Eugene Lin, Ph.D.
Research
About Me
Artificial Intelligence
Conduct research in the intersection of artificial intelligence and medicine
Machine Learning
Ensemble Machine Learning Framework
I Conduct research in the intersection of
artificial intelligence and medicine...
using single-cell RNA sequencing, multi-omics, neuroimaging, Taiwan Biobank,
genome-wide association studies, and whole genome sequencing.
I also develop algorithms in R, Python, and TensorFlow
for machine learning, computational biology, genetics, biostatistics,
statistical genetics, artificial intelligence, data visualization, bioinformatics,
statistical learning, multi-omics, computational genomics, deep learning,
computer vision, and natural language processing. (The code)
Recent works
Selected Publications
(*Corresponding author)
Lin E, Hwang JN, Chang MW. In search for proper boundary conditions of pharyngeal bolus movement using neural network inversion. International Journal of Knowledge Based Intelligent Engineering Systems. 1999;3(3):172-177.
Yuan C, Lin E, Millard J, Hwang JN. Closed contour edge detection of blood vessel lumen and outer wall boundaries in black-blood MR images. Magnetic Resonance Imaging. 1999;17(2):257-66.
Chang MW, Lin E, Hwang JN. Contour tracking using a knowledge-based snake algorithm to construct three-dimensional pharyngeal bolus movement. Dysphagia. 1999;14(4):219-27.
Kang X, Polissar NL, Han C, Lin E, Yuan C. Analysis of the measurement precision of arterial lumen and wall areas using high-resolution MRI. Magnetic Resonance in Medicine. 2000;44(6):968-72.
Lin E, Hwang Y, Tzeng CM. A case study of the utility of the HapMap database for pharmacogenomic haplotype analysis in the Taiwanese population. Molecular Diagnosis & Therapy. 2006;10(6):367-70.
Lin E, Hwang Y, Wang SC, Gu ZJ, Chen EY. An artificial neural network approach to the drug efficacy of interferon treatments. Pharmacogenomics. 2006;7(7):1017-24.
Lin E, Hwang Y, Liang KH, Chen EY. Pattern-recognition techniques with haplotype analysis in pharmacogenomics. Pharmacogenomics. 2007;8(1):75-83.
Lin E, Hwang Y, Chen EY. Gene-gene and gene-environment interactions in interferon therapy for chronic hepatitis C. Pharmacogenomics. 2007;8(10):1327-35.
Lin E, Hwang Y. A support vector machine approach to assess drug efficacy of interferon-alpha and ribavirin combination therapy. Molecular Diagnosis & Therapy. 2008;12(4):219-23.
Lin E, Chen PS, Huang LC, Hsu SY. Association study of a brain-derived neurotrophic-factor polymorphism and short-term antidepressant response in major depressive disorders. Pharmacogenomics and Personalized Medicine. 2008;1:1-6.
Lin E, Chen PS. Pharmacogenomics with antidepressants in the STAR*D study. Pharmacogenomics. 2008;9(7):935-46.
Lin E, Hsu SY. A Bayesian approach to gene-gene and gene-environment interactions in chronic fatigue syndrome. Pharmacogenomics. 2009;10(1):35-42.
Lin E, Pei D, Huang YJ, Hsieh CH, Wu LS. Gene-gene interactions among genetic variants from obesity candidate genes for nonobese and obese populations in type 2 diabetes. Genetic Testing and Molecular Biomarkers. 2009;13(4):485-93.
Hsiao DJ, Wu LS, Huang SY, Lin E*. Weight loss and body fat reduction under sibutramine therapy in obesity with the C825T polymorphism in the GNB3 gene. Pharmacogenetics and Genomics. 2009;19(9):730-3.
Huang LC, Hsu SY, Lin E*. A comparison of classification methods for predicting Chronic Fatigue Syndrome based on genetic data. Journal of Translational Medicine. 2009;7:81.
Lin E, Chen PS, Chang HH, Gean PW, Tsai HC, Yang YK, Lu RB. Interaction of serotonin-related genes affects short-term antidepressant response in major depressive disorder. Progress in Neuropsychopharmacology & Biological Psychiatry. 2009;33(7):1167-72.
Wu LS, Hsieh CH, Pei D, Hung YJ, Kuo SW, Lin E*. Association and interaction analyses of genetic variants in ADIPOQ, ENPP1, GHSR, PPARgamma and TCF7L2 genes for diabetic nephropathy in a Taiwanese population with type 2 diabetes. Nephrology Dialysis Transplantation. 2009;24(11):3360-6.
Lin E, Hong CJ, Hwang JP, Liou YJ, Yang CH, Cheng D, Tsai SJ. Gene-gene interactions of the brain-derived neurotrophic-factor and neurotrophic tyrosine kinase receptor 2 genes in geriatric depression. Rejuvenation Research. 2009;12(6):387-93.
Hsiao TJ, Wu LS, Hwang Y, Huang SY, Lin E*. Effect of the common -866G/A polymorphism of the uncoupling protein 2 gene on weight loss and body composition under sibutramine therapy in an obese Taiwanese population. Molecular Diagnosis & Therapy. 2010;14(2):101-6.
Chi MH, Lee SY, Chang HH, Yang YK, Lin E, Chen PS. Comparison of antidepressant efficacy-related SNPs among Taiwanese and four populations in the HapMap database. Journal of the Formosan Medical Association. 2011;110(7):478-82.
Lane HY, Tsai GE, Lin E*. Assessing gene-gene interactions in pharmacogenomics. Molecular Diagnosis & Therapy. 2012;16(1):15-27.
Liou YJ, Bai YM, Lin E, Chen JY, Chen TT, Hong CJ, Tsai SJ. Gene-gene interactions of the INSIG1 and INSIG2 in metabolic syndrome in schizophrenic patients treated with atypical antipsychotics. The Pharmacogenomics Journal. 2012;12(1):54-61.
Wang CH, Ke WS, Lin E*. Evaluation of the ENPP1 and PLIN single nucleotide polymorphisms with type 2 diabetes in a Taiwanese population: evidence for replication and gene-gene interaction. Journal of Investigative Medicine. 2012;60(8):1169-73.
Hsiao TJ, Hwang Y, Liu CH, Chang HM, Lin E*. Association of the C825T polymorphism in the GNB3 gene with obesity and metabolic phenotypes in a Taiwanese population. Genes & Nutrition. 2013;8(1):137-44.
Hsiao TJ, Hwang Y, Chang HM, Lin E*. Association of the rs6235 variant in the proprotein convertase subtilisin/kexin type 1 (PCSK1) gene with obesity and related traits in a Taiwanese population. Gene. 2014;533(1):32-7.
Hsiao TJ, Lin E*. Evaluation of the glutamine 27 glutamic acid polymorphism in the adrenoceptor β2 surface gene on obesity and metabolic phenotypes in Taiwan. Journal of Investigative Medicine. 2014;62(2):310-5.
Lin E, Lane HY. Genome-wide association studies in pharmacogenomics of antidepressants. Pharmacogenomics. 2015;16(5):555-66.
Hsiao TJ, Lin E*. The Pro12Ala polymorphism in the peroxisome proliferator-activated receptor gamma (PPARG) gene in relation to obesity and metabolic phenotypes in a Taiwanese population. Endocrine. 2015;48(3):786-93.
Lin E, Tsai SJ. Genome-wide microarray analysis of gene expression profiling in major depression and antidepressant therapy. Progress in Neuro-Psychopharmacology and Biological Psychiatry. 2016;64:334-40.
Hsiao TJ, Lin E*. Association of a common rs9939609 variant in the fat mass and obesity-associated (FTO) gene with obesity and metabolic phenotypes in a Taiwanese population: a replication study. Journal of Genetics. 2016;95(3):595-601.
Hsiao TJ, Lin E*. The ENPP1 K121Q polymorphism is associated with type 2 diabetes and related metabolic phenotypes in a Taiwanese population. Molecular and Cellular Endocrinology. 2016;433:20-5.
Lin E*, Kuo PH, Liu YL, Yang AC, Kao CF, Tsai SJ. Association and interaction of APOA5, BUD13, CETP, LIPA and health-related behavior with metabolic syndrome in a Taiwanese population. Scientific Reports. 2016;6:36830.
Hsiao TJ, Lin E*. A Validation Study of Adiponectin rs266729 Gene Variant with Type 2 Diabetes, Obesity, and Metabolic Phenotypes in a Taiwanese Population. Biochemical Genetics. 2016;54(6):830-841.
Lin E, Lane HY. Machine learning and systems genomics approaches for multi-omics data. Biomarker Research. 2017;5:2.
Hsiao TJ, Lin E*. A common rs7903146 variant of the transcription factor 7-like 2 gene is associated with type 2 diabetes mellitus and fasting glucose in a Taiwanese population. Diabetes & Metabolism. 2017;43(1):83-85.
Lin E*, Tsai SJ, Kuo PH, Liu YL, Yang AC, Kao CF, Yang CH. The rs1277306 Variant of the REST Gene Confers Susceptibility to Cognitive Aging in an Elderly Taiwanese Population. Dementia and Geriatric Cognitive Disorders. 2017;43(3-4):119-127.
Lin E*, Tsai SJ, Kuo PH, Liu YL, Yang AC, Kao CF. Association and interaction effects of Alzheimer's disease-associated genes and lifestyle on cognitive aging in older adults in a Taiwanese population. Oncotarget. 2017;8(15):24077-24087.
Lin E*, Tsai SJ, Kuo PH, Liu YL, Yang AC, Kao CF, Yang CH. The ADAMTS9 gene is associated with cognitive aging in the elderly in a Taiwanese population. PLoS One. 2017;12(2):e0172440.
Lin E*, Kuo PH, Liu YL, Yang AC, Kao CF, Tsai SJ. Effects of circadian clock genes and environmental factors on cognitive aging in old adults in a Taiwanese population. Oncotarget. 2017;8(15):24088-24098.
Lin E*, Kuo PH, Liu YL, Yang AC, Kao CF, Tsai SJ. Effects of circadian clock genes and health-related behavior on metabolic syndrome in a Taiwanese population. PLoS One. 2017;12(3):e0173861.
Lin E*, Kuo PH, Liu YL, Yang AC, Tsai SJ. Transforming growth factor-β signaling pathway-associated genes SMAD2 and TGFBR2 are implicated in metabolic syndrome in a Taiwanese population. Scientific Reports. 2017;7(1):13589.
Lin E*, Kuo PH, Liu YL, Yang AC, Tsai SJ. Detection of susceptibility loci on APOA5 and COLEC12 associated with metabolic syndrome using a genome-wide association study in a Taiwanese population. Oncotarget. 2017;8(55):93349-93359.
Lin CH, Lin E, Lane HY. Genetic biomarkers on age-related cognitive decline. Frontiers in Psychiatry. 2017;8:247.
Lin E*, Kuo PH, Liu YL, Yu YWY, Yang AC, Tsai SJ. A deep learning approach for predicting antidepressant response in major depression using clinical and genetic biomarkers. Frontiers in Psychiatry 2018;9:290.
Lin E, Lin CH, Lai YL, Huang CH, Huang YJ, Lane HY. Combination of G72 Genetic Variation and G72 Protein Level to Detect Schizophrenia: Machine Learning Approaches. Frontiers in Psychiatry 2018;9:566.
Lin E*, Kuo PH, Liu YL, Yang AC, Tsai SJ. Polymorphisms of the DNA repair gene EXO1 modulate cognitive aging in old adults in a Taiwanese population. DNA Repair (Amst). 2019;78:1-6.
Lin E*, Kuo PH, Liu YL, Yang AC, Tsai SJ. Association and interaction effects of interleukin-12 related genes and physical activity on cognitive aging in old adults in the Taiwanese population. Frontiers in Neurology. 2019; 10, 1065.
Lin E, Lin CH, Lane HY. Precision Psychiatry Applications with Pharmacogenomics: Artificial Intelligence and Machine Learning Approaches. International Journal of Molecular Sciences 2020; 21 (3), 969.
Lin E, Mukherjee S, Kannan S. A deep adversarial variational autoencoder model for dimensionality reduction in single-cell RNA sequencing analysis. BMC Bioinformatics 2020; 21 (1), 1-11.
Hou SJ, Tsai SJ, Kuo PH, Liu YL, Yang AC, Lin E*, Lan TH. An association study in the Taiwan Biobank reveals RORA as a novel locus for sleep duration in the Taiwanese Population. Sleep Medicine 2020; 73:70-75.
Lin E, Lin CH, CC Hung, Lane HY. An ensemble approach to predict schizophrenia using protein data in the N-methyl-D-aspartate receptor (NMDAR) and tryptophan catabolic pathways. Frontiers in Bioengineering and Biotechnology 2020; 8, 569.
Lin E, Lin CH, Lane HY. Relevant Applications of Generative Adversarial Networks in Drug Design and Discovery: Molecular De Novo Design, Dimensionality Reduction, and De Novo Peptide and Protein Design. Molecules 2020; 25 (14), 3250.
Lin E*, Kuo PH, Liu YL, Yu YWY, Yang AC, Tsai SJ. Prediction of Antidepressant Treatment Response and Remission Using an Ensemble Machine Learning Framework. Pharmaceuticals 2020; 13 (10), 305.
Contacts
You will find the latest information about me on this page. My research is constantly evolving and growing. I conduct a wide range of research topics. My mission is to provide the best solution that helps improve human health. If you want to contact me, please fill out the contact form on the website. I wish you a good day!
