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Novichkov PS(*), Chandonia JM(*), Arkin AP. 2022. CORAL: A framework for rigorous self-validated data modeling and integrative, reproducible data analysis. Gigascience 2022 Oct 17;11:giac089. doi: 10.1093/gigascience/giac089. [PubMed]|[PDF]|[Supplementary information] * = co-first authors
Goff JL, Szink EG, Thorgersen MP, Putt AD, Fan Y, Lui LM, Nielsen TN, Hunt KA, Michael JP, Wang Y, Ning D, Fu Y, Van Nostrand JD, Poole FL 2nd, Chandonia JM, Hazen TC, Stahl DA, Zhou J, Arkin AP, Adams MWW. 2022. Ecophysiological and genomic analyses of a representative isolate of highly abundant Bacillus cereus strains in contaminated subsurface sediments. Environ Microbiol 2022 Nov;24(11):5546-5560. doi: 10.1111/1462-2920.16173. [PubMed]|[PDF]
Goff JL, Lui LM, Nielsen TN, Thorgersen MP, Szink EG, Chandonia JM, Poole FL 2nd, Zhou J, Hazen TC, Arkin AP, Adams MWW. 2022. Complete Genome Sequence of Bacillus cereus Strain CPT56D-587-MTF, Isolated from a Nitrate- and Metal-Contaminated Subsurface Environment. Microbiol Resour Announc 2022 May 19;11(5):e0014522. doi: 10.1128/mra.00145-22. [PubMed]|[PDF]
Chandonia JM, Guan L, Lin S, Yu C, Fox NK, Brenner SE. 2022. SCOPe: Improvements to the Structural Classification of Proteins-extended Database to facilitate Variant Interpretation and Machine Learning. Nucleic Acids Research 2022 Jan 7;50(D1):D553–D559. doi: 10.1093/nar/gkab1054. [PubMed]|[PDF]
Kothari A, Roux S, Zhang H, Prieto A, Soneja D, Chandonia J-M,, Spencer S, Wu X, Altenburg S, Fields MW, Deutschbauer AM, Arkin AP, Alm EJ, Chakraborty R, Mukhopadhyay A, 2021. Ecogenomics of Groundwater Phages Suggests Niche Differentiation Linked to Specific Environmental Tolerance. mSystems. 2021 Jun 29;6(3):e0053721. doi: 10.1128/mSystems.00537-21. [PubMed]
Vangay P, Burgin J, Johnston A, Beck KL, Berrios DC, Blumberg K, Canon S, Chain P, Chandonia JM, Christianson D, Costes SV, Damerow J, Duncan WD, Dundore-Arias JP, Fagnan K, Galazka JM, Gibbons SM, Hays D, Hervey J, Hu B, Hurwitz BL, Jaiswal P, Joachimiak MP, Kinkel L, Ladau J, Martin SL, McCue LA, Miller K, Mouncey N, Mungall C, Pafilis E, Reddy TBK, Richardson L, Roux S, Shaffer JP, Sundaramurthi JC, Thompson LR, Timme RE, Zheng J, Wood-Charlson EM, Eloe-Fadrosh EA. 2021. Microbiome Metadata Standards: Report of the National Microbiome Data Collaborative's Workshop and Follow-On Activities. mSystems. 2021 Feb 23;6(1):e01194-20. doi: 10.1128/mSystems.01194-20. [PubMed]
Ge X, Thorgersen MP, Poole FL 2nd, Deutschbauer AM, Chandonia JM, Novichkov PS, Gushgari-Doyle S, Lui LM, Nielsen T, Chakraborty R, Adams PD, Arkin AP, Hazen TC, Adams MWW. 2020. Characterization of a Metal-Resistant Bacillus Strain With a High Molybdate Affinity ModA From Contaminated Sediments at the Oak Ridge Reservation. Front Microbiol. 2020 Oct 19;11:587127. doi: 10.3389/fmicb.2020.587127. eCollection 2020. [PubMed]
Ge X, Thorgersen MP, Poole FL 2nd, Deutschbauer AM, Chandonia JM, Novichkov PS, Adams PD, Arkin AP, Hazen TC, Adams MWW. 2020. Draft Genome Sequence of Bacillus sp. Strain EB106-08-02-XG196, Isolated from High-Nitrate-Contaminated Sediment. Microbiol Resour Announc. 2020 Oct 29;9(44):e01149-20. doi: 10.1128/MRA.01149-20. [PubMed]
Kothari A, Wu YW, Chandonia JM, Charrier M, Rajeev L, Rocha AM, Joyner DC, Hazen TC, Singer SW, Mukhopadhyay A. 2019. Large Circular Plasmids from Groundwater Plasmidomes Span Multiple Incompatibility Groups and Are Enriched in Multimetal Resistance Genes. MBio. 2019 Feb 26;10(1). pii: e02899-18. doi: 10.1128/mBio.02899-18. [PubMed]
Chandonia JM, Fox NK, Brenner SE. 2019. SCOPe: classification of large macromolecular structures in the structural classification of proteins-extended database. Nucleic Acids Res. 2019 Jan 8;47(D1):D475-D481. doi: 10.1093/nar/gky1134. [PubMed]
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. 2018. KBase: The United States Department of Energy Systems Biology Knowledgebase. Nat Biotechnol. Jul 6. doi: 10.1038/nbt.4163. [PubMed]
Chandonia JM, Adhikari A, Carraro M, Chhibber A, Cutting GR, Function 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. 2017. Lessons from the CAGI-4 Hopkins clinical panel challenge. Hum Mutat. Apr 11. doi: 10.1002/humu.23225. [PubMed]
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. 2017. Temporal Dynamics of In-Field Bioreactor Populations Reflect the Groundwater System and Respond Predictably to Perturbation. Environ Sci Technol. Available online 10 Feb 2017. [PubMed]
Chandonia JM, Fox NK, Brenner SE. 2017. SCOPe: Manual Curation and Artifact Removal in the Structural Classification of Proteins – extended Database. Journal of Molecular Biology. J Mol Biol. 2017 Feb 3;429(3):348-355. Available online 30 November 2016, ISSN 0022-2836, doi:0.1016/j.jmb.2016.11.023 [PDF]
Shatsky M, Dong M, Liu H, Yang LL, Choi M, Singer ME, Geller JT, Fisher SJ, Hall SC, Hazen TC, Brenner SE, Butland GP, Jin J, Witkowska HE, Chandonia JM, Biggin MD. 2016. Quantitative tagless co-purification: a method to validate and identify protein-protein interactions. Mol Cell Proteomics mcp.M115.057117. First Published on April 20, 2016, doi:10.1074/mcp.M115.057117. [PDF]|[Supporting information]
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 GP. 2016. Bacterial interactomes: interacting protein partners share similar function and are validated in independent assays more frequently than previously reported. Mol Cell Proteomics mcp.M115.054692. First Published on February 12, 2016, doi:10.1074/mcp.M115.054692. [PDF]|[Supporting information]
Fox NK, Brenner SE, Chandonia JM. 2015. The value of protein structure classification information-surveying the scientific literature. Proteins. doi: 10.1002/prot.24915. [PDF]|[Supporting information]
Fox NK, Brenner SE, Chandonia JM. 2013. SCOPe: Structural Classification of Proteins—extended, integrating SCOP and ASTRAL data and classification of new structures. Nucl. Acids Res. doi: 10.1093/nar/gkt1240. [PDF]
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. 2012. 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. doi: 10.1021/pr300548d. Epub 2012 Oct 25. [PDF]
Chhabra SR, Butland GP, Elias D, Chandonia JM, Fok OY, Juba T, Gorur A, Allen S, Leung CM, Keller K, Reveco SA, Zane GM, Semkiw ES, 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. 2011. Generalized Schemes for High Throughput Manipulation of the Desulfovibrio vulgaris Hildenborough Genome. Applied and Environmental Microbiology. 2011 November; 77(21): 7595-7604. [PDF]
Chhabra SR, Joachimiak MP, Petzold CJ, Zane GM, Price MN, Reveco SA, Fok V, Johanson AR, Batth S, Singer M, Chandonia JM, Joyner D, Hazen TC, Arkin AP, Wall DJ, Singh AK, Keasling JD. 2011. Towards a Rigorous Network of Protein-Protein Interactions of the Model Sulfate Reducer Desulfovibrio vulgaris Hildenborough. PLoS ONE 6(6): e21470. doi:10.1371/journal.pone.0021470.[PDF]
Huang YW, Arkin AP, Chandonia JM. 2011. WIST: toolkit for rapid, customized LIMS development. Bioinformatics 27(3): 437-438. doi: 10.1093/bioinformatics/btq676.[PDF]
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. 2009. Survey of large protein complexes in D. vulgaris reveals great structural diversity. PNAS doi: 10.1073/pnas.0813068106. [PDF]|[Supporting information]
Kim SH, Shin DH, Kim R, Adams P, Chandonia JM. 2008. Structural genomics of minimal organisms: pipeline and results. Methods Mol Biol. 426:475-96. [PDF]|[PubMed]
Andreeva A, Howorth D, Chandonia JM, Brenner SE, Hubbard TJP, Chothia C, Murzin AG. 2008. Data growth and its impact on the SCOP database: new developments. Nucleic Acids Res Jan;36(Database issue):D419-25. Epub 2007 Nov 13. [PDF]|[PubMed]
Chandonia JM. 2007. StrBioLib: a Java library for development of custom computational structural biology applications. Bioinformatics 23: 2018-20. [Preprint PDF]|[PubMed]|[abstract]
Lowery TJ, Pelton JG, Chandonia JM, Kim R, Yokota H, Wemmer DE. 2007. NMR structure of the N-terminal domain of the replication initiator protein DnaA. J Struct Funct Genomics [PDF]|[PubMed]|[abstract]
Shin DH, Hou J, Chandonia JM, Das D, Choi IG, Kim R, Kim SH. 2007. Structure-based inference of molecular functions of proteins of unknown function from Berkeley Structural Genomics Center. J Struct Funct Genomics [PDF]|[PubMed]|[abstract]
Yooseph S, ... (13 authors) ..., Mashiyama ST, Joachimiak MP, van Belle C, Chandonia JM, Soergel DA, ... (6 authors) ..., Brenner SE, ... (6 authors) ..., Venter JC. 2007. The Sorcerer II Global Ocean Sampling Expedition: Expanding the Universe of Protein Families. PLoS Biol 5:e16. [PDF]|[PubMed]|[abstract]
Chandonia JM, Brenner SE. 2006. The impact of structural genomics: expectations and outcomes. Science 311:347-51. [PDF]|[Supplementary Info]|[TOC PDF]|[PubMed]|[abstract]
Chandonia JM, Kim SH, Brenner SE. 2006. Target selection and deselection at the Berkeley Structural Genomics Center. Proteins 62:356-370. [PDF]|[Supplementary Info]|[PubMed]|[abstract]
Chandonia JM, Kim SH. 2006. Structural proteomics of minimal organisms: conservation of protein fold usage and evolutionary implications. BMC Struct Biol 6:7. [PDF]|[PubMed]
Smith A, Chandonia JM, Brenner SE. 2006. ANDY: a general, fault-tolerant tool for database searching on computer clusters. Bioinformatics 22:618-620. [PDF]|[Supplementary Info]|[PubMed]|[abstract]
Chandonia JM, Brenner SE. 2005. Update on the Pfam5000 Strategy for Selection of Structural Genomics Targets. Proceedings of the 2005 IEEE Engineering in Medicine and Biology 27th Annual Conference, Shanghai, China [PDF]|[abstract]
Chandonia JM, Brenner SE. 2005. Implications of structural genomics target selection strategies: Pfam5000, whole genome, and random approaches. Proteins 58:166-79. [PDF]|[Supplementary data]|[PubMed]|[abstract]
Zhang Y, Chandonia JM, Ding C, Holbrook SR. 2005. Comparative mapping of sequence-based and structure-based protein domains. BMC Bioinformatics 6: 77. [PDF]|[PubMed]|[abstract]
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 IC, Chandonia JM, Hou J, Gold B, Yokota H, Brenner SE, Adams PD, Kim R. 2005. Structural Genomics of Minimal Organisms and Protein Fold Space. J Struct Funct Genomics 6:63-70. [PDF]|[PubMed]
Chandonia JM, Hon G, Walker NS, Lo Conte L, Koehl P, Levitt M, Brenner SE. 2004. The ASTRAL Compendium in 2004. Nucleic Acids Res 32 Database issue:D189-92. [PDF]|[PubMed]|[abstract]
Chandonia JM, Earnest TN, Brenner SE. 2004. Structural genomics and structural biology: compare and contrast. Genome Biology 5:343. [PDF]|[PubMed]
Crooks GE, Hon G, Chandonia JM, Brenner SE. 2004. WebLogo: a sequence logo generator. Genome Res 14:1188-90. [PDF]|[PubMed]|[abstract]
Chandonia JM, Cohen FE. 2003. New local potential useful for genome annotation and 3D modeling. J Mol Biol 332:835-50. [PDF]|[abstract]
Chandonia JM, Walker NS, Lo Conte L, Koehl P, Levitt M, Brenner SE. 2002. ASTRAL compendium enhancements. Nucleic Acids Res 30:260-3. [PDF]|[PubMed]|[abstract]
Chandonia JM, Karplus M. 1999. New methods for accurate prediction of protein secondary structure. Proteins 35:293-306. [PDF]|[abstract]
Schwartz HL, Chandonia JM, Kash SF, Kanaani J, Tunnell E, ... Richter W, Baekkeskov S. 1999. High-resolution autoreactive epitope mapping and structural modeling of the 65 kDa form of human glutamic acid decarboxylase. J Mol Biol 287:983-99. [PDF]|[abstract]
Chandonia JM, Karplus M. 1996. The importance of larger data sets for protein secondary structure prediction with neural networks. Protein Sci 5:768-74. [OCR PDF]|[PDF]|[abstract]
Chandonia JM, Karplus M. 1995. Neural networks for secondary structure and structural class predictions. Protein Sci 4:275-85. [OCR PDF]|[PDF]|[abstract]