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RNA as a Complex Polymer with Coupled Dynamics of Ions and Water in the Outer Solvation Sphere.

Lammert H, Wang A, Mohanty U, Onuchic JN.

J Phys Chem B. 2018 Aug 13. doi: 10.1021/acs.jpcb.8b06874. [Epub ahead of print]


A mechanism-based computational model to capture the interconnections among epithelial-mesenchymal transition, cancer stem cells and Notch-Jagged signaling.

Bocci F, Jolly MK, George JT, Levine H, Onuchic JN.

Oncotarget. 2018 Jul 6;9(52):29906-29920. doi: 10.18632/oncotarget.25692. eCollection 2018 Jul 6.


Atomistic simulations indicate the functional loop-to-coiled-coil transition in influenza hemagglutinin is not downhill.

Lin X, Noel JK, Wang Q, Ma J, Onuchic JN.

Proc Natl Acad Sci U S A. 2018 Jul 16. pii: 201805442. doi: 10.1073/pnas.1805442115. [Epub ahead of print]


Anomalous diffusion, spatial coherence, and viscoelasticity from the energy landscape of human chromosomes.

Di Pierro M, Potoyan DA, Wolynes PG, Onuchic JN.

Proc Natl Acad Sci U S A. 2018 Jul 24;115(30):7753-7758. doi: 10.1073/pnas.1806297115. Epub 2018 Jul 9.


Uncovering the molecular mechanisms behind disease-associated leptin variants.

Haglund E, Nguyen L, Schafer NP, Lammert H, Jennings PA, Onuchic JN.

J Biol Chem. 2018 Jun 27. pii: jbc.RA118.003957. doi: 10.1074/jbc.RA118.003957. [Epub ahead of print]


RACIPE: a computational tool for modeling gene regulatory circuits using randomization.

Huang B, Jia D, Feng J, Levine H, Onuchic JN, Lu M.

BMC Syst Biol. 2018 Jun 19;12(1):74. doi: 10.1186/s12918-018-0594-6.


PAGE4 and Conformational Switching: Insights from Molecular Dynamics Simulations and Implications for Prostate Cancer.

Lin X, Roy S, Jolly MK, Bocci F, Schafer NP, Tsai MY, Chen Y, He Y, Grishaev A, Weninger K, Orban J, Kulkarni P, Rangarajan G, Levine H, Onuchic JN.

J Mol Biol. 2018 Aug 3;430(16):2422-2438. doi: 10.1016/j.jmb.2018.05.011. Epub 2018 Jun 5.


Targeting CPT1A-mediated fatty acid oxidation sensitizes nasopharyngeal carcinoma to radiation therapy.

Tan Z, Xiao L, Tang M, Bai F, Li J, Li L, Shi F, Li N, Li Y, Du Q, Lu J, Weng X, Yi W, Zhang H, Fan J, Zhou J, Gao Q, Onuchic JN, Bode AM, Luo X, Cao Y.

Theranostics. 2018 Mar 22;8(9):2329-2347. doi: 10.7150/thno.21451. eCollection 2018.


The Energetics and Physiological Impact of Cohesin Extrusion.

Vian L, Pękowska A, Rao SSP, Kieffer-Kwon KR, Jung S, Baranello L, Huang SC, El Khattabi L, Dose M, Pruett N, Sanborn AL, Canela A, Maman Y, Oksanen A, Resch W, Li X, Lee B, Kovalchuk AL, Tang Z, Nelson S, Di Pierro M, Cheng RR, Machol I, St Hilaire BG, Durand NC, Shamim MS, Stamenova EK, Onuchic JN, Ruan Y, Nussenzweig A, Levens D, Aiden EL, Casellas R.

Cell. 2018 May 17;173(5):1165-1178.e20. doi: 10.1016/j.cell.2018.03.072. Epub 2018 Apr 26.


Rotation-Activated and Cooperative Zipping Characterize Class I Viral Fusion Protein Dynamics.

Eddy NR, Onuchic JN.

Biophys J. 2018 Apr 24;114(8):1878-1888. doi: 10.1016/j.bpj.2018.03.005.


Role of metabolic spatiotemporal dynamics in regulating biofilm colony expansion.

Bocci F, Suzuki Y, Lu M, Onuchic JN.

Proc Natl Acad Sci U S A. 2018 Apr 17;115(16):4288-4293. doi: 10.1073/pnas.1706920115. Epub 2018 Apr 2.


Phylogenetic analysis of the CDGSH iron-sulfur binding domain reveals its ancient origin.

Sengupta S, Nechushtai R, Jennings PA, Onuchic JN, Padilla PA, Azad RK, Mittler R.

Sci Rep. 2018 Mar 19;8(1):4840. doi: 10.1038/s41598-018-23305-6.


NEET Proteins: A New Link Between Iron Metabolism, Reactive Oxygen Species, and Cancer.

Mittler R, Darash-Yahana M, Sohn YS, Bai F, Song L, Cabantchik IZ, Jennings PA, Onuchic JN, Nechushtai R.

Antioxid Redox Signal. 2018 Mar 29. doi: 10.1089/ars.2018.7502. [Epub ahead of print]


The unique fold and lability of the [2Fe-2S] clusters of NEET proteins mediate their key functions in health and disease.

Karmi O, Marjault HB, Pesce L, Carloni P, Onuchic JN, Jennings PA, Mittler R, Nechushtai R.

J Biol Inorg Chem. 2018 Jun;23(4):599-612. doi: 10.1007/s00775-018-1538-8. Epub 2018 Feb 12. Review.


Fluorescent Proteins Detect Host Structural Rearrangements via Electrostatic Mechanism.

Simine L, Lammert H, Sun L, Onuchic JN, Rossky PJ.

J Am Chem Soc. 2018 Jan 31;140(4):1203-1206. doi: 10.1021/jacs.7b10851. Epub 2018 Jan 22.


Structure of the human monomeric NEET protein MiNT and its role in regulating iron and reactive oxygen species in cancer cells.

Lipper CH, Karmi O, Sohn YS, Darash-Yahana M, Lammert H, Song L, Liu A, Mittler R, Nechushtai R, Onuchic JN, Jennings PA.

Proc Natl Acad Sci U S A. 2018 Jan 9;115(2):272-277. doi: 10.1073/pnas.1715842115. Epub 2017 Dec 19.


Numb prevents a complete epithelial-mesenchymal transition by modulating Notch signalling.

Bocci F, Jolly MK, Tripathi SC, Aguilar M, Hanash SM, Levine H, Onuchic JN.

J R Soc Interface. 2017 Nov;14(136). pii: 20170512. doi: 10.1098/rsif.2017.0512.


De novo prediction of human chromosome structures: Epigenetic marking patterns encode genome architecture.

Di Pierro M, Cheng RR, Lieberman Aiden E, Wolynes PG, Onuchic JN.

Proc Natl Acad Sci U S A. 2017 Nov 14;114(46):12126-12131. doi: 10.1073/pnas.1714980114. Epub 2017 Oct 31.


Molecular Simulations Suggest a Force-Dependent Mechanism of Vinculin Activation.

Sun L, Noel JK, Levine H, Onuchic JN.

Biophys J. 2017 Oct 17;113(8):1697-1710. doi: 10.1016/j.bpj.2017.08.037.


Molecular origin of the weak susceptibility of kinesin velocity to loads and its relation to the collective behavior of kinesins.

Wang Q, Diehl MR, Jana B, Cheung MS, Kolomeisky AB, Onuchic JN.

Proc Natl Acad Sci U S A. 2017 Oct 10;114(41):E8611-E8617. doi: 10.1073/pnas.1710328114. Epub 2017 Sep 27. Erratum in: Proc Natl Acad Sci U S A. 2018 Aug 13;:.


Cooperation between Magnesium and Metabolite Controls Collapse of the SAM-I Riboswitch.

Roy S, Onuchic JN, Sanbonmatsu KY.

Biophys J. 2017 Jul 25;113(2):348-359. doi: 10.1016/j.bpj.2017.06.044.


Modeling the response of a tumor-suppressive network to mitogenic and oncogenic signals.

Tian X, Huang B, Zhang XP, Lu M, Liu F, Onuchic JN, Wang W.

Proc Natl Acad Sci U S A. 2017 May 23;114(21):5337-5342. doi: 10.1073/pnas.1702412114. Epub 2017 May 8.


Interactions between mitoNEET and NAF-1 in cells.

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.

PLoS One. 2017 Apr 20;12(4):e0175796. doi: 10.1371/journal.pone.0175796. eCollection 2017.


Interrogating the topological robustness of gene regulatory circuits by randomization.

Huang B, Lu M, Jia D, Ben-Jacob E, Levine H, Onuchic JN.

PLoS Comput Biol. 2017 Mar 31;13(3):e1005456. doi: 10.1371/journal.pcbi.1005456. eCollection 2017 Mar.


A magnesium-induced triplex pre-organizes the SAM-II riboswitch.

Roy S, Lammert H, Hayes RL, Chen B, LeBlanc R, Dayie TK, Onuchic JN, Sanbonmatsu KY.

PLoS Comput Biol. 2017 Mar 1;13(3):e1005406. doi: 10.1371/journal.pcbi.1005406. eCollection 2017 Mar.


Phylogenetic analysis of eukaryotic NEET proteins uncovers a link between a key gene duplication event and the evolution of vertebrates.

Inupakutika MA, Sengupta S, Nechushtai R, Jennings PA, Onuchic JN, Azad RK, Padilla P, Mittler R.

Sci Rep. 2017 Feb 16;7:42571. doi: 10.1038/srep42571.


Modeling the Genetic Regulation of Cancer Metabolism: Interplay between Glycolysis and Oxidative Phosphorylation.

Yu L, Lu M, Jia D, Ma J, Ben-Jacob E, Levine H, Kaipparettu BA, Onuchic JN.

Cancer Res. 2017 Apr 1;77(7):1564-1574. doi: 10.1158/0008-5472.CAN-16-2074. Epub 2017 Feb 15.


Distinguishing mechanisms underlying EMT tristability.

Jia D, Jolly MK, Tripathi SC, Den Hollander P, Huang B, Lu M, Celiktas M, Ramirez-Peña E, Ben-Jacob E, Onuchic JN, Hanash SM, Mani SA, Levine H.

Cancer Converg. 2017;1(1):2. doi: 10.1186/s41236-017-0005-8. Epub 2017 Nov 1.


Pierced Lasso Topology Controls Function in Leptin.

Haglund E, Pilko A, Wollman R, Jennings PA, Onuchic JN.

J Phys Chem B. 2017 Feb 2;121(4):706-718. doi: 10.1021/acs.jpcb.6b11506. Epub 2017 Jan 18.


Elucidating the druggable interface of protein-protein interactions using fragment docking and coevolutionary analysis.

Bai F, Morcos F, Cheng RR, Jiang H, Onuchic JN.

Proc Natl Acad Sci U S A. 2016 Dec 13;113(50):E8051-E8058. Epub 2016 Nov 29.


Protein Folding and Structure Prediction from the Ground Up II: AAWSEM for α/β Proteins.

Chen M, Lin X, Lu W, Onuchic JN, Wolynes PG.

J Phys Chem B. 2017 Apr 20;121(15):3473-3482. doi: 10.1021/acs.jpcb.6b09347. Epub 2016 Nov 11.


Transferable model for chromosome architecture.

Di Pierro M, Zhang B, Aiden EL, Wolynes PG, Onuchic JN.

Proc Natl Acad Sci U S A. 2016 Oct 25;113(43):12168-12173. Epub 2016 Sep 29.


Breast cancer tumorigenicity is dependent on high expression levels of NAF-1 and the lability of its Fe-S clusters.

Darash-Yahana M, Pozniak Y, Lu M, Sohn YS, Karmi O, Tamir S, Bai F, Song L, Jennings PA, Pikarsky E, Geiger T, Onuchic JN, Mittler R, Nechushtai R.

Proc Natl Acad Sci U S A. 2016 Sep 27;113(39):10890-5. doi: 10.1073/pnas.1612736113. Epub 2016 Sep 12.


Connecting the Sequence-Space of Bacterial Signaling Proteins to Phenotypes Using Coevolutionary Landscapes.

Cheng RR, Nordesjö O, Hayes RL, Levine H, Flores SC, Onuchic JN, Morcos F.

Mol Biol Evol. 2016 Dec;33(12):3054-3064. Epub 2016 Sep 7.


Lowered pH Leads to Fusion Peptide Release and a Highly Dynamic Intermediate of Influenza Hemagglutinin.

Lin X, Noel JK, Wang Q, Ma J, Onuchic JN.

J Phys Chem B. 2016 Sep 15;120(36):9654-60. doi: 10.1021/acs.jpcb.6b06775. Epub 2016 Sep 1.


Strain Mediated Adaptation Is Key for Myosin Mechanochemistry: Discovering General Rules for Motor Activity.

Jana B, Onuchic JN.

PLoS Comput Biol. 2016 Aug 5;12(8):e1005035. doi: 10.1371/journal.pcbi.1005035. eCollection 2016 Aug.


Gambogic acid identifies an isoform-specific druggable pocket in the middle domain of Hsp90β.

Yim KH, Prince TL, Qu S, Bai F, Jennings PA, Onuchic JN, Theodorakis EA, Neckers L.

Proc Natl Acad Sci U S A. 2016 Aug 16;113(33):E4801-9. doi: 10.1073/pnas.1606655113. Epub 2016 Jul 27.


Notch-Jagged signalling can give rise to clusters of cells exhibiting a hybrid epithelial/mesenchymal phenotype.

Boareto M, Jolly MK, Goldman A, Pietilä M, Mani SA, Sengupta S, Ben-Jacob E, Levine H, Onuchic JN.

J R Soc Interface. 2016 May;13(118). pii: 20151106. doi: 10.1098/rsif.2015.1106.


Protein Folding and Structure Prediction from the Ground Up: The Atomistic Associative Memory, Water Mediated, Structure and Energy Model.

Chen M, Lin X, Zheng W, Onuchic JN, Wolynes PG.

J Phys Chem B. 2016 Aug 25;120(33):8557-65. doi: 10.1021/acs.jpcb.6b02451. Epub 2016 May 13.


Preface to Special Topic on Protein Dynamics: Beyond Static Snapshots in Structural Biology.

Phillips GN Jr, Onuchic JN.

Struct Dyn. 2016 Feb 26;3(1):011901. doi: 10.1063/1.4942424. eCollection 2016 Jan. No abstract available.


SMOG 2: A Versatile Software Package for Generating Structure-Based Models.

Noel JK, Levi M, Raghunathan M, Lammert H, Hayes RL, Onuchic JN, Whitford PC.

PLoS Comput Biol. 2016 Mar 10;12(3):e1004794. doi: 10.1371/journal.pcbi.1004794. eCollection 2016 Mar.


Sequence co-evolutionary information is a natural partner to minimally-frustrated models of biomolecular dynamics.

Noel JK, Morcos F, Onuchic JN.

F1000Res. 2016 Jan 26;5. pii: F1000 Faculty Rev-106. doi: 10.12688/f1000research.7186.1. eCollection 2016. Review.


Periodic, Quasi-periodic and Chaotic Dynamics in Simple Gene Elements with Time Delays.

Suzuki Y, Lu M, Ben-Jacob E, Onuchic JN.

Sci Rep. 2016 Feb 15;6:21037. doi: 10.1038/srep21037.


Information and redundancy in the burial folding code of globular proteins within a wide range of shapes and sizes.

Ferreira DC, van der Linden MG, de Oliveira LC, Onuchic JN, de Araújo AF.

Proteins. 2016 Apr;84(4):515-31. doi: 10.1002/prot.24998. Epub 2016 Feb 15.


Constructing a folding model for protein S6 guided by native fluctuations deduced from NMR structures.

Lammert H, Noel JK, Haglund E, Schug A, Onuchic JN.

J Chem Phys. 2015 Dec 28;143(24):243141. doi: 10.1063/1.4936881.


Geometrical Frustration in Interleukin-33 Decouples the Dynamics of the Functional Element from the Folding Transition State Ensemble.

Fisher KM, Haglund E, Noel JK, Hailey KL, Onuchic JN, Jennings PA.

PLoS One. 2015 Dec 2;10(12):e0144067. doi: 10.1371/journal.pone.0144067. eCollection 2015.


Modeling the Transitions between Collective and Solitary Migration Phenotypes in Cancer Metastasis.

Huang B, Jolly MK, Lu M, Tsarfaty I, Ben-Jacob E, Onuchic JN.

Sci Rep. 2015 Dec 2;5:17379. doi: 10.1038/srep17379.


Activation of apoptosis in NAF-1-deficient human epithelial breast cancer cells.

Holt SH, Darash-Yahana M, Sohn YS, Song L, Karmi O, Tamir S, Michaeli D, Luo Y, Paddock ML, Jennings PA, Onuchic JN, Azad RK, Pikarsky E, Cabantchik IZ, Nechushtai R, Mittler R.

J Cell Sci. 2016 Jan 1;129(1):155-65. doi: 10.1242/jcs.178293. Epub 2015 Nov 30.


Cancer-Related NEET Proteins Transfer 2Fe-2S Clusters to Anamorsin, a Protein Required for Cytosolic Iron-Sulfur Cluster Biogenesis.

Lipper CH, Paddock ML, Onuchic JN, Mittler R, Nechushtai R, Jennings PA.

PLoS One. 2015 Oct 8;10(10):e0139699. doi: 10.1371/journal.pone.0139699. eCollection 2015.


Dimeric interactions and complex formation using direct coevolutionary couplings.

dos Santos RN, Morcos F, Jana B, Andricopulo AD, Onuchic JN.

Sci Rep. 2015 Sep 4;5:13652. doi: 10.1038/srep13652.

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