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Jose Onuchic

Title(s)Emeritus Professor, Physics
SchoolVc-academic Affairs
Address9500 Gilman Drive #
La Jolla CA 92093
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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
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    1. A data-driven chromatin model reveals spatial and dynamic features of genome organization. Proc Natl Acad Sci U S A. 2026 Jan 27; 123(4):e2530583123. Oliveira Junior AB, Mello MF, Oliveira RJ, Dodero-Rojas E, Brahmachari S, Contessoto VG, Onuchic JN. PMID: 41576073; PMCID: PMC12846836.
      View in: PubMed   Mentions:
    2. Sequence-based calculation of local energetic frustration in proteins. Struct Dyn. 2025 Nov; 12(6):064101. Kuhn AM, Contessoto VG, Onuchic JN, Phillips GN. PMID: 41312536; PMCID: PMC12657058.
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    3. Mapping the energy landscape of a fold-switching protein MAD2. Protein Sci. 2025 Nov; 34(11):e70329. Pereira AF, Contessoto VG, Martínez L, Onuchic JN. PMID: 41074798; PMCID: PMC12514843.
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    4. Critical Role of Mg2+ Ions in RNA Folding Transitions: Anchoring the A-Minor Twist in the SAM-II Riboswitch. J Phys Chem B. 2025 Sep 11; 129(36):9058-9067. Viegas RG, Sinha A, Mainan A, Sanbonmatsu KY, Onuchic JN, Roy S, Leite VBP. PMID: 40892043; PMCID: PMC12434664.
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    5. Conformational ligand-directed targeting of calcium-dependent receptors in acute trauma. Med. 2025 Jul 11; 6(7):100638. Pasqualini R, Markosian C, Staquicini DI, Dobroff AS, Dodero-Rojas E, Whitford PC, Barbu EM, Bronk JK, Cardó-Vila M, Christianson DR, Dias-Neto E, Driessen WHP, Guzman-Rojas L, Marchiò S, Nunes DN, de Oliveira FS, Ozawa MG, Proneth B, Rangel R, Smith TL, Souza GR, Staquicini FI, Tang FHF, Baze WB, Setubal JC, Burns JW, Dubick MA, Gelovani JG, Batchinsky AI, Mogford JE, Wade CE, Holcomb JB, Burley SK, Onuchic JN, Arap W. PMID: 40609540.
      View in: PubMed   Mentions:    Fields:    Translation:AnimalsCells
    6. Conformational heterogeneity in the dGsw purine riboswitch: role of Mg2+ and 2'-dG in aptamer folding. RNA. 2025 Apr 16; 31(5):724-733. Chaudhury SN, Ding E, Jespersen NE, Onuchic JN, Sanbonmatsu KY. PMID: 40021341; PMCID: PMC12001964.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    7. Simulating biomolecules for physiological timescales. Curr Opin Struct Biol. 2025 Jun; 92:103039. Whitford PC, Onuchic JN. PMID: 40215701; PMCID: PMC12997101.
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    8. The need to implement FAIR principles in biomolecular simulations. Nat Methods. 2025 Apr; 22(4):641-645. Amaro RE, Åqvist J, Bahar I, Battistini F, Bellaiche A, Beltran D, Biggin PC, Bonomi M, Bowman GR, Bryce RA, Bussi G, Carloni P, Case DA, Cavalli A, Chang CA, Cheatham TE, Cheung MS, Chipot C, Chong LT, Choudhary P, Cisneros GA, Clementi C, Collepardo-Guevara R, Coveney P, Covino R, Crawford TD, Dal Peraro M, de Groot BL, Delemotte L, De Vivo M, Essex JW, Fraternali F, Gao J, Gelpí JL, Gervasio FL, González-Nilo FD, Grubmüller H, Guenza MG, Guzman HV, Harris S, Head-Gordon T, Hernandez R, Hospital A, Huang N, Huang X, Hummer G, Iglesias-Fernández J, Jensen JH, Jha S, Jiao W, Jorgensen WL, Kamerlin SCL, Khalid S, Laughton C, Levitt M, Limongelli V, Lindahl E, Lindorff-Larsen K, Loverde S, Lundborg M, Luo YL, Luque FJ, Lynch CI, MacKerell AD, Magistrato A, Marrink SJ, Martin H, McCammon JA, Merz K, Moliner V, Mulholland AJ, Murad S, Naganathan AN, Nangia S, Noe F, Noy A, Oláh J, O'Mara ML, Ondrechen MJ, Onuchic JN, Onufriev A, Osuna S, Palermo G, Panchenko AR, Pantano S, Parish C, Parrinello M, Perez A, Perez-Acle T, Perilla JR, Pettitt BM, Pietropaolo A, Piquemal JP, Poma AB, Praprotnik M, Ramos MJ, Ren P, Reuter N, Roitberg A, Rosta E, Rovira C, Roux B, Rothlisberger U, Sanbonmatsu KY, Schlick T, Shaytan AK, Simmerling C, Smith JC, Sugita Y, Swiderek K, Taiji M, Tao P, Tieleman DP, Tikhonova IG, Tirado-Rives J, Tuñón I, van der Kamp MW, van der Spoel D, Velankar S, Voth GA, Wade R, Warshel A, Welborn VV, Wetmore SD, Wheeler TJ, Wong CF, Yang LW, Zacharias M, Orozco M. PMID: 40175561.
      View in: PubMed   Mentions: 7     Fields:    
    9. The need to implement FAIR principles in biomolecular simulations. Nat Methods. 2025 Apr; 22(4):641-645. Amaro RE, Åqvist J, Bahar I, Battistini F, Bellaiche A, Beltran D, Biggin PC, Bonomi M, Bowman GR, Bryce RA, Bussi G, Carloni P, Case DA, Cavalli A, Chang CA, Cheatham TE, Cheung MS, Chipot C, Chong LT, Choudhary P, Cisneros GA, Clementi C, Collepardo-Guevara R, Coveney P, Covino R, Crawford TD, Dal Peraro M, de Groot BL, Delemotte L, De Vivo M, Essex JW, Fraternali F, Gao J, Gelpí JL, Gervasio FL, González-Nilo FD, Grubmüller H, Guenza MG, Guzman HV, Harris S, Head-Gordon T, Hernandez R, Hospital A, Huang N, Huang X, Hummer G, Iglesias-Fernández J, Jensen JH, Jha S, Jiao W, Jorgensen WL, Kamerlin SCL, Khalid S, Laughton C, Levitt M, Limongelli V, Lindahl E, Lindorff-Larsen K, Loverde S, Lundborg M, Luo YL, Luque FJ, Lynch CI, MacKerell AD, Magistrato A, Marrink SJ, Martin H, McCammon JA, Merz K, Moliner V, Mulholland AJ, Murad S, Naganathan AN, Nangia S, Noe F, Noy A, Oláh J, O'Mara ML, Ondrechen MJ, Onuchic JN, Onufriev A, Osuna S, Palermo G, Panchenko AR, Pantano S, Parish C, Parrinello M, Perez A, Perez-Acle T, Perilla JR, Pettitt BM, Pietropaolo A, Piquemal JP, Poma AB, Praprotnik M, Ramos MJ, Ren P, Reuter N, Roitberg A, Rosta E, Rovira C, Roux B, Rothlisberger U, Sanbonmatsu KY, Schlick T, Shaytan AK, Simmerling C, Smith JC, Sugita Y, Swiderek K, Taiji M, Tao P, Tieleman DP, Tikhonova IG, Tirado-Rives J, Tuñón I, van der Kamp MW, van der Spoel D, Velankar S, Voth GA, Wade R, Warshel A, Welborn VV, Wetmore SD, Wheeler TJ, Wong CF, Yang LW, Zacharias M, Orozco M. PMID: 40175561; PMCID: PMC12950262.
      View in: PubMed   Mentions: 7     Fields:    
    10. The synergy between compartmentalization and motorization in chromatin architecture. J Chem Phys. 2025 Mar 21; 162(11). Oliveira RJ, Oliveira Junior AB, Contessoto VG, Onuchic JN. PMID: 40105139.
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    11. Energy landscape analysis of the development of the chromosome structure across the cell cycle. Proc Natl Acad Sci U S A. 2025 Mar 25; 122(12):e2425225122. Contessoto VG, Oliveira AB, Brahmachari S, Wolynes PG, Di Pierro M, Onuchic JN. PMID: 40112110; PMCID: PMC11962442.
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    12. Evolving concepts of the protein universe. iScience. 2025 Mar 21; 28(3):112012. Kulkarni P, Porter L, Chou TF, Chong S, Chiti F, Schafer JW, Mohanty A, Ramisetty S, Onuchic JN, Tuite M, Uversky VN, Weninger KR, Koonin EV, Orban J, Salgia R. PMID: 40124498; PMCID: PMC11926713.
      View in: PubMed   Mentions: 1  
    13. Biguanides antithetically regulate tumor properties by the dose-dependent mitochondrial reprogramming-driven c-Src pathway. Cell Rep Med. 2025 Feb 18; 6(2):101941. Park JH, Jung KH, Jia D, Yang S, Attri KS, Ahn S, Murthy D, Samanta T, Dutta D, Ghidey M, Chatterjee S, Han SY, Pedroza DA, Tiwari A, Lee JV, Davis C, Li S, Putluri V, Creighton CJ, Putluri N, Dobrolecki LE, Lewis MT, Rosen JM, Onuchic JN, Goga A, Kaipparettu BA. PMID: 39933530; PMCID: PMC11866546.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansAnimalsCells
    14. Trapped-ion quantum simulation of electron transfer models with tunable dissipation. Sci Adv. 2024 Dec 20; 10(51):eads8011. So V, Duraisamy Suganthi M, Menon A, Zhu M, Zhuravel R, Pu H, Wolynes PG, Onuchic JN, Pagano G. PMID: 39705352; PMCID: PMC11661436.
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    15. Designing proteins: Mimicking natural protein sequence heterogeneity. J Chem Phys. 2024 Nov 21; 161(19). Lequerica-Mateos M, Martin J, Onuchic JN, Morcos F, Coluzza I. PMID: 39546369; PMCID: PMC11568883.
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    16. Structure and inhibition of SARS-CoV-2 spike refolding in membranes. Science. 2024 08 16; 385(6710):757-765. Grunst MW, Qin Z, Dodero-Rojas E, Ding S, Prévost J, Chen Y, Hu Y, Pazgier M, Wu S, Xie X, Finzi A, Onuchic JN, Whitford PC, Mothes W, Li W. PMID: 39146425; PMCID: PMC11449073.
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    17. Magnesium ions mitigate metastable states in the regulatory landscape of mRNA elements. RNA. 2024 07 16; 30(8):992-1010. Ding E, Chaudhury SN, Prajapati JD, Onuchic JN, Sanbonmatsu KY. PMID: 38777381; PMCID: PMC11251524.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    18. Germline BARD1 variants predispose to mesothelioma by impairing DNA repair and calcium signaling. Proc Natl Acad Sci U S A. 2024 Jul 16; 121(29):e2405231121. Novelli F, Yoshikawa Y, Vitto VAM, Modesti L, Minaai M, Pastorino S, Emi M, Kim JH, Kricek F, Bai F, Onuchic JN, Bononi A, Suarez JS, Tanji M, Favaron C, Zolondick AA, Xu R, Takanishi Y, Wang Z, Sakamoto G, Gaudino G, Grzymski J, Grosso F, Schrump DS, Pass HI, Atanesyan L, Smout J, Savola S, Sarin KY, Abolhassani H, Hammarström L, Pan-Hammarström Q, Giorgi C, Pinton P, Yang H, Carbone M. PMID: 38990952; PMCID: PMC11260134.
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    19. Three-dimensional genome architecture persists in a 52,000-year-old woolly mammoth skin sample. Cell. 2024 Jul 11; 187(14):3541-3562.e51. Sandoval-Velasco M, Dudchenko O, Rodríguez JA, Pérez Estrada C, Dehasque M, Fontsere C, Mak SST, Khan R, Contessoto VG, Oliveira Junior AB, Kalluchi A, Zubillaga Herrera BJ, Jeong J, Roy RP, Christopher I, Weisz D, Omer AD, Batra SS, Shamim MS, Durand NC, O'Connell B, Roca AL, Plikus MV, Kusliy MA, Romanenko SA, Lemskaya NA, Serdyukova NA, Modina SA, Perelman PL, Kizilova EA, Baiborodin SI, Rubtsov NB, Machol G, Rath K, Mahajan R, Kaur P, Gnirke A, Garcia-Treviño I, Coke R, Flanagan JP, Pletch K, Ruiz-Herrera A, Plotnikov V, Pavlov IS, Pavlova NI, Protopopov AV, Di Pierro M, Graphodatsky AS, Lander ES, Rowley MJ, Wolynes PG, Onuchic JN, Dalén L, Marti-Renom MA, Gilbert MTP, Aiden EL. PMID: 38996487; PMCID: PMC12128189.
      View in: PubMed   Mentions: 9     Fields:    Translation:HumansAnimalsCells
    20. Nucleosomes play a dual role in regulating transcription dynamics. Proc Natl Acad Sci U S A. 2024 Jul 09; 121(28):e2319772121. Brahmachari S, Tripathi S, Onuchic JN, Levine H. PMID: 38968124; PMCID: PMC11252751.
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    21. Machine learning in biological physics: From biomolecular prediction to design. Proc Natl Acad Sci U S A. 2024 Jul 02; 121(27):e2311807121. Martin J, Lequerica Mateos M, Onuchic JN, Coluzza I, Morcos F. PMID: 38913893; PMCID: PMC11228481.
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    22. CISD3/MiNT is required for complex I function, mitochondrial integrity, and skeletal muscle maintenance. Proc Natl Acad Sci U S A. 2024 May 28; 121(22):e2405123121. Nechushtai R, Rowland L, Karmi O, Marjault HB, Nguyen TT, Mittal S, Ahmed RS, Grant D, Manrique-Acevedo C, Morcos F, Onuchic JN, Mittler R. PMID: 38781208; PMCID: PMC11145280.
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    23. RACER-m leverages structural features for sparse T cell specificity prediction. Sci Adv. 2024 05 17; 10(20):eadl0161. Wang A, Lin X, Chau KN, Onuchic JN, Levine H, George JT. PMID: 38748791; PMCID: PMC11095454.
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    24. Residue coevolution and mutational landscape for OmpR and NarL response regulator subfamilies. Biophys J. 2024 03 19; 123(6):681-692. Shibata M, Lin X, Onuchic JN, Yura K, Cheng RR. PMID: 38291753; PMCID: PMC10995415.
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    25. Theoretical and computational tools to model multistable gene regulatory networks. ArXiv. 2023 Jun 26. Bocci F, Jia D, Nie Q, Jolly MK, Onuchic J. PMID: 36824430; PMCID: PMC9949162.
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    26. Key aspects of the past 30 years of protein design. Rep Prog Phys. 2022 07 06; 85(8). Magi Meconi G, Sasselli IR, Bianco V, Onuchic JN, Coluzza I. PMID: 35704983.
      View in: PubMed   Mentions: 3     Fields:    Translation:Cells
    27. Intrinsically disordered proteins: Ensembles at the limits of Anfinsen's dogma. Biophys Rev (Melville). 2022 Mar; 3(1):011306. Kulkarni P, Leite VBP, Roy S, Bhattacharyya S, Mohanty A, Achuthan S, Singh D, Appadurai R, Rangarajan G, Weninger K, Orban J, Srivastava A, Jolly MK, Onuchic JN, Uversky VN, Salgia R. PMID: 38505224; PMCID: PMC10903413.
      View in: PubMed   Mentions: 14  
    28. BAP1 forms a trimer with HMGB1 and HDAC1 that modulates gene × environment interaction with asbestos. Proc Natl Acad Sci U S A. 2021 11 30; 118(48). Novelli F, Bononi A, Wang Q, Bai F, Patergnani S, Kricek F, Haglund E, Suarez JS, Tanji M, Xu R, Takanishi Y, Minaai M, Pastorino S, Morris P, Sakamoto G, Pass HI, Barbour H, Gaudino G, Giorgi C, Pinton P, Onuchic JN, Yang H, Carbone M. PMID: 34815344; PMCID: PMC8640737.
      View in: PubMed   Mentions: 17     Fields:    Translation:AnimalsCells
    29. SMOG 2 and OpenSMOG: Extending the limits of structure-based models. Protein Sci. 2022 01; 31(1):158-172. de Oliveira AB, Contessoto VG, Hassan A, Byju S, Wang A, Wang Y, Dodero-Rojas E, Mohanty U, Noel JK, Onuchic JN, Whitford PC. PMID: 34655449; PMCID: PMC8740843.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansAnimalsCells
    30. Sterically confined rearrangements of SARS-CoV-2 Spike protein control cell invasion. Elife. 2021 08 31; 10. Dodero-Rojas E, Onuchic JN, Whitford PC. PMID: 34463614; PMCID: PMC8456623.
      View in: PubMed   Mentions: 27     Fields:    Translation:HumansCells
    31. Exploring chromosomal structural heterogeneity across multiple cell lines. Elife. 2020 10 13; 9. Cheng RR, Contessoto VG, Lieberman Aiden E, Wolynes PG, Di Pierro M, Onuchic JN. PMID: 33047670; PMCID: PMC7593087.
      View in: PubMed   Mentions: 25     Fields:    Translation:HumansCells
    32. Decoding the mechanisms underlying cell-fate decision-making during stem cell differentiation by random circuit perturbation. J R Soc Interface. 2020 08; 17(169):20200500. Huang B, Lu M, Galbraith M, Levine H, Onuchic JN, Jia D. PMID: 32781932; PMCID: PMC7482558.
      View in: PubMed   Mentions: 13     Fields:    Translation:AnimalsCells
    33. Consensus report of the 8 and 9th Weinman Symposia on Gene x Environment Interaction in carcinogenesis: novel opportunities for precision medicine. Cell Death Differ. 2018 11; 25(11):1885-1904. Carbone M, Amelio I, Affar EB, Brugarolas J, Cannon-Albright LA, Cantley LC, Cavenee WK, Chen Z, Croce CM, Andrea A, Gandara D, Giorgi C, Jia W, Lan Q, Mak TW, Manley JL, Mikoshiba K, Onuchic JN, Pass HI, Pinton P, Prives C, Rothman N, Sebti SM, Turkson J, Wu X, Yang H, Yu H, Melino G. PMID: 30323273; PMCID: PMC6219489.
      View in: PubMed   Mentions: 19     Fields:    Translation:Humans
    34. Phylogenetic analysis of the CDGSH iron-sulfur binding domain reveals its ancient origin. Sci Rep. 2018 03 19; 8(1):4840. Sengupta S, Nechushtai R, Jennings PA, Onuchic JN, Padilla PA, Azad RK, Mittler R. PMID: 29556009; PMCID: PMC5859297.
      View in: PubMed   Mentions: 11     Fields:    Translation:HumansCells
    35. The unique fold and lability of the [2Fe-2S] clusters of NEET proteins mediate their key functions in health and disease. J Biol Inorg Chem. 2018 06; 23(4):599-612. Karmi O, Marjault HB, Pesce L, Carloni P, Onuchic JN, Jennings PA, Mittler R, Nechushtai R. PMID: 29435647; PMCID: PMC6006223.
      View in: PubMed   Mentions: 31     Fields:    Translation:HumansCells
    36. Interactions between mitoNEET and NAF-1 in cells. PLoS One. 2017; 12(4):e0175796. Karmi O, Holt SH, Song L, Tamir S, Luo Y, Bai F, Adenwalla A, Darash-Yahana M, Sohn YS, Jennings PA, Azad RK, Onuchic JN, Morcos F, Nechushtai R, Mittler R. PMID: 28426722; PMCID: PMC5398536.
      View in: PubMed   Mentions: 30     Fields:    Translation:HumansCells
    37. Interrogating the topological robustness of gene regulatory circuits by randomization. PLoS Comput Biol. 2017 03; 13(3):e1005456. Huang B, Lu M, Jia D, Ben-Jacob E, Levine H, Onuchic JN. PMID: 28362798; PMCID: PMC5391964.
      View in: PubMed   Mentions: 99     Fields:    Translation:Humans
    38. Phylogenetic analysis of eukaryotic NEET proteins uncovers a link between a key gene duplication event and the evolution of vertebrates. Sci Rep. 2017 02 16; 7:42571. Inupakutika MA, Sengupta S, Nechushtai R, Jennings PA, Onuchic JN, Azad RK, Padilla P, Mittler R. PMID: 28205535; PMCID: PMC5311916.
      View in: PubMed   Mentions: 25     Fields:    Translation:HumansAnimalsCells
    39. Connecting the Sequence-Space of Bacterial Signaling Proteins to Phenotypes Using Coevolutionary Landscapes. Mol Biol Evol. 2016 12; 33(12):3054-3064. Cheng RR, Nordesjö O, Hayes RL, Levine H, Flores SC, Onuchic JN, Morcos F. PMID: 27604223; PMCID: PMC5100047.
      View in: PubMed   Mentions: 37     Fields:    Translation:Cells
    40. Notch-Jagged signalling can give rise to clusters of cells exhibiting a hybrid epithelial/mesenchymal phenotype. J R Soc Interface. 2016 05; 13(118). Boareto M, Jolly MK, Goldman A, Pietilä M, Mani SA, Sengupta S, Ben-Jacob E, Levine H, Onuchic JN. PMID: 27170649; PMCID: PMC4892257.
      View in: PubMed   Mentions: 71     Fields:    Translation:HumansCells
    41. Sequence co-evolutionary information is a natural partner to minimally-frustrated models of biomolecular dynamics. F1000Res. 2016; 5. Noel JK, Morcos F, Onuchic JN. PMID: 26918164; PMCID: PMC4755392.
      View in: PubMed   Mentions: 9     Fields:    
    42. Modeling the Transitions between Collective and Solitary Migration Phenotypes in Cancer Metastasis. Sci Rep. 2015 Dec 02; 5:17379. Huang B, Jolly MK, Lu M, Tsarfaty I, Ben-Jacob E, Onuchic JN. PMID: 26627083; PMCID: PMC4667179.
      View in: PubMed   Mentions: 33     Fields:    Translation:HumansAnimals
    43. Integrating molecular dynamics simulations with chemical probing experiments using SHAPE-FIT. Methods Enzymol. 2015; 553:215-34. Kirmizialtin S, Hennelly SP, Schug A, Onuchic JN, Sanbonmatsu KY. PMID: 25726467; PMCID: PMC4777697.
      View in: PubMed   Mentions: 10     Fields:    Translation:Cells
    44. The physics of bacterial decision making. Front Cell Infect Microbiol. 2014; 4:154. Ben-Jacob E, Lu M, Schultz D, Onuchic JN. PMID: 25401094; PMCID: PMC4214203.
      View in: PubMed   Mentions: 13     Fields:    Translation:Cells
    45. Structure-function analysis of NEET proteins uncovers their role as key regulators of iron and ROS homeostasis in health and disease. Biochim Biophys Acta. 2015 Jun; 1853(6):1294-315. Tamir S, Paddock ML, Darash-Yahana-Baram M, Holt SH, Sohn YS, Agranat L, Michaeli D, Stofleth JT, Lipper CH, Morcos F, Cabantchik IZ, Onuchic JN, Jennings PA, Mittler R, Nechushtai R. PMID: 25448035.
      View in: PubMed   Mentions: 97     Fields:    Translation:HumansCells
    46. Toward decoding the principles of cancer metastasis circuits. Cancer Res. 2014 Sep 01; 74(17):4574-87. Lu M, Jolly MK, Onuchic J, Ben-Jacob E. PMID: 25183783.
      View in: PubMed   Mentions: 32     Fields:    Translation:Humans
    47. Allosteric control in a metalloprotein dramatically alters function. Proc Natl Acad Sci U S A. 2013 Jan 15; 110(3):948-53. Baxter EL, Zuris JA, Wang C, Vo PL, Axelrod HL, Cohen AE, Paddock ML, Nechushtai R, Onuchic JN, Jennings PA. PMID: 23271805; PMCID: PMC3549116.
      View in: PubMed   Mentions: 13     Fields:    Translation:Cells
    48. Energy landscape of knotted protein folding. Proc Natl Acad Sci U S A. 2012 Oct 30; 109(44):17783-8. Sulkowska JI, Noel JK, Onuchic JN. PMID: 22891304; PMCID: PMC3497829.
      View in: PubMed   Mentions: 42     Fields:    Translation:Cells
    49. Conservation of complex knotting and slipknotting patterns in proteins. Proc Natl Acad Sci U S A. 2012 Jun 26; 109(26):E1715-23. Sulkowska JI, Rawdon EJ, Millett KC, Onuchic JN, Stasiak A. PMID: 22685208; PMCID: PMC3387036.
      View in: PubMed   Mentions: 96     Fields:    Translation:Cells
    50. Computational modeling of phosphotransfer complexes in two-component signaling. Methods Enzymol. 2010; 471:43-58. Schug A, Weigt M, Hoch JA, Onuchic JN, Hwa T, Szurmant H. PMID: 20946841.
      View in: PubMed   Mentions: 12     Fields:    Translation:Cells
    51. A novel disulfide bond in the SH2 Domain of the C-terminal Src kinase controls catalytic activity. J Mol Biol. 2007 Feb 02; 365(5):1460-8. Mills JE, Whitford PC, Shaffer J, Onuchic JN, Adams JA, Jennings PA. PMID: 17137590; PMCID: PMC2741090.
      View in: PubMed   Mentions: 27     Fields:    Translation:HumansCells
    52. Exploring biomolecular machines: energy landscape control of biological reactions. Philos Trans R Soc Lond B Biol Sci. 2006 Aug 29; 361(1472):1439-43. Onuchic JN, Kobayashi C, Miyashita O, Jennings P, Baldridge KK. PMID: 16873130; PMCID: PMC1647308.
      View in: PubMed   Mentions: 10     Fields:    Translation:Cells
    53. Multiple-basin energy landscapes for large-amplitude conformational motions of proteins: Structure-based molecular dynamics simulations. Proc Natl Acad Sci U S A. 2006 Aug 08; 103(32):11844-9. Okazaki K, Koga N, Takada S, Onuchic JN, Wolynes PG. PMID: 16877541; PMCID: PMC1567665.
      View in: PubMed   Mentions: 129     Fields:    Translation:HumansCells
    54. Multiple routes lead to the native state in the energy landscape of the beta-trefoil family. Proc Natl Acad Sci U S A. 2006 Jul 05; 103(27):10254-10258. Chavez LL, Gosavi S, Jennings PA, Onuchic JN. PMID: 16801558; PMCID: PMC1502444.
      View in: PubMed   Mentions: 38     Fields:    Translation:Cells
    55. Self-regulating gene: an exact solution. Phys Rev E Stat Nonlin Soft Matter Phys. 2005 Nov; 72(5 Pt 1):051907. Hornos JE, Schultz D, Innocentini GC, Wang J, Walczak AM, Onuchic JN, Wolynes PG. PMID: 16383645.
      View in: PubMed   Mentions: 82     Fields:    Translation:HumansAnimalsCells
    56. The folding and dimerization of HIV-1 protease: evidence for a stable monomer from simulations. J Mol Biol. 2004 Jun 25; 340(1):67-79. Levy Y, Caflisch A, Onuchic JN, Wolynes PG. PMID: 15184023.
      View in: PubMed   Mentions: 28     Fields:    Translation:Cells
    57. Solvation in protein folding analysis: combination of theoretical and experimental approaches. Proc Natl Acad Sci U S A. 2004 Mar 02; 101(9):2834-9. Fernández-Escamilla AM, Cheung MS, Vega MC, Wilmanns M, Onuchic JN, Serrano L. PMID: 14978284; PMCID: PMC365706.
      View in: PubMed   Mentions: 32     Fields:    Translation:Cells
    58. Theory of protein folding. Curr Opin Struct Biol. 2004 Feb; 14(1):70-5. Onuchic JN, Wolynes PG. PMID: 15102452.
      View in: PubMed   Mentions: 438     Fields:    Translation:Cells
    59. Nonlinear elasticity, proteinquakes, and the energy landscapes of functional transitions in proteins. Proc Natl Acad Sci U S A. 2003 Oct 28; 100(22):12570-5. Miyashita O, Onuchic JN, Wolynes PG. PMID: 14566052; PMCID: PMC240658.
      View in: PubMed   Mentions: 218     Fields:    Translation:Cells
    60. Science education. Educating future scientists. Science. 2003 Sep 12; 301(5639):1485. Sung NS, Gordon JI, Rose GD, Getzoff ED, Kron SJ, Mumford D, Onuchic JN, Scherer NF, Sumners DL, Kopell NJ. PMID: 12970550.
      View in: PubMed   Mentions: 7     Fields:    Translation:Humans
    61. Probing the folding free energy landscape of the Src-SH3 protein domain. Proc Natl Acad Sci U S A. 2002 Dec 10; 99(25):16064-8. Shea JE, Onuchic JN, Brooks CL. PMID: 12446834; PMCID: PMC138565.
      View in: PubMed   Mentions: 48     Fields:    Translation:AnimalsCells
    62. Different scenarios for inter-protein electron tunneling: the effect of water-mediated pathways. J Biol Phys. 2002 Sep; 28(3):383-94. Miyashita O, Axelrod HL, Onuchic JN. PMID: 23345783; PMCID: PMC3456736.
      View in: PubMed   Mentions: 1     Fields:    
    63. Prediction of folding mechanism for circular-permuted proteins. J Mol Biol. 2001 Aug 24; 311(4):879-90. Clementi C, Jennings PA, Onuchic JN. PMID: 11518537.
      View in: PubMed   Mentions: 29     Fields:    Translation:Cells
    64. Statistical thermodynamics. Taking a walk on a landscape. Science. 2001 Jul 27; 293(5530):612-3. Brooks CL, Onuchic JN, Wales DJ. PMID: 11474087.
      View in: PubMed   Mentions: 47     Fields:    Translation:Cells
    65. Dynamically controlled protein tunneling paths in photosynthetic reaction centers. Science. 2000 Oct 06; 290(5489):114-7. Balabin IA, Onuchic JN. PMID: 11021791.
      View in: PubMed   Mentions: 66     Fields:    Translation:Cells
    66. Investigation of routes and funnels in protein folding by free energy functional methods. Proc Natl Acad Sci U S A. 2000 Jun 06; 97(12):6509-14. Plotkin SS, Onuchic JN. PMID: 10841554; PMCID: PMC18640.
      View in: PubMed   Mentions: 30     Fields:    Translation:Cells
    67. How native-state topology affects the folding of dihydrofolate reductase and interleukin-1beta. Proc Natl Acad Sci U S A. 2000 May 23; 97(11):5871-6. Clementi C, Jennings PA, Onuchic JN. PMID: 10811910; PMCID: PMC18526.
      View in: PubMed   Mentions: 73     Fields:    Translation:Cells
    68. Topological and energetic factors: what determines the structural details of the transition state ensemble and "en-route" intermediates for protein folding? An investigation for small globular proteins. J Mol Biol. 2000 May 19; 298(5):937-53. Clementi C, Nymeyer H, Onuchic JN. PMID: 10801360.
      View in: PubMed   Mentions: 429     Fields:    Translation:Cells
    69. Landscape approaches for determining the ensemble of folding transition states: success and failure hinge on the degree of frustration. Proc Natl Acad Sci U S A. 2000 Jan 18; 97(2):634-9. Nymeyer H, Socci ND, Onuchic JN. PMID: 10639131; PMCID: PMC15382.
      View in: PubMed   Mentions: 33     Fields:    Translation:Cells
    70. The energy landscape theory of protein folding: insights into folding mechanisms and scenarios. Adv Protein Chem. 2000; 53:87-152. Onuchic JN, Nymeyer H, García AE, Chahine J, Socci ND. PMID: 10751944.
      View in: PubMed   Mentions: 67     Fields:    Translation:HumansAnimalsCells
    71. Pressure-induced protein-folding/unfolding kinetics. Proc Natl Acad Sci U S A. 1999 Dec 21; 96(26):14848-53. Hillson N, Onuchic JN, García AE. PMID: 10611301; PMCID: PMC24736.
      View in: PubMed   Mentions: 18     Fields:    Translation:Cells
    72. Exploring the origins of topological frustration: design of a minimally frustrated model of fragment B of protein A. Proc Natl Acad Sci U S A. 1999 Oct 26; 96(22):12512-7. Shea JE, Onuchic JN, Brooks CL. PMID: 10535953; PMCID: PMC22965.
      View in: PubMed   Mentions: 88     Fields:    Translation:Cells
    73. Stretching lattice models of protein folding. Proc Natl Acad Sci U S A. 1999 Mar 02; 96(5):2031-5. Socci ND, Onuchic JN, Wolynes PG. PMID: 10051589; PMCID: PMC26731.
      View in: PubMed   Mentions: 18     Fields:    Translation:Cells
    74. Chemical physics of protein folding. Proc Natl Acad Sci U S A. 1998 Sep 15; 95(19):11037-8. Brooks CL, Gruebele M, Onuchic JN, Wolynes PG. PMID: 9736683; PMCID: PMC33893.
      View in: PubMed   Mentions: 40     Fields:    Translation:Cells
    75. Proposed mechanism for stability of proteins to evolutionary mutations. Proc Natl Acad Sci U S A. 1998 Sep 01; 95(18):10682-6. Nelson ED, Onuchic JN. PMID: 9724764; PMCID: PMC27955.
      View in: PubMed   Mentions: 11     Fields:    Translation:Cells
    76. Protein folding mechanisms and the multidimensional folding funnel. Proteins. 1998 Aug 01; 32(2):136-58. Socci ND, Onuchic JN, Wolynes PG. PMID: 9714155.
      View in: PubMed   Mentions: 53     Fields:    Translation:Cells
    77. Folding funnels and frustration in off-lattice minimalist protein landscapes. Proc Natl Acad Sci U S A. 1998 May 26; 95(11):5921-8. Nymeyer H, García AE, Onuchic JN. PMID: 9600893; PMCID: PMC34496.
      View in: PubMed   Mentions: 98     Fields:    Translation:HumansAnimalsCells
    78. Contacting the protein folding funnel with NMR. Proc Natl Acad Sci U S A. 1997 Jul 08; 94(14):7129-31. Onuchic JN. PMID: 9207055; PMCID: PMC34098.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansAnimalsCells
    79. Theory of protein folding: the energy landscape perspective. Annu Rev Phys Chem. 1997; 48:545-600. Onuchic JN, Luthey-Schulten Z, Wolynes PG. PMID: 9348663.
      View in: PubMed   Mentions: 633     Fields:    Translation:Cells
    80. Fast-folding experiments and the topography of protein folding energy landscapes. Chem Biol. 1996 Jun; 3(6):425-32. Wolynes P, Luthey-Schulten Z, Onuchic J. PMID: 8807873.
      View in: PubMed   Mentions: 26     Fields:    Translation:Cells
    81. Protein folding funnels: the nature of the transition state ensemble. Fold Des. 1996; 1(6):441-50. Onuchic JN, Socci ND, Luthey-Schulten Z, Wolynes PG. PMID: 9080190.
      View in: PubMed   Mentions: 98     Fields:    Translation:HumansAnimalsCells
    82. Electron tunneling in azurin: the coupling across a beta-sheet. Chem Biol. 1995 Jul; 2(7):489-96. Regan JJ, Di Bilio AJ, Langen R, Skov LK, Winkler JR, Gray HB, Onuchic JN. PMID: 9383451.
      View in: PubMed   Mentions: 28     Fields:    Translation:Cells
    83. Response. Science. 1995 May 19; 268(5213):960-1. Wolynes PG, Onuchic JN, Thirumalai D. PMID: 17774212.
      View in: PubMed   Mentions: 1     Fields:    
    84. Toward an outline of the topography of a realistic protein-folding funnel. Proc Natl Acad Sci U S A. 1995 Apr 11; 92(8):3626-30. Onuchic JN, Wolynes PG, Luthey-Schulten Z, Socci ND. PMID: 7724609; PMCID: PMC42220.
      View in: PubMed   Mentions: 142     Fields:    Translation:Cells
    85. Navigating the folding routes. Science. 1995 Mar 17; 267(5204):1619-20. Wolynes PG, Onuchic JN, Thirumalai D. PMID: 7886447.
      View in: PubMed   Mentions: 295     Fields:    Translation:Cells
    86. Funnels, pathways, and the energy landscape of protein folding: a synthesis. Proteins. 1995 Mar; 21(3):167-95. Bryngelson JD, Onuchic JN, Socci ND, Wolynes PG. PMID: 7784423.
      View in: PubMed   Mentions: 778     Fields:    Translation:Cells
    87. Protein folding funnels: a kinetic approach to the sequence-structure relationship. Proc Natl Acad Sci U S A. 1992 Sep 15; 89(18):8721-5. Leopold PE, Montal M, Onuchic JN. PMID: 1528885; PMCID: PMC49992.
      View in: PubMed   Mentions: 271     Fields:    Translation:Cells
    88. Pathway analysis of protein electron-transfer reactions. Annu Rev Biophys Biomol Struct. 1992; 21:349-77. Onuchic JN, Beratan DN, Winkler JR, Gray HB. PMID: 1326356.
      View in: PubMed   Mentions: 61     Fields:    Translation:AnimalsCells
    89. Long-range electron transfer in myoglobin. Ann N Y Acad Sci. 1988; 550:68-84. Cowan JA, Upmacis RK, Beratan DN, Onuchic JN, Gray HB. PMID: 3245652.
      View in: PubMed   Mentions: 7     Fields:    Translation:Cells
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