Selected Publications

(* First Author; # Corresponding Author)


Preprint: 

Somatic cancer driver mutations are enriched and associated with inflammatory states in Alzheimer's disease microglia

Huang AY*, Zhou Z*, Talukdar M*, Miller MB, Chhouk B, Enyenihi L, Rosen I, Stronge E, Zhao B, Kim D, Choi J, Khoshkhoo S, Kim J, Ganz J, Travaglini KJ, Gabitto M, Hodge RD, Kaplan E, Lein E, De Jager P, Bennett DA, Lee EA#, Walsh CA#. bioRxiv. 2024


Analysis of DNA from brain tissue on stereo-EEG electrodes reveals mosaic epilepsy-related variants

D'Gama AM*, Phillips HW*, Wang Y*, Chiu MY, Chahine Y, Swanson AC, Smith RS, Pearl PL, Tsuboyama M, Madsen JR, Lidov H, Lee EA, Prabhu SP, Huang AY#, Stone SSD#, Walsh CA#, Poduri A#. medRxiv. 2024


Somatic Mosaicism in Amyotrophic Lateral Sclerosis and Frontotemporal Dementia Reveals Widespread Degeneration from Focal Mutations

Zhou Z*, Kim J*, Huang AY*, Nolan M, Park J, Doan R, Shin T, Miller MB, Chhouk B, Morillo K, Yeh RC, Kenny C, Neil JE, Lee C-Z, Ohkubo T, Ravits J, Ansorge O, Ostrow LW, Lagier-Tourenne C#, Lee EA#, Walsh CA#. bioRxiv. 2023



Peer-reviewed:

Neuropathologically-directed profiling of PRNP somatic and germline variants in sporadic human prion disease

McDonough GA*, Cheng Y*, Morillo K, Doan RN, Kenny CJ, Foutz A, Kim C, Cohen ML, Appleby BS, Walsh CA, Safar JG, Huang AY#, Miller MB#. Acta Neuropathol. (In press)


Somatic Mosaicism in PIK3CA Variant Correlates With Stereoelectroencephalography-Derived Electrophysiology

Phillips HW*, D'Gama AM*, Wang Y*, Chahine Y, Chiu M, Swanson AC, Ahtam B, Bolton JB, Madsen JR, Lee EA, Prabhu SP, Lidov HG, Papadakis J, Huang AY#, Poduri A#, Stone SS#, Walsh CA#. Neurol Genet. 2023


Somatic genomic changes in single Alzheimer’s disease neurons

Miller MB*, Huang AY*, Kim J, Zhou Z, Kirkham SL, Maury EA, Ziegenfuss JS, Reed HC, Neil JE, Rento L, Ryu SC, Ma CC, Luquette LJ, Ames HM, Oakley DH, Frosch MP, Hyman BT, Lodato MA#, Lee EA#, Walsh CA#. Nature. 2022


Somatic mutations in single human cardiomyocytes reveal a rapid increase in age-associated DNA damage and widespread oxidative genotoxicity

Choudhury S*#, Huang AY*, Kim J, Zhou Z, Morillo K, Maury EA, Tsai JW, Miller MB, Lodato MA,  Araten S, Hilal N, Lee EA#, Chen MH#, Walsh CA#. Nat Aging. 2022


Identification of Somatic Mutations From Bulk and Single-Cell Sequencing Data

Huang AY*, Lee EA#. Front Aging. 2022


Parallel RNA and DNA analysis after Deep-sequencing (PRDD-seq) reveals cell type-specific lineage patterns in human brain

Huang AY*, Li P*, Rodin RE, Kim SN, Dou Y, Kenny CJ, Akula SK, Hodge RD, Bakken TE, Miller JA, Lein ES, Park PJ, Lee EA, Walsh CA#. PNAS. 2020


MosaicBase: A Knowledgebase of Postzygotic Mosaic Variants in Noncancer Diseases and Asymptomatic Human Individuals

Yang X*, Yang C*, Zheng X*, Xiong L, Tao Y, Wang M, Ye AY, Wu Q, Dou Y, Luo J, Wei L#, Huang AY#. Genom Proteom Bioinf. 2020


Somatic LINE-1 retrotransposition in cortical neurons and non-brain tissues of Rett patients and healthy individuals

Zhao B*, Wu Q, Ye AY, Guo J, Zheng X, Yang X, Yan L, Liu QR, Hyde TM, Wei L#, Huang AY#. PLoS Genet. 2019


A model for postzygotic mosaicisms quantifies the allele fraction drift, mutation rate, and contribution to de novo mutations

Ye AY*, Dou Y*, Yang X, Wang S, Huang AY#, Wei L#. Genome Res. 2018


Distinctive types of postzygotic single-nucleotide mosaicisms in healthy individuals revealed by genome-wide profiling of multiple organs

Huang AY*#, Yang X*, Wang S, Zheng X, Wu Q, Ye AY, Wei L#. PLoS Genet. 2018


Somatic MAP2K1 Mutations Are Associated with Extracranial Arteriovenous Malformation

Couto JA*, Huang AY*, Konczyk DJ, Goss JA, Fishman SJ, Mulliken, JB, Warman ML, Greene AK#. Am J Hum Genet, 2017


MosaicHunter: accurate detection of postzygotic single-nucleotide mosaicism through next-generation sequencing of unpaired, trio, and paired samples

Huang AY*, Zhang Z*, Ye AY*, Dou Y*, Yan L, Yang X, Zhang Y, Wei L#. Nucleic Acids Res. 2017


Postzygotic single‐nucleotide mosaicisms contribute to the etiology of autism spectrum disorder and autistic traits and the origin of mutations

Dou Y*, Yang X, Li Z, Wang S, Zhang Z, Ye AY, Yan L, Yang C, Wu Q, Li J, Zhao B, Huang AY#, Wei L#. Hum Mutat. 2017 


Postzygotic single-nucleotide mosaicism in whole-genome sequences of clinically unremarkable individuals

Huang AY*, Xu X*, Ye AY*, Wu Q*, Yan L, Zhao B, Yang X, He Y, Wang S, Zhang Z, Gu B, Zhao HQ, Wang  M, Gao H, Gao G, Zhang Z, Yang X, Wu X, Zhang Y#, Wei L#. Cell Res. 2014


Recent adaptive events in human brain revealed by meta-analysis of positively selected genes

Huang Y*, Xie C, Ye AY, Li CY, Gao G, Wei L#. PLoS One. 2013