Hi there! My name is Siddharth Kaipa, and I graduated from UCSD this past June, with a major in Bioinformatics. I have always been passionate about genetics and its effects on everyday life. I want to spend my life helping people and making an impact around me, and I look forward to using this degree to help tackle diseases and make the world a healthier place!

Studying various aspects of bioinformatics, including biology, genetics, physiology, and computer science

UC San Diego

Assisted in researching and developing new Covid testing techniques, emphasizing viral load quantification and variant typing

*   Utilized SnapGene to identify mutations in diverse Covid sequence genomes, reducing data
*   Compartmentalization and enhancing comprehensive analysis of genetic variations
*   Conducted in-depth analysis of PCR probes to determine the specific variant types of Covid-19 for improved diagnostic accuracy

Bioinformatics Intern

Leading a senior design project focused on developing handmade probes and primers for Covid variant testing. Utilizing machine learning to generate probes and primers and comparing their effectiveness for accurate testing

*   Designing multiple probes for a portable PCR machine to enable precise and rapid at-home testing
*   Developing novel methods for PCR variant detection
*   Preparing research findings for publication in a scientific journal

Senior Design Project Leader

**Genomic Sequencing Data Analysis**
Preprocessed and analyzed genomic data to ensure sequence quality and integrity.
Applied FastQC for quality control, Sickle for read trimming, and conducted k-mer analysis using Jellyfish and Kmergenie to determine optimal parameters for genome assembly.
Assembled high-quality genomic data using Minia, optimizing parameters for accuracy.
**Variant Analysis and Population Genetics**
Analyzed genetic variations within human genomes to uncover population-specific structures and disease implications.
Extracted and analyzed ~5000 variants using bcftools and plink.
Performed PCA for genetic diversity insights, conducted GWAS with population structure adjustments to reduce biases, and utilized SNP clumping to identify independent genetic signals.
**Differential Gene Expression Analysis**
Analyzed RNA-seq data to identify differentially expressed genes under various conditions.
Retrieved and processed data from GEO, used DESeq2 in R for gene expression analysis, visualized alignments with Integrative Genomics Viewer, and performed Gene Ontology using PANTHER to reveal functional impacts of differential expression.
**Identification of Cancer-Related Genes through BED File Analysis**
Parsed BED files of cancer cell lines, converted a reference genome from GFF3 to BED format, and identified intersecting genes.
Compiled gene frequencies into a dictionary and studied their effects on cancer progression.
Successfully identified key genes with selective advantages, providing insights into their roles in cancer
**AlignFix: A High-Performance DNA Sequence Alignment Tool**
Developed AlignFix, leveraging suffix arrays and affine gap penalties for precise sequence alignment.
Packaged the tool for easy pip installation, benchmarked against BWA-MEM, and achieved an 83% alignment rate.

*   Successfully validated a high-performance tool surpassing BWA-MEM in speed and alignment percentage, making it accessible for the research community.

Student

Raised funds for a homeless shelter project

*   Wrote and designed a play highlighting the importance of hygiene products for homeless communities
*   Secured 2nd place in the State-level competition and participated in the Global competition

Nationally Ranked

Siddharth Kaipa

English

Bioinformatician

Post Doc

Programming

Adobe Illustrator

Python

UNIX

Linux

Data Analysis

Experience with one or more general purpose programming languages including but not limited to: Java, C/C++, C#, Objective C, Python, JavaScript, or Go.

Written Communication

MS Word

Data structures

Machine Learning

customer service

Data Visualization

Public speaking

Data Mining

Algorithm development

Statistical modeling

PowerPoint

Genomics

Bioinformatics

Laboratory research

script coverage

R programming

Next-Generation Sequencing

RNA seq

Communication

Conflict Resolution

Leadership

Time management

Self-motivated, strong work ethic and able to work independently with minimal supervision

Team player willing to learn new tasks

Interpersonal Skills

Ability to exhibit a positive, friendly and helpful attitude with customers and to be sensitive to their needs.

Siddharth Kaipa

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