JAYARAM KANCHERLA

Sr. Research Software Engineer, Engineering Lead

South San Francisco, US.

About

Highly accomplished Senior Research Software Engineer and Engineering Lead with extensive experience in bioinformatics, specializing in full-stack development of high-performance web applications for genomic and multi-modal single-cell datasets. Proven leader in designing scalable systems, integrating AI/ML models, and delivering intuitive scientific user experiences to computational biologists and analysts. Expert in Python, JavaScript, and R, with a strong track record of developing open-source tools and driving data-driven insights for complex scientific challenges.

Work

Genentech Research and Early Development (gRED), A Member of Roche Group

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Sr. Research Software Engineer, Engineering Lead

South San Francisco, CA, US

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Summary

Led the full-stack engineering and development of high-performance web applications for bioinformatics, integrating AI/ML models and harmonizing diverse datasets to deliver scalable scientific user experiences.

Highlights

Led engineering initiatives to develop scalable and interactive applications for indexing, searching, and harmonizing public and internal collections of multi-modal single-cell datasets.

Spearheaded the integration of interactive analytical workflows and AI/ML models across extensive multi-modal dataset collections, enhancing data utility for biologists.

Developed and launched open-source interactive exploratory tools, including Kana (https://github.com/kanaverse), for browser-based analysis and visualization of multi-modal single-cell datasets utilizing WebAssembly.

Directed Python development efforts at gRED to enable Bioconductor workflows and establish language-agnostic data storage systems, with significant contributions open-sourced in BiocPy (https://github.com/biocpy).

University of Maryland

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Faculty Specialist

College Park, MD, US

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Summary

Advanced bioinformatics tools and methodologies as a Research Software Engineer at the Center for Bioinformatics and Computational Biology, leading software engineering initiatives for omic dataset visualization.

Highlights

Led software engineering initiatives for the creation of reusable web components and systems, enabling interactive visual analysis of genomic and genetic datasets.

Developed and maintained Epiviz (http://www.epiviz.org) for interactive visualization of genetic and epigenetic datasets, enhancing research capabilities.

Created the Metaviz (http://www.metaviz.org) suite of tools specifically designed for metagenomic analyses, expanding data interpretation capabilities.

National Center for Computational Toxicology (NCCT), U.S. Environmental Protection Agency

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Oakridge Science Research Fellow

Durham, NC, US

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Summary

Developed interactive dashboard systems and data mining processes to visualize and update High Throughput Screening (HTS) data for the ToxCast program.

Highlights

Developed interactive dashboard systems for exploring and visualizing High Throughput Screening (HTS) data from the ToxCast program, improving data accessibility.

Engineered robust data mining processes to continuously update toxicity and compound information from thousands of sources within the ACTOR database, ensuring data currency and reliability.

National Center for Environmental Assessment (NCEA), U.S. Environmental Protection Agency

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Student Research Trainee

Arlington, VA, US

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Summary

Collaborated with the US Census & sustainable communities to develop a platform for sharing environmental data and facilitating sustainable decision-making.

Highlights

Identified key use cases and co-created an ideation platform to engage stakeholders and communities in making sustainable environmental decisions.

Developed interactive tools to visualize shared environmental data, enhancing public access and understanding of critical information.

Education

North Carolina State University

Raleigh, NC, United States of America
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Masters Computer Science

V.R. Siddhartha Engineering College, Affiliated to Nagarjuna University

Vijayawada, Andhra Pradesh, India
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Bachelors Computer Science and Engineering

Publications

metavizr: R Interface to the metaviz web app for interactive metagenomics data analysis and visualization

Bioconductor

An R package providing an interface to the Metaviz web application for interactive metagenomic data analysis and visualization.

epivizrChart: R interface to epiviz web components

Bioconductor

An R package providing an interface to Epiviz web components for interactive genomic data visualization.

epivizr: R Interface to epiviz web app

Bioconductor

An R package facilitating interaction with the Epiviz web application for genomic data analysis and visualization.

epivizrStandalone: Run Epiviz Interactive Genomic Data Visualization App within R

Bioconductor

An R package that enables running the Epiviz Interactive Genomic Data Visualization App directly within the R environment.

Skills

Programming Languages

JavaScript, Python, R, Golang.

Data Management

Neo4j, MySQL, DuckDB.

Web Frameworks & Technologies

React, d3Js, Lit (Web components), WebGL, WebAssembly.

DevOps & Cloud

Terraform, AWS.

Bioinformatics & Genomics

Single-Cell RNA-seq analysis, Genomic Data Visualization, Epigenetic Data, Metagenomic Analysis, Bioconductor Workflows, Omic Datasets, High Throughput Screening (HTS).

Software Engineering

Full Stack Development, Scalable Applications, Backend Systems, Web Components, Open Source Development, AI/ML Integration, Data Mining, System Design.

Projects

Kana: Single-Cell RNA-seq analysis in the browser

Summary

An application designed for single-cell RNA-seq analysis directly within the web browser.

scTreeViz: Interactive Hierarchical exploration of single cell RNA-seq expression datasets

Summary

A tool for interactive hierarchical exploration of single-cell RNA-seq expression datasets.

Epiviz File Server: Query and Transform directly from indexed genomic files

Summary

A file server designed to query and transform data directly from indexed genomic files.

Epiviz Feed: Proactive interactive and statistical visualization of genomic data

Summary

An application for proactive, interactive, and statistical visualization of genomic data, specifically for cancer epigenetics.

CDGnet: Network visualization for precision medicine

Summary

A network visualization tool for precision medicine applications.

Epiviz Components: Web Components for interactive visualization of genomic data

Summary

A collection of web components, including Epiviz Chart and an R package, for interactive genomic data visualization.