Publications

Construction and iterative redesign of synXVI a 903 kb synthetic Saccharomyces cerevisiae chromosome

Goold, H and Kroukamp, H and Erpf, P E and Zhao, Yu and Kelso, P and Calame, J and Timmins, J JB and Wightman, E LI and Peng, K and Carpenter, A C and ... and Stracquadanio, G and Bader, J S and Mitchell, L A and Boeke, J D and Williams, T C and Paulsen, I and Pretorius, I S

Nature Communications

APEX: Automated Protein EXpression in Escherichia coli

Kasprzyk, Martyna and Herrera, Michael A and Stracquadanio, Giovanni

ACS Synthetic Biology

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

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

Dirichlet latent modelling enables effective learning and sampling of the functional protein design space

Lobzaev, Evgenii and Stracquadanio, Giovanni

Nature Communications

Protein engineering using variational free energy approximation

Lobzaev, Evgenii and Herrera Michael and Kasprzyk, Martyna and Stracquadanio, Giovanni

Nature Communications

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

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

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

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

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

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

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

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

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

The landscape of the heritable cancer genome

Fanfani, V., Citi, L., Harris, A. L., Pezzella, F. and Stracquadanio, G.

Cancer Research

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

Design and assembly of DNA molecules using multi-objective optimisation

Gaeta, A., Zulkower, V. and Stracquadanio, G.

Synthetic Biology

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

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

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

PyGNA: a unified framework for geneset network analysis

Fanfani, V., Cassano, F. & Stracquadanio, G.

BMC Bioinformatics

Computer Aided Assembly and Verification of Synthetic Chromosomes

Stracquadanio, G. & Zulkower, V

Computational Methods in Synthetic Biology, Springer

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

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

Stochastic Methods for Global Optimization and Problem Solving

Stracquadanio, G. and Pardalos, P.

Encyclopedia of Bioinformatics and Computational Biology

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

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

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

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

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

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

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

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

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

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

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

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

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

BioPartsBuilder: a synthetic biology tool for combinatorial assembly of biological parts

Yang¹, Kun; Stracquadanio¹, Giovanni; Luo, Jingchuan; Boeke, Jef D; Bader, Joel S

Bioinformatics

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

Bose-Einstein condensation in satisfiability problems

Angione, C., Occhipinti, A., Stracquadanio, G., Nicosia, G.

European Journal of Operational Research

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

Semiconductor device design using the BiMADS algorithm

Stracquadanio, G., Romano, V., Nicosia, G.

Journal of Computational Physics

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

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

Computational energy-based redesign of robust proteins

Stracquadanio, G., Nicosia, G.

Computers and Chemical Engineering

Generalized pattern search algorithm for peptide structure prediction

Nicosia, G., Stracquadanio³, G.

Biophysical Journal

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

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

Polymer physics of structural evolution in synthetic yeast chromosomes

Stracquadanio, G., Yang, K., Boeke, J. D., Koszul, R., Bader, J.S.

bioRxiv

Discovering cancer driver genes and pathways using stochastic block model graph neural networks

Fanfani, V., Vinas Torne, R., Lio’, P. and Stracquadanio, G.

biorXiv

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

A unified framework for geneset network analysis

Fanfani, V. and Stracquadanio, G.

biorXiv

Large scale agent-based modeling of the humoral and cellular immune response

Stracquadanio, G., Umeton, R., Costanza, J., Annibali, V., Mechelli, R., Pavone, M., Zammataro, L., Nicosia, G.

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Design of robust metabolic pathways

Umeton, R., Stracquadanio, G., Sorathiya, A., Papini, A., Liò, P., Nicosia, G.

Proceedings - Design Automation Conference

Design of robust space trajectories

Stracquadanio, G., La Ferla, A., De Felice, M., Nicosia, G.

Res. and Dev. in Intelligent Syst. XXVIII: Incorporating Applications and Innovations in Intel. Sys. XIX - AI 2011, 31st SGAI Int. Conf. on Innovative Techniques and Applications of Artificial Intel.

Robust bio-active peptide prediction using multi-objective optimization

Narzisi, G., Nicosia, G., Stracquadanio, G.

2010 International Conference on Biosciences, BioSciencesWorld 2010

An information-theoretic approach for clonal selection algorithms

Cutello, V., Nicosia, G., Pavone, M., Stracquadanio³, G.

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Multi-objective optimization of doping profile in semiconductor design GECCO track: Real world applications

Stracquadanio, G., Drago, C., Romano, V., Nicosia, G.

Proceedings of the 12th Annual Genetic and Evolutionary Computation Conference, GECCO '10

An immunological algorithm for doping profile optimization in semiconductors design

Stracquadanio, G., Drago, C., Romano, V., Nicosia, G.

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Analysis and optimization of C3 photosynthetic carbon metabolism

Stracquadanio, G., Umeton, R., Papini, A., Lio, P., Nicosia, G.

10th IEEE International Conference on Bioinformatics and Bioengineering 2010, BIBE 2010

Effective design of semiconductor devices using evolutionary-based derivative free optimization

Stracquadanio, G., Drago, C., Romano, V., Nicosia, G.

2010 IEEE World Congress on Computational Intelligence, WCCI 2010 - 2010 IEEE Congress on Evolutionary Computation, CEC 2010

Entropic divergence for population based optimization algorithms

Cutello, V., Nicosia, G., Pavone, M., Stracquadanio³, G.

2010 IEEE World Congress on Computational Intelligence, WCCI 2010 - 2010 IEEE Congress on Evolutionary Computation, CEC 2010

A design-for-yield algorithm to assess and improve the structural and energetic robustness of proteins and drugs

Nicosia, G., Stracquadanio³, G.

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Doping profile optimization in semiconductor design

Stracquadanio, G., Drago, C., Romano, V., Nicosia, G.

2009 16th IEEE International Conference on Electronics, Circuits and Systems, ICECS 2009

Nominal-yield-area tradeoff in automatic synthesis of analog circuits: A genetic programming approach using immune-inspired operators

Conca, P., Nicosia, G., Stracquadanio³, G., Timmis, J.

Proceedings - 2009 NASA/ESA Conference on Adaptive Hardware and Systems, AHS 2009

An advanced clonal selection algorithm with ad-hoc network-based hypermutation operators for synthesis of topology and sizing of analog electrical circuits

Ciccazzo, A., Conca, P., Nicosia, G., Stracquadanio³, G.

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

New coupled EM and circuit simulation flow for integrated spiral inductor by introducing symbolic simplified expressions

Ciccazzo, A., Halfmann, T., Marotta, A., Nicosia, G., Rinaudo, S., Stracquadanio³, G., Venturi, A.

IEEE International Symposium on Industrial Electronics

Generalized pattern search and mesh adaptive direct search algorithms for protein structure prediction

Nicosia, G., Stracquadanio³, G.

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)