ORCID Profile
0000-0002-8509-2543
Current Organisations
Monash University
,
University of Sydney
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Publisher: Elsevier BV
Date: 12-2021
Publisher: Springer Science and Business Media LLC
Date: 12-2012
DOI: 10.1186/1471-2105-13-S17-S24
Abstract: The transcriptome of an organism can be studied with the analysis of expressed sequence tag (EST) data sets that offers a rapid and cost effective approach with several new and updated bioinformatics approaches and tools for assembly and annotation. The comprehensive analyses comprehend an organism along with the genome and proteome analysis. With the advent of large-scale sequencing projects and generation of sequence data at protein and cDNA levels, automated analysis pipeline is necessary to store, organize and annotate ESTs. TranSeqAnnotator is a workflow for large-scale analysis of transcriptomic data with the most appropriate bioinformatics tools for data management and analysis. The pipeline automatically cleans, clusters, assembles and generates consensus sequences, conceptually translates these into possible protein products and assigns putative function based on various DNA and protein similarity searches. Excretory/secretory (ES) proteins inferred from ESTs/short reads are also identified. The TranSeqAnnotator accepts FASTA format raw and quality ESTs along with protein and short read sequences and are analysed with user selected programs. After pre-processing and assembly, the dataset is annotated at the nucleotide, protein and ES protein levels. TranSeqAnnotator has been developed in a Linux cluster, to perform an exhaustive and reliable analysis and provide detailed annotation. TranSeqAnnotator outputs gene ontologies, protein functional identifications in terms of mapping to protein domains and metabolic pathways. The pipeline is applied to annotate large EST datasets to identify several novel and known genes with therapeutic experimental validations and could serve as potential targets for parasite intervention. TransSeqAnnotator is freely available for the scientific community at estexplorer.biolinfo.org/TranSeqAnnotator/ .
Publisher: Elsevier BV
Date: 08-2009
Publisher: Impact Journals, LLC
Date: 27-09-2017
Publisher: Elsevier BV
Date: 07-2009
DOI: 10.1016/J.BIOTECHADV.2009.03.005
Abstract: Parasitic nematodes infect humans, other animals and plants, and impose a significant public health and economic burden worldwide due to the diseases that they cause. A better understanding of parasite genomes, host-parasite relationships and the molecular biology of parasites themselves will enable the rational development of diagnostic tests and/or safe anti-parasitic compounds, following the functional annotation of parasite genomic sequences. With only a few completely sequenced nematode genomes, expressed sequence tag (EST) datasets provide a low-cost alternative ("poor man's genome") to whole genome sequences and a glimpse of the transcriptome of an organism. EST data require a number of computational methods for their pre-processing, clustering, assembly and annotation to yield biologically relevant information. In this article, we review the steps involved in EST data analysis, the development of new semi-automated bioinformatic pipelines and their application to parasitic nematodes of major socio-economic significance, focused on identifying molecules involved in key biological processes or pathways that might serve as targets for new drugs or vaccines.
Publisher: Elsevier BV
Date: 04-2016
Publisher: American Society of Tropical Medicine and Hygiene
Date: 05-12-2018
Publisher: Springer Science and Business Media LLC
Date: 12-2012
DOI: 10.1186/1471-2164-13-S7-S10
Abstract: Teladorsagia circumcincta (order Strongylida) is an economically important parasitic nematode of small ruminants (including sheep and goats) in temperate climatic regions of the world. Improved insights into the molecular biology of this parasite could underpin alternative methods required to control this and related parasites, in order to circumvent major problems associated with anthelmintic resistance. The aims of the present study were to define the transcriptome of the adult stage of T. circumcincta and to infer the main pathways linked to molecules known to be expressed in this nematode. Since sheep develop acquired immunity against T. circumcincta , there is some potential for the development of a vaccine against this parasite. Hence, we infer excretory/secretory molecules for T. circumcincta as possible immunogens and vaccine candidates. A total of 407,357 ESTs were assembled yielding 39,852 putative gene sequences. Conceptual translation predicted 24,013 proteins, which were then subjected to detailed annotation which included pathway mapping of predicted proteins (including 112 excreted/secreted [ES] and 226 transmembrane peptides), domain analysis and GO annotation was carried out using InterProScan along with BLAST2GO. Further analysis was carried out for secretory signal peptides using SignalP and non-classical sec pathway using SecretomeP tools. For ES proteins, key pathways, including Fc epsilon RI, T cell receptor, and chemokine signalling as well as leukocyte transendothelial migration were inferred to be linked to immune responses, along with other pathways related to neurodegenerative diseases and infectious diseases, which warrant detailed future studies. KAAS could identify new and updated pathways like phagosome and protein processing in endoplasmic reticulum. Domain analysis for the assembled dataset revealed families of serine, cysteine and proteinase inhibitors which might represent targets for parasite intervention. InterProScan could identify GO terms pertaining to the extracellular region. Some of the important domain families identified included the SCP-like extracellular proteins which belong to the pathogenesis-related proteins (PRPs) superfamily along with C-type lectin, saposin-like proteins. The 'extracellular region' that corresponds to allergen V5/Tpx-1 related, considered important in parasite-host interactions, was also identified. Six cysteine motif (SXC1) proteins, transthyretin proteins, C-type lectins, activation-associated secreted proteins (ASPs), which could represent potential candidates for developing novel anthelmintics or vaccines were few other important findings. Of these, SXC1, protein kinase domain-containing protein, trypsin family protein, trypsin-like protease family member (TRY-1), putative major allergen and putative lipid binding protein were identified which have not been reported in the published T. circumcincta proteomics analysis. Detailed analysis of 6,058 raw EST sequences from dbEST revealed 315 putatively secreted proteins. Amongst them, C-type single domain activation associated secreted protein ASP3 precursor, activation-associated secreted proteins (ASP-like protein), cathepsin B-like cysteine protease, cathepsin L cysteine protease, cysteine protease, TransThyretin-Related and Venom-Allergen-like proteins were the key findings. We have annotated a large dataset ESTs of T. circumcincta and undertaken detailed comparative bioinformatics analyses. The results provide a comprehensive insight into the molecular biology of this parasite and disease manifestation which provides potential focal point for future research. We identified a number of pathways responsible for immune response. This type of large-scale computational scanning could be coupled with proteomic and metabolomic studies of this parasite leading to novel therapeutic intervention and disease control strategies. We have also successfully affirmed the use of bioinformatics tools, for the study of ESTs, which could now serve as a benchmark for the development of new computational EST analysis pipelines.
Publisher: Elsevier BV
Date: 10-2019
DOI: 10.1016/J.JBI.2019.103288
Abstract: Bluetooth low energy (BLE) beacons have been used to track the locations of in iduals in indoor environments for clinical applications such as workflow analysis and infectious disease modelling. Most current approaches use the received signal strength indicator (RSSI) to track locations. When using the RSSI to track indoor locations, devices need to be calibrated to account for complex interference patterns, which is a laborious process. Our aim was to investigate an alternative method for indoor location tracking of a moving user using BLE beacons in dynamic indoor environments. We developed a new method based on the received number of signals indicator (RNSI) and compared it to a standard RSSI-based method for predicting a user's location. Experiments were performed in an office environment and a tertiary hospital. Both RNSI and RSSI were compared at various distances from BLE beacons. In moving user experiments, a user wearing a beacon walked from one location to another based on a pre-defined route. Performance in predicting user locations was measured based on accuracy. RNSI values decreased substantially with distance from the BLE beacon than RSSI values. Moving user experiments in the office environment demonstrated that the RNSI-based method produced higher accuracy (80.0%) than the RSSI-based method (76.2%). In the hospital, where the environment may introduce signal quality problems due to increased signal interference, the RNSI-based method still outperformed (83.3%) the RSSI-based method (51.9%). Our results suggest that the RNSI-based method could be useful to track the locations of a moving user without involving complex calibration, especially when deploying within a new environment. RNSI has the potential to be used together with other methods in more robust indoor positioning systems.
Publisher: Elsevier BV
Date: 03-2019
No related grants have been discovered for Ranjeeta Menon.