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CD4+ T cell-mediated HLA class II cross-restriction in HIV controllers.

Galperin M, Farenc C, Mukhopadhyay M, Jayasinghe D, Decroos A, Benati D, Tan LL, Ciacchi L, Reid HH, Rossjohn J, Chakrabarti LA, Gras S.

Sci Immunol. 2018 Jun 8;3(24). pii: eaat0687. doi: 10.1126/sciimmunol.aat0687.


On simulation of local fluxes in molecular junctions.

Cabra G, Jensen A, Galperin M.

J Chem Phys. 2018 May 28;148(20):204103. doi: 10.1063/1.5029252.


A High Frequency of HIV-Specific Circulating Follicular Helper T Cells Is Associated with Preserved Memory B Cell Responses in HIV Controllers.

Claireaux M, Galperin M, Benati D, Nouël A, Mukhopadhyay M, Klingler J, de Truchis P, Zucman D, Hendou S, Boufassa F, Moog C, Lambotte O, Chakrabarti LA.

MBio. 2018 May 8;9(3). pii: e00317-18. doi: 10.1128/mBio.00317-18.


A bacterial coat that is not pure cotton.

Galperin MY, Shalaeva DN.

Science. 2018 Jan 19;359(6373):276-277. doi: 10.1126/science.aar5253. No abstract available.


Phyletic Distribution and Lineage-Specific Domain Architectures of Archaeal Two-Component Signal Transduction Systems.

Galperin MY, Makarova KS, Wolf YI, Koonin EV.

J Bacteriol. 2018 Mar 12;200(7). pii: e00681-17. doi: 10.1128/JB.00681-17. Print 2018 Apr 1.


Proposed Role for KaiC-Like ATPases as Major Signal Transduction Hubs in Archaea.

Makarova KS, Galperin MY, Koonin EV.

MBio. 2017 Dec 5;8(6). pii: e01959-17. doi: 10.1128/mBio.01959-17.


DNA Vaccination by Electroporation Amplifies Broadly Cross-Restricted Public TCR Clonotypes Shared with HIV Controllers.

Mukhopadhyay M, Galperin M, Patgaonkar M, Vasan S, Ho DD, Nouël A, Claireaux M, Benati D, Lambotte O, Huang Y, Chakrabarti LA.

J Immunol. 2017 Nov 15;199(10):3437-3452. doi: 10.4049/jimmunol.1700953. Epub 2017 Oct 9.


Microbial genome analysis: the COG approach.

Galperin MY, Kristensen DM, Makarova KS, Wolf YI, Koonin EV.

Brief Bioinform. 2017 Sep 14. doi: 10.1093/bib/bbx117. [Epub ahead of print]


Discovery of the Second Messenger Cyclic di-GMP.

Römling U, Galperin MY.

Methods Mol Biol. 2017;1657:1-8. doi: 10.1007/978-1-4939-7240-1_1. Review.


Towards Noise Simulation in Interacting Nonequilibrium Systems Strongly Coupled to Baths.

Miwa K, Chen F, Galperin M.

Sci Rep. 2017 Aug 29;7(1):9735. doi: 10.1038/s41598-017-09060-0.


Stand-Alone EAL Domain Proteins Form a Distinct Subclass of EAL Proteins Involved in Regulation of Cell Motility and Biofilm Formation in Enterobacteria.

El Mouali Y, Kim H, Ahmad I, Brauner A, Liu Y, Skurnik M, Galperin MY, Römling U.

J Bacteriol. 2017 Aug 22;199(18). pii: e00179-17. doi: 10.1128/JB.00179-17. Print 2017 Sep 15.


Emergence of cytochrome bc complexes in the context of photosynthesis.

Dibrova DV, Shalaeva DN, Galperin MY, Mulkidjanian AY.

Physiol Plant. 2017 Sep;161(1):150-170. doi: 10.1111/ppl.12586. Epub 2017 Jul 4.


Photonics and spectroscopy in nanojunctions: a theoretical insight.

Galperin M.

Chem Soc Rev. 2017 Jul 3;46(13):4000-4019. doi: 10.1039/c7cs00067g. Review.


The 24th annual Nucleic Acids Research database issue: a look back and upcoming changes.

Galperin MY, Fernández-Suárez XM, Rigden DJ.

Nucleic Acids Res. 2017 May 19;45(9):5627. doi: 10.1093/nar/gkx021. No abstract available.


Genome Sequence of Uric Acid-Fermenting Eubacterium angustum DSM 1989T (MK-1).

Poehlein A, Galperin MY, Andreesen JR, Daniel R.

Genome Announc. 2017 Jan 12;5(2). pii: e01439-16. doi: 10.1128/genomeA.01439-16.


The 24th annual Nucleic Acids Research database issue: a look back and upcoming changes.

Galperin MY, Fernández-Suárez XM, Rigden DJ.

Nucleic Acids Res. 2017 Jan 4;45(D1):D1-D11. doi: 10.1093/nar/gkw1188. Erratum in: Nucleic Acids Res. 2017 May 19;45(9):5627.


Sustained sensing as an emerging principle in second messenger signaling systems.

Orr MW, Galperin MY, Lee VT.

Curr Opin Microbiol. 2016 Dec;34:119-126. doi: 10.1016/j.mib.2016.08.010. Epub 2016 Oct 1. Review.


Nucleotide binding by the widespread high-affinity cyclic di-GMP receptor MshEN domain.

Wang YC, Chin KH, Tu ZL, He J, Jones CJ, Sanchez DZ, Yildiz FH, Galperin MY, Chou SH.

Nat Commun. 2016 Aug 31;7:12481. doi: 10.1038/ncomms12481.


On the widths of Stokes lines in Raman scattering from molecules adsorbed at metal surfaces and in molecular conduction junctions.

Gao Y, Galperin M, Nitzan A.

J Chem Phys. 2016 Jun 28;144(24):244114. doi: 10.1063/1.4954912.


Simulation of optical response functions in molecular junctions.

Gao Y, Galperin M.

J Chem Phys. 2016 Jun 28;144(24):244106. doi: 10.1063/1.4954407.


Optical spectroscopy of molecular junctions: Nonequilibrium Green's functions perspective.

Gao Y, Galperin M.

J Chem Phys. 2016 May 7;144(17):174113. doi: 10.1063/1.4948469.


Public T cell receptors confer high-avidity CD4 responses to HIV controllers.

Benati D, Galperin M, Lambotte O, Gras S, Lim A, Mukhopadhyay M, Nouël A, Campbell KA, Lemercier B, Claireaux M, Hendou S, Lechat P, de Truchis P, Boufassa F, Rossjohn J, Delfraissy JF, Arenzana-Seisdedos F, Chakrabarti LA.

J Clin Invest. 2016 Jun 1;126(6):2093-108. doi: 10.1172/JCI83792. Epub 2016 Apr 25.


The 2016 database issue of Nucleic Acids Research and an updated molecular biology database collection.

Rigden DJ, Fernández-Suárez XM, Galperin MY.

Nucleic Acids Res. 2016 Jan 4;44(D1):D1-6. doi: 10.1093/nar/gkv1356.


Nuclear Dynamics at Molecule-Metal Interfaces: A Pseudoparticle Perspective.

Galperin M, Nitzan A.

J Phys Chem Lett. 2015 Dec 17;6(24):4898-903. doi: 10.1021/acs.jpclett.5b02331. Epub 2015 Nov 25.


Systematic Identification of Cyclic-di-GMP Binding Proteins in Vibrio cholerae Reveals a Novel Class of Cyclic-di-GMP-Binding ATPases Associated with Type II Secretion Systems.

Roelofs KG, Jones CJ, Helman SR, Shang X, Orr MW, Goodson JR, Galperin MY, Yildiz FH, Lee VT.

PLoS Pathog. 2015 Oct 27;11(10):e1005232. doi: 10.1371/journal.ppat.1005232. eCollection 2015 Oct.


Eukaryotic G protein-coupled receptors as descendants of prokaryotic sodium-translocating rhodopsins.

Shalaeva DN, Galperin MY, Mulkidjanian AY.

Biol Direct. 2015 Oct 15;10:63. doi: 10.1186/s13062-015-0091-4.


Effects of Electromagnetic Coupling on Conductance Switching of a Gated Tunnel Junction.

Baratz A, White AJ, Galperin M, Baer R.

J Phys Chem Lett. 2014 Oct 16;5(20):3545-50. doi: 10.1021/jz501652y. Epub 2014 Oct 6. No abstract available.


Pump-Probe Noise Spectroscopy of Molecular Junctions.

Ochoa MA, Selzer Y, Peskin U, Galperin M.

J Phys Chem Lett. 2015 Feb 5;6(3):470-6. doi: 10.1021/jz502484z. Epub 2015 Jan 21.


Systematic Nomenclature for GGDEF and EAL Domain-Containing Cyclic Di-GMP Turnover Proteins of Escherichia coli.

Hengge R, Galperin MY, Ghigo JM, Gomelsky M, Green J, Hughes KT, Jenal U, Landini P.

J Bacteriol. 2015 Jul 6;198(1):7-11. doi: 10.1128/JB.00424-15. Print 2016 Jan 1.


Bacterial cellulose biosynthesis: diversity of operons, subunits, products, and functions.

Römling U, Galperin MY.

Trends Microbiol. 2015 Sep;23(9):545-57. doi: 10.1016/j.tim.2015.05.005. Epub 2015 Jun 12. Review.


Ancient Systems of Sodium/Potassium Homeostasis as Predecessors of Membrane Bioenergetics.

Dibrova DV, Galperin MY, Koonin EV, Mulkidjanian AY.

Biochemistry (Mosc). 2015 May;80(5):495-516. doi: 10.1134/S0006297915050016.


Diversity of Cyclic Di-GMP-Binding Proteins and Mechanisms.

Chou SH, Galperin MY.

J Bacteriol. 2016 Jan 1;198(1):32-46. Review.


Modeling of interaction between cytochrome c and the WD domains of Apaf-1: bifurcated salt bridges underlying apoptosome assembly.

Shalaeva DN, Dibrova DV, Galperin MY, Mulkidjanian AY.

Biol Direct. 2015 May 27;10:29. doi: 10.1186/s13062-015-0059-4.


Comment on "Frequency-domain stimulated and spontaneous light emission signals at molecular junctions" [J. Chem. Phys. 141, 074107 (2014)].

Galperin M, Ratner MA, Nitzan A.

J Chem Phys. 2015 Apr 7;142(13):137101. doi: 10.1063/1.4916523. No abstract available.


Quantum thermodynamics: a nonequilibrium Green's function approach.

Esposito M, Ochoa MA, Galperin M.

Phys Rev Lett. 2015 Feb 27;114(8):080602. Epub 2015 Feb 25.


The 2015 Nucleic Acids Research Database Issue and molecular biology database collection.

Galperin MY, Rigden DJ, Fernández-Suárez XM.

Nucleic Acids Res. 2015 Jan;43(Database issue):D1-5. doi: 10.1093/nar/gku1241.


Expanded microbial genome coverage and improved protein family annotation in the COG database.

Galperin MY, Makarova KS, Wolf YI, Koonin EV.

Nucleic Acids Res. 2015 Jan;43(Database issue):D261-9. doi: 10.1093/nar/gku1223. Epub 2014 Nov 26.


Seed transmission of Pseudoperonospora cubensis.

Cohen Y, Rubin AE, Galperin M, Ploch S, Runge F, Thines M.

PLoS One. 2014 Oct 17;9(10):e109766. doi: 10.1371/journal.pone.0109766. eCollection 2014.


A non-equilibrium equation-of-motion approach to quantum transport utilizing projection operators.

Ochoa MA, Galperin M, Ratner MA.

J Phys Condens Matter. 2014 Nov 12;26(45):455301. doi: 10.1088/0953-8984/26/45/455301. Epub 2014 Oct 16.


GIL, a new c-di-GMP-binding protein domain involved in regulation of cellulose synthesis in enterobacteria.

Fang X, Ahmad I, Blanka A, Schottkowski M, Cimdins A, Galperin MY, Römling U, Gomelsky M.

Mol Microbiol. 2014 Aug;93(3):439-52. doi: 10.1111/mmi.12672. Epub 2014 Jul 1.


Phylogenomic reconstruction of archaeal fatty acid metabolism.

Dibrova DV, Galperin MY, Mulkidjanian AY.

Environ Microbiol. 2014 Apr;16(4):907-18. doi: 10.1111/1462-2920.12359.


Raman scattering in molecular junctions: a pseudoparticle formulation.

White AJ, Tretiak S, Galperin M.

Nano Lett. 2014 Feb 12;14(2):699-703. doi: 10.1021/nl4039532. Epub 2014 Jan 28.


The 2014 Nucleic Acids Research Database Issue and an updated NAR online Molecular Biology Database Collection.

Fernández-Suárez XM, Rigden DJ, Galperin MY.

Nucleic Acids Res. 2014 Jan;42(Database issue):D1-6. doi: 10.1093/nar/gkt1282. Epub 2013 Dec 6.


Genome Diversity of Spore-Forming Firmicutes.

Galperin MY.

Microbiol Spectr. 2013 Dec;1(2). doi: 10.1128/microbiolspectrum.TBS-0015-2012.


Transient thermal sympathectomy as a possible mechanism for hypotension after kyphoplasty: a case report.

Soto E, Galperin M, Portenoy RK.

Clin J Pain. 2013 Dec;29(12):e49-53. doi: 10.1097/AJP.0000000000000031.


The COMBREX project: design, methodology, and initial results.

Anton BP, Chang YC, Brown P, Choi HP, Faller LL, Guleria J, Hu Z, Klitgord N, Levy-Moonshine A, Maksad A, Mazumdar V, McGettrick M, Osmani L, Pokrzywa R, Rachlin J, Swaminathan R, Allen B, Housman G, Monahan C, Rochussen K, Tao K, Bhagwat AS, Brenner SE, Columbus L, de Crécy-Lagard V, Ferguson D, Fomenkov A, Gadda G, Morgan RD, Osterman AL, Rodionov DA, Rodionova IA, Rudd KE, Söll D, Spain J, Xu SY, Bateman A, Blumenthal RM, Bollinger JM, Chang WS, Ferrer M, Friedberg I, Galperin MY, Gobeill J, Haft D, Hunt J, Karp P, Klimke W, Krebs C, Macelis D, Madupu R, Martin MJ, Miller JH, O'Donovan C, Palsson B, Ruch P, Setterdahl A, Sutton G, Tate J, Yakunin A, Tchigvintsev D, Plata G, Hu J, Greiner R, Horn D, Sjölander K, Salzberg SL, Vitkup D, Letovsky S, Segrè D, DeLisi C, Roberts RJ, Steffen M, Kasif S.

PLoS Biol. 2013;11(8):e1001638. doi: 10.1371/journal.pbio.1001638. Epub 2013 Aug 27. No abstract available.

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