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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.


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 Feb 12. doi: 10.1007/s00775-018-1538-8. [Epub ahead of print] 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.


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.


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.


Implications of the Hybrid Epithelial/Mesenchymal Phenotype in Metastasis.

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

Front Oncol. 2015 Jul 20;5:155. doi: 10.3389/fonc.2015.00155. eCollection 2015. Review.


Constructing sequence-dependent protein models using coevolutionary information.

Cheng RR, Raghunathan M, Noel JK, Onuchic JN.

Protein Sci. 2016 Jan;25(1):111-22. doi: 10.1002/pro.2758. Epub 2015 Aug 10.


Generalized Manning Condensation Model Captures the RNA Ion Atmosphere.

Hayes RL, Noel JK, Mandic A, Whitford PC, Sanbonmatsu KY, Mohanty U, Onuchic JN.

Phys Rev Lett. 2015 Jun 26;114(25):258105. Epub 2015 Jun 26.


Jagged mediates differences in normal and tumor angiogenesis by affecting tip-stalk fate decision.

Boareto M, Jolly MK, Ben-Jacob E, Onuchic JN.

Proc Natl Acad Sci U S A. 2015 Jul 21;112(29):E3836-44. doi: 10.1073/pnas.1511814112. Epub 2015 Jul 7.


47 The energy landscape for protein folding and biomolecular machines.

Onuchic JN.

J Biomol Struct Dyn. 2015;33 Suppl 1:33. doi: 10.1080/07391102.2015.1032596. No abstract available.


The Fe-S cluster-containing NEET proteins mitoNEET and NAF-1 as chemotherapeutic targets in breast cancer.

Bai F, Morcos F, Sohn YS, Darash-Yahana M, Rezende CO, Lipper CH, Paddock ML, Song L, Luo Y, Holt SH, Tamir S, Theodorakis EA, Jennings PA, Onuchic JN, Mittler R, Nechushtai R.

Proc Natl Acad Sci U S A. 2015 Mar 24;112(12):3698-703. doi: 10.1073/pnas.1502960112. Epub 2015 Mar 11.


Integrating molecular dynamics simulations with chemical probing experiments using SHAPE-FIT.

Kirmizialtin S, Hennelly SP, Schug A, Onuchic JN, Sanbonmatsu KY.

Methods Enzymol. 2015;553:215-34. doi: 10.1016/bs.mie.2014.10.061. Epub 2015 Feb 7.


Jagged-Delta asymmetry in Notch signaling can give rise to a Sender/Receiver hybrid phenotype.

Boareto M, Jolly MK, Lu M, Onuchic JN, Clementi C, Ben-Jacob E.

Proc Natl Acad Sci U S A. 2015 Feb 3;112(5):E402-9. doi: 10.1073/pnas.1416287112. Epub 2015 Jan 20.


What protein folding teaches us about biological function and molecular machines.

Whitford PC, Onuchic JN.

Curr Opin Struct Biol. 2015 Feb;30:57-62. doi: 10.1016/ Epub 2015 Jan 2. Review.


Connecting thermal and mechanical protein (un)folding landscapes.

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

Biophys J. 2014 Dec 16;107(12):2950-61. doi: 10.1016/j.bpj.2014.10.021.


Structure-function analysis of NEET proteins uncovers their role as key regulators of iron and ROS homeostasis in health and disease.

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.

Biochim Biophys Acta. 2015 Jun;1853(6):1294-315. doi: 10.1016/j.bbamcr.2014.10.014. Epub 2014 Oct 23. Review.


The physics of bacterial decision making.

Ben-Jacob E, Lu M, Schultz D, Onuchic JN.

Front Cell Infect Microbiol. 2014 Oct 30;4:154. doi: 10.3389/fcimb.2014.00154. eCollection 2014. Review.


Physics transforming the life sciences.

Onuchic JN.

Phys Biol. 2014 Oct 8;11(5):053006. doi: 10.1088/1478-3975/11/5/053006.


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