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Items: 44

1.

High-coverage, long-read sequencing of Han Chinese trio reference samples.

Wang YC, Olson ND, Deikus G, Shah H, Wenger AM, Trow J, Xiao C, Sherry S, Salit ML, Zook JM, Smith M, Sebra R.

Sci Data. 2019 Jun 14;6(1):91. doi: 10.1038/s41597-019-0098-2.

2.

Mce3R Stress-Resistance Pathway Is Vulnerable to Small-Molecule Targeting That Improves Tuberculosis Drug Activities.

Yang X, Yuan T, Ma R, Chacko KI, Smith M, Deikus G, Sebra R, Kasarskis A, van Bakel H, Franzblau SG, Sampson NS.

ACS Infect Dis. 2019 Jul 12;5(7):1239-1251. doi: 10.1021/acsinfecdis.9b00099. Epub 2019 May 3.

3.

A physical and genetic map of Cannabis sativa identifies extensive rearrangements at the THC/CBD acid synthase loci.

Laverty KU, Stout JM, Sullivan MJ, Shah H, Gill N, Holbrook L, Deikus G, Sebra R, Hughes TR, Page JE, van Bakel H.

Genome Res. 2019 Jan;29(1):146-156. doi: 10.1101/gr.242594.118. Epub 2018 Nov 8.

4.

Genome Plasticity of agr-Defective Staphylococcus aureus during Clinical Infection.

Altman DR, Sullivan MJ, Chacko KI, Balasubramanian D, Pak TR, Sause WE, Kumar K, Sebra R, Deikus G, Attie O, Rose H, Lewis M, Fulmer Y, Bashir A, Kasarskis A, Schadt EE, Richardson AR, Torres VJ, Shopsin B, van Bakel H.

Infect Immun. 2018 Sep 21;86(10). pii: e00331-18. doi: 10.1128/IAI.00331-18. Print 2018 Oct.

5.

Mapping and characterizing N6-methyladenine in eukaryotic genomes using single-molecule real-time sequencing.

Zhu S, Beaulaurier J, Deikus G, Wu TP, Strahl M, Hao Z, Luo G, Gregory JA, Chess A, He C, Xiao A, Sebra R, Schadt EE, Fang G.

Genome Res. 2018 Jul;28(7):1067-1078. doi: 10.1101/gr.231068.117. Epub 2018 May 15.

6.

Coupling of Single Molecule, Long Read Sequencing with IMGT/HighV-QUEST Analysis Expedites Identification of SIV gp140-Specific Antibodies from scFv Phage Display Libraries.

Han SY, Antoine A, Howard D, Chang B, Chang WS, Slein M, Deikus G, Kossida S, Duroux P, Lefranc MP, Sebra RP, Smith ML, Fofana IBF.

Front Immunol. 2018 Mar 1;9:329. doi: 10.3389/fimmu.2018.00329. eCollection 2018.

7.

Metagenomic binning and association of plasmids with bacterial host genomes using DNA methylation.

Beaulaurier J, Zhu S, Deikus G, Mogno I, Zhang XS, Davis-Richardson A, Canepa R, Triplett EW, Faith JJ, Sebra R, Schadt EE, Fang G.

Nat Biotechnol. 2018 Jan;36(1):61-69. doi: 10.1038/nbt.4037. Epub 2017 Dec 11.

8.

HIV-1 Infection of Primary CD4+ T Cells Regulates the Expression of Specific Human Endogenous Retrovirus HERV-K (HML-2) Elements.

Young GR, Terry SN, Manganaro L, Cuesta-Dominguez A, Deikus G, Bernal-Rubio D, Campisi L, Fernandez-Sesma A, Sebra R, Simon V, Mulder LCF.

J Virol. 2017 Dec 14;92(1). pii: e01507-17. doi: 10.1128/JVI.01507-17. Print 2018 Jan 1.

9.

Identification of a novel RASD1 somatic mutation in a USP8-mutated corticotroph adenoma.

Uzilov AV, Cheesman KC, Fink MY, Newman LC, Pandya C, Lalazar Y, Hefti M, Fowkes M, Deikus G, Lau CY, Moe AS, Kinoshita Y, Kasai Y, Zweig M, Gupta A, Starcevic D, Mahajan M, Schadt EE, Post KD, Donovan MJ, Sebra R, Chen R, Geer EB.

Cold Spring Harb Mol Case Stud. 2017 May;3(3):a001602. doi: 10.1101/mcs.a001602.

10.

Capturing pairwise and multi-way chromosomal conformations using chromosomal walks.

Olivares-Chauvet P, Mukamel Z, Lifshitz A, Schwartzman O, Elkayam NO, Lubling Y, Deikus G, Sebra RP, Tanay A.

Nature. 2016 Dec 8;540(7632):296-300. doi: 10.1038/nature20158. Epub 2016 Nov 30.

PMID:
27919068
11.

Extensive sequencing of seven human genomes to characterize benchmark reference materials.

Zook JM, Catoe D, McDaniel J, Vang L, Spies N, Sidow A, Weng Z, Liu Y, Mason CE, Alexander N, Henaff E, McIntyre AB, Chandramohan D, Chen F, Jaeger E, Moshrefi A, Pham K, Stedman W, Liang T, Saghbini M, Dzakula Z, Hastie A, Cao H, Deikus G, Schadt E, Sebra R, Bashir A, Truty RM, Chang CC, Gulbahce N, Zhao K, Ghosh S, Hyland F, Fu Y, Chaisson M, Xiao C, Trow J, Sherry ST, Zaranek AW, Ball M, Bobe J, Estep P, Church GM, Marks P, Kyriazopoulou-Panagiotopoulou S, Zheng GX, Schnall-Levin M, Ordonez HS, Mudivarti PA, Giorda K, Sheng Y, Rypdal KB, Salit M.

Sci Data. 2016 Jun 7;3:160025. doi: 10.1038/sdata.2016.25.

12.

Development and clinical application of an integrative genomic approach to personalized cancer therapy.

Uzilov AV, Ding W, Fink MY, Antipin Y, Brohl AS, Davis C, Lau CY, Pandya C, Shah H, Kasai Y, Powell J, Micchelli M, Castellanos R, Zhang Z, Linderman M, Kinoshita Y, Zweig M, Raustad K, Cheung K, Castillo D, Wooten M, Bourzgui I, Newman LC, Deikus G, Mathew B, Zhu J, Glicksberg BS, Moe AS, Liao J, Edelmann L, Dudley JT, Maki RG, Kasarskis A, Holcombe RF, Mahajan M, Hao K, Reva B, Longtine J, Starcevic D, Sebra R, Donovan MJ, Li S, Schadt EE, Chen R.

Genome Med. 2016 Jun 1;8(1):62. doi: 10.1186/s13073-016-0313-0.

13.

Complete Genome Sequence of KPC-Producing Klebsiella pneumoniae Strain CAV1193.

Sheppard AE, Stoesser N, Sebra R, Kasarskis A, Deikus G, Anson L, Walker AS, Peto TE, Crook DW, Mathers AJ.

Genome Announc. 2016 Jan 28;4(1). pii: e01649-15. doi: 10.1128/genomeA.01649-15.

14.

Methicillin-Susceptible, Vancomycin-Resistant Staphylococcus aureus, Brazil.

Panesso D, Planet PJ, Diaz L, Hugonnet JE, Tran TT, Narechania A, Munita JM, Rincon S, Carvajal LP, Reyes J, Londoño A, Smith H, Sebra R, Deikus G, Weinstock GM, Murray BE, Rossi F, Arthur M, Arias CA.

Emerg Infect Dis. 2015 Oct;21(10):1844-8. doi: 10.3201/eid2110.141914.

15.

Whole-genome sequencing identifies emergence of a quinolone resistance mutation in a case of Stenotrophomonas maltophilia bacteremia.

Pak TR, Altman DR, Attie O, Sebra R, Hamula CL, Lewis M, Deikus G, Newman LC, Fang G, Hand J, Patel G, Wallach F, Schadt EE, Huprikar S, van Bakel H, Kasarskis A, Bashir A.

Antimicrob Agents Chemother. 2015 Nov;59(11):7117-20. doi: 10.1128/AAC.01723-15. Epub 2015 Aug 31.

16.

Assembly and diploid architecture of an individual human genome via single-molecule technologies.

Pendleton M, Sebra R, Pang AW, Ummat A, Franzen O, Rausch T, Stütz AM, Stedman W, Anantharaman T, Hastie A, Dai H, Fritz MH, Cao H, Cohain A, Deikus G, Durrett RE, Blanchard SC, Altman R, Chin CS, Guo Y, Paxinos EE, Korbel JO, Darnell RB, McCombie WR, Kwok PY, Mason CE, Schadt EE, Bashir A.

Nat Methods. 2015 Aug;12(8):780-6. doi: 10.1038/nmeth.3454. Epub 2015 Jun 29.

17.

Single molecule-level detection and long read-based phasing of epigenetic variations in bacterial methylomes.

Beaulaurier J, Zhang XS, Zhu S, Sebra R, Rosenbluh C, Deikus G, Shen N, Munera D, Waldor MK, Chess A, Blaser MJ, Schadt EE, Fang G.

Nat Commun. 2015 Jun 15;6:7438. doi: 10.1038/ncomms8438.

18.

Parallel Epidemics of Community-Associated Methicillin-Resistant Staphylococcus aureus USA300 Infection in North and South America.

Planet PJ, Diaz L, Kolokotronis SO, Narechania A, Reyes J, Xing G, Rincon S, Smith H, Panesso D, Ryan C, Smith DP, Guzman M, Zurita J, Sebra R, Deikus G, Nolan RL, Tenover FC, Weinstock GM, Robinson DA, Arias CA.

J Infect Dis. 2015 Dec 15;212(12):1874-82. doi: 10.1093/infdis/jiv320. Epub 2015 Jun 5.

19.

Transmission of methicillin-resistant Staphylococcus aureus via deceased donor liver transplantation confirmed by whole genome sequencing.

Altman DR, Sebra R, Hand J, Attie O, Deikus G, Carpini KW, Patel G, Rana M, Arvelakis A, Grewal P, Dutta J, Rose H, Shopsin B, Daefler S, Schadt E, Kasarskis A, van Bakel H, Bashir A, Huprikar S.

Am J Transplant. 2014 Nov;14(11):2640-4. doi: 10.1111/ajt.12897. Epub 2014 Sep 22.

20.

Global analysis of mRNA decay intermediates in Bacillus subtilis wild-type and polynucleotide phosphorylase-deletion strains.

Liu B, Deikus G, Bree A, Durand S, Kearns DB, Bechhofer DH.

Mol Microbiol. 2014 Oct;94(1):41-55. doi: 10.1111/mmi.12748. Epub 2014 Aug 21.

21.

Evolution of hypervirulence by a MRSA clone through acquisition of a transposable element.

Benson MA, Ohneck EA, Ryan C, Alonzo F 3rd, Smith H, Narechania A, Kolokotronis SO, Satola SW, Uhlemann AC, Sebra R, Deikus G, Shopsin B, Planet PJ, Torres VJ.

Mol Microbiol. 2014 Aug;93(4):664-81. doi: 10.1111/mmi.12682. Epub 2014 Jul 16.

22.

Genome Sequence of Bacterial Interference Strain Staphylococcus aureus 502A.

Parker D, Narechania A, Sebra R, Deikus G, Larussa S, Ryan C, Smith H, Prince A, Mathema B, Ratner AJ, Kreiswirth B, Planet PJ.

Genome Announc. 2014 Apr 10;2(2). pii: e00284-14. doi: 10.1128/genomeA.00284-14.

23.

HIV-1 interacts with human endogenous retrovirus K (HML-2) envelopes derived from human primary lymphocytes.

Brinzevich D, Young GR, Sebra R, Ayllon J, Maio SM, Deikus G, Chen BK, Fernandez-Sesma A, Simon V, Mulder LC.

J Virol. 2014 Jun;88(11):6213-23. doi: 10.1128/JVI.00669-14. Epub 2014 Mar 19.

24.

Genome-wide mapping of methylated adenine residues in pathogenic Escherichia coli using single-molecule real-time sequencing.

Fang G, Munera D, Friedman DI, Mandlik A, Chao MC, Banerjee O, Feng Z, Losic B, Mahajan MC, Jabado OJ, Deikus G, Clark TA, Luong K, Murray IA, Davis BM, Keren-Paz A, Chess A, Roberts RJ, Korlach J, Turner SW, Kumar V, Waldor MK, Schadt EE.

Nat Biotechnol. 2012 Dec;30(12):1232-9. doi: 10.1038/nbt.2432. Epub 2012 Nov 8. Erratum in: Nat Biotechnol. 2013 Jun;31(6):566.

25.

5' End-independent RNase J1 endonuclease cleavage of Bacillus subtilis model RNA.

Deikus G, Bechhofer DH.

J Biol Chem. 2011 Oct 7;286(40):34932-40. doi: 10.1074/jbc.M111.287409. Epub 2011 Aug 23.

26.

Antagonistic roles of four SR proteins in the biosynthesis of alternatively spliced tissue factor transcripts in monocytic cells.

Chandradas S, Deikus G, Tardos JG, Bogdanov VY.

J Leukoc Biol. 2010 Jan;87(1):147-52. doi: 10.1189/jlb.0409252. Epub 2009 Oct 20.

27.

Bacillus subtilis trp Leader RNA: RNase J1 endonuclease cleavage specificity and PNPase processing.

Deikus G, Bechhofer DH.

J Biol Chem. 2009 Sep 25;284(39):26394-401. doi: 10.1074/jbc.M109.015875. Epub 2009 Jul 28.

28.

Bacillus subtilis polynucleotide phosphorylase 3'-to-5' DNase activity is involved in DNA repair.

Cardenas PP, Carrasco B, Sanchez H, Deikus G, Bechhofer DH, Alonso JC.

Nucleic Acids Res. 2009 Jul;37(12):4157-69. doi: 10.1093/nar/gkp314. Epub 2009 May 11.

29.

Assay of Bacillus subtilis ribonucleases in vitro.

Condon C, Pellegrini O, Mathy N, Bénard L, Redko Y, Oussenko IA, Deikus G, Bechhofer DH.

Methods Enzymol. 2008;447:277-308. doi: 10.1016/S0076-6879(08)02215-5.

PMID:
19161849
30.

Analysis of mRNA decay in Bacillus subtilis.

Bechhofer DH, Oussenko IA, Deikus G, Yao S, Mathy N, Condon C.

Methods Enzymol. 2008;447:259-76. doi: 10.1016/S0076-6879(08)02214-3.

PMID:
19161848
31.

Role of Bacillus subtilis RNase J1 endonuclease and 5'-exonuclease activities in trp leader RNA turnover.

Deikus G, Condon C, Bechhofer DH.

J Biol Chem. 2008 Jun 20;283(25):17158-67. doi: 10.1074/jbc.M801461200. Epub 2008 Apr 29.

32.

SR proteins ASF/SF2 and SRp55 participate in tissue factor biosynthesis in human monocytic cells.

Tardos JG, Eisenreich A, Deikus G, Bechhofer DH, Chandradas S, Zafar U, Rauch U, Bogdanov VY.

J Thromb Haemost. 2008 May;6(5):877-84. doi: 10.1111/j.1538-7836.2008.02946.x. Epub 2008 Mar 1.

33.

Initiation of decay of Bacillus subtilis trp leader RNA.

Deikus G, Bechhofer DH.

J Biol Chem. 2007 Jul 13;282(28):20238-44. Epub 2007 May 16.

34.

Adaptive gene expression in Bacillus subtilis strains deleted for tetL.

Wei Y, Deikus G, Powers B, Shelden V, Krulwich TA, Bechhofer DH.

J Bacteriol. 2006 Oct;188(20):7090-100.

35.

Structural dynamics of the manganese-stabilizing protein-effect of pH, calcium, and manganese.

Shutova T, Nikitina J, Deikus G, Andersson B, Klimov V, Samuelsson G.

Biochemistry. 2005 Nov 22;44(46):15182-92.

PMID:
16285721
36.

Recycling of a regulatory protein by degradation of the RNA to which it binds.

Deikus G, Babitzke P, Bechhofer DH.

Proc Natl Acad Sci U S A. 2004 Mar 2;101(9):2747-51. Epub 2004 Feb 19.

37.

Ultraviolet illumination-induced reduction of alpha-lactalbumin disulfide bridges.

Permyakov EA, Permyakov SE, Deikus GY, Morozova-Roche LA, Grishchenko VM, Kalinichenko LP, Uversky VN.

Proteins. 2003 Jun 1;51(4):498-503.

PMID:
12784209
38.

Constrained analysis of fluorescence anisotropy decay:application to experimental protein dynamics.

Feinstein E, Deikus G, Rusinova E, Rachofsky EL, Ross JB, Laws WR.

Biophys J. 2003 Jan;84(1):599-611.

39.

Origin and properties of fluorescence emission from the extrinsic 33 kDa manganese stabilizing protein of higher plant water oxidizing complex.

Shutova T, Deikus G, Irrgang KD, Klimov VV, Renger G.

Biochim Biophys Acta. 2001 Apr 2;1504(2-3):371-8.

40.

pH-induced transition and Zn2+-binding properties of bovine prolactin.

Permyakov EA, Veprintsev DB, Deikus GY, Permyakov SE, Kalinichenko LP, Grishchenko VM, Brooks CL.

FEBS Lett. 1997 Apr 1;405(3):273-6.

41.

Interactions of alpha-lactalbumins with lipid vesicles studied by tryptophan fluorescence.

Grishchenko VM, Kalinichenko LP, Deikus GY, Veprintsev DB, Cawthern KM, Berliner LJ, Permyakov EA.

Biochem Mol Biol Int. 1996 Mar;38(3):453-66.

PMID:
8829604
42.

[Study of conformation transitions in proteins by tryptophan fluorescence and phosphorescence at low temperatures].

Permiakov EA, Deĭkus GIu.

Mol Biol (Mosk). 1995 Mar-Apr;29(2):339-44. Russian.

PMID:
7783738
43.

[Analytical description of electron-vibrational protein spectra].

Permiakov EA, Deĭkus GIu.

Mol Biol (Mosk). 1995 Jan-Feb;29(1):159-67. Russian.

PMID:
7723756
44.

[Kinetics of dissociation of parvalbumin complexes with calcium and magnesium ions].

Permiakov EA, Ostrovskiĭ AV, Kalinichenko LP, Deĭkus GIu.

Mol Biol (Mosk). 1987 Jul-Aug;21(4):1017-22. Russian.

PMID:
3657779

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