My Research Interests

• Bioinformatics
• Metagenomics
• Data Mining and Information Retrieval
• Machine Learning
• Data Structures and Algorithms
• Software Architecture

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Published Projects

ConDiGA: Contigs Directed Gene Annotation

• ConDiGA (Contigs Directed Gene Annotation) is an accurate taxonomic annotation pipeline from metagenomic data to construct accurate protein sequence databases for deep metaproteomic coverage.
• Technologies used: Python 3
• View project
• View Microbiome journal publication

Phables: from fragmented assemblies to high-quality bacteriophage genomes

• Phables is a tool developed to resolve bacteriophage genomes using assembly graphs of viral metagenomic data.
• Phables models phage-like components in the viral metagenomic assembly as flow networks, models as a minimum flow decomposition problem and resolves genomic paths corresponding to flow paths determined.
• Technologies used: Python 3, Snaketool
• View project
• View Bioinformatics journal publication
• View ABACBS 2023 conference presentation

MetaCoAG: Binning Metagenomic Contigs via Composition, Coverage and Assembly Graphs

• MetaCoAG is an NGS data-based metagenomic contig binning tool that makes use of the connectivity information found in assembly graphs, apart from the composition and coverage information.
• MetaCoAG makes use of single-copy marker genes along with a graph matching technique and a label propagation technique to bin contigs.
• Technologies used: Python 3
• View project
• View RECOMB 2022 conference presentation
• View RECOMB 2022 conference publication
• View extended journal publication

GraphBin2: Refined and Overlapped Binning of Metagenomic Contigs Using Assembly Graphs

• GraphBin2 is an extension of GraphBin which refines the binning results obtained from existing tools and can 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.
• Technologies used: Python 3
• View project
• View WABI 2020 conference presentation
• View WABI 2020 conference publication
• View extended journal publication

GraphBin: Refined Binning of Metagenomic Contigs using Assembly Graphs

• GraphBin is a metagenomic contig binning tool that makes use of the contig connectivity information from the assembly graph to bin contigs.
• It utilizes the binning result of an existing binning tool and a label propagation algorithm to correct mis-binned contigs and predict the labels of contigs that are discarded due to the short length.
• Technologies used: Python 3
• View project
• View Bioinformatics publication
• Seminar Talk

Pipeline Monitor

• A scheduler to execute and run a pipeline of commands in a supercomputing facility.
• The program can schedule a graph-like execution sequence.
• View project

An Interactive Workflow Solution to Support Bioinformatics Analyses

• A generic software framework that can be used to construct bioinformatics workflows by both biologists and bioinformaticians with any level of programming expertise.
• This framework incorporates novel web application development technologies to support specific requirements of bioinformatics software for workflow creation.
• View project
• View publication

Change Detection in Distributed Digital Collections

• An efficient change detection and notification system to track changes occurring in web pages and notify interested users.
• Final Year Project carried out for the completion of the degree BSc. Engineering (Hons.) in Computer Science and Engineering.
• Technologies used include Java, H2O.ai, Jsoup, AngularJS, PHP, HTML, CSS, MySQL
• View ACM CSUR survey paper

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View My Work