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Items: 1 to 50 of 294

1.

Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction.

Sigalova OM, Chaplin AV, Bochkareva OO, Shelyakin PV, Filaretov VA, Akkuratov EE, Burskaia V, Gelfand MS.

BMC Genomics. 2019 Sep 12;20(1):710. doi: 10.1186/s12864-019-6059-5.

2.

Predictive models of protease specificity based on quantitative protease-activity profiling data.

Fedonin GG, Eroshkin A, Cieplak P, Matveev EV, Ponomarev GV, Gelfand MS, Ratnikov BI, Kazanov MD.

Biochim Biophys Acta Proteins Proteom. 2019 Nov;1867(11):140253. doi: 10.1016/j.bbapap.2019.07.006. Epub 2019 Jul 19.

PMID:
31330204
3.

Re: 'Cefazolin versus anti-staphylococcal penicillins for the treatment of patients with Staphylococcus aureus bacteremia' by Weis et al.

Gelfand MS, Cleveland KO.

Clin Microbiol Infect. 2020 Feb;26(2):258-259. doi: 10.1016/j.cmi.2019.07.017. Epub 2019 Jul 19. No abstract available.

PMID:
31330190
4.

Comparative Genomic Analysis of the Regulation of Aromatic Metabolism in Betaproteobacteria.

Suvorova IA, Gelfand MS.

Front Microbiol. 2019 Mar 29;10:642. doi: 10.3389/fmicb.2019.00642. eCollection 2019.

5.

Micro-evolution of three Streptococcus species: selection, antigenic variation, and horizontal gene inflow.

Shelyakin PV, Bochkareva OO, Karan AA, Gelfand MS.

BMC Evol Biol. 2019 Mar 27;19(1):83. doi: 10.1186/s12862-019-1403-6.

6.

Nuclear lamina integrity is required for proper spatial organization of chromatin in Drosophila.

Ulianov SV, Doronin SA, Khrameeva EE, Kos PI, Luzhin AV, Starikov SS, Galitsyna AA, Nenasheva VV, Ilyin AA, Flyamer IM, Mikhaleva EA, Logacheva MD, Gelfand MS, Chertovich AV, Gavrilov AA, Razin SV, Shevelyov YY.

Nat Commun. 2019 Mar 12;10(1):1176. doi: 10.1038/s41467-019-09185-y.

7.

Genome rearrangements and selection in multi-chromosome bacteria Burkholderia spp.

Bochkareva OO, Moroz EV, Davydov II, Gelfand MS.

BMC Genomics. 2018 Dec 27;19(1):965. doi: 10.1186/s12864-018-5245-1.

8.

Microbiomes of gall-inducing copepod crustaceans from the corals Stylophora pistillata (Scleractinia) and Gorgonia ventalina (Alcyonacea).

Shelyakin PV, Garushyants SK, Nikitin MA, Mudrova SV, Berumen M, Speksnijder AGCL, Hoeksema BW, Fontaneto D, Gelfand MS, Ivanenko VN.

Sci Rep. 2018 Aug 1;8(1):11563. doi: 10.1038/s41598-018-29953-y.

9.

Neanderthal and Denisovan ancestry in Papuans: A functional study.

Akkuratov EE, Gelfand MS, Khrameeva EE.

J Bioinform Comput Biol. 2018 Apr;16(2):1840011. doi: 10.1142/S0219720018400115.

PMID:
29739306
10.

Comparative Genomic Analysis of Holospora spp., Intranuclear Symbionts of Paramecia.

Garushyants SK, Beliavskaia AY, Malko DB, Logacheva MD, Rautian MS, Gelfand MS.

Front Microbiol. 2018 Apr 16;9:738. doi: 10.3389/fmicb.2018.00738. eCollection 2018.

11.

Genome rearrangements and phylogeny reconstruction in Yersinia pestis.

Bochkareva OO, Dranenko NO, Ocheredko ES, Kanevsky GM, Lozinsky YN, Khalaycheva VA, Artamonova II, Gelfand MS.

PeerJ. 2018 Mar 27;6:e4545. doi: 10.7717/peerj.4545. eCollection 2018.

12.

Pangenomic Definition of Prokaryotic Species and the Phylogenetic Structure of Prochlorococcus spp.

Moldovan MA, Gelfand MS.

Front Microbiol. 2018 Mar 12;9:428. doi: 10.3389/fmicb.2018.00428. eCollection 2018.

13.

Comparative genomic analysis of fungal TPP-riboswitches.

Moldovan MA, Petrova SA, Gelfand MS.

Fungal Genet Biol. 2018 May;114:34-41. doi: 10.1016/j.fgb.2018.03.004. Epub 2018 Mar 13.

PMID:
29548845
14.

Cooption of heat shock regulatory system for anhydrobiosis in the sleeping chironomid Polypedilum vanderplanki.

Mazin PV, Shagimardanova E, Kozlova O, Cherkasov A, Sutormin R, Stepanova VV, Stupnikov A, Logacheva M, Penin A, Sogame Y, Cornette R, Tokumoto S, Miyata Y, Kikawada T, Gelfand MS, Gusev O.

Proc Natl Acad Sci U S A. 2018 Mar 6;115(10):E2477-E2486. doi: 10.1073/pnas.1719493115. Epub 2018 Feb 20.

15.

The genes of the sulphoquinovose catabolism in Escherichia coli are also associated with a previously unknown pathway of lactose degradation.

Kaznadzey A, Shelyakin P, Belousova E, Eremina A, Shvyreva U, Bykova D, Emelianenko V, Korosteleva A, Tutukina M, Gelfand MS.

Sci Rep. 2018 Feb 16;8(1):3177. doi: 10.1038/s41598-018-21534-3.

16.

Conservation, evolution, and regulation of splicing during prefrontal cortex development in humans, chimpanzees, and macaques.

Mazin PV, Jiang X, Fu N, Han D, Guo M, Gelfand MS, Khaitovich P.

RNA. 2018 Apr;24(4):585-596. doi: 10.1261/rna.064931.117. Epub 2018 Jan 23.

17.

Sugar Lego: gene composition of bacterial carbohydrate metabolism genomic loci.

Kaznadzey A, Shelyakin P, Gelfand MS.

Biol Direct. 2017 Nov 25;12(1):28. doi: 10.1186/s13062-017-0200-7.

18.

Neurological adverse events associated with metronidazole.

Gelfand MS, Cleveland KO.

Int J Antimicrob Agents. 2017 Oct;50(4):598. doi: 10.1016/j.ijantimicag.2017.08.028. Epub 2017 Aug 25. No abstract available.

PMID:
28847696
19.

Genome analysis of E. coli isolated from Crohn's disease patients.

Rakitina DV, Manolov AI, Kanygina AV, Garushyants SK, Baikova JP, Alexeev DG, Ladygina VG, Kostryukova ES, Larin AK, Semashko TA, Karpova IY, Babenko VV, Ismagilova RK, Malanin SY, Gelfand MS, Ilina EN, Gorodnichev RB, Lisitsyna ES, Aleshkin GI, Scherbakov PL, Khalif IL, Shapina MV, Maev IV, Andreev DN, Govorun VM.

BMC Genomics. 2017 Jul 19;18(1):544. doi: 10.1186/s12864-017-3917-x.

20.

Activation of the alpha-globin gene expression correlates with dramatic upregulation of nearby non-globin genes and changes in local and large-scale chromatin spatial structure.

Ulianov SV, Galitsyna AA, Flyamer IM, Golov AK, Khrameeva EE, Imakaev MV, Abdennur NA, Gelfand MS, Gavrilov AA, Razin SV.

Epigenetics Chromatin. 2017 Jul 11;10(1):35. doi: 10.1186/s13072-017-0142-4.

21.

Genomic Analysis of Caldithrix abyssi, the Thermophilic Anaerobic Bacterium of the Novel Bacterial Phylum Calditrichaeota.

Kublanov IV, Sigalova OM, Gavrilov SN, Lebedinsky AV, Rinke C, Kovaleva O, Chernyh NA, Ivanova N, Daum C, Reddy TB, Klenk HP, Spring S, Göker M, Reva ON, Miroshnichenko ML, Kyrpides NC, Woyke T, Gelfand MS, Bonch-Osmolovskaya EA.

Front Microbiol. 2017 Feb 20;8:195. doi: 10.3389/fmicb.2017.00195. eCollection 2017.

22.

Application of sorting and next generation sequencing to study 5΄-UTR influence on translation efficiency in Escherichia coli.

Evfratov SA, Osterman IA, Komarova ES, Pogorelskaya AM, Rubtsova MP, Zatsepin TS, Semashko TA, Kostryukova ES, Mironov AA, Burnaev E, Krymova E, Gelfand MS, Govorun VM, Bogdanov AA, Sergiev PV, Dontsova OA.

Nucleic Acids Res. 2017 Apr 7;45(6):3487-3502. doi: 10.1093/nar/gkw1141.

23.

Small Open Reading Frames, Non-Coding RNAs and Repetitive Elements in Bradyrhizobium japonicum USDA 110.

Hahn J, Tsoy OV, Thalmann S, Čuklina J, Gelfand MS, Evguenieva-Hackenberg E.

PLoS One. 2016 Oct 27;11(10):e0165429. doi: 10.1371/journal.pone.0165429. eCollection 2016.

24.

Identification of Position-Specific Correlations between DNA-Binding Domains and Their Binding Sites. Application to the MerR Family of Transcription Factors.

Korostelev YD, Zharov IA, Mironov AA, Rakhmaininova AB, Gelfand MS.

PLoS One. 2016 Sep 30;11(9):e0162681. doi: 10.1371/journal.pone.0162681. eCollection 2016.

25.

Nitrogen Fixation and Molecular Oxygen: Comparative Genomic Reconstruction of Transcription Regulation in Alphaproteobacteria.

Tsoy OV, Ravcheev DA, Čuklina J, Gelfand MS.

Front Microbiol. 2016 Aug 26;7:1343. doi: 10.3389/fmicb.2016.01343. eCollection 2016.

26.

Evolution of the Exon-Intron Structure in Ciliate Genomes.

Bondarenko VS, Gelfand MS.

PLoS One. 2016 Sep 7;11(9):e0161476. doi: 10.1371/journal.pone.0161476. eCollection 2016.

27.

Changes in segmentation and setation along the anterior/posterior axis of the homonomous trunk limbs of a remipede (Crustacea, Arthropoda).

Ivanenko VN, Antonenko EA, Gelfand MS, Yager J, Ferrari FD.

PeerJ. 2016 Aug 10;4:e2305. doi: 10.7717/peerj.2305. eCollection 2016.

28.

Genome-wide transcription start site mapping of Bradyrhizobium japonicum grown free-living or in symbiosis - a rich resource to identify new transcripts, proteins and to study gene regulation.

Čuklina J, Hahn J, Imakaev M, Omasits U, Förstner KU, Ljubimov N, Goebel M, Pessi G, Fischer HM, Ahrens CH, Gelfand MS, Evguenieva-Hackenberg E.

BMC Genomics. 2016 Apr 23;17:302. doi: 10.1186/s12864-016-2602-9.

29.

History of chromosome rearrangements reflects the spatial organization of yeast chromosomes.

Khrameeva EE, Fudenberg G, Gelfand MS, Mirny LA.

J Bioinform Comput Biol. 2016 Apr;14(2):1641002. doi: 10.1142/S021972001641002X. Epub 2016 Jan 28.

30.

Reversion From Methicillin Susceptibility to Methicillin Resistance in Staphylococcus aureus.

Gelfand MS, Cleveland KO.

J Infect Dis. 2016 May 15;213(10):1671. No abstract available.

PMID:
26962235
31.

Detection of homologous recombination in closely related strains.

Kalinina AS, Suvorikova AL, Spokoiny VG, Gelfand MS.

J Bioinform Comput Biol. 2016 Apr;14(2):1641001. doi: 10.1142/S0219720016410018. Epub 2016 Jan 14.

PMID:
26952964
32.

Changes in snoRNA and snRNA Abundance in the Human, Chimpanzee, Macaque, and Mouse Brain.

Zhang B, Han D, Korostelev Y, Yan Z, Shao N, Khrameeva E, Velichkovsky BM, Chen YP, Gelfand MS, Khaitovich P.

Genome Biol Evol. 2016 Mar 23;8(3):840-50. doi: 10.1093/gbe/evw038.

33.

Genomic study of the Ket: a Paleo-Eskimo-related ethnic group with significant ancient North Eurasian ancestry.

Flegontov P, Changmai P, Zidkova A, Logacheva MD, Altınışık NE, Flegontova O, Gelfand MS, Gerasimov ES, Khrameeva EE, Konovalova OP, Neretina T, Nikolsky YV, Starostin G, Stepanova VV, Travinsky IV, Tříska M, Tříska P, Tatarinova TV.

Sci Rep. 2016 Feb 11;6:20768. doi: 10.1038/srep20768.

34.

Streptococcus pyogenes: Acute Proctosigmoiditis, Bacteremia and Death in a Healthy Adult.

Gelfand MS, Cleveland KO.

Am J Med Sci. 2016 Jan;351(1):120-1. doi: 10.1016/j.amjms.2015.10.001. No abstract available.

PMID:
26802769
35.

Active chromatin and transcription play a key role in chromosome partitioning into topologically associating domains.

Ulianov SV, Khrameeva EE, Gavrilov AA, Flyamer IM, Kos P, Mikhaleva EA, Penin AA, Logacheva MD, Imakaev MV, Chertovich A, Gelfand MS, Shevelyov YY, Razin SV.

Genome Res. 2016 Jan;26(1):70-84. doi: 10.1101/gr.196006.115. Epub 2015 Oct 30.

36.

Cryptococcus uniguttulatus Meningitis.

Animalu C, Mazumder S, Cleveland KO, Gelfand MS.

Am J Med Sci. 2015 Nov;350(5):421-2. doi: 10.1097/MAJ.0000000000000564. No abstract available.

PMID:
26371608
37.

GntR Family of Bacterial Transcription Factors and Their DNA Binding Motifs: Structure, Positioning and Co-Evolution.

Suvorova IA, Korostelev YD, Gelfand MS.

PLoS One. 2015 Jul 7;10(7):e0132618. doi: 10.1371/journal.pone.0132618. eCollection 2015.

38.

Dynasty Foundation: Russian science loses to politics.

Kondrashov FA, Kondrashov AS, Gelfand MS.

Nature. 2015 Jun 25;522(7557):419. doi: 10.1038/522419a. No abstract available.

PMID:
26108844
39.

Horizontal gene transfer and genome evolution in Methanosarcina.

Garushyants SK, Kazanov MD, Gelfand MS.

BMC Evol Biol. 2015 Jun 5;15:102. doi: 10.1186/s12862-015-0393-2.

40.

Ceftolozane/Tazobactam Therapy of Respiratory Infections due to Multidrug-Resistant Pseudomonas aeruginosa.

Gelfand MS, Cleveland KO.

Clin Infect Dis. 2015 Sep 1;61(5):853-5. doi: 10.1093/cid/civ411. Epub 2015 May 28. No abstract available.

PMID:
26021991
41.

Confused by Weissella confusa Bacteremia.

Gelfand MS, Cleveland KO.

J Clin Microbiol. 2015 Jun;53(6):2001. doi: 10.1128/JCM.00509-15. No abstract available.

42.

Bacterial meningitis in the USA.

Gelfand MS, Cleveland KO.

Lancet Infect Dis. 2015 May;15(5):509. doi: 10.1016/S1473-3099(15)70151-9. Epub 2015 Apr 19. No abstract available.

PMID:
25932582
43.

Natural variation of gene models in Drosophila melanogaster.

Kurmangaliyev YZ, Favorov AV, Osman NM, Lehmann KV, Campo D, Salomon MP, Tower J, Gelfand MS, Nuzhdin SV.

BMC Genomics. 2015 Mar 17;16:198. doi: 10.1186/s12864-015-1415-6.

44.

Serum-derived bovine immunoglobulin/protein isolate should be considered in patients with HIV gut barrier dysfunction.

Gelfand MS, Burnett BP.

Infection. 2015 Apr;43(2):253-4. doi: 10.1007/s15010-015-0732-7. Epub 2015 Jan 30. No abstract available.

PMID:
25633465
45.

Football lingo in the medical world.

Cleveland KO, Gelfand MS.

Am J Med. 2015 Jan;128(1):e25. doi: 10.1016/j.amjmed.2014.10.005. No abstract available.

PMID:
25553636
46.

Comparative genomics of transcriptional regulation of methionine metabolism in Proteobacteria.

Leyn SA, Suvorova IA, Kholina TD, Sherstneva SS, Novichkov PS, Gelfand MS, Rodionov DA.

PLoS One. 2014 Nov 20;9(11):e113714. doi: 10.1371/journal.pone.0113714. eCollection 2014.

47.

Macrolides and the placenta.

Gelfand MS, Cleveland KO.

Expert Opin Drug Saf. 2014 Dec;13(12):1763-4. doi: 10.1517/14740338.2014.978487. Epub 2014 Nov 4. No abstract available.

PMID:
25366668
48.

Bacteriuria in delirious individuals.

Gelfand MS, Mazumder SA, Cleveland KO.

Am J Med. 2014 Oct;127(10):e15. doi: 10.1016/j.amjmed.2014.04.023. No abstract available.

PMID:
25311069
49.

Evaluation of the treatment of methicillin-resistant Staphylococcus aureus bacteremia.

Usery JB, Vo NH, Finch CK, Cleveland KO, Gelfand MS, Self TH.

Am J Med Sci. 2015 Jan;349(1):36-41. doi: 10.1097/MAJ.0000000000000338.

PMID:
25233042
50.

Comparative genomics and evolution of regulons of the LacI-family transcription factors.

Ravcheev DA, Khoroshkin MS, Laikova ON, Tsoy OV, Sernova NV, Petrova SA, Rakhmaninova AB, Novichkov PS, Gelfand MS, Rodionov DA.

Front Microbiol. 2014 Jun 11;5:294. doi: 10.3389/fmicb.2014.00294. eCollection 2014.

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