Publication List

Yao Z, Di Poto C, Mavodza G, Oliver E, Ressom HW, Sherif ZA (2019). DNA methylation activates TP73 expression in hepatocellular carcinoma and gastrointestinal cancer. Scientific Reports 2019 Dec 18;9(1):19367. PMID: 31852961

Barefoot ME, Chen Y, Varghese RS, Zhou Y, and Ressom HW (2019). Integrative analysis of DNA methylation and gene expression patterns in tissues from hepatocellular carcinoma patients. Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine (BIBM), San Diego, CA, Nov. 18-21, 2019, pp. 267-274.

Fan Z, Ghaffari K, Alley A, Ressom HW (2019). Metabolite identification using artificial neural network. Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine (BIBM), San Diego, CA, Nov. 18-21, 2019, pp. 244-248.

Barefoot ME, Varghese RS, Zhou Y, Di Poto C, Ferrarini A, Ressom HW (2019). Multi-omic pathway and network analysis to identify biomarkers for hepatocellular carcinoma. Conf Proc IEEE Eng Med Biol Soc. 2019 Jul;2019:1350-1354. doi: 10.1109/EMBC.2019.8856576. PMID: 31946143

Fan, Z, Zhou Y, Ressom HW (2019). MOTA: Multi-omic integrative analysis for biomarker discovery. Conf Proc IEEE Eng Med Biol Soc. 2019 Jul;2019:243-247. doi: 10.1109/EMBC.2019.8857049. PMID: 31945887

Su S, Di Poto C, Kroemer AH, Cui W, Roy R, Liu X, Ressom HW (2019). Establishment of ornithine transcarbamylase deficiency-derived primary human hepatocyte with hepatic functions. Exp Cell Res. 2019 Nov 1;384(1):111621. doi: 10.1016/j.yexcr.2019.111621. Epub 2019 Sep 9. PMID: 31513782

Thangarajh M, Zhang A, Gill K, Ressom HW, Li Z, Varghese RS, Hoffman EP, Nagaraju K, Hathout Y, Boca SM (2019). Discovery of potential urine-accessible metabolite biomarkers associated with muscle disease and corticosteroid response in the mdx mouse model for Duchenne. PLoS One. 2019 Jul 16;14(7):e0219507. doi: 10.1371/journal.pone.0219507. eCollection 2019. PMID: 31310630

Ferrarini A, Di Poto C, He S, Tu C, Varghese RS, Kara Balla A, Jayatilake M, Li Z, Ghaffari K, Fan Z, Sherif ZA, Kumar D, Kroemer A, Tadesse MG, Ressom HW (2019). Metabolomic Analysis of liver tissues for characterization of hepatocellular carcinoma. J Proteome Res. 2019 Aug 2;18(8):3067-3076. doi: 10.1021/acs.jproteome.9b00185. Epub 2019 Jul 1. PMID: 31188000

Su S, Di Poto C, Roy R, Liu X, Cui W, Kroemer A, Ressom HW (2019). Highlight article: Long-term culture and characterization of patient-derived primary hepatocytes using conditional reprogramming. Exp Biol Med (Maywood). 2019 Aug;244(11):857-864. doi: 10.1177/1535370219855398. Epub 2019 Jun 11. PMID: 31184925

White SM, Avantaggiati ML, Nemazanyy I, Di Poto C, Yang Y, Pende M, Gibney GT, Ressom HW, Field J, Atkins MB, Yi C (2019). YAP/TAZ inhibition induces metabolic and signaling rewiring resulting in targetable vulnerabilities in NF2-deficient tumor cells. Dev Cell. 2019 May 6;49(3):425-443.e9. doi: 10.1016/j.devcel.2019.04.014. PMID: 31063758

Tricoli L, Niture S, Chimeh U, Ressom H, Kumar D (2019). Role of microRNAs in the development of hepatocellular carcinoma and drug resistance. Front Biosci (Landmark Ed). 24:382-391. Review. PMID: 30468662

Li Z, Zuo Y, Xu C, Varghese RS, Ressom HW (2018). INDEED: R package for network based differential expression analysis. Proceedings (IEEE Int Conf Bioinformatics Biomed). 2018 Dec;2018:2709-2712. doi: 10.1109/BIBM.2018.8621426. Epub 2019 Jan 24. PMID: 31179159

Fernandez HR, Gadre SM, Tan M, Graham GT, Mosaoa R, Ongkeko MS, Kim KA, Riggins RB, Parasido E, Petrini I, Pacini S, Cheema A, Varghese R, Ressom HW, Zhang Y, Albanese C, Uren A, Paige M, Giaccone G, Avantaggiati ML (2018). The mitochondrial citrate carrier, SLC25A1, drives stemness and therapy resistance in non-small cell lung cancer. Cell Death Differ. 25(7):1239-1258. PMID: 29651165

Di Poto C, He S, Varghese RS, Zhao Y, Ferrarini A, Su S, Karabala A, Redi M, Mamo H, Rangnekar AS, Fishbein TM, Kroemer AH, Tadesse MG, Roy R, Sherif ZA, Kumar D, Ressom HW (2018). Identification of race-associated metabolite biomarkers for hepatocellular carcinoma in patients with liver cirrhosis and hepatitis C virus infection. PLoS One 13(3):e0192748. PMID: 29538406

Niture S, Gyamfi M, Kedir H, Arthur E, Ressom H, Deep G, Kumar D. Serotonin induced hepatic steatosis is associated with modulation of autophagy and Notch signaling pathway. Cell Communication and Signaling.2018 Nov 8;16(1):78. doi: 10.1186/s12964-018-0282-6. PMID: 30409162

Misiak MM, Hipolito MS, Ressom HW, Obisesan TO, Manaye KF, Nwulia EA. Apo E4 Alleles and Impaired Olfaction as Predictors of Alzheimer's Disease. Clin Exp Psychol. 2017;3(4). pii: 169. doi: 10.4172/2471-2701.1000169. Epub 2017 Oct 19. PMID: 29423459

Zuo Y, Cui Y, Yu G, Li R, Ressom HW* (2017). Incorporating prior biological knowledge for network-based differential gene expression analysis using differentially weighted graphical LASSO. BMC Bioinformatics. 2017 Feb 10;18(1):99. PMID: 28187708

Varghese RS, Zuo Y, Zhao Y, Zhang YW, Jablonski SA, Pierobon M, Petricoin EF, Ressom HW*, Weiner LM* (2017). Protein network construction using reverse phase protein array data. Methods 124:89-99. PMID: 28651964

Di Poto C, Ferrarini A, Zhao Y, Varghese RS, Tu C, Zuo Y, Wang M, Nezami Ranjbar MR, Luo Y, Zhang C, Desai CS, Shetty K, Tadesse MG, Ressom HW* (2017). Metabolomic characterization of hepatocellular carcinoma in patients with liver cirrhosis for biomarker discovery. Cancer Epidemiol Biomarkers Prev. 26(5):675-683. PMID: 27913395

Azizan KA, Ressom HW, Mendoza ER, Baharum SN (2017). 13C based proteinogenic amino acid (PAA) and metabolic flux ratio analysis of Lactococcus lactis reveals changes in pentose phosphate (PP) pathway in response to agitation and temperature related stresses. PeerJ. 2017 Jul 5;5:e3451. doi: 10.7717/peerj.3451. eCollection 2017. PMID: 28695065

Hsu PC, Lan RS, Brasky TM, Marian C, Cheema AK, Ressom HW, Loffredo CA, Pickworth WB, Shields PG (2017). Metabolomic profiles of current cigarette smokers. Mol Carcinog. 2017 Feb;56(2):594-606. doi: 10.1002/MID: 27341184

Hsu PC, Lan RS, Brasky TM, Marian C, Cheema AK, Ressom HW, Loffredo CA, Pickworth WB, Shields PG (2017). Menthol Smokers: Metabolomic profiling and smoking behavior. Cancer Epidemiol Biomarkers Prev. 2017 Jan;26(1):51-60. doi: 10.1158/1055-9965.EPI-16-0124. PMID: 27628308

Day TF, Mewani RR, Starr J, Li X, Chakravarty D, Ressom H, Zou X, Eidelman O, Pollard HB, Srivastava M, Kasid UN*. Transcriptome and proteome analyses of TNFAIP8 knockdown cancer cells reveal new insights into molecular determinants of cell survival and tumor progression. Methods Mol Biol. 2017;1513:83-100. PMID: 27807832

Wang M, Di Poto C, Ferrarini A, Yu G, Ressom HW (2016). Metabolomic data deconvolution using probabilistic purification models. Oral Presentation in the Proceedings of the 2016 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Shenzhen, China, December 15-18, 2016. (Awarded the Best Student Paper, 1/361)

Wang M, Tsai TH, Di Poto C, Ferrarini A, Yu G, Ressom HW (2016). Topic model-based mass spectrometric data analysis in cancer biomarker discovery studies. BMC Genomics, 17(Suppl 4):545.

Wang M, Yu G, Ressom HW (2016). Integrative analysis of proteomic, glycomic, and metabolomic data for biomarker discovery. IEEE J Biomed Health Inform, 20(5), 1225-1231. PMID: 27249841

Ressom HW, Di Poto C, Ferrarini A, Hu Y, Nezami Ranjbar MR, Song E, Varghese RS, Wang M, Zhou S, Zhu R, Zuo Y, Tadesse MG, Mechref Y (2016). Multi-omic approaches for characterization of hepatocellular carcinoma. Oral Presentation in the Proceedings of the 38th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, Orlando, Florida, August 16-20, 2016.

Varghese RS, Di Poto C, Tu C, Nezami Ranjbar MR, Luo Y, Choi J, Tadesse MG, Ressom HW (2016). Assessment of GC-MS in detecting changes in the levels of metabolites using a spike-in experiment in human plasma. Accepted for Publication in Metabolomics: Open Access.

Zuo Y, Cui Y, Di Poto C, Varghese RS, Yu G, Li R, and Ressom HW (2016). INDEED: Integrated differential expression and differential network analysis of omic data for biomarker discovery. METHODS. 2016 Dec 1;111:12-20. doi: 10.1016/j.ymeth.2016.08.015. PMID: 27592383

Zuo Y, Cui Y, Yu G, Li R, and Ressom HW (2016). Integrating prior biological knowledge for network-based differential gene expression analysis using weighted graphical LASSO. BMC Bioinformatics. 2017 Feb 10;18(1):99. PMID: 28187708

Tsai TH, Wang M, Ressom HW (2016). Preprocessing and Analysis of LC-MS-Based Proteomic Data. Methods Mol Biol. 2016;1362:63-76. doi: 10.1007/978-1-4939-3106-4_3. PMID: 26519169, PMCID: PMC4838194

Zhao Y, Tsai TH, Di Poto C, Pannell LK, Tadesse MG, and Ressom HW (2016). Variability assessment of label-free LC-MS experiments for difference detection. In: Statistical Analysis of Proteomics, Metabolomics, and Lipidomics Data Using Mass Spectrometry. Eds. Datta S and Mertens BJA: Springer, 2016: 157-176

Varghese RS, Zuo Y, Zhao Y, Zhang YW, Jablonski SA, Pierobon M, Petricoin E, Ressom HW, Weiner LM (2016). Network-based analysis of reverse phase protein array data. Proceedings of the 2016 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Shenzhen, China, December 15-18, 2016.

Ferrarini A, Di Poto C, Varghese RS, Nezami Ranjbar MR, Alonso DE, Binkley J, Ressom HW (2015). A multi-platform approach for metabolomic analysis of human liver tissues. Chromatography Today. August/September 2015.

Korba B, Shetty K, Medvedev A, Viswanathan P, Varghese RS, Zhou B, Roy R, Makambi K, Ressom HW, Loffredo C (2015). Hepatitis C virus genotype 1a core gene nucleotide patterns associated with hepatocellular carcinoma risk. Journal of General Virology. [Epub ahead of print] PMID: 26296571

Zhang YW, Nasto RE, Varghese R, Jablonski SA, Serebriiskii IG, Surana R, Calvert VS, Bebu I, Murray J, Jin L, Johnson M, Riggins R, Ressom HW, Petricoin E, Clarke R, Golemis EA, Weiner LM (2015). Acquisition of estrogen independence induces TOB1-related mechanisms supporting breast cancer cell proliferation. Oncogene. [Epub ahead of print] PMID: 26165839

Enquobahrie DA, Denis M, Tadesse MG, Gelaye B, Ressom HW, Williams MA (2015). Maternal early pregnancy serum metabolites and risk of gestational diabetes mellitus. J Clin Endocrinol Metab.

Wang M, Tsai TH, Yu G, Ressom HW (2015). Purification of LC/GC-MS based Biomolecular Expression Profiles Using a Topic Model. To appear in the Proceedings of the 2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Washington D.C., USA, November 9-12, 2015.

Zuo Y, Yu G, and Ressom HW (2015). Integrating prior biological knowledge and graphical LASSO for network inference. To appear in the Proceedings of the 6th Workshop on Integrative Data Analysis in System Biology (IDASB), Washington DC, November 9-12, 2015.

Tsai TH, Wang M, Ressom HW (2015). Preprocessing and Analysis of LC-MS-Based Proteomic Data. Statistical Analysis in Proteomics (Methods in Molecular Biology), Editor: Klaus Jung, 1st Edition. ISBN-13: 978-1493931057.

Nezami Ranjbar MR, Di Poto C, Wang Y, Ressom HW (2015). SIMAT: GC-SIM-MS data analysis tool. BMC Bioinformatics 2015, 16:259. PMID: 26283310

Nezami Ranjbar MR, Luo Y, Di Poto C, Varghese RS, Ferrarini A, Zhang C, Sarhan NI, Soliman H, Tadesse MG, Ziada DH, Roy R, Ressom HW (2015). GC-MS based plasma metabolomics for identification of candidate biomarkers for hepatocellular carcinoma in Egyptian cohort. PLoS One 10(6):e0127299. PMID: 26030804

Wang M, Yu G, Ressom HW (2015). Integrative analysis of LC-MS based glycomic and proteomic data. To appear in the Proceedings of the 37th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, Milano, Italy, August 25-29, 2015.

Tsai TH, Song E, Zhu R, Di Poto C, Wang M, Luo Y, Varghese RS, Tadesse MG, Ziada DH, Desai CS, Shetty K, Mechref Y, Ressom HW (2015). LC-MS/MS based Serum Proteomics for Identification of Candidate Biomarkers for Hepatocellular Carcinoma. Proteomics. 15(13), 2369-2381. PMID: 25778709

Wang J, Zuo Y, Man Y-G., Avital I, Stojadinovic A, Liu M, Yang X, Varghese RS, Tadesse MG, Ressom HW (2015). Pathway and network approaches for identification of cancer signature markers from omics data. Journal of Cancer 6(1): 54-65. PMID: 25553089

Nezami Ranjbar MR, Tadesse MG, Wang Y, Ressom HW (2015). Bayesian normalization model for Label-free quantitative analysis by LC-MS. IEEE/ACM Trans Comput Biol Bioinform. 12(4), 914-927. DOI 10.1109/TCBB.2014.2377723.

Zuo Y, Yu G, Zhang C, Ressom HW (2014). A new approach for multi-omic data integration. Proceedings of the 2014 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Belfast, UK, November 2014, pp. 214-217. DOI: 10.1109/BIBM.2014.6999157

Tsai TH, Wang M, Di Poto C, Hu Y, Zhou S, Zhao Y, Varghese RS, Luo Y, Tadesse MG, Ziada DH, Desai CS, Shetty K, Mechref Y, Ressom HW (2014). LC-MS Profiling of N-Glycans Derived from Human Serum Samples for Biomarker Discovery in Hepatocellular Carcinoma. J Proteome Res. PMID: 25077556

Zuo, Y, Yu, G, Tadesse, MG, Ressom, HW (2014). Biological network inference using low order partial correlation. Methods. PMID: 25003577

Wang, J, Zuo, Y, Liu, L, Man, Y, Tadesse, MG, Ressom, HW (2014). Identification of Functional Modules by Integration of Multiple Data Sources Using a Bayesian Network Classifier. Circulation: Cardiovascular Genetics,7(2), 206-217. PMID: 24736851

Xiao JF, Zhao Y, Varghese RS, Zhou B, Di Poto C, Zhang L, Tadesse MG, Ziada DH, Shetty K, Ressom HW (2014). Evaluation of metabolite biomarkers for hepatocellular carcinoma through stratified analysis by gender, race and alcoholic cirrhosis. Cancer Epidemiol Biomarkers Prev. 23(1):64-72. PMID: 24186894

Tsai TH, Tadesse MG, Di Poto C, Pannell LK, Mechref Y, Wang Y, Ressom HW (2013). Multi-profile Bayesian alignment model for LC-MS data analysis with integration of internal standards. Bioinformatics 29(21):2774-80. PMID: 24013927

Zhang Z, Xuan J, Clarke R, Ressom HW (2013). Module-based breast cancer classification. Int J Data Min Bioinform. 7(3):284-302. PMID: 23819260

Nezami Ranjbar MR, Zhao Y, Tadesse MG, Wang Y, Ressom HW (2013). Gaussian process regression model for normalization of LC-MS data using scan-level information. Proteome Science 2013, 11(Suppl 1):S13.

Tsai TH, Tadesse MG, Wang Y, Ressom HW (2013). Profile-based LC-MS data alignment--a Bayesian approach. IEEE/ACM Trans Comput Biol Bioinform. 10(2):494-503. PMID: 23929872

MacArthur L, Ressom H, Shah S, Federoff HJ (2013). Network modeling to identify new mechanisms and therapeutic targets for Parkinson's disease. Expert Rev Neurother. 13(6):685-93. PMID: 23739005

Cheema AK, Varghese RS, Timofeeva O, Zhang L, Kirilyuk A, Zandkarimi F, Kaur P, Ressom HW, Jung M, Dritschilo A. (2013) Functional proteomics analysis to study ATM dependent signaling in response to ionizing radiation. Radiat Res. 179(6):674-83. PMID: 23642045

Zhou B, Xiao JF, Ressom HW. Prioritization of putative metabolite identifications in LC-MS/MS experiments using a computational pipeline. Proteomics. 2013 Jan;13(2):248-60. PMID: 23307777

Wu FX, Ressom H, Dunn MJ. Focus on bioinformatics in proteomics. Proteomics. 2013 Jan;13(2):219-20. PMID: 23341066

Hsu PC, Zhou B, Zhao Y, Ressom HW, Cheema AK, Pickworth W, Shields PG. Feasibility of Identifying the Tobacco-related Global Metabolome in Blood by UPLC-QTOF-MS. J Proteome Res. 2013 Feb 1;12(2):679-91.PMID: 23240883

Zuo Y, Yu G, Tadesse MG, Ressom HW (2013). "Reconstructing biological networks using low order partial correlation", Proceedings of the 2013 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Shanghai, China, December 2013, pp. 171-175.

Wang M, Yu G, Mechref Y, Ressom HW (2013). "GPA: an algorithm for LC/MS based glycan profile annotation", Proceedings of the 2013 IEEE International Conference on Bioinformatics and Biomedicine Workshop (BIBMW), Shanghai, China, December 2013, pp. 16-22.

Xiao JF, Varghese RS, Zhou B, Nezami Ranjbar MR; Zhao Y, Tsai T-H,Di Poto C, Wang J, Goerlitz D, Luo Y, Cheema A, Sarhan N, Soliman H,Tadesse MG, Ziada DH, Ressom HW (2012). LC-MS based serum metabo-lomics for identification of hepatocellular carcinoma biomarkers in Egyptian cohort. J Proteome Res. 11(12):5914-23. PMID:23078175

Kaur P, Rizk NM, Ibrahim S, Younes N, Uppal A, Dennis K, Karve T,Blakeslee K, Kwagyan J, Zirie M, Ressom HW, Cheema AK (2012). iTRAQ-based quantitative protein expression profiling and MRM verification of markers in Type 2 diabetes. J Proteome Res. 11(11):5527-39. PMID: 23050762

Nezami Ranjbar MR, Zhao Y, Tadesse MG, Wang Y, Ressom HW (2012). Evaluation of normalization methods for analysis of LC-MS data. Proceedings of the 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshop (BIBMW), Philadelphia, PA, October 2012, pp. 610-617.

Zhao Y, Tsai T-H, Di Poto C, Pannell L, Tadesse MG, Ressom HW (2012). Variability assessment of LC-MS experiments and its application to experimental design and difference detection. Proceedings of the 2012 IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS), Washington, DC, December 2012, 195-198.

Nezami Ranjbar MR, Tadesse MG, Wang Y, Ressom HW (2012). Normalization of LC-MS data using Gaussian process. Proceedings of the 2012 IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS), Washington, DC, December 2012, pp. 1870190.

Wang J, Yuan H, Tadesse MG, Ressom HW (2012). Integration of multiple data sources for identifying functional modules using Bayesian network. Proceedings of the 2012 IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS), Washington DC, December 2012, pp. 13-17.

Ressom HW, Xiao JF, Tuli L, Varghese RS, Zhou B, Tsai T-H, Nezami Ranjbar MR, Zhao Y, Wang J, Di Poto C, Cheema AK, Tadesse MG, Goldman R, Shetty K (2012). Utilization of metabolomics to identify serum biomarkers for hepatocellular carcinoma in patients with liver cirrhosis. Anal Chim Acta. 2012 Sep 19;743C:90-100. PMID: 22882828

Zhou B, Wang J, Ressom HW (2012). MetaboSearch: Tool for mass-based metabolite identification using multiple databases. PLoS One 7(6): e40096. doi:10.1371/journal.pone.0040096. PMID: 22768229

Tuli L, Tsai T-H, Varghese R, Xiao JF, Cheema A, and Ressom HW (2012). Using a spike-in experiment to evaluate analysis of LC-MS data. Proteome Science. Proteome Science 10(1):13.

Zhang Z, Xuan J, Clarke R, Ressom HW (2012). Module-based breast cancer classification. Int J Data Min Bioinform. 2013;7(3):284-302. PMID: 23819260

Varghese RS, Zhou B, Nezami Ranjbar MR, Zhao Y, Ressom HW (2012). Ion annotation-assisted analysis of LC-MS based metabolomic experiment. Proteome Sci. 2012 Jun 21;10 Suppl 1:S8.

Scholz SW, Mhyre T, Ressom H, Shah S, Federoff HJ (2012). Genomics and bioinformatics of Parkinson's disease. Cold Spring Harb Perspect Med. 2012 Jul;2(7):a009449.

Wang J, Zhang y, Marian C, Ressom HW (2012). Identification of aberrant pathways and network activities from high-throughput data. Briefings in Bioinformatics. 13(4):406-19. PMID: 22287794

Xiao JF, Zhou B, Ressom HW (2012). Metabolite identification and quantitation in LC-MS/MS-based metabolomics. Trends Analyt Chem 32:1-14.

Zhou B, Xiao JF, Tuli L, Ressom HW (2012). LC-MS-based metabolomics. LC-MS-based metabolomics. Mol. BioSyst. 8(2) 470-481.

Kaur P, Sheikh K, Kirilyuk A, Kirilyuk K, Kallakury B, Ressom HW, Cheema A (2012). Metabolomic profiling for biomarker discovery in pancreatic cancer. International Journal of Mass Spectrometry 310: 44-51.

Kamalru AA, Baharum SN, Ressom HW, Noor NM (2012). GC-MS analysis and PLS-DA validation of the trimethyl silyl-derivatization techniques. American Journal of Applied Sciences. American Journal of Applied Sciences 9 (7): 1124-1136, 2012.

Patacsil D, Tran AT, Cho YS, Suy S, Saenz F, Malyukova I, Ressom H, Collins SP, Clarke R, Kumar D (2012). Gamma-tocotrienol induced apoptosis is associated with unfolded protein response in human breast cancer cells. J Nutr Biochem. 2012 Jan;23(1):93-100. Epub 2011 Mar 22.

Befekadu GK, Tadesse MG, Tsai T-H, Ressom HW (2011). Probabilistic mixture regression models for alignment of LC-MS data. IEEE/ACM Trans Comput Biol Bioinform 8(5):1417-24.

Tang Z, Zhang L, Cheema A, Ressom HW (2011). A new method for alignment of LC-MALDI-TOF data. Proteome Science 9 (Suppl 1):S1.

Cheema AK, Timofeeva O, Varghese R, Dimtchev A, Shiekh K, Shulaev V, Suy S, Collins S, Ressom H, Jung M, Dritschilo A* (2011). Integrated analysis of ATM mediated gene and protein expression impacting cellular metabolism. J Proteome Res. 2011 May 6;10(5):2651-7. Epub 2011 Mar 7.

Ochs MF, Karchin R, Ressom H, Gentleman R (2011). Identification of aberrant pathway and network activity from high-througput data - workshop introduction. Pac Symp Biocomput. 2011:364-8.

Tsai T-H, Tadesse MG, Wang Y, and Ressom HW (2011). Bayesian alignment model for LC-MS data. Proceedings of the IEEE International Conference on Bioinformatics & Biomedicine, Atlanta, GA, November 12-15, 2011, pp. 261-264.

Zhou B, Xiao JF, Ressom HW (2011). A computational pipeline for LC-MS/MS based metabolite identification. Proceedings of the IEEE International Conference on Bioinformatics & Biomedicine, Atlanta, GA, November 12-15, 2011, pp. 247-251.

Varghese RS, Zhou B, Ressom HW (2011). Meta-analysis of LC-MS based metabolomic experiments. Proceedings of the Third International Workshop on Data Mining for Biomarker Discovery (DMBD 2011), Atlanta, GA, November 12-15, 2011, pp. 157-164.

Patacsil D, Tran AT, Cho YS, Suy S, Saenz F, Malyukova I, Ressom H, Collins SP, Clarke R, Kumar D (2011). Gamma-tocotrienol induced apoptosis is associated with unfolded protein response in human breast cancer cells. J Nutr Biochem. 2011 Mar 21. [Epub ahead of print] PMID:21429729

Cheema AK, Timofeeva O, Varghese R, Dimtchev A, Shiekh K, Shulaev V, Suy S, Collins S, Ressom H, Jung M, Dritschilo A (2011). Integrated analysis of ATM mediated gene and protein expression impacting cellular metabolism. J Proteome Res. 2011 Mar 7. [Epub ahead of print]

Ochs MF, Karchin R, Ressom H, Gentleman R (2011). Identification of aberrant pathway and network activity from high-througput data - workshop introduction. Pac Symp Biocomput. 2011:364-8.

Varghese RS and Ressom HW (2011). LC-MS data analysis for differential protein expression detection. Methods Mol Biol. 2011;694:139-50.

Varghese RS, Cheema A, Cheema P, Bourbeau M, Tuli L, Zhou B, Jung M, Dritschilo A, Ressom HW (2010). Analysis of LC-MS data for characterizing the metabolic changes in response to radiation. J Proteome Res. 9(5):2786-93.

Zhang Y, Xuan J, de los Reyes BG, Clarke R, Ressom HW (2010). Reconstruction of gene regulatory modules in cancer cell cycle by multi-source data integration. PLoS One 5(4):e10268.

Tang Z, Varghese RS, Bekesova S, Loffredo CA, Abdel-Hamid M, Kyselova Z, Mechref Y, Novotny M, Goldman R, Ressom HW (2010). Identification of N-glycan serum markers associated with hepatocellular carcinoma from mass spectrometry data. J Proteome Res. 9(1):104-12.

Prahalad P, Dakshanamurthy S, Ressom H, Byers SW (2010). Retinoic acid mediates regulation of network formation by COUP-TFII and VE-cadherin expression by TGFbeta receptor kinase in breast cancer cells. PLoS One 5(4):e1002.

Befekadu GK, Tadesse MG, Tsai T-H, Ressom HW. Probabilistic mixture regression models for alignment of LC-MS data. IEEE/ACM Trans Comput Biol Bioinform. 2010 Sep 8. [Epub ahead of print] PMID: 20837998

Zhou B, Cheema A, Ressom HW (2010). SVM-based spectral matching for metabolite identification. Proceedings of the 32nd Annual Conference of the IEEE Engineering in Medicine and Biology Society, Buenos Aires, Argentina, August 31 - September 4, 2010, pp. 756-759.

Tang Z, Zhang L, Cheema A, Ressom HW (2010). A new method for alignment of LC-MALDI-TOF data. Proceedings of the IEEE International Conference on Bioinformatics & Biomedicine, December 18-21, Hong Kong. 2010, pp.346-351.

Zhang Y, Xuan J, Clarke R, Ressom HW (2010). Module-based biomarker discovery in breast cancer. Proceedings of the IEEE International Conference on Bioinformatics & Biomedicine, December 18-21, Hong Kong. 2010, pp.352-356.

Tuli L, Tsai T-H, Varghese R, Cheema A, and Ressom HW (2010). Using a spike-in experiment to evaluate analysis of LC-MS data. Proceedings of the IEEE International Workshop on Computational Proteomics, December 18-21, Hong Kong. 2010, pp.67-72.

Kaur P, Sheikh K, Kirilyuk A, Kirilyuk K, Kallakury B, Ressom HW, Cheema A (2010). Metabolomic profiling for biomarker discovery in pancreatic cancer. Proceedings of the IEEE International Conference on Bioinformatics & Biomedicine, December 18-21, Hong Kong. 2010. pp. 505-509.