Carles Boix Adserà

Postdoc, Harvard Medical School

carles_boix [AT] hms.harvard.edu

I am a postdoc at Harvard Medical School working with Shamil Sunyaev.

I develop computational approaches, methods, and resources to study the genetic and molecular underpinnings of human disease, with a focus on neurodegeneration. I am particularly interested in understanding the impacts of genetic variation across a spectrum of varying molecular and cellular contexts. My research interests include:

  • Mapping molecular mechanisms to endophenotypes in a context-specific manner
  • Progression, resilience, and vulnerability to neurodegeneration
  • Convergence of disease-associated variation onto common mechanisms
  • Proximal mechanisms of disease-associated variation
  • Learning structured representations of molecular processes

    • Before this, I received my Ph.D. from MIT in Computational and Systems Biology under the supervision of Manolis Kellis. My research focused on understanding Alzheimer's disease progression and the role of DNA damage in neurodegeneration, in collaboration with Li-Huei Tsai's group. I also developed epigenomic references and methods for understanding gene regulation and complex disease.

    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. *indicates equal contribution.

    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

    HTML Code Data/Website

    Neuronal DNA double-strand breaks lead to genome structural variations and 3D genome disruption in neurodegeneration

    Vishnu Dileep*, Carles A. Boix*, Hansruedi Mathys, Asaf Marco, [...], David A. Bennett, Manolis Kellis, Li-Huei Tsai. Cell, 2023

    HTML Data/Website

    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

    HTML Data/Website

    Single-cell atlas reveals correlates of high cognitive function, dementia, and resilience to Alzheimer’s disease pathology

    Hansruedi Mathys*, Zhuyu Peng*, Carles A. Boix*, Matheus B. Victor, [...], David A. Bennett, Manolis Kellis, Li-Huei Tsai. Cell, 2023

    HTML Data/Website

    The ENCODE Imputation Challenge: a critical assessment of methods for cross-cell type imputation of epigenomic profiles

    Jacob Schreiber*, Carles A. Boix*, Jin wook Lee, Hongyang Li, [...], Manolis Kellis, William Stafford, Anshul Kundaje. Genome Biology, 2023

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    Neurons burdened by DNA double-strand breaks incite microglia activation through antiviral-like signaling in neurodegeneration

    Gwyneth M. Welch, Carles A. Boix, Eloi Schmauch, Jose Davila-Velderrain, [...], Andreas R. Pfenning, Manolis Kellis, Li-Huei Tsai. Science Advances, 2023

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    Single-cell mosaicism analysis reveals cell-type-specific somatic mutational burden in Alzheimer’s Dementia

    Maria Kousi*, Carles A. Boix*, Yongjin P. Park, Hansruedi Mathys, Samuel Sledzieski, Zhuyu Peng, David A. Bennett, Li-Huei Tsai, Manolis Kellis. BioRxiv, 2022

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    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

    HTML Code Data/Website

    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

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    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

    HTML Code Data/Website

    Neuronal DNA double-strand breaks lead to genome structural variations and 3D genome disruption in neurodegeneration

    Vishnu Dileep*, Carles A. Boix*, Hansruedi Mathys, Asaf Marco, [...], David A. Bennett, Manolis Kellis, Li-Huei Tsai. Cell, 2023

    HTML Data/Website

    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

    HTML Data/Website

    Single-cell atlas reveals correlates of high cognitive function, dementia, and resilience to Alzheimer’s disease pathology

    Hansruedi Mathys*, Zhuyu Peng*, Carles A. Boix*, Matheus B. Victor, [...], David A. Bennett, Manolis Kellis, Li-Huei Tsai. Cell, 2023

    HTML Data/Website

    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

    HTML Data/Website

    Multitissue H3K27ac profiling of GTEx samples links epigenomic variation to disease

    Lei Hou*, Xushen Xiong*, Yongjin Park, Carles Boix, [...], Chad Nusbaum, François Aguet, Kristin G. Ardlie & Manolis Kellis. Nature Genetics, 2023

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    The ENCODE Imputation Challenge: a critical assessment of methods for cross-cell type imputation of epigenomic profiles

    Jacob Schreiber*, Carles A. Boix*, Jin wook Lee, Hongyang Li, [...], Manolis Kellis, William Stafford, Anshul Kundaje. Genome Biology, 2023

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    GENCODE: reference annotation for the human and mouse genomes in 2023

    One of many in GENCODE. Nucleic Acids Research, 2023

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    Neurons burdened by DNA double-strand breaks incite microglia activation through antiviral-like signaling in neurodegeneration

    Gwyneth M. Welch, Carles A. Boix, Eloi Schmauch, Jose Davila-Velderrain, [...], Andreas R. Pfenning, Manolis Kellis, Li-Huei Tsai. Science Advances, 2023

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    Single-cell mosaicism analysis reveals cell-type-specific somatic mutational burden in Alzheimer’s Dementia

    Maria Kousi*, Carles A. Boix*, Yongjin P. Park, Hansruedi Mathys, Samuel Sledzieski, Zhuyu Peng, David A. Bennett, Li-Huei Tsai, Manolis Kellis. BioRxiv, 2022

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    Single-cell dissection of live human hearts in ischemic heart disease and heart failure reveals cell-type-specific driver genes and pathways

    Suvi Linna-Kuosmanen*, Eloi Schmauch*, Kyriakitsa Galani, Carles A Boix, [...], Guillermo Garcia-Cardena, Tuomas Kiviniemi, Manolis Kellis. BioRxiv, 2021

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    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

    HTML Code Data/Website

    GENCODE 2021

    One of many in GENCODE. Nucleic Acids Research, 2021

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    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

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    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

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    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

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    Resources

    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

    This website uses the website template and design from Martin Saveski
    Carles Boix Adserà
    carles_boix [AT] hms.harvard.edu