ORCID Profile
0000-0002-2651-8719
Current Organisations
Flinders University
,
University of Barcelona
,
Universitat de Barcelona
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Publisher: Cold Spring Harbor Laboratory
Date: 04-04-2023
DOI: 10.1101/2023.04.04.535632
Abstract: Microbial communities found within the human gut have a strong influence on human health. Intestinal bacteria and viruses influence gastrointestinal diseases such as inflammatory bowel disease. Viruses infecting bacteria, known as bacteriophages, play a key role in modulating bacterial communities within the human gut. However, the identification and characterisation of novel bacteriophages remain a challenge. Available tools use similarities between sequences, nucleotide composition, and the presence of viral genes roteins. Most available tools consider in idual contigs to determine whether they are of viral origin. As a result of the challenges in viral assembly, fragmentation of viral genomes can occur, leading to the need for new approaches in viral identification. We introduce Phables, a new computational method to resolve bacteriophage genomes from fragmented viral metagenomic assemblies. Phables identifies bacteriophage-like components in the assembly graph, models each component as a flow network, and uses graph algorithms and flow decomposition techniques to identify genomic paths. Experimental results of viral metagenomic s les obtained from different environments show that over 80% of the bacteriophage genomes resolved by Phables have high quality and are longer than the in idual contigs identified by existing viral identification tools. Phables is available on GitHub at github.com/Vini2 hables (DOI: 10.5281/zenodo.7645166). vijini.mallawaarachchi@flinders.edu.au
Publisher: Elsevier BV
Date: 10-2022
DOI: 10.1016/J.COMPBIOLCHEM.2022.107734
Abstract: Metagenomics has enabled culture-independent analysis of micro-organisms present in environmental s les. Metagenomics binning, which involves the grouping of contigs into bins that represent different taxonomic groups, is an important step of a typical metagenomic workflow followed after assembly. The majority of the metagenomic binning tools represent the composition and coverage information of contigs as feature vectors consisting of a large number of dimensions. However, these tools use traditional Euclidean distance or Manhattan distance metrics which become unreliable in the high dimensional space. We propose CH-Bin, a binning approach that leverages the benefits of using convex hull distance for binning contigs represented by high dimensional feature vectors. We demonstrate using experimental evidence on simulated and real datasets that the use of high dimensional feature vectors to represent contigs can preserve additional information, and result in improved binning results. We further demonstrate that the convex hull distance based binning approach can be effectively utilized in binning such high dimensional data. To the best of our knowledge, this is the first time that composition information from oligonucleotides of multiple sizes has been used in representing the composition information of contigs and a convex hull distance based binning algorithm has been used to bin metagenomic contigs. The source code of CH-Bin is available at dsuneraavinash/CH-Bin.
Publisher: IEEE
Date: 12-2018
Publisher: University of Buckingham Press
Date: 15-06-2022
Abstract: This paper presents the numerical study on the hydrodynamic coefficients of the submarine hull form “DARPA SUBOFF” when deeply submerged and near the free surface when travelling straight ahead and at a range of drift angles. The Computational Fluid Dynamics (CFD)-based numerical model was validated with experimental data existing in the public domain for the SUBOFF, travelling over a range of drift angles when deeply submerged at a constant speed and in a straight line near the free surface over a range of speeds. The free surface effect on the hydrodynamic behaviour of the SUBOFF was then investigated throughout a range of speeds, drift angles and submergence depths. Results show that the effects of the free surface diminish rapidly with submergence and the near free surface hydrodynamic behaviour of the SUBOFF is highly Froude number dependent.
Publisher: IEEE
Date: 06-2017
Publisher: Springer International Publishing
Date: 2022
Publisher: IEEE
Date: 07-2018
Publisher: Cold Spring Harbor Laboratory
Date: 06-03-2023
DOI: 10.1101/2023.03.05.531146
Abstract: Bacteroides, the prominent bacteria in the human gut, play a crucial role in degrading complex polysaccharides. Their abundance is influenced by phages belonging to the Crassvirales order. Despite identifying over 600 Crassvirales genomes computationally, only few have been successfully isolated. Continued efforts in isolation of more Crassvirales genomes can provide insights into phage-host-evolution and infection mechanisms. We focused on wastewater s les, as potential sources of phages infecting various Bacteroides hosts. Sequencing, assembly, and characterization of isolated phages revealed 14 complete genomes belonging to three novel Crassvirales species infecting Bacteroides cellulosilyticus WH2. These species, Kehishuvirus sp. ‘tikkala’ strain Bc01, Kolpuevirus sp. ‘frurule’ strain Bc03, and ‘Rudgehvirus jaberico’ strain Bc11, spanned two families, and three genera, displaying a broad range of virion productions. Upon testing all successfully cultured Crassvirales species and their respective bacterial hosts, we discovered that they do not exhibit co-evolutionary patterns with their bacterial hosts. Furthermore, we observed variations in gene similarity, with greater shared similarity observed within genera. However, despite belonging to different genera, the three novel species shared a unique structural gene that encodes the tail spike protein. When investigating the relationship between this gene and host interaction, we discovered evidence of purifying selection, indicating its functional importance. Moreover, our analysis demonstrated that this tail spike protein binds to the TonB-dependent receptors present on the bacterial host surface. Combining these observations, our findings provide insights into phage-host interactions and present three Crassvirales species as an ideal system for controlled infectivity experiments on one of the most dominant members of the human enteric virome. Bacteriophages play a crucial role in shaping microbial communities within the human gut. Among the most dominant bacteriophages in the human gut microbiome are Crassvirales phages, which infect Bacteroides. Despite being widely distributed, only a few Crassvirales genomes have been isolated, leading to a limited understanding of their biology, ecology, and evolution. This study isolated and characterized three novel Crassvirales genomes belonging to two different families, and three genera, but infecting one bacterial host, Bacteroides cellulosilyticus WH2. Notably, the observation confirmed the phages are not co-evolving with their bacterial hosts, rather have a shared ability to exploit similar features in their bacterial host. Additionally, the identification of a critical viral protein undergoing purifying selection and interacting with the bacterial receptors opens doors to targeted therapies against bacterial infections. Given Bacteroides role in polysaccharide degradation in the human gut, our findings advance our understanding of the phage-host interactions and could have important implications for the development of phage-based therapies. These discoveries may hold implications for improving gut health and metabolism to support overall well-being. The genomes used in this research are available on Sequence Read Archive (SRA) within the project, PRJNA737576. Bacteroides cellulosilyticus WH2, Kehishuvirus sp. ‘tikkala’ strain Bc01, Kolpuevirus sp. ‘ frurule’ strain Bc03, and ‘Rudgehvirus jaberico’ strain Bc11 are all available on GenBank with accessions NZ_CP072251.1 ( B. cellulosilyticus WH2), QQ198717 (Bc01), QQ198718 (Bc03), and QQ198719 (Bc11), and we are working on making the strains available through ATCC. The 3D protein structures for the three Crassvirales genomes are available to download at 0.25451/flinders.21946034.
Publisher: American Chemical Society (ACS)
Date: 12-11-2021
Publisher: IEEE
Date: 09-2018
Publisher: Cold Spring Harbor Laboratory
Date: 20-04-2023
DOI: 10.1101/2023.04.19.537311
Abstract: Microbiota are closely associated to human health and disease. Metaproteomics can provide a direct means to identify microbial proteins in microbiota for compositional and functional characterization. However, in-depth and accurate metaproteomics is still limited due to the extreme complexity and high ersity of microbiota s les. One of the main challenges is constructing a protein sequence database that best fits the microbiota s le. Herein, we proposed an accurate taxonomic annotation pipeline from metagenomic data for deep metaproteomic coverage, namely contigs directed gene annotation (ConDiGA). We mixed 12 known bacterial species to derive a synthetic microbial community to benchmark metagenomic and metaproteomic pipelines. With the optimized taxonomic annotation strategy by ConDiGA, we built a protein sequence database from the metagenomic data for metaproteomic analysis and identified about 12,000 protein groups, which was very close to the result obtained with the reference proteome protein sequence database of the 12 species. We also demonstrated the practicability of the method in real fecal s les, achieved deep proteome coverage of human gut microbiome, and compared the function and taxonomy of gut microbiota at metagenomic level and metaproteomic level. Our study can tackle the current taxonomic annotation reliability problem in metagenomics-derived protein sequence database for metaproteomics. The unique dataset of metagenomic and the metaproteomic data of the 12 bacterial species is publicly available as a standard benchmarking s le for evaluating various analysis pipelines. The code of ConDiGA is open access at GitHub for the analysis of real microbiota s les.
Publisher: Institute of Electrical and Electronics Engineers (IEEE)
Date: 07-2018
Publisher: Public Library of Science (PLoS)
Date: 15-12-2022
Publisher: IEEE
Date: 03-2019
Publisher: Frontiers Media SA
Date: 09-01-2023
DOI: 10.3389/FMICB.2022.1098268
Abstract: Daqu , the Chinese liquor fermentation starter, contains complex microbial communities that are important for the yield, quality, and unique flavor of produced liquor. However, the composition and metabolism of microbial communities in the different types of high-temperature Daqu (i.e., white, yellow, and black Daqu ) have not been well understood. Herein, we used quantitative metaproteomics based on data-independent acquisition (DIA) mass spectrometry to analyze a total of 90 s les of white, yellow, and black Daqu collected in spring, summer, and autumn, revealing the taxonomic and metabolic profiles of different types of Daqu across seasons. Taxonomic composition differences were explored across types of Daqu and seasons, where the under-fermented white Daqu showed the higher microbial ersity and seasonal stability. It was demonstrated that yellow Daqu had higher abundance of saccharifying enzymes for raw material degradation. In addition, considerable seasonal variation of microbial protein abundance was discovered in the over-fermented black Daqu , suggesting elevated carbohydrate and amino acid metabolism in autumn black Daqu . We expect that this study will facilitate the understanding of the key microbes and their metabolism in the traditional fermentation process of Chinese liquor production.
Publisher: IEEE
Date: 09-2019
Publisher: American Chemical Society (ACS)
Date: 03-07-2018
DOI: 10.1021/ACS.INORGCHEM.8B01147
Abstract: A kineticomechanistic study of reversible electron-transfer processes undergone by the water-soluble, cyanido-bridged mixed-valence [{Co
Publisher: Informa UK Limited
Date: 06-01-2021
Publisher: Oxford University Press (OUP)
Date: 27-06-2023
DOI: 10.1093/BIOINFORMATICS/BTAD409
Abstract: With recent advances in sequencing technologies, it is now possible to obtain near-perfect complete bacterial chromosome assemblies cheaply and efficiently by combining a long-read-first assembly approach with short-read polishing. However, existing methods for assembling bacterial plasmids from long-read-first assemblies often misassemble or even miss bacterial plasmids entirely and accordingly require manual curation. Plassembler was developed to provide a tool that automatically assembles and outputs bacterial plasmids using a hybrid assembly approach. It achieves increased accuracy and computational efficiency compared to the existing gold standard tool Unicycler by removing chromosomal reads from the input read sets using a mapping approach. Plassembler is implemented in Python and is installable as a bioconda package using ‘conda install -c bioconda plassembler’. The source code is available on GitHub at bouras13 lassembler. The full benchmarking pipeline can be found at bouras13 lassembler_simulation_benchmarking, while the benchmarking input FASTQ and output files can be found at 0.5281/zenodo.7996690.
Publisher: Springer Science and Business Media LLC
Date: 04-05-2021
DOI: 10.1186/S13015-021-00185-6
Abstract: Metagenomic sequencing allows us to study the structure, ersity and ecology in microbial communities without the necessity of obtaining pure cultures. In many metagenomics studies, the reads obtained from metagenomics sequencing are first assembled into longer contigs and these contigs are then binned into clusters of contigs where contigs in a cluster are expected to come from the same species. As different species may share common sequences in their genomes, one assembled contig may belong to multiple species. However, existing tools for binning contigs only support non-overlapped binning, i.e., each contig is assigned to at most one bin (species). In this paper, we introduce GraphBin2 which refines the binning results obtained from existing tools and, more importantly, is able to assign contigs to multiple bins. GraphBin2 uses the connectivity and coverage information from assembly graphs to adjust existing binning results on contigs and to infer contigs shared by multiple species. Experimental results on both simulated and real datasets demonstrate that GraphBin2 not only improves binning results of existing tools but also supports to assign contigs to multiple bins. GraphBin2 incorporates the coverage information into the assembly graph to refine the binning results obtained from existing binning tools. GraphBin2 also enables the detection of contigs that may belong to multiple species. We show that GraphBin2 outperforms its predecessor GraphBin on both simulated and real datasets. GraphBin2 is freely available at github.com/Vini2/GraphBin2 .
Publisher: IEEE
Date: 07-2019
Publisher: Frontiers Media SA
Date: 02-03-2023
DOI: 10.3389/FMICB.2023.1031711
Abstract: Marine host-associated microbiomes are affected by a combination of species-specific (e.g., host ancestry, genotype) and habitat-specific features (e.g., environmental physiochemistry and microbial biogeography). The stingray epidermis provides a gradient of characteristics from high dermal denticles coverage with low mucus to reduce dermal denticles and high levels of mucus. Here we investigate the effects of host phylogeny and habitat by comparing the epidermal microbiomes of Myliobatis californica (bat rays) with a mucus rich epidermis, and Urobatis halleri (round rays) with a mucus reduced epidermis from two locations, Los Angeles and San Diego, California (a 150 km distance). We found that host microbiomes are species-specific and distinct from the water column, however composition of M. californica microbiomes showed more variability between in iduals compared to U. halleri. The variability in the microbiome of M. californica caused the microbial taxa to be similar across locations, while U. halleri microbiomes were distinct across locations. Despite taxonomic differences, Shannon ersity is the same across the two locations in U. halleri microbiomes suggesting the taxonomic composition are locally adapted, but ersity is maintained by the host. Myliobatis californica and U. halleri microbiomes maintain functional similarity across Los Angeles and San Diego and each ray showed several unique functional genes. Myliobatis californica has a greater relative abundance of RNA Polymerase III-like genes in the microbiome than U. halleri , suggesting specific adaptations to a heavy mucus environment. Construction of Metagenome Assembled Genomes (MAGs) identified novel microbial species within Rhodobacteraceae , Moraxellaceae , Caulobacteraceae , Alcanivoracaceae and Gammaproteobacteria. All MAGs had a high abundance of active RNA processing genes, heavy metal, and antibiotic resistant genes, suggesting the stingray mucus supports high microbial growth rates, which may drive high levels of competition within the microbiomes increasing the antimicrobial properties of the microbes.
Publisher: American Chemical Society (ACS)
Date: 13-01-2020
DOI: 10.1021/ACS.INORGCHEM.9B03274
Abstract: Novel types of water-soluble anionic cubic cages, K
Publisher: International Association of Online Engineering (IAOE)
Date: 19-06-2020
DOI: 10.3991/IJOE.V16I07.13807
Abstract: Phylogenetics is one of the dominant data engineering research disciplines based on biological information. More particularly here, we consider raw DNA sequences and do comparative analysis in order to come up with important conclusions. When representing evolutionary relationships among different organisms in a concise manner, the phylogenetic tree helps significantly. When constructing phylogenetic trees, the elementary step is to calculate the genetic distance among species. Alignment-based sequencing and alignment-free sequencing are the two main distance computation methods that are used to find genetic relatedness of different species. In this paper we propose a novel alignment-free, pairwise, distance calculation method based on k-mers and a state of art machine learning-based phylogenetic tree construction mechanism. With the proposed approach we can convert longer DNA sequences into compendious k-mer forests which gear up the efficiency of comparison. Later we construct the phylogenetic tree based on calculated distances with the help of an algorithm build upon k-medoid clustering, which guaranteed significant efficiency and accuracy compared to traditional phylogenetic tree construction methods.
Publisher: Microbiology Society
Date: 04-09-2023
Publisher: Mary Ann Liebert Inc
Date: 12-2022
Abstract: Metagenomics enables the recovery of various genetic materials from different species, thus providing valuable insights into microbial communities. Metagenomic binning group sequences belong to different organisms, which is an important step in the early stages of metagenomic analysis pipelines. The classic pipeline followed in metagenomic binning is to assemble short reads into longer contigs and then bin these resulting contigs into groups representing different taxonomic groups in the metagenomic s le. Most of the currently available binning tools are designed to bin metagenomic contigs, but they do not make use of the assembly graphs that produce such assemblies. In this study, we propose MetaCoAG, a metagenomic binning tool that uses assembly graphs with the composition and coverage information of contigs. MetaCoAG estimates the number of initial bins using single-copy marker genes, assigns contigs into bins iteratively, and adjusts the number of bins dynamically throughout the binning process. We show that MetaCoAG significantly outperforms state-of-the-art binning tools by producing similar or more high-quality bins than the second-best binning tool on both simulated and real datasets. To the best of our knowledge, MetaCoAG is the first stand-alone contig-binning tool that directly makes use of the assembly graph information along with other features of the contigs.
Publisher: Inderscience Publishers
Date: 2017
Publisher: Royal Institution of Naval Architects
Date: 2015
DOI: 10.3940/RINA.IJME.2015.A4.320
Abstract: "When an Autonomous Underwater Vehicle (AUV) is operating close to a moving submarine, the hydrodynamic interaction between the two vehicles can prevent the AUV from maintaining its desired trajectory. This can lead to mission failure and, in extreme cases, collision with the submarine. This paper outlines the transient interaction influence on the hydrodynamic coefficients of an AUV operating in close proximity and in relative motion to a larger moving submarine. The effects of relative motion on the interaction behaviour were investigated via two manoeuvres, i.e. the AUV overtaking and being overtaken by the submarine at different relative forward velocities and lateral distances. The results presented are from a series of Computational Fluid Dynamics (CFD) simulations on axisymmetric AUV and submarine hull forms, with validation of the CFD model carried out through scaled captive model experiments. The results showed that an AUV becomes less susceptible to the interaction influence when overtaking at speeds higher than the submarine. The implications of the interaction influence on the AUV’s ability to safely manoeuvre around the submarine are also discussed."
Publisher: IEEE
Date: 08-2017
Publisher: Cold Spring Harbor Laboratory
Date: 11-09-2021
DOI: 10.1101/2021.09.10.459728
Abstract: Metagenomics binning has allowed us to study and characterize various genetic material of different species and gain insights into microbial communities. While existing binning tools bin metagenomics de novo assemblies, they do not make use of the assembly graphs that produce such assemblies. Here we propose MetaCoAG, a tool that utilizes assembly graphs with the composition and coverage information to bin metagenomic contigs. MetaCoAG uses single-copy marker genes to estimate the number of initial bins, assigns contigs into bins iteratively and adjusts the number of bins dynamically throughout the binning process. Experimental results on simulated and real datasets demonstrate that MetaCoAG significantly outperforms state-of-the-art binning tools, producing more high-quality bins than the second-best tool, with an average median F1-score of 88.40%. To the best of our knowledge, MetaCoAG is the first stand-alone binning tool to make direct use of the assembly graph information. MetaCoAG is available at github.com/Vini2/MetaCoAG .
Publisher: Elsevier BV
Date: 12-2016
Publisher: Frontiers Media SA
Date: 24-05-2023
DOI: 10.3389/FMICB.2023.963173
Abstract: The gut virome is an incredibly complex part of the gut ecosystem. Gut viruses play a role in many disease states, but it is unknown to what extent the gut virome impacts everyday human health. New experimental and bioinformatic approaches are required to address this knowledge gap. Gut virome colonization begins at birth and is considered unique and stable in adulthood. The stable virome is highly specific to each in idual and is modulated by varying factors such as age, diet, disease state, and use of antibiotics. The gut virome primarily comprises bacteriophages, predominantly order Crassvirales, also referred to as crAss-like phages, in industrialized populations and other Caudoviricetes (formerly Caudovirales ). The stability of the virome’s regular constituents is disrupted by disease. Transferring the fecal microbiome, including its viruses, from a healthy in idual can restore the functionality of the gut. It can alleviate symptoms of chronic illnesses such as colitis caused by Clostridiodes difficile . Investigation of the virome is a relatively novel field, with new genetic sequences being published at an increasing rate. A large percentage of unknown sequences, termed ‘viral dark matter’, is one of the significant challenges facing virologists and bioinformaticians. To address this challenge, strategies include mining publicly available viral datasets, untargeted metagenomic approaches, and utilizing cutting-edge bioinformatic tools to quantify and classify viral species. Here, we review the literature surrounding the gut virome, its establishment, its impact on human health, the methods used to investigate it, and the viral dark matter veiling our understanding of the gut virome.
Publisher: Frontiers Media SA
Date: 06-2023
DOI: 10.3389/FNUT.2023.1139836
Abstract: The special flavor and fragrance of Chinese liquor are closely related to microorganisms in the fermentation starter Daqu . The changes of microbial community can affect the stability of liquor yield and quality. In this study, we used data-independent acquisition mass spectrometry (DIA-MS) for cohort study of the microbial communities of a total of 42 Daqu s les in six production cycles at different times of a year. The DIA MS data were searched against a protein database constructed by metagenomic sequencing. The microbial composition and its changes across production cycles were revealed. Functional analysis of the differential proteins was carried out and the metabolic pathways related to the differential proteins were explored. These metabolic pathways were related to the saccharification process in liquor fermentation and the synthesis of secondary metabolites to form the unique flavor and aroma in the Chinese liquor. We expect that the metaproteome profiling of Daqu from different production cycles will serve as a guide for the control of fermentation process of Chinese liquor in the future.
Publisher: Marine Technology Society
Date: 03-2016
DOI: 10.4031/MTSJ.50.2.3
Abstract: Abstract Autonomous underwater vehicles (AUVs) use secondary velocity over ground measurements to aid the Inertial Navigation System (INS) to avoid unbounded drift in the point-to-point navigation solution. When operating in deep open ocean (i.e., in blue water—beyond the frequency-specific instrument range), the velocity measurements are either based on water column velocities or completely unavailable. In such scenarios, the velocity-relative-to-water measurements from an acoustic Doppler current profiler (ADCP) are often used for INS aiding. ADCPs have a blanking distance (typically ranging between 0.5 and 5 m) in proximity to the device in which the flow velocity data are undetectable. Hence, water velocities used to aid the INS solution can be significantly different from that near the vehicle and are subjected to significant noise. Previously, the authors introduced a nonacoustic method to calculate the w ater v elocity components of a turbulent water column within the ADCP dead zone using the A UV m otion response (referred to as the WVAM method). The current study analyzes the feasibility of incorporating the WVAM method within the INS by investigating the accuracy of it at different turbulence levels of the water column. Findings of this work demonstrate that the threshold limits of the method can be improved in the nonlinear ranges (i.e., at low and high levels of energy) however, by estimating a more accurate representation of vehicle hydrodynamic coefficients, this method has proven robust in a range of tidally induced flow conditions. The WVAM method, in its current state, offers significant potential to make a key contribution to blue water navigation when integrated within the vehicle's INS.
Publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
Date: 2020
Publisher: Association for Computing Machinery (ACM)
Date: 06-02-2021
DOI: 10.1145/3369876
Abstract: The majority of currently available webpages are dynamic in nature and are changing frequently. New content gets added to webpages, and existing content gets updated or deleted. Hence, people find it useful to be alert for changes in webpages that contain information that is of value to them. In the current context, keeping track of these webpages and getting alerts about different changes have become significantly challenging. Change Detection and Notification (CDN) systems were introduced to automate this monitoring process and to notify users when changes occur in webpages. This survey classifies and analyzes different aspects of CDN systems and different techniques used for each aspect. Furthermore, the survey highlights the current challenges and areas of improvement present within the field of research.
Publisher: Elsevier BV
Date: 05-2017
Publisher: Oxford University Press (OUP)
Date: 07-2020
DOI: 10.1093/BIOINFORMATICS/BTAA441
Abstract: Metagenomics studies have provided key insights into the composition and structure of microbial communities found in different environments. Among the techniques used to analyse metagenomic data, binning is considered a crucial step to characterize the different species of micro-organisms present. The use of short-read data in most binning tools poses several limitations, such as insufficient species-specific signal, and the emergence of long-read sequencing technologies offers us opportunities to surmount them. However, most current metagenomic binning tools have been developed for short reads. The few tools that can process long reads either do not scale with increasing input size or require a database with reference genomes that are often unknown. In this article, we present MetaBCC-LR, a scalable reference-free binning method which clusters long reads directly based on their k-mer coverage histograms and oligonucleotide composition. We evaluate MetaBCC-LR on multiple simulated and real metagenomic long-read datasets with varying coverages and error rates. Our experiments demonstrate that MetaBCC-LR substantially outperforms state-of-the-art reference-free binning tools, achieving ∼13% improvement in F1-score and ∼30% improvement in ARI compared to the best previous tools. Moreover, we show that using MetaBCC-LR before long-read assembly helps to enhance the assembly quality while significantly reducing the assembly cost in terms of time and memory usage. The efficiency and accuracy of MetaBCC-LR pave the way for more effective long-read-based metagenomics analyses to support a wide range of applications. The source code is freely available at: nuradhawick/MetaBCC-LR. Supplementary data are available at Bioinformatics online.
Publisher: IEEE
Date: 05-2017
Publisher: Elsevier BV
Date: 03-2017
Publisher: IEEE
Date: 09-2018
Publisher: Elsevier BV
Date: 06-2015
Publisher: International Association of Online Engineering (IAOE)
Date: 20-12-2018
Abstract: Bioinformatics is focused on deriving biological understanding from large amounts of data with specialized skills and computational tools. Students, who wish to pursue a career as a bioinformatician, are required to have a good understanding in biology and computer science. One of the challenging areas for a student learning in bioinformatics is complex workflow modelling and analysis it incorporates several threshold concepts and liminal spaces for student learning, which demands higher levels of cognitive skills, active exploration and reflective reinforcement in student learning. Hence, proper learning material and interactive tools are required to support student learning through active exploration and experiential learning. The study presents the successful use of such a learner support tool, BioWorkflow [1], we developed to be used in bioinformatics teaching and research. An evaluation was done with a student s le (n=80), where the first group (n1=40) was given only the relevant course material and the second group (n2=40) was given the course material along with BioWorkflow to visualize concepts relevant to sequence alignment and workflow modelling. Better learning engagement during the experiment, better performance at advanced questions and a positive user response were observed from the students who used BioWorkflow tool, compared to the control group. Student feedback strongly supported the fact that tools similar to BioWorkflow are an essential element for enhancing teaching and learner support in bioinformatics students appreciated the tool usability and its help obtained for scoring high grades at the assessment.
Publisher: IEEE
Date: 09-2018
Publisher: Association for the Advancement of Artificial Intelligence (AAAI)
Date: 28-06-2022
Abstract: Mixed communities of organisms are found in many environments -- from the human gut to marine ecosystems -- and can have profound impact on human health and the environment. Metagenomics studies the genomic material of such communities through high-throughput sequencing that yields DNA subsequences for subsequent analysis. A fundamental problem in the standard workflow, called binning, is to discover clusters, of genomic subsequences, associated with the constituent organisms. Inherent noise in the subsequences, various biological constraints that need to be imposed on them and the skewed cluster size distribution exacerbate the difficulty of this unsupervised learning problem. In this paper, we present a new formulation using a graph where the nodes are subsequences and edges represent homophily information. In addition, we model biological constraints providing heterophilous signal about nodes that cannot be clustered together. We solve the binning problem by developing new algorithms for (i) graph representation learning that preserves both homophily relations and heterophily constraints (ii) constraint-based graph clustering method that addresses the problems of skewed cluster size distribution. Extensive experiments, on real and synthetic datasets, demonstrate that our approach, called RepBin, outperforms a wide variety of competing methods. Our constraint-based graph representation learning and clustering methods, that may be useful in other domains as well, advance the state-of-the-art in both metagenomics binning and graph representation learning.
Publisher: ACM
Date: 08-02-2018
Publisher: Elsevier BV
Date: 09-2015
Publisher: Oxford University Press (OUP)
Date: 21-09-2023
Publisher: ACM
Date: 27-07-2018
Publisher: Royal Society of Chemistry (RSC)
Date: 2023
DOI: 10.1039/D3DT02442C
No related grants have been discovered for Vijini Mallawaarachchi.