J. Chandonia

发表

The ASTRAL Compendium in 2004

Patrice Koehl, Steven E. Brenner, Michael Levitt, 2003, Nucleic Acids Res..

WebLogo: a sequence logo generator.

G. Crooks, S. Brenner, G. Hon, 2004, Genome research.

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

Steven E Brenner, John-Marc Chandonia, Naomi K Fox, 2017, Journal of molecular biology.

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

M. Shatsky, S. Brenner, K. Downing, 2009, Proceedings of the National Academy of Sciences.

WIST: toolkit for rapid, customized LIMS development

Adam P. Arkin, John-Marc Chandonia, Y. Wayne Huang, 2011, Bioinform..

The Sorcerer II Global Ocean Sampling Expedition: Expanding the Universe of Protein Families

Benjamin J. Raphael, Susan S. Taylor, David A W Soergel, 2007, PLoS biology.

Overview of Structural Genomics: Landscape, Premises, and Current Direction

Sung-Hou Kim, J. Chandonia, P. Adams, 2005 .

Implications of structural genomics target selection strategies: Pfam5000, whole genome, and random approaches

S. Brenner, J. Chandonia, 2004, Proteins.

KBase: The United States Department of Energy Systems Biology Knowledgebase

Rick L. Stevens, James J. Davis, Kevin P. Keegan, 2018, Nature Biotechnology.

ASTRAL compendium enhancements

Patrice Koehl, Steven E. Brenner, Michael Levitt, 2002, Nucleic Acids Res..

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

F. Cohen, J. Chandonia, Fred E Cohen, 2003, Journal of molecular biology.

Characterization of a Metal-Resistant Bacillus Strain With a High Molybdate Affinity ModA From Contaminated Sediments at the Oak Ridge Reservation

A. Arkin, A. Deutschbauer, J. Chandonia, 2020, Frontiers in Microbiology.

Lawrence Berkeley National Laboratory Title The Sorcerer II Global Ocean Sampling Expedition : Expanding the Universe of Protein Families Permalink

Benjamin J. Raphael, Susan S. Taylor, David A W Soergel, 2007 .

Towards a Rigorous Network of Protein-Protein Interactions of the Model Sulfate Reducer Desulfovibrio vulgaris Hildenborough

J. Keasling, A. Arkin, A. Singh, 2011, PloS one.

Structural Genomics of Minimal Organisms and Protein Fold Space

Paul D. Adams, Steven E. Brenner, Stephen R. Holbrook, 2005, Journal of Structural and Functional Genomics.

Structural genomics of minimal organisms: pipeline and results.

Sung-Hou Kim, J. Chandonia, P. Adams, 2007, Methods in molecular biology.

Update on the Pfam5000 Strategy for Selection of Structural Genomics Targets

S. Brenner, J. Chandonia, 2005, 2005 IEEE Engineering in Medicine and Biology 27th Annual Conference.

Quantitative tagless co-purification : a method to validate and identify protein-protein interactions

G. Butland, S. Brenner, M. Biggin, 2016 .

Large-scale Genetic Characterization of a Model Sulfate-Reducing Bacterium

Kelly M. Wetmore, A. Arkin, G. Butland, 2021, bioRxiv.

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

Steven E Brenner, Steven C Hall, Susan J Fisher, 2016, Molecular & Cellular Proteomics.

Metrics Progress Report Q 1 : 01 / 12 / 2022 SFA Laboratory Research Manager :

N. Baliga, A. Deutschbauer, D. Stahl, 2022 .

Ecogenomics of groundwater viruses suggests niche differentiation linked to specific environmental tolerance

Sara D. Altenburg, A. Arkin, A. Deutschbauer, 2020, bioRxiv.

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

J. Chandonia, Yu-Wei Wu, S. Singer, 2019, mBio.

Draft Genome Sequence of Bacillus sp. Strain EB106-08-02-XG196, Isolated from High-Nitrate-Contaminated Sediment

A. Arkin, A. Deutschbauer, J. Chandonia, 2020, Microbiology Resource Announcements.

Complete Genome Sequence of Bacillus cereus Strain CPT56D-587-MTF, Isolated from a Nitrate- and Metal-Contaminated Subsurface Environment

A. Arkin, Jizhong Zhou, J. Chandonia, 2022, Microbiology resource announcements.

CORAL: A framework for rigorous self-validated data modeling and integrative, reproducible data analysis

J. Chandonia, P. Novichkov, Adam P Arkin, 2022, GigaScience.

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

Tim J. P. Hubbard, Steven E. Brenner, Alexey G. Murzin, 2007, Nucleic Acids Res..

Lessons from the CAGI‐4 Hopkins clinical panel challenge

Hugo Y. K. Lam, David T. Jones, Aashish N. Adhikari, 2017, Human mutation.

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

G. Butland, S. Brenner, M. Biggin, 2016, Molecular & Cellular Proteomics.

Target selection and deselection at the Berkeley Structural Genomics Center

Steven E Brenner, John-Marc Chandonia, S. Brenner, 2005, Proteins.

Structural proteomics of minimal organisms: Conservation of protein fold usage and evolutionary implications

John-Marc Chandonia, Sung-Hou Kim, J. Chandonia, 2006, BMC Structural Biology.

Ecophysiological and genomic analyses of a representative isolate of highly abundant Bacillus cereus strains in contaminated subsurface sediments

K. A. Hunt, A. Arkin, D. Stahl, 2022, Environmental microbiology.

The DOE Systems Biology Knowledgebase (KBase)

Fangfang Xia, Rick Stevens, Mark Gerstein, 2016, bioRxiv.

Ecogenomics of Groundwater Phages Suggests Niche Differentiation Linked to Specific Environmental Tolerance

Sara D. Altenburg, A. Arkin, A. Deutschbauer, 2021, mSystems.

SCOPe: improvements to the structural classification of proteins – extended database to facilitate variant interpretation and machine learning

S. Brenner, J. Chandonia, Changhua Yu, 2021, Nucleic Acids Res..

Microbiome Metadata Standards: Report of the National Microbiome Data Collaborative’s Workshop and Follow-On Activities

Luke R. Thompson, William D. Duncan, Stanton L. Martin, 2021, mSystems.

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

Steven E. Brenner, Naomi Fox, John-Marc Chandonia, 2018, Nucleic Acids Res..

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

Steven E. Brenner, Naomi Fox, John-Marc Chandonia, 2013, Nucleic Acids Res..

The value of protein structure classification information—Surveying the scientific literature

Steven E. Brenner, Naomi K. Fox, John‐Marc Chandonia, 2015, Proteins.

The Impact of Structural Genomics: Expectations and Outcomes

Steven E Brenner, John-Marc Chandonia, S. Brenner, 2005, Science.

Generalized Schemes for High-Throughput Manipulation of the Desulfovibrio vulgaris Genome

J. Keasling, A. Arkin, M. Ouellet, 2011, Applied and Environmental Microbiology.

The importance of larger data sets for protein secondary structure prediction with neural networks

J M Chandonia, M Karplus, M. Karplus, 1996, Protein science : a publication of the Protein Society.

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

A. Arkin, Jizhong Zhou, J. Chandonia, 2017, Environmental science & technology.

High-throughput Isolation and Characterization of Untagged Membrane Protein Complexes: Outer Membrane Complexes of Desulfovibrio vulgaris

S. Brenner, M. Biggin, J. Chandonia, 2012, Journal of proteome research.

New methods for accurate prediction of protein secondary structure

J M Chandonia, M Karplus, M. Karplus, 1999, Proteins.

Large-scale genetic characterization of the model sulfate-reducing bacterium, Desulfovibrio vulgaris Hildenborough

Kelly M. Wetmore, A. Arkin, G. Butland, 2023, Frontiers in Microbiology.

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

F. Cohen, S. Kash, J. Chandonia, 1999, Journal of molecular biology.

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

J. Chandonia, D. Wemmer, H. Yokota, 2007, Journal of Structural and Functional Genomics.

Protein Secondary Structures: Prediction

John-Marc Chandonia, J. Chandonia, 2001 .

Neural networks for secondary structure and structural class predictions

J M Chandonia, M Karplus, M. Karplus, 1995, Protein science : a publication of the Protein Society.

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

In-Geol Choi, John-Marc Chandonia, Sung-Hou Kim, 2007, Journal of Structural and Functional Genomics.

Correction for Vangay et al., “Microbiome Metadata Standards: Report of the National Microbiome Data Collaborative’s Workshop and Follow-On Activities”

Luke R. Thompson, William D. Duncan, Stanton L. Martin, 2021, mSystems.

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

John-Marc Chandonia, J. Chandonia, 2007, Bioinform..

The Impact of Structural Genomics: Expectations and Outcomes

S. Brenner, J. Chandonia, 2005, Science.

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

S. Brenner, J. Chandonia, Naomi Fox, 2017, Journal of molecular biology.

Structural genomics of minimal organisms: pipeline and results.

Sung-Hou Kim, J. Chandonia, P. Adams, 2007, Methods in molecular biology.

CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods

Silvio C. E. Tosatto, Julius O. B. Jacobsen, Nicholas A. Sinnott-Armstrong, 2024, Genome biology.

CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods

Nicholas A. Sinnott-Armstrong, Jonathan M. Mudge, Hui Ting Grace Yeo, 2022, Genome biology.