PrimeOmicX, LLC

Bioinformatics × Applied AI Practice

Arun Boddapati · Founder & Principal

Executive Summary: PrimeOmicX is an independent computational biology practice closing the gap between data generation and deployed intelligence. Backed by 9 years of omics research and pipeline engineering at NIH/NIAID, Emory University, and the CDC National Wastewater Surveillance System, we provide single-expert accountability across reproducible pipelines, clinical variant agents, and private on-device language models.

§ 01 · Practice Areas & Capabilities

Omics Analysis

From raw data to publication-ready figures, with the methods, code and environment needed to reproduce them.

WGS / WESBulk & single-cell RNA-seqATAC / ChIP / methylationMetagenomics

Pipeline Engineering

Production-grade Nextflow, Snakemake and WDL workflows that run the same on a laptop, a SLURM cluster and the cloud.

Nextflow / nf-coreSnakemakeWDLContainers

Agentic RAG Systems

Question answering over your papers, protocols, LIMS and results, grounded in citations and deployable on-prem.

Hybrid retrievalLive database toolsCitationsEvaluation

AI Agents

Tool-using agents that run analyses, triage QC failures, draft reports and file the paperwork, with humans in the loop.

Pipeline operatorsQC triageReport draftingMCP tools

On-device AI Models

Small language models, around 3B parameters, fine-tuned on your domain and running on Apple Silicon. No data leaves the machine.

~3B parametersFine-tuningMLX / llama.cpp / Core MLOffline

Codaris (Nextflow Workbench)

Tool

Proprietary deterministic Nextflow DSL2 / nf-core engineering environment with automated module resolution, lint loops, and container testing.

DSL2nf-coreLangGraph

§ 02 · Selected Track Record & Peer-Reviewed Research

Aquascope

CDC · National Wastewater Surveillance System

Principal architect of the national SARS-CoV-2 wastewater genomic surveillance pipeline, versions 1.0 to 3.1. Published in Emerging Infectious Diseases, 2025.

github.com/CDCgov/aquascope ↗

KIF5A plasma proteomics

Emory School of Medicine · Pant Lab

Targeted plasma proteomics using the multiplex NULISA platform to uncover biomarker signatures in KIF5A-linked SPG10 and ALS spectrum disorders. Published in Human Genetics and Genomics Advances, 2026.

PubMed: 40873038 ↗

AIVA clinical benchmarking

Mamidi Health

Benchmarked agentic ACMG variant classification, co-authored the preprint evaluation study, and guided product direction and go-to-market strategy.

Preprint PDF ↗

IMPACC immune transcriptomics

Emory National Primate Research Center

Lead bioinformatician on a 5,000-patient study across 15 centres; built the QC and processing pipeline on AWS with Snakemake. Cell Reports Medicine and Nature Communications.

Baricitinib in rhesus macaques

Emory National Primate Research Center

Co-first author on the Cell 2021 single-cell and CITE-seq study of lower-airway inflammation in SARS-CoV-2 infection.

Analysis code ↗

Clinical exome pipeline

NIH / NIAID Clinical Sequencing Initiative

Whole-exome variant calling and automated QC for 1,200 clinical patients.

github.com/arunbodd/NIAID ↗

§ 03 · Core Platforms & Execution Environments

Pipelines & Workflow: Nextflow (DSL2 / nf-core), Snakemake, WDL, nf-test · Omics & Multi-Omics: GATK, DeepVariant, STAR, Salmon, DESeq2, Seurat, Scanpy, NULISA, MACS3 · AI & Models: Claude Agent SDK, LangGraph, Model Context Protocol (MCP), PyTorch, MLX, llama.cpp, Core ML · Infrastructure: SLURM, AWS Batch, Google Cloud, Docker, Apptainer, Seqera Platform, Apple Silicon (M1–M4).

§ 04 · Engagement Structures & Guarantees

Project

Fixed scope, fixed price, defined deliverables. Best for a dataset to analyse, a pipeline to build, or a model to ship.

Typically 2 to 12 weeks

Embedded

One senior bioinformatician on a monthly retainer, in your Slack and your repository, with weekly planning.

Monthly, cancel any time

Advisory & training

Architecture reviews, pipeline audits and hands-on workshops on Nextflow, single-cell analysis, agents and MLX.

Half-day to one week