Biologically informed NeuralODEs for genome-wide regulatory dynamics von Hossain, Intekhab, Fanfani, Viola, Fischer, Jonas, Quackenbush, John, Burkholz, Rebekka

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PyGNA: a unified framework for geneset network analysis von Fanfani, Viola, Cassano, Fabio, Stracquadanio, Giovanni

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The Network Zoo: a multilingual package for the inference and analysis of gene regulatory networks von Ben Guebila, Marouen, Wang, Tian, Lopes-Ramos, Camila M, Fanfani, Viola, Weighill, Des, Burkholz, Rebekka, Schlauch, Daniel, Paulson, Joseph N, Altenbuchinger, Michael, Shutta, Katherine H, Sonawane, Abhijeet R, Lim, James, Calderer, Genis, van IJzendoorn, David G P, Morgan, Daniel, Marin, Alessandro, Chen, Cho-Yi, Song, Qi, Saha, Enakshi, DeMeo, Dawn L, Padi, Megha, Platig, John, Kuijjer, Marieke L, Glass, Kimberly, Quackenbush, John

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Gene regulatory networks reveal sex difference in lung adenocarcinoma von Saha, Enakshi, Ben Guebila, Marouen, Fanfani, Viola, Fischer, Jonas, Shutta, Katherine H, Mandros, Panagiotis, DeMeo, Dawn L, Quackenbush, John, Lopes-Ramos, Camila M

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The Landscape of the Heritable Cancer Genome von Fanfani, Viola, Citi, Luca, Harris, Adrian L., Pezzella, Francesco, Stracquadanio, Giovanni

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Dissecting the heritable risk of breast cancer: From statistical methods to susceptibility genes von Fanfani, Viola, Zatopkova, Martina, Harris, Adrian L., Pezzella, Francesco, Stracquadanio, Giovanni

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Machine learning and large scale cancer omic data: decoding the biological mechanisms underpinning cancer von Fanfani, Viola

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Debugging and consolidating multiple synthetic chromosomes reveals combinatorial genetic interactions von Zhao, Yu, Coelho, Camila, Hughes, Amanda L., Lazar-Stefanita, Luciana, Yang, Sandy, Brooks, Aaron N., Walker, Roy S.K., Zhang, Weimin, Lauer, Stephanie, Hernandez, Cindy, Cai, Jitong, Mitchell, Leslie A., Agmon, Neta, Shen, Yue, Sall, Joseph, Fanfani, Viola, Jalan, Anavi, Rivera, Jordan, Liang, Feng-Xia, Bader, Joel S., Stracquadanio, Giovanni, Steinmetz, Lars M., Cai, Yizhi, Boeke, Jef D.

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Systematic analysis of the IL‐17 receptor signalosome reveals a robust regulatory feedback loop von Draberova, Helena, Janusova, Sarka, Knizkova, Daniela, Semberova, Tereza, Pribikova, Michaela, Ujevic, Andrea, Harant, Karel, Knapkova, Sofija, Hrdinka, Matous, Fanfani, Viola, Stracquadanio, Giovanni, Drobek, Ales, Ruppova, Klara, Stepanek, Ondrej, Draber, Peter

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Manipulating the 3D organization of the largest synthetic yeast chromosome von Zhang, Weimin, Lazar-Stefanita, Luciana, Yamashita, Hitoyoshi, Shen, Michael J, Mitchell, Leslie A, Kurasawa, Hikaru, Lobzaev, Evgenii, Fanfani, Viola, Haase, Max A B, Sun, Xiaoji, Jiang, Qingwen, Goldberg, Gregory W, Ichikawa, David M, Lauer, Stephanie L, McCulloch, Laura H, Easo, Nicole, Lin, S Jiaming, Camellato, Brendan R, Zhu, Yinan, Cai, Jitong, Xu, Zhuwei, Zhao, Yu, Sacasa, Maya, Noyes, Marcus B, Bader, Joel S, Deutsch, Samuel, Stracquadanio, Giovanni, Aizawa, Yasunori, Dai, Junbiao, Boeke, Jef D

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Synthetic yeast chromosome XI design provides a testbed for the study of extrachromosomal circular DNA dynamics von Blount, Benjamin A., Lu, Xinyu, Driessen, Maureen R.M., Jovicevic, Dejana, Sanchez, Mateo I., Ciurkot, Klaudia, Zhao, Yu, Lauer, Stephanie, McKiernan, Robert M., Gowers, Glen-Oliver F., Sweeney, Fiachra, Fanfani, Viola, Lobzaev, Evgenii, Palacios-Flores, Kim, Walker, Roy S.K., Hesketh, Andy, Cai, Jitong, Oliver, Stephen G., Cai, Yizhi, Stracquadanio, Giovanni, Mitchell, Leslie A., Bader, Joel S., Boeke, Jef D., Ellis, Tom

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Consequences of a telomerase-related fitness defect and chromosome substitution technology in yeast synIX strains von McCulloch, Laura H, Sambasivam, Vijayan, Hughes, Amanda L, Annaluru, Narayana, Ramalingam, Sivaprakash, Fanfani, Viola, Lobzaev, Evgenii, Mitchell, Leslie A, Cai, Jitong, Jiang, Hua, LaCava, John, Taylor, Martin S, Bishai, William R, Stracquadanio, Giovanni, Steinmetz, Lars M, Bader, Joel S, Zhang, Weimin, Boeke, Jef D, Chandrasegaran, Srinivasan

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Context-dependent neocentromere activity in synthetic yeast chromosome VIII von Lauer, Stephanie, Luo, Jingchuan, Lazar-Stefanita, Luciana, Zhang, Weimin, McCulloch, Laura H, Fanfani, Viola, Lobzaev, Evgenii, Haase, Max A B, Easo, Nicole, Zhao, Yu, Yu, Fangzhou, Cai, Jitong, Bader, Joel S, Stracquadanio, Giovanni, Boeke, Jef D

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Mutation landscape of multiple myeloma measurable residual disease: identification of targets for precision medicine von Zátopková, Martina, Ševčíková, Tereza, Fanfani, Viola, Chyra, Zuzana, Říhová, Lucie, Bezděková, Renata, Žihala, David, Growková, Kateřina, Filipová, Jana, Černá, Lucie, Broskevičova, Lucie, Kryukov, Fedor, Minařík, Jiří, Smejkalová, Jana, Maisnar, Vladimír, Harvanová, Ĺubica, Pour, Luděk, Jungova, Alexandra, Popková, Tereza, Bago, Juli Rodriguez, Anilkumar Sithara, Anjana, Hrdinka, Matouš, Jelínek, Tomáš, Šimíček, Michal, Stracquadanio, Giovanni, Hájek, Roman

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BONOBO: Bayesian Optimized Sample-Specific Networks Obtained by Omics Data von Saha, Enakshi, Fanfani, Viola, Mandros, Panagiotis, Ben-Guebila, Marouen, Fischer, Jonas, Shutta, Katherine H., Glass, Kimberly, DeMeo, Dawn L., Lopes-Ramos, Camila M., Quackenbush, John

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BONOBO replication data von Fanfani, Viola, Saha, Enakshi

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Data and scripts used for the node2vec2rank paper von Mandros, Panagiotis, Fanfani, Viola, Chen, Chen

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Heritability analysis of the 38 cancers in the UK Biobank von Fanfani, Viola, Stracquadanio, Giovanni

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PyGNA: a unified framework for geneset network analysis von Fanfani, Viola, Cassano, Fabio, Stracquadanio, Giovanni

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The Network Zoo: a multilingual package for the inference and analysis of gene regulatory networks von Ben Guebila, Marouen, Wang, Tian, Lopes-Ramos, Camila M, Fanfani, Viola, Weighill, Des, Burkholz, Rebekka, Schlauch, Daniel, Paulson, Joseph N, Altenbuchinger, Michael, Shutta, Katherine H, Sonawane, Abhijeet R, Lim, James, Calderer, Genis, van IJzendoorn, David G, Morgan, Daniel, Marin, Alessandro, Chen, Cho-Yi, Song, Qi, Saha, Enakshi, DeMeo, Dawn L, Padi, Megha, Platig, John, Kuijjer, Marieke L, Glass, Kimberly, Quackenbush, John

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