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Component 1:
Cvetkovic A., Shanmukh S., Menon A.L., Poole F.L., Scott J.W., Praissman J., Jenney F.E. Jr., Trauger S.A., Kalisiak E., Apon J.V., Siuzdak G., Adams M.W.W.
The metalloproteome of microorganisms is largely uncharacterized
Science, 2008, (to be submitted 05/2008)
Menon A.L., Poole F.L., Cvetkovic A., Trauger S.A., Kalisiak E., Scott J.W., Shanmukh S., Praissman J., Jenney F.E. Jr., 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
Molecular and Cellular Proteomics, 2008, (to be submitted 05/2008)
Menon A.L., Poole F.L., Cvetkovic A., Shanmukh S., Scott J., Adams M.W.W.
MAGGIE Component 1: Identification and Purification of Native and Recombinant Multiprotein Complexes and Modified Proteins from Pyrococcus furiosus
Component 3:
Bonneau R, Facciotti MT, Reiss DJ, Schmid AK, Pan M, Kaur A, Thorsson T, Shannon P, Johnson MH, Bare CJ, Longabaugh W, Vuthoori M, Whitehead K, Madar A, Suzuki L, Mori T, Chang DE, DiRuggiero J, Johnson CH, Hood L, Baliga NS
A predictive model for transcriptional control of physiology in a free living cell
Cell., 2007 Dec 28, 131(7), 1354-65
PMID: 18160043 [PubMed - in process]
Reiss DJ, Facciotti MT, Baliga NS
Model-based deconvolution of genome-wide DNA binding
Bioinformatics, 2008 Feb1, 24(3), 396-403
PMID: 18056063 [PubMed - as supplied by publisher]
Bare JC, Shannon P, Schmid A, Baliga NS
The Firegoose: two-way integration of diverse data from different bioinformatics web resources with desktop applications
BMC Bioinformatics, 2007 Nov 19, 8(1), 456
PMID: 18021453 [PubMed - as supplied by publisher]
Schmid AK, Reiss DJ, Kaur A, Pan M, King N, Van PT, Hohmann L, Martin DB, Baliga NS
The anatomy of microbial cell state transitions in response to oxygen
Genome Research, 2007 Oct, 17(10), 1399-413, Epub 2007 Sep 4
PMID: 17785531 [PubMed- indexed for MEDLINE]
Facciotti MT, Reiss DJ, Pan M, Kaur A, Vuthoori M, Bonneau R, Shannon P, Srivastava A, Donohoe SM, Hood LE, Baliga NS
General transcription factor specified global gene regulation in archaea
Proc Natl Acad Sci USA, 2007, 104(11), 4630-4635
PMID: 17360575
Amy K. Schmid and Nitin S. Baliga
Prokaryotic Systems Biology
Cell Engineering, 2007, 5, 395-423
Kaur A, Pan M, Meislin M, Facciotti MT, El-Geweley R, Baliga NS
A systems view of haloarchaeal strategies to withstand stress from transition metals
Genome Research, 2006 July, 16, 841-854
PMID: 16751342
Reiss DJ, Baliga NS, Bonneau R
Integrated biclustering of heterogeneous genome-wide datasets for the inference of global regulatory networks
BMC Bioinformatics, 2006 Jun 2, 7, 280
PMID: 16749936
Bonneau R*, Reiss D, Shannon P, Facciotti MT, Hood L, Baliga NS, Thorsson V
The Inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data-sets
Genome Biology, 2006 May 10, 7(5), R36
PMID: 16686963 [PubMed - indexed for MEDLINE]
Shannon P, Reiss D, Bonneau R, Baliga N
Gaggle: An open-source software system for integrating bioinformatics software and data sources
BMC Bioinformatics, 2006 Mar 28, 7(1), 176
PMID: 16569235 [PubMed - as supplied by publisher]
Kenia Whitehead, Adrienne Kish, Min Pan, Amardeep Kaur, David J Reiss, Nichole King, Laura Hohmann, Jocelyne DiRuggiero, Nitin S Baliga
An integrated systems approach for understanding cellular responses to gamma radiation
Molecular Systems Biology, 2006, 2, 47
PMID: 16969339
Component 4:
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
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
Nordstrom A., He L., Siuzdak G.
Desorption/Ionization on Silicon (DIOS)
Encyclopedia of Mass Spectrometry, Editor Michael Gross, in press, 2007
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, in press, 2007
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
O'Maille G., Hoang L., Nordstrom A., Go E.P., Qin C., Siuzdak G.
Enhanced Metabolite Profiling via Chemical Derivatization and Isotope Labeling
submitted, 2007
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
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
Nordstrom A., O'Maille G., Qin C., Siuzdak G.
Non-linear Data Alignment for UPLC-MS and HPLC-MS based Metabolomics: Quantitative Analysis of Endogenous and Exogenous Metabolites in Human Serum
Analytical Chemistry, 2006, 78, 7289-3295
Lee J-C.,Wu C-Y., Apon J.V., Siuzdak G., Wong C-H.
Reactivity-Based One-Pot Synthesis of Tumor-Associated Antigen N3 Minor Octasaccharide: A Case Study of DIOS-MS Sugar Array**
Angew Chem Int Ed, 2006, 45, 2753 - 2757
Want E.J., Smith C., Siuzdak G.
Phospholipid Capture Combined with Non-Linear Chromatographic Correction for Improved Metabolite Profiling
Metabolomics, 2006, in press
Cohen L., Go E.P. , Siuzdak G.
Small Molecule Desorption/Ionization Mass Analysis
MALDI-MS Franz Hillenkamp - editor, 2006, XVI, 346
Siuzdak G.
The Expanding Role of Mass Spectrometry in Biotechnology - 2nd Edition
MCC Press, San Diego, 2006, , 1-252
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
Component 5:
Fan, L., Fuss, J.O., Cheng, Q.J., Arvai, A.S., Hammel M., Roberts, V.A., Cooper; P.K., and Tainer, JA.
XPD Helicase Structures and Activities Provide Insights into Cancer and Aging Phenotypes from XPD Mutations
Cell, 2008, in press.
Williams, RS., Williams, JS., and Tainer, JA.
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
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, 2007, in press
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
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
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
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, in press, 2006
Component 6:
Zeng E, Ding C, Narasimhan G, Holbrook SR
Estimating Support for Protein-Protein Interaction Data with Applications to Function Prediction
LSS Computational Systems Bioinformatics Conference, CSB2008
Wang C, Ding C, Yang Q, Holbrook SR
Consistent dissection of the protein interaction network by combining global and local metrics
Genome Biol., 2007, 8, R271
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
Ding C, He X, Xiong H, Peng H, Holbrook SR
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
Ding C, Zhang AY, 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
Zhang Y, Ding C, Holbrook S
Simultaneously Relating Domains and Protein complexes through Biclique Discovery
Bioinformatics, 2006, 1-6
Ding C, He X, Meraz RF, Holbrook SR
A Unified Representation of Multiprotein Complex Data for Modeling Interaction Networks
PROTEINS: Structure, Function, and Bioinformatics, 2004, 57, 99-108
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