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Kumar R, Jayaraman M, Ramadas K, Chandrasekaran A. Computational identification and analysis of deleterious non-synonymous single nucleotide polymorphisms (nsSNPs) in the human POR gene: a structural and functional impact. J Biomol Struct Dyn 2024; 42:1518-1532. [PMID: 37173831 DOI: 10.1080/07391102.2023.2211674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 04/02/2023] [Indexed: 05/15/2023]
Abstract
Cytochrome P450 oxidoreductase (POR) protein is essential for steroidogenesis, and POR gene mutations are frequently associated with P450 Oxidoreductase Deficiency (PORD), a disorder of hormone production. To our knowledge, no previous attempt has been made to identify and analyze the deleterious/pathogenic non-synonymous single nucleotide polymorphisms (nsSNPs) in the human POR gene through an extensive computational approach. Computational algorithms and tools were employed to identify, characterize, and validate the pathogenic SNPs associated with certain diseases. To begin with, all the high-confidence SNPs were collected, and their structural and functional impacts on the protein structures were explored. The results of various in silico analyses affirm that the A287P and R457H variants of POR could destabilize the interactions between the amino acids and the hydrogen bond networks, resulting in functional deviations of POR. The literature study further confirms that the pathogenic mutations (A287P and R457H) are associated with the onset of PORD. Molecular dynamics simulations (MDS) and essential dynamics (ED) studies characterized the structural consequences of prioritized deleterious mutations, representing the structural destabilization that might disrupt POR biological function. The identified deleterious mutations at the cofactor's binding domains might interfere with the essential interactions between the protein and cofactors, thus inhibiting POR catalytic activity. The consolidated insights from the computational analyses can be used to predict potential deleterious mutants and understand the disease's pathological basis and the molecular mechanism of drug metabolism for the application of personalized medication. HIGHLIGHTSNADPH cytochrome P450 oxidoreductase (POR) mutations are associated with a broad spectrum of human diseasesIdentified and analyzed the most deleterious nsSNPs of POR through the sequence and structure-based prediction toolsInvestigated the structural and functional impacts of the most significant mutations (A287P and R457H) associated with PORDMolecular dynamics and PCA-based FEL analysis were utilized to probe the mutation-induced structural alterations in PORCommunicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Rajalakshmi Kumar
- Central Inter-Disciplinary Research Facility, Sri Balaji Vidyapeeth (Deemed to be University), Pillayarkuppam, Puducherry, India
| | - Manikandan Jayaraman
- Department of Bioinformatics, School of Life Sciences, Pondicherry University, Kalapet, Puducherry, India
| | - Krishna Ramadas
- Department of Bioinformatics, School of Life Sciences, Pondicherry University, Kalapet, Puducherry, India
| | - Adithan Chandrasekaran
- Central Inter-Disciplinary Research Facility, Sri Balaji Vidyapeeth (Deemed to be University), Pillayarkuppam, Puducherry, India
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Das P, Majumder R, Sen N, Nandi SK, Ghosh A, Mandal M, Basak P. A computational analysis to evaluate deleterious SNPs of GSK3β, a multifunctional and regulatory protein, for metabolism, wound healing, and migratory processes. Int J Biol Macromol 2024; 256:128262. [PMID: 37989431 DOI: 10.1016/j.ijbiomac.2023.128262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 10/04/2023] [Accepted: 11/17/2023] [Indexed: 11/23/2023]
Abstract
This study focused on GSK-3β, a critical serine/threonine kinase with diverse cellular functions. However, there is limited understanding of the impact of non-synonymous single nucleotide polymorphisms (nsSNPs) on its structure and function. Through an exhaustive in-silico investigation 12 harmful nsSNPs were predicted from a pool of 172 acquired from the NCBI dbSNP database using 12 established tools that detects deleterious SNPs. Consistently, these nsSNPs were discovered in locations with high levels of conservation. Notably, the three harmful nsSNPs F67C, A83T, and T138I were situated in the active/binding site of GSK-3β, which may affect the protein's capacity to bind to substrates and other proteins. Molecular dynamics simulations revealed that the F67C and T138I mutants had stable structures, indicating rigidness, whereas the A83T mutant was unstable. Analysis of secondary structures revealed different modifications in all mutant forms, which may affect the stability, functioning, and interactions of the protein. These mutations appear to alter the structural dynamics of GSK-3β, which may have functional ramifications, such as the formation of novel secondary structures and variations in coil-to-helix transitions. In conclusion, this study illuminates the possible structural and functional ramifications of these GSK-3 nsSNPs, revealing how protein compactness, stiffness, and interactions may affect biological activities.
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Affiliation(s)
- Pratik Das
- School of Bioscience and Engineering, Jadavpur University, Kolkata, India
| | - Ranabir Majumder
- Cancer Biology Lab, School of Medical Science & Technology, Indian Institute of Technology Kharagpur, India
| | - Nandita Sen
- Molecular biology wing, Dept of Biotechnology, PES University, Bangalore, India
| | - Samit Kumar Nandi
- Department of Veterinary Surgery & Radiology, West Bengal University of Animal and Fishery Sciences, Kolkata, India
| | - Arabinda Ghosh
- Department of Computational Biology and Biotechnology, Mahapurusha Srimanta Sankaradeva Viswavidyalaya, Guwahati Unit, Guwahati, Assam, India
| | - Mahitosh Mandal
- Cancer Biology Lab, School of Medical Science & Technology, Indian Institute of Technology Kharagpur, India
| | - Piyali Basak
- School of Bioscience and Engineering, Jadavpur University, Kolkata, India.
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Bano N, Kumar A. Immunoinformatics study to explore dengue (DENV-1) proteome to design multi-epitope vaccine construct by using CD4+ epitopes. J Genet Eng Biotechnol 2023; 21:128. [PMID: 37987878 PMCID: PMC10663418 DOI: 10.1186/s43141-023-00592-9] [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: 04/24/2023] [Accepted: 11/06/2023] [Indexed: 11/22/2023]
Abstract
BACKGROUND Immunoinformatics is an emerging interdisciplinary field which integrates immunology, bioinformatics, and computational biology to study the immune system. In this study, we apply immunoinformatics approaches to explore the dengue proteome in order to design a multi-epitope vaccine construct. METHODS We used existing databases and algorithms to predict potential epitopes on dengue proteins and used a bioinformatics approach to identify the most promising epitopes. We then used molecular modelling to develop a multi-epitope construct which could be used as a potential vaccine. The results of this study demonstrate that immunoinformatics is a powerful tool for exploring and designing potential vaccines for infectious diseases like dengue. RESULTS Here, we found four CD4+ epitopes NLKYSVIVTVHTGDQ, ANPIVTDKEKPVNIE, LDPVVYDAKFEKQL, and VGAIALDFKPGTSGS that were used to design vaccine construct. The vaccine construct docked with TLR5. RMSD values suggest that docked complex of TLR5 and vaccine construct have putative stable interaction to induce immunogenic effects on host. CONCLUSIONS Furthermore, our study provides a proof of concept for the use of immunoinformatics approaches in DENV vaccine design. This vaccine can be effective in treating patients infected with DENV virus.
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Affiliation(s)
- Nishat Bano
- Department of Biotechnology, Faculty of Engineering and Technology Rama University, G.T. Road, Kanpur, 209217, India
| | - Ajay Kumar
- Department of Biotechnology, Faculty of Engineering and Technology Rama University, G.T. Road, Kanpur, 209217, India.
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Wu SC, Lai SW, Lu XJ, Lai HF, Chen YG, Chen PH, Ho CL, Wu YY, Chiu YL. Profiling of miRNAs and their interfering targets in peripheral blood mononuclear cells from patients with chronic myeloid leukaemia. Front Oncol 2023; 13:1173970. [PMID: 37476380 PMCID: PMC10356106 DOI: 10.3389/fonc.2023.1173970] [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: 02/25/2023] [Accepted: 06/16/2023] [Indexed: 07/22/2023] Open
Abstract
Introduction MicroRNAs may be implicated in the acquisition of drug resistance in chronic myeloid leukemia as they regulate the expression of not only BCR-ABL1 but also genes associated with the activation of drug transfer proteins or essential signaling pathways. Methods To understand the impact of specifically expressed miRNAs in chronic myeloid leukemia and their target genes, we collected peripheral blood mononuclear cells (PBMC) from patients diagnosed with chronic myeloid leukemia (CML) and healthy donors to determine whole miRNA expression by small RNA sequencing and screened out 31 differentially expressed microRNAs (DE-miRNAs) with high expression. With the utilization of miRNA set enrichment analysis tools, we present here a comprehensive analysis of the relevance of DE-miRNAs to disease and biological function. Furthermore, the literature-based miRNA-target gene database was used to analyze the overall target genes of the DE-miRNAs and to define their associated biological responses. We further integrated DE-miRNA target genes to identify CML miRNA targeted gene signature singscore (CMTGSS) and used gene-set enrichment analysis (GSEA) to analyze the correlation between CMTGSS and Hallmark gene-sets in PBMC samples from clinical CML patients. Finally, the association of CMTGSS stratification with multiple CML cell lineage gene sets was validated in PBMC samples from CML patients using GSEA. Results Although individual miRNAs have been reported to have varying degrees of impact on CML, overall, our results show that abnormally upregulated miRNAs are associated with apoptosis and aberrantly downregulated miRNAs are associated with cell cycle. The clinical database shows that our defined DE-miRNAs are associated with the prognosis of CML patients. CMTGSS-based stratification analysis presented a tendency for miRNAs to affect cell differentiation in the blood microenvironment. Conclusion Collectively, this study defined differentially expressed miRNAs by miRNA sequencing from clinical samples and comprehensively analyzed the biological functions of the differential miRNAs in association with the target genes. The analysis of the enrichment of specific myeloid differentiated cells and immune cells also suggests the magnitude and potential targets of differentially expressed miRNAs in the clinical setting. It helps us to make links between the different results obtained from the multi-faceted studies to provide more potential research directions.
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Affiliation(s)
- Sheng-Cheng Wu
- Division of Hematology and Oncology, Department of Internal Medicine, Tri-Service General Hospital Penghu Branch, Magong City, Taiwan
| | - Shiue-Wei Lai
- Division of Hematology and Oncology, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei City, Taiwan
| | - Xin-Jie Lu
- Department of Biochemistry, National Defense Medical Center, Taipei City, Taiwan
| | - Hsing-Fan Lai
- Department of Biochemistry, National Defense Medical Center, Taipei City, Taiwan
| | - Yu-Guang Chen
- Division of Hematology and Oncology, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei City, Taiwan
| | - Po-Huang Chen
- Division of Hematology and Oncology, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei City, Taiwan
| | - Ching-Liang Ho
- Division of Hematology and Oncology, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei City, Taiwan
| | - Yi-Ying Wu
- Division of Hematology and Oncology, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei City, Taiwan
| | - Yi-Lin Chiu
- Department of Biochemistry, National Defense Medical Center, Taipei City, Taiwan
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Zhong FM, Yao FY, Yang YL, Liu J, Li MY, Jiang JY, Zhang N, Xu YM, Li SQ, Cheng Y, Xu S, Huang B, Wang XZ. Molecular subtypes predict therapeutic responses and identifying and validating diagnostic signatures based on machine learning in chronic myeloid leukemia. Cancer Cell Int 2023; 23:61. [PMID: 37024911 PMCID: PMC10080819 DOI: 10.1186/s12935-023-02905-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 03/27/2023] [Indexed: 04/08/2023] Open
Abstract
Chronic myeloid leukemia (CML) is a hematological tumor derived from hematopoietic stem cells. The aim of this study is to analyze the biological characteristics and identify the diagnostic markers of CML. We obtained the expression profiles from the Gene Expression Omnibus (GEO) database and identified 210 differentially expressed genes (DEGs) between CML and normal samples. These DEGs are mainly enriched in immune-related pathways such as Th1 and Th2 cell differentiation, primary immunodeficiency, T cell receptor signaling pathway, antigen processing and presentation pathways. Based on these DEGs, we identified two molecular subtypes using a consensus clustering algorithm. Cluster A was an immunosuppressive phenotype with reduced immune cell infiltration and significant activation of metabolism-related pathways such as reactive oxygen species, glycolysis and mTORC1; Cluster B was an immune activating phenotype with increased infiltration of CD4 + and CD8 + T cells and NK cells, and increased activation of signaling pathways such as interferon gamma (IFN-γ) response, IL6-JAK-STAT3 and inflammatory response. Drug prediction results showed that patients in Cluster B had a higher therapeutic response to anti-PD-1 and anti-CTLA4 and were more sensitive to imatinib, nilotinib and dasatinib. Support Vector Machine Recursive Feature Elimination (SVM-RFE), Least Absolute Shrinkage Selection Operator (LASSO) and Random Forest (RF) algorithms identified 4 CML diagnostic genes (HDC, SMPDL3A, IRF4 and AQP3), and the risk score model constructed by these genes improved the diagnostic accuracy. We further validated the diagnostic value of the 4 genes and the risk score model in a clinical cohort, and the risk score can be used in the differential diagnosis of CML and other hematological malignancies. The risk score can also be used to identify molecular subtypes and predict response to imatinib treatment. These results reveal the characteristics of immunosuppression and metabolic reprogramming in CML patients, and the identification of molecular subtypes and biomarkers provides new ideas and insights for the clinical diagnosis and treatment.
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Affiliation(s)
- Fang-Min Zhong
- Jiangxi Province Key Laboratory of Laboratory Medicine, Center for Laboratory Medicine, Department of Clinical Laboratory, Jiangxi Provincial Clinical Research, The Second Affiliated Hospital of Nanchang University, No. 1 Minde Road, Nanchang, 330006, Jiangxi Provence, China
| | - Fang-Yi Yao
- Jiangxi Province Key Laboratory of Laboratory Medicine, Center for Laboratory Medicine, Department of Clinical Laboratory, Jiangxi Provincial Clinical Research, The Second Affiliated Hospital of Nanchang University, No. 1 Minde Road, Nanchang, 330006, Jiangxi Provence, China
| | - Yu-Lin Yang
- Jiangxi Province Key Laboratory of Laboratory Medicine, Center for Laboratory Medicine, Department of Clinical Laboratory, Jiangxi Provincial Clinical Research, The Second Affiliated Hospital of Nanchang University, No. 1 Minde Road, Nanchang, 330006, Jiangxi Provence, China
| | - Jing Liu
- Jiangxi Province Key Laboratory of Laboratory Medicine, Center for Laboratory Medicine, Department of Clinical Laboratory, Jiangxi Provincial Clinical Research, The Second Affiliated Hospital of Nanchang University, No. 1 Minde Road, Nanchang, 330006, Jiangxi Provence, China
| | - Mei-Yong Li
- Jiangxi Province Key Laboratory of Laboratory Medicine, Center for Laboratory Medicine, Department of Clinical Laboratory, Jiangxi Provincial Clinical Research, The Second Affiliated Hospital of Nanchang University, No. 1 Minde Road, Nanchang, 330006, Jiangxi Provence, China
| | - Jun-Yao Jiang
- Jiangxi Province Key Laboratory of Laboratory Medicine, Center for Laboratory Medicine, Department of Clinical Laboratory, Jiangxi Provincial Clinical Research, The Second Affiliated Hospital of Nanchang University, No. 1 Minde Road, Nanchang, 330006, Jiangxi Provence, China
| | - Nan Zhang
- Jiangxi Province Key Laboratory of Laboratory Medicine, Center for Laboratory Medicine, Department of Clinical Laboratory, Jiangxi Provincial Clinical Research, The Second Affiliated Hospital of Nanchang University, No. 1 Minde Road, Nanchang, 330006, Jiangxi Provence, China
| | - Yan-Mei Xu
- Jiangxi Province Key Laboratory of Laboratory Medicine, Center for Laboratory Medicine, Department of Clinical Laboratory, Jiangxi Provincial Clinical Research, The Second Affiliated Hospital of Nanchang University, No. 1 Minde Road, Nanchang, 330006, Jiangxi Provence, China
| | - Shu-Qi Li
- Jiangxi Province Key Laboratory of Laboratory Medicine, Center for Laboratory Medicine, Department of Clinical Laboratory, Jiangxi Provincial Clinical Research, The Second Affiliated Hospital of Nanchang University, No. 1 Minde Road, Nanchang, 330006, Jiangxi Provence, China
| | - Ying Cheng
- Jiangxi Province Key Laboratory of Laboratory Medicine, Center for Laboratory Medicine, Department of Clinical Laboratory, Jiangxi Provincial Clinical Research, The Second Affiliated Hospital of Nanchang University, No. 1 Minde Road, Nanchang, 330006, Jiangxi Provence, China
| | - Shuai Xu
- Jiangxi Province Key Laboratory of Laboratory Medicine, Center for Laboratory Medicine, Department of Clinical Laboratory, Jiangxi Provincial Clinical Research, The Second Affiliated Hospital of Nanchang University, No. 1 Minde Road, Nanchang, 330006, Jiangxi Provence, China
| | - Bo Huang
- Jiangxi Province Key Laboratory of Laboratory Medicine, Center for Laboratory Medicine, Department of Clinical Laboratory, Jiangxi Provincial Clinical Research, The Second Affiliated Hospital of Nanchang University, No. 1 Minde Road, Nanchang, 330006, Jiangxi Provence, China.
| | - Xiao-Zhong Wang
- Jiangxi Province Key Laboratory of Laboratory Medicine, Center for Laboratory Medicine, Department of Clinical Laboratory, Jiangxi Provincial Clinical Research, The Second Affiliated Hospital of Nanchang University, No. 1 Minde Road, Nanchang, 330006, Jiangxi Provence, China.
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Styk J, Pös Z, Pös O, Radvanszky J, Turnova EH, Buglyó G, Klimova D, Budis J, Repiska V, Nagy B, Szemes T. Microsatellite instability assessment is instrumental for Predictive, Preventive and Personalised Medicine: status quo and outlook. EPMA J 2023; 14:143-165. [PMID: 36866160 PMCID: PMC9971410 DOI: 10.1007/s13167-023-00312-w] [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: 08/31/2022] [Accepted: 01/06/2023] [Indexed: 01/26/2023]
Abstract
A form of genomic alteration called microsatellite instability (MSI) occurs in a class of tandem repeats (TRs) called microsatellites (MSs) or short tandem repeats (STRs) due to the failure of a post-replicative DNA mismatch repair (MMR) system. Traditionally, the strategies for determining MSI events have been low-throughput procedures that typically require assessment of tumours as well as healthy samples. On the other hand, recent large-scale pan-tumour studies have consistently highlighted the potential of massively parallel sequencing (MPS) on the MSI scale. As a result of recent innovations, minimally invasive methods show a high potential to be integrated into the clinical routine and delivery of adapted medical care to all patients. Along with advances in sequencing technologies and their ever-increasing cost-effectiveness, they may bring about a new era of Predictive, Preventive and Personalised Medicine (3PM). In this paper, we offered a comprehensive analysis of high-throughput strategies and computational tools for the calling and assessment of MSI events, including whole-genome, whole-exome and targeted sequencing approaches. We also discussed in detail the detection of MSI status by current MPS blood-based methods and we hypothesised how they may contribute to the shift from conventional medicine to predictive diagnosis, targeted prevention and personalised medical services. Increasing the efficacy of patient stratification based on MSI status is crucial for tailored decision-making. Contextually, this paper highlights drawbacks both at the technical level and those embedded deeper in cellular/molecular processes and future applications in routine clinical testing.
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Affiliation(s)
- Jakub Styk
- Institute of Medical Biology, Genetics and Clinical Genetics, Faculty of Medicine, Comenius University, 811 08 Bratislava, Slovakia ,Comenius University Science Park, 841 04 Bratislava, Slovakia ,Geneton Ltd, 841 04 Bratislava, Slovakia
| | - Zuzana Pös
- Comenius University Science Park, 841 04 Bratislava, Slovakia ,Geneton Ltd, 841 04 Bratislava, Slovakia ,Institute of Clinical and Translational Research, Biomedical Research Centre, Slovak Academy of Sciences, 845 05 Bratislava, Slovakia
| | - Ondrej Pös
- Comenius University Science Park, 841 04 Bratislava, Slovakia ,Geneton Ltd, 841 04 Bratislava, Slovakia
| | - Jan Radvanszky
- Comenius University Science Park, 841 04 Bratislava, Slovakia ,Institute of Clinical and Translational Research, Biomedical Research Centre, Slovak Academy of Sciences, 845 05 Bratislava, Slovakia ,Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, 841 04 Bratislava, Slovakia
| | - Evelina Hrckova Turnova
- Comenius University Science Park, 841 04 Bratislava, Slovakia ,Slovgen Ltd, 841 04 Bratislava, Slovakia
| | - Gergely Buglyó
- Department of Human Genetics, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
| | - Daniela Klimova
- Institute of Medical Biology, Genetics and Clinical Genetics, Faculty of Medicine, Comenius University, 811 08 Bratislava, Slovakia
| | - Jaroslav Budis
- Comenius University Science Park, 841 04 Bratislava, Slovakia ,Geneton Ltd, 841 04 Bratislava, Slovakia ,Slovak Centre of Scientific and Technical Information, 811 04 Bratislava, Slovakia
| | - Vanda Repiska
- Institute of Medical Biology, Genetics and Clinical Genetics, Faculty of Medicine, Comenius University, 811 08 Bratislava, Slovakia ,Medirex Group Academy, NPO, 949 05 Nitra, Slovakia
| | - Bálint Nagy
- Comenius University Science Park, 841 04 Bratislava, Slovakia ,Department of Human Genetics, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
| | - Tomas Szemes
- Comenius University Science Park, 841 04 Bratislava, Slovakia ,Geneton Ltd, 841 04 Bratislava, Slovakia ,Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, 841 04 Bratislava, Slovakia
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T-Cell Epitopes Based Vaccine Candidate’s Prediction for Treatment Against Burkholderia pseudomallei: Causative Agent of Melioidosis. Int J Pept Res Ther 2022. [DOI: 10.1007/s10989-022-10400-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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