Genomics & informatics最新文献

Analyzing COVID-19 progression with Markov multistage models: insights from a Korean cohort.

Genomics & informatics Pub Date : 2025-01-27 DOI: 10.1186/s44342-024-00035-y

Frank Aimee Rodrigue Ndagijimana, Taesung Park

{"title":"Analyzing COVID-19 progression with Markov multistage models: insights from a Korean cohort.","authors":"Frank Aimee Rodrigue Ndagijimana, Taesung Park","doi":"10.1186/s44342-024-00035-y","DOIUrl":"10.1186/s44342-024-00035-y","url":null,"abstract":"Background: Understanding the progression and recovery process of COVID-19 is crucial for guiding public health strategies and developing targeted interventions. This longitudinal cohort study aims to elucidate the dynamics of COVID-19 severity progression and evaluate the impact of underlying health conditions on these transitions, providing critical insights for more effective disease management.Methods: Data from 4549 COVID-19 patients admitted to Seoul National University Boramae Medical Center between February 5th, 2020, and October 30th, 2021, were analyzed using a 5-state continuous-time Markov multistate model. The model estimated instantaneous transition rates between different levels of COVID-19 severity, predicted probabilities of state transitions, and determined hazard ratios associated with underlying comorbidities.Results: The analysis revealed that most patients stabilized in their initial state, with 72.2% of patients with moderate symptoms remaining moderate. Patients with hypertension had a 67.6% higher risk of progressing from moderate to severe, while those with diabetes had an 89.9% higher risk of deteriorating from severe to critical. Although transition rates to death were low early in hospitalization, these comorbidities significantly increased the likelihood of worsening conditions.Conclusion: This study highlights the utility of continuous-time Markov multistate models in assessing COVID-19 severity progression among hospitalized patients. The findings indicate that patients are more likely to recover than to experience worsening conditions. However, hypertension and diabetes significantly increase the risk of severe outcomes, underscoring the importance of managing these conditions in COVID-19 patients.","PeriodicalId":94288,"journal":{"name":"Genomics & informatics","volume":"23 1","pages":"2"},"PeriodicalIF":0.0,"publicationDate":"2025-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11786383/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143076668","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Structural insights into antibody-based immunotherapy for hepatocellular carcinoma. 基于抗体的肝细胞癌免疫治疗的结构见解。

Genomics & informatics Pub Date : 2025-01-20 DOI: 10.1186/s44342-024-00033-0

Masaud Shah, Muhammad Hussain, Hyun Goo Woo

{"title":"Structural insights into antibody-based immunotherapy for hepatocellular carcinoma.","authors":"Masaud Shah, Muhammad Hussain, Hyun Goo Woo","doi":"10.1186/s44342-024-00033-0","DOIUrl":"10.1186/s44342-024-00033-0","url":null,"abstract":"Hepatocellular carcinoma (HCC) is one of the most common types of primary liver cancer and remains a leading cause of cancer-related deaths worldwide. While traditional approaches like surgical resection and tyrosine kinase inhibitors struggle against the tumor's immune evasion, monoclonal antibody (mAb)-based immunotherapies have emerged as promising alternatives. Several therapeutic antibodies that counter the immunosuppressive tumor microenvironment have demonstrated efficacy in clinical trials, leading to FDA approvals for advanced HCC treatment. A crucial aspect of advancing these therapies lies in understanding the structural interactions between antibodies and their targets. Recent findings indicate that mAbs and bispecific antibodies (bsAbs) can target different, non-overlapping epitopes on immune checkpoints such as PD-1 and CTLA-4. This review delves into the epitope-paratope interactions of structurally unresolved mAbs and bsAbs, and discusses the potential for combination therapies based on their non-overlapping epitopes. By leveraging this unique feature, combination therapies could enhance immune activation, reduce resistance, and improve overall efficacy, marking a new direction for antibody-based immunotherapy in HCC.","PeriodicalId":94288,"journal":{"name":"Genomics & informatics","volume":"23 1","pages":"1"},"PeriodicalIF":0.0,"publicationDate":"2025-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11744992/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143019311","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

DeepDoublet identifies neighboring cell-dependent gene expression. DeepDoublet识别邻近细胞依赖性基因表达。

Genomics & informatics Pub Date : 2024-12-18 DOI: 10.1186/s44342-024-00031-2

Linbu Liao, Junyoung Kim, Kanghee Cho, Junil Kim, Byung-Kwan Lim, Kyoung Jae Won

引用次数: 0

Rore: robust and efficient antioxidant protein classification via a novel dimensionality reduction strategy based on learning of fewer features. 摘要：基于学习更少特征的新型降维策略，实现抗氧化蛋白的鲁棒和高效分类。

Genomics & informatics Pub Date : 2024-12-04 DOI: 10.1186/s44342-024-00026-z

Chaolu Meng, Yongqi Hou, Quan Zou, Lei Shi, Xi Su, Ying Ju

{"title":"Rore: robust and efficient antioxidant protein classification via a novel dimensionality reduction strategy based on learning of fewer features.","authors":"Chaolu Meng, Yongqi Hou, Quan Zou, Lei Shi, Xi Su, Ying Ju","doi":"10.1186/s44342-024-00026-z","DOIUrl":"10.1186/s44342-024-00026-z","url":null,"abstract":"In protein identification, researchers increasingly aim to achieve efficient classification using fewer features. While many feature selection methods effectively reduce the number of model features, they often cause information loss caused by merely selecting or discarding features, which limits classifier performance. To address this issue, we present Rore, an algorithm based on a feature-dimensionality reduction strategy. By mapping the original features to a latent space, Rore retains all relevant feature information while using fewer representations of the latent features. This approach significantly preserves the original information and overcomes the information loss problem associated with previous feature selection. Through extensive experimental validation and analysis, Rore demonstrated excellent performance on an antioxidant protein dataset, achieving an accuracy of 95.88% and MCC of 91.78%, using vectors including only 15 features. The Rore algorithm is available online at http://112.124.26.17:8021/Rore .","PeriodicalId":94288,"journal":{"name":"Genomics & informatics","volume":"22 1","pages":"29"},"PeriodicalIF":0.0,"publicationDate":"2024-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11616364/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142782245","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Rare disease genomics and precision medicine. 罕见病基因组学和精准医学。

Genomics & informatics Pub Date : 2024-12-03 DOI: 10.1186/s44342-024-00032-1

Juhyeon Hong, Dajun Lee, Ayoung Hwang, Taekeun Kim, Hong-Yeoul Ryu, Jungmin Choi

引用次数: 0

Common genetic etiologies of sensorineural hearing loss in Koreans. 韩国人感音神经性听力损失的常见遗传病因。

Genomics & informatics Pub Date : 2024-11-28 DOI: 10.1186/s44342-024-00030-3

Seung Hyun Jang, Kuhn Yoon, Heon Yung Gee

引用次数: 0

Dissecting non-B DNA structural motifs in untranslated regions of eukaryotic genomes. 剖析真核生物基因组非翻译区中的非 B 型 DNA 结构图案。

Genomics & informatics Pub Date : 2024-11-27 DOI: 10.1186/s44342-024-00028-x

Aruna Sesha Chandrika Gummadi, Divya Kumari Muppa, Venakata Rajesh Yella

{"title":"Dissecting non-B DNA structural motifs in untranslated regions of eukaryotic genomes.","authors":"Aruna Sesha Chandrika Gummadi, Divya Kumari Muppa, Venakata Rajesh Yella","doi":"10.1186/s44342-024-00028-x","DOIUrl":"10.1186/s44342-024-00028-x","url":null,"abstract":"The untranslated regions (UTRs) of genes significantly impact various biological processes, including transcription, posttranscriptional control, mRNA stability, localization, and translation efficiency. In functional areas of genomes, non-B DNA structures such as cruciform, curved, triplex, G-quadruplex, and Z-DNA structures are common and have an impact on cellular physiology. Although the role of these structures in cis-regulatory regions such as promoters is well established in eukaryotic genomes, their prevalence within UTRs across different eukaryotic classes has not been extensively documented. Our study investigated the prevalence of various non-B DNA motifs within the 5' and 3' UTRs across diverse eukaryotic species. Our comparative analysis encompassed the 5'-UTRs and 3'UTRs of 360 species representing diverse eukaryotic domains of life, including Arthropoda (Diptera, Hemiptera, and Hymenoptera), Chordata (Artiodactyla, Carnivora, Galliformes, Passeriformes, Primates, Rodentia, Squamata, Testudines), Magnoliophyta (Brassicales), Fabales (Poales), and Nematoda (Rhabditida), on the basis of datasets derived from the UTRdb. We observed that species belonging to taxonomic orders such as Rhabditida, Diptera, Brassicales, and Hemiptera present a prevalence of curved DNA motifs in their UTRs, whereas orders such as Testudines, Galliformes, and Rodentia present a preponderance of G-quadruplexes in both UTRs. The distribution of motifs is conserved across different taxonomic classes, although species-specific variations in motif preferences were also observed. Our research unequivocally illuminates the prevalence and potential functional implications of non-B DNA motifs, offering invaluable insights into the evolutionary and biological significance of these structures.","PeriodicalId":94288,"journal":{"name":"Genomics & informatics","volume":"22 1","pages":"25"},"PeriodicalIF":0.0,"publicationDate":"2024-11-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11603647/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142741945","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Genomic characteristics of Vibrio vulnificus strains isolated from clinical and environmental sources. 从临床和环境来源分离的弧菌菌株的基因组特征。

Genomics & informatics Pub Date : 2024-11-27 DOI: 10.1186/s44342-024-00029-w

Jinkyeong Lee, Jeong-Ih Shin, Woo Young Cho, Kun Taek Park, Yeun-Jun Chung, Seung-Hyun Jung

{"title":"Genomic characteristics of Vibrio vulnificus strains isolated from clinical and environmental sources.","authors":"Jinkyeong Lee, Jeong-Ih Shin, Woo Young Cho, Kun Taek Park, Yeun-Jun Chung, Seung-Hyun Jung","doi":"10.1186/s44342-024-00029-w","DOIUrl":"10.1186/s44342-024-00029-w","url":null,"abstract":"Vibrio vulnificus, a gram-negative pathogenic bacterium, transmitted via undercooked seafood or contaminated seawater, causes septicemia and wound infections. In this study, we analyzed 15 clinical and 11 environmental isolates. In total, 20 sequence types (STs), including eight novel STs, were identified. Antibiotic resistance gene analysis commonly detected the cyclic AMP receptor protein (CRP) in both the clinical and environmental isolates. Interestingly, clinical and environmental isolates were non-susceptible to third-generation cephalosporins, such as ceftazidime and cefotaxime, complicating the treatment of V. vulnificus infection. Multiple antibiotic resistance (MAR) index ranged from 0.1 to 0.5, with clinical isolates showing a higher mean MAR index than the environmental isolates, indicating their broader spectrum of resistance. Notable, no quantitative (124.3 vs. 126.5) and qualitative (adherence, antiphagocytosis, and chemotaxis/motility) differences in virulence factors were observed between the environmental and clinical strains. The molecular characteristics identified in this study provide insights into the virulence of V. vulnificus strains in South Korea, highlighting the need for continuous surveillance of antibiotic resistance in emerging V. vulnificus strains.","PeriodicalId":94288,"journal":{"name":"Genomics & informatics","volume":"22 1","pages":"26"},"PeriodicalIF":0.0,"publicationDate":"2024-11-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11603906/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142741946","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Neuromuscular diseases: genomics-driven advances. 神经肌肉疾病：基因组学驱动的进步。

Genomics & informatics Pub Date : 2024-11-26 DOI: 10.1186/s44342-024-00027-y

Anna Cho

{"title":"Neuromuscular diseases: genomics-driven advances.","authors":"Anna Cho","doi":"10.1186/s44342-024-00027-y","DOIUrl":"10.1186/s44342-024-00027-y","url":null,"abstract":"Neuromuscular diseases (NMDs) are a group of rare disorders characterized by significant genetic and clinical complexity. Advances in genomics have revolutionized both the diagnosis and treatment of NMDs. While fewer than 30 NMDs had known genetic causes before the 1990s, more than 600 have now been identified, largely due to the adoption of next-generation sequencing (NGS) technologies such as whole-exome sequencing (WES) and whole-genome sequencing (WGS). These technologies have enabled more precise and earlier diagnoses, although the genetic complexity of many NMDs continues to pose challenges. Gene therapy has been a transformative breakthrough in the treatment of NMDs. In spinal muscular atrophy (SMA), therapies like nusinersen, onasemnogene abeparvovec, and risdiplam have dramatically improved patient outcomes. Similarly, Duchenne muscular dystrophy (DMD) has seen significant progress, most notably with the FDA approval of delandistrogene moxeparvovec, the first micro-dystrophin gene therapy. Despite these advancements, challenges remain, including the rarity of many NMDs, genetic heterogeneity, and the high costs associated with genomic technologies and therapies. Continued progress in gene therapy, RNA-based therapeutics, and personalized medicine holds promise for further breakthroughs in the management of these debilitating diseases.","PeriodicalId":94288,"journal":{"name":"Genomics & informatics","volume":"22 1","pages":"24"},"PeriodicalIF":0.0,"publicationDate":"2024-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11600827/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142735453","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Examining HPO by organ and system to facilitate practical use by clinicians. 按器官和系统检查 HPO，以方便临床医生实际使用。

Genomics & informatics Pub Date : 2024-11-12 DOI: 10.1186/s44342-024-00024-1

Eisuke Dohi, Terue Takatsuki, Yuka Tateisi, Toyofumi Fujiwara, Yasunori Yamamoto

{"title":"Examining HPO by organ and system to facilitate practical use by clinicians.","authors":"Eisuke Dohi, Terue Takatsuki, Yuka Tateisi, Toyofumi Fujiwara, Yasunori Yamamoto","doi":"10.1186/s44342-024-00024-1","DOIUrl":"10.1186/s44342-024-00024-1","url":null,"abstract":"The Human Phenotype Ontology (HPO) is widely used for annotating clinical text data, and sufficient annotation is crucial for the effective utilization of clinical texts. It was known that the use of LLMs can successfully extract symptoms and findings, but cannot annotate them with the HPO. We hypothesized that one of the potential issue for this is the lack of appropriate terms in the HPO. Therefore, during the Biomedical Linked Annotation Hackathon 8 (BLAH8), we attempted the following two tasks in order to grasp the overall picture of HPO. (1) Extract all HPO terms for each of the 23 HPO subclasses (defined as categories) directly under the HPO \"Phenotypic abnormality\" and then (2) search for major attributes in each of 23 categories. We employed LLM for these two tasks related to examining HPO and, at the same time, found that LLM didn't work well without ingenuity for tasks that lacked sentences and context. A manual search for terms within each category revealed that the HPO contains a mix of terms with four major attributes: (1) Disease Name, (2) Condition, (3) Test Data, and (4) Symptoms and Findings. Manual curation showed that the ratio of symptoms and findings varied from 0 to 93.1% across categories. For clinicians, who are end-users of medical terminology including HPO, it is difficult to understand ontologies. However, for good quality ontology is also important for good-quality data, and a clinician's help is essential. It is also important to make the overall picture and limitations of ontologies easy to understand in order to bring out the explanatory power of LLMs and artificial intelligence.","PeriodicalId":94288,"journal":{"name":"Genomics & informatics","volume":"22 1","pages":"23"},"PeriodicalIF":0.0,"publicationDate":"2024-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11559069/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142635517","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0