At Axiotl we find
hidden patterns
in genetic data

Axiotl is an R&D company that finds targets for new therapies using AI and genetic data. We work with pharma and academia to address unmet needs in heart disease and cancer. 3D genomics is our specialty, you can check out one of our recent analyses here:

research article

Single-cell variant-to-enhancer -to-gene map for coronary artery disease

Amrute et al. 2026

Nature

in press

Finding good targets from genetic data requires accurate models of gene regulation. We are co-leading the design and training of AI models on Icelandic data at Amgen deCODE Genetics. In May 2026 we presented at the CSHL AI in Biology symposium.

poster

Training on 13,000 transcriptomes increases prediction accuracy in sequence-to-function models

Jónsson et al. 2026

CSHL Symposium: AI in Biology

meetings.cshl.edu

If you’d like to work with us, please reach out at hello@axiotl.com

We are: Alexandra D’Yan Laura Morgan Maharshi Chakraborty Marquis Dodson Richard Sallari Ruth Gómez Quin Scacheri

We build most of the tools we use as part of our research system. You’re welcome to try them. The easiest way is to jump on a public Tinker box and prompt a new analysis on reference data.

research article

AQuA Tools: clear and reliable BEDPE operations for 3D genomics

Chakraborty and Morgan et al. 2025

Bioinformatics

doi.org/10.1093/bioinformatics/btaf510

code

Tinker platform

A collection of tools and services built from the ground up for 3D genomics

tinker.axiotl.com/

code

AQuA tools

A toolkit for 3D genomics. Developed in collaboration with the Gryder lab at CWRU.

github.com/axiotl/aqua-tools

docs

Tool documentation

docs.axiotl.com/

We choose projects that address substantial societal burdens: cancer, primarily colorectal, breast, and prostate, in addition to cardiometabolic diseases. We are especially interested in causes that suffer from inattention, such as deaths from opioids during the coronavirus pandemic.

research article

Interlocking host and viral cis-regulatory networks drive Merkel cell carcinoma

Miao et al. 2025

J Clin Invest

doi.org/10.1172/JCI188924

research article

Small-molecule disruption of androgen receptor–dependent chromatin clusters

Kohrt et al. 2024

PNAS

doi.org/10.1073/pnas.2406239121

research article

PAX3-FOXO1 uses its activation domain to recruit CBP/P300 and shape RNA Pol2 cluster distribution

Asante et al. 2023

Nature Communications

doi.org/10.1038/s41467-023-43780-4

research article

Oncogenic reactivation of young L1s is a hallmark of colon cancer

Neu et al. 2023

bioRxiv

doi.org/10.1101/2023.05.17.541189

research article

Convergence of case-specific epigenetic alterations identify a confluence of genetic vulnerabilities tied to opioid overdose

Corradin et al. 2022

Molecular Psychiatry

doi.org/10.1038/s41380-022-01477-y

collaborator talk

The Genetics of Opioid Addiction: What We Know, What We Are Learning

Olivia Corradin

Professor, MIT

youtube.com/watch?v=8MKF16y_QR4

research article

A regulatory variant at 3q21.1 confers an increased pleiotropic risk for hyperglycemia and altered bone mineral density​

Sinnott-Armstrong et al. 2021

Cell Metabolism

doi.org/10.1016/j.cmet.2021.01.001

research article

Convergent mutations in tissue-specific regulatory regions reveal novel cancer drivers

Sinnott-Armstrong et al. 2020

bioRxiv

doi.org/10.1101/2020.08.21.239954

research article

Functional Enhancers Shape Extrachromosomal Oncogene Amplifications

Morton et al. 2019

Cell

doi.org/10.1016/j.cell.2019.10.039

Axiotl’s roots are in academia. The following papers lay out the conceptual foundation of the work we do in human genetics, cancer genomics and target discovery.

research article

Convergence of Dispersed Regulatory Mutations Predicts Driver Genes in Prostate Cancer

Sallari et al. 2016

bioRxiv

doi.org/10.1101/097451

research article

Noncoding Somatic And Inherited Single-Nucleotide Variants Converge To Promote ESR1 Expression In Breast Cancer​

Bailey et al. 2016

Nature Genetics

doi.org/10.1038/ng.3650

research article

Breast cancer risk–associated SNPs modulate the affinity of chromatin for FOXA1 and alter gene expression

Sallari et al. 2012

Nature Genetics

doi.org/10.1038/ng.2416

research article

Layers of epistasis: genome-wide regulatory networks and network approaches to genome-wide association studies

Sallari et al. 2010

WIREs Syst Biol Med

doi.org/10.1002/wsbm.132