Selected publications

A selected list of publications is provided below. The complete list of publications is available on Google Scholar.

Peer-reviewed articles

  1. Protein engineering using variational free energy approximation. Lobzaev, Evgenii and Herrera Michael and Kasprzyk, Martyna and Stracquadanio, Giovanni, Nature Communications, 2024.
  2. Dirichlet latent modelling enables effective learning and sampling of the functional protein design space. Lobzaev, Evgenii and Stracquadanio, Giovanni, Nature Communications, 2024.
  3. Beyond the marrow: insights from comprehensive next-generation sequencing of extramedullary multiple myeloma tumors. Jelinek, T and Zihala, D and Sevcikova, T and Anilkumar Sithara, A and Kapustova, V and Sahinbegovic, H and Venglar, O and Muronova, L and Broskevicova, L and Nenarokov, S and, ..., Stracquadanio, G and Simicek, M and Hajek, R, Leukemia, 2024.
  4. Biofoundry-Scale DNA Assembly Validation Using Cost-Effective High-Throughput Long-Read Sequencing. Vegh, P and Donovan, S and Rosser, S and Stracquadanio, G and Fragkoudis, R, ACS Synthetic Biology, 2024.
  5. Debugging and consolidating multiple synthetic chromosomes reveals combinatorial genetic interactions. Zhao, Y., Coelho, C., Hughes, A. L., Lazar-Stefanita, L., Yang, S., Brooks, A. N., Walker, R. S. K., Zhang, W., Lauer, S., Hernandez, C., Mitchell, L. A., Agmon, N., Shen, Y., Sall, J., Fanfani, V., Jalan, A., Rivera, J., Liang, F.-X., Stracquadanio, G., Steinmetz, L. M., Cai, Y. P. & Boeke, J. D., Cell, 2023.
  6. Manipulating the 3D organization of the largest synthetic yeast chromosome. Zhang, W., Lazar-Stefanita, L., Yamashita, H., Shen, M. J., Mitchell, L. A., Kurasawa, H., Haase, M. A. B., Sun, X., Jiang, Q., Lauer, S. L., McCulloch, L. H., Zhao, Y., Ichikawa, D., Easo, N., Lin, S. J., Fanfani, V., Camellato, B. R., Zhu, Y., Cai, J., Xu, Z., Sacasa, M., Accardo, R., Ahn, J. Y., Annadanam, S., Brammer Basta, L. A., Bello, N. R., Cai, L., Cerritos, S., Cornwell, M., D’Amato, A., Hacker, M., Hersey, K., Kennedy, E., Kianercy, A., Kim, D., Lim, H. S., McCutcheon, G., McGirr, K., Meaney, N., Meyer, L., Moyer, A., Nimer, M., Sabbatini, C., Scheifele, L., Shores, L. S., Silvestrone, C., Snee, A., Spina, A., Staiti, A., Stuver, M., Tian, E., Whearty, D., Zhao, C., Zheng, T., Zhou, V., Zeller, K., Bader, J. S., Stracquadanio, G., Deutsch, S., Dai, J., Aizawa, Y., Boeke, J.D., Molecular Cell, 2023.
  7. Parallel laboratory evolution and rational debugging reveal genomic plasticity to S. cerevisiae synthetic chromosome XIV defects. Williams, T. C., Kroukamp, H., Xu, X., Wightman, E. L. I., Llorente, B., Borneman, A. R., Carpenter, A. C., Van Wyk, N., Espinosa, M. I., Daniel, E. L., Walker, R. S. K., Cai, Y., Nevalainen, H. K. M., Curach, N. C., Deveson, I. W., Mercer, T. R., Johnson, D. L., Mitchell, L. A., Bader, J. S., Stracquadanio, G., Boeke, J. D., Goold, H. D., Pretorius, I. S. & Paulsen, I. T., Cell Genomics, 2023.
  8. Consequences of a telomerase-related fitness defect and chromosome substitu- tion technology in yeast synIX strains.. McCulloch, L., Sambasivam, V., ... Stracquadanio, G., Steinmetz, L. M., Bader, J. S., Zhang Weimin Boeke, J. D. & Chandrasegaran, S., Cell Genomics, 2023.
  9. Synthetic yeast chromosome XI design enables extrachromosomal circular DNA formation on demand.. Blount, B. A., Lu, X., Driessen, M. R. M., Jovicevic, D., Sanchez, M. I., Ciurkot, K., Zhao, Y., Lauer, S., McKier- nan, R. M., Gowers, G.-O. F., Sweeney, F., Fanfani, V., Lobzaev, E., Palacios-Flores, K., Walker, R., Hesketh, A., Oliver, S. G., Cai, Y., Stracquadanio, G., Mitchell, L. A., Bader, J. S., Boeke, J. D. & Ellis, T., Cell Genomics, 2023.
  10. SynXV fusion and fission to establish chromosome-scale design-build-test-learn cycles. Foo, J. L., Kitano, S., Vicanatalita Susanto, A., ..., Stracquadanio, G., Bader, J. S., Boeke, J. D., Dai, J. & Chang, M., Cell Genomics, 2023.
  11. Context-dependent neocentromere activity in synthetic yeast chromosome VIII. Lauer, S., Luo, J., Lazar-Stefanita, L., ..., Bader, J. S., Stracquadanio, G. & Boeke, J. D., Cell Genomics, 2023.
  12. Synthetic chromosome fusion: Effects on mitotic and meiotic genome structure and function. Luo, J., Mercy, G., Vale-Silva, L. A., Sun, X., Agmon, N., Zhang, W., Yang, K., Stracquadanio, G., Thierry, A., Ahn, J. Y., et al., Cell Genomics, 2023.
  13. Design and assembly of DNA molecules using multi-objective optimisation. Gaeta, A., Zulkower, V. and Stracquadanio, G., Synthetic Biology, 2021.
  14. Mutation landscape of multiple myeloma measurable residual disease: identification of targets for precision medicine. Zátopková, M., Ševčíková, T., Fanfani, V., Chyra, Z., Rihova, L., Bezdekova, R., Žihala, D., Growková, K., Filipova, J., Černá, L. ..., Stracquadanio, G. and Hajek, R., Blood Advances, 2021.
  15. The landscape of the heritable cancer genome. Fanfani, V., Citi, L., Harris, A. L., Pezzella, F. and Stracquadanio, G., Cancer Research, 2021.
  16. Germline and somatic genetic variants in the p53 pathway interact to affect cancer risk, progression, and drug response. Zhang, P., Kitchen-Smith, I., Xiong, L., Stracquadanio, G. ..., Tomlinson, I., Turnbull, C., Carter, H. and Bond, G., Cancer Research, 2021.
  17. Computer Aided Assembly and Verification of Synthetic Chromosomes. Stracquadanio, G. & Zulkower, V, Computational Methods in Synthetic Biology, Springer, 2020.
  18. PyGNA: a unified framework for geneset network analysis. Fanfani, V., Cassano, F. & Stracquadanio, G., BMC Bioinformatics, 2020.
  19. Systematic analysis of the IL-17 receptor signalosome reveals a robust regulatory feedback loop. Draberova, H., Janusova, S., Knizkova, D., Semberova, T., Pribikova, T., Ujevic, A., Harant, K., Knapkova, S., Hrdinka, M., Fanfani, V., Stracquadanio, G., Drobek, A., Ruppova, K., Stepanek, O. and Draber, P., The EMBO Journal, 2020.
  20. Dissecting the heritable risk of breast cancer: from statistical methods to susceptibility genes. Fanfani, V., Zatopkova, M., Harris, ALH, Pezzella, F. and Stracquadanio, G., Seminars in Cancer Biology, 2020.
  21. Heritable genetic variants in key cancer genes link cancer risk with anthropometric traits. Di Giovannantonio, M., Harris, B HL, and Zhang, P., Kitchen-Smith, I., Xiong, L., Sahgal, N., Stracquadanio, G., Wallace, M., Blagden, S., Lord, S., Harris, D., Harris, A.H.L., Buffa, F.M. and Bond, Gareth L., Journal of Medical Genetics, 2020.
  22. Technological challenges and milestones for writing genomes. Ostrov, N., Beal, J., Ellis, T., Gordon, D. B., Karas, B. J., Lee, H. H., Lenaghan, S.C., Schloss, J.A., Stracquadanio, G., Trefzer, A., Bader, J. S., Church, G. M., Coelho, C. M., Efcavitch, J. W., Güell, M., Mitchell, L. A., Nielsen, A. A. K., Peck, B., Smith, A. C., Neal Stewart Jr., C. , Tekotte, H., Science, 2019.
  23. Stochastic Methods for Global Optimization and Problem Solving. Stracquadanio, G. and Pardalos, P., Encyclopedia of Bioinformatics and Computational Biology, 2018.
  24. Synthetic chromosome fusion: effects on genome structure and function. Luo, J and Mercy, G and Vale-Silva, L. A. and Sun, X. and Agmon, N. and Zhang, W. and Yang, K. and Stracquadanio, G. and Thierry, A. and Ahn, J.Y. and Adoff, G and DAvino, A. and Berger, H. and Chen, Y. and Chickering, M. and Fishman, O. and Greeno, R. V. and Kim, S. and Kim, S. and Lim, H. and Im, J. and Meyer, L. and Moyer, A. and Mullangi, S. and Murphy, N.A. and Natov, P. and Nimer, M. and Radley, A. and Tripathy, A. and Wang, T. and Wilkerson, N. and Zheng, T. and Zhou, V. and Kaback, D. B. and Bader, J. S. and Mitchell, L. A. and Mozziconacci, J. and Hochwagen, A. and Koszul, R, and Boeke, J. D., biorXiv, 2018.
  25. Design of a synthetic yeast genome. Richardson1, Sarah M. and Mitchell1, Leslie A. and Stracquadanio1, Giovanni and Yang1, Kun and Dymond, Jessica S. and DiCarlo, James E. and Lee, Dongwon and Huang, Cheng Lai Victor and Chandrasegaran, Srinivasan and Cai, Yizhi and Boeke, Jef D. and Bader, Joel S., Science, 2017.
  26. Synthesis, debugging, and effects of synthetic chromosome consolidation: synVI and beyond. Mitchell, Leslie A. and Wang, Ann and Stracquadanio, Giovanni and Kuang, Zheng and Wang, Xuya and Yang, Kun and Richardson, Sarah and Martin, J. Andrew and Zhao, Yu and Walker, Roy and Luo, Yisha and Dai, Hongjiu and Dong, Kang and Tang, Zuojian and Yang, Yanling and Cai, Yizhi and Heguy, Adriana and Ueberheide, Beatrix and Fenyö, David and Dai, Junbiao and Bader, Joel S. and Boeke, Jef D., Science, 2017.
  27. Deep functional analysis of synII, a 770-kilobase synthetic yeast chromosome. Shen, Yue and Wang, Yun and Chen, Tai and Gao, Feng and Gong, Jianhui and Abramczyk, Dariusz and Walker, Roy and Zhao, Hongcui and Chen, Shihong and Liu, Wei and Luo, Yisha and Müller, Carolin A. and Paul-Dubois-Taine, Adrien and Alver, Bonnie and Stracquadanio, Giovanni and ... and Boeke, Jef D. and Xu, Xun and Cai, Yizhi and Yang, Huanming, Science, 2017.
  28. Bug mapping and fitness testing of chemically synthesized chromosome X. Wu, Yi and Li, Bing-Zhi and Zhao, Meng and Mitchell, Leslie A. and Xie, Ze-Xiong and Lin, Qiu-Hui and Wang, Xia and Xiao, Wen-Hai and Wang, Ying and Zhou, Xiao and Liu, Hong and Li, Xia and Ding, Ming-Zhu and Liu, Duo and Zhang, Lu and Liu, Bao-Li and Wu, Xiao-Le and Li, Fei-Fei and Dong, Xiu-Tao and Jia, Bin and Zhang, Wen-Zheng and Jiang, Guo-Zhen and Liu, Yue and Bai, Xue and Song, Tian-Qing and Chen, Yan and Zhou, Si-Jie and Zhu, Rui-Ying and Gao, Feng and Kuang, Zheng and Wang, Xuya and Shen, Michael and Yang, Kun and Stracquadanio, Giovanni and ... and Bader, Joel S. and Boeke, Jef D. and Yuan, Ying-Jin, Science, 2017.
  29. Perfect designer chromosome V and behavior of a ring derivative. Xie, Ze-Xiong and Li, Bing-Zhi and Mitchell, Leslie A. and Wu, Yi and Qi, Xin and Jin, Zhu and Jia, Bin and Wang, Xia and Zeng, Bo-Xuan and Liu, Hui-Min and Wu, Xiao-Le and Feng, Qi and Zhang, Wen-Zheng and Liu, Wei and Ding, Ming-Zhu and Li, Xia and Zhao, Guang-Rong and Qiao, Jian-Jun and Cheng, Jing-Sheng and Zhao, Meng and Kuang, Zheng and Wang, Xuya and Martin, J. Andrew and Stracquadanio, Giovanni and ... and Bader, Joel S. and Boeke, Jef D. and Yuan, Ying-Jin, Science, 2017.
  30. Low escape-rate genome safeguards with minimal molecular perturbation of Saccharomyces cerevisiae. Agmon, Neta and Tang, Zuojian and Yang, Kun and Sutter, Ben and Ikushima, Shigehito and Cai, Yizhi and Caravelli, Katrina and Martin, James A. and Sun, Xiaoji and Choi, Woo Jin and Zhang, Allen and Stracquadanio, Giovanni and Hao, Haiping and Tu, Benjamin P. and Fenyo, David and Bader, Joel S. and Boeke, Jef D., Proceedings of the National Academy of Sciences of the United States of America, 2017.
  31. BioPartsDB: a synthetic biology workflow web-application for education and research. Stracquadanio, G. and Yang, K. and Boeke, J. D. and Bader, J. S., Bioinformatics, 2016.
  32. CD44 SNP rs187115: A novel biomarker signature that predicts survival in resectable pancreatic ductal adenocarcinoma. Stracquadanio, G., Vrugt, B., Flury, R., Schraml, P., Wu ̈rl, P., Mu ̈ller, T. H., Knippschild, U., Henne- Bruns, D., Breitenstein, S., Clavien, P.-A., Graf, R., Bond, G. L., Grochola, L. F., Clinical Cancer Research, 2016.
  33. The importance of p53 pathway genetics in inherited and somatic cancer genomes. Stracquadanio1, G., Wang1, Wallace, M., Grawenda, A., Zhang, P., Hewitt, J., Zeron-Medina, J., Castro-Giner, F., Tomlinson, I., Goding, C., Cygan, K., Fairbrother, W., Thomas, L., Saetrom, P., Gemignani, F., Landi, S., Schuster-Bockler, B., Bell, D., Bond, G., , Nature Reviews Cancer, 2016.
  34. SCRaMbLE generates designed combinatorial stochastic diversity in synthetic chromosomes. Shen1, Y., Stracquadanio1, G., Wang1, Y., Yang, K., Mitchell, L.; Xue, Y., Cai, Y., Chen, T., Dymond, J. S., Kang, K., Gong, J., Zeng, X., Zhang, Y., Li, Y.; Feng, Q., Xu, X., Wang, J., Wang, J., Yang, H., Boeke, J. D., Bader, J.S., Genome Research, 2016.
  35. BioPartsBuilder: a synthetic biology tool for combinatorial assembly of biological parts. Yang1, Kun; Stracquadanio1, Giovanni; Luo, Jingchuan; Boeke, Jef D; Bader, Joel S, Bioinformatics, 2015.
  36. Yeast Golden Gate (yGG) for the Efficient Assembly of S. cerevisiae Transcription Units. Agmon, N., Mitchell, L.A., Cai, Y., Ikushima, S., Chuang, J., Zheng, A., Choi, W.-J., Martin, J.A., Caravelli, K., Stracquadanio, G., Boeke, J.D., ACS Synthetic Biology, 2015.
  37. Intrinsic biocontainment: Multiplex genome safeguards combine transcriptional and recombinational control of essential yeast genes. Cai, Y., Agmon, N., Choi, W.J., Ubide, A., Stracquadanio, G., Caravelli, K., Hao, H., Bader, J.S., Boeke, J.D., Proceedings of the National Academy of Sciences of the United States of America, 2015.
  38. RADOM, an efficient in vivo method for assembling designed DNA fragments up to 10 kb long in saccharomyces cerevisiae. Lin, Q., Jia, B., Mitchell, L.A., Luo, J., Yang, K., Zeller, K.I., Zhang, W., Xu, Z., Stracquadanio, G., Bader, J.S., Boeke, J.D., Yuan, Y.-J., ACS Synthetic Biology, 2015.
  39. Total synthesis of a functional designer eukaryotic chromosome. Annaluru, N., Muller, H., Mitchell, L.A., Ramalingam, S., Stracquadanio, G., Richardson, S.M., Dymond, J.S., Kuang, Z., Scheifele, L.Z., Cooper, E.M., Cai, Y., Zeller, K., Agmon, N., Han, J.S., 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, J.A., Bilgel, M., Bohutski, P., Boulier, K.M., Capaldo, B.J., Chang, J., Charoen, K., Choi, W.J., Deng, P., DiCarlo, J.E., Doong, J., Dunn, J., Feinberg, J.I., Fernandez, C., Floria, C.E., Gladowski, D., Hadidi, P., Ishizuka, I., Jabbari, J., Lau, C.Y.L., Lee, P.A., Li, S., Lin, D., Linder, M.E., Ling, J., Liu, J., Liu, J., London, M., Henry, M., Mao, J., McDade, J.E., McMillan, A., Moore, A.M., Oh, W.C., Ouyang, Y., Patel, R., Paul, M., Paulsen, L.C., Qiu, J., Rhee, A., Rubashkin, M.G., Soh, I.Y., Sotuyo, N.E., Srinivas, V., Suarez, A., Wong, A., Wong, R., Xie, W.R., Xu, Y., Yu, A.T., Koszul, R., Bader, J.S., Boeke, J.D., Chandrasegaran, S., Science, 2014.
  40. Semiconductor device design using the BiMADS algorithm. Stracquadanio, G., Romano, V., Nicosia, G., Journal of Computational Physics, 2013.
  41. Efficient behavior of photosynthetic organelles via pareto optimality, identifiability, and sensitivity analysis. Carapezza, G., Umeton, R., Costanza, J., Angione, C., Stracquadanio, G., Papini, A., Lió, P., Nicosia, G., ACS Synthetic Biology, 2013.
  42. Bose-Einstein condensation in satisfiability problems. Angione, C., Occhipinti, A., Stracquadanio, G., Nicosia, G., European Journal of Operational Research, 2013.
  43. A Mesh Adaptive Basin Hopping Method for the Design of Circular Antenna Arrays. Stracquadanio, G., Pappalardo, E., Pardalos, P.M., Journal of Optimization Theory and Applications, 2012.
  44. Identification of sensitive enzymes in the photosynthetic carbon metabolism. Umeton, R., Stracquadanio, G., Papini, A., Costanza, J., Liò, P., Nicosia, G., Advances in Experimental Medicine and Biology, 2012.
  45. Computational energy-based redesign of robust proteins. Stracquadanio, G., Nicosia, G., Computers and Chemical Engineering, 2011.
  46. Generalized pattern search algorithm for peptide structure prediction. Nicosia, G., Stracquadanio3, G., Biophysical Journal, 2008.

Preprints

  1. APEX: Automated Protein EXpression in Escherichia coli. Kasprzyk, Martyna and Herrera, Michael A and Stracquadanio, Giovanni, bioRxiv, 2024.
  2. Synthetic genome modules designed for programmable silencing of functions and chromosomes. Lu, X and Shaw, W M and Sutradhar, A and Stracquadanio, Giovanni and Ellis, Tom, bioRxiv, 2024.
  3. Polymer physics of structural evolution in synthetic yeast chromosomes. Stracquadanio, G., Yang, K., Boeke, J. D., Koszul, R., Bader, J.S., bioRxiv, 2022.
  4. Designing human Sphingosine-1-phosphate lyases using a temporal Dirichlet variational autoencoder. Lobzaev, Evgenii and Herrera, Michael A. and Campopiano, Dominic J. and Stracquadanio, Giovanni, bioRxiv, 2022.
  5. Discovering cancer driver genes and pathways using stochastic block model graph neural networks. Fanfani, V., Vinas Torne, R., Lio’, P. and Stracquadanio, G., biorXiv, 2021.
  6. Gene-level heritability analysis explains the polygenic architecture of cancer. Fanfani, V. and Citi, L. Harris, A. L. and Pezzella, F. and Stracquadanio, G., biorXiv, 2020.
  7. A unified framework for geneset network analysis. Fanfani, V. and Stracquadanio, G., biorXiv, 2019.

Books and contributed chapters

  1. Designing groundwater supply systems using the mesh adaptive basin hopping algorithm. Pappalardo, E., Stracquadanio, G., Optimization in Science and Engineering: In Honor of the 60th Birthday of Panos M. Pardalos, 2014.
  2. Optimization approaches for solving string selection problems. Pappalardo, E., Pardalos, M., Stracquadanio, G., SpringerBriefs in Optimization, 2013.

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