José Nelson Onuchic (José N Onuchic, Jose N Onuchic)

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 73

Top Topics

Molecular Dynamics Simulations

Duchenne Muscular Dystrophy

Intellectual Disability

Top Venues

Proceedings of the National Academy of Sciences of the United States of America

The journal of physical chemistry. B

Nature communications

This page only lists publications with an associated author ORCID identifier.

Publications

Tae-Yun Kang, Federico Bocci, Qing Nie, José Nelson Onuchic, Andre Levchenko
Spatial-temporal order-disorder transition in angiogenic NOTCH signaling controls cell fate specification. eLife 12 (2024)
Flavia Novelli, Yoshie Yoshikawa, Veronica Angela Maria Vitto, Lorenzo Modesti, Michael Minaai, Sandra Pastorino, Mitsuru Emi, Jin-Hee Kim, Franz Kricek, Fang Bai, José Nelson Onuchic, Angela Bononi, Joelle D Sacks, Mika Tanji, Cristina Favaron, Alicia A Zolondick, Ronghui Xu, Yasutaka Takanishi, Zhanwei Wang, Greg Sakamoto, Giovanni Gaudino, Joseph Grzymski, Federica Grosso, David S Schrump, Harvey I Pass, Lilit Atanesyan, Jan Smout, Laura Chiecchio, Kavita Y Sarin, Hassan Abolhassani, Lennart Hammarström, Qiang Pan-Hammarström, Carlotta Giorgi, Paolo Pinton, Haining Yang, Michele Carbone
Germline BARD1 variants predispose to mesothelioma by impairing DNA repair and calcium signaling. Proceedings of the National Academy of Sciences of the United States of America 121 (29) (2024)
Flavia Novelli, Yoshie Yoshikawa, Veronica Angela Maria Vitto, Lorenzo Modesti, Michael Minaai, Sandra Pastorino, Mitsuru Emi, Jin-Hee Kim, Franz Kricek, Fang Bai, José Nelson Onuchic, Angela Bononi, Joelle D Sacks, Mika Tanji, Cristina Favaron, Alicia A Zolondick, Ronghui Xu, Yasutaka Takanishi, Zhanwei Wang, Greg Sakamoto, Giovanni Gaudino, Joseph Grzymski, Federica Grosso, David S Schrump, Harvey I Pass, Lilit Atanesyan, Jan Smout, Laura Chiecchio, Kavita Y Sarin, Hassan Abolhassani, Lennart Hammarström, Qiang Pan-Hammarström, Carlotta Giorgi, Paolo Pinton, Haining Yang, Michele Carbone
Germline BARD1 variants predispose to mesothelioma by impairing DNA repair and calcium signaling. Proceedings of the National Academy of Sciences of the United States of America 121 (29) (2024)
Jonathan Martin, Marcos Lequerica Mateos, José Nelson Onuchic, Ivan Coluzza, Faruck Morcos
Machine learning in biological physics: From biomolecular prediction to design. Proceedings of the National Academy of Sciences of the United States of America 121 (27) (2024)
Rachel Nechushtai, Linda Rowland, Ola Karmi, Henri-Baptiste Marjault, Thi Thao Nguyen, Shubham Mittal, Raheel S Ahmed, DeAna Grant, Camila Manrique-Acevedo, Faruck Morcos, José Nelson Onuchic, Ron Mittler
CISD3/MiNT is required for complex I function, mitochondrial integrity, and skeletal muscle maintenance. Proceedings of the National Academy of Sciences of the United States of America 121 (22) (2024)
Michael W Grunst, Zhuan Qin, Esteban Dodero-Rojas, Shilei Ding, Jérémie Prévost, Yaozong Chen, Yanping Hu, Marzena E Pazgier, Shenping Wu, Xuping Xie, Andrés Finzi, José Nelson Onuchic, Paul Charles Whitford, Walther Mothes, Wenwei Li
Structure and inhibition of SARS-CoV-2 spike refolding in membranes. Science (New York, N.Y.) 385 (6710) (2024)
Ailun Wang, Xingcheng Lin, Kevin Ng Chau, José Nelson Onuchic, Herbert Levine, Jason T George
RACER-m leverages structural features for sparse T cell specificity prediction. Science advances 10 (20) (2024)
Jonathan Martin, Marcos Lequerica Mateos, José Nelson Onuchic, Ivan Coluzza, Faruck Morcos
Machine learning in biological physics: From biomolecular prediction to design. Proceedings of the National Academy of Sciences of the United States of America 121 (27) (2024)
Ailun Wang, Xingcheng Lin, Kevin Ng Chau, José Nelson Onuchic, Herbert Levine, Jason T George
RACER-m leverages structural features for sparse T cell specificity prediction. Science advances 10 (20) (2024)
Flavia Novelli, Yoshie Yoshikawa, Veronica Angela Maria Vitto, Lorenzo Modesti, Michael Minaai, Sandra Pastorino, Mitsuru Emi, Jin-Hee Kim, Franz Kricek, Fang Bai, José Nelson Onuchic, Angela Bononi, Joelle D Sacks, Mika Tanji, Cristina Favaron, Alicia A Zolondick, Ronghui Xu, Yasutaka Takanishi, Zhanwei Wang, Greg Sakamoto, Giovanni Gaudino, Joseph Grzymski, Federica Grosso, David S Schrump, Harvey I Pass, Lilit Atanesyan, Jan Smout, Laura Chiecchio, Kavita Y Sarin, Hassan Abolhassani, Lennart Hammarström, Qiang Pan-Hammarström, Carlotta Giorgi, Paolo Pinton, Haining Yang, Michele Carbone
Germline BARD1 variants predispose to mesothelioma by impairing DNA repair and calcium signaling. Proceedings of the National Academy of Sciences of the United States of America 121 (29) (2024)
Rachel Nechushtai, Linda Rowland, Ola Karmi, Henri-Baptiste Marjault, Thi Thao Nguyen, Shubham Mittal, Raheel S Ahmed, DeAna Grant, Camila Manrique-Acevedo, Faruck Morcos, José Nelson Onuchic, Ron Mittler
CISD3/MiNT is required for complex I function, mitochondrial integrity, and skeletal muscle maintenance. Proceedings of the National Academy of Sciences of the United States of America 121 (22) (2024)
Sumitabha Brahmachari, Shubham Tripathi, José Nelson Onuchic, Herbert Levine
Nucleosomes play a dual role in regulating transcription dynamics. Proceedings of the National Academy of Sciences of the United States of America 121 (28) (2024)
Sumitabha Brahmachari, Shubham Tripathi, José Nelson Onuchic, Herbert Levine
Nucleosomes play a dual role in regulating transcription dynamics. Proceedings of the National Academy of Sciences of the United States of America 121 (28) (2024)
Jonathan Martin, Marcos Lequerica Mateos, José Nelson Onuchic, Ivan Coluzza, Faruck Morcos
Machine learning in biological physics: From biomolecular prediction to design. Proceedings of the National Academy of Sciences of the United States of America 121 (27) (2024)
Rachel Nechushtai, Linda Rowland, Ola Karmi, Henri-Baptiste Marjault, Thi Thao Nguyen, Shubham Mittal, Raheel S Ahmed, DeAna Grant, Camila Manrique-Acevedo, Faruck Morcos, José Nelson Onuchic, Ron Mittler
CISD3/MiNT is required for complex I function, mitochondrial integrity, and skeletal muscle maintenance. Proceedings of the National Academy of Sciences of the United States of America 121 (22) (2024)
Flavia Novelli, Yoshie Yoshikawa, Veronica Angela Maria Vitto, Lorenzo Modesti, Michael Minaai, Sandra Pastorino, Mitsuru Emi, Jin-Hee Kim, Franz Kricek, Fang Bai, José Nelson Onuchic, Angela Bononi, Joelle D Sacks, Mika Tanji, Cristina Favaron, Alicia A Zolondick, Ronghui Xu, Yasutaka Takanishi, Zhanwei Wang, Greg Sakamoto, Giovanni Gaudino, Joseph Grzymski, Federica Grosso, David S Schrump, Harvey I Pass, Lilit Atanesyan, Jan Smout, Laura Chiecchio, Kavita Y Sarin, Hassan Abolhassani, Lennart Hammarström, Qiang Pan-Hammarström, Carlotta Giorgi, Paolo Pinton, Haining Yang, Michele Carbone
Germline BARD1 variants predispose to mesothelioma by impairing DNA repair and calcium signaling. Proceedings of the National Academy of Sciences of the United States of America 121 (29) (2024)
Rachel Nechushtai, Linda Rowland, Ola Karmi, Henri-Baptiste Marjault, Thi Thao Nguyen, Shubham Mittal, Raheel S Ahmed, DeAna Grant, Camila Manrique-Acevedo, Faruck Morcos, José Nelson Onuchic, Ron Mittler
CISD3/MiNT is required for complex I function, mitochondrial integrity, and skeletal muscle maintenance. Proceedings of the National Academy of Sciences of the United States of America 121 (22) (2024)
Ailun Wang, Xingcheng Lin, Kevin Ng Chau, José Nelson Onuchic, Herbert Levine, Jason T George
RACER-m leverages structural features for sparse T cell specificity prediction. Science advances 10 (20) (2024)
Rachel Nechushtai, Linda Rowland, Ola Karmi, Henri-Baptiste Marjault, Thi Thao Nguyen, Shubham Mittal, Raheel S Ahmed, DeAna Grant, Camila Manrique-Acevedo, Faruck Morcos, José Nelson Onuchic, Ron Mittler
CISD3/MiNT is required for complex I function, mitochondrial integrity, and skeletal muscle maintenance. Proceedings of the National Academy of Sciences of the United States of America 121 (22) (2024)
Sumitabha Brahmachari, Shubham Tripathi, José Nelson Onuchic, Herbert Levine
Nucleosomes play a dual role in regulating transcription dynamics. Proceedings of the National Academy of Sciences of the United States of America 121 (28) (2024)
Tae-Yun Kang, Federico Bocci, Qing Nie, José Nelson Onuchic, Andre Levchenko
Spatial-temporal order-disorder transition in angiogenic NOTCH signaling controls cell fate specification. eLife 12 (2024)
Flavia Novelli, Yoshie Yoshikawa, Veronica Angela Maria Vitto, Lorenzo Modesti, Michael Minaai, Sandra Pastorino, Mitsuru Emi, Jin-Hee Kim, Franz Kricek, Fang Bai, José Nelson Onuchic, Angela Bononi, Joelle D Sacks, Mika Tanji, Cristina Favaron, Alicia A Zolondick, Ronghui Xu, Yasutaka Takanishi, Zhanwei Wang, Greg Sakamoto, Giovanni Gaudino, Joseph Grzymski, Federica Grosso, David S Schrump, Harvey I Pass, Lilit Atanesyan, Jan Smout, Laura Chiecchio, Kavita Y Sarin, Hassan Abolhassani, Lennart Hammarström, Qiang Pan-Hammarström, Carlotta Giorgi, Paolo Pinton, Haining Yang, Michele Carbone
Germline BARD1 variants predispose to mesothelioma by impairing DNA repair and calcium signaling. Proceedings of the National Academy of Sciences of the United States of America 121 (29) (2024)
Rachel Nechushtai, Linda Rowland, Ola Karmi, Henri-Baptiste Marjault, Thi Thao Nguyen, Shubham Mittal, Raheel S Ahmed, DeAna Grant, Camila Manrique-Acevedo, Faruck Morcos, José Nelson Onuchic, Ron Mittler
CISD3/MiNT is required for complex I function, mitochondrial integrity, and skeletal muscle maintenance. Proceedings of the National Academy of Sciences of the United States of America 121 (22) (2024)
Tae-Yun Kang, Federico Bocci, Qing Nie, José Nelson Onuchic, Andre Levchenko
Spatial-temporal order-disorder transition in angiogenic NOTCH signaling controls cell fate specification. eLife 12 (2024)
Michael W Grunst, Zhuan Qin, Esteban Dodero-Rojas, Shilei Ding, Jérémie Prévost, Yaozong Chen, Yanping Hu, Marzena E Pazgier, Shenping Wu, Xuping Xie, Andrés Finzi, José Nelson Onuchic, Paul Charles Whitford, Walther Mothes, Wenwei Li
Structure and inhibition of SARS-CoV-2 spike refolding in membranes. Science (New York, N.Y.) 385 (6710) (2024)
Michael W Grunst, Zhuan Qin, Esteban Dodero-Rojas, Shilei Ding, Jérémie Prévost, Yaozong Chen, Yanping Hu, Marzena E Pazgier, Shenping Wu, Xuping Xie, Andrés Finzi, José Nelson Onuchic, Paul Charles Whitford, Walther Mothes, Wenwei Li
Structure and inhibition of SARS-CoV-2 spike refolding in membranes. Science (New York, N.Y.) 385 (6710) (2024)
Tae-Yun Kang, Federico Bocci, Qing Nie, José Nelson Onuchic, Andre Levchenko
Spatial-temporal order-disorder transition in angiogenic NOTCH signaling controls cell fate specification. eLife 12 (2024)
Angela Bononi, Qian Wang, Alicia A Zolondick, Fang Bai, Mika Steele-Tanji, Joelle D Sacks, Sandra Pastorino, Abigail Sipes, Valentina Signorato, Angelica Ferro, Flavia Novelli, Jin-Hee Kim, Michael Minaai, Yasutaka Takinishi, Laura Pellegrini, Andrea Napolitano, Ronghui Xu, Christine E Farrar, Chandra Goparaju, Cristian Bassi, Massimo Negrini, Ian S Pagano, Greg Sakamoto, Giovanni Gaudino, Harvey I Pass, José Nelson Onuchic, Haining Yang, Michele Carbone
BAP1 is a novel regulator of HIF-1α. Proceedings of the National Academy of Sciences of the United States of America 120 (4) (2023)
Angela Bononi, Qian Wang, Alicia A Zolondick, Fang Bai, Mika Steele-Tanji, Joelle D Sacks, Sandra Pastorino, Abigail Sipes, Valentina Signorato, Angelica Ferro, Flavia Novelli, Jin-Hee Kim, Michael Minaai, Yasutaka Takinishi, Laura Pellegrini, Andrea Napolitano, Ronghui Xu, Christine E Farrar, Chandra Goparaju, Cristian Bassi, Massimo Negrini, Ian S Pagano, Greg Sakamoto, Giovanni Gaudino, Harvey I Pass, José Nelson Onuchic, Haining Yang, Michele Carbone
BAP1 is a novel regulator of HIF-1α. Proceedings of the National Academy of Sciences of the United States of America 120 (4) (2023)
Angela Bononi, Qian Wang, Alicia A Zolondick, Fang Bai, Mika Steele-Tanji, Joelle D Sacks, Sandra Pastorino, Abigail Sipes, Valentina Signorato, Angelica Ferro, Flavia Novelli, Jin-Hee Kim, Michael Minaai, Yasutaka Takinishi, Laura Pellegrini, Andrea Napolitano, Ronghui Xu, Christine E Farrar, Chandra Goparaju, Cristian Bassi, Massimo Negrini, Ian S Pagano, Greg Sakamoto, Giovanni Gaudino, Harvey I Pass, José Nelson Onuchic, Haining Yang, Michele Carbone
BAP1 is a novel regulator of HIF-1α. Proceedings of the National Academy of Sciences of the United States of America 120 (4) (2023)
Vinícius de Godoi Contessoto, Olga Dudchenko, Erez Lieberman Aiden, Peter G Wolynes, José Nelson Onuchic, Michele Di Pierro
Interphase chromosomes of the Aedes aegypti mosquito are liquid crystalline and can sense mechanical cues. Nature communications 14 (1) (2023)
Vinícius de Godoi Contessoto, Olga Dudchenko, Erez Lieberman Aiden, Peter G Wolynes, José Nelson Onuchic, Michele Di Pierro
Interphase chromosomes of the Aedes aegypti mosquito are liquid crystalline and can sense mechanical cues. Nature communications 14 (1) (2023)
Vinícius de Godoi Contessoto, Olga Dudchenko, Erez Lieberman Aiden, Peter G Wolynes, José Nelson Onuchic, Michele Di Pierro
Interphase chromosomes of the Aedes aegypti mosquito are liquid crystalline and can sense mechanical cues. Nature communications 14 (1) (2023)
Angela Bononi, Qian Wang, Alicia A Zolondick, Fang Bai, Mika Steele-Tanji, Joelle D Sacks, Sandra Pastorino, Abigail Sipes, Valentina Signorato, Angelica Ferro, Flavia Novelli, Jin-Hee Kim, Michael Minaai, Yasutaka Takinishi, Laura Pellegrini, Andrea Napolitano, Ronghui Xu, Christine E Farrar, Chandra Goparaju, Cristian Bassi, Massimo Negrini, Ian S Pagano, Greg Sakamoto, Giovanni Gaudino, Harvey I Pass, José Nelson Onuchic, Haining Yang, Michele Carbone
BAP1 is a novel regulator of HIF-1α. Proceedings of the National Academy of Sciences of the United States of America 120 (4) (2023)
Angela Bononi, Qian Wang, Alicia A Zolondick, Fang Bai, Mika Steele-Tanji, Joelle D Sacks, Sandra Pastorino, Abigail Sipes, Valentina Signorato, Angelica Ferro, Flavia Novelli, Jin-Hee Kim, Michael Minaai, Yasutaka Takinishi, Laura Pellegrini, Andrea Napolitano, Ronghui Xu, Christine E Farrar, Chandra Goparaju, Cristian Bassi, Massimo Negrini, Ian S Pagano, Greg Sakamoto, Giovanni Gaudino, Harvey I Pass, José Nelson Onuchic, Haining Yang, Michele Carbone
BAP1 is a novel regulator of HIF-1α. Proceedings of the National Academy of Sciences of the United States of America 120 (4) (2023)
Vinícius de Godoi Contessoto, Olga Dudchenko, Erez Lieberman Aiden, Peter G Wolynes, José Nelson Onuchic, Michele Di Pierro
Interphase chromosomes of the Aedes aegypti mosquito are liquid crystalline and can sense mechanical cues. Nature communications 14 (1) (2023)
Angela Bononi, Qian Wang, Alicia A Zolondick, Fang Bai, Mika Steele-Tanji, Joelle D Sacks, Sandra Pastorino, Abigail Sipes, Valentina Signorato, Angelica Ferro, Flavia Novelli, Jin-Hee Kim, Michael Minaai, Yasutaka Takinishi, Laura Pellegrini, Andrea Napolitano, Ronghui Xu, Christine E Farrar, Chandra Goparaju, Cristian Bassi, Massimo Negrini, Ian S Pagano, Greg Sakamoto, Giovanni Gaudino, Harvey I Pass, José Nelson Onuchic, Haining Yang, Michele Carbone
BAP1 is a novel regulator of HIF-1α. Proceedings of the National Academy of Sciences of the United States of America 120 (4) (2023)
Vinícius de Godoi Contessoto, Olga Dudchenko, Erez Lieberman Aiden, Peter G Wolynes, José Nelson Onuchic, Michele Di Pierro
Interphase chromosomes of the Aedes aegypti mosquito are liquid crystalline and can sense mechanical cues. Nature communications 14 (1) (2023)
Angela Bononi, Qian Wang, Alicia A Zolondick, Fang Bai, Mika Steele-Tanji, Joelle D Sacks, Sandra Pastorino, Abigail Sipes, Valentina Signorato, Angelica Ferro, Flavia Novelli, Jin-Hee Kim, Michael Minaai, Yasutaka Takinishi, Laura Pellegrini, Andrea Napolitano, Ronghui Xu, Christine E Farrar, Chandra Goparaju, Cristian Bassi, Massimo Negrini, Ian S Pagano, Greg Sakamoto, Giovanni Gaudino, Harvey I Pass, José Nelson Onuchic, Haining Yang, Michele Carbone
BAP1 is a novel regulator of HIF-1α. Proceedings of the National Academy of Sciences of the United States of America 120 (4) (2023)
Angela Bononi, Qian Wang, Alicia A Zolondick, Fang Bai, Mika Steele-Tanji, Joelle D Sacks, Sandra Pastorino, Abigail Sipes, Valentina Signorato, Angelica Ferro, Flavia Novelli, Jin-Hee Kim, Michael Minaai, Yasutaka Takinishi, Laura Pellegrini, Andrea Napolitano, Ronghui Xu, Christine E Farrar, Chandra Goparaju, Cristian Bassi, Massimo Negrini, Ian S Pagano, Greg Sakamoto, Giovanni Gaudino, Harvey I Pass, José Nelson Onuchic, Haining Yang, Michele Carbone
BAP1 is a novel regulator of HIF-1α. Proceedings of the National Academy of Sciences of the United States of America 120 (4) (2023)
Frederico Campos Freitas, Michelli Maldonado, Antonio Bento Oliveira Junior, José Nelson Onuchic, Ronaldo Junio de Oliveira
Biotin-painted proteins have thermodynamic stability switched by kinetic folding routes. The Journal of chemical physics 156 (19) (2022)
Rabindra Nath Manna, José Nelson Onuchic, Biman Jana
Road-blocker HSP disease mutation disrupts pre-organization for ATP hydrolysis in kinesin through a second sphere control. Proceedings of the National Academy of Sciences of the United States of America 120 (1) (2022)
Rabindra Nath Manna, José Nelson Onuchic, Biman Jana
Road-blocker HSP disease mutation disrupts pre-organization for ATP hydrolysis in kinesin through a second sphere control. Proceedings of the National Academy of Sciences of the United States of America 120 (1) (2022)
Frederico Campos Freitas, Michelli Maldonado, Antonio Bento Oliveira Junior, José Nelson Onuchic, Ronaldo Junio de Oliveira
Erratum: "Biotin-painted proteins have thermodynamic stability switched by kinetic folding routes" [J. Chem. Phys. 156, 195101 (2022)]. The Journal of chemical physics 157 (4) (2022)
Ola Karmi, Henri-Baptiste Marjault, Fang Bai, Susmita Roy, Yang-Sung Sohn, Merav Darash Yahana, Faruck Morcos, Konstantinos Ioannidis, Yaakov Nahmias, Patricia A Jennings, Ron Mittler, José Nelson Onuchic, Rachel Nechushtai
A VDAC1-mediated NEET protein chain transfers [2Fe-2S] clusters between the mitochondria and the cytosol and impacts mitochondrial dynamics. Proceedings of the National Academy of Sciences of the United States of America 119 (7) (2022)
Rabindra Nath Manna, José Nelson Onuchic, Biman Jana
Road-blocker HSP disease mutation disrupts pre-organization for ATP hydrolysis in kinesin through a second sphere control. Proceedings of the National Academy of Sciences of the United States of America 120 (1) (2022)
Rabindra Nath Manna, José Nelson Onuchic, Biman Jana
Road-blocker HSP disease mutation disrupts pre-organization for ATP hydrolysis in kinesin through a second sphere control. Proceedings of the National Academy of Sciences of the United States of America 120 (1) (2022)
Madeline Galbraith, Federico Bocci, José Nelson Onuchic
Stochastic fluctuations promote ordered pattern formation of cells in the Notch-Delta signaling pathway. PLoS computational biology 18 (7) (2022)
Giulia Magi Meconi, Ivan Ramos Sasselli, Valentino Bianco, José Nelson Onuchic, Ivan Coluzza
Key aspects of the past 30 years of protein design. Reports on progress in physics. Physical Society (Great Britain) 85 (8) (2022)
Rabindra Nath Manna, José Nelson Onuchic, Biman Jana
Road-blocker HSP disease mutation disrupts pre-organization for ATP hydrolysis in kinesin through a second sphere control. Proceedings of the National Academy of Sciences of the United States of America 120 (1) (2022)
Claire Hoencamp, Olga Dudchenko, Ahmed M O Elbatsh, Sumitabha Brahmachari, Jonne A Raaijmakers, Tom van Schaik, Ángela Sedeño Cacciatore, Vinícius de Godoi Contessoto, Roy G H P van Heesbeen, Bram van den Broek, Aditya N Mhaskar, Hans Teunissen, Brian Glenn St Hilaire, David Weisz, Arina D Omer, Melanie Pham, Zane Colaric, Zhenzhen Yang, Suhas S P Rao, Namita Mitra, Christopher G Lui, Weijie Yao, Ruqayya Khan, Leonid L Moroz, Andrea Kohn, Judy St Leger, Alexandria Mena, Karen Holcroft, Maria Cristina Gambetta, Fabian Lim, Emma Kirsten Farley, Nils Stein, Alexander Haddad, Daniel Chauss, Ayse Sena Mutlu, Meng C Wang, Neil David Young, Evin Hildebrandt, Hans H Cheng, Christopher J Knight, Theresa L U Burnham, Kevin A Hovel, Andrew J Beel, Pierre-Jean Mattei, Roger D Kornberg, Wesley C Warren, Veronica F Hinman, José Luis Gómez-Skarmeta, Veronica F Hinman, Kerstin Lindblad-Toh, Federica Di Palma, Kazuhiro Maeshima, Asha S Multani, Sen Pathak, Liesl Nel-Themaat, Richard R Behringer, Parwinder Kaur, René H Medema, Bas van Steensel, Elzo de Wit, José Nelson Onuchic, Michele Di Pierro, Erez Lieberman Aiden, Benjamin D Rowland
3D genomics across the tree of life reveals condensin II as a determinant of architecture type. Science (New York, N.Y.) 372 (6545) (2021)
Samuel A Vilchez Mercedes, Federico Bocci, Herbert Levine, José Nelson Onuchic, Mohit Kumar Jolly, Pak Kin Wong
Decoding leader cells in collective cancer invasion. Nature reviews. Cancer 21 (9) (2021)
Antonio Bento Oliveira Junior, Vinícius de Godoi Contessoto, Asem Hassan, Sandra Byju, Ailun Wang, Yang Wang, Esteban Dodero-Rojas, Udayan Mohanty, Jeffrey K Noel, José Nelson Onuchic, Paul Charles Whitford
SMOG 2 and OpenSMOG: Extending the limits of structure-based models. Protein science : a publication of the Protein Society (2021)
Flavia Novelli, Angela Bononi, Qian Wang, Fang Bai, Simone Patergnani, Franz Kricek, Ellinor Haglund, Joelle D Sacks, Mika Tanji, Ronghui Xu, Yasutaka Takanishi, Michael Minaai, Sandra Pastorino, Paul Morris, Greg Sakamoto, Harvey I Pass, Haithem Barbour, Giovanni Gaudino, Carlotta Giorgi, Paolo Pinton, José Nelson Onuchic, Haining Yang, Michele Carbone
BAP1 forms a trimer with HMGB1 and HDAC1 that modulates gene × environment interaction with asbestos. Proceedings of the National Academy of Sciences of the United States of America 118 (48) (2021)
Kareem M Mehrabiani, Ryan R Cheng, José Nelson Onuchic
Expanding Direct Coupling Analysis to Identify Heterodimeric Interfaces from Limited Protein Sequence Data. The journal of physical chemistry. B 125 (41) (2021)
Murilo Nogueira Sanches, Kaitlin Knapp, Antonio B Oliveira, Peter G Wolynes, José Nelson Onuchic, Ingrid B S Martins
Examining the Ensembles of Amyloid-β Monomer Variants and Their Propensities to Form Fibers Using an Energy Landscape Visualization Method. The journal of physical chemistry. B 126 (1) (2021)
Esteban Dodero-Rojas, José Nelson Onuchic, Paul Charles Whitford
Sterically confined rearrangements of SARS-CoV-2 Spike protein control cell invasion. eLife 10 (2021)
Antonio B Oliveira Junior, Xingcheng Lin, Prakash Kulkarni, José Nelson Onuchic, Susmita Roy, Ingrid B S Martins
Exploring Energy Landscapes of Intrinsically Disordered Proteins: Insights into Functional Mechanisms. Journal of chemical theory and computation 17 (5) (2021)
Daniela I Staquicini, Fenny H F Tang, Christopher Markosian, Virginia J Yao, Fernanda I Staquicini, Esteban Dodero-Rojas, Vinícius G Contessoto, Deodate Davis, Paul O'Brien, Nazia Habib, Tracey L Smith, Natalie Bruiners, Richard L Sidman, Maria Laura Gennaro, Edmund C Lattime, Steven K Libutti, Paul Charles Whitford, Stephen K Burley, José Nelson Onuchic, Wadih Arap, Renata Pasqualini
Design and proof of concept for targeted phage-based COVID-19 vaccination strategies with a streamlined cold-free supply chain. Proceedings of the National Academy of Sciences of the United States of America 118 (30) (2021)
Dongya Jia, Jun Hyoung Park, Harsimran Kaur, Kwang Hwa Jung, Sukjin Yang, Shubham Tripathi, Madeline Galbraith, Youyuan Deng, Mohit Kumar Jolly, Benny Abraham Kaipparettu, José Nelson Onuchic, Herbert Levine
Towards decoding the coupled decision-making of metabolism and epithelial-to-mesenchymal transition in cancer. British journal of cancer 124 (12) (2021)
Antonio B Oliveira Junior, Cynthia Perez Estrada, Erez Lieberman Aiden, Vinícius de Godoi Contessoto, José Nelson Onuchic
Chromosome Modeling on Downsampled Hi-C Maps Enhances the Compartmentalization Signal. The journal of physical chemistry. B 125 (31) (2021)
Mandira Dutta, Susan P Gilbert, José Nelson Onuchic, Biman Jana
Mechanistic basis of propofol-induced disruption of kinesin processivity. Proceedings of the National Academy of Sciences of the United States of America 118 (5) (2021)
Raju Sarkar, Akhilesh Jaiswar, Scott P Hennelly, José Nelson Onuchic, Karissa Y Sanbonmatsu, Susmita Roy
Chelated Magnesium Logic Gate Regulates Riboswitch Pseudoknot Formation. The journal of physical chemistry. B 125 (24) (2021)
Khoa Ngo, Fernando Bruno da Silva, Ingrid B S Martins, Vinícius de Godoi Contessoto, José Nelson Onuchic
Improving the Thermostability of Xylanase A from Bacillus subtilis by Combining Bioinformatics and Electrostatic Interactions Optimization. The journal of physical chemistry. B 125 (17) (2021)
Shikai Jin, Mingchen Chen, Xun Chen, Carlos Bueno, Wei Lu, Nicholas P Schafer, Xingcheng Lin, José Nelson Onuchic, Peter G Wolynes
Protein Structure Prediction in CASP13 Using AWSEM-Suite. Journal of chemical theory and computation 16 (6) (2020)
José Nelson Onuchic, Igor V Rubtsov, Michael J Therien
Tribute to David N. Beratan. The journal of physical chemistry. B 124 (17) (2020)
Ryan R Cheng, Vinícius de Godoi Contessoto, Erez Lieberman Aiden, Peter G Wolynes, Michele Di Pierro, José Nelson Onuchic
Exploring chromosomal structural heterogeneity across multiple cell lines. eLife 9 (2020)
Ana Mandic, Ryan L Hayes, Heiko Lammert, Ryan R Cheng, José Nelson Onuchic
Structure-Based Model of RNA Pseudoknot Captures Magnesium-Dependent Folding Thermodynamics. The journal of physical chemistry. B 123 (7) (2019)
Heiko Lammert, Ailun Wang, Udayan Mohanty, José Nelson Onuchic
RNA as a Complex Polymer with Coupled Dynamics of Ions and Water in the Outer Solvation Sphere. The journal of physical chemistry. B 122 (49) (2018)
Guy Nir, Irene Farabella, Cynthia Pérez Estrada, Carl G Ebeling, Brian J Beliveau, Hiroshi M Sasaki, S Dean Lee, Son C Nguyen, Ruth B McCole, Shyamtanu Chattoraj, Jelena Erceg, Jumana AlHaj Abed, Nuno M C Martins, Huy Q Nguyen, Mohammed A Hannan, Sheikh Russell, Neva C Durand, Suhas S P Rao, Jocelyn Y Kishi, Paula Soler-Vila, Michele Di Pierro, José Nelson Onuchic, Steven P Callahan, John M Schreiner, Jeff A Stuckey, Peng Yin, Erez Lieberman Aiden, Marc A Marti-Renom, Chao-Ting Wu
Walking along chromosomes with super-resolution imaging, contact maps, and integrative modeling. PLoS genetics 14 (12) (2018)
Ryan R Cheng, Ellinor Haglund, Nicholas S Tiee, Faruck Morcos, Herbert Levine, Joseph A Adams, Patricia A Jennings, José Nelson Onuchic
Designing bacterial signaling interactions with coevolutionary landscapes. PloS one 13 (8) (2018)
Mingchen Chen, Xingcheng Lin, Wei Lu, Nicholas P Schafer, José Nelson Onuchic, Peter G Wolynes
Template-Guided Protein Structure Prediction and Refinement Using Optimized Folding Landscape Force Fields. Journal of chemical theory and computation 14 (11) (2018)
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