The detection of identity-by-descent(IBD)segments is widely used to infer relatedness in many fields,including forensics and ancient DNA analysis.However,existing methods are often ineffective for poor-quality DNA sam...The detection of identity-by-descent(IBD)segments is widely used to infer relatedness in many fields,including forensics and ancient DNA analysis.However,existing methods are often ineffective for poor-quality DNA samples.Here,we propose a method,clusIBD,which can robustly detect IBD segments using unphased genetic data with a high rate of genotyping error.We evaluated and compared the performance of clusIBD with that of IBIS,TRUFFLE,and IBDseq using simulated data,artificial poor-quality materials,and ancient DNA samples.The results show that clusIBD outperforms these existing tools and could be used for kinship inference in fields such as ancient DNA analysis and criminal investigation.clusIBD is publicly available at GitHub(https://github.com/Ryan620/clusIBD/)and BioCode(https://ngdc.cncb.ac.cn/biocode/tool/BT007882).展开更多
The paper utilized a standardized methodology to identify prognostic biomarkers in hepatocellular carcinoma(HCC)by analyzing transcriptomic and clinical data from The Cancer Genome Atlas(TCGA)database.The approach,whi...The paper utilized a standardized methodology to identify prognostic biomarkers in hepatocellular carcinoma(HCC)by analyzing transcriptomic and clinical data from The Cancer Genome Atlas(TCGA)database.The approach,which included stringent data preprocessing,differential gene expression analysis,and Kaplan-Meier survival analysis,provided valuable insights into the genetic underpinnings of HCC.The comprehensive analysis of a dataset involving 370 HCC patients uncovered correlations between survival status and pathological characteristics,including tumor size,lymph node involvement,and distant metastasis.The processed transcriptome dataset,comprising 420 samples and annotating 26,783 genes,served as a robust platform for identifying differential gene expression patterns.Among the significant differential expression genes,the key genes such as FBXO43,HAGLROS,CRISPLD1,LRRC3.DT,and ERN2,were pinpointed,which showed significant associations with patient survival outcomes,indicating their potential as novel prognostic biomarkers.This study can not only enhance the understanding of HCC’s genetic landscape but also establish a blueprint for a standardized process to discover prognostic biomarkers of various diseases using genetic big data.Future research should focus on validating these biomarkers through independent cohorts and exploring their utility in the development of personalized treatment strategies.展开更多
The primary focus of this paper is to design a progressive restoration plan for an enterprise data center environment following a partial or full disruption. Repairing and restoring disrupted components in an enterpri...The primary focus of this paper is to design a progressive restoration plan for an enterprise data center environment following a partial or full disruption. Repairing and restoring disrupted components in an enterprise data center requires a significant amount of time and human effort. Following a major disruption, the recovery process involves multiple stages, and during each stage, the partially recovered infrastructures can provide limited services to users at some degraded service level. However, how fast and efficiently an enterprise infrastructure can be recovered de- pends on how the recovery mechanism restores the disrupted components, considering the inter-dependencies between services, along with the limitations of expert human operators. The entire problem turns out to be NP- hard and rather complex, and we devise an efficient meta-heuristic to solve the problem. By considering some real-world examples, we show that the proposed meta-heuristic provides very accurate results, and still runs 600-2800 times faster than the optimal solution obtained from a general purpose mathematical solver [1].展开更多
The completion of genome sequences and subsequent high-throughput mapping of molecular networks have allowed us to study biology from the network perspective. Experimental, statistical and mathematical modeling approa...The completion of genome sequences and subsequent high-throughput mapping of molecular networks have allowed us to study biology from the network perspective. Experimental, statistical and mathematical modeling approaches have been employed to study the structure, function and dynamics of molecular networks, and begin to reveal important links of various network properties to the functions of the biological systems. In agreement with these functional links, evolutionary selection of a network is apparently based on the function, rather than directly on the structure of the network. Dynamic modularity is one of the prominent features of molecular networks. Taking advantage of such a feature may simplify network-based biological studies through construction of process-specific modular networks and provide functional and mechanistic insights linking genotypic variations to complex traits or diseases, which is likely to be a key approach in the next wave of understanding complex human diseases. With the development of ready-to-use network analysis and modeling tools the networks approaches will be infused into everyday biological research in the near future.展开更多
基金funded by the National Natural Science Foundation of China(Grant No.82302125)the National Key R&D Program of China(Grant No.2024YFC3306702).
文摘The detection of identity-by-descent(IBD)segments is widely used to infer relatedness in many fields,including forensics and ancient DNA analysis.However,existing methods are often ineffective for poor-quality DNA samples.Here,we propose a method,clusIBD,which can robustly detect IBD segments using unphased genetic data with a high rate of genotyping error.We evaluated and compared the performance of clusIBD with that of IBIS,TRUFFLE,and IBDseq using simulated data,artificial poor-quality materials,and ancient DNA samples.The results show that clusIBD outperforms these existing tools and could be used for kinship inference in fields such as ancient DNA analysis and criminal investigation.clusIBD is publicly available at GitHub(https://github.com/Ryan620/clusIBD/)and BioCode(https://ngdc.cncb.ac.cn/biocode/tool/BT007882).
基金the 2023 Inner Mongolia Public Institution High-Level Talent Introduction Scientific Research Support Project with the start-up funding from Linyi Vocational College。
文摘The paper utilized a standardized methodology to identify prognostic biomarkers in hepatocellular carcinoma(HCC)by analyzing transcriptomic and clinical data from The Cancer Genome Atlas(TCGA)database.The approach,which included stringent data preprocessing,differential gene expression analysis,and Kaplan-Meier survival analysis,provided valuable insights into the genetic underpinnings of HCC.The comprehensive analysis of a dataset involving 370 HCC patients uncovered correlations between survival status and pathological characteristics,including tumor size,lymph node involvement,and distant metastasis.The processed transcriptome dataset,comprising 420 samples and annotating 26,783 genes,served as a robust platform for identifying differential gene expression patterns.Among the significant differential expression genes,the key genes such as FBXO43,HAGLROS,CRISPLD1,LRRC3.DT,and ERN2,were pinpointed,which showed significant associations with patient survival outcomes,indicating their potential as novel prognostic biomarkers.This study can not only enhance the understanding of HCC’s genetic landscape but also establish a blueprint for a standardized process to discover prognostic biomarkers of various diseases using genetic big data.Future research should focus on validating these biomarkers through independent cohorts and exploring their utility in the development of personalized treatment strategies.
文摘The primary focus of this paper is to design a progressive restoration plan for an enterprise data center environment following a partial or full disruption. Repairing and restoring disrupted components in an enterprise data center requires a significant amount of time and human effort. Following a major disruption, the recovery process involves multiple stages, and during each stage, the partially recovered infrastructures can provide limited services to users at some degraded service level. However, how fast and efficiently an enterprise infrastructure can be recovered de- pends on how the recovery mechanism restores the disrupted components, considering the inter-dependencies between services, along with the limitations of expert human operators. The entire problem turns out to be NP- hard and rather complex, and we devise an efficient meta-heuristic to solve the problem. By considering some real-world examples, we show that the proposed meta-heuristic provides very accurate results, and still runs 600-2800 times faster than the optimal solution obtained from a general purpose mathematical solver [1].
文摘The completion of genome sequences and subsequent high-throughput mapping of molecular networks have allowed us to study biology from the network perspective. Experimental, statistical and mathematical modeling approaches have been employed to study the structure, function and dynamics of molecular networks, and begin to reveal important links of various network properties to the functions of the biological systems. In agreement with these functional links, evolutionary selection of a network is apparently based on the function, rather than directly on the structure of the network. Dynamic modularity is one of the prominent features of molecular networks. Taking advantage of such a feature may simplify network-based biological studies through construction of process-specific modular networks and provide functional and mechanistic insights linking genotypic variations to complex traits or diseases, which is likely to be a key approach in the next wave of understanding complex human diseases. With the development of ready-to-use network analysis and modeling tools the networks approaches will be infused into everyday biological research in the near future.
