HARIE VIGNESH
Research Assistant
Lyngby
Summary
A diligent and keen goal-oriented individual trying to address fundamental questions in developmental biology and epigenetics by unlocking the potential of Genomics and transcriptomics. Aspiring to be a scientist contributing to the development of real-time solutions to existing problems at the intersection of medicine, biology, and engineering.
Overview
6
6
years of professional experience
5
5
years of post-secondary education
Work History
Research Assistant
Technical University of Denmark
Lyngby, Copenhagen
2 2024 - Current
- Implemented simultaneous profiling of mRNA and ATAC libraries from time-course human and mammalian iPSCs(microglia precursors and embryonic stem cells), an improvised version of Smartseq2
- Collaborated with Industrial partners in a cooperative project focusing on developmental cell fate specifications of the CNS
- Provided library prep and sequencing support in this project
- Implemented single-cell RNA seq(Smartseq3') and plate based ATAC-seq workflow for fast and robust profiling of chromatin accessibility
- Handled high-throughput liquid dispensing system (iDOT, ECHO)
- Conducted drop count test for different liquid reagents and assigned distinct liquid classes for them
- Experienced in utilizing High-Performance Computing (HPC) for large-scale data analysis and processing
- Co-authored a review article exploring the developments in the field of spatial and single technologies in exploring TMEs.
Project Associate-I
Sridhar Sivasubbu Lab, CSIR-IGIB
01.2022 - 12.2023
- Worked with an interdisciplinary team of collaborators consisting of clinical experts, molecular biologists and informaticians to execute population scale rare+genetic disorders screening project.
- Performed whole exome and whole genome library preparation, sequencing, and sequencing analysis from probands provisionally diagnosed for cardiac channelopathies
- Proficient in linux programming environment, and executing bioinformatic pipelines to analyze whole genome, exome sequencing data to fetch out putative variations and annotate them in accordance to the ACMG/AMP guidelines for the interpretation of variants
- Carried out Sanger Sequencing to confirm the variant segregation in proband and family members.
- Experienced in writing genetic reports.
- Spearheaded various genome sequencing projects
- Developed and optimized sequencing assays for rare-genetic disorders such as cardiac channelopathies, familial hypercholesterolemia, autoinflammatory diseases, and viral diseases such as the lumpy skin disease virus
- Have been a part of the GenomeIndia Program performing whole genome sequencing of self-declared healthy individuals from culturally diverse backgrounds in India.
- Have co+authored 4 publication in this role.
Graduate Student Researcher
Molecular Motors Lab, ASK-II, SASTRA deemed to be University
12.2018 - 05.2021
- Expressed target protein Eg5 through pET-21B construct in yeast model
- Employed basic molecular biology techniques such as primer design, PCR, cloning, transformation, gene expression, and protein purification to obtain protein
- Carried out ligand binding assays such as ITC-50 to check binding affinity of inhibitors to the allosteric binding pockets of the protein
- Developed a therapeutic peptide mimicking the role of hepcidins to treat FRDA patients suffering from iron dyshomeostasis
- Observed the stability and the ADME properties of this peptide through molecular dynamics simulation and various in-silico pharmacokinetic studies
- Fetched Frataxin-Hepcidin complex from PDB, extracted the hepcidin co-ordinates from the complex in PyMol, and used the structure to perform molecular docking and simulations
- Established structural similarities between different Kinesin Spindle Family Proteins involved in the metaphase to anaphase transition of the cell-cycle such as the Eg5, MKLP-I, MKLP-II and CENP-E to optimize the drug discovery process for cancer targets
Education
BTech+MTech. (Integrated 5 Yrs) - Biotechnology
SASTRA University
Thanjavur India 07.2016 - 06.2021
Skills
Bioinformatics skills:GATK best practices for WGS, WES, and RNA-Seq, DRAGEN workflow Building and customizing variant filtering pipelines for genomic variant discovery Linux programming environment Bioconductor, Seurat, vignettes such as scTransform, batch integration
Programming Languages: Linux programming, Python, R
Wet lab Skills: gDNA, RNA, and plasmid isolation from biological samples, cDNA preparation, zebrafish injections, gene-cloning, primer design, long-range PCR, library preparation techniques (WGS, WES, RNASeq, ATACseq, scRNA and scATAC seq plate-based), protein expression and purification
Project Planning, Collaborative mindset, Creative solutions, Report Writing, Organization skills, Collaborative mindset
Publications
- Whole genome sequencing of families diagnosed with cardiac channelopathies reveals structural variants missed by whole exome sequencing, Senthivel, V., Jolly, B., VR, A., et al., J Hum Genet, 2024, https://doi.org/10.1038/s10038-024-01265-2
- The genome sequence of lumpy skin disease virus from an outbreak in India suggests a distinct lineage of the virus, Bhatt, L., Bhoyar, R.C., Jolly, B., H.Vignesh, et al., Arch Virol, 2023, https://doi.org/10.1007/s00705-023-05705-w
- Scalable non-invasive amplicon-based precision sequencing (SNAPseq) for genetic diagnosis and screening of β-thalassemia and sickle cell disease using a next-generation sequencing platform, Pragya, et al., https://www.frontiersin.org/journals/molecular-biosciences/articles/10.3389/fmolb.2023.1244244/full
- Crosstalk between tumor and microenvironment: Insights from spatial transcriptomics. https://www.sciencedirect.com/science/article/pii/S0065230X24000277?dgcid=author
References
- Dr. Sridhar Sivasubbu PhD, Senior consultant, Viswananthan cancer care foundation, sridhar@igib.in, +91-9871780662
- Dr. Vinod Scaria PhD, Senior-consultant, Viswanathan cancer care foundation, vinods@igib.in, +91-9650466002
- Dr. Venkatasubramanian PhD, Associate Professor, SASTRA University, venkat@scbt.sastra.edu, +91-9443615312
Languages
Tamil
Native language
English
Proficient
C2
Danish
Beginner
A1
Timeline
Project Associate-I
Sridhar Sivasubbu Lab, CSIR-IGIB
01.2022 - 12.2023
Graduate Student Researcher
Molecular Motors Lab, ASK-II, SASTRA deemed to be University
12.2018 - 05.2021
BTech+MTech. (Integrated 5 Yrs) - Biotechnology
SASTRA University
07.2016 - 06.2021
Research Assistant
Technical University of Denmark
2 2024 - Current
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