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View article: IFN-γ drives long-term bone marrow niche dysfunction following chemotherapy
IFN-γ drives long-term bone marrow niche dysfunction following chemotherapy Open
Since their introduction in the 1960s, chemotherapy agents have remained a cornerstone of treatment for hematopoietic malignancies. However, their non-specific cytotoxic effects extend beyond malignant cells, inflicting collateral damage o…
View article: Stabilized marker gene identification and functional annotation from single-cell transcriptomic data
Stabilized marker gene identification and functional annotation from single-cell transcriptomic data Open
With the rapid emergence of single-cell transcriptomics datasets, reproducible marker genes and functional annotation of cell type or state is becoming increasingly important. Conventional methods that rely on differential gene expression …
View article: Neurodevelopmental hijacking of oligodendrocyte lineage programs drives glioblastoma infiltration
Neurodevelopmental hijacking of oligodendrocyte lineage programs drives glioblastoma infiltration Open
Glioblastoma (GBM) is an aggressive brain tumor with a highly invasive nature. Despite the clinical relevance of this behavior, the molecular underpinnings of infiltrating GBM cells in the peritumoral zone remain underexplored in patients.…
View article: iSHARC: Integrating scMultiome data for heterogeneity and regulatory analysis in cancer
iSHARC: Integrating scMultiome data for heterogeneity and regulatory analysis in cancer Open
Summary The 10x Genomics single cell Multiome (scMultiome) assay enables the simultaneous profiling of chromatin accessibility and gene expression from the same nucleus, and has increasingly been utilized in revealing cellular heterogeneit…
View article: EPCO-28. UNVEILING INVASIVE MECHANISMS OF GLIOBLASTOMA CELLS THROUGH MULTIMODAL SINGLE-CELL SEQUENCING
EPCO-28. UNVEILING INVASIVE MECHANISMS OF GLIOBLASTOMA CELLS THROUGH MULTIMODAL SINGLE-CELL SEQUENCING Open
Glioblastoma (GBM) is the most common malignancy of the central nervous system, characterized by a dismal prognosis and inevitable recurrence despite aggressive standard-of-care therapy. Extensive colonization of the surrounding brain pare…
View article: Stabilized marker gene identification and functional annotation from single-cell transcriptomic data
Stabilized marker gene identification and functional annotation from single-cell transcriptomic data Open
With the rapid emergence of single-cell transcriptomics datasets, reproducible marker genes and functional annotation of cell type or state are becoming increasingly important. Conventional methods that rely on differential gene expression…
View article: An expression-directed linear mixed model discovering low-effect genetic variants
An expression-directed linear mixed model discovering low-effect genetic variants Open
Detecting genetic variants with low-effect sizes using a moderate sample size is difficult, hindering downstream efforts to learn pathology and estimating heritability. In this work, by utilizing informative weights learned from training g…
View article: cLD: Rare-variant linkage disequilibrium between genomic regions identifies novel genomic interactions
cLD: Rare-variant linkage disequilibrium between genomic regions identifies novel genomic interactions Open
Linkage disequilibrium (LD) is a fundamental concept in genetics; critical for studying genetic associations and molecular evolution. However, LD measurements are only reliable for common genetic variants, leaving low-frequency variants un…
View article: XA4C: eXplainable representation learning via Autoencoders revealing Critical genes
XA4C: eXplainable representation learning via Autoencoders revealing Critical genes Open
Machine Learning models have been frequently used in transcriptome analyses. Particularly, Representation Learning (RL), e.g., autoencoders, are effective in learning critical representations in noisy data. However, learned representations…
View article: Cover Image
Cover Image Open
The cover image is based on the Research Article Enterolactone and trabectedin suppress epithelial ovarian cancer synergistically via upregulating THBS1 by Zheng Zeng and Caiji Lin et al., https://doi.org/10.1002/ptr.7942 . image
View article: IBAS: Interaction-bridged association studies discovering novel genes underlying complex traits
IBAS: Interaction-bridged association studies discovering novel genes underlying complex traits Open
The contribution of genetic variants to a complex phenotype may be mediated by various forms of complicated interactions. Currently, the discovery of genetic variants underlying interaction is limited, partly due to that the real interacti…
View article: XA4C: eXplainable representation learning via Autoencoders revealing Critical genes
XA4C: eXplainable representation learning via Autoencoders revealing Critical genes Open
Machine Learning models have been frequently used in transcriptome analyses. Particularly, Representation Learning (RL), e.g., autoencoders, are effective in learning critical representations in noisy data. However, learned representations…
View article: An expression-directed linear mixed model (edLMM) discovering low-effect genetic variants
An expression-directed linear mixed model (edLMM) discovering low-effect genetic variants Open
Detecting genetic variants with low effect sizes using a moderate sample size is difficult, hindering downstream efforts to learn pathology and estimating heritability. In this work, by utilizing informative weights learned from training g…
View article: Stabilized COre gene and Pathway Election uncovers pan-cancer shared pathways and a cancer-specific driver
Stabilized COre gene and Pathway Election uncovers pan-cancer shared pathways and a cancer-specific driver Open
Approaches systematically characterizing interactions via transcriptomic data usually follow two systems: (i) coexpression network analyses focusing on correlations between genes and (ii) linear regressions (usually regularized) to select …
View article: ptsuite: Fast Tail Index Estimation for Power Law Distributions in R
ptsuite: Fast Tail Index Estimation for Power Law Distributions in R Open
Power law distributions, in particular Pareto distributions, describe data across diverse areas of study. We have developed a package, ptsuite, in R to estimate the tail index for such datasets which: a) uses a variety of estimation method…
View article: SCOPE: Stabilized COre gene and Pathway Election
SCOPE: Stabilized COre gene and Pathway Election Open
This repository contains code (SCOPE_Functions.R) and TCGA data required to run SCOPE reflecting the results produced in the "Stabilized COre gene and Pathway Election uncovers pan-cancer shared pathways and a cancer specific driver" manus…
View article: cLD: Rare-variant disequilibrium between genomic regions identifies novel genomic interactions
cLD: Rare-variant disequilibrium between genomic regions identifies novel genomic interactions Open
Linkage disequilibrium (LD) is a fundamental concept in genetics; critical for studying genetic associations and molecular evolution. However, LD measurements are only reliable for common genetic variants, leaving low-frequency variants un…
View article: Explainable autoencoder-based representation learning for gene expression data
Explainable autoencoder-based representation learning for gene expression data Open
Modern machine learning methods have been extensively utilized in gene expression data analysis. In particular, autoencoders (AE) have been employed in processing noisy and heterogenous RNA-Seq data. However, AEs usually lead to “black-box…
View article: Stabilized COre gene and Pathway Election uncovers pan-cancer shared pathways and a cancer specific driver
Stabilized COre gene and Pathway Election uncovers pan-cancer shared pathways and a cancer specific driver Open
Summary Approaches systematically characterizing interactions via transcriptomic data usually follow two systems: (1) co-expression network analyses focusing on correlations between genes; (2) linear regressions (usually regularized) to se…
View article: Disentangling genetic feature selection and aggregation in transcriptome-wide association studies
Disentangling genetic feature selection and aggregation in transcriptome-wide association studies Open
The success of transcriptome-wide association studies (TWAS) has led to substantial research toward improving the predictive accuracy of its core component of genetically regulated expression (GReX). GReX links expression information with …
View article: kTWAS: Integrating kernel-machine with transcriptome-wide association studies improves statistical power and reveals novel genes
kTWAS: Integrating kernel-machine with transcriptome-wide association studies improves statistical power and reveals novel genes Open
The power of genotype-phenotype association mapping studies increases greatly when contributions from multiple variants in a focal region are meaningfully aggregated. Currently, there are two popular categories of variant aggregation metho…
View article: Fast Tail Index Estimation for Power Law Distributions in R
Fast Tail Index Estimation for Power Law Distributions in R Open
Power law distributions, in particular Pareto distributions, describe data across diverse areas of study. We have developed a package in R to estimate the tail index for such datasets focusing on speed (in particular with large datasets), …
View article: Evaluation of A Phylogenetic Pipeline to Examine Transmission Networks in A Canadian HIV Cohort
Evaluation of A Phylogenetic Pipeline to Examine Transmission Networks in A Canadian HIV Cohort Open
Modern computational methods using patient Human Immunodeficiency Virus type 1 (HIV-1) genetic sequences can model population-wide viral transmission dynamics. Accurate transmission inferences can play a critical role in the characterizati…
View article: Revisiting Feller Diffusion: Derivation and Simulation
Revisiting Feller Diffusion: Derivation and Simulation Open
We propose a simpler derivation of the probability density function of Feller Diffusion by using the Fourier Transform on the associated Fokker-Planck equation and then solving the resulting equation via the Method of Characteristics. We u…