Summary
Overview
Work History
Education
Skills
Publications
Timeline
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Mihika Sharma

Bioinformatics Scientist | Computational Biologist | Data Scientist
San Jose,CA

Summary

Committed to remaining at the forefront of computational biology by staying abreast of the latest advancements in genomics, bioinformatics, and data science. Demonstrated impactful contributions as a Bioinformatics Analyst, primarily focused on leveraging computational and analytical methodologies to bolster research initiatives in Biomedical Informatics (BMI) at Cincinnati Children's Hospital Medical Center. Skilled in the analysis of diverse genomic datasets, encompassing Single Cell RNA-Seq, Spatial Transcriptomic Data, Bulk RNA-Seq, and other Omics data. Recognized for effective communication and collaboration abilities, adept at bridging the gap between computational and biological spheres. Known for being a quick learner, readily adaptable to assimilating new technologies and methodologies.

Overview

8
8
years of professional experience
4
4
Languages

Work History

Sabbatical

Self Employed
01.2023 - Current

Took a deliberate gap year to explore personal interests, focus on health and gain valuable life experiences. During this time:

  • Focused on physical and mental well-being
  • Learnt and honed skills for handmade products to harness creative skills
  • Launched a small business to sell handmade products
  • Gained important experience with business, marketing and customer-base
  • Contributed to fundraising with knitting for Children's Research
  • Developed strong communication and interpersonal skills through interactions with diverse communities


The sabbatical served as a transformative and productive period, providing insights to business, enhancing people skills and giving an outlet to creative side. Excited to bring the gained skills and enriched outlook to new professional opportunities.

Bioinformatics Analyst

Cincinnati Children's Hospital Medical Center
03.2020 - 12.2022
  • Conducted comprehensive analysis of multi-omics Next-Generation Sequencing (NGS) datasets, both in-house and publicly available, to support various research projects.
  • Applied single-cell analysis techniques to investigate ~40 cases of Idiopathic Pulmonary Fibrosis (IPF) and other disease states, aiming to unveil Gene Regulatory Networks (GRNs) for potential drug repurposing strategies.
  • Performed transcriptomic analysis on COVID-19 datasets to identify differential regulators implicated in disease progression.
  • Employed CellChat and Niche-Net methodologies to elucidate cell-cell communication patterns in IPF and other disease states, comparing them with wild-type conditions.
  • Utilized spatial single-cell and transcriptomic analyses in tandem to resolve the spatial-expression complexities of cells within the lung.
  • Implemented Weighted Gene Correlation Network Analysis (WGCNA) to identify significant modules of genes involved in expression-based network construction, particularly in Ulcerative Colitis and other disease models.
  • Integrated outputs from image analysis to derive gene correlation network regulations, contributing to a comprehensive understanding of cellular interactions and regulatory mechanisms.

Bioinformatics Research Assistant II

Cincinnati Children's Hospital Medical Center
02.2019 - 03.2020
  • Conducted single-cell RNA sequencing (scRNA-seq) to assess the induction of human stem cells through co-culturing human induced pluripotent stem cells (iPSCs) and mouse embryonic stem cells (ESCs), elucidating the cellular dynamics and gene expression changes involved in this process.
  • Employed organoid models to conduct multi-drug screening analyses, aiming to evaluate the efficacy and toxicity of various compounds and identify potential candidates for therapeutic intervention.
  • Investigated the lineage diversification within gastro-hepatic cells to develop in vitro model boundary organoids, leveraging single-cell RNA sequencing (scRNA-seq) techniques to characterize cell populations and their differentiation trajectories.
  • Analyzed SNP-Chip Microarray data obtained from pooled iPSC samples, identifying subpopulations harboring disease-associated Single Nucleotide Polymorphisms (SNPs) and discerning their potential implications in disease susceptibility and pathology.
  • Conduct experiments following research protocols, maintaining accurate records, and analyzing data for statistical insights.
  • Manage laboratory operations, troubleshoot equipment issues, and oversee inventory and cell cultures.
  • Serve as a knowledgeable resource within the department, fostering teamwork and providing excellent customer service to stakeholders.

Junior Programmer

GlaxoSmithKline Pharmaceuticals Pvt. Ltd.
07.2016 - 08.2018
  • Proficient in creating analysis datasets and generating Tables, Listings, and Figures from raw data, ensuring accuracy and compliance with study protocols.
  • Demonstrated comprehension of study design and related documents such as the Report and Analysis Plan (RAP) and Protocol.
  • Experienced in respiratory clinical data analysis across various domains including Adverse Events, Lab, Vital Signs, ECG, Concomitant Medications, and Subject Disposition.
  • Skilled in handling parallel, blinded, unblinded, and device studies, ensuring adherence to study protocols and regulatory requirements.
  • Developed SAS Macros to streamline processing and standardize code, enhancing efficiency in data analysis.
  • Actively involved in maintaining and updating the Web Forum, contributing to the enhancement of the website's functionality.
  • Recognized for innovation and collaboration, winning the in-house competition 'Innovation Growth League' for developing a drug dispensing device controlled by a Telegram bot, and contributing to AI processing for its development and training.
  • Received a Bronze recognition award for significant contributions to a high-priority study, showcasing dedication and excellence in work performance.

Education

Master of Science - Bioinformatics And Applied Biotechnology

IBAB
Bengaluru
07.2014 - 2016.07

Bachelor of Science - Biotechnology

Jaipur National University
Jaipur
07.2011 - 2014.07

Skills

    NGS Analysis

Publications

  • Development of an optimal machine learning model using treatment naïve diagnostic pathology images to predict steroid-free clinical remission at one year in pediatric Ulcerative Colitis, Gastroenterology [2023/4]

Jasbir Dhaliwal, Xiaoxuan Liu, Jim Reigle, Mihika Sharma, Oscar Lopez-Nunez, Tom Walters, Margaret Collins, Jeffrey Hyams, Iram Siddiqui, Lee Denson, Anil Jegga, Surya Prasath

  • Targeted Assessment of Mucosal Immune Gene Expression Predicts Clinical Outcomes in Children with Ulcerative Colitis, Journal of Crohn's and Colitis [2022/11]

Kathryn Clarkston, Rebekah Karns, Anil G Jegga, Mihika Sharma , Sejal Fox, Babajide A Ojo, Phillip Minar, Thomas D Walters, Anne M Griffiths, David R Mack, Brendan Boyle, Neal S LeLeiko, James Markowitz, Joel R Rosh, Ashish S Patel, Sapana Shah, Robert N Baldassano, Marian Pfefferkorn, Cary Sauer, Subra Kugathasan, Yael Haberman, Jeffrey S Hyams, Lee A Denson, Michael J Rosen

  • Unsupervised Gene Co-expression Network Analysis Identifies Gene Modules Associated With Villiform Changes and Remission in Ulcerative Colitis, Gastroenterology Conference [2022/5/1]

Jasbir Dhaliwal, Mihika Sharma , Margaret H Collins, Yael Haberman, Jeffrey S Hyams, Lee A Denson, Anil Jegga

  • Consensus Gene Co-Expression Network Analysis Identifies Novel Genes Associated with Severity of Fibrotic Lung Disease, International Journal of Molecular Sciences [2022/5/13]

Sudhir Ghandikota, Mihika Sharma , Harshavardhana H Ediga, Satish K Madala, Anil G Jegga

  • Computational workflow for functional characterization of COVID-19 through secondary data analysis, STAR Protocols [2021/12/17]

Sudhir Ghandikota, Mihika Sharma , Anil G Jegga

  • Secondary analysis of transcriptomes of SARS-CoV-2 infection models to characterize COVID-19, Patterns [2021/5/14]

Sudhir Ghandikota, Mihika Sharma , Anil G Jegga

Timeline

Sabbatical

Self Employed
01.2023 - Current

Bioinformatics Analyst

Cincinnati Children's Hospital Medical Center
03.2020 - 12.2022

Bioinformatics Research Assistant II

Cincinnati Children's Hospital Medical Center
02.2019 - 03.2020

Junior Programmer

GlaxoSmithKline Pharmaceuticals Pvt. Ltd.
07.2016 - 08.2018

Master of Science - Bioinformatics And Applied Biotechnology

IBAB
07.2014 - 2016.07

Bachelor of Science - Biotechnology

Jaipur National University
07.2011 - 2014.07
Mihika SharmaBioinformatics Scientist | Computational Biologist | Data Scientist