publications
2023
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Proteome-wide discovery of cortical proteins that may provide motor resilience to offset the negative effects of pathologies in older adultsThe Journals of Gerontology: Series A, 2023Proteome -
Estrogen receptor genes, cognitive decline, and Alzheimer diseaseNeurology, 2023Transcriptome -
How far are we from personalized gene expression prediction using sequence-to-expression deep neural networks?bioRxiv, 2023GenomeTranscriptome -
The associations of VGF with neuropathologies and cognitive health in older adultsAnnals of Neurology, 2023Proteome -
Polygenic Risk Associated with Alzheimer’s Disease and Other Traits Influences Genes Involved in T Cell Signaling and ActivationbioRxiv, 2023GenomeTranscriptome -
Unconventional Source of Neurotoxic Protein Aggregation from Organelle Off-Target Bax∆ 2 in Alzheimer’s DiseaseBiomolecules, 2023Transcriptome -
The MIND diet, brain transcriptomic alterations, and dementiamedRxiv, 2023GenomeTranscriptome -
SR-TWAS: Leveraging Multiple Reference Panels to Improve TWAS Power by Ensemble Machine LearningmedRxiv, 2023GenomeTranscriptome -
A Molecular Basis of Human Brain ConnectivitybioRxiv, 2023GenomeTranscriptomeProteome -
Spatial Transcriptomics of Human Postmortem Brain Tissue Uncovers Molecular Pathways Associated with Amyloid-Beta PlaquesIn Alzheimer’s Association International Conference, 2023Transcriptome -
Explainable deep learning approach for extracting cognitive features from hand-drawn images of intersecting pentagonsNPJ Digital Medicine, 2023 -
Chasing the cell type-specific molecular networks involved in Alzheimer’s DiseaseIn Alzheimer’s Association International Conference, 2023Transcriptome -
Investigating the role of structural variants in Alzheimer’s Disease and AD-Related traitsIn Alzheimer’s Association International Conference, 2023Genome -
A Three-Stage Algorithm for Quantification of the MMSE Interlocking Pentagon AreasmedRxiv, 2023 -
Associations of cortical SPP1 and ITGAX with cognition and common neuropathologies in older adultsAlzheimer’s & Dementia, 2023TranscriptomeProteome -
Differential gene expression analysis based on linear mixed model corrects false positive inflation for studying quantitative traitsScientific Reports, 2023Transcriptome -
Robust, scalable, and informative clustering for diverse biological networksGenome Biology, 2023Transcriptome
2022
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Inferring protein expression changes from mRNA in Alzheimer’s dementia using deep neural networksNature Communications, 2022TranscriptomeProteome -
The molecular genetic landscape of human brain size variationbioRxiv, 2022GenomeTranscriptome -
Omnibus proteome-wide association study (PWAS-O) identified 43 risk genes for Alzheimer’s disease dementiamedRxiv, 2022GenomeProteome
2021
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Cortical proteins may provide motor resilience in older adultsScientific reports, 2021Proteome -
Stem cell-derived neurons reflect features of protein networks, neuropathology, and cognitive outcome of their aged human donorsNeuron, 2021GenomeTranscriptomeProteome -
Cascading epigenomic analysis for identifying disease genes from the regulatory landscape of GWAS variantsPLoS Genetics, 2021GenomeTranscriptomeDNA Methylation
2020
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Identification of novel genes associated with dysregulation of B cells in patients with primary Sjögren’s syndromeArthritis Research & Therapy, 2020Transcriptome -
Cortical proteins associated with cognitive resilience in community-dwelling older personsJAMA psychiatry, 2020Proteome -
Deep learning decodes the principles of differential gene expressionNature Machine Intelligence, 2020GenomeTranscriptome
2019
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Gene expression and DNA methylation are extensively coordinated with MRI-based brain microstructural characteristicsBrain imaging and behavior, 2019TranscriptomeDNA Methylation -
Association of cortical β-amyloid protein in the absence of insoluble deposits with Alzheimer diseaseJAMA neurology, 2019Proteome -
Transgenic mice overexpressing miR-137 in the brain show schizophrenia-associated behavioral deficits and transcriptome profilesPloS one, 2019Transcriptome -
Cognition may link cortical IGFBP5 levels with motor function in older adultsPLoS One, 2019Proteome -
Using transcriptomic hidden variables to infer context-specific genotype effects in the brainThe American Journal of Human Genetics, 2019GenomeTranscriptome -
Genetic risk for Alzheimer’s dementia predicts motor deficits through multi-omic systems in older adultsTranslational psychiatry, 2019GenomeTranscriptomeDNA MethylationHistone Modifications -
Sleep fragmentation, microglial aging, and cognitive impairment in adults with and without Alzheimer’s dementiaScience advances, 2019Transcriptome
2018
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A molecular network of the aging human brain provides insights into the pathology and cognitive decline of Alzheimer’s diseaseNature neuroscience, 2018Transcriptome -
Multi-omic directed networks describe features of gene regulation in aged brains and expand the set of genes driving cognitive declineFrontiers in genetics, 2018GenomeTranscriptomeDNA MethylationHistone Modifications -
Multi-omics monitoring of drug response in rheumatoid arthritis in pursuit of molecular remissionNature communications, 2018TranscriptomeProteome -
Seasonal plasticity of cognition and related biological measures in adults with and without Alzheimer disease: Analysis of multiple cohortsPLoS medicine, 2018Transcriptome -
The molecular and neuropathological consequences of genetic risk for Alzheimer’s dementiaFrontiers in neuroscience, 2018GenomeTranscriptomeProteomeDNA MethylationHistone Modifications
2017
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CLK-dependent exon recognition and conjoined gene formation revealed with a novel small molecule inhibitorNature Communications, 2017Transcriptome -
Multiomic disease signatures converge to cytotoxic CD8 T cells in primary Sjögren’s syndromeAnnals of the Rheumatic Diseases, 2017GenomeTranscriptomeProteome
2015
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Bayesian network reconstruction using systems genetics data: comparison of MCMC methodsGenetics, 2015GenomeTranscriptome
2012
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Phosphoproteome-based systems analysis of signal transduction networksFrontiers in Physiology, 2012Phosphoproteome
2010
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Phosphoproteome-based modeling defines the regulatory mechanism underlying aberrant EGFR signalingPloS one, 2010Phosphoproteome -
Tyrosine-Phosphoproteome DynamicsSystems Biology for Signaling Networks, 2010Phosphoproteome
2009
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Temporal perturbation of tyrosine phosphoproteome dynamics reveals the system-wide regulatory networksMolecular & Cellular Proteomics, 2009Phosphoproteome
2006
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Modeling and estimation of dynamic EGFR pathway by data assimilation approach using time series proteomic dataGenome Informatics, 2006Phosphoproteome -
High-throughput temporal analysis of phosphotyrosine-dependent signaling networks by gel-free quantitative proteomicsIn MOLECULAR & CELLULAR PROTEOMICS, 2006Phosphoproteome
