Background

I am a Professor of Computing Science and Synthetic Biology at the School of Computing Science and a Royal Academy of Engineering Chair in Emerging Technologies

I am Director of Newcastle's Interdisciplinary Computing and Complex BioSystems (ICOS) Research Group and of the Centre for Synthetic Biology and the Bioeconomy. I am associated with the Centre for Bacterial Cell Biology.

My research activities lie at the interface of Computing Science and the Natural Sciences, e.g. Biology, Chemistry and  Physics. I apply my expertise on Machine Intelligence (e.g. optimisation, data mining, big data, evolutionary learning), Complex Systems and Unconventional Computing (e.g. biocomputing) to Bioinformatics, Systems and Synthetic Biology.

For details on my publications and externally funded research projects please visit my personal webpages.

Google Scholar Profile

Research

I am a Professor of Computing Science and Synthetic Biology at the School of Computing Science.

I am director of Newcastle's Interdisciplinary Computing and Complex BioSystems (ICOS) Research Group and of the Centre for Synthetic Biology and the Bioeconomy.    I am associated  with the Centre for Bacterial Cell Biology.

My research activities lie at the interface of Computing Science and the Natural Sciences, e.g. Biology, Chemistry and  Physics. I apply my expertise on Machine Intelligence (e.g. optimisation, data mining, big data, evolutionary learning), Complex Systems and Unconventional Computing (e.g. biocomputing) to Bioinformatics, Systems and Synthetic Biology.

I am currently PI on an EPSRC programme grant Portabolomics, I hold a Royal Academy of Engineering Chair in Emerging Technologies in the project EnDROIDS and also PI on an H2020 project called DESTINATION and an Innovate UK KTP project on nucleic acids nanotechnology for drug delivery systems.

My Google Scholar Profile

Publications

• Lopiccolo A, Shirt-Ediss B, Torelli E, Olulana AFA, Castronovo M, Fellermann H, Krasnogor N. A last-in first-out stack data structure implemented in DNA. Nature Communications 2021, 12(1), 4861.
• Callaghan MM, Koch B, Hackett KT, Klimowicz AK, Schaub RE, Krasnogor N, Dillard JP. Expression, Localization, and Protein Interactions of the Partitioning Proteins in the Gonococcal Type IV Secretion System. Frontiers in Microbiology 2021, 12, 784483.
• de Lorenzo V, Krasnogor N, Schmidt M. For the sake of the Bioeconomy: define what a Synthetic Biology Chassis is!. New Biotechnology 2021, 60, 44-51.
• Velazquez E, Al-Ramahi Y, Tellechea-Luzardo J, Krasnogor N, De Lorenzo V. Targetron-Assisted Delivery of Exogenous DNA Sequences into Pseudomonas putida through CRISPR-Aided Counterselection. ACS Synthetic Biology 2021, 10(10), 2552-2565.
• Konur S, Mierla L, Fellermann H, Ladroue C, Brown B, Wipat A, Twycross J, Dun BP, Kalvala S, Gheorghe M, Krasnogor N. Toward Full-Stack In Silico Synthetic Biology: Integrating Model Specification, Simulation, Verification, and Biological Compilation. ACS Synthetic Biology 2021, 10(8), 1931-1945.
• Choo SW, Mohammed WK, Mutha NVR, Rostami N, Ahmed H, Krasnogor N, Tan GYA, Jakubovics NS. Transcriptomic Responses to Coaggregation between Streptococcus gordonii and Streptococcus oralis. Applied and Environmental Microbiology 2021, 87(22), e01558-21.
• Jiang S, Kaiser M, Yang S, Kollias S, Krasnogor N. A Scalable Test Suite for Continuous Dynamic Multiobjective Optimization. IEEE Transactions on Cybernetics 2020, 50(6), 2814-2826.
• Jiang S, Li H, Guo J, Zhong M, Yang S, Kaiser M, Krasnogor N. AREA: An adaptive reference-set based evolutionary algorithm for multiobjective optimisation. Information Sciences 2020, 515, 365-387.
• Franco MA, Krasnogor N, Bacardit J. Automatic Tuning of Rule-Based Evolutionary Machine Learning via Problem Structure Identification. IEEE Computational Intelligence Magazine 2020, 15(3), 28-46.
• Torelli E, Kozyra JW, Shirt-Ediss B, Piantanida L, Voïtchovsky K, Krasnogor N. Co-transcriptional folding of a bio-orthogonal fluorescent scaffolded RNA origami. ACS Synthetic Biology 2020, 9(7), 1682-1692.
• Zerti D, Dorgau B, Felemban M, Ghareeb AE, Yu M, Ding Y, Kranogor N, LAko M. Developing a simple method to enhance the generation of cone and rod photoreceptors in pluripotent stem cell‐derived retinal organoids . Stem Cells 2020, 38(1), 45-51.
• White MG, Maheshwari RR, Anderson SJ, Berlinguer-Palmini R, Jones C, Richardson SJ, Rotti PG, Armour SL, Ding Y, Krasnogor N, Engelhardt JF, Gray MA, Morgan NG, Shaw JAM. In situ analysis reveals that CFTR is expressed in only a small minority of β-cells in normal adult human pancreas. Journal of Clinical Endocrinology and Metabolism 2020, 105(5), 1366-1374.
• Tellechea-Luzardo J, Winterhalter C, Widera P, Kozyra J, de Lorenzo V, Krasnogor N. Linking Engineered Cells to Their Digital Twins: A Version Control System for Strain Engineering. ACS synthetic biology 2020, 9(3), 536-545.
• Jiang S, Wang Y, Kaiser M, Krasnogor N. NIHBA: a network interdiction approach for metabolic engineering design. Bioinformatics 2020, 36(11), 3482-3492.
• Koch B, Callaghan MM, Tellechea-Luzardo J, Seeger AY, Dillard JP, Krasnogor N. Protein interactions within and between two F-type type IV secretion systems. Molecular Microbiology 2020, 114(5), 823-838.
• Armour SL, Anderson SJ, Richardson SJ, Ding Y, Carey C, Lyon J, Maheshwari RR, Al-Jahdami N, Krasnogor N, Morgan NG, MacDonald P, Shaw JAM, White MG. Reduced expression of the co-regulator TLE1 in type 2 diabetes is associated with increased islet α-cell number. Endocrinology 2020, 161(4), bqaa011.
• Shirt-Ediss B, Elezgaray J, Connolly J, Torelli E, Krasnogor N. REVNANO: An Algorithm to Reverse Engineer Scaffolded DNA/RNA Origami Designs from Sequence Information Only. In: 26th International Conference on DNA Computing and Molecular Programming. 2020, Online: IOP.
• Torelli E, Kozyra JW, Shirt-Ediss B, Piantanida L, Voïtchovsky K, Krasnogor N. Towards in vivo origami: bio-orthogonal scaffolded RNA nanoribbons self-assembled via co-transcriptional folding. In: The 1st International Biodesign Research Conference. 2020.
• Torelli E, Kozyra JW, Shirt-Ediss B, Piantanida L, Voïtchovsky K, Krasnogor N. Towards in vivo origami: co-transcriptional folding of a bio-orthogonal scaffolded RNA nanoribbon. In: Functional DNA Nanotechnology, FDN 2020. 2020, Rome, Italy.
• Dorgau B, Felemban M, Hilgen G, Kienning N, Zert D, Hunt N, Doherty M, Whifield P, Hallam D, White K, Ding Y, Krasnogor N, Alaama J, Asfour HZ, Sernagor E, Lako M. Decellularised extracellular matrix-derived peptides from neural retina and retinal pigment epithelium enhance the expression of synaptic markers and light responsiveness of human pluripotent stem cell derived retinal organoids. Biomaterials 2019, 199, 63-75.
• Naylor J, Fellermann H, Krasnogor N. Easybiotics: a GUI for 3D physical modelling of multi-species bacterial populations. Bioinformatics 2019, 35(19), 3859-3860.
• Swan DJ, Aschenbrenner D, Lamb CA, Chakraborty K, Clark J, Pandey S, Engelhardt KR, Chen R, Cavounidis A, Ding Y, Krasnogor N, Carey CD, Acres M, Needham S, Cant AJ, Arkwright PD, Chandra A, Okkenhaug K, Uhlig HH, Hambleton S. Immunodeficiency, autoimmune thrombocytopenia and enterocolitis caused by autosomal recessive deficiency of PIK3CD-encoded phosphoinositide 3-kinase δ. Haematologica 2019, 104(10), e483-e486.
• Torelli E, Kozyra JW, Gu JY, Stimming U, Piantanida L, Voïtchovsky K, Krasnogor N. Switchable 2D/3D DNA origami nanodevices and light-up bio-orthogonal RNA nanoribbon. In: Nantech 2019. 2019, Helsinki, Finland.
• Mutha NVR, Mohammed WK, Krasnogor NK, Tan GYA, Wee WY, Li Y, Choo SW, Jakubovics NS. Transcriptional profiling of coaggregation interactions between Streptococcus gordonii and Veillonella parvula by Dual RNA-Seq. Scientific Reports 2019, 9, 7664.
• Torelli E, Kozyra JW, Gu JY, Stimming U, Piantanida L, Voïtchovsky K, Krasnogor N. Walk on the Origami Side: From Switchable DNA Nanodevices to Light-up Bio-orthogonal RNA Nanoribbon. In: 2019 RNA Nanotechnologies, New Frontiers in RNA Nanotechnology-Based Therapeutics and Diagnostics, Gordon Research Seminar and Conference. 2019, Ventura, CA, US: Gordon Research Conferences.
• Mohammed WK, Krasnogor N, Jakubovics NS. Streptococcus gordonii Challisin protease is required for sensing cell-cell contact with Actinomyces oris. FEMS Microbiology Ecology 2018, 94(5), fiy043.
• Jiang S, Kaiser M, Wan S, Guo J, Yang S, Krasnogor N. An Empirical Study of Dynamic Triobjective Optimisation Problems. In: 2018 IEEE Congress on Evolutionary Computation, CEC 2018 - Proceedings. 2018, Rio de Janeiro, Brazil: IEEE.
• Bakir ME, Konur S, Gheorghe M, Krasnogor N, Stannett M. Automatic Selection of Verification Tools for Efficient Analysis of Biochemical Models. Bioinformatics 2018, 34(18), 3187-3195.
• Buskin A, Zhu L, Chichagova V, Basu B, Mozaffari-Jovin S, Dolan D, Droop A, Collin J, Bronstein V, Mehrotra S, Farkas M, Hilgen G, White K, Pan KT, Treumann A, Hallam D, Bialas K, Chung G, Mellough C, Ding Y, Krasnogor N, Pryzborski S, Zwolinski S, Alharthi S, Al-Aama J, Xu Y, Wheway G, Szymanska K, McKibbin M, Inglehearn CF, Elliott DJ, Lindsay S, Ali R, Steel DH, Armstrong L, Sernagor E, Urlaub H, Pierce E, Luehrmann R, Grellscheid SN, Johnson CA, Lako M. Disrupted alternative splicing for genes implicated in splicing and ciliogenesis causes PRPF31 retinitis pigmentosa. Nature Communications 2018, 9, 4234.
• Buskin A, Zhu L, Chichagova V, Basu B, Mozaffari-Jovin S, Dolan D, Droop A, Collin J, Bronstein R, Mehrotra S, Farkas M, Hilgen G, White K, Pan K-T, Treumann A, Hallam D, Bialas K, Chung G, Mellough C, Ding Y, Krasnogor N, Przyborski S, Zwolinski S, Al-Aama J, Alharthi S, Xu Y, Wheway G, Szymanska K, McKibbin M, Inglehearn CF, Elliott DJ, Lindsay S, Ali RR, Steel DH, Armstrong L, Sernagor E, Urlaub H, Pierce E, Luhrmann R, Grellscheid S-N, Johnson CA, Lako M. Disrupted alternative splicing for genes implicated in splicing and ciliogenesis causes PRPF31 retinitis pigmentosa. Nature Communications 2018, 9, 4234.
• Felemban M, Dorgau B, Hunt NC, Hallam D, Zerti D, Bauer R, Ding Y, Collin J, Steel DH, Krasnogor N, Al-Aama J, Lindsay S, Mellough C, Lako M. Extracellular matrix components expression in human pluripotent stem cell-derived retinal organoids recapitulates retinogenesis in vivo and reveals an important role for IMPG1 and CD44 in the development of photoreceptors and interphotoreceptor matrix. Acta Biomaterialia 2018, 74, 207-221.
• Torelli E, Kozyra JW, Gu J-Y, Stimming U, Piantanida L, Voitchovsky K, Krasnogor N. Isothermal folding of a light-up bio-orthogonal RNA origami nanoribbon. Scientific Reports 2018, 8, 6989.
• Torelli E, Kozyra JW, Gu JY, Stimming U, Piantanida L, Voïtchovsky K, Krasnogor N. Isothermal folding of a light-up bio-orthogonal RNA origami nanoribbon. In: 3rd Functional DNA Nanotechnology Workshop. 2018, Rome, Italy.
• Jiang S, Kaiser M, Guo J, Yang S, Krasnogor N. Less detectable environmental changes in dynamic multiobjective optimisation. In: GECCO 2018 - Proceedings of the 2018 Genetic and Evolutionary Computation Conference. 2018, Kyoto, Japan: Association for Computing Machinery, Inc.
• Hordijk W, Naylor J, Krasnogor N, Fellermann H. Population Dynamics of Autocatalytic Sets in a Compartmentalized Spatial World. Life 2018, 8(3), 33.
• Markovitch O, Krasnogor N. Predicting species emergence in simulated complex pre-biotic networks. PLoS ONE 2018, 13(2), e0192871.
• Torres M, Jiang S, Pelta D, Kaiser M, Krasnogor N. Strain design as multiobjective network interdiction problem: A preliminary approach. In: 18th Conference of the Spanish Association for Artificial Intelligence. 2018, Granada, Spain: Springer Verlag.
• Shirt-Ediss B, Krasnogor N, Fellermann H. The fittest, the common, and the dullest: Selection dynamics of exact autocatalytic replicators. In: The 2018 Conference on Artificial Life. 2018, Tokyo, Japan: MIT Press.
• Mutha NVR, Mohammed WK, Krasnogor N, Tan GYA, Choo SW, Jakubovics NS. Transcriptional Responses of Streptococcus gordonii and Fusobacterium nucleatum to Coaggregation. Molecular Oral Microbiology 2018, 33(6), 450-464.
• Konur S, Fellermann H, Mierla LM, Sanassy D, Ladroue C, Kalvala S, Gheorghe M, Krasnogor N. An integrated in silico simulation and biomatter compilation approach to cellular computation. In: Adamatzky A, ed. Advances in Unconventional Computing. Cham: Springer, 2017, pp.655-676.
• Goni-Moreno A, Wipat A, Krasnogor N. CSBB: Synthetic biology research at Newcastle University. Biochemical Society Transactions 2017, 45(3), 781-783.
• Kozyra J, Ceccarelli A, Torelli E, Lopiccolo A, Gu JY, Fellermann H, Stimming U, Krasnogor N. Designing uniquely addressable Bio-orthogonal Synthetic Scaffolds for DNA and RNA Origami. ACS Synthetic Biology 2017, 6(7), 1140-1149.
• Torelli E, Krasnogor N. DNA origami as device at the nanoscale. In: Bio-X Conference. 2017, Netanya, Israel.
• Kozyra J, Fellermann H, Shirt-Ediss B, Lopiccolo A, Krasnogor N. Optimizing nucleic acid sequences for a molecular data recorder. In: GECCO'17 Genetic and Evolutionary Computation Conference. 2017, Berlin, Germany: ACM.
• Naylor J, Fellermann H, Ding Y, Mohammed W, Jakubovics N, Mukherjee J, Biggs C, Wright P, Krasnogor N. Simbiotics: A Multiscale Integrative Platform for 3D Modeling of Bacterial Populations. ACS Synthetic Biology 2017, 6(7), 1194-1210.
• Kozyra J, Ceccarelli A, Torelli E, Lopiccolo A, Fellermann H, Shirt-Ediss B, Krasnogor N. Toward in vivo nanostructures: hybrid origami scaffolds on De Bruijn sequence. In: BioOrigami Workshop. 2017, Ljubljana, Slovenia.
• Fellermann H, Lopiccolo A, Kozyra J, Krasnogor N. In vitro implementation of a stack data structure based on DNA strand displacement. In: Unconventional Computation and Natural Computation: 15th International Conference, UCNC 2016. 2016, Manchester, UK: Springer.
• Lazzarini N, Widera P, Williamson S, Heer R, Krasnogor N, Bacardit J. Functional networks inference from machine learning models. BioData Mining 2016, 9, 28.
• Ben Yehezkel T, Rival A, Raz O, Cohen R, Marx Z, Camara M, Dubern JF, Koch B, Heeb S, Krasnogor N, Delattre C, Shapiro E. Synthesis and cell-free cloning of DNA libraries using programmable microfluidics. Nucleic Acids Research 2016, 44(4), e35-e35.
• Coello CAC, Franco G, Krasnogor N, Pavone M. Algorithms and models for complex natural systems. Natural Computing 2015, 14(3), 339-340.
• Lui LT, Terrazas G, Zenil H, Alexander C, Krasnogor N. Complexity Measurement Based on Information Theory and Kolmogorov Complexity. Artificial Life 2015, 21(2), 205-224.
• Sanassy D, Widera P, Krasnogor N. Meta-Stochastic Simulation of Biochemical Models for Systems and Synthetic Biology. ACS Synthetic Biology 2015, 4(1), 39-47.
• Konur S, Gheorghe M, Dragomir C, Mierla L, Ipate F, Krasnogor N. Qualitative and Quantitative Analysis of Systems and Synthetic Biology Constructs using P Systems. ACS Synthetic Biology 2015, 4(1), 83-92.
• Contreras I, Arnaldo I, Krasnogor N, Hidalgo JI. Blind optimisation problem instance classification via enhanced universal similarity metric. Memetic Computing 2014, 6(4), 263-276.
• Fellermann H, Krasnogor N. Chemical Production and Molecular Computing in Addressable Reaction Compartments. Lecture Notes in Computer Science 2014, 8493, 173-182.
• Konur S, Gheorghe M, Dragomir C, Ipate F, Krasnogor N. Conventional Verification for Unconventional Computing: a Genetic XOR Gate Example. Fundamenta Informaticae 2014, 134(1-2), 97-110.
• Krasnogor N. Executable biology for rapid model prototyping in synthetic biology: implications for regenerative medicine and tissue engineering. In: Tissue Engineering & Regenerative Medicine International Society, European Chapter Meeting. 2014, Genova, Italy: Wiley-Blackwell Publishing Ltd.
• Fellermann H, Hadorn M, Fuchslin RM, Krasnogor N. Formalizing Modularization and Data Hiding in Synthetic Biology. ACM Journal on Emerging Technologies in Computing Systems (JETC) 2014, 11(3), 24.
• Bacardit J, Widera P, Lazzarini N, Krasnogor N. Hard Data Analytics Problems Make for Better Data Analysis Algorithms: Bioinformatics as an Example. Big Data 2014, 2(3), 164-176.
• Blakes J, Raz O, Feige U, Bacardit J, Widera P, Ben-Yehezkel T, Shapiro E, Krasnogor N. Heuristic for Maximizing DNA Reuse in Synthetic DNA Library Assembly. ACS Synthetic Biology 2014, 3(8), 529-542.
• Winterhalter C, Widera P, Krasnogor N. JEPETTO: a Cytoscape plugin for gene set enrichment and topological analysis based on interaction networks. Bioinformatics 2014, 30(7), 1029-1030.
• Konur S, Ladroue C, Fellermann H, Sanassy D, Mierla LM, Ipate F, Kalvala S, Gheorghe M, Krasnogor N. Modeling and Analysis of Genetic Boolean Gates using Infobiotics Workbench. In: Workshop on Verification of Engineered Molecular Devices and Programs 2014. 2014, Vienna, Austria.
• Sanassy D, Fellermann H, Krasnogor N, Konur S, Mierla LM, Gheorghe M, Ladroue C, Kalvala S. Modelling and stochastic simulation of synthetic biological Boolean gates. In: 2014 IEEE International Conference on High Performance Computing and Communications. 2014, Paris: IEEE.
• Chaplin JC, Krasnogor N, Russell NA. Photochromic molecular implementations of universal computation. Biosystems 2014, 126, 12-26.
• Lui LT, Xue X, Sui C, Brown A, Pritchard DI, Halliday N, Winzer K, Howdle SM, Fernandez-Trillo F, Krasnogor N, Alexander C. Bacteria clustering by polymers induces the expression of quorum-sensing-controlled phenotypes. Nature Chemistry 2013, 5(12), 1058-1065.
• Terrazas G, Zenil H, Krasnogor N. Exploring programmable self-assembly in non-DNA based molecular computing. Natural Computing 2013, 12(4), 499-515.
• Franco MA, Krasnogor N, Bacardit J. GAssist vs. BioHEL: critical assessment of two paradigms of genetics-based machine learning. Soft Computing 2013, 17(6), 953-981.
• Franco MA, Krasnogor N, Bacardit J. Analysing BioHEL using challenging boolean functions. Evolutionary Intelligence 2012, 5(2), 87-102.
• Bacardit J, Widera P, Márquez-Chamorro A, Divina F, Aguilar-Ruiz JS, Krasnogor N. Contact map prediction using a large-scale ensemble of rule sets and the fusion of multiple predicted structural features. Bioinformatics 2012, 28(19), 2441-2448.
• Markovitch O, Sorek D, Lui L, Lancet D, Krasnogor N. Is there an optimal level of open-endedness in prebiotic evolution?. Origins of Life and Evolution of Biospheres 2012, 42, 469.
• Franco MA, Krasnogor N, Bacardit J. Post-processing operators for decision lists. In: Fourteenth International Conference on Genetic and Evolutionary Computation - GECCO '12. 2012.
• Glaab E, Bacardit J, Garibaldi JM, Krasnogor N. Using Rule-Based Machine Learning for Candidate Disease Gene Prioritization;Sample Classification of Cancer Gene Expression Data. PLoS ONE 2012, 7(7), e39932.
• Woolley RAJ, Stirling J, Radocea A, Krasnogor N, Moriarty P. Automated probe microscopy via evolutionary optimization at the atomic scale. Applied Physics Letters 2011, 98, 253104.
• Bassel GW, Lan H, Glaab E, Gibbs DJ, Gerjets T, Krasnogor N, Bonner AJ, Holdsworth MJ, Provart NJ. Genome-wide network model capturing seed germination reveals coordinated regulation of plant cellular phase transitions. Proceedings of the National Academy of Sciences 2011, 108(23), 9709-9714.
• Franco MA, Krasnogor N, Bacardit J. Modelling the initialisation stage of the ALKR representation for discrete domains and GABIL encoding. In: 13th Annual Conference on Genetic and Evolutionary Computation - GECCO '11. 2011.
• Smith RE, Jiang MK, Bacardit J, Stout M, Krasnogor N, Hirst JD. A learning classifier system with mutual-information-based fitness. Evolutionary Intelligence 2010, 3(1), 31-50.
• Cao H, Romero-Campero FJ, Heeb S, Cámara M, Krasnogor N. Evolving cell models for systems and synthetic biology. Systems and Synthetic Biology 2010, 4(1), 55-84.
• Franco MA, Krasnogor N, Bacardit J. Speeding up the evaluation of evolutionary learning systems using GPGPUs. In: 12th Annual Conference on Genetic and Evolutionary Computation. 2010.
• Bacardit J, Krasnogor N. A mixed discrete-continuous attribute list representation for large scale classification domains. In: 11th Annual Conference on Genetic and Evolutionary Computation - GECCO '09. 2009.
• Bacardit J, Stout M, Hirst JD, Valencia A, Smith RE, Krasnogor N. Automated Alphabet Reduction for Protein Datasets. BMC Bioinformatics 2009, 10, 6.
• Bacardit J, Burke EK, Krasnogor N. Improving the scalability of rule-based evolutionary learning. Memetic Computing 2009, 1(1), 55-67.