: 26313554; PMCID: PMC4609302.
      6. Fox NK, Brenner SE, Chandonia J. SCOPe: Structural Classification of Proteins--extended, integrating SCOP and ASTRAL data and classification of new structures. Nucleic Acids Res. 2014 Jan; 42(Database issue):D304-9. PMID: 24304899; PMCID: PMC3965108.
      7. 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 J, 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 07; 11(12):5720-35. PMID: 23098413; PMCID: PMC3516867.
      8. Chhabra SR, Butland G, Elias DA, Chandonia J, 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. PMID: 21908633; PMCID: PMC3209177.
      9. Chhabra SR, Joachimiak MP, Petzold CJ, Zane GM, Price MN, Reveco SA, Fok V, Johanson AR, Batth TS, Singer M, Chandonia J, 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. PMID: 21738675; PMCID: PMC3125180.
      10. Huang YW, Arkin AP, Chandonia J. WIST: toolkit for rapid, customized LIMS development. Bioinformatics. 2011 Feb 01; 27(3):437-8. PMID: 21258060; PMCID: PMC3031042.
      11. 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 J, 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. PMID: 19805340; PMCID: PMC2742403.
      12. Kim SH, Shin DH, Kim R, Adams P, Chandonia J. Structural genomics of minimal organisms: pipeline and results. Methods Mol Biol. 2008; 426:475-96. PMID: 18542885.
        View in: PubMed
      13. Andreeva A, Howorth D, Chandonia J, 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. PMID: 18000004; PMCID: PMC2238974.
      14. Shin DH, Hou J, Chandonia J, 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. PMID: 17764033.
        View in: PubMed
      15. Lowery TJ, Pelton JG, Chandonia J, 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. PMID: 17680349.
        View in: PubMed
      16. Chandonia J. StrBioLib: a Java library for development of custom computational structural biology applications. Bioinformatics. 2007 Aug 01; 23(15):2018-20. PMID: 17537750; PMCID: PMC4566930.
      17. 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 J, 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. PMID: 17355171; PMCID: PMC1821046.
      18. Chandonia J, Kim SH. Structural proteomics of minimal organisms: conservation of protein fold usage and evolutionary implications. BMC Struct Biol. 2006 Mar 28; 6:7. PMID: 16566839; PMCID: PMC1488858.
      19. Chandonia J, Kim SH, Brenner SE. Target selection and deselection at the Berkeley Structural Genomics Center. Proteins. 2006 Feb 01; 62(2):356-70. PMID: 16276528.
        View in: PubMed
      20. Chandonia J, Brenner SE. The impact of structural genomics: expectations and outcomes. Science. 2006 Jan 20; 311(5759):347-51. PMID: 16424331.
        View in: PubMed
      21. Smith A, Chandonia J, Brenner SE. ANDY: a general, fault-tolerant tool for database searching on computer clusters. Bioinformatics. 2006 Mar 01; 22(5):618-20. PMID: 16397008.
        View in: PubMed
      22. Zhang Y, Chandonia J, Ding C, Holbrook SR. Comparative mapping of sequence-based and structure-based protein domains. BMC Bioinformatics. 2005 Mar 25; 6:77. PMID: 15790427; PMCID: PMC1087832.
      23. Chandonia J, Brenner SE. Implications of structural genomics target selection strategies: Pfam5000, whole genome, and random approaches. Proteins. 2005 Jan 01; 58(1):166-79. PMID: 15521074.
        View in: PubMed
      24. 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 J, 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. PMID: 16211501.
        View in: PubMed
      25. Chandonia J, Brenner S. Update on the pfam5000 strategy for selection of structural genomics targets. Conf Proc IEEE Eng Med Biol Soc. 2005; 1:751-5. PMID: 17282292.
        View in: PubMed
      26. Chandonia J, Earnest TN, Brenner SE. Structural genomics and structural biology: compare and contrast. Genome Biol. 2004; 5(9):343. PMID: 15345043; PMCID: PMC522866.
      27. Crooks GE, Hon G, Chandonia J, Brenner SE. WebLogo: a sequence logo generator. Genome Res. 2004 Jun; 14(6):1188-90. PMID: 15173120; PMCID: PMC419797.
      28. Chandonia J, Hon G, Walker NS, Lo Conte L, Koehl P, Levitt M, Brenner SE. The ASTRAL Compendium in 2004. Nucleic Acids Res. 2004 Jan 01; 32(Database issue):D189-92. PMID: 14681391; PMCID: PMC308768.
      29. Chandonia J, Cohen FE. New local potential useful for genome annotation and 3D modeling. J Mol Biol. 2003 Sep 26; 332(4):835-50. PMID: 12972255.
        View in: PubMed
      30. Chandonia J, Walker NS, Lo Conte L, Koehl P, Levitt M, Brenner SE. ASTRAL compendium enhancements. Nucleic Acids Res. 2002 Jan 01; 30(1):260-3. PMID: 11752310; PMCID: PMC99063.
      31. Chandonia J, Karplus M. New methods for accurate prediction of protein secondary structure. Proteins. 1999 May 15; 35(3):293-306. PMID: 10328264.
        View in: PubMed
      32. Schwartz HL, Chandonia J, 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. PMID: 10222205.
        View in: PubMed
      33. Chandonia J, Karplus M. The importance of larger data sets for protein secondary structure prediction with neural networks. Protein Sci. 1996 Apr; 5(4):768-74. PMID: 8845767; PMCID: PMC2143390.
      34. Chandonia J, Karplus M. Neural networks for secondary structure and structural class predictions. Protein Sci. 1995 Feb; 4(2):275-85. PMID: 7757016; PMCID: PMC2143056.
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