Riley J. Mangan | Evolutionary & Regulatory Genomics

Evolutionary & regulatory genomics

Understanding the regulatory changes that shaped the human brain.

I seek to understand the gene regulatory changes that shaped human neurodevelopment and how their evolutionary history influences susceptibility to neurological and neuropsychiatric disease.

My research combines comparative genomics, functional genomics, and genomic deep learning to identify consequential regulatory variants, determine their molecular and cellular mechanisms, and uncover how regulatory innovations reshape functional constraint.

I work with Prof. Manolis Kellis in the MIT Computational Biology Group and at the Broad Institute. I received my Ph.D. in Molecular Genetics and Microbiology from Duke University, advised by Prof. Craig Lowe.

Research

Discovering human regulatory innovations

Identify evolutionary changes in regulatory function, from rapidly evolved DNA to consequential variants overlooked by sequence divergence alone.

Connecting sequence to cellular function

Combine sequence-to-function deep learning with functional genomics, including in vivo scSTARR-seq, to reveal the mechanisms of regulatory change.

Linking evolution, constraint, and disease

Investigate how regulatory innovations reshape functional constraint and influence susceptibility to neurological and neuropsychiatric disease.

Selected publications

Full list

* Co-first author · † Co-corresponding author

bioRxiv2026Preprint

Sequence-to-function deep learning decodes human cis-regulatory evolution

Mangan RJ^†, Thoduguli N, Ivanov D, Li B, Vasudev K, Zeerow T, Shankar J, Lin Y, Liu Z, Wohlwend M, Song JHT^†, Kellis M^†

Predicting lineage-specific regulatory activity to uncover functional changes beyond elevated sequence divergence.

Preprint

Cell Genomics2026

Intraspecific sequence variation and complete genomes refine the identification of rapidly evolved regions in humans

Luo Y*, Mangan RJ*, Weaver S, Zhao SA, Mosti F, Thomas MC, Karra R, Silver DL, Kellis M, Lowe CB

Using complete ape genomes and within-species variation to refine the search for human regulatory innovation.

Paper

Nature2025

Complete sequencing of ape genomes

Yoo D, Rhie A, Hebbar P, et al. (including Mangan RJ)

Paper Full author list

Bioinformatics2023

Gonomics: uniting high performance and readability for genomics with Go

Au EH*, Fauci C*, Luo Y*, Mangan RJ*, Snellings DA*, Shoben CR, Weaver S, Simpson S, Lowe CB

Paper Code

Cell2022

Adaptive sequence divergence forged new neurodevelopmental enhancers in humans

Mangan RJ, Alsina FC, Mosti F, Sotelo-Fonseca JE, Snellings DA, Au EH, Carvalho J, Sathyan L, Johnson GD, Reddy TE, Silver DL, Lowe CB

Discovering Human Ancestor Quickly Evolved Regions (HAQERs) and testing their enhancer activity in the developing brain.

Paper

All publications and manuscripts

Software

Gonomics

I am a lead developer of Gonomics, an open-source collection of high-performance genomics tools written in Go. The project brings together readable code and scalable methods for genomic data analysis.

GitHub

Selected talks

All presentations

2027
UC Santa Cruz · Genomics Institute UpcomingSequence-to-function deep learning decodes human cis-regulatory evolution
2026
Harvard · Human Evolutionary BiologySequence-to-function deep learning decodes human cis-regulatory evolution
2026
EMBL · Reconstructing the human pastDeep learning prediction of cis-regulatory turnover in human evolution
2025
American Society of Human GeneticsSingle-cell-resolved phenotypes for Alzheimer’s disease across 599 patients and 3.4 million cells
2025
Broad Institute · Medical and Population GeneticsTransdiagnostic genomics of psychiatric disorders

Riley Mangan presenting a platform talk at ASHG 2025 — Platform presentation at the 2025 American Society of Human Genetics Annual Meeting, Boston.

Curriculum vitae

View full CV

Appointments

2026–present

Research Scientist · MITComputational Biology Group · Manolis Kellis

2023–present

Postdoctoral Scholar · Broad InstituteLaboratory of Manolis Kellis

2023–2026

Postdoctoral Associate / Fellow · MITComputational Biology Group · Manolis Kellis

2024–2026

Research Fellow · Harvard Medical SchoolGenetics Training Program · Manolis Kellis & Jordan Smoller
July 2024–June 2025; September 2025–August 2026

Education

2023

Ph.D. · Duke UniversityMolecular Genetics and Microbiology · Craig Lowe

2016

B.S. · Davidson CollegeBiology · Magna cum laude

Teaching, mentorship, awards & service

Teaching & mentorship

I mentor undergraduate and graduate researchers, visiting scholars, and high-school students in computational genomics, evolutionary genomics, and machine learning. At MIT, I developed curriculum and lecture materials for Machine Learning for Computational Biology in 2024 and 2025 and mentored semester-long student projects. I also delivered an invited lecture on human evolutionary neuroscience at Davidson College.

Selected fellowships & awards

ASHG Trainee Research Excellence Award semifinalist, 2025
Harvard Medical School Genetics Training Program T32 Postdoctoral Fellowship, 2024–2026
Triangle Center for Evolutionary Medicine Graduate Student Award, 2020
Sigma Xi Grants-in-Aid of Research, 2019

Service

Founder and Director, MIT Genomic Deep Learning Journal Club
Member, Kellis Lab Postdoctoral Search Committee
Co-Director, Duke Graduate Peer Mentoring Program
Reviewer for Genome Biology, Cell Reports, and Nature

Full teaching, mentorship, and service record