M Aghayev, A Arias-Alvarado, S Ilchenko, J Lepp, I Scott, Y-R Chen, G-F Zhang, T-H Tsai, T Kasumov (2023). A high-fat diet increases hepatic mitochondrial turnover through restricted acetylation in a NAFLD mouse model. American Journal of Physiology-Endocrinology and Metabolism, 325(1):E83–E98. [Link] [PubMed]
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V Verma, D Dahal, R Radha Krishnan, B Lussem, T-H Tsai (2022). Accurate and reproducible mobility estimation enables high-throughput analysis of organic field-effect transistors. Computational Material Science, 214:111689. [Link]
J Bao, S Jegede, J Hawks, B Dade, Q Guan, S Middaugh, Z Qiu, A Levina, T-H Tsai (2022). Detecting cochlear synaptopathy through curvature quantification of the auditory brainstem response. Frontiers in Cellular Neuroscience, 16:851500. [Link] [PubMed]
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M Choi, J Carver, C Chiva, M Tzouros, T Huang, T-H Tsai, B Pullman, O Bernhardt, R Huttenhain, G Teo, Y Perez-Riverol, J Muntel, M Muller, S Goetze, M Pavlou, E Verschueren, B Wollscheid, A Nesvizhskii, L Reiter, T Dunkley, E Sabido, N Bandeira, O Vitek (2020). MassIVE.quant: a community resource of quantitative mass spectrometry-based proteomics datasets. Nature Methods, 17:981–984. [Link] [PubMed]
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M Wang, T-H Tsai, C Di Poto, A Ferrarini, G Yu, HW Ressom (2016). Topic model-based mass spectrometric data analysis in cancer biomarker discovery studies. BMC Genomics, 17(Suppl 4):545. [Link] [PubMed]
T-H Tsai, E Song, Z Rui, C Di Poto, M Wang, Y Luo, RS Varghese, MG Tadesse, DH Ziada, CS Desai, K Shetty, Y Mechref, HW Ressom (2015). LC-MS/MS based serum proteomics for identification of candidate biomarkers for hepatocellular carcinoma. Proteomics, 15(13):2369–2381. [Link] [PubMed]
T-H Tsai, M Wang, C Di Poto, Y Hu, S Zhou, Y Zhao, RS Varghese, Y Luo, MG Tadesse, DH Ziada, CS Desai, K Shetty, Y Mechref, HW Ressom (2014). LC-MS profiling of N-glycans derived from human serum samples for biomarker discovery in hepatocellular carcinoma. Journal of Proteome Research, 13(11):4859–4868. [Link] [PubMed]
T-H Tsai, MG Tadesse, C Di Poto, LK Pannell, Y Mechref, Y Wang, HW Ressom (2013). Multi-profile Bayesian alignment model for LC-MS data analysis with integration of internal standards. Bioinformatics, 29(21):2774–2780. [Link] [PubMed]
T-H Tsai, MG Tadesse, Y Wang, HW Ressom (2013). Profile-based LC-MS data alignment — A Bayesian approach. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 10(2):494–503. [Link] [PubMed]
JF Xiao, RS Varghese, B Zhou, MR Ranjbar, Y Zhao, T-H Tsai, C Di Poto, J Wang, D Goerlitz, Y Luo, AK Cheema, N Sarhan, H Soliman, MG Tadesse, DH Ziada, HW Ressom (2012). LC-MS based serum metabolomics for identification of hepatocellular carcinoma biomarkers in Egyptian cohort. Journal of Proteome Research, 11(12):5914–5923. [Link] [PubMed]
HW Ressom, JF Xiao, L Tuli, RS Varghese, B Zhou, T-H Tsai, MR Ranjbar, Y Zhao, J Wang, C Di Poto, AK Cheema, MG Tadesse, R Goldman, K Shetty (2012). Utilization of metabolomics to identify serum biomarkers for hepatocellular carcinoma in patients with liver cirrhosis. Analytica Chimica Acta, 743:90–100. [Link] [PubMed]
L Tuli, T-H Tsai, RS Varghese, JF Xiao, AK Cheema, HW Ressom (2012). Using a spike-in experiment to evaluate analysis of LC-MS data. Proteome Science, 10(13). [Link] [PubMed]
GK Befekadu, MG Tadesse, T-H Tsai, HW Ressom (2011). Probabilistic mixture regression models for alignment of LC-MS data. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 8(5):1417–1424. [Link] [PubMed]
T-T Liu, Y-H Lin, C-S Hung, T-J Liu, Y Chen, Y-C Huang, T-H Tsai, H-H Wang, D-W Wang, J-K Wang, Y-L Wang, C-H Lin (2009). A high speed detection platform based on surface-enhanced Raman scattering for monitoring antibiotic-induced chemical changes in bacteria cell wall. PLoS One, 4(5):e5470. [Link] [PubMed]
Y-H Yi, P-Y Ho, T-W Chen, W-J Lin, V Gukassyan, T-H Tsai, D-W Wang, T-S Liu, C-Y Tang, SJ Lo, T-Y Chen, F-J Kao, C-H Lin (2009). Membrane targeting and coupling of NHE1-integrin\(\alpha_{\text{IIb}}\beta_{3}\)-NCX1 by lipid rafts following integrin-ligand interactions trigger Ca\(^{2+}\) oscillations. Journal of Biological Chemistry, 284(6):3855–3864. [Link] [PubMed]
Y Fu, T-H Tsai, C Mao, SK Mun, HW Ressom, M Wang, Z Zhang, Y Wang (2020). Biological Computing. In Biomedical Information Technology (Ed. D.D. Feng), Academic Press, pp. 81–104. [Link]
Y Zhao, T-H Tsai, C Di Poto, LK Pannell, MG Tadesse, HW Ressom (2017). Variability Assessment of Label-free LC-MS Experiments for Difference Detection. In Statistical Analysis of Proteomics, Metabolomics and Lipidomics Data using Mass Spectrometry (Eds. S. Datta and B.J.A. Mertens), Springer, pp. 157–176. [Link]
T-H Tsai, M Wang, HW Ressom (2016). Preprocessing and Analysis of LC-MS-based Proteomic Data. In Statistical Analysis in Proteomics (Ed. K. Jung), Springer, pp. 63–76. [Link] [PubMed]