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
2022.01 - 2023.12
- 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
2018.12 - 2021.05
- 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 2016.07 - 2021.06
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
2022.01 - 2023.12
Graduate Student Researcher
Molecular Motors Lab, ASK-II, SASTRA deemed to be University
2018.12 - 2021.05
BTech+MTech. (Integrated 5 Yrs) - Biotechnology
SASTRA University
2016.07 - 2021.06
Research Assistant
Technical University of Denmark
2 2024 - Current
Similar Profiles
Elizabeth Rees ChinElizabeth Rees Chin
PhD Fellow at Technical University Of Denmark (DTU)PhD Fellow at Technical University Of Denmark (DTU)
Babak RezaeiBabak Rezaei
Assistant Professor at Biomaterials and Microsystems group, DTU Nanolab, Technical University of DenmarkAssistant Professor at Biomaterials and Microsystems group, DTU Nanolab, Technical University of Denmark
Madhu VeettikazhyMadhu Veettikazhy
Postdoctoral Researcher at Technical University of DenmarkPostdoctoral Researcher at Technical University of Denmark