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Items: 1 to 50 of 263

1.

Redox-dependent gating of VDAC by mitoNEET.

Lipper CH, Stofleth JT, Bai F, Sohn YS, Roy S, Mittler R, Nechushtai R, Onuchic JN, Jennings PA.

Proc Natl Acad Sci U S A. 2019 Oct 1;116(40):19924-19929. doi: 10.1073/pnas.1908271116. Epub 2019 Sep 16.

2.

A biophysical model uncovers the size distribution of migrating cell clusters across cancer types.

Bocci F, Kumar Jolly M, Onuchic JN.

Cancer Res. 2019 Sep 3. pii: canres.1726.2019. doi: 10.1158/0008-5472.CAN-19-1726. [Epub ahead of print]

PMID:
31481500
3.

NRF2 activates a partial epithelial-mesenchymal transition and is maximally present in a hybrid epithelial/mesenchymal phenotype.

Bocci F, Tripathi SC, Vilchez Mercedes SA, George JT, Casabar JP, Wong PK, Hanash SM, Levine H, Onuchic JN, Jolly MK.

Integr Biol (Camb). 2019 Jun 1;11(6):251-263. doi: 10.1093/intbio/zyz021.

4.

Quantifying Cancer Epithelial-Mesenchymal Plasticity and its Association with Stemness and Immune Response.

Jia D, Li X, Bocci F, Tripathi S, Deng Y, Jolly MK, Onuchic JN, Levine H.

J Clin Med. 2019 May 22;8(5). pii: E725. doi: 10.3390/jcm8050725. Review.

5.

The role of coevolutionary signatures in protein interaction dynamics, complex inference, molecular recognition, and mutational landscapes.

Morcos F, Onuchic JN.

Curr Opin Struct Biol. 2019 Jun;56:179-186. doi: 10.1016/j.sbi.2019.03.024. Epub 2019 Apr 28. Review.

PMID:
31029927
6.

Forging tools for refining predicted protein structures.

Lin X, Schafer NP, Lu W, Jin S, Chen X, Chen M, Onuchic JN, Wolynes PG.

Proc Natl Acad Sci U S A. 2019 May 7;116(19):9400-9409. doi: 10.1073/pnas.1900778116. Epub 2019 Apr 18.

7.

Structural and Dynamical Order of a Disordered Protein: Molecular Insights into Conformational Switching of PAGE4 at the Systems Level.

Lin X, Kulkarni P, Bocci F, Schafer NP, Roy S, Tsai MY, He Y, Chen Y, Rajagopalan K, Mooney SM, Zeng Y, Weninger K, Grishaev A, Onuchic JN, Levine H, Wolynes PG, Salgia R, Rangarajan G, Uversky V, Orban J, Jolly MK.

Biomolecules. 2019 Feb 22;9(2). pii: E77. doi: 10.3390/biom9020077.

8.

The anti-apoptotic proteins NAF-1 and iASPP interact to drive apoptosis in cancer cells.

Iosub-Amir A, Bai F, Sohn YS, Song L, Tamir S, Marjault HB, Mayer G, Karmi O, Jennings PA, Mittler R, Onuchic JN, Friedler A, Nechushtai R.

Chem Sci. 2018 Nov 20;10(3):665-673. doi: 10.1039/c8sc03390k. eCollection 2019 Jan 21.

9.

Elucidating cancer metabolic plasticity by coupling gene regulation with metabolic pathways.

Jia D, Lu M, Jung KH, Park JH, Yu L, Onuchic JN, Kaipparettu BA, Levine H.

Proc Natl Acad Sci U S A. 2019 Feb 26;116(9):3909-3918. doi: 10.1073/pnas.1816391116. Epub 2019 Feb 7.

10.

Structure-Based Model of RNA Pseudoknot Captures Magnesium-Dependent Folding Thermodynamics.

Mandic A, Hayes RL, Lammert H, Cheng RR, Onuchic JN.

J Phys Chem B. 2019 Feb 21;123(7):1505-1511. doi: 10.1021/acs.jpcb.8b10791. Epub 2019 Feb 7.

PMID:
30676755
11.

Quantitative Characteristic of ncRNA Regulation in Gene Regulatory Networks.

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

Methods Mol Biol. 2019;1912:341-366. doi: 10.1007/978-1-4939-8982-9_14.

PMID:
30635901
12.

Magnesium controls aptamer-expression platform switching in the SAM-I riboswitch.

Roy S, Hennelly SP, Lammert H, Onuchic JN, Sanbonmatsu KY.

Nucleic Acids Res. 2019 Apr 8;47(6):3158-3170. doi: 10.1093/nar/gky1311.

13.

Toward understanding cancer stem cell heterogeneity in the tumor microenvironment.

Bocci F, Gearhart-Serna L, Boareto M, Ribeiro M, Ben-Jacob E, Devi GR, Levine H, Onuchic JN, Jolly MK.

Proc Natl Acad Sci U S A. 2019 Jan 2;116(1):148-157. doi: 10.1073/pnas.1815345116. Epub 2018 Dec 26.

14.

Walking along chromosomes with super-resolution imaging, contact maps, and integrative modeling.

Nir G, Farabella I, Pérez Estrada C, Ebeling CG, Beliveau BJ, Sasaki HM, Lee SD, Nguyen SC, McCole RB, Chattoraj S, Erceg J, AlHaj Abed J, Martins NMC, Nguyen HQ, Hannan MA, Russell S, Durand NC, Rao SSP, Kishi JY, Soler-Vila P, Di Pierro M, Onuchic JN, Callahan SP, Schreiner JM, Stuckey JA, Yin P, Aiden EL, Marti-Renom MA, Wu CT.

PLoS Genet. 2018 Dec 26;14(12):e1007872. doi: 10.1371/journal.pgen.1007872. eCollection 2018 Dec.

15.

Testing the gene expression classification of the EMT spectrum.

Jia D, George JT, Tripathi SC, Kundnani DL, Lu M, Hanash SM, Onuchic JN, Jolly MK, Levine H.

Phys Biol. 2019 Jan 18;16(2):025002. doi: 10.1088/1478-3975/aaf8d4.

PMID:
30557866
16.

Deciphering the structure of the condensin protein complex.

Krepel D, Cheng RR, Di Pierro M, Onuchic JN.

Proc Natl Acad Sci U S A. 2018 Nov 20;115(47):11911-11916. doi: 10.1073/pnas.1812770115. Epub 2018 Nov 1.

17.

Structural consequences of hereditary spastic paraplegia disease-related mutations in kinesin.

Dutta M, Diehl MR, Onuchic JN, Jana B.

Proc Natl Acad Sci U S A. 2018 Nov 13;115(46):E10822-E10829. doi: 10.1073/pnas.1810622115. Epub 2018 Oct 26.

18.

Consensus report of the 8 and 9th Weinman Symposia on Gene x Environment Interaction in carcinogenesis: novel opportunities for precision medicine.

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.

Cell Death Differ. 2018 Nov;25(11):1885-1904. doi: 10.1038/s41418-018-0213-5. Epub 2018 Oct 15. Review.

PMID:
30323273
19.

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 Sep 20;175(1):292-294. doi: 10.1016/j.cell.2018.09.002. No abstract available.

20.

Template-Guided Protein Structure Prediction and Refinement Using Optimized Folding Landscape Force Fields.

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

J Chem Theory Comput. 2018 Nov 13;14(11):6102-6116. doi: 10.1021/acs.jctc.8b00683. Epub 2018 Oct 8.

21.

Molecular mechanisms of the interhead coordination by interhead tension in cytoplasmic dyneins.

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

Proc Natl Acad Sci U S A. 2018 Oct 2;115(40):10052-10057. doi: 10.1073/pnas.1806688115. Epub 2018 Sep 17.

22.

Designing bacterial signaling interactions with coevolutionary landscapes.

Cheng RR, Haglund E, Tiee NS, Morcos F, Levine H, Adams JA, Jennings PA, Onuchic JN.

PLoS One. 2018 Aug 20;13(8):e0201734. doi: 10.1371/journal.pone.0201734. eCollection 2018.

23.

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 Dec 13;122(49):11218-11227. doi: 10.1021/acs.jpcb.8b06874. Epub 2018 Aug 27.

PMID:
30102033
24.

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.

25.

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 Aug 21;115(34):E7905-E7913. doi: 10.1073/pnas.1805442115. Epub 2018 Jul 16.

26.

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.

27.

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 Aug 17;293(33):12919-12933. doi: 10.1074/jbc.RA118.003957. Epub 2018 Jun 27.

28.

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.

29.

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.

30.

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.

31.

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. Erratum in: Cell. 2018 Sep 20;175(1):292-294.

32.

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.

33.

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.

34.

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.

35.

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. 2019 Mar 10;30(8):1083-1095. doi: 10.1089/ars.2018.7502. Epub 2018 Mar 29.

PMID:
29463105
36.

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.

37.

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.

PMID:
29328673
38.

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.

39.

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.

40.

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.

41.

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.

42.

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 21;115(34):E8104.

43.

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.

44.

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.

45.

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.

46.

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.

47.

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.

48.

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.

49.

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.

50.

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.

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