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Batch effects correction in scRNA-seq based on biological-noise decoupling autoencoder and central-cross loss 基于生物噪声解耦自动编码器和中心交叉损失的 scRNA-seq 批次效应校正。
IF 2.6 4区 生物学
Computational Biology and Chemistry Pub Date : 2024-10-19 DOI: 10.1016/j.compbiolchem.2024.108261
Zhangjie Di , Bo Yang , Meng Li , Yue Wu , Hong Ji
{"title":"Batch effects correction in scRNA-seq based on biological-noise decoupling autoencoder and central-cross loss","authors":"Zhangjie Di ,&nbsp;Bo Yang ,&nbsp;Meng Li ,&nbsp;Yue Wu ,&nbsp;Hong Ji","doi":"10.1016/j.compbiolchem.2024.108261","DOIUrl":"10.1016/j.compbiolchem.2024.108261","url":null,"abstract":"<div><div>Technical or biologically irrelevant differences caused by different experiments, times, or sequencing platforms can generate batch effects that mask the true biological information. Therefore, batch effects are typically removed when analyzing single-cell RNA sequencing (scRNA-seq) datasets for downstream tasks. Existing batch correction methods usually mitigate batch effects by reducing the data from different batches to a lower dimensional space before clustering, potentially leading to the loss of rare cell types. To address this problem, we introduce a novel single-cell data batch effect correction model using Biological-noise Decoupling Autoencoder (BDA) and Central-cross Loss termed BDACL. The model initially reconstructs raw data using an auto-encoder and conducts preliminary clustering. We then construct a similarity matrix and a hierarchical clustering tree to delineate relationships within and between different batches. Finally, we introduce a Central-cross Loss (CL). This loss leverages cross-entropy loss to prompt the model to better distinguish between different cluster labels. Additionally, it employs the Central Loss to encourage samples to form more compact clusters in the embedding space, thereby enhancing the consistency and interpretability of clustering results to mitigate differences between different batches. The primary innovation of this model lies in reconstructing data with an auto-encoder and gradually merging smaller clusters into larger ones using a hierarchical clustering tree. By using reallocated cluster labels as training labels and employing the Central-cross Loss, the model effectively eliminates batch effects in an unsupervised manner. Compared to current methods, BDACL can mitigate batch effects without losing rare cell types.</div></div>","PeriodicalId":10616,"journal":{"name":"Computational Biology and Chemistry","volume":"113 ","pages":"Article 108261"},"PeriodicalIF":2.6,"publicationDate":"2024-10-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142514742","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Construction and validation of a prognostic model based on immune-metabolic-related genes in oral squamous cell carcinoma 基于口腔鳞状细胞癌免疫代谢相关基因的预后模型的构建与验证
IF 2.6 4区 生物学
Computational Biology and Chemistry Pub Date : 2024-10-19 DOI: 10.1016/j.compbiolchem.2024.108258
Bo Yang, Yu Wan, Jieqiong Wang, Yun Liu, Shaohua Wang
{"title":"Construction and validation of a prognostic model based on immune-metabolic-related genes in oral squamous cell carcinoma","authors":"Bo Yang,&nbsp;Yu Wan,&nbsp;Jieqiong Wang,&nbsp;Yun Liu,&nbsp;Shaohua Wang","doi":"10.1016/j.compbiolchem.2024.108258","DOIUrl":"10.1016/j.compbiolchem.2024.108258","url":null,"abstract":"<div><div>Oral squamous cell carcinoma (OSCC), a significant type of head and neck cancer, has witnessed increasing incidence and mortality rates. Immune-related genes (IRGs) and metabolic-related genes (MRGs) play essential roles in the pathogenesis, metastasis, and progression of OSCC. This study exploited data from The Cancer Genome Atlas (TCGA) to identify IRGs and MRGs related to OSCC through differential analysis. Univariate Cox analysis was utilized to determine immune-metabolic-related genes (IMRGs) associated with patient prognosis. A prognostic model for OSCC was constructed using Lasso-Cox regression and subsequently validated with datasets from the Gene Expression Omnibus (GEO). Non-Negative Matrix Factorization (NMF) clustering identified three molecular subtypes of OSCC, among which the C2 subtype showed better overall survival (OS) and progression-free survival (PFS). A prognostic model based on nine IMRGs was developed to categorize OSCC patients into high- and low-risk groups, with the low-risk group demonstrating significantly longer OS in both training and testing cohorts. The model showed strong predictive capabilities, and the risk score served as an independent prognostic factor. Additionally, expression levels of programmed death 1 (PD1) and cytotoxic T-lymphocyte-associated antigen 4 (CTLA4) differed between the risk groups. Gene Set Enrichment Analysis (GSEA) indicated distinct enriched pathways between high-risk and low-risk groups, highlighting the crucial roles of immune and metabolic processes in OSCC. The nine IMRGs prognostic model presented excellent predictive performance and has potential for clinical application.</div></div>","PeriodicalId":10616,"journal":{"name":"Computational Biology and Chemistry","volume":"113 ","pages":"Article 108258"},"PeriodicalIF":2.6,"publicationDate":"2024-10-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142514746","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Comparative in Silico study of apigenin and its dimeric forms on PIM1 kinase in glioblastoma multiform 芹菜素及其二聚体形式对多形性胶质母细胞瘤 PIM1 激酶的硅学比较研究
IF 2.6 4区 生物学
Computational Biology and Chemistry Pub Date : 2024-10-18 DOI: 10.1016/j.compbiolchem.2024.108253
Mohammad-Sadegh Lotfi , Majid Jafari-Sabet
{"title":"Comparative in Silico study of apigenin and its dimeric forms on PIM1 kinase in glioblastoma multiform","authors":"Mohammad-Sadegh Lotfi ,&nbsp;Majid Jafari-Sabet","doi":"10.1016/j.compbiolchem.2024.108253","DOIUrl":"10.1016/j.compbiolchem.2024.108253","url":null,"abstract":"<div><div>This study aimed to investigate and compare the binding affinity of apigenin and its dimeric flavonoid forms to PIM1 kinase in glioblastoma multiforme (GBM), an aggressive and lethal brain cancer. Apigenin is a natural herbal product that has demonstrated anti-cancer effects in numerous studies, both in vitro and in vivo, on various cancers. Our in silico analysis showed that PIM1 expression was significantly higher in GBM tumor tissue compared to normal brain tissue, and high PIM1 expression correlated with worse survival rates in patients with GBM. Also, our molecular docking studies showed that apigenin and its dimeric flavonoids, such as amentoflavone and hinokiflavone, can bind to the ATP-binding site of PIM1 with significant binding affinity and form various intermolecular interactions with key amino acid residues. Notably, dimeric flavonoids have a stronger binding affinity than apigenin, indicating their potential as potent PIM1 inhibitors. Our findings demonstrated the therapeutic potential of apigenin and its dimeric flavonoid forms in treating GBM by targeting PIM1 kinase. The observed inhibitory effects of PIM1 can inhibit tumor growth, induce cell cycle arrest, and promote apoptosis. However, further in vitro and in vivo studies are needed to confirm their anticancer potentials and elucidate the underlying molecular mechanisms of these compounds in GBM treatment.</div></div>","PeriodicalId":10616,"journal":{"name":"Computational Biology and Chemistry","volume":"113 ","pages":"Article 108253"},"PeriodicalIF":2.6,"publicationDate":"2024-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142514743","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Computational insights into human UCP1 activators through molecular docking, MM-GBSA, and molecular dynamics simulation studies 通过分子对接、MM-GBSA 和分子动力学模拟研究对人类 UCP1 激活剂的计算研究。
IF 2.6 4区 生物学
Computational Biology and Chemistry Pub Date : 2024-10-18 DOI: 10.1016/j.compbiolchem.2024.108252
Utkarsh A. Jagtap , Sanket Rathod , Ravi Shukla , Atish T. Paul
{"title":"Computational insights into human UCP1 activators through molecular docking, MM-GBSA, and molecular dynamics simulation studies","authors":"Utkarsh A. Jagtap ,&nbsp;Sanket Rathod ,&nbsp;Ravi Shukla ,&nbsp;Atish T. Paul","doi":"10.1016/j.compbiolchem.2024.108252","DOIUrl":"10.1016/j.compbiolchem.2024.108252","url":null,"abstract":"<div><div>The prevalence of obesity is rapidly increasing worldwide. Brown adipose tissue activates uncoupling protein 1 (UCP1) to generate heat through bypassing ATP synthesis, offering a potential target for obesity treatment. Targeting UCP1 activation to induce thermogenesis through small molecules presents a promising approach for obesity management. In this study, molecular docking of UCP1 activators, using 2,4-dinitrophenol (DNP) as a reference ligand (PDB ID: 8J1N, docking score: −5.343 kcal/mol), identified seven top-scoring compounds: naringin (-7.284 kcal/mol), quercetin (-6.661 kcal/mol), salsalate (-6.017 kcal/mol), rhein (-5.798 kcal/mol), mirabegron (-5.535 kcal/mol), curcumin (-5.479 kcal/mol), and formoterol (-5.451 kcal/mol). Prime MM-GBSA calculation of the top-scored molecule (i.e., naringin) in the docking study showed ΔGBind of −70.48 kcal/mol. Key interactions of these top 7 activators with UCP1 binding pocket residues Trp280, Arg276, Glu190, Arg83, and Arg91 were observed. Molecular dynamics simulations performed for 100 ns confirmed complex stability, with RMSD values below 6 Å. Additionally, most activators showed favorable intestinal absorption (&gt;90 %) and lipophilicity (LogP 2–4), with pKa values supporting their pharmacological potential as UCP1-targeting therapeutics for obesity. These findings provide a foundation for designing potent UCP1 activators by integrating docking scores, interaction profiles, statistical profiles from MD simulations, and physicochemical assessments to develop effective anti-obesity therapies.</div></div>","PeriodicalId":10616,"journal":{"name":"Computational Biology and Chemistry","volume":"113 ","pages":"Article 108252"},"PeriodicalIF":2.6,"publicationDate":"2024-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142514744","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Gene-expression profile analysis to disclose diagnostics and therapeutics biomarkers for thyroid carcinoma 通过基因表达谱分析发现甲状腺癌的诊断和治疗生物标记物。
IF 2.6 4区 生物学
Computational Biology and Chemistry Pub Date : 2024-10-18 DOI: 10.1016/j.compbiolchem.2024.108245
Sabkat Mahmud , Alvira Ajadee , Md. Bayazid Hossen , Md. Saiful Islam , Reaz Ahmmed , Md. Ahad Ali , Md. Manir Hossain Mollah , Md. Selim Reza , Md. Nurul Haque Mollah
{"title":"Gene-expression profile analysis to disclose diagnostics and therapeutics biomarkers for thyroid carcinoma","authors":"Sabkat Mahmud ,&nbsp;Alvira Ajadee ,&nbsp;Md. Bayazid Hossen ,&nbsp;Md. Saiful Islam ,&nbsp;Reaz Ahmmed ,&nbsp;Md. Ahad Ali ,&nbsp;Md. Manir Hossain Mollah ,&nbsp;Md. Selim Reza ,&nbsp;Md. Nurul Haque Mollah","doi":"10.1016/j.compbiolchem.2024.108245","DOIUrl":"10.1016/j.compbiolchem.2024.108245","url":null,"abstract":"<div><div>The most frequent endocrine cancer of the head and neck is thyroid carcinoma (THCA). Although there is increasing evidence linking THCA to genetic alterations, the exact molecular mechanism behind this relationship is not yet completely known to the researchers. There is still much to learn about THCA's molecular roots and genetic biomarkers. Though drug therapies are the best choice after metastasis, unfortunately, the majority of the patients progressively develop resistance against the therapeutic drugs after receiving them for a few years. Therefore, multi-targeted different variants of therapeutic drugs may be essential for effective treatment against THCA. To understand molecular mechanisms of THCA development and progression and explore multi-targeted different variants of therapeutic drugs, we detected 80 common differentially expressed genes (cDEGs) between THCA and non-THCA samples from six microarray gene expression datasets using the statistical LIMMA approach. Through protein-protein interaction (PPI) network analysis, we identified the top-ranked eight differentially expressed genes (TIMP1, FN1, THBS1, RUNX2, SHANK2, TOP2A, LRP2, and ACTN1) as the THCA-causing key genes (KGs), where 6 KGs (TIMP1, TOP2A, FN1, ACTN1, RUNX2, THBS1) are upregulated and 2 KGs (LRP2, SHANK2) are downregulated. The expression pattern analysis of KGs with the independent TCGA database by Box plots also confirmed their upregulated and downregulated patterns. The expression analysis of KGs in different stages of THCA development indicated that these KGs might be utilized as early diagnostic and prognostic biomarkers. The pan-cancer analysis of KGs indicated a substantial correlation of KGs with multiple cancers, including THCA. Some transcription factors (TFs) and microRNAs were detected as the key transcriptional and post-transcriptional regulators of KGs using gene regulatory network (GRN) analysis. The enrichment analysis of the cDEGs revealed several key molecular functions, biological processes, cellular components, and pathways significantly associated with THCA. These findings highlight critical mechanisms influenced by the identified key genes (KGs), providing deeper insight into their roles in THCA development. Then we detected 6 repurposable drug molecules (Entrectinib, Imatinib, Ponatinib, Sorafenib, Retevmo, and Pazopanib) by molecular docking with KGs-mediated receptor proteins, ADME/T analysis, and cross-validation with the independent receptors. Therefore, these findings might be useful resources for wet lab researchers and clinicians to consider an effective treatment strategy against THCA.</div></div>","PeriodicalId":10616,"journal":{"name":"Computational Biology and Chemistry","volume":"113 ","pages":"Article 108245"},"PeriodicalIF":2.6,"publicationDate":"2024-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142514760","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Optimization and correction of breast dynamic optical imaging projection data based on deep learning 基于深度学习的乳腺动态光学成像投影数据优化与校正
IF 2.6 4区 生物学
Computational Biology and Chemistry Pub Date : 2024-10-17 DOI: 10.1016/j.compbiolchem.2024.108259
Tong Hu , Jianguo Chen , Lili Qiao
{"title":"Optimization and correction of breast dynamic optical imaging projection data based on deep learning","authors":"Tong Hu ,&nbsp;Jianguo Chen ,&nbsp;Lili Qiao","doi":"10.1016/j.compbiolchem.2024.108259","DOIUrl":"10.1016/j.compbiolchem.2024.108259","url":null,"abstract":"<div><div>Breast cancer poses a significant health threat to women, necessitating advancements in diagnostic technologies. Breast dynamic optical imaging (DOI) technology, recognized for its non-invasive and radiation-free properties, is extensively utilized for the early screening and quantitative analysis of breast tumors. The integration of deep learning, a robust technology for automatic image feature extraction, with breast DOI has the potential to enhance tumor detection and diagnosis significantly. This paper introduces a deep learning-enhanced image optimization approach to overcome challenges such as poor image quality and distorted projection data commonly encountered in existing DOI methods. The approach utilizes convolutional neural networks (CNNs) to extract features from raw images and employs generative adversarial networks (GANs) to enhance these images, thereby improving their quality and contrast. Additionally, a novel correction algorithm is developed to address projection data distortion, enabling the reconstruction and correction of this data for more accurate and reliable imaging results. Experimental findings confirm that the proposed method markedly enhances both image quality and projection data accuracy in breast DOI, offering a reliable foundation for clinical diagnosis. This study not only provides a new perspective and methodology for the early screening and diagnosis of breast cancer but also holds substantial clinical importance and prospective applications.</div></div>","PeriodicalId":10616,"journal":{"name":"Computational Biology and Chemistry","volume":"113 ","pages":"Article 108259"},"PeriodicalIF":2.6,"publicationDate":"2024-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142560564","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Computational insights into irinotecan's interaction with UBE2I in ovarian and endometrial cancers 通过计算深入了解伊立替康与卵巢癌和子宫内膜癌中 UBE2I 的相互作用。
IF 2.6 4区 生物学
Computational Biology and Chemistry Pub Date : 2024-10-16 DOI: 10.1016/j.compbiolchem.2024.108250
Tamizhini Loganathan , Madhulekha S. , Hatem Zayed , George Priya Doss C
{"title":"Computational insights into irinotecan's interaction with UBE2I in ovarian and endometrial cancers","authors":"Tamizhini Loganathan ,&nbsp;Madhulekha S. ,&nbsp;Hatem Zayed ,&nbsp;George Priya Doss C","doi":"10.1016/j.compbiolchem.2024.108250","DOIUrl":"10.1016/j.compbiolchem.2024.108250","url":null,"abstract":"<div><div>Endometrial and Ovarian cancers are two highly prevalent and fatal reproductive diseases with poor prognoses among women. Elevated estrogen levels in Ovarian Cancer (OC) stimulate the endometrium, causing Endometrial Cancer (EC). Although numerous studies have reported the crucial genes and pathways in this cancer, the pathogenesis of this disease remains unclear. In this study, used bioinformatics tools to analyse GSE63678, GSE115810, GSE36389, GSE26712, GSE36668, GSE27651, GSE6008, GSE69429, GSE69428, GSE18521, GSE185209, GSE54388 gene expression microarray datasets for both the cancers. We analyzed the differential gene expression, functional association, and structural studies. The analysis identified crucial differentially expressed genes (DEGs) in both cancers associated with DNA damage, DNA integrity, and cell-cycle checkpoint signaling pathways. <em>CLDN7, UBE2I, WT1, JAM2, FOXL2, F11R, JAM3, ZFPM2, MEF2C</em>, and <em>PIAS1</em> are the top 10 hub genes commonly identified in both cancer types. Only <em>CLDN7</em> and <em>F11R</em> are upregulated, whereas the remaining hub genes are downregulated in both cancers, suggesting a common framework for contributing to tumorigenesis. Molecular docking and dynamics were performed on the UBE2I protein with Irinotecan Hydrochloride, which could serve as the new approach for treating and managing both cancers. The study reveals the common molecular pathways, pointing out the role of cell cycle and DNA damage and integrity checkpoint signaling in the pathogenesis of both cancer types. This study explored the <em>UBE2I</em> gene as a potential biomarker in OC and EC. Further, this study concludes that the irinotecan hydrochloride drug has higher therapeutic effects on UBE2I protein through docking and dynamics studies.</div></div>","PeriodicalId":10616,"journal":{"name":"Computational Biology and Chemistry","volume":"113 ","pages":"Article 108250"},"PeriodicalIF":2.6,"publicationDate":"2024-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142549484","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Cycle-ESM: Generation-assisted classification of antifungal peptides using ESM protein language model Cycle-ESM:使用 ESM 蛋白语言模型对抗真菌肽进行世代辅助分类。
IF 2.6 4区 生物学
Computational Biology and Chemistry Pub Date : 2024-10-16 DOI: 10.1016/j.compbiolchem.2024.108240
YiMing Wang, Chun Fang
{"title":"Cycle-ESM: Generation-assisted classification of antifungal peptides using ESM protein language model","authors":"YiMing Wang,&nbsp;Chun Fang","doi":"10.1016/j.compbiolchem.2024.108240","DOIUrl":"10.1016/j.compbiolchem.2024.108240","url":null,"abstract":"<div><div>The rising prevalence of invasive fungal infections and the emergence of antifungal resistance highlight the urgent need for new antifungal medications. Antifungal peptides have emerged as promising alternatives to traditional antimicrobial agents. The identification of natural or synthetic antifungal peptides is crucial for advancing antifungal drug development. Typically, the availability of antifungal samples is limited, and significant sequence diversity exists among antifungal peptides, posing challenges for high-throughput screening. To address the identification challenge of antifungal peptides with limited sample availability, this study introduces the Cycle ESM method. Initially, the method utilises the ESM protein language model to generate additional data on antifungal peptides, serving as a data augmentation technique to enhance model training effectiveness. Subsequently, the ESM is employed in conjunction with a textCNN model to construct a classifier for peptide prediction, with a comprehensive exploration of peptide characteristics to improve prediction accuracy. Experimental results demonstrate that the performance of the Cycle ESM method surpasses that of existing methods across three distinct antifungal peptide datasets. This study presents a novel approach to antifungal peptide prediction and offers innovative insights for addressing classification problems with limited sample availability.</div></div>","PeriodicalId":10616,"journal":{"name":"Computational Biology and Chemistry","volume":"113 ","pages":"Article 108240"},"PeriodicalIF":2.6,"publicationDate":"2024-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142514758","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Multi-omics data integration and analysis pipeline for precision medicine: Systematic review 精准医疗的多组学数据整合与分析管道:系统综述。
IF 2.6 4区 生物学
Computational Biology and Chemistry Pub Date : 2024-10-16 DOI: 10.1016/j.compbiolchem.2024.108254
Esraa Hamdi Abdelaziz , Rasha Ismail , Mai S. Mabrouk , Eman Amin
{"title":"Multi-omics data integration and analysis pipeline for precision medicine: Systematic review","authors":"Esraa Hamdi Abdelaziz ,&nbsp;Rasha Ismail ,&nbsp;Mai S. Mabrouk ,&nbsp;Eman Amin","doi":"10.1016/j.compbiolchem.2024.108254","DOIUrl":"10.1016/j.compbiolchem.2024.108254","url":null,"abstract":"<div><div>Precision medicine has gained considerable popularity since the \"one-size-fits-all\" approach did not seem very effective or reflective of the complexity of the human body. Subsequently, since single-omics does not reflect the complexity of the human body’s inner workings, it did not result in the expected advancement in the medical field. Therefore, the multi-omics approach has emerged. The multi-omics approach involves integrating data from different omics technologies, such as DNA sequencing, RNA sequencing, mass spectrometry, and others, using computational methods and then analyzing the integrated result for different downstream analysis applications such as survival analysis, cancer classification, or biomarker identification. Most of the recent reviews were constrained to discussing one aspect of the multi-omics analysis pipeline, such as the dimensionality reduction step, the integration methods, or the interpretability aspect; however, very few provide a comprehensive review of every step of the analysis. This study aims to give an overview of the multi-omics analysis pipeline, starting with the most popular multi-omics databases used in recent literature, dimensionality reduction techniques, details the different types of data integration techniques and their downstream analysis applications, describes the most commonly used evaluation metrics, highlights the importance of model interpretability, and lastly discusses the challenges and potential future work for multi-omics data integration in precision medicine.</div></div>","PeriodicalId":10616,"journal":{"name":"Computational Biology and Chemistry","volume":"113 ","pages":"Article 108254"},"PeriodicalIF":2.6,"publicationDate":"2024-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142514762","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
An efficient interpretable stacking ensemble model for lung cancer prognosis 肺癌预后的高效可解释堆积集合模型
IF 2.6 4区 生物学
Computational Biology and Chemistry Pub Date : 2024-10-15 DOI: 10.1016/j.compbiolchem.2024.108248
Umair Arif , Chunxia Zhang , Sajid Hussain , Abdul Rauf Abbasi
{"title":"An efficient interpretable stacking ensemble model for lung cancer prognosis","authors":"Umair Arif ,&nbsp;Chunxia Zhang ,&nbsp;Sajid Hussain ,&nbsp;Abdul Rauf Abbasi","doi":"10.1016/j.compbiolchem.2024.108248","DOIUrl":"10.1016/j.compbiolchem.2024.108248","url":null,"abstract":"<div><div>Lung cancer significantly contributes to global cancer mortality, posing challenges in clinical management. Early detection and accurate prognosis are crucial for improving patient outcomes. This study develops an interpretable stacking ensemble model (SEM) for lung cancer prognosis prediction and identifies key risk factors. Using a Kaggle dataset of 1000 patients with 22 variables, the model classifies prognosis into Low, Medium, and High-risk categories. The bootstrap method was employed for evaluation metrics, while SHAP (Shapley Additive Explanations) and LIME (Local Interpretable Model-agnostic Explanations) assessed model interpretability. Results showed SEM's superior interpretability over traditional models, such as Random Forest, Logistic Regression, Decision Tree, Gradient Boosting Machine, Extreme Gradient Boosting Machine, and Light Gradient Boosting Machine. SEM achieved an accuracy of 98.90 %, precision of 98.70 %, F1 score of 98.85 %, sensitivity of 98.77 %, specificity of 95.45 %, Cohen’s kappa value of 94.56 %, and an AUC of 98.10 %. The SEM demonstrated robust performance in lung cancer prognosis, revealing chronic lung cancer and genetic risk as major factors.</div></div>","PeriodicalId":10616,"journal":{"name":"Computational Biology and Chemistry","volume":"113 ","pages":"Article 108248"},"PeriodicalIF":2.6,"publicationDate":"2024-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142483221","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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