Items where Author is "Stracquadanio, Giovanni"
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Article
Fanfani, Viola and Citi, Luca and Harris, Adrian L and Pezzella, Francesco and Stracquadanio, Giovanni (2021) The landscape of the heritable cancer genome. Cancer Research, 81 (10). pp. 2588-2599. DOI https://doi.org/10.1158/0008-5472.CAN-20-3348
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 Richardson, Sarah M and Lin, Yicong and Wang, Lihui and Walker, Roy and Luo, Yisha and Ma, Ping-Sheng and Yang, Huanming and Cai, Yizhi and Dai, Junbiao and Bader, Joel S and Boeke, Jef D and Yuan, Ying-Jin (2017) Bug mapping and fitness testing of chemically synthesized chromosome X. Science, 355 (6329). eaaf4706-. DOI https://doi.org/10.1126/science.aaf4706
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 Mitchell, Leslie A and Luo, Zhouqing and Fan, Yanqun and Zhou, Baojin and Wen, Bo and Tan, Fengji and Wang, Yujia and Zi, Jin and Xie, Zexiong and Li, Bingzhi and Yang, Kun and Richardson, Sarah M and Jiang, Hui and French, Christopher E and Nieduszynski, Conrad A and Koszul, Romain and Marston, Adele L and Yuan, Yingjin and Wang, Jian and Bader, Joel S and Dai, Junbiao and Boeke, Jef D and Xu, Xun and Cai, Yizhi and Yang, Huanming (2017) Deep functional analysis of synII, a 770-kilobase synthetic yeast chromosome. Science, 355 (6329). eaaf4791-. DOI https://doi.org/10.1126/science.aaf4791
Richardson, Sarah M and Mitchell, Leslie A and Stracquadanio, Giovanni and Yang, 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 (2017) Design of a synthetic yeast genome. Science, 355 (6329). pp. 1040-1044. DOI https://doi.org/10.1126/science.aaf4557
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 Yang, Kun and Bai, Xue and Zhao, Juan and Hu, Meng-Long and Lin, Qiu-Hui and Zhang, Wen-Qian and Shen, Ming-Hua and Chen, Si and Su, Wan and Wang, En-Xu and Guo, Rui and Zhai, Fang and Guo, Xue-Jiao and Du, Hao-Xing and Zhu, Jia-Qing and Song, Tian-Qing and Dai, Jun-Jun and Li, Fei-Fei and Jiang, Guo-Zhen and Han, Shi-Lei and Liu, Shi-Yang and Yu, Zhi-Chao and Yang, Xiao-Na and Chen, Ken and Hu, Cheng and Li, Da-Shuai and Jia, Nan and Liu, Yue and Wang, Lin-Ting and Wang, Su and Wei, Xiao-Tong and Fu, Mei-Qing and Qu, Lan-Meng and Xin, Si-Yu and Liu, Ting and Tian, Kai-Ren and Li, Xue-Nan and Zhang, Jin-Hua and Song, Li-Xiang and Liu, Jin-Gui and Lv, Jia-Fei and Xu, Hang and Tao, Ran and Wang, Yan and Zhang, Ting-Ting and Deng, Ye-Xuan and Wang, Yi-Ran and Li, Ting and Ye, Guang-Xin and Xu, Xiao-Ran and Xia, Zheng-Bao and Zhang, Wei and Yang, Shi-Lan and Liu, Yi-Lin and Ding, Wen-Qi and Liu, Zhen-Ning and Zhu, Jun-Qi and Liu, Ning-Zhi and Walker, Roy and Luo, Yisha and Wang, Yun and Shen, Yue and Yang, Huanming and Cai, Yizhi and Ma, Ping-Sheng and Zhang, Chun-Ting and Bader, Joel S and Boeke, Jef D and Yuan, Ying-Jin (2017) “Perfect” designer chromosome V and behavior of a ring derivative. Science, 355 (6329). eaaf4704-. DOI https://doi.org/10.1126/science.aaf4704
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 (2017) Synthesis, debugging, and effects of synthetic chromosome consolidation: synVI and beyond. Science, 355 (6329). eaaf4831-. DOI https://doi.org/10.1126/science.aaf4831
Stracquadanio, Giovanni and Wang, Xuting and Wallace, Marsha D and Grawenda, Anna M and Zhang, Ping and Hewitt, Juliet and Zeron-Medina, Jorge and Castro-Giner, Francesc and Tomlinson, Ian P and Goding, Colin R and Cygan, Kamil J and Fairbrother, William G and Thomas, Laurent F and Sætrom, Pål and Gemignani, Federica and Landi, Stefano and Schuster-Böckler, Benjamin and Bell, Douglas A and Bond, Gareth L (2016) The importance of p53 pathway genetics in inherited and somatic cancer genomes. Nature Reviews Cancer, 16 (4). pp. 251-265. DOI https://doi.org/10.1038/nrc.2016.15
Yang, Kun and Stracquadanio, Giovanni and Luo, Jingchuan and Boeke, Jef D and Bader, Joel S (2016) BioPartsBuilder: a synthetic biology tool for combinatorial assembly of biological parts. Bioinformatics, 32 (6). pp. 937-939. DOI https://doi.org/10.1093/bioinformatics/btv664
Shen, Yue and Stracquadanio, Giovanni and Wang, Yun and Yang, Kun and Mitchell, Leslie A and Xue, Yaxin and Cai, Yizhi and Chen, Tai and Dymond, Jessica S and Kang, Kang and Gong, Jianhui and Zeng, Xiaofan and Zhang, Yongfen and Li, Yingrui and Feng, Qiang and Xu, Xun and Wang, Jun and Wang, Jian and Yang, Huanming and Boeke, Jef D and Bader, Joel S (2016) SCRaMbLE generates designed combinatorial stochastic diversity in synthetic chromosomes. Genome Research, 26 (1). pp. 36-49. DOI https://doi.org/10.1101/gr.193433.115
Agmon, Neta and Mitchell, Leslie A and Cai, Yizhi and Ikushima, Shigehito and Chuang, James and Zheng, Allen and Choi, Woo-Jin and Martin, J Andrew and Caravelli, Katrina and Stracquadanio, Giovanni and Boeke, Jef D (2015) Yeast Golden Gate (yGG) for the Efficient Assembly of <i>S. cerevisiae</i> Transcription Units. ACS Synthetic Biology, 4 (7). pp. 853-859. DOI https://doi.org/10.1021/sb500372z
Lin, Qiuhui and Jia, Bin and Mitchell, Leslie A and Luo, Jingchuan and Yang, Kun and Zeller, Karen I and Zhang, Wenqian and Xu, Zhuwei and Stracquadanio, Giovanni and Bader, Joel S and Boeke, Jef D and Yuan, Ying-Jin (2015) RADOM, an Efficient <i>In Vivo</i> Method for Assembling Designed DNA Fragments up to 10 kb Long in <i>Saccharomyces cerevisiae</i>. ACS Synthetic Biology, 4 (3). pp. 213-220. DOI https://doi.org/10.1021/sb500241e
Cai, Yizhi and Agmon, Neta and Choi, Woo Jin and Ubide, Alba and Stracquadanio, Giovanni and Caravelli, Katrina and Hao, Haiping and Bader, Joel S and Boeke, Jef D (2015) Intrinsic biocontainment: Multiplex genome safeguards combine transcriptional and recombinational control of essential yeast genes. Proceedings of the National Academy of Sciences, 112 (6). pp. 1803-1808. DOI https://doi.org/10.1073/pnas.1424704112
Annaluru, Narayana and Muller, Héloïse and Mitchell, Leslie A and Ramalingam, Sivaprakash and Stracquadanio, Giovanni and Richardson, Sarah M and Dymond, Jessica S and Kuang, Zheng and Scheifele, Lisa Z and Cooper, Eric M and Cai, Yizhi and Zeller, Karen and Agmon, Neta and Han, Jeffrey S and Hadjithomas, Michalis and Tullman, Jennifer and Caravelli, Katrina and Cirelli, Kimberly and Guo, Zheyuan and London, Viktoriya and Yeluru, Apurva and Murugan, Sindurathy and Kandavelou, Karthikeyan and Agier, Nicolas and Fischer, Gilles and Yang, Kun and Martin, J Andrew and Bilgel, Murat and Bohutskyi, Pavlo and Boulier, Kristin M and Capaldo, Brian J and Chang, Joy and Charoen, Kristie and Choi, Woo Jin and Deng, Peter and DiCarlo, James E and Doong, Judy and Dunn, Jessilyn and Feinberg, Jason I and Fernandez, Christopher and Floria, Charlotte E and Gladowski, David and Hadidi, Pasha and Ishizuka, Isabel and Jabbari, Javaneh and Lau, Calvin YL and Lee, Pablo A and Li, Sean and Lin, Denise and Linder, Matthias E and Ling, Jonathan and Liu, Jaime and Liu, Jonathan and London, Mariya and Ma, Henry and Mao, Jessica and McDade, Jessica E and McMillan, Alexandra and Moore, Aaron M and Oh, Won Chan and Ouyang, Yu and Patel, Ruchi and Paul, Marina and Paulsen, Laura C and Qiu, Judy and Rhee, Alex and Rubashkin, Matthew G and Soh, Ina Y and Sotuyo, Nathaniel E and Srinivas, Venkatesh and Suarez, Allison and Wong, Andy and Wong, Remus and Xie, Wei Rose and Xu, Yijie and Yu, Allen T and Koszul, Romain and Bader, Joel S and Boeke, Jef D and Chandrasegaran, Srinivasan (2014) Total Synthesis of a Functional Designer Eukaryotic Chromosome. Science, 344 (6179). pp. 55-58. DOI https://doi.org/10.1126/science.1249252
Stracquadanio, Giovanni and Romano, Vittorio and Nicosia, Giuseppe (2013) Semiconductor device design using the BiMADS algorithm. Journal of Computational Physics, 242. pp. 304-320. DOI https://doi.org/10.1016/j.jcp.2013.01.025
Carapezza, Giovanni and Umeton, Renato and Costanza, Jole and Angione, Claudio and Stracquadanio, Giovanni and Papini, Alessio and Lió, Pietro and Nicosia, Giuseppe (2013) Efficient Behavior of Photosynthetic Organelles via Pareto Optimality, Identifiability, and Sensitivity Analysis. ACS Synthetic Biology, 2 (5). pp. 274-288. DOI https://doi.org/10.1021/sb300102k
Angione, Claudio and Occhipinti, Annalisa and Stracquadanio, Giovanni and Nicosia, Giuseppe (2013) Bose–Einstein condensation in satisfiability problems. European Journal of Operational Research, 227 (1). pp. 44-54. DOI https://doi.org/10.1016/j.ejor.2012.11.039
Stracquadanio, Giovanni and Pappalardo, Elisa and Pardalos, Panos M (2012) A Mesh Adaptive Basin Hopping Method for the Design of Circular Antenna Arrays. Journal of Optimization Theory and Applications, 155 (3). pp. 1008-1024. DOI https://doi.org/10.1007/s10957-012-0112-8
Umeton, Renato and Stracquadanio, Giovanni and Papini, Alessio and Costanza, Jole and Liò, Pietro and Nicosia, Giuseppe (2012) Identification of Sensitive Enzymes in the Photosynthetic Carbon Metabolism. Advances in Experimental Medicine and Biology, 736. pp. 441-459. DOI https://doi.org/10.1007/978-1-4419-7210-1_26
Stracquadanio, Giovanni and Nicosia, Giuseppe (2011) Computational energy-based redesign of robust proteins. Computers & Chemical Engineering, 35 (3). pp. 464-473. DOI https://doi.org/10.1016/j.compchemeng.2010.04.005
Nicosia, Giuseppe and Stracquadanio, Giovanni (2008) Generalized Pattern Search Algorithm for Peptide Structure Prediction. Biophysical Journal, 95 (10). pp. 4988-4999. DOI https://doi.org/10.1529/biophysj.107.124016
Book Section
Rinaudo, Salvatore and Martino, Valeria Cinnera and Fiorante, Franco and Stracquadanio, Giovanni and Nicosia, Giuseppe (2015) Optimization Methods and Applications to Microelectronics CAD. In: Mathematics in Industry. Springer Berlin Heidelberg, 435 - 451.
Conference or Workshop Item
Umeton, Renato and Stracquadanio, Giovanni and Sorathiya, Anilkumar and Liò, Pietro and Papini, Alessio and Nicosia, Giuseppe (2011) Design of robust metabolic pathways. In: DAC '11: The 48th Annual Design Automation Conference 2011, ? - ?.
Stracquadanio, Giovanni and La Ferla, Angelo and De Felice, Matteo and Nicosia, Giuseppe (2011) Design of Robust Space Trajectories. In: UNSPECIFIED, ? - ?.
Stracquadanio, Giovanni and Umeton, Renato and Costanza, Jole and Annibali, Viviana and Mechelli, Rosella and Pavone, Mario and Zammataro, Luca and Nicosia, Giuseppe (2011) Large Scale Agent-Based Modeling of the Humoral and Cellular Immune Response. In: UNSPECIFIED, ? - ?.
Stracquadanio, Giovanni and Drago, Concetta and Romano, Vittorio and Nicosia, Giuseppe (2010) Multi-objective optimization of doping profile in semiconductor design. In: GECCO '10: Genetic and Evolutionary Computation Conference, ? - ?.
Cutello, Vincenzo and Nicosia, Giuseppe and Pavone, Mario and Stracquadanio, Giovanni (2010) Entropic divergence for population based optimization algorithms. In: 2010 IEEE Congress on Evolutionary Computation (CEC), 2010-07-18 - 2010-07-23.
Stracquadanio, Giovanni and Umeton, Renato and Papini, Alessio and Liò, Pietro and Nicosia, Giuseppe (2010) Analysis and Optimization of C3 Photosynthetic Carbon Metabolism. In: 2010 IEEE International Conference on BioInformatics and BioEngineering, 2010-05-31 - 2010-06-03.
Stracquadanio, Giovanni and Drago, Concetta and Romano, Vittorio and Nicosia, Giuseppe (2010) An Immunological Algorithm for Doping Profile Optimization in Semiconductors Design. In: UNSPECIFIED, ? - ?.
Cutello, Vincenzo and Nicosia, Giuseppe and Pavone, Mario and Stracquadanio, Giovanni (2010) An Information-Theoretic Approach for Clonal Selection Algorithms. In: UNSPECIFIED, ? - ?.
Nicosia, Giuseppe and Stracquadanio, Giovanni (2009) A Design-for-Yield Algorithm to Assess and Improve the Structural and Energetic Robustness of Proteins and Drugs. In: UNSPECIFIED, ? - ?.
Ciccazzo, Angelo and Conca, Piero and Nicosia, Giuseppe and Stracquadanio, Giovanni (2008) An Advanced Clonal Selection Algorithm with Ad-Hoc Network-Based Hypermutation Operators for Synthesis of Topology and Sizing of Analog Electrical Circuits. In: UNSPECIFIED, ? - ?.
Ciccazzo, Angelo and Halfmann, Thomas and Marotta, Angelo and Nicosia, Giuseppe and Rinaudo, Salvatore and Stracquadanio, Giovanni and Venturi, Alberto (2008) New coupled EM and circuit simulation flow for integrated spiral inductor by introducing symbolic simplified expressions. In: 2008 IEEE International Symposium on Industrial Electronics (ISIE 2008), 2008-06-30 - 2008-07-02.
Nicosia, Giuseppe and Stracquadanio, Giovanni (2007) Generalized Pattern Search and Mesh Adaptive Direct Search Algorithms for Protein Structure Prediction. In: UNSPECIFIED, ? - ?.