Nishant Panwar
Somerville
Summary
Accomplished Senior Bioinformatics Engineer at Generate:Biomedicines, specializing in designing cutting-edge NGS assays and creating scalable Python tools. Demonstrated expertise in enhancing data integrity and optimizing workflows through advanced machine learning techniques and effective collaboration. Acknowledged for implementing best practices and conducting impactful training sessions for multidisciplinary teams.
Overview
8
8
years of professional experience
Work History
Senior Bioinformatics Engineer I
Generate:Biomedicines
Somerville
07.2024 - Current
- Designed novel NGS-based assays with wet lab scientists to characterize multiplexed protein variant libraries.
- Established protocols for integrating analyzed assay data with data science and machine learning teams.
- Identified key assay variables, assessing their influence on phenotype discernment.
- Collaborated with Generate scientists to identify molecules for pharmaceutical applications.
- Codified best practices for NGS-based assays within Computational Biology team to enhance program consistency.
- Communicated assay capabilities and applications to multidisciplinary scientists and management.
- Evaluated project requirements, recommending suitable assays to meet research objectives.
- Developed scalable Python tools with schema validation using pydantic to ensure data integrity.
Bioinformatics Engineer
Generate:Biomedicines
Somerville
06.2022 - Current
- Orchestrated UMI-aware FASTQ processing pipelines for Oxford Nanopore, PacBio, and Illumina platforms.
- Designed workflows to resolve variants, mapping assay-specific features to phenotype clusters.
- Managed parallel runs and DAGs using Prefect for high-throughput QC and consensus generation.
- Collaborated with cross-functional teams to streamline product development processes.
Senior Associate Scientist II
2Seventy Bio
Cambridge
11.2021 - 06.2022
- Developed and maintained in-house production pipelines for analyzing high-throughput NGS data, including RNA-seq and WGS.
- Optimized scalable, parameterizable pipelines to ensure production readiness using workflow languages on AWS.
- Leveraged AWS to facilitate secure data transfer and scalable computational resources.
- Collaborated with researchers and data scientists to ensure informatics tools met scientific objectives.
- Delivered training sessions on pipeline usage, documentation, and troubleshooting for users.
- Presented analytical findings to internal and external stakeholders to support informed decision-making.
- Contributed to development of infrastructure and tooling for comprehensive analytics within data science team.
Bioinformatics Data Scientist
Precision BioSciences
Durham
08.2021 - 11.2021
- Designed assays for genome editing outcomes using computational approaches.
- Analyzed NGS data from GUIDE-Seq, SITE-Seq, One-Seq, and indel profiling.
- Developed custom tools to support various internal genomics projects.
- Created visual analytics dashboards to enhance genome editing workflows.
Bioinformatician
Velsera (formerly PierianDX)
St Louis
10.2019 - 07.2021
- Developed clinical bioinformatics solutions to enable personalized diagnostics using NGS and cloud computing frameworks.
- Productized workflows for Illumina TSO500, TST170, ArcherDX, SOPHiA, and Pillar Biosciences.
- Designed pipelines for read alignment, variant calling, annotation, and statistical analysis with varied tools.
- Contributed to software development utilizing Git-based version control and AWS for deployment.
- Built NoSQL and SQL integration layers for efficient data storage and reporting.
- Followed Agile methodologies and SDLC practices to enhance code quality and delivery.
Bioinformatics Scientist
MOgene LC
St. Louis
09.2017 - 10.2019
- Designed and maintained NGS pipelines for de novo assembly, RNA-seq, metagenomics, and 16S workflows.
- Delivered variant analysis tools for SNPs, indels, CNVs, and insertion sites.
- Processed sequencing data from Illumina and PacBio to support lab quality control.
- Optimized pipelines by troubleshooting low-quality datasets in collaboration with bench scientists.
- Provided clear technical reports and experimental insights based on collaborative efforts.
Education
MS - Bioinformatics
University of The Sciences in Philadelphia
Philadelphia, PA01.2017
MS - Biotechnology
Sardar Patel University
India01.2014
BS - Biotechnology
Sardar Patel University
India01.2012
Skills
- Programming languages: Python, R, BASH
- Data manipulation tools: Pydantic, Pandas, NumPy, Regex
- High throughput technology: Illumina, Oxford Nanopore, PacBio, mass spectrometry
- Machine learning frameworks: PyTorch, TensorFlow, scikit-learn
- Web technologies: Flask, Django, AWS (Batch, Lambda, S3, ECR, Step)
- Containerization and CI/CD: Docker, Jenkins, Bitbucket
- Genomic analysis tools: GATK, Samtools, STAR, BWA
- Bioinformatics utilities: Bedtools, Pindel, Freebayes
- Data visualization tools: Matplotlib, Seaborn, Streamlit
- Workflow management frameworks: WDL (Cromwell), CWL (Seven Bridges), Prefect
- Database systems: MongoDB, PostgreSQL
- Development methodologies: SDLC, Agile
Publications
Chroma: Contributor to generative protein design model (Nature, 2024)
Performed high-throughput pooled expression and solubility profiling of >300 de novo Chroma-designed proteins using a split-GFP fluorescence assay coupled with Oxford Nanopore long-read sequencing. Designed and executed the full wet- and dry-lab pipeline: DNA digestion, AMPure cleanup, barcode ligation (EXP-NBD104), and MinION sequencing using Bonito (basecalling) and Minimap2 (alignment). Developed a custom demultiplexing and quantification pipeline using SeqKit, samtools, and pysam to compute enrichment scores across FACS-sorted fluorescence bins. Implemented normalization strategies and bin-weighted scoring to resolve protein-level solubility phenotypes in a pooled format, enabling structure-function insights at scale. Supported three sequencing runs totaling >30M reads across unconditional and semantically conditioned designs.
BIO
I'm a Senior Bioinformatics Engineer with 8+ years crafting production-grade NGS and AI/LLM-driven pipelines, bridging bench and data science to accelerate protein/DNA design and assay development.
Timeline
Senior Bioinformatics Engineer I
Generate:Biomedicines
07.2024 - Current
Bioinformatics Engineer
Generate:Biomedicines
06.2022 - Current
Senior Associate Scientist II
2Seventy Bio
11.2021 - 06.2022
Bioinformatics Data Scientist
Precision BioSciences
08.2021 - 11.2021
Bioinformatician
Velsera (formerly PierianDX)
10.2019 - 07.2021
Bioinformatics Scientist
MOgene LC
09.2017 - 10.2019
MS - Bioinformatics
University of The Sciences in Philadelphia
MS - Biotechnology
Sardar Patel University
BS - Biotechnology
Sardar Patel University
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