Nandeeni Suryawanshi

Nandeeni Suryawanshi

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Bioinformatics Associate | Graduate Student of Bioinformatics at Northeastern University
Augusta, Georgia, United States
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Jobs verified_user 0% verified
  • I
    Bioinformatics Research Associate
    Immunology Center of Georgia AU
    Sep 2024 - Current (2 years 1 month)
    • Led biomarker and therapeutic target discovery in sarcoidosis by integrating multi-omics datasets (Olink proteomics, lipidomics, bulk RNA-seq, and single-cell TCR/RNA-seq), uncovering disease associated signatures and immune dysregulation patterns.
    • Designed and implemented automated NGS data processing pipelines using Nextflow, Snakemake, and GATK, enabling high-throughput variant calling and accelerating biomarker identification across oncology and rare disease studies.
    • Developed and deployed scalable, end-to-end data pipelines using Python, SQL, and AWS (EC2, S3), reducing processing time and improving reproducibility and scalability for large healthcare and genomics datasets.
    • Applied differential expression analysi
  • Regeneron
    Computational Biologist Co-op
    Regeneron
    Jan 2024 - Aug 2024 (8 months)
    • Designed and implemented a robust MySQL-backed RNA-binding protein (RBP) motif database by integrating public and proprietary datasets, enhancing accessibility for regulatory genomics studies.
    • Improved the performance and usability of the Splice Variant Atlas (SVA) web portal using Flask and AWS, increasing data visualization efficiency and end-user engagement.
    • Built a scalable Python-based pipeline leveraging RBPmap to quantify the effects of genetic variants on RBP binding affinity, enabling high-throughput variant impact analysis.
    • Conducted transcriptome-wide analysis of the GHS liver dataset to assess the influence of genetic variants on splicing mechanisms and gene expression modulation.
    • Executed comprehen
  • Regeneron
    Data Scientist - Bioinformatics
    Regeneron
    Jan 2024 - Aug 2024 (8 months)
    • Led large-scale analysis of exome sequences using Hail, BGEN, and GATK, identifying novel loss-of-function variants associated with lipid metabolism and Type 2 diabetes across diverse populations.
    • Designed and deployed custom data pipelines in Python to process terabyte-scale genotype–phenotype datasets on Google Cloud Platform (GCP), reducing variant processing time.
    • Performed Genome-Wide Association Studies (GWAS) using UK Biobank and internal datasets, uncovering statistically significant gene–disease associations to support early drug target validation.
    • Prioritized rare, pathogenic variants by integrating PolyPhen-2, CADD, and REVEL scores, supporting functional validation efforts for antibody-based therapies.
  • Northeastern University
    Instructional Assistant
    Northeastern University
    Aug 2023 - Dec 2023 (5 months)
  • The Janssen Pharmaceutical Companies of Johnson Johnson
    Data Scientist
    The Janssen Pharmaceutical Companies of Johnson Johnson
    May 2023 - Jul 2023 (3 months)
    • Standardized and harmonized large-scale clinical genomics datasets—including NGS, EHR, and medical imaging—using FHIR standards and the OMOP Common Data Model (CDM) to enhance real-world evidence (RWE) analytics and regulatory reporting.
    • Conducted graph-based modeling of molecular pathways and disease networks using igraph and tidygraph, generating actionable insights for drug repurposing across immunology and oncology therapeutic areas.
    • Automated high-throughput variant annotation pipelines using Ensembl VEP, ClinVar, and gnomAD, ensuring compliance with CLIA/CAP standards and improving genomic data throughput and accuracy.
    • Ensured reproducible bioinformatics workflows by using GitHub for version control and structur
  • Johnson Johnson Innovative Medicine
    Data Scientist
    Johnson Johnson Innovative Medicine
    May 2023 - Jul 2023 (3 months)
    • Analyzed high-throughput mass spectrometry-based proteomics datasets using R to uncover novel therapeutic targets for acute myeloid leukemia (AML), supporting data-driven drug discovery.
    • Performed differential expression analysis using DESeq2 to compare NPM1 mutant vs. non-mutant AML patient samples, identifying candidate biomarkers for precision medicine.
    • Integrated organoid and cell line datasets and developed two interactive RShiny dashboards on Domino Data Lab, enabling real time exploration of AML proteomics data.
    • Compiled in-depth target evaluation reports utilizing biomedical databases such as MGI, cBioPortal, BloodSpot, Human Protein Atlas, and UniProt to inform experimental prioritization.
    • Collaborated
  • Springer Nature
    Editorial Associate
    Springer Nature
    Jul 2019 - Jan 2022 (2 years 7 months)
    • Reviewed biomedical manuscripts for scientific integrity and formatting accuracy, ensuring 95% adherence to submission standards.
    • Managed peer-review logistics, communications, and reviewer performance tracking using custom editorial tools.
    • Analyzed backlog trends and optimized review timelines through internal reporting, reducing manuscript turnaround time.
    • Produced detailed documentation of editorial workflows and standard operating procedures, improving operational consistency across departments.
    • Created Tableau-based visual summaries of editorial performance, supporting leadership in decision-making and planning.
    • Maintained databases for reviewer payments and author records, ensuring secure and accur
Education verified_user 0% verified
  • Northeastern University
    Master of Science - MS, Bioinformatics
    Northeastern University
    Jan 2022 - Current (4 years 9 months)
    Courses taken: Bioinformatics Methods (section 1 and 2) Bioinformatics Programming Introduction to Data mining and machine learning Professional Development for co-op Ethics in Biological Research The Biotechnology Enterprise
  • Savitribai Phule Pune University
    Msc, Microbiology, General
    Savitribai Phule Pune University
    Jan 2017 - Dec 2019 (3 years)
  • Savitribai Phule Pune University
    Bachelor of Science, Microbiology, General
    Savitribai Phule Pune University
    Jan 2014 - Dec 2017 (4 years)
Projects (professional or personal) verified_user 0% verified
  • M
    Machine Learning Project - Heart Failure Prediction
    Oct 2023 - Dec 2023 (3 months)
    • Employed k-NN, Naive Bayes, and Random Forest models to predict heart failure survival.
    • Implemented robust data preprocessing techniques and k-fold cross-validation for reliable model assessment.
    • Achieved competitive model accuracy and precision through meticulous evaluation, highlighting expertise in healthcare analytics. Dataset Information: https://archive.ics.uci.edu/dataset/519/heart+failure+clinical+records
  • D
    Developed a pipeline for Listeria monocytogenes bacteria to analyze DNA seq and RNA seq raw data
    Oct 2022 - Dec 2022 (3 months)
    • Performed Genome assembly from DNA-seq data. (Trimmomatic, Spades, Quast)
    • Performed Transcriptome assembly from RNA-seq data. (Trinity)
    • Annotated Genes using BLAST, Transdecoder, pfamScan tools.
    • Protein function prediction by using KEGG API.
  • S
    Study of AM biodiversity associated with Xerophytes and study its effects on water intensive plant (Wheat)
    Oct 2018 - Mar 2019 (6 months)
    • Studied the biodiversity of AM fungi associated with the Xerophytes and isolated and Identified AM Fungal species.
    • Produced Mass Inoculum using Maize as host plant and checked its effects on Wheat crop.
    • Also studied the use of AM inoculum for cultivation under water stress conditions. (Pot experiment)