Publications

 
According to Component Total Publications
 
  1. Menon A.L., Poole F.L., Cvetkovic A., Trauger S.A., Kalisiak E., Scott J.W., Shanmukh S., Praissman J., Jenney F.E., Wikoff W.R, Apon J.V., Siuzdak G., Adams M.W.W.
    Novel protein complexes identified in the hyperthermophilic archaeon Pyrococcus furiosus by non-denaturing fractionation of the native proteome
    Mol. Cell. Proteomics, 2008, (in press:  Nov 28. Epub ahead of print)
  2. Cvetkovic A., Shanmukh S., Menon A.L., Poole F.L., Scott J.W., Thorgersen M., Jenney F.E., Yannone S.M., Tainer J.A., Trauger S.A., Kalisiak E., Apon J.V., Siuzdak G., Adams M.W.W.
    "Metalloterra incognito: the metalloproteomes of microorganisms are largely uncharacterized"
    Nature, 10/2008, submitted
  3. Trauger S.A., Kalisiak E., Kalisiak J., Morita H., Weinbergb M.V., Menon A.L., Poole F.L. II, Adams M.W.W., Siuzdak G.
    Correlating the Transcriptome, Proteome, and Metabolome in the Environmental Adaptation of a Hyperthermophile
    Journal of Proteome Research, 2008, 7, 1027-1035
  4. Kalisiak J., Trauger S., Kalisiak E., Morita H., Fokin V., Adams M.M., Sharpless K.B., Siuzdak G.
    The identification of a new endogenous metabolite and the characterization of its protein interactions through an immobilization approach
    Journal of the Americal Chemical Society, 2008, in press
  5. Fan L., Fuss J.O., Cheng Q.J., Arvai A.S., Hammel M., Roberts V.A., Cooper P.K., Tainer J.A.
    XPD Helicase Structures and Activities Provide Insights into Cancer and Aging Phenotypes from XPD Mutations
    Cell, May 30 2008, 133(5), 789-800.
  6. Pascal J.M., Tsodikov O.V., Hura G.L., Song W., Cotner E.A., Classen S., Tomkinson A.E., Tainer J.A., Ellenberger T.
    A Flexible Interface between DNA Ligase and PCNA Supports Conformational Switching and Efficient Ligation of DNA
    Molecular Cell, 2006, 24, 279-291
  7. Northen T.R., Lee J-C, Hoang L., Raymond J., Hwang D-R, Yannone S.M., Wong C-H, Siuzdak G.
    A Nanostructure-Initiator Mass Spectrometry-Based Enzyme Activity Assay
    PNAS, 2008, 105(10), 3678-3683
  8. Reiss D.J., Facciotti M.T., Baliga N.S.
    Model-based deconvolution of genome-wide DNA binding
    Bioinformatics, Feb 1 2008, 24(3), 396-403
  9. Bonneau R., Facciotti M.T., Reiss D.J., Schmid A.K., Pan M., Kaur A., Thorsson T., Shannon P., Johnson M.H., Bare C.J., Longabaugh W., Vuthoori M., Whitehead K., Madar A., Suzuki L., Mori T., Chang D.E., DiRuggiero J., Johnson C.H., Hood L., Baliga N.S.
    A predictive model for transcriptional control of physiology in a free living cell
    Cell, Dec 28 2007, 131(7), 1354-65
  10. Bare J.C., Shannon P., Schmid A., Baliga N.S.
    The Firegoose: two-way integration of diverse data from different bioinformatics web resources with desktop applications
    BMC Bioinformatics, Nov 19 2007, 8(1), 456
  11. Schmid A.K., Reiss D.J., Kaur A., Pan M., King N., Van P.T., Hohmann L., Martin D.B., Baliga N.S.
    The anatomy of microbial cell state transitions in response to oxygen
    Genome Research, Oct 2007, 17(10), 1399-413 (Epub 2007 Sep 4)
  12. Facciotti M.T., Reiss D.J., Pan M., Kaur A., Vuthoori M., Bonneau R., Shannon P., Srivastava A., Donohoe S.M., Hood L.E., Baliga N.S.
    General transcription factor specified global gene regulation in archaea
    Proc Natl Acad Sci U S A, 2007, 104(11), 4630-4635
  13. Schmid A.K., Baliga N.S.
    Prokaryotic Systems Biology
    Cell Engineering, 2007, Vol. 5: Systems Biology, 395-423, M. Al-Rubeai and M. Fussenegger (ed.), Springer Press, New York, NY
  14. Kaur A., Pan M., Meislin M., Facciotti M.T., El-Geweley R., Baliga N.S.
    A systems view of haloarchaeal strategies to withstand stress from transition metals
    Genome Research, July 2006, 16, 841-854
  15. Reiss D.J., Baliga N.S., Bonneau R.
    Integrated biclustering of heterogeneous genome-wide datasets for the inference of global regulatory networks
    BMC Bioinformatics, Jun 2 2006, 7, 280
  16. Bonneau R., Reiss D., Shannon P., Facciotti M.T., Hood L., Baliga N.S., Thorsson V.
     The Inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data-sets
    Genome Biology, May 10 2006, 7(5), R36
  17. Shannon P., Reiss D., Bonneau R., Baliga N.
    Gaggle: An open-source software system for integrating bioinformatics software and data sources
    BMC Bioinformatics, Mar 28 2006, 7(1), 176
  18. Whitehead K., Kish A., Pan M., Kaur A., Reiss D.J., King N., Hohmann L., DiRuggiero J., Baliga N.S.
    An integrated systems approach for understanding cellular responses to gamma radiation
    Molecular Systems Biology, 2006, 2, 47
  19. Bunner A.E., Trauger S.A., Siuzdak G., Williamson J.R.
    Quantitative ESI-TOF Analysis of Macromolecular Assembly Kinetics
    Analytical Chemistry, 2008, in press
  20. Benton H.P., Wong D.M., Siuzdak G.
    XCMS: Processing Tandem Mass Spectrometry Data for Metabolite Identification and Structural Characterization
    Analytical Chemistry, 2008, 80(16), 6382-6389
  21. Woo H.K., Northen T.R., Yanes O., Siuzdak G.
    Nanostructure-initiator mass spectrometry: a protocol for preparing and applying NIMS surfaces for high-sensitivity mass analysis
    Nature Protocols, 2008, 3(8), 1341-1349
  22. Nordstrom A. Want E., Northen T., Lehtio J., Siuzdak G.
    Multiple Ionization Mass Spectrometry Strategy Reveals the Complexity of Metabolomics
    Analytical Chemistry, 2008, 80, 421-429
  23. Trauger S.A., Kalisiak E., Kalisiak J., Morita H., Weinbergb M.V., Menon A.L., Poole F.L. II, Adams M.W.W., Siuzdak G.
    Correlating the Transcriptome, Proteome, and Metabolome in the Environmental Adaptation of a Hyperthermophile
    Journal of Proteome Research, 2008, 7, 1027-1035
  24. O'Maille G., Go E.P., Hoang L., Want E.J., Smith C., O'Maille P., Nordstrom A., Morita H., Qin C., Uritboonthai W., Apon J., Moore R., Garrett J., Siuzdak G.
    Metabolomics relative quantitation with mass spectrometry using chemical derivatization and isotope labeling
    Spectroscopy - An International Journal, 2008, 22(5), 327-343
  25. Go E.P., Uritboonthai W., Apon J.A., Trauger S.A., Nordstrom A., O'Maille G., Brittain S., Peters E.C., Siuzdak G.
    Selective Metabolite and Peptide Capture/Mass Detection Using Fluorous Affinity Tags
    Journal of Proteome Research, 2007, 6, 1492-1499
  26. Northen T.R., Northen M.T., Marrinucci D.C., Nordstrom A., Golledge S., Siuzdak G.
    Clathrate Nanostructures for Mass Spectrometry
    Nature, 2007, 449, 1033-1036
  27. Want E.J., Nordstrom A., Morita H., Siuzdak G.
    From Exogenous to Endogenous: The Inevitable Imprint of Mass Spectrometry in Metabolomics
    Journal of Proteome Research, 2007, 6(2), 459-468
  28. Northen T.R., Northen M.T., Nordstrom A., Uritboonthai W., Turner K., Siuzdak G.
    High Surface Energy of Porous Silicon Drives Desorption of Intact Biomolecules
    Journal of the American Society of Mass Spectrometry, 2007, 18, 1945-49
  29. Go E.P., Uritboonthai W., Apon J.A., Trauger S.A., Nordstrom A., O'Maille G., Brittain S., Peters E.C., Siuzdak G.
    Selective Metabolite and Peptide Capture/Mass Detection Using Fluorous Affinity Tags
    Journal of Proteome Research, 2007, 6, 1492-1499
  30. Go E.P., Wikoff W., Shen Z., O'Maille G., Morita H., Conrads T.P., Nordstrom A., Trauger S.A., Uritboonthai W., Lucas D., Chan K.C., Veenstra T.D., Lewicki H., Oldstone M.B., Schneemann A., Siuzdak G.
    Mass Spectrometry Reveals Specific and Global Molecular Transformations during Viral Infection
    Journal of Proteome Research, 2006, 5 (9), 2405-2416
  31. Smith C.A., Want E.J., O'Maille G., Abagyan R., Siuzdak G.
    XCMS: Processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching and identification
    Analytical Chemistry, 2006, 78, 779-787
  32. Want E.J., Smith C., Siuzdak G.
    Phospholipid Capture Combined with Non-Linear Chromatographic Correction for Improved Metabolite Profiling Metabolomics, 2006, 2, 145-154
  33. Nordstrom A., Apon J.V., Uritboonthai W., Go E.P., Siuzdak G.
    Surfactant Enhanced Desorption/Ionization on Silicon (DIOS) Mass Spectrometry Analytical Chemistry, 2006, 78, 272-278
  34. Williams R.S., Moncalian G., Williams J.S., Yamada Y., Limbo O., Shin D.S., Groocock L.M., Cahill D., Hitomi C., Guenther G., Moiani D., Carney J.P., Russell P., Tainer J.A.
    Mre11 dimers coordinate DNA end bridging and nuclease processing in double-strand-break repair
    Cell, Oct 3 2008, 135(1), 97-109
  35. Fan L., Fuss J.O., Cheng Q.J., Arvai A.S., Hammel M., Roberts V.A., Cooper P.K., Tainer J.A.
    XPD Helicase Structures and Activities Provide Insights into Cancer and Aging Phenotypes from XPD Mutations
    Cell, May 30 2008, 133(5), 789-800
  36. Fan L., Williams R.S., Shin D.S., Chapados B.R., Tainer J.A.
    Master keys to DNA replication,  repair, and recombination from the structural biology  of enzymes from thermophilesIn Thermophiles:  Biology and Technology at High Temperatures (Robb, F. T., Antranikian, G., Grogan, D. & Driessen, A., eds), 2008, 239–263, CRC Press, Boca Raton, FL
  37. Williams R.S., Williams J.S., Tainer J.A.
    Mre11/Rad50/Nbs1 is a keystone complex connecting DNA repair machinery, double strand break signaling, and the chromatin template
    Biochem. Cell Biol, 2007, 85, 509-520
  38. Putnam C.D., Hammel M., Hura G.L., Tainer J.A.
    Solution scattering (SAXS) combined with crystallography and computation: defining accurate macromolecular structures, conformations and assemblies in solution
    Quarterly Reviews in Biophysics, Aug 2007, 40(3), 191-285
  39. Williams R., Sengerova B., Osborne S., Syson K., Ault S., Kilgour A., Chapados B.R., Tainer J.A., Sayers J.R., Grasby J.A.
    Comparison of the catalytic parameters and reaction specificities of a phage and an archaeal flap endonuclease
    J Mol Biol., 2007 Aug 3, 371(1), 34-48 (Epub 2007 May 1)
  40. Yamagata A., Tainer J.A.
    Hexameric structures of the archaeal secretion ATPase GspE and implications for a universal secretion mechanism
    EMBO Journal, 2007, 26(3), 878-890
  41. Fan L., Arvai A., , Cooper P.K., Iwai S., Hanaoka F., Tainer J.A.
    Conserved XPB Core Structure and Motifs for DNA Unwinding: Implications for Pathway Selection of Transcription or Excision Repair
    Molecular Cell, 2006, 22, 27-37
  42. Pascal J.M., Tsodikov O.V., Hura G.L., Song W., Cotner E.A., Classen S., Tomkinson A.E., Tainer J.A., Ellenberger T.
    A Flexible Interface between DNA Ligase and PCNA Supports Conformational Switching and Efficient Ligation of DNA
    Molecular Cell, 2006, 24, 279-291
  43. Tsutakawa S.E., Hura G.L., Frankel K.A., Cooper P.K., Tainer J.A.
    Structural analysis of flexible proteins in solution by small angle X-ray scattering combined with crystallography
    J. Structural Biology, May 2007, 158(2), 214-23
  44. Wang C., Ding C., Holbrook S.
    Dissecting Protein Interaction Networks With A Robust Algorithm
    PLOS ONE, 2008, submitted
  45. Zeng E., Ding C., Narasimhan G., Holbrook S.R.
    Estimating Support for Protein-Protein Interaction Data with Applications to Function Prediction
    LSS Computational Systems Bioinformatics Conference, CSB2008
  46. Wang C., Ding C., Yang Q., Holbrook S.R.
    Consistent dissection of the protein interaction network by combining global and local metrics
    Genome Biol., 2007, 8, R271
  47. Francis-Lyon P., Cristianini N., Holbrook S.
    Terminator Detection by Support Vector Machine Utilizing a Stochastic Context-Free Grammar 2007
    Pacific Symposium on Biocomputing 12, 2007
  48. Ding C., He X., Xiong H., Peng H., Holbrook S.R.
    Transitive Closure and Metric Inequality of Weighted Graphs - Detecting Protein Interaction Modules Using Cliques
    Int. J. Data Mining and Bioinformatics, 2006, 1(2), 162-177
  49. Ding C., Zhang A.Y., Holbrook S.
    Biclustering Protein Complex Interactions with a Biclique Finding Algorithm, 2006 IEEE International Conference on Data Mining
    IEEE Computer Society Press, 2006, 178-187
    50. Zhang Y., Ding C., Holbrook S.
    Simultaneously Relating Domains and Protein complexes through Biclique Discovery
    Bioinformatics, 2006, 1-6

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