Publications

Journal Publications

• L.T. Lui, X. Xue, C. Sui, A. Brown, D.I. Pritchard, N. Halliday, K. Winzer, S.M. Howdle, F. Fernandez-Trillo, N. Krasnogor, C. Alexander, Bacteria clustering by polymers induces the expression of quorum-sensing-controlled phenotypes in Nature Chemistry, 5(12):1058-1065, 2013

• J. C. Kort, D. Esser, T. K. Pham, J. Noirel, P. C. Wrigh, & B. Siebers, Cool tool for hot and sour archaea: proteomics of Sulfolobus solfataricus, Proteomics 3(18-19), 2831-50, 2013

• J. Reimann, D. Esser, A. Orell, F. Amman, T. K. Pham, J. Noirel, A. C. Lindås, R. Bernander, P. C.Wright, B. Siebers, & S. V. Albers, Archaeal signal transduction: impact of protein phosphatase deletions on cell size, motility and energy metabolism in Sulfolobus acidocaldarius, Mol. Cell. Proteomics, 12(12), 3908-23, 2013.

• 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. ACS Synthetic Biology, 2014.

• S. Konur, A Property-Driven Methodology for Formal Analysis of Synthetic Biology Systems. IEEE/ACM Transactions on Biology and Bioinformatics, 2014.

• S. Konur, M. Gheorghe, C. Dragomir, F. Ipate, N. Krasnogor. Conventional Verification for Unconventional Computing: A Genetic XOR Gate Example. Fundamenta Informaticae, vol. 134, pp. 97-110, 2014.

• S. Konur. Towards light-weight probabilistic model checking. Special issue on Intelligent Modeling and Verification, Journal of Applied Mathematics, 15 pages, 2014.

• D. Sanassy, P. Widera & N. Krasnogor. Meta-stochastic Simulation of Biochemical Models for Systems & Synthetic Biology, ACS Synthetic Biology, 2014.

• H. Fellermann, M. Hadorn, R. Füchslin & N. Krasnogor, Formalising Modularisation and Data Hiding for Synthetic Biology, ACM J. Emerg. Tech. Comp. Sys (in press)

• S. Konur, M. Gheorghe, H. Fellermann, D. Sanassy, N. Krasnogor, C. Ladroue, S. Kalvala, L. M. Mierla & Florentin Ipate, In Silico Design and Analysis of Genetic Boolean Gates: Membrane Computing Approach, J. Theor. Comp. Sci. (submitted)

• M. Raut, N. Couto, T. K. Pham, C. Evans, J. Noirel, & P. C. Wright, Influence of lignin on the Clostridium acetobutylicum ATCC 824 proteome: a quantitative proteomics analysis, J. Proteome Res., (submitted)

Book Chapters

• J. Blakes, Jamie Twycross, S. Konur, F. J. Romero-Campero, N. Krasnogor, M. Gheorghe. Infobiotics Workbench: A P systems based tool for systems and synthetic biology. Applications of Membrane Computing in Systems and Synthetic Biology, Springer, 7, pp. 1-41, 2014.

Conference Proceedings

• C. Dragomir, F. Ipate, S. Konur, R. Lefticaru, L. Mierla. Model Checking Kernel P Systems. Proceedings of 14th International Conference on Membrane Computing, LNCS, vol. 8340, pp. 151-172, Chisinau, Moldova, August 2013.

• H. Fellermann & N. Krasnogor, Chemical Synthesis and Molecular Computing in Programmable Bioreactors, Lect. Notes Comp. Sci. 8493:173-182, 2014

• D. Sanassy, H. Fellermann, S. Konur, C. Ladroue, L. Mierla, S. Kalvala, M. Gheorghe, N. Krasnogor. Modelling and stochastic simulation of synthetic biological Boolean gates. Proceedings of 16th IEEE International Conference on High Performance Computing and Communications, pp. 404-408, Paris, France, 2014.
• I. Niculescu, F. Ipate, M. Bakir, S. Konur, M. Gheorghe. High Performance Simulations of Kernel P Systems. Proceedings of 16th IEEE International Conference on High Performance Computing and Communications, pp. 409-412, Paris, France, 2014.
• S. Konur, C. Ladroue, Harold Fellermann, D. Sanassy, L. Mierla, F. Ipate, S. Kalvala, M. Gheorghe and N. Krasnogor. Modeling and Analysis of Genetic Boolean Gates using Infobiotics Workbench. Proceedings of Workshop on Verification of Engineered Molecular Devices and Programs 2014 (CAV 2014), pp. 26-37, Vienna, Austria, 2014.
• M. Bakir, I. Niculescu, L. Mierla, S. Konur, F. Ipate. Modeling and Analysis of Biological Systems using Kernel P Systems. Proceedings of 15th International Conference on Membrane Computing, pp. 135-151, Prague, Czech Republic, 2014.
• L. Miearla, F. Ipate, M. Bakir, S. Konur, M. Gheorghe. An Integrated Model Checking Toolset for Kernel P Systems. 30th ACM Symposium on Applied Computing. (submitted)

Oral Presentations

• H. Fellermann, DNA Addressable Reaction Compartments for Bottom-Up Synthetic Biology, Researchers Links, British Council Workshop, Cali, Colombia, March 2014.
• M. Camara, Bacterial signalling and pharmaceutical biotechnology, Researchers Links, British Council Workshop, Cali, Colombia, March 2014.
• M. Camara, Impact of Quorum Sensing in different industrial sectors, ERASMUS SUMMER INTENSIVE COURSE ‘Towards a Scientific Career: an Introductory Course for Research in Biomedicine and Biotechnology - BIOMED-TECH’ Granada, Spain, 2nd – 14th June, 2014

• H. Fellermann, Molecular Computing & Chemical Production in Addressable Nanobioreactors, Computability in Europe, Budapest, Hungary, June 23 - 27, 2014

• L. Nicholas, Speculative Cultures: Writing Future Ethnographies for Synthetic Biologists, European Association of Social Anthropologists Biennial 2014, Tallinn, Estonia, July 31st- August 3, 2014

Poster Presentations

• C. Ladroue, S. Kalvala, ATGC: Assistant To Genetic Compilation, SB6.0, London, UK. July 2013

• S. Higgins, S. Heeb, P. Williams, N. Krasnogor, M. Camara. Computational modelling and new molecular tools unravel the connection between quorum sensing and phenazine production in Pseudomonas aeruginosa, ESF BACNET, Poland 2013.

• H. Fellermann, D. Sanassy, N. Krasnogor, S. Konur, L. Mierla, M. Gheorghe, C. Ladroue, S. Kalvala, Integrating design, verification, and compilation of synthetic biological circuits, 10th International Symposium on Integrative Bioinformatics, Newcastle upon Tyne, UK, 2014

• D. Sanassy, J. Twycross, P. Widera, J. Blakes & N. Krasnogor. Principled Selection of Stochastic Simulation Algorithms for Systems and Synthetic Biology. 10th International Symposium on Integrative Bioinformatics, Newcastle upon Tyne, UK, 2014.

• T. K. Pham, M. Serys-Kubertavicius, J. Mukherjee, C. A. Biggs, F. Dafhnis-Calas, S. Heeb, M. Camara, N. Krasnogor, P. C. Wright, Improvements of salicylic acid detection in engineered Escherichia coli cells using HPLC and GC-MS techniques, 62nd ASMS conference, Baltimore, USA, 14-19 June 2014
• W. Qiu, T. K. Pham, P. C. Wright, -Omics study of Sulfolobus solfataricus species under different carbon sources, 62nd ASMS conference, Baltimore, USA, 14-19 June 2014
• L.Foster, C. Ladroue, S. Kalvala, Predicting Promoter Activity from Sequence Analysis, SB6.0, London, UK. July 2013