Publications

According to Component

Total Publications

Component 1: Mike Adams - Pyrococcus

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)

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

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

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

Component 2: Steve Yannone - Sulfolobus

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.

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

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

Component 3: Nitin Baliga – Halobacerium, Gaggle

Whitehead K., Min P., Masumura K., Bonneau R., Baliga N.S.
Diurnally entrained anticipatory behavior in Archaea
PLoS One, in press

Schmid A.K., Pan M., Baliga N.S.
Metabolic regulation, (in preparation, supplemental data)

Koide T., Pang W.L., Baliga N.S.
The role of predictive modelling in rationally re-engineering biological systems
Nature Reviews Microbiology, 2009 Apr, 7(4), 297-305

Van P., Schmid A.K., King N., Kaur A., Pan M., Whitehead K., Koide T., Facciotti M., Goo Y.A., Deutsch E., Reiss D.J., Mallick P., Baliga N.S.
Halobacterium salinarium NRC-1 PeptideAtlas: toward strategies for targeted proteomics and improved proteome coverage
Journal of Proteome Research, 2008 Sep, 7(9), 3755-64

Baliga N.S.
Perspectives: Microbiology - Scale of Prediction
Science, 2008 June 6, 320(5880), 1297-1298

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

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

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

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)

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

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

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

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

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

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

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

Component 4: Gary Siuzdak – Mass Spectrometry

Bunner A.E., Trauger S.A., Siuzdak G., Williamson J.R.
Quantitative ESI-TOF Analysis of Macromolecular Assembly Kinetics
Analytical Chemistry, 2008, in press

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

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

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

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

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

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

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

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

Want E.J., Smith C., Siuzdak G.
Phospholipid Capture Combined with Non-Linear Chromatographic Correction for Improved Metabolite Profiling Metabolomics, 2006, 2, 145-154

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

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

Component 5: John Tainer, Greg Hura - SAXS

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, (submitted)

Hura G.L., Menon A.L., Hammel M., Rambo R.P., Poole F.L., Tsutakawa S.E., Jenney F.E., Frankel K.A., Hopkins R.C., Scott J.O., Dillard B.D., Classen S., Adams M.W.W., Tainer J.A.
Rapid and robust proteomics-scale solution structural analyses determined efficiently by x-ray scattering (SAXS)
Nature Methods, 2009, in press

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

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

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

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

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)

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

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

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, 2008, submitted

Component 6: Steve Holbrook - Bioinformatics

Wang C., Ding C., Holbrook S.
Dissecting Protein Interaction Networks With A Robust Algorithm
PLOS ONE, 2008, submitted

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

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

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 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

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

Zhang Y., Ding C., Holbrook S.
Simultaneously Relating Domains and Protein complexes through Biclique Discovery
Bioinformatics, 2006, 1-6