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J. Chandonia · SciRah

Researcher profile · Semantic Scholar

J. Chandonia

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J. Chandonia — researcher profile on SciRah

h-index: 26
Works: 71
Citations: 19K

Most-cited papers

WebLogo: a sequence logo generator.
G. Crooks, G. Hon, J. Chandonia, S. Brenner
2004Genome Research13K citations Open access
Semantic Scholar
KBase: The United States Department of Energy Systems Biology Knowledgebase
A. Arkin, R. Cottingham, C. Henry, N. Harris +77 more
2018Nature Biotechnology1,445 citations Open access
Semantic Scholar
Data growth and its impact on the SCOP database: new developments
A. Andreeva, Dave Howorth, J. Chandonia, S. Brenner +3 more
2007Nucleic Acids Res.976 citations Open access
Semantic Scholar
The Sorcerer II Global Ocean Sampling Expedition: Expanding the Universe of Protein Families
S. Yooseph, G. Sutton, D. Rusch, A. Halpern +29 more
2007PLoS Biology865 citations Open access
Semantic Scholar
SCOPe: Structural Classification of Proteins—extended, integrating SCOP and ASTRAL data and classification of new structures
N. Fox, S. Brenner, J. Chandonia
2013Nucleic Acids Res.762 citations Open access
Semantic Scholar
The ASTRAL Compendium in 2004
J. Chandonia, G. Hon, Nigel S. Walker, L. Conte +3 more
2003Nucleic Acids Res.572 citations Open access
Semantic Scholar
The Impact of Structural Genomics: Expectations and Outcomes
J. Chandonia, S. Brenner
2005Science394 citations
Semantic Scholar
SCOPe: improvements to the structural classification of proteins – extended database to facilitate variant interpretation and machine learning
J. Chandonia, Lindsey Guan, Shi-Ruei Lin, Changhua Yu +2 more
2021Nucleic Acids Res.169 citations Open access
Semantic Scholar
SCOPe: classification of large macromolecular structures in the structural classification of proteins—extended database
J. Chandonia, N. Fox, S. Brenner
2018Nucleic Acids Res.157 citations Open access
Semantic Scholar
ASTRAL compendium enhancements
J. Chandonia, Nigel S. Walker, L. Conte, P. Koehl +2 more
2002Nucleic Acids Res.144 citations Open access
Semantic Scholar
New methods for accurate prediction of protein secondary structure
J. Chandonia, M. Karplus
1999Proteins: Structure, Function, and Bioinformatics130 citations Open access
Semantic Scholar
Neural networks for secondary structure and structural class predictions
J. Chandonia, M. Karplus
1995Protein Science122 citations Open access
Semantic Scholar
High-resolution autoreactive epitope mapping and structural modeling of the 65 kDa form of human glutamic acid decarboxylase.
H. L. Schwartz, J. Chandonia, S. Kash, J. Kanaani +7 more
1999Journal of Molecular Biology114 citations Open access
Semantic Scholar
SCOPe: Manual Curation and Artifact Removal in the Structural Classification of Proteins – extended Database
J. Chandonia, N. Fox, S. Brenner
2016Journal of Molecular Biology101 citations Open access
Semantic Scholar
Structural proteomics of minimal organisms: Conservation of protein fold usage and evolutionary implications
J. Chandonia, Sung-Hou Kim
2006BMC Structural Biology97 citations Open access
Semantic Scholar
The DOE Systems Biology Knowledgebase (KBase)
A. Arkin, Rick L. Stevens, R. Cottingham, S. Maslov +75 more
2016bioRxiv68 citations Open access
Semantic Scholar
Implications of structural genomics target selection strategies: Pfam5000, whole genome, and random approaches
J. Chandonia, Steven E. Brenner
2004Proteins: Structure, Function, and Bioinformatics68 citations Open access
Semantic Scholar
Microbiome Metadata Standards: Report of the National Microbiome Data Collaborative’s Workshop and Follow-On Activities
P. Vangay, J. Burgin, Anjanette Johnston, Kristen L. Beck +38 more
2021mSystems60 citations Open access
Semantic Scholar
Large Circular Plasmids from Groundwater Plasmidomes Span Multiple Incompatibility Groups and Are Enriched in Multimetal Resistance Genes
A. Kothari, Yu-Wei Wu, J. Chandonia, M. Charrier +6 more
2019mBio46 citations Open access
Semantic Scholar
The importance of larger data sets for protein secondary structure prediction with neural networks
J. Chandonia, M. Karplus
1996Protein Science44 citations Open access
Semantic Scholar
Survey of large protein complexes in D. vulgaris reveals great structural diversity
B. Han, M. Dong, Haichuan Liu, Lauren E. Camp +13 more
2009Proceedings of the National Academy of Sciences of the United States of America42 citations Open access
Semantic Scholar
WebLogo: A sequence logo generator - eScholarship
G. Crooks, G. Hon, J. Chandonia, S. Brenner
200441 citations
Semantic Scholar
High-throughput Isolation and Characterization of Untagged Membrane Protein Complexes: Outer Membrane Complexes of Desulfovibrio vulgaris
P. Walian, S. Allen, Maxim Shatsky, Lucy Zeng +13 more
2012Journal of Proteome Research32 citations Open access
Semantic Scholar
Structure-based inference of molecular functions of proteins of unknown function from Berkeley Structural Genomics Center
D. Shin, Jing-Tong Hou, J. Chandonia, D. Das +3 more
2007Journal of Structural and Functional Genomics29 citations
Semantic Scholar
Target selection and deselection at the Berkeley Structural Genomics Center
J. Chandonia, Sung-Hou Kim, Steven E. Brenner
2005Proteins: Structure, Function, and Bioinformatics29 citations Open access
Semantic Scholar
Structural Genomics of Minimal Organisms and Protein Fold Space
Sung-Hou Kim, D. Shin, Jin-Yu Liu, V. Oganesyan +23 more
2005Journal of Structural and Functional Genomics26 citations
Semantic Scholar
The value of protein structure classification information—surveying the scientific literature
N. Fox, S. Brenner, J. Chandonia
2015Proteins: Structure, Function, and Bioinformatics24 citations Open access
Semantic Scholar
Bacterial Interactomes: Interacting Protein Partners Share Similar Function and Are Validated in Independent Assays More Frequently Than Previously Reported*
Maxim Shatsky, S. Allen, B. Gold, Nancy L. Liu +23 more
2016Molecular & Cellular Proteomics21 citations Open access
Semantic Scholar
Comparative mapping of sequence-based and structure-based protein domains
Ya Zhang, J. Chandonia, C. Ding, S. Holbrook
2005BMC Bioinformatics21 citations Open access
Semantic Scholar
Characterization of a Metal-Resistant Bacillus Strain With a High Molybdate Affinity ModA From Contaminated Sediments at the Oak Ridge Reservation
X. Ge, M. Thorgersen, F. Poole, A. Deutschbauer +10 more
2020Frontiers in Microbiology18 citations Open access
Semantic Scholar
Ecogenomics of Groundwater Phages Suggests Niche Differentiation Linked to Specific Environmental Tolerance
A. Kothari, S. Roux, Han-Qiao Zhang, A. Prieto +11 more
2021mSystems14 citations Open access
Semantic Scholar
Towards a Rigorous Network of Protein-Protein Interactions of the Model Sulfate Reducer Desulfovibrio vulgaris Hildenborough
S. Chhabra, marcin p. joachimiak, C. Petzold, G. Zane +13 more
2011PLoS ONE14 citations Open access
Semantic Scholar
Generalized Schemes for High-Throughput Manipulation of the Desulfovibrio vulgaris Genome
S. Chhabra, G. Butland, Dwayne A Elias, J. Chandonia +24 more
2011Applied and Environmental Microbiology14 citations Open access
Semantic Scholar
NMR structure of the N-terminal domain of the replication initiator protein DnaA
T. Lowery, J. Pelton, J. Chandonia, R. Kim +2 more
2007Journal of Structural and Functional Genomics12 citations
Semantic Scholar
Genomic and environmental controls on Castellaniella biogeography in an anthropogenically disturbed subsurface
Jennifer L. Goff, Elizabeth G. Szink, Konnor L. Durrence, L. Lui +12 more
2024bioRxiv11 citations Open access
Semantic Scholar
Temporal Dynamics of In-Field Bioreactor Populations Reflect the Groundwater System and Respond Predictably to Perturbation.
A. King, S. Preheim, K. Bailey, M. Robeson +22 more
2017Environmental Science and Technology11 citations Open access
Semantic Scholar
Quantitative Tagless Copurification: A Method to Validate and Identify Protein-Protein Interactions
Maxim Shatsky, M. Dong, Haichuan Liu, Lee Yang +12 more
2016Molecular & Cellular Proteomics11 citations Open access
Semantic Scholar
Large-scale genetic characterization of the model sulfate-reducing bacterium, Desulfovibrio vulgaris Hildenborough
Valentine V. Trotter, Maxim Shatsky, M. Price, T. Juba +12 more
2023Frontiers in Microbiology9 citations Open access
Semantic Scholar
Ecophysiological and genomic analyses of a representative isolate of highly abundant Bacillus cereus strains in contaminated subsurface sediments
Jennifer L. Goff, Elizabeth G. Szink, M. Thorgersen, A. D. Putt +16 more
2022Environmental Microbiology8 citations Open access
Semantic Scholar
Lessons from the CAGI-4 Hopkins clinical panel challenge
J. Chandonia, Aashish N. Adhikari, Marco Carraro, A. Chhibber +16 more
2017Human Mutation8 citations Open access
Semantic Scholar
Complete Genome Sequence of Bacillus cereus Strain CPT56D-587-MTF, Isolated from a Nitrate- and Metal-Contaminated Subsurface Environment
Jennifer L. Goff, L. Lui, T. Nielsen, M. Thorgersen +7 more
2022Microbiology Resource Announcements7 citations Open access
Semantic Scholar
WIST: toolkit for rapid, customized LIMS development
Y. Huang, A. Arkin, J. Chandonia
2011Bioinform.7 citations Open access
Semantic Scholar
Structural genomics and structural biology: compare and contrast
J. Chandonia, T. Earnest, S. Brenner
2004Genome Biology7 citations Open access
Semantic Scholar
Large-scale Genetic Characterization of a Model Sulfate-Reducing Bacterium
Valentine V. Trotter, Maxim Shatsky, M. Price, T. Juba +12 more
2021bioRxiv6 citations Open access
Semantic Scholar
Update on the Pfam5000 Strategy for Selection of Structural Genomics Targets
J. Chandonia, Steven E. Brenner
20052005 IEEE Engineering in Medicine and Biology 27th Annual Conference6 citations Open access
Semantic Scholar
Correction for Vangay et al., “Microbiome Metadata Standards: Report of the National Microbiome Data Collaborative’s Workshop and Follow-On Activities”
P. Vangay, J. Burgin, Anjanette Johnston, Kristen L. Beck +38 more
2021mSystems4 citations Open access
Semantic Scholar
Structural genomics of minimal organisms: pipeline and results.
Sung-Hou Kim, D. Shin, R. Kim, P. Adams +1 more
2007Methods in molecular biology3 citations Open access
Semantic Scholar
Computational Structural Genomics of a Complete Minimal Organism
J. Chandonia, D. Konerding, D. Grant Allen, I. Choi +2 more
20023 citations
Semantic Scholar
CORAL: A framework for rigorous self-validated data modeling and integrative, reproducible data analysis
P. Novichkov, J. Chandonia, A. Arkin
2022GigaScience2 citations Open access
Semantic Scholar
ANDY: a general, fault-tolerant tool for database searching on computer clusters
Andrew Smith, J. Chandonia, S. Brenner
2005Bioinform.2 citations Open access
Semantic Scholar

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