Multi-omics Lead  (Principal Scientist)

Camila Farias Amorim, Ph.D.

Century Therapeutics  ·  Philadelphia, PA

Multi-omics computational biologist with experience spanning single-cell genomics, translational biomarker discovery, and AI-augmented analytical workflows — from study design through (pre)clinical readout.

Camila Farias Amorim

Scientist. Analyst.
Translational lead.

I am a computational biologist currently serving as Multi-omics Lead (Principal Scientist) at Century Therapeutics. I work at the intersection of high-dimensional genomics, translational biology, and data science — supporting iPSC-derived cell therapy programs for auto-immune (T1D) and oncology diseases (CAR-NK, CAR-αβT cell, and SC-islet) from early pre-clinical research through IND-enabling studies and into first-in-human trial support.

My work spans the full pre-clinical and translational continuum: in vitro and in vivo omics characterization of cell therapy products, in silico multi-omics integration for biomarker discovery and predictive modeling, and manufacturing analytics for process development and lot release. On the early clinical side, I contribute to PK/PD biomarker strategy, translational pharmacology frameworks, and data packages that bridge pre-clinical findings to clinical success. I thrive in fast-paced, cross-functional biotech environments where scientific rigor, data analytics and operational execution are equally valued.

I integrate AI-based tools and agentic workflows into routine omics operations and data analysis — prioritizing reproducibility, automation, and decisions grounded in well-structured data.

End-to-end omics program design Study architecture, technology selection, and analysis across single-cell RNA-seq, CITE-seq, spatial transcriptomics, bulk RNA-seq, and WGS — across multiple concurrent programs.
Cross-functional scientific leadership Bridging iPSC biology, immunology, manufacturing, and clinical teams. Founder and lead of a company-wide Research/Omics Forum (20+ scientists).
AI-augmented workflows Active integration of LLMs and agentic tooling into omics operations, data pipelines, and logistics — with reproducibility and automation as core principles.
12+ years, bench to bioinformatics PhD in Immunology, 20+ peer-reviewed publications, postdoctoral research at the University of Pennsylvania, 5 years teaching NGS bioinformatics.

What I do

Single-Cell & Multi-Omics Genomics

Design and execute high-dimensional sequencing studies from sample collection through data deliverable. Technologies include scRNA-seq, CITE-seq, spatial transcriptomics, bulk RNA-seq, and whole-genome sequencing — applied across iPSC-derived cell therapy and SC-islet programs.

scRNA-seq CITE-seq Spatial transcriptomics Bulk RNA-seq WGS

Computational Analysis & Biomarker Discovery

Multi-omics data integration, dimensionality reduction, differential expression, and supervised ML for clinical outcome prediction. I develop reproducible analytical pipelines and translate findings into actionable scientific and regulatory narratives.

R / Python Seurat / Scanpy DESeq2 / edgeR ML modeling GSEA / pathway analysis

Assay Translation & Technology Development

Translating NGS-derived biomarker findings into rapid, scalable molecular assay formats. This includes converting transcriptomic signatures into qPCR and ddPCR panels suitable for manufacturing QC, identity testing, and early clinical monitoring.

qPCR ddPCR NGS-to-assay translation Assay development

Program Operations & Scientific Management

Full budget ownership, CRO and technology vendor management, data submission and receipt workflows, and sample inventory coordination across multiple sites. Responsible for contract oversight and ensuring cross-site data comparability.

Budget ownership CRO management Study design Cross-site coordination

Scientific Leadership & AI-Augmented Operations

Managing "wet and dry-bench" professionals and facilitating cross-disciplinary alignment through a company-wide omics forum (20+ scientists). I use agentic coding environments to automate analytical pipelines, data logistics, and reporting workflows — reducing manual overhead and improving reproducibility across projects.

People management Claude Code Aider Agentic coding Pipeline automation Reproducible research

Skills & technologies

Programming languages

R Python Bash C++ SQL Shell scripting Unix/Linux

Single-cell & genomics frameworks

Seurat Scanpy Cell Ranger Bioconductor DESeq2 edgeR / limma clusterProfiler Harmony Monocle3

Data science & visualization

tidyverse ggplot2 ComplexHeatmap Shiny R Markdown / Quarto git / GitHub Cloud computing / HPC AWS / EC2 / S3buckets GEO / NCBI deposition

Omics technologies

scRNA-seq CITE-seq Spatial transcriptomics Bulk RNA-seq Dual RNA-seq WGS 16S rRNA-seq Illumina sequencing qPCR ddPCR

Analytical methods

Multi-omics integration Read mapping / alignment Differential expression GSEA / GO enrichment Dimensionality reduction Batch correction / integration Hierarchical clustering Supervised / unsupervised ML Pattern recognition Linear & mixed-effects modeling Statistical inference Pseudotime / trajectory analysis Cell type deconvolution Biomarker discovery Predictive modeling

AI & automation

Claude Code / Anthropic Aider LLMs Agentic workflows Nextflow / Snakemake Docker / containerization Pipeline automation Reproducible research

Selected science

A selection of first-author publications demonstrating multi-omics data integration, ML-based clinical prediction, and translational biomarker discovery from complex human datasets.

Featured industry work

Century Therapeutics · Keystone Symposia 2025

iPSC-derived CD4+, CD8+ αβT cells that expand upon antigen stimulation and exhibit in vivo tumor control

Omics lead for the translational characterization behind this program — single-cell and multi-omics profiling of iPSC-derived CAR-αβT cell products, from study design through analysis, supporting the demonstration of antigen-driven expansion and in vivo tumor control.

Keystone 2025 poster · View poster (PDF)

Selected publications

Multi-omic profiling paper figure

Science Translational Medicine · 2023

Multi-omic profiling of cutaneous leishmaniasis infections reveals microbiota-driven mechanisms underlying disease severity

Integrated analysis of host transcriptomics (RNA-seq), microbiome profiling (16S rRNA-seq, WGS), and clinical metadata from a single patient cohort, using multivariate linear regression and supervised ML to identify predictors of clinical outcome. This work reflects my approach to multi-modal omics integration: aligning heterogeneous data types, reducing dimensionality jointly, and extracting clinically meaningful structure under a unified statistical framework.

Farias Amorim et al. 2023 · DOI: 10.1126/scitranslmed.adh1469

Variable gene expression paper figure

Science Translational Medicine · 2019

Variable gene expression and parasite load predict treatment outcome in cutaneous leishmaniasis

Dual RNA-seq profiling of human skin lesions — simultaneously mapping host transcriptome and pathogen burden — combined with variable gene expression analysis and dimensionality reduction to build a predictive model of treatment response. This was my first publication integrating computational and immunological approaches to clinical biomarker discovery, and it established the analytical framework I continue to refine.

Farias Amorim et al. 2019 · DOI: 10.1126/scitranslmed.aax4204 · Code (CodeOcean)

Systemic IFN-gamma signature paper figure

PLoS Neglected Tropical Diseases · 2021

Localized skin inflammation during cutaneous leishmaniasis drives a chronic, systemic IFN-γ signature

Parallel RNA-seq profiling of tissue (skin lesion) and peripheral blood, coupled with cross-cohort comparison against publicly available disease transcriptomes. The analysis combined linear modeling, statistical inference, and data visualization to isolate disease-specific transcriptional signatures — a cross-tissue, multi-context approach to understanding systemic immune responses.

Farias Amorim et al. 2021 · DOI: 10.1371/journal.pntd.0009321

Career timeline

2024 – present

Multi-omics Lead  (Principal Scientist)

Century Therapeutics · Philadelphia, PA
Leading the omics program across iPSC-derived CAR-NK, CAR-αβT cell, and SC-islet programs, with responsibility for study design, computational analysis, assay development, and cross-functional coordination.

2017 – 2024

Postdoctoral Researcher → Research Associate

Beiting Lab & Scott Lab · University of Pennsylvania
Multi-omics of infectious disease immunopathology; 5 years as Teaching Assistant for NGS & bioinformatics (DIYtranscriptomics.com).

2011 – 2017

Masters & Ph.D. in Immunology

Federal University of Bahia, Brazil
Immunopathogenesis of cutaneous leishmaniasis; clinical cohort design and translational immunology research.

Recognition & credentials

AAI Oral Presentation Award — 1st place
ASTMH Scientific Excellence Award
NIH travel awards (multiple)
20+ peer-reviewed publications (Science Translational Medicine, JEM, PLoS Pathogens)
5 years teaching NGS/bioinformatics at University of Pennsylvania — co-author on open-source bioinformatics curriculum (mBio, 2021)

Philadelphia, PA  ·  originally from Salvador, Bahia, Brazil

Get in touch

Open to scientific conversations and collaborations.