George C. Tseng

Novel transplantable mouse cell line model recapitulates invasive lobular breast carcinoma (ILC) phenotype and immune microenvironment.

The paper develops a novel mouse cell line model of invasive lobular breast carcinoma that recapitulates human tumor phenotype and immune microenvironment, offering a preclinical platform for therapy evaluation.

Systemic and local chronic inflammation and hormone disposition promote a tumor-permissive environment for breast cancer in older women

This study shows that chronic inflammation and hormonal changes in older women create a tumor-permissive environment for ER+ breast cancer by increasing local estradiol and immune dysfunction.

Gene-specific exponent-corrected normalization for library size in bulk RNA-seq

The paper introduces gecco, a gene-specific normalization method for bulk RNA-seq that reduces library size bias while preserving biological signal, improving differential expression and pathway analysis.

Estrogen receptor-positive cell line xenograft models recapitulate metastatic dissemination and endocrine response of invasive lobular breast carcinoma

This study shows that ER-positive ILC xenograft models replicate metastatic patterns and endocrine response of human invasive lobular breast carcinoma.

AI-guided analysis of human pancreatic islet sociology reveals distinct cell compositional changes in type 1 diabetes

The paper uses AI to analyze pancreatic islet composition in type 1 diabetes, finding age, sex, and region-dependent changes and beta-cell loss with reciprocal cell expansion.

Early-life mucosal T cells direct intestinal stem cell fate via a coordinated developmental program

This study shows that early-life mucosal T cells promote intestinal stem cell renewal and secretory differentiation through direct interactions and signaling, with impaired function in NEC and adult T cells.

Benchmarking scRNA-seq Copy Number Inference: A Comprehensive Evaluation and Practitioner Guide

This study benchmarks 12 scRNA-seq CNV inference methods across 28 datasets, finding allele-aware tools perform better with high-quality allelic data, while expression-centric tools are reliable with raw data.

Unraveling Tissue-Specific Molecular Signatures and Convergent Pathway Enrichments in Suicidal Behavior

This study identifies tissue-specific molecular signatures and convergent pathways in suicide by analyzing transcriptomic data from blood and brain tissues.

Bayesian rhythmic model for jointly detecting circadian biomarkers and predicting molecular circadian time in human post-mortem brain transcriptome

BayCT detects circadian biomarkers and estimates molecular circadian time in human brain transcriptomes, outperforming existing methods by jointly addressing both tasks.

Deep Disentangled Representation Learning Reveals Neuron Subtype-Specific Nuclear Morphologies Across Aging in Mice and Humans

The paper develops a computational pipeline to link nuclear morphology to mRNA expression in neurons across aging in mice and humans, revealing subtype-specific morphology differences and age-related interactions.

Molecular and cellular rhythms in excitatory and inhibitory neurons in the mouse prefrontal cortex

This study identifies cell-type and sex-specific gene expression and electrophysiological rhythms in mouse prefrontal cortex neurons, showing differences in rhythmic transcripts and biological processes between excitatory pyramidal cells and inhibitory PV interneurons.

In utero human intestine contains maternally derived bacterial metabolites

The paper shows that microbial metabolites in fetal intestines are maternally derived and may regulate fetal immunity and prepare the gut for postnatal microbes.

Comparative transcriptomic rhythms in the mouse and human prefrontal cortex

This study compares circadian transcriptomic rhythms in mouse and human prefrontal cortex subregions, finding conserved signaling with sex-specific phase shifts and species-specific rhythmic transcript identities.

Comprehensive evaluation and practical guideline of gating methods for high-dimensional cytometry data: manual gating, unsupervised clustering, and auto-gating

This study evaluates manual gating, unsupervised clustering, and auto-gating methods for high-dimensional cytometry data using six datasets and provides practical guidelines for selecting appropriate methods.

Identification of the MRTFA/SRF pathway as a critical regulator of quiescence in cancer.

This study identifies the MRTFA/SRF pathway as a regulator of quiescence in cancer and shows that inhibiting it induces quiescence and reduces tumor growth.

Mutual information for detecting multi-class biomarkers when integrating multiple bulk or single-cell transcriptomic studies

The paper introduces MICA, a method to detect multi-class biomarkers across multiple transcriptomic studies, showing improved accuracy and biological insights in both bulk and single-cell data.

Sex-specific Regulation of Fentanyl Reward by the Circadian Transcription Factor NPAS2

This study identifies sex-specific roles of NPAS2 in fentanyl reward and addiction mechanisms in mice and humans.

IFDlong: an isoform and fusion detector for accurate annotation and quantification of long-read RNA-seq data

IFDlong is a tool for detecting and quantifying isoform and fusion transcripts in long-read RNA-seq data, showing high accuracy and performance in simulations and real datasets.

An EEG Signature of MCH Neuron Activities Predicts Cocaine Seeking

This study identifies an EEG signature that tracks MCH neuron activity and predicts cocaine seeking behavior in rats.

Single nuclei transcriptomics in human and non-human primate striatum implicates neuronal DNA damage and proinflammatory signaling in opioid use disorder

The paper uses single nuclei RNA-sequencing to identify striatal cell types in humans and rhesus macaques and finds molecular changes linked to opioid use disorder.

Differential Effects of Cocaine and Morphine on the Diurnal Regulation of the Mouse Nucleus Accumbens Proteome

This study examines how cocaine and morphine affect diurnal proteome rhythms in the mouse nucleus accumbens, revealing distinct pathway alterations.

Circadian rhythm disruptions associated with opioid use disorder in the synaptic proteomes of the human dorsolateral prefrontal cortex and nucleus accumbens

The paper identifies synaptic protein alterations and circadian rhythm disruptions in brain regions associated with opioid use disorder using proteomics.

A sparse negative binomial classifier with covariateadjustment for RNA-seq data

The paper develops a sparse negative binomial classifier for RNA-seq data that adjusts for covariates and improves prediction accuracy and feature selection.

The ultradian transcriptome of the human prefrontal cortex and abnormalities in schizophrenia

The paper identifies 12-hour ultradian rhythms in the human prefrontal cortex and shows disruptions in schizophrenia affecting genes related to protein processing and mitochondrial function.

Molecular rhythm alterations in prefrontal cortex and nucleus accumbens associated with opioid use disorder

The paper investigates molecular rhythm alterations in the prefrontal cortex and nucleus accumbens of individuals with opioid use disorder, finding distinct rhythmic transcript patterns and associations with sleep and neurotransmitter systems.

High-dimension to high-dimension screening for detecting genome-wide epigenetic regulators of gene expression

The paper introduces a screening method to identify genome-wide epigenetic regulators of gene expression by reducing dimensionality in both predictors and responses.

Experimental Design and Power Calculation in Omics Circadian Rhythmicity Detection

This paper introduces CircaPower, a statistical method for power calculation in circadian rhythmicity detection, validated through simulations and real data.

CAMO: A molecular congruence analysis framework for evaluating model organisms

CAMO evaluates omics congruence between model organisms and humans by analyzing differential analysis, concordance, pathway investigations, and subnetwork detection.

Transcriptional alterations in opioid use disorder reveal an interplay between neuroinflammation and synaptic remodeling

This study identifies transcriptional changes in opioid use disorder brains, linking neuroinflammation and synaptic remodeling through RNA-seq and integrative analyses.

Likelihood-based Tests for Detecting CircadianRhythmicity and Differential Circadian Patterns in Transcriptomic Applications

This paper introduces likelihood-based methods to detect circadian rhythmicity and differential circadian patterns in transcriptomic data, showing improved error control and power in simulations and real data.