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List of works by John-Marc Chandonia

ANDY: a general, fault-tolerant tool for database searching on computer clusters

scientific article published on 5 January 2006

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

scientific journal article

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

scientific article published in 2022

Comparative mapping of sequence-based and structure-based protein domains

scientific article

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

scientific article published in 2021

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

scientific article published on 29 June 2021

Generalized schemes for high-throughput manipulation of the Desulfovibrio vulgaris genome

scientific article

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

scientific article published on 01 April 1999

High-throughput isolation and characterization of untagged membrane protein complexes: outer membrane complexes of Desulfovibrio vulgaris

scientific article

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

scientific article published in January 2005

KBase: The United States Department of Energy Systems Biology Knowledgebase

article

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

article

Lessons from the CAGI-4 Hopkins clinical panel challenge

scientific article published on 11 April 2017

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

scientific article published on 22 February 2021

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

scientific article

Neural networks for secondary structure and structural class predictions.

scientific article published on February 1995

New local potential useful for genome annotation and 3D modeling

scientific article

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

scientific journal article

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

scientific article published on 30 November 2016

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

scientific article

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

scholarly article by John-Marc Chandonia et al published 8 January 2019 in Nucleic Acids Research

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

scientific article published on 01 January 2022

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

scientific article

Structural genomics and structural biology: compare and contrast

scientific article

Structural genomics of minimal organisms and protein fold space

scientific article published in January 2005

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

scientific article published on 28 March 2006

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

scholarly article

Target selection and deselection at the Berkeley Structural Genomics Center

scientific article published in February 2006

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

scientific article published on 23 January 2017

The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families

scientific article published in March 2007

The impact of structural genomics: expectations and outcomes

scientific article

The value of protein structure classification information-Surveying the scientific literature.

scientific article

Towards a rigorous network of protein-protein interactions of the model sulfate reducer Desulfovibrio vulgaris Hildenborough

scientific article

WIST: toolkit for rapid, customized LIMS development ⬇️

scientific article published on January 21, 2011

WebLogo: A Sequence Logo Generator

scientific article (publication date: June 2004)

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