Publication List

Year 2016

  • Wang M, Di Poto C, Ferrarini A, Yu G, Ressom HW (2016). Metabolomic data deconvolution using probabilistic puri cation 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.
  • Di Poto C, Ferrarini A, Zhao Y, Varghese RS, Tu C, Zuo Y, Wang M, et al (2016). Metabolomic characterization of hepatocellular carcinoma in patients with liver cirrhosis for biomarker discovery. Cancer Epidemiol Biomarkers Prev , DOI: 10.1158/1055-9965.EPI-16-0366.
  • 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. In review
  • 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. In review.
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    Year 2015

  • 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.
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    Year 2014

  • 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
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    Year 2013

  • 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.
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    Year 2012

  • 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.
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    Year 2011

  • 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.
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    Year 2010

  • 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.
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    Year 2009

  • Tuli L and Ressom HW (2009). LCS based detection of differential protein expression. Journal of Proteomics and Bioinformatics 2(10); 416-438.
  • Goldman R, Ressom HW, Varghese RS, Goldman L, Bascug G, Loffredo CA, Abdel-Hamid M, Gouda I, Ezzat S, Kyselova Z, Mechref Y, Novotny MV (2009). Detection of hepatocellular carcinoma using glycomic analysis. Clin Cancer Res. 15(5):1808-13.
  • Zhang Y, Xuan J, de Los Reyes BG, Clarke R, Ressom HW (2009). Reverse engineering module networks by PSO-RNN hybrid modeling. BMC Genomics 10(Suppl 1):S15.
  • Solomon DA, Kim JS, Ressom HW, Sibenaller Z, Ryken T, Jean W, Bigner D, Yan H, Waldman T (2009). Sample type bias in the analysis of cancer genomes. Cancer Res. 69(14):5630-3.
  • Timofeeva OA, Zhang X, Ressom HW, Varghese RS, Kallakury BV, Wang K, Ji Y, Cheema A, Jung M, Brown ML, Rhim JS, Dritschilo A (2009). Enhanced expression of SOS1 is detected in prostate cancer epithelial cells from African-American men. Int J Oncol. 35(4):751-60.
  • Ressom HW, Varghese RS, Goldman R (2009). Computational methods for analysis of MALDI-TOF spectra to discover peptide serum biomarkers. Protein Protocols Handbook 3rd Ed. (J.M. Walker, Ed.), Humana Press. 2009.
  • Ressom HW, Befekadu GK, Tadesse MG (2009). Analysis of LC-MS data using probabilistic-based mixture regression models. at ?Automatisierungstechnik 57(9): 453-465.
  • Befekadu GK, Tadesse MG, Hathout Y, Ressom HW (2009). A Bayesian based functional mixed-effects model for analysis of LC-MS data. Conf Proc IEEE Eng Med Biol Soc. 2009; 6743-6746.
  • An, Yanming, Ressom, HW, Goldman R (2009). Enrichment of serum peptides and analysis by MALDI-TOF mass spectrometry. Protein Protocols Handbook 3rd Ed. (J.M. Walker, Ed.), Humana Press. 2009.
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    Year 2008

  • Zhang Y, Xuan J, de Los Reyes BG, Clarke R, Ressom HW (2008). Network motif-based identification of transcription factor-target gene relationships by integrating multi-source biological data. BMC Bioinformatics 9(1):203.
  • Solomon DA, Kim JS, Cronin JC, Sibenaller Z, Ryken T, Rosenberg SA, Ressom H, Jean W, Bigner D, Yan H, Samuels Y, Waldman T (2008). Mutational Inactivation of PTPRD in Glioblastoma Multiforme and Malignant Melanoma. Cancer Res. 68(24):10300-6.
  • Ressom HW, Varghese RS, Goldman L, Loffredo CA, Abdel-Hamid M, Kyselova Z, Mechref Y, Novotny M, Goldman R (2008). Analysis of MALDI-TOF mass spectrometry data for detection of glycan biomarkers. Pacific Symposium on Biocomputing 13:216-227.
  • Ressom HW, Varghese RS, Zhang Y, Xuan J, Clarke R (2008). Classification algorithms for phenotype prediction in genomics and proteomics. Frontiers in Biosciences 13:691-708.
  • Ressom HW, Varghese RS, Goldman L, Yanming A, Loffredo CA, Abdel-Hamid M, Kyselova Z, Mechref Y, Novotny M, Drake, S, Goldman R (2008). Analysis of MALDI-TOF mass spectrometry data for discovery of peptide and glycan biomarkers of hepatocellular carcinoma. Journal of Proteome Research 7(2) 603-610.
  • Solomon DA, Kim JS, Jenkins S, Ressom H, Huang M, Coppa N, Mabanta L, Bigner D, Yan H, Jean W, Waldman T (2008). Identification of p18 INK4c as a tumor suppressor gene in glioblastoma multiforme. Cancer Res 68(8):2564-9.
  • Song J., Liu H., Ressom H., Tiwari S., Ecelbarger CA (2008). Chronic rosiglitazone therapy normalizes expression of ACE1, SCD1 and other genes in the kidney of obese Zucker rats as determined by microarray analysis. Experimental and Clinical Endocrinology & Diabetes 116:315-325.
  • Clarke R, Ressom HW, Wang A, Xuan J, Liu MC, Gehan EA, Wang Y (2008). The properties of very high dimensional data spaces: implications for exploring gene and protein expression data. Nature Reviews Cancer 8(1):37-49.
  • Tang Y, Kitisin K, Jogunoori W, Li C, Deng CX, Mueller SC, Ressom HW, Rashid A, He AR, Mendelson JS, Jessup JM, Shetty K, Zasloff M, Mishra B, Reddy EP, Johnson L, Mishra L (2008). Progenitor/stem cells give rise to liver cancer due to aberrant TGF-beta and IL-6 signaling. PNAS 105(7): 2445-2450.
  • Varghese RS, Goldman L, An Y, Loffredo CA, Abdel-Hamid M, Kyselova Z, Mechref Y, Novotny M, Drake SK, Goldman R, Ressom HW (2008). Integrated peptide and glycan biomarker discovery using MALDI-TOF mass spectrometry. Conf Proc IEEE Eng Med Biol Soc. 2008;1:3791-3794.
  • Befekadu GK, Tadesse MG, Hathout Y, Ressom HW (2008). Multi-class alignment of LC-MS data using probabilistic-based mixture regression models. Conf Proc IEEE Eng Med Biol Soc. 2008;1:4094-4097.
  • Zhang Y, Xuan J, de los Reyes BG, Clarke R, Ressom HW (2008). Network motif-based identification of breast cancer susceptibility genes. Conf Proc IEEE Eng Med Biol Soc. 2008;1:5696-5699.
  • Befekadu GK, Tadesse MG, Ressom HW (2008). Probabilistic-based mixture regression models for multi-class alignment of LC-MS data. Proceedings of the 2008 International Conference on Bioinformatics and Computational Biology (BIOCOMP'08), Las Vegas, NV, July 14-17, 2008, 368-373.
  • Zhang Y, Xuan J, de los Reyes BG, Clarke R, Ressom HW (2008). Reverse engineering module networks by PSO-RNN hybrid modeling. Proceedings of the 2008 International Conference on Bioinformatics and Computational Biology (BIOCOMP'08), Las Vegas, NV, July 14-17, 2008, 401-407.
  • De Los Reyes BG, Lakshman D, Yun SJ, Ressom H (2008). Agricultural genomic. In: Textbook of Agricultural Biotechnology, (A. Nag, Ed.), PHI Learning, New Delhi, India, pp. 55-88.
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    Year 2007

  • Ressom HW, Varghese RS, Drake SK, Hortin GL, Abdel-Hamid M, Loffredo CA, and Goldman R (2007). Peak selection from MALDI-TOF mass spectra using ant colony optimization. Bioinformatics 23(5):619-626.
  • Goldman R, Ressom HW, Abdel-Hamid M, Goldman L, Wang A, Varghese RS, An Y, Loffredo CA, Drake SK, Eissa SA, Gouda I, Ezzat S, Seillier-Moiseiwitsch F (2007). Candidate markers for the detection of hepatocellular carcinoma in low molecular weight fraction of serum. Carcinogenesis 28(10):2149-53.
  • Kim JS, Lee C, Bonifant CL, Ressom H, Waldman T (2007). Activation of p53-Dependent Growth Suppression in Human Cells by Mutations in PTEN or PIK3CA.Mol Cell Biol 27(2): 662-677.
  • Xu J, Gao M, Fan S, Meng Q, Goldberg ID, Abounader R, Ressom H, Laterra JJ, Rosen EM (2007). Effect of Akt inhibition on scatter factor-regulated gene expression in DU-145 human prostate cancer cells. Oncogene 26(20): 2925-2938.
  • Cheng C, Yun K-Y, Ressom HW, Mohanty B, Bajic VB, Jia Y, Yun SJ, de los Reyes BG (2007). An early response regulatory cluster induced by low temperature and hydrogen peroxide in seedlings of chilling-tolerant japonica rice. BMC Genomics 8: 175.
  • Musavi MT, Ressom H, Srirangam S, Natarajan P, Virnstein RW, Morris LJ, and Tweedale W (2007). Neural network-based light attenuation model for monitoring seagrass population in the Indian river lagoon. J Intell Inf Syst. 29: 63-77.
  • Ressom HW, Varghese RS, Goldman L, Loffredo CA, Abdel-Hamid M, Kyselova Z, Mechref Y, Novotny M, Goldman R (2007). Analysis of mass spectrometry data for serum biomarker discovery. Proceedings The third IEEE-NIH LIfe Science Systems and Applications (LISSA'07) Workshop, Nov 2007, Bethesda, MD.
  • Ressom HW, Zhang Y, Xuan J, Wang J, Clarke R (2007). Integrating multi-source biological data for transcriptional regulatory module discovery. Proceedings The third IEEE-NIH LIfe Science Systems and Applications (LISSA'07) Workshop, Nov 2007, Bethesda, MD.
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    Year 2006

  • Ressom HW, Fyfe SK, Srirangam S, Natarajan P, and Musavi MT (2006). Neural network-based estimation of photosynthetic efficiency. International Journal of Ocean and Oceanography 1(3), Sep. 06. http://www.ripublication.com/Volume/ijoov1n3.htm.
  • Orvisky E, Drake SK, Martin BM, Ressom H, Varghese RS, Saha D, Hortin GL, Loffredo CA, Goldman R (2006). Enrichment of low molecular weight fraction of serum for mass spectrometric analysis of peptides associated with hepatocellular carcinoma. Proteomics 6(9) 2895-2902.
  • Ressom HW, Zhang Y, Xuan J, Wang J, Clarke R (2006). Inferring network interactions using recurrent neural networks and swarm intelligence. Proceedings of the 28th IEEE Engineering in Medicine and Biology Society Annual International Conference, New York, NY, 4241-4244.
  • Ressom HW, Varghese RS, Orvisky E, Drake SK, Hortin GL, Abdel-Hamid M, Loffredo CA, and Goldman R (2006). Ant colony optimization for biomarker identification from MALDI-TOF mass spectra. Proceedings of the 28th IEEE Engineering in Medicine and Biology Society Annual International Conference, New York, NY, 4560-4563.
  • Ressom HW, Varghese RS, Orvisky E, Drake SK, Hortin GL, Abdel-Hamid M, Loffredo CA, and Goldman R (2006). Biomarker identification and rule extraction from mass spectral serum profiles. Proceedings of the 2006 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, Toronto, ON, 164-170.
  • Ressom HW, Zhang Y, Xuan J, Wang J, Clarke R (2006). Inference of gene regulatory networks from time course gene expression data using neural networks and swarm intelligence. Proceedings of the 2006 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, Toronto, ON, 435-442.
  • Ressom HW, Turner K, and Musavi MT (2006). Estimation of ocean water chlorophyll-a concentration using computational intelligence. Proceedings of Oceans '06 MTS/IEEE, Boston, MA, 1-6.
  • Ressom HW, Turner K, and Musavi MT (2006). Estimation of ocean water chlorophyll-a concentration using fuzzy c-means clustering and artificial neural networks. Proceedings of the International Joint Conference on Neural Networks, Vancouver, BC, Canada, 4118-4125.
  • Ressom HW, Zhang Y, Xuan J, Wang J, Clarke R (2006). Inferring network interactions using recurrent neural networks and particle swarm optimization. Proceedings of the First International Conference on Computational Systems Biology, Shanghai, China.
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    Year 2005

  • Ressom HW, Varghese RS, Abdel-Hamid M, Abdel-Latif Eissa S, Saha D, Goldman L, Petricoin EF, Conrads TP, Veenstra TD, Loffredo CA, Goldman R (2005). Analysis of mass spectral serum profiles for biomarker selection. Bioinformatics 21(21):4039-4045.
  • Ressom H, Natarjan P, Varghese RS, and Musavi MT (2005). Applications of fuzzy logic in genomics. Journal of Fuzzy Sets and Systems 152: 125-138.
  • Ressom H, Miller RL, Natarajan P, and Slade WH (2005). Computational intelligence and its application in remote sensing. In: Remote Sensing of Coastal Aquatic Environments: Technologies, Techniques and Applications. Series: Remote Sensing and Digital Image Processing, Vol. 7, Miller, Richard L.; Del Castillo, Carlos E.; McKee, Brent A. (Eds.), XVIII, 347 p., ISBN: 1-4020-3099-1, Springer, Berlin.
  • Ressom HW and Natarajan P (2005). Gene expression clustering using computational intelligence. In: Bioinformatics: New Research, Editor: Yan, Peter V., pp. 1-25, ISBN 1-59454-242-2, Nova Science Publishers Inc., New York.
  • Ressom HW, Varghese RS, Orvisky E, Drake SK, Hortin GL, Abdel-Hamid M, Loffredo CA, and Goldman R (2005). Analysis of MALDI-TOF serum profiles for biomarker selection and sample classification. Proceedings of the IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, La Jolla, CA, pp. 378-384.
  • Ressom H, Varghese RS, Saha D, Orvisky E, Goldman L, Petricoin EF, Conrads TP, Veenstra TD, Abdel-Hamid M, Loffredo CA, Goldman R (2005). Particle swarm optimization for analysis of mass spectral serum profiles. In Proceedings of the Genetic and Evolutionary Computation Conference, GECCO-2005, Beyer, H.G. et al. (Editors), ACM Press, New York, vol. 1, pp. 431-438.
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    Year 2004

  • Slade WH, Ressom H, Musavi MT, and Miller RL (2004). Inversion of ocean color observations using particle swarm optimization. IEEE Transactions on Geoscience and Remote Sensing 42(9):1915-1923.
  • Slade WH, Ressom H, M.T, Musavi, and Miller RL (2004). Ocean color inversion by particle swarm optimization. Proceedings of 2004 IEEE Congress on Evolutionary Computation (CEC 2004), Portland, Oregon, June 19-23, 2004, pp. 971-977.
  • Varghese RS, Musavi MT, and Ressom H (2004). Fuzzy confidence value for DNA bases. Proceedings of IEEE International conference on Fuzzy Systems (FUZZ-IEEE 2004), Budapest, Hungary, July 25-29, 2004. IEEE Catalog # 04CH37542C, ISBN 0-7803-8354-0, CD-ROM Edition.
  • Ressom H, Natarjan P, Srirangam S, Musavi MT, Virnstein RW, Morris LJ, and Tweedale W (2004). Neural network based light attenuation model for monitoring seagrass health. Proceedings of the International Joint Conference on Neural Networks (IJCNN 2004), Budapest, Hungary, July 25-29, 2004, IEEE Catalog # 04CH37541C, ISBN 0-7803-8360-5, CD-ROM Edition.
  • Ressom H, Fyfe SK, Srirangam S, Musavi MT, and Natarjan P (2004). Estimation of photosynthetic efficiency for monitoring seagrass health using neural networks. Proceedings of IASTED International Conference on Neural Networks and Computational Intelligence (NCI 2004), Grindelwald, Switzerland, Feb. 23-25, 2004, pp. 232-237.
  • Slade WH, Miller RL, Ressom H, and Natarjan P (2004). Neural network retrieval of phytoplankton abundance from remotely-sensed ocean radiance. Proceedings of IASTED International Conference on Neural Networks and Computational Intelligence (NCI 2004), Grindelwald, Switzerland, Feb. 23-25, 2004, pp. 226-231.
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    Year 2003

  • Ressom H, Wang D, and Natarjan P (2003). Adaptive double self-organizing maps for clustering gene expression profiles. Neural Networks 16(5-6):633-640.
  • Ressom H, Reynolds R, and Varghese RS (2003). Increasing the efficiency of fuzzy logic-based gene expression data analysis. Physiological Genomics 13:107-117.
  • Ressom H, Wang D, and Natarjan P (2003). Clustering gene expression data using adaptive double self-organizing map. Physiological Genomics 14:35-46.
  • Ressom H, Wang D, and Natarjan P (2003). Adaptive double self-organizing map and its application in clustering gene expression data. Proceedings of International Joint Conference on Neural Networks (IJCNN), Portland, OR, July 20-24, 2003, IEEE Catalog # 03CH37464C, ISBN 0-7803-7899-7, CD-ROM Edition, pp. 39-44.
  • Ressom H, Fyfe SK, Natarjan P, and Srirangam S (2003). Monitoring seagrass health using neural networks. Proceedings of International Joint Conference on Neural Networks (IJCNN), Portland, OR, July 20-24, 2003, IEEE Catalog # 03CH37464C, ISBN 0-7803-7899-7, CD-ROM Edition, pp. 1019-1024.
  • Srirangam S, Ressom H, Natarjan P, Musavi MT, Virnstein RW, Morris LJ, and Tweedale W (2003). Neural network-based estimation of light attenuation coefficient. Proceedings of International Joint Conference on Neural Networks (IJCNN), Portland, OR, July 20-24, 2003, IEEE Catalog # 03CH37464C, ISBN 0-7803-7899-7, CD-ROM Edition, pp. 590-595.
  • Slade WH, Miller RL, Ressom H, and Natarjan P (2003). Ensemble neural network methods for satellite-derived estimation of chlorophyll a. Proceedings of International Joint Conference on Neural Networks (IJCNN), Portland, OR, July 20-24, 2003, IEEE Catalog # 03CH37464C, ISBN 0-7803-7899-7, CD-ROM Edition, pp. 547-552.
  • Ressom H, Wang D, Varghese RS, and Reynolds R (2003). Fuzzy logic-based gene regulatory network. Proceedings of IEEE International Conference on Fuzzy Systems, St. Louis, MO, May 25-28, 2003, pp. 1210-1215.
  • Ressom H, Wang D, and Natarjan P (2003). Computational methods for identifying number of clusters in gene expression data. Proceedings of IASTED International Conference on Neural Networks and Computational Intelligence (NCI 2003), Cancun, Mexico, May 19-21, 2003, pp. 233-238.
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    Year 2002

  • Xiong N, Litz L, and Ressom H (2002). Learning premises of fuzzy rules for knowledge acquisition in classification problems. Knowledge and Information Systems 4(1): 96-111.
  • Slade WH, Miller RL, Ressom H, and Natarjan P (2002). Improved modeling of satellite-derived chlorophyll a concentration using neural networks. Ocean Optics XVI CD from ONR, Ocean Optics XVI, Santa Fe, NM, November 18-22, 2002.
  • French BD, Domnisoru C, Ressom H, and Musavi MT (2002). Confidence value prediction of called genetic bases using a fuzzy predication system," Proceedings of the International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences (METMBS '02), Las Vegas, NV, June 24-27, 2002, CSREA Press, ISBN 1-892512-39-4, H.R. Arabnia (Ed.), pp. 203-209.
  • Wang D, Ressom H, Musavi MT, and Domnisoru C (2002). Double self-organizing maps to cluster gene expression data. Proceedings of 10th European Symposium on Artificial Neural Networks (ESANN 2002), Bruges, Belgium, April 2002, d-side publi., ISBN 2-930307-02-1, pp. 45-50.
  • Reynolds R, Ressom H, Musavi MT, and Domnisoru C (2002). Improving robustness of fuzzy gene modeling. Proceedings of 10th European Symposium on Artificial Neural Networks (ESANN 2002), Bruges, Belgium, April 2002, d-side publi., ISBN 2-930307-02-1, pp. 51-56.
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    Year 2001

  • Ressom H, Musavi MT, Natarjan P (2001). Neural network-based estimation of phytoplankton primary production. Proceedings of SPIE, San Diego, CA, August 2001, vol. 4488, pp. 213-220.
  • Musavi MT, R. Miller, Ressom H, Natarjan P. (2001) Neural network-based estimation of chlorophyll-a concentration in coastal waters," Proceedings of SPIE, San Diego, CA, August 2001, vol. 4488, pp. 176-183.
  • Reynolds R, Ressom H, Musavi MT, and Domnisoru C (2001). Use of clustering to improve performance in fuzzy gene expression analysis. Proceedings of International Joint Conference on Neural Networks, Washington, DC, July 2001, pp. 2738-2743.
  • Ressom H, Musavi MT, and Khan S (2001). Intelligent control of critical dimension in photolithography process," Proceedings of International Joint Conference on Neural Networks, Washington, DC, July 2001, pp. 486-490.
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    Year 2000

  • Khan S, Musavi MT, and Ressom H (2000). Critical dimension control in semiconductor manufacturing. Intelligent Engineering Systems Through Artificial Neural Networks, vol. 10, editors: C.H. Dagli et al, ASME Press Series, pp. 995-1000.
  • Ressom H (2000). Neural network-based on-line quality prediction in nonwoven production. Intelligent Engineering Systems Through Artificial Neural Networks, vol. 10, editors: C.H. Dagli et al, ASME Press Series, pp. 1031-1036.
  • Ressom H, Voos H, Litz L, and Schmitt P (2000). On-line estimation of key quality parameters in nonwoven production. Proceedings of IEEE International Conference on Systems, Man, and Cybernetics, Nashville, TN, October 2000, pp. 1745-1749.
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    Year 1999

  • Martin Becker, Andreas Diehl, and Habtom Ressom (1999). Modeling a refrigeration system using recurrent neural networks. atp-Automatisierungstechnische Praxis 41(9):22-31. (in German)
  • Habtom Ressom, Holger Voos, and Lothar Litz, NeuroIdentifier: A software tool for neural network-based identification of dynamic systems,?at - Automatisierungstechnik, Oldenbourg-Verlag, vol. 47, No. 4, pp. 181-182, 1999. (in German)
  • Habtom Ressom (1999) Dynamic system and virtual sensor modeling using neural networks, VDI Fortschritt-Berichte, Series 8, No. 771, VDI-Verlag, Duesseldorf.
  • Habtom Ressom (1999). Modeling a compression plant using recurrent neural networks. Proceedings of International Joint Conference on Neural Networks (IJCNN), Washington DC, July 10-16, 1999, IEEE Catalog # 99CH36339C, ISBN 0-7803-5532-6, CD-ROM Edition
  • Holger Voos, Habtom Ressom, and Lothar Litz (1999). Development of an engineering tool for the design and optimization of knowledge-based control systems: a perspective. Proceedings of the 11th International Conference on Software Engineering and Knowledge Engineering, Kaiserslautern, Germany, 1999, pp. 327-331.
  • Habtom Ressom (1999). Soft-sensing using recurrent neural networks. Proceedings of IEEE International Symposium on Intelligent Control, Gaithersburg, MD, 1999. pp. 342-347.
  • Habtom Ressom (1999). Modeling a refrigeration system using recurrent neural networks. In: Lecture notes in computer science 1625: Editor: B. Reusch, Springer-Verlag, vol. 1625, pp. 47-52.
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    Year 1998

  • Habtom Ressom and Lothar Litz (1998). Neural network-based inferential sensing. In: Perspective in Neural Computing, Editors: L. Niklasson et al., Springer-Verlag, pp. 785-790.
  • Habtom Ressom and Lothar Litz (1998). Virtual sensors based on recurrent neural networks and the extended Kalman filter. Proceedings of IEEE International Conference on Control Applications, Trieste, Italy, 1998. pp. 163-167.
  • Lothar Litz, Klaus-Peter Klaan, and Habtom Ressom (1998). Methodik und Einsatzpotential von Fuzzy Control, Neuronalen Netzen und Neuro-Fuzzy. In: Fuzzy Control und Neuronale Netze zur Optimierung der Stickstoff- und Phosphorelimination, Schriftenreihe des Fachgebietes Siedlungswasserwirtschaft, Universit Kaiserslautern, Editors: T. G. Schmitt and J. Hansen, vol. 11, pp. 23-38.
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    Year 1997

  • Ressom Habtom and Lothar Litz (1997). Neurocontrol of nonlinear dynamic systems subject to unmeasured disturbance inputs. Lecture notes in computer science, Editor: Gerstner, vol. 1327, Springer-Verlag, pp. 855-860.
  • Ressom Habtom and Lothar Litz, (1997) Estimation of unmeasured inputs using recurrent neural networks and the extended Kalman filter. Proceedings of IEEE International Conference on Neural Networks, Houston, TX, 1997, pp. 2067-2071.
  • Habtom Ressom and Lothar Litz (1997). Neural network-based control of nonlinear dynamic systems with unmeasured inputs. Proceedings of 12th International Conference on Systems Engineering, Coventry, U.K., 1997, pp. 296-300.
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