Works matching AU Chandonia, John-Marc

Results: 21

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

Published in:

PLoS Biology, 2007, v. 5, n. 3, p. 0432, doi. 10.1371/journal.pbio.0050016

By:

Yooseph, Shibu;
Sutton, Granger;
Rusch, Douglas B.;
Halpern, Aaron L.;
Williamson, Shannon J.;
Remington, Karin;
Eisen, Jonathan A.;
Heidelberg, Karla B.;
Manning, Gerard;
Li, Weizhong;
Jaroszewski, Lukasz;
Cieplak, Piotr;
Miller, Christopher S.;
Li, Huiying;
Mashiyama, Susan T.;
Joachimiak, Marcin P.;
van Belle, Christopher;
Chandonia, John-Marc;
Soergel, David A.;
Zhai, Yufeng

Publication type:

Article

Genomic and environmental controls on Castellaniella biogeography in an anthropogenically disturbed subsurface.

Published in:

Environmental Microbiome, 2024, v. 19, n. 1, p. 1, doi. 10.1186/s40793-024-00570-9

By:

Goff, Jennifer L.;
Szink, Elizabeth G.;
Durrence, Konnor L.;
Lui, Lauren M.;
Nielsen, Torben N.;
Kuehl, Jennifer V.;
Hunt, Kristopher A.;
Chandonia, John-Marc;
Huang, Jiawen;
Thorgersen, Michael P.;
Poole II, Farris L.;
Stahl, David A.;
Chakraborty, Romy;
Deutschbauer, Adam M.;
Arkin, Adam P.;
Adams, Michael W. W.

Publication type:

Article

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

Published in:

GigaScience, 2022, v. 11, p. 1, doi. 10.1093/gigascience/giac089

By:

Novichkov, Pavel S;
Chandonia, John-Marc;
Arkin, Adam P

Publication type:

Article

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

Published in:

Frontiers in Microbiology, 2020, v. 11, p. N.PAG, doi. 10.3389/fmicb.2020.587127

By:

Ge, Xiaoxuan;
Thorgersen, Michael P.;
Poole II, Farris L.;
Deutschbauer, Adam M.;
Chandonia, John-Marc;
Novichkov, Pavel S.;
Gushgari-Doyle, Sara;
Lui, Lauren M.;
Nielsen, Torben;
Chakraborty, Romy;
Adams, Paul D.;
Arkin, Adam P.;
Hazen, Terry C.;
Adams, Michael W. W.

Publication type:

Article

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

Published in:

Nucleic Acids Research, 2008, v. 36, p. D419

By:

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

Publication type:

Article

The ASTRAL Compendium in 2004.

Published in:

Nucleic Acids Research, 2004, v. 32, n. suppl 1, p. d189

By:

Chandonia, John‐Marc;
Hon, Gary;
Walker, Nigel S.;
Lo Conte, Loredana;
Koehl, Patrice;
Levitt, Michael;
Brenner, Steven E.

Publication type:

Article

ASTRAL compendium enhancements.

Published in:

Nucleic Acids Research, 2002, v. 30, n. 1, p. 260, doi. 10.1093/nar/30.1.260

By:

Chandonia, John-Marc;
Walker, Nigel S.;
Conte, Loredana Lo;
Koehl, Patrice;
Levitt, Michael;
Brenner, Steven E.

Publication type:

Article

Target selection and deselection at the Berkeley Structural Genomics Center.

Published in:

Proteins, 2006, v. 62, n. 2, p. 356, doi. 10.1002/prot.20674

By:

Chandonia, John-Marc;
Kim, Sung-Hou;
Brenner, Steven E.

Publication type:

Article

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

Published in:

Proteins, 2005, v. 58, n. 1, p. 166, doi. 10.1002/prot.20298

By:

Chandonia, John-Marc;
Brenner, Steven E.

Publication type:

Article

New methods for accurate prediction of protein secondary structure.

Published in:

Proteins, 1999, v. 35, n. 3, p. 293, doi. 10.1002/(SICI)1097-0134(19990515)35:3<293::AID-PROT3>3.0.CO;2-L

By:

Chandonia, John-Marc;
Karplus, Martin

Publication type:

Article

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

Published in:

Environmental Microbiology, 2022, v. 24, n. 11, p. 5546, doi. 10.1111/1462-2920.16173

By:

Goff, Jennifer L.;
Szink, Elizabeth G.;
Thorgersen, Michael P.;
Putt, Andrew D.;
Fan, Yupeng;
Lui, Lauren M.;
Nielsen, Torben N.;
Hunt, Kristopher A.;
Michael, Jonathan P.;
Wang, Yajiao;
Ning, Daliang;
Fu, Ying;
Van Nostrand, Joy D.;
Poole, Farris L.;
Chandonia, John‐Marc;
Hazen, Terry C.;
Stahl, David A.;
Zhou, Jizhong;
Arkin, Adam P.;
Adams, Michael W. W.

Publication type:

Article

WIST: toolkit for rapid, customized LIMS development.

Published in:

Bioinformatics, 2011, v. 27, n. 3, p. 437, doi. 10.1093/bioinformatics/btq676

By:

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

Publication type:

Article

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

Published in:

Proteins, 2015, v. 83, n. 11, p. 2025, doi. 10.1002/prot.24915

By:

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

Publication type:

Article

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

Published in:

BMC Bioinformatics, 2005, v. 6, p. 77, doi. 10.1186/1471-2105-6-77

By:

Ya Zhang;
Chandonia, John-Marc;
Chris6 Ding;
Holbrook, Stephen R.

Publication type:

Article

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

Published in:

Nucleic Acids Research, 2022, v. 50, n. D1, p. D553, doi. 10.1093/nar/gkab1054

By:

Chandonia, John-Marc;
Guan, Lindsey;
Lin, Shiangyi;
Yu, Changhua;
Fox, Naomi K;
Brenner, Steven E

Publication type:

Article

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

Published in:

Nucleic Acids Research, 2019, v. 47, n. D1, p. D475, doi. 10.1093/nar/gky1134

By:

Chandonia, John-Marc;
Fox, Naomi K;
Brenner, Steven E

Publication type:

Article

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

Published in:

Nucleic Acids Research, 2014, v. 42, n. D1, p. D304, doi. 10.1093/nar/gkt1240

By:

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

Publication type:

Article

Novel aspects of iron sulfur cluster biosynthesis in sulfate reducing bacteria (768.17).

Published in:

FASEB Journal, 2014, v. 28, p. N.PAG, doi. 10.1096/fasebj.28.1_supplement.768.17

By:

Butland, Gareth;
Saini, Avneesh;
Trotter, Valentine;
Price, Morgan;
He, Jennifer;
Kuehl, Jennifer;
Wetmore, Kelly;
Liu, Nancy;
Zane, Grant;
Fels, Samuel;
Juba, Thomas;
Shatsky, Maxim;
Arkin, Adam;
Chandonia, John‐Marc;
Wall, Judy;
Deutschbauer, Adam

Publication type:

Article

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

Published in:

PLoS ONE, 2011, v. 6, n. 6, p. 1, doi. 10.1371/journal.pone.0021470

By:

Chhabra, Swapnil R.;
Joachimiak, Marcin P.;
Petzold, Christopher J.;
Zane, Grant M.;
Price, Morgan N.;
Reveco, Sonia A.;
Fok, Veronica;
Johanson, Alyssa R.;
Batth, Tanveer S.;
Singer, Mary;
Chandonia, John-Marc;
Joyner, Dominique;
Hazen, Terry C.;
Arkin, Adam P.;
Wall, Judy D.;
Singh, Anup K.;
Keasling, Jay D.

Publication type:

Article

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

Published in:

Frontiers in Microbiology, 2023, v. 14, p. 1, doi. 10.3389/fmicb.2023.1095191

By:

Trotter, Valentine V.;
Shatsky, Maxim;
Price, Morgan N.;
Juba, Thomas R.;
Zane, Grant M.;
De León, Kara B.;
Majumder, Erica L.-W.;
Gui, Qin;
Ali, Rida;
Wetmore, Kelly M.;
Kuehl, Jennifer V.;
Arkin, Adam P.;
Wall, Judy D.;
Deutschbauer, Adam M.;
Chandonia, John-Marc;
Butland, Gareth P.

Publication type:

Article

Lessons from the CAGI-4 Hopkins clinical panel challenge.

Published in:

Human Mutation, 2017, v. 38, n. 9, p. 1155, doi. 10.1002/humu.23225

By:

Chandonia, John‐Marc;
Adhikari, Aashish;
Carraro, Marco;
Chhibber, Aparna;
Cutting, Garry R.;
Fu, Yao;
Gasparini, Alessandra;
Jones, David T.;
Kramer, Andreas;
Kundu, Kunal;
Lam, Hugo Y. K.;
Leonardi, Emanuela;
Moult, John;
Pal, Lipika R.;
Searls, David B.;
Shah, Sohela;
Sunyaev, Shamil;
Tosatto, Silvio C. E.;
Yin, Yizhou;
Buckley, Bethany A.

Publication type:

Article