1. 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

  2. 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

  3. 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

  4. 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

  5. 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

  6. 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

  7. 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

  8. 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

  9. 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

  10. 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

  11. 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

  12. 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.

  13. 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

  14. 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

  15. 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

  16. 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

  17. 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

  18. 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

  19. 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

  20. 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

  21. 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

  22. 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

  23. 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

  24. 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

  25. 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

  26. 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

  27. 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.

  28. 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

  29. 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

  30. 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

  31. 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

  32. 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

  33. 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.

  34. 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

  35. 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

  36. 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

  37. 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.

  38. 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

  39. 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.

  40. 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

  41. 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.

  42. 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

  43. 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


  44. 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

  45. 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,

  46. 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

  47. 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.

  48. 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

  49. 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

  50. 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

  51. 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

  52. 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.

  53. 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

  54. 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

  55. Eugene C. Yi*, M Hackett “Rapid isolation method for lipopolysaccharide and lipid A from gram-negative bacteria” Analyst. (2000) Apr ;125(4):651-6.

  56. 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.

  57. 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


  58. Daniel H. Rogers, Eugene C. Yi, Dale Poulter “Enantioselective synthesis of (+)-presqualene diphosphate” J.Org.Chem.(1995) Feb ;60(4):941-945.


  59. 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.