COPASI

COPASI's Use In Genomics

2024
An H, Pires JC, Conant GC (2024) Gene expression bias between the subgenomes of allopolyploid hybrids is an emergent property of the kinetics of expression. PLOS Computational Biology 20:e1011803 Genetics Genomics Link

1 publication
2023

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2022

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2021

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2020

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2019

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2018
Acón M, Siles-Canales F, Mora-Rodríguez R (2018) Modeling Gene Dosage Compensation Mediated by Sensor Loops in Large-Scale Mathematical Models of MicroRNA-Transcription Factor Networks. 2018 IEEE International Work Conference on Bioinspired Intelligence (IWOBI) doi:10.1109/IWOBI.2018.8464210 Genomics Link
Bogantes-Vidal MA, Mora-Rodríguez R, Aeón MS (2018) In-Silico Modeling for the Identification of Regulatory Microrna Targets in Epithelial Mesenchymal Transition. 2018 IEEE International Work Conference on Bioinspired Intelligence (IWOBI) doi:10.1109/IWOBI.2018.8464202 Genomics Link
Jiménez-Vargas D, Acón M, Sahin Ö, Eyüpoğlu E, Riazalhosseini Y, Molina-Mora JA, Guevara-Coto J, Mora-Rodríguez R (2018) Modules of Correlated Genes in a Gene Expression Regulatory Network of CDDP-Resistant Cancer Cells. 2018 IEEE International Work Conference on Bioinspired Intelligence (IWOBI). doi:10.1109/IWOBI.2018.8464190 Genomics Link
Vargas-Mora C, Acón M, Mora-Rodríguez R, Quirós-Barrantes S (2018) A Transcriptional Regulatory Network Model Reveals miR-34a as a Potential Regulator of Proliferation in Cancer Cell Lines. 2018 IEEE International Work Conference on Bioinspired Intelligence (IWOBI) doi:10.1109/IWOBI.2018.8464205 Genomics Link

4 publications
2017
Badet T, Peyraud R, Mbengue M, Navaud O, Derbyshire M, Oliver RP, Barbacci A, Raffaele S (2017) Codon optimization underpins generalist parasitism in fungi. eLife 6:e22472 Genomics Theory Macromolecular Biochemistry Link
Man-Sai A, Siles-Canales F, Mora-Rodríguez R (2017) A biocomputational platform for the automated construction of large-scale mathematical models of miRNA-transcription factor networks for studies on gene dosage compensation. 2016 IEEE 36th Central American and Panama Convention (CONCAPAN XXXVI), San Jose, 2016, pp. 1-7 Genomics Link

2 publications
2016
Pires JC, Conant GC (2016) Robust yet fragile: expression noise, protein misfolding, and gene dosage in the evolution of genomes. Annual Review of Genetics 50:113–131 Genetics Genomics Link

1 publication
2015

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2014
Fadda A, Ryten M, Droll D, Rojas F, Färber V, Haanstra JR, Merce C, Bakker BM, Matthews KR, Clayton C (2014) Transcriptome-wide analysis of trypanosome mRNA decay reveals complex degradation kinetics and suggests a role for co-transcriptional degradation in determining mRNA levels. Molecular Microbiology 94:307-326 Microbiology Genomics Link
Ligon TS, Leonhardt C, Rädler JO (2014) Multi-level kinetic model of mRNA delivery via transfection of lipoplexes. PLoS One 9:e107148 Cell Biology Genomics Link
Shinde S, Mol M, Singh S (2014) Regulatory networks, genes and glycerophospholipid biosynthesis pathway in schistosomiasis: A systems biology view for pharmacological intervention. Gene 550:214-22. Pharmacology Genomics Link

3 publications
2013
LeBaron R, Villareal G, Roberson DJ, Phelix CF (2013) Abstract 5224: Breast cancer biomarkers from biosimulations: transcriptome-to-reactomeâ„¢ technology. Cancer Research 73:5224 Genomics Computational Method Link

1 publication
2012
Cristovao M, Sisamakis E, Hingorani MM, Marx AD, Jung CP, Rothwell PJ, Seidel CAM, Friedhoff P (2012) Single-molecule multiparameter fluorescence spectroscopy reveals directional MutS binding to mismatched bases in DNA. Nucleic Acids Research 40:5448-5464 Genomics Link
Viladomiu M, Hontecillas R, Pedragosa M, Carbo A, Hoops S, Michalak P, Michalak K, Guerrant RL, Roche JK, Warren CA, Bassaganya-Riera J (2012) Modeling the Role of Peroxisome Proliferator-Activated Receptor γ and MicroRNA-146 in Mucosal Immune Responses to Clostridium difficile. PLoS One 7:e47525 Genomics Immunology Link

2 publications
2011
Lee MV, Topper SE, Hubler SL, Hose J, Wenger CD, Coon JJ, Gasch AP (2011) A dynamic model of proteome changes reveals new roles for transcript alteration in yeast. Molecular Systems Biology 7:514 Genomics Link

1 publication
2010
Samorodnitsky E, Pugh BF (2010) Genome-Wide Modeling of Transcription Preinitiation Complex Disassembly Mechanisms using ChIP-chip Data. PLoS Computational Biology 6:e1000733 Macromolecular Biochemistry Genomics Link
Smallbone K, Simeonidis E, Swainston N, Mendes P (2010) Towards a genome-scale kinetic model of cellular metabolism. BMC Systems Biology 4:6 Genomics Whole-Cell Models Metabolism Link

2 publications
2009

0 publication
2008
Long J, Roth M (2008) Synthetic microarray data generation with RANGE and NEMO. Bioinformatics 24:132–134 Computational Method Genomics Link

1 publication
2007

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2006

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2005

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