Proteomics & Metabolomics Shared Resource

2006

Orvisky E, Drake SK, Martin BM, Abdel-Hamid M, Ressom HW, Varghese RS, An Y, Saha D, Hortin GL, Loffredo CA, Goldman R. Enrichment of low molecular weight fraction of serum for MS analysis of peptides associated with hepatocellular carcinoma. Proteomics 2006;6:2895-2902.

Ressom HW, Varghese RS, Orvisky E, Drake SK, Hortin GL, Abdel-Hamid M, Loffredo CA, Goldman R. Ant colony optimization for biomarker identification from MALDI-TOF mass spectra. Conf Proc IEEE Eng Med Biol Soc 2006;1:4560-4563.

2007

Emami A, Dyba M. Cheema AK, Pan J, Nath RG, Chung FL. Detection of the acrolein-derived cyclic DNA adduct by a quantitative 32P-postlabeling/solid-phase extraction/HPLC method: blocking its artifact formation with glutathione. Anal Biochem 2008 Mar 1;374(1):163-72. Epub 2007 Oct 24.

Goldman R, Ressom HW, Abdel-Hamid M, Goldman L, Wang A, Varghese RS, An Y, Loffredo CA, Drake SK, Eissa SA, Gouda S, Moisewitsch FS. Candidate markers for the detection of hepatocellular carcinoma in low-molecular weight fraction of serum. Carcinogenesis 2007;28:2149-2153.

Li HH, Aubrecht J, Fornace AJ, Jr. Toxicogenomics: overview and potential applications for the study of non-covalent DNA interacting chemicals. Mutat Res 2007;623:98-108.

Ressom HW, Varghese RS, Drake SK, Hortin GL, Abdel-Hamid M, Loffredo CA, Goldman R. Peak selection from MALDI-TOF mass spectra using ant colony optimization. Bioinformatics 2007;23:619-626.

Wong CM, Cheema AK, Zhang L, Suzuki YJ. Protein carbonylation as a novel mechanism in redox signaling. Circ Res. 2008 Feb 15;102(3):310-8. Epub 2007 Dec 13.

2008

Patterson AD, Li H, Eichler GS, Krausz KW, Weinstein JN, Fornace AJ, Jr. Gonzalez FJ, Idle JR. UPLC-ESI-TOFMS-based metabolomics and gene expression dynamics inspector self-organizing metabolomic maps as tools for understanding the cellular response to ionizing radiation. Anal Chem 2008;80:665-674.

Ressom HW, Varghese RS, Goldman L, An Y, Loffredo CA, Abdel-Hamid M, Kyselova Z, Mechref Y, Novotny M, Drake SK, Goldman R. Analysis of MALDI-TOF mass spectrometry data for discovery of peptide and glycan biomarkers of hepatocellular carcinoma. J Proteome Res 2008;7:603-610.

Tyburski JB, Patterson AD, Krausz KW, Slavik J, Fornace AJ, Jr. Gonzalez FJ, Idle JR. Radiation metabolomics. 1. Identification of minimally invasive urine biomarkers for gamma-radiation exposure in mice. Radiat Res 2008;170:1-14.

Zhang-Zhi Hu, Hongzhan Huang, Amrita Cheema, Mira Jung, Anatoly Dritschilo, Cathy H. Wu Integrated Bioinformatics for Radiation-Induced Pathway Analysis from Proteomics and Microarray Data. J Proteomics & Bioinformatics 2008

2009

Amrita K. Cheema, Jason Catania, Siva Dakshanamurthy, Weiping Shen, Brigitte Simons, Chad Knights, Christopher Albanese, and Maria Laura Avantaggiati. A SUMO-1 Acetylated Motif, SAM, Regulates SUMO-1 Ubiquitination, Stability, and DNA-Damage. Tolerance J.Biol. Chem. 2009. (under revision)

Rahul Balal, Amrita Cheema and Tapas Saha Fluorescent Oligonucleotides Can Serve As Suitable Alternative to Hazardous Radioactivity. J.Biomol.Tech. 2009. (in press)

Lixin Mi, Nanqin Gan, Amrita Cheema, Sivanesan Dakshanamurthy, David C. H. Yang, Fung-Lung Chung. Cancer preventive isothiocyanates induce selective degradation of cellular alpha- and beta-tubulins by proteasomes J.Biol. Chem. 2009. (accepted, in press)