Format
Sort by
Items per page

Send to

Choose Destination

Search results

Items: 1 to 50 of 340

1.

Combined Analysis of Antigen Presentation and T-cell Recognition Reveals Restricted Immune Responses in Melanoma.

Kalaora S, Wolf Y, Feferman T, Barnea E, Greenstein E, Reshef D, Tirosh I, Reuben A, Patkar S, Levy R, Quinkhardt J, Omokoko T, Qutob N, Golani O, Zhang J, Mao X, Song X, Bernatchez C, Haymaker C, Forget MA, Creasy C, Greenberg P, Carter BW, Cooper ZA, Rosenberg SA, Lotem M, Sahin U, Shakhar G, Ruppin E, Wargo JA, Friedman N, Admon A, Samuels Y.

Cancer Discov. 2018 Sep 12. doi: 10.1158/2159-8290.CD-17-1418. [Epub ahead of print]

PMID:
30209080
2.

Physical foundations of biological complexity.

Wolf YI, Katsnelson MI, Koonin EV.

Proc Natl Acad Sci U S A. 2018 Sep 11;115(37):E8678-E8687. doi: 10.1073/pnas.1807890115. Epub 2018 Aug 27.

3.

Comparative genomics and evolution of trans-activating RNAs in Class 2 CRISPR-Cas systems.

Faure G, Shmakov SA, Makarova KS, Wolf YI, Crawley AB, Barrangou R, Koonin EV.

RNA Biol. 2018 Aug 14:1-14. doi: 10.1080/15476286.2018.1493331. [Epub ahead of print]

PMID:
30103650
4.

Escherichia coli ItaT is a type II toxin that inhibits translation by acetylating isoleucyl-tRNAIle.

Wilcox B, Osterman I, Serebryakova M, Lukyanov D, Komarova E, Gollan B, Morozova N, Wolf YI, Makarova KS, Helaine S, Sergiev P, Dubiley S, Borukhov S, Severinov K.

Nucleic Acids Res. 2018 Sep 6;46(15):7873-7885. doi: 10.1093/nar/gky560.

5.

Insights into the Kinetics of the Resistance Formation of Bacteria against Ciprofloxacin Poly(2-methyl-2-oxazoline) Conjugates.

Schmidt M, Romanovska A, Wolf Y, Nguyen TD, Krupp A, Tumbrink HL, Lategahn J, Volmer J, Rauh D, Luetz S, Krumm C, Tiller JC.

Bioconjug Chem. 2018 Aug 15;29(8):2671-2678. doi: 10.1021/acs.bioconjchem.8b00361. Epub 2018 Jul 11.

PMID:
29927244
6.

Systematic prediction of genes functionally linked to CRISPR-Cas systems by gene neighborhood analysis.

Shmakov SA, Makarova KS, Wolf YI, Severinov KV, Koonin EV.

Proc Natl Acad Sci U S A. 2018 Jun 5;115(23):E5307-E5316. doi: 10.1073/pnas.1803440115. Epub 2018 May 21.

PMID:
29784811
7.

Microglial MHC class II is dispensable for experimental autoimmune encephalomyelitis and cuprizone-induced demyelination.

Wolf Y, Shemer A, Levy-Efrati L, Gross M, Kim JS, Engel A, David E, Chappell-Maor L, Grozovski J, Rotkopf R, Biton I, Eilam-Altstadter R, Jung S.

Eur J Immunol. 2018 Aug;48(8):1308-1318. doi: 10.1002/eji.201847540. Epub 2018 Jun 7.

PMID:
29697861
8.

Taxonomy of the family Arenaviridae and the order Bunyavirales: update 2018.

Maes P, Alkhovsky SV, Bào Y, Beer M, Birkhead M, Briese T, Buchmeier MJ, Calisher CH, Charrel RN, Choi IR, Clegg CS, de la Torre JC, Delwart E, DeRisi JL, Di Bello PL, Di Serio F, Digiaro M, Dolja VV, Drosten C, Druciarek TZ, Du J, Ebihara H, Elbeaino T, Gergerich RC, Gillis AN, Gonzalez JJ, Haenni AL, Hepojoki J, Hetzel U, Hồ T, Hóng N, Jain RK, Jansen van Vuren P, Jin Q, Jonson MG, Junglen S, Keller KE, Kemp A, Kipar A, Kondov NO, Koonin EV, Kormelink R, Korzyukov Y, Krupovic M, Lambert AJ, Laney AG, LeBreton M, Lukashevich IS, Marklewitz M, Markotter W, Martelli GP, Martin RR, Mielke-Ehret N, Mühlbach HP, Navarro B, Ng TFF, Nunes MRT, Palacios G, Pawęska JT, Peters CJ, Plyusnin A, Radoshitzky SR, Romanowski V, Salmenperä P, Salvato MS, Sanfaçon H, Sasaya T, Schmaljohn C, Schneider BS, Shirako Y, Siddell S, Sironen TA, Stenglein MD, Storm N, Sudini H, Tesh RB, Tzanetakis IE, Uppala M, Vapalahti O, Vasilakis N, Walker PJ, Wáng G, Wáng L, Wáng Y, Wèi T, Wiley MR, Wolf YI, Wolfe ND, Wú Z, Xú W, Yang L, Yāng Z, Yeh SD, Zhāng YZ, Zhèng Y, Zhou X, Zhū C, Zirkel F, Kuhn JH.

Arch Virol. 2018 Aug;163(8):2295-2310. doi: 10.1007/s00705-018-3843-5. Epub 2018 Apr 21.

PMID:
29680923
9.

Estimation of universal and taxon-specific parameters of prokaryotic genome evolution.

Sela I, Wolf YI, Koonin EV.

PLoS One. 2018 Apr 13;13(4):e0195571. doi: 10.1371/journal.pone.0195571. eCollection 2018.

10.

Taxonomy of the order Mononegavirales: update 2018.

Amarasinghe GK, Aréchiga Ceballos NG, Banyard AC, Basler CF, Bavari S, Bennett AJ, Blasdell KR, Briese T, Bukreyev A, Caì Y, Calisher CH, Campos Lawson C, Chandran K, Chapman CA, Chiu CY, Choi KS, Collins PL, Dietzgen RG, Dolja VV, Dolnik O, Domier LL, Dürrwald R, Dye JM, Easton AJ, Ebihara H, Echevarría JE, Fooks AR, Formenty PBH, Fouchier RAM, Freuling CM, Ghedin E, Goldberg TL, Hewson R, Horie M, Hyndman TH, Jiāng D, Kityo R, Kobinger GP, Kondō H, Koonin EV, Krupovic M, Kurath G, Lamb RA, Lee B, Leroy EM, Maes P, Maisner A, Marston DA, Mor SK, Müller T, Mühlberger E, Ramírez VMN, Netesov SV, Ng TFF, Nowotny N, Palacios G, Patterson JL, Pawęska JT, Payne SL, Prieto K, Rima BK, Rota P, Rubbenstroth D, Schwemmle M, Siddell S, Smither SJ, Song Q, Song T, Stenglein MD, Stone DM, Takada A, Tesh RB, Thomazelli LM, Tomonaga K, Tordo N, Towner JS, Vasilakis N, Vázquez-Morón S, Verdugo C, Volchkov VE, Wahl V, Walker PJ, Wang D, Wang LF, Wellehan JFX, Wiley MR, Whitfield AE, Wolf YI, Yè G, Zhāng YZ, Kuhn JH.

Arch Virol. 2018 Aug;163(8):2283-2294. doi: 10.1007/s00705-018-3814-x. Epub 2018 Apr 11.

PMID:
29637429
11.

Proteomic Analysis of Methanonatronarchaeum thermophilum AMET1, a Representative of a Putative New Class of Euryarchaeota, "Methanonatronarchaeia".

Ferrer M, Sorokin DY, Wolf YI, Ciordia S, Mena MC, Bargiela R, Koonin EV, Makarova KS.

Genes (Basel). 2018 Jan 23;9(2). pii: E28. doi: 10.3390/genes9020028.

12.

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.

13.

Diverse functions of homologous actin isoforms are defined by their nucleotide, rather than their amino acid sequence.

Vedula P, Kurosaka S, Leu NA, Wolf YI, Shabalina SA, Wang J, Sterling S, Dong DW, Kashina A.

Elife. 2017 Dec 15;6. pii: e31661. doi: 10.7554/eLife.31661.

14.

Inevitability of the emergence and persistence of genetic parasites caused by evolutionary instability of parasite-free states.

Koonin EV, Wolf YI, Katsnelson MI.

Biol Direct. 2017 Dec 4;12(1):31. doi: 10.1186/s13062-017-0202-5.

15.

Phylogenomics of Cas4 family nucleases.

Hudaiberdiev S, Shmakov S, Wolf YI, Terns MP, Makarova KS, Koonin EV.

BMC Evol Biol. 2017 Nov 28;17(1):232. doi: 10.1186/s12862-017-1081-1.

16.

Net Evolutionary Loss of Residue Polarity in Drosophilid Protein Cores Indicates Ongoing Optimization of Amino Acid Composition.

Yampolsky LY, Wolf YI, Bouzinier MA.

Genome Biol Evol. 2017 Oct 1;9(10):2879-2892. doi: 10.1093/gbe/evx191.

17.

Extreme Deviations from Expected Evolutionary Rates in Archaeal Protein Families.

Petitjean C, Makarova KS, Wolf YI, Koonin EV.

Genome Biol Evol. 2017 Oct 1;9(10):2791-2811. doi: 10.1093/gbe/evx189.

18.

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]

PMID:
28968633
19.

The CRISPR Spacer Space Is Dominated by Sequences from Species-Specific Mobilomes.

Shmakov SA, Sitnik V, Makarova KS, Wolf YI, Severinov KV, Koonin EV.

MBio. 2017 Sep 19;8(5). pii: e01397-17. doi: 10.1128/mBio.01397-17.

20.

High-quality genome sequence of the radioresistant bacterium Deinococcus ficus KS 0460.

Matrosova VY, Gaidamakova EK, Makarova KS, Grichenko O, Klimenkova P, Volpe RP, Tkavc R, Ertem G, Conze IH, Brambilla E, Huntemann M, Clum A, Pillay M, Palaniappan K, Varghese N, Mikhailova N, Stamatis D, Reddy T, Daum C, Shapiro N, Ivanova N, Kyrpides N, Woyke T, Daligault H, Davenport K, Erkkila T, Goodwin LA, Gu W, Munk C, Teshima H, Xu Y, Chain P, Woolbert M, Gunde-Cimerman N, Wolf YI, Grebenc T, Gostinčar C, Daly MJ.

Stand Genomic Sci. 2017 Jul 28;12:46. doi: 10.1186/s40793-017-0258-y. eCollection 2017.

21.

Induced-Pluripotent-Stem-Cell-Derived Primitive Macrophages Provide a Platform for Modeling Tissue-Resident Macrophage Differentiation and Function.

Takata K, Kozaki T, Lee CZW, Thion MS, Otsuka M, Lim S, Utami KH, Fidan K, Park DS, Malleret B, Chakarov S, See P, Low D, Low G, Garcia-Miralles M, Zeng R, Zhang J, Goh CC, Gul A, Hubert S, Lee B, Chen J, Low I, Shadan NB, Lum J, Wei TS, Mok E, Kawanishi S, Kitamura Y, Larbi A, Poidinger M, Renia L, Ng LG, Wolf Y, Jung S, Önder T, Newell E, Huber T, Ashihara E, Garel S, Pouladi MA, Ginhoux F.

Immunity. 2017 Jul 18;47(1):183-198.e6. doi: 10.1016/j.immuni.2017.06.017.

22.

'ARMAN' archaea depend on association with euryarchaeal host in culture and in situ.

Golyshina OV, Toshchakov SV, Makarova KS, Gavrilov SN, Korzhenkov AA, La Cono V, Arcadi E, Nechitaylo TY, Ferrer M, Kublanov IV, Wolf YI, Yakimov MM, Golyshin PN.

Nat Commun. 2017 Jul 5;8(1):60. doi: 10.1038/s41467-017-00104-7.

23.

Evolutionary Genomics of Defense Systems in Archaea and Bacteria.

Koonin EV, Makarova KS, Wolf YI.

Annu Rev Microbiol. 2017 Sep 8;71:233-261. doi: 10.1146/annurev-micro-090816-093830. Epub 2017 Jun 28. Review.

24.

Discovery of extremely halophilic, methyl-reducing euryarchaea provides insights into the evolutionary origin of methanogenesis.

Sorokin DY, Makarova KS, Abbas B, Ferrer M, Golyshin PN, Galinski EA, Ciordia S, Mena MC, Merkel AY, Wolf YI, van Loosdrecht MCM, Koonin EV.

Nat Microbiol. 2017 May 30;2:17081. doi: 10.1038/nmicrobiol.2017.81.

25.

Brown-adipose-tissue macrophages control tissue innervation and homeostatic energy expenditure.

Wolf Y, Boura-Halfon S, Cortese N, Haimon Z, Sar Shalom H, Kuperman Y, Kalchenko V, Brandis A, David E, Segal-Hayoun Y, Chappell-Maor L, Yaron A, Jung S.

Nat Immunol. 2017 Jun;18(6):665-674. doi: 10.1038/ni.3746. Epub 2017 May 1.

26.

Early vertebrate origin and diversification of small transmembrane regulators of cellular ion transport.

Pirkmajer S, Kirchner H, Lundell LS, Zelenin PV, Zierath JR, Makarova KS, Wolf YI, Chibalin AV.

J Physiol. 2017 Jul 15;595(14):4611-4630. doi: 10.1113/JP274254. Epub 2017 May 29.

27.

Alternatively activated macrophages do not synthesize catecholamines or contribute to adipose tissue adaptive thermogenesis.

Fischer K, Ruiz HH, Jhun K, Finan B, Oberlin DJ, van der Heide V, Kalinovich AV, Petrovic N, Wolf Y, Clemmensen C, Shin AC, Divanovic S, Brombacher F, Glasmacher E, Keipert S, Jastroch M, Nagler J, Schramm KW, Medrikova D, Collden G, Woods SC, Herzig S, Homann D, Jung S, Nedergaard J, Cannon B, Tschöp MH, Müller TD, Buettner C.

Nat Med. 2017 May;23(5):623-630. doi: 10.1038/nm.4316. Epub 2017 Apr 17.

28.

Reconstruction of the evolution of microbial defense systems.

Puigbò P, Makarova KS, Kristensen DM, Wolf YI, Koonin EV.

BMC Evol Biol. 2017 Apr 4;17(1):94. doi: 10.1186/s12862-017-0942-y.

29.

Autonomous TNF is critical for in vivo monocyte survival in steady state and inflammation.

Wolf Y, Shemer A, Polonsky M, Gross M, Mildner A, Yona S, David E, Kim KW, Goldmann T, Amit I, Heikenwalder M, Nedospasov S, Prinz M, Friedman N, Jung S.

J Exp Med. 2017 Apr 3;214(4):905-917. doi: 10.1084/jem.20160499. Epub 2017 Mar 22.

30.

Diversity and evolution of class 2 CRISPR-Cas systems.

Shmakov S, Smargon A, Scott D, Cox D, Pyzocha N, Yan W, Abudayyeh OO, Gootenberg JS, Makarova KS, Wolf YI, Severinov K, Zhang F, Koonin EV.

Nat Rev Microbiol. 2017 Mar;15(3):169-182. doi: 10.1038/nrmicro.2016.184. Epub 2017 Jan 23.

31.

ATGC database and ATGC-COGs: an updated resource for micro- and macro-evolutionary studies of prokaryotic genomes and protein family annotation.

Kristensen DM, Wolf YI, Koonin EV.

Nucleic Acids Res. 2017 Jan 4;45(D1):D210-D218. doi: 10.1093/nar/gkw934. Epub 2016 Oct 18.

32.

Positive and strongly relaxed purifying selection drive the evolution of repeats in proteins.

Persi E, Wolf YI, Koonin EV.

Nat Commun. 2016 Nov 18;7:13570. doi: 10.1038/ncomms13570.

33.

Two fundamentally different classes of microbial genes.

Wolf YI, Makarova KS, Lobkovsky AE, Koonin EV.

Nat Microbiol. 2016 Nov 7;2:16208. doi: 10.1038/nmicrobiol.2016.208.

PMID:
27819663
34.

Theory of prokaryotic genome evolution.

Sela I, Wolf YI, Koonin EV.

Proc Natl Acad Sci U S A. 2016 Oct 11;113(41):11399-11407. Epub 2016 Oct 4.

35.

Inevitability of Genetic Parasites.

Iranzo J, Puigbò P, Lobkovsky AE, Wolf YI, Koonin EV.

Genome Biol Evol. 2016 Sep 26;8(9):2856-2869.

36.

Microglia contribute to circuit defects in Mecp2 null mice independent of microglia-specific loss of Mecp2 expression.

Schafer DP, Heller CT, Gunner G, Heller M, Gordon C, Hammond T, Wolf Y, Jung S, Stevens B.

Elife. 2016 Jul 26;5. pii: e15224. doi: 10.7554/eLife.15224.

37.

Microglia replenished OHSC: A culture system to study in vivo like adult microglia.

Masuch A, van der Pijl R, Füner L, Wolf Y, Eggen B, Boddeke E, Biber K.

Glia. 2016 Aug;64(8):1285-97. doi: 10.1002/glia.23002. Epub 2016 May 5.

PMID:
27145902
38.

Macrophage precursor cells from the left atrial appendage of the heart spontaneously reprogram into a C-kit+/CD45- stem cell-like phenotype.

Leinonen JV, Korkus-Emanuelov A, Wolf Y, Milgrom-Hoffman M, Lichtstein D, Hoss S, Lotan C, Tzahor E, Jung S, Beeri R.

Int J Cardiol. 2016 Apr 15;209:296-306. doi: 10.1016/j.ijcard.2016.02.040. Epub 2016 Feb 4.

PMID:
26913371
39.

Just how Lamarckian is CRISPR-Cas immunity: the continuum of evolvability mechanisms.

Koonin EV, Wolf YI.

Biol Direct. 2016 Feb 24;11(1):9. doi: 10.1186/s13062-016-0111-z.

40.

Evolvability of an Optimal Recombination Rate.

Lobkovsky AE, Wolf YI, Koonin EV.

Genome Biol Evol. 2015 Dec 10;8(1):70-7. doi: 10.1093/gbe/evv249.

41.

Discovery and Functional Characterization of Diverse Class 2 CRISPR-Cas Systems.

Shmakov S, Abudayyeh OO, Makarova KS, Wolf YI, Gootenberg JS, Semenova E, Minakhin L, Joung J, Konermann S, Severinov K, Zhang F, Koonin EV.

Mol Cell. 2015 Nov 5;60(3):385-97. doi: 10.1016/j.molcel.2015.10.008. Epub 2015 Oct 22.

42.

An updated evolutionary classification of CRISPR-Cas systems.

Makarova KS, Wolf YI, Alkhnbashi OS, Costa F, Shah SA, Saunders SJ, Barrangou R, Brouns SJ, Charpentier E, Haft DH, Horvath P, Moineau S, Mojica FJ, Terns RM, Terns MP, White MF, Yakunin AF, Garrett RA, van der Oost J, Backofen R, Koonin EV.

Nat Rev Microbiol. 2015 Nov;13(11):722-36. doi: 10.1038/nrmicro3569. Epub 2015 Sep 28. Review.

43.

Adaptive Immune Regulation of Mammary Postnatal Organogenesis.

Plaks V, Boldajipour B, Linnemann JR, Nguyen NH, Kersten K, Wolf Y, Casbon AJ, Kong N, van den Bijgaart RJ, Sheppard D, Melton AC, Krummel MF, Werb Z.

Dev Cell. 2015 Sep 14;34(5):493-504. doi: 10.1016/j.devcel.2015.07.015. Epub 2015 Aug 27.

44.

Mapping vaccinia virus DNA replication origins at nucleotide level by deep sequencing.

Senkevich TG, Bruno D, Martens C, Porcella SF, Wolf YI, Moss B.

Proc Natl Acad Sci U S A. 2015 Sep 1;112(35):10908-13. doi: 10.1073/pnas.1514809112. Epub 2015 Aug 18.

45.

Genetic Cell Ablation Reveals Clusters of Local Self-Renewing Microglia in the Mammalian Central Nervous System.

Bruttger J, Karram K, Wörtge S, Regen T, Marini F, Hoppmann N, Klein M, Blank T, Yona S, Wolf Y, Mack M, Pinteaux E, Müller W, Zipp F, Binder H, Bopp T, Prinz M, Jung S, Waisman A.

Immunity. 2015 Jul 21;43(1):92-106. doi: 10.1016/j.immuni.2015.06.012. Epub 2015 Jul 7.

46.

Functional Diversity of Haloacid Dehalogenase Superfamily Phosphatases from Saccharomyces cerevisiae: BIOCHEMICAL, STRUCTURAL, AND EVOLUTIONARY INSIGHTS.

Kuznetsova E, Nocek B, Brown G, Makarova KS, Flick R, Wolf YI, Khusnutdinova A, Evdokimova E, Jin K, Tan K, Hanson AD, Hasnain G, Zallot R, de Crécy-Lagard V, Babu M, Savchenko A, Joachimiak A, Edwards AM, Koonin EV, Yakunin AF.

J Biol Chem. 2015 Jul 24;290(30):18678-98. doi: 10.1074/jbc.M115.657916. Epub 2015 Jun 12.

47.

Methyl-CpG Binding Protein 2 Regulates Microglia and Macrophage Gene Expression in Response to Inflammatory Stimuli.

Cronk JC, Derecki NC, Ji E, Xu Y, Lampano AE, Smirnov I, Baker W, Norris GT, Marin I, Coddington N, Wolf Y, Turner SD, Aderem A, Klibanov AL, Harris TH, Jung S, Litvak V, Kipnis J.

Immunity. 2015 Apr 21;42(4):679-91. doi: 10.1016/j.immuni.2015.03.013.

48.

Babela massiliensis, a representative of a widespread bacterial phylum with unusual adaptations to parasitism in amoebae.

Pagnier I, Yutin N, Croce O, Makarova KS, Wolf YI, Benamar S, Raoult D, Koonin EV, La Scola B.

Biol Direct. 2015 Mar 31;10:13. doi: 10.1186/s13062-015-0043-z.

49.

Immunity, suicide or both? Ecological determinants for the combined evolution of anti-pathogen defense systems.

Iranzo J, Lobkovsky AE, Wolf YI, Koonin EV.

BMC Evol Biol. 2015 Mar 13;15:43. doi: 10.1186/s12862-015-0324-2.

Supplemental Content

Support Center