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Showing 1 to 12 of 23 entries
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SBpipe: a collection of pipelines for automating repetitive simulation and analysis tasks.

BMC systems biology

Dalle Pezze P, Le Novère N.
PMID: 28395655
BMC Syst Biol. 2017 Apr 10;11(1):46. doi: 10.1186/s12918-017-0423-3.

BACKGROUND: The rapid growth of the number of mathematical models in Systems Biology fostered the development of many tools to simulate and analyse them. The reliability and precision of these tasks often depend on multiple repetitions and they can...

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Dalle Pezze P, Le Novère N. SBpipe: a collection of pipelines for automating repetitive simulation and analysis tasks. BMC Syst Biol. 2017;11(1):46doi: 10.1186/s12918-017-0423-3.
Dalle Pezze, P., & Le Novère, N. (2017). SBpipe: a collection of pipelines for automating repetitive simulation and analysis tasks. BMC systems biology, 11(1), 46. https://doi.org/10.1186/s12918-017-0423-3
Dalle Pezze, Piero, and Le Novère, Nicolas. "SBpipe: a collection of pipelines for automating repetitive simulation and analysis tasks." BMC systems biology vol. 11,1 (2017): 46. doi: https://doi.org/10.1186/s12918-017-0423-3
Dalle Pezze P, Le Novère N. SBpipe: a collection of pipelines for automating repetitive simulation and analysis tasks. BMC Syst Biol. 2017 Apr 10;11(1):46. doi: 10.1186/s12918-017-0423-3. PMID: 28395655; PMCID: PMC5387271.
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SysBioMed report: advancing systems biology for medical applications.

IET systems biology

Wolkenhauer O, Fell D, De Meyts P, Blüthgen N, Herzel H, Le Novère N, Höfer T, Schürrle K, van Leeuwen I.
PMID: 19449974
IET Syst Biol. 2009 May;3(3):131-6. doi: 10.1049/iet-syb.2009.0005.

The following report selects and summarises some of the conclusions and recommendations generated throughout a series of workshops and discussions that have lead to the publication of the Science Policy Briefing (SPB) Nr. 35, published by the European Science...

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Wolkenhauer O, Fell D, De Meyts P, et al. SysBioMed report: advancing systems biology for medical applications. IET Syst Biol. 2009;3(3):131-6doi: 10.1049/iet-syb.2009.0005.
Wolkenhauer, O., Fell, D., De Meyts, P., Blüthgen, N., Herzel, H., Le Novère, N., Höfer, T., Schürrle, K., & van Leeuwen, I. (2009). SysBioMed report: advancing systems biology for medical applications. IET systems biology, 3(3), 131-6. https://doi.org/10.1049/iet-syb.2009.0005
Wolkenhauer, O, et al. "SysBioMed report: advancing systems biology for medical applications." IET systems biology vol. 3,3 (2009): 131-6. doi: https://doi.org/10.1049/iet-syb.2009.0005
Wolkenhauer O, Fell D, De Meyts P, Blüthgen N, Herzel H, Le Novère N, Höfer T, Schürrle K, van Leeuwen I. SysBioMed report: advancing systems biology for medical applications. IET Syst Biol. 2009 May;3(3):131-6. doi: 10.1049/iet-syb.2009.0005. PMID: 19449974.
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Software that goes with the flow in systems biology.

BMC biology

Hucka M, Le Novère N.
PMID: 21114874
BMC Biol. 2010 Nov 29;8:140. doi: 10.1186/1741-7007-8-140.

A recent article in BMC Bioinformatics describes new advances in workflow systems for computational modeling in systems biology. Such systems can accelerate, and improve the consistency of, modeling through automation not only at the simulation and results-production stages, but...

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Hucka M, Le Novère N. Software that goes with the flow in systems biology. BMC Biol. 2010;8:140doi: 10.1186/1741-7007-8-140.
Hucka, M., & Le Novère, N. (2010). Software that goes with the flow in systems biology. BMC biology, 8140. https://doi.org/10.1186/1741-7007-8-140
Hucka, Michael, and Le Novère, Nicolas. "Software that goes with the flow in systems biology." BMC biology vol. 8 (2010): 140. doi: https://doi.org/10.1186/1741-7007-8-140
Hucka M, Le Novère N. Software that goes with the flow in systems biology. BMC Biol. 2010 Nov 29;8:140. doi: 10.1186/1741-7007-8-140. PMID: 21114874; PMCID: PMC2993668.
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Meeting report from the first meetings of the Computational Modeling in Biology Network (COMBINE).

Standards in genomic sciences

Le Novère N, Hucka M, Anwar N, Bader GD, Demir E, Moodie S, Sorokin A.
PMID: 22180826
Stand Genomic Sci. 2011 Nov 30;5(2):230-42. doi: 10.4056/sigs.2034671.

The Computational Modeling in Biology Network (COMBINE), is an initiative to coordinate the development of the various community standards and formats in computational systems biology and related fields. This report summarizes the activities pursued at the first annual COMBINE...

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Le Novère N, Hucka M, Anwar N, et al. Meeting report from the first meetings of the Computational Modeling in Biology Network (COMBINE). Stand Genomic Sci. 2011;5(2):230-42doi: 10.4056/sigs.2034671.
Le Novère, N., Hucka, M., Anwar, N., Bader, G. D., Demir, E., Moodie, S., & Sorokin, A. (2011). Meeting report from the first meetings of the Computational Modeling in Biology Network (COMBINE). Standards in genomic sciences, 5(2), 230-42. https://doi.org/10.4056/sigs.2034671
Le Novère, Nicolas, et al. "Meeting report from the first meetings of the Computational Modeling in Biology Network (COMBINE)." Standards in genomic sciences vol. 5,2 (2011): 230-42. doi: https://doi.org/10.4056/sigs.2034671
Le Novère N, Hucka M, Anwar N, Bader GD, Demir E, Moodie S, Sorokin A. Meeting report from the first meetings of the Computational Modeling in Biology Network (COMBINE). Stand Genomic Sci. 2011 Nov 30;5(2):230-42. doi: 10.4056/sigs.2034671. PMID: 22180826; PMCID: PMC3235518.
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Community-driven roadmap for integrated disease maps.

Briefings in bioinformatics

Ostaszewski M, Gebel S, Kuperstein I, Mazein A, Zinovyev A, Dogrusoz U, Hasenauer J, Fleming RMT, Le Novère N, Gawron P, Ligon T, Niarakis A, Nickerson D, Weindl D, Balling R, Barillot E, Auffray C, Schneider R.
PMID: 29688273
Brief Bioinform. 2019 Mar 25;20(2):659-670. doi: 10.1093/bib/bby024.

The Disease Maps Project builds on a network of scientific and clinical groups that exchange best practices, share information and develop systems biomedicine tools. The project aims for an integrated, highly curated and user-friendly platform for disease-related knowledge. The...

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Ostaszewski M, Gebel S, Kuperstein I, et al. Community-driven roadmap for integrated disease maps. Brief Bioinform. 2019;20(2):659-670doi: 10.1093/bib/bby024.
Ostaszewski, M., Gebel, S., Kuperstein, I., Mazein, A., Zinovyev, A., Dogrusoz, U., Hasenauer, J., Fleming, R. M. T., Le Novère, N., Gawron, P., Ligon, T., Niarakis, A., Nickerson, D., Weindl, D., Balling, R., Barillot, E., Auffray, C., & Schneider, R. (2019). Community-driven roadmap for integrated disease maps. Briefings in bioinformatics, 20(2), 659-670. https://doi.org/10.1093/bib/bby024
Ostaszewski, Marek, et al. "Community-driven roadmap for integrated disease maps." Briefings in bioinformatics vol. 20,2 (2019): 659-670. doi: https://doi.org/10.1093/bib/bby024
Ostaszewski M, Gebel S, Kuperstein I, Mazein A, Zinovyev A, Dogrusoz U, Hasenauer J, Fleming RMT, Le Novère N, Gawron P, Ligon T, Niarakis A, Nickerson D, Weindl D, Balling R, Barillot E, Auffray C, Schneider R. Community-driven roadmap for integrated disease maps. Brief Bioinform. 2019 Mar 25;20(2):659-670. doi: 10.1093/bib/bby024. PMID: 29688273; PMCID: PMC6556900.
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BioModels: expanding horizons to include more modelling approaches and formats.

Nucleic acids research

Glont M, Nguyen TVN, Graesslin M, Hälke R, Ali R, Schramm J, Wimalaratne SM, Kothamachu VB, Rodriguez N, Swat MJ, Eils J, Eils R, Laibe C, Malik-Sheriff RS, Chelliah V, Le Novère N, Hermjakob H.
PMID: 29106614
Nucleic Acids Res. 2018 Jan 04;46:D1248-D1253. doi: 10.1093/nar/gkx1023.

BioModels serves as a central repository of mathematical models representing biological processes. It offers a platform to make mathematical models easily shareable across the systems modelling community, thereby supporting model reuse. To facilitate hosting a broader range of model...

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Glont M, Nguyen TVN, Graesslin M, et al. BioModels: expanding horizons to include more modelling approaches and formats. Nucleic Acids Res. 2018;46:D1248-D1253doi: 10.1093/nar/gkx1023.
Glont, M., Nguyen, T. V. N., Graesslin, M., Hälke, R., Ali, R., Schramm, J., Wimalaratne, S. M., Kothamachu, V. B., Rodriguez, N., Swat, M. J., Eils, J., Eils, R., Laibe, C., Malik-Sheriff, R. S., Chelliah, V., Le Novère, N., & Hermjakob, H. (2018). BioModels: expanding horizons to include more modelling approaches and formats. Nucleic acids research, 46D1248-D1253. https://doi.org/10.1093/nar/gkx1023
Glont, Mihai, et al. "BioModels: expanding horizons to include more modelling approaches and formats." Nucleic acids research vol. 46 (2018): D1248-D1253. doi: https://doi.org/10.1093/nar/gkx1023
Glont M, Nguyen TVN, Graesslin M, Hälke R, Ali R, Schramm J, Wimalaratne SM, Kothamachu VB, Rodriguez N, Swat MJ, Eils J, Eils R, Laibe C, Malik-Sheriff RS, Chelliah V, Le Novère N, Hermjakob H. BioModels: expanding horizons to include more modelling approaches and formats. Nucleic Acids Res. 2018 Jan 04;46:D1248-D1253. doi: 10.1093/nar/gkx1023. PMID: 29106614; PMCID: PMC5753244.
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Structure, function, and behaviour of computational models in systems biology.

BMC systems biology

Knüpfer C, Beckstein C, Dittrich P, Le Novère N.
PMID: 23721297
BMC Syst Biol. 2013 May 31;7:43. doi: 10.1186/1752-0509-7-43.

BACKGROUND: Systems Biology develops computational models in order to understand biological phenomena. The increasing number and complexity of such "bio-models" necessitate computer support for the overall modelling task. Computer-aided modelling has to be based on a formal semantic description...

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Knüpfer C, Beckstein C, Dittrich P, et al. Structure, function, and behaviour of computational models in systems biology. BMC Syst Biol. 2013;7:43doi: 10.1186/1752-0509-7-43.
Knüpfer, C., Beckstein, C., Dittrich, P., & Le Novère, N. (2013). Structure, function, and behaviour of computational models in systems biology. BMC systems biology, 743. https://doi.org/10.1186/1752-0509-7-43
Knüpfer, Christian, et al. "Structure, function, and behaviour of computational models in systems biology." BMC systems biology vol. 7 (2013): 43. doi: https://doi.org/10.1186/1752-0509-7-43
Knüpfer C, Beckstein C, Dittrich P, Le Novère N. Structure, function, and behaviour of computational models in systems biology. BMC Syst Biol. 2013 May 31;7:43. doi: 10.1186/1752-0509-7-43. PMID: 23721297; PMCID: PMC3716781.
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Multi-Omics and Genome-Scale Modeling Reveal a Metabolic Shift During .

Frontiers in molecular biosciences

Hastings J, Mains A, Virk B, Rodriguez N, Murdoch S, Pearce J, Bergmann S, Le Novère N, Casanueva O.
PMID: 30788345
Front Mol Biosci. 2019 Feb 06;6:2. doi: 10.3389/fmolb.2019.00002. eCollection 2019.

In this contribution, we describe a multi-omics systems biology study of the metabolic changes that occur during aging in

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Hastings J, Mains A, Virk B, et al. Multi-Omics and Genome-Scale Modeling Reveal a Metabolic Shift During . Front Mol Biosci. 2019;6:2doi: 10.3389/fmolb.2019.00002.
Hastings, J., Mains, A., Virk, B., Rodriguez, N., Murdoch, S., Pearce, J., Bergmann, S., Le Novère, N., & Casanueva, O. (2019). Multi-Omics and Genome-Scale Modeling Reveal a Metabolic Shift During . Frontiers in molecular biosciences, 62. https://doi.org/10.3389/fmolb.2019.00002
Hastings, Janna, et al. "Multi-Omics and Genome-Scale Modeling Reveal a Metabolic Shift During ." Frontiers in molecular biosciences vol. 6 (2019): 2. doi: https://doi.org/10.3389/fmolb.2019.00002
Hastings J, Mains A, Virk B, Rodriguez N, Murdoch S, Pearce J, Bergmann S, Le Novère N, Casanueva O. Multi-Omics and Genome-Scale Modeling Reveal a Metabolic Shift During . Front Mol Biosci. 2019 Feb 06;6:2. doi: 10.3389/fmolb.2019.00002. eCollection 2019. PMID: 30788345; PMCID: PMC6372924.
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The Systems Biology Graphical Notation.

Nature biotechnology

Le Novère N, Hucka M, Mi H, Moodie S, Schreiber F, Sorokin A, Demir E, Wegner K, Aladjem MI, Wimalaratne SM, Bergman FT, Gauges R, Ghazal P, Kawaji H, Li L, Matsuoka Y, Villéger A, Boyd SE, Calzone L, Courtot M, Dogrusoz U, Freeman TC, Funahashi A, Ghosh S, Jouraku A, Kim S, Kolpakov F, Luna A, Sahle S, Schmidt E, Watterson S, Wu G, Goryanin I, Kell DB, Sander C, Sauro H, Snoep JL, Kohn K, Kitano H.
PMID: 19668183
Nat Biotechnol. 2009 Aug;27(8):735-41. doi: 10.1038/nbt.1558. Epub 2009 Aug 07.

Circuit diagrams and Unified Modeling Language diagrams are just two examples of standard visual languages that help accelerate work by promoting regularity, removing ambiguity and enabling software tool support for communication of complex information. Ironically, despite having one of...

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Le Novère N, Hucka M, Mi H, et al. The Systems Biology Graphical Notation. Nat Biotechnol. 2009;27(8):735-41doi: 10.1038/nbt.1558.
Le Novère, N., Hucka, M., Mi, H., Moodie, S., Schreiber, F., Sorokin, A., Demir, E., Wegner, K., Aladjem, M. I., Wimalaratne, S. M., Bergman, F. T., Gauges, R., Ghazal, P., Kawaji, H., Li, L., Matsuoka, Y., Villéger, A., Boyd, S. E., Calzone, L., Courtot, M., Dogrusoz, U., Freeman, T. C., Funahashi, A., Ghosh, S., Jouraku, A., Kim, S., Kolpakov, F., Luna, A., Sahle, S., Schmidt, E., Watterson, S., Wu, G., Goryanin, I., Kell, D. B., Sander, C., Sauro, H., Snoep, J. L., Kohn, K., & Kitano, H. (2009). The Systems Biology Graphical Notation. Nature biotechnology, 27(8), 735-41. https://doi.org/10.1038/nbt.1558
Le Novère, Nicolas, et al. "The Systems Biology Graphical Notation." Nature biotechnology vol. 27,8 (2009): 735-41. doi: https://doi.org/10.1038/nbt.1558
Le Novère N, Hucka M, Mi H, Moodie S, Schreiber F, Sorokin A, Demir E, Wegner K, Aladjem MI, Wimalaratne SM, Bergman FT, Gauges R, Ghazal P, Kawaji H, Li L, Matsuoka Y, Villéger A, Boyd SE, Calzone L, Courtot M, Dogrusoz U, Freeman TC, Funahashi A, Ghosh S, Jouraku A, Kim S, Kolpakov F, Luna A, Sahle S, Schmidt E, Watterson S, Wu G, Goryanin I, Kell DB, Sander C, Sauro H, Snoep JL, Kohn K, Kitano H. The Systems Biology Graphical Notation. Nat Biotechnol. 2009 Aug;27(8):735-41. doi: 10.1038/nbt.1558. Epub 2009 Aug 07. PMID: 19668183.
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BioModels: Content, Features, Functionality, and Use.

CPT: pharmacometrics & systems pharmacology

Juty N, Ali R, Glont M, Keating S, Rodriguez N, Swat MJ, Wimalaratne SM, Hermjakob H, Le Novère N, Laibe C, Chelliah V.
PMID: 26225232
CPT Pharmacometrics Syst Pharmacol. 2015 Feb;4(2):e3. doi: 10.1002/psp4.3. Epub 2015 Feb 26.

BioModels is a reference repository hosting mathematical models that describe the dynamic interactions of biological components at various scales. The resource provides access to over 1,200 models described in literature and over 140,000 models automatically generated from pathway resources....

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Juty N, Ali R, Glont M, et al. BioModels: Content, Features, Functionality, and Use. CPT Pharmacometrics Syst Pharmacol. 2015;4(2):e3doi: 10.1002/psp4.3.
Juty, N., Ali, R., Glont, M., Keating, S., Rodriguez, N., Swat, M. J., Wimalaratne, S. M., Hermjakob, H., Le Novère, N., Laibe, C., & Chelliah, V. (2015). BioModels: Content, Features, Functionality, and Use. CPT: pharmacometrics & systems pharmacology, 4(2), e3. https://doi.org/10.1002/psp4.3
Juty, N, et al. "BioModels: Content, Features, Functionality, and Use." CPT: pharmacometrics & systems pharmacology vol. 4,2 (2015): e3. doi: https://doi.org/10.1002/psp4.3
Juty N, Ali R, Glont M, Keating S, Rodriguez N, Swat MJ, Wimalaratne SM, Hermjakob H, Le Novère N, Laibe C, Chelliah V. BioModels: Content, Features, Functionality, and Use. CPT Pharmacometrics Syst Pharmacol. 2015 Feb;4(2):e3. doi: 10.1002/psp4.3. Epub 2015 Feb 26. PMID: 26225232; PMCID: PMC4360671.
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The health care and life sciences community profile for dataset descriptions.

PeerJ

Dumontier M, Gray AJG, Marshall MS, Alexiev V, Ansell P, Bader G, Baran J, Bolleman JT, Callahan A, Cruz-Toledo J, Gaudet P, Gombocz EA, Gonzalez-Beltran AN, Groth P, Haendel M, Ito M, Jupp S, Juty N, Katayama T, Kobayashi N, Krishnaswami K, Laibe C, Le Novère N, Lin S, Malone J, Miller M, Mungall CJ, Rietveld L, Wimalaratne SM, Yamaguchi A.
PMID: 27602295
PeerJ. 2016 Aug 16;4:e2331. doi: 10.7717/peerj.2331. eCollection 2016.

Access to consistent, high-quality metadata is critical to finding, understanding, and reusing scientific data. However, while there are many relevant vocabularies for the annotation of a dataset, none sufficiently captures all the necessary metadata. This prevents uniform indexing and...

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Dumontier M, Gray AJG, Marshall MS, et al. The health care and life sciences community profile for dataset descriptions. PeerJ. 2016;4:e2331doi: 10.7717/peerj.2331.
Dumontier, M., Gray, A. J. G., Marshall, M. S., Alexiev, V., Ansell, P., Bader, G., Baran, J., Bolleman, J. T., Callahan, A., Cruz-Toledo, J., Gaudet, P., Gombocz, E. A., Gonzalez-Beltran, A. N., Groth, P., Haendel, M., Ito, M., Jupp, S., Juty, N., Katayama, T., Kobayashi, N., Krishnaswami, K., Laibe, C., Le Novère, N., Lin, S., Malone, J., Miller, M., Mungall, C. J., Rietveld, L., Wimalaratne, S. M., & Yamaguchi, A. (2016). The health care and life sciences community profile for dataset descriptions. PeerJ, 4e2331. https://doi.org/10.7717/peerj.2331
Dumontier, Michel, et al. "The health care and life sciences community profile for dataset descriptions." PeerJ vol. 4 (2016): e2331. doi: https://doi.org/10.7717/peerj.2331
Dumontier M, Gray AJG, Marshall MS, Alexiev V, Ansell P, Bader G, Baran J, Bolleman JT, Callahan A, Cruz-Toledo J, Gaudet P, Gombocz EA, Gonzalez-Beltran AN, Groth P, Haendel M, Ito M, Jupp S, Juty N, Katayama T, Kobayashi N, Krishnaswami K, Laibe C, Le Novère N, Lin S, Malone J, Miller M, Mungall CJ, Rietveld L, Wimalaratne SM, Yamaguchi A. The health care and life sciences community profile for dataset descriptions. PeerJ. 2016 Aug 16;4:e2331. doi: 10.7717/peerj.2331. eCollection 2016. PMID: 27602295; PMCID: PMC4991880.
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The promises of quantitative systems pharmacology modelling for drug development.

Computational and structural biotechnology journal

Knight-Schrijver VR, Chelliah V, Cucurull-Sanchez L, Le Novère N.
PMID: 27761201
Comput Struct Biotechnol J. 2016 Sep 23;14:363-370. doi: 10.1016/j.csbj.2016.09.002. eCollection 2016.

Recent growth in annual new therapeutic entity (NTE) approvals by the U.S. Food and Drug Administration (FDA) suggests a positive trend in current research and development (R&D) output. Prior to this, the cost of each NTE was considered to...

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Knight-Schrijver VR, Chelliah V, Cucurull-Sanchez L, et al. The promises of quantitative systems pharmacology modelling for drug development. Comput Struct Biotechnol J. 2016;14:363-370doi: 10.1016/j.csbj.2016.09.002.
Knight-Schrijver, V. R., Chelliah, V., Cucurull-Sanchez, L., & Le Novère, N. (2016). The promises of quantitative systems pharmacology modelling for drug development. Computational and structural biotechnology journal, 14363-370. https://doi.org/10.1016/j.csbj.2016.09.002
Knight-Schrijver, V R, et al. "The promises of quantitative systems pharmacology modelling for drug development." Computational and structural biotechnology journal vol. 14 (2016): 363-370. doi: https://doi.org/10.1016/j.csbj.2016.09.002
Knight-Schrijver VR, Chelliah V, Cucurull-Sanchez L, Le Novère N. The promises of quantitative systems pharmacology modelling for drug development. Comput Struct Biotechnol J. 2016 Sep 23;14:363-370. doi: 10.1016/j.csbj.2016.09.002. eCollection 2016. PMID: 27761201; PMCID: PMC5064996.
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