Advanced Search
Display options
Filter resources
Text Availability
Article type
Publication date
Species
Language
Sex
Age
Showing 1 to 12 of 18 entries
Sorted by: Best Match Show Resources per page
Computational Metabolomics Operations at BioCyc.org.

Metabolites

Karp PD, Billington R, Holland TA, Kothari A, Krummenacker M, Weaver D, Latendresse M, Paley S.
PMID: 26011592
Metabolites. 2015 May 22;5(2):291-310. doi: 10.3390/metabo5020291.

BioCyc.org is a genome and metabolic pathway web portal covering 5500 organisms, including Homo sapiens, Arabidopsis thaliana, Saccharomyces cerevisiae and Escherichia coli. These organism-specific databases have undergone variable degrees of curation. The EcoCyc (Escherichia coli Encyclopedia) database is the...

Cite
Karp PD, Billington R, Holland TA, et al. Computational Metabolomics Operations at BioCyc.org. Metabolites. 2015;5(2):291-310doi: 10.3390/metabo5020291.
Karp, P. D., Billington, R., Holland, T. A., Kothari, A., Krummenacker, M., Weaver, D., Latendresse, M., & Paley, S. (2015). Computational Metabolomics Operations at BioCyc.org. Metabolites, 5(2), 291-310. https://doi.org/10.3390/metabo5020291
Karp, Peter D, et al. "Computational Metabolomics Operations at BioCyc.org." Metabolites vol. 5,2 (2015): 291-310. doi: https://doi.org/10.3390/metabo5020291
Karp PD, Billington R, Holland TA, Kothari A, Krummenacker M, Weaver D, Latendresse M, Paley S. Computational Metabolomics Operations at BioCyc.org. Metabolites. 2015 May 22;5(2):291-310. doi: 10.3390/metabo5020291. PMID: 26011592; PMCID: PMC4495374.
Copy Download .nbib Format: NLM
Construction and completion of flux balance models from pathway databases.

Bioinformatics (Oxford, England)

Latendresse M, Krummenacker M, Trupp M, Karp PD.
PMID: 22262672
Bioinformatics. 2012 Feb 01;28(3):388-96. doi: 10.1093/bioinformatics/btr681. Epub 2012 Jan 18.

MOTIVATION: Flux balance analysis (FBA) is a well-known technique for genome-scale modeling of metabolic flux. Typically, an FBA formulation requires the accurate specification of four sets: biochemical reactions, biomass metabolites, nutrients and secreted metabolites. The development of FBA models...

Cite
Latendresse M, Krummenacker M, Trupp M, et al. Construction and completion of flux balance models from pathway databases. Bioinformatics. 2012;28(3):388-96doi: 10.1093/bioinformatics/btr681.
Latendresse, M., Krummenacker, M., Trupp, M., & Karp, P. D. (2012). Construction and completion of flux balance models from pathway databases. Bioinformatics (Oxford, England), 28(3), 388-96. https://doi.org/10.1093/bioinformatics/btr681
Latendresse, Mario, et al. "Construction and completion of flux balance models from pathway databases." Bioinformatics (Oxford, England) vol. 28,3 (2012): 388-96. doi: https://doi.org/10.1093/bioinformatics/btr681
Latendresse M, Krummenacker M, Trupp M, Karp PD. Construction and completion of flux balance models from pathway databases. Bioinformatics. 2012 Feb 01;28(3):388-96. doi: 10.1093/bioinformatics/btr681. Epub 2012 Jan 18. PMID: 22262672; PMCID: PMC3268246.
Copy Download .nbib Format: NLM
A Comparison of Microbial Genome Web Portals.

Frontiers in microbiology

Karp PD, Ivanova N, Krummenacker M, Kyrpides N, Latendresse M, Midford P, Ong WK, Paley S, Seshadri R.
PMID: 30853946
Front Microbiol. 2019 Feb 22;10:208. doi: 10.3389/fmicb.2019.00208. eCollection 2019.

Microbial genome web portals have a broad range of capabilities that address a number of information-finding and analysis needs for scientists. This article compares the capabilities of the major microbial genome web portals to aid researchers in determining which...

Cite
Karp PD, Ivanova N, Krummenacker M, et al. A Comparison of Microbial Genome Web Portals. Front Microbiol. 2019;10:208doi: 10.3389/fmicb.2019.00208.
Karp, P. D., Ivanova, N., Krummenacker, M., Kyrpides, N., Latendresse, M., Midford, P., Ong, W. K., Paley, S., & Seshadri, R. (2019). A Comparison of Microbial Genome Web Portals. Frontiers in microbiology, 10208. https://doi.org/10.3389/fmicb.2019.00208
Karp, Peter D, et al. "A Comparison of Microbial Genome Web Portals." Frontiers in microbiology vol. 10 (2019): 208. doi: https://doi.org/10.3389/fmicb.2019.00208
Karp PD, Ivanova N, Krummenacker M, Kyrpides N, Latendresse M, Midford P, Ong WK, Paley S, Seshadri R. A Comparison of Microbial Genome Web Portals. Front Microbiol. 2019 Feb 22;10:208. doi: 10.3389/fmicb.2019.00208. eCollection 2019. PMID: 30853946; PMCID: PMC6395428.
Copy Download .nbib Format: NLM
The EcoCyc Database in 2021.

Frontiers in microbiology

Keseler IM, Gama-Castro S, Mackie A, Billington R, Bonavides-Martínez C, Caspi R, Kothari A, Krummenacker M, Midford PE, Muñiz-Rascado L, Ong WK, Paley S, Santos-Zavaleta A, Subhraveti P, Tierrafría VH, Wolfe AJ, Collado-Vides J, Paulsen IT, Karp PD.
PMID: 34394059
Front Microbiol. 2021 Jul 28;12:711077. doi: 10.3389/fmicb.2021.711077. eCollection 2021.

The EcoCyc model-organism database collects and summarizes experimental data for

Cite
Keseler IM, Gama-Castro S, Mackie A, et al. The EcoCyc Database in 2021. Front Microbiol. 2021;12:711077doi: 10.3389/fmicb.2021.711077.
Keseler, I. M., Gama-Castro, S., Mackie, A., Billington, R., Bonavides-Martínez, C., Caspi, R., Kothari, A., Krummenacker, M., Midford, P. E., Muñiz-Rascado, L., Ong, W. K., Paley, S., Santos-Zavaleta, A., Subhraveti, P., Tierrafría, V. H., Wolfe, A. J., Collado-Vides, J., Paulsen, I. T., & Karp, P. D. (2021). The EcoCyc Database in 2021. Frontiers in microbiology, 12711077. https://doi.org/10.3389/fmicb.2021.711077
Keseler, Ingrid M, et al. "The EcoCyc Database in 2021." Frontiers in microbiology vol. 12 (2021): 711077. doi: https://doi.org/10.3389/fmicb.2021.711077
Keseler IM, Gama-Castro S, Mackie A, Billington R, Bonavides-Martínez C, Caspi R, Kothari A, Krummenacker M, Midford PE, Muñiz-Rascado L, Ong WK, Paley S, Santos-Zavaleta A, Subhraveti P, Tierrafría VH, Wolfe AJ, Collado-Vides J, Paulsen IT, Karp PD. The EcoCyc Database in 2021. Front Microbiol. 2021 Jul 28;12:711077. doi: 10.3389/fmicb.2021.711077. eCollection 2021. PMID: 34394059; PMCID: PMC8357350.
Copy Download .nbib Format: NLM
Exceptional fossil assemblages confirm the existence of complex Early Triassic ecosystems during the early Spathian.

Scientific reports

Smith CPA, Laville T, Fara E, Escarguel G, Olivier N, Vennin E, Goudemand N, Bylund KG, Jenks JF, Stephen DA, Hautmann M, Charbonnier S, Krumenacker LJ, Brayard A.
PMID: 34608207
Sci Rep. 2021 Oct 04;11(1):19657. doi: 10.1038/s41598-021-99056-8.

The mass extinction characterizing the Permian/Triassic boundary (PTB; ~ 252 Ma) corresponds to a major faunal shift between the Palaeozoic and the Modern evolutionary fauna. The temporal, spatial, environmental, and ecological dynamics of the associated biotic recovery remain highly...

Cite
Smith CPA, Laville T, Fara E, et al. Exceptional fossil assemblages confirm the existence of complex Early Triassic ecosystems during the early Spathian. Sci Rep. 2021;11(1):19657doi: 10.1038/s41598-021-99056-8.
Smith, C. P. A., Laville, T., Fara, E., Escarguel, G., Olivier, N., Vennin, E., Goudemand, N., Bylund, K. G., Jenks, J. F., Stephen, D. A., Hautmann, M., Charbonnier, S., Krumenacker, L. J., & Brayard, A. (2021). Exceptional fossil assemblages confirm the existence of complex Early Triassic ecosystems during the early Spathian. Scientific reports, 11(1), 19657. https://doi.org/10.1038/s41598-021-99056-8
Smith, Christopher P A, et al. "Exceptional fossil assemblages confirm the existence of complex Early Triassic ecosystems during the early Spathian." Scientific reports vol. 11,1 (2021): 19657. doi: https://doi.org/10.1038/s41598-021-99056-8
Smith CPA, Laville T, Fara E, Escarguel G, Olivier N, Vennin E, Goudemand N, Bylund KG, Jenks JF, Stephen DA, Hautmann M, Charbonnier S, Krumenacker LJ, Brayard A. Exceptional fossil assemblages confirm the existence of complex Early Triassic ecosystems during the early Spathian. Sci Rep. 2021 Oct 04;11(1):19657. doi: 10.1038/s41598-021-99056-8. PMID: 34608207; PMCID: PMC8490361.
Copy Download .nbib Format: NLM
Prediction of Means and Variances of Crosses With Genome-Wide Marker Effects in Barley.

Frontiers in plant science

Osthushenrich T, Frisch M, Zenke-Philippi C, Jaiser H, Spiller M, Cselényi L, Krumnacker K, Boxberger S, Kopahnke D, Habekuß A, Ordon F, Herzog E.
PMID: 30627135
Front Plant Sci. 2018 Dec 21;9:1899. doi: 10.3389/fpls.2018.01899. eCollection 2018.

No abstract available.

Cite
Osthushenrich T, Frisch M, Zenke-Philippi C, et al. Prediction of Means and Variances of Crosses With Genome-Wide Marker Effects in Barley. Front Plant Sci. 2018;9:1899doi: 10.3389/fpls.2018.01899.
Osthushenrich, T., Frisch, M., Zenke-Philippi, C., Jaiser, H., Spiller, M., Cselényi, L., Krumnacker, K., Boxberger, S., Kopahnke, D., Habekuß, A., Ordon, F., & Herzog, E. (2018). Prediction of Means and Variances of Crosses With Genome-Wide Marker Effects in Barley. Frontiers in plant science, 91899. https://doi.org/10.3389/fpls.2018.01899
Osthushenrich, Tanja, et al. "Prediction of Means and Variances of Crosses With Genome-Wide Marker Effects in Barley." Frontiers in plant science vol. 9 (2018): 1899. doi: https://doi.org/10.3389/fpls.2018.01899
Osthushenrich T, Frisch M, Zenke-Philippi C, Jaiser H, Spiller M, Cselényi L, Krumnacker K, Boxberger S, Kopahnke D, Habekuß A, Ordon F, Herzog E. Prediction of Means and Variances of Crosses With Genome-Wide Marker Effects in Barley. Front Plant Sci. 2018 Dec 21;9:1899. doi: 10.3389/fpls.2018.01899. eCollection 2018. PMID: 30627135; PMCID: PMC6309237.
Copy Download .nbib Format: NLM
The BioCyc collection of microbial genomes and metabolic pathways.

Briefings in bioinformatics

Karp PD, Billington R, Caspi R, Fulcher CA, Latendresse M, Kothari A, Keseler IM, Krummenacker M, Midford PE, Ong Q, Ong WK, Paley SM, Subhraveti P.
PMID: 29447345
Brief Bioinform. 2019 Jul 19;20(4):1085-1093. doi: 10.1093/bib/bbx085.

BioCyc.org is a microbial genome Web portal that combines thousands of genomes with additional information inferred by computer programs, imported from other databases and curated from the biomedical literature by biologist curators. BioCyc also provides an extensive range of...

Cite
Karp PD, Billington R, Caspi R, et al. The BioCyc collection of microbial genomes and metabolic pathways. Brief Bioinform. 2019;20(4):1085-1093doi: 10.1093/bib/bbx085.
Karp, P. D., Billington, R., Caspi, R., Fulcher, C. A., Latendresse, M., Kothari, A., Keseler, I. M., Krummenacker, M., Midford, P. E., Ong, Q., Ong, W. K., Paley, S. M., & Subhraveti, P. (2019). The BioCyc collection of microbial genomes and metabolic pathways. Briefings in bioinformatics, 20(4), 1085-1093. https://doi.org/10.1093/bib/bbx085
Karp, Peter D, et al. "The BioCyc collection of microbial genomes and metabolic pathways." Briefings in bioinformatics vol. 20,4 (2019): 1085-1093. doi: https://doi.org/10.1093/bib/bbx085
Karp PD, Billington R, Caspi R, Fulcher CA, Latendresse M, Kothari A, Keseler IM, Krummenacker M, Midford PE, Ong Q, Ong WK, Paley SM, Subhraveti P. The BioCyc collection of microbial genomes and metabolic pathways. Brief Bioinform. 2019 Jul 19;20(4):1085-1093. doi: 10.1093/bib/bbx085. PMID: 29447345; PMCID: PMC6781571.
Copy Download .nbib Format: NLM
The EcoCyc Database in 2021.

Frontiers in microbiology

Keseler IM, Gama-Castro S, Mackie A, Billington R, Bonavides-Martínez C, Caspi R, Kothari A, Krummenacker M, Midford PE, Muñiz-Rascado L, Ong WK, Paley S, Santos-Zavaleta A, Subhraveti P, Tierrafría VH, Wolfe AJ, Collado-Vides J, Paulsen IT, Karp PD.
PMID: 34394059
Front Microbiol. 2021 Jul 28;12:711077. doi: 10.3389/fmicb.2021.711077. eCollection 2021.

The EcoCyc model-organism database collects and summarizes experimental data for

Cite
Keseler IM, Gama-Castro S, Mackie A, et al. The EcoCyc Database in 2021. Front Microbiol. 2021;12:711077doi: 10.3389/fmicb.2021.711077.
Keseler, I. M., Gama-Castro, S., Mackie, A., Billington, R., Bonavides-Martínez, C., Caspi, R., Kothari, A., Krummenacker, M., Midford, P. E., Muñiz-Rascado, L., Ong, W. K., Paley, S., Santos-Zavaleta, A., Subhraveti, P., Tierrafría, V. H., Wolfe, A. J., Collado-Vides, J., Paulsen, I. T., & Karp, P. D. (2021). The EcoCyc Database in 2021. Frontiers in microbiology, 12711077. https://doi.org/10.3389/fmicb.2021.711077
Keseler, Ingrid M, et al. "The EcoCyc Database in 2021." Frontiers in microbiology vol. 12 (2021): 711077. doi: https://doi.org/10.3389/fmicb.2021.711077
Keseler IM, Gama-Castro S, Mackie A, Billington R, Bonavides-Martínez C, Caspi R, Kothari A, Krummenacker M, Midford PE, Muñiz-Rascado L, Ong WK, Paley S, Santos-Zavaleta A, Subhraveti P, Tierrafría VH, Wolfe AJ, Collado-Vides J, Paulsen IT, Karp PD. The EcoCyc Database in 2021. Front Microbiol. 2021 Jul 28;12:711077. doi: 10.3389/fmicb.2021.711077. eCollection 2021. PMID: 34394059; PMCID: PMC8357350.
Copy Download .nbib Format: NLM
Isolated extratesticular hematoma from intraoperative positioning during lumbar spinal surgery.

Radiology case reports

Qi-Huang S, Danilenko A, Watson C, Krumenacker J.
PMID: 34630811
Radiol Case Rep. 2021 Oct 02;16(12):3746-3750. doi: 10.1016/j.radcr.2021.09.011. eCollection 2021 Dec.

Scrotal injury is present in less than 1% of all trauma-related injuries. Traumatic injuries of the scrotum are most commonly seen in penetrating or blunt injury but may also occur after iatrogenic causes such as in the intraoperative setting....

Cite
Qi-Huang S, Danilenko A, Watson C, et al. Isolated extratesticular hematoma from intraoperative positioning during lumbar spinal surgery. Radiol Case Rep. 2021;16(12):3746-3750doi: 10.1016/j.radcr.2021.09.011.
Qi-Huang, S., Danilenko, A., Watson, C., & Krumenacker, J. (2021). Isolated extratesticular hematoma from intraoperative positioning during lumbar spinal surgery. Radiology case reports, 16(12), 3746-3750. https://doi.org/10.1016/j.radcr.2021.09.011
Qi-Huang, Sunny, et al. "Isolated extratesticular hematoma from intraoperative positioning during lumbar spinal surgery." Radiology case reports vol. 16,12 (2021): 3746-3750. doi: https://doi.org/10.1016/j.radcr.2021.09.011
Qi-Huang S, Danilenko A, Watson C, Krumenacker J. Isolated extratesticular hematoma from intraoperative positioning during lumbar spinal surgery. Radiol Case Rep. 2021 Oct 02;16(12):3746-3750. doi: 10.1016/j.radcr.2021.09.011. eCollection 2021 Dec. PMID: 34630811; PMCID: PMC8493494.
Copy Download .nbib Format: NLM
Lack of standardisation in interpretation and reporting of autoantibody assays: a survey analysis of Australasian laboratories with focus on line immunoassays.

Pathology

Krummenacher M, Lee FJ, Wienholt L, Hissaria P.
PMID: 33994175
Pathology. 2021 Dec;53(7):883-888. doi: 10.1016/j.pathol.2021.01.018. Epub 2021 May 14.

Autoantibody assays are reported in a variety of formats. Results only slightly above established cut-offs provide lower likelihood ratios; therefore, their clinical significance may be more uncertain, which is not readily communicated with dichotomous qualitative reporting. Line immunoassays (LIA)...

Cite
Krummenacher M, Lee FJ, Wienholt L, et al. Lack of standardisation in interpretation and reporting of autoantibody assays: a survey analysis of Australasian laboratories with focus on line immunoassays. Pathology. 2021;53(7):883-888doi: 10.1016/j.pathol.2021.01.018.
Krummenacher, M., Lee, F. J., Wienholt, L., & Hissaria, P. (2021). Lack of standardisation in interpretation and reporting of autoantibody assays: a survey analysis of Australasian laboratories with focus on line immunoassays. Pathology, 53(7), 883-888. https://doi.org/10.1016/j.pathol.2021.01.018
Krummenacher, Matthew, et al. "Lack of standardisation in interpretation and reporting of autoantibody assays: a survey analysis of Australasian laboratories with focus on line immunoassays." Pathology vol. 53,7 (2021): 883-888. doi: https://doi.org/10.1016/j.pathol.2021.01.018
Krummenacher M, Lee FJ, Wienholt L, Hissaria P. Lack of standardisation in interpretation and reporting of autoantibody assays: a survey analysis of Australasian laboratories with focus on line immunoassays. Pathology. 2021 Dec;53(7):883-888. doi: 10.1016/j.pathol.2021.01.018. Epub 2021 May 14. PMID: 33994175.
Copy Download .nbib Format: NLM
Pathway Tools Visualization of Organism-Scale Metabolic Networks.

Metabolites

Paley S, Billington R, Herson J, Krummenacker M, Karp PD.
PMID: 33499002
Metabolites. 2021 Jan 22;11(2). doi: 10.3390/metabo11020064.

Metabolomics, synthetic biology, and microbiome research demand information about organism-scale metabolic networks. The convergence of genome sequencing and computational inference of metabolic networks has enabled great progress toward satisfying that demand by generating metabolic reconstructions from the genomes of...

Cite
Paley S, Billington R, Herson J, et al. Pathway Tools Visualization of Organism-Scale Metabolic Networks. Metabolites. 2021;11(2)doi: 10.3390/metabo11020064.
Paley, S., Billington, R., Herson, J., Krummenacker, M., & Karp, P. D. (2021). Pathway Tools Visualization of Organism-Scale Metabolic Networks. Metabolites, 11(2), . https://doi.org/10.3390/metabo11020064
Paley, Suzanne, et al. "Pathway Tools Visualization of Organism-Scale Metabolic Networks." Metabolites vol. 11,2 (2021). doi: https://doi.org/10.3390/metabo11020064
Paley S, Billington R, Herson J, Krummenacker M, Karp PD. Pathway Tools Visualization of Organism-Scale Metabolic Networks. Metabolites. 2021 Jan 22;11(2). doi: 10.3390/metabo11020064. PMID: 33499002; PMCID: PMC7911265.
Copy Download .nbib Format: NLM
Exceptional fossil assemblages confirm the existence of complex Early Triassic ecosystems during the early Spathian.

Scientific reports

Smith CPA, Laville T, Fara E, Escarguel G, Olivier N, Vennin E, Goudemand N, Bylund KG, Jenks JF, Stephen DA, Hautmann M, Charbonnier S, Krumenacker LJ, Brayard A.
PMID: 34608207
Sci Rep. 2021 Oct 04;11(1):19657. doi: 10.1038/s41598-021-99056-8.

The mass extinction characterizing the Permian/Triassic boundary (PTB; ~ 252 Ma) corresponds to a major faunal shift between the Palaeozoic and the Modern evolutionary fauna. The temporal, spatial, environmental, and ecological dynamics of the associated biotic recovery remain highly...

Cite
Smith CPA, Laville T, Fara E, et al. Exceptional fossil assemblages confirm the existence of complex Early Triassic ecosystems during the early Spathian. Sci Rep. 2021;11(1):19657doi: 10.1038/s41598-021-99056-8.
Smith, C. P. A., Laville, T., Fara, E., Escarguel, G., Olivier, N., Vennin, E., Goudemand, N., Bylund, K. G., Jenks, J. F., Stephen, D. A., Hautmann, M., Charbonnier, S., Krumenacker, L. J., & Brayard, A. (2021). Exceptional fossil assemblages confirm the existence of complex Early Triassic ecosystems during the early Spathian. Scientific reports, 11(1), 19657. https://doi.org/10.1038/s41598-021-99056-8
Smith, Christopher P A, et al. "Exceptional fossil assemblages confirm the existence of complex Early Triassic ecosystems during the early Spathian." Scientific reports vol. 11,1 (2021): 19657. doi: https://doi.org/10.1038/s41598-021-99056-8
Smith CPA, Laville T, Fara E, Escarguel G, Olivier N, Vennin E, Goudemand N, Bylund KG, Jenks JF, Stephen DA, Hautmann M, Charbonnier S, Krumenacker LJ, Brayard A. Exceptional fossil assemblages confirm the existence of complex Early Triassic ecosystems during the early Spathian. Sci Rep. 2021 Oct 04;11(1):19657. doi: 10.1038/s41598-021-99056-8. PMID: 34608207; PMCID: PMC8490361.
Copy Download .nbib Format: NLM
Showing 1 to 12 of 18 entries