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Caetano-Anollés G. Are Viruses Taxonomic Units? A Protein Domain and Loop-Centric Phylogenomic Assessment. Viruses 2024; 16:1061. [PMID: 39066224 PMCID: PMC11281659 DOI: 10.3390/v16071061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Revised: 06/26/2024] [Accepted: 06/27/2024] [Indexed: 07/28/2024] Open
Abstract
Virus taxonomy uses a Linnaean-like subsumption hierarchy to classify viruses into taxonomic units at species and higher rank levels. Virus species are considered monophyletic groups of mobile genetic elements (MGEs) often delimited by the phylogenetic analysis of aligned genomic or metagenomic sequences. Taxonomic units are assumed to be independent organizational, functional and evolutionary units that follow a 'natural history' rationale. Here, I use phylogenomic and other arguments to show that viruses are not self-standing genetically-driven systems acting as evolutionary units. Instead, they are crucial components of holobionts, which are units of biological organization that dynamically integrate the genetics, epigenetic, physiological and functional properties of their co-evolving members. Remarkably, phylogenomic analyses show that viruses share protein domains and loops with cells throughout history via massive processes of reticulate evolution, helping spread evolutionary innovations across a wider taxonomic spectrum. Thus, viruses are not merely MGEs or microbes. Instead, their genomes and proteomes conduct cellularly integrated processes akin to those cataloged by the GO Consortium. This prompts the generation of compositional hierarchies that replace the 'is-a-kind-of' by a 'is-a-part-of' logic to better describe the mereology of integrated cellular and viral makeup. My analysis demands a new paradigm that integrates virus taxonomy into a modern evolutionarily centered taxonomy of organisms.
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Affiliation(s)
- Gustavo Caetano-Anollés
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, C. R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL 61801, USA
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2
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Caetano-Anollés G, Claverie JM, Nasir A. A critical analysis of the current state of virus taxonomy. Front Microbiol 2023; 14:1240993. [PMID: 37601376 PMCID: PMC10435761 DOI: 10.3389/fmicb.2023.1240993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 07/20/2023] [Indexed: 08/22/2023] Open
Abstract
Taxonomical classification has preceded evolutionary understanding. For that reason, taxonomy has become a battleground fueled by knowledge gaps, technical limitations, and a priorism. Here we assess the current state of the challenging field, focusing on fallacies that are common in viral classification. We emphasize that viruses are crucial contributors to the genomic and functional makeup of holobionts, organismal communities that behave as units of biological organization. Consequently, viruses cannot be considered taxonomic units because they challenge crucial concepts of organismality and individuality. Instead, they should be considered processes that integrate virions and their hosts into life cycles. Viruses harbor phylogenetic signatures of genetic transfer that compromise monophyly and the validity of deep taxonomic ranks. A focus on building phylogenetic networks using alignment-free methodologies and molecular structure can help mitigate the impasse, at least in part. Finally, structural phylogenomic analysis challenges the polyphyletic scenario of multiple viral origins adopted by virus taxonomy, defeating a polyphyletic origin and supporting instead an ancient cellular origin of viruses. We therefore, prompt abandoning deep ranks and urgently reevaluating the validity of taxonomic units and principles of virus classification.
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Affiliation(s)
- Gustavo Caetano-Anollés
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences and C.R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Jean-Michel Claverie
- Structural and Genomic Information Laboratory (UMR7256), Mediterranean Institute of Microbiology (FR3479), IM2B, IOM, Aix Marseille University, CNRS, Marseille, France
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3
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Villalobos-Cid M, Dorn M, Contreras Á, Inostroza-Ponta M. An evolutionary algorithm based on parsimony for the multiobjective phylogenetic network inference problem. Appl Soft Comput 2023. [DOI: 10.1016/j.asoc.2023.110270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2023]
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4
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Li S, Chang M, Tong L, Wang Y, Wang M, Wang F. Screening potential lncRNA biomarkers for breast cancer and colorectal cancer combining random walk and logistic matrix factorization. Front Genet 2023; 13:1023615. [PMID: 36744179 PMCID: PMC9895102 DOI: 10.3389/fgene.2022.1023615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Accepted: 10/10/2022] [Indexed: 01/21/2023] Open
Abstract
Breast cancer and colorectal cancer are two of the most common malignant tumors worldwide. They cause the leading causes of cancer mortality. Many researches have demonstrated that long noncoding RNAs (lncRNAs) have close linkages with the occurrence and development of the two cancers. Therefore, it is essential to design an effective way to identify potential lncRNA biomarkers for them. In this study, we developed a computational method (LDA-RWLMF) by integrating random walk with restart and Logistic Matrix Factorization to investigate the roles of lncRNA biomarkers in the prognosis and diagnosis of the two cancers. We first fuse disease semantic and Gaussian association profile similarities and lncRNA functional and Gaussian association profile similarities. Second, we design a negative selection algorithm to extract negative LncRNA-Disease Associations (LDA) based on random walk. Third, we develop a logistic matrix factorization model to predict possible LDAs. We compare our proposed LDA-RWLMF method with four classical LDA prediction methods, that is, LNCSIM1, LNCSIM2, ILNCSIM, and IDSSIM. The results from 5-fold cross validation on the MNDR dataset show that LDA-RWLMF computes the best AUC value of 0.9312, outperforming the above four LDA prediction methods. Finally, we rank all lncRNA biomarkers for the two cancers after determining the performance of LDA-RWLMF, respectively. We find that 48 and 50 lncRNAs have the highest association scores with breast cancer and colorectal cancer among all lncRNAs known to associate with them on the MNDR dataset, respectively. We predict that lncRNAs HULC and HAR1A could be separately potential biomarkers for breast cancer and colorectal cancer and need to biomedical experimental validation.
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5
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Yang P, Lang J, Li H, Lu J, Lin H, Tian G, Bai H, Yang J, Ning K. TCM-Suite: A comprehensive and holistic platform for Traditional Chinese Medicine component identification and network pharmacology analysis. IMETA 2022; 1:e47. [PMID: 38867910 PMCID: PMC10989960 DOI: 10.1002/imt2.47] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 07/05/2022] [Accepted: 07/20/2022] [Indexed: 06/14/2024]
Abstract
DNA-based biological ingredient identification and downstream pharmacology network analysis are commonly used in research for Traditional Chinese Medicine preparations (TCM formulas). Advancements in bioinformatics tools and the accumulation of related data have become driving forces for progress in this field. However, a lack of a platform integrating biological ingredient identification and downstream pharmacology network analysis hinders the deep understanding of TCM. In this study, we developed the TCM-Suite platform composed of two sub-databases, Holmes-Suite and Watson-Suite, for TCM biological ingredient identification and network pharmacology investigation, respectively, both are among the most complete: In the Holmes-Suite, we collected and processed six types of marker gene sequences, accounting for 1,251,548 marker gene sequences. In the Watson-Suite, we curated and integrated a massive number of entries from more than 10 public databases. Importantly, we developed a comprehensive pipeline to integrate TCM biological ingredient identification and downstream network pharmacology research, allowing users to simultaneously identify components of a TCM formula and analyze its potential pharmacology mechanism. Furthermore, we designed search engines and a user-friendly platform to better search and visualize these rich resources. TCM-Suite is a comprehensive and holistic platform for TCM-based drug discovery and repurposing. TCM-Suite website: http://TCM-Suite.AImicrobiome.cn.
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Affiliation(s)
- Pengshuo Yang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular‐imaging, Center for Artificial Intelligence Biology, Department of Bioinformatics and Systems BiologyCollege of Life Science and Technology, Huazhong University of Science and TechnologyWuhanChina
| | - Jidong Lang
- Geneis Beijing Co., Ltd.BeijingChina
- Department of sciencesQingdao Genesis Institute of Big Data Mining and PrecisionQingdaoShandongChina
- Academician WorkstationChangsha Medical UniversityChangshaChina
| | - Hongjun Li
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular‐imaging, Center for Artificial Intelligence Biology, Department of Bioinformatics and Systems BiologyCollege of Life Science and Technology, Huazhong University of Science and TechnologyWuhanChina
| | - Jinxiang Lu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular‐imaging, Center for Artificial Intelligence Biology, Department of Bioinformatics and Systems BiologyCollege of Life Science and Technology, Huazhong University of Science and TechnologyWuhanChina
| | - Hanyang Lin
- Sequenxe Biological Technology Co., Ltd.XiamenChina
| | - Geng Tian
- Geneis Beijing Co., Ltd.BeijingChina
- Department of sciencesQingdao Genesis Institute of Big Data Mining and PrecisionQingdaoShandongChina
| | - Hong Bai
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular‐imaging, Center for Artificial Intelligence Biology, Department of Bioinformatics and Systems BiologyCollege of Life Science and Technology, Huazhong University of Science and TechnologyWuhanChina
| | - Jialiang Yang
- Geneis Beijing Co., Ltd.BeijingChina
- Department of sciencesQingdao Genesis Institute of Big Data Mining and PrecisionQingdaoShandongChina
- Academician WorkstationChangsha Medical UniversityChangshaChina
| | - Kang Ning
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular‐imaging, Center for Artificial Intelligence Biology, Department of Bioinformatics and Systems BiologyCollege of Life Science and Technology, Huazhong University of Science and TechnologyWuhanChina
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6
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Zhai S, Li X, Wu Y, Shi X, Ji B, Qiu C. Identifying potential microRNA biomarkers for colon cancer and colorectal cancer through bound nuclear norm regularization. Front Genet 2022; 13:980437. [PMID: 36313468 PMCID: PMC9614659 DOI: 10.3389/fgene.2022.980437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 08/01/2022] [Indexed: 11/17/2022] Open
Abstract
Colon cancer and colorectal cancer are two common cancer-related deaths worldwide. Identification of potential biomarkers for the two cancers can help us to evaluate their initiation, progression and therapeutic response. In this study, we propose a new microRNA-disease association identification method, BNNRMDA, to discover potential microRNA biomarkers for the two cancers. BNNRMDA better combines disease semantic similarity and Gaussian Association Profile Kernel (GAPK) similarity, microRNA function similarity and GAPK similarity, and the bound nuclear norm regularization model. Compared to other five classical microRNA-disease association identification methods (MIDPE, MIDP, RLSMDA, GRNMF, AND LPLNS), BNNRMDA obtains the highest AUC of 0.9071, demonstrating its strong microRNA-disease association identification performance. BNNRMDA is applied to discover possible microRNA biomarkers for colon cancer and colorectal cancer. The results show that all 73 known microRNAs associated with colon cancer in the HMDD database have the highest association scores with colon cancer and are ranked as top 73. Among 137 known microRNAs associated with colorectal cancer in the HMDD database, 129 microRNAs have the highest association scores with colorectal cancer and are ranked as top 129. In addition, we predict that hsa-miR-103a could be a potential biomarker of colon cancer and hsa-mir-193b and hsa-mir-7days could be potential biomarkers of colorectal cancer.
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Affiliation(s)
- Shengyong Zhai
- Department of General Surgery, Weifang People’s Hospital, Shandong, China
| | - Xiaoling Li
- The Second Department of Oncology, Beidahuang Industry Group General Hospital, Harbin, China,Heilongjiang Second Cancer Hospital, Harbin, China
| | - Yan Wu
- Geneis Beijing Co., Ltd., Beijing, China
| | - Xiaoli Shi
- Geneis Beijing Co., Ltd., Beijing, China
| | - Binbin Ji
- Geneis Beijing Co., Ltd., Beijing, China
| | - Chun Qiu
- Department of Oncology, Hainan General Hospital, Haikou, China,*Correspondence: Chun Qiu,
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7
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Unified K-means coupled self-representation and neighborhood kernel learning for clustering single-cell RNA-sequencing data. Neurocomputing 2022. [DOI: 10.1016/j.neucom.2022.06.046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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8
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Guo Z, Hui Y, Kong F, Lin X. Finding Lung-Cancer-Related lncRNAs Based on Laplacian Regularized Least Squares With Unbalanced Bi-Random Walk. Front Genet 2022; 13:933009. [PMID: 35938010 PMCID: PMC9355720 DOI: 10.3389/fgene.2022.933009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 06/03/2022] [Indexed: 11/13/2022] Open
Abstract
Lung cancer is one of the leading causes of cancer-related deaths. Thus, it is important to find its biomarkers. Furthermore, there is an increasing number of studies reporting that long noncoding RNAs (lncRNAs) demonstrate dense linkages with multiple human complex diseases. Inferring new lncRNA-disease associations help to identify potential biomarkers for lung cancer and further understand its pathogenesis, design new drugs, and formulate individualized therapeutic options for lung cancer patients. This study developed a computational method (LDA-RLSURW) by integrating Laplacian regularized least squares and unbalanced bi-random walk to discover possible lncRNA biomarkers for lung cancer. First, the lncRNA and disease similarities were computed. Second, unbalanced bi-random walk was, respectively, applied to the lncRNA and disease networks to score associations between diseases and lncRNAs. Third, Laplacian regularized least squares were further used to compute the association probability between each lncRNA-disease pair based on the computed random walk scores. LDA-RLSURW was compared using 10 classical LDA prediction methods, and the best AUC value of 0.9027 on the lncRNADisease database was obtained. We found the top 30 lncRNAs associated with lung cancers and inferred that lncRNAs TUG1, PTENP1, and UCA1 may be biomarkers of lung neoplasms, non-small–cell lung cancer, and LUAD, respectively.
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9
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Lang J, Li Y, Yang W, Dong R, Liang Y, Liu J, Chen L, Wang W, Ji B, Tian G, Che N, Meng B. Genomic and resistome analysis of Alcaligenes faecalis strain PGB1 by Nanopore MinION and Illumina Technologies. BMC Genomics 2022; 23:316. [PMID: 35443609 PMCID: PMC9022240 DOI: 10.1186/s12864-022-08507-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 03/28/2022] [Indexed: 12/24/2022] Open
Abstract
Background Drug-resistant bacteria are important carriers of antibiotic-resistant genes (ARGs). This fact is crucial for the development of precise clinical drug treatment strategies. Long-read sequencing platforms such as the Oxford Nanopore sequencer can improve genome assembly efficiency particularly when they are combined with short-read sequencing data. Results Alcaligenes faecalis PGB1 was isolated and identified with resistance to penicillin and three other antibiotics. After being sequenced by Nanopore MinION and Illumina sequencer, its entire genome was hybrid-assembled. One chromosome and one plasmid was assembled and annotated with 4,433 genes (including 91 RNA genes). Function annotation and comparison between strains were performed. A phylogenetic analysis revealed that it was closest to A. faecalis ZD02. Resistome related sequences was explored, including ARGs, Insert sequence, phage. Two plasmid aminoglycoside genes were determined to be acquired ARGs. The main ARG category was antibiotic efflux resistance and β-lactamase (EC 3.5.2.6) of PGB1 was assigned to Class A, Subclass A1b, and Cluster LSBL3. Conclusions The present study identified the newly isolated bacterium A. faecalis PGB1 and systematically annotated its genome sequence and ARGs. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08507-7.
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Affiliation(s)
- Jidong Lang
- Geneis (Beijing) Co., Ltd, Beijing, 100102, China.,Qingdao Geneis Institute of Big Data Mining and Precision Medicine, Qingdao, People's Republic of China
| | - Yanju Li
- School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Wenjuan Yang
- Geneis (Beijing) Co., Ltd, Beijing, 100102, China
| | - Ruyi Dong
- Geneis (Beijing) Co., Ltd, Beijing, 100102, China.,Qingdao Geneis Institute of Big Data Mining and Precision Medicine, Qingdao, People's Republic of China
| | - Yuebin Liang
- Geneis (Beijing) Co., Ltd, Beijing, 100102, China.,Qingdao Geneis Institute of Big Data Mining and Precision Medicine, Qingdao, People's Republic of China
| | - Jia Liu
- Geneis (Beijing) Co., Ltd, Beijing, 100102, China
| | - Lanyou Chen
- Geneis (Beijing) Co., Ltd, Beijing, 100102, China
| | - Weiwei Wang
- Geneis (Beijing) Co., Ltd, Beijing, 100102, China
| | - Binbin Ji
- Geneis (Beijing) Co., Ltd, Beijing, 100102, China
| | - Geng Tian
- Geneis (Beijing) Co., Ltd, Beijing, 100102, China.,Qingdao Geneis Institute of Big Data Mining and Precision Medicine, Qingdao, People's Republic of China
| | - Nanying Che
- Department of Pathology, Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, 101149, China.
| | - Bo Meng
- Geneis (Beijing) Co., Ltd, Beijing, 100102, China.
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10
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Lang J, Zhu R, Sun X, Zhu S, Li T, Shi X, Sun Y, Yang Z, Wang W, Bing P, He B, Tian G. Evaluation of the MGISEQ-2000 Sequencing Platform for Illumina Target Capture Sequencing Libraries. Front Genet 2021; 12:730519. [PMID: 34777467 PMCID: PMC8578046 DOI: 10.3389/fgene.2021.730519] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 09/24/2021] [Indexed: 01/19/2023] Open
Abstract
Illumina is the leading sequencing platform in the next-generation sequencing (NGS) market globally. In recent years, MGI Tech has presented a series of new sequencers, including DNBSEQ-T7, MGISEQ-2000 and MGISEQ-200. As a complex application of NGS, cancer-detecting panels pose increasing demands for the high accuracy and sensitivity of sequencing and data analysis. In this study, we used the same capture DNA libraries constructed based on the Illumina protocol to evaluate the performance of the Illumina Nextseq500 and MGISEQ-2000 sequencing platforms. We found that the two platforms had high consistency in the results of hotspot mutation analysis; more importantly, we found that there was a significant loss of fragments in the 101-133 bp size range on the MGISEQ-2000 sequencing platform for Illumina libraries, but not for the capture DNA libraries prepared based on the MGISEQ protocol. This phenomenon may indicate fragment selection or low fragment ligation efficiency during the DNA circularization step, which is a unique step of the MGISEQ-2000 sequence platform. In conclusion, these different sequencing libraries and corresponding sequencing platforms are compatible with each other, but protocol and platform selection need to be carefully evaluated in combination with research purpose.
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Affiliation(s)
- Jidong Lang
- Bioinformatics and R and D Department, Geneis (Beijing) Co. Ltd., Beijing, China.,Qingdao Geneis Institute of Big Data Mining and Precision Medicine, Qingdao, China.,Academician Workstation, Changsha Medical University, Changsha, China
| | - Rongrong Zhu
- Vascular Surgery Department, Tsinghua University Affiliated Beijing Tsinghua Changgung Hospital, Beijing, China
| | - Xue Sun
- Bioinformatics and R and D Department, Geneis (Beijing) Co. Ltd., Beijing, China
| | - Siyu Zhu
- Department of Medicine, School of Medicine, University of California at San Diego, La Jolla, CA, United States
| | - Tianbao Li
- Bioinformatics and R and D Department, Geneis (Beijing) Co. Ltd., Beijing, China.,Qingdao Geneis Institute of Big Data Mining and Precision Medicine, Qingdao, China
| | - Xiaoli Shi
- Bioinformatics and R and D Department, Geneis (Beijing) Co. Ltd., Beijing, China
| | - Yanqi Sun
- Bioinformatics and R and D Department, Geneis (Beijing) Co. Ltd., Beijing, China
| | - Zhou Yang
- Bioinformatics and R and D Department, Geneis (Beijing) Co. Ltd., Beijing, China
| | - Weiwei Wang
- Bioinformatics and R and D Department, Geneis (Beijing) Co. Ltd., Beijing, China.,Qingdao Geneis Institute of Big Data Mining and Precision Medicine, Qingdao, China
| | - Pingping Bing
- Academician Workstation, Changsha Medical University, Changsha, China
| | - Binsheng He
- Academician Workstation, Changsha Medical University, Changsha, China
| | - Geng Tian
- Bioinformatics and R and D Department, Geneis (Beijing) Co. Ltd., Beijing, China.,Qingdao Geneis Institute of Big Data Mining and Precision Medicine, Qingdao, China
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11
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Yu L, Shi X, Liu X, Jin W, Jia X, Xi S, Wang A, Li T, Zhang X, Tian G, Sun D. Artificial Intelligence Systems for Diagnosis and Clinical Classification of COVID-19. Front Microbiol 2021; 12:729455. [PMID: 34650534 PMCID: PMC8507494 DOI: 10.3389/fmicb.2021.729455] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 08/17/2021] [Indexed: 01/14/2023] Open
Abstract
Objectives: COVID-19 is highly infectious and has been widely spread worldwide, with more than 159 million confirmed cases and more than 3 million deaths as of May 11, 2021. It has become a serious public health event threatening people's lives and safety. Due to the rapid transmission and long incubation period, shortage of medical resources would easily occur in the short term of discovering disease cases. Therefore, we aimed to construct an artificial intelligent framework to rapidly distinguish patients with COVID-19 from common pneumonia and non-pneumonia populations based on computed tomography (CT) images. Furthermore, we explored artificial intelligence (AI) algorithms to integrate CT features and laboratory findings on admission to predict the clinical classification of COVID-19. This will ease the burden of doctors in this emergency period and aid them to perform timely and appropriate treatment on patients. Methods: We collected all CT images and clinical data of novel coronavirus pneumonia cases in Inner Mongolia, including domestic cases and those imported from abroad; then, three models based on transfer learning to distinguish COVID-19 from other pneumonia and non-pneumonia population were developed. In addition, CT features and laboratory findings on admission were combined to predict clinical types of COVID-19 using AI algorithms. Lastly, Spearman's correlation test was applied to study correlations of CT characteristics and laboratory findings. Results: Among three models to distinguish COVID-19 based on CT, vgg19 showed excellent diagnostic performance, with area under the curve (AUC) of the receiver operating characteristic (ROC) curve at 95%. Together with laboratory findings, we were able to predict clinical types of COVID-19 with AUC of the ROC curve at 90%. Furthermore, biochemical markers, such as C-reactive protein (CRP), LYM, and lactic dehydrogenase (LDH) were identified and correlated with CT features. Conclusion: We developed an AI model to identify patients who were positive for COVID-19 according to the results of the first CT examination after admission and predict the progression combined with laboratory findings. In addition, we obtained important clinical characteristics that correlated with the CT image features. Together, our AI system could rapidly diagnose COVID-19 and predict clinical types to assist clinicians perform appropriate clinical management.
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Affiliation(s)
- Lan Yu
- Clinical Medical Research Center/Inner Mongolia Key Laboratory of Gene Regulation of the Metabolic Diseases, Inner Mongolia People's Hospital, Hohhot, China.,Department of Endocrinology, Inner Mongolia People's Hospital, Hohhot, China
| | - Xiaoli Shi
- Geneis (Beijing) Co., Ltd., Beijing, China.,Qingdao Geneis Institute of Big Data Mining and Precision Medicine, Qingdao, China
| | - Xiaoling Liu
- Department of Otolaryngology, Inner Mongolia People's Hospital, Hohhot, China
| | - Wen Jin
- Clinical Medical Research Center/Inner Mongolia Key Laboratory of Gene Regulation of the Metabolic Diseases, Inner Mongolia People's Hospital, Hohhot, China
| | - Xiaoqing Jia
- Baotou City Hospital for Infectious Diseases, Baotou, China
| | - Shuxue Xi
- Geneis (Beijing) Co., Ltd., Beijing, China.,Qingdao Geneis Institute of Big Data Mining and Precision Medicine, Qingdao, China
| | - Ailan Wang
- Geneis (Beijing) Co., Ltd., Beijing, China.,Qingdao Geneis Institute of Big Data Mining and Precision Medicine, Qingdao, China
| | - Tianbao Li
- Geneis (Beijing) Co., Ltd., Beijing, China.,Qingdao Geneis Institute of Big Data Mining and Precision Medicine, Qingdao, China
| | - Xiao Zhang
- Clinical Medical Research Center/Inner Mongolia Key Laboratory of Gene Regulation of the Metabolic Diseases, Inner Mongolia People's Hospital, Hohhot, China
| | - Geng Tian
- Geneis (Beijing) Co., Ltd., Beijing, China.,Qingdao Geneis Institute of Big Data Mining and Precision Medicine, Qingdao, China
| | - Dejun Sun
- Department of Pulmonary and Critical Care Medicine/Key Laboratory of National Health Commission for the Diagnosis & Treatment of COPD, Inner Mongolia People's Hospital, Hohhot, China
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12
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Qi R, Wu J, Guo F, Xu L, Zou Q. A spectral clustering with self-weighted multiple kernel learning method for single-cell RNA-seq data. Brief Bioinform 2020; 22:5916937. [PMID: 33003206 DOI: 10.1093/bib/bbaa216] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 08/14/2020] [Accepted: 08/14/2020] [Indexed: 12/26/2022] Open
Abstract
Single-cell RNA-sequencing (scRNA-seq) data widely exist in bioinformatics. It is crucial to devise a distance metric for scRNA-seq data. Almost all existing clustering methods based on spectral clustering algorithms work in three separate steps: similarity graph construction; continuous labels learning; discretization of the learned labels by k-means clustering. However, this common practice has potential flaws that may lead to severe information loss and degradation of performance. Furthermore, the performance of a kernel method is largely determined by the selected kernel; a self-weighted multiple kernel learning model can help choose the most suitable kernel for scRNA-seq data. To this end, we propose to automatically learn similarity information from data. We present a new clustering method in the form of a multiple kernel combination that can directly discover groupings in scRNA-seq data. The main proposition is that automatically learned similarity information from scRNA-seq data is used to transform the candidate solution into a new solution that better approximates the discrete one. The proposed model can be efficiently solved by the standard support vector machine (SVM) solvers. Experiments on benchmark scRNA-Seq data validate the superior performance of the proposed model. Spectral clustering with multiple kernels is implemented in Matlab, licensed under Massachusetts Institute of Technology (MIT) and freely available from the Github website, https://github.com/Cuteu/SMSC/.
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Affiliation(s)
- Ren Qi
- College of Intelligence and Computing, Tianjin University
| | - Jin Wu
- School of Management, Shenzhen Polytechnic
| | - Fei Guo
- College of Intelligence and Computing, Tianjin University
| | - Lei Xu
- School of Electronic and Communication Engineering, Shenzhen Polytechnic
| | - Quan Zou
- University of Electronic Science and Technology of China
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13
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Tan M, Long H, Liao B, Cao Z, Yuan D, Tian G, Zhuang J, Yang J. QS-Net: Reconstructing Phylogenetic Networks Based on Quartet and Sextet. Front Genet 2019; 10:607. [PMID: 31396256 PMCID: PMC6667645 DOI: 10.3389/fgene.2019.00607] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 06/11/2019] [Indexed: 01/27/2023] Open
Abstract
Phylogenetic networks are used to estimate evolutionary relationships among biological entities or taxa involving reticulate events such as horizontal gene transfer, hybridization, recombination, and reassortment. In the past decade, many phylogenetic tree and network reconstruction methods have been proposed. Despite that they are highly accurate in reconstructing simple to moderate complex reticulate events, the performance decreases when several reticulate events are present simultaneously. In this paper, we proposed QS-Net, a phylogenetic network reconstruction method taking advantage of information on the relationship among six taxa. To evaluate the performance of QS-Net, we conducted experiments on three artificial sequence data simulated from an evolutionary tree, an evolutionary network involving three reticulate events, and a complex evolutionary network involving five reticulate events. Comparison with popular phylogenetic methods including Neighbor-Joining, Split-Decomposition, Neighbor-Net, and Quartet-Net suggests that QS-Net is comparable with other methods in reconstructing tree-like evolutionary histories, while it outperforms them in reconstructing reticulate events. In addition, we also applied QS-Net in real data including a bacterial taxonomy data consisting of 36 bacterial species and the whole genome sequences of 22 H7N9 influenza A viruses. The results indicate that QS-Net is capable of inferring commonly believed bacterial taxonomy and influenza evolution as well as identifying novel reticulate events. The software QS-Net is publically available at https://github.com/Tmyiri/QS-Net.
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Affiliation(s)
- Ming Tan
- College of Computer Science and Electronic Engineering, Hunan University, Changsha, China
| | - Haixia Long
- School of Information Science and Technology , Hainan Normal University, Haikou, China
| | - Bo Liao
- College of Computer Science and Electronic Engineering, Hunan University, Changsha, China.,School of Information Science and Technology , Hainan Normal University, Haikou, China
| | - Zhi Cao
- College of Computer Science and Electronic Engineering, Hunan University, Changsha, China
| | - Dawei Yuan
- Geneis (Beijing) Co. Ltd., Beijing, China
| | - Geng Tian
- Geneis (Beijing) Co. Ltd., Beijing, China
| | - Jujuan Zhuang
- Department of Mathematics, Dalian Martine University, Dalian, China
| | - Jialiang Yang
- School of Information Science and Technology , Hainan Normal University, Haikou, China.,Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
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Qi R, Ma A, Ma Q, Zou Q. Clustering and classification methods for single-cell RNA-sequencing data. Brief Bioinform 2019; 21:1196-1208. [PMID: 31271412 DOI: 10.1093/bib/bbz062] [Citation(s) in RCA: 101] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 04/24/2019] [Accepted: 04/25/2019] [Indexed: 12/12/2022] Open
Abstract
Appropriate ways to measure the similarity between single-cell RNA-sequencing (scRNA-seq) data are ubiquitous in bioinformatics, but using single clustering or classification methods to process scRNA-seq data is generally difficult. This has led to the emergence of integrated methods and tools that aim to automatically process specific problems associated with scRNA-seq data. These approaches have attracted a lot of interest in bioinformatics and related fields. In this paper, we systematically review the integrated methods and tools, highlighting the pros and cons of each approach. We not only pay particular attention to clustering and classification methods but also discuss methods that have emerged recently as powerful alternatives, including nonlinear and linear methods and descending dimension methods. Finally, we focus on clustering and classification methods for scRNA-seq data, in particular, integrated methods, and provide a comprehensive description of scRNA-seq data and download URLs.
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Affiliation(s)
- Ren Qi
- School of Computer Science and Technology, College of Intelligence and Computing, Tianjin University, Tianjin, China
| | - Anjun Ma
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, USA
| | - Qin Ma
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China
| | - Quan Zou
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
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15
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Ru X, Li L, Wang C. Identification of Phage Viral Proteins With Hybrid Sequence Features. Front Microbiol 2019; 10:507. [PMID: 30972038 PMCID: PMC6443926 DOI: 10.3389/fmicb.2019.00507] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Accepted: 02/27/2019] [Indexed: 02/01/2023] Open
Abstract
The uniqueness of bacteriophages plays an important role in bioinformatics research. In real applications, the function of the bacteriophage virion proteins is the main area of interest. Therefore, it is very important to classify bacteriophage virion proteins and non-phage virion proteins accurately. Extracting comprehensive and effective sequence features from proteins plays a vital role in protein classification. In order to more fully represent protein information, this paper is more comprehensive and effective by combining the features extracted by the feature information representation algorithm based on sequence information (CCPA) and the feature representation algorithm based on sequence and structure information. After extracting features, the Max-Relevance-Max-Distance (MRMD) algorithm is used to select the optimal feature set with the strongest correlation between class labels and low redundancy between features. Given the randomness of the samples selected by the random forest classification algorithm and the randomness features for producing each node variable, a random forest method is employed to perform 10-fold cross-validation on the bacteriophage protein classification. The accuracy of this model is as high as 93.5% in the classification of phage proteins in this study. This study also found that, among the eight physicochemical properties considered, the charge property has the greatest impact on the classification of bacteriophage proteins These results indicate that the model discussed in this paper is an important tool in bacteriophage protein research.
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Affiliation(s)
- Xiaoqing Ru
- School of Information and Electrical Engineering, Hebei University of Engineering, Handan, China
| | - Lihong Li
- School of Information and Electrical Engineering, Hebei University of Engineering, Handan, China
| | - Chunyu Wang
- School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China
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16
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Genetic Polymorphism Study on Aedes albopictus of Different Geographical Regions Based on DNA Barcoding. BIOMED RESEARCH INTERNATIONAL 2018; 2018:1501430. [PMID: 30003088 PMCID: PMC5996416 DOI: 10.1155/2018/1501430] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Accepted: 03/19/2018] [Indexed: 12/01/2022]
Abstract
Aedes albopictus is a very important vector for pathogens of many infectious diseases including dengue fever. In this study, we explored the genetic polymorphism of Aedes albopictus strains in different geographical regions using DNA barcoding of mitochondrial COI (MT-COI) gene. We collected MT-COI sequence of 106 Aedes albopictus mosquitos from 6 provinces in China including Fujian, Guangdong, Hainan, Yunnan, and Taiwan. The length of the sequences is 709bp with the content of A+T (67.7%) greater than that of G+C (32.3%). We identified mutations in 90 (13.68%) loci, of which 57 (63.33%) are transitions, 28 (31.11%) are transversions, and 5 (5.56%) are hypervariable loci. In addition, we obtained 42 haplotypes, 4 (9.52%) of which are shared among different populations. The haplotype diversity of Aedes albopictus is 0.882 and nucleotide diversity is 0.01017. Moreover, the pedigree network diagram shows that most haplotypes are under parallel evolution, suggesting a local expansion of Aedes albopictus in history. Finally, the Neighbor-Joining tree of MT-COI haplotypes reveals a certain correlation between haplotype clusters and geographical distribution, and there are differences among Aedes albopictus in different geographical regions. In conclusion, DNA barcoding of MT-COI gene is an effective method to study the genetic structure of Aedes albopictus.
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De Novo Sequencing of a Sparassis latifolia Genome and Its Associated Comparative Analyses. CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY 2018; 2018:1857170. [PMID: 29682127 PMCID: PMC5845502 DOI: 10.1155/2018/1857170] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 10/30/2017] [Accepted: 11/02/2017] [Indexed: 12/16/2022]
Abstract
Known to be rich in β-glucan, Sparassis latifolia (S. latifolia) is a valuable edible fungus cultivated in East Asia. A few studies have suggested that S. latifolia is effective on antidiabetic, antihypertension, antitumor, and antiallergen medications. However, it is still unclear genetically why the fungus has these medical effects, which has become a key bottleneck for its further applications. To provide a better understanding of this fungus, we sequenced its whole genome, which has a total size of 48.13 megabases (Mb) and contains 12,471 predicted gene models. We then performed comparative and phylogenetic analyses, which indicate that S. latifolia is closely related to a few species in the antrodia clade including Fomitopsis pinicola, Wolfiporia cocos, Postia placenta, and Antrodia sinuosa. Finally, we annotated the predicted genes. Interestingly, the S. latifolia genome encodes most enzymes involved in carbohydrate and glycoconjugate metabolism and is also enriched in genes encoding enzymes critical to secondary metabolite biosynthesis and involved in indole, terpene, and type I polyketide pathways. As a conclusion, the genome content of S. latifolia sheds light on its genetic basis of the reported medicinal properties and could also be used as a reference genome for comparative studies on fungi.
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Wu XM, Chen QY, Chen RJ, Che YL, Wang LB, Wang CY, Yan S, Liu YT, Xiu JS, Zhou LJ. Pathogenicity and Whole Genome Sequence Analysis of a Pseudorabies Virus Strain FJ-2012 Isolated from Fujian, Southern China. THE CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY = JOURNAL CANADIEN DES MALADIES INFECTIEUSES ET DE LA MICROBIOLOGIE MEDICALE 2017; 2017:9073172. [PMID: 29527230 PMCID: PMC5804112 DOI: 10.1155/2017/9073172] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 09/18/2017] [Accepted: 09/26/2017] [Indexed: 01/03/2023]
Abstract
The outbreaks of pseudorabies have been frequently reported in Bartha-K61-vaccinated farms in China since 2011. To study the pathogenicity and evolution of the circulating pseudorabies viruses in Fujian Province, mainland China, we isolated and sequenced the whole genome of a wild-type pseudorabies virus strain named "FJ-2012." We then conducted a few downstream bioinformatics analyses including phylogenetic analysis and pathogenic analysis and used the virus to infect 6 pseudorabies virus-free piglets. FJ-2012-infected piglets developed symptoms like high body temperature and central nervous system disorders and had high mortality rate. In addition, we identified typical micropathological changes such as multiple gross lesions in infected piglets through pathological analysis and conclude that the FJ-2012 genome is significantly different from known pseudorabies viruses, in which insertions, deletions, and substitutions are observed in multiple immune and virulence genes. In summary, this study shed lights on the molecular basis of the prevalence and pathology of the pseudorabies virus strain FJ-2012. The genome of FJ-2012 could be used as a reference to study the evolution of pseudorabies viruses, which is critical to the vaccine development of new emerging pseudorabies viruses.
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Affiliation(s)
- Xue-min Wu
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agriculture Sciences/Fujian Animal Disease Control Technology Development Center, Fuzhou 350013, China
| | - Qiu-yong Chen
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agriculture Sciences/Fujian Animal Disease Control Technology Development Center, Fuzhou 350013, China
| | - Ru-jing Chen
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agriculture Sciences/Fujian Animal Disease Control Technology Development Center, Fuzhou 350013, China
| | - Yong-liang Che
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agriculture Sciences/Fujian Animal Disease Control Technology Development Center, Fuzhou 350013, China
| | - Long-bai Wang
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agriculture Sciences/Fujian Animal Disease Control Technology Development Center, Fuzhou 350013, China
| | - Chen-yan Wang
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agriculture Sciences/Fujian Animal Disease Control Technology Development Center, Fuzhou 350013, China
| | - Shan Yan
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agriculture Sciences/Fujian Animal Disease Control Technology Development Center, Fuzhou 350013, China
| | - Yu-tao Liu
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agriculture Sciences/Fujian Animal Disease Control Technology Development Center, Fuzhou 350013, China
| | - Jin-sheng Xiu
- College of Animal Sciences, Fujian Agricultural and Forestry University, Fuzhou, Fujian 350002, China
| | - Lun-jiang Zhou
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agriculture Sciences/Fujian Animal Disease Control Technology Development Center, Fuzhou 350013, China
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Schliep K, Potts AJ, Morrison DA, Grimm GW. Intertwining phylogenetic trees and networks. Methods Ecol Evol 2017. [DOI: 10.1111/2041-210x.12760] [Citation(s) in RCA: 119] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Willems M, Tahiri N, Makarenkov V. A new efficient algorithm for inferring explicit hybridization networks following the Neighbor-Joining principle. J Bioinform Comput Biol 2014; 12:1450024. [PMID: 25219384 DOI: 10.1142/s0219720014500243] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Several algorithms and software have been developed for inferring phylogenetic trees. However, there exist some biological phenomena such as hybridization, recombination, or horizontal gene transfer which cannot be represented by a tree topology. We need to use phylogenetic networks to adequately represent these important evolutionary mechanisms. In this article, we present a new efficient heuristic algorithm for inferring hybridization networks from evolutionary distance matrices between species. The famous Neighbor-Joining concept and the least-squares criterion are used for building networks. At each step of the algorithm, before joining two given nodes, we check if a hybridization event could be related to one of them or to both of them. The proposed algorithm finds the exact tree solution when the considered distance matrix is a tree metric (i.e. it is representable by a unique phylogenetic tree). It also provides very good hybrids recovery rates for large trees (with 32 and 64 leaves in our simulations) for both distance and sequence types of data. The results yielded by the new algorithm for real and simulated datasets are illustrated and discussed in detail.
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Affiliation(s)
- Matthieu Willems
- Département d'informatique, Université du Québec à Montréal, Case postale 8888, Succursale Centre-ville, Montréal (Québec) H3C 3P8, Canada
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Yang J, Grünewald S, Xu Y, Wan XF. Quartet-based methods to reconstruct phylogenetic networks. BMC SYSTEMS BIOLOGY 2014; 8:21. [PMID: 24555518 PMCID: PMC3941989 DOI: 10.1186/1752-0509-8-21] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2013] [Accepted: 02/12/2014] [Indexed: 11/11/2022]
Abstract
BACKGROUND Phylogenetic networks are employed to visualize evolutionary relationships among a group of nucleotide sequences, genes or species when reticulate events like hybridization, recombination, reassortant and horizontal gene transfer are believed to be involved. In comparison to traditional distance-based methods, quartet-based methods consider more information in the reconstruction process and thus have the potential to be more accurate. RESULTS We introduce QuartetSuite, which includes a set of new quartet-based methods, namely QuartetS, QuartetA, and QuartetM, to reconstruct phylogenetic networks from nucleotide sequences. We tested their performances and compared them with other popular methods on two simulated nucleotide sequence data sets: one generated from a tree topology and the other from a complicated evolutionary history containing three reticulate events. We further validated these methods to two real data sets: a bacterial data set consisting of seven concatenated genes of 36 bacterial species and an influenza data set related to recently emerging H7N9 low pathogenic avian influenza viruses in China. CONCLUSION QuartetS, QuartetA, and QuartetM have the potential to accurately reconstruct evolutionary scenarios from simple branching trees to complicated networks containing many reticulate events. These methods could provide insights into the understanding of complicated biological evolutionary processes such as bacterial taxonomy and reassortant of influenza viruses.
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Affiliation(s)
- Jialiang Yang
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State
University, Mississippi State, MS 39762, USA
- Current Address: Department of Genetics and Genomic Sciences, Icahn School of
Medicine at Mount Sinai, New York, NY 10029, USA
| | - Stefan Grünewald
- CAS-MPG Partner Institute for Computational Biology, Key Laboratory of
Computational Biology, Shanghai Institutes for Biological Sciences, Chinese
Academy of Sciences, Shanghai 200031, China
| | - Yifei Xu
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State
University, Mississippi State, MS 39762, USA
| | - Xiu-Feng Wan
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State
University, Mississippi State, MS 39762, USA
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