Li Shen

This study identifies KMT2E as a reader of H3K4me3Q5ser, showing its role in regulating chromatin dynamics and neurodevelopmental gene expression in ODLURO syndrome.

The paper uses deconvolution of bulk RNA-seq to generate cell-type-specific targets for predicting gene expression from personal genome sequences, finding that sequence-derived models outperform genotype-feature baselines.

The paper maps R-loop landscapes in the developing human brain and shows their role in neural differentiation and gene expression programs.

This study identifies QR2 as a reader of H3Q5ser, showing its role in human neuron development through transcriptional and electrophysiological effects.

This study identifies transcriptional differences in mice with antidepressant resistance using RNA sequencing of brain regions after stress and drug treatment.

The paper identifies a shared transcriptional network in the nucleus accumbens that supports stress resilience in both sexes and shows causal effects of hub genes.

This study identifies how GBM cells use Plexin-D1 and Plexin-B2 to gain mechanocompliance, enabling immune-silent invasion through tissue.

This study performs a cell-type-aware transcriptome-wide association study (TWAS) of mammographic density phenotypes, identifying novel genes and prioritizing known GWAS loci through cell-type-specific gene expression analysis.

The paper uses CRISPR-based epigenetic editing to manipulate Cartpt expression in mice, showing it affects cocaine memory acquisition and extinction.

This study shows that oxidation of ΔFOSB at Cys172 regulates its DNA binding and gene expression in the hippocampus, affecting cognitive function under oxidative stress.

This study identifies cortical tension as a mechanical barrier that prevents premature neuronal differentiation during neurogenesis, showing that reducing it accelerates neuronal lineage commitment and differentiation.

AlphaGenome improves gene expression prediction over Enformer but still underperforms compared to models trained on individual-level data.

This paper develops a 3D brain vascular niche model to study GBM invasion and gene signatures, revealing glia-vascular contact influences transcriptional adaptation and poor prognosis.

The paper identifies ZBTB7A as a key regulator of MDD-specific chromatin signatures and astrocyte-mediated stress vulnerability in the orbitofrontal cortex.

This study uses a Transformer-based model to predict 3D chromatin interactions from DNA sequences, improving accuracy over convolutional models by capturing long-range genomic interactions.

This study identifies a novel epigenetic mechanism by which chronic cocaine exposure alters gene expression in nucleus accumbens neurons through H2A.Z depletion and chromatin changes.

This study identifies H3K27me1 as a chromatin scar that mediates lifelong stress susceptibility through its role in altering gene expression in the nucleus accumbens.

FABEL forecasts animal behaviors and locomotion from video using deep learning, showing promise in predicting food interactions and trajectories.

The paper compares gene expression in the nucleus accumbens during cocaine withdrawal and extinction in rats, identifying distinct transcriptional patterns associated with different behavioral outcomes.

The paper shows that serotonin transporter-dependent H3 serotonylation in placenta regulates neurodevelopmental gene networks in embryos.

DeepRegFinder uses deep learning to predict enhancers and promoters from genomic data, outperforming existing methods across multiple cell types.

This study identifies AhR as a regulator of axon regeneration by balancing stress and growth responses after injury, showing that its inhibition promotes regeneration in nerve and spinal cord injury models.

The paper examines transcriptomic changes in D1 and D2 medium spiny neurons of the nucleus accumbens after cocaine and morphine exposure, revealing shared and divergent regulatory patterns.

This study compares transcriptional and cellular changes in brain regions of SARS-CoV-2 infected, Alzheimer's disease, and SARS-CoV-2 infected Alzheimer's disease individuals to identify shared neuroinflammatory and blood-brain barrier alterations.

This study identifies transcriptional changes in the brain reward circuit across heroin exposure and seeking behaviors in mice, revealing molecular mechanisms and potential therapeutic targets for opioid use disorder.

The paper investigates how serotonin modifies histone H3K4me3Q5ser dynamics in the dorsal raphe nucleus under stress and antidepressant exposure, showing its role in gene expression and behavior.

This study identifies RXR as a key regulator of drug reward sensitivity in the nucleus accumbens through transcriptional control of neuronal excitability in mice.

A single enzyme, TGM2, bidirectionally controls H3 monoaminylation dynamics, which, in turn, facilitate neural rhythmicity.

The paper identifies FEDORA, a lncRNA with sex- and cell-type-specific effects on depression in females.