Siri Thatavarthy
Broomfield,CO
Summary
Detail-oriented Researcher with hands-on experience performing computational and laboratory work to advance research goals.
Overview
5
5
years of professional experience
Work History
Professional Research Assistant
Dr. Halil Aydin's Lab (CU Boulder)
06.2023 - Current
- Designed precise PCR primers for site directed mutagenesis, showcasing a meticulous approach to genetic modifications and ensuring accuracy in experimental results.
- Conducted extensive experiments using cutting-edge methodologies including Size exclusion chromatography (Supersose6, Superdex200), Ion exchange chromatography and His column affinity chromatography.
- Established and maintained insect cell lines for protein expression using baculovirus expression systems.
- Transfected insect cells with cloned genes, optimized conditions for efficient expression, and scaled up cell cultures for protein production and purification.
- Played a key role in the preparation of negative stain and cryo-EM grids, showcasing sample preparation for structural studies.
- Applied advanced software tools such as CryoSPARC and RELION to process and analyze cryo EM data analysis, contributing to the lab's proficiency in high-resolution structural analysis.
- Employed tools such as PyMOL and ChimeraX to conduct docking studies, explore protein-protein interactions, and visualize and manipulate three-dimensional protein structures.
- Developed and optimized computational pipelines, streamlining data analysis processes for increased efficiency and accuracy.
Research Associate II
Laronde Inc.
09.2021 - 05.2022
- Design, cloning and generate pooled RNA libraries for downstream high-throughput functional screens.
- Analyzing NGS data – (e.g; Illumina and PacBio) for quality control of pooled libraries.
- Apply commercial Illumina kits (Nextera XT, Trueseq)or custom amplicon-sequencing strategies to prepare NGS libraries.
- Performed nested PCRs and bacterial transformations, troubleshoot primer design, readied products for DNA sequencing.
- Developed Computational Pipelines for barcode sequencing and discovery of DNA/RNA libraries from Illumina, Pac Bio and Nanopore datasets.
- Demonstrated Experience with AWS Cloud technologies.
- Applied complex chromatography techniques such as anion exchange chromatography, oligoDT and reverse purification to remove impurities from nucleic acid.
- Maintain open and active communication with managers and reports regarding workflow, issues, and opportunities for improvement.
- Experience with handling the Hamilton Automation for fully automated workflows such as DNA Digestions and In Vitro Transcription (IVT).
Graduate Researcher
Dr. Yuzhen Ye's Lab (IUB)
10.2019 - 05.2021
- Worked on a computational pipeline that predicts putative anti-CRISPR genes in a genome, applying existing tools to predict CRISPR- Cas systems and prophage regions.
- Implemented various data mining methods such as supervised, unsupervised, and dimensionality reduction techniques on microarray gene expression data (brain cancer dataset).
- Applied clustering, deep learning techniques, and unsupervised manifold alignment algorithm (MMD- MA) on scRNA- seq and scATAC- seq data.
- Executed spectral clustering methods on Yeast proteins for DIP (Database of interacting proteins) to find functional modules in protein interacting networks.
Education
Master of Science - Bioinformatics
Indiana University Bloomington
Bloomington, IN05.2021
Bachelor of Science - Biotechnology
Sir M Visvesvaraya Institute of Technology
India07.2018
Skills
Wet Lab Skills
- Molecular Biology Lab Techniques: RT-qPCR/ddPCR, Western Blotting, Southern Blotting, ELISA, In Vitro Transcription (IVT), DNA Digestions, Agarose gel Electrophoresis, SDS PAGE, DNA extraction and Purification, Recombinant DNA expression and purification, Fragment Analyzer
- Purification of RNA using AKTA, FPLC, AEX (Gilson)and HPLC
- Purification of Protein using Size Exclusion, Anion Exchange and His column affinity chromatography
- Microbiology Lab Techniques: Streaking, Inoculation, Gram staining, Serial dilution, Bacterial Transformations,
- Cell Culture Techniques: Insect cell culture, Mammalian cell culture of common immortalized cell lines, FACS
- High-throughput sequencing library preparation
- Polysome Profiling using Sucrose Gradient
- Preparing negative stain and cryo-EM grid, showcasing sample preparation
- Trained on Transmission Electron Microscopy and cryo-Electron Microscopy
Dry Lab Skills
- Programming Languages: Python, R- Programming, Bash, SQL
- Platforms: Windows, Linux, MacOS
- Sequencing Data Analysis: Illumina, Pac Bio, Sanger, Nanopore
- Bioinformatics Tools: Samtools, PYMOL, Discovery studio, Spdbv, Hexdock, Chimerax, MEGA-X, RCSB PDB, Phylogenyfr, BLAST, Megahit, CRISPRone, FragGeneScan, Virsorter2, Phaster, Diamond, Bowtie2, CD-HIT, Alphafold2, SnapGene
- File Formats: FASTQ, FASTA, FNA, BAM, SAM, CRT, M8
- Machine Learning: Supervised Algorithms (SVM, Linear Regression, etc), Unsupervised Algorithms ( kmeans, hierarchical, etc), Spectral Clustering (PCA, tSNE, UMAP) sklearn, scanpy, scAlign, Deep Learning ( Convolutional Neural Networks)
- AWS Cloud Computing
- Use of advanced tools such as RELION and CRYOSPARC to perform cryo-EM data analysis
Timeline
Professional Research Assistant
Dr. Halil Aydin's Lab (CU Boulder)
06.2023 - Current
Research Associate II
Laronde Inc.
09.2021 - 05.2022
Graduate Researcher
Dr. Yuzhen Ye's Lab (IUB)
10.2019 - 05.2021
Master of Science - Bioinformatics
Indiana University Bloomington
Bachelor of Science - Biotechnology
Sir M Visvesvaraya Institute of Technology
Similar Profiles
Shaughnessy DunnShaughnessy Dunn
Spectrograph Design & Agile Software Development at Astronomical Instrumentation Lab - CU BoulderSpectrograph Design & Agile Software Development at Astronomical Instrumentation Lab - CU Boulder
Ben StearnsBen Stearns
Tutor at CU Boulder and Boulder High SchoolTutor at CU Boulder and Boulder High School
Chandanie WijesekaraChandanie Wijesekara
Lead Teacher at CU Childrens Center CU BoulderLead Teacher at CU Childrens Center CU Boulder