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BARNETT
INSTITUTE RESEARCH PUBLICATIONS
(2003 - present)
Contents:
Prof. Barry L. Karger
Prof. William S. Hancock
Prof. Graham Jones
Prof. Roger Giese
Prof. Bill Giessen
Prof. Paul Vouros
Prof. John Engen
Prof. Zhaohui Sunny Zhou
Professor
Barry L. Karger
Csanky,
E., Olivova, P., Rajnavolgyi, E., Hempel, W., Tardieu,
N., Katalin, E.T., Jullien, A., Malderez-Bloes, C.,
Kuras, M., Duval, M.X., Nagy, L., Scholtz, B., Hancock,
W.S., Karger, B.L., Guttman, A., Takacs, L., "Monoclonal
Antibody Proteomics: Discovery and Prevalidation of
Chronic Obstructive Pulmonary Disease Biomarkers in
a Single Step", Electrophoresis, 28, #23,
4401-4406, (2007). pubmed
Gu,
Y., Wu, S-L., Meyer, J.L., Hancock, W.S., Burg, L.J.,
Linder, J, Hanlon, D.W., and Karger B.L.
"Proteomic analysis of high-grade dysplastic
cervical cells obtained from ThinPrep slides using
laser capture microdissection and mass spectrometry."
J. Proteome Res. 6(11):4256-68, (2007). pubmed
Wu,
S-L., Hühmer, A.F., Hao, Z., and Karger, B.L. "On-line
LC-MS approach combining collision-induced dissociation
(CID), electron-transfer dissociation (ETD), and CID
of an isolated charge-reduced species for the trace-level
characterization of proteins with post-translational
modifications." J. Proteome Res.
6(11):4230-44, (2007). pubmed
Zvonok,
N., Yaddanapudi, S., Williams, J., Dai, S., Dong,
K., Rejtar, T., Karger, B.L. and Makriyannis, A.,
" Comprehensive Proteomic Mass Spectrometric
Chracterization of Human Cannabinoid CB2 Receptor",
J. Proteome Research, 2068-2079, (2007).pubmed
Zhang,
J., Wu, S., Kim, J. and Karger, B.L., "Ultratrace
liquid chromatography/mass spectrometry analysis of
large peptides with post-translational modifications
using narrow-bore poly(styrene- divinylbenzene) monolithic
columns and extended range proteomic analysis",
J. Chromatogr A., 1154, 295-307, (2007).pubmed
Luo,
Q., Yue, G., Valaskovic, G., Gu, Y., Wu., S-L. and
Karger, B.L. "On-Line 1D and 2D PLOT/LC-ESI-MS
Using 10 µm i.d. Poly(styrene-divinylbenzene)
Porous Layer Open Tubular (PLOT) columns for Ultrasensitive
Proteomic Analysis", Anal. Chem., ASAP
Article; DOI:
10.1021/ac070583w (2007).
Ren, J.M., Rejtar, T., Li, L. and Karger, B.L. "Automated
N-Glycan Structure Annotation of Glycopeptides Using
a Linearized Structure database (GlyDB)", J.
of Proteome Research, 6, 3162-3173, (2007).
Andreev,
V., Li, L., Cao, L., Gu, Y., Rejtar, T., Wu, S-L.
And Karger, B.L. " A New Algorithm Using Cross-Assignment
for Label-Free Quantitation with LC/LTQ-FT MS",
J. of Proteome Res., 6, 2186-2194
(2007).
Li,
L., Li, Q., Rohlin, L., Kim, U., Salmon, K., Rejtar,
T., Gunsalus, R.P., Karger, B.L. and Ferry, J.G.
"Quantitative proteomic and microarray analysis
of the archaeon Methanosarcina acetivorans grown
with acetate versus methanol", J. of Proteome
Res, 6, 759-771, (2007).
Yue, G. Luo, Q., Zhang, J., Wu, S. And Karger B.L.,"Ultratrace
LC/MS Proteomic Analysis Using 10 µm i.d.
Porous Layer Open Tubular (PLOT) Poly(styrene-divinylbenzene)
Capillary Columns", Anal. Chem, 79 (3),
938-946, (2007).
Lessner,
D., Li, L., Li, Q., Rejtar, T., Andreev, A., Reichlen,
M., Hill, K., Moran, J., Karger, B.L. and Ferry,
J. G. "An Unconventional Pathway for Reduction
of CO2 to Methane in CO-grown Methanosarcina Acetivorans
Revealed by Proteomics" PNAS (103) 17921,
(2006).
Correia,
F., D'Onofrio, A., Rejtar,T., Li, L., Karger, B.L.,
Makarova, K., Koonin, E.V., and Lewis, K., "Kinase
Activity of Overexpressed HipA is Required for Growth
Arrest and Multidrug Tolerance in Escherichia coli",
J. of Bacteriology, vol. 188 (24) 8360-8367,
(2006).
Wu,
S.L., Kim, J., Bandle, R., Liotta, L., Petricoin,
E. And Karger, B.L., "Dynamic profiling of
the post-translational modifications and interaction
partners of epidermal growth factor receptor signaling
after stimulation by EGF using extended range proteomic
analysis (ERPA)", Mol. Cell,. 5,
1610-1627, (2006).
Andreev, V., Li, L., Cao, L., Gu, Y., Kim, J., Rejtar,
T., Wu, S. And Karger, B.L., "A New Algorithm
for 15N/14N Quantitation with LC-ESI-MS Using an
LTQ-FT Mass Spectrometer", J. of Proteome
Res, 5; 2039-2045, (2006).
Moskovets,
E., Preisler, J., Chen, H.S., Rejtar, T., Andreev,
V. and Karger. B.L., "High-Throughput Axial
MALDI-TOF MS Using a 2 kHz Repetition Rate Laser",
Anal. Chem., 78, 912-919 (2006).
Karger, Barry L. "Shigeru Terabe, a Colleague
and Outstanding Scientist", J. of Chrom,
A., 3, 1106 (2006).
Li, Q., Li, L., Rejtar, T., Lessner, D., Karger,
B.L. and Ferry, J.G., "Electron Transport in
the Pathway of Acetate Conversion to Methane in
the Marine Archaeon Methanosarcina acetivorans",
J. of Bacteriol., 188(2), 702-710,
(2005).
Chen, H., Rejtar, T., Andreev, V., Moskovets, E.
and Karger, B.L., "A New Strategy for Enhanced
Characterization of Complex Proteomic Samples Using
LC-MALDI MS/MS: Exclusion of Redundant Peptides
from MS/MS Analysis in Replicate Runs" Anal.
Chem, 77, 7816 -7825 (2005).
Wu, S., Kim, J., Hancock, W.S., Karger, B.L., "Extended
Range Proteomic Analysis (ERPA): New anad Sensitive
LC-MS Platform for High Seqeucne Coverage of Complex
Proteins with Extensive Posttranslational Modifications
-Comprehensive Analysis of Beta-Caesin and Epidermal
Growth Factor Receptor", J. of Proteome
Res., 4(4); 1155-1170 (2005).
Li-Sucholeiki, X., Tomita-Mitchell, A., Arnold,
K., Glassner, B., Thompson, T., Murthy, J., Berk,
L., Lange, C., Leong-Morgenthaler, P., MacDougall,
D., Munro, J., Cannon, D., Mistry, T., Miller, A.,
Deka, C., Karger, B.L., Gillespie, K., Ekstrom,
P., Todd, J. and Thilly, W. " Detection and
Frequency Estimation of Rare Varients in Pools of
Genomic DNA from Large Populations Using Mutational
Spectrometry", Mutation Research, 570,
267-280 (2005).
Li, Q., Deka, C., Glassner, B., Arnold, K., Li-Sucholeiki,
X., Tomita-Mitchell, A., Thilly, W. and Karger,
B.L., "Design of an Automated Instrument with
Fraction Collection for DNA Mutation Discovery by
Constant Denaturant Capillary Electrophoresis (CDCE)."
J. of Separation Science, 28 1375-1389
(2005).
Chen, H., Rejtar, T., Andreev, V., Moskovets, E.
and Karger, B.L. "High Speed - High Resolution
Monolithic Capillary LC-MALDI MS Using an Off-line
Continuous Deposition Interface for Proteomic Analysis",
Anal. Chem., 77, 2323-2331 (2005).
Pashkova, A., Chen, H., Rejtar, T., Zang, X., Giese,
R. Andreev, V., Moskovets, E. and Karger, B.L. "Coumarin
Tags for Improved Analysis of Peptides by MALDI-TOF
MS and MS/MS. II. Alexa Fluor 350 Tag for Increased
Peptide and Protein Identification by LC-MALDI-TOF/TOF
MS", Anal. Chem., 77(7); 2085-2096,
(2005).
Li , Q, Li, L, Rejtar, T, Karger, B.L. and Ferry,
J. "The Proteome of Methanosarcina acetivorans.
Part II, Comparison of Protein Abundance in Acetate-
and Methanol-Grown Cells", J. of Proteome
Res., 4(1); 129-135 (2005).
Li, Q, Li, L, Rejtar, T, Karger, B.L. and Ferry,
J. "The Proteome of Methanosarcina
acetivorans.
Part I, An Expanded View of the Biology
of the Cell" J. of Proteome Res., 4(1),
112-128 (2005).
Kautz, R., Goetzinger, W. and Karger, B.L. "High
Throughput Microcoil NMR of Compound Libraries Using
Zero-Dispersion Segmented Flow Analysis", The
Journal of Combinatorial Chemistry, 7(1); 14-20.
(2005).
Wu, S., Jardine, I., Hancock, W.I. and Karger, B.L.
"A New and Sensitive On-Line LC-MS Approach
for Top-Down Protein Analysis: The Comprehensive
Analysis of Human Growth Hormone in an E. coli Lysate
Using a Hybrid Linear Ion Trap Fourier Transform
Ion Cyclotron Resonance (FTICR) Mass Spectrometer",
Rapid Comm. Mass Spec., 19, 2201-2207
(2004).
Rejtar, T., Chen, H., Andreev, V., Moskovets, E.,
and Karger, B.L. "Increased Identification
by Peptides by Enhanced Data Processing of High
Resolution MALDI TOF/TOF Mass Spectra Prior to Database
Searching", Anal. Chem., 76,
6017-6028 (2004).
Pashkova, A., Moskovets, E. Karger, Barry L. "Coumarin
Tags for Improved Analysis of Peptides by MALDI-TOF
MS and MS/MS I. Enhancement in MALDI MS Signal Intensities",
Anal. Chem., 76, 4550-4557 (2004).
Zang, L., Palmer-Toy, D., Hancock, W.S., Sgroi,
D. and Karger, B.L. "Proteomic Analysis of
Ductal Carcinoma of the Breast Using Laser Capture
Microdissection, LC-MS and 16O/18O
Isotopic Labeling", J. Proteome Res.,3,
604-612 (2004).
Paba, J.; Ricart, C. A. O., Fontes, W., Santana,
J. M., Teixeira, A. R. L.,. Marchese, J., Williamson,
B., Hunt, T., Karger, B. L., Sousa, M. V., "Proteomic
Analysis of Trypanosoma cruzi Developmental
Stages Using Isotope-Coded Affinity Tag Reagents",
J. Proteome Res., 3, 517-524 (2004).
Lazar, I.M., Horvath,C., Yang, Y., Karger, B.L.,
"Microfluidic Device for Capillary Electrochromatography-Mass
Spectrometry", Electrophoresis, 24,
3655-3662 (2003).
Moskovets, E., Chen, H., Pashkova, A., Rejtar, T.,
Andreev, V.P., Karger, B.L., "Closely Spaced
External Standard: A Universal Method of Achieving
5 ppm Mass Accuracy Over the Entire MALDI Plate
in MALDI-TOF MS", Rapid Commun. in Mass
Spect., 17, 2177-2187 (2003).
Andreev, V.P., Rejtar, T., Moskovets, E., Ivanov,
A., Karger, B.L., "A Universal Denoising and
Peak Picking Algorithm for LC-MS Based on Matched
Filtration in the Chromatographic Time Domain",
Anal. Chem., 75(22), 6314-6326 (2003).
Ivanov, A., Zang, L., Karger, B.L., "Low Attomole
ESI-MS and MS/MS Analysis of Protein Digests Using
20-µm I.D. Polystyrene-Divinylbenzene Monolithic
Capillary Columns", Anal. Chem., 75(20),
5306-5316 (2003).
Ivanov, A., Horvath, C., Karger, B.L., " High-Efficiency
Peptide Analysis on MonolithicMulti-Mode Capillary
Columns: Pressure Assisted CEC/CE Coupled to UV
and ESI-MS", Electrophoresis, 24,
3663-3673 (2003).
Guttman, A., Karger, B.L., "Capillary Electrophoresis
and the Human Genome Project", Genomic/Proteomic
Tech., 3, 12-20, April/May (2003).
Karger, B.L. " Some Personal Words on the Career
of Stellan Hjerten", J. Chromatogr A.
1004, 7-8 (2003).
Moskovets, E., Karger, B.L. "Mass calibration
of MALDI-TOF MS Including Rise Time of the Delayed
Extraction Pulse", Rapid Commun. in Mass
Spec., 17, 229-237 (2003).
Professor
William Hancock
Hancock,
W.S. and Hincapie, M., "A Two Step Fractionation
Approach for Plasma Proteomics Using Immunodepletion
of Abundant Proteins and Multi-lectin Affinity Chromatography
(M-LAC) : Application to the Analysis of Obesity,
Diabetes and Hypertension, Dayarathna, MKD",
J. Sep. Science, (2008), in press.
Orazine, C.I., Hincapie, M., Hancock, W.S., Hattersley, M.,
and Hanke, J.A, "Proteomic Analysis of the
Plasma Glycoproteins of a MCF-7 Mouse Xenograft
: A Model System for the Detection of Tumor Markers",
J.Prot.Res., (2008), in press.
Lu, C., Murugesan, N., Macdonald, J.
A., Wu, S-L., Pachter, J., and Hancock, W.
S., "Analysis of Mouse Brain Microvascular
Endothelium Using Immuno-Laser Capture Microdissection
Coupled to a Hybrid LTQ-FT MS Proteomics Platform",
Electrophoresis (2008), in press.
Wu, S.-L., Gu, Y., Hanlon, D., Meyer, J., Linder,
J., Hancock, W.S., and Karger, B.L., "Proteomic
Analysis of High-Grade Dysplastic Cervical Cells
Obtained From ThinPrep® Slides Using Laser Capture
Microdissection and Mass Spectrometry", J
Proteome Res., 6, 4256-68 (2007).
Plavina, T., Wakeshull, E., Hancock, W.S., Hincapie, M.,
"Combination of Abundant Protein Depletion
and Multi-Lectin Affinity Chromatography (M-LAC)
for Plasma Protein Biomarker Discovery", J.
Proteome Res., 662-671 (2007).
Zheng,
X., Baker, H., and Hancock, W. S., "Analysis
of the Low Molecular Weight Serum Peptidome Using
Ultrafiltration and a Hybrid Ion Trap-Fourier Transform
Mass Spectrometer", J. Chromatogr.,
1120, 173-184 (2006).
Plymoth,
A, Yang, Z, Lofdahl, C. G, Ekberg-Jansson, A, Dahlback,
M,, Fehniger, T. E., Marko-Varga, G., Hancock, W.
S., "Rapid Proteome Analysis of Bronchoalveolar
Lavage Samples of Lifelong Smokers and Never-Smokers
by Micro-Scale Liquid Chromatography and Mass Spectrometry",
Clin. Chem., 52, 671-679 (2006).
Wang,
Y., Wu, S. L. and Hancock, W. S., "Approaches
to the Study of N-linked Glycoproteins in Human
Plasma Using Lectin Affinity Chromatography and
Nano-HPLC Coupled to Electrospray Linear Ion Trap
- Fourier Transform Mass Spectrometry (LTQ/FTMS)",
Glycobiology, 16, 514-523 (2006).
Wang,
Y., Wu, S .L. and Hancock, W. S., "Monitoring
of Glycoprotein Products in Cell Culture Lysates
Using Lectin Affinity Chromatography and Capillary-HPLC
Coupled to Electrospray Linear Ion Trap - Fourier
Transform Mass Spectrometry (LTQ/FTMS)", Biotechnology
Progress, 22, 873-880 (2006).
Zheng,
X., Wu, S. L., and Hancock, W. S., "Glycation
of Interferon-beta-1b and human serum albumin in
a lyophilized glucose formulation", Int.
J. Pharmaceutics, 322, 136-145 (2006).
Yang,
Z., Harris, L. E., Palmer-Toy, D. E. and Hancock,
W. S., "Characterization of Multiple Glycoprotein
Biomarker Candidates in Serum from Breast Cancer
Patients Using Multi-lectin Affinity Chromatography
(M-LAC)", Clin. Chem., 52, 1897-1905
(2006).
Wang,
Y., Dai, D., Sadee, W. and Hancock, W.S., "A
Pharmacoproteomics Study of the Cancer Cell Line
EKVX", Mol. Pharmaceutics, 5,
566-578 (2006).
Zheng,
X., Baker, H., Hancock, W. S., Fawaz, F., McCaman,
M. and Pungor, E., "Proteomic Analysis for
the Assessment of Different Lots of Fetal Bovine
Serum as a Raw Material for Cell Culture",
Biotechnology Progress, 5, 1294-1300
(2006).
Hancock,
W. S., Wang,Y., Yang, Y., and Gruia-Gray, J, "Multidimensional
Liquid Chromatography: A High-Resolution, Reroducible,
and Versatile Technique for Proteomic Analysis of
Complex Biological Samples, American Laboratory,
16-19 (2005).
Wang, ,Y.,Wu, S.-L. Hancock, W.S., Trala, R., Kessler,
M., Taylor, A.H., and Aon, J.C., "Proteomic Profiling
of Escherichia coli Proteins under High Cell Density
Fed-batch Cultivation with Overexpression of Phosphogluconolactonase",
Biotech. Progr., 5, 1401 - 1411 (2005).
Ping P, Vondriska T.M., Creighton C.J., Gandhi T,
Yang Z, Menon R, Kwon M.S., Cho S.Y., Drwal G, Kellmann
M, Peri S, Suresh S, Gronborg M, Molina H, Chaerkady
R, Rekha B, Shet A.S., Gerszten R.E., Wu H, Raftery
M, Wasinger V, Schulz-Knappe P, Hanash S.M., Paik
Y.K., Hancock W.S., States D.J., Omenn G.S., Pandey
A., "A functional annotation of subproteomes
in human plasma", Proteomics. 13 :3506-19
(2005).
Omenn GS, States DJ, Adamski M, Blackwell TW, Menon
R, Hermjakob H, Apweiler R, Haab BB, Simpson RJ, Eddes
JS, Kapp EA, Moritz RL, Chan DW, Rai AJ, Admon A,
Aebersold R, Eng J, Hancock WS, Hefta SA, Meyer H,
Paik YK, Yoo JS, Ping P, Pounds J, Adkins J, Qian
X, Wang R, Wasinger V, Wu CY, Zhao X, Zeng R, Archakov
A, Tsugita A, Beer I, Pandey A, Pisano M, Andrews
P, Tammen H, Speicher DW, Hanash SM, "Overview
of the HUPO Plasma Proteome Project: Results from
the pilot phase with 35 collaborating laboratories
and multiple analytical groups, generating a core
dataset of 3020 proteins and a publicly-available
database", Proteomics, 5(13) 3226-45
(2005).
Wu, S.-L, Kim, J.K., Hancock, W.S., and Karger, B.L.,"Extended
Range Proteomic Analysis (ERPA): A New and Sensitive
LC-MS Platform for High Sequence Coverage of Complex
Proteins with Extensive Posttranslational Modifications
- Comprehensive Analysis of Beta-Casein and Epidermal
Growth Factor Receptor (EGFR)", J.Proteome
Res., 4(4) 1155-1170 (2005).
Hancock, W.S., Wang,Y., Yang, Z., and Gruia-Gray,"Multidimensional
Liquid Chromatography: A High-Resolution, Reproducible,
and Versatile Technique for Proteomic Analysis of
Complex Biological Samples", American Laboratory,
16-19 (2005).
Yang, Z., Hancock, W.S., Richmond-Chew, T., Bonilla,
L., "A Study of Glycoproteins in Human Serum
and Plasma Reference Standards (HUPO) using Multi-Lectin
Affinity Chromatography Coupled with RPLC-MS/MS",
Proteomics, (13):3353-66.(2005).
Yang, Z.. and Hancock, W.S "Monitoring Glycosylation
Pattern Changes of Glycoproteins Using Multi-lectin
Affinity Columns", J. Chromatogr. A, 1070,
57-64 (2005).
Baker, H., Patel, V., Molinolo, A.A., Shillitoe, E.J.,
Ensley, J.F., Yoo, G.H., Meneses-Garcia, A., Myers,
J.N., El-Naggar, A.K., Silvio Gutkind, J. and Hancock,
W.S., "Proteome-Wide Analysis of Head and Neck Squamous
Cell Carcinomas Using Laser-Capture Microdissection
and Tandem Mass-Spectrometry", J. Proteome Res.,
41, 183-199 (2005).
Yang, Z-P. and Hancock, W.S. "Approach to the Comprehensive
Analysis of Glycoproteins Isolated from Human Serum
Using a Multi-lectin Affinity Column", J. Chromatogr.
A, 1053, 79-88 (2004).
Wang, Y., Hancock, W.S., Weber, G., Eckerskorn, C.
and Palmer-Toy, D., "Free Flow Electrophoresis Coupled
with Liquid Chromatography-Mass Spectrometry for a
Proteomic Study of the Human Cell Line (K562/CR3)",
J. Chromatogr. A, 1053, 269-278, (2004).
Wu, S.-L, Jardine, I., Hancock, W.S., and Karger,
B.L."A New and Sensitive On-Line Liquid Chromatography/Mass
Spectrometric Approach for Top-Down Protein Analysis:
The Comprehensive Analysis of Human Growth Hormone
in an E.coli Lysate Using a Hybrid Linear Ion
Trap/Fourier Transform Ion Cyclotron Resonance (FTICR)
Mass Spectrometer", Rapid Commun. Mass Spectrom.,
19, 2201-2207 (2004).
Zang, L., Palmer-Toy, D., Hancock, W.S., Sgroi, D.
and Karger, B, "Proteomic Analysis of Ductal Carcinoma
of the Breast Using Laser Capture Microdissection,
LC-MS and 16O/18O Isotopic Labeling, J.Proteome Res.,
3, 604-612 (2004).
Wu, S.-L., Choudhary, G., Ramström, M., Bergquist,
J. and Hancock, W.S., "An Evaluation of Shotgun
Sequencing for Proteomic Analysis of Human Plasma
Using HPLC Coupled with Either Ion Trap Or Fourier
Transform Mass Spectrometry", J. Proteome
Res., 2 383-393 (2003).
Stanley, R. and Hancock, W.S., "Bioinformatics
in the Clinic: Challenges and Opportunities for Improved
Trials and Clinical Care", Genomic/Proteomic
Technology, 3, 36 (2003).
Wu, S.-L., Shieh, P. Hancock, W.S., Kunitaki, S.T.,
and Goodrich, G.G., "A Proteomic Approach to
the Detection of Novel Marker Proteins in a Breast
Cancer Cell Line (SKBR-3)", Proteomics,
3, 1037-46 (2003).
Choudhary, G., Wu, S.-L., Shieh, P., and Hancock,
W.S., "Multiple Enzymatic Digestion for Enhanced
Sequence Coverage of Proteins in Complex Proteomic
Mixtures using Capillary LC with Ion Trap MS/MS",
J. Proteome Res., 2, 59-67 (2003).
Professor John Engen
Weis, D. D., Kass, I. J. and Engen, J. R., "Semi-automated
analysis of hydrogen exchange mass spectra using
HX-Express", J. Am. Soc. Mass Spectrom.,
17(12), 1700-1703 (2006).
Weis,
D. D., Kjellen, P., Sefton, B. M., and Engen, J.
R., "Altered dynamics in Lck SH3 upon binding
to the LBD1 domain of Herpesvirus saimiri Tip",
Protein Sci., 15(10), 2402-2410 (2006).
Meyn,
M. A., Wilson, M. B., Abdi, F. A., Fahey, N., Schiavone,
A. P., Wu, J., Hochrein, J. M., Engen, J. R., and
Smithgall, T. E., "Src-family kinases phosphorylate
Bcr-Abl SH3-SH2 region and modulate Bcr-Abl transforming
activity", J. Biol. Chem., 281(41),
30907-16 (2006).
Hochrein,
J. M., Wales, T. E., Lerner, E. C., Schiavone, A.
P., Smithgall, T. E. and Engen, J. R., "Conformational
features of the full-length HIV and SIV Nef proteins
by mass spectrometry", Biochemistry,
45(25), 7733-7739 (2006).
Wu,
Y., Hobbins, W. B. and Engen, J. R., "Ultra
performance liquid chromatography (UPLC) further
improves hydrogen/deuterium exchange mass spectrometry",
J. Am. Soc. Mass Spectrom. 17(2), 163-167
(2006).
Wales,
T. E. and Engen, J. R., "Hydrogen exchange
mass spectrometry for the analysis of protein dynamics",
Mass Spectrom. Rev., 25(1), 158-170 (2006).
Professor Roger Giese
Yong,
L. C., Schulte, P. A., Kao, C-K., Giese, R. W., Boeniger,
M. F., Strauss, G. H.S., Petersen, M. R., Wiencke,
J. K., "DNA Adducts in Granulocytes of Hospital
Workers Exposed to Ethylene Oxide", Am. J.
Ind. Med., 50, 293-302.09 (2007).
Shao, G., Kautz, R., Peng, S., Cui, G., Giese, R.
W., "Calibration by NMR for quantitative analysis:
p-Toluenesulfonic acid as a reference substance",
J. Chromatogr. A, 1138, 305-308 (2007).
Murugaiah, V., Naim, A., Peng, S., Cui, G., Giese,
R. W., "4-(4'-Methyltetrafluorophenyl)-2,3,5,6-tetrafluorobenzyl
bromide: A new electrophoric derivatizing reagent",
J. Chromatogr113. A, 4, 338-340 (2006).
Shimelis,
O., Giese, R. W., "Nuclease P1 digestion/high-performance
liquid chromatography, a practical method for DNA
quantitation", J. Chromatogr. A., 1117,
132-136 (2006).
Pashkova, A., Chen, H., Rejtar, T., Zang, X., Giese,
R., Andreev, V., Moskovets, E. Karger, Barry L.
"Coumarin Tags for Improved Analysis of Peptides
by MALDI-TOF MS and MS/MS. II. Alexa Fluor 350 Tag
for Increased Peptide and Protein Identification
by LC-MALDI-TOF/TOF MS", Anal. Chem.,
4(1), 129-135 (2005).
Kao, C-Y., Giese, R.W., Measurement of N7(2-Hydroxyethyl)guanine
in Human DNA by Gas Chromatography Electron Capture
Mass Spectrometry, Chem. Res. Toxicol, 18,
70-75 (2005).
Guttman, A., Giese, R. W. eds. Bioanalytical Chemistry:
Perspectives and Recent Advances, J. Chromatogr.
A, 1053 (2004).
Shimeilis, O., Zhou, X., Li, G., Giese, R. W. Phenolic
extraction of DNA from mammalian tissues and conversion
to deoxyribonucleoside-5'-monophosphates devoid
of ribonucleotides, J. Chromatogr. A., 1053,
143-149 (2004).
Shao, G., Giese, R. W. Trace Detection of Glycolic
Acid by Electrophore Labeling Gas Chromatography-Electron
Capture Mass Spectrometry, Anal. Chem., 76,
3049-3054 (2004).
Li, G., Shimelis, O., Zhou, X., Giese, R. W. Scaled-Down
Nuclease P1 for Scaled-Up DNA Digestion, BioTechniques
34, 908-909 (2003).
Li, G., Gao, J., Zhou, X., Shimelis, O., Giese,
R. W. Handling and detection of 25 amol of near-infrared
dye deoxynucleotide conjugates by capillary electrophoresis
with laser-induced fluorescence detection, J.
Chromatogr. A, 1004, 47-50 (2003).
Giese, Roger W. Measurement of endogenous estrogens:
analytical challenges and recent advances, J.
Chromatogr. A, 1000, 401-412 (2003).
Professor Graham Jones
Zhang, N., Lin, Y., Xiao, Z., Jones, G. B., and
Goldberg, I. H., "Solution Structure of a Designed
Spirocyclic Helical Ligand Binding at a Two-Base
Bulge Site in DNA", Biochemistry, 46,
561 (2007).
Jones, G. B., Lin, Y., Xiao, Z., Kappen, L., and
Goldberg, I. H., "Molecular Probes of DNA Bulges:
Functional Assay and Spectroscopic Analysis",
Bioorg Med Chem., 15, 784 (2007).
Xiao, Z., Zhang, N., Lin, Y. Jones, G.B., and
Goldberg, I. H., "Spirocyclic Helical Compounds
as Binding Agents for Bulged RNA, Including HIV-2
TAR", Chem Commun., 4431 (2006).
Swamy, N., Purohit, A., Fernandez-Gacio, A., Jones,
G. B., and Ray, R., "Nuclear Estrogen Recepter
Targeted Photodynamic Therapy: Selective Uptake
and Killing of MCF-7 Breast Cancer Cells by a C17a-Alkynylestradiol-Porphyrin
Conjugate", Journal of Cellular Biochemistry,
99, 966 (2006).
Torregrossa, J., Bubley, G. J., and Jones G. B.,"Microwave
Expedited Synthesis of 5-Aminocamptothecin Analogs:
Inhimbitors of Hypoxia Inducible Factor HIF-1a",
Bioorganic & Medicinal Chemistry Letters.,
16, 6082-6085 (2006).
Jones,
G. B., Crasto, C. F., Mathews, J. E., Xie, L., Mitchell,
M. O., El-Shafey, A., D'Amico, A. V., and Bubley,
G. J., "An Image contrast agent selectively
activated by prostate specific antigen (PSA)",
Bioorganic and Medicinal Chemistry, 14,
418 (2006).
Shenoy, D., Fu, W., Crasto, C., Sridhar, S., Amiji,
M., Li, J., Weinberg, J., Jones, G., "Functionalized
heterobifunctional poly[ethylene glycol] templates
for use in cellular trafficking and imaging studies",
Int. Journal of Nanomedicine, 1, 51
(2006).
Xie, L. and Jones, G.B., "Exploiting Shielding
Interactions: A Highly Selective Chiral Auxiliary
derived from a Biogenic Building Block", Tetrahedron
Lett. 46, 3579 (2005).
Li, J., Crasto, C. F., Weinberg, J., Amiji, M.,
Shenoy, D., Sridhar, S., and Jones, G. B., "An
Approach to Heterobifunctional Poly(ethyleneglycol)
Bioconjugates", Bioorg. Med. Chem. Lett.
, 15, 5558 (2005).
Fouad, F. S., Wright, J. M., Plourde, G., II., Purohit,
A. D., Wyatt, J. K.; El-Shafey, A., Hynd, G., Crasto,
C. F., Lin, Y., Jones, G. B., "Synthesis and
Protein Degradation Capacity of Photoactivated Enediynes",
.J. Org. Chem.; 70, 9789 (2005).
Lin, Y., Jones, G. B., Hwang, G.-S., Kappen, L.,
Goldberg, I. H., "Convenient Synthesis of NCS-Chromophore
Metabolite Isosteres: Binding Agents for Bulged
DNA Microenvironments", Org. Lett.,
7, 71 (2005).
Oh, W. K., Kantoff, P. W., Weinberg, V., Jones,
G., Rini, B. I., Derynck, Robert Bok, Matthew R.
Smith, Glenn J. Bubley, Robert T. Rosen, M. K.,
DiPaola, R. S., Small, E. J., "A Prospective,
Multicenter, Randomized Phase II Trial of the Herbal
Supplement, PC-SPES, and Diethylstilbestrol in Patients
with Androgen-Independent Prostate Cancer",
, J. Clin. Oncol., 22, 3705 (2004).
Oh, W. K., Kantoff, P. W., Weinberg, V., Jones,
G., Rini, B. I., Derynck, Robert Bok, Matthew R.
Smith, Glenn J. Bubley, Robert T. Rosen, M. K.,
DiPaola, R. S., Small, E. J., "A Prospective,
Multicenter, Randomized Phase II Trial of the Herbal
Supplement, PC-SPES, and Diethylstilbestrol in Patients
with Androgen-Independent Prostate Cancer",
, J. Clin. Oncol., 22, 3705 (2004).
Hwang, G.-S., Jones, G. B., and Goldberg, I. H.,
"Sterochemical Control of Small Molecule Binding
to Bulged DNA: Comparison of Structures of Spirocyclic
Enantiomer-Bulged DNA Complexes", Biochemistry,
43, 641 (2004).
Jones, G. B., and Fouad, F. S., "Designed Enediyne
Antitumor Agents", Frontiers in Medicinal
Chemistry, 1, 189 (2004).
Crasto, C. F., and Jones, G. B., "A Practical
method for preparation of ?-glycosides of N-Acetylglucosamine",
Tetrahedron Lett , 45, 4891 (2004).
.
Jones, G. B., Xie, L., El-Shafey, A., Crasto, C.
F., Bubley, G. J., and D'Amico, A. V., "Image
contrast agents activated by prostate specific antigen
(PSA)", Bioorg. Med. Chem. Lett., 14,
3081 (2004).
Fouad, F. S., Xie, Z., Goldberg, I. H., and Jones,
G. B., "Preparation of Alkylation Agents for
Bulged DNA Microenvironments", Bioorg. Med.
Chem. Lett., 14, 3337 (2004).
Fouad, F. S., Crasto, C. F., Lin, Y., and Jones,
G.B.,"Photoactivated Enediynes: Targeted Chimeras
which undergo PhotoBergman Cyclization", Tetrahedron
Lett, 45, 7753 (2004).
Jones, G.B., Russell, K.C., "The Photo Bergman
Cycloaromatization of Enediynes", CRC Handbook
of Photochemistry, 29-1 (2003).
Kappen, L.S., Xi, Z., Jones, G.B., Goldberg, I.H.,
"Stimulation of DNA Strand Slippage Synthesis
by a Bulge Binding Synthetic Agent", Biochemistry,
42, 2166 (2003).
Hu, Y., Dehal, S. S., Hynd, G., Jones, G. B, .Kupfer,
D., "CYP2D6 - catalyzes tamoxifen aromatic
hydroxylation with an NIH-Shift", Xenobiotica,
33, 141 (2003).
Hwang, G-S, Jones, G. B., Goldberg, I. H., "Solution
structure of a wedge-shaped synthetic molecule at
a two-base bulge site in DNA", Biochemistry,
42, 8472 (2003).
Professor Bill Giessen
B. C. Giessen, K. Xu, J. Chen, J. Yao, Z. Zhao,
T. Yu, and K. Dadkhah, "Short Time Segment
Price Forecasts Using Spline Fit Interactions Which
Simulate Cycle Analysis", in: "Practical
Fruits of Econophysics, Business Models in the 21st
Century - Risk Management and Expectations for Econophysics",
Proc. 3rd Nikkei Econophysics Symp., H. Takayasu,
ed., Springer, Tokyo (2006) p. 111.
B.C. Giessen, Z. Zhao, J. Chen, J. Yao, K. Xu, T.
Yu, and K. Dadkhah, "Successful Price Cycle
Forecasts in S&P Futures Using "TFX",
a Family of Pattern Recognition Algorithms Based
on the KNN Method", in: "Practical Fruits
of Econophysics, Business Models in the 21st Century
- Risk Management and Expectations for Econophysics",
Proc. 3rd Nikkei Econophysics Symp., H. Takayasu,
ed., Springer, Tokyo (2006) p. 116.
J. Yao, J. Chen, K. Xu, Z. Zhao, T. Yu, B. C. Giessen,
and K. Dadkhah, "Market Cycle Turning Point
Forecasts by an Interactively Learning Algorithm
as a Trading Tool for S&P Futures", in:
"Practical Fruits of Econophysics, Business
Models in the 21st Century - Risk Management and
Expectations for Econophysics", Proc. 3rd Nikkei
Econophysics Symp., H. Takayasu, ed., Springer,
Tokyo (2006) p. 131.
B.C. Giessen and R. Hidalgo, "Alloys",
Chapter in "Encyclopedia of Inorganic Chemistry,
2nd Ed.", Wiley (2005).
S-Q. Wang, B. C. Giessen and R. S. Markiewicz, "Phase
equilibrium in Y-Ba-Cu-O system", Mater. Lett.,
57 (2003) 2110-2115.
S-Q. Wang, R. A. Bigelow, R. S. Markiewicz and B.
C. Giessen, "Magnetic-alignment properties
of REBa2Cu4O8 (RE=Ho,
Er)", Mater. Lett., 57 (2003) 3449-3454. S-Q.
Wang, R. S. Markiewicz and B. C. Giessen, "Phase
equilibrium in Eu-Ba-Cu-O system", J. Cryst.
Growth, 254 (2003) 279-284.
Professor
Paul Vouros
Liao, Q., Chiu, N. H. L., Shen, C., and Vouros,
P., “Investigation of the Enzymatic Behavior
of Benzonase /Alkaline Phosphatase in the Digestion
of DNA and DNA Adducts by ESI-LC/MS”, Anal.
Chem., 79, 1907-1917 (2007).
Andrews, C.L., Li, F., Yu, C.P., Yang, E., and Vouros,
P., “Incorporation of a Nanosplitter Interface
into an LC-RD-MS System to Facilitate Drug Metabolism
Studies”, Journal of Mass Spectrom.
41, 43-49 (2006).
Levin,
D.S., Vouros, P., Miller, R.A., Nazarov, E.G., Morris,
J.C., “Characterization of gas phase interactions
utilizing a novel nanoelectrospray ionization -
differential mobility - mass spectrometer (nanoESI-DMS-MS)
system”, Anal. Chem., 78, 96-106
(2006).
Ricicki,
E.M., Andrews, C.L., Schiavo, S., and Vouros, P.,
“Analysis of DNA Adducts”, in Encyclopedia
of Mass Spectrometry, Volume 3, Biological Applications
Part B: Carbohydrates, Nucleic Acids and other Biological
Compounds, Series editors: Caprioli, R. and Gross,
M., Elsevier Ltd., Oxford, 2006, pp. 61-85.
Simionato,A.V.C.
, de Souza, G.D., Rodrigues-Filho,E., Glick, J.,
Vouros, P., and Carrilho, E., “Tandem mass
spectrometry of coprogen and deferoxamine hydroxamic
siderophores”, Rapid Commun. Mass Spectrom.,
20, 193-199 (2006).
Levin,
D.S., Miller, R.A., Nazarov, E.G. and Vouros, P.,
“Rapid separation and quantitative analysis
of peptides using a new nanoelectrospray –
differential mobility spectrometer– mass spectrometer
system” Anal. Chem., 78, 5443-5452
(2006).
Ricicki,
E.M., Luo, W., Zarbl, H., and Vouros, P., “Quantification
of N-(deoxyguanosin-8-yl)-4-aminobiphenyl Adducts
in Human Lymphoblastoid TK6 Cells Dosed with N-hydroxy-4-aminobiphenyl
and their Relationship to Mutation, Toxicity, and
Gene Expression Profiling”, Anal. Chem.,
78, 6422-6432 (2006).
Williams,
J., Pandarinathan, L., Wood, J.A., Vouros, P, Makriyannis,
A., “Endocannabinoid Metabolomics: A Novel
Liquid Chromatography–Mass Spectrometry Reagent
for Fatty Acid Analysis", AAPS Journal.
2006; 8(4): E655-E660. DOI: 10.1208/aapsj080474.
Brown,
A. J., Ritter, C.S., Weiskopf, A.S., Vouros, P,
Sasso, G. J., Uskokovic. M.R., Wang, G, Reddy, G.
S. “Isolation and identification of 1alpha-hydroxy-3-epi-vitamin
D3, a potent suppressor of parathyroid hormone secretion.”,
J. Cell. Biochem. 96(3) :569-78 (2005).
Ricicki, E.M., Andrews, C.L., Schiavo, S., and Vouros,
P., “Analysis of DNA Adducts”, in Encyclopedia
of Mass Spectrometry, Volume 3, Biological Applications
Part B: Carbohydrates, Nucleic Acids and other Biological
Compounds, Series editors: Caprioli, R. and Gross,
M., Elsevier Ltd., Oxford, 2005, 61-85.
Rozen, S., Cudcowicz, M.E., Bogdanov, M., Matson,
W.R., Kristal, B. S., Beecher, C., Harrison, S.,
Vouros, P., Flarakos, J., Vigneau-Callahan, K.,
Matson, T.R., Newhall, K.M., Beal, M.F., Brown,
R.H. and Kaddurah-Daouk, R., "Metabolomic analysis
and signatures in motor neuron disease", Metabolomics,
1, 101-108 (2005).
Argoti, D., Liang, L., Conteh, A., Chen, L., Bershas,
D., Yu, C-P., Vouros, P., Yang, E. “Cyanide
Trapping of Iminium Ion Reactive Intermediates Followed
by Detection and Structure Identification Using
Liquid Chromatography-Mass Spectrometry (LC/MS)”,
Chem. Res. Toxicol., 18, 1537-1544
(2005).
Luo, W., Fan, W., Xie, H., Jing, L.; Zhao, L.P.,
Ricicki, E., Vouros, P. and Zarbl, H., "Phenotypic
Anchoring of Global Gene Expression Profiles Induced
by N-hydroxy-4-acetylaminobiphenyl and Benzo(a)pyrene
Diol Epoxide Reveals Correlations between Expression
Profiles and Mechanism of Toxicity", Chem.
Res. Toxicol. 18, 619-629 (2005).
Flarakos, J., Xiong, W., Glick, J., and Vouros,
P. "A Novel Deoxynucleotide Derivatization
Methodology for Improving LC-ESI-MS Detection",
Anal. Chem., 77, 2373-2380 (2005).
Ricicki, E.M., Soglia, J.R., Teitel, C., Kane, R.,
Kadlubar, F. and Vouros, P., "Detection and
Quantification of N-(deoxyguanosine-8-yl)-4-aminobiphenyl
Adducts in Human Pancreas Tissue Using Capillary
Liquid Chromatography-Microelectrospray Mass Spectrometry",
Chem. Res. Toxicol. 18, 692-699, (2005).
Flarakos, J., Morand, K. and Vouros, P., "High
Throughput Solution-Based Medicinal Library Screening
against Human Serum Albumin", Anal. Chem.,
77, 1345-1353 (2005).
Astecker, N., Bobrovnikova, E.A., Omdahl, J.L.,
Gennaro, L.A., Vouros, P., Schuster, I., S., Ishizuka,
Wang, G., Reddy, G.S., “C-25 Hydroxylation of the
Antipsoriatic Drug 1á,24(R)-Dihydroxyvitamin D3
Is Catalyzed by 25-Hydroxyvitamin D3-24-Hydroxylase
(CYP24A1): Metabolism Studies with Human Keratinocytes
and Recombinant CYP24A1”, Archives Biochem. Biophys.,
431, 261-270 (2004).
Andrews, C.L., Yu, C-P., Yang, E., and Vouros, P.,
“Improved liquid chromatography–mass spectrometry
performance in quantitative analysis using a nanosplitter
interface”, Journal of Chromatography A,
1053, 151-159 (2004).
Andrews, C.L., Harsch, A. and Vouros, P., "Analysis
of the in vitro Digestion of Modified DNA to Oligonucleotides
by LC-MS and LC-MS/MS", Intern. J. Mass Spectrom.,
231, (2-3), 169-177 (2004).
Gennaro, L.A., Vadhanam, M., Gupta, R.C. and Vouros,
P., "Selective Digestion and Novel Cleanup Techniques
for Detection of Benzo[a]pyrene Diol Epoxide-DNA
Adducts by CE/MS", Rapid Commun. Mass Spectrom.,
18, 1541-1547 (2004).
Flarakos , J., Luo, W., Aman, M., Svinarov, D.,
Gerber, N., and Vouros, P., "Quantification of Risperidone
and 9-Hydroxyrisperidone in Plasma and Saliva from
Adult and Pediatric Patients by Liquid Chromatography/
Mass Spectrometry", J. Chromatogr. A, 1026,
175-181 (2004).
Turesky, R.J. and Vouros, P., "Formation and
Analysis of Heterocyclic Aromatic Amine- DNA Adducts
in vitro and in vivo", J.
Chromatogr. B, 802 (1) 155-166
(2004).
Marzilli, L.A., Fay, L. B., Dionisi, F. and Vouros,
P., "Structural Characterization of Triacylglycerols
Using Electrospray Ionization-MSn Ion Trap MS",
J. Assoc. Off. Anal. Chem., 80, 195-202
(2003)
Gennaro, L.A., Harvey, D.J. and Vouros, P., "Reversed-
phase ion-pairing liquid chromatography/ion trap
mass spectrometry for the analysis of negatively
charged, derivatized glycans", Rapid Commun.
Mass Spectrom., 17, 1528-1534 (2003).
Professor
Zhaohui Sunny Zhou
Dorgan,
K.M., Wooderchak, W.L, Wynn, D.P., Karschner, E.L.,
Alfaro, J.F., Cui, Y., Zhou, Z.S., Hevel, J.M.,
"An enzyme-coupled continuous spectrophotometric
assay for S-adenosylmethionine-dependent methyltransferases",
Anal Biochem., Mar 15;350(2):249-55 (2006).
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