Advanced Search
Display options
Filter resources
Text Availability
Article type
Publication date
Species
Language
Sex
Age
Showing 1 to 12 of 14 entries
Sorted by: Best Match Show Resources per page
CoCo-MD: A Simple and Effective Method for the Enhanced Sampling of Conformational Space.

Journal of chemical theory and computation

Shkurti A, Styliari ID, Balasubramanian V, Bethune I, Pedebos C, Jha S, Laughton CA.
PMID: 30620585
J Chem Theory Comput. 2019 Apr 09;15(4):2587-2596. doi: 10.1021/acs.jctc.8b00657. Epub 2019 Mar 05.

CoCo ("complementary coordinates") is a method for ensemble enrichment based on principal component analysis (PCA) that was developed originally for the investigation of NMR data. Here we investigate the potential of the CoCo method, in combination with molecular dynamics...

Cite
Shkurti A, Styliari ID, Balasubramanian V, et al. CoCo-MD: A Simple and Effective Method for the Enhanced Sampling of Conformational Space. J Chem Theory Comput. 2019;15(4):2587-2596doi: 10.1021/acs.jctc.8b00657.
Shkurti, A., Styliari, I. D., Balasubramanian, V., Bethune, I., Pedebos, C., Jha, S., & Laughton, C. A. (2019). CoCo-MD: A Simple and Effective Method for the Enhanced Sampling of Conformational Space. Journal of chemical theory and computation, 15(4), 2587-2596. https://doi.org/10.1021/acs.jctc.8b00657
Shkurti, Ardita, et al. "CoCo-MD: A Simple and Effective Method for the Enhanced Sampling of Conformational Space." Journal of chemical theory and computation vol. 15,4 (2019): 2587-2596. doi: https://doi.org/10.1021/acs.jctc.8b00657
Shkurti A, Styliari ID, Balasubramanian V, Bethune I, Pedebos C, Jha S, Laughton CA. CoCo-MD: A Simple and Effective Method for the Enhanced Sampling of Conformational Space. J Chem Theory Comput. 2019 Apr 09;15(4):2587-2596. doi: 10.1021/acs.jctc.8b00657. Epub 2019 Mar 05. PMID: 30620585.
Copy Download .nbib Format: NLM
Light transmission in multiple or single subwavelength trefoil channels of microstructured fibers.

Optics express

Moison JM, Apetrei AM, Levenson JA, Melin G, Pedeboseq P, Fleureau A, Lempereur S, Gasca L.
PMID: 19494989
Opt Express. 2005 Feb 21;13(4):1193-201. doi: 10.1364/opex.13.001193.

We evaluate the trefoil channels present between the holes of microstructured fibers as a potential dense array of small waveguides. In channels with an inner radius of 330nm, calculations indicate possible propagation with a mode waist of ~350nm at...

Cite
Moison JM, Apetrei AM, Levenson JA, et al. Light transmission in multiple or single subwavelength trefoil channels of microstructured fibers. Opt Express. 2005;13(4):1193-201doi: 10.1364/opex.13.001193.
Moison, J. M., Apetrei, A. M., Levenson, J. A., Melin, G., Pedeboseq, P., Fleureau, A., Lempereur, S., & Gasca, L. (2005). Light transmission in multiple or single subwavelength trefoil channels of microstructured fibers. Optics express, 13(4), 1193-201. https://doi.org/10.1364/opex.13.001193
Moison, J M, et al. "Light transmission in multiple or single subwavelength trefoil channels of microstructured fibers." Optics express vol. 13,4 (2005): 1193-201. doi: https://doi.org/10.1364/opex.13.001193
Moison JM, Apetrei AM, Levenson JA, Melin G, Pedeboseq P, Fleureau A, Lempereur S, Gasca L. Light transmission in multiple or single subwavelength trefoil channels of microstructured fibers. Opt Express. 2005 Feb 21;13(4):1193-201. doi: 10.1364/opex.13.001193. PMID: 19494989.
Copy Download .nbib Format: NLM
Year-long COVID-19 infection reveals within-host evolution of SARS-CoV-2 in a patient with B cell depletion.

medRxiv : the preprint server for health sciences

Nussenblatt V, Roder AE, Das S, de Wit E, Youn JH, Banakis S, Mushegian A, Mederos C, Wang W, Chung M, Pérez-Pérez L, Palmore T, Brudno JN, Kochenderfer JN, Ghedin E.
PMID: 34642697
medRxiv. 2021 Oct 05; doi: 10.1101/2021.10.02.21264267.

BACKGROUND: B-cell depleting therapies may lead to protracted disease and prolonged viral shedding in individuals infected with SARS-CoV-2. Viral persistence in the setting of immunosuppression raises concern for viral evolution.METHODS: Amplification of sub-genomic transcripts for the E gene (sgE)...

Cite
Nussenblatt V, Roder AE, Das S, et al. Year-long COVID-19 infection reveals within-host evolution of SARS-CoV-2 in a patient with B cell depletion. medRxiv. 2021;doi: 10.1101/2021.10.02.21264267.
Nussenblatt, V., Roder, A. E., Das, S., de Wit, E., Youn, J. H., Banakis, S., Mushegian, A., Mederos, C., Wang, W., Chung, M., Pérez-Pérez, L., Palmore, T., Brudno, J. N., Kochenderfer, J. N., & Ghedin, E. (2021). Year-long COVID-19 infection reveals within-host evolution of SARS-CoV-2 in a patient with B cell depletion. medRxiv : the preprint server for health sciences, . https://doi.org/10.1101/2021.10.02.21264267
Nussenblatt, Veronique, et al. "Year-long COVID-19 infection reveals within-host evolution of SARS-CoV-2 in a patient with B cell depletion." medRxiv : the preprint server for health sciences vol. (2021). doi: https://doi.org/10.1101/2021.10.02.21264267
Nussenblatt V, Roder AE, Das S, de Wit E, Youn JH, Banakis S, Mushegian A, Mederos C, Wang W, Chung M, Pérez-Pérez L, Palmore T, Brudno JN, Kochenderfer JN, Ghedin E. Year-long COVID-19 infection reveals within-host evolution of SARS-CoV-2 in a patient with B cell depletion. medRxiv. 2021 Oct 05; doi: 10.1101/2021.10.02.21264267. PMID: 34642697; PMCID: PMC8509089.
Copy Download .nbib Format: NLM
Making it Rain: Cloud-Based Molecular Simulations for Everyone.

Journal of chemical information and modeling

Arantes PR, Polêto MD, Pedebos C, Ligabue-Braun R.
PMID: 34595915
J Chem Inf Model. 2021 Oct 25;61(10):4852-4856. doi: 10.1021/acs.jcim.1c00998. Epub 2021 Oct 01.

We present a user-friendly front-end for running molecular dynamics (MD) simulations using the OpenMM toolkit on the Google Colab framework. Our goals are (1) to highlight the usage of a cloud-computing scheme for educational purposes for a hands-on approach...

Cite
Arantes PR, Polêto MD, Pedebos C, et al. Making it Rain: Cloud-Based Molecular Simulations for Everyone. J Chem Inf Model. 2021;61(10):4852-4856doi: 10.1021/acs.jcim.1c00998.
Arantes, P. R., Polêto, M. D., Pedebos, C., & Ligabue-Braun, R. (2021). Making it Rain: Cloud-Based Molecular Simulations for Everyone. Journal of chemical information and modeling, 61(10), 4852-4856. https://doi.org/10.1021/acs.jcim.1c00998
Arantes, Pablo R, et al. "Making it Rain: Cloud-Based Molecular Simulations for Everyone." Journal of chemical information and modeling vol. 61,10 (2021): 4852-4856. doi: https://doi.org/10.1021/acs.jcim.1c00998
Arantes PR, Polêto MD, Pedebos C, Ligabue-Braun R. Making it Rain: Cloud-Based Molecular Simulations for Everyone. J Chem Inf Model. 2021 Oct 25;61(10):4852-4856. doi: 10.1021/acs.jcim.1c00998. Epub 2021 Oct 01. PMID: 34595915.
Copy Download .nbib Format: NLM
Year-long COVID-19 infection reveals within-host evolution of SARS-CoV-2 in a patient with B cell depletion.

The Journal of infectious diseases

Nussenblatt V, Roder AE, Das S, de Wit E, Youn JH, Banakis S, Mushegian A, Mederos C, Wang W, Chung M, Pérez-Pérez L, Palmore T, Brudno JN, Kochenderfer JN, Ghedin E.
PMID: 34940844
J Infect Dis. 2021 Dec 23; doi: 10.1093/infdis/jiab622. Epub 2021 Dec 23.

B-cell depleting therapies may lead to prolonged disease and viral shedding in individuals infected with SARS-CoV-2 and this viral persistence raises concern for viral evolution. We report on the sequencing of early and late samples from a 335-day infection...

Cite
Nussenblatt V, Roder AE, Das S, et al. Year-long COVID-19 infection reveals within-host evolution of SARS-CoV-2 in a patient with B cell depletion. J Infect Dis. 2021;doi: 10.1093/infdis/jiab622.
Nussenblatt, V., Roder, A. E., Das, S., de Wit, E., Youn, J. H., Banakis, S., Mushegian, A., Mederos, C., Wang, W., Chung, M., Pérez-Pérez, L., Palmore, T., Brudno, J. N., Kochenderfer, J. N., & Ghedin, E. (2021). Year-long COVID-19 infection reveals within-host evolution of SARS-CoV-2 in a patient with B cell depletion. The Journal of infectious diseases, . https://doi.org/10.1093/infdis/jiab622
Nussenblatt, Veronique, et al. "Year-long COVID-19 infection reveals within-host evolution of SARS-CoV-2 in a patient with B cell depletion." The Journal of infectious diseases vol. (2021). doi: https://doi.org/10.1093/infdis/jiab622
Nussenblatt V, Roder AE, Das S, de Wit E, Youn JH, Banakis S, Mushegian A, Mederos C, Wang W, Chung M, Pérez-Pérez L, Palmore T, Brudno JN, Kochenderfer JN, Ghedin E. Year-long COVID-19 infection reveals within-host evolution of SARS-CoV-2 in a patient with B cell depletion. J Infect Dis. 2021 Dec 23; doi: 10.1093/infdis/jiab622. Epub 2021 Dec 23. PMID: 34940844; PMCID: PMC8755281.
Copy Download .nbib Format: NLM
Year-long COVID-19 infection reveals within-host evolution of SARS-CoV-2 in a patient with B cell depletion.

medRxiv : the preprint server for health sciences

Nussenblatt V, Roder AE, Das S, de Wit E, Youn JH, Banakis S, Mushegian A, Mederos C, Wang W, Chung M, Pérez-Pérez L, Palmore T, Brudno JN, Kochenderfer JN, Ghedin E.
PMID: 34642697
medRxiv. 2021 Oct 05; doi: 10.1101/2021.10.02.21264267.

BACKGROUND: B-cell depleting therapies may lead to protracted disease and prolonged viral shedding in individuals infected with SARS-CoV-2. Viral persistence in the setting of immunosuppression raises concern for viral evolution.METHODS: Amplification of sub-genomic transcripts for the E gene (sgE)...

Cite
Nussenblatt V, Roder AE, Das S, et al. Year-long COVID-19 infection reveals within-host evolution of SARS-CoV-2 in a patient with B cell depletion. medRxiv. 2021;doi: 10.1101/2021.10.02.21264267.
Nussenblatt, V., Roder, A. E., Das, S., de Wit, E., Youn, J. H., Banakis, S., Mushegian, A., Mederos, C., Wang, W., Chung, M., Pérez-Pérez, L., Palmore, T., Brudno, J. N., Kochenderfer, J. N., & Ghedin, E. (2021). Year-long COVID-19 infection reveals within-host evolution of SARS-CoV-2 in a patient with B cell depletion. medRxiv : the preprint server for health sciences, . https://doi.org/10.1101/2021.10.02.21264267
Nussenblatt, Veronique, et al. "Year-long COVID-19 infection reveals within-host evolution of SARS-CoV-2 in a patient with B cell depletion." medRxiv : the preprint server for health sciences vol. (2021). doi: https://doi.org/10.1101/2021.10.02.21264267
Nussenblatt V, Roder AE, Das S, de Wit E, Youn JH, Banakis S, Mushegian A, Mederos C, Wang W, Chung M, Pérez-Pérez L, Palmore T, Brudno JN, Kochenderfer JN, Ghedin E. Year-long COVID-19 infection reveals within-host evolution of SARS-CoV-2 in a patient with B cell depletion. medRxiv. 2021 Oct 05; doi: 10.1101/2021.10.02.21264267. PMID: 34642697; PMCID: PMC8509089.
Copy Download .nbib Format: NLM
Year-long COVID-19 infection reveals within-host evolution of SARS-CoV-2 in a patient with B cell depletion.

The Journal of infectious diseases

Nussenblatt V, Roder AE, Das S, de Wit E, Youn JH, Banakis S, Mushegian A, Mederos C, Wang W, Chung M, Pérez-Pérez L, Palmore T, Brudno JN, Kochenderfer JN, Ghedin E.
PMID: 34940844
J Infect Dis. 2021 Dec 23; doi: 10.1093/infdis/jiab622. Epub 2021 Dec 23.

B-cell depleting therapies may lead to prolonged disease and viral shedding in individuals infected with SARS-CoV-2 and this viral persistence raises concern for viral evolution. We report on the sequencing of early and late samples from a 335-day infection...

Cite
Nussenblatt V, Roder AE, Das S, et al. Year-long COVID-19 infection reveals within-host evolution of SARS-CoV-2 in a patient with B cell depletion. J Infect Dis. 2021;doi: 10.1093/infdis/jiab622.
Nussenblatt, V., Roder, A. E., Das, S., de Wit, E., Youn, J. H., Banakis, S., Mushegian, A., Mederos, C., Wang, W., Chung, M., Pérez-Pérez, L., Palmore, T., Brudno, J. N., Kochenderfer, J. N., & Ghedin, E. (2021). Year-long COVID-19 infection reveals within-host evolution of SARS-CoV-2 in a patient with B cell depletion. The Journal of infectious diseases, . https://doi.org/10.1093/infdis/jiab622
Nussenblatt, Veronique, et al. "Year-long COVID-19 infection reveals within-host evolution of SARS-CoV-2 in a patient with B cell depletion." The Journal of infectious diseases vol. (2021). doi: https://doi.org/10.1093/infdis/jiab622
Nussenblatt V, Roder AE, Das S, de Wit E, Youn JH, Banakis S, Mushegian A, Mederos C, Wang W, Chung M, Pérez-Pérez L, Palmore T, Brudno JN, Kochenderfer JN, Ghedin E. Year-long COVID-19 infection reveals within-host evolution of SARS-CoV-2 in a patient with B cell depletion. J Infect Dis. 2021 Dec 23; doi: 10.1093/infdis/jiab622. Epub 2021 Dec 23. PMID: 34940844.
Copy Download .nbib Format: NLM
Year-long COVID-19 infection reveals within-host evolution of SARS-CoV-2 in a patient with B cell depletion.

The Journal of infectious diseases

Nussenblatt V, Roder AE, Das S, de Wit E, Youn JH, Banakis S, Mushegian A, Mederos C, Wang W, Chung M, Pérez-Pérez L, Palmore T, Brudno JN, Kochenderfer JN, Ghedin E.
PMID: 34940844
J Infect Dis. 2021 Dec 23; doi: 10.1093/infdis/jiab622. Epub 2021 Dec 23.

B-cell depleting therapies may lead to prolonged disease and viral shedding in individuals infected with SARS-CoV-2 and this viral persistence raises concern for viral evolution. We report on the sequencing of early and late samples from a 335-day infection...

Cite
Nussenblatt V, Roder AE, Das S, et al. Year-long COVID-19 infection reveals within-host evolution of SARS-CoV-2 in a patient with B cell depletion. J Infect Dis. 2021;doi: 10.1093/infdis/jiab622.
Nussenblatt, V., Roder, A. E., Das, S., de Wit, E., Youn, J. H., Banakis, S., Mushegian, A., Mederos, C., Wang, W., Chung, M., Pérez-Pérez, L., Palmore, T., Brudno, J. N., Kochenderfer, J. N., & Ghedin, E. (2021). Year-long COVID-19 infection reveals within-host evolution of SARS-CoV-2 in a patient with B cell depletion. The Journal of infectious diseases, . https://doi.org/10.1093/infdis/jiab622
Nussenblatt, Veronique, et al. "Year-long COVID-19 infection reveals within-host evolution of SARS-CoV-2 in a patient with B cell depletion." The Journal of infectious diseases vol. (2021). doi: https://doi.org/10.1093/infdis/jiab622
Nussenblatt V, Roder AE, Das S, de Wit E, Youn JH, Banakis S, Mushegian A, Mederos C, Wang W, Chung M, Pérez-Pérez L, Palmore T, Brudno JN, Kochenderfer JN, Ghedin E. Year-long COVID-19 infection reveals within-host evolution of SARS-CoV-2 in a patient with B cell depletion. J Infect Dis. 2021 Dec 23; doi: 10.1093/infdis/jiab622. Epub 2021 Dec 23. PMID: 34940844.
Copy Download .nbib Format: NLM
Lightning initiation: Strong pulses of VHF radiation accompany preliminary breakdown.

Scientific reports

Kolmašová I, Santolík O, Defer E, Rison W, Coquillat S, Pedeboy S, Lán R, Uhlíř L, Lambert D, Pinty JP, Prieur S, Pont V.
PMID: 29483561
Sci Rep. 2018 Feb 26;8(1):3650. doi: 10.1038/s41598-018-21972-z.

We analyze lightning initiation process using magnetic field waveforms of preliminary breakdown (PB) pulses observed at time scales of a few tens of microseconds by a broad-band receiver. We compare these pulses with sources of narrow-band very high frequency...

Cite
Kolmašová I, Santolík O, Defer E, et al. Lightning initiation: Strong pulses of VHF radiation accompany preliminary breakdown. Sci Rep. 2018;8(1):3650doi: 10.1038/s41598-018-21972-z.
Kolmašová, I., Santolík, O., Defer, E., Rison, W., Coquillat, S., Pedeboy, S., Lán, R., Uhlíř, L., Lambert, D., Pinty, J. P., Prieur, S., & Pont, V. (2018). Lightning initiation: Strong pulses of VHF radiation accompany preliminary breakdown. Scientific reports, 8(1), 3650. https://doi.org/10.1038/s41598-018-21972-z
Kolmašová, Ivana, et al. "Lightning initiation: Strong pulses of VHF radiation accompany preliminary breakdown." Scientific reports vol. 8,1 (2018): 3650. doi: https://doi.org/10.1038/s41598-018-21972-z
Kolmašová I, Santolík O, Defer E, Rison W, Coquillat S, Pedeboy S, Lán R, Uhlíř L, Lambert D, Pinty JP, Prieur S, Pont V. Lightning initiation: Strong pulses of VHF radiation accompany preliminary breakdown. Sci Rep. 2018 Feb 26;8(1):3650. doi: 10.1038/s41598-018-21972-z. PMID: 29483561; PMCID: PMC5827727.
Copy Download .nbib Format: NLM
Erratum: A TRAF-like motif of the inducible costimulator ICOS controls development of germinal center TFH cells via the kinase TBK1.

Nature immunology

Pedros C, Zhang Y, Hu JK, Choi YS, Canonigo-Balancio AJ, Yates JR, Altman A, Crotty S, Kong KF.
PMID: 27434013
Nat Immunol. 2016 Jul 19;17(8):1005. doi: 10.1038/ni0816-1005b.

No abstract available.

Cite
Pedros C, Zhang Y, Hu JK, et al. Erratum: A TRAF-like motif of the inducible costimulator ICOS controls development of germinal center TFH cells via the kinase TBK1. Nat Immunol. 2016;17(8):1005doi: 10.1038/ni0816-1005b.
Pedros, C., Zhang, Y., Hu, J. K., Choi, Y. S., Canonigo-Balancio, A. J., Yates, J. R., Altman, A., Crotty, S., & Kong, K. F. (2016). Erratum: A TRAF-like motif of the inducible costimulator ICOS controls development of germinal center TFH cells via the kinase TBK1. Nature immunology, 17(8), 1005. https://doi.org/10.1038/ni0816-1005b
Pedros, Christophe, et al. "Erratum: A TRAF-like motif of the inducible costimulator ICOS controls development of germinal center TFH cells via the kinase TBK1." Nature immunology vol. 17,8 (2016): 1005. doi: https://doi.org/10.1038/ni0816-1005b
Pedros C, Zhang Y, Hu JK, Choi YS, Canonigo-Balancio AJ, Yates JR, Altman A, Crotty S, Kong KF. Erratum: A TRAF-like motif of the inducible costimulator ICOS controls development of germinal center TFH cells via the kinase TBK1. Nat Immunol. 2016 Jul 19;17(8):1005. doi: 10.1038/ni0816-1005b. PMID: 27434013.
Copy Download .nbib Format: NLM
Development of GROMOS-Compatible Parameter Set for Simulations of Chalcones and Flavonoids.

The journal of physical chemistry. B

Arantes PR, Polêto MD, John EBO, Pedebos C, Grisci BI, Dorn M, Verli H.
PMID: 30624922
J Phys Chem B. 2019 Feb 07;123(5):994-1008. doi: 10.1021/acs.jpcb.8b10139. Epub 2019 Jan 25.

Chalcones and flavonoids constitute a large family of plant secondary metabolites that have been explored as a potential source of novel pharmaceutical products. While the simulation of these compounds by molecular dynamics (MD) can be a valuable strategy to...

Cite
Arantes PR, Polêto MD, John EBO, et al. Development of GROMOS-Compatible Parameter Set for Simulations of Chalcones and Flavonoids. J Phys Chem B. 2019;123(5):994-1008doi: 10.1021/acs.jpcb.8b10139.
Arantes, P. R., Polêto, M. D., John, E. B. O., Pedebos, C., Grisci, B. I., Dorn, M., & Verli, H. (2019). Development of GROMOS-Compatible Parameter Set for Simulations of Chalcones and Flavonoids. The journal of physical chemistry. B, 123(5), 994-1008. https://doi.org/10.1021/acs.jpcb.8b10139
Arantes, Pablo R, et al. "Development of GROMOS-Compatible Parameter Set for Simulations of Chalcones and Flavonoids." The journal of physical chemistry. B vol. 123,5 (2019): 994-1008. doi: https://doi.org/10.1021/acs.jpcb.8b10139
Arantes PR, Polêto MD, John EBO, Pedebos C, Grisci BI, Dorn M, Verli H. Development of GROMOS-Compatible Parameter Set for Simulations of Chalcones and Flavonoids. J Phys Chem B. 2019 Feb 07;123(5):994-1008. doi: 10.1021/acs.jpcb.8b10139. Epub 2019 Jan 25. PMID: 30624922.
Copy Download .nbib Format: NLM
Modifying the catalytic preference of alpha-amylase toward n-alkanes for bioremediation purposes using in silico strategies.

Journal of computational chemistry

Pinto ÉSM, Feltes BC, Pedebos C, Dorn M.
PMID: 34018199
J Comput Chem. 2021 Aug 15;42(22):1540-1551. doi: 10.1002/jcc.26562. Epub 2021 May 20.

Since the beginning of oil exploration, whole ecosystems have been affected by accidents and bad practices involving petroleum compounds. In this sense, bioremediation stands out as the cheapest and most eco-friendly alternatives to reverse the damage done in oil-impacted...

Cite
Pinto ÉSM, Feltes BC, Pedebos C, et al. Modifying the catalytic preference of alpha-amylase toward n-alkanes for bioremediation purposes using in silico strategies. J Comput Chem. 2021;42(22):1540-1551doi: 10.1002/jcc.26562.
Pinto, �. �. S. M., Feltes, B. C., Pedebos, C., & Dorn, M. (2021). Modifying the catalytic preference of alpha-amylase toward n-alkanes for bioremediation purposes using in silico strategies. Journal of computational chemistry, 42(22), 1540-1551. https://doi.org/10.1002/jcc.26562
Pinto, Éderson Sales Moreira, et al. "Modifying the catalytic preference of alpha-amylase toward n-alkanes for bioremediation purposes using in silico strategies." Journal of computational chemistry vol. 42,22 (2021): 1540-1551. doi: https://doi.org/10.1002/jcc.26562
Pinto ÉSM, Feltes BC, Pedebos C, Dorn M. Modifying the catalytic preference of alpha-amylase toward n-alkanes for bioremediation purposes using in silico strategies. J Comput Chem. 2021 Aug 15;42(22):1540-1551. doi: 10.1002/jcc.26562. Epub 2021 May 20. PMID: 34018199.
Copy Download .nbib Format: NLM
Showing 1 to 12 of 14 entries