COPASI

COPASI's Use In Genetics

2021
Chushak Y, Harbaugh S, Zimlich K, Alfred B, Chávez J, Kelley-Loughnane N (2021) Characterization of synthetic riboswitch in cell-free protein expression systems. RNA Biology doi:10.1080/15476286.2020.1868149 Biochemistry Genetics Link

1 publication
2020
Arya S, Todman H, Baker M, Hooton S, Millard A, Kreft J-U, Hobman JL, Stekel DJ (2020) A generalised model for generalised transduction: the importance of co-evolution and stochasticity in phage mediated antimicrobial resistance transfer. FEMS Microbiology Ecology 96:fiaa100 Microbiology Genetics Link
Carlson-Stevermer J, Das A, Abdeen AA, Fiflis D, Grindel BI, Saxena S, Akcan T, Alam T, Kletzien H, Kohlenberg L, Goedland M, Dombroe MJ, Saha K (2020) Design of efficacious somatic cell genome editing strategies for recessive and polygenic diseases. Nature Communications 11:6277 Laboratory Method Genetics Link

2 publications
2019
Anderson R, Lagnado A, Maggiorani D, Walaszczyk A, Dookun E, Chapman J, Birch J, Salmonowicz H, Ogrodnik M, Jurk D, Proctor C, Correia-Melo C, Victorelli S, Fielder E, Berlinguer-Palmini R, Owens A, Greaves LC, Kolsky KL, Parini A, Douin-Echinard V, LeBrasseur NK, Arthur HM, Tual-Chalot S, Schafer MJ, Roos CM, Miller JD, Robertson N, Mann J, Adams PD, Tchkonia T, Kirkland JL, Mialet-Perez J, Richardson GD, Passos JF (2019) Length-independent telomere damage drives post-mitotic cardiomyocyte senescence. The EMBO Journal 38:e100492 Genetics Physiology Link
Lebar T, Verbič A, Ljubetič A, Jerala R (2019) Polarized displacement by transcription activator-like effectors for regulatory circuits. Nature Chemical Biology 15:80–87 Synthetic Biology Genetics Link

2 publications
2018
Buriticá DCC, Mejía BV, Rojas LM, Sáenz L, Yosa J (2018) Análisis determinístico de la red de regulación génica involucrada en la expresión y función del factor de transcripción σ^ 32 en E. coli. Revista Cuarzo 23:7–15 Genetics Microbiology Link
Yeom K-H, Mitchell S, Linares AJ, Zheng S, Lin C-H, Wang X-J, Hoffmann A, Black DL (2018) Polypyrimidine tract-binding protein blocks miRNA-124 biogenesis to enforce its neuronal-specific expression in the mouse. Proceedings of the National Academy of Sciences USA 115:E11061–E11070 Genetics Biochemistry Link

2 publications
2017
Orlenko A, Chi PB, Liberles DA (2017) Characterizing the roles of changing population size and selection on the evolution of flux control in metabolic pathways. BMC Evolutionary Biology 17:117 Biochemistry Genetics Link
Proctor CJ, Goljanek-Whysall K (2017) Using computer simulation models to investigate the most promising microRNAs to improve muscle regeneration during ageing. Scientific Reports 7:12314 Genetics Signaling Link
Proctor CJ, Smith GR (2017) Computer simulation models as a tool to investigate the role of microRNAs in osteoarthritis. PLOS One 12:e0187568 Genetics Signaling Link

3 publications
2016
Boross G, Papp B (2016) No evidence that protein noise-induced epigenetic epistasis constrains gene expression evolution. Molecular Biology and Evolution 34:380–390 Metabolism Genetics Link
Chizzolini F (2016) The relationship between genotype and phenotype in cell-free transcription-translation reactions. PhD Thesis, University of Trento Genetics Link
Lloréns-Rico V, Cano J, Kamminga T, Gil R, Latorre A, Chen W-H, Bork P, Glass JI, Serrano L, Lluch-Senar M (2016) Bacterial antisense RNAs are mainly the product of transcriptional noise. Science Advances 2:e1501363 Microbiology Genetics Link
Orlenko A, Teufel AI, Chi PB, Liberles DA (2016) Selection on metabolic pathway function in the presence of mutation-selection-drift balance leads to rate-limiting steps that are not evolutionarily stable. Biology Direct 11:31 Genetics Metabolism Link
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
Rantasalo A, Czeizler E, Virtanen R, Rousu J, Lähdesmäki H, Penttilä M, Jäntti J, Mojzita D (2016) Synthetic Transcription Amplifier System for Orthogonal Control of Gene Expression in Saccharomyces cerevisiae. PLOS One 11:e0148320 Genetics Microbiology Synthetic Biology Link

6 publications
2015
Dornseifer S, Willkomm S, Far RK, Liebschwager J, Beltsiou F, Frank K, Laufer SD, Martinetz T, Sczakiel G, Claussen JC, Restle T (2015) RNAi revised - target mRNA-dependent enhancement of gene silencing. Nucleic Acids Research 43:10623-32. Macromolecular Biochemistry Genetics Link
Mandlik V, Gurav M, Singh S (2015) Regulatory dynamics of network architecture and function in tristable genetic circuit of Leishmania: a mathematical biology approach. Journal of Biomolecular Structure and Dynamics 33:2554-62 Synthetic Biology Genetics Metabolism Link
Rastgou Talemi S, Kollarovic G, Lapytsko A, Schaber J (2015) Development of a robust DNA damage model including persistent telomere-associated damage with application to secondary cancer risk assessment. Scientific Reports 5:13540 Genetics Macromolecular Biochemistry Link

3 publications
2014

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2013

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2012
Ray JCJ, Igoshin OA (2012) Interplay of Gene Expression Noise and Ultrasensitive Dynamics Affects Bacterial Operon Organization. PLOS Computational Biology 8:e1002672 Microbiology Genetics Link

1 publication
2011

0 publication
2010
Tiwari A, Balázsi G, Gennaro ML, Igoshin OA (2010) The interplay of multiple feedback loops with post-translational kinetics results in bistability of mycobacterial stress response. Physical Biology 7:36005 Microbiology Genetics Link

1 publication
2009
Kovács K, Hurst LD, Papp B (2009) Stochasticity in Protein Levels Drives Colinearity of Gene Order in Metabolic Operons of Escherichia coli. PLOS Biology 7:e1000115 Genetics Link

1 publication
2008

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2007

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2006

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