MyMedR

Displaying publications 1 - 20 of 25 in total

Abstract:

Sort:

Fulltext Using bioconductor package BiGGR for metabolic flux estimation based on gene expression changes in brain

Gavai AK, Supandi F, Hettling H, Murrell P, Leunissen JA, van Beek JH

PLoS One, 2015;10(3):e0119016.
PMID: 25806817 DOI: 10.1371/journal.pone.0119016

Predicting the distribution of metabolic fluxes in biochemical networks is of major interest in systems biology. Several databases provide metabolic reconstructions for different organisms. Software to analyze flux distributions exists, among others for the proprietary MATLAB environment. Given the large user community for the R computing environment, a simple implementation of flux analysis in R appears desirable and will facilitate easy interaction with computational tools to handle gene expression data. We extended the R software package BiGGR, an implementation of metabolic flux analysis in R. BiGGR makes use of public metabolic reconstruction databases, and contains the BiGG database and the reconstruction of human metabolism Recon2 as Systems Biology Markup Language (SBML) objects. Models can be assembled by querying the databases for pathways, genes or reactions of interest. Fluxes can then be estimated by maximization or minimization of an objective function using linear inverse modeling algorithms. Furthermore, BiGGR provides functionality to quantify the uncertainty in flux estimates by sampling the constrained multidimensional flux space. As a result, ensembles of possible flux configurations are constructed that agree with measured data within precision limits. BiGGR also features automatic visualization of selected parts of metabolic networks using hypergraphs, with hyperedge widths proportional to estimated flux values. BiGGR supports import and export of models encoded in SBML and is therefore interoperable with different modeling and analysis tools. As an application example, we calculated the flux distribution in healthy human brain using a model of central carbon metabolism. We introduce a new algorithm termed Least-squares with equalities and inequalities Flux Balance Analysis (Lsei-FBA) to predict flux changes from gene expression changes, for instance during disease. Our estimates of brain metabolic flux pattern with Lsei-FBA for Alzheimer's disease agree with independent measurements of cerebral metabolism in patients. This second version of BiGGR is available from Bioconductor.

Matched MeSH terms: Systems Biology
Discovery of Antimalarial Drugs from Streptomycetes Metabolites Using a Metabolomic Approach

Ahmad SJ, Abdul Rahim MBH, Baharum SN, Baba MS, Zin NM

J Trop Med, 2017;2017:2189814.
PMID: 29123551 DOI: 10.1155/2017/2189814

Natural products continue to play an important role as a source of biologically active substances for the development of new drug. Streptomyces, Gram-positive bacteria which are widely distributed in nature, are one of the most popular sources of natural antibiotics. Recently, by using a bioassay-guided fractionation, an antimalarial compound, Gancidin-W, has been discovered from these bacteria. However, this classical method in identifying potentially novel bioactive compounds from the natural products requires considerable effort and is a time-consuming process. Metabolomics is an emerging "omics" technology in systems biology study which integrated in process of discovering drug from natural products. Metabolomics approach in finding novel therapeutics agent for malaria offers dereplication step in screening phase to shorten the process. The highly sensitive instruments, such as Liquid Chromatography-Mass Spectrophotometry (LC-MS), Gas Chromatography-Mass Spectrophotometry (GC-MS), and Nuclear Magnetic Resonance ((1)H-NMR) spectroscopy, provide a wide range of information in the identification of potentially bioactive compounds. The current paper reviews concepts of metabolomics and its application in drug discovery of malaria treatment as well as assessing the antimalarial activity from natural products. Metabolomics approach in malaria drug discovery is still new and needs to be initiated, especially for drug research in Malaysia.

Matched MeSH terms: Systems Biology
Fulltext Why metabonomics?

Yap, Ivan K.S.

International e-Journal of Science, Medicine & Education, 2011;5(1):17-26.
MyJurnal

Metabonomics can be used to quantitatively measure dynamic biochemical responses of living organisms to physiological or pathological stimuli. A range of analytical tools such as high-resolution nuclear magnetic resonance (NMR) spectroscopy and mass spectrometry (MS) combined with multivariate statistical analysis can be employed to create comprehensive metabolic signatures of biological samples including urine, plasma, faecal water and tissue extracts. These metabolic signatures can reflect the physiological or pathological condition of the organism and indicate imbalances in the homeostatic regulation of tissues and extracellular fluids. This technology has been employed in a diverse range of application areas including investigation of disease mechanisms, diagnosis/prognosis of pathologies, nutritional interventions and drug toxicity. Metabolic profiling is becoming increasingly important in identifying biomarkers of disease progression and drug intervention, and can provide additional information to support or aid the interpretation of genomic and proteomic data. With the new generation of postgenomic technologies, the paradigm in many biological fields has shifted to either top down systems biology approaches, aiming to achieve a general understanding of the global and integrated response of an organism or to bottom up modelling of specific pathways and networks using a priori knowledge based on mining large bodies of literature. Whilst metabolic profiling lends itself to either approach, using it in an exploratory and hypothesis generating capacity clearly allows new mechanisms to be uncovered.

Matched MeSH terms: Systems Biology
Metabolomics - the complementary field in systems biology: a review on obesity and type 2 diabetes

Abu Bakar MH, Sarmidi MR, Cheng KK, Ali Khan A, Suan CL, Zaman Huri H, et al.

Mol Biosyst, 2015 Jul;11(7):1742-74.
PMID: 25919044 DOI: 10.1039/c5mb00158g

Metabolomic studies on obesity and type 2 diabetes mellitus have led to a number of mechanistic insights into biomarker discovery and comprehension of disease progression at metabolic levels. This article reviews a series of metabolomic studies carried out in previous and recent years on obesity and type 2 diabetes, which have shown potential metabolic biomarkers for further evaluation of the diseases. Literature including journals and books from Web of Science, Pubmed and related databases reporting on the metabolomics in these particular disorders are reviewed. We herein discuss the potential of reported metabolic biomarkers for a novel understanding of disease processes. These biomarkers include fatty acids, TCA cycle intermediates, carbohydrates, amino acids, choline and bile acids. The biological activities and aetiological pathways of metabolites of interest in driving these intricate processes are explained. The data from various publications supported metabolomics as an effective strategy in the identification of novel biomarkers for obesity and type 2 diabetes. Accelerating interest in the perspective of metabolomics to complement other fields in systems biology towards the in-depth understanding of the molecular mechanisms underlying the diseases is also well appreciated. In conclusion, metabolomics can be used as one of the alternative approaches in biomarker discovery and the novel understanding of pathophysiological mechanisms in obesity and type 2 diabetes. It can be foreseen that there will be an increasing research interest to combine metabolomics with other omics platforms towards the establishment of detailed mechanistic evidence associated with the disease processes.

Matched MeSH terms: Systems Biology
A Q-marker screening strategy based on ADME studies and systems biology for Chinese herbal medicine, taking Qianghuo Shengshi decoction in treating rheumatoid arthritis as an example

Wang J, Tao C, Xu G, Ling J, Tong J, Goh BH, et al.

Mol Omics, 2023 Dec 04;19(10):769-786.
PMID: 37498608 DOI: 10.1039/d3mo00029j

Chinese herbal medicine (CHM) exhibits a broad spectrum of clinical applications and demonstrates favorable therapeutic efficacy. Nonetheless, elucidating the underlying mechanism of action (MOA) of CHM in disease treatment remains a formidable task due to its inherent characteristics of multi-level, multi-linked, and multi-dimensional non-linear synergistic actions. In recent years, the concept of a Quality marker (Q-marker) proposed by Liu et al. has significantly contributed to the monitoring and evaluation of CHM products, thereby fostering the advancement of CHM research. Within this study, a Q-marker screening strategy for CHM formulas has been introduced, particularly emphasising efficacy and biological activities, integrating absorption, distribution, metabolism, and excretion (ADME) studies, systems biology, and experimental verification. As an illustrative case, the Q-marker screening of Qianghuo Shengshi decoction (QHSSD) for treating rheumatoid arthritis (RA) has been conducted. Consequently, from a pool of 159 compounds within QHSSD, five Q-markers exhibiting significant in vitro anti-inflammatory effects have been identified. These Q-markers encompass notopterol, isoliquiritin, imperatorin, cimifugin, and glycyrrhizic acid. Furthermore, by employing an integrated analysis of network pharmacology and metabolomics, several instructive insights into pharmacological mechanisms have been gleaned. This includes the identification of key targets and pathways through which QHSSD exerts its crucial roles in the treatment of RA. Notably, the inhibitory effect of QHSSD on AKT1 and MAPK3 activation has been validated through western blot analysis, underscoring its potential to mitigate RA-related inflammatory responses. In summary, this research demonstrates the proposed strategy's feasibility and provides a practical reference model for the systematic investigation of CHM formulas.

Matched MeSH terms: Systems Biology
Fulltext Exploring Ayurvedic Knowledge on Food and Health for Providing Innovative Solutions to Contemporary Healthcare

Payyappallimana U, Venkatasubramanian P

Front Public Health, 2016;4:57.
PMID: 27066472 DOI: 10.3389/fpubh.2016.00057

Ayurveda, a traditional system of medicine that originated over three millennia ago in the South Asian region, offers extensive insights about food and health based on certain unique conceptual as well as theoretical positions. Health is defined as a state of equilibrium with one's self (svasthya) but which is inextricably linked to the environment. Ayurvedic principles, such as the tridosa (three humors) theory, provide the relationship between the microcosm and the macrocosm that can be applied in day-to-day practice. Classical Ayurveda texts cover an array of themes on food ranging from diversity of natural sources, their properties in relation to seasons and places and to their specific function both in physiological and pathological states. The epistemic perspective on health and nutrition in Ayurveda is very different from that of biomedicine and modern nutrition. However, contemporary knowledge is reinventing and advancing several of these concepts in an era of systems biology, personalized medicine, and the broader context of a more holistic transition in sciences in general. Trans-disciplinary research could be important not only for pushing the boundaries of food and health sciences but also for providing practical solutions for contemporary health conditions. This article briefly reviews the parallels in Ayurveda and biomedicine and draws attention to the need for a deeper engagement with traditional knowledge systems, such as Ayurveda. It points out that recreation of the methodologies that enabled the holistic view point about health in Ayurveda may unravel some of the complex connections with Nature.

Matched MeSH terms: Systems Biology
Fulltext Towards big data science in the decade ahead from ten years of InCoB and the 1st ISCB-Asia Joint Conference

Ranganathan S, Schönbach C, Kelso J, Rost B, Nathan S, Tan TW

BMC Bioinformatics, 2011;12 Suppl 13:S1.
PMID: 22372736 DOI: 10.1186/1471-2105-12-S13-S1

The 2011 International Conference on Bioinformatics (InCoB) conference, which is the annual scientific conference of the Asia-Pacific Bioinformatics Network (APBioNet), is hosted by Kuala Lumpur, Malaysia, is co-organized with the first ISCB-Asia conference of the International Society for Computational Biology (ISCB). InCoB and the sequencing of the human genome are both celebrating their tenth anniversaries and InCoB's goalposts for the next decade, implementing standards in bioinformatics and globally distributed computational networks, will be discussed and adopted at this conference. Of the 49 manuscripts (selected from 104 submissions) accepted to BMC Genomics and BMC Bioinformatics conference supplements, 24 are featured in this issue, covering software tools, genome/proteome analysis, systems biology (networks, pathways, bioimaging) and drug discovery and design.

Matched MeSH terms: Systems Biology
Fulltext Challenges of the next decade for the Asia Pacific region: 2010 International Conference in Bioinformatics (InCoB 2010)

Ranganathan S, Schönbach C, Nakai K, Tan TW

BMC Genomics, 2010;11 Suppl 4:S1.
PMID: 21143792 DOI: 10.1186/1471-2164-11-S4-S1

The 2010 annual conference of the Asia Pacific Bioinformatics Network (APBioNet), Asia's oldest bioinformatics organisation formed in 1998, was organized as the 9th International Conference on Bioinformatics (InCoB), Sept. 26-28, 2010 in Tokyo, Japan. Initially, APBioNet created InCoB as forum to foster bioinformatics in the Asia Pacific region. Given the growing importance of interdisciplinary research, InCoB2010 included topics targeting scientists in the fields of genomic medicine, immunology and chemoinformatics, supporting translational research. Peer-reviewed manuscripts that were accepted for publication in this supplement, represent key areas of research interests that have emerged in our region. We also highlight some of the current challenges bioinformatics is facing in the Asia Pacific region and conclude our report with the announcement of APBioNet's 100 BioDatabases (BioDB100) initiative. BioDB100 will comply with the database criteria set out earlier in our proposal for Minimum Information about a Bioinformatics and Investigation (MIABi), setting the standards for biocuration and bioinformatics research, on which we will report at the next InCoB, Nov. 27 - Dec. 2, 2011 at Kuala Lumpur, Malaysia.

Matched MeSH terms: Systems Biology
Fulltext Emerging strengths in Asia Pacific bioinformatics

Ranganathan S, Hsu WL, Yang UC, Tan TW

BMC Bioinformatics, 2008;9 Suppl 12:S1.
PMID: 19091008 DOI: 10.1186/1471-2105-9-S12-S1

The 2008 annual conference of the Asia Pacific Bioinformatics Network (APBioNet), Asia's oldest bioinformatics organisation set up in 1998, was organized as the 7th International Conference on Bioinformatics (InCoB), jointly with the Bioinformatics and Systems Biology in Taiwan (BIT 2008) Conference, Oct. 20-23, 2008 at Taipei, Taiwan. Besides bringing together scientists from the field of bioinformatics in this region, InCoB is actively involving researchers from the area of systems biology, to facilitate greater synergy between these two groups. Marking the 10th Anniversary of APBioNet, this InCoB 2008 meeting followed on from a series of successful annual events in Bangkok (Thailand), Penang (Malaysia), Auckland (New Zealand), Busan (South Korea), New Delhi (India) and Hong Kong. Additionally, tutorials and the Workshop on Education in Bioinformatics and Computational Biology (WEBCB) immediately prior to the 20th Federation of Asian and Oceanian Biochemists and Molecular Biologists (FAOBMB) Taipei Conference provided ample opportunity for inducting mainstream biochemists and molecular biologists from the region into a greater level of awareness of the importance of bioinformatics in their craft. In this editorial, we provide a brief overview of the peer-reviewed manuscripts accepted for publication herein, grouped into thematic areas. As the regional research expertise in bioinformatics matures, the papers fall into thematic areas, illustrating the specific contributions made by APBioNet to global bioinformatics efforts.

Matched MeSH terms: Systems Biology
Converting differential-equation models of biological systems to membrane computing

Muniyandi RC, Zin AM, Sanders JW

Biosystems, 2013 Dec;114(3):219-26.
PMID: 24120990 DOI: 10.1016/j.biosystems.2013.09.008

This paper presents a method to convert the deterministic, continuous representation of a biological system by ordinary differential equations into a non-deterministic, discrete membrane computation. The dynamics of the membrane computation is governed by rewrite rules operating at certain rates. That has the advantage of applying accurately to small systems, and to expressing rates of change that are determined locally, by region, but not necessary globally. Such spatial information augments the standard differentiable approach to provide a more realistic model. A biological case study of the ligand-receptor network of protein TGF-β is used to validate the effectiveness of the conversion method. It demonstrates the sense in which the behaviours and properties of the system are better preserved in the membrane computing model, suggesting that the proposed conversion method may prove useful for biological systems in particular.

Matched MeSH terms: Systems Biology/methods*
Fulltext A bioinformatics potpourri

Schönbach C, Li J, Ma L, Horton P, Sjaugi MF, Ranganathan S

BMC Genomics, 2018 01 19;19(Suppl 1):920.
PMID: 29363432 DOI: 10.1186/s12864-017-4326-x

The 16th International Conference on Bioinformatics (InCoB) was held at Tsinghua University, Shenzhen from September 20 to 22, 2017. The annual conference of the Asia-Pacific Bioinformatics Network featured six keynotes, two invited talks, a panel discussion on big data driven bioinformatics and precision medicine, and 66 oral presentations of accepted research articles or posters. Fifty-seven articles comprising a topic assortment of algorithms, biomolecular networks, cancer and disease informatics, drug-target interactions and drug efficacy, gene regulation and expression, imaging, immunoinformatics, metagenomics, next generation sequencing for genomics and transcriptomics, ontologies, post-translational modification, and structural bioinformatics are the subject of this editorial for the InCoB2017 supplement issues in BMC Genomics, BMC Bioinformatics, BMC Systems Biology and BMC Medical Genomics. New Delhi will be the location of InCoB2018, scheduled for September 26-28, 2018.

Matched MeSH terms: Systems Biology/methods*
Fulltext Insight into plant cell wall degradation and pathogenesis of Ganoderma boninense via comparative genome analysis

Ramzi AB, Che Me ML, Ruslan US, Baharum SN, Nor Muhammad NA

PeerJ, 2019;7:e8065.
PMID: 31879570 DOI: 10.7717/peerj.8065

Background: G. boninense is a hemibiotrophic fungus that infects oil palms (Elaeis guineensis Jacq.) causing basal stem rot (BSR) disease and consequent massive economic losses to the oil palm industry. The pathogenicity of this white-rot fungus has been associated with cell wall degrading enzymes (CWDEs) released during saprophytic and necrotrophic stage of infection of the oil palm host. However, there is a lack of information available on the essentiality of CWDEs in wood-decaying process and pathogenesis of this oil palm pathogen especially at molecular and genome levels.
Methods: In this study, comparative genome analysis was carried out using the G. boninense NJ3 genome to identify and characterize carbohydrate-active enzyme (CAZymes) including CWDE in the fungal genome. Augustus pipeline was employed for gene identification in G. boninense NJ3 and the produced protein sequences were analyzed via dbCAN pipeline and PhiBase 4.5 database annotation for CAZymes and plant-host interaction (PHI) gene analysis, respectively. Comparison of CAZymes from G. boninense NJ3 was made against G. lucidum, a well-studied model Ganoderma sp. and five selected pathogenic fungi for CAZymes characterization. Functional annotation of PHI genes was carried out using Web Gene Ontology Annotation Plot (WEGO) and was used for selecting candidate PHI genes related to cell wall degradation of G. boninense NJ3.
Results: G. boninense was enriched with CAZymes and CWDEs in a similar fashion to G. lucidum that corroborate with the lignocellulolytic abilities of both closely-related fungal strains. The role of polysaccharide and cell wall degrading enzymes in the hemibiotrophic mode of infection of G. boninense was investigated by analyzing the fungal CAZymes with necrotrophic Armillaria solidipes, A. mellea, biotrophic Ustilago maydis, Melampsora larici-populina and hemibiotrophic Moniliophthora perniciosa. Profiles of the selected pathogenic fungi demonstrated that necrotizing pathogens including G. boninense NJ3 exhibited an extensive set of CAZymes as compared to the more CAZymes-limited biotrophic pathogens. Following PHI analysis, several candidate genes including polygalacturonase, endo β-1,3-xylanase, β-glucanase and laccase were identified as potential CWDEs that contribute to the plant host interaction and pathogenesis.
Discussion: This study employed bioinformatics tools for providing a greater understanding of the biological mechanisms underlying the production of CAZymes in G. boninense NJ3. Identification and profiling of the fungal polysaccharide- and lignocellulosic-degrading enzymes would further facilitate in elucidating the infection mechanisms through the production of CWDEs by G. boninense. Identification of CAZymes and CWDE-related PHI genes in G. boninense would serve as the basis for functional studies of genes associated with the fungal virulence and pathogenicity using systems biology and genetic engineering approaches.

Matched MeSH terms: Systems Biology
Recent Development in Omics Studies

Aizat WM, Ismail I, Noor NM

Adv Exp Med Biol, 2018 11 2;1102:1-9.
PMID: 30382565 DOI: 10.1007/978-3-319-98758-3_1

The central dogma of molecular biology (DNA, RNA, protein and metabolite) has engraved our understanding of genetics in all living organisms. While the concept has been embraced for many decades, the development of high-throughput technologies particularly omics (genomics, transcriptomics, proteomics and metabolomics) has revolutionised the field to incorporate big data analysis including bioinformatics and systems biology as well as synthetic biology area. These omics approaches as well as systems and synthetic biology areas are now increasingly popular as seen by the growing numbers of publication throughout the years. Several journals which have published most of these related fields are also listed in this chapter to overview their impact and target journals.

Matched MeSH terms: Systems Biology
Fulltext The Use of System Dynamics Methodology in Building a COVID-19 Confirmed Case Model

Mohd Yusoff MI

Comput Math Methods Med, 2020;2020:9328414.
PMID: 33224268 DOI: 10.1155/2020/9328414

Researchers used a hybrid model (a combination of health resource demand model and disease transmission model), Bayesian model, and susceptible-exposed-infectious-removed (SEIR) model to predict health service utilization and deaths and mixed-effect nonlinear regression. Further, they used the mixture model to predict the number of confirmed cases and deaths or to predict when the curve would flatten. In this article, we show, through scenarios developed using system dynamics methodology, besides close to real-world results, the detrimental effects of ignoring social distancing guidelines (in terms of the number of people infected, which decreased as the percentage of noncompliance decreased).

Matched MeSH terms: Systems Biology/methods
Genome-scale metabolic models as platforms for strain design and biological discovery

Mienda BS

J Biomol Struct Dyn, 2017 Jul;35(9):1863-1873.
PMID: 27251747 DOI: 10.1080/07391102.2016.1197153

Genome-scale metabolic models (GEMs) have been developed and used in guiding systems' metabolic engineering strategies for strain design and development. This strategy has been used in fermentative production of bio-based industrial chemicals and fuels from alternative carbon sources. However, computer-aided hypotheses building using established algorithms and software platforms for biological discovery can be integrated into the pipeline for strain design strategy to create superior strains of microorganisms for targeted biosynthetic goals. Here, I described an integrated workflow strategy using GEMs for strain design and biological discovery. Specific case studies of strain design and biological discovery using Escherichia coli genome-scale model are presented and discussed. The integrated workflow presented herein, when applied carefully would help guide future design strategies for high-performance microbial strains that have existing and forthcoming genome-scale metabolic models.

Matched MeSH terms: Systems Biology*
Functional Genomics

Goh HH, Ng CL, Loke KK

Adv Exp Med Biol, 2018 11 2;1102:11-30.
PMID: 30382566 DOI: 10.1007/978-3-319-98758-3_2

Functional genomics encompasses diverse disciplines in molecular biology and bioinformatics to comprehend the blueprint, regulation, and expression of genetic elements that define the physiology of an organism. The deluge of sequencing data in the postgenomics era has demanded the involvement of computer scientists and mathematicians to create algorithms, analytical software, and databases for the storage, curation, and analysis of biological big data. In this chapter, we discuss on the concept of functional genomics in the context of systems biology and provide examples of its application in human genetic disease studies, molecular crop improvement, and metagenomics for antibiotic discovery. An overview of transcriptomics workflow and experimental considerations is also introduced. Lastly, we present an in-house case study of transcriptomics analysis of an aromatic herbal plant to understand the effect of elicitation on the biosynthesis of volatile organic compounds.

Matched MeSH terms: Systems Biology
Fulltext Getting the most out of RNA-seq data analysis

Khang TF, Lau CY

PeerJ, 2015;3:e1360.
PMID: 26539333 DOI: 10.7717/peerj.1360

Background. A common research goal in transcriptome projects is to find genes that are differentially expressed in different phenotype classes. Biologists might wish to validate such gene candidates experimentally, or use them for downstream systems biology analysis. Producing a coherent differential gene expression analysis from RNA-seq count data requires an understanding of how numerous sources of variation such as the replicate size, the hypothesized biological effect size, and the specific method for making differential expression calls interact. We believe an explicit demonstration of such interactions in real RNA-seq data sets is of practical interest to biologists. Results. Using two large public RNA-seq data sets-one representing strong, and another mild, biological effect size-we simulated different replicate size scenarios, and tested the performance of several commonly-used methods for calling differentially expressed genes in each of them. We found that, when biological effect size was mild, RNA-seq experiments should focus on experimental validation of differentially expressed gene candidates. Importantly, at least triplicates must be used, and the differentially expressed genes should be called using methods with high positive predictive value (PPV), such as NOISeq or GFOLD. In contrast, when biological effect size was strong, differentially expressed genes mined from unreplicated experiments using NOISeq, ASC and GFOLD had between 30 to 50% mean PPV, an increase of more than 30-fold compared to the cases of mild biological effect size. Among methods with good PPV performance, having triplicates or more substantially improved mean PPV to over 90% for GFOLD, 60% for DESeq2, 50% for NOISeq, and 30% for edgeR. At a replicate size of six, we found DESeq2 and edgeR to be reasonable methods for calling differentially expressed genes at systems level analysis, as their PPV and sensitivity trade-off were superior to the other methods'. Conclusion. When biological effect size is weak, systems level investigation is not possible using RNAseq data, and no meaningful result can be obtained in unreplicated experiments. Nonetheless, NOISeq or GFOLD may yield limited numbers of gene candidates with good validation potential, when triplicates or more are available. When biological effect size is strong, NOISeq and GFOLD are effective tools for detecting differentially expressed genes in unreplicated RNA-seq experiments for qPCR validation. When triplicates or more are available, GFOLD is a sharp tool for identifying high confidence differentially expressed genes for targeted qPCR validation; for downstream systems level analysis, combined results from DESeq2 and edgeR are useful.

Matched MeSH terms: Systems Biology
Proteomics in Systems Biology

Aizat WM, Hassan M

Adv Exp Med Biol, 2018 11 2;1102:31-49.
PMID: 30382567 DOI: 10.1007/978-3-319-98758-3_3

Proteomics is the study of proteins, the workhorses of cells. Proteins can be subjected to various post-translational modifications, making them dynamic to external perturbation. Proteomics can be divided into four areas: sequence, structural, functional and interaction and expression proteomics. These different areas used different instrumentations and have different focuses. For example, sequence and structural proteomics mainly focus on elucidating a particular protein sequence and structure, respectively. Meanwhile, functional and interaction proteomics concentrate on protein function and interaction partners, whereas expression proteomics allows the cataloguing of total proteins in any given samples, hence providing a holistic overview of various proteins in a cell. The application of expression proteomics in cancer and crop research is detailed in this chapter. The general workflow of expression proteomics consisting the use of mass spectrometry instrumentation has also been described, and some examples of proteomics studies are also presented.

Matched MeSH terms: Systems Biology*
Integrative Multi-Omics Through Bioinformatics

Goh HH

Adv Exp Med Biol, 2018 11 2;1102:69-80.
PMID: 30382569 DOI: 10.1007/978-3-319-98758-3_5

This chapter introduces different aspects of bioinformatics with a brief discussion in the systems biology context. Example applications in network pharmacology of traditional Chinese medicine, systems metabolic engineering, and plant genome-scale modelling are described. Lastly, this chapter concludes on how bioinformatics helps to integrate omics data derived from various studies described in previous chapters for a holistic understanding of secondary metabolite production in P. minus.

Matched MeSH terms: Systems Biology*
Fulltext Understanding Host-Pathogen Interactions in Brassica napus in the Omics Era

Neik TX, Amas J, Barbetti M, Edwards D, Batley J

Plants (Basel), 2020 Oct 10;9(10).
PMID: 33050509 DOI: 10.3390/plants9101336

Brassica napus (canola/oilseed rape/rapeseed) is an economically important crop, mostly found in temperate and sub-tropical regions, that is cultivated widely for its edible oil. Major diseases of Brassica crops such as Blackleg, Clubroot, Sclerotinia Stem Rot, Downy Mildew, Alternaria Leaf Spot and White Rust have caused significant yield and economic losses in rapeseed-producing countries worldwide, exacerbated by global climate change, and, if not remedied effectively, will threaten global food security. To gain further insights into the host-pathogen interactions in relation to Brassica diseases, it is critical that we review current knowledge in this area and discuss how omics technologies can offer promising results and help to push boundaries in our understanding of the resistance mechanisms. Omics technologies, such as genomics, proteomics, transcriptomics and metabolomics approaches, allow us to understand the host and pathogen, as well as the interaction between the two species at a deeper level. With these integrated data in multi-omics and systems biology, we are able to breed high-quality disease-resistant Brassica crops in a more holistic, targeted and accurate way.

Matched MeSH terms: Systems Biology

Filters

Please provide feedback to Administrator (afdal@afpm.org.my)

External Links