Siril Arockiam, Ph.D.

Siril Arockiam.

Ph.D. · Postdoctoral Research Scholar, Biodesign Institute, Arizona State University

I build computational systems for cancer immunogenomics, from GPU-accelerated sequence alignment to neoepitope discovery, grounded in wet-lab validation and cGMP industry experience.

GPU Genomics · Independent2025–26

GenoCache: learned-embedding long-read aligner

A learned encoder that aligns long reads at near-minimap2 speed, no hand-tuned seeds.

A GPU-accelerated alignment engine that replaces hand-tuned seeding with a lightweight learned encoder (0.5M params, 128-D embeddings) plus FAISS vector search, DP-chaining, and edlib verification, with full SAM/CIGAR output. Built at the NVIDIA AI x Bio Hackathon and continued as independent research; awarded $15K in AWS and Modal cloud credits.

1D CNN encoderFAISS / IVF-PQfp16 tensor-core searchnumba JITedlib91.8M-vector GRCh38 index

95.0%Locus accuracy, real ONT reads

9.0 msPer read on A100 (0.85x minimap2)

4.8xSpeedup from profiling & tuning

Immunogenomics2025–26

HPV neoepitope discovery pipeline

Turns HPV integration junctions into ranked, HLA-matched immunotherapy targets.

End-to-end pipeline from whole-genome sequencing to MHC-I binding: VIRUSBreakend/GRIDSS for integration detection, OptiType for HLA typing, pVACtools and NetMHCpan for prediction. Found 9 junction-spanning neoepitopes across HPV16/18 integration hotspots (GLI2, KLF5, MYC), plus novel E6/E7 epitopes for under-studied alleles. Now scaling to TCGA-CESC/HNSC (n>600).

5.98 nMTop binder, A*68:02

9Junction neoepitopes

n>600TCGA cohort scale-up

WGSpVACtoolsNetMHCpanHLA typing

Sequencing Dx2025–26

Rapid TB drug-resistance detection

Same-visit rifampicin-resistance calls, read straight off the sequencer.

LAMP amplification coupled to Oxford Nanopore MinION with an optimized rapid library prep. Detected the rifampicin-resistance mutation S450L at 66,000x depth within 30 seconds of sequencing, with sample-to-mutation in under two hours, a route to same-visit resistance profiling in low-resource settings.

<30 sTo first resistance call

66,000xDepth at S450L

<2 hrSample to answer

LAMPNanopore MinIONrpoB / S450L

Point-of-Care Dx2020–25

SPRINT-HPV point-of-care platform

Lab-grade cervical cancer screening with no lab and no cold chain.

A microfluidic cartridge ($10–20/test) with a battery-powered detector ($200–300) for cervical cancer screening where cold-chain and labs are scarce. Field-validated on 150+ patient samples at AIIMS against Roche Cobas, with a multiplex LAMP assay covering 11 high-risk HPV types down to 2.5 copies/uL.

100%Sensitivity vs Cobas

94.5%Specificity, cervical

<60 minSample to answer

Multiplex LAMPMicrofluidicsLyophilized reagentsField-tested

Single-Cell ML2026

scFM-Bench: single-cell annotation benchmark

A benchmark for cell-type annotation on PBMC scRNA-seq comparing reference-mapping (Seurat v5, CellTypist) against MLP baselines, with a focus on how methods behave when reference panels are small. PyTorch MLP baseline reaches 0.84 macro F1; extending to single-cell foundation models (scGPT).

0.84Macro F1, held-out cells

scGPTFoundation-model track

Scanpy / AnnDataSeuratCellTypistPyTorch

Structural Immunology2026

TCR-pMHC structural analysis

Analyzed 109 TCR-pMHC crystal structures from the PDB to map CDR-loop contact patterns at the peptide interface, confirming the P4–P8 dominant contact window. Exploring whether TCR sequence features correlate with 3D binding motifs, to push immunogenicity prediction beyond binding affinity alone.

109Crystal structures

P4–P8Contact window mapped

PDB analysisChimeraXContact mapping

Let's build something that reads biology and acts on it.

I am looking for postdoctoral and industry roles in computational immuno-oncology, ML for genomics, and translational diagnostics. If your work lives at that intersection, I would love to talk.

Siril Arockiam.

Learned representations of biological sequence and structure

Projects that turn sequence into decisions

GenoCache: learned-embedding long-read aligner

HPV neoepitope discovery pipeline

Rapid TB drug-resistance detection

SPRINT-HPV point-of-care platform

scFM-Bench: single-cell annotation benchmark

TCR-pMHC structural analysis

Peer-reviewed work, patents, and preprints

Patents

In Preparation

Research & professional experience

Postdoctoral Research Scholar

Ph.D. · Graduate Research Assistant

Scientist II (Associate)

Research Assistant · M.S. Thesis

Research Intern

Building, funding, and translating

Let's build something that reads biology and acts on it.