Shaping the genome via lengthwise compaction, phase separation, and lamina adhesion
Brahmachari, Sumitabha, Contessoto, Vinícius G, Di Pierro, Michele, Onuchic, José N
Published in Nucleic acids research (06.05.2022)
Published in Nucleic acids research (06.05.2022)
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Journal Article
Interphase chromosomes of the Aedes aegypti mosquito are liquid crystalline and can sense mechanical cues
Contessoto, Vinícius G, Dudchenko, Olga, Aiden, Erez Lieberman, Wolynes, Peter G, Onuchic, José N, Di Pierro, Michele
Published in Nature communications (19.01.2023)
Published in Nature communications (19.01.2023)
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Journal Article
The Nucleome Data Bank: web-based resources to simulate and analyze the three-dimensional genome
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
Published in Nucleic acids research (08.01.2021)
Published in Nucleic acids research (08.01.2021)
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Journal Article
Improving the Thermostability of Xylanase A from Bacillus subtilis by Combining Bioinformatics and Electrostatic Interactions Optimization
Ngo, Khoa, Bruno da Silva, Fernando, Leite, Vitor B. P, Contessoto, Vinícius G, Onuchic, José N
Published in The journal of physical chemistry. B (06.05.2021)
Published in The journal of physical chemistry. B (06.05.2021)
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Journal Article
PyMEGABASE: Predicting Cell-Type-Specific Structural Annotations of Chromosomes Using the Epigenome
Dodero-Rojas, Esteban, Mello, Matheus F., Brahmachari, Sumitabha, Oliveira Junior, Antonio B., Contessoto, Vinícius G., Onuchic, José N.
Published in Journal of molecular biology (01.08.2023)
Published in Journal of molecular biology (01.08.2023)
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Journal Article
SMOG 2 and OpenSMOG: Extending the limits of structure‐based models
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.
Published in Protein science (01.01.2022)
Published in Protein science (01.01.2022)
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Journal Article
Structural reorganization and relaxation dynamics of axially stressed chromosomes
Ruben, Benjamin S., Brahmachari, Sumitabha, Contessoto, Vinícius G., Cheng, Ryan R., Oliveira Junior, Antonio B., Di Pierro, Michele, Onuchic, José N.
Published in Biophysical journal (02.05.2023)
Published in Biophysical journal (02.05.2023)
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Journal Article
Three-dimensional genome architecture persists in a 52,000-year-old woolly mammoth skin sample
Sandoval-Velasco, Marcela, Dudchenko, Olga, Rodríguez, Juan Antonio, Pérez Estrada, Cynthia, Dehasque, Marianne, Fontsere, Claudia, Mak, Sarah S.T., Khan, Ruqayya, Contessoto, Vinícius G., Oliveira Junior, Antonio B., Kalluchi, Achyuth, Zubillaga Herrera, Bernardo J., Jeong, Jiyun, Roy, Renata P., Christopher, Ishawnia, Weisz, David, Omer, Arina D., Batra, Sanjit S., Shamim, Muhammad S., Durand, Neva C., O’Connell, Brendan, Roca, Alfred L., Plikus, Maksim V., Kusliy, Mariya A., Romanenko, Svetlana A., Lemskaya, Natalya A., Serdyukova, Natalya A., Modina, Svetlana A., Perelman, Polina L., Kizilova, Elena A., Baiborodin, Sergei I., Rubtsov, Nikolai B., Machol, Gur, Rath, Krisha, Mahajan, Ragini, Kaur, Parwinder, Gnirke, Andreas, Garcia-Treviño, Isabel, Coke, Rob, Flanagan, Joseph P., Pletch, Kelcie, Ruiz-Herrera, Aurora, Plotnikov, Valerii, Pavlov, Innokentiy S., Pavlova, Naryya I., Protopopov, Albert V., Di Pierro, Michele, Graphodatsky, Alexander S., Lander, Eric S., Rowley, M. Jordan, Wolynes, Peter G., Onuchic, José N., Dalén, Love, Marti-Renom, Marc A., Gilbert, M. Thomas P., Aiden, Erez Lieberman
Published in Cell (11.07.2024)
Published in Cell (11.07.2024)
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TKSA‐MC: A web server for rational mutation through the optimization of protein charge interactions
Contessoto, Vinícius G., Oliveira, Vinícius M., Fernandes, Bruno R., Slade, Gabriel G., Leite, Vitor B. P.
Published in Proteins, structure, function, and bioinformatics (01.11.2018)
Published in Proteins, structure, function, and bioinformatics (01.11.2018)
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Journal Article
3D genomics across the tree of life reveals condensin II as a determinant of architecture type
Hoencamp, Claire, Dudchenko, Olga, Elbatsh, Ahmed M O, Brahmachari, Sumitabha, Raaijmakers, Jonne A, van Schaik, Tom, Sedeño Cacciatore, Ángela, Contessoto, Vinícius G, van Heesbeen, Roy G H P, van den Broek, Bram, Mhaskar, Aditya N, Teunissen, Hans, St Hilaire, Brian Glenn, Weisz, David, Omer, Arina D, Pham, Melanie, Colaric, Zane, Yang, Zhenzhen, Rao, Suhas S P, Mitra, Namita, Lui, Christopher, Yao, Weijie, Khan, Ruqayya, Moroz, Leonid L, Kohn, Andrea, St Leger, Judy, Mena, Alexandria, Holcroft, Karen, Gambetta, Maria Cristina, Lim, Fabian, Farley, Emma, Stein, Nils, Haddad, Alexander, Chauss, Daniel, Mutlu, Ayse Sena, Wang, Meng C, Young, Neil D, Hildebrandt, Evin, Cheng, Hans H, Knight, Christopher J, Burnham, Theresa L U, Hovel, Kevin A, Beel, Andrew J, Mattei, Pierre-Jean, Kornberg, Roger D, Warren, Wesley C, Cary, Gregory, Gómez-Skarmeta, José Luis, Hinman, Veronica, Lindblad-Toh, Kerstin, Di Palma, Federica, Maeshima, Kazuhiro, Multani, Asha S, Pathak, Sen, Nel-Themaat, Liesl, Behringer, Richard R, Kaur, Parwinder, Medema, René H, van Steensel, Bas, de Wit, Elzo, Onuchic, José N, Di Pierro, Michele, Lieberman Aiden, Erez, Rowland, Benjamin D
Published in Science (American Association for the Advancement of Science) (28.05.2021)
Published in Science (American Association for the Advancement of Science) (28.05.2021)
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Design and proof of concept for targeted phage-based COVID-19 vaccination strategies with a streamlined cold-free supply chain
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
Published in Proceedings of the National Academy of Sciences - PNAS (27.07.2021)
Published in Proceedings of the National Academy of Sciences - PNAS (27.07.2021)
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Genetic and Structural Analysis of SARS-CoV-2 Spike Protein for Universal Epitope Selection
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
Published in Molecular biology and evolution (03.05.2022)
Published in Molecular biology and evolution (03.05.2022)
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