Publications containing data produced in the Proteomics Center

Publications of Emily Chen Ph.D. and Antonius Koller Ph.D.


  • Golebiewska U, Guo Y, Khalikaprasad N, Zurawsky C, Yerramilli VS, Scarlata S. (2012) gamma-Synuclein interacts with Phospholipase Cbeta2 to Modulate G Protein Activation. PlosOne 7(8): e41067.
  • Doege CA, Inoue K, Yamashita T, Rhee DB, Travis S, Fujita R., Guarnieri P, Bhagat G, Vanti WB, Shih A, Levine RL, Nik S, Chen EI, Abeliovich A. (2012) Early-stage epigenetic modification during smatic cell reprogramming by Parp1 and Tet2. Nature in press.
  • Xu X, Gnatenko DV, Ju J, Hitchcock IS, Martin DW, Zhu W, Bahou WF. (2012) Systematic analysis of microRNA fingerprints in thrombocythemic platelets using integrated platforms. Blood, in press.
  • Corthals A, Koller A, Martin DW, Rieger R, Chen EI, Bernaski M, Recagno G, Davalos LM, (2012) Detecting The Immune System Response Of A 500 Year-old Inca Mummy, PlosOne, 7(7): e41244.
  • Xie, G, Wong CC, Cheng KW, Huang L, Constantinides PP, Rigas B. (2012) In vitro and in vivo Metabolic Studies of Phospho-aspirin (MDC-22). Pharm. Res. in press.
  • Quitschke WW. (2012) Curcuminoid binding to embryonal carcinoma cells: reductive metabolism, induction of apoptosis, senescence, and inhibition of cell proliferation. PlosOne, 7(6):e39568.
  • Macri LK, Sheihet L, Singer AJ, Kohn J, Clark RA. (2012) Ultrafast and fast bioerodible electrospun fiber mats for topical delivery of a hydrophilic peptide. J. Control Release, 161:813-820.
  • Svetlanov A, Puri N, Mena P, Koller A, Karzai AW. (2012) Francisella tularensis tmRNA System Mutants are Vulnerable to Stress, Avirulent in Mice, and Provide Effective Immune Protections. Mol. Microbiol. 85:122-141.
  • Wu M, Nissen JC, Chen EI, Tsirka SE. (2012) Tuftsin promotes an anti-Inflammatory switch and attenuates symptoms in experimental autoimmune encephalomyelitis. PLOS ONE, 7(4):e34933.
  • Bikkavilli RK, Malbon CC. (2012) Wnt3a-stimulated LRP6 phosphorylation is dependent upon arginine methylation of G3BP2. J. Cell Science, 125:2446-2456.
  • Baumann Z, Koller A, Fisher NS. (2012) Factors influencing the assimilation of arsenic in a deposit-feeding polychaete. Comp Biochem and Physiology, Part C, 156:42-50.
  • Xie G, Wong CC, Cheng KW, Huang L, Constantinides PP, Rigas B. (2012) Regioselective oxidation of phospho-NSAIDs by human cytochrome P450 and flavin monooxygenase isoforms: Implications for their pharmacokinetic properties and safety. Brit. J. of Pharmacology, in press.
  • Sinnamon JR, Waddell CB, Nik S, Chen EI, Czaplinski K. (2012) Hnrap regulates neural development and neuron cell survival after glutamate stimulation. RNA, 18:704-719.
  • Xie G, Nie T, Mackenzie GG, Sun Y, Huang L, Ouyang N, Alston N, Zhu C, Murray OT, Constantinides PP, Kopelovich L, Rigas B. (2012) The metabolism and pharmacokinetics of phospho-sulindac (OXT-328) and the effect of difluoromethylornithine. Brit. J. of Pharmacology, 165:2152-2166.


  • Lukin M, Zaliznyak T, Johnson F, de los Santos CR. (2011) Incorporation of 3-aminobenzanthrone into 2'-deoxyoligonucleotides and its impact on duplex stability. J Nucleic Acids, Article ID 521035.
  • Szema AM, Hamidi SA, Koller A, Martin DW. (2011) Vasoactive Intestinal Peptide Knockout (VIP KO) Mouse Model of Sulfite-Sensitive Asthma: Up-regulation of Novel Lung Carbonyl Reductase. BMC Immunology, 12:66.
  • Thomas ST, VanderVen BC, Sherman DR, Russell DG, Sampson NS. (2011) Pathway Profiling in Mycobacterium tuberculosis: Elucidation of a Cholesterol-derived Catabolite and the Enzymes that Catalyze its Metabolism. JBC, 286:43668-43678.
  • Takeuchi H, Fernandez-Valdivia RC, Caswell DS, Nita-Lazar A, Rana NA, Garner TP, Weldeghiorghis TK, Macnaughtan MA, Jafar-Nejad H, Haltiwanger RS. (2011) Rumi functions as both a protein O-glucosyltransferase and a protein O-xylosyltransferase. PNAS 108:16600-16605.
  • Roma-Mateo C, Solaz-Fuster MC, Gimeno-Alcaniz JV, Dukhande V, Donderis J, Marina A, Criado O, Koller A, Rodriguez de Cordoba S, Gentry MS, Sanz P. (2011) Laforin, a dual specificity protein phosphatase involved in Lafora disease, is phosphorylated at Ser25 by AMP-activated kinase. Biochem. J. 439:265-275.
  • Bikkavilli RK, Malbon CC. (2011) Arginine methylation of G3BP1 in response to Wnt3a regulates b-catenin mRNA. J. Cell Science. 124:2310-2320.
  • Banerjee PS, Ostapchuck P, Hearing P, Carrico IS. (2011) Unnatural Amino Acid Incorporation onto Adenoviral (Ad) Coat Proteins Facilitates Chemoselective Modification and Retargeting of Ad Type 5 Vectors. J. of Virology. 85:7546-7554.
  • Xie G, Sun Y, Nie T, Mackenzie GG, Huang L, Kopelovich L, Komninou D, Rigas B. (2011) Phospho-ibuprofen (MDC-917) is a novel agent against colon cancer: Efficacy, metabolism and pharmacokinetics in mouse models. JPET 337:876-886.
  • Zhao S, Ramakrishnan G, Su D, Rieger R, Koller A, Orlov A. (2011) Novel Photocatalytic Applications of Sub-Nanometer Gold Particles for Environmental Liquid and Gas Phase Reactions. Applied Catalysis B: Environmental. 104:239-244.
  • Song A, Walker SG, Parker KA, Sampson NS. (2011) Antibacterial Studies of Cationic Polymers with Alternating, Random and Uniform Backbones. ACS Chem. Biol. 6:590-599.
  • Srinivasan M, Mehta P, Yu Y, Prugar E, Koonin EV, Karzai AW, Sternglanz R. (2011) The highly conserved KEOPS/EKC complex is essential for a universal tRNA modification, t6A. EMBO Journal 30:873-881.


  • Beliveau A, Mott JD, Lo A, Chen EI, Koller AA, Yaswen P, Muschler J, Bissell MJ. (2010) Raf-induced MMP9 disrupts tissue architecture of human breast cells in three-dimensional culture and is necessary for tumor growth in vivo. Genes Dev. 15:2800-2811.
  • Bikkavilli RK, Malbon CC. (2010) Dishevelled-KSRP complex regulates Wnt signaling through post-transcriptional stabilization of b-catenin mRNA. J. Cell Science. 123:1352-1362.
  • Guainazzi A, Campbell AJ, Angelov T, Simmerling C, Schaerer OD (2010) Synthesis and Molecular Modeling of a Nitrogen Mustard DNA Interstrand Crosslink. Chemistry - A European Journal, 16: 12100-12103.
  • Shibutani S, Bonala RR, Rosenquist T, Rieger R, Suzuki N, Johnson F, Miller F, Grollman AP. (2010) Detoxification of aristolochich acid I by O-demethylation: Less nephrotoxicity and genotoxicity of aristolochic acid Ia in rodents. Int. J. of Cancer 127:1021-1027..
  • Lukin M, de los Santos C. (2010) Stereoselective nucleoside deuteration for NMR studies of DNA. Nucleosides Nucleotides Nucleic Acids. 29:562-573.
  • Song A, Parker, KA, Sampson NS. (2010) Cyclic alternating ring-opening metathesis polymerization (CAROMP). Rapid access to functionalized cyclic polymers. Org Lett. 12:3729-31.
  • Taskent-Sezgin H, Chung J, Banerjee PS, Nagarajan S, Dyer RB, Carrico I, Raleigh DP. (2010) Azidohomoalanine: A Conformationally Sensitive IR Probe of Protein Folding, Protein Structure, and Electrostatics. Angew Chem Int Ed Engl. 49:7473-7475.
  • Zeituni AE, McCaig W, Scisci E, Thanassi DG, Cutler CW. (2010) The Native 67-Kilodalton Minor Fimbria of Porphyromonas gingivalis Is a Novel Glycoprotein with DC-SIGN-Targeting Motifs. J. Baceriology. 192:4103-4110.


  • Worby CA, Mattoo S, Kruger RP, Corbeil LB, Koller A, Mendez JC, Zekarias B, Lazar C, Dixon JE. (2009) The fic domain: regulation of cell signaling by adenylylation. Mol Cell. 34:93-103.
  • Yang X, Nesbitt NM, Dubnau E, Smith I, Sampson NS. (2009) Cholesterol metabolism increases the metabolic pool of propionate in Mycobacterium tuberculosis. Biochemistry. 48:3819-3821.
  • Rithidech KN, Honikel L, Rieger R, Xie W, Fischer T, Simon SR. (2009) Protein-expression profiles in mouse blood-plasma following acute whole-body exposure to (137)Cs gamma rays. Int J Radiat Biol. 85:432-447.
  • Rithidech KN, Honikel L, Milazzo M, Madigan D, Troxell R, Krupp LB. (2009) Protein expression profiles in pediatric multiple sclerosis: potential biomarkers. Mult Scler. 15:455-464.
  • Yokoyama N, Malbon CC. (2009) Dishevelled-2 docks and activates Src in a Wnt-dependent manner. J. Cell Science. 122:4439-4451.
  • Taskent-Sezgin H, Chung J, Patsalo V, Miyake-Stoner SJ, Miller AM, Brewer SH, Mehl RA, Green DF, Raleigh DP, Carrico I. (2009) Interpretation of p-Cyanophenylalanine Fluorescence in Proteins in Terms of Solvent Exposure and Contribution of Side-Chain Quenchers: A Combined Fluorescence, IR and Molecular Dynamics Study. Biochemistry, 48:9040-9046.
  • Angelov T, Guainazzi A, Schaerer OD. (2009) Generation of DNA Interstarnd Cross-Links by Post-Synthetic Reductive Amination. Org. Lett. 11:661-664.

2008 and older

  • Watkins J, Basu S, Bogenhagen, DF. (2008) A Quantitative Proteomic Analysis of Mitochondrial Participation in P19 Cell Neuronal Differentiation. J Proteome Res. 7:328-338.
  • Rithidech KN, Honikel L, Simon SR. (2007) Radiation leukemogenesis: A proteomic approach. Exp Hematol. 35:117-124.
  • Rieger RA, Zaika EI, Xie W, Johnson F, Grollman AP, Iden CR, Zharkov DO. (2006) Proteomic approach to identification of proteins reactive for abasic sites in DNA. Mol&Cell. Proteomics. 5:858-867.
  • Kodani S, Lodato MA, Durrant MC, Picart F, Willey JM. (2005) SapT, a lanthionine-containing peptide involved in aerial hyphae formation in the streptomycetes. Mol Microbiol. 58:1368-1380.
  • Wang X, Connelly JJ, Wang CL, Sternglanz R. (2004) Importance of the Sir3 N-terminus and its acetylation for yeast transcriptional silencing. Genetics. 168:547-551.
  • Kodani S, Hudson ME, Durrant MC, Buttner MJ, Nodwell JR, Willey JM. (2004) The SapB morphogen is a lantibiotic-like peptide derived from the product of the developmental gene ramS in Streptomyces coelicolor. Proc Natl Acad Sci U S A. 101:11448-11453.
  • Bogenhagen DF, Wangy, Shen EL, Kobayashi R. (2003) Protein components of mitochondrial DNA nucleoids in higher eukaryotes. Mol Cell Proteomics. 2:1205-1216.
  • Song OK, Wang X, Waterborg JH, Sternglanz R. (2003) An Nalpha-acetyltransferase responsible for acetylation of the N-terminal residues of histones H4 and H2A. J Biol Chem. 278:38109-38112.
  • Yokoyama N, Miller WT. (2003) Biochemical properties of the Cdc42-associated tyrosine kinase ACK1. Substrate specificity, authphosphorylation, and interaction with Hck. J Biol Chem. 278:47713-47723