Cameron S. Brandt, Myriam Baratin, Eugene C. Yi,
Jacob Kennedy, Zeren Gao, Brian Fox, Betty Haldeman, Craig D. Ostrander,
Tomonori Kaifu, Christian Chabannon, Alessandro Moretta, Robert West, WenFeng
Xu, Eric Vivier, and Steven D. Levin “The B7 family
member B7-H6 is a tumor cell ligand for the activating natural killer cell
receptor NKp30 in humans” The
Journal of Experimental Medicine. (2009) Jul 6;206(7):1495-503. PMID:
19528259
Eugene
C. Yi* and
Jacob Kennedy Book Chapter “Use
of gas-phase-fractionation to increase protein identifications: Application to
the peroxisome” Organelle Proteomics, Humana Press, (2008), 217-228. PMID: 18370021
Ming-Chang
Chiang, Chiun-Gung Juo, Hao-Hung Chang, Hui-Mei Chen, Eugene C. Yi, Yijuang Chern
“Systematic Uncovering of Multiple Pathways underlying the Pathology of
Huntington’s Disease by Acid-cleavable Isotope-coded affinity tag Approach” Mol Cell Proteomics. (2007)
May;6(5):781-97. PMID: 17272267
D.
R. Goodlett, Eugene C. Yi
and P. Mottay “Preparation and use of an integrated microcapillary HPLC column
and electrospray ionization device for proteomic analysis” CSH Protoc. (2007) May 1;2007:pdb.prot4617. PMID: 21357072
Pei Wang, Marc
Coram, Hua Tang, Matthew P Fitzgibbon, Hui Zhang, Eugene
C. Yi, Ruedi Aebersold , Martin
McIntosh “A statistical method for chromatographic
alignment of LC-MS data.” Biostatistics.
(2007) Apr;8(2):357-67. PMID: 16880200
Hui Zhang, Paul Loriaux, Jimmy Eng, David Campbell,
Andrew Keller, Pat Moss, Richard Bonneau, Ning Zhang, Yong, Zhou, Bernd
Wollscheid, Kelly Cooke, Eugene C. Yi, Hookeun Lee, Elaine R. Peskind, Jing Zhang,
Richard D. Smith, and Ruedi
Aebersold “UniPep, a database for human N-linked glycosites: A Resource
for Biomarker Discovery” Genome Biol.
(2006) Aug 10;7(8):R73. PMID: 16901351
Ru Chen, Sheng
Pan, Eugene C. Yi, Samuel Donohoe, Mary P Bronner, John D Potter, David R Goodlett, Ruedi Aebersold, Teresa A Brentnall “Quantitative proteomic profiling of pancreatic cancer juice” Proteomics. (2006) Jul;6(13):3871-9.
PMID: 16739137
Rueichi
R Gan, Eugene C. Yi, Yulun Chiu, Hookeun Lee, Yu-Chieh P Kao, Timothy H
Wu, Ruedi Aebersold, David R Goodlett, Wailap V Ng “ Proteome analysis of
Halobacterium sp. NRC-1 facilitated by the biomodules analysis tool BMSorter” Mol Cell Proteomics. (2006)
Jun;5(6):987-97. PMID: 16497792
Sharon
Chen, Eric Deutsch, Eugene C. Yi, Xiao-Jun Li, David
Goodlett, Ruedi Aebersold “Improving
Mass and Liquid Chromatography Based Identification of Proteins Using Bayesian
Scoring” J Proteome Res.
(2005) Dec 12;4(6):2174-2184. PMID: 16335964
David
J Dilworth, Alan J Tackett, Richard S Rogers, Eugene C. Yi, Rowan H Christmas, Jennifer J Smith, Andrew F
Siegel, Brian T Chait, Richard W Wozniak, John D Aitchison “The mobile nucleoporin Nup2p and
chromatin-bound Prp20p function in endogenous NPC-mediated transcriptional
control” J Cell Biol. (2005)
Dec ;019;171(6):955-65. PMID: 16365162
Ru
Chen, Eugene C. Yi, Samuel Donohoe, Sheng Pan, Jimmy Eng, Kelly
Cooke, David A Crispin, Zhaoli Lane, David R Goodlett, Mary P Bronner, Ruedi
Aebersold, Teresa A Brentnall “Pancreatic
cancer proteome: the proteins that underlie invasion, metastasis, and immunologic
escape” Gastroenterology.
(2005) Oct ;129(4):1187-97. PMID: 16230073
Eric W Deutsch, Jimmy K Eng, Hui Zhang, Nichole L
King, Alexey I Nesvizhskii, Biaoyang Lin, Hookeun Lee, Eugene C. Yi, Reto Ossola,
Ruedi Aebersold “Human Plasma Peptide Atlas” Proteomics. (2005) Aug ;5(13):03497-500.
Xiao-jun
Li, Eugene C. Yi, Christopher J Kemp, Hui Zhang, Ruedi Aebersold “A software suite for the generation and
comparison of peptide arrays from sets of data collected by liquid
chromatography-mass spectrometry” Mol
Cell Proteomics. (2005) Sep ;4(9):1328-40. PMID: 16048906
Kevin
D Welch, Bo Wen, David R Goodlett, Eugene C. Yi, Hookeun Lee, Timothy P Reilly, Sidney D Nelson,
Lance R Pohl “Proteomic identification
of potential susceptibility factors in drug-induced liver disease” Chem Res Toxicol. (2005) Jun
;18(6):924-33. PMID: 15962927
Biaoyang Lin, James T White, Wei Lu, Tao Xie,
Angelita G Utleg, Xiaowei Yan, Eugene C. Yi, Paul
Shannon, Irina Khrebtukova, Paul H Lange, David R Goodlett, Daixing Zhou,
Thomas J Vasicek, Leroy Hood “Evidence for the presence of disease-perturbed
networks in prostate cancer cells by genomic and proteomic analyses: a systems
approach to disease” Cancer Res.
(2005) Apr 15;65(8):3081-91. PMID: 15833837
Yaroslav
Sydorskyy, David J Dilworth, Brendan Halloran, Eugene C. Yi, Taras Makhnevych, Richard W Wozniak, John D
Aitchison “Nop53p is a novel nucleolar
60S ribosomal subunit biogenesis protein” Biochem J. (2005) Jun 15;388(Pt3 ):819-26. PMID: 15686447
Eugene C. Yi*, Xiao-Jun Li, Kelly Cooke, Hookeun Lee, Brian
Raught, Andrew Page, Victoria Aneliunas, Phil Hieter, David R Goodlett, Ruedi
Aebersold “Increased
quantitative proteome coverage with (13)C/(12)C-based, acid-cleavable
isotope-coded affinity tag reagent and modified data acquisition scheme”
Proteomics. (2005) Feb ;5(2):380-7.
PMID: 15648049
Frank
Desiere, Eric W Deutsch, Alexey I Nesvizhskii, Parag Mallick, Nichole L King,
Jimmy K Eng, Alan Aderem, Rose Boyle, Erich Brunner, Samuel Donohoe, Nelson
Fausto, Ernst Hafen, Lee Hood, Michael G Katze, Kathleen A Kennedy, Floyd
Kregenow, Hookeun Lee, Biaoyang Lin, Dan Martin, Jeffrey A Ranish, David J
Rawlings, Lawrence E Samelson, Yuzuru Shiio, Julian D Watts, Bernd Wollscheid,
Michael E Wright, Wei Yan, Lihong Yang, Eugene C. Yi, Hui Zhang, Ruedi Aebersold “Integration with the human genome of peptide
sequences obtained by high-throughput mass spectrometry” Genome Biol. (2005) ;6(1):R9. PMID:
15642101
Hui
Zhang, Eugene C. Yi, Xiao-jun Li, Parag Mallick, Karen S
Kelly-Spratt, Christophe D Masselon, David G Camp 2nd, Richard D Smith,
Christopher J Kemp, Ruedi Aebersold “High
throughput quantitative analysis of serum proteins using glycopeptide capture
and liquid chromatography mass spectrometry” Mol Cell Proteomics. (2005) Feb ;4(2):144-55. PMID: 15608340
Jing
Zhang, David R Goodlett, Elaine R Peskind, Joseph F Quinn, Yong Zhou, Qin Wang,
Catherine Pan, Eugene C. Yi, Jimmy Eng, Ruedi H
Aebersold, Thomas J Montine “Quantitative
proteomic analysis of age-related changes in human cerebrospinal fluid” Neurobiol Aging. (2005) Feb
;26(2):207-27. PMID: 15582749
Jing
Zhang, Dave R Goodlett, Joseph F Quinn, Elaine Peskind, Jeffrey A Kaye, Yong
Zhou, Catherine Pan, Eugene C. Yi, Jimmy Eng, Qin Wang,
Ruedi H Aebersold, Thomas J Montine “Quantitative
proteomics of cerebrospinal fluid from patients with Alzheimer disease” J Alzheimers Dis. (2005) Apr ;7(2):125-33;
discussion 173-80. PMID: 15851850
D.
B. Martin, D. R. Gifford, M. E. Wright, A. Keller, Eugene C. Yi, D. R. Goodlett, R. Aebersold, P. S. Nelson
“Quantitative Proteomic Analysis of Proteins Released by Neoplastic Prostate
Epithelium” Cancer Res. (2004) Jan;
64(1), 347-355. PMID: 14729644
Marcello
Marelli, Jennifer J Smith, Sunhee Jung, Eugene C. Yi, Alexey I Nesvizhskii, Rowan H Christmas, Ramsey A
Saleem, Yuen Yi C Tam, Andrei Fagarasanu, David R Goodlett, Ruedi Aebersold,
Richard A Rachubinski, John D Aitchison “Quantitative mass spectrometry reveals a role for the GTPase Rho1p in
actin organization on the peroxisome membrane” J Cell Biol. (2004) Dec 20;167(6):1099-112. PMID: 15596542
Wei-Chun
Kao, Yet-Ran Chen, Eugene C. Yi, Hookeun Lee, Qiang
Tian, Keh-Ming Wu, Shih-Feng Tsai, Steve S-F Yu, Yu-Ju Chen, Ruedi Aebersold,
Sunney I Chan “Quantitative Proteomic Analysis of Metabolic Regulation by
Copper Ions in Methylococcus capsulatus (Bath)” J Biol Chem. (2004) Dec 3;279(49):51554-60. PMID: 15385566
Bernd
Wollscheid, Priska D von Haller, Eugene
C. Yi, Samuel Donohoe, Kelly Vaughn, Andrew Keller, Alexey I Nesvizhskii,
Jimmy Eng, Xiao-jun Li, David R Goodlett, Ruedi Aebersold, Julian D Watts
“Lipid raft proteins and their identification in T lymphocytes” Subcell Biochem. (2004) ;37:121-52.
PMID: 15376619
Wei
Yan, Hookeun Lee, Eugene C. Yi, David Reiss, Paul
Shannon, Bartlomiej K Kwieciszewski, Carlos Coito, Xiao-jun Li, Andrew Keller,
Jimmy Eng, Timothy Galitski, David R Goodlett, Ruedi Aebersold, Michael G Katze
“System-based proteomic analysis of the
interferon response in human liver cells” Genome Biol. (2004) ;5:R54. PMID: 15287976
Qiang
Tian, Serguel B. Stepaniants, Mao Mao, Lee Weng, Megan C. Feeham, Michelle J
Doyle, Eugene C. Yi, Hongyue Dai, Vesteinn Thorsson, Jimmy Eng, David
Goodlett, Joel P Berger, Bert Gunter, Peter S Linseley, Roland B Stoughton,
Ruedi Aebersold, Steven J Collins, William A Hanlon, Leroy E Hood “Integrated
genomic and proteomic analyses of gene expression in Mammalian cells” Mol Cell Proteomics. (2004) Oct
;3(10):960-9.
Xiao-Jun
Li, Patrick G A Pedrioli, Jimmy Eng, Dan Martin, Eugene C. Yi, Hookeun Lee, Ruedi Aebersold “A tool to visualize and evaluate data
obtained by liquid chromatography-electrospray ionization-mass spectrometry” Anal Chem. (2004) Jul 1;76(36):3856-60.
PMID: 15228367
Jeffrey
A Ranish, Steven Hahn, Yu Lu, Eugene C. Yi, Xiao-Jun Li, Jimmy
Eng, Ruedi Aebersold “Identification of
TFB5, a new component of general transcription and DNA repair factor IIH” Nat Genet. (2004) Jul ;36(7):707-13.
PMID: 15220919
Hookeun
Lee, Eugene C. Yi, Bo Wen, Timothy P Reily, Lance Pohl, Sidney
Nelson, Ruedi Aebersold, David R Goodlett “Optimization of reversed-phase microcapillary liquid chromatography for
quantitative proteomics” J
Chromatogr B Analyt Technol Biomed Life Sci. (2004) Apr 15;803(1):101-10.
PMID: 15026003
Eugene C. Yi*, K. Cooke, H. Zhang, D. R. Goodlett, R.
Aebersold Book Chapter “Quantitative Analysis of Proteomes and Subproteoms by Isotope
Coded Affinity Tag (ICAT) and Solid-Phase Glycoprotein Capture” Methods in Molecular Biology/ Methods in
Molecular Medicine, Humana Press, (2004) Feb;Chapter 23:Unit 23.2
Anthony
P Fejes, Eugene C. Yi, David R Goodlett, J
Thomas Beatty “Shotgun proteomic
analysis of a chromatophore-enriched preparation from the purple phototrophic
bacterium Rhodopseudomonas palustris” Photosynth Res. (2003) ;78(3):195-203. PMID: 16245051
D.
R. Goodlett and Eugene C. Yi*,
Review article: “Stable Isotope Labeling and Mass Spectrometry as a Means to
Determine Differences in Protein Expression” Trends in Analytical Chemistry (2003), 22 (5), 282-290.
Eugene
Kolker, Samuel Purvine, Michael Y Galperin, Serg Stolyar, David R Goodlett,
Alexey I Nesvizhskii, Andrew Keller, Tao Xie, Jimmy K Eng, Eugene C. Yi, Leroy Hood, Alex
F Picone, Tim Cherny, Brian C Tjaden, Andrew F Siegel, Thomas J Reilly, Kira S
Makarova, Bernhard O Palsson, Arnold L Smith “Initial proteome analysis of
model microorganism Haemophilus influenzae strain Rd KW20” J Bacteriol. (2003) Aug ;185(15):4593-602. PMID: 12867470
P.
D. Von Haller, Eugene C. Yi,
S. Donohoe, K. Vaughn, A. Keller, A. I. Nesvizskii, J. Eng, X. J. Li, D. R,
Goodlett, R. Aebersold, J. D. Watts “The Application of New Software Tools to
Quantitative Protein Profiling Via Isotope-coded Affinity Tag (ICAT) and Tandem
Mass Spectrometry: I. Statistically Annotated Datasets for Peptide Sequences
and Proteins Identified via the Application of ICAT and Tandem Mass
Spectrometry to Proteins Copurifying with T Cell Lipid Rafts” Mol. Cell. Proteomics, (2003), 2(7),
426-427. PMID: 12832456
Eugene C. Yi*, Hookeun Lee, Ruedi Aebersold, David R
Goodlett “A microcapillary trap cartridge-microcapillary high-performance liquid
chromatography electrospray ionization emitter device capable of peptide tandem
mass spectrometry at the attomole level on an ion trap mass spectrometer with
automated routine operation” Rapid
Commun Mass Spectrom. (2003) ;17(18):2093-8. PMID: 12955739
Young
Ah Goo, Eugene C. Yi, Nitin S Baliga, Weiguo A Tao, Min Pan, Ruedi
Aebersold, David R Goodlett, Leroy Hood, Wailap V Ng “Proteomic Analysis of an Extreme Halophilic Archaeon, Halobacterium sp.
NRC-1” Mol Cell Proteomics.
(2003) Aug ;2(8):506-24.
Tina
Guina, Manhong Wu, Samuel I Miller, Samuel O Purvine, Eugene C. Yi, Jimmy Eng, David R Goodlett, Ruedi Aebersold,
Robert K Ernst, Kimberly A Lee “Proteomic
analysis of Pseudomonas aeruginosa grown under magnesium limitation” J Am Soc Mass Spectrom. (2003) Jul
;14(7):742-51. PMID: 12837596
Yuzuru
Shiio, Robert N Eisenman, Eugene C. Yi, Sam Donohoe, David R
Goodlett, Ruedi Aebersold “Quantitative
proteomic analysis of chromatin-associated factors” J Am Soc Mass Spectrom. (2003) Jul ;14(7):696-703.
Samuel Purvine, Jason-Thomas Eppel, Eugene C. Yi, David R
Goodlett “Shotgun collision-induced dissociation of peptides using a time of
flight mass analyzer” Proteomics.
(2003) Jun ;3(6):847-50. PMID: 12833507
Angelita
G Utleg, Eugene C. Yi, Tao
Xie, Paul Shannon, James T White, David R Goodlett, Leroy Hood, Biaoyang Lin
“Proteomic analysis of human prostasomes” Prostate.
(2003) Jul 1;56(2):150-61.
Y
Sydorskyy, D J Dilworth, Eugene
C. Yi, D R Goodlett, R W Wozniak, J D Aitchison “Intersection of the
Kap123p-mediated nuclear import and ribosome export pathways” Mol Cell Biol. (2003) Mar
;23(6):2042-54. PMID: 12612077
Tina Guina, Samuel O Purvine, Eugene C. Yi, Jimmy Eng, David R Goodlett, Ruedi Aebersold, Samuel I Miller “Quantitative proteomic analysis indicates increased synthesis of a quinolone by Pseudomonas aeruginosa isolates from cystic fibrosis airways” Proc Natl Acad Sci U S A. (2003) Mar 4;100(5):2771-6. PMID: 12601166
Jeffrey
A Ranish, Eugene C. Yi,
Deena M Leslie, Samuel O Purvine, David R Goodlett, Jimmy Eng, Ruedi Aebersold
“The study of macromolecular complexes by quantitative proteomics” Nat Genet. (2003) Mar ;33(3):349-55.
PMID: 12590263
Eugene C. Yi*, David R.
Goodlett “Quantitative Protein Profile Comparisons Using ICAT and Related
Methods” Book Chapter, Current Protocols
in Protein Science, (2003).UNIT 23.3,
Nitin
S Baliga, Min Pan, Young Ah Goo, Eugene
C. Yi, David R Goodlett, Krassen Dimitrov, Paul Shannon, Ruedi Aebersold,
Wailap Victor Ng, Leroy Hood “Coordinate regulation of energy transduction
modules in Halobacterium sp. analyzed by a global systems approach” Proc Natl Acad Sci U S A. (2002) Nov
12;99(23):14913-8. PMID: 12403819
Yuzuru
Shiio, Sam Donohoe, Eugene C.
Yi, David R Goodlett, Ruedi Aebersold, Robert N Eisenman “Quantitative
proteomic analysis of Myc oncoprotein function” EMBO J. (2002) Oct 1;21(19):5088-96.
Eugene C. Yi*, Marcello
Marelli, Hookeun Lee, Samuel O Purvine, Ruedi Aebersold, John D Aitchison,
David R Goodlett “Approaching complete peroxisome characterization by gas-phase
fractionation” Electrophoresis.
(2002) Sep ;23(18):3205-16. PMID: 12298092
David
R Goodlett, Eugene C. Yi*
“Proteomics without polyacrylamide : qualitative and quantitative uses of
tandem mass spectrometry in proteome analysis” Funct Integr Genomics. (2002) Sep;2(4-5):138-53. PMID: 12192588
D
R Goodlett, A Keller, J D Watts, R Newitt, Eugene C. Yi, S Purvine, J K
Eng, P von Haller , R Aebersold, E Kolker “Differential stable isotope labeling
of peptides for quantitation and de novo sequence derivation” Rapid Commun Mass Spectrom. (2001)
;15(14):1214-21. PMID: 11445905
K
M Kim, Eugene C. Yi, D
Baker, K Y Zhang “Post-translational modification of the N-terminal His tag
interferes with the crystallization of the wild-type and mutant SH3 domains
from chicken src tyrosine kinase” Acta
Crystallogr D Biol Crystallogr. (2001) May ;57(Pt 5):759-62. PMID: 11320329
F
Hayashi, K D Smith, A Ozinsky, T R Hawn, Eugene C. Yi, D R Goodlett, J
K Eng, S Akira, D M Underhill, A Aderem “The innate immune response to
bacterial flagellin is mediated by Toll-like receptor 5” Nature. (2001) Apr 26;410(6832):1099-103.
T
Guina, Eugene C. Yi, H
Wang, M Hackett, S I Miller “A PhoP-regulated outer membrane protease of
Salmonella enterica serovar typhimurium promotes resistance to alpha-helical
antimicrobial peptides” J Bacteriol.
(2000) Jul ;182(14):4077-86. PMID: 10869088
H
Wang, Eugene C. Yi, C A
Ibarra, M Hackett “A remote flow cell for UV absorbance detection with
capillary HPLC based on a single strand fiber optic” Analyst. (2000) Jun ;125(6):1061-4. PMID: 10932851
Eugene
C. Yi*, M Hackett “Rapid isolation method for lipopolysaccharide and lipid A
from gram-negative bacteria” Analyst.
(2000) Apr ;125(4):651-6.
R
K Ernst, Eugene C. Yi, L Guo, K B Lim, J L Burns, M Hackett, S I Miller
“Specific lipopolysaccharide found in cystic fibrosis airway Pseudomonas
aeruginosa” Science. (1999) Nov
19;286:1561-5.
R al-Asadi, Eugene C. Yi, J L Merchant “Sp1 affinity for GC-rich elements correlates with ornithine decarboxylase promoter activity” Biochem Biophys Res Commun. (1995) Sep 14;214(2):324-30. PMID: 7677738
Daniel H. Rogers, Eugene C. Yi, Dale Poulter “Enantioselective synthesis of (+)-presqualene diphosphate” J.Org.Chem.(1995) Feb ;60(4):941-945.
S. C. Rasmussen, M. M. Ritcher, Eugene. C. Yi, H. Place, K. J. Brewer “Synthesis and Characterization of a Series of Novel Rhodium and Iridium Complexes Containing Polypyridyl Bridging Ligands: Potential Uses in the Development of Multimetal Catalysts for Carbon Dioxide” In org. Chem. (1990) Oct ; 29(20):3926-3932.