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5th International Conference on Complex, Intelligent and Software Intensive Systems, CISIS 2011

作者： Tsai, Zing Tsung-Yeh Huang, Grace Tzu-Wei Tsai, Huai-Kuang Institute of Information Science Academia Sinica Taipei 115 Taiwan Bioinformatics Program Taiwan International Graduate Program Taiwan Institute of Biomedical Informatics National Yang-Ming University Taiwan Joint CMU-Pitt PhD Program in Computational Biology University of Pittsburgh Carnegie Mellon University Pittsburgh PA United States Research Center for Information Technology Innovation Taipei 115 Taiwan Computer Science and Engineering National Taiwan Ocean University Keelung 202 Taiwan

ISBN: (纸本)9780769543734

Identifying transcription factor binding sites (TFBSs) is crucial for understanding the mechanism of transcriptional regulation. It is known that transcription factors (TFs) often cooperate to regulate genes. While traditional approaches can be used to discover binding motifs of a group of co-regulated genes, they often fail to accurately assign motifs to the corresponding TFs. Here, we consider two TFs together to infer their TFBSs and their synergistic relationship simultaneously. The basic idea is that if two TFs interact, their TFBSs, if distinct, would be conserved across species and coincided in the promoter regions of the genes they co-regulated. Applying our method to Saccharomyces cerevisiae chromatin immunoprecipitation data, we predicted 110 TF pairs with statistically significant motif assignments. A majority of these TF pairs have literature support to be synergistic, and the designated motifs to TFs match well with their known consensus. We further examined the synergism of predicted TF pairs in seven experimental conditions using ANOVA, and identified significant interactions. © 2011 IEEE.

关键词： Yeast

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Molecular Evolution of Cystine-Stabilized Miniproteins as Stable Proteinaceous Binders

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Structure 2009年第4期17卷 620-631页

作者： Chang, Hung-Ju Hsu, Hung-Ju Chang, Chi-Fon Peng, Hung-Pin Sun, Yi-Kun Yu, Hui-Ming Shih, Hsi-Chang Song, Chun-Ying Lin, Yi-Ting Chen, Chu-Chun Wang, Chia-Hung Yang, An-Suei Genomics Research Center Academia Sinica Taipei 115 Taiwan Taiwan International Graduate Program Academia Sinica Taipei 115 Taiwan Institute of Biochemical Science National Taiwan University Taipei 106 Taiwan Graduate Institute of Life Sciences National Defence Medical Center Taipei 114 Taiwan Institute of BioMedical Informatics National Yang-Ming University Taipei 112 Taiwan Institute of Biochemistry and Molecular Biology National Yang-Ming University Taipei 112 Taiwan

Small cystine-stabilized proteins are desirable scaffolds for therapeutics and diagnostics. Specific folding and binding properties of the proteinaceous binders can be engineered with combinatorial protein libraries in connection with artificial molecular evolution. The combinatorial protein libraries are composed of scaffold variants with random sequence variation, which inevitably produces a portion of the library sequences incompatible with the parent structure. Here, we used artificial molecular evolution to elucidate structure-determining residues in a smallest cystine-stabilized scaffold. The structural determinant information was then applied to designing cystine-stabilized miniproteins binding to human vascular endothelial growth factor. This work demonstrated a general methodology on engineering artificial cystine-stabilized proteins as antibody mimetics with simultaneously enhanced folding and binding properties. © 2009 Elsevier Ltd. All rights reserved.

关键词： PROTEINS

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Corrigendum to "Novel model of multiple sclerosis induced by EBV-like virus generate a unique B cell population" [Journal of Neuroimmunology volume 394 (2024) 578408]

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Journal of neuroimmunology 2025年 404卷 578625页

作者： J L Deffenbaugh K-J Jung S P Murphy Y Liu C N Rau C Petersen-Cherubini P L Collins D Chung A E Lovett-Racke Department of Microbial Infection & Immunity The Ohio State University Wexner Medical Center USA. Department of Computer Science and Engineering The Ohio State University USA. Department of Microbial Infection & Immunity The Ohio State University Wexner Medical Center USA Neuroscience Graduate Program The Ohio State University USA. Department of Biomedical Informatics The Ohio State University Wexner Medical Center USA Pelotonia Institute for Immuno-Oncology The Ohio State University Wexner Medical Center USA. Department of Neuroscience The Ohio State University Wexner Medical Center USA. Electronic address: amylovettracke@***.

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Towards Precision Cancer Therapy: Prottrans and Multi-Window Scanning Convolutional Neural Networks Transforming Protein-Peptide Interaction Predictions

SSRN

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SSRN 2024年

作者： Van Le, The Zi Zhan, Jun Yu Ou, Yen Department of Computer Science and Engineering Yuan Ze University Chung-Li32003 Taiwan Graduate Program in Biomedical Informatics Yuan Ze University Chung-Li32003 Taiwan

This study delves into the prediction of protein-peptide interactions using advanced machine learning techniques, comparing models such as sequence-based, standard CNNs, and traditional classifiers. Leveraging pre-trained language models and multi-view window scanning CNNs, our approach yields significant improvements, with ProtTrans standing out based on 2.1 billion protein sequences and 393 billion amino acids. The integrated model achieves an impressive AUC of 0.855 and 0.822 on Set_1 and Set_2 datasets, outperforming previous methods. Beyond this, we explore the application of this model in cancer therapy, particularly in identifying peptide interactions for selective targeting of cancer cells. The findings of this study contribute to bioinformatics, providing valuable insights for drug discovery and therapeutic development. © 2024, The Authors. All rights reserved.

关键词： Machine learning

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Deepepiil13: Deep Learning for Prediction of Il-13 Inducing Epitopes Using Pre-Trained Language Models and Multi-Window Convolutional Neural Networks

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SSRN 2024年

作者： Chuang, Cheng-Che Ou, Yu-Yen Department of Computer Science and Engineering Yuan Ze University Chung-Li32003 Taiwan Graduate Program in Biomedical Informatics Yuan Ze University Chung-Li32003 Taiwan

Interleukin-13 (IL-13) is a key cytokine involved in allergic inflammation and the cytokine storm associated with severe COVID-19. Identifying antigenic epitopes capable of inducing IL-13 holds therapeutic potential for developing epitope-based vaccines and immunomodulatory treatments. However, conventional methods for epitope prediction are often inefficient and inaccurate. This study presents DeepEpiIL13, a novel deep learning framework that integrates pre-trained language models and multi-window convolutional neural networks (CNNs) to rapidly and accurately predict IL-13-inducing epitopes from protein sequences. The ProtTrans pre-trained language model was employed to generate high-dimensional embeddings that capture rich contextual information from protein sequences. These embeddings were then inputted into a multi-window CNN architecture, enabling the efficient exploration of local and global sequence patterns associated with IL-13 induction. The proposed approach was rigorously evaluated using benchmark datasets and an independent SARS-CoV-2 dataset. DeepEpiIL13 achieved superior performance compared to traditional methods, with an impressive Matthews correlation coefficient (MCC) of 0.52 and an area under the receiver operating characteristic curve (AUC) of 0.86 on the benchmark dataset. On the independent SARS-CoV-2 dataset, DeepEpiIL13 demonstrated remarkable robustness, attaining an MCC of 0.63 and an AUC of 0.92, highlighting its potential applicability in the context of COVID-19 research. This study introduces a powerful deep learning framework for accurate epitope prediction, offering new avenues for the development of epitope-based vaccines and immunotherapies targeting IL-13-mediated disorders. The successful identification of IL-13-inducing epitopes paves the way for novel therapeutic interventions against allergic diseases, inflammatory conditions, and potentially severe viral infections like COVID-19. © 2024, The Authors. All rights reserved.

关键词： COVID-19

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Constructing an Automated Method for Interpreting Alzheimer’s Disease Based on Deep Learning Models and Image Processing 24

Constructing an Automated Method for Interpreting Alzheimer...

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8th International Conference on Medical and Health informatics, ICMHI 2024

作者： Yi, Chia-Pin Ting, Hsien-Wei Yang, Tzu-Fang Chien, Ting-Ying Department of Computer Science and Engineering Yuan Ze University Taoyuan City Taiwan Department of Neurosurgery Taipei Hospital Ministry of Health and Welfare New Taipei City242 Taiwan Graduate Program in Biomedical Informatics Yuan Ze University Taoyuan City Taiwan TaiwanInnovation Center for Big Data and Digital Convergence Yuan Ze University Taoyuan City Taiwan

ISBN: (纸本)9798400716874

Alzheimer’s disease (AD) often presents only mild symptoms in its early stages, and as there is no direct diagnostic method currently available, many patients are diagnosed only after the condition has worsened. Considering that magnetic resonance imaging (MRI) can provide key information in the diagnosis of AD, but the condition may go undiagnosed under manual interpretation due to the subtleness of symptoms and the reliance on radiologists to interpret MRI images, this study aimed to develop an automated method for interpreting brain MR images, hoping to screen for potential AD patients. By combining image processing, the U-Net model, YOLOv8 model, various CNN model architectures, and ensemble data statistics, our method was able to identify features related to AD and predict whether a patient has the disease. Our method can process a complete set of MR images and automatically extract important slices for prediction, making it practical for medical applications. Furthermore, we tested the accuracy and reliability of the method with additional datasets. © 2024 Copyright ACM.

关键词： Magnetic resonance imaging

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Constructing a Segmentation Model for Patients with Leukoaraiosis Using Deep Learning Algorithms 24

Constructing a Segmentation Model for Patients with Leukoara...

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8th International Conference on Medical and Health informatics, ICMHI 2024

作者： Lo, Li-Ting Tsai, Yi-Chia Chang, Yi-Jou Ting, Hsien-Wei Chien, Ting-Ying Department of Computer Science and Engineering Yuan Ze University Taoyuan City Taiwan Graduate Program in Biomedical Informatics Yuan Ze University Taoyuan City Taiwan Department of Neurosurgery Taipei Hospital Ministry of Health and Welfare New Taipei City242 Taiwan Innovation Center for Big Data and Digital Convergence Yuan Ze University Taoyuan City Taiwan

ISBN: (纸本)9798400716874

Many patients with leukoaraiosis (LA) exhibit mild and difficult-to-detect symptoms in the early stages, and due to the lack of effective detection methods, the optimal timing for treatment is often missed. This not only makes later treatment more difficult but, in severe cases, can even lead to mild to severe dementia. Therefore, in addition to relying on radiologists to manually interpret magnetic resonance imaging (MRI) scans, finding more effective detection methods has become extremely urgent. This study aimed to combine image processing and deep learning technologies to develop a model capable of accurately identifying and segmenting white matter hyperintensities (WMHs) to assist doctors in the early diagnosis of LA. We first performed efficient preprocessing on MR image slices from two different series and used the ResNet18 model to identify key slices containing WMHs, ultimately achieving precise segmentation of WMH areas with the U-Net model. This research focused on developing innovative preprocessing techniques, improving the accuracy by 12.3% with a limited dataset through preprocessing. Ultimately, the ResNet18 model achieved an F1 score of 0.829, while the U-Net model’s intersection over union (IoU) and Dice coefficient reached 0.750 and 0.857, respectively, showing the potential of this architecture. We propose improvements in the final chapter to construct a more comprehensive model. © 2024 Copyright ACM.

关键词： Deep learning

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A deep learning approach to Lung Nodule Growth Prediction using CT image combined with Demographic and image features 23

A deep learning approach to Lung Nodule Growth Prediction us...

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7th International Conference on Medical and Health informatics, ICMHI 2023

作者： Li, Ai-Hsien Adams Nguyen, Duc-Khanh Lai, Yen-Jun Chien, Ting-Ying Chiu, Yen-Ling Chan, Chien-Lung Yang, Pan-Chyr Division of Cardiology Far Eastern Memorial Hospital Taipei220 Taiwan Graduate Program in Biomedical Informatics Yuan Ze University Taoyuan City Taiwan Department of Information Management Yuan Ze University Taoyuan320 Taiwan Department of Radiology Far Eastern Memorial Hospital Taipei220 Taiwan Department of Computer Science and Engineering Yuan Ze University Taoyuan City Taiwan Innovation Center for Big Data and Digital Convergence Yuan Ze University Taoyuan City Taiwan Graduate Institute of Medicine and Graduate Program in Biomedical Informatics Yuan Ze University Taoyuan Taiwan Department of Medical Research Far Eastern Memorial Hospital Taipei Taiwan Innovation Center for Big Data and Digital Convergence Yuan Ze University Taoyuan320 Taiwan Institute of Biomedical Sciences Academia Sinica Taipei106 Taiwan Department of Internal Medicine College of Medicine National Taiwan University Taipei100 Taiwan Center of Genomic Medicine National Taiwan University Taipei100 Taiwan

ISBN: (纸本)9798400700712

Lung cancer remains a significant global public health concern, being the leading cause of cancer-related deaths worldwide. Despite recent medical advancements, the disease still has a high mortality rate, making early detection and treatment critical for improving patient outcomes. Accurate prediction of nodule growth is key to early lung cancer treatment, but current assessments offer unclear indications of future growth, leading physicians to recommend costly and anxiety-provoking follow-up appointments every 3 to 12 months. To address this need, this study develops an ensemble deep learning approach that combines demographic data with existing CT images to predict whether lung nodules will grow, potentially reducing unnecessary examinations and easing the burden on patients. Our study, conducted on 862 patients with 1004 nodules, produced promising preliminary results with Accuracy, Sensitivity, Precision, F1 Score, and AUC of 0.66, 0.66, 0.67, 0.66, and 0.71, respectively. The proposed method provides a promising support system to empower patients to make informed decisions about seeking medical attention and helps physicians facilitate early treatment regimens, leading to improved patient outcomes and potentially saving lives. © 2023 ACM.

关键词： Forecasting

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Multiomics Reveals Induction of Neuroblastoma SK-N-BE(2)C Cell Death by Mitochondrial Division Inhibitor 1 through Multiple Effects

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Journal of Proteome Research 2024年第1期23卷 301-315页

作者： Wang, Wei-Hsuan Kao, Yi-Chun Hsieh, Chiao-Hui Tsai, Shin-Yu Cheung, Chantal Hoi Yin Huang, Hsuan-Cheng Juan, Hsueh-Fen Genome and Systems Biology Degree Program Academia Sinica and National Taiwan University Taipei 106 Taiwan Department of Life Science National Taiwan University Taipei 106 Taiwan Center for Computational and Systems Biology National Taiwan University Taipei 106 Taiwan Institute of Biomedical Informatics National Yang Ming Chiao Tung University Taipei 112 Taiwan Graduate Institute of Biomedical Electronics and Bioinformatics National Taiwan University Taipei 106 Taiwan Center for Advanced Computing and Imaging in Biomedicine National Taiwan University Taipei 106 Taiwan

Mitochondrial division inhibitor 1 (Mdivi-1) is a well-known synthetic compound aimed at inhibiting dynamin-related protein 1 (Drp1) to suppress mitochondrial fission, making it a valuable tool for studying mitochondrial dynamics. However, its specific effects beyond Drp1 inhibition remain to be confirmed. In this study, we employed integrative proteomics and phosphoproteomics to delve into the molecular responses induced by Mdivi-1 in SK-N-BE(2)C cells. A total of 3070 proteins and 1945 phosphorylation sites were identified, with 880 of them represented as phosphoproteins. Among these, 266 proteins and 97 phosphorylation sites were found to be sensitive to the Mdivi-1 treatment. Functional enrichment analysis unveiled their involvement in serine biosynthesis and extrinsic apoptotic signaling pathways. Through targeted metabolomics, we observed that Mdivi-1 enhanced intracellular serine biosynthesis while reducing the production of C24:1-ceramide. Within these regulated phosphoproteins, dynamic dephosphorylation of proteasome subunit alpha type 3 serine 250 (PSMA3-S250) occurred after Mdivi-1 treatment. Further site-directed mutagenesis experiments revealed that the dephosphorylation-deficient mutant PSMA3-S250A exhibited a decreased cell survival. This research confirms that Mdivi-1’s inhibition of mitochondrial division leads to various side effects, ultimately influencing cell survival, rather than solely targeting Drp1 inhibition. © 2023 American Chemical Society.

关键词： Mdivi-1 multiomics neuroblastoma phosphoproteome proteome targeted metabolome

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Constructing Coronary Artery Vessel Segmentation Based on Deep Learning Models and Image Processing 24

Constructing Coronary Artery Vessel Segmentation Based on De...

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8th International Conference on Medical and Health informatics, ICMHI 2024

作者： Peng, Kang-Syuan Chang, Hsiao-Huang Hsu, Ying-Kai Chien, Ting-Ying Department of Computer Science and Engineering Yuan Ze University Taoyuan City Taiwan Cardiovascular Surgery Department Taipei Veterans General Hospital Taipei City TaiwanTaipei Medical University Taipei City Taiwan Graduate Program in Biomedical Informatics Yuan Ze University Taoyuan City Taiwan TaiwanInnovation Center for Big Data and Digital Convergence Yuan Ze University Taoyuan City Taiwan

ISBN: (纸本)9798400716874

Narrowing of the coronary arteries is an important indicator of the severity of coronary artery disease (CAD) in patients. Previous research using deep learning to identify narrowed vessels has primarily been based on object detection, but this approach has several problems, such as the inability to detect multivessel narrowing, calculate the actual rate of narrowing, and determine the exact location of occurrence. Therefore, we believe that the determination of narrowing should return to the original method, namely, calculating the maximum and minimum diameters around the vessel. However, to automate this task, a preprocessing step for separating each vessel is needed, especially for the complex structure of the left coronary artery. We designed a deep learning model capable of analyzing an entire coronary angiography (CAG) image for the separation and tracking of vessels. This not only serves as a preprocessing step for calculating narrowing but also allows for the analysis of different vessel flow directions, providing doctors with comprehensive assessment indicators. © 2024 Copyright ACM.

关键词： Image segmentation

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