Genomics, Proteomics & Bioinformatics最新文献

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Acid–base Homeostasis and Implications to the Phenotypic Behaviors of Cancer 酸碱平衡及其对癌症表型行为的影响
IF 11.5 2区 生物学
Genomics, Proteomics & Bioinformatics Pub Date : 2023-12-01 DOI: 10.1016/j.gpb.2022.06.003
Yi Zhou , Wennan Chang , Xiaoyu Lu , Jin Wang , Chi Zhang , Ying Xu
{"title":"Acid–base Homeostasis and Implications to the Phenotypic Behaviors of Cancer","authors":"Yi Zhou ,&nbsp;Wennan Chang ,&nbsp;Xiaoyu Lu ,&nbsp;Jin Wang ,&nbsp;Chi Zhang ,&nbsp;Ying Xu","doi":"10.1016/j.gpb.2022.06.003","DOIUrl":"10.1016/j.gpb.2022.06.003","url":null,"abstract":"<div><div><strong>Acid–base homeostasis</strong> is a fundamental property of living cells, and its persistent disruption in human cells can lead to a wide range of diseases. In this study, we conducted a computational modeling analysis of transcriptomic data of 4750 human tissue samples of 9 cancer types in The Cancer Genome Atlas (TCGA) database. Built on our previous study, we quantitatively estimated the average production rate of OH<sup>−</sup> by cytosolic <strong>Fenton reactions</strong>, which continuously disrupt the intracellular pH (pH<sub>i</sub>) homeostasis. Our predictions indicate that all or at least a subset of 43 reprogrammed metabolisms (RMs) are induced to produce net protons (H<sup>+</sup>) at comparable rates of Fenton reactions to keep the pH<sub>i</sub> stable. We then discovered that a number of well-known phenotypes of cancers, including increased growth rate, metastasis rate, and local immune cell composition, can be naturally explained in terms of the Fenton reaction level and the induced RMs. This study strongly suggests the possibility to have a unified framework for studies of cancer-inducing stressors, adaptive <strong>metabolic reprogramming</strong>, and cancerous behaviors. In addition, strong evidence is provided to demonstrate that a popular view that Na<sup>+</sup>/H<sup>+</sup> exchangers along with lactic acid exporters and carbonic anhydrases are responsible for the intracellular alkalization and extracellular acidification in cancer may not be justified.</div></div>","PeriodicalId":12528,"journal":{"name":"Genomics, Proteomics & Bioinformatics","volume":"21 6","pages":"Pages 1133-1148"},"PeriodicalIF":11.5,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11082410/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40480520","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
A Review of Machine Learning and Algorithmic Methods for Protein Phosphorylation Site Prediction 蛋白质磷酸化位点预测的机器学习和算法方法综述。
IF 11.5 2区 生物学
Genomics, Proteomics & Bioinformatics Pub Date : 2023-12-01 DOI: 10.1016/j.gpb.2023.03.007
Farzaneh Esmaili , Mahdi Pourmirzaei , Shahin Ramazi , Seyedehsamaneh Shojaeilangari , Elham Yavari
{"title":"A Review of Machine Learning and Algorithmic Methods for Protein Phosphorylation Site Prediction","authors":"Farzaneh Esmaili ,&nbsp;Mahdi Pourmirzaei ,&nbsp;Shahin Ramazi ,&nbsp;Seyedehsamaneh Shojaeilangari ,&nbsp;Elham Yavari","doi":"10.1016/j.gpb.2023.03.007","DOIUrl":"10.1016/j.gpb.2023.03.007","url":null,"abstract":"<div><div><strong>Post-translational modifications</strong> (PTMs) have key roles in extending the functional diversity of proteins and, as a result, regulating diverse cellular processes in prokaryotic and eukaryotic organisms. <strong>Phosphorylation</strong> modification is a vital PTM that occurs in most proteins and plays a significant role in many biological processes. Disorders in the phosphorylation process lead to multiple diseases, including neurological disorders and cancers. The purpose of this review is to organize this body of knowledge associated with phosphorylation site (p-site) prediction to facilitate future research in this field. At first, we comprehensively review all related <strong>databases</strong> and introduce all steps regarding dataset creation, data preprocessing, and method evaluation in p-site prediction. Next, we investigate p-site prediction methods, which are divided into two computational groups: algorithmic and <strong>machine learning</strong> (ML). Additionally, it is shown that there are basically two main approaches for p-site prediction by ML: conventional and end-to-end <strong>deep learning</strong> methods, both of which are given an overview. Moreover, this review introduces the most important feature extraction techniques, which have mostly been used in p-site prediction. Finally, we create three test sets from new proteins related to the released version of the database of protein post-translational modifications (dbPTM) in 2022 based on general and human species. Evaluating online p-site prediction tools on newly added proteins introduced in the dbPTM 2022 release, distinct from those in the dbPTM 2019 release, reveals their limitations. In other words, the actual performance of these online p-site prediction tools on unseen proteins is notably lower than the results reported in their respective research papers.</div></div>","PeriodicalId":12528,"journal":{"name":"Genomics, Proteomics & Bioinformatics","volume":"21 6","pages":"Pages 1266-1285"},"PeriodicalIF":11.5,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11082408/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49686555","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Multi-omics Data Reveal the Effect of Sodium Butyrate on Gene Expression and Protein Modification in Streptomyces 多组学数据揭示丁酸钠对链霉菌基因表达和蛋白质修饰的影响
IF 11.5 2区 生物学
Genomics, Proteomics & Bioinformatics Pub Date : 2023-12-01 DOI: 10.1016/j.gpb.2022.09.002
Jiazhen Zheng , Yue Li , Ning Liu , Jihui Zhang , Shuangjiang Liu , Huarong Tan
{"title":"Multi-omics Data Reveal the Effect of Sodium Butyrate on Gene Expression and Protein Modification in Streptomyces","authors":"Jiazhen Zheng ,&nbsp;Yue Li ,&nbsp;Ning Liu ,&nbsp;Jihui Zhang ,&nbsp;Shuangjiang Liu ,&nbsp;Huarong Tan","doi":"10.1016/j.gpb.2022.09.002","DOIUrl":"10.1016/j.gpb.2022.09.002","url":null,"abstract":"<div><div>Streptomycetes possess numerous gene clusters and the potential to produce a large amount of natural products. Histone deacetylase (HDAC) inhibitors play an important role in the regulation of histone modifications in fungi, but their roles in prokaryotes remain poorly understood. Here, we investigated the global effects of the HDAC inhibitor, <strong>sodium butyrate</strong> (SB), on marine-derived <strong><em>Streptomyces</em></strong> <em>olivaceus</em> FXJ 8.021, particularly focusing on the activation of secondary metabolite biosynthesis. The antiSMASH analysis revealed 33 secondary metabolite biosynthetic gene clusters (BGCs) in strain FXJ 8.021, among which the silent lobophorin BGC was activated by SB. Transcriptomic data showed that the expression of genes involved in lobophorin biosynthesis (<em>ge00097–ge00139</em>) and CoA-ester formation (<em>e.g.</em>, <em>ge02824</em>), as well as the glycolysis/gluconeogenesis pathway (<em>e.g</em>., <em>ge01661</em>), was significantly up-regulated in the presence of SB. Intracellular CoA-ester analysis confirmed that SB triggered the biosynthesis of CoA-ester, thereby increasing the precursor supply for lobophorin biosynthesis. Further acetylomic analysis revealed that the acetylation levels on 218 sites of 190 proteins were up-regulated and those on 411 sites of 310 proteins were down-regulated. These acetylated proteins were particularly enriched in transcriptional and translational machinery components (<em>e.g</em>., elongation factor GE04399), and their correlations with the proteins involved in lobophorin biosynthesis were established by protein–protein interaction network analysis, suggesting that SB might function via a complex hierarchical regulation to activate the expression of lobophorin BGC. These findings provide solid evidence that acetylated proteins triggered by SB could affect the expression of genes involved in the biosynthesis of primary and secondary metabolites in prokaryotes.</div></div>","PeriodicalId":12528,"journal":{"name":"Genomics, Proteomics & Bioinformatics","volume":"21 6","pages":"Pages 1149-1162"},"PeriodicalIF":11.5,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11082262/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40363021","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Revolutionizing Antibody Discovery: An Innovative AI Model for Generating Robust Libraries 革命性的抗体发现:一种用于生成鲁棒库的创新AI模型。
IF 11.5 2区 生物学
Genomics, Proteomics & Bioinformatics Pub Date : 2023-10-01 DOI: 10.1016/j.gpb.2023.06.001
Yaojun Wang , Shiwei Sun
{"title":"Revolutionizing Antibody Discovery: An Innovative AI Model for Generating Robust Libraries","authors":"Yaojun Wang ,&nbsp;Shiwei Sun","doi":"10.1016/j.gpb.2023.06.001","DOIUrl":"10.1016/j.gpb.2023.06.001","url":null,"abstract":"","PeriodicalId":12528,"journal":{"name":"Genomics, Proteomics & Bioinformatics","volume":"21 5","pages":"Pages 910-912"},"PeriodicalIF":11.5,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10928364/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9671806","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Omics Views of Mechanisms for Cell Fate Determination in Early Mammalian Development Omics 对哺乳动物早期发育中细胞命运决定机制的看法。
IF 11.5 2区 生物学
Genomics, Proteomics & Bioinformatics Pub Date : 2023-10-01 DOI: 10.1016/j.gpb.2023.03.001
Lin-Fang Ju , Heng-Ji Xu , Yun-Gui Yang , Ying Yang
{"title":"Omics Views of Mechanisms for Cell Fate Determination in Early Mammalian Development","authors":"Lin-Fang Ju ,&nbsp;Heng-Ji Xu ,&nbsp;Yun-Gui Yang ,&nbsp;Ying Yang","doi":"10.1016/j.gpb.2023.03.001","DOIUrl":"10.1016/j.gpb.2023.03.001","url":null,"abstract":"<div><div>During mammalian preimplantation development, a totipotent zygote undergoes several cell cleavages and two rounds of <strong>cell fate determination</strong>, ultimately forming a mature blastocyst. Along with compaction, the establishment of apicobasal <strong>cell polarity</strong> breaks the symmetry of an embryo and guides subsequent cell fate choice. Although the lineage segregation of the inner cell mass (ICM) and trophectoderm (TE) is the first symbol of cell differentiation, several molecules have been shown to bias the early cell fate through their inter-cellular variations at much earlier stages, including the 2- and 4-cell stages. The underlying mechanisms of early cell fate determination have long been an important research topic. In this review, we summarize the molecular events that occur during early embryogenesis, as well as the current understanding of their regulatory roles in cell fate decisions. Moreover, as powerful tools for early embryogenesis research, <strong>single-cell omics</strong> techniques have been applied to both mouse and human preimplantation embryos and have contributed to the discovery of cell fate regulators. Here, we summarize their applications in the research of preimplantation embryos, and provide new insights and perspectives on cell fate regulation.</div></div>","PeriodicalId":12528,"journal":{"name":"Genomics, Proteomics & Bioinformatics","volume":"21 5","pages":"Pages 950-961"},"PeriodicalIF":11.5,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10928378/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10101436","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
MicroRNA–disease Network Analysis Repurposes Methotrexate for the Treatment of Abdominal Aortic Aneurysm in Mice 微RNA-疾病网络分析将甲氨蝶呤重新用于治疗小鼠腹主动脉瘤
IF 11.5 2区 生物学
Genomics, Proteomics & Bioinformatics Pub Date : 2023-10-01 DOI: 10.1016/j.gpb.2022.08.002
Yicong Shen , Yuanxu Gao , Jiangcheng Shi , Zhou Huang , Rongbo Dai , Yi Fu , Yuan Zhou , Wei Kong , Qinghua Cui
{"title":"MicroRNA–disease Network Analysis Repurposes Methotrexate for the Treatment of Abdominal Aortic Aneurysm in Mice","authors":"Yicong Shen ,&nbsp;Yuanxu Gao ,&nbsp;Jiangcheng Shi ,&nbsp;Zhou Huang ,&nbsp;Rongbo Dai ,&nbsp;Yi Fu ,&nbsp;Yuan Zhou ,&nbsp;Wei Kong ,&nbsp;Qinghua Cui","doi":"10.1016/j.gpb.2022.08.002","DOIUrl":"10.1016/j.gpb.2022.08.002","url":null,"abstract":"<div><div><strong>Abdominal aortic aneurysm</strong> (AAA) is a permanent dilatation of the abdominal aorta and is highly lethal. The main purpose of the current study is to search for noninvasive medical therapies for AAA, for which there is currently no effective drug therapy. <strong>Network medicine</strong> represents a cutting-edge technology, as analysis and modeling of disease networks can provide critical clues regarding the etiology of specific diseases and therapeutics that may be effective. Here, we proposed a novel algorithm to quantify disease relations based on a large accumulated microRNA–disease association dataset and then built a disease network covering 15 disease classes and 304 diseases. Analysis revealed some patterns for these diseases. For instance, diseases tended to be clustered and coherent in the network. Surprisingly, we found that AAA showed the strongest similarity with rheumatoid arthritis and systemic lupus erythematosus, both of which are <strong>autoimmune diseases</strong>, suggesting that AAA could be one type of autoimmune diseases in etiology. Based on this observation, we further hypothesized that drugs for autoimmune diseases could be repurposed for the prevention and therapy of AAA. Finally, animal experiments confirmed that <strong>methotrexate</strong>, a drug for autoimmune diseases, was able to alleviate the formation and development of AAA.</div></div>","PeriodicalId":12528,"journal":{"name":"Genomics, Proteomics & Bioinformatics","volume":"21 5","pages":"Pages 1030-1042"},"PeriodicalIF":11.5,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10928436/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40425409","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Patient Assessment and Therapy Planning Based on Homologous Recombination Repair Deficiency 基于同源重组修复缺陷的患者评估和治疗计划
IF 11.5 2区 生物学
Genomics, Proteomics & Bioinformatics Pub Date : 2023-10-01 DOI: 10.1016/j.gpb.2023.02.004
Wenbin Li , Lin Gao , Xin Yi , Shuangfeng Shi , Jie Huang , Leming Shi , Xiaoyan Zhou , Lingying Wu , Jianming Ying
{"title":"Patient Assessment and Therapy Planning Based on Homologous Recombination Repair Deficiency","authors":"Wenbin Li ,&nbsp;Lin Gao ,&nbsp;Xin Yi ,&nbsp;Shuangfeng Shi ,&nbsp;Jie Huang ,&nbsp;Leming Shi ,&nbsp;Xiaoyan Zhou ,&nbsp;Lingying Wu ,&nbsp;Jianming Ying","doi":"10.1016/j.gpb.2023.02.004","DOIUrl":"10.1016/j.gpb.2023.02.004","url":null,"abstract":"<div><div>Defects in genes involved in the <strong>DNA damage response</strong> cause <strong>homologous recombination repair deficiency</strong> (HRD). HRD is found in a subgroup of cancer patients for several tumor types, and it has a clinical relevance to cancer prevention and therapies. Accumulating evidence has identified HRD as a <strong>biomarker</strong> for assessing the therapeutic response of tumor cells to <strong>poly</strong><strong>(ADP-ribose) polymerase inhibitors</strong> and platinum-based chemotherapies. Nevertheless, the biology of HRD is complex, and its applications and the benefits of different HRD biomarker assays are controversial. This is primarily due to inconsistencies in HRD assessments and definitions (gene-level tests, genomic scars, mutational signatures, or a combination of these methods) and difficulties in assessing the contribution of each genomic event. Therefore, we aim to review the biological rationale and clinical evidence of HRD as a biomarker. This review provides a blueprint for the standardization and <strong>harmonization</strong> of HRD assessments.</div></div>","PeriodicalId":12528,"journal":{"name":"Genomics, Proteomics & Bioinformatics","volume":"21 5","pages":"Pages 962-975"},"PeriodicalIF":11.5,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10928375/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10737665","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
HPC-Atlas: Computationally Constructing A Comprehensive Atlas of Human Protein Complexes HPC图谱:计算构建人类蛋白质复合物的综合图谱。
IF 11.5 2区 生物学
Genomics, Proteomics & Bioinformatics Pub Date : 2023-10-01 DOI: 10.1016/j.gpb.2023.05.001
Yuliang Pan , Ruiyi Li , Wengen Li , Liuzhenghao Lv , Jihong Guan , Shuigeng Zhou
{"title":"HPC-Atlas: Computationally Constructing A Comprehensive Atlas of Human Protein Complexes","authors":"Yuliang Pan ,&nbsp;Ruiyi Li ,&nbsp;Wengen Li ,&nbsp;Liuzhenghao Lv ,&nbsp;Jihong Guan ,&nbsp;Shuigeng Zhou","doi":"10.1016/j.gpb.2023.05.001","DOIUrl":"10.1016/j.gpb.2023.05.001","url":null,"abstract":"<div><div>A fundamental principle of biology is that proteins tend to form complexes to play important roles in the core functions of cells. For a complete understanding of human cellular functions, it is crucial to have a comprehensive atlas of <strong>human protein complexes</strong>. Unfortunately, we still lack such a comprehensive atlas of experimentally validated protein complexes, which prevents us from gaining a complete understanding of the compositions and functions of human protein complexes, as well as the underlying biological mechanisms. To fill this gap, we built Human Protein Complexes Atlas (HPC-Atlas), as far as we know, the most accurate and comprehensive atlas of human protein complexes available to date. We integrated two latest <strong>protein interaction networks</strong>, and developed a novel computational method to identify nearly 9000 protein complexes, including many previously uncharacterized complexes. Compared with the existing methods, our method achieved outstanding performance on both testing and independent datasets. Furthermore, with HPC-Atlas we identified 751 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-affected human protein complexes, and 456 <strong>multifunctional proteins</strong> that contain many potential moonlighting proteins. These results suggest that HPC-Atlas can serve as not only a computing framework to effectively identify biologically meaningful protein complexes by integrating multiple protein data sources, but also a valuable resource for exploring new biological findings. The HPC-Atlas webserver is freely available at <span><span>http://www.yulpan.top/HPC-Atlas</span><svg><path></path></svg></span>.</div></div>","PeriodicalId":12528,"journal":{"name":"Genomics, Proteomics & Bioinformatics","volume":"21 5","pages":"Pages 976-990"},"PeriodicalIF":11.5,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10928439/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41124619","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
OBIA: An Open Biomedical Imaging Archive OBIA:一个开放的生物医学成像档案。
IF 11.5 2区 生物学
Genomics, Proteomics & Bioinformatics Pub Date : 2023-10-01 DOI: 10.1016/j.gpb.2023.09.003
Enhui Jin , Dongli Zhao , Gangao Wu , Junwei Zhu , Zhonghuang Wang , Zhiyao Wei , Sisi Zhang , Anke Wang , Bixia Tang , Xu Chen , Yanling Sun , Zhe Zhang , Wenming Zhao , Yuanguang Meng
{"title":"OBIA: An Open Biomedical Imaging Archive","authors":"Enhui Jin ,&nbsp;Dongli Zhao ,&nbsp;Gangao Wu ,&nbsp;Junwei Zhu ,&nbsp;Zhonghuang Wang ,&nbsp;Zhiyao Wei ,&nbsp;Sisi Zhang ,&nbsp;Anke Wang ,&nbsp;Bixia Tang ,&nbsp;Xu Chen ,&nbsp;Yanling Sun ,&nbsp;Zhe Zhang ,&nbsp;Wenming Zhao ,&nbsp;Yuanguang Meng","doi":"10.1016/j.gpb.2023.09.003","DOIUrl":"10.1016/j.gpb.2023.09.003","url":null,"abstract":"<div><div>With the development of artificial intelligence (AI) technologies, <strong>biomedical imaging</strong> data play an important role in scientific research and clinical application, but the available resources are limited. Here we present <strong>Open Biomedical Imaging Archive</strong> (OBIA), a repository for archiving biomedical imaging and related clinical data. OBIA adopts five data objects (Collection, Individual, Study, Series, and Image) for data organization, and accepts the submission of biomedical images of multiple modalities, organs, and diseases. In order to protect personal privacy, OBIA has formulated a unified <strong>de-identification</strong> and <strong>quality control</strong> process. In addition, OBIA provides friendly and intuitive web interfaces for data submission, browsing, and retrieval, as well as image retrieval. As of September 2023, OBIA has housed data for a total of 937 individuals, 4136 studies, 24,701 series, and 1,938,309 images covering 9 modalities and 30 anatomical sites. Collectively, OBIA provides a reliable platform for biomedical imaging data management and offers free open access to all publicly available data to support research activities throughout the world. OBIA can be accessed at <span><span>https://ngdc.cncb.ac.cn/obia</span><svg><path></path></svg></span>.</div></div>","PeriodicalId":12528,"journal":{"name":"Genomics, Proteomics & Bioinformatics","volume":"21 5","pages":"Pages 1059-1065"},"PeriodicalIF":11.5,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10928373/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41147344","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
AB-Gen: Antibody Library Design with Generative Pre-trained Transformer and Deep Reinforcement Learning AB-Gen:利用生成式预训练变换器和深度强化学习设计抗体库。
IF 11.5 2区 生物学
Genomics, Proteomics & Bioinformatics Pub Date : 2023-10-01 DOI: 10.1016/j.gpb.2023.03.004
Xiaopeng Xu , Tiantian Xu , Juexiao Zhou , Xingyu Liao , Ruochi Zhang , Yu Wang , Lu Zhang , Xin Gao
{"title":"AB-Gen: Antibody Library Design with Generative Pre-trained Transformer and Deep Reinforcement Learning","authors":"Xiaopeng Xu ,&nbsp;Tiantian Xu ,&nbsp;Juexiao Zhou ,&nbsp;Xingyu Liao ,&nbsp;Ruochi Zhang ,&nbsp;Yu Wang ,&nbsp;Lu Zhang ,&nbsp;Xin Gao","doi":"10.1016/j.gpb.2023.03.004","DOIUrl":"10.1016/j.gpb.2023.03.004","url":null,"abstract":"<div><div>Antibody leads must fulfill multiple desirable properties to be clinical candidates. Primarily due to the low throughput in the experimental procedure, the need for such multi-property optimization causes the bottleneck in preclinical antibody discovery and development, because addressing one issue usually causes another. We developed a <strong>reinforcement learning</strong> (RL) method, named AB-Gen, for antibody library design using a generative pre-trained <strong>transformer</strong> (GPT) as the policy network of the RL agent. We showed that this model can learn the antibody space of heavy chain complementarity determining region 3 (CDRH3) and generate sequences with similar property distributions. Besides, when using human epidermal growth factor receptor-2 (HER2) as the target, the agent model of AB-Gen was able to generate novel CDRH3 sequences that fulfill multi-property constraints. Totally, 509 generated sequences were able to pass all property filters, and three highly conserved residues were identified. The importance of these residues was further demonstrated by molecular dynamics simulations, consolidating that the agent model was capable of grasping important information in this complex optimization task. Overall, the AB-Gen method is able to design novel antibody sequences with an improved success rate than the traditional propose-then-filter approach. It has the potential to be used in practical antibody design, thus empowering the antibody discovery and development process. The source code of AB-Gen is freely available at Zenodo (<span><span>https://doi.org/10.5281/zenodo.7657016</span><svg><path></path></svg></span>) and BioCode (<span><span>https://ngdc.cncb.ac.cn/biocode/tools/BT007341</span><svg><path></path></svg></span>).</div></div>","PeriodicalId":12528,"journal":{"name":"Genomics, Proteomics & Bioinformatics","volume":"21 5","pages":"Pages 1043-1053"},"PeriodicalIF":11.5,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10928431/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10045398","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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