Vicky Yao
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View article: Interpretable phenotype decoding from multicondition sequencing data with ALPINE
Interpretable phenotype decoding from multicondition sequencing data with ALPINE Open
As sequencing techniques advance in precision, affordability, and diversity, an abundance of heterogeneous sequencing data has become available, encompassing a wide range of phenotypic features and biological perturbations. Unfortunately, …
View article: Influenza A Virus (<scp>H1N1</scp>) Infection Induces Ferroptosis to Promote Developmental Injury in Fetal Tissues
Influenza A Virus (<span>H1N1</span>) Infection Induces Ferroptosis to Promote Developmental Injury in Fetal Tissues Open
H1N1, a globally pervasive subtype of influenza A virus (IAV), poses an ongoing threat to human health and occasionally leads to multi‐organ dysfunction in severe cases. Evidence confirms that the H1N1 virus is enabled to penetrate the pla…
View article: Characterization of the NFAT Gene Family in Grass Carp (Ctenopharyngodon idellus) and Functional Analysis of NFAT1 During GCRV Infection
Characterization of the NFAT Gene Family in Grass Carp (Ctenopharyngodon idellus) and Functional Analysis of NFAT1 During GCRV Infection Open
Nuclear factors of activated T cells (NFATs) are pivotal regulatory factors of immune responses, primarily by modulating T cell activity and regulating inflammatory cytokine gene transcription. The grass carp reovirus (GCRV) triggers a ser…
View article: Ontology-aware DNA methylation classification with a curated atlas of human tissues and cell types
Ontology-aware DNA methylation classification with a curated atlas of human tissues and cell types Open
A bstract DNA methylation (DNAm) is a core gene regulatory mechanism that captures cellular responses to short- and long-term stimuli such as environmental exposures, aging, and cellular differentiation. Although DNAm has proven valuable a…
View article: Gut Microbiota Dysbiosis: Pathogenesis, Diseases, Prevention, and Therapy
Gut Microbiota Dysbiosis: Pathogenesis, Diseases, Prevention, and Therapy Open
Dysbiosis refers to the disruption of the gut microbiota balance and is the pathological basis of various diseases. The main pathogenic mechanisms include impaired intestinal mucosal barrier function, inflammation activation, immune dysreg…
View article: Interpretable phenotype decoding from multi-condition sequencing data with ALPINE
Interpretable phenotype decoding from multi-condition sequencing data with ALPINE Open
As sequencing techniques advance in precision, affordability, and diversity, an abundance of heterogeneous sequencing data has become available, encompassing a wide range of phenotypic features and biological perturbations. Unfortunately, …
View article: Benchmarking gene embeddings from sequence, expression, network, and text models for functional prediction tasks
Benchmarking gene embeddings from sequence, expression, network, and text models for functional prediction tasks Open
Accurate, data-driven representations of genes are critical for interpreting high-throughput biological data, yet no consensus exists on the most effective embedding strategy for common functional prediction tasks. Here, we present a syste…
View article: A best-match approach for gene set analyses in embedding spaces
A best-match approach for gene set analyses in embedding spaces Open
Embedding methods have emerged as a valuable class of approaches for distilling essential information from complex high-dimensional data into more accessible lower-dimensional spaces. Applications of embedding methods to biological data ha…
View article: Disentangling associations between complex traits and cell types with<i>seismic</i>
Disentangling associations between complex traits and cell types with<i>seismic</i> Open
A bstract Integrating single-cell RNA sequencing (scRNA-seq) with Genome-Wide Association Studies (GWAS) can help reveal GWAS-associated cell types, furthering our understanding of the cell-type-specific biological processes underlying com…
View article: A cell autonomous regulator of neuronal excitability modulates tau in Alzheimer’s disease vulnerable neurons
A cell autonomous regulator of neuronal excitability modulates tau in Alzheimer’s disease vulnerable neurons Open
Neurons from layer II of the entorhinal cortex (ECII) are the first to accumulate tau protein aggregates and degenerate during prodromal Alzheimer’s disease. Gaining insight into the molecular mechanisms underlying this vulnerability will …
View article: Splitpea: quantifying protein interaction network rewiring changes due to alternative splicing in cancer
Splitpea: quantifying protein interaction network rewiring changes due to alternative splicing in cancer Open
Protein-protein interactions play an essential role in nearly all biological processes, and it has become increasingly clear that in order to better understand the fundamental processes that underlie disease, we must develop a strong under…
View article: ANDES: a novel best-match approach for enhancing gene set analysis in embedding spaces
ANDES: a novel best-match approach for enhancing gene set analysis in embedding spaces Open
A bstract Embedding methods have emerged as a valuable class of approaches for distilling essential information from complex high-dimensional data into more accessible lower-dimensional spaces. Applications of embedding methods to biologic…
View article: Splitpea: quantifying protein interaction network rewiring changes due to alternative splicing in cancer
Splitpea: quantifying protein interaction network rewiring changes due to alternative splicing in cancer Open
Protein-protein interactions play an essential role in nearly all biological processes, and it has become increasingly clear that in order to better understand the fundamental processes that underlie disease, we must develop a strong under…
View article: Into the Single Cell Multiverse: an End-to-End Dataset for Procedural Knowledge Extraction in Biomedical Texts
Into the Single Cell Multiverse: an End-to-End Dataset for Procedural Knowledge Extraction in Biomedical Texts Open
Many of the most commonly explored natural language processing (NLP) information extraction tasks can be thought of as evaluations of declarative knowledge, or fact-based information extraction. Procedural knowledge extraction, i.e., break…
View article: Joint embedding of biological networks for cross-species functional alignment
Joint embedding of biological networks for cross-species functional alignment Open
Motivation Model organisms are widely used to better understand the molecular causes of human disease. While sequence similarity greatly aids this cross-species transfer, sequence similarity does not imply functional similarity, and thus, …
View article: Oral mucosal breaks trigger anti-citrullinated bacterial and human protein antibody responses in rheumatoid arthritis
Oral mucosal breaks trigger anti-citrullinated bacterial and human protein antibody responses in rheumatoid arthritis Open
Periodontal disease is more common in individuals with rheumatoid arthritis (RA) who have detectable anti-citrullinated protein antibodies (ACPAs), implicating oral mucosal inflammation in RA pathogenesis. Here, we performed paired analysi…
View article: The proto-oncogene DEK regulates neuronal excitability and tau accumulation in Alzheimer’s disease vulnerable neurons
The proto-oncogene DEK regulates neuronal excitability and tau accumulation in Alzheimer’s disease vulnerable neurons Open
SUMMARY Neurons from layer II of the entorhinal cortex (ECII) are the first to accumulate tau protein aggregates and degenerate during prodromal Alzheimer’s disease. Here, we use a data-driven functional genomics approach to model ECII neu…
View article: Joint embedding of biological networks for cross-species functional alignment
Joint embedding of biological networks for cross-species functional alignment Open
Model organisms are widely used to better understand the molecular causes of human disease. While sequence similarity greatly aids this transfer, sequence similarity does not imply functional similarity, and thus, several current approache…
View article: RNA Identification of PRIME Cells Predicting Rheumatoid Arthritis Flares
RNA Identification of PRIME Cells Predicting Rheumatoid Arthritis Flares Open
Longitudinal genomic analysis of rheumatoid arthritis flares revealed PRIME cells in the blood during the period before a flare and suggested a model in which these cells become activated by B cells in the weeks before a flare and subseque…
View article: Accurate genome-wide predictions of spatio-temporal gene expression during embryonic development
Accurate genome-wide predictions of spatio-temporal gene expression during embryonic development Open
Comprehensive information on the timing and location of gene expression is fundamental to our understanding of embryonic development and tissue formation. While high-throughput in situ hybridization projects provide invaluable information …
View article: Selective neuronal vulnerability in Alzheimer’s disease: a network-based analysis
Selective neuronal vulnerability in Alzheimer’s disease: a network-based analysis Open
A major obstacle to treating Alzheimer’s disease (AD) is our lack of understanding of the molecular mechanisms underlying selective neuronal vulnerability, which is a key characteristic of the disease. Here we present a framework to integr…
View article: Transcriptome analysis of adult Caenorhabditis elegans cells reveals tissue-specific gene and isoform expression
Transcriptome analysis of adult Caenorhabditis elegans cells reveals tissue-specific gene and isoform expression Open
The biology and behavior of adults differ substantially from those of developing animals, and cell-specific information is critical for deciphering the biology of multicellular animals. Thus, adult tissue-specific transcriptomic data are c…
View article: A loop-counting method for covariate-corrected low-rank biclustering of gene-expression and genome-wide association study data
A loop-counting method for covariate-corrected low-rank biclustering of gene-expression and genome-wide association study data Open
A common goal in data-analysis is to sift through a large data-matrix and detect any significant submatrices (i.e., biclusters) that have a low numerical rank. We present a simple algorithm for tackling this biclustering problem. Our algor…
View article: Transcriptome Analysis of Adult <i>C. elegans</i> Cells Reveals Tissue-specific Gene and Isoform Expression
Transcriptome Analysis of Adult <i>C. elegans</i> Cells Reveals Tissue-specific Gene and Isoform Expression Open
The biology and behavior of adults differ substantially from those of developing animals, and cell-specific information is critical for deciphering the biology of multicellular animals. Thus, adult tissue-specific transcriptomic data are c…