Publications

2024

  • DOI BibTeX
    C. Siachisumo, S. Luzzi, S. Aldalaqan, G. Hysenaj, C. Dalgliesh, K. Cheung, M.R. Gazzara, I.D. Yonchev, K. James, M. Kheirollahi Chadegani, I.E. Ehrmann, G.R. Smith, S.J. Cockell, J. Munkley, S.A. Wilson, Y. Barash, D.J. Elliott
    An anciently diverged family of RNA binding proteins maintain correct splicing of a class of ultra-long exons through cryptic splice site repression
    in eLife, 12, October 2024
    @ARTICLE{Siachisumo2024,
  title = {An anciently diverged family of RNA binding proteins maintain correct splicing of a class of ultra-long exons through cryptic splice site repression},
  author = {Siachisumo, Chileleko and Luzzi, Sara and Aldalaqan, Saad and Hysenaj, Gerald and Dalgliesh, Caroline and Cheung, Kathleen and Gazzara, Matthew R and Yonchev, Ivaylo D and James, Katherine and Kheirollahi Chadegani, Mahsa and Ehrmann, Ingrid E and Smith, Graham R and Cockell, Simon J and Munkley, Jennifer and Wilson, Stuart A and Barash, Yoseph and Elliott, David J},
  year = 2024,
  doi = {10.7554/eLife.89705.3},
  month = oct,
  journal = {eLife},
  volume = {12}

2023

  • BibTeX
    S. Scheidegger, S. Mingo Barba, H. Fellermann, U. Gaipl
    Influence of the Antigen Pattern Vector on the Dynamics in a Perceptron-Based Artificial Immune - Tumour- Ecosystem During and After Radiation Therapy
    in Artificial Life and Evolutionary Computation. WIVACE 2021, p.195-206, Cham., January 2023
    @INPROCEEDINGS{Scheidegger2023,
  title = {Influence of the Antigen Pattern Vector on the Dynamics in a Perceptron-Based Artificial Immune - Tumour- Ecosystem During and After Radiation Therapy},
  author = {Scheidegger, Stephan and Mingo Barba, Sergio and Fellermann, Harold and Gaipl , Udo},
  year = 2023,
  month = jan,
  booktitle = {Artificial Life and Evolutionary Computation. WIVACE 2021},
  pages = {195--206},
  address = {Cham.}
}
  • DOI BibTeX
    Y. Huang, N. Sinha, A. Wipat, J. Bacardit
    A knowledge integration strategy for the selection of a robust multi-stress biomarkers panel for Bacillus subtilis
    in Synthetic and Systems Biotechnology, 8(1):97-106, March 2023
    @ARTICLE{Huang2023,
  title = {A knowledge integration strategy for the selection of a robust multi-stress biomarkers panel for Bacillus subtilis},
  author = {Huang, Yiming and Sinha, Nishant and Wipat, Anil and Bacardit, Jaume},
  year = 2023,
  doi = {10.1016/j.synbio.2022.12.001},
  month = mar,
  journal = {Synthetic and Systems Biotechnology},
  volume = {8},
  number = {1},
  pages = {97--106}
}

2022

  • DOI BibTeX
    S. Jiang, I. Otero-Muras, J.R. Banga, Y. Wang, M. Kaiser, N. Krasnogor
    OptDesign: Identifying Optimum Design Strategies in Strain Engineering for Biochemical Production
    in ACS Synthetic Biology, 11(4):1531-1541, April 2022
    @ARTICLE{Jiang2022,
  title = {OptDesign: Identifying Optimum Design Strategies in Strain Engineering for Biochemical Production},
  author = {Jiang, Shouyong and Otero-Muras, Irene and Banga, Julio R. and Wang, Yong and Kaiser, Marcus and Krasnogor, Natalio},
  year = 2022,
  doi = {10.1021/acssynbio.1c00610},
  month = apr,
  journal = {ACS Synthetic Biology},
  volume = {11},
  number = {4},
  pages = {1531--1541}
}
  • DOI BibTeX
    K. James, J. Muñoz-Muñoz
    Computational Network Inference for Bacterial Interactomics
    in mSystems, 7(2), April 2022
    @ARTICLE{James2022,
  title = {Computational Network Inference for Bacterial Interactomics},
  author = {James, Katherine and Muñoz-Muñoz, Jose},
  year = 2022,
  doi = {10.1128/msystems.01456-21},
  month = apr,
  journal = {mSystems},
  volume = {7},
  number = {2}
  • DOI BibTeX
    H. Fellermann, R.M. Füchslin
    Editorial: The 2019 Conference on Artificial Life Special Issue
    in Artificial Life, 28(2):171-172, June 2022
    @ARTICLE{Fellermann2022,
  title = {Editorial: The 2019 Conference on Artificial Life Special Issue},
  author = {Fellermann, Harold and Füchslin, Rudolf M.},
  year = 2022,
  doi = {10.1162/artl_e_00380},
  month = jun,
  journal = {Artificial Life},
  volume = {28},
  number = {2},
  pages = {171--172}
}
  • DOI BibTeX
    K. James, A. Wipat, S.J. Cockell
    Expanding interactome analyses beyond model eukaryotes
    in Briefings in Functional Genomics, 21(4):243-269, July 2022
    @ARTICLE{James2022b,
  title = {Expanding interactome analyses beyond model eukaryotes},
  author = {James, Katherine and Wipat, Anil and Cockell, Simon J},
  year = 2022,
  doi = {10.1093/bfgp/elac007},
  month = jul,
  journal = {Briefings in Functional Genomics},
  volume = {21},
  number = {4},
  pages = {243--269}
}
  • DOI BibTeX
    F. Shmarov, G.R. Smith, S.C. Weatherhead, N.J. Reynolds, P. Zuliani
    Individualised computational modelling of immune mediated disease onset, flare and clearance in psoriasis
    in PLOS Computational Biology, 18(9):e1010267, September 2022
    @ARTICLE{Shmarov2022,
  title = {Individualised computational modelling of immune mediated disease onset, flare and clearance in psoriasis},
  author = {Shmarov, Fedor and Smith, Graham R. and Weatherhead, Sophie C. and Reynolds, Nick J. and Zuliani, Paolo},
  year = 2022,
  doi = {10.1371/journal.pcbi.1010267},
  month = sep,
  journal = {PLOS Computational Biology},
  volume = {18},
  number = {9},
  pages = {e1010267}
}
  • DOI BibTeX
    Y. Xia, P.G. Jayathilake, B. Li, P. Zuliani, D. Deehan, J. Longyear, P. Stoodley, J. Chen
    Coupled CFD‐DEM modeling to predict how EPS affects bacterial biofilm deformation, recovery and detachment under flow conditions
    in Biotechnology and Bioengineering, 119(9):2551-2563, September 2022
    @ARTICLE{Xia2022,
  title = {Coupled CFD‐DEM modeling to predict how EPS affects bacterial biofilm deformation, recovery and detachment under flow conditions},
  author = {Xia, Yuqing and Jayathilake, Pahala G. and Li, Bowen and Zuliani, Paolo and Deehan, David and Longyear, Jennifer and Stoodley, Paul and Chen, Jinju},
  year = 2022,
  doi = {10.1002/bit.28146},
  month = sep,
  journal = {Biotechnology and Bioengineering},
  volume = {119},
  number = {9},
  pages = {2551--2563}
}
  • DOI BibTeX
    K. James, A. Alsobhe, S.J. Cockell, A. Wipat, M. Pocock
    Integration of probabilistic functional networks without an external Gold Standard
    in BMC Bioinformatics, 23(1), December 2022
    @ARTICLE{James2022a,
  title = {Integration of probabilistic functional networks without an external Gold Standard},
  author = {James, Katherine and Alsobhe, Aoesha and Cockell, Simon J and Wipat, Anil and Pocock, Matthew},
  year = 2022,
  doi = {10.1186/s12859-022-04834-4},
  month = dec,
  journal = {BMC Bioinformatics},
  volume = {23},
  number = {1}

2021

  • DOI BibTeX
    Y. Xia, P.G. Jayathilake, B. Li, P. Zuliani, J. Chen
    CFD–DEM modelling of biofilm streamer oscillations and their cohesive failure in fluid flow
    in Biotechnology and Bioengineering, 118(2):918-929, February 2021
    @ARTICLE{Xia2021,
  title = {CFD–DEM modelling of biofilm streamer oscillations and their cohesive failure in fluid flow},
  author = {Xia, Yuqing and Jayathilake, Pahala G. and Li, Bowen and Zuliani, Paolo and Chen, Jinju},
  year = 2021,
  doi = {10.1002/bit.27619},
  month = feb,
  journal = {Biotechnology and Bioengineering},
  volume = {118},
  number = {2},
  pages = {918--929}
}
  • DOI BibTeX
    S. Konur, L. Mierla, H. Fellermann, C. Ladroue, B. Brown, A. Wipat, J. Twycross, B.P. Dun, S. Kalvala, M. Gheorghe, N. Krasnogor
    Toward Full-Stack In Silico Synthetic Biology: Integrating Model Specification, Simulation, Verification, and Biological Compilation
    in ACS Synthetic Biology, 10(8):1931-1945, August 2021
    @ARTICLE{Konur2021,
  title = {Toward Full-Stack In Silico Synthetic Biology: Integrating Model Specification, Simulation, Verification, and Biological Compilation},
  author = {Konur, Savas and Mierla, Laurentiu and Fellermann, Harold and Ladroue, Christophe and Brown, Bradley and Wipat, Anil and Twycross, Jamie and Dun, Boyang Peter and Kalvala, Sara and Gheorghe, Marian and Krasnogor, Natalio},
  year = 2021,
  doi = {10.1021/acssynbio.1c00143},
  month = aug,
  journal = {ACS Synthetic Biology},
  volume = {10},
  number = {8},
  pages = {1931--1945}
}
  • DOI BibTeX
    S.W. Choo, W.K. Mohammed, N.V.R. Mutha, N. Rostami, H. Ahmed, N. Krasnogor, G.Y.A. Tan, N.S. Jakubovics
    Transcriptomic Responses to Coaggregation between Streptococcus gordonii and Streptococcus oralis
    in Applied and Environmental Microbiology, 87(22), October 2021
    @ARTICLE{Choo2021,
  title = {Transcriptomic Responses to Coaggregation between Streptococcus gordonii and Streptococcus oralis},
  author = {Choo, Siew Woh and Mohammed, Waleed K. and Mutha, Naresh V. R. and Rostami, Nadia and Ahmed, Halah and Krasnogor, Natalio and Tan, Geok Yuan Annie and Jakubovics, Nicholas S.},
  year = 2021,
  doi = {10.1128/AEM.01558-21},
  month = oct,
  journal = {Applied and Environmental Microbiology},
  volume = {87},
  number = {22}
  • DOI BibTeX
    N. Watson, N. Wilson, F. Shmarov, P. Zuliani, N.J. Reynolds, S.C. Weatherhead
    The use of psoriasis biomarkers, including trajectory of clinical response, to predict clearance and remission duration to UVB phototherapy
    in Journal of the European Academy of Dermatology and Venereology, 35(11):2250-2258, November 2021
    @ARTICLE{Watson2021,
  title = {The use of psoriasis biomarkers, including trajectory of clinical response, to predict clearance and remission duration to UVB phototherapy},
  author = {Watson, N. and Wilson, N. and Shmarov, F. and Zuliani, P. and Reynolds, N. J. and Weatherhead, S. C.},
  year = 2021,
  doi = {10.1111/jdv.17519},
  month = nov,
  journal = {Journal of the European Academy of Dermatology and Venereology},
  volume = {35},
  number = {11},
  pages = {2250--2258}
}

2020

  • DOI BibTeX
    S. Jiang, Y. Wang, M. Kaiser, N. Krasnogor
    NIHBA: a network interdiction approach for metabolic engineering design
    in Bioinformatics, 36(11):3482-3492, June 2020
    @ARTICLE{Jiang2020,
  title = {NIHBA: a network interdiction approach for metabolic engineering design},
  author = {Jiang, Shouyong and Wang, Yong and Kaiser, Marcus and Krasnogor, Natalio},
  year = 2020,
  doi = {10.1093/bioinformatics/btaa163},
  month = jun,
  journal = {Bioinformatics},
  volume = {36},
  number = {11},
  pages = {3482--3492}
}
  • DOI BibTeX
    M. Vasileva, F. Shmarov, P. Zuliani
    Probabilistic Reachability for Uncertain Stochastic Hybrid Systems via Gaussian Processes
    in 2020 18th ACM-IEEE International Conference on Formal Methods and Models for System Design (MEMOCODE), p.1-11, Jaipur, India, December 2020
    @INPROCEEDINGS{Vasileva2020,
  title = {Probabilistic Reachability for Uncertain Stochastic Hybrid Systems via Gaussian Processes},
  author = {Vasileva, Mariia and Shmarov, Fedor and Zuliani, Paolo},
  year = 2020,
  doi = {10.1109/MEMOCODE51338.2020.9315182},
  month = dec,
  booktitle = {2020 18th ACM-IEEE International Conference on Formal Methods and Models for System Design (MEMOCODE)},
  pages = {1--11},
  address = {Jaipur, India}
}
  • DOI BibTeX
    F. Shmarov, S. Soudjani, N. Paoletti, E. Bartocci, S. Lin, S.A. Smolka, P. Zuliani
    Automated Synthesis of Safe Digital Controllers for Sampled-Data Stochastic Nonlinear Systems
    in IEEE Access, 8:180825-180843, 2020
    @ARTICLE{Shmarov2020,
  title = {Automated Synthesis of Safe Digital Controllers for Sampled-Data Stochastic Nonlinear Systems},
  author = {Shmarov, Fedor and Soudjani, Sadegh and Paoletti, Nicola and Bartocci, Ezio and Lin, Shan and Smolka, Scott A. and Zuliani, Paolo},
  year = 2020,
  doi = {10.1109/ACCESS.2020.3028476},
  journal = {IEEE Access},
  volume = {8},
  pages = {180825--180843}
}
  • DOI BibTeX
    S. Scheidegger, A. Mikos, H. Fellermann
    Modelling Artificial Immune – Tumor Ecosystem Interaction During Radiation Therapy Using a Perceptron – Based Antigen Pattern Recognition
    in The 2020 Conference on Artificial Life, p.541-548, Online, 2020
    @INPROCEEDINGS{Scheidegger2020,
  title = {Modelling Artificial Immune – Tumor Ecosystem Interaction During Radiation Therapy Using a Perceptron – Based Antigen Pattern Recognition},
  author = {Scheidegger, Stephan and Mikos, Alexander and Fellermann, Harold},
  year = 2020,
  doi = {10.1162/isal_a_00271},
  booktitle = {The 2020 Conference on Artificial Life},
  pages = {541--548},
  address = {Online}
}

2019

  • DOI BibTeX
    O.K. Oyebamiji, D.J. Wilkinson, B. Li, P.G. Jayathilake, P. Zuliani, T.P. Curtis
    Bayesian emulation and calibration of an individual-based model of microbial communities
    in Journal of Computational Science, 30(C):194-208, January 2019
    @ARTICLE{Oyebamiji2019,
  title = {Bayesian emulation and calibration of an individual-based model of microbial communities},
  author = {Oyebamiji, O. K. and Wilkinson, D. J. and Li, B. and Jayathilake, P. G. and Zuliani, P. and Curtis, T. P.},
  year = 2019,
  doi = {10.1016/j.jocs.2018.12.007},
  month = jan,
  journal = {Journal of Computational Science},
  volume = {30},
  number = {C},
  pages = {194--208}
}
  • DOI BibTeX
    P.G. Jayathilake, B. Li, P. Zuliani, T. Curtis, J. Chen
    Modelling bacterial twitching in fluid flows: a CFD-DEM approach
    in Scientific Reports, 9(1), October 2019
    @ARTICLE{Jayathilake2019,
  title = {Modelling bacterial twitching in fluid flows: a CFD-DEM approach},
  author = {Jayathilake, Pahala Gedara and Li, Bowen and Zuliani, Paolo and Curtis, Tom and Chen, Jinju},
  year = 2019,
  doi = {10.1038/s41598-019-51101-3},
  month = oct,
  journal = {Scientific Reports},
  volume = {9},
  number = {1}
  • DOI BibTeX
    J. Naylor, H. Fellermann, N. Krasnogor
    Easybiotics: a GUI for 3D physical modelling of multi-species bacterial populations
    in Bioinformatics, 35(19):3859-3860, October 2019
    @ARTICLE{Naylor2019,
  title = {Easybiotics: a GUI for 3D physical modelling of multi-species bacterial populations},
  author = {Naylor, Jonathan and Fellermann, Harold and Krasnogor, Natalio},
  year = 2019,
  doi = {10.1093/bioinformatics/btz131},
  month = oct,
  journal = {Bioinformatics},
  volume = {35},
  number = {19},
  pages = {3859--3860}
}
  • DOI BibTeX
    L. Grozinger, M. Amos, T.E. Gorochowski, P. Carbonell, D.A. Oyarzún, R. Stoof, H. Fellermann, P. Zuliani, H. Tas, A. Goñi-Moreno
    Pathways to cellular supremacy in biocomputing
    in Nature Communications, 10(1), November 2019
    @ARTICLE{Grozinger2019,
  title = {Pathways to cellular supremacy in biocomputing},
  author = {Grozinger, Lewis and Amos, Martyn and Gorochowski, Thomas E. and Carbonell, Pablo and Oyarzún, Diego A. and Stoof, Ruud and Fellermann, Harold and Zuliani, Paolo and Tas, Huseyin and Goñi-Moreno, Angel},
  year = 2019,
  doi = {10.1038/s41467-019-13232-z},
  month = nov,
  journal = {Nature Communications},
  volume = {10},
  number = {1}
  • DOI BibTeX
    S. Scheidegger, H. Fellermann
    Optimizing Radiation Therapy Treatments by Exploring Tumour Ecosystem Dynamics in – silico
    in The 2019 Conference on Artificial Life, p.236-242, Newcastle, United Kingdom, 2019
    @INPROCEEDINGS{Scheidegger2019,
  title = {Optimizing Radiation Therapy Treatments by Exploring Tumour Ecosystem Dynamics in – silico},
  author = {Scheidegger, Stephan and Fellermann, Harold},
  year = 2019,
  doi = {10.1162/isal_a_00167},
  booktitle = {The 2019 Conference on Artificial Life},
  pages = {236--242},
  address = {Newcastle, United Kingdom}
}

2018

  • DOI BibTeX
    O.K. Oyebamiji, D.J. Wilkinson, P.G. Jayathilake, S.P. Rushton, B. Bridgens, B. Li, P. Zuliani
    A Bayesian approach to modelling the impact of hydrodynamic shear stress on biofilm deformation
    in PLOS ONE, 13(4):e0195484, April 2018
    @ARTICLE{Oyebamiji2018,
  title = {A Bayesian approach to modelling the impact of hydrodynamic shear stress on biofilm deformation},
  author = {Oyebamiji, Oluwole K. and Wilkinson, Darren J. and Jayathilake, Pahala Gedara and Rushton, Steve P. and Bridgens, Ben and Li, Bowen and Zuliani, Paolo},
  year = 2018,
  doi = {10.1371/journal.pone.0195484},
  month = apr,
  journal = {PLOS ONE},
  volume = {13},
  number = {4},
  pages = {e0195484}
}
  • DOI BibTeX
    B. Shirt-Ediss, N. Krasnogor, H. Fellermann
    The fittest, the common, and the dullest: Selection dynamics of exact autocatalytic replicators
    in The 2018 Conference on Artificial Life, p.370-371, Tokyo, Japan, 2018
    @INPROCEEDINGS{Shirt-Ediss2018,
  title = {The fittest, the common, and the dullest: Selection dynamics of exact autocatalytic replicators},
  author = {Shirt-Ediss, Ben and Krasnogor, Natalio and Fellermann, Harold},
  year = 2018,
  doi = {10.1162/isal_a_00070},
  booktitle = {The 2018 Conference on Artificial Life},
  pages = {370--371},
  address = {Tokyo, Japan}
}
  • DOI BibTeX
    J. Revell, P. Zuliani
    Stochastic Rate Parameter Inference Using the Cross-Entropy Method
    in Computational Methods in Systems Biology, Lecture Notes in Computer Science 11095, p.146-164, 2018
    @INCOLLECTION{Revell2018,
  title = {Stochastic Rate Parameter Inference Using the Cross-Entropy Method},
  author = {Revell, Jeremy and Zuliani, Paolo},
  year = 2018,
  doi = {10.1007/978-3-319-99429-1_9},
  booktitle = {Computational Methods in Systems Biology},
  publisher = {Springer International Publishing},
  volume = {11095},
  series = {Lecture Notes in Computer Science},
  pages = {146--164}
}

2017

  • DOI code BibTeX
    J. Naylor, H. Fellermann, Y. Ding, W.K. Mohammed, N.S. Jakubovics, J. Mukherjee, C.A. Biggs, P.C. Wright, N. Krasnogor
    Simbiotics: A Multiscale Integrative Platform for 3D Modeling of Bacterial Populations
    in ACS Synthetic Biology, 6(7):1194-1210, July 2017
    @ARTICLE{Naylor2017,
  title = {Simbiotics: A Multiscale Integrative Platform for 3D Modeling of Bacterial Populations},
  author = {Naylor, Jonathan and Fellermann, Harold and Ding, Yuchun and Mohammed, Waleed K. and Jakubovics, Nicholas S. and Mukherjee, Joy and Biggs, Catherine A. and Wright, Phillip C. and Krasnogor, Natalio},
  year = 2017,
  doi = {10.1021/acssynbio.6b00315},
  month = jul,
  journal = {ACS Synthetic Biology},
  volume = {6},
  number = {7},
  pages = {1194--1210}
}
  • DOI BibTeX
    P.G. Jayathilake, P. Gupta, B. Li, C. Madsen, O. Oyebamiji, R. González-Cabaleiro, S. Rushton, B. Bridgens, D. Swailes, B. Allen, A.S. McGough, P. Zuliani, I.D. Ofiteru, D. Wilkinson, J. Chen, T. Curtis
    A mechanistic Individual-based Model of microbial communities
    in PLOS ONE, 12(8):e0181965, August 2017
    @ARTICLE{Jayathilake2017,
  title = {A mechanistic Individual-based Model of microbial communities},
  author = {Jayathilake, Pahala Gedara and Gupta, Prashant and Li, Bowen and Madsen, Curtis and Oyebamiji, Oluwole and González-Cabaleiro, Rebeca and Rushton, Steve and Bridgens, Ben and Swailes, David and Allen, Ben and McGough, A. Stephen and Zuliani, Paolo and Ofiteru, Irina Dana and Wilkinson, Darren and Chen, Jinju and Curtis, Tom},
  year = 2017,
  doi = {10.1371/journal.pone.0181965},
  month = aug,
  journal = {PLOS ONE},
  volume = {12},
  number = {8},
  pages = {e0181965}
}
  • DOI BibTeX
    H. Fellermann, S. Tanaka, S. Rasmussen
    Sequence selection by dynamical symmetry breaking in an autocatalytic binary polymer model
    in Physical Review E, 96(6), December 2017
    @ARTICLE{Fellermann2017,
  title = {Sequence selection by dynamical symmetry breaking in an autocatalytic binary polymer model},
  author = {Fellermann, Harold and Tanaka, Shinpei and Rasmussen, Steen},
  year = 2017,
  doi = {10.1103/PhysRevE.96.062407},
  month = dec,
  journal = {Physical Review E},
  volume = {96},
  number = {6}
  • DOI BibTeX
    F. Shmarov, N. Paoletti, E. Bartocci, S. Lin, S.A. Smolka, P. Zuliani
    SMT-based Synthesis of Safe and Robust PID Controllers for Stochastic Hybrid Systems
    in Hardware and Software: Verification and Testing, Lecture Notes in Computer Science 10629, p.131-146, 2017
    @INCOLLECTION{Shmarov2017,
  title = {SMT-based Synthesis of Safe and Robust PID Controllers for Stochastic Hybrid Systems},
  author = {Shmarov, Fedor and Paoletti, Nicola and Bartocci, Ezio and Lin, Shan and Smolka, Scott A. and Zuliani, Paolo},
  year = 2017,
  doi = {10.1007/978-3-319-70389-3_9},
  booktitle = {Hardware and Software: Verification and Testing},
  publisher = {Springer International Publishing},
  volume = {10629},
  series = {Lecture Notes in Computer Science},
  pages = {131--146}
}

2016

  • DOI BibTeX
    G. Misirli, M. Cavaliere, W. Waites, M. Pocock, C. Madsen, O. Gilfellon, R. Honorato-Zimmer, P. Zuliani, V. Danos, A. Wipat
    Annotation of rule-based models with formal semantics to enable creation, analysis, reuse and visualization
    in Bioinformatics, 32(6):908-917, March 2016
    @ARTICLE{Misirli2015,
  title = {Annotation of rule-based models with formal semantics to enable creation, analysis, reuse and visualization},
  author = {Misirli, Goksel and Cavaliere, Matteo and Waites, William and Pocock, Matthew and Madsen, Curtis and Gilfellon, Owen and Honorato-Zimmer, Ricardo and Zuliani, Paolo and Danos, Vincent and Wipat, Anil},
  year = 2016,
  doi = {10.1093/bioinformatics/btv660},
  month = mar,
  journal = {Bioinformatics},
  volume = {32},
  number = {6},
  pages = {908--917}
}
  • DOI BibTeX
    A. Best, K. James, G. Hysenaj, A. Tyson-Capper, D.J. Elliott
    Transformer2 proteins protect breast cancer cells from accumulating replication stress by ensuring productive splicing of checkpoint kinase 1
    in Frontiers of Chemical Science and Engineering, 10(2):186-195, June 2016
    @ARTICLE{Best2015,
  title = {Transformer2 proteins protect breast cancer cells from accumulating replication stress by ensuring productive splicing of checkpoint kinase 1},
  author = {Best, Andrew and James, Katherine and Hysenaj, Gerald and Tyson-Capper, Alison and Elliott, David J.},
  year = 2016,
  doi = {10.1007/s11705-015-1540-4},
  month = jun,
  journal = {Frontiers of Chemical Science and Engineering},
  volume = {10},
  number = {2},
  pages = {186--195}
}
  • DOI eprint code BibTeX
    N. Lazzarini, P. Widera, S. Williamson, R. Heer, N. Krasnogor, J. Bacardit
    Functional networks inference from rule-based machine learning models
    in BioData Mining, 9(1), December 2016
    @ARTICLE{Lazzarini2016,
  title = {Functional networks inference from rule-based machine learning models},
  author = {Lazzarini, Nicola and Widera, Paweł and Williamson, Stuart and Heer, Rakesh and Krasnogor, Natalio and Bacardit, Jaume},
  year = 2016,
  doi = {10.1186/s13040-016-0106-4},
  month = dec,
  journal = {BioData Mining},
  volume = {9},
  number = {1}
  • DOI BibTeX
    F. Shmarov, P. Zuliani
    Probabilistic Hybrid Systems Verification via SMT and Monte Carlo Techniques
    in Hardware and Software: Verification and Testing, Lecture Notes in Computer Science 10028, p.152-168, 2016
    @INCOLLECTION{Shmarov2016,
  title = {Probabilistic Hybrid Systems Verification via SMT and Monte Carlo Techniques},
  author = {Shmarov, Fedor and Zuliani, Paolo},
  year = 2016,
  doi = {10.1007/978-3-319-49052-6_10},
  booktitle = {Hardware and Software: Verification and Testing},
  publisher = {Springer International Publishing},
  volume = {10028},
  series = {Lecture Notes in Computer Science},
  pages = {152--168}
}

2015

  • DOI eprint code BibTeX
    D. Sanassy, P. Widera, N. Krasnogor
    Meta-Stochastic Simulation of Biochemical Models for Systems and Synthetic Biology
    in ACS Synthetic Biology, 4(1):39-47, January 2015
    @ARTICLE{Sanassy2014,
  title = {Meta-Stochastic Simulation of Biochemical Models for Systems and Synthetic Biology},
  author = {Sanassy, Daven and Widera, Paweł and Krasnogor, Natalio},
  year = 2015,
  doi = {10.1021/sb5001406},
  month = jan,
  journal = {ACS Synthetic Biology},
  volume = {4},
  number = {1},
  pages = {39--47}
}
  • DOI BibTeX
    S. Konur, M. Gheorghe, C. Dragomir, L. Mierla, F. Ipate, N. Krasnogor
    Qualitative and Quantitative Analysis of Systems and Synthetic Biology Constructs using P Systems
    in ACS Synthetic Biology, 4(1):83-92, January 2015
    @ARTICLE{Konur2015,
  title = {Qualitative and Quantitative Analysis of Systems and Synthetic Biology Constructs using P Systems},
  author = {Konur, Savas and Gheorghe, Marian and Dragomir, Ciprian and Mierla, Laurentiu and Ipate, Florentin and Krasnogor, Natalio},
  year = 2015,
  doi = {10.1021/sb500134w},
  month = jan,
  journal = {ACS Synthetic Biology},
  volume = {4},
  number = {1},
  pages = {83--92}
}

2014

  • DOI eprint code BibTeX
    C. Winterhalter, P. Widera, N. Krasnogor
    JEPETTO: a Cytoscape plugin for gene set enrichment and topological analysis based on interaction networks
    in Bioinformatics, 30(7):1029-1030, April 2014
    @ARTICLE{Winterhalter2013,
  title = {JEPETTO: a Cytoscape plugin for gene set enrichment and topological analysis based on interaction networks},
  author = {Winterhalter, C. and Widera, P. and Krasnogor, N.},
  year = 2014,
  doi = {10.1093/bioinformatics/btt732},
  month = apr,
  journal = {Bioinformatics},
  volume = {30},
  number = {7},
  pages = {1029--1030}
}
  • DOI BibTeX
    A. Best, K. James, C. Dalgliesh, E. Hong, M. Kheirolahi-Kouhestani, T. Curk, Y. Xu, M. Danilenko, R. Hussain, B. Keavney, A. Wipat, R. Klinck, I.G. Cowell, K. Cheong Lee, C.A. Austin, J.P. Venables, B. Chabot, M. Santibanez Koref, A. Tyson-Capper, D.J. Elliott
    Human Tra2 proteins jointly control a CHEK1 splicing switch among alternative and constitutive target exons
    in Nature Communications, 5:4760, September 2014
    @ARTICLE{Best2014,
  title = {Human Tra2 proteins jointly control a CHEK1 splicing switch among alternative and constitutive target exons},
  author = {Best, Andrew and James, Katherine and Dalgliesh, Caroline and Hong, Elaine and Kheirolahi-Kouhestani, Mahsa and Curk, Tomaz and Xu, Yaobo and Danilenko, Marina and Hussain, Rafiq and Keavney, Bernard and Wipat, Anil and Klinck, Roscoe and Cowell, Ian G. and Cheong Lee, Ka and Austin, Caroline A. and Venables, Julian P. and Chabot, Benoit and Santibanez Koref, Mauro and Tyson-Capper, Alison and Elliott, David J.},
  year = 2014,
  doi = {10.1038/ncomms5760},
  month = sep,
  journal = {Nature Communications},
  volume = {5},
  pages = {4760}
}
  • DOI BibTeX
    S. Konur, M. Gheorge, C. Dragomir, F. Ipate, N. Krasnogor
    Conventional verification for unconventional computing: a genetic XOR gate example
    in Fundamenta Informaticae, 134(1-2):97-110, November 2014
    @ARTICLE{Konur2014,
  title = {Conventional verification for unconventional computing: a genetic XOR gate example},
  author = {Konur, Savas and Gheorge, Marian and Dragomir, Ciprian and Ipate, Florin and Krasnogor, Natalio},
  year = 2014,
  doi = {10.3233/FI-2014-1093},
  month = nov,
  journal = {Fundamenta Informaticae},
  volume = {134},
  number = {1-2},
  pages = {97--110}
}
  • DOI BibTeX
    R. Bauer, M. Kaiser, E. Stoll
    A Computational Model Incorporating Neural Stem Cell Dynamics Reproduces Glioma Incidence across the Lifespan in the Human Population
    in PLoS ONE, 9(11):e111219, November 2014
    @ARTICLE{Bauer2014a,
  title = {A Computational Model Incorporating Neural Stem Cell Dynamics Reproduces Glioma Incidence across the Lifespan in the Human Population},
  author = {Bauer, Roman and Kaiser, Marcus and Stoll, Elizabeth},
  year = 2014,
  doi = {10.1371/journal.pone.0111219},
  month = nov,
  journal = {PLoS ONE},
  volume = {9},
  number = {11},
  pages = {e111219}
}
  • DOI BibTeX
    R. Bauer, F. Zubler, S. Pfister, A. Hauri, M. Pfeiffer, D.R. Muir, R.J. Douglas
    Developmental Self-Construction and -Configuration of Functional Neocortical Neuronal Networks
    in PLoS Computational Biology, 10(12):e1003994, December 2014
    @ARTICLE{Bauer2014b,
  title = {Developmental Self-Construction and -Configuration of Functional Neocortical Neuronal Networks},
  author = {Bauer, Roman and Zubler, Frédéric and Pfister, Sabina and Hauri, Andreas and Pfeiffer, Michael and Muir, Dylan R. and Douglas, Rodney J.},
  year = 2014,
  doi = {10.1371/journal.pcbi.1003994},
  month = dec,
  journal = {PLoS Computational Biology},
  volume = {10},
  number = {12},
  pages = {e1003994}
}
  • DOI BibTeX
    B. Liu, S. Kong, S. Gao, P. Zuliani, E.M. Clarke
    Parameter Synthesis for Cardiac Cell Hybrid Models Using δ-Decisions
    in Computational Methods in Systems Biology, Lecture Notes in Computer Science 8859, p.99-113, 2014
    @INCOLLECTION{Liu2014,
  title = {Parameter Synthesis for Cardiac Cell Hybrid Models Using δ-Decisions},
  author = {Liu, Bing and Kong, Soonho and Gao, Sicun and Zuliani, Paolo and Clarke, Edmund M.},
  year = 2014,
  doi = {10.1007/978-3-319-12982-2_8},
  booktitle = {Computational Methods in Systems Biology},
  publisher = {Springer International Publishing},
  volume = {8859},
  series = {Lecture Notes in Computer Science},
  pages = {99--113}
}
  • DOI BibTeX
    R. Gross, I. Fouxon, D. Lancet, O. Markovitch
    Quasispecies in population of compositional assemblies
    in BMC Evolutionary Biology, 14(1):265, 2014
    @ARTICLE{Gross2014,
  title = {Quasispecies in population of compositional assemblies},
  author = {Gross, Renan and Fouxon, Itzhak and Lancet, Doron and Markovitch, Omer},
  year = 2014,
  doi = {10.1186/s12862-014-0265-1},
  journal = {BMC Evolutionary Biology},
  volume = {14},
  number = {1},
  pages = {265}
}
  • URL BibTeX
    G. Misirli, J. Hallinan, R. Röttger, J. Baumbach, A. Wipat
    BacillusRegNet: A transcriptional regulation database and analysis platform for Bacillus species
    in Journal of Integrative Bioinformatics, 11(2):244, 2014
    @ARTICLE{Misirli2014,
  title = {BacillusRegNet: A transcriptional regulation database and analysis platform for Bacillus species},
  author = {Misirli, G. and Hallinan, J. and Röttger, R. and Baumbach, J. and Wipat, A.},
  year = 2014,
  url = {http://journal.imbio.de/article.php?aid=244},
  journal = {Journal of Integrative Bioinformatics},
  volume = {11},
  number = {2},
  pages = {244}
}
  • DOI BibTeX
    J. Blakes, J. Twycross, S. Konur, F.J. Romero-Campero, N. Krasnogor, M. Gheorghe
    Infobiotics Workbench: A P Systems Based Tool for Systems and Synthetic Biology
    in Applications of Membrane Computing in Systems and Synthetic Biology, Emergence, Complexity and Computation 7, p.1-41, 2014
    @INCOLLECTION{Blakes2014a,
  title = {Infobiotics Workbench: A P Systems Based Tool for Systems and Synthetic Biology},
  author = {Blakes, Jonathan and Twycross, Jamie and Konur, Savas and Romero-Campero, Francisco Jose and Krasnogor, Natalio and Gheorghe, Marian},
  year = 2014,
  doi = {10.1007/978-3-319-03191-0_1},
  booktitle = {Applications of Membrane Computing in Systems and Synthetic Biology},
  publisher = {Springer International Publishing},
  volume = {7},
  series = {Emergence, Complexity and Computation},
  pages = {1--41}
}

2013

  • DOI BibTeX
    H. Gong, P. Zuliani, E. M. Clarke
    Model Checking a Synchronous Diabetes-Cancer Logical Network
    in Current Bioinformatics, 8(1):9-15, February 2013
    @ARTICLE{Gong2013,
  title = {Model Checking a Synchronous Diabetes-Cancer Logical Network},
  author = {Gong, Haijun and Zuliani, Paolo and M. Clarke, Edmund},
  year = 2013,
  doi = {10.2174/157489313804871542},
  month = feb,
  journal = {Current Bioinformatics},
  volume = {8},
  number = {1},
  pages = {9--15}
}
  • DOI BibTeX
    B.J.W. Dekkers, S. Pearce, R.P. van Bolderen-Veldkamp, A. Marshall, P. Widera, J. Gilbert, H.-. Drost, G.W. Bassel, K. Muller, J.R. King, A.T.A. Wood, I. Grosse, M. Quint, N. Krasnogor, G. Leubner-Metzger, M.J. Holdsworth, L. Bentsink
    Transcriptional Dynamics of Two Seed Compartments with Opposing Roles in Arabidopsis Seed Germination
    in PLANT PHYSIOLOGY, 163(1):205-215, September 2013
    @ARTICLE{Dekkers2013,
  title = {Transcriptional Dynamics of Two Seed Compartments with Opposing Roles in Arabidopsis Seed Germination},
  author = {Dekkers, B. J. W. and Pearce, S. and van Bolderen-Veldkamp, R. P. and Marshall, A. and Widera, P. and Gilbert, J. and Drost, H. -g. and Bassel, G. W. and Muller, K. and King, J. R. and Wood, A. T. A. and Grosse, I. and Quint, M. and Krasnogor, N. and Leubner-Metzger, G. and Holdsworth, M. J. and Bentsink, L.},
  year = 2013,
  doi = {10.1104/pp.113.223511},
  month = sep,
  journal = {PLANT PHYSIOLOGY},
  volume = {163},
  number = {1},
  pages = {205--215}
}
  • DOI BibTeX
    G. Misirli, A. Wipat, J. Mullen, K. James, M. Pocock, W. Smith, N. Allenby, J. Hallinan
    BacillOndex: An Integrated Data Resource for Systems and Synthetic Biology
    in Journal of Integrative Bioinformatics, 10(2):224, 2013
    @ARTICLE{Misirli2013,
  title = {BacillOndex: An Integrated Data Resource for Systems and Synthetic Biology},
  author = {Misirli, G. and Wipat, A. and Mullen, J. and James, K. and Pocock, M. and Smith, W. and Allenby, N. and Hallinan, J.},
  year = 2013,
  doi = {10.2390/biecoll-jib-2013-224},
  journal = {Journal of Integrative Bioinformatics},
  volume = {10},
  number = {2},
  pages = {224}
}

2012

  • DOI BibTeX
    E. Glaab, A. Baudot, N. Krasnogor, R. Schneider, A. Valencia
    EnrichNet: network-based gene set enrichment analysis
    in Bioinformatics, 28(18):i451-i457, September 2012
    @ARTICLE{Glaab2012a,
  title = {EnrichNet: network-based gene set enrichment analysis},
  author = {Glaab, E. and Baudot, A. and Krasnogor, N. and Schneider, R. and Valencia, A.},
  year = 2012,
  doi = {10.1093/bioinformatics/bts389},
  month = sep,
  journal = {Bioinformatics},
  volume = {28},
  number = {18},
  pages = {i451--i457}
}
  • DOI BibTeX
    O. Markovitch, D. Sorek, L.T. Lui, D. Lancet, N. Krasnogor
    Is There an Optimal Level of Open-Endedness in Prebiotic Evolution?
    in Origins of Life and Evolution of Biospheres, 42(5):469-474, October 2012
    @ARTICLE{Markovitch2012,
  title = {Is There an Optimal Level of Open-Endedness in Prebiotic Evolution?},
  author = {Markovitch, Omer and Sorek, Daniel and Lui, Leong Ting and Lancet, Doron and Krasnogor, Natalio},
  year = 2012,
  doi = {10.1007/s11084-012-9309-y},
  month = oct,
  journal = {Origins of Life and Evolution of Biospheres},
  volume = {42},
  number = {5},
  pages = {469--474}
}
  • DOI BibTeX
    H. Gong, P. Zuliani, A. Komuravelli, J.R. Faeder, E.M. Clarke
    Computational Modeling and Verification of Signaling Pathways in Cancer
    in Algebraic and Numeric Biology, Lecture Notes in Computer Science 6479, p.117-135, 2012
    @INCOLLECTION{Gong2012,
  title = {Computational Modeling and Verification of Signaling Pathways in Cancer},
  author = {Gong, Haijun and Zuliani, Paolo and Komuravelli, Anvesh and Faeder, James R. and Clarke, Edmund M.},
  year = 2012,
  doi = {10.1007/978-3-642-28067-2_7},
  booktitle = {Algebraic and Numeric Biology},
  publisher = {Springer Berlin Heidelberg},
  volume = {6479},
  series = {Lecture Notes in Computer Science},
  pages = {117--135}
}
  • DOI BibTeX
    K. James, A. Wipat, J. Hallinan
    Is newer better?—evaluating the effects of data curation on integrated analyses in Saccharomyces cerevisiae
    in Integrative Biology, 4(7):715, 2012
    @ARTICLE{James2012,
  title = {Is newer better?—evaluating the effects of data curation on integrated analyses in Saccharomyces cerevisiae},
  author = {James, Katherine and Wipat, Anil and Hallinan, Jennifer},
  year = 2012,
  doi = {10.1039/c2ib00123c},
  journal = {Integrative Biology},
  volume = {4},
  number = {7},
  pages = {715}
}

2011

  • DOI
    M. Hucka, C. Laibe, N. Juty, W. Liebermeister, S. Keating, C. Lloyd, C. Knuepfer, G. Misirli, M. Schulz, D. Waltemath, M. Taschuk, N. Swainston, N. Le Novère, A. Lister, F. Bergmann, R. Henkel, F. Krause, S. Hoops
    SBML Level 3 Package Proposal: Annotation
    in Nature Precedings, available online since January 2011
  • DOI BibTeX
    G.W. Bassel, H. Lan, E. Glaab, D.J. Gibbs, T. Gerjets, N. Krasnogor, A.J. Bonner, M.J. Holdsworth, N.J. Provart
    Genome-wide network model capturing seed germination reveals coordinated regulation of plant cellular phase transitions
    in Proceedings of the National Academy of Sciences, 108(23):9709-9714, June 2011
    @ARTICLE{Bassel2011a,
  title = {Genome-wide network model capturing seed germination reveals coordinated regulation of plant cellular phase transitions},
  author = {Bassel, G. W. and Lan, H. and Glaab, E. and Gibbs, D. J. and Gerjets, T. and Krasnogor, N. and Bonner, A. J. and Holdsworth, M. J. and Provart, N. J.},
  year = 2011,
  doi = {10.1073/pnas.1100958108},
  month = jun,
  journal = {Proceedings of the National Academy of Sciences},
  volume = {108},
  number = {23},
  pages = {9709--9714}
}
  • DOI BibTeX
    H.O. Habashy, D.G. Powe, E. Glaab, G. Ball, I. Spiteri, N. Krasnogor, J.M. Garibaldi, E.A. Rakha, A.R. Green, C. Caldas, I.O. Ellis
    RERG (Ras-like, oestrogen-regulated, growth-inhibitor) expression in breast cancer: a marker of ER-positive luminal-like subtype
    in Breast Cancer Research and Treatment, 128(2):315-326, July 2011
    @ARTICLE{Habashy2011,
  title = {RERG (Ras-like, oestrogen-regulated, growth-inhibitor) expression in breast cancer: a marker of ER-positive luminal-like subtype},
  author = {Habashy, Hany Onsy and Powe, Desmond G. and Glaab, Enrico and Ball, Graham and Spiteri, Inmaculada and Krasnogor, Natalio and Garibaldi, Jonathan M. and Rakha, Emad A. and Green, Andrew R. and Caldas, C. and Ellis, Ian O.},
  year = 2011,
  doi = {10.1007/s10549-010-1073-y},
  month = jul,
  journal = {Breast Cancer Research and Treatment},
  volume = {128},
  number = {2},
  pages = {315--326}
}
  • DOI BibTeX
    F. Dupeux, J. Santiago, K. Betz, J. Twycross, S. Park, L. Rodriguez, M. Gonzalez-Guzman, M.R. Jensen, N. Krasnogor, M. Blackledge, M. Holdsworth, S.R. Cutler, P.L. Rodriguez, J.A. Márquez
    A thermodynamic switch modulates abscisic acid receptor sensitivity
    in The EMBO Journal, 30(20):4171-4184, October 2011
    @ARTICLE{Dupeux2011,
  title = {A thermodynamic switch modulates abscisic acid receptor sensitivity},
  author = {Dupeux, Florine and Santiago, Julia and Betz, Katja and Twycross, Jamie and Park, Sang-Youl and Rodriguez, Lesia and Gonzalez-Guzman, Miguel and Jensen, Malene Ringkjøbing and Krasnogor, Natalio and Blackledge, Martin and Holdsworth, Michael and Cutler, Sean R and Rodriguez, Pedro L and Márquez, José Antonio},
  year = 2011,
  doi = {10.1038/emboj.2011.294},
  month = oct,
  journal = {The EMBO Journal},
  volume = {30},
  number = {20},
  pages = {4171--4184}
}
  • DOI BibTeX
    H. Gong, P. Zuliani, Q. Wang, E.M. Clarke
    Formal analysis for logical models of pancreatic cancer
    in IEEE Conference on Decision and Control and European Control Conference, p.4855-4860, Orlando, FL, USA, December 2011
    @INPROCEEDINGS{Gong2011,
  title = {Formal analysis for logical models of pancreatic cancer},
  author = {Gong, Haijun and Zuliani, Paolo and Wang, Qinsi and Clarke, Edmund M.},
  year = 2011,
  doi = {10.1109/CDC.2011.6161052},
  month = dec,
  booktitle = {IEEE Conference on Decision and Control and European Control Conference},
  pages = {4855--4860},
  address = {Orlando, FL, USA}
}

2010

  • DOI BibTeX
    H. Cao, F.J. Romero-Campero, S. Heeb, M. Cámara, N. Krasnogor
    Evolving cell models for systems and synthetic biology
    in Systems and Synthetic Biology, 4(1):55-84, March 2010
    @ARTICLE{Cao2010,
  title = {Evolving cell models for systems and synthetic biology},
  author = {Cao, Hongqing and Romero-Campero, Francisco J. and Heeb, Stephan and Cámara, Miguel and Krasnogor, Natalio},
  year = 2010,
  doi = {10.1007/s11693-009-9050-7},
  month = mar,
  journal = {Systems and Synthetic Biology},
  volume = {4},
  number = {1},
  pages = {55--84}
}
  • DOI eprint BibTeX
    E. Glaab, A. Baudot, N. Krasnogor, A. Valencia
    TopoGSA: network topological gene set analysis
    in Bioinformatics, 26(9):1271-1272, May 2010
    @ARTICLE{Glaab2010a,
  title = {TopoGSA: network topological gene set analysis},
  author = {Glaab, E. and Baudot, A. and Krasnogor, N. and Valencia, A.},
  year = 2010,
  doi = {10.1093/bioinformatics/btq131},
  month = may,
  journal = {Bioinformatics},
  volume = {26},
  number = {9},
  pages = {1271--1272}
}
  • DOI BibTeX
    E. Glaab, A. Baudot, N. Krasnogor, A. Valencia
    Extending pathways and processes using molecular interaction networks to analyse cancer genome data
    in BMC Bioinformatics, 11(1):597, 2010
    @ARTICLE{Glaab2010,
  title = {Extending pathways and processes using molecular interaction networks to analyse cancer genome data},
  author = {Glaab, Enrico and Baudot, Anaïs and Krasnogor, Natalio and Valencia, Alfonso},
  year = 2010,
  doi = {10.1186/1471-2105-11-597},
  journal = {BMC Bioinformatics},
  volume = {11},
  number = {1},
  pages = {597}
}
  • DOI BibTeX
    H. Gong, P. Zuliani, A. Komuravelli, J.R. Faeder, E.M. Clarke
    Analysis and verification of the HMGB1 signaling pathway
    in BMC Bioinformatics, 11(Suppl 7):S10, 2010
    @ARTICLE{Gong2010,
  title = {Analysis and verification of the HMGB1 signaling pathway},
  author = {Gong, Haijun and Zuliani, Paolo and Komuravelli, Anvesh and Faeder, James R and Clarke, Edmund M},
  year = 2010,
  doi = {10.1186/1471-2105-11-S7-S10},
  journal = {BMC Bioinformatics},
  volume = {11},
  number = {Suppl 7},
  pages = {S10}
}
  • DOI BibTeX
    C. García-Martínez, C. Lima, J. Twycross, N. Krasnogor, M. Lozano
    P system model optimisation by means of evolutionary based search algorithms
    in Proceedings of the 12th annual conference on Genetic and evolutionary computation - GECCO '10, p.187, Portland, Oregon, USA, 2010
    @INPROCEEDINGS{Garcia-Martinez2010,
  title = {P system model optimisation by means of evolutionary based search algorithms},
  author = {García-Martínez, Carlos and Lima, Claudio and Twycross, Jamie and Krasnogor, Natalio and Lozano, Manuel},
  year = 2010,
  doi = {10.1145/1830483.1830517},
  booktitle = {Proceedings of the 12th annual conference on Genetic and evolutionary computation - GECCO '10},
  pages = {187},
  address = {Portland, Oregon, USA}
}
  • DOI BibTeX
    J. Twycross, L.R. Band, M.J. Bennett, J.R. King, N. Krasnogor
    Stochastic and deterministic multiscale models for systems biology: an auxin-transport case study
    in BMC Systems Biology, 4(1):34, 2010
    @ARTICLE{Twycross2010,
  title = {Stochastic and deterministic multiscale models for systems biology: an auxin-transport case study},
  author = {Twycross, Jamie and Band, Leah R and Bennett, Malcolm J and King, John R and Krasnogor, Natalio},
  year = 2010,
  doi = {10.1186/1752-0509-4-34},
  journal = {BMC Systems Biology},
  volume = {4},
  number = {1},
  pages = {34}
}

2009

  • DOI BibTeX
    F.J. Romero-Campero, J. Twycross, M. Cámara, M. Bennett, M. Gheorghe, N. Krasnogor
    Modular Assembly Of Cell Systems Biology Models Using P Systems
    in International Journal of Foundations of Computer Science, 20(03):427-442, June 2009
    @ARTICLE{Romero-Campero2009,
  title = {Modular Assembly Of Cell Systems Biology Models Using P Systems},
  author = {Romero-Campero, Francisco J. and Twycross, Jamie and Cámara, Miguel and Bennett, Malcolm and Gheorghe, Marian and Krasnogor, Natalio},
  year = 2009,
  doi = {10.1142/S0129054109006668},
  month = jun,
  journal = {International Journal of Foundations of Computer Science},
  volume = {20},
  number = {03},
  pages = {427--442}
}
  • DOI BibTeX
    F.J. Romero-Campero, J. Twycross, H. Cao, J. Blakes, N. Krasnogor
    A Multiscale Modeling Framework Based on P Systems
    in Membrane Computing, Lecture Notes in Computer Science 5391, p.63-77, 2009
    @INCOLLECTION{Romero-Campero2009a,
  title = {A Multiscale Modeling Framework Based on P Systems},
  author = {Romero-Campero, Francisco José and Twycross, Jamie and Cao, Hongqing and Blakes, Jonathan and Krasnogor, Natalio},
  year = 2009,
  doi = {10.1007/978-3-540-95885-7_5},
  booktitle = {Membrane Computing},
  publisher = {Springer Berlin Heidelberg},
  volume = {5391},
  series = {Lecture Notes in Computer Science},
  pages = {63--77}
}
  • DOI BibTeX
    S.K. Jha, E.M. Clarke, C.J. Langmead, A. Legay, A. Platzer, P. Zuliani
    A Bayesian Approach to Model Checking Biological Systems
    in Computational Methods in Systems Biology, Lecture Notes in Computer Science 5688, p.218-234, 2009
    @INCOLLECTION{Jha2009,
  title = {A Bayesian Approach to Model Checking Biological Systems},
  author = {Jha, Sumit K. and Clarke, Edmund M. and Langmead, Christopher J. and Legay, Axel and Platzer, André and Zuliani, Paolo},
  year = 2009,
  doi = {10.1007/978-3-642-03845-7_15},
  booktitle = {Computational Methods in Systems Biology},
  publisher = {Springer Berlin Heidelberg},
  volume = {5688},
  series = {Lecture Notes in Computer Science},
  pages = {218--234}
}
  • DOI BibTeX
    K. James, A. Wipat, J. Hallinan
    Integration of Full-Coverage Probabilistic Functional Networks with Relevance to Specific Biological Processes
    in Data Integration in the Life Sciences, Lecture Notes in Computer Science 5647, p.31-46, 2009
    @INCOLLECTION{James2009,
  title = {Integration of Full-Coverage Probabilistic Functional Networks with Relevance to Specific Biological Processes},
  author = {James, Katherine and Wipat, Anil and Hallinan, Jennifer},
  year = 2009,
  doi = {10.1007/978-3-642-02879-3_4},
  booktitle = {Data Integration in the Life Sciences},
  publisher = {Springer Berlin Heidelberg},
  volume = {5647},
  series = {Lecture Notes in Computer Science},
  pages = {31--46}
}
  • DOI BibTeX
    E. Glaab, J.M. Garibaldi, N. Krasnogor
    ArrayMining: a modular web-application for microarray analysis combining ensemble and consensus methods with cross-study normalization
    in BMC Bioinformatics, 10(1):358, 2009
    @ARTICLE{Glaab2009,
  title = {ArrayMining: a modular web-application for microarray analysis combining ensemble and consensus methods with cross-study normalization},
  author = {Glaab, Enrico and Garibaldi, Jonathan M and Krasnogor, Natalio},
  year = 2009,
  doi = {10.1186/1471-2105-10-358},
  journal = {BMC Bioinformatics},
  volume = {10},
  number = {1},
  pages = {358}
}

2008

  • DOI eprint BibTeX
    N. Krasnogor, A. Shah, D. Barthel, P. Lukasiak, J. Blazewicz
    Web and Grid Technologies in Bioinformatics, Computational and Systems Biology: A Review
    in Current Bioinformatics, 3(1):10-31, January 2008
    @ARTICLE{Krasnogor2008b,
  title = {Web and Grid Technologies in Bioinformatics, Computational and Systems Biology: A Review},
  author = {Krasnogor, Natalio and Shah, Azhar and Barthel, Daniel and Lukasiak, Piotr and Blazewicz, Jacek},
  year = 2008,
  doi = {10.2174/157489308783329850},
  month = jan,
  journal = {Current Bioinformatics},
  volume = {3},
  number = {1},
  pages = {10--31}
}
  • DOI eprint BibTeX
    F.J. Romero-Campero, H. Cao, M. Camara, N. Krasnogor
    Structure and parameter estimation for cell systems biology models
    in Proceedings of the 10th annual conference on Genetic and evolutionary computation - GECCO '08, p.331, Atlanta, GA, USA, 2008
    @INPROCEEDINGS{Romero-Campero2008,
  title = {Structure and parameter estimation for cell systems biology models},
  author = {Romero-Campero, Francisco J. and Cao, Hongqing and Camara, Miguel and Krasnogor, Natalio},
  year = 2008,
  doi = {10.1145/1389095.1389153},
  booktitle = {Proceedings of the 10th annual conference on Genetic and evolutionary computation - GECCO '08},
  pages = {331},
  address = {Atlanta, GA, USA}
}
  • DOI BibTeX
    J. Smaldon, J. Blakes, N. Krasnogor, D. Lancet
    A multi-scaled approach to artificial life simulation with P systems and dissipative particle dynamics
    in Proceedings of the 10th annual conference on Genetic and evolutionary computation - GECCO '08, p.249, Atlanta, GA, USA, 2008
    @INPROCEEDINGS{Smaldon2008,
  title = {A multi-scaled approach to artificial life simulation with P systems and dissipative particle dynamics},
  author = {Smaldon, James and Blakes, Jonathan and Krasnogor, Natalio and Lancet, Doron},
  year = 2008,
  doi = {10.1145/1389095.1389134},
  booktitle = {Proceedings of the 10th annual conference on Genetic and evolutionary computation - GECCO '08},
  pages = {249},
  address = {Atlanta, GA, USA}
}

2007

  • DOI eprint BibTeX
    F. Bernardini, M. Gheorghe, N. Krasnogor
    Quorum sensing P systems
    in Theoretical Computer Science, 371(1-2):20-33, February 2007
    @ARTICLE{Bernardini2007,
  title = {Quorum sensing P systems},
  author = {Bernardini, Francesco and Gheorghe, Marian and Krasnogor, Natalio},
  year = 2007,
  doi = {10.1016/j.tcs.2006.10.012},
  month = feb,
  journal = {Theoretical Computer Science},
  volume = {371},
  number = {1-2},
  pages = {20--33}
}

2006

  • DOI BibTeX
    F. Bernardini, M. Gheorghe, N. Krasnogor, R.C. Muniyandi, M.J. Pérez-Jímenez, F.J. Romero-Campero
    On P Systems as a Modelling Tool for Biological Systems
    in Membrane Computing, Lecture Notes in Computer Science 3850, p.114-133, 2006
    @INCOLLECTION{Bernardini2006,
  title = {On P Systems as a Modelling Tool for Biological Systems},
  author = {Bernardini, Francesco and Gheorghe, Marian and Krasnogor, Natalio and Muniyandi, Ravie C. and Pérez-Jímenez, Mario J. and Romero-Campero, Francisco José},
  year = 2006,
  doi = {10.1007/11603047_8},
  booktitle = {Membrane Computing},
  publisher = {Springer Berlin Heidelberg},
  volume = {3850},
  series = {Lecture Notes in Computer Science},
  pages = {114--133}
}
  • DOI BibTeX
    L. Bianco, D. Pescini, P. Siepmann, N. Krasnogor, F.J. Romero-Campero, M. Gheorghe
    Towards a P Systems Pseudomonas Quorum Sensing Model
    in Membrane Computing, Lecture Notes in Computer Science 4361, p.197-214, 2006
    @INCOLLECTION{Bianco2006,
  title = {Towards a P Systems Pseudomonas Quorum Sensing Model},
  author = {Bianco, Luca and Pescini, Dario and Siepmann, Peter and Krasnogor, Natalio and Romero-Campero, Francisco J. and Gheorghe, Marian},
  year = 2006,
  doi = {10.1007/11963516_13},
  booktitle = {Membrane Computing},
  publisher = {Springer Berlin Heidelberg},
  volume = {4361},
  series = {Lecture Notes in Computer Science},
  pages = {197--214}
}

2005

  • DOI eprint BibTeX
    G. Terrazas, N. Krasnogor, M. Gheorghe, F. Bernardini, S. Diggle, M. Cámara
    An Environment Aware P-System Model of Quorum Sensing
    in New Computational Paradigms, Lecture Notes in Computer Science 3526, p.479-485, 2005
    @INCOLLECTION{Terrazas2005,
  title = {An Environment Aware P-System Model of Quorum Sensing},
  author = {Terrazas, German and Krasnogor, Natalio and Gheorghe, Marian and Bernardini, Francesco and Diggle, Steve and Cámara, Miguel},
  year = 2005,
  doi = {10.1007/11494645_59},
  booktitle = {New Computational Paradigms},
  publisher = {Springer Berlin Heidelberg},
  volume = {3526},
  series = {Lecture Notes in Computer Science},
  pages = {479--485}
}