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Ronald M. Levy - Publications

Affiliations: 
1980-2014 Rutgers University, New Brunswick, New Brunswick, NJ, United States 
 2014- Temple University, Philadelphia, PA, United States 
Area:
Computational chemistry, biophysics
Website:
https://ronlevygroup.cst.temple.edu/levygroup.html
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Year Citation  Score
2023 Li M, Oliveira Passos D, Shan Z, Smith SJ, Sun Q, Biswas A, Choudhuri I, Strutzenberg TS, Haldane A, Deng N, Li Z, Zhao XZ, Briganti L, Kvaratskhelia M, Burke TR, ... Levy RM, et al. Mechanisms of HIV-1 integrase resistance to dolutegravir and potent inhibition of drug-resistant variants. Science Advances. 9: eadg5953. PMID 37478179 DOI: 10.1126/sciadv.adg5953  0.602
2022 Choudhuri I, Biswas A, Haldane A, Levy RM. Contingency and Entrenchment of Drug-Resistance Mutations in HIV Viral Proteins. The Journal of Physical Chemistry. B. 126: 10622-10636. PMID 36493468 DOI: 10.1021/acs.jpcb.2c06123  0.614
2021 Haldane A, Levy RM. Mi3-GPU: MCMC-based inverse Ising inference on GPUs for protein covariation analysis Computer Physics Communications. 260: 107312. DOI: 10.1016/J.Cpc.2020.107312  0.334
2020 Tse C, Wickstrom L, Kvaratskhelia M, Gallicchio E, Levy R, Deng N. Exploring the Free-Energy Landscape and Thermodynamics of Protein-Protein Association. Biophysical Journal. PMID 32877664 DOI: 10.1016/J.Bpj.2020.08.005  0.665
2020 Zhang BW, Matubayasi N, Levy RM. Cavity Particle in Aqueous Solution with a Hydrophobic Solute: Structure, Energetics, and Functionals. The Journal of Physical Chemistry. B. PMID 32469519 DOI: 10.1021/Acs.Jpcb.0C02721  0.316
2020 Levy RM. Insights into the energy landscapes of chromosome organization proteins from coevolutionary sequence variation and structural modeling. Proceedings of the National Academy of Sciences of the United States of America. PMID 31924744 DOI: 10.1073/Pnas.1921727117  0.368
2019 Narayan B, Fathizadeh A, Templeton C, He P, Arasteh S, Elber R, Buchete NV, Levy RM. The transition between active and inactive conformations of Abl kinase studied by rock climbing and Milestoning. Biochimica Et Biophysica Acta. General Subjects. 129508. PMID 31884066 DOI: 10.1016/J.Bbagen.2019.129508  0.507
2019 Cui D, Zhang BW, Tan Z, Levy RM. Ligand Binding Thermodynamic Cycles: Hysteresis, LWHAM, and the Overlapping States Matrix. Journal of Chemical Theory and Computation. PMID 31743019 DOI: 10.1021/Acs.Jctc.9B00740  0.37
2019 Sakae Y, Zhang BW, Levy RM, Deng N. Absolute Protein Binding Free Energy Simulations for Ligands with Multiple Poses, a Thermodynamic Path That Avoids Exhaustive Enumeration of the Poses. Journal of Computational Chemistry. PMID 31621932 DOI: 10.1002/Jcc.26078  0.395
2019 Ishii Y, Yamamoto N, Matubayasi N, Zhang BW, Cui D, Levy RM. Spatially-Decomposed Free Energy of Solvation Based on the Endpoint Density-Functional Method. Journal of Chemical Theory and Computation. PMID 30990682 DOI: 10.1021/Acs.Jctc.8B01309  0.348
2019 Zhang BW, Arasteh S, Levy RM. The UWHAM and SWHAM Software Package. Scientific Reports. 9: 2803. PMID 30808938 DOI: 10.1038/S41598-019-39420-X  0.329
2019 Xia J, Flynn W, Gallicchio E, Uplinger K, Armstrong JD, Forli S, Olson AJ, Levy RM. Massive-Scale Binding Free Energy Simulations of HIV Integrase Complexes Using Asynchronous Replica Exchange Framework Implemented on the IBM WCG Distributed Network. Journal of Chemical Information and Modeling. PMID 30758197 DOI: 10.1021/Acs.Jcim.8B00817  0.675
2018 He P, Zhang BW, Arasteh S, Wang L, Abel R, Levy RM. Conformational Free Energy Changes via an Alchemical Path without Reaction Coordinates. The Journal of Physical Chemistry Letters. PMID 30024165 DOI: 10.1021/Acs.Jpclett.8B01851  0.337
2018 Xia J, Flynn WF, Levy RM. On Improving Prediction Accuracy of Binding Free Energies and Poses of HIV Integrase Complexes Using the Binding Energy Distribution Analysis Method with Flattening Potentials. Journal of Chemical Information and Modeling. PMID 29927237 DOI: 10.1021/Acs.Jcim.8B00194  0.455
2018 Deng N, Cui D, Zhang BW, Xia J, Cruz J, Levy R. Comparing alchemical and physical pathway methods for computing the absolute binding free energy of charged ligands. Physical Chemistry Chemical Physics : Pccp. PMID 29896599 DOI: 10.1039/C8Cp01524D  0.389
2018 Zhang BW, Cui D, Matubayasi N, Levy RM. The Excess Chemical Potential of Water at the Interface with a Protein from Endpoint Simulations. The Journal of Physical Chemistry. B. PMID 29634902 DOI: 10.1021/Acs.Jpcb.8B02666  0.378
2017 Cui D, Zhang BW, Matubayasi N, Levy RM. The Role of Interfacial Water in Protein-Ligand Binding: Insights from the Indirect Solvent Mediated PMF. Journal of Chemical Theory and Computation. PMID 29262255 DOI: 10.1021/Acs.Jctc.7B01076  0.373
2017 Zhang BW, Deng N, Tan Z, Levy RM. Stratified UWHAM and Its Stochastic Approximation for Multicanonical Simulations Which are Far from Equilibrium. Journal of Chemical Theory and Computation. PMID 28902500 DOI: 10.1021/Acs.Jctc.7B00651  0.407
2017 Levy RM, Cui D, Zhang BW, Matubayasi N. The Relationship Between Solvation Thermodynamics from IST and DFT Perspectives. The Journal of Physical Chemistry. B. PMID 28186751 DOI: 10.1021/Acs.Jpcb.6B12889  0.346
2016 Harris RC, Deng N, Levy RM, Ishizuka R, Matubayasi N. Computing conformational free energy differences in explicit solvent: An efficient thermodynamic cycle using an auxiliary potential and a free energy functional constructed from the end points. Journal of Computational Chemistry. PMID 28008630 DOI: 10.1002/Jcc.24668  0.374
2016 Levy RM, Haldane A, Flynn WF. Potts Hamiltonian models of protein co-variation, free energy landscapes, and evolutionary fitness. Current Opinion in Structural Biology. 43: 55-62. PMID 27870991 DOI: 10.1016/J.Sbi.2016.11.004  0.353
2016 Pal RK, Haider K, Kaur D, Flynn W, Xia J, Levy RM, Taran T, Wickstrom L, Kurtzman T, Gallicchio E. Erratum to: A combined treatment of hydration and dynamical effects for the modeling of host-guest binding thermodynamics: the SAMPL5 blinded challenge. Journal of Computer-Aided Molecular Design. PMID 27815770 DOI: 10.1007/s10822-016-9987-z  0.779
2016 Pal RK, Haider K, Kaur D, Flynn W, Xia J, Levy RM, Taran T, Wickstrom L, Kurtzman T, Gallicchio E. A combined treatment of hydration and dynamical effects for the modeling of host-guest binding thermodynamics: the SAMPL5 blinded challenge. Journal of Computer-Aided Molecular Design. PMID 27696239 DOI: 10.1007/S10822-016-9956-6  0.8
2016 Deng N, Flynn WF, Xia J, Vijayan RS, Zhang B, He P, Mentes A, Gallicchio E, Levy RM. Large scale free energy calculations for blind predictions of protein-ligand binding: the D3R Grand Challenge 2015. Journal of Computer-Aided Molecular Design. PMID 27562018 DOI: 10.1007/S10822-016-9952-X  0.653
2016 Deng N, Hoyte A, Mansour YE, Mohamed MS, Fuchs JR, Engelman AN, Kvaratskhelia M, Levy R. Allosteric HIV-1 integrase inhibitors promote aberrant protein multimerization by directly mediating inter-subunit interactions: Structural and thermodynamic modeling studies. Protein Science : a Publication of the Protein Society. 25: 1911-1917. PMID 27503276 DOI: 10.1002/Pro.2997  0.367
2016 Haldane A, Flynn WF, He P, Vijayan RS, Levy RM. Structural Propensities of Kinase Family Proteins from a Potts Model of Residue Co-Variation. Protein Science : a Publication of the Protein Society. PMID 27241634 DOI: 10.1002/Pro.2954  0.378
2016 Zhang BW, Dai W, Gallicchio E, He P, Xia J, Tan Z, Levy RM. Simulating Replica Exchange: Markov State Models, Proposal Schemes and the Infinite Swapping Limit. The Journal of Physical Chemistry. B. PMID 27079355 DOI: 10.1021/Acs.Jpcb.6B02015  0.654
2016 Mentes A, Deng NJ, Vijayan RS, Xia J, Gallicchio E, Levy RM. Binding Energy Distribution Analysis Method (BEDAM): Hamiltonian replica exchange with torsional flattening for binding mode prediction and binding free energy estimation. Journal of Chemical Theory and Computation. PMID 27070865 DOI: 10.1021/Acs.Jctc.6B00134  0.679
2016 Xia J, Flynn WF, Gallicchio E, Zhang BW, He P, Tan Z, Levy RM. Large-Scale Asynchronous and Distributed Multidimensional Replica Exchange Molecular Simulations and Efficiency Analysis. Journal of Computational Chemistry. 37. PMID 26860348 DOI: 10.1002/jcc.24336  0.578
2016 Tan Z, Xia J, Zhang BW, Levy RM. Locally weighted histogram analysis and stochastic solution for large-scale multi-state free energy estimation. The Journal of Chemical Physics. 144: 034107. PMID 26801020 DOI: 10.1063/1.4939768  0.398
2016 Wickstrom L, Deng N, He P, Mentes A, Nguyen C, Gilson MK, Kurtzman T, Gallicchio E, Levy RM. Parameterization of an effective potential for protein-ligand binding from host-guest affinity data. Journal of Molecular Recognition : Jmr. 29: 10-21. PMID 26256816 DOI: 10.1002/Jmr.2489  0.658
2015 Gallicchio E, Xia J, Flynn WF, Zhang B, Samlalsingh S, Mentes A, Levy RM. Asynchronous Replica Exchange Software for Grid and Heterogeneous Computing. Computer Physics Communications. 196: 236-246. PMID 27103749 DOI: 10.1016/J.Cpc.2015.06.010  0.628
2015 Zhang BW, Xia J, Tan Z, Levy RM. A Stochastic Solution to the Unbinned WHAM Equations. The Journal of Physical Chemistry Letters. 6: 3834-3840. PMID 26722879 DOI: 10.1021/Acs.Jpclett.5B01771  0.385
2015 Dai W, Sengupta AM, Levy RM. First Passage Times, Lifetimes, and Relaxation Times of Unfolded Proteins. Physical Review Letters. 115: 048101. PMID 26252709 DOI: 10.1103/Physrevlett.115.048101  0.337
2015 Deng N, Zhang BW, Levy RM. Connecting Free Energy Surfaces in Implicit and Explicit Solvent: an Efficient Method to Compute Conformational and Solvation Free Energies. Journal of Chemical Theory and Computation. 11: 2868-2878. PMID 26236174 DOI: 10.1021/Acs.Jctc.5B00264  0.417
2015 Xia J, Flynn WF, Gallicchio E, Zhang BW, He P, Tan Z, Levy RM. Large-scale asynchronous and distributed multidimensional replica exchange molecular simulations and efficiency analysis. Journal of Computational Chemistry. PMID 26149645 DOI: 10.1002/Jcc.23996  0.65
2015 Gallicchio E, Chen H, Chen H, Fitzgerald M, Gao Y, He P, Kalyanikar M, Kao C, Lu B, Niu Y, Pethe M, Zhu J, Levy RM. BEDAM binding free energy predictions for the SAMPL4 octa-acid host challenge. Journal of Computer-Aided Molecular Design. 29: 315-25. PMID 25726024 DOI: 10.1007/S10822-014-9795-2  0.645
2015 Vijayan RS, He P, Modi V, Duong-Ly KC, Ma H, Peterson JR, Dunbrack RL, Levy RM. Conformational analysis of the DFG-out kinase motif and biochemical profiling of structurally validated type II inhibitors. Journal of Medicinal Chemistry. 58: 466-79. PMID 25478866 DOI: 10.1021/Jm501603H  0.566
2015 Deng N, Forli S, He P, Perryman A, Wickstrom L, Vijayan RS, Tiefenbrunn T, Stout D, Gallicchio E, Olson AJ, Levy RM. Distinguishing binders from false positives by free energy calculations: fragment screening against the flap site of HIV protease. The Journal of Physical Chemistry. B. 119: 976-88. PMID 25189630 DOI: 10.1021/Jp506376Z  0.659
2015 Gallicchio E, Xia J, Flynn WF, Zhang B, Samlalsingh S, Mentes A, Levy RM. Asynchronous replica exchange software for grid and heterogeneous computing Computer Physics Communications. DOI: 10.1016/j.cpc.2015.06.010  0.531
2015 Wickstrom L, Deng N, He P, Mentes A, Nguyen C, Gilson MK, Kurtzman T, Gallicchio E, Levy RM. Parameterization of an effective potential for protein-ligand binding from host-guest affinity data Journal of Molecular Recognition. DOI: 10.1002/jmr.2489  0.585
2014 Xia J, Levy RM. Molecular dynamics of the proline switch and its role in Crk signaling. The Journal of Physical Chemistry. B. 118: 4535-45. PMID 24702481 DOI: 10.1021/Jp5013297  0.325
2014 Gallicchio E, Deng N, He P, Wickstrom L, Perryman AL, Santiago DN, Forli S, Olson AJ, Levy RM. Virtual screening of integrase inhibitors by large scale binding free energy calculations: the SAMPL4 challenge. Journal of Computer-Aided Molecular Design. 28: 475-90. PMID 24504704 DOI: 10.1007/S10822-014-9711-9  0.672
2013 Wickstrom L, He P, Gallicchio E, Levy RM. Large scale affinity calculations of cyclodextrin host-guest complexes: Understanding the role of reorganization in the molecular recognition process. Journal of Chemical Theory and Computation. 9: 3136-3150. PMID 25147485 DOI: 10.1021/Ct400003R  0.673
2013 Yi G, Lapelosa M, Bradley R, Mariano TM, Dietz DE, Hughes S, Wrin T, Petropoulos C, Gallicchio E, Levy RM, Arnold E, Arnold GF. Correction: Chimeric Rhinoviruses Displaying MPER Epitopes Elicit Anti-HIV Neutralizing Responses. Plos One. 8. PMID 24116242 DOI: 10.1371/Annotation/57Fc0148-19Fe-4B8B-B2F4-Bb5F60Baa971  0.563
2013 Yi G, Lapelosa M, Bradley R, Mariano TM, Dietz DE, Hughes S, Wrin T, Petropoulos C, Gallicchio E, Levy RM, Arnold E, Arnold GF. Chimeric rhinoviruses displaying MPER epitopes elicit anti-HIV neutralizing responses. Plos One. 8: e72205. PMID 24039745 DOI: 10.1371/Journal.Pone.0072205  0.563
2013 Deng NJ, Dai W, Levy RM. How kinetics within the unfolded state affects protein folding: an analysis based on markov state models and an ultra-long MD trajectory. The Journal of Physical Chemistry. B. 117: 12787-99. PMID 23705683 DOI: 10.1021/Jp401962K  0.365
2013 Xia J, Deng NJ, Levy RM. NMR relaxation in proteins with fast internal motions and slow conformational exchange: model-free framework and Markov state simulations. The Journal of Physical Chemistry. B. 117: 6625-34. PMID 23638941 DOI: 10.1021/Jp400797Y  0.42
2013 Radak BK, Romanus M, Gallicchio E, Lee TS, Weidner O, Deng NJ, He P, Dai W, York DM, Levy RM, Jha S. A framework for flexible and scalable replica-exchange on production distributed CI Acm International Conference Proceeding Series. DOI: 10.1145/2484762.2484830  0.641
2012 Narayanan C, Weinstock DS, Wu KP, Baum J, Levy RM. Investigation of the Polymeric Properties of α-Synuclein and Comparison with NMR Experiments: A Replica Exchange Molecular Dynamics Study. Journal of Chemical Theory and Computation. 8: 3929-3942. PMID 23162382 DOI: 10.1021/Ct300241T  0.748
2012 Tan Z, Gallicchio E, Lapelosa M, Levy RM. Theory of binless multi-state free energy estimation with applications to protein-ligand binding. The Journal of Chemical Physics. 136: 144102. PMID 22502496 DOI: 10.1063/1.3701175  0.661
2012 Lapelosa M, Gallicchio E, Levy RM. Conformational Transitions and Convergence of Absolute Binding Free Energy Calculations. Journal of Chemical Theory and Computation. 8: 47-60. PMID 22368530 DOI: 10.1021/Ct200684B  0.68
2012 Gallicchio E, Levy RM. Prediction of SAMPL3 host-guest affinities with the binding energy distribution analysis method (BEDAM). Journal of Computer-Aided Molecular Design. 26: 505-16. PMID 22354755 DOI: 10.1007/S10822-012-9552-3  0.675
2012 Wickstrom L, Gallicchio E, Levy RM. The linear interaction energy method for the prediction of protein stability changes upon mutation. Proteins. 80: 111-25. PMID 22038697 DOI: 10.1002/Prot.23168  0.624
2012 Bell JA, Cao Y, Gunn JR, Day T, Gallicchio E, Zhou Z, Levy R, Farid R. PrimeX and the Schrödinger computational chemistry suite of programs International Tables For Crystallography. DOI: 10.1107/97809553602060000864  0.612
2011 Gallicchio E, Levy RM. Recent theoretical and computational advances for modeling protein-ligand binding affinities. Advances in Protein Chemistry and Structural Biology. 85: 27-80. PMID 21920321 DOI: 10.1016/B978-0-12-386485-7.00002-8  0.655
2011 Deng NJ, Zheng W, Gallicchio E, Levy RM. Insights into the dynamics of HIV-1 protease: a kinetic network model constructed from atomistic simulations. Journal of the American Chemical Society. 133: 9387-94. PMID 21561098 DOI: 10.1021/Ja2008032  0.413
2011 Gallicchio E, Levy RM. Advances in all atom sampling methods for modeling protein-ligand binding affinities. Current Opinion in Structural Biology. 21: 161-6. PMID 21339062 DOI: 10.1016/J.Sbi.2011.01.010  0.662
2011 Zheng W, Gallicchio E, Deng N, Andrec M, Levy RM. Kinetic network study of the diversity and temperature dependence of Trp-Cage folding pathways: combining transition path theory with stochastic simulations. The Journal of Physical Chemistry. B. 115: 1512-23. PMID 21254767 DOI: 10.1021/Jp1089596  0.653
2010 Gallicchio E, Lapelosa M, Levy RM. The Binding Energy Distribution Analysis Method (BEDAM) for the Estimation of Protein-Ligand Binding Affinities. Journal of Chemical Theory and Computation. 6: 2961-2977. PMID 21116484 DOI: 10.1021/Ct1002913  0.656
2010 Lapelosa M, Arnold GF, Gallicchio E, Arnold E, Levy RM. Antigenic characteristics of rhinovirus chimeras designed in silico for enhanced presentation of HIV-1 gp41 epitopes [corrected]. Journal of Molecular Biology. 397: 752-66. PMID 20138057 DOI: 10.1016/J.Jmb.2010.01.064  0.623
2010 Okumura H, Gallicchio E, Levy RM. Conformational populations of ligand-sized molecules by replica exchange molecular dynamics and temperature reweighting. Journal of Computational Chemistry. 31: 1357-67. PMID 19882731 DOI: 10.1002/Jcc.21419  0.66
2010 Sheridan RP, Levy RM, Englander SW. Normal mode paths for hydrogen exchange in the peptide ferrichrome. Proceedings of the National Academy of Sciences of the United States of America. 80: 5569-72. PMID 16593367 DOI: 10.1073/Pnas.80.18.5569  0.31
2010 Levy RM, Perahia D, Karplus M. Molecular dynamics of an alpha-helical polypeptide: Temperature dependence and deviation from harmonic behavior. Proceedings of the National Academy of Sciences of the United States of America. 79: 1346-50. PMID 16593164 DOI: 10.1073/Pnas.79.4.1346  0.629
2010 Lapelosa M, Arnold GF, Gallicchio E, Arnold E, Levy RM. Erratum to “Antigenic Characteristics of Rhinovirus Chimeras Designed in silico for Enhanced Presentation of HIV-1 gp41 Epitopes” [J. Mol. Biol. 397 (2010) 752–766] Journal of Molecular Biology. 398: 623-624. DOI: 10.1016/J.Jmb.2010.03.044  0.551
2010 Zheng W, Gallicchio E, Andrec M, Levy RM. Exploring the Kinetics and Folding Pathways of Trp-cage using a Kinetic Network Model Biophysical Journal. 98: 634a. DOI: 10.1016/J.Bpj.2009.12.3472  0.628
2009 Gallicchio E, Paris K, Levy RM. The AGBNP2 Implicit Solvation Model. Journal of Chemical Theory and Computation. 5: 2544-2564. PMID 20419084 DOI: 10.1021/Ct900234U  0.654
2009 Paris KA, Haq O, Felts AK, Das K, Arnold E, Levy RM. Conformational landscape of the human immunodeficiency virus type 1 reverse transcriptase non-nucleoside inhibitor binding pocket: lessons for inhibitor design from a cluster analysis of many crystal structures. Journal of Medicinal Chemistry. 52: 6413-20. PMID 19827836 DOI: 10.1021/Jm900854H  0.327
2009 Frenkel YV, Gallicchio E, Das K, Levy RM, Arnold E. Molecular dynamics study of non-nucleoside reverse transcriptase inhibitor 4-[[4-[[4-[(E)-2-cyanoethenyl]-2,6-dimethylphenyl]amino]-2-pyrimidinyl]amino]benzonitrile (TMC278/rilpivirine) aggregates: correlation between amphiphilic properties of the drug and oral bioavailability. Journal of Medicinal Chemistry. 52: 5896-905. PMID 19739675 DOI: 10.1021/Jm900282Z  0.606
2009 Zheng W, Andrec M, Gallicchio E, Levy RM. Recovering kinetics from a simplified protein folding model using replica exchange simulations: a kinetic network and effective stochastic dynamics. The Journal of Physical Chemistry. B. 113: 11702-9. PMID 19655770 DOI: 10.1021/Jp900445T  0.625
2009 Wu KP, Weinstock DS, Narayanan C, Levy RM, Baum J. Structural reorganization of alpha-synuclein at low pH observed by NMR and REMD simulations. Journal of Molecular Biology. 391: 784-96. PMID 19576220 DOI: 10.1016/J.Jmb.2009.06.063  0.728
2009 Lapelosa M, Gallicchio E, Arnold GF, Arnold E, Levy RM. In silico vaccine design based on molecular simulations of rhinovirus chimeras presenting HIV-1 gp41 epitopes. Journal of Molecular Biology. 385: 675-91. PMID 19026659 DOI: 10.1016/J.Jmb.2008.10.089  0.627
2008 Felts AK, Gallicchio E, Chekmarev D, Paris KA, Friesner RA, Levy RM. Prediction of Protein Loop Conformations using the AGBNP Implicit Solvent Model and Torsion Angle Sampling. Journal of Chemical Theory and Computation. 4: 855-868. PMID 18787648 DOI: 10.1021/Ct800051K  0.666
2008 Weinstock DS, Narayanan C, Baum J, Levy RM. Correlation between 13Calpha chemical shifts and helix content of peptide ensembles. Protein Science : a Publication of the Protein Society. 17: 950-4. PMID 18436960 DOI: 10.1110/Ps.073365408  0.745
2008 Knight JL, Zhou Z, Gallicchio E, Himmel DM, Friesner RA, Arnold E, Levy RM. Exploring structural variability in X-ray crystallographic models using protein local optimization by torsion-angle sampling. Acta Crystallographica. Section D, Biological Crystallography. 64: 383-96. PMID 18391405 DOI: 10.1107/S090744490800070X  0.639
2008 Zheng W, Andrec M, Gallicchio E, Levy RM. Simple continuous and discrete models for simulating replica exchange simulations of protein folding. The Journal of Physical Chemistry. B. 112: 6083-93. PMID 18251533 DOI: 10.1021/Jp076377+  0.657
2008 Gallicchio E, Levy RM, Parashar M. Asynchronous replica exchange for molecular simulations. Journal of Computational Chemistry. 29: 788-94. PMID 17876761 DOI: 10.1002/Jcc.20839  0.613
2007 Su Y, Gallicchio E, Das K, Arnold E, Levy RM. Linear Interaction Energy (LIE) Models for Ligand Binding in Implicit Solvent:  Theory and Application to the Binding of NNRTIs to HIV-1 Reverse Transcriptase. Journal of Chemical Theory and Computation. 3: 256-77. PMID 26627170 DOI: 10.1021/Ct600258E  0.646
2007 Zheng W, Andrec M, Gallicchio E, Levy RM. Simulating replica exchange simulations of protein folding with a kinetic network model. Proceedings of the National Academy of Sciences of the United States of America. 104: 15340-5. PMID 17878309 DOI: 10.1073/Pnas.0704418104  0.659
2007 Andrec M, Snyder DA, Zhou Z, Young J, Montelione GT, Levy RM. A large data set comparison of protein structures determined by crystallography and NMR: statistical test for structural differences and the effect of crystal packing. Proteins. 69: 449-65. PMID 17623851 DOI: 10.1002/Prot.21507  0.323
2007 Weinstock DS, Narayanan C, Felts AK, Andrec M, Levy RM, Wu KP, Baum J. Distinguishing among structural ensembles of the GB1 peptide: REMD simulations and NMR experiments. Journal of the American Chemical Society. 129: 4858-9. PMID 17402734 DOI: 10.1021/Ja0677517  0.753
2007 Ravindranathan KP, Gallicchio E, McDermott AE, Levy RM. Conformational dynamics of substrate in the active site of cytochrome P450 BM-3/NPG complex: Insights from NMR order parameters Journal of the American Chemical Society. 129: 474-475. PMID 17226994 DOI: 10.1021/Ja0672371  0.634
2006 Himmel DM, Sarafianos SG, Dharmasena S, Hossain MM, McCoy-Simandle K, Ilina T, Clark AD, Knight JL, Julias JG, Clark PK, Krogh-Jespersen K, Levy RM, Hughes SH, Parniak MA, Arnold E. HIV-1 reverse transcriptase structure with RNase H inhibitor dihydroxy benzoyl naphthyl hydrazone bound at a novel site. Acs Chemical Biology. 1: 702-12. PMID 17184135 DOI: 10.1021/Cb600303Y  0.304
2006 Ravindranathan KP, Gallicchio E, Friesner RA, McDermott AE, Levy RM. Conformational equilibrium of cytochrome P450 BM-3 complexed with N-palmitoylglycine: a replica exchange molecular dynamics study. Journal of the American Chemical Society. 128: 5786-91. PMID 16637647 DOI: 10.1021/Ja058465I  0.646
2006 Zhang L, Parashar M, Gallicchio E, Levy RM. Salsa: Scalable asynchronous replica exchange for parallel molecular dynamics applications Proceedings of the International Conference On Parallel Processing. 127-134. DOI: 10.1109/ICPP.2006.63  0.569
2005 Gallicchio E, Andrec M, Felts AK, Levy RM. Temperature weighted histogram analysis method, replica exchange, and transition paths. The Journal of Physical Chemistry. B. 109: 6722-31. PMID 16851756 DOI: 10.1021/Jp045294F  0.642
2005 Banks JL, Beard HS, Cao Y, Cho AE, Damm W, Farid R, Felts AK, Halgren TA, Mainz DT, Maple JR, Murphy R, Philipp DM, Repasky MP, Zhang LY, Berne BJ, ... ... Levy RM, et al. Integrated Modeling Program, Applied Chemical Theory (IMPACT). Journal of Computational Chemistry. 26: 1752-80. PMID 16211539 DOI: 10.1002/Jcc.20292  0.696
2005 Ravindranathan KP, Gallicchio E, Levy RM. Conformational equilibria and free energy profiles for the allosteric transition of the ribose-binding protein. Journal of Molecular Biology. 353: 196-210. PMID 16157349 DOI: 10.1016/J.Jmb.2005.08.009  0.671
2005 Andrec M, Felts AK, Gallicchio E, Levy RM. Protein folding pathways from replica exchange simulations and a kinetic network model. Proceedings of the National Academy of Sciences of the United States of America. 102: 6801-6. PMID 15800044 DOI: 10.1073/Pnas.0408970102  0.649
2005 Knight JL, Mekler V, Mukhopadhyay J, Ebright RH, Levy RM. Distance-restrained docking of rifampicin and rifamycin SV to RNA polymerase using systematic FRET measurements: developing benchmarks of model quality and reliability. Biophysical Journal. 88: 925-38. PMID 15542547 DOI: 10.1529/Biophysj.104.050187  0.338
2004 Felts AK, Harano Y, Gallicchio E, Levy RM. Free energy surfaces of beta-hairpin and alpha-helical peptides generated by replica exchange molecular dynamics with the AGBNP implicit solvent model. Proteins. 56: 310-21. PMID 15211514 DOI: 10.1002/Prot.20104  0.636
2004 Gallicchio E, Levy RM. AGBNP: an analytic implicit solvent model suitable for molecular dynamics simulations and high-resolution modeling. Journal of Computational Chemistry. 25: 479-99. PMID 14735568 DOI: 10.1002/Jcc.10400  0.68
2004 Chekmarev DS, Ishida T, Levy RM. Long-Time Conformational Transitions of Alanine Dipeptide in Aqueous Solution:  Continuous and Discrete-State Kinetic Models The Journal of Physical Chemistry B. 108: 19487-19495. DOI: 10.1021/Jp048540W  0.406
2003 Andrec M, Levy RM, Talaga DS. Direct Determination of Kinetic Rates from Single-Molecule Photon Arrival Trajectories Using Hidden Markov Models. The Journal of Physical Chemistry. A. 107: 7454-7464. PMID 19626138 DOI: 10.1021/Jp035514+  0.303
2003 Levy RM, Zhang LY, Gallicchio E, Felts AK. On the nonpolar hydration free energy of proteins: surface area and continuum solvent models for the solute-solvent interaction energy. Journal of the American Chemical Society. 125: 9523-30. PMID 12889983 DOI: 10.1021/Ja029833A  0.677
2003 Du P, Andrec M, Levy RM. Have we seen all structures corresponding to short protein fragments in the Protein Data Bank? An update. Protein Engineering. 16: 407-14. PMID 12874373 DOI: 10.1093/Protein/Gzg052  0.305
2002 Andrec M, Harano Y, Jacobson MP, Friesner RA, Levy RM. Complete protein structure determination using backbone residual dipolar couplings and sidechain rotamer prediction. Journal of Structural and Functional Genomics. 2: 103-11. PMID 12836667 DOI: 10.1023/A:1020435630054  0.378
2002 Andrec M, Levy RM. Protein sequential resonance assignments by combinatorial enumeration using 13C alpha chemical shifts and their (i, i-1) sequential connectivities. Journal of Biomolecular Nmr. 23: 263-70. PMID 12398347 DOI: 10.1023/A:1020236105735  0.323
2002 Felts AK, Gallicchio E, Wallqvist A, Levy RM. Distinguishing native conformations of proteins from decoys with an effective free energy estimator based on the OPLS all-atom force field and the Surface Generalized Born solvent model. Proteins. 48: 404-22. PMID 12112706 DOI: 10.1002/Prot.10171  0.655
2002 Gallicchio E, Zhang LY, Levy RM. The SGB/NP hydration free energy model based on the surface generalized born solvent reaction field and novel nonpolar hydration free energy estimators. Journal of Computational Chemistry. 23: 517-29. PMID 11948578 DOI: 10.1002/Jcc.10045  0.661
2002 Andrec M, Du P, Levy RM. Protein backbone structure determination using only residual dipolar couplings from one ordering medium. Journal of Biomolecular Nmr. 21: 335-47. PMID 11824753 DOI: 10.1023/A:1013334513610  0.349
2002 Kubo M, Levy RM, Rossky PJ, Matubayasi N, Nakahara M. Chloride ion hydration and diffusion in supercritical water using a polarizable water model Journal of Physical Chemistry B. 106: 3979-3986. DOI: 10.1021/Jp013743V  0.507
2001 Andrec M, Du P, Levy RM. Protein structural motif recognition via NMR residual dipolar couplings. Journal of the American Chemical Society. 123: 1222-9. PMID 11456677 DOI: 10.1021/Ja003979X  0.35
2001 Zhou R, Friesner RA, Ghosh A, Rizzo RC, Jorgensen WL, Levy RM. New linear interaction method for binding affinity calculations using a continuum solvent model Journal of Physical Chemistry B. 105: 10388-10397. DOI: 10.1021/Jp011480Z  0.367
2001 Zhang LY, Gallicchio E, Friesner RA, Levy RM. Solvent models for protein-ligand binding: Comparison of implicit solvent poisson and surface generalized born models with explicit solvent simulations Journal of Computational Chemistry. 22: 591-607. DOI: 10.1002/Jcc.1031  0.676
2000 Andrec M, Inman KG, Weber DJ, Levy RM, Montelione GT. A Bayesian statistical method for the detection and quantification of rotational diffusion anisotropy from NMR relaxation data. Journal of Magnetic Resonance (San Diego, Calif. : 1997). 146: 66-80. PMID 10968959 DOI: 10.1006/Jmre.2000.2113  0.303
2000 Andrec M, Montelione GT, Levy RM. Estimation of dynamic parameters from NMR relaxation data using the Lipari-Szabo model-free approach and Bayesian statistical methods. Journal of Magnetic Resonance (San Diego, Calif. : 1997). 139: 408-21. PMID 10423379 DOI: 10.1006/Jmre.1999.1839  0.309
2000 Lockwood DM, Rossky PJ, Levy RM. Functional Group Contributions to Partial Molar Compressibilities of Alcohols in Water Journal of Physical Chemistry B. 104: 4210-4217. DOI: 10.1021/Jp994197X  0.506
2000 Gallicchio E, Kubo MM, Levy RM. Enthalpy−Entropy and Cavity Decomposition of Alkane Hydration Free Energies:  Numerical Results and Implications for Theories of Hydrophobic Solvation The Journal of Physical Chemistry B. 104: 6271-6285. DOI: 10.1021/Jp0006274  0.646
1999 Levy RM, Gallicchio E. Computer simulations with explicit solvent: recent progress in the thermodynamic decomposition of free energies and in modeling electrostatic effects. Annual Review of Physical Chemistry. 49: 531-67. PMID 9933909 DOI: 10.1146/Annurev.Physchem.49.1.531  0.665
1999 Jin D, Andrec M, Montelione GT, Levy RM. Propagation of experimental uncertainties using the Lipari-Szabo model-free analysis of protein dynamics. Journal of Biomolecular Nmr. 12: 471-92. PMID 9862126 DOI: 10.1023/A:1008313319334  0.327
1999 Murphy LR, Li N, Baum J, Levy RM. Tertiary contacts in alpha-lactalbumin at pH 7 and pH 2: a molecular dynamics study. Journal of Biomolecular Structure & Dynamics. 16: 355-65. PMID 9833674 DOI: 10.1080/07391102.1998.10508253  0.339
1998 Murphy LR, Matubayasi N, Payne VA, Levy RM. Protein hydration and unfolding--insights from experimental partial specific volumes and unfolded protein models. Folding & Design. 3: 105-18. PMID 9565755 DOI: 10.1016/S1359-0278(98)00016-9  0.332
1998 Matubayasi N, Gallicchio E, Levy RM. On the local and nonlocal components of solvation thermodynamics and their relation to solvation shell models The Journal of Chemical Physics. 109: 4864-4872. DOI: 10.1063/1.477097  0.607
1998 Gallicchio E, Kubo MM, Levy RM. Entropy−Enthalpy Compensation in Solvation and Ligand Binding Revisited Journal of the American Chemical Society. 120: 4526-4527. DOI: 10.1021/Ja974061H  0.606
1997 Figueirido F, Levy RM, Zhou R, Berne BJ. Erratum: “Large scale simulation of macromolecules in solution: Combining the periodic fast multipole method with multiple time step integrators” [J. Chem. Phys. 106, 9835 (1997)] The Journal of Chemical Physics. 107: 7002-7002. DOI: 10.1063/1.475334  0.502
1997 Figueirido F, Levy RM, Zhou R, Berne BJ. Large scale simulation of macromolecules in solution: Combining the periodic fast multipole method with multiple time step integrators The Journal of Chemical Physics. 106: 9835-9849. DOI: 10.1063/1.474115  0.429
1997 Figueirido F, Levy RM, Zhou R, Berne BJ. Large scale simulation of macromolecules in solution: Combining the periodic fast multipole method with multiple time step integrators Journal of Chemical Physics. 106: 9835-9849. DOI: 10.1063/1.474115  0.524
1997 Kubo MM, Gallicchio E, Levy RM. Thermodynamic Decomposition of Hydration Free Energies by Computer Simulation:  Application to Amines, Oxides, and Sulfides The Journal of Physical Chemistry B. 101: 10527-10534. DOI: 10.1021/Jp972598B  0.393
1997 Figueirido F, Del Buono GS, Levy RM. On Finite-Size Corrections to the Free Energy of Ionic Hydration The Journal of Physical Chemistry B. 101: 5622-5623. DOI: 10.1021/Jp970882X  0.331
1997 Jin D, Figueirido F, Montelione GT, Levy RM. Impact of the Precision in NMR Relaxation Measurements on the Interpretation of Protein Dynamics Journal of the American Chemical Society. 119: 6923-6924. DOI: 10.1021/Ja970947+  0.313
1996 Fadel AR, Jin DQ, Montelione GT, Levy RM. Crankshaft motions of the polypeptide backbone in molecular dynamics simulations of human type-alpha transforming growth factor. Journal of Biomolecular Nmr. 6: 221-6. PMID 8589611 DOI: 10.1007/Bf00211787  0.303
1996 Figueirido F, Del Buono GS, Levy RM. Prediction of pKaShifts without Truncation of Electrostatic Interactions:  An Explicit Solvent Calculation for Succinic Acid The Journal of Physical Chemistry. 100: 6389-6392. DOI: 10.1021/Jp9600524  0.392
1995 Suri AK, Levy RM. A Relaxation-Matrix Analysis of Distance-Constraint Ranges for NOEs in Proteins at Long Mixing Times Journal of Magnetic Resonance, Series B. 106: 24-31. PMID 7850172 DOI: 10.1006/Jmrb.1995.1004  0.311
1995 Del Buono GS, Figueirido FE, Levy RM. Intrinsic pKas of ionizable residues in proteins: an explicit solvent calculation for lysozyme. Proteins. 20: 85-97. PMID 7824525 DOI: 10.1002/Prot.340200109  0.431
1995 Figueirido F, Del Buono GS, Levy RM. On finite‐size effects in computer simulations using the Ewald potential The Journal of Chemical Physics. 103: 6133-6142. DOI: 10.1063/1.470721  0.309
1995 Ding Y, Bernardo DN, Krogh-Jespersen K, Levy RM. Solvation Free Energies of Small Amides and Amines from Molecular Dynamics/Free Energy Perturbation Simulations Using Pairwise Additive and Many-Body Polarizable Potentials The Journal of Physical Chemistry. 99: 11575-11583. DOI: 10.1021/J100029A040  0.37
1994 Chen Y, Suri AK, Kominos D, Sanyal G, Naylor AM, Pitzenberger SM, Garsky VM, Levy RM, Baum J. Three-dimensional structure of echistatin and dynamics of the active site. Journal of Biomolecular Nmr. 4: 307-24. PMID 8019139 DOI: 10.1007/Bf00179342  0.379
1994 Figueirido F, Del Buono GS, Levy RM. Molecular mechanics and electrostatic effects. Biophysical Chemistry. 51: 235-41. PMID 7919034 DOI: 10.1016/0301-4622(94)00044-1  0.332
1994 Matubayasi N, Reed LH, Levy RM. Thermodynamics of the Hydration Shell. 1. Excess Energy of a Hydrophobic Solute The Journal of Physical Chemistry. 98: 10640-10649. DOI: 10.1021/J100092A040  0.309
1994 Bernardo DN, Ding Y, Krogh-Jespersen K, Levy RM. An Anisotropic Polarizable Water Model: Incorporation of All-Atom Polarizabilities into Molecular Mechanics Force Fields The Journal of Physical Chemistry. 98: 4180-4187. DOI: 10.1021/J100066A043  0.346
1993 Smith-Brown MJ, Kominos D, Levy RM. Global folding of proteins using a limited number of distance constraints. Protein Engineering. 6: 605-14. PMID 7694274 DOI: 10.1093/Protein/6.6.605  0.325
1992 Kitchen DB, Reed LH, Levy RM. Molecular dynamics simulation of solvated protein at high pressure. Biochemistry. 31: 10083-93. PMID 1382594 DOI: 10.1021/Bi00156A031  0.313
1992 Figueirido FE, Levy RM. Vibrational relaxation and Bloch–Redfield theory The Journal of Chemical Physics. 97: 703-706. DOI: 10.1063/1.463566  0.309
1992 Kominos D, Suri AK, Kitchen DB, Bassolino D, Levy RM. Simulating the effect of the two-spin approximation on the generation of protein structures from NOE data Journal of Magnetic Resonance (1969). 97: 398-410. DOI: 10.1016/0022-2364(92)90325-2  0.778
1991 Levy RM, Belhadj M, Kitchen DB. Gaussian fluctuation formula for electrostatic free‐energy changes in solution The Journal of Chemical Physics. 95: 3627-3633. DOI: 10.1063/1.460813  0.302
1991 Levy RM, Westbrook JD, Kitchen DB, Krogh-Jespersen K. Solvent effects on the adiabatic free energy difference between the ground and excited states of methylindole in water The Journal of Physical Chemistry. 95: 6756-6758. DOI: 10.1021/J100171A005  0.397
1991 Belhadj M, Alper HE, Levy RM. Molecular dynamics simulations of water with Ewald summation for the long range electrostatic interactions Chemical Physics Letters. 179: 13-20. DOI: 10.1016/0009-2614(91)90284-G  0.362
1990 Kominos D, Bassolino DA, Levy RM, Pardi A. Analysis of side-chain conformational distributions in neutrophil peptide-5 NMR structures. Biopolymers. 29: 1807-22. PMID 2207287 DOI: 10.1002/Bip.360291412  0.782
1990 Metzler WJ, Wang C, Kitchen DB, Levy RM, Pardi A. Determining local conformational variations in DNA. Nuclear magnetic resonance structures of the DNA duplexes d(CGCCTAATCG) and d(CGTCACGCGC) generated using back-calculation of the nuclear Overhauser effect spectra, a distance geometry algorithm and constrained molecular dynamics. Journal of Molecular Biology. 214: 711-36. PMID 2167379 DOI: 10.1016/0022-2836(90)90288-W  0.348
1990 Levy RM, Kitchen DB, Blair JT, Krogh-Jespersen K. Molecular dynamics simulation of time-resolved fluorescence and nonequilibrium solvation of formaldehyde in water The Journal of Physical Chemistry. 94: 4470-4476. DOI: 10.1021/J100374A023  0.353
1990 Blair JT, Levy RM, Krogh-Jespersen K. Molecular mechanics parameters for electronically excited states: The (n, π*) singlet state of formaldehyde Chemical Physics Letters. 166: 429-436. DOI: 10.1016/0009-2614(90)85056-I  0.325
1990 Kitchen DB, Hirata F, Westbrook JD, Levy R, Kofke D, Yarmush M. Conserving energy during molecular dynamics simulations of water, proteins, and proteins in water Journal of Computational Chemistry. 11: 1169-1180. DOI: 10.1002/Jcc.540111009  0.351
1990 Perahia D, Levy RM, Karplus M. Motions of an ?-helical polypeptide: Comparison of molecular and harmonic dynamics Biopolymers. 29: 645-677. DOI: 10.1002/Bip.360290402  0.638
1989 Levy RM, Bassolino DA, Kitchen DB, Pardi A. Solution structures of proteins from NMR data and modeling: alternative folds for neutrophil peptide 5. Biochemistry. 28: 9361-72. PMID 2611235 DOI: 10.1021/Bi00450A017  0.788
1989 Alper HE, Levy RM. Computer simulations of the dielectric properties of water: Studies of the simple point charge and transferrable intermolecular potential models The Journal of Chemical Physics. 91: 1242-1251. DOI: 10.1063/1.457198  0.33
1989 Blair JT, Krogh-Jespersen K, Levy RM. Solvent effects on optical absorption spectra: the 1A1 .fwdarw. 1A2 transition of formaldehyde in water Journal of the American Chemical Society. 111: 6948-6956. DOI: 10.1021/Ja00200A009  0.331
1989 Blair JT, Westbrook JD, Levy RM, Krogh-Jespersen K. Simple models for solvation effects on electronic transition energies: Formaldehyde and water Chemical Physics Letters. 154: 531-535. DOI: 10.1016/0009-2614(89)87146-5  0.355
1988 Bassolino DA, Hirata F, Kitchen DB, Kominos D, Pardi A, Levy RM. Determination of Protein Structures in Solution Using Nmr Data and Impact The International Journal of Supercomputing Applications. 2: 41-61. DOI: 10.1177/109434208800200204  0.791
1988 Hirata F, Redfern P, Levy RM. Viewing the born model for ion hydration through a microscope International Journal of Quantum Chemistry. 34: 179-190. DOI: 10.1002/Qua.560340716  0.334
1987 Westhof E, Chevrier B, Gallion SL, Weiner PK, Levy RM. Temperature-dependent molecular dynamics and restrained X-ray refinement simulations of a Z-DNA hexamer. Journal of Molecular Biology. 191: 699-712. PMID 3806679 DOI: 10.1016/0022-2836(86)90454-7  0.349
1986 Kuriyan J, Petsko GA, Levy RM, Karplus M. Effect of anisotropy and anharmonicity on protein crystallographic refinement. An evaluation by molecular dynamics. Journal of Molecular Biology. 190: 227-54. PMID 3795269 DOI: 10.1016/0022-2836(86)90295-0  0.625
1986 Levy RM. Computer Simulations of Macromolecular Dynamics: Models for Vibrational Spectroscopy and X‐Ray Refinement Annals of the New York Academy of Sciences. 482: 24-43. PMID 3471107 DOI: 10.1111/J.1749-6632.1986.Tb20934.X  0.378
1986 Rojas OL, Levy RM, Szabo A. Corrections to the quasiharmonic approximation for evaluating molecular entropies The Journal of Chemical Physics. 85: 1037-1043. DOI: 10.1063/1.451296  0.364
1986 Weiner PK, Gallion SL, Westhof E, Levy RM. Visualization of energetics and conformations from molecular computer simulations Journal of Molecular Graphics. 4: 203-207. DOI: 10.1016/0263-7855(86)80041-8  0.405
1986 Levy RM. Using Macromolecular Dynamics Simulations to Interpret Experiments Israel Journal of Chemistry. 27: 173-179. DOI: 10.1002/Ijch.198600026  0.375
1985 Levy RM, Sheridan RP, Keepers JW, Dubey GS, Swaminathan S, Karplus M. Molecular dynamics of myoglobin at 298 degrees K. Results from a 300-ps computer simulation. Biophysical Journal. 48: 509-18. PMID 3840041 DOI: 10.1016/S0006-3495(85)83806-6  0.516
1984 Levy RM, Srinivasan AR, Olson WK, McCammon JA. Quasi-harmonic method for studying very low frequency modes in proteins. Biopolymers. 23: 1099-112. PMID 6733249 DOI: 10.1002/Bip.360230610  0.453
1984 Levy RM, Karplus M, Kushick J, Perahia D. Evaluation of the configurational entropy for proteins: application to molecular dynamics simulations of an α-helix Macromolecules. 17: 1370-1374. DOI: 10.1021/Ma00137A013  0.64
1984 Olejniczak ET, Dobson CM, Karplus M, Levy RM. Motional averaging of proton nuclear Overhauser effects in proteins. Predictions from a molecular dynamics simulation of lysozyme Journal of the American Chemical Society. 106: 1923-1930. DOI: 10.1021/Ja00319A004  0.487
1984 OLEJNICZAK ET, DOBSON CM, KARPLUS M, LEVY RM. ChemInform Abstract: MOTIONAL AVERAGING OF PROTON NUCLEAR OVERHAUSER EFFECTS IN PROTEINS. PREDICTIONS FROM A MOLECULAR DYNAMICS SIMULATION OF LYSOZYME Chemischer Informationsdienst. 15. DOI: 10.1002/chin.198427055  0.412
1982 Sheridan RP, Levy RM, Salemme FR. alpha-Helix dipole model and electrostatic stabilization of 4-alpha-helical proteins. Proceedings of the National Academy of Sciences of the United States of America. 79: 4545-4549. PMID 6956878 DOI: 10.1073/Pnas.79.15.4545  0.329
1982 Levy RM, Dobson CM, Karplus M. Dipolar NMR relaxation of nonprotonated aromatic carbons in proteins. Structural and dynamical effects. Biophysical Journal. 39: 107-13. PMID 6179550 DOI: 10.1016/S0006-3495(82)84496-2  0.489
1982 Lipari G, Szabo A, Levy RM. Protein dynamics and NMR relaxation: comparison of simulations with experiment Nature. 300: 197-198. DOI: 10.1038/300197A0  0.393
1982 LEVY RM, KARPLUS M, WOLYNES PG. ChemInform Abstract: NMR RELAXATION PARAMETERS IN MOLECULES WITH INTERNAL MOTION: EXACT LANGEVIN TRAJECTORY RESULTS COMPARED WITH SIMPLIFIED RELAXATION MODELS Chemischer Informationsdienst. 13. DOI: 10.1002/chin.198203044  0.377
1981 Levy RM, Karplus M, Wolynes PG. NMR relaxation parameters in molecules with internal motion: exact Langevin trajectory results compared with simplified relaxation models Journal of the American Chemical Society. 103: 5998-6011. DOI: 10.1021/Ja00410A002  0.455
1981 Levy RM, Karplus M, McCammon JA. Increase of carbon-13 NMR relaxation times in proteins due to picosecond motional averaging Journal of the American Chemical Society. 103: 994-996. DOI: 10.1021/Ja00394A072  0.528
1981 LEVY RM, KARPLUS M, MCCAMMON JA. ChemInform Abstract: INCREASE OF CARBON-13 NMR RELAXATION TIMES IN PROTEINS DUE TO PICOSECOND MOTIONAL AVERAGING Chemischer Informationsdienst. 12. DOI: 10.1002/chin.198122050  0.475
1981 Pear MR, Northrup SH, McCammon JA, Karplus M, Levy RM. Correlated helix-coil transitions in polypeptides Biopolymers. 20: 629-632. DOI: 10.1002/Bip.1981.360200314  0.51
1980 Levy RM, Karplus M, McCammon JA. Molecular dynamics studies of NMR relaxation in proteins. Biophysical Journal. 32: 628-30. PMID 19431400 DOI: 10.1016/S0006-3495(80)84998-8  0.572
1980 McCammon JA, Northrup SH, Karplus M, Levy RM. Helix-coil transitions in a simple polypeptide model Biopolymers. 19: 2033-2045. DOI: 10.1002/Bip.1980.360191108  0.594
1979 Levy RM, Karplus M, Andrew McCammon J. Diffusive langevin dynamics of model alkanes Chemical Physics Letters. 65: 4-11. DOI: 10.1016/0009-2614(79)80114-1  0.453
1979 Levy RM, Karplus M. Vibrational approach to the dynamics of an ?-helix Biopolymers. 18: 2465-2495. DOI: 10.1002/Bip.1979.360181008  0.47
1976 Levy RM, Kushmerick MJ. Induction of contractile activity by rigor complexes in myofibrils. Biochemical and Biophysical Research Communications. 76: 512-9. PMID 141286 DOI: 10.1016/0006-291X(77)90754-9  0.532
1976 Levy RM, Umazume Y, Kushmerick MJ. Ca2+ dependence of tension and ADP production in segments of chemically skinned muscle fibers. Biochimica Et Biophysica Acta. 430: 352-65. PMID 132189 DOI: 10.1016/0005-2728(76)90091-8  0.517
Low-probability matches (unlikely to be authored by this person)
2022 Gizzio J, Thakur A, Haldane A, Levy RM. Evolutionary divergence in the conformational landscapes of tyrosine vs serine/threonine kinases. Elife. 11. PMID 36562610 DOI: 10.7554/eLife.83368  0.299
1995 Bernardo DN, Ding Y, Krogh-Jespersen K, Levy RM. Evaluating polarizable potentials on distributed memory parallel computers: Program development and applications Journal of Computational Chemistry. 16: 1141-1152. DOI: 10.1002/Jcc.540160908  0.298
2015 Flynn WF, Chang MW, Tan Z, Oliveira G, Yuan J, Okulicz JF, Torbett BE, Levy RM. Deep sequencing of protease inhibitor resistant HIV patient isolates reveals patterns of correlated mutations in Gag and protease. Plos Computational Biology. 11: e1004249. PMID 25894830 DOI: 10.1371/Journal.Pcbi.1004249  0.297
2007 Zhou Z, Felts AK, Friesner RA, Levy RM. Comparative performance of several flexible docking programs and scoring functions: enrichment studies for a diverse set of pharmaceutically relevant targets. Journal of Chemical Information and Modeling. 47: 1599-608. PMID 17585856 DOI: 10.1021/Ci7000346  0.296
2019 Arasteh S, He P, Haldane A, Levy RM. Protein Kinase Free Energy Landscapes: The Role of the Activation Loop Biophysical Journal. 116: 436a. DOI: 10.1016/J.Bpj.2018.11.2348  0.296
2019 Haldane A, Levy RM. Influence of multiple-sequence-alignment depth on Potts statistical models of protein covariation. Physical Review. E. 99: 032405. PMID 30999494 DOI: 10.1103/Physreve.99.032405  0.294
2001 Wallqvist A, Fukunishi Y, Murphy LR, Fadel A, Levy RM. Iterative sequence/secondary structure search for protein homologs: comparison with amino acid sequence alignments and application to fold recognition in genome databases. Bioinformatics (Oxford, England). 16: 988-1002. PMID 11159310 DOI: 10.1093/Bioinformatics/16.11.988  0.293
1986 Gallion SL, Levy RM, Weiner PK, Hirata F. Implementation of a macromolecular mechanics program on a cyber 205 supercomputer Computers & Chemistry. 10: 165-173. DOI: 10.1016/0097-8485(86)80008-0  0.292
1988 Zhang P, Levy RM, Friesner RA. Variable quadratic propagator for quantum Monte Carlo simulations Chemical Physics Letters. 144: 236-242. DOI: 10.1016/0009-2614(88)87147-1  0.29
1996 Matubayasi N, Levy RM. Thermodynamics of the Hydration Shell. 2. Excess Volume and Compressibility of a Hydrophobic Solute The Journal of Physical Chemistry. 100: 2681-2688. DOI: 10.1021/Jp951618B  0.29
2011 Felts AK, Labarge K, Bauman JD, Patel DV, Himmel DM, Arnold E, Parniak MA, Levy RM. Identification of alternative binding sites for inhibitors of HIV-1 ribonuclease H through comparative analysis of virtual enrichment studies. Journal of Chemical Information and Modeling. 51: 1986-98. PMID 21714567 DOI: 10.1021/Ci200194W  0.289
2013 Levy RM, Dai W, Deng NJ, Makarov DE. How long does it take to equilibrate the unfolded state of a protein? Protein Science : a Publication of the Protein Society. 22: 1459-65. PMID 23963761 DOI: 10.1002/Pro.2335  0.288
2001 Wallqvist A, Gallicchio E, Levy RM. A Model for Studying Drying at Hydrophobic Interfaces:  Structural and Thermodynamic Properties† The Journal of Physical Chemistry B. 105: 6745-6753. DOI: 10.1021/Jp010945I  0.286
1987 Hirata F, Levy RM. A new RISM integral equation for solvated polymers Chemical Physics Letters. 136: 267-273. DOI: 10.1016/0009-2614(87)80249-X  0.286
2014 Slaughter A, Jurado KA, Deng N, Feng L, Kessl JJ, Shkriabai N, Larue RC, Fadel HJ, Patel PA, Jena N, Fuchs JR, Poeschla E, Levy RM, Engelman A, Kvaratskhelia M. The mechanism of H171T resistance reveals the importance of Nδ-protonated His171 for the binding of allosteric inhibitor BI-D to HIV-1 integrase. Retrovirology. 11: 100. PMID 25421939 DOI: 10.1186/S12977-014-0100-1  0.284
1992 Westbrook JD, Levy RM, Krogh-Jespersen K. Molecular electrostatic potentials and partial atomic charges from correlated wave functions: Applications to the electronic ground and excited states of 3-methylindole Journal of Computational Chemistry. 13: 979-989. DOI: 10.1002/Jcc.540130808  0.283
2012 Haq O, Andrec M, Morozov AV, Levy RM. Correlated electrostatic mutations provide a reservoir of stability in HIV protease. Plos Computational Biology. 8: e1002675. PMID 22969420 DOI: 10.1371/Journal.Pcbi.1002675  0.283
1984 Levy RM, De la Luz Rojas O, Friesner RA. Quasi-harmonic method for calculating vibrational spectra from classical simulations on multi-dimensional anharmonic potential surfaces The Journal of Physical Chemistry. 88: 4233-4238. DOI: 10.1021/J150663A009  0.281
2016 Patel D, Antwi J, Koneru PC, Serrao E, Forli S, Kessl JJ, Feng L, Deng N, Levy RM, Fuchs JR, Olson AJ, Engelman AN, Bauman JD, Kvaratskhelia M, Arnold E. A New Class of Allosteric HIV-1 Integrase Inhibitors Identified by Crystallographic Fragment Screening of the Catalytic Core Domain. The Journal of Biological Chemistry. 291: 23569-23577. PMID 27645997 DOI: 10.1074/Jbc.M116.753384  0.28
1993 Alper H, Levy RM. Dielectric and thermodynamic response of a generalized reaction field model for liquid state simulations The Journal of Chemical Physics. 99: 9847-9852. DOI: 10.1063/1.465468  0.277
1984 Friesner RA, Levy RM. An optimized harmonic reference system for the evaluation of discretized path integrals The Journal of Chemical Physics. 80: 4488-4495. DOI: 10.1063/1.447232  0.277
2017 Flynn WF, Haldane A, Torbett BE, Levy RM. Inference of Epistatic Effects Leading to Entrenchment and Drug Resistance in HIV-1 Protease. Molecular Biology and Evolution. PMID 28369521 DOI: 10.1093/Molbev/Msx095  0.275
2021 Sun Q, Levy RM, Kirby KA, Wang Z, Sarafianos SG, Deng N. Molecular Dynamics Free Energy Simulations Reveal the Mechanism for the Antiviral Resistance of the M66I HIV-1 Capsid Mutation. Viruses. 13. PMID 34063519 DOI: 10.3390/v13050920  0.274
2018 Haldane A, Flynn WF, He P, Levy RM. Coevolutionary Landscape of Kinase Family Proteins: Sequence Probabilities and Functional Motifs. Biophysical Journal. 114: 21-31. PMID 29320688 DOI: 10.1016/J.Bpj.2017.10.028  0.273
2000 Murphy LR, Wallqvist A, Levy RM. Simplified amino acid alphabets for protein fold recognition and implications for folding. Protein Engineering. 13: 149-52. PMID 10775656 DOI: 10.1093/Protein/13.3.149  0.272
1988 Levy RM. Biomolecular processes: dynamics of proteins and nucleic acids. Science. 241: 234-235. PMID 17841055 DOI: 10.1126/Science.241.4862.234  0.269
1997 Payne VA, Matubayasi N, Murphy LR, Levy RM. Monte Carlo Study of the Effect of Pressure on Hydrophobic Association The Journal of Physical Chemistry B. 101: 2054-2060. DOI: 10.1021/Jp962977P  0.268
1991 Belhadj M, Kitchen DB, Krogh-Jespersen K, Levy RM. A molecular dynamics study of pressure effects on solvation and optical spectra: the ground and excited states of formaldehyde in water The Journal of Physical Chemistry. 95: 1082-1089. DOI: 10.1021/J100156A013  0.266
1987 Hirata F, Levy RM. Ionic association in methanol and related solvents: an extended RISM analysis The Journal of Physical Chemistry. 91: 4788-4795. DOI: 10.1021/J100302A028  0.263
1983 Levy RM, Sheridan RP. Combined effect of restricted rotational diffusion plus jumps on nuclear magnetic resonance and fluorescence probes of aromatic ring motions in proteins Biophysical Journal. 41: 217-221. PMID 6838964 DOI: 10.1016/S0006-3495(83)84422-1  0.263
2019 Koneru PC, Francis AC, Deng N, Rebensburg SV, Hoyte AC, Lindenberger J, Adu-Ampratwum D, Larue RC, Wempe MF, Engelman AN, Lyumkis D, Fuchs JR, Levy RM, Melikyan GB, Kvaratskhelia M. HIV-1 integrase tetramers are the antiviral target of pyridine-based allosteric integrase inhibitors. Elife. 8. PMID 31120420 DOI: 10.7554/Elife.46344  0.26
1996 Del Buono GS, Figueirido FE, Levy RM. Dielectric response of solvent surrounding an ion pair: Ewald potential versus spherical truncation Chemical Physics Letters. 263: 521-529. DOI: 10.1016/S0009-2614(96)01234-1  0.259
2019 Biswas A, Haldane A, Arnold E, Levy RM. Epistasis and entrenchment of drug resistance in HIV-1 subtype B. Elife. 8. PMID 31591964 DOI: 10.7554/Elife.50524  0.258
2005 Andrec M, Kholodenko BN, Levy RM, Sontag E. Inference of signaling and gene regulatory networks by steady-state perturbation experiments: structure and accuracy. Journal of Theoretical Biology. 232: 427-41. PMID 15572066 DOI: 10.1016/J.Jtbi.2004.08.022  0.257
2009 Haq O, Levy RM, Morozov AV, Andrec M. Pairwise and higher-order correlations among drug-resistance mutations in HIV-1 subtype B protease. Bmc Bioinformatics. 10: S10. PMID 19758465 DOI: 10.1186/1471-2105-10-S8-S10  0.251
2024 Sun Q, Biswas A, Lyumkis D, Levy R, Deng N. Elucidating the Molecular Determinants of the Binding Modes of a Third-Generation HIV-1 Integrase Strand Transfer Inhibitor: The Importance of Side Chain and Solvent Reorganization. Viruses. 16. PMID 38257776 DOI: 10.3390/v16010076  0.25
1993 Suri AK, Levy RM. Estimation of Interatomic Distances in Proteins from NOE Spectra at Longer Mixing Times Using an Empirical Two-Spin Equation Journal of Magnetic Resonance, Series B. 101: 320-324. DOI: 10.1006/Jmrb.1993.1050  0.249
2020 Levy RM, Matubayasi N, Zhang BW. Solvation Thermodynamics from the Perspective of Endpoints DFT. The Journal of Physical Chemistry. B. PMID 33306906 DOI: 10.1021/acs.jpcb.0c08988  0.249
2023 Sun Q, Biswas A, Lyumkis D, Levy R, Deng N. Elucidating the molecular determinants for binding modes of a third-generation HIV-1 integrase strand transfer inhibitor: Importance of side chain and solvent reorganization. Biorxiv : the Preprint Server For Biology. PMID 38077045 DOI: 10.1101/2023.11.29.569269  0.248
2002 Mekler V, Kortkhonjia E, Mukhopadhyay J, Knight J, Revyakin A, Kapanidis AN, Niu W, Ebright YW, Levy R, Ebright RH. Structural organization of bacterial RNA polymerase holoenzyme and the RNA polymerase-promoter open complex. Cell. 108: 599-614. PMID 11893332 DOI: 10.1016/S0092-8674(02)00667-0  0.248
2001 Andrec M, Montelione GT, Levy RM. Lipari-Szabo mapping: A graphical approach to Lipari-Szabo analysis of NMR relaxation data using reduced spectral density mapping. Journal of Biomolecular Nmr. 18: 83-100. PMID 11101213 DOI: 10.1023/A:1008302101116  0.247
2005 Himmel DM, Sarafianos SG, Dharmasena S, Hossain M, McCoy-Simandle K, Clark PK, Clark Jr AD, Knight JL, Levy RM, Hughes SH, Parniak MA, Arnold E. X-ray structure for an RNase H inhibitor bound to HIV-1 reverse transcriptase Acta Crystallographica Section a Foundations of Crystallography. 61: c249-c249. DOI: 10.1107/S0108767305089397  0.239
2004 Mukhopadhyay J, Sineva E, Knight J, Levy RM, Ebright RH. Antibacterial peptide microcin J25 inhibits transcription by binding within and obstructing the RNA polymerase secondary channel. Molecular Cell. 14: 739-51. PMID 15200952 DOI: 10.1016/J.Molcel.2004.06.010  0.239
1982 Levy RM, Szabo A. Initial fluorescence depolarization of tyrosines in proteins Journal of the American Chemical Society. 104: 2073-2075. DOI: 10.1021/Ja00371A070  0.229
2019 Koneru PC, Francis AC, Deng N, Rebensburg SV, Hoyte AC, Lindenberger J, Adu-Ampratwum D, Larue RC, Wempe MF, Engelman AN, Lyumkis D, Fuchs JR, Levy RM, Melikyan GB, Kvaratskhelia M. Author response: HIV-1 integrase tetramers are the antiviral target of pyridine-based allosteric integrase inhibitors Elife. DOI: 10.7554/Elife.46344.029  0.228
1989 Hirata F, Levy RM. Salt-induced conformational changes in DNA: analysis using the polymer RISM theory The Journal of Physical Chemistry. 93: 479-484. DOI: 10.1021/J100338A092  0.223
2020 Sun Q, Vijayan RSK, Levy R, Deng N. Computational Design of Small Molecular Modulators of Protein-Protein Interactions with a Novel Thermodynamic Cycle: Allosteric Inhibitors of HIV-1 Integrase. Protein Science : a Publication of the Protein Society. PMID 33244804 DOI: 10.1002/pro.4004  0.222
2019 Haldane A, He P, Flynn WF, Levy RM. Coevolutionary Landscapes of Kinase Family Proteins Biophysical Journal. 116: 168a. DOI: 10.1016/J.Bpj.2018.11.936  0.22
2022 Sun Q, Biswas A, Vijayan RSK, Craveur P, Forli S, Olson AJ, Castaner AE, Kirby KA, Sarafianos SG, Deng N, Levy R. Structure-based virtual screening workflow to identify antivirals targeting HIV-1 capsid. Journal of Computer-Aided Molecular Design. PMID 35262811 DOI: 10.1007/s10822-022-00446-5  0.218
2017 Post CB, Levy RM. Editorial overview: Theory & computation. Current Opinion in Structural Biology. 43: iv-vi. PMID 28477855 DOI: 10.1016/J.Sbi.2017.04.008  0.213
2019 Biswas A, Haldane A, Arnold E, Levy RM. Author response: Epistasis and entrenchment of drug resistance in HIV-1 subtype B Elife. DOI: 10.7554/Elife.50524.030  0.212
2021 Haldane A, Levy RM. Mi3-GPU: MCMC-based Inverse Ising Inference on GPUs for protein covariation analysis. Computer Physics Communications. 260. PMID 33716309 DOI: 10.1016/j.cpc.2020.107312  0.209
1990 Alper HE, Levy RM. Field strength dependence of dielectric saturation in liquid water The Journal of Physical Chemistry. 94: 8401-8403. DOI: 10.1021/J100385A008  0.208
2024 Thakur A, Gizzio J, Levy RM. Potts Hamiltonian Models and Molecular Dynamics Free Energy Simulations for Predicting the Impact of Mutations on Protein Kinase Stability. The Journal of Physical Chemistry. B. 128: 1656-1667. PMID 38350894 DOI: 10.1021/acs.jpcb.3c08097  0.205
1982 Finn OJ, Levy R. Multiple HLA-DR antigens: detection with monoclonal antibodies and translation in vitro. Proceedings of the National Academy of Sciences of the United States of America. 79: 2658-62. PMID 6979750 DOI: 10.1073/Pnas.79.8.2658  0.204
2010 Irish JM, Myklebust JH, Alizadeh AA, Houot R, Sharman JP, Czerwinski DK, Nolan GP, Levy R. B-cell signaling networks reveal a negative prognostic human lymphoma cell subset that emerges during tumor progression. Proceedings of the National Academy of Sciences of the United States of America. 107: 12747-54. PMID 20543139 DOI: 10.1073/Pnas.1002057107  0.196
2021 Do HN, Haldane A, Levy RM, Miao Y. Unique features of different classes of G-protein-coupled receptors revealed from sequence coevolutionary and structural analysis. Proteins. PMID 34599827 DOI: 10.1002/prot.26256  0.181
1991 Fan P, Kominos D, Kitchen DB, Levy RM, Baum J. Stabilization of α-helical secondary structure during high-temperature molecular-dynamics simulations of α-lactalbumin Chemical Physics. 158: 295-301. DOI: 10.1016/0301-0104(91)87073-5  0.176
2021 Arasteh S, Zhang BW, Levy RM. Protein Loop Conformational Free Energy Changes via an Alchemical Path without Reaction Coordinates. The Journal of Physical Chemistry Letters. 4368-4377. PMID 33938761 DOI: 10.1021/acs.jpclett.1c00778  0.164
2022 Biswas A, Haldane A, Levy RM. Limits to detecting epistasis in the fitness landscape of HIV. Plos One. 17: e0262314. PMID 35041711 DOI: 10.1371/journal.pone.0262314  0.161
2021 McGee F, Hauri S, Novinger Q, Vucetic S, Levy RM, Carnevale V, Haldane A. The generative capacity of probabilistic protein sequence models. Nature Communications. 12: 6302. PMID 34728624 DOI: 10.1038/s41467-021-26529-9  0.151
2009 Patel KG, Ng PP, Kuo CC, Levy S, Levy R, Swartz JR. Cell-free production of Gaussia princeps luciferase--antibody fragment bioconjugates for ex vivo detection of tumor cells. Biochemical and Biophysical Research Communications. 390: 971-6. PMID 19852937 DOI: 10.1016/J.Bbrc.2009.10.087  0.134
2024 Biswas A, Choudhuri I, Arnold E, Lyumkis D, Haldane A, Levy RM. Kinetic coevolutionary models predict the temporal emergence of HIV-1 resistance mutations under drug selection pressure. Proceedings of the National Academy of Sciences of the United States of America. 121: e2316662121. PMID 38557187 DOI: 10.1073/pnas.2316662121  0.133
2014 Pyne S, Lee SX, Wang K, Irish J, Tamayo P, Nazaire MD, Duong T, Ng SK, Hafler D, Levy R, Nolan GP, Mesirov J, McLachlan GJ. Joint modeling and registration of cell populations in cohorts of high-dimensional flow cytometric data. Plos One. 9: e100334. PMID 24983991 DOI: 10.1371/Journal.Pone.0100334  0.131
1993 Smith MJ, Krogh-Jespersen K, Levy RM. Solvent effects on the torsional dynamics of a twisted intramolecular charge transfer (TICT) molecule: bianthryl in acetonitrile Chemical Physics. 171: 97-106. DOI: 10.1016/0301-0104(93)85134-T  0.129
2024 Gizzio J, Thakur A, Haldane A, Levy RM. Evolutionary sequence and structural basis for the distinct conformational landscapes of Tyr and Ser/Thr kinases. Biorxiv : the Preprint Server For Biology. PMID 38559238 DOI: 10.1101/2024.03.08.584161  0.12
2015 Dai W, Sengupta AM, Levy RM. First Passage Times, Lifetimes, and Relaxation Times of Unfolded Proteins Physical Review Letters. 115. DOI: 10.1103/PhysRevLett.115.048101  0.112
2019 Chen B, Khodadoust MS, Olsson N, Wagar LE, Fast E, Liu CL, Muftuoglu Y, Sworder BJ, Diehn M, Levy R, Davis MM, Elias JE, Altman RB, Alizadeh AA. Predicting HLA class II antigen presentation through integrated deep learning. Nature Biotechnology. PMID 31611695 DOI: 10.1038/S41587-019-0280-2  0.102
2022 Testa S, Haabeth OAW, Blake TR, Del Castillo TJ, Czerwinski DK, Rajapaksa R, Wender PA, Waymouth RM, Levy R. Fingolimod-Conjugated Charge-Altering Releasable Transporters Efficiently and Specifically Deliver mRNA to Lymphocytes In Vivo and In Vitro. Biomacromolecules. PMID 35748182 DOI: 10.1021/acs.biomac.2c00469  0.102
2007 Natkunam Y, Vainer G, Chen J, Zhao S, Marinelli RJ, Hammer AS, Hamilton-Dutoit S, Pikarsky E, Amir G, Levy R, Yisraeli JK, Lossos IS. Expression of the RNA-binding protein VICKZ in normal hematopoietic tissues and neoplasms. Haematologica. 92: 176-83. PMID 17296566 DOI: 10.3324/HAEMATOL.10724  0.097
2005 Yang J, Kanter G, Voloshin A, Michel-Reydellet N, Velkeen H, Levy R, Swartz JR. Rapid expression of vaccine proteins for B-cell lymphoma in a cell-free system. Biotechnology and Bioengineering. 89: 503-11. PMID 15669088 DOI: 10.1002/Bit.20283  0.096
2018 Kurtz DM, Scherer F, Jin MC, Soo J, Craig AFM, Esfahani MS, Chabon JJ, Stehr H, Liu CL, Tibshirani R, Maeda LS, Gupta NK, Khodadoust MS, Advani RH, Levy R, et al. Circulating Tumor DNA Measurements As Early Outcome Predictors in Diffuse Large B-Cell Lymphoma. Journal of Clinical Oncology : Official Journal of the American Society of Clinical Oncology. JCO2018785246. PMID 30125215 DOI: 10.1200/Jco.2018.78.5246  0.088
2011 Patel KG, Ng PP, Levy S, Levy R, Swartz JR. Escherichia coli-based production of a tumor idiotype antibody fragment--tetanus toxin fragment C fusion protein vaccine for B cell lymphoma. Protein Expression and Purification. 75: 15-20. PMID 20851769 DOI: 10.1016/J.Pep.2010.09.005  0.088
2023 Blake TR, Haabeth OAW, Sallets A, McClellan RL, Del Castillo TJ, Vilches-Moure JG, Ho WC, Wender PA, Levy R, Waymouth RM. Lysine-Derived Charge-Altering Releasable Transporters: Targeted Delivery of mRNA and siRNA to the Lungs. Bioconjugate Chemistry. PMID 36996808 DOI: 10.1021/acs.bioconjchem.3c00019  0.087
2008 Malumbres R, Chen J, Tibshirani R, Johnson NA, Sehn LH, Natkunam Y, Briones J, Advani R, Connors JM, Byrne GE, Levy R, Gascoyne RD, Lossos IS. Paraffin-based 6-gene model predicts outcome in diffuse large B-cell lymphoma patients treated with R-CHOP. Blood. 111: 5509-14. PMID 18445689 DOI: 10.1182/Blood-2008-02-136374  0.087
2017 Khodadoust MS, Olsson N, Wagar LE, Haabeth OA, Chen B, Swaminathan K, Rawson K, Liu CL, Steiner D, Lund P, Rao S, Zhang L, Marceau C, Stehr H, Newman AM, ... ... Levy R, et al. Antigen presentation profiling reveals recognition of lymphoma immunoglobulin neoantigens. Nature. PMID 28329770 DOI: 10.1038/Nature21433  0.086
2010 Anderson MW, Zhao S, Ai WZ, Tibshirani R, Levy R, Lossos IS, Natkunam Y. C-C chemokine receptor 1 expression in human hematolymphoid neoplasia. American Journal of Clinical Pathology. 133: 473-83. PMID 20154287 DOI: 10.1309/Ajcp1Ta3Floqtmhf  0.085
2012 Ng PP, Jia M, Patel KG, Brody JD, Swartz JR, Levy S, Levy R. A vaccine directed to B cells and produced by cell-free protein synthesis generates potent antilymphoma immunity. Proceedings of the National Academy of Sciences of the United States of America. 109: 14526-31. PMID 22875703 DOI: 10.1073/Pnas.1211018109  0.084
2007 Kanter G, Yang J, Voloshin A, Levy S, Swartz JR, Levy R. Cell-free production of scFv fusion proteins: an efficient approach for personalized lymphoma vaccines. Blood. 109: 3393-9. PMID 17164345 DOI: 10.1182/Blood-2006-07-030593  0.083
2003 McCormick AA, Reinl SJ, Cameron TI, Vojdani F, Fronefield M, Levy R, Tusé D. Individualized human scFv vaccines produced in plants: humoral anti-idiotype responses in vaccinated mice confirm relevance to the tumor Ig. Journal of Immunological Methods. 278: 95-104. PMID 12957399 DOI: 10.1016/s0022-1759(03)00208-4  0.08
2016 Scherer F, Kurtz DM, Newman AM, Stehr H, Craig AF, Esfahani MS, Lovejoy AF, Chabon JJ, Klass DM, Liu CL, Zhou L, Glover C, Visser BC, Poultsides GA, Advani RH, ... ... Levy R, et al. Distinct biological subtypes and patterns of genome evolution in lymphoma revealed by circulating tumor DNA. Science Translational Medicine. 8: 364ra155. PMID 27831904 DOI: 10.1126/Scitranslmed.Aai8545  0.079
2008 Natkunam Y, Farinha P, Hsi ED, Hans CP, Tibshirani R, Sehn LH, Connors JM, Gratzinger D, Rosado M, Zhao S, Pohlman B, Wongchaowart N, Bast M, Avigdor A, Schiby G, ... ... Levy R, et al. LMO2 protein expression predicts survival in patients with diffuse large B-cell lymphoma treated with anthracycline-based chemotherapy with and without rituximab. Journal of Clinical Oncology : Official Journal of the American Society of Clinical Oncology. 26: 447-54. PMID 18086797 DOI: 10.1200/Jco.2007.13.0690  0.079
2006 Natkunam Y, Zhao S, Mason DY, Chen J, Taidi B, Jones M, Hammer AS, Hamilton Dutoit S, Lossos IS, Levy R. The oncoprotein LMO2 is expressed in normal germinal-center B cells and in human B-cell lymphomas. Blood. 109: 1636-42. PMID 17038524 DOI: 10.1182/blood-2006-08-039024  0.078
2018 Olsson N, Schultz LM, Zhang L, Khodadoust MS, Narayan R, Czerwinski DK, Levy R, Elias JE. T-cell immunopeptidomes reveal cell subtype surface markers derived from intracellular proteins. Proteomics. PMID 29493099 DOI: 10.1002/Pmic.201700410  0.077
2016 Torchia J, Weiskopf K, Levy R. Targeting lymphoma with precision using semisynthetic anti-idiotype peptibodies. Proceedings of the National Academy of Sciences of the United States of America. 113: 5376-81. PMID 27114517 DOI: 10.1073/Pnas.1603335113  0.077
2004 Lossos IS, Czerwinski DK, Alizadeh AA, Wechser MA, Tibshirani R, Botstein D, Levy R. Prediction of survival in diffuse large-B-cell lymphoma based on the expression of six genes. The New England Journal of Medicine. 350: 1828-37. PMID 15115829 DOI: 10.1056/Nejmoa032520  0.076
2004 Yang J, Kanter G, Voloshin A, Levy R, Swartz JR. Expression of active murine granulocyte-macrophage colony-stimulating factor in an Escherichia coli cell-free system. Biotechnology Progress. 20: 1689-96. PMID 15575700 DOI: 10.1021/Bp034350B  0.076
2022 Hong WX, Sagiv-Barfi I, Czerwinski DK, Sallets A, Levy R. Neoadjuvant Intratumoral Immunotherapy with TLR9 Activation and Anti-OX40 Antibody Eradicates Metastatic Cancer. Cancer Research. PMID 35135810 DOI: 10.1158/0008-5472.CAN-21-1382  0.071
2006 Natkunam Y, Hsi ED, Aoun P, Zhao S, Elson P, Pohlman B, Naushad H, Bast M, Levy R, Lossos IS. Expression of the human germinal center-associated lymphoma (HGAL) protein identifies a subset of classic Hodgkin lymphoma of germinal center derivation and improved survival. Blood. 109: 298-305. PMID 16954503 DOI: 10.1182/BLOOD-2006-04-014977  0.071
2011 Morton LM, Cerhan JR, Hartge P, Vasef MA, Neppalli VT, Natkunam Y, Dogan A, Dave BJ, Jain S, Levy R, Lossos IS, Cozen W, Davis S, Schenk MJ, Maurer MJ, et al. Immunostaining to identify molecular subtypes of diffuse large B-cell lymphoma in a population-based epidemiologic study in the pre-rituximab era. International Journal of Molecular Epidemiology and Genetics. 2: 245-52. PMID 21915363  0.069
2003 Lossos IS, Natkunam Y, Levy R, Lopez CD. Apoptosis stimulating protein of p53 (ASPP2) expression differs in diffuse large B-cell and follicular center lymphoma: correlation with clinical outcome. Leukemia & Lymphoma. 43: 2309-17. PMID 12613517 DOI: 10.1080/1042819021000040017  0.069
2015 Kurtz DM, Green MR, Bratman SV, Scherer F, Liu CL, Kunder CA, Takahashi K, Glover C, Keane C, Kihira S, Visser B, Callahan J, Kong KA, Faham M, Corbelli KS, ... ... Levy R, et al. Noninvasive monitoring of diffuse large B-cell lymphoma by immunoglobulin high-throughput sequencing. Blood. 125: 3679-87. PMID 25887775 DOI: 10.1182/Blood-2015-03-635169  0.067
2009 Alizadeh AA, Gentles AJ, Lossos IS, Levy R. Molecular outcome prediction in diffuse large-B-cell lymphoma. The New England Journal of Medicine. 360: 2794-5. PMID 19553658 DOI: 10.1056/NEJMc0902616  0.067
2005 Natkunam Y, Lossos IS, Taidi B, Zhao S, Lu X, Ding F, Hammer AS, Marafioti T, Byrne GE, Levy S, Warnke RA, Levy R. Expression of the human germinal center-associated lymphoma (HGAL) protein, a new marker of germinal center B-cell derivation. Blood. 105: 3979-86. PMID 15677569 DOI: 10.1182/BLOOD-2004-08-3112  0.066
2004 Reddy SA, Levy R. Molecular rescue of tumour-specific T cell receptor idiotype from T cell lymphomas. British Journal of Haematology. 124: 626-8. PMID 14871249 DOI: 10.1111/j.1365-2141.2004.04830.x  0.066
2009 Gentles AJ, Alizadeh AA, Lee SI, Myklebust JH, Shachaf CM, Shahbaba B, Levy R, Koller D, Plevritis SK. A pluripotency signature predicts histologic transformation and influences survival in follicular lymphoma patients. Blood. 114: 3158-66. PMID 19636063 DOI: 10.1182/Blood-2009-02-202465  0.065
2007 Weinberg OK, Ai WZ, Mariappan MR, Shum C, Levy R, Arber DA. ''Minor'' BCL2 breakpoints in follicular lymphoma: frequency and correlation with grade and disease presentation in 236 cases. The Journal of Molecular Diagnostics : Jmd. 9: 530-7. PMID 17652637 DOI: 10.2353/jmoldx.2007.070038  0.065
2021 Vences-Catalán F, Rajapaksa R, Kuo CC, Miller CL, Lee A, Ramani VC, Jeffrey SS, Levy R, Levy S. Targeting the tetraspanin CD81 reduces cancer invasion and metastasis. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 34099563 DOI: 10.1073/pnas.2018961118  0.063
2021 Haebe SE, Shree T, Sathe A, Day G, Czerwinski DK, Grimes S, Lee H, Binkley MS, Long SR, Martin BA, Ji HP, Levy R. Single Cell Analysis Can Define Distinct Evolution of Tumor Sites in Follicular Lymphoma. Blood. PMID 33728464 DOI: 10.1182/blood.2020009855  0.061
2023 Haebe SE, Day G, Czerwinski DK, Sathe A, Grimes SM, Chen T, Long SR, Martin BA, Ozawa MG, Ji HP, Shree T, Levy R. Follicular lymphoma evolves with a surmountable dependency on acquired glycosylation motifs in the B cell receptor. Blood. PMID 37683139 DOI: 10.1182/blood.2023020360  0.061
2012 Kohrt HE, Houot R, Marabelle A, Cho HJ, Osman K, Goldstein M, Levy R, Brody J. Combination strategies to enhance antitumor ADCC Immunotherapy. 4: 511-527. PMID 22642334 DOI: 10.2217/Imt.12.38  0.061
2021 Miller CL, Sagiv-Barfi I, Neuhöfer P, Czerwinski DK, Artandi SE, Bertozzi CR, Levy R, Cochran JR. Systemic delivery of a targeted synthetic immunostimulant transforms the immune landscape for effective tumor regression. Cell Chemical Biology. PMID 34774126 DOI: 10.1016/j.chembiol.2021.10.012  0.06
2022 Mentz M, Keay W, Strobl CD, Antoniolli M, Adolph L, Heide M, Lechner A, Haebe S, Osterode E, Kridel R, Ziegenhain C, Wange LE, Hildebrand JA, Shree T, Silkenstedt E, ... ... Levy R, et al. PARP14 is a novel target in STAT6 mutant follicular lymphoma. Leukemia. PMID 35851155 DOI: 10.1038/s41375-022-01641-x  0.06
2011 Brody J, Kohrt H, Marabelle A, Levy R. Active and passive immunotherapy for lymphoma: proving principles and improving results. Journal of Clinical Oncology : Official Journal of the American Society of Clinical Oncology. 29: 1864-75. PMID 21482977 DOI: 10.1200/JCO.2010.33.4623  0.058
2015 Sagiv-Barfi I, Kohrt HE, Burckhardt L, Czerwinski DK, Levy R. Ibrutinib enhances the antitumor immune response induced by intratumoral injection of a TLR9 ligand in mouse lymphoma. Blood. 125: 2079-86. PMID 25662332 DOI: 10.1182/blood-2014-08-593137  0.058
2003 Lossos IS, Alizadeh AA, Rajapaksa R, Tibshirani R, Levy R. HGAL is a novel interleukin-4-inducible gene that strongly predicts survival in diffuse large B-cell lymphoma. Blood. 101: 433-40. PMID 12509382 DOI: 10.1182/Blood-2002-06-1931  0.057
2002 Briones J, Timmerman JM, Hilbert DM, Levy R. BLyS and BLyS receptor expression in non-Hodgkin's lymphoma. Experimental Hematology. 30: 135-41. PMID 11823048 DOI: 10.1016/S0301-472X(01)00774-3  0.057
2013 Tan D, Horning SJ, Hoppe RT, Levy R, Rosenberg SA, Sigal BM, Warnke RA, Natkunam Y, Han SS, Yuen A, Plevritis SK, Advani RH. Improvements in observed and relative survival in follicular grade 1-2 lymphoma during 4 decades: the Stanford University experience. Blood. 122: 981-7. PMID 23777769 DOI: 10.1182/Blood-2013-03-491514  0.057
2009 Weng WK, Levy R. Genetic polymorphism of the inhibitory IgG Fc receptor FccRIIb is not associated with clinical outcome in patients with follicular lymphoma treated with rituximab Leukemia and Lymphoma. 50: 723-727. PMID 19452316 DOI: 10.1080/10428190902829441  0.056
2003 Weng WK, Levy R. Two immunoglobulin G fragment C receptor polymorphisms independently predict response to rituximab in patients with follicular lymphoma. Journal of Clinical Oncology : Official Journal of the American Society of Clinical Oncology. 21: 3940-7. PMID 12975461 DOI: 10.1200/JCO.2003.05.013  0.056
2011 Alizadeh AA, Gentles AJ, Alencar AJ, Liu CL, Kohrt HE, Houot R, Goldstein MJ, Zhao S, Natkunam Y, Advani RH, Gascoyne RD, Briones J, Tibshirani RJ, Myklebust JH, Plevritis SK, ... ... Levy R, et al. Prediction of survival in diffuse large B-cell lymphoma based on the expression of 2 genes reflecting tumor and microenvironment. Blood. 118: 1350-8. PMID 21670469 DOI: 10.1182/Blood-2011-03-345272  0.056
2014 Marabelle A, Kohrt H, Levy R. New insights into the mechanism of action of immune checkpoint antibodies. Oncoimmunology. 3: e954869. PMID 25610751 DOI: 10.4161/21624011.2014.954869  0.056
2004 Davis TA, Kaminski MS, Leonard JP, Hsu FJ, Wilkinson M, Zelenetz A, Wahl RL, Kroll S, Coleman M, Goris M, Levy R, Knox SJ. The radioisotope contributes significantly to the activity of radioimmunotherapy. Clinical Cancer Research : An Official Journal of the American Association For Cancer Research. 10: 7792-8. PMID 15585610 DOI: 10.1158/1078-0432.CCR-04-0756  0.055
2003 Do B, Lossos IS, Thorstenson Y, Oefner PJ, Levy R. Analysis of FAS (CD95) gene mutations in higher-grade transformation of follicle center lymphoma Leukemia and Lymphoma. 44: 1317-1323. PMID 12952224 DOI: 10.1080/1042819031000090228  0.055
2022 Sagiv-Barfi I, Czerwinski DK, Shree T, Lohmeyer JJK, Levy R. Intratumoral immunotherapy relies on B and T cell collaboration. Science Immunology. 7: eabn5859. PMID 35622903 DOI: 10.1126/sciimmunol.abn5859  0.055
2002 Timmerman JM, Czerwinski DK, Davis TA, Hsu FJ, Benike C, Hao ZM, Taidi B, Rajapaksa R, Caspar CB, Okada CY, van Beckhoven A, Liles TM, Engleman EG, Levy R. Idiotype-pulsed dendritic cell vaccination for B-cell lymphoma: clinical and immune responses in 35 patients. Blood. 99: 1517-26. PMID 11861263  0.055
2009 Ai WZ, Tibshirani R, Taidi B, Czerwinski D, Levy R. Anti-idiotype antibody response after vaccination correlates with better overall survival in follicular lymphoma. Blood. 113: 5743-6. PMID 19346494 DOI: 10.1182/Blood-2009-01-201988  0.054
2010 Durnick DK, Law ME, Maurer MJ, Natkunam Y, Levy R, Lossos IS, Kurtin PJ, McPhail ED. Expression of LMO2 is associated with t(14;18)/IGH-BCL2 fusion but not BCL6 translocations in diffuse large B-cell lymphoma. American Journal of Clinical Pathology. 134: 278-81. PMID 20660332 DOI: 10.1309/AJCPATUP1D0HGCUG  0.054
2002 Timmerman JM, Singh G, Hermanson G, Hobart P, Czerwinski DK, Taidi B, Rajapaksa R, Caspar CB, Van Beckhoven A, Levy R. Immunogenicity of a plasmid DNA vaccine encoding chimeric idiotype in patients with B-cell lymphoma. Cancer Research. 62: 5845-52. PMID 12384547  0.054
2015 Zhang BW, Xia J, Tan Z, Levy RM. A Stochastic Solution to the Unbinned WHAM Equations Journal of Physical Chemistry Letters. 6: 3834-3840. DOI: 10.1021/acs.jpclett.5b01771  0.053
2018 Haabeth OAW, Blake TR, McKinlay CJ, Waymouth RM, Wender PA, Levy R. mRNA vaccination with charge-altering releasable transporters elicits human T cell responses and cures established tumors in mice. Proceedings of the National Academy of Sciences of the United States of America. PMID 30201728 DOI: 10.1073/Pnas.1810002115  0.053
2013 Green MR, Gentles AJ, Nair RV, Irish JM, Kihira S, Liu CL, Kela I, Hopmans ES, Myklebust JH, Ji H, Plevritis SK, Levy R, Alizadeh AA. Hierarchy in somatic mutations arising during genomic evolution and progression of follicular lymphoma. Blood. 121: 1604-11. PMID 23297126 DOI: 10.1182/Blood-2012-09-457283  0.053
2018 S Alam I, T Mayer A, Sagiv-Barfi I, Wang K, Vermesh O, K Czerwinski D, M Johnson E, L James M, Levy R, S Gambhir S. Imaging activated T cells predicts response to cancer vaccines. The Journal of Clinical Investigation. PMID 29596062 DOI: 10.1172/Jci98509  0.052
2016 Myklebust JH, Brody J, Kohrt HE, Kolstad A, Czerwinski DK, Wälchli S, Green MR, Trøen G, Liestøl K, Beiske K, Houot R, Delabie J, Alizadeh AA, Irish JM, Levy R. Distinct patterns of B-cell receptor signaling in non-Hodgkins' lymphomas identified by single cell profiling. Blood. PMID 28011673 DOI: 10.1182/Blood-2016-05-718494  0.052
2020 Hong WX, Haebe S, Lee A, Westphalen B, Norton JA, Jiang W, Levy R. Intratumoral immunotherapy for early stage solid tumors. Clinical Cancer Research : An Official Journal of the American Association For Cancer Research. PMID 32071116 DOI: 10.1158/1078-0432.CCR-19-3642  0.052
2014 Lim SH, Levy R. Translational medicine in action: anti-CD20 therapy in lymphoma. Journal of Immunology (Baltimore, Md. : 1950). 193: 1519-24. PMID 25086174 DOI: 10.4049/jimmunol.1490027  0.052
2003 Briones J, Timmerman JM, Panicalli DL, Levy R. Antitumor immunity after vaccination with B lymphoma cells overexpressing a triad of costimulatory molecules. Journal of the National Cancer Institute. 95: 548-55. PMID 12671023  0.051
2003 Lossos IS, Levy R. Diffuse large B-cell lymphoma: insights gained from gene expression profiling. International Journal of Hematology. 77: 321-9. PMID 12774918 DOI: 10.1007/BF02982638  0.051
2015 Crittenden M, Kohrt H, Levy R, Jones J, Camphausen K, Dicker A, Demaria S, Formenti S. Current clinical trials testing combinations of immunotherapy and radiation. Seminars in Radiation Oncology. 25: 54-64. PMID 25481267 DOI: 10.1016/j.semradonc.2014.07.003  0.051
2016 Boyiadzis M, Bishop MR, Abonour R, Anderson KC, Ansell SM, Avigan D, Barbarotta L, Barrett AJ, Van Besien K, Bergsagel PL, Borrello I, Brody J, Brufsky J, Cairo M, Chari A, ... ... Levy R, et al. The Society for Immunotherapy of Cancer consensus statement on immunotherapy for the treatment of hematologic malignancies: multiple myeloma, lymphoma, and acute leukemia. Journal For Immunotherapy of Cancer. 4: 90. PMID 28018601 DOI: 10.1186/s40425-016-0188-z  0.051
2016 Mackrides N, Campuzano-Zuluaga G, Maque-Acosta Y, Moul A, Hijazi N, Ikpatt FO, Levy R, Verdun RE, Kunkalla K, Natkunam Y, Lossos IS, Vega F, Chapman J. Epstein-Barr virus-positive follicular lymphoma. Modern Pathology : An Official Journal of the United States and Canadian Academy of Pathology, Inc. PMID 27982024 DOI: 10.1038/modpathol.2016.214  0.05
2018 Sagiv-Barfi I, Czerwinski DK, Levy S, Alam IS, Mayer AT, Gambhir SS, Levy R. Eradication of spontaneous malignancy by local immunotherapy. Science Translational Medicine. 10. PMID 29386357 DOI: 10.1126/Scitranslmed.Aan4488  0.05
2004 Lambert SL, Okada CY, Levy R. TCR vaccines against a murine T cell lymphoma: a primary role for antibodies of the IgG2c class in tumor protection. Journal of Immunology (Baltimore, Md. : 1950). 172: 929-36. PMID 14707065 DOI: 10.4049/jimmunol.172.2.929  0.05
2009 Brody J, Levy R. Lymphoma immunotherapy: Vaccines, adoptive cell transfer and immunotransplant Immunotherapy. 1: 809-824. PMID 20636025 DOI: 10.2217/IMT.09.50  0.049
2023 Shree T, Haebe SE, Czerwinski DK, Eckhert E, Day G, Sathe A, Grimes SM, Frank MJ, Maeda L, Alizadeh AA, Advani RH, Hoppe RT, Long SR, Martin BA, Ozawa MG, ... ... Levy R, et al. A clinical trial of therapeutic vaccination in lymphoma with serial tumor sampling and single cell analysis. Blood Advances. PMID 37939259 DOI: 10.1182/bloodadvances.2023011589  0.049
2007 Liu A, Guardino A, Chinsangaram L, Goldstein MJ, Panicali D, Levy R. Therapeutic vaccination against murine lymphoma by intratumoral injection of recombinant fowlpox virus encoding CD40 ligand. Cancer Research. 67: 7037-44. PMID 17638917 DOI: 10.1158/0008-5472.CAN-07-0224  0.048
2020 Timmerman J, Herbaux C, Ribrag V, Zelenetz AD, Houot R, Neelapu SS, Logan T, Lossos IS, Urba W, Salles G, Ramchandren R, Jacobson C, Godwin J, Carpio C, Lathers D, ... ... Levy R, et al. Urelumab alone or in combination with rituximab in patients with relapsed or refractory B-cell lymphoma. American Journal of Hematology. PMID 32052473 DOI: 10.1002/ajh.25757  0.048
2021 Haabeth OAW, Lohmeyer JJK, Sallets A, Blake TR, Sagiv-Barfi I, Czerwinski DK, McCarthy B, Powell AE, Wender PA, Waymouth RM, Levy R. An mRNA SARS-CoV-2 Vaccine Employing Charge-Altering Releasable Transporters with a TLR-9 Agonist Induces Neutralizing Antibodies and T Cell Memory. Acs Central Science. 7: 1191-1204. PMID 34341771 DOI: 10.1021/acscentsci.1c00361  0.048
2008 Baecklund E, Natkunam Y, Backlin C, Iliadou A, Askling J, Ekbom A, Feltelius N, Klareskog L, Enblad G, Lossos IS, Levy R, Sundström C, Rosenquist R. Expression of the human germinal-centre-associated lymphoma protein in diffuse large B-cell lymphomas in patients with rheumatoid arthritis. British Journal of Haematology. 141: 69-72. PMID 18324968 DOI: 10.1111/j.1365-2141.2008.07011.x  0.048
2008 Houot R, Levy R. T-cell modulation combined with intratumoral CpG cures lymphoma in a mouse model without the need for chemotherapy. Blood. 113: 3546-52. PMID 18941113 DOI: 10.1182/blood-2008-07-170274  0.047
2008 Friedberg JW, Sharman J, Schaefer-Cutillo J, Johnston PB, De Vos S, LaCasce A, Leonard JP, Cripe LD, Sinha R, Gregory SA, Sweetenham J, Vose JM, Lowe AM, Levy R, Shipp MA. Fostamatinib Disodium (FosD), An Oral Inhibitor of Syk, Is Well-Tolerated and Has Significant Clinical Activity in Diffuse Large B Cell Lymphoma (DLBCL) and Chronic Lymphocytic Leukemia (SLL/CLL) Blood. 112: 3-3. DOI: 10.1182/Blood.V112.11.3.3  0.047
2011 Weng WK, Weng WK, Levy R. Immunoglobulin G Fc receptor polymorphisms do not correlate with response to chemotherapy or clinical course in patients with follicular lymphoma. Leukemia & Lymphoma. 50: 1494-500. PMID 19672774 DOI: 10.1080/10428190903128660  0.047
2010 Brody JD, Ai WZ, Czerwinski DK, Torchia JA, Levy M, Advani RH, Kim YH, Hoppe RT, Knox SJ, Shin LK, Wapnir I, Tibshirani RJ, Levy R. In situ vaccination with a TLR9 agonist induces systemic lymphoma regression: a phase I/II study. Journal of Clinical Oncology : Official Journal of the American Society of Clinical Oncology. 28: 4324-32. PMID 20697067 DOI: 10.1200/Jco.2010.28.9793  0.047
2000 Waldmann TA, Levy R, Coller BS. Emerging Therapies: Spectrum of Applications of Monoclonal Antibody Therapy Hematology. 2000: 394-408. PMID 11701553 DOI: 10.1182/Asheducation-2000.1.394  0.047
2017 Neelapu SS, Locke FL, Bartlett NL, Lekakis LJ, Miklos DB, Jacobson CA, Braunschweig I, Oluwole OO, Siddiqi T, Lin Y, Timmerman JM, Stiff PJ, Friedberg JW, Flinn IW, Goy A, ... ... Levy R, et al. Axicabtagene Ciloleucel CAR T-Cell Therapy in Refractory Large B-Cell Lymphoma. The New England Journal of Medicine. PMID 29226797 DOI: 10.1056/Nejmoa1707447  0.047
2004 Lossos IS, Levy R. Higher grade transformation of follicular lymphoma: phenotypic tumor progression associated with diverse genetic lesions. Seminars in Cancer Biology. 13: 191-202. PMID 12959350 DOI: 10.1016/S1044-579X(03)00015-4  0.047
2018 Sallets A, Robinson S, Kardosh A, Levy R. Enhancing immunotherapy of STING agonist for lymphoma in preclinical models. Blood Advances. 2: 2230-2241. PMID 30194137 DOI: 10.1182/bloodadvances.2018020040  0.046
2018 Andor N, Simonds EF, Czerwinski DK, Chen J, Grimes SM, Wood-Bouwens C, Zheng GXY, Kubit MA, Greer S, Weiss WA, Levy R, Ji HP. Single-cell RNA-Seq of lymphoma cancers reveals malignant B cell types and co-expression of T cell immune checkpoints. Blood. PMID 30591526 DOI: 10.1182/Blood-2018-08-862292  0.046
2023 Abu-Saleh N, Kuo CC, Jiang W, Levy R, Levy S. The molecular mechanism of CD81 antibody inhibition of metastasis. Proceedings of the National Academy of Sciences of the United States of America. 120: e2305042120. PMID 37339209 DOI: 10.1073/pnas.2305042120  0.046
2023 Grimes SM, Kim HS, Roy S, Sathe A, Ayala CI, Bai X, Almeda-Notestine AF, Haebe S, Shree T, Levy R, Lau BT, Ji HP. Single-cell multi-gene identification of somatic mutations and gene rearrangements in cancer. Nar Cancer. 5: zcad034. PMID 37435532 DOI: 10.1093/narcan/zcad034  0.045
2017 Vences-Catalán F, Duault C, Kuo CC, Rajapaksa R, Levy R, Levy S. CD81 as a tumor target. Biochemical Society Transactions. 45: 531-535. PMID 28408492 DOI: 10.1042/BST20160478  0.045
2012 Kim YH, Gratzinger D, Harrison C, Brody JD, Czerwinski DK, Ai WZ, Morales A, Abdulla F, Xing L, Navi D, Tibshirani RJ, Advani RH, Lingala B, Shah S, Hoppe RT, ... Levy R, et al. In situ vaccination against mycosis fungoides by intratumoral injection of a TLR9 agonist combined with radiation: A phase 1/2 study Blood. 119: 355-363. PMID 22045986 DOI: 10.1182/Blood-2011-05-355222  0.045
2018 Segal NH, He AR, Doi T, Levy R, Bhatia S, Pishvaian MJ, Cesari R, Chen Y, Davis CB, Huang B, Thall AD, Gopal AK. Phase I Study of Single-Agent Utomilumab (PF-05082566), a 4-1BB/CD137 Agonist, in Patients with Advanced Cancer. Clinical Cancer Research : An Official Journal of the American Association For Cancer Research. PMID 29549159 DOI: 10.1158/1078-0432.Ccr-17-1922  0.045
2002 Lossos IS, Thorstenson YR, Wayne TL, Oefner PJ, Levy R, Chu G. Mutation of the ATM gene is not involved in the pathogenesis of either follicle center lymphoma or its transformation to higher-grade lymphoma. Leukemia & Lymphoma. 43: 1079-85. PMID 12148890 DOI: 10.1080/10428190290021623  0.045
2014 Kohrt HE, Thielens A, Marabelle A, Sagiv-Barfi I, Sola C, Chanuc F, Fuseri N, Bonnafous C, Czerwinski D, Rajapaksa A, Waller E, Ugolini S, Vivier E, Romagné F, Levy R, et al. Anti-KIR antibody enhancement of anti-lymphoma activity of natural killer cells as monotherapy and in combination with anti-CD20 antibodies. Blood. 123: 678-86. PMID 24326534 DOI: 10.1182/blood-2013-08-519199  0.044
2003 Akasaka T, Lossos IS, Levy R. BCL6 gene translocation in follicular lymphoma: a harbinger of eventual transformation to diffuse aggressive lymphoma. Blood. 102: 1443-8. PMID 12738680 DOI: 10.1182/BLOOD-2002-08-2482  0.043
2012 Anderson MW, Zhao S, Freud AG, Czerwinski DK, Kohrt H, Alizadeh AA, Houot R, Azambuja D, Biasoli I, Morais JC, Spector N, Molina-Kirsch HF, Warnke RA, Levy R, Natkunam Y. CD137 is expressed in follicular dendritic cell tumors and in classical Hodgkin and T-cell lymphomas: diagnostic and therapeutic implications. The American Journal of Pathology. 181: 795-803. PMID 22901750 DOI: 10.1016/J.Ajpath.2012.05.015  0.043
2007 Li J, Song W, Czerwinski DK, Varghese B, Uematsu S, Akira S, Krieg AM, Levy R. Lymphoma immunotherapy with CpG oligodeoxynucleotides requires TLR9 either in the host or in the tumor itself. Journal of Immunology (Baltimore, Md. : 1950). 179: 2493-500. PMID 17675511 DOI: 10.4049/jimmunol.179.4.2493  0.042
1989 BLAIR JT, KROGH-JESPERSEN K, LEVY RM. ChemInform Abstract: Solvent Effects on Optical Absorption Spectra: The 1A1 → 1A2 Transition of Formaldehyde in Water. Cheminform. 20. DOI: 10.1002/CHIN.198948035  0.042
2014 Marabelle A, Kohrt H, Caux C, Levy R. Intratumoral immunization: a new paradigm for cancer therapy. Clinical Cancer Research : An Official Journal of the American Association For Cancer Research. 20: 1747-56. PMID 24691639 DOI: 10.1158/1078-0432.CCR-13-2116  0.042
2015 Green MR, Kihira S, Liu CL, Nair RV, Salari R, Gentles AJ, Irish J, Stehr H, Vicente-Dueñas C, Romero-Camarero I, Sanchez-Garcia I, Plevritis SK, Arber DA, Batzoglou S, Levy R, et al. Mutations in early follicular lymphoma progenitors are associated with suppressed antigen presentation. Proceedings of the National Academy of Sciences of the United States of America. 112: E1116-25. PMID 25713363 DOI: 10.1073/Pnas.1501199112  0.042
2008 Houot R, Levy R. Vaccines for lymphomas: idiotype vaccines and beyond. Blood Reviews. 23: 137-42. PMID 18951668 DOI: 10.1016/j.blre.2008.09.001  0.042
2021 Haabeth OAW, Lohmeyer JJK, Sallets A, Blake TR, Sagiv-Barfi I, Czerwinski DK, Powell AE, Wender PA, Waymouth RM, Levy R. An mRNA SARS-CoV-2 vaccine employing a novel delivery vehicle with a TLR-9 agonist induces neutralizing antibodies and T cell memory. Biorxiv : the Preprint Server For Biology. PMID 33880472 DOI: 10.1101/2021.04.14.439891  0.042
2015 Sagiv-Barfi I, Kohrt HE, Czerwinski DK, Ng PP, Chang BY, Levy R. Therapeutic antitumor immunity by checkpoint blockade is enhanced by ibrutinib, an inhibitor of both BTK and ITK. Proceedings of the National Academy of Sciences of the United States of America. 112: E966-72. PMID 25730880 DOI: 10.1073/pnas.1500712112  0.042
2011 Houot R, Kohrt H, Goldstein MJ, Levy R. Immunomodulating antibodies and drugs for the treatment of hematological malignancies. Cancer Metastasis Reviews. 30: 97-109. PMID 21271352 DOI: 10.1007/s10555-011-9274-3  0.041
2014 Kohrt HE, Colevas AD, Houot R, Weiskopf K, Goldstein MJ, Lund P, Mueller A, Sagiv-Barfi I, Marabelle A, Lira R, Troutner E, Richards L, Rajapaska A, Hebb J, Chester C, ... ... Levy R, et al. Targeting CD137 enhances the efficacy of cetuximab. The Journal of Clinical Investigation. 124: 2668-82. PMID 24837434 DOI: 10.1172/Jci73014  0.041
2002 Huang JZ, Sanger WG, Greiner TC, Staudt LM, Weisenburger DD, Pickering DL, Lynch JC, Armitage JO, Warnke RA, Alizadeh AA, Lossos IS, Levy R, Chan WC. The t(14;18) defines a unique subset of diffuse large B-cell lymphoma with a germinal center B-cell gene expression profile. Blood. 99: 2285-90. PMID 11895757 DOI: 10.1182/Blood.V99.7.2285  0.041
2016 Segal NH, Logan TF, Hodi FS, McDermott DF, Melero I, Hamid O, Schmidt H, Robert C, Chiarion-Sileni V, Ascierto PA, Maio M, Urba WJ, Gangadhar TC, Suryawanshi S, Neely J, ... ... Levy R, et al. Results From an Integrated Safety Analysis of Urelumab, an Agonist Anti-CD137 Monoclonal Antibody. Clinical Cancer Research : An Official Journal of the American Association For Cancer Research. PMID 27756788 DOI: 10.1158/1078-0432.CCR-16-1272  0.041
2009 Houot R, Goldstein MJ, Kohrt HE, Myklebust JH, Alizadeh AA, Lin JT, Irish JM, Torchia JA, Kolstad A, Chen L, Levy R. Therapeutic effect of CD137 immunomodulation in lymphoma and its enhancement by Treg depletion. Blood. 114: 3431-8. PMID 19641184 DOI: 10.1182/Blood-2009-05-223958  0.041
2018 Frank MJ, Reagan PM, Bartlett NL, Gordon LI, Friedberg JW, Czerwinski DK, Long SR, Hoppe RT, Janssen RS, Candia AF, Coffman RL, Levy R. In Situ Vaccination with a TLR 9 Agonist and Local Low Dose Radiation Induces Systemic Responses in Untreated Indolent Lymphoma. Cancer Discovery. PMID 30154192 DOI: 10.1158/2159-8290.Cd-18-0743  0.041
2010 Luo RF, Zhao S, Tibshirani R, Myklebust JH, Sanyal M, Fernandez R, Gratzinger D, Marinelli RJ, Lu ZS, Wong A, Levy R, Levy S, Natkunam Y. CD81 protein is expressed at high levels in normal germinal center B cells and in subtypes of human lymphomas. Human Pathology. 41: 271-80. PMID 20004001 DOI: 10.1016/J.Humpath.2009.07.022  0.041
2011 Goldstein MJ, Varghese B, Brody JD, Rajapaksa R, Kohrt H, Czerwinski DK, Levy S, Levy R. A CpG-loaded tumor cell vaccine induces antitumor CD4+ T cells that are effective in adoptive therapy for large and established tumors. Blood. 117: 118-27. PMID 20876455 DOI: 10.1182/blood-2010-06-288456  0.04
2011 Ai WZ, Kohrt HE, Timmerman J, Hwang J, Hsu FJ, Czerwinski DD, Taidi B, Levy R. Prolonged disease-free survival and overall survival with CVP alternating with fludarabine in advanced follicular lymphoma. American Journal of Hematology. 86: 515-8. PMID 21538469 DOI: 10.1002/ajh.22017  0.04
2008 Gor NV, Levy RM, Ahn J, Kogan D, Dodson SF, Cohen SM. Biliary cast syndrome following liver transplantation: Predictive factors and clinical outcomes. Liver Transplantation : Official Publication of the American Association For the Study of Liver Diseases and the International Liver Transplantation Society. 14: 1466-72. PMID 18825683 DOI: 10.1002/lt.21492  0.04
2020 Neelapu SS, Adkins S, Ansell SM, Brody J, Cairo MS, Friedberg JW, Kline JP, Levy R, Porter DL, van Besien K, Werner M, Bishop MR. Society for Immunotherapy of Cancer (SITC) clinical practice guideline on immunotherapy for the treatment of lymphoma. Journal For Immunotherapy of Cancer. 8. PMID 33361336 DOI: 10.1136/jitc-2020-001235  0.039
2002 Auffermann-Gretzinger S, Lossos IS, Vayntrub TA, Leong W, Grumet FC, Blume KG, Stockerl-Goldstein KE, Levy R, Shizuru JA. Rapid establishment of dendritic cell chimerism in allogeneic hematopoietic cell transplant recipients. Blood. 99: 1442-8. PMID 11830498 DOI: 10.1182/Blood.V99.4.1442  0.039
2005 Song W, Levy R. Therapeutic vaccination against murine lymphoma by intratumoral injection of naive dendritic cells. Cancer Research. 65: 5958-64. PMID 15994975 DOI: 10.1158/0008-5472.CAN-05-0406  0.039
2014 Levy R, Ganjoo KN, Leonard JP, Vose JM, Flinn IW, Ambinder RF, Connors JM, Berinstein NL, Belch AR, Bartlett NL, Nichols C, Emmanouilides CE, Timmerman JM, Gregory SA, Link BK, et al. Active idiotypic vaccination versus control immunotherapy for follicular lymphoma. Journal of Clinical Oncology : Official Journal of the American Society of Clinical Oncology. 32: 1797-803. PMID 24799467 DOI: 10.1200/Jco.2012.43.9273  0.038
2023 Miller CL, Sagiv-Barfi I, Neuhöfer P, Czerwinski DK, Bertozzi CR, Cochran JR, Levy R. Targeted TLR9 Agonist Elicits Effective Antitumor Immunity against Spontaneously Arising Breast Tumors. Journal of Immunology (Baltimore, Md. : 1950). PMID 37256255 DOI: 10.4049/jimmunol.2200950  0.038
2012 Sachen KL, Strohman MJ, Singletary J, Alizadeh AA, Kattah NH, Lossos C, Mellins ED, Levy S, Levy R. Self-antigen recognition by follicular lymphoma B-cell receptors. Blood. 120: 4182-90. PMID 23024238 DOI: 10.1182/blood-2012-05-427534  0.038
2010 Friedberg JW, Sharman J, Sweetenham J, Johnston PB, Vose JM, Lacasce A, Schaefer-Cutillo J, De Vos S, Sinha R, Leonard JP, Cripe LD, Gregory SA, Sterba MP, Lowe AM, Levy R, et al. Inhibition of Syk with fostamatinib disodium has significant clinical activity in non-Hodgkin lymphoma and chronic lymphocytic leukemia. Blood. 115: 2578-85. PMID 19965662 DOI: 10.1182/Blood-2009-08-236471  0.038
2011 Kohrt HE, Houot R, Goldstein MJ, Weiskopf K, Alizadeh AA, Brody J, Müller A, Pachynski R, Czerwinski D, Coutre S, Chao MP, Chen L, Tedder TF, Levy R. CD137 stimulation enhances the antilymphoma activity of anti-CD20 antibodies. Blood. 117: 2423-32. PMID 21193697 DOI: 10.1182/Blood-2010-08-301945  0.038
2006 Weng WK, Czerwinski D, Levy R. Humoral immune response and immunoglobulin G Fc receptor genotype are associated with better clinical outcome following idiotype vaccination in follicular lymphoma patients regardless of their response to induction chemotherapy. Blood. 109: 951-3. PMID 17032925 DOI: 10.1182/blood-2006-03-013136  0.037
2018 Kooreman NG, Kim Y, de Almeida PE, Termglinchan V, Diecke S, Shao NY, Wei TT, Yi H, Dey D, Nelakanti R, Brouwer TP, Paik DT, Sagiv-Barfi I, Han A, Quax PHA, ... ... Levy R, et al. Autologous iPSC-Based Vaccines Elicit Anti-tumor Responses In Vivo. Cell Stem Cell. PMID 29456158 DOI: 10.1016/J.Stem.2018.01.016  0.037
2019 Haabeth OAW, Blake TR, McKinlay CJ, Tveita AA, Sallets A, Waymouth RM, Wender PA, Levy R. Local delivery of OX40L, CD80, and CD86 mRNA kindles global anti-cancer immunity. Cancer Research. PMID 30692215 DOI: 10.1158/0008-5472.Can-18-2867  0.037
2019 Vences-Catalán F, Kuo CC, Rajapaksa R, Duault C, Andor N, Czerwinski DK, Levy R, Levy S. CD81 is a novel immunotherapeutic target for B cell lymphoma. The Journal of Experimental Medicine. PMID 31123084 DOI: 10.1084/jem.20190186  0.036
2002 Briones J, Timmerman J, Levy R. In vivo antitumor effect of CD40L-transduced tumor cells as a vaccine for B-cell lymphoma. Cancer Research. 62: 3195-9. PMID 12036933  0.036
2018 Turaj AH, Cox KL, Penfold CA, French RR, Mockridge CI, Willoughby JE, Tutt AL, Griffiths J, Johnson PWM, Glennie MJ, Levy R, Cragg MS, Lim SH. Augmentation of CD134 (OX40)-dependent NK anti-tumour activity is dependent on antibody cross-linking. Scientific Reports. 8: 2278. PMID 29396470 DOI: 10.1038/s41598-018-20656-y  0.036
2021 Mooney KL, Czerwinski DK, Shree T, Frank MJ, Haebe S, Martin BA, Testa S, Levy R, Long SR. Serial FNA allows direct sampling of malignant and infiltrating immune cells in patients with B-cell lymphoma receiving immunotherapy. Cancer Cytopathology. PMID 34780125 DOI: 10.1002/cncy.22531  0.036
2010 Younes SF, Beck AH, Lossos IS, Levy R, Warnke RA, Natkunam Y. Immunoarchitectural patterns in follicular lymphoma: efficacy of HGAL and LMO2 in the detection of the interfollicular and diffuse components. The American Journal of Surgical Pathology. 34: 1266-76. PMID 20697248 DOI: 10.1097/PAS.0b013e3181e9343d  0.035
2021 Ribas A, Dhodapkar MV, Campbell KM, Davies FE, Gore SD, Levy R, Greenberger LM. How to Provide the Needed Protection from COVID-19 to Patients with Hematologic Malignancies. Blood Cancer Discovery. 2: 562-567. PMID 34778796 DOI: 10.1158/2643-3230.BCD-21-0166  0.035
2013 Marabelle A, Kohrt H, Sagiv-Barfi I, Ajami B, Axtell RC, Zhou G, Rajapaksa R, Green MR, Torchia J, Brody J, Luong R, Rosenblum MD, Steinman L, Levitsky HI, Tse V, ... Levy R, et al. Depleting tumor-specific Tregs at a single site eradicates disseminated tumors. The Journal of Clinical Investigation. 123: 2447-63. PMID 23728179 DOI: 10.1172/Jci73340  0.035
2013 Marabelle A, Kohrt H, Levy R. Intratumoral anti-CTLA-4 therapy: enhancing efficacy while avoiding toxicity. Clinical Cancer Research : An Official Journal of the American Association For Cancer Research. 19: 5261-3. PMID 23965900 DOI: 10.1158/1078-0432.CCR-13-1923  0.035
2015 Weinstock DM, Dalla-Favera R, Gascoyne RD, Leonard JP, Levy R, Lossos IS, Melnick AM, Nowakowski GS, Press OW, Savage KJ, Shipp MA, Staudt LM. A roadmap for discovery and translation in lymphoma. Blood. 125: 2175-7. PMID 25814490 DOI: 10.1182/Blood-2015-01-623777  0.035
2011 Houot R, Kohrt HE, Marabelle A, Levy R. Targeting immune effector cells to promote antibody-induced cytotoxicity in cancer immunotherapy. Trends in Immunology. 32: 510-6. PMID 21907000 DOI: 10.1016/j.it.2011.07.003  0.035
2006 Irish JM, Czerwinski DK, Nolan GP, Levy R. Kinetics of B cell receptor signaling in human B cell subsets mapped by phosphospecific flow cytometry. Journal of Immunology (Baltimore, Md. : 1950). 177: 1581-9. PMID 16849466 DOI: 10.4049/Jimmunol.177.3.1581  0.035
2014 Kohrt HE, Sagiv-Barfi I, Rafiq S, Herman SE, Butchar JP, Cheney C, Zhang X, Buggy JJ, Muthusamy N, Levy R, Johnson AJ, Byrd JC. Ibrutinib antagonizes rituximab-dependent NK cell-mediated cytotoxicity. Blood. 123: 1957-60. PMID 24652965 DOI: 10.1182/Blood-2014-01-547869  0.035
2014 Ng PP, Kuo CC, Wang S, Einav S, Arcaini L, Paulli M, Portlock CS, Marcotrigiano J, Tarr A, Ball J, Levy R, Levy S. B-cell receptors expressed by lymphomas of hepatitis C virus (HCV)-infected patients rarely react with the viral proteins. Blood. 123: 1512-5. PMID 24449209 DOI: 10.1182/Blood-2013-10-532895  0.034
2016 Houot R, Gaulard P, Schreiber R, Mellman I, Lambotte O, Coulie PG, Fest T, Korman A, Levy R, Shipp M, Tarte K, Kohrt H, Marabelle A, Ansell S, Watier H, et al. Immunomodulatory antibodies for the treatment of lymphoma: Report on the CALYM Workshop. Oncoimmunology. 5: e1186323. PMID 27622041 DOI: 10.1080/2162402X.2016.1186323  0.034
2004 Weng WK, Czerwinski D, Timmerman J, Hsu FJ, Levy R. Clinical outcome of lymphoma patients after idiotype vaccination is correlated with humoral immune response and immunoglobulin G Fc receptor genotype. Journal of Clinical Oncology : Official Journal of the American Society of Clinical Oncology. 22: 4717-24. PMID 15483014 DOI: 10.1200/JCO.2004.06.003  0.034
2019 Josefsson SE, Beiske K, Blaker YN, Førsund MS, Holte H, Østenstad B, Kimby E, Köksal H, Wälchli S, Bai B, Smeland EB, Levy R, Kolstad A, Huse K, Myklebust JH. TIGIT and PD-1 mark intratumoral T cells with reduced effector function in B-cell non-Hodgkin lymphoma. Cancer Immunology Research. PMID 30659053 DOI: 10.1158/2326-6066.CIR-18-0351  0.034
2019 Kohrt HE, Houot R, Weiskopf K, Goldstein MJ, Scheeren F, Czerwinski D, Colevas AD, Weng WK, Clarke MF, Carlson RW, Stockdale FE, Mollick JA, Chen L, Levy R. Stimulation of natural killer cells with a CD137-specific antibody enhances trastuzumab efficacy in xenotransplant models of breast cancer. The Journal of Clinical Investigation. 129: 2595. PMID 31157620 DOI: 10.1172/JCI129688  0.034
2022 Shree T, Shankar V, Lohmeyer JJ, Czerwinski DK, Schroers-Martin JG, Rodriguez GM, Beygi S, Kanegai AM, Corbelli KS, Gabriel E, Kurtz DM, Khodadoust MS, Gupta NK, Maeda LS, Advani RH, ... ... Levy R, et al. CD20-Targeted Therapy Ablates De Novo Antibody Response to Vaccination but Spares Pre-Established Immunity. Blood Cancer Discovery. PMID 35015688 DOI: 10.1158/2643-3230.BCD-21-0222  0.034
2015 Vences-Catalan F, Rajapaksa R, Srivastava MK, Marabelle A, Kuo CC, Levy R, Levy S. Tetraspanin CD81 promotes tumor growth and metastasis by modulating the functions of T regulatory and myeloid-derived suppressor cells. Cancer Research. PMID 26329536 DOI: 10.1158/0008-5472.Can-15-1021  0.034
2002 Lossos IS, Alizadeh AA, Diehn M, Warnke R, Thorstenson Y, Oefner PJ, Brown PO, Botstein D, Levy R. Transformation of follicular lymphoma to diffuse large-cell lymphoma: alternative patterns with increased or decreased expression of c-myc and its regulated genes. Proceedings of the National Academy of Sciences of the United States of America. 99: 8886-91. PMID 12077300 DOI: 10.1073/Pnas.132253599  0.033
2020 Shree T, Li Q, Glaser SL, Brunson A, Maecker HT, Haile RW, Levy R, Keegan THM. Impaired Immune Health in Survivors of Diffuse Large B-Cell Lymphoma. Journal of Clinical Oncology : Official Journal of the American Society of Clinical Oncology. JCO1901937. PMID 32083991 DOI: 10.1200/Jco.19.01937  0.033
2011 Younes SF, Beck AH, Ohgami RS, Lossos IS, Levy R, Warnke RA, Natkunam Y. The efficacy of HGAL and LMO2 in the separation of lymphomas derived from small B cells in nodal and extranodal sites, including the bone marrow. American Journal of Clinical Pathology. 135: 697-708. PMID 21502424 DOI: 10.1309/AJCP7Z2BIBUNQPLZ  0.033
2020 Wilk AJ, Weidenbacher NL, Vergara R, Haabeth OAW, Levy R, Waymouth RM, Wender PA, Blish CA. Charge-altering releasable transporters enable phenotypic manipulation of natural killer cells for cancer immunotherapy. Blood Advances. 4: 4244-4255. PMID 32898247 DOI: 10.1182/Bloodadvances.2020002355  0.033
2022 Schultz LM, Czerwinski DK, Levy R, Levy S. CD81 costimulation skews CAR transduction toward naive T cells. Proceedings of the National Academy of Sciences of the United States of America. 119. PMID 35091467 DOI: 10.1073/pnas.1910844119  0.033
2009 Cohen SM, Levy RM, Jovanovich JF, Ahn J. Fatal lactic acidosis associated with the use of combination oral medications to treat reactivation of hepatitis B. Journal of Clinical Gastroenterology. 43: 1008-10. PMID 19461528 DOI: 10.1097/MCG.0b013e31819c3945  0.032
2020 Frank MJ, Khodadoust MS, Czerwinski DK, Haabeth OAW, Chu MP, Miklos DB, Advani RH, Alizadeh AA, Gupta NK, Maeda LS, Reddy SA, Laport GG, Meyer EH, Negrin RS, Rezvani AR, ... ... Levy R, et al. Autologous tumor cell vaccine induces antitumor T cell immune responses in patients with mantle cell lymphoma: A phase I/II trial. The Journal of Experimental Medicine. 217. PMID 32558897 DOI: 10.1084/Jem.20191712  0.032
2010 Chao MP, Alizadeh AA, Tang C, Myklebust JH, Varghese B, Gill S, Jan M, Cha AC, Chan CK, Tan BT, Park CY, Zhao F, Kohrt HE, Malumbres R, Briones J, ... ... Levy R, et al. Anti-CD47 antibody synergizes with rituximab to promote phagocytosis and eradicate non-Hodgkin lymphoma. Cell. 142: 699-713. PMID 20813259 DOI: 10.1016/J.Cell.2010.07.044  0.032
2012 Kohrt HE, Houot R, Weiskopf K, Goldstein MJ, Scheeren F, Czerwinski D, Colevas AD, Weng WK, Clarke MF, Carlson RW, Stockdale FE, Mollick JA, Chen L, Levy R. Stimulation of natural killer cells with a CD137-specific antibody enhances trastuzumab efficacy in xenotransplant models of breast cancer. The Journal of Clinical Investigation. 122: 1066-75. PMID 22326955 DOI: 10.1172/Jci61226  0.031
2009 Brody JD, Goldstein MJ, Czerwinski DK, Levy R. Immunotransplantation preferentially expands T-effector cells over T-regulatory cells and cures large lymphoma tumors. Blood. 113: 85-94. PMID 18812472 DOI: 10.1182/blood-2008-05-155457  0.031
2009 Timmerman JM, Vose JM, Czerwinski DK, Weng WK, Ingolia D, Mayo M, Denney DW, Levy R. Tumor-specific recombinant idiotype immunisation after chemotherapy as initial treatment for follicular non-Hodgkin lymphoma. Leukemia & Lymphoma. 50: 37-46. PMID 19125383 DOI: 10.1080/10428190802563355  0.03
2003 Martinez-Climent JA, Alizadeh AA, Segraves R, Blesa D, Rubio-Moscardo F, Albertson DG, Garcia-Conde J, Dyer MJ, Levy R, Pinkel D, Lossos IS. Transformation of follicular lymphoma to diffuse large cell lymphoma is associated with a heterogeneous set of DNA copy number and gene expression alterations. Blood. 101: 3109-17. PMID 12406872 DOI: 10.1182/blood-2002-07-2119  0.03
2013 Myklebust JH, Irish JM, Brody J, Czerwinski DK, Houot R, Kohrt HE, Timmerman J, Said J, Green MR, Delabie J, Kolstad A, Alizadeh AA, Levy R. High PD-1 expression and suppressed cytokine signaling distinguish T cells infiltrating follicular lymphoma tumors from peripheral T cells. Blood. 121: 1367-76. PMID 23297127 DOI: 10.1182/Blood-2012-04-421826  0.029
2006 Irish JM, Czerwinski DK, Nolan GP, Levy R. Altered B-cell receptor signaling kinetics distinguish human follicular lymphoma B cells from tumor-infiltrating nonmalignant B cells. Blood. 108: 3135-42. PMID 16835385 DOI: 10.1182/Blood-2006-02-003921  0.029
2008 Racila E, Link BK, Weng WK, Witzig TE, Ansell S, Maurer MJ, Huang J, Dahle C, Halwani A, Levy R, Weiner GJ. A polymorphism in the complement component C1qA correlates with prolonged response following rituximab therapy of follicular lymphoma. Clinical Cancer Research : An Official Journal of the American Association For Cancer Research. 14: 6697-703. PMID 18927313 DOI: 10.1158/1078-0432.CCR-08-0745  0.028
2015 Knox SJ, Levy R. CCR 20th anniversary commentary: Radioactive Drones for B-cell lymphoma. Clinical Cancer Research : An Official Journal of the American Association For Cancer Research. 21: 493-4. PMID 25646179 DOI: 10.1158/1078-0432.CCR-14-2547  0.028
2017 Josefsson SE, Huse K, Kolstad A, Beiske K, Pende D, Steen CB, Inderberg EM, Lingjærde OC, Østenstad B, Smeland EB, Levy R, Irish JM, Myklebust JH. T cells expressing checkpoint receptor TIGIT are enriched in follicular lymphoma tumors and characterized by reversible suppression of T-cell receptor signaling. Clinical Cancer Research : An Official Journal of the American Association For Cancer Research. PMID 29217528 DOI: 10.1158/1078-0432.Ccr-17-2337  0.027
2018 Khodadoust MS, Olsson N, Chen B, Sworder B, Shree T, Liu CL, Zhang L, Czerwinski DK, Davis MM, Levy R, Elias JE, Alizadeh AA. B cell lymphomas present immunoglobulin neoantigens. Blood. PMID 30545830 DOI: 10.1182/Blood-2018-06-845156  0.027
2020 Houot R, Levy R, Cartron G, Armand P. Could anti-CD20 therapy jeopardise the efficacy of a SARS-CoV-2 vaccine? European Journal of Cancer (Oxford, England : 1990). 136: 4-6. PMID 32619884 DOI: 10.1016/j.ejca.2020.06.017  0.025
2017 Frank M, Khodadoust M, Chu M, Kohrt H, Advani R, Alizadeh A, Reddy S, Maeda L, Gupta N, Laport G, Meyer E, Miklos D, Negrin R, Rezvani A, Weng W, ... ... Levy R, et al. PHASE I/II CLINICAL TRIAL OF AN ACTIVATED WHOLE TUMOR CELL VACCINE FOLLOWED BY TRANSFER OF IMMUNE T CELLS IN PATIENTS WITH MANTLE CELL LYMPHOMA Hematological Oncology. 35: 207-208. DOI: 10.1002/Hon.2438_72  0.024
2009 Ai WZ, Hou JZ, Zeiser R, Czerwinski D, Negrin RS, Levy R. Follicular lymphoma B cells induce the conversion of conventional CD4+ T cells to T-regulatory cells. International Journal of Cancer. 124: 239-44. PMID 18814264 DOI: 10.1002/ijc.23881  0.023
2009 Varghese B, Widman A, Do J, Taidi B, Czerwinski DK, Timmerman J, Levy S, Levy R. Generation of CD8+ T cell-mediated immunity against idiotype-negative lymphoma escapees. Blood. 114: 4477-85. PMID 19762487 DOI: 10.1182/blood-2009-05-223263  0.023
2012 Sagi Y, Landrigan A, Levy R, Levy S. Complementary costimulation of human T-cell subpopulations by cluster of differentiation 28 (CD28) and CD81. Proceedings of the National Academy of Sciences of the United States of America. 109: 1613-8. PMID 22307619 DOI: 10.1073/pnas.1121307109  0.023
2012 Goldstein MJ, Kohrt HE, Houot R, Varghese B, Lin JT, Swanson E, Levy R. Adoptive cell therapy for lymphoma with CD4 T cells depleted of CD137-expressing regulatory T cells. Cancer Research. 72: 1239-47. PMID 22232735 DOI: 10.1158/0008-5472.CAN-11-3375  0.023
2009 Gratzinger D, Zhao S, West R, Rouse RV, Vogel H, Gil EC, Levy R, Lossos IS, Natkunam Y. The transcription factor LMO2 is a robust marker of vascular endothelium and vascular neoplasms and selected other entities. American Journal of Clinical Pathology. 131: 264-78. PMID 19141387 DOI: 10.1309/Ajcp5Fp3Naxaxrje  0.023
2003 Bohen SP, Troyanskaya OG, Alter O, Warnke R, Botstein D, Brown PO, Levy R. Variation in gene expression patterns in follicular lymphoma and the response to rituximab. Proceedings of the National Academy of Sciences of the United States of America. 100: 1926-30. PMID 12571354 DOI: 10.1073/Pnas.0437875100  0.023
2020 Gopal AK, Levy R, Houot R, Patel SP, Popplewell L, Jacobson C, Mu XJ, Deng S, Ching KA, Chen Y, Davis CB, Huang B, Fly KD, Thall A, Woolfson A, et al. First-in-Human Study of Utomilumab, a 4-1BB/CD137 Agonist, in Combination with Rituximab in Patients with Follicular and Other CD20 Non-Hodgkin Lymphomas. Clinical Cancer Research : An Official Journal of the American Association For Cancer Research. PMID 32144134 DOI: 10.1158/1078-0432.Ccr-19-2973  0.022
2010 Levy R. Profile of Ronald Levy. Interview by Beth Azar Proceedings of the National Academy of Sciences of the United States of America. 107: 12745-12746. PMID 20624971 DOI: 10.1073/pnas.1008810107  0.021
2007 Levy RM, Cohen SM, Van Thiel DH, Ahn J. Fatal Lactic Acidosis Associated with Combination Oral Antiviral Therapy for Hepatitis B Reactivation Following Chemotherapy American Journal of Gastroenterology. 102: S325. DOI: 10.14309/00000434-200709002-00566  0.019
2019 Kohrt HE, Colevas AD, Houot R, Weiskopf K, Goldstein MJ, Lund P, Mueller A, Sagiv-Barfi I, Marabelle A, Lira R, Troutner E, Richards L, Rajapaska A, Hebb J, Chester C, ... ... Levy R, et al. Targeting CD137 enhances the efficacy of cetuximab. The Journal of Clinical Investigation. 129: 2595. PMID 31157621 DOI: 10.1172/JCI129689  0.018
2009 Houot R, Levy R. Idiotype vaccination for lymphoma: moving towards optimisation. Leukemia & Lymphoma. 50: 1-2. PMID 19172492 DOI: 10.1080/10428190802517807  0.016
1971 Levy RM. Diazepam for L.S.D. intoxication. Lancet (London, England). 1: 1297. PMID 4104747 DOI: 10.1016/S0140-6736(71)91810-1  0.015
2016 Vences-Catalán F, Rajapaksa R, Srivastava MK, Marabelle A, Kuo CC, Levy R, Levy S. Tetraspanin CD81, a modulator of immune suppression in cancer and metastasis. Oncoimmunology. 5: e1120399. PMID 27467918 DOI: 10.1080/2162402X.2015.1120399  0.015
2013 Rezvani K, Brody JD, Kohrt HE, Logan AC, Advani R, Czerwinski DK, Weng WK, Negrin RS, Carlton V, Faham M, Levy R, Barrett J. Cancer vaccines and T cell therapy. Biology of Blood and Marrow Transplantation : Journal of the American Society For Blood and Marrow Transplantation. 19: S97-S101. PMID 23041602 DOI: 10.1016/j.bbmt.2012.09.020  0.013
2015 Levy RM. Recollection. Protein Science : a Publication of the Protein Society. PMID 26575588 DOI: 10.1002/pro.2844  0.01
2010 Marini H, Bitto A, Altavilla D, Burnett BP, Polito F, Di Stefano V, Minutoli L, Atteritano M, Levy RM, Frisina N, Mazzaferro S, Frisina A, D'Anna R, Cancellieri F, Cannata ML, et al. Efficacy of genistein aglycone on some cardiovascular risk factors and homocysteine levels: A follow-up study. Nutrition, Metabolism, and Cardiovascular Diseases : Nmcd. 20: 332-40. PMID 19631515 DOI: 10.1016/j.numecd.2009.04.012  0.01
2007 Levy RM, Komanduri S. Images in clinical medicine. Trichobezoar. The New England Journal of Medicine. 357: e23. PMID 18032760 DOI: 10.1056/NEJMicm067796  0.01
2005 Timmerman JM, Levy R. Cancer vaccines: pessimism in check. Nature Medicine. 10: 1279; author reply 1. PMID 15682512 DOI: 10.1038/nm1204-1279a  0.01
2004 Levy R. Vaccines in lymphoma Clinical Advances in Hematology &Amp; Oncology : H&Amp;O. 2. PMID 16163215  0.01
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