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Items: 36

1.

Extracting the Strongest Signals from Omics Data: Differentially Expressed Pathways and Beyond.

Glazko G, Rahmatallah Y, Zybailov B, Emmert-Streib F.

Methods Mol Biol. 2017;1613:125-159. doi: 10.1007/978-1-4939-7027-8_7.

2.

GSAR: Bioconductor package for Gene Set analysis in R.

Rahmatallah Y, Zybailov B, Emmert-Streib F, Glazko G.

BMC Bioinformatics. 2017 Jan 24;18(1):61. doi: 10.1186/s12859-017-1482-6.

3.

Evidence That G-quadruplex DNA Accumulates in the Cytoplasm and Participates in Stress Granule Assembly in Response to Oxidative Stress.

Byrd AK, Zybailov BL, Maddukuri L, Gao J, Marecki JC, Jaiswal M, Bell MR, Griffin WC, Reed MR, Chib S, Mackintosh SG, MacNicol AM, Baldini G, Eoff RL, Raney KD.

J Biol Chem. 2016 Aug 19;291(34):18041-57. doi: 10.1074/jbc.M116.718478. Epub 2016 Jul 1.

4.

Protein-protein interaction analysis for functional characterization of helicases.

Zybailov BL, Byrd AK, Glazko GV, Rahmatallah Y, Raney KD.

Methods. 2016 Oct 1;108:56-64. doi: 10.1016/j.ymeth.2016.04.014. Epub 2016 Apr 20. Review.

5.

Analysis of Protein-protein Interaction Interface between Yeast Mitochondrial Proteins Rim1 and Pif1 Using Chemical Cross-linking Mass Spectrometry.

Zybailov B, Gokulan K, Wiese J, Ramanagoudr-Bhojappa R, Byrd AK, Glazko G, Jaiswal M, Mackintosh S, Varughese KI, Raney KD.

J Proteomics Bioinform. 2015 Nov;8(11):243-252. Epub 2015 Nov 19.

6.

Yeast transcription co-activator Sub1 and its human homolog PC4 preferentially bind to G-quadruplex DNA.

Gao J, Zybailov BL, Byrd AK, Griffin WC, Chib S, Mackintosh SG, Tackett AJ, Raney KD.

Chem Commun (Camb). 2015 Apr 28;51(33):7242-4. doi: 10.1039/c5cc00742a.

7.

XLPM: efficient algorithm for the analysis of protein-protein contacts using chemical cross-linking mass spectrometry.

Jaiswal M, Crabtree N, Bauer MA, Hall R, Raney KD, Zybailov BL.

BMC Bioinformatics. 2014;15 Suppl 11:S16. doi: 10.1186/1471-2105-15-S11-S16. Epub 2014 Oct 21.

8.

[G4-quadruplexes and genome instability].

Zybań≠lov BL, Sherpa MD, Glazko GV, Raney KD, Glazko VI.

Mol Biol (Mosk). 2013 Mar-Apr;47(2):224-31. Russian.

9.

Large Scale Chemical Cross-linking Mass Spectrometry Perspectives.

Zybailov BL, Glazko GV, Jaiswal M, Raney KD.

J Proteomics Bioinform. 2013 Feb 8;6(Suppl 2):001.

10.

Computational prediction of polycomb-associated long non-coding RNAs.

Glazko GV, Zybailov BL, Rogozin IB.

PLoS One. 2012;7(9):e44878. doi: 10.1371/journal.pone.0044878. Epub 2012 Sep 13.

11.

The functional network of the Arabidopsis plastoglobule proteome based on quantitative proteomics and genome-wide coexpression analysis.

Lundquist PK, Poliakov A, Bhuiyan NH, Zybailov B, Sun Q, van Wijk KJ.

Plant Physiol. 2012 Mar;158(3):1172-92. doi: 10.1104/pp.111.193144. Epub 2012 Jan 24.

13.

Subunits of the plastid ClpPR protease complex have differential contributions to embryogenesis, plastid biogenesis, and plant development in Arabidopsis.

Kim J, Rudella A, Ramirez Rodriguez V, Zybailov B, Olinares PD, van Wijk KJ.

Plant Cell. 2009 Jun;21(6):1669-92. doi: 10.1105/tpc.108.063784. Epub 2009 Jun 12.

14.

Large scale comparative proteomics of a chloroplast Clp protease mutant reveals folding stress, altered protein homeostasis, and feedback regulation of metabolism.

Zybailov B, Friso G, Kim J, Rudella A, Rodríguez VR, Asakura Y, Sun Q, van Wijk KJ.

Mol Cell Proteomics. 2009 Aug;8(8):1789-1810. doi: 10.1074/mcp.M900104-MCP200.

15.

PPDB, the Plant Proteomics Database at Cornell.

Sun Q, Zybailov B, Majeran W, Friso G, Olinares PD, van Wijk KJ.

Nucleic Acids Res. 2009 Jan;37(Database issue):D969-74. doi: 10.1093/nar/gkn654. Epub 2008 Oct 2.

16.

Consequences of C4 differentiation for chloroplast membrane proteomes in maize mesophyll and bundle sheath cells.

Majeran W, Zybailov B, Ytterberg AJ, Dunsmore J, Sun Q, van Wijk KJ.

Mol Cell Proteomics. 2008 Sep;7(9):1609-38. doi: 10.1074/mcp.M800016-MCP200. Epub 2008 May 2.

17.

Sorting signals, N-terminal modifications and abundance of the chloroplast proteome.

Zybailov B, Rutschow H, Friso G, Rudella A, Emanuelsson O, Sun Q, van Wijk KJ.

PLoS One. 2008 Apr 23;3(4):e1994. doi: 10.1371/journal.pone.0001994.

18.

An ortholog of the Ro autoantigen functions in 23S rRNA maturation in D. radiodurans.

Chen X, Wurtmann EJ, Van Batavia J, Zybailov B, Washburn MP, Wolin SL.

Genes Dev. 2007 Jun 1;21(11):1328-39. Epub 2007 May 17.

19.

Quantitative shotgun proteomics using a protease with broad specificity and normalized spectral abundance factors.

Zybailov BL, Florens L, Washburn MP.

Mol Biosyst. 2007 May;3(5):354-60. Epub 2007 Apr 10.

PMID:
17460794
20.

Statistical analysis of membrane proteome expression changes in Saccharomyces cerevisiae.

Zybailov B, Mosley AL, Sardiu ME, Coleman MK, Florens L, Washburn MP.

J Proteome Res. 2006 Sep;5(9):2339-47.

PMID:
16944946
21.
22.

Principles and applications of multidimensional protein identification technology.

Paoletti AC, Zybailov B, Washburn MP.

Expert Rev Proteomics. 2004 Oct;1(3):275-82.

PMID:
15966824
23.
24.

A set of consensus mammalian mediator subunits identified by multidimensional protein identification technology.

Sato S, Tomomori-Sato C, Parmely TJ, Florens L, Zybailov B, Swanson SK, Banks CA, Jin J, Cai Y, Washburn MP, Conaway JW, Conaway RC.

Mol Cell. 2004 Jun 4;14(5):685-91.

25.

A mammalian mediator subunit that shares properties with Saccharomyces cerevisiae mediator subunit Cse2.

Tomomori-Sato C, Sato S, Parmely TJ, Banks CA, Sorokina I, Florens L, Zybailov B, Washburn MP, Brower CS, Conaway RC, Conaway JW.

J Biol Chem. 2004 Feb 13;279(7):5846-51. Epub 2003 Nov 24.

26.

Electron transfer in cyanobacterial photosystem I: II. Determination of forward electron transfer rates of site-directed mutants in a putative electron transfer pathway from A0 through A1 to FX.

Xu W, Chitnis PR, Valieva A, van der Est A, Brettel K, Guergova-Kuras M, Pushkar YN, Zech SG, Stehlik D, Shen G, Zybailov B, Golbeck JH.

J Biol Chem. 2003 Jul 25;278(30):27876-87. Epub 2003 Apr 29.

27.

Electron transfer in cyanobacterial photosystem I: I. Physiological and spectroscopic characterization of site-directed mutants in a putative electron transfer pathway from A0 through A1 to FX.

Xu W, Chitnis P, Valieva A, van der Est A, Pushkar YN, Krzystyniak M, Teutloff C, Zech SG, Bittl R, Stehlik D, Zybailov B, Shen G, Golbeck JH.

J Biol Chem. 2003 Jul 25;278(30):27864-75. Epub 2003 Apr 29.

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32.

Electron transfer may occur in the chlorosome envelope: the CsmI and CsmJ proteins of chlorosomes are 2Fe-2S ferredoxins.

Vassilieva EV, Antonkine ML, Zybailov BL, Yang F, Jakobs CU, Golbeck JH, Bryant DA.

Biochemistry. 2001 Jan 16;40(2):464-73.

PMID:
11148041
33.

Recruitment of a foreign quinone into the A1 site of photosystem I. Altered kinetics of electron transfer in phylloquinone biosynthetic pathway mutants studied by time-resolved optical, EPR, and electrometric techniques.

Semenov AY, Vassiliev IR, van Der Est A, Mamedov MD, Zybailov B, Shen G, Stehlik D, Diner BA, Chitnis PR, Golbeck JH.

J Biol Chem. 2000 Aug 4;275(31):23429-38.

34.
35.

Recruitment of a foreign quinone into the A(1) site of photosystem I. I. Genetic and physiological characterization of phylloquinone biosynthetic pathway mutants in Synechocystis sp. pcc 6803.

Johnson TW, Shen G, Zybailov B, Kolling D, Reategui R, Beauparlant S, Vassiliev IR, Bryant DA, Jones AD, Golbeck JH, Chitnis PR.

J Biol Chem. 2000 Mar 24;275(12):8523-30.

36.

Menaquinone-7 in the reaction center complex of the green sulfur bacterium Chlorobium vibrioforme functions as the electron acceptor A1.

Kjaer B, Frigaard NU, Yang F, Zybailov B, Miller M, Golbeck JH, Scheller HV.

Biochemistry. 1998 Mar 10;37(10):3237-42.

PMID:
9536963

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