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Items: 1 to 50 of 56

1.

Complete Genome Sequence and Methylome Analysis of Thermoactinomyces vulgaris 2H.

Mankai H, Anton BP, Wu V, Vincze T, Roberts RJ, Limam F, Fomenkov A.

Microbiol Resour Announc. 2019 Aug 8;8(32). pii: e00657-19. doi: 10.1128/MRA.00657-19.

2.

Methylomes of Two Extremely Halophilic Archaea Species, Haloarcula marismortui and Haloferax mediterranei.

DasSarma S, Fomenkov A, DasSarma SL, Vincze T, DasSarma P, Roberts RJ.

Microbiol Resour Announc. 2019 Jul 3;8(27). pii: e00577-19. doi: 10.1128/MRA.00577-19.

3.

The labile zinc pool in plant cells.

Zlobin IE, Kartashov AV, Nosov AV, Fomenkov AA, Kuznetsov VV.

Funct Plant Biol. 2019 May 10. doi: 10.1071/FP19064. [Epub ahead of print]

PMID:
31072451
4.

Complete Genome Sequence and Methylome Analysis of Deinococcus wulumuqiensis 479.

Fomenkov A, Luyten Y, Vincze T, Anton BP, Roberts RJ, Morgan RD.

Microbiol Resour Announc. 2019 Mar 21;8(12). pii: e00066-19. doi: 10.1128/MRA.00066-19.

5.

Complete Genome Sequences of Two Rhodobacter Strains.

Anton BP, Roberts RJ, Fomenkov A, Humbert A, Stoian N, Zeilstra-Ryalls J.

Microbiol Resour Announc. 2018 Sep 27;7(12). pii: e01162-18. doi: 10.1128/MRA.01162-18. eCollection 2018 Sep.

6.

Complete Genome Sequence of the Freshwater Bacterium Beggiatoa leptomitoformis Strain D-401.

Fomenkov A, Sun Z, Vincze T, Dubinina G, Orlova M, Tarlachkov SV, Anton BP, Grabovich MY, Roberts RJ.

Genome Announc. 2018 Apr 26;6(17). pii: e00311-18. doi: 10.1128/genomeA.00311-18.

7.

Correction for Fomenkov et al., "Complete Genome Sequence of the Freshwater Colorless Sulfur Bacterium Beggiatoa leptomitoformis Neotype Strain D-402T".

Fomenkov A, Vincze T, Grabovich MY, Dubinina G, Orlova M, Belousova E, Roberts RJ.

Genome Announc. 2018 Apr 19;6(16). pii: e00312-18. doi: 10.1128/genomeA.00312-18. No abstract available.

8.

Complete Genome Sequence and Methylome Analysis of Bacillus caldolyticus NEB414.

Fomenkov A, Vincze T, Mersha F, Roberts RJ.

Genome Announc. 2018 Feb 8;6(6). pii: e01605-17. doi: 10.1128/genomeA.01605-17.

9.

The non-specific adenine DNA methyltransferase M.EcoGII.

Murray IA, Morgan RD, Luyten Y, Fomenkov A, Corrêa IR Jr, Dai N, Allaw MB, Zhang X, Cheng X, Roberts RJ.

Nucleic Acids Res. 2018 Jan 25;46(2):840-848. doi: 10.1093/nar/gkx1191.

10.

Restriction-modification mediated barriers to exogenous DNA uptake and incorporation employed by Prevotella intermedia.

Johnston CD, Skeete CA, Fomenkov A, Roberts RJ, Rittling SR.

PLoS One. 2017 Sep 21;12(9):e0185234. doi: 10.1371/journal.pone.0185234. eCollection 2017.

11.

The third restriction-modification system from Thermus aquaticus YT-1: solving the riddle of two TaqII specificities.

Skowron PM, Anton BP, Czajkowska E, Zebrowska J, Sulecka E, Krefft D, Jezewska-Frackowiak J, Zolnierkiewicz O, Witkowska M, Morgan RD, Wilson GG, Fomenkov A, Roberts RJ, Zylicz-Stachula A.

Nucleic Acids Res. 2017 Sep 6;45(15):9005-9018. doi: 10.1093/nar/gkx599.

12.

Whole-Genome Sequence and Methylome Analysis of the Freshwater Colorless Sulfur Bacterium Thioflexothrix psekupsii D3.

Fomenkov A, Vincze T, Grabovich MY, Dubinina G, Orlova M, Belousova E, Roberts RJ.

Genome Announc. 2017 Aug 31;5(35). pii: e00904-17. doi: 10.1128/genomeA.00904-17.

13.

EcoBLMcrX, a classical modification-dependent restriction enzyme in Escherichia coli B: Characterization in vivo and in vitro with a new approach to cleavage site determination.

Fomenkov A, Sun Z, Dila DK, Anton BP, Roberts RJ, Raleigh EA.

PLoS One. 2017 Jun 27;12(6):e0179853. doi: 10.1371/journal.pone.0179853. eCollection 2017.

14.

Nitric Oxide Has a Concentration-Dependent Effect on the Cell Cycle Acting via EIN2 in Arabidopsis thaliana Cultured Cells.

Novikova GV, Mur LA, Nosov AV, Fomenkov AA, Mironov KS, Mamaeva AS, Shilov ES, Rakitin VY, Hall MA.

Front Physiol. 2017 Mar 10;8:142. doi: 10.3389/fphys.2017.00142. eCollection 2017.

15.

Complete Genome Sequence and Methylome Analysis of Acinetobacter calcoaceticus 65.

Fomenkov A, Vincze T, Degtyarev SK, Roberts RJ.

Genome Announc. 2017 Mar 23;5(12). pii: e00060-17. doi: 10.1128/genomeA.00060-17.

16.

Complete Genome and Methylome Analysis of Psychrotrophic Bacterial Isolates from Lake Untersee in Antarctica.

Fomenkov A, Akimov VN, Vasilyeva LV, Andersen DT, Vincze T, Roberts RJ.

Genome Announc. 2017 Mar 16;5(11). pii: e01753-16. doi: 10.1128/genomeA.01753-16.

17.

Complete Genome Sequence of the Engineered Escherichia coli SHuffle Strains and Their Wild-Type Parents.

Anton BP, Fomenkov A, Raleigh EA, Berkmen M.

Genome Announc. 2016 Mar 31;4(2). pii: e00230-16. doi: 10.1128/genomeA.00230-16.

18.

The Epigenomic Landscape of Prokaryotes.

Blow MJ, Clark TA, Daum CG, Deutschbauer AM, Fomenkov A, Fries R, Froula J, Kang DD, Malmstrom RR, Morgan RD, Posfai J, Singh K, Visel A, Wetmore K, Zhao Z, Rubin EM, Korlach J, Pennacchio LA, Roberts RJ.

PLoS Genet. 2016 Feb 12;12(2):e1005854. doi: 10.1371/journal.pgen.1005854. eCollection 2016 Feb. Erratum in: PLoS Genet. 2016 May;12(5):e1006064.

19.

Complete Genome Sequence of a Strain of Azospirillum thiophilum Isolated from a Sulfide Spring.

Fomenkov A, Vincze T, Grabovich M, Anton BP, Dubinina G, Orlova M, Belousova E, Roberts RJ.

Genome Announc. 2016 Jan 7;4(1). pii: e01521-15. doi: 10.1128/genomeA.01521-15.

20.

Complete Genome Sequence of the Freshwater Colorless Sulfur Bacterium Beggiatoa leptomitoformis [corrected] Neotype Strain D-402T.

Fomenkov A, Vincze T, Grabovich MY, Dubinina G, Orlova M, Belousova E, Roberts RJ.

Genome Announc. 2015 Dec 10;3(6). pii: e01436-15. doi: 10.1128/genomeA.01436-15. Erratum in: Genome Announc. 2018 Apr 19;6(16):.

21.

Complete Genome Sequence of ER2796, a DNA Methyltransferase-Deficient Strain of Escherichia coli K-12.

Anton BP, Mongodin EF, Agrawal S, Fomenkov A, Byrd DR, Roberts RJ, Raleigh EA.

PLoS One. 2015 May 26;10(5):e0127446. doi: 10.1371/journal.pone.0127446. eCollection 2015.

22.

Complete Genome Sequence Analysis of Bacillus subtilis T30.

Xu SY, Boitano M, Clark TA, Vincze T, Fomenkov A, Kumar S, Too PH, Gonchar D, Degtyarev SK, Roberts RJ.

Genome Announc. 2015 May 7;3(3). pii: e00395-15. doi: 10.1128/genomeA.00395-15.

23.

Biochemical characterization of a Naegleria TET-like oxygenase and its application in single molecule sequencing of 5-methylcytosine.

Pais JE, Dai N, Tamanaha E, Vaisvila R, Fomenkov AI, Bitinaite J, Sun Z, Guan S, Corrêa IR Jr, Noren CJ, Cheng X, Roberts RJ, Zheng Y, Saleh L.

Proc Natl Acad Sci U S A. 2015 Apr 7;112(14):4316-21. doi: 10.1073/pnas.1417939112. Epub 2015 Mar 23.

24.

[The level of genetic variability of cells in prolonged suspension culture of Arabidopsis thaliana].

Sedov KA, Fomenkov AA, Solov'eva AI, Nosov AV, Dolgikh IuI.

Izv Akad Nauk Ser Biol. 2014 Nov-Dec;(6):565-72. Russian.

PMID:
25739305
25.

Complete genome sequence and methylome analysis of bacillus strain x1.

Fomenkov A, Lunnen KD, Zhu Z, Anton BP, Wilson GG, Vincze T, Roberts RJ.

Genome Announc. 2015 Feb 19;3(1). pii: e01593-14. doi: 10.1128/genomeA.01593-14.

26.

Gill bacteria enable a novel digestive strategy in a wood-feeding mollusk.

O'Connor RM, Fung JM, Sharp KH, Benner JS, McClung C, Cushing S, Lamkin ER, Fomenkov AI, Henrissat B, Londer YY, Scholz MB, Posfai J, Malfatti S, Tringe SG, Woyke T, Malmstrom RR, Coleman-Derr D, Altamia MA, Dedrick S, Kaluziak ST, Haygood MG, Distel DL.

Proc Natl Acad Sci U S A. 2014 Nov 25;111(47):E5096-104. doi: 10.1073/pnas.1413110111. Epub 2014 Nov 10.

27.

Structure and mutagenesis of the DNA modification-dependent restriction endonuclease AspBHI.

Horton JR, Nugent RL, Li A, Mabuchi MY, Fomenkov A, Cohen-Karni D, Griggs RM, Zhang X, Wilson GG, Zheng Y, Xu SY, Cheng X.

Sci Rep. 2014 Mar 7;4:4246. doi: 10.1038/srep04246.

28.

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.

29.

The methylomes of six bacteria.

Murray IA, Clark TA, Morgan RD, Boitano M, Anton BP, Luong K, Fomenkov A, Turner SW, Korlach J, Roberts RJ.

Nucleic Acids Res. 2012 Dec;40(22):11450-62. doi: 10.1093/nar/gks891. Epub 2012 Oct 2. Erratum in: Nucleic Acids Res. 2014 Apr;42(6):4140.

30.

Phytohormone interplay controls proliferation of in vitro cultivated cells of Arabidopsis thaliana ethylene-insensitive mutants.

Stepanchenko NS, Fomenkov AA, Moshkov IE, Rakitin VY, Novikova GV, Nosov AV.

Dokl Biol Sci. 2012 Jan-Feb;442:46-9. doi: 10.1134/S0012496612010139. Epub 2012 Mar 17. No abstract available.

PMID:
22427223
31.

Characterization of DNA methyltransferase specificities using single-molecule, real-time DNA sequencing.

Clark TA, Murray IA, Morgan RD, Kislyuk AO, Spittle KE, Boitano M, Fomenkov A, Roberts RJ, Korlach J.

Nucleic Acids Res. 2012 Feb;40(4):e29. doi: 10.1093/nar/gkr1146. Epub 2011 Dec 7.

32.

Characterization of type II and III restriction-modification systems from Bacillus cereus strains ATCC 10987 and ATCC 14579.

Xu SY, Nugent RL, Kasamkattil J, Fomenkov A, Gupta Y, Aggarwal A, Wang X, Li Z, Zheng Y, Morgan R.

J Bacteriol. 2012 Jan;194(1):49-60. doi: 10.1128/JB.06248-11. Epub 2011 Oct 28.

33.

The MspJI family of modification-dependent restriction endonucleases for epigenetic studies.

Cohen-Karni D, Xu D, Apone L, Fomenkov A, Sun Z, Davis PJ, Kinney SR, Yamada-Mabuchi M, Xu SY, Davis T, Pradhan S, Roberts RJ, Zheng Y.

Proc Natl Acad Sci U S A. 2011 Jul 5;108(27):11040-5. doi: 10.1073/pnas.1018448108. Epub 2011 Jun 20.

34.
35.

Targeting DNA 5mCpG sites with chimeric endonucleases.

Fomenkov A, Too PH, Chan SH, Vaisvila R, Cantin BA, Mazzola L, Tam V, Xu SY.

Anal Biochem. 2008 Oct 1;381(1):135-41. doi: 10.1016/j.ab.2008.06.035. Epub 2008 Jul 2.

PMID:
18638441
36.

AEC-associated p63 mutations lead to alternative splicing/protein stabilization of p63 and modulation of Notch signaling.

Huang YP, Kim Y, Li Z, Fomenkov T, Fomenkov A, Ratovitski EA.

Cell Cycle. 2005 Oct;4(10):1440-7. Epub 2005 Oct 9.

PMID:
16177572
37.

Differential recognition of response elements determines target gene specificity for p53 and p63.

Osada M, Park HL, Nagakawa Y, Yamashita K, Fomenkov A, Kim MS, Wu G, Nomoto S, Trink B, Sidransky D.

Mol Cell Biol. 2005 Jul;25(14):6077-89.

38.

p63-specific activation of the BPAG-1e promoter.

Osada M, Nagakawa Y, Park HL, Yamashita K, Wu G, Kim MS, Fomenkov A, Trink B, Sidransky D.

J Invest Dermatol. 2005 Jul;125(1):52-60.

39.

DeltaNp63alpha up-regulates the Hsp70 gene in human cancer.

Wu G, Osada M, Guo Z, Fomenkov A, Begum S, Zhao M, Upadhyay S, Xing M, Wu F, Moon C, Westra WH, Koch WM, Mantovani R, Califano JA, Ratovitski E, Sidransky D, Trink B.

Cancer Res. 2005 Feb 1;65(3):758-66.

40.

Altered sumoylation of p63alpha contributes to the split-hand/foot malformation phenotype.

Huang YP, Wu G, Guo Z, Osada M, Fomenkov T, Park HL, Trink B, Sidransky D, Fomenkov A, Ratovitski EA.

Cell Cycle. 2004 Dec;3(12):1587-96. Epub 2004 Dec 7.

PMID:
15539951
41.

RACK1 and stratifin target DeltaNp63alpha for a proteasome degradation in head and neck squamous cell carcinoma cells upon DNA damage.

Fomenkov A, Zangen R, Huang YP, Osada M, Guo Z, Fomenkov T, Trink B, Sidransky D, Ratovitski EA.

Cell Cycle. 2004 Oct;3(10):1285-95. Epub 2004 Oct 6. Erratum in: Cell Cycle. 2007 Feb;6(4):497-8.

PMID:
15467455
42.

CDC91L1 (PIG-U) is a newly discovered oncogene in human bladder cancer.

Guo Z, Linn JF, Wu G, Anzick SL, Eisenberger CF, Halachmi S, Cohen Y, Fomenkov A, Hoque MO, Okami K, Steiner G, Engles JM, Osada M, Moon C, Ratovitski E, Trent JM, Meltzer PS, Westra WH, Kiemeney LA, Schoenberg MP, Sidransky D, Trink B.

Nat Med. 2004 Apr;10(4):374-81. Epub 2004 Mar 14. Erratum in: Nat Med. 2004 Oct;10(10):1139.

PMID:
15034568
43.

P63 alpha mutations lead to aberrant splicing of keratinocyte growth factor receptor in the Hay-Wells syndrome.

Fomenkov A, Huang YP, Topaloglu O, Brechman A, Osada M, Fomenkova T, Yuriditsky E, Trink B, Sidransky D, Ratovitski E.

J Biol Chem. 2003 Jun 27;278(26):23906-14. Epub 2003 Apr 10.

44.

DeltaNp63 induces beta-catenin nuclear accumulation and signaling.

Patturajan M, Nomoto S, Sommer M, Fomenkov A, Hibi K, Zangen R, Poliak N, Califano J, Trink B, Ratovitski E, Sidransky D.

Cancer Cell. 2002 May;1(4):369-79.

45.

[New technological means in medical diagnosis].

Fedorov VA, Antonov IuN, Gavorkian MV, Fomin AV, Babaev AB, Fomenkov AV, Golov IuS, Sliusar IB, Khramtsov PI, Krokhin LA.

Med Tekh. 1999 Nov-Dec;(6):34-41. Russian.

PMID:
10693125
46.
47.

The XmnI restriction-modification system: cloning, expression, sequence organization and similarity between the R and M genes.

Nwankwo DO, Lynch JJ, Moran LS, Fomenkov A, Slatko BE.

Gene. 1996 Sep 16;173(2):121-7.

PMID:
8964488
48.
49.
50.

Nucleotide sequence of a small plasmid isolated from Acetobacter pasteurianus.

Fomenkov A, Xiao JP, Xu SY.

Gene. 1995 May 26;158(1):143-4.

PMID:
7789800

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