People

Dr Giovanni Stracquadanio

Lecturer
School of Computer Science and Electronic Engineering (CSEE)
Dr Giovanni Stracquadanio
  • Email

  • Telephone

    +44 (0) 1206 872342

  • Location

    5B.534, Colchester Campus

  • Academic support hours

    Tue, 11am -12pm Wed, 11am -12pm

Profile

Biography

Giovanni Stracquadanio is a Lecturer in Computer Science and Artificial Intelligence at University of Essex and the Head of the Computational Intelligence Lab for Biology and Medicine (CIBM). His research work focuses on computational methods to analyse big biological data and design synthetic biological systems. His lab is currently working on multi-omics Bayesian inference to identify genetic mutations increasing the risk of cancer, and computer aided design (CAD) methods for whole genome engineering. Dr Stracquadanio obtained a Ph.D. in computer science from the University of Catania in Italy. From 2010, he was a postdoctoral fellow at Johns Hopkins University, working on the synthetic yeast project (Sc2.0) with Joel Bader and Jef Boeke, and later at the University of Oxford, focusing on cancer genetics with Gareth Bond. In 2017, Dr Stracquadanio received the Wellcome Trust Seed Award in Science. Awards 2016. Keystone Future of Science Scholarship. Keystone Genomics and Personalized Medicine Meeting, Banff, Canada 2015. Best Poster Award. Cancer Research UK, Oxford, UK 2015. Best postdoc talk prize at the 31st Genes & Cancer Conference. Nature Reviews Cancer, Cambridge, UK 2012. AutoDesk IdeaStudio grant. AutoDesk Inc, CA, USA 2011. Travel Award. Synthetic Biology 5.0, Stanford, CA, USA 2009. Parallel Algorithms for Biological Pathways Analysis. HPC-Europa, UK 2007. Travel Award. Synthetic Biology 3.0, ETH, Zurich, Switzerland 2006-2009. Ph.D. Fellowship. Ministero dell'Istruzione, dell'Universita' e della Ricerca, Italy 2001-2006. Scholarship for Excellent Student Career. Universita' degli Studi di Catania, Italy

Qualifications

  • 2010 - Ph.D. in Computer Science, University of Catania, Italy

  • 2006- M.Sc. in Computer Science, University of Catania, Italy. Summa cum laude

Appointments

University of Essex

  • Lecturer in Computer Science and Artificial Intelligence, School of Computer Science and Electronic Engineering University of Essex ( 1/11/2016 - present )

Other academic

  • Senior Postdoctoral Fellow, Ludwig Institute for Cancer Research University of Oxford ( 18/7/2014 - 30/9/2016 )

  • Postdoctoral Fellow, Department of Biomedical Engineering Johns Hopkins University ( 20/8/2010 - 20/5/2014 )

  • Postdoctoral Fellow, School of Medicine Johns Hopkins University ( 20/8/2010 - 20/5/2014 )

Research and professional activities

Current research

Computational Biology

Bioinformatics

Biostatistics

Machine learning

Graph theory

Optimisation

Conferences and presentations

Computer Aided Design and Analysis Methods for Synthetic Genomics. Synthetic Genome Summer School. July 6, 2016. Edinburgh, UK

Polymorphisms in the p53 Pathway are Enriched in Cancer Susceptibility Loci and Share Characteristics with Somatic Pathway Mutations. 31st Genes & Cancer Conference. April 13, 2015. Cambridge, UK

Computational Challenges in Synthetic Biology. Synthetic Genomics Inc.. April 23, 2014. La Jolla, CA, USA

Computational Analysis and Validation of Structural Variations in Synthetic Yeast Genomes. 2nd International Conference on Computational Medicine. January 24, 2013. University of Florida. Gainesville, FL, USA

Design and Synthesis of Vitamin A in Yeast. NASA Workshop on Food Production in Space. September 20, 2012. NASA Ames Research Center, Mountain View, CA, USA

Structural Variation Analysis of a Synthetic Yeast Chromosome. Joint Genome Institute (JGI). September 18, 2012. Walnut Creek, CA, USA.

Teaching and supervision

  • Network Fundamentals (CE155)

  • ICT Systems Integration and Management (CE219)

  • Placement Year (CE300)

Publications

Journal articles (26)

Mitchell, LA., Wang, A., Stracquadanio, G., Kuang, Z., Wang, X., Yang, K., Richardson, S., Martin, JA., Zhao, Y., Walker, R., Luo, Y., Dai, H., Dong, K., Tang, Z., Yang, Y., Cai, Y., Heguy, A., Ueberheide, B., Fenyö, D., Dai, J., Bader, JS. and Boeke, JD., (2017). Synthesis, debugging, and effects of synthetic chromosome consolidation: synVI and beyond. Science. 355 (6329), eaaf4831-eaaf4831

Richardson, SM., Mitchell, LA., Stracquadanio, G., Yang, K., Dymond, JS., DiCarlo, JE., Lee, D., Huang, CLV., Chandrasegaran, S., Cai, Y., Boeke, JD. and Bader, JS., (2017). Design of a synthetic yeast genome. Science. 355 (6329), 1040-1044

Shen, Y., Wang, Y., Chen, T., Gao, F., Gong, J., Abramczyk, D., Walker, R., Zhao, H., Chen, S., Liu, W., Luo, Y., Müller, CA., Paul-Dubois-Taine, A., Alver, B., Stracquadanio, G., Mitchell, LA., Luo, Z., Fan, Y., Zhou, B., Wen, B., Tan, F., Wang, Y., Zi, J., Xie, Z., Li, B., Yang, K., Richardson, SM., Jiang, H., French, CE., Nieduszynski, CA., Koszul, R., Marston, AL., Yuan, Y., Wang, J., Bader, JS., Dai, J., Boeke, JD., Xu, X., Cai, Y. and Yang, H., (2017). Deep functional analysis of synII, a 770-kilobase synthetic yeast chromosome. Science. 355 (6329), eaaf4791-eaaf4791

Wu, Y., Li, B-Z., Zhao, M., Mitchell, LA., Xie, Z-X., Lin, Q-H., Wang, X., Xiao, W-H., Wang, Y., Zhou, X., Liu, H., Li, X., Ding, M-Z., Liu, D., Zhang, L., Liu, B-L., Wu, X-L., Li, F-F., Dong, X-T., Jia, B., Zhang, W-Z., Jiang, G-Z., Liu, Y., Bai, X., Song, T-Q., Chen, Y., Zhou, S-J., Zhu, R-Y., Gao, F., Kuang, Z., Wang, X., Shen, M., Yang, K., Stracquadanio, G., Richardson, SM., Lin, Y., Wang, L., Walker, R., Luo, Y., Ma, P-S., Yang, H., Cai, Y., Dai, J., Bader, JS., Boeke, JD. and Yuan, Y-J., (2017). Bug mapping and fitness testing of chemically synthesized chromosome X. Science. 355 (6329), eaaf4706-eaaf4706

Xie, Z-X., Li, B-Z., Mitchell, LA., Wu, Y., Qi, X., Jin, Z., Jia, B., Wang, X., Zeng, B-X., Liu, H-M., Wu, X-L., Feng, Q., Zhang, W-Z., Liu, W., Ding, M-Z., Li, X., Zhao, G-R., Qiao, J-J., Cheng, J-S., Zhao, M., Kuang, Z., Wang, X., Martin, JA., Stracquadanio, G., Yang, K., Bai, X., Zhao, J., Hu, M-L., Lin, Q-H., Zhang, W-Q., Shen, M-H., Chen, S., Su, W., Wang, E-X., Guo, R., Zhai, F., Guo, X-J., Du, H-X., Zhu, J-Q., Song, T-Q., Dai, J-J., Li, F-F., Jiang, G-Z., Han, S-L., Liu, S-Y., Yu, Z-C., Yang, X-N., Chen, K., Hu, C., Li, D-S., Jia, N., Liu, Y., Wang, L-T., Wang, S., Wei, X-T., Fu, M-Q., Qu, L-M., Xin, S-Y., Liu, T., Tian, K-R., Li, X-N., Zhang, J-H., Song, L-X., Liu, J-G., Lv, J-F., Xu, H., Tao, R., Wang, Y., Zhang, T-T., Deng, Y-X., Wang, Y-R., Li, T., Ye, G-X., Xu, X-R., Xia, Z-B., Zhang, W., Yang, S-L., Liu, Y-L., Ding, W-Q., Liu, Z-N., Zhu, J-Q., Liu, N-Z., Walker, R., Luo, Y., Wang, Y., Shen, Y., Yang, H., Cai, Y., Ma, P-S., Zhang, C-T., Bader, JS., Boeke, JD. and Yuan, Y-J., (2017). “Perfect” designer chromosome V and behavior of a ring derivative. Science. 355 (6329), eaaf4704-eaaf4704

Agmon, N., Tang, Z., Yang, K., Sutter, B., Ikushima, S., Cai, Y., Caravelli, K., Martin, JA., Sun, X., Choi, WJ., Zhang, A., Stracquadanio, G., Hao, H., Tu, BP., Fenyo, D., Bader, JS. and Boeke, JD., (2017). Low escape-rate genome safeguards with minimal molecular perturbation of Saccharomyces cerevisiae. Proceedings of the National Academy of Sciences of the United States of America. 114 (8), E1470-E1479

Agmon, N., Tang, Z., Yang, K., Sutter, B., Ikushima, S., Cai, Y., Caravelli, K., Martin, JA., Sun, X., Choi, WJ., Zhang, A., Stracquadanio, G., Hao, H., Tu, BP., Fenyo, D., Bader, JS. and Boeke, JD., (2017). Low escape-rate genome safeguards with minimal molecular perturbation of Saccharomyces cerevisiae. Proceedings of the National Academy of Sciences, creators-Stracquadanio=3AGiovanni=3A=3A

Stracquadanio, G., Vrugt, B., Flury, R., Schraml, P., Wu rl, P., Mu ller, TH., Knippschild, U., Henne-Bruns, D., Breitenstein, S., Clavien, P-A., Graf, R., Bond, GL. and Grochola, LF., (2016). CD44 SNPrs187115: A Novel Biomarker Signature that Predicts Survival in Resectable Pancreatic Ductal Adenocarcinoma. Clinical Cancer Research. 22 (24), 6069-6077

Stracquadanio, G., Yang, K., Boeke, JD. and Bader, JS., (2016). BioPartsDB: a synthetic biology workflow web-application for education and research. Bioinformatics. 32 (22), btw394-btw394

Stracquadanio, G., Wang, X., Wallace, MD., Grawenda, AM., Zhang, P., Hewitt, J., Zeron-Medina, J., Castro-Giner, F., Tomlinson, IP., Goding, CR., Cygan, KJ., Fairbrother, WG., Thomas, LF., Sætrom, P., Gemignani, F., Landi, S., Schuster-Böckler, B., Bell, DA. and Bond, GL., (2016). The importance of p53 pathway genetics in inherited and somatic cancer genomes. Nature Reviews Cancer. 16 (4), 251-265

Yang, K., Stracquadanio, G., Luo, J., Boeke, JD. and Bader, JS., (2016). BioPartsBuilder: a synthetic biology tool for combinatorial assembly of biological parts. Bioinformatics. 32 (6), 937-939

Shen, Y., Stracquadanio, G., Wang, Y., Yang, K., Mitchell, LA., Xue, Y., Cai, Y., Chen, T., Dymond, JS., Kang, K., Gong, J., Zeng, X., Zhang, Y., Li, Y., Feng, Q., Xu, X., Wang, J., Wang, J., Yang, H., Boeke, JD. and Bader, JS., (2016). SCRaMbLE generates designed combinatorial stochastic diversity in synthetic chromosomes. Genome Research. 26 (1), 36-49

Stracquadanio, G., Yang, K., Boeke, JD. and Bader, JS., (2016). BioPartsDB: a synthetic biology workflow web-application for education and research. Bioinformatics. 32 (22), 3519-3521

Agmon, N., Mitchell, LA., Cai, Y., Ikushima, S., Chuang, J., Zheng, A., Choi, W-J., Martin, JA., Caravelli, K., Stracquadanio, G. and Boeke, JD., (2015). Yeast Golden Gate (yGG) for the Efficient Assembly of S. cerevisiae Transcription Units. ACS Synthetic Biology. 4 (7), 853-859

Lin, Q., Jia, B., Mitchell, LA., Luo, J., Yang, K., Zeller, KI., Zhang, W., Xu, Z., Stracquadanio, G., Bader, JS., Boeke, JD. and Yuan, Y-J., (2015). RADOM, an Efficient In Vivo Method for Assembling Designed DNA Fragments up to 10 kb Long in Saccharomyces cerevisiae. ACS Synthetic Biology. 4 (3), 213-220

Cai, Y., Agmon, N., Choi, WJ., Ubide, A., Stracquadanio, G., Caravelli, K., Hao, H., Bader, JS. and Boeke, JD., (2015). Intrinsic biocontainment: Multiplex genome safeguards combine transcriptional and recombinational control of essential yeast genes. Proceedings of the National Academy of Sciences. 112 (6), 1803-1808

Annaluru, N., Muller, H., Mitchell, LA., Ramalingam, S., Stracquadanio, G., Richardson, SM., Dymond, JS., Kuang, Z., Scheifele, LZ., Cooper, EM., Cai, Y., Zeller, K., Agmon, N., Han, JS., Hadjithomas, M., Tullman, J., Caravelli, K., Cirelli, K., Guo, Z., London, V., Yeluru, A., Murugan, S., Kandavelou, K., Agier, N., Fischer, G., Yang, K., Martin, JA., Bilgel, M., Bohutskyi, P., Boulier, KM., Capaldo, BJ., Chang, J., Charoen, K., Choi, WJ., Deng, P., DiCarlo, JE., Doong, J., Dunn, J., Feinberg, JI., Fernandez, C., Floria, CE., Gladowski, D., Hadidi, P., Ishizuka, I., Jabbari, J., Lau, CYL., Lee, PA., Li, S., Lin, D., Linder, ME., Ling, J., Liu, J., Liu, J., London, M., Ma, H., Mao, J., McDade, JE., McMillan, A., Moore, AM., Oh, WC., Ouyang, Y., Patel, R., Paul, M., Paulsen, LC., Qiu, J., Rhee, A., Rubashkin, MG., Soh, IY., Sotuyo, NE., Srinivas, V., Suarez, A., Wong, A., Wong, R., Xie, WR., Xu, Y., Yu, AT., Koszul, R., Bader, JS., Boeke, JD. and Chandrasegaran, S., (2014). Total Synthesis of a Functional Designer Eukaryotic Chromosome. Science. 344 (6179), 55-58

(2014). Erratum for the Research Article: "Total Synthesis of a Functional Designer Eukaryotic Chromosome" by N. Annaluru, H. Muller, L. A. Mitchell, S. Ramalingam, G. Stracquadanio, S. M. Richardson, J. S. Dymond, Z. Kuang, L. Z. Scheifele, E. M. Cooper, Y. Cai, K. Zeller, N. Agmon, J. S. Han, M. Hadjithomas, J. Tullman, K. Caravelli, K. Cirelli, Z. Guo, V. London, A. Yeluru, S. Murugan, K. Kandavelou, N. Agier, G. Fischer, K. Yang, J. A. Martin, M. Bilgel, P. Bohutskyi, K. M. Boulier, B. J. Capaldo, J. Chang, K. Charoen, W. J. Choi, P. Deng, J. E. DiCarlo, J. Doong, J. Dunn, J. I. Feinberg, C. Fernandez, C. E. Floria, D. Gladowski, P. Hadidi, I. Ishizuka, J. Jabbari, C. Y. L. Lau, P. A. Lee, S. Li, D. Lin, M. E. Linder, J. Ling, J. Liu, J. Liu, M. London, H. Ma, J. Mao, J. E. McDade, A. McMillan, A. M. Moore, W. C. Oh, Y. Ouyang, R. Patel, M. Paul, L. C. Paulsen, J. Qiu, A. Rhee, M. G. Rubashkin, I. Y. Soh, N. E. Sotuyo, V. Srinivas, A. Suarez, A. Wong, R. Wong, W. R. Xie, Y. Xu, A. T. Yu, R. Koszul, J. S. Bader, J. D. Boeke, S. Chandrasegaran. Science. 344 (6181), 1254596-1254596

Carapezza, G., Umeton, R., Costanza, J., Angione, C., Stracquadanio, G., Papini, A., Lió, P. and Nicosia, G., (2013). Efficient Behavior of Photosynthetic Organelles via Pareto Optimality, Identifiability, and Sensitivity Analysis. ACS Synthetic Biology. 2 (5), 274-288

Stracquadanio, G., Romano, V. and Nicosia, G., (2013). Semiconductor device design using the BiMADS algorithm. Journal of Computational Physics. 242, 304-320

Angione, C., Occhipinti, A., Stracquadanio, G. and Nicosia, G., (2013). Bose-Einstein condensation in satisfiability problems.. European Journal of Operational Research. 227, 44-54

Angione, C., Occhipinti, A., Stracquadanio, G. and Nicosia, G., (2013). Bose–Einstein condensation in satisfiability problems. European Journal of Operational Research. 227 (1), 44-54

Umeton, R., Stracquadanio, G., Papini, A., Costanza, J., Liò, P. and Nicosia, G., (2012). Identification of sensitive enzymes in the photosynthetic carbon metabolism. Advances in Experimental Medicine and Biology. 736, 441-459

Stracquadanio, G., Pappalardo, E. and Pardalos, PM., (2012). A Mesh Adaptive Basin Hopping Method for the Design of Circular Antenna Arrays. Journal of Optimization Theory and Applications. 155 (3), 1008-1024

Stracquadanio, G. and Nicosia, G., (2011). Computational energy-based redesign of robust proteins. Computers & Chemical Engineering. 35 (3), 464-473

Nicosia, G. and Stracquadanio, G., (2008). Generalized Pattern Search Algorithm for Peptide Structure Prediction. Biophysical Journal. 95 (10), 4988-4999

Books (1)

Pappalardo, E., Pardalos, PM. and Stracquadanio, G., (2013). Optimization Approaches for Solving String Selection Problems. Springer. 978-1-4614-9052-4

Book chapters (2)

Rinaudo, S., Martino, VC., Fiorante, F., Stracquadanio, G. and Nicosia, G., (2015). Optimization Methods and Applications to Microelectronics CAD. In: Coupled Multiscale Simulation and Optimization in Nanoelectronics. Editors: G�nther, M., . Springer Berlin. 435- 451

Pappalardo, E. and Stracquadanio, G., (2014). Designing groundwater supply systems using the mesh adaptive basin hopping algorithm. In: Optimization in Science and Engineering: In Honor of the 60th Birthday of Panos M. Pardalos. 407- 421. 9781493908080

Conferences (21)

Stracquadanio, G., Greco, O., Conca, P., Cutello, V., Pavone, M. and Nicosia, G., (2016). Packing equal disks in a unit square: An immunological optimization approach

Conca, P., Stracquadanio, G. and Nicosia, G., (2015). Automatic tuning of algorithms through sensitivity minimization

Stracquadanio, G., La Ferla, A., De Felice, M. and Nicosia, G., (2011). Design of robust space trajectories

Stracquadanio, G., Umeton, R., Costanza, J., Annibali, V., Mechelli, R., Pavone, M., Zammataro, L. and Nicosia, G., (2011). Large scale agent-based modeling of the humoral and cellular immune response

Stracquadanio, G., La Ferla, A., De Felice, M. and Nicosia, G., (2011). Design of Robust Space Trajectories

Umeton, R., Stracquadanio, G., Sorathiya, A., Papini, A., Liò, P. and Nicosia, G., (2011). Design of robust metabolic pathways

Narzisi, G., Nicosia, G. and Stracquadanio, G., (2010). Robust bio-active peptide prediction using multi-objective optimization

Stracquadanio, G., Drago, C., Romano, V. and Nicosia, G., (2010). Multi-objective optimization of doping profile in semiconductor design GECCO track: Real world applications

Cutello, V., Nicosia, G., Pavone, M. and Stracquadanio, G., (2010). Entropic divergence for population based optimization algorithms

Stracquadanio, G., Drago, C., Romano, V. and Nicosia, G., (2010). Effective design of semiconductor devices using evolutionary-based derivative free optimization

Stracquadanio, G., Umeton, R., Papini, A., Lio, P. and Nicosia, G., (2010). Analysis and optimization of C3 photosynthetic carbon metabolism

Cutello, V., Nicosia, G., Pavone, M. and Stracquadanio, G., (2010). An information-theoretic approach for clonal selection algorithms

Stracquadanio, G., Drago, C., Romano, V. and Nicosia, G., (2010). An immunological algorithm for doping profile optimization in semiconductors design

Papini, A., Nicosia, G., Stracquadanio, G., Liò, P. and Umeton, R., (2010). Key Enzymes for the Optimization of CO2 Uptake and Nitrogen Consumption in the C3 Photosynthetic Carbon Metabolism

Stracquadanio, G., Drago, C., Romano, V. and Nicosia, G., (2009). Doping profile optimization in semiconductor design

Conca, P., Nicosia, G., Stracquadanio, G. and Timmis, J., (2009). Nominal-Yield-Area Tradeoff in Automatic Synthesis of Analog Circuits: A Genetic Programming Approach Using Immune-Inspired Operators

Nicosia, G. and Stracquadanio, G., (2009). A design-for-yield algorithm to assess and improve the structural and energetic robustness of proteins and drugs

Ciccazzo, A., Halfmann, T., Marotta, A., Nicosia, G., Rinaudo, S., Stracquadanio, G. and Venturi, A., (2008). New coupled EM and circuit simulation flow for integrated spiral inductor by introducing symbolic simplified expressions

Ciccazzo, A., Conca, P., Nicosia, G. and Stracquadanio, G., (2008). An advanced clonal selection algorithm with ad-hoc network-based hypermutation operators for synthesis of topology and sizing of analog electrical circuits

Ciccazzo, A., Halfmann, T., Marotta, A., Nicosia, G., Rinaudo, S., Stracquadanio, G., Venturi, A. and IEEE, (2008). New Coupled EM and Circuit Simulation Flow for Integrated Spiral Inductor by Introducing Symbolic Simplified Expressions

Nicosia, G. and Stracquadanio, G., (2007). Generalized pattern search and mesh adaptive direct search algorithms for protein structure prediction

Grants and funding

2017

Network analysis of the effect of hypoxia and nutrient deprivation on motility and metabolic switching of cancer cells

Wellcome Trust

Network Analysis of the effect of hypoxia and nutrient deprivation on motility and metabolic switching of cancer cells

Wellcome Trust

Contact

g.stracquadanio@essex.ac.uk
+44 (0) 1206 872342

Location:

5B.534, Colchester Campus

Academic support hours:

Tue, 11am -12pm Wed, 11am -12pm