Non-Native Cooperative Interactions Modulate Protein Folding Rates von Bruno da Silva, Fernando, Contessoto, Vinícius G, de Oliveira, Vinícius M, Clarke, Jane, Leite, Vitor B. P

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Design and proof of concept for targeted phage-based COVID-19 vaccination strategies with a streamlined cold-free supply chain von Staquicini, Daniela I., Tang, Fenny H. F., Markosian, Christopher, Yao, Virginia J., Staquicini, Fernanda I., Dodero-Rojas, Esteban, Contessoto, Vinícius G., Davis, Deodate, O’Brien, Paul, Habib, Nazia, Smith, Tracey L., Bruiners, Natalie, Sidman, Richard L., Gennaro, Maria L., Lattime, Edmund C., Libutti, Steven K., Whitford, Paul C., Burley, Stephen K., Onuchic, José N., Arap, Wadih, Pasqualini, Renata

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NTL9 Folding at Constant pH: The Importance of Electrostatic Interaction and pH Dependence von Contessoto, Vinícius G, de Oliveira, Vinícius M, de Carvalho, Sidney J, Oliveira, Leandro C, Leite, Vitor B. P

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Exploring chromosomal structural heterogeneity across multiple cell lines von Cheng, Ryan R, Contessoto, Vinicius G, Lieberman Aiden, Erez, Wolynes, Peter G, Di Pierro, Michele, Onuchic, Jose N

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Genetic and Structural Analysis of SARS-CoV-2 Spike Protein for Universal Epitope Selection von Markosian, Christopher, Staquicini, Daniela I., Dogra, Prashant, Dodero-Rojas, Esteban, Lubin, Joseph H., Tang, Fenny H.F., Smith, Tracey L., Contessoto, Vinícius G., Libutti, Steven K., Wang, Zhihui, Cristini, Vittorio, Khare, Sagar D., Whitford, Paul C., Burley, Stephen K., Onuchic, José N., Pasqualini, Renata, Arap, Wadih

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Analyzing the effect of homogeneous frustration in protein folding von Contessoto, Vinícius G., Lima, Debora T., Oliveira, Ronaldo J., Bruni, Aline T., Chahine, Jorge, Leite, Vitor B. P.

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Shaping the genome via lengthwise compaction, phase separation, and lamina adhesion von Brahmachari, Sumitabha, Contessoto, Vinícius G, Di Pierro, Michele, Onuchic, José N

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Small Neutral Crowding Solute Effects on Protein Folding Thermodynamic Stability and Kinetics von Contessoto, Vinícius G, Ferreira, Paulo H. B, Chahine, Jorge, Leite, Vitor B. P, Oliveira, Ronaldo J

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Uncovering the statistical physics of 3D chromosomal organization using data-driven modeling von Contessoto, Vinícius G., Cheng, Ryan R., Onuchic, José N.

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A Scalable Computational Approach for Simulating Complexes of Multiple Chromosomes von Oliveira Junior, Antonio B., Contessoto, Vinícius G., Mello, Matheus F., Onuchic, José N.

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Interphase chromosomes of the Aedes aegypti mosquito are liquid crystalline and can sense mechanical cues von Contessoto, Vinicius G., Dudchenko, Olga, Aiden, Erez, Wolynes, Peter G., Onuchic, Jose N., Di Pierro, Michele

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Interphase chromosomes of the Aedes aegypti mosquito are liquid crystalline and can sense mechanical cues von Contessoto, Vinícius G., Dudchenko, Olga, Aiden, Erez Lieberman, Wolynes, Peter G., Onuchic, José N., Di Pierro, Michele

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The Nucleome Data Bank: web-based resources to simulate and analyze the three-dimensional genome von Contessoto, Vinícius G, Cheng, Ryan R, Hajitaheri, Arya, Dodero-Rojas, Esteban, Mello, Matheus F, Lieberman-Aiden, Erez, Wolynes, Peter G, Di Pierro, Michele, Onuchic, José N

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Improving the Thermostability of Xylanase A from Bacillus subtilis by Combining Bioinformatics and Electrostatic Interactions Optimization von Ngo, Khoa, Bruno da Silva, Fernando, Leite, Vitor B. P, Contessoto, Vinícius G, Onuchic, José N

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Chromosome Modeling on Downsampled Hi‑C Maps Enhances the Compartmentalization Signal von Oliveira Junior, Antonio B, Estrada, Cynthia Perez, Aiden, Erez Lieberman, Contessoto, Vinícius G, Onuchic, José N

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PyMEGABASE: Predicting Cell-Type-Specific Structural Annotations of Chromosomes Using the Epigenome von Dodero-Rojas, Esteban, Mello, Matheus F., Brahmachari, Sumitabha, Oliveira Junior, Antonio B., Contessoto, Vinícius G., Onuchic, José N.

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Modeling Chikungunya control strategies and Mayaro potential outbreak in the city of Rio de Janeiro von Dodero-Rojas, Esteban, Ferreira, Luiza G, Leite, Vitor B P, Onuchic, José N, Contessoto, Vinícius G

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AWSEM-Suite: a protein structure prediction server based on template-guided, coevolutionary-enhanced optimized folding landscapes von Jin, Shikai, Contessoto, Vinicius G, Chen, Mingchen, Schafer, Nicholas P, Lu, Wei, Chen, Xun, Bueno, Carlos, Hajitaheri, Arya, Sirovetz, Brian J, Davtyan, Aram, Papoian, Garegin A, Tsai, Min-Yeh, Wolynes, Peter G

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Rational Design of Chymotrypsin Inhibitor 2 by Optimizing Non-Native Interactions von B. da Silva, Fernando, M. de Oliveira, Vinícius, Sanches, Murilo N, Contessoto, Vinícius G, Leite, Vitor B. P

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SMOG 2 and OpenSMOG: Extending the limits of structure‐based models von Oliveira, Antonio B., Contessoto, Vinícius G., Hassan, Asem, Byju, Sandra, Wang, Ailun, Wang, Yang, Dodero‐Rojas, Esteban, Mohanty, Udayan, Noel, Jeffrey K., Onuchic, Jose N., Whitford, Paul C.

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