MATHANAKUMARA
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Bioinformatician / Molecular Genetics Scientist
About Me
About Me
Biological researcher specialized in the field of bioinformatics, molecular genetics and immunology.
Proven track record with 3 years of experience in analyzing large-scale transcriptomics data and interpreting complex genomics and transcriptomics information through bioinformatics.
Experienced in hands-on wet lab molecular techniques to conduct genomics and transcriptomics studies.
Looking for PhD opportunities to contribute to the development and validation of cutting-edge bioinformatics tools on NGS data. Also, open to work as a freelance bioinformatician as part time (Link above in Upwork).
2021-2024
2021-2024
M.Sc. Biology and Biochemistry (University Malaya)
Project title:
Genome wide identification and characterisation of host circular RNAs involved in monocyte-derived macrophages in response to H1N1 Influenza A virus induced innate immune response
Bioinformatics:
Analyzed bulk RNA-seq data to profile circRNAs in IAV-infected macrophages at multiple timepoints corresponding to innate immune response
Designed and benchmarked novel transcriptomics bioinformatics pipeline through simulation study
Utilisation of genomics and transcriptomics aligners to align RNA-seq reads
Statistical analysis of circRNA expression
In-silico characterized and functionally annotated detected circRNAs
Developed customized scripts to run downstream analyses
Generate publication worthy plots to address the quality of RNA-seq reads and downstream characterisation and functional annotation of DE circRNAs
Wet-lab:
Cultured an immortalized monocytic cell-line, THP1
Induced differentiation of THP1 monocytes into macrophages using PMA
Virus culture of IAV in MDCK cells
Infected differentiated THP1 macrophages with cultured IAV at distinct timepoints
RNA extraction and cDNA conversion using kit
Primer design in primer3plus that hybridizes to the backsplice junction of circRNAs
Run PCR, RT-PCR, gel electrophoresis and Sanger sequencing for key circRNA validation
Research outcome:
Macrophage cells such as MDM (an innate immune cell) generally plays an inflammatory role in perturbing IAV infection by translocating to the lungs. This is the first study to address and characterize circRNAs expressed in MDM cells during IAV infection. Highlighted key circRNAs that can potentially act as diagnostic or prognostic markers.
2020-2021
2020-2021
Internship (Universiti Sains Malaysia, INFORMM)
Project title:
Biopanning and phage display
Assisted in identifying complex antibody fragments that bind to Human Papillomavirus (HPV) that causes cervical cancer (Successfully completed this methodology section)
Developed competent bacterial cells
Research outcome:
Developed target specific antibody complexes that binds to HPV antigens for adaptive immune response-mediated clearance.
2019-2020
2019-2020
B.Sc. Genetics and Molecular Biology (University Malaya)
CGPA: 3.60
Final Year Project:
Molecular characterisation of multidrug-resistant bacteria isolated from domestic sewage effluent
Collected sewage samples
Cultured bacteria using LB, R2A and MacConkey agar
Characterized bacteria through:
Gram-staining
Morphology
Antibiotic sensitivity tests (based on Kirby-Bauer test)
16s rRNA PCR
Phylogenetic analysis using MEGA
Research outcome:
Profiled and characterized culturable multidrug-resistant bacteria currently residing in the sewage system located at the Klang Valley area that may pose a threat to public health in the future.
Key Skills and Experience
Extensive research experience in bioinformatics, transcriptomics, virology, immunology and the identification of diagnostic and prognostic biomarkers.
Proficient in analyzing and interpreting genomics and transcriptomics data to provide valuable insights and contribute to advancements in immunological research.
Strong expertise in mammalian cellular genome with minimal experience in bacterial research.
Studying the diverse coding and non-coding RNA species and their interactions with pathogens (IAV) during the innate immune phase.
Skilled in performing genome and transcriptomic assemblies in model organisms, leveraging cutting-edge tools and techniques to generate high-quality genome sequences.
Proficient in data processing, analysis, and visualization using R, Python, Perl, and Bash scripting, enabling efficient and reproducible research workflows.
Competency in Linux (Local and HPC SLURM), Conda and Nextflow environments.
Experienced in implementing statistical analysis to derive meaningful conclusions from complex biological datasets.
Proven ability to communicate scientific findings through presentations, scientific reports, and publication in reputable journals.
Able to be independent and work as a team in engaging interdisciplinary research project.
Committed to staying updated with the latest advancements in the field of bioinformatics and adopting innovative approaches to address research challenges.
NGS Technology
Data analysis and statistics
Visualization
Wet-lab
Experienced with Next-Generation Sequencing (NGS) data analysis in bulk and single-cell RNA-sequencing from Illumina, Oxford Nanopore technology, PacBio and 10x Genomics.
Identified circRNAs and mRNAs during host pathogen interactions and integrate these two RNA species to understand their underlying relationship. This experience has allowed me to explore and highlight key circRNAs involved in the innate immune reaction in macrophage cells upon IAV infection.
Extensive experience in comprehensive data analysis across transcriptomics, genomics, immunology and mammalian genetics.
Proficient in processing and cleaning large-scale biological datasets for statistical tests
Programming skills in R, Python, Perl, and Bash.
Experienced in simulating RNA-seq reads based on specific distribution patterns, ex. normal and Poisson distribution, to benchmark novel circRNA pipeline.
Skilled in integrating and analyzing multi-omics data, leveraging bioinformatics tools such as integrating circRNA and mRNA data.
Proficient in computational platforms such as Linux (Both local PC and HPC SLURM), Conda and Nextflow environment.
Applied various statistical measures such as ANOVA, distribution models, time-series, edgeR, deseq2.
Collaboration and interdisciplinary teamwork are integral to my work, where I have contributed my data analysis expertise in research projects and also as a freelancer. Documented most of my scripts in my personal GitHub page (Github link).
Experienced in data visualization techniques to extract meaningful insights from complex biological data and effectively communicate research findings to both technical and non-technical audiences.
Communication is primarily through PowerPoints, but also occasionally through video platforms with proper annotations.
Mainly worked in R using ggplot2, ggpubr, pheatmap and base R. Not limited to that, I am proficient in Python's seaborn, matplotlib and plotly
Bioinformatics is not my only forte, as I have extensive experience in hands-on wet lab skills.
Trained molecular techniques include cell culturing mainly on immortalized mammalian cell line, THP1 and A549. Minimal experience in bacterial culture in LB, R2A and MacConkey agar and virus culture and propagation in MDCK cell line.
Performed virology experiments, followed by RNA extraction and cDNA conversion afterwards.
Designed primer probes using primer3plus that targets the unique backsplice junction region of circRNAs.
To validate circRNAs or bacterial 16s rRNA, I have performed PCR, RT PCR, agarose gel electrophoresis and sanger sequencing.
Academic, Scientific, and Social Impact of my Research
Academic, Scientific, and Social Impact of my Research
As a fresh graduate bioinformatician and molecular scientist, specializing in eukaryotic genomics, I have just started making significant contributions to the academic, scientific, and social community. Current highlights of my career include:
With a Bachelor's degree in Genetics and Molecular Biology and a Masters in Biology and Biochemistry, I focused on non-coding RNA expression profiling due to infectious disease related matter in an immunology context.
Published a video article in JoVE demonstrating methods to conduct circRNA analysis on RNA-seq data by downloading materials and algorithms application. scientific journals, showcasing the quality and impact of my research. JoVE Journal is indexed in PubMed, Web of Science, SciFinder, Scopus, and SCI Expanded as Journal of Visualized Experiments.
Advancing our understanding of the roles played by non-coding RNAs, and their downstream regulation that leads to further understanding of disease progression and ultimately may potentially serve as a prognosis and personalized treatments.
Currently writing two research articles:
Addressing role of circRNAs on a type of epithelial cells (a type that has not been investigated before) in H1N1 and innate immunology context and
A bioinformatics algorithm aimed at identifying potential regulatory functions of circRNAs .
Disseminating my findings at prestigious international conferences, to maximize their reach and impact (Link at page header).
Getting in touch
Getting in touch
Personal Github account
Connect with me on LinkedIn
Personal email account
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