The Shadow Map: A General Contact Definition for Capturing the Dynamics of Biomolecular Folding and Function von Noel, Jeffrey K, Whitford, Paul C, Onuchic, José N

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Anomalous diffusion, spatial coherence, and viscoelasticity from the energy landscape of human chromosomes von Di Pierro, Michele, Potoyan, Davit A., Wolynes, Peter G., Onuchic, José N.

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Implications of the Hybrid Epithelial/Mesenchymal Phenotype in Metastasis von Jolly, Mohit Kumar, Boareto, Marcelo, Huang, Bin, Jia, Dongya, Lu, Mingyang, Ben-Jacob, Eshel, Onuchic, José N, Levine, Herbert

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De novo prediction of human chromosome structures: Epigenetic marking patterns encode genome architecture von Di Pierro, Michele, Cheng, Ryan R., Aiden, Erez Lieberman, Wolynes, Peter G., Onuchic, José N.

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SMOG 2: A Versatile Software Package for Generating Structure-Based Models von Noel, Jeffrey K, Levi, Mariana, Raghunathan, Mohit, Lammert, Heiko, Hayes, Ryan L, Onuchic, José N, Whitford, Paul C

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Stochastic fluctuations promote ordered pattern formation of cells in the Notch-Delta signaling pathway von Galbraith, Madeline, Bocci, Federico, Onuchic, José N

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Coevolutionary signals across protein lineages help capture multiple protein conformations von Morcos, Faruck, Jana, Biman, Hwa, Terence, Onuchic, José N.

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Toward rationally redesigning bacterial two-component signaling systems using coevolutionary information von Cheng, Ryan R., Morcos, Faruck, Levine, Herbert, Onuchic, José N.

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Redox-dependent gating of VDAC by mitoNEET von Lipper, Colin H., Stofleth, Jason T., Bai, Fang, Sohn, Yang-Sung, Roy, Susmita, Mittler, Ron, Nechushtai, Rachel, Onuchic, José N., Jennings, Patricia A.

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Jagged mediates differences in normal and tumor angiogenesis by affecting tip-stalk fate decision von Boareto, Marcelo, Mohit Kumar Jolly, Eshel Ben-Jacob, Joséé N. Onuchic

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MicroRNA-based regulation of epithelial–hybrid–mesenchymal fate determination von Lu, Mingyang, Jolly, Mohit Kumar, Levine, Herbert, Onuchic, José N., Ben-Jacob, Eshel

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Genomics-aided structure prediction von Sułkowska, Joanna I, Morcos, Faruck, Weigt, Martin, Hwa, Terence, Onuchic, José N

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Numb prevents a complete epithelial–mesenchymal transition by modulating Notch signalling von Bocci, Federico, Jolly, Mohit K., Tripathi, Satyendra C., Aguilar, Mitzi, Hanash, Samir M., Levine, Herbert, Onuchic, José N.

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NEET Proteins: A New Link Between Iron Metabolism, Reactive Oxygen Species, and Cancer von Mittler, Ron, Darash-Yahana, Merav, Sohn, Yang Sung, Bai, Fang, Song, Luhua, Cabantchik, Ioav Z, Jennings, Patricia A, Onuchic, José N, Nechushtai, Rachel

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Towards decoding the coupled decision-making of metabolism and epithelial-to-mesenchymal transition in cancer von Jia, Dongya, Park, Jun Hyoung, Kaur, Harsimran, Jung, Kwang Hwa, Yang, Sukjin, Tripathi, Shubham, Galbraith, Madeline, Deng, Youyuan, Jolly, Mohit Kumar, Kaipparettu, Benny Abraham, Onuchic, José N., Levine, Herbert

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Strain Mediated Adaptation Is Key for Myosin Mechanochemistry: Discovering General Rules for Motor Activity von Jana, Biman, Onuchic, José N

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Coevolutionary information, protein folding landscapes, and the thermodynamics of natural selection von Morcos, Faruck, Schafer, Nicholas P., Cheng, Ryan R., Onuchic, José N., Wolynes, Peter G.

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An associative memory Hamiltonian model for DNA and nucleosomes von Lu, Weiqi, Onuchic, José N, Di Pierro, Michele

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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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High-resolution protein complexes from integrating genomic information with molecular simulation von Schug, Alexander, Weigt, Martin, Onuchic, José N, Hwa, Terence, Szurmant, Hendrik

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