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All papers authored by John-Marc Chandonia

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2021 Pajau Vangay

ORCID

, Josephine Burgin

ORCID

, Anjanette Johnston, Kristen L. Beck

ORCID

, Daniel C. Berrios

ORCID

ORCID

, Shane Canon, Patrick Chain, John-Marc Chandonia

ORCID

, Danielle Christianson, Sylvain V. Costes, Joan Damerow, William D. Duncan, Jose Pablo Dundore-Arias

ORCID

, Kjiersten Fagnan and 27 other authors

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

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Pajau Vangay

ORCID

, Josephine Burgin

ORCID

, Anjanette Johnston, Kristen L. Beck

ORCID

, Daniel C. Berrios

ORCID

ORCID

, Shane Canon, Patrick Chain, John-Marc Chandonia

ORCID

, Danielle Christianson, Sylvain V. Costes, Joan Damerow, William D. Duncan, Jose Pablo Dundore-Arias

ORCID

, Kjiersten Fagnan and 27 other authors

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

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2019 Ankita Kothari

ORCID

, Yu-Wei Wu, John-Marc Chandonia

ORCID

, Marimikel Charrier

ORCID

, Lara Rajeev, Andrea M. Rocha, Dominique C. Joyner, Terry C. Hazen

ORCID

, Steven W. Singer, Aindrila Mukhopadhyay

ORCID

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

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2018 John-Marc Chandonia

ORCID

, Naomi K. Fox, Steven E. Brenner

ORCID

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

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Adam P. Arkin

ORCID

, Robert W. Cottingham, Christopher S. Henry, Nomi L. Harris

ORCID

, Michael W. Sneddon, Matthew L. Henderson, William J. Riehl, David J. Weston, Rick L. Stevens, Dan Murphy-Olson, Stephen Y. Chan, Roy T. Kamimura, Sergei Maslov, Sunita Kumari, Meghan M. Drake and 67 other authors

KBase: The United States Department of Energy Systems Biology Knowledgebase

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2017 Andrew J. King, Sarah P. Preheim, Kathryn L. Bailey, Michael S. Robeson

ORCID

, Taniya Roy Chowdhury, Bryan R. Crable, Richard A. Hurt, Tonia Mehlhorn, Kenneth A. Lowe, Tommy J. Phelps, Anthony V. Palumbo, Craig C. Brandt, Steven D. Brown, Mircea Podar, Ping Zhang

ORCID

and 11 other authors

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

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John-Marc Chandonia

ORCID

, Naomi K. Fox, Steven E. Brenner

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

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2016 Maxim Shatsky, Ming Dong, Haichuan Liu, Lee Lisheng Yang, Megan Choi, Mary E. Singer, Jil T. Geller, Susan J. Fisher, Steven C. Hall, Terry C. Hazen, Steven E. Brenner, Gareth Butland, Jian Jin, H. Ewa Witkowska, John-Marc Chandonia

ORCID

and 1 other authors

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

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Maxim Shatsky, Simon Allen, Barbara L. Gold, Nancy L. Liu, Thomas R. Juba, Sonia A. Reveco, Dwayne A. Elias, Ramadevi Prathapam, Jennifer He, Whenhong Yang, Evelin D. Szakal, Haichuan Liu, Mary E. Singer, Jil T. Geller, Bonita R. Lam and 13 other authors

Bacterial interactomes: interacting protein partners share similar function and are validated in independent assays more frequently than previously reported

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

ORCID

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

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2013 Naomi K. Fox, Steven E. Brenner, John-Marc Chandonia

ORCID

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

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2011 S. R. Chhabra, G. Butland, D. A. Elias

ORCID

, J.-M. Chandonia

ORCID

, O.-Y. Fok, T. R. Juba, A. Gorur, S. Allen, C. M. Leung, K. L. Keller, S. Reveco, G. M. Zane, E. Semkiw, R. Prathapam, B. Gold and 13 other authors

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

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Swapnil R. Chhabra, Marcin P. Joachimiak, Christopher J. Petzold, Grant M. Zane, Morgan N. Price, Sonia A. Reveco, Veronica Fok, Alyssa R. Johanson, Tanveer S. Batth, Mary Singer, John-Marc Chandonia

ORCID

, Dominique Joyner, Terry C. Hazen, Adam P. Arkin, Judy D. Wall and 2 other authors

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

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

ORCID

WIST: toolkit for rapid, customized LIMS development

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2009 Bong-Gyoon Han, Ming Dong, Haichuan Liu, Lauren Camp, Jil Geller, Mary Singer, Terry C. Hazen, Megan Choi, H. Ewa Witkowska, H. Ewa Witkowska, David A. Ball, Dieter Typke, Kenneth H. Downing, Maxim Shatsky, Steven E. Brenner and 3 other authors

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

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2007 Antonina Andreeva, Dave Howorth, Steven E. Brenner, John-Marc; Andreeva Antonina; Howorth Dave; Chandonia Marc; Brenner Steven E.; Hubbard Tim J. P.; Chothia Cyrus; Murzin Alexey G. Chandonia

ORCID

, Tim J. P. Hubbard, Cyrus Chothia, Alexey G. Murzin

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

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Dong Hae Shin, Jingtong Hou, John-Marc Chandonia

ORCID

, Debanu Das, In-Geol Choi

ORCID

, Rosalind Kim, Sung-Hou Kim, Sung-Hou; Shin Dong Hae; Hou Jingtong; Chandonia John-Marc; Das Debanu; Choi In-Geol; Kim Rosalind; Kim Sung-Hou Kim

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

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Thomas J. Lowery, Jeffrey G. Pelton, John-Marc Chandonia

ORCID

, Rosalind Kim, Hisao Yokota, David E.; Lowery Thomas J.; Pelton Jeffrey G.; Chandonia John-Marc; Kim Rosalind; Yokota Hisao; Wemmer E. Wemmer

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

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John-Marc Chandonia

ORCID

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

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Shibu Yooseph, Granger Sutton, Douglas B. Rusch, Aaron L. Halpern, Shannon J. Williamson, Karin Remington, Jonathan A. Eisen, Karla B. Heidelberg

ORCID

, Gerard Manning

ORCID

, Weizhong Li, Lukasz Jaroszewski, Piotr Cieplak, Christopher S. Miller, Huiying Li, Susan T. Mashiyama and 19 other authors

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

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