Neelakshi Soni
Ontario,CA
Summary
A driven and passionate Programmer Analyst with 8+ Years of robust background in data analysis, particularly within the healthcare and banking sectors. With expertise in integrations and analyzing complex multi-omics datasets, I have played a key role in pioneering research on Alzheimer’s disease at UCLA, utilizing spatial transcriptomics to unlock deep insights into disease mechanisms. My dedication to advancing healthcare research is reflected in my leadership in developing computational methods and creating dynamic data visualization tools to enhance disease understanding and treatment strategies. As a self-motivated professional, I have consistently improved operational and clinical performance metrics, demonstrating a strong ability to synthesize cross-functional team inputs into actionable insights.
Overview
10
10
years of professional experience
Work History
Applications Programmer 2
Semel Institute for Neuroscience & Human Behavior
03.2024 - Current
- Spearheaded the integration and analysis of multi-omics datasets, including genomics, proteomics, and transcriptomics, specifically focusing on Alzheimer's disease models to uncover molecular mechanisms and biomarkers.
- Collaborated with cross-functional teams comprising biologists, data scientists, and clinicians to synthesize findings from spatial transcriptomics with other omics data, driving forward the research into Alzheimer’s disease progression and potential therapeutic targets.
- Created intuitive data visualization tools and interactive dashboards that allow for the dynamic exploration of complex biological data, thereby facilitating deeper insights into Alzheimer’s disease mechanisms.
Programmer Analyst 2
Geschwind Lab, AMRF Functional Genomics Common Research Resource at David Geffen School of Medicine at UCLA
09.2023 - 03.2024
- Designed, executed and analyzed spatial transcriptomics experiments, including sample preparation, library construction, sequencing.
- Developed and optimized protocols for spatially resolved transcriptomic analysis, leveraging techniques such as spatially barcoded RNA sequencing (SBS-seq), spatial transcriptomics imaging, and single-cell spatial transcriptomics.
- Performed data analysis and interpretation to identify spatially distinct gene expression patterns and cellular interactions within tissues.
- Contributed to the development of novel computational methods and analytical pipelines for spatial transcriptomics data analysis.
- Integrated and harmonized multi-omic data from diverse experimental platforms to identify correlations and associations between different molecular layers.
- Performed statistical analysis and data mining to identify patterns, biomarkers, and biological pathways underlying complex biological phenomena.
Graduate Student Researcher
Green Lab, University of California, Irvine
06.2018 - 06.2023
- Effectively communicated computational research findings through presentations; authored peer-reviewed scientific articles; and collaborated with interdisciplinary teams to develop clear and accessible reports on the impact of genetic diversity on disease susceptibility.
- Collaborated with external partners at JAX to integrate omics data to develop a custom transcriptome for data analysis; enable seamless analysis for a collaborative research project; and actively contributed to lab meetings, providing valuable feedback on experimental design.
- Demonstrated problem-solving proficiency by developing pipelines and automated algorithms to characterize microglial transcriptional profiles across neurodegenerative diseases; resolving data quality issues in large-scale genomics datasets; and utilizing statistical analysis techniques and data visualization to uncover significant gene expression patterns for potential therapeutic targets.
- Demonstrated adaptability by quickly acquiring proficiency in Python and R, developing custom computational pipelines for high-throughput sequencing data analysis; successfully adjusting workflows and allocating resources to meet changing project priorities and timelines; and proactively integrating new bioinformatics tools and methodologies, enhancing data analysis capabilities and optimizing research efficiency.
- Conducted thorough quality control assessments on genomics datasets, implemented rigorous statistical validation methods, and maintained meticulous documentation to ensure data integrity, robust computational predictions, and reproducibility.
- Orchestrated multiple concurrent projects with strict deadlines, coordinating experimental design, data analysis, and reporting across diverse research teams; prioritized tasks based on objectives and urgency, optimizing time and resource allocation for timely completion; and leveraged project management tools to track progress, identify bottlenecks, and streamline workflows, fostering improved efficiency and productivity.
- Facilitated collaborations, fostering a positive team environment with open communication and knowledge sharing; and led the development and implementation of a standardized bioinformatics pipeline as the primary bioinformatician, improving data processing efficiency and reproducibility.
Intern
Alchem International PVT. LTD.
06.2015 - 08.2015
- Developed expertise in pharmacological product management and manufacturing, demonstrating proficiency in coordinating and overseeing the production process, quality control, and regulatory compliance.
- Applied strong production logistics skills to optimize supply chain operations, ensuring timely and efficient delivery of materials, components, and finished products, while minimizing costs and maintaining quality standards.
- Exhibited collaborative competency by effectively communicating with cross-functional teams, adapting to dynamic environments, resolving conflicts constructively, and applying creative problem-solving skills to drive successful outcomes in biotechnological operations.
Education
Ph.D. - MCSB, Center of Complex Biology
University of California, Irvine
Irvine, CA09-2023
Bachelor of Technology - Biotechnology
Vellore Institute of Technology
Vellore, India07-2017
Skills
- Language: Python, C, R, SQL, SAS
- Statistical Methods:Hypothetical Testing, ANOVA, Time Series
- Machine Learning:Regression analysis, Bayesian Method, Decision Tree, Random Forests, Support Vector Machine, Neural Network, Sentiment Analysis, K-Means Clustering, KNN, Classification, SVM, Naive Bayes, Natural Language Processing (NLP), LLM, CNN, XGBoost
- Packages: NumPy, Pandas, Matplotlib, SciPy, ggplot2, Scikit-Learn, PyTorch, TensorFlow, Keras, Spark
- Visualization/Other Tools:Tableau, Power BI, Jira, Microsoft Excel Cloud Technologies: AWS, GCP Database: MySQL, SQL Server, Oracle, MongoDB
- Software/Other Skills:Data Cleaning, Data Wrangling, Critical Thinking, Communication Skills, Presentation Skills, Problem-solving, Decision-Making, EDA, Communication Skills, Databricks, Data Visualization, Predictive Analytics, Pattern Recognition, JMP, Data Integrity, Quantitative Data, Data Science, Statistics, Statistical Analysis, Data Analytics, Data Modeling, Big Query, Snowflake
- Laboratory Skills: PCR and Gel Electrophoresis, Protein, and Microglial RNA Isolation, Western blot (whole brain and cell lysate), Immunohistochemistry, MSD assays, Microtome sectioning, Mouse handling, and tissue harvesting, Confocal and slide scanner Microscopy, Image analysis via Bitplane Imaris, and Image J
- Operating System: Windows, Linux
Professional and Outreach Affiliations
- UCI Graduate Professional Success in STEM (UCI-GPS-STEM)
- UCI California State Summer School for Mathematics and Science (UCI COSMOS)
- University of California Institute for Memory Impairments and Neurological Disorders (UCI MIND)
- Research and Education in Memory Impairments and Neurological Disorders (ReMIND)
- Diverse Educational Community and Doctoral Experience (DECADE)
- Mentoring Excellence Program (MEP)
Publications
1. Soni N, Hohsfield LA, Tran KM, et al. Genetic diversity promotes resilience in a mouse model of Alzheimer's disease. Alzheimer's Dement. 2024; 1-23. https://doi.org/10.1002/alz.13753
2. Hanningfield CM, Arreola MA, Soni N, Spangenberg EE, Green KN. Microglia-specific ApoE knock-out does not alter Alzheimer's disease plaque pathogenesis or gene expression. Glia. 2022 Feb;70(2):287-302. doi: 10.1002/glia.24105. Epub 2021 Oct 13. PMID: 34643971; PMCID: PMC9308171.
3. Hohsfield LA, Najafi AR, Ghorbanian Y, Soni N, Crapser J, Figueroa Velez DX, Jiang S, Royer SE, Kim SJ, Hanningfield CM, Anderson A, Gandhi SP, Mortazavi A, Inlay MA, Green KN. Subventricular zone/white matter microglia reconstitute the empty adult microglial niche in a dynamic wave. Elife. 2021 Aug 23;10: e66738. doi: 10.7554/eLife.66738. PMID: 34423781; PMCID: PMC8425950.
4. Arreola MA, Soni N, Crapser JD, Hohsfield LA, Elmore MRP, Matheos DP, Wood MA, Swarup V, Mortazavi A, Green KN. Microglial dyshomeostasis drives the perineuronal net and synaptic loss in a CSF1R+/- mouse model of ALSP, which can be rescued via CSF1R inhibitors. Sci Adv. 2021 Aug 25;7(35): eabg1601. doi: 10.1126/sciadv. abg1601. PMID: 34433559; PMCID: PMC8386924.
5. Crapser JD, Ochaba J, Soni N, Reidling JC, Thompson LM, Green KN. Microglial depletion prevents extracellular matrix changes and striatal volume reduction in a model of Huntington's disease. Brain. 2020 Jan 1;143(1):266-288. doi: 10.1093/brain/awz363. Erratum in: Brain. 2020 Mar 1;143(3): e24. PMID: 31848580; PMCID: PMC6935750.
6. Hohsfield LA, Najafi AR, Ghorbanian Y, Soni N, Hingco EE, Kim SJ, Jue AD, Swarup V, Inlay MA, Green KN. Effects of long-term and brain-wide colonization of peripheral bone marrow-derived myeloid cells in the CNS. J Neuroinflammation. 2020 Sep 20;17(1):279. doi: 10.1186/s12974-020-01931-0. PMID: 32951604; PMCID: PMC7504855.
7. Henningfield CM, Soni N, Lee RW, Sharma R, Cleland JL, Green KN. Selective targeting and modulation of plaque-associated microglia via systemic hydroxyl dendrimer administration in an Alzheimer's disease mouse model. Alzheimers Res Ther. 2024 May 6;16(1):101. doi: 10.1186/s13195-024-01470-3. PMID: 38711159; PMCID: PMC11071231.
Timeline
Applications Programmer 2
Semel Institute for Neuroscience & Human Behavior
03.2024 - Current
Programmer Analyst 2
Geschwind Lab, AMRF Functional Genomics Common Research Resource at David Geffen School of Medicine at UCLA
09.2023 - 03.2024
Graduate Student Researcher
Green Lab, University of California, Irvine
06.2018 - 06.2023
Intern
Alchem International PVT. LTD.
06.2015 - 08.2015
Ph.D. - MCSB, Center of Complex Biology
University of California, Irvine
Bachelor of Technology - Biotechnology
Vellore Institute of Technology
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