Riley J. Mangan

Education

Duke University, Durham, North Carolina · 2023

Ph.D. - Molecular Genetics and Microbiology

Graduate Program in Cell and Molecular Biology

Advised by Craig B. Lowe, Ph.D.

Dissertation: Divergence, Mutation, Function, Selection: The Evolution of the Human Genome

Davidson College, Davidson, North Carolina · 2016

B.S. - Biology, Magna Cum Laude

Professional Experience

Massachusetts Institute of Technology, Cambridge, Massachusetts · Oct 2023 – Present

Research Scientist · Sep 2026 – Present

Postdoctoral Fellow · Jul 2024 – Jun 2025 ; Sep 2025 – Aug 2026

Postdoctoral Associate · Oct 2023 – Jun 2024 ; Jul 2025 – Aug 2025

MIT Computational Biology Group, Laboratory of Manolis Kellis, Ph.D.

Developed computational approaches leveraging regulatory deep learning models to predict lineage-specific cis-regulatory elements across human and great ape evolution (Mangan et al, BioRxiv 2026).

Identified rapidly evolving regions in the human genome using state-of-the-art primate assemblies as a leading analyst for the Telomere-to-Telomere (T2T) Consortium (Luo*, Mangan* et al, Cell Genomics 2026; Yoo et al, Nature 2025).

Contributed to single-cell multi-omic analyses to uncover epigenomic erosion in Alzheimer's disease (Liu et al, Cell 2025) and circadian dysregulation in breast cancer (Liang et al, BioRxiv 2026).

Contributed to major genomic consortia, including the International Human Epigenome Consortium (IHEC et al, BioRxiv 2026) and GENCODE (Mudge et al, NAR 2025).

Broad Institute of MIT and Harvard, Cambridge, Massachusetts · Oct 2023 – Present

Postdoctoral Scholar, Laboratory of Manolis Kellis, Ph.D.

Harvard Medical School, Boston, Massachusetts · Jul 2024 – Jun 2025 ; Sep 2025 – Aug 2026

Research Fellow, Genetics Training Program

Co-advised by Manolis Kellis, Ph.D. (MIT) and Jordan Smoller, M.D., Sc.D. (MGH/HMS).

Duke University School of Medicine, Durham, North Carolina · Aug 2018 – Oct 2023

Ph.D. Candidate, Laboratory of Craig B. Lowe, Ph.D.

Discovered HAQERs, the fastest-evolved regions of the human genome, demonstrating their role in encoding human-specific functional elements and driving human neurodevelopment and disease (Mangan et al, Cell 2022).

Developed in vivo scSTARR-seq, a high-throughput, single-cell, multiplex enhancer assay to quantify the cell type-specific enhancer activity of DNA sequences in developing brain tissue.

Led development of Gonomics, an open-source initiative to produce high-performance genomics software in the Go programming language (Au*, Fauci*, Luo*, Mangan*, Snellings* et al, Bioinformatics 2023).

Duke Human Vaccine Institute, Durham, North Carolina · May 2016 – Jul 2018

Research Technician II, Laboratory of Sallie R. Permar, MD., Ph.D.

Davidson College Biology Department, Davidson, North Carolina · Aug 2015 – Dec 2015

Student Research Assistant, Laboratory of Rachid El Bejjani, Ph.D.

University of Illinois at Chicago, Chicago, Illinois · May 2015 – Aug 2015

Division of Gastroenterology and Hepatology, Department of Medicine

Summer Research Intern, Laboratory of Paul Grippo, Ph.D.

Northwestern University, Chicago, Illinois · May 2012 – Aug 2014

Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine

Summer Research Intern, Laboratory of Paul Grippo, Ph.D.

Grants, fellowships, and awards

K99/R00 Pathway to Independence Award, NIH · Submitted June 2026, Under Review

Cell-state-resolved regulatory deep learning and cross-disorder single-cell genomics for noncoding psychiatric risk variant interpretation.

Role: PI.

NIH R01 (PA-25-301). PIs: Manolis Kellis, Ph.D. and Brad Ruzicka, M.D., Ph.D. · Pending

Computational, experimental, and genetic dissection of single-cell molecular hallmarks and therapeutic outcomes for precision psychiatry

Conceptualized the project and led proposal writing.

Funded proposals contributed to as a member of the Kellis Lab

GENCODE: comprehensive reference genome annotation for human and mouse. NIH/EBI (U24HG007234).

Multi-resolution pathway-centric biomarker discovery for Parkinson's Disease. Michael J. Fox Foundation.

FlyBase: A Drosophila Genomic and Genetic Database. NIH/Harvard University (U24HG013300).

AI-Guided Regulatory Circuitry Design for Precision Genomic Medicine. MIT Health and Life Sciences Collaborative.

Multi-modal patient embeddings for precision patient stratification in Parkinson's disease. Sanofi.

Trainee Research Excellence Award, Semifinalist. · Oct 2025

2025 Annual Meeting, American Society of Human Genetics.

Harvard Medical School Genetics Training Program T32 Postdoctoral Fellowship · Jul 2024 – Aug 2026

NIGMS-funded fellowship (T32 GM007748, PI: Cynthia Morton) supporting advanced research and training in medical and human genetics.

Co-advised by Manolis Kellis, Ph.D. (MIT), and Jordan Smoller, M.D., Sc.D. (MGH/HMS)

Triangle Center for Evolutionary Medicine Graduate Student Award · Fall 2020

Sigma Xi Grants-In-Aid of Research. · 2019

Matching contribution from the Duke Graduate School.

Publications and manuscripts

Preprints and submitted manuscripts

36. Liu Z, Galani K, Linville RM, James BT, Mangan RJ, Grayson A, Fass SB, Zhang S, Ho L, Heiman M, Gabuzda DH, Kellis M. (2026) Single-cell multiomic brain atlas of HIV and opioid use disorder reveals region- and cell-type-specific vulnerability. In Preparation.

35. Wohlwend M, Zhao B, Mangan RJ, Tanigawa Y, Han X, Kelly S, Tian X, Ho LL, Saarela J, Pentelute B, Kellis M. (2026) Human genetics of the noncoding human exome implicates novel RNA molecules in brain diseases. In Preparation.

34. Frankish A, Carbonell-Sala S, Diekhans M, Martinez JG, Merritt R, Hunt T, Jungreis I, Loveland JE, Mudge JM, Perteghella T, Arnan C, Barnes I, Bennett R, Berry A, Borsari B, Burgess J, Carpenter J, Cerdan-Velez D, Clauwaert J, Cochran K, Cortes LT, Davidson C, Degalez F, Diamantaskis S, Donaldson S, Fatima R, Hao T, Hardy M, Hebbar P, Hollis Z, James BT, Jiang Y, Johnson R, Kassa-Belaouchat T, Kaur G, Burhi SK, Kay M, Lopes Novo C, Lumbreras Iglesias P, Mangan RJ, Maquedano M, Mathlouthi N, Murray R, Nurtdinov R, Palumbo E, Quigley S, Simpson M, Sisu C, Spirohn-Fizgerald K, Suner MM, Tanzer A, Uszczynska-Ratajczak B, Valls CF, Wider N, Yang YT, Yu X, Zhang Y, Finn RD, Gerstein M, Guigo R, Hill DE, Hubbard TJP, Kellis M, Kundaje A, Ljungman M, Paten B, Presner JR, Tress ML, Vidal M, Martin FJ. (2026) GENCODE 2027: reference gene annotation for human and mouse. In Preparation.

33. Lou Y, Li Q, Wang H, Liu Z, Hao Z, Su Z, Ong JS, Wohlwend M, Bian B, Mangan RJ, Kellis M, Han X. (2026) A multistage genetic architecture of human life history. Submitted.

32. Liu Z, Mangan RJ, Insawang B, Tanigawa Y, Liu M, Yan M, Ong JS, Gharahkhani P, Zeng J, Hewitt AW, Mackey DA, MacGregor S, Kellis M, Han X. (2026) Ancient genomes reveal stable polygenic susceptibility to myopia over 15,000 years. In Revisions.

31. Liu M, Mangan RJ, Boix CA, MacGregor S, Kellis M, Han X. (2026) A gene-level framework for statistical pleiotropy in humans with application to aging-related traits. In Revisions.

30. Mangan RJ†, Thoduguli N, Ivanov D, Li B, Vasudev K, Zeerow T, Shankar J, Lin Y, Liu Z, Wohlwend M, Song JHT†, Kellis M†. (2026) Sequence-to-function deep learning decodes human cis-regulatory evolution. BioRxiv. https://doi.org/10.64898/2026.08.24.746818 †Indicates co-corresponding.

29. International Human Epigenome Consortium, Manz Q*, Bilenky M*, Hecker D*, Aggarwal N, Arcila-Galvis JE, Ashrafiyan S, Baumgarten N, Behjati Ardakani F, Branco Lins PR, Breeze CE, Brownlee D, Bujold D, Chapman AR, Chow SHC, Dincer TU, Dupras C, Frosi G, Fu J, Gérard D, Hauduc A, Hyacinthe J, Jaroszewicz A, Li R, Mangan RJ, Mikulasova A, Moghul I, Needhamsen M, Palmour N, Pacheco MP, Quon J, Raby J, Reynolds A, Rumpf L, Salhab A, Shi CH, Sinkkonen L, Tanigawa Y, Tanner RM, Vu H, White F, Aw JTM, Badii S, Bowlby R, Boyle M, Brown C, Chand D, Calingo M, Cao Q, Carles A, Caron M, Carreira M, Cheng ASL, Cheng CCY, Cheng D, Cheng Y, Cheung MF, Choe G, Chuah E, Dali R, Deng A, Gakkhar S, Gut M, He A, Heath SC, Ho V, Intan AG, Ito CY, Jiang Q, Kluiver JL, Lee J, Lee S, Leung Z, Li I, Lorzadeh A, McKerricher D, Mishra N, Mungall K, Nagai LAE, Ngubo M, Palmquist D, Pang J, Park V, Plettner P, Puri A, Redensek A, Sharafian Z, Simon M-M, Steif J, Su E, Tam SKM, Tam SST, Van den Berg A, Wong R, Wong T, Wu JKH, Zhu A, Kwan T, Moksa M, Aherne STA, Aparicio S, Arima T, Chung HR, Costello JF, Eaves CJ, Fisher SJ, Gut IG, Harrison PW, Horsthemke B, Ilsley GR, Jagodic M, Karsan A, Lavoie PM, Leung D, Libbrecht MW, Manke T, Marra MA, Meuleman W, Müller F, Nakato R, Okae H, Rico D, Rosenstiel P, Sasaki H, Sauter T, Schreiber S, Scott DW, Stanford WL, Steidl C, Stunnenberg HG, Suyama M, Tran F, Ushijima T, Weng AP, Wiseman SM, Wu AR, Yip KY, Yip S, Beck S, Bourque G, Ernst J, Jacques P-É, Joly Y, Kellis M, List M, Perkins TJ, Schulz MH, Walter J, Hirst M. (2026) EpiATLAS – a reference for human epigenomic research. BioRxiv. https://doi.org/10.64898/2026.06.22.729579.

28. Liang C*, Liu Z*, Xu X, Xu Z, Zhang Q, Zhang T, Mangan RJ, Xiu B, Wu G, Akhshi T, Sandusky Z, Gray GK, Zhang N, Kuziel G, Traphagen N, Fass SB, Grayson A, Ho LL, Gu SS, Wang S, Sheng ZZ, Zhang Y, Chen T, Jeselsohn R, Kellis M, Brown M. (2026) Circadian misalignment underlies immune escape in breast cancer. BioRxiv. https://doi.org/10.64898/2026.05.26.726543 *Indicates co-first author

27. Mangan RJ*, Bouland GA*, Schubert T, Anwer D, Bai J, Ekiz G, Pigadas N, Dattatri A, Polster A, Mahfouz A, Reinders MJT, Kellis M. (2026) Cell-projected phenotypes link transcriptional and phenotypic heterogeneity in Alzheimer's disease. SSRN. https://dx.doi.org/10.2139/ssrn.6615879. *Indicates co-first author

26. Abeykoon Y, Dzikowski N, Luo Y, Sinniah E, Weaver S, Pavlovic BJ, Wallace JL, Mangan RJ, Lowe CB, Pollen AA. (2025) Interrogating the regulatory function of HAQERs during human cortical development. BioRxiv. https://doi.org/10.1101/2025.11.30.691411.

Published and in-press works

25. Mangan RJ, Kannan S, Calef R, Tanigawa Y, & Kellis M. (2026). Artificial Intelligence for Genetics and Genomic Medicine. Chapter In Vogel and Motulsky’s Human Genetics, 5th Edition. Springer. In Press.

24. Liu M, Mangan RJ, Fullard JF, Zeng J, Li A, Daskalakis N, Liu Z, Smoller J, Ruzicka WB, Roussos P, Kellis M, Han X. (2026) Single-cell genomics provides new insights into psychiatric disorders. Nature Reviews Genetics, In Press.

23. Luo Y*, Mangan RJ*, Weaver S, Zhao SA, Mosti F, Thomas MC, Karra R, Silver DL, Kellis M, Lowe CB. (2026) Intraspecific sequence variation and complete genomes refine the identification of rapidly evolved regions in humans. Cell Genomics. https://doi.org/10.1016/j.xgen.2026.101363. *Indicates co-first author

22. Pacheco MP, Gerard D, Mangan RJ, Chapman AR, Hecker D, Kellis M, Schulz MH, Sinkkonen L, Sauter T. (2026) Epigenetic control of metabolic identity across cell types. BMC Genomics. 27:22. https://doi.org/10.1186/s12864-025-12155-y.

21. Liu Z, James BT, Zhang S, Galani K, Mangan RJ, Fass SB, Liang C, Wagle MM, Boix CA, Tanigawa Y, Yun S, Sung Y, Xiong X, Sun N, Hou L, Wohlwend M, Qiu M, Han X, Xiong L, Preka E, Huang L, Li WF, Ho LL, Grayson A, Mantero J, Kozlenkov A, Mathys H, Chen T, Dracheva S, Bennett DA, Tsai LH, Kellis M. (2025) Single-cell multiregion epigenomic rewiring in Alzheimer’s disease progression and cognitive resilience. Cell. https://doi.org/10.1016/j.cell.2025.06.031.

20. Au EH, Weaver S, Katikaneni A, Wucherpfennig JI, Luo Y, Mangan RJ, Wund MA, Bell MA, Lowe CB. (2025) Genome sequence of a marine threespine stickleback (Gasterosteus aculeatus) from Rabbit Slough in the Cook Inlet. G3: Genes, Genomes, Genetics. jkaf114, https://doi.org/10.1093/g3journal/jkaf114.

19. Yoo D, Rhie A, Hebbar P, Antonacci F, Logsdon GA, Solar SJ, Antipov D, Pickett BD, Safonova Y, Montinaro F, Luo Y, Malukiewicz J, Storer JM, Lin J, Sequeira AN, Mangan RJ, Hickey G, Monfort Anez G, Balachandran P, Bankevich A, Beck CR, Biddanda A, Borchers M, Bouffard GG, Brannan E, Brooks SY, Carbone L, Carrel L, Chan AP, Crawford J, Diekhans M, Engelbrecht E, Feschotte C, Formenti G, Garcia GH, de Gennaro L, Gilbert D, Green RE, Guarracino A, Gupta I, Haddad D, Han J, Harris RS, Hartley GA, Harvey WT, Hiller M, Hoekzema K, Houck ML, Jeong H, Kamali K, Kellis M, Kille B, Lee C, Lee Y, Lees W, Lewis AP, Li Q, Loftus M, Loh YHE, Loucks H, Ma J, Mao Y, Martinez JFI, Masterson P, McCoy RC, McGrath B, McKinney S, Meyer BS, Miga KH, Mohanty SK, Munson KM, Pal K, Pennell M, Pevzner PA, Porubsky D, Potapova T, Ringeling FR, Rocha JL, Ryder OA, Sacco S, Saha S, Sasaki T, Schatz MC, Schork NJ, Shanks C, Smeds L, Son DR, Steiner C, Sweeten AP, Tassia MG, Thibaud-Nissen F, Torres-González E, Trivedi M, Wei W, Wertz J, Yang M, Zhang P, Zhang S, Zhang Y, Zhang Z, Zhao SA, Zhu Y, Jarvis ED, Gerton JL, Rivas-González I, Paten B, Szpiech ZA, Huber CD, Lenz TL, Konkel MK, Yi SV, Canzar S, Watson CT, Sudmant PH, Molloy E, Garrison E, Lowe CB, Ventura M, O’Neill RJ, Koren S, Makova KD, Phillippy AM, Eichler EE. (2025) Complete sequencing of ape genomes. Nature. https://doi.org/10.1038/s41586-025-08816-3.

18. Mudge JM, Carbonell-Sala S, Diekhans M, Gonzalez Martinez J, Hunt T, Jungreis I, Loveland JE, Arnan C, Barnes I, Bennett R, Berry A, Bignell A, Cerdán-Vélez D, Cochran K, Cortés LT, Davidson C, Donaldson S, Dursun C, Fatima R, Hardy M, Hebbar P, Hollis Z, James BT, Jiang Y, Johnson R, Kaur G, Kay M, Mangan RJ, Maquedano M, Martínez Gómez L, Mathlouthi N, Merritt R, Ni P, Palumbo E, Perteghella T, Pozo F, Sisu C, Steed E, Sumathipala D, Suner MM, Uszczynska-Ratajczak B, Wass E, Yang YT, Zhang D, Finn RD, Gerstein M, Guigó R, Hubbard TJP, Kellis M, Kundaje A, Paten B, Tress ML, Martin FJ, Frankish A. (2024) GENCODE 2025: reference gene annotation for human and mouse. Nucleic Acids Research. gkae1078.

17. Singh T, Miller IG, Venkatayogi S, Webster H, Heimsath HJ, Eudailey JA, Dudley DM, Kumar A, Mangan RJ, Thein A, Aliota MT, Newman CM, Mohns MS, Breitbach ME, Berry M, Wiehe K, O’Connor DH, and Permar SR. (2024) Prior dengue virus serotype 3 infection modulates subsequent plasmablast responses to Zika virus infection in rhesus macaques. mBio. e03160-23.

16. Au EH*, Fauci C*, Luo Y*, Mangan RJ*, Snellings DA*, Shoben CR, Weaver S, Simpson S, Lowe CB. (2023) Gonomics: uniting high performance and readability for genomics with Go. Bioinformatics. Volume 39, Issue 8, August 2023, btad516. *Co-first author, listed alphabetically.

15. 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. (2022) Adaptive sequence divergence forged new neurodevelopmental enhancers in humans. Cell. 185: 4587–4603. *Indicates co-second author.

14. Nelson AN, Dennis M, Mangold JF, Li K, Saha PT, Cronin K, Kumar A, Mangan RJ, Shaw GM, Bar K, Haynes B, Moody MA, Alam M, Pollara J, Hudgens MG, Van Rompay KKA, De Paris K, Permar SR. (2022) Leveraging antigenic seniority for maternal vaccination to prevent mother-to-child transmission of HIV-1. NPJ Vaccines. 7(1): 87.

13. Berendam S*, Morgan-Asiedue PK*, Mangan RJ, Li S, Heimsath H, Luo K, Curtis A, Eudailey J, Faison W, Fox C, Phillips B, Tomai M, Kunz E, Itell H, Hudgens M, Cronin K, Wiehe K, Alam SM, Van Rompay KKA, De Paris K, Permar SR, Moody MA, Fouda GG. (2021) Different adjuvanted pediatric HIV envelope vaccines induced distinct plasma antibody responses despite similar B cell receptor repertoires in infant rhesus macaques. PLOS One. 16(12):e0256885. *Indicates co-first author.

12. Itell HL, Berenz A, Mangan RJ, Permar SR, Kaufman D. (2021) Systemic and mucosal levels of lactoferrin in very low birth weight infants supplemented with bovine lactoferrin. Biochemistry and Cell Biology. 99(1):25-34.

11. Martinez DR, Tu JJ, Kumar A, Mangold JF, Mangan RJ, Goswami R, Giorgi EE, Chen J, Mengual M, Douglas AO, Heimsath H, Saunders KO, Nicely NI, Eudailey J, Hernandez G, Morgan-Asiedu PK, Wiehe K, Haynes BF, Moody MA, LaBranche C, Montefiori DC, Gao F, Permar SR. (2020) Maternal broadly neutralizing responses select for neutralization-resistant infant transmitted/founder HIV variants. mBio. 111(2):e00176-20.

10. Goswami R, Nelson AN, Tu JJ, Dennis M, Feng L, Kumar A, Mangold J, Mangan RJ, Mattingly C, Curtis AD, Obregon-Perko V, Mavigner M, Pollara J, Shaw GM, Bar K, Chahroudi A, De Paris K, Chan C, Van Rompay KKA, Permar SR. (2019) Analytical treatment interruption of postnatal SHIV infection after short-term anti-retroviral therapy in an infant rhesus macaque model. mBio. 10(5): e01971-19.

9. Nelson AN, Goswami R, Dennis M, Tu J, Mangan RJ, Saha P, Cain DW, Shen X, Bar K, Hudgens M, Pollara J, De Paris K, Van Rompay KKA, and Permar SR. (2019) SHIV CH505 infected infant and adult rhesus macaques exhibit similar HIV Env-specific antibody kinetics, despite distinct T follicular helper (Tfh) and germinal center B cell landscapes. Journal of Virology. 93(15): e00168-19.

8. Mangan RJ, Stamper L, Ohashi T, Eudailey JA, Go EP, Jeager F, Itell HL, Watts BE, Fouda GG, Erickson HP, Alam SM, Desaire H, Permar SR. (2019) Determinants of tenascin-C and HIV Env binding and neutralization. Mucosal Immunology. 12: 1004-1012.

7. Kim J*, Chun A*, Mangan RJ, Doyle H, Mourao B, and El Bejjani R. (2019) A retromer-independent function for RAB-6.2/RAB6 in C. elegans epidermis integrity. Journal of Cell Science. 8(3): 3826-2839. *Indicates co-first author.

6. Himes JE, Goswami R*, Mangan RJ*, Kumar A, Jeffries TL, Eudailey JA, Hemsath H, Nguyen QN, Pollara J, LaBranche C, Chen M, Vandergrift NA, Schiro F, Midkiff C, Ferrari G, Montefiori DC, Alvarez-Hernandez X, Aye PP, Permar SR. (2018) Polyclonal anti-HIV envelope breast milk antibodies limit founder SHIV acquisition and cell-associated virus loads in infant rhesus monkeys. Mucosal Immunology. 11(6): 1716-1726. *Co-second author.

5. Nguyen QN, Martinez DR, Himes JE, Edwards RW, Han Q, Kumar A, Mangan R, Nicely NI, Shen X, Pollara J, Permar SR. (2018) Predominant envelope variable loop 2-specific and antibody-dependent cellular cytotoxicity antibody responses in acutely SIV-infected African green monkeys. Retrovirology. 15(1): 24.

4. Principe DR, Diaz AM, Torres C, Mangan RJ, DeCant B, McKinney R, Tsao MS, Lowy A, Munshi HG, Grippo PJ. (2017) TGFβ engages MEK/ERK to differentially regulate benign and malignant pancreas cell function. Oncogene. 36(30):4336-4348.

3. Principe DR, Mangan RJ, Grippo PJ. (2017) Transforming Growth Factor β. Chapter in Cancer Therapeutic Targets, Springer. https://doi.org/10.1007/978-1-4419-0717-2_137.

2. Principe DR, DeCant B, Staudacher J, Vitello D, Mangan RJ, Wayne E, Mascariñas E, Diaz AM, Bauer J, McKinney RD, Khazaie K, Pasche B, Dawson DW, Munshi HG, Grippo PJ, Jung B. (2016) Loss of TGFβ signaling promotes colon cancer progression and tumor-associated inflammation. Oncotarget. 8(3):3826-3839.

1. Principe DR, Decant B, Diaz AM, Mangan RJ, Hwang R, Lowy A, Shetuni BB, Sreekumar BK, Chung C, Bentrem DJ, Munshi HG, Jung B, Grippo PJ, Bishehsari F. (2016) PEDF inhibits pancreatic tumorigenesis by attenuating the fibroinflammatory reaction. Oncotarget. 7(19): 28218-28234.

Presentations

Oral Presentations and Invited Talks

2027 Upcoming invited seminar. Genomics Institute, University of California Santa Cruz. Santa Cruz, CA. “Sequence-to-function deep learning decodes human cis-regulatory evolution."

2026 Invited Seminar Speaker. Department of Human Evolutionary Biology, Harvard University. Cambridge, MA. “Sequence-to-function deep learning decodes human cis-regulatory evolution."

2026 Selected Oral Presentation. EMBL Symposium, Reconstructing the human past: using ancient and modern genomics. Heidelberg, Germany. “Deep learning prediction of cis-regulatory turnover in human evolution."

2025 Platform Presentation. Annual Meeting, American Society of Human Genetics. Boston, MA. “Single-cell-resolved phenotypes for Alzheimer’s disease across 599 patients and 3.4 million cells.”

2025 Platform Presentation, CSAIL Alliances Annual Meeting, Massachusetts Institute of Technology, Cambridge, MA. "Enabling Precision Psychiatry with AI and Genomics."

2025 Invited Speaker, Medical and Population Genetics Seminar Series, Broad Institute of MIT and Harvard, Cambridge, MA. “Transdiagnostic genomics of psychiatric disorders."

2024 Invited Speaker, Center for Precision Psychiatry, Massachusetts General Hospital, Boston, MA. “Pathway-centric personalized precision psychiatry by single-cell multiomis-genetics-EHR integration."

2024 Invited Speaker, Boston Evolutionary Genomics Supergroup, Harvard Medical School, Boston, MA. “Recent gene-regulatory innovations in the human lineage."

2023 Invited Speaker, Altenberg Workshop in Theoretical Biology, Konrad Lorenz Institute, Klosterneuberg, Austria. “Directionality in Genomics and Macroevolution.”

2022 Platform Presentation. Annual Meeting, American Society of Human Genetics. “Adaptive sequence divergence forged new neurodevelopmental enhancers in humans.”

2020 Duke University Division of Human Genetics Retreat. “High-throughput functional analysis of the fastest evolving regions of the human genome.”

2019 Duke University Department of Molecular Genetics and Microbiology Research Retreat. “Exploring the fastest evolving regions of the human genome.”

Poster Presentations

2025 The Biology of Genomes, Cold Spring Harbor Laboratory

2023 The Biology of Genomes, Cold Spring Harbor Laboratory

2019 Duke University Division of Human Genetics Retreat

2017 and 2018 Duke University Department of Pediatrics Research Retreat

2016, 2017, and 2018 Center for AIDS Research (CFAR) Retreat, Duke University

2016 Math and Science Research Symposium, Davidson College Biology Department

2016 Community-Based Learning Poster Session, Davidson College Department of Mathematics and Computer Science

Teaching and Mentorship

Overview: Primary research mentor to undergraduate and graduate researchers, visiting scholars, and high-school students in computational genomics, evolutionary genomics, and machine learning.

Teaching

2023 Invited Guest Lecture, course in Cell and Molecular Neuroscience, Davidson College. “Human Evolutionary Neuroscience: Genomic Insights.”

Developed curriculum and slide decks for Machine Learning for Computational Biology (MIT course number 6.8700 / 6.8701 / 20.s900 / 20.s948 / HST.507), taught by Prof. Manolis Kellis, for both the Fall 2024 and Fall 2025 semesters.

I served as a project mentor for two semester-long student research projects for Machine Learning for Computational Biology (MIT course number 6.8700 / 6.8701 / 20.s900 / 20.s948 / HST.507).

Graduate Research Mentoring:

Sarah Zhao (MIT, 2024–2025). Primary research mentor, first as an undergraduate researcher and subsequently as a master's student. Developed computational methods for comparative genomics, ancestral sequence reconstruction, and analysis of rapid divergence on the human lineage. Received the 2025 Anna Pogosyants UROP Award for outstanding undergraduate research in MIT EECS and the 2026 David Adler Thesis Award for an outstanding M.Eng. thesis in MIT EECS. Received a Fulbright Research Fellowship to conduct research at EMBL and the Skaggs-Oxford Scholarship, providing five years of funding for doctoral study at Scripps Research and the University of Oxford. Now pursuing a Ph.D. at Scripps Research and a D.Phil. at the University of Oxford. Co-authored Yoo et al. Nature 2025 and Luo et al. Cell Genomics 2026.

Tim Schubert (MIT, 2025). Primary research mentor during a four-month visiting graduate research internship investigating Alzheimer's disease heterogeneity using single-cell, metabolomic, and cognitive data. Co-authored Mangan et al. SSRN 2026. Now completing an M.D./Ph.D. at Heidelberg University.

Jesús Emiliano Sotelo-Fonseca (Duke University, 2021). Ph.D. rotation student under my primary research supervision for two months. Discovered enrichments between rapidly evolved regions of the human genome and neuropsychiatric risk loci. Co-authored Mangan et al. Cell 2022. Subsequently completed an M.S. at Duke University and began Ph.D. training at the Centre for Genomic Regulation (CRG), Barcelona, Spain.

Zichen Deng (MIT, 2026–present). Zichen is a current Master's student at the Harvard T.H. Chan School of Public Health who is co-advised by Dr. Frank Hu (Harvard) and Prof. Manolis Kellis (MIT). I have served as his primary research mentor on the MIT side of the collaboration, where he has worked on two projects: the first related to evaluating cross-disorder similarities in transcriptional dysregulation in schizophrenia and bipolar disorder, and the second investigating interactions between food compounds and the human proteome using a contrastive learning-based protein-small molecule affinity prediction approach.

Enrique Mondragon-Estrada (MIT, 2026). Primary research mentor for a first-year Kellis lab rotation for the MIT Ph.D. program in Electrical Engineering and Computer Science (EECS). Enrique is exploring deep learning-based in silico prioritization of regulatory variants from GWAS summary statistics, with specific applications to latent genetic risk factors for neuropsychiatric disorders.

Undergraduate Research Mentoring:

Nikitha Thoduguli (MIT, 2023–present). Primary research mentor for undergraduate research in computational genomics and sequence-to-function deep learning. Received the 2025 Merck Prize for outstanding research and academic performance in biophysical or bioinformatics sciences and the 2025 Morais '86 and Rosenblum '86 UROP Award in recognition of an outstanding undergraduate research project. Selected for a platform presentation at the 2025 Annual Meeting of the American Society of Human Genetics and as one of MIT's official nominees for the Rhodes Scholarship for the Class of 2027. Co-authored Mangan et al. Under Review 2026.

Shea Simpson (Duke University, 2022–2023). Primary research mentor for undergraduate thesis research investigating causal noncoding variants associated with nervous system disease using evolutionary analysis, epigenomic annotation, and in vivo scSTARR-seq. Awarded Best Undergraduate Thesis in Evolutionary Anthropology at Duke University for research conducted under my supervision. Now pursuing a Doctor of Medicine at NYU Grossman School of Medicine. Co-authored Au et al. Bioinformatics 2023.

Saathvik Kannan (MIT, 2024–present). Co-mentor for undergraduate research in multimodal deep learning for computational chemistry, meeting weekly to guide project design and analysis. Saathvik has led the development of AffinityNet, a contrastive learning model that predicts protein-small molecule binding affinities. Co-authored Mangan et al. Vogel & Motulsky's Human Genetics, 2026.

Yuru Lin (MIT, 2023–present). Primary research mentor for undergraduate research in regulatory and evolutionary genomics, developing computational methods to integrate sequence-to-function deep learning, transcription factor binding motifs, and evolutionary conservation to interpret noncoding genetic variation. Featured speaker, 2026 MIT Biology Undergraduate Research Symposium. Co-authored Mangan et al. Under Review 2026.

Jayashabari Shankar (MIT, 2023–2024). Primary research mentor for undergraduate research developing computational methods to measure lineage-specific enhancer activity using large pre-trained sequence-to-function models. Co-authored Mangan et al. Under Review, 2026.

Bessie Li (MIT, 2026–present). Primary research mentor for undergraduate research in regulatory and evolutionary genomics. Guided the development of contrastive language-image pre-training (CLIP) models to interoperate between gene expression embedding space and natural language descriptions of single cells based on marker gene expression. Directed computational analyses of evolutionary and functional features of lineage-specific cis-regulatory elements. Co-authored Mangan et al. Under Review 2026.

Krish Vasudev (MIT, 2026). Primary research mentor during a three-month visiting undergraduate research internship investigating deep learning approaches to identify lineage-specific cis-regulatory elements. Co-authored Mangan et al. (Under Review) 2026. Now an undergraduate at Brown University.

Laya Sathyan (Duke University, 2020-2021). Primary research mentor in regulatory epigenomics. I trained her in plasmid preparation, molecular cloning, library preparation, and next generation sequencing to perform in vivo scSTARR-seq assays. Co-authored Mangan et al. Cell 2022. Now a Life Sciences Consulting Analyst with the Dedham Group.

High School Research Mentoring:

Gulfum Ekiz (MIT Research Science Institute, 2025). Primary research mentor during the Research Science Institute. Co-authored Mangan et al. (SSRN, 2026). Now an undergraduate at the University of Oxford.

Judy Bai (MIT Research Science Institute, 2025). Primary research mentor during the Research Science Institute. Co-authored Mangan et al. (SSRN, 2026). Now an undergraduate at Harvard University.

Amogh Dattatri (MIT Research Science Institute, 2026). Primary research mentor during the Research Science Institute. Co-authored Mangan et al. (SSRN, 2026).

Adrita Samanta (MIT, 2025–present). Primary research mentor for high school research project. Supervised the development of CLIP models connecting gene expression embedding spaces to natural language descriptions of single cells using a cell2sentence approach, with application to the Fly Cell Atlas. Currently collaborating to deploy this framework as a public resource for FlyBase.

Institutional & Scholarly Service

Reviewer for scientific journals, including Genome Biology, Cell Reports, and Nature.

Founder and Director, MIT Genomic Deep Learning Journal Club.

Organized and led regular discussions on genomic representation learning, sequence-to-function modeling, single-cell foundation models, electronic health records and precision medicine, and agentic approaches to biomedicine.

Member, Postdoctoral Search Committee, Kellis Lab (MIT). Evaluated and interviewed over 10 postdoctoral candidates, advising on lab recruitment and strategic hiring.

Co-Director, Graduate Peer Mentoring Program (Duke University). Co-directed an institutional initiative pairing senior graduate students with incoming cohorts to facilitate successful lab rotations.

Designed and led training workshops, including seminars on the NSF GRFP application, choosing a graduate mentor, stress and time management, and an overview of career and professional development resources available to students at Duke.

Maintained and expanded a historical database of rotation outcomes to optimize student-PI matching.

Software & Computational Resources

Bioinformatics & Software Engineering

Lead developer of Gonomics, an open-source, high-performance genomics software platform written in Go.

Extensive experience developing scalable computational pipelines for single-cell multi-omics, large-scale comparative genomics, phylogenetics, and sequence-to-function deep learning models.

Languages & Infrastructure

Programming: Python, Go, R, bash/csh.

Infrastructure: High-performance cluster computing (Slurm), Git version control, LaTeX.