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Affiliation(s)
- Hsin-Hsiung Huang
- Department of Statistics, University of Central Florida, Orlando, FL, USA
| | - Zijing Wang
- Department of Statistics, University of Central Florida, Orlando, FL, USA
| | - Wingyan Chung
- Institute for Simulation and Training, University of Central Florida, Orlando, FL, USA
- Department of Computer Science, Faculty of Engineering, The University of Hong Kong, Hong Kong
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Groot M, Zhang D, Jin Y. Long Non-Coding RNA Review and Implications in Lung Diseases. JSM BIOINFORMATICS, GENOMICS AND PRETEOMICS 2018; 3:1033. [PMID: 30854513 PMCID: PMC6404970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Non-coding genes occupy the majority of the human genome and have recently garnered increased attention for their implications in a range of diseases. This review illustrates the current scientific landscape concerning long non-coding RNA biogenesis, regulation, and degradation, as well as their functional roles in lung pathogenesis. LncRNAs share many similar biogenesis and regulatory processes with mRNA, such as capping, polyadenylation, post-transcriptional modifications, and exonuclease degradation. Evidence suggests that these lncRNAs become dysregulated in lung diseases such as Acute Lung Injury, Idiopathic Pulmonary Fibrosis, COPD, Lung Cancer, and Pulmonary Arterial Fiypertension. Some lncRNAs have known functions, but the overwhelming majority requires further research to completely understand.
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Affiliation(s)
| | | | - Yang Jin
- Corresponding author Yang Jin, Department of Medicine, Boston University Medical Campus, Boston, MA 02118, USA, Tel: 1-617-414-3298; Fax: 1-617-536-8093;
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Huang G, Li J, Zhao C. Computational Prediction and Analysis of Associations between Small Molecules and Binding-Associated S-Nitrosylation Sites. Molecules 2018; 23:molecules23040954. [PMID: 29671802 PMCID: PMC6017196 DOI: 10.3390/molecules23040954] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Revised: 03/30/2018] [Accepted: 04/09/2018] [Indexed: 01/12/2023] Open
Abstract
Interactions between drugs and proteins occupy a central position during the process of drug discovery and development. Numerous methods have recently been developed for identifying drug–target interactions, but few have been devoted to finding interactions between post-translationally modified proteins and drugs. We presented a machine learning-based method for identifying associations between small molecules and binding-associated S-nitrosylated (SNO-) proteins. Namely, small molecules were encoded by molecular fingerprint, SNO-proteins were encoded by the information entropy-based method, and the random forest was used to train a classifier. Ten-fold and leave-one-out cross validations achieved, respectively, 0.7235 and 0.7490 of the area under a receiver operating characteristic curve. Computational analysis of similarity suggested that SNO-proteins associated with the same drug shared statistically significant similarity, and vice versa. This method and finding are useful to identify drug–SNO associations and further facilitate the discovery and development of SNO-associated drugs.
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Affiliation(s)
- Guohua Huang
- Provincial Key Laboratory of Informational Service for Rural Area of Southwestern Hunan, Shaoyang University, Shaoyang 422000, China.
- College of Information Engineering, Shaoyang University, Shaoyang 422000, China.
| | - Jincheng Li
- Provincial Key Laboratory of Informational Service for Rural Area of Southwestern Hunan, Shaoyang University, Shaoyang 422000, China.
- College of Information Engineering, Shaoyang University, Shaoyang 422000, China.
| | - Chenglin Zhao
- Provincial Key Laboratory of Informational Service for Rural Area of Southwestern Hunan, Shaoyang University, Shaoyang 422000, China.
- College of Information Engineering, Shaoyang University, Shaoyang 422000, China.
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Valente C, Alvarez L, Marques PI, Gusmão L, Amorim A, Seixas S, João Prata M. Genes from the TAS1R and TAS2R Families of Taste Receptors: Looking for Signatures of Their Adaptive Role in Human Evolution. Genome Biol Evol 2018; 10:1139-1152. [PMID: 29635333 PMCID: PMC5905477 DOI: 10.1093/gbe/evy071] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/27/2018] [Indexed: 02/06/2023] Open
Abstract
Taste perception is crucial in monitoring food intake and, hence, is thought to play a significant role in human evolution. To gain insights into possible adaptive signatures in genes encoding bitter, sweet, and umami taste receptors, we surveyed the available sequence variation data from the 1000 Genomes Project Phase 3 for TAS1R (TAS1R1-3) and TAS2R (TAS2R16 and TAS2R38) families. Our study demonstrated that genes from these two families have experienced contrasting evolutionary histories: While TAS1R1 and TAS1R3 showed worldwide evidence of positive selection, probably correlated with improved umami and sweet perception, the patterns of variation displayed by TAS2R16 and TAS2R38 were more consistent with scenarios of balancing selection that possibly conferred a heterozygous advantage associated with better capacity to perceive a wide range of bitter compounds. In TAS2R16, such adaptive events appear to have occurred restrictively in mainland Africa, whereas the strongest evidence in TAS2R38 was detected in Europe. Despite plausible associations between taste perception and the TAS1R and TAS2R selective signatures, we cannot discount other biological mechanisms as driving the evolutionary trajectories of those TAS1R and TAS2R members, especially given recent findings of taste receptors behaving as the products of pleiotropic genes involved in many functions outside the gustatory system.
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Affiliation(s)
- Cristina Valente
- I3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal
- IPATIMUP, Institute of Molecular Pathology and Immunology, University of Porto, Portugal
- Faculty of Sciences, University of Porto, Portugal
| | - Luis Alvarez
- I3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal
- IPATIMUP, Institute of Molecular Pathology and Immunology, University of Porto, Portugal
| | - Patrícia Isabel Marques
- I3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal
- IPATIMUP, Institute of Molecular Pathology and Immunology, University of Porto, Portugal
| | - Leonor Gusmão
- DNA Diagnostic Laboratory (LDD), State University of Rio de Janeiro (UERJ), Brazil
| | - António Amorim
- I3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal
- IPATIMUP, Institute of Molecular Pathology and Immunology, University of Porto, Portugal
- Faculty of Sciences, University of Porto, Portugal
| | - Susana Seixas
- I3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal
- IPATIMUP, Institute of Molecular Pathology and Immunology, University of Porto, Portugal
| | - Maria João Prata
- I3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal
- IPATIMUP, Institute of Molecular Pathology and Immunology, University of Porto, Portugal
- Faculty of Sciences, University of Porto, Portugal
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Investigation of copy number variation in subjects with major depression based on whole-genome sequencing data. J Affect Disord 2017; 220:38-42. [PMID: 28578134 DOI: 10.1016/j.jad.2017.05.044] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 04/26/2017] [Accepted: 05/28/2017] [Indexed: 01/12/2023]
Abstract
BACKGROUND Despite recent intensive research using genome-wide association studies, the underlying biological basis of major depressive disorder (MDD) still remains unknown. In contrast to genotyping platforms which identify specific variations, whole-genome sequencing (WGS) allows us to detect all private genetic variations within an individual. So far there have been no studies investigating copy number variations (CNVs) in subjects with MDD using WGS data. METHODS We obtained complete WGS paired-end reads data of 15 MDD patients and 10 ethnically matched healthy controls. We performed alignments for the sequencing reads and used GASV package to call CNVs including deletion, inversion, translocation and divergence for those subjects. RESULTS Our results show that, in the Mexican-American sample, deletion CNVs were significantly richer in MDD cases than healthy controls on each of 23 chromosomes. However, other types of CNVs failed to reach any significance. In the Australian sample, there was no statistically significant difference of CNVs between MDD cases and controls. Furthermore, we found that the Australian group had significantly more deletion CNVs than the Mexican-American group. LIMITATIONS High quality WGS costs limited obtaining larger datasets. The GASV package does not currently support duplication or insertion CNVs. CONCLUSIONS To our knowledge this is the first time that CNVs detected by WGS data are used to study major depression. The conclusion that deletion CNVs are significantly richer in MDD cases than healthy controls is consistent with the previous finding about recurrent depressive disorder by genome-wide association analysis of CNVs on a large genotyping microarray data.
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Yu C, Baune BT, Licinio J, Wong ML. Single-nucleotide variant proportion in genes: a new concept to explore major depression based on DNA sequencing data. J Hum Genet 2017; 62:577-580. [PMID: 28148926 DOI: 10.1038/jhg.2017.2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 12/21/2016] [Accepted: 12/26/2016] [Indexed: 01/03/2023]
Abstract
Major depressive disorder (MDD) is a common psychiatric illness with significant medical and socioeconomic impact. Genetic factors are likely to play important roles in the development of this condition. DNA sequencing technology has the ability to identify all private genetic mutations and provides new channels for studying the biology of MDD. In this proof-of-concept study we proposed a novel concept, single-nucleotide variant proportion (SNVP), to investigate MDD based on whole-genome sequencing (WGS) data. Our SNVP-based approach can be used to test newly found candidate genes as a complement to genome-wide genotyping analysis. Furthermore, we performed cluster analysis for MDD patients and ethnically matched healthy controls, and found that clusters based on SNVP may predict MDD diagnosis. Our results suggest that SNVP may be used as a potential biomarker associated with major depression. Our methodology could be a valuable predictive/diagnostic tool as one can test whether a new subject falls within or close to an existing MDD cluster. Advances in this study design have the potential to personalized treatments and could include the ability to diagnose patients based on their full or part DNA sequencing data.
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Affiliation(s)
- Chenglong Yu
- Mind and Brain Theme, South Australian Health and Medical Research Institute, North Terrace, Adelaide, SA, Australia.,School of Medicine, Flinders University, Bedford Park, SA, Australia
| | - Bernhard T Baune
- Discipline of Psychiatry, School of Medicine, University of Adelaide, Adelaide, SA, Australia
| | - Julio Licinio
- Mind and Brain Theme, South Australian Health and Medical Research Institute, North Terrace, Adelaide, SA, Australia.,School of Medicine, Flinders University, Bedford Park, SA, Australia
| | - Ma-Li Wong
- Mind and Brain Theme, South Australian Health and Medical Research Institute, North Terrace, Adelaide, SA, Australia.,School of Medicine, Flinders University, Bedford Park, SA, Australia
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Li M, Lu X, Wang X, Lu S, Zhong N. Biomedical classification application and parameters optimization of mixed kernel SVM based on the information entropy particle swarm optimization. Comput Assist Surg (Abingdon) 2016. [DOI: 10.1080/24699322.2016.1240300] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Affiliation(s)
- Mi Li
- Department of Automation, Faculty of Information Technology, Beijing University of Technology, Beijing, China
- Beijing International Collaboration Base on Brain Informatics and Wisdom Services, Beijing, China
- Beijing Key Laboratory of MRI and Brain Informatics, Beijing, China
| | - Xiaofeng Lu
- Department of Automation, Faculty of Information Technology, Beijing University of Technology, Beijing, China
- Beijing International Collaboration Base on Brain Informatics and Wisdom Services, Beijing, China
- Beijing Key Laboratory of MRI and Brain Informatics, Beijing, China
| | - Xiaodong Wang
- Department of Automation, Faculty of Information Technology, Beijing University of Technology, Beijing, China
- Beijing International Collaboration Base on Brain Informatics and Wisdom Services, Beijing, China
- Beijing Key Laboratory of MRI and Brain Informatics, Beijing, China
| | - Shengfu Lu
- Department of Automation, Faculty of Information Technology, Beijing University of Technology, Beijing, China
- Beijing International Collaboration Base on Brain Informatics and Wisdom Services, Beijing, China
- Beijing Key Laboratory of MRI and Brain Informatics, Beijing, China
| | - Ning Zhong
- Department of Automation, Faculty of Information Technology, Beijing University of Technology, Beijing, China
- Beijing International Collaboration Base on Brain Informatics and Wisdom Services, Beijing, China
- Beijing Key Laboratory of MRI and Brain Informatics, Beijing, China
- Department of Life Science and Informatics, Maebashi Institute of Technology, Maebashi, Japan
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