Carles Boix Adserà
Postdoc, Harvard Medical School
carles_boix [AT] hms.harvard.edu
I am a postdoc at Harvard Medical School working for 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:
Before this, I received my Ph.D. from MIT under the supervision of Manolis Kellis in Computational and Systems Biology, where I studied disease progression and the role of DNA damage in neurodegeneration (with Li-Huei Tsai) and 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.
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, Gwyneth Margaret Welch, Hiruy S. Meharena, Anjanet Loon, Ritika Jeloka, Zhuyu Peng, 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, Kyriaki Galani, Matheus B. Victor, Na Sun, Lei Hou, Li-Lun Ho, Julio Mantero, Aine Ni Scannail, Vishnu Dileep, Weixiu Dong, Hansruedi Mathys, David A. Bennett, Li-Huei Tsai, Manolis Kellis. Cell, 2023
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, Noelle Leary, Sudhagar Babu, Ghada Abdelhady, Xueqiao Jiang, Ayesha P. Ng, Kimia Ghafari, Alexander K. Kunisky, Julio Mantero, Kyriaki Galani, Vanshika N. Lohia, Gabrielle E. Fortier, Yasmine Lotfi, Jason Ivey, Hannah P. Brown, Pratham R. Patel, Nehal Chakraborty, Jacob I. Beaudway, Elizabeth J. Imhoff, Cameron F. Keeler, Maren M. McChesney, Haishal H. Patel, Sahil P. Patel, Megan T. Thai, David A. Bennett, Manolis Kellis, Li-Huei Tsai. Cell, 2023
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, Yuanfang Guan, Chun-Chieh Chang, Jen-Chien Chang, Alex Hawkins-Hooker, Bernhard Schölkopf, Gabriele Schweikert, Mateo Rojas Carulla, Arif Canakoglu, Francesco Guzzo, Luca Nanni, Marco Masseroli, Mark James Carman, Pietro Pinoli, Chenyang Hong, Kevin Y Yip, Jeffrey P Spence, Sanjit Singh Batra, Yun S Song, Shaun Mahony, Zheng Zhang, Wuwei Tan, Yang Shen, Yuanfei Sun, Minyi Shi, Jessika Adrian, Richard Sandstrom, Nina Farrell, Jessica Halow, Kristen Lee, Lixia Jiang, Xinqiong Yang, Charles Epstein, J Seth Strattan, Bradley Bernstein, Michael Snyder, Manolis Kellis, William Stafford, Anshul Kundaje. Genome Biology, 2023
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, Matheus B. Victor, Vishnu Dileep, P. Lorenzo Bozzelli, Qiao Su, Jemmie D. Cheng, Audrey Lee, Noelle S. Leary, Andreas R. Pfenning, Manolis Kellis, Li-Huei Tsai. Science Advances, 2023
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
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
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, Gwyneth Margaret Welch, Hiruy S. Meharena, Anjanet Loon, Ritika Jeloka, Zhuyu Peng, 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, Kyriaki Galani, Matheus B. Victor, Na Sun, Lei Hou, Li-Lun Ho, Julio Mantero, Aine Ni Scannail, Vishnu Dileep, Weixiu Dong, Hansruedi Mathys, David A. Bennett, Li-Huei Tsai, Manolis Kellis. Cell, 2023
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, Noelle Leary, Sudhagar Babu, Ghada Abdelhady, Xueqiao Jiang, Ayesha P. Ng, Kimia Ghafari, Alexander K. Kunisky, Julio Mantero, Kyriaki Galani, Vanshika N. Lohia, Gabrielle E. Fortier, Yasmine Lotfi, Jason Ivey, Hannah P. Brown, Pratham R. Patel, Nehal Chakraborty, Jacob I. Beaudway, Elizabeth J. Imhoff, Cameron F. Keeler, Maren M. McChesney, Haishal H. Patel, Sahil P. Patel, Megan T. Thai, 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, Aine Ni Scannail, Noelle Leary, Shaniah Prosper, Soujanya Viswanathan, Xochitl Luna, Carles A. Boix, Benjamin T. James, Yosuke Tanigawa, Kyriaki Galani, Hansruedi Mathys, Xueqiao Jiang, Ayesha P. Ng, 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, Benjamin James, Na Sun, Liang He, Aman Patel, Zhizhuo Zhang, Benoit Molinie, Nicholas Van Wittenberghe, Scott Steelman, Chad Nusbaum, François Aguet, Kristin G. Ardlie & Manolis Kellis. Nature Genetics, 2023
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, Yuanfang Guan, Chun-Chieh Chang, Jen-Chien Chang, Alex Hawkins-Hooker, Bernhard Schölkopf, Gabriele Schweikert, Mateo Rojas Carulla, Arif Canakoglu, Francesco Guzzo, Luca Nanni, Marco Masseroli, Mark James Carman, Pietro Pinoli, Chenyang Hong, Kevin Y Yip, Jeffrey P Spence, Sanjit Singh Batra, Yun S Song, Shaun Mahony, Zheng Zhang, Wuwei Tan, Yang Shen, Yuanfei Sun, Minyi Shi, Jessika Adrian, Richard Sandstrom, Nina Farrell, Jessica Halow, Kristen Lee, Lixia Jiang, Xinqiong Yang, Charles Epstein, J Seth Strattan, Bradley Bernstein, Michael Snyder, Manolis Kellis, William Stafford, Anshul Kundaje. Genome Biology, 2023
GENCODE: reference annotation for the human and mouse genomes in 2023
One of many in GENCODE. Nucleic Acids Research, 2023
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, Matheus B. Victor, Vishnu Dileep, P. Lorenzo Bozzelli, Qiao Su, Jemmie D. Cheng, Audrey Lee, Noelle S. Leary, Andreas R. Pfenning, Manolis Kellis, Li-Huei Tsai. Science Advances, 2023
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
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, Lei Hou, Tiit Örd, Anu Toropainen, Lindsey K Stolze, Elamaran Meibalan, Julio C Mantero, Ashley Renfro, Johannes Ojanen, Leandro Z Agudelo, Maija Hollmen, Juho Jalkanen, Jarmo Gunn, Pasi Tavi, Casey E Romanoski, Calum A MacRae, Minna U Kaikkonen, Guillermo Garcia-Cardena, Tuomas Kiviniemi, Manolis Kellis. BioRxiv, 2021
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
GENCODE 2021
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, Michael Alexanian, Gaia Andreoletti, Sophie Shen, Yuliangzi Sun, Brad Balderson, Carles Boix, Guangdun Peng, Naihe Jing, Yuliang Wang, Manolis Kellis, Patrick PL Tam, Aaron Smith, Michael Piper, Lionel Christiaen, 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
