I am a computational biologist and postdoctoral research fellow in the Department of Biomedical Informatics at Harvard Medical School, working with Shamil Sunyaev and supported by an NIA K99/R00 Pathway to Independence award.
I develop statistical genetics methods, mechanistic interpretability tools for AI models, and genomic resources to study the molecular basis of human disease, with a focus on neurodegeneration. My research interests include:
- Partitioning traits into molecular mechanisms. Developing methods that use the shared effects of genetic variants across traits to identify molecular pathways underlying complex disease, model disease heterogeneity, and find genes whose loss protects against disease.
- Sequence-level mechanisms of variation. Dissecting how variants alter DNA, RNA, and protein function, from biophysical effects to gene regulation in specific cellular contexts, both individually and in combination.
- Learning new biology from sequence models. Building tools to interpret biological sequence models and using these models to understand the molecular effects of variants and their interactions.
- 3′UTRs in neuronal function. Mapping how alternative polyadenylation shapes mRNA localization and local translation in neurons, identifying the sequence determinants of these downstream functions of 3′UTRs, and understanding how these processes are disrupted in neurodegeneration.
- Selective neuronal vulnerability. Identifying the molecular mechanisms that make specific neuronal populations vulnerable in Parkinson's and Alzheimer's disease, and how genetic risk converges on these cell types.
Before this, I received my Ph.D. in Computational and Systems Biology from MIT with Manolis Kellis. There, I built EpiMap, linking disease loci to the tissues and enhancer programs through which they act, and developed methods for atlas-scale single-cell data. With Li-Huei Tsai's group, I co-led single-cell studies of more than 400 aged and Alzheimer's brains, identified selectively vulnerable neurons, and helped map how DNA double-strand breaks disrupt neuronal genome organization in AD.
I received my undergraduate degree from Princeton University, where I worked with John Storey on statistics for high-dimensional genomic data.
Publications
A full set of publications can be found on Google Scholar.
* equal contribution; + co-corresponding author
Single-cell profiling and genetic regulation of alternative polyadenylation in the human brain
Jiuhong Nan*, Carles A. Boix*+, Shaohui Shi*, Xiaoxi Fan, , Shamil Sunyaev, Jingyun Li, Xushen Xiong+. Nature Genetics, 2026
Single-cell multiregion dissection of Alzheimer’s disease
Hansruedi Mathys*, Carles A. Boix*, Leyla Anne Akay*, Ziting Xia, , David A. Bennett, Li-Huei Tsai+, Manolis Kellis+. Nature, 2024
Vishnu Dileep*+, Carles A. Boix*, Hansruedi Mathys, Asaf Marco, , David A. Bennett, Manolis Kellis+, Li-Huei Tsai+. Cell, 2023
Epigenomic dissection of Alzheimer’s disease pinpoints causal variants and reveals epigenome erosion
Xushen Xiong*, Benjamin T. James*, Carles A. Boix*, Yongjin P. Park, , David A. Bennett, Li-Huei Tsai+, Manolis Kellis+. Cell, 2023
Hansruedi Mathys*+, Zhuyu Peng*, Carles A. Boix*, Matheus B. Victor, , David A. Bennett, Manolis Kellis+, Li-Huei Tsai+. Cell, 2023
Jacob Schreiber*+, Carles A. Boix*, Jin wook Lee, Hongyang Li, , William Stafford, Anshul Kundaje, ENCODE Imputation Challenge Participants. Genome Biology, 2023
Gwyneth M. Welch, Carles A. Boix, Eloi Schmauch, Jose Davila-Velderrain, , Andreas R. Pfenning, Manolis Kellis, Li-Huei Tsai. Science Advances, 2023
Maria Kousi*, Carles A. Boix*, Yongjin P. Park, Hansruedi Mathys, Samuel Sledzieski, Zhuyu Peng, David A. Bennett, Li-Huei Tsai, Manolis Kellis. BioRxiv, 2022
Regulatory genomic circuitry of human disease loci by integrative epigenomics
Carles A. Boix, Benjamin T. James, Yongjin P. Park, Wouter Meuleman, Manolis Kellis. Nature, 2021
Strain-level diversity drives alternative community types in millimetre-scale granular biofilms
Gabriel E. Leventhal, Carles A. Boix, Urs Kuechler, Tim N. Enke, Elzbieta Sliwerska, Christof Holliger, Otto X. Cordero. Nature Microbiology, 2018
Single-cell profiling and genetic regulation of alternative polyadenylation in the human brain
Jiuhong Nan*, Carles A. Boix*+, Shaohui Shi*, Xiaoxi Fan, , Shamil Sunyaev, Jingyun Li, Xushen Xiong+. Nature Genetics, 2026
Alice E Stanton*, Jinyoung Kang*, Joel W Blanchard*, Carles A Boix, , Robert Langer, Edward Boyden+, Li-Huei Tsai+. BioRxiv, 2026
Molecular hallmarks of excitatory and inhibitory neuronal resilience to Alzheimer’s disease
Isabel Castanho*, Pourya Naderi Yeganeh*, Carles A Boix, Sarah L Morgan, , Manolis Kellis, Rudolph E Tanzi+, Winston Hide+. Molecular Neurodegeneration, 2025
ABCA7 variants impact phosphatidylcholine and mitochondria in neurons
Djuna Von Maydell, Shannon E Wright, Ping-Chieh Pao, Colin Staab, , George Samaan, Manolis Kellis, Li-Huei Tsai. Nature, 2025
Zunpeng Liu*+, Shanshan Zhang*, Benjamin T James, Kyriaki Galani, , David A Bennett, Li-Huei Tsai+, Manolis Kellis+. Cell, 2025
Jialin He*, Lei Xiong*+, Shaohui Shi, Chengyu Li, , Manolis Kellis, Jingyun Li, Xushen Xiong+. Nature Machine Intelligence, 2024
Suvi Linna-Kuosmanen*+, Eloi Schmauch*, Kyriakitsa Galani, Johannes Ojanen, , Pasi Tavi, Tuomas Kiviniemi, Manolis Kellis+. Cell Reports Medicine, 2024
Single-cell multiregion dissection of Alzheimer’s disease
Hansruedi Mathys*, Carles A. Boix*, Leyla Anne Akay*, Ziting Xia, , David A. Bennett, Li-Huei Tsai+, Manolis Kellis+. Nature, 2024
Vishnu Dileep*+, Carles A. Boix*, Hansruedi Mathys, Asaf Marco, , David A. Bennett, Manolis Kellis+, Li-Huei Tsai+. Cell, 2023
Epigenomic dissection of Alzheimer’s disease pinpoints causal variants and reveals epigenome erosion
Xushen Xiong*, Benjamin T. James*, Carles A. Boix*, Yongjin P. Park, , David A. Bennett, Li-Huei Tsai+, Manolis Kellis+. Cell, 2023
Hansruedi Mathys*+, Zhuyu Peng*, Carles A. Boix*, Matheus B. Victor, , David A. Bennett, Manolis Kellis+, Li-Huei Tsai+. Cell, 2023
Human Microglial State Dynamics in Alzheimer’s Disease Progression
Na Sun*, Matheus B. Victor*, Yongjin P. Park, Xushen Xiong, , David A. Bennett, Li-Huei Tsai+, Manolis Kellis+. Cell, 2023
Multitissue H3K27ac profiling of GTEx samples links epigenomic variation to disease
Lei Hou*, Xushen Xiong*, Yongjin Park, Carles Boix, , François Aguet, Kristin G. Ardlie, Manolis Kellis. Nature Genetics, 2023
Jacob Schreiber*+, Carles A. Boix*, Jin wook Lee, Hongyang Li, , William Stafford, Anshul Kundaje, ENCODE Imputation Challenge Participants. Genome Biology, 2023
GENCODE: reference annotation for the human and mouse genomes in 2023
Adam Frankish+, Sílvia Carbonell-Sala, Mark Diekhans, Irwin Jungreis,... (one of many in GENCODE). Nucleic Acids Research, 2023
Gwyneth M. Welch, Carles A. Boix, Eloi Schmauch, Jose Davila-Velderrain, , Andreas R. Pfenning, Manolis Kellis, Li-Huei Tsai. Science Advances, 2023
Maria Kousi*, Carles A. Boix*, Yongjin P. Park, Hansruedi Mathys, Samuel Sledzieski, Zhuyu Peng, David A. Bennett, Li-Huei Tsai, Manolis Kellis. BioRxiv, 2022
Regulatory genomic circuitry of human disease loci by integrative epigenomics
Carles A. Boix, Benjamin T. James, Yongjin P. Park, Wouter Meuleman, Manolis Kellis. Nature, 2021
Adam Frankish, Mark Diekhans, Irwin Jungreis, Julien Lagarde,... (one of many in GENCODE). Nucleic Acids Research, 2021
Conserved epigenetic regulatory logic infers genes governing cell identity
Woo Jun Shim, Enakshi Sinniah, Jun Xu, Burcu Vitrinel, , Quan Nguyen, Mikael Bodén, Nathan J Palpant. Cell systems, 2020
Expanded encyclopaedias of DNA elements in the human and mouse genomes
JE Moore, MJ Purcaro, HE Pratt, CB Epstein, N Shoresh, J Adrian, T Kawli, ... ENCODE Consortium (one of many in ENCODE). Nature, 2020
Strain-level diversity drives alternative community types in millimetre-scale granular biofilms
Gabriel E. Leventhal, Carles A. Boix, Urs Kuechler, Tim N. Enke, Elzbieta Sliwerska, Christof Holliger, Otto X. Cordero. Nature Microbiology, 2018
Resources
Single-cell atlas of alternative polyadenylation in the brain
Single-cell atlas of AD progression across brain regions
scdemon: module detection in scRNA-seq
Single-cell epigenomic landscape of AD
Single-cell atlas of AD and aging PFC
Genomic instability in neurodegeneration
EpiMap data/resources
EpiMap data browser