BaDoi N. Phan

A molecular and spinal circuit basis for the functional segregation of itch and pain

The paper identifies functionally distinct subtypes within Grpr+ neurons in the dorsal horn that mediate itch and mechanical allodynia, demonstrating the utility of genomic enhancer-based strategies for modality-specific targeting.

An Epigenetic Signature of Vulnerable Neurons is Under Selective Pressure Associated with Longevity Across Placental Mammals.

The paper identifies cell-type-specific epigenetic signatures linked to neuronal vulnerability and longevity across placental mammals using epigenomics and AI.

Fine-mapping candidate neuropsychiatric regulatory variants using cell type-aware comparative genomics

The paper introduces CTACIT to fine-map neuropsychiatric regulatory variants by integrating conservation scores with cell type-specific open chromatin data across species.

Local control of dopamine release in nucleus accumbens gates opioid withdrawal aversion

The paper identifies Tshz1 neurons in the nucleus accumbens as critical for withdrawal aversion by modulating dopamine release and mGluR8 activity, offering a new therapeutic target for opioid use disorder.

Context-dependent regulatory variants in Alzheimer's disease

The paper identifies context-dependent regulatory variants in Alzheimer's disease by analyzing their effects across different cellular contexts using MPRAs and machine learning.

Characterization of astrocyte density in the Pitt-Hopkins Syndrome mouse model of ASD

This study investigates the effect of germline TCF4 mutations on astrocyte lineage in a Pitt-Hopkins Syndrome mouse model, finding no significant impact on astrocyte markers or distribution.

Combining Machine Learning and Multiplexed, In Situ Profiling to Engineer Cell Type and Behavioral Specificity

The paper develops a platform combining machine learning and multiplexed in situ screening to identify enhancers with cell-type and behavioral specificity for neural circuit engineering.

Cell Type Specific Enhancers for Dorsolateral Prefrontal Cortex.

The paper identifies cell type-specific enhancers for the DLPFC in NHPs using single nucleus RNA-Seq and ATAC-Seq, validates them with AAV injections, and demonstrates functional expression in specific neuron types.

An in vivo massively parallel platform for deciphering tissue-specific regulatory function

The paper introduces WhAMPRA, an in vivo MPRA platform in mice, to assess tissue-specific regulatory functions of genetic variants and enhancers.

Spatial, transcriptomic and epigenomic analyses link dorsal horn neurons to chronic pain genetic predisposition

The paper links chronic pain genetic variants to dorsal horn neuron subtypes using multi-species single-cell and spatial transcriptomic analyses.

Regression convolutional neural network models implicate peripheral immune regulatory variants in the predisposition to Alzheimer's disease

The paper uses CNN regression models to predict the impact of AD-associated variants on open chromatin in different cell types, finding greater effects in peripheral cells than in microglia or neurons.

Vocal learning-associated convergent evolution in mammalian proteins and regulatory elements

The paper identifies proteins and regulatory elements associated with vocal learning by analyzing bat neural activity and epigenomic data.

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.

Integrative multi-dimensional characterization of striatal projection neuron heterogeneity in adult brain

The paper characterizes striatal projection neuron heterogeneity in mice using single-nuclei multi-omics and spatial mapping, revealing distinct subtypes with unique receptor expression and disease risk contributions.

Integrating gene annotation with orthology inference at scale

TOGA integrates gene annotation and orthology inference across hundreds of genomes, improving ortholog detection and creating large comparative gene resources.

Relating enhancer genetic variation across mammals to complex phenotypes using machine learning

A machine learning approach identifies enhancer-phenotype associations across mammals, revealing links to brain size and behavior evolution.

Insights into mammalian TE diversity via the curation of 248 mammalian genome assemblies

The paper curates TE content in 248 mammalian genomes, finding trends in recent TE accumulation and associations with dietary habits.

Evolutionary constraint and innovation across hundreds of placental mammals

A 240-species placental mammal alignment resolves constraint to single bases, estimating at least 10.7% of the human genome is constrained, with 48.5% of constrained bases unannotated.

Title: Leveraging Base Pair Mammalian Constraint to Understand Genetic Variation and Human Disease

The paper uses evolutionary constraint scores to identify functional genomic regions and finds they are enriched for variants associated with common diseases.

Chiropterans are a hotspot for horizontal transfer of DNA transposons in Mammalia

The paper identifies bats as a hotspot for horizontal transfer of DNA transposons, finding over 200 putative elements and shared transposons across mammals and reptiles.

Machine learning sequence prioritization for cell type-specific enhancer design

The paper introduces SNAIL, a virus-based method using machine learning to design cell type-specific enhancer probes for targeted nuclear isolation and characterization.

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.

Induction of Bdnf from promoter I following electroconvulsive seizures contributes to structural plasticity in neurons of the piriform cortex

The paper shows that Bdnf exon 1 expression is necessary for ECS-induced dendritic spine plasticity in piriform cortex neurons.

Addiction-associated genetic variants implicate brain cell type- and region-specific cis-regulatory elements in addiction neurobiology

The paper identifies addiction-associated genetic variants in brain cell type- and region-specific cis-regulatory elements using GWAS and machine learning.

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.

SPEAQeasy: a Scalable Pipeline for Expression Analysis and Quantification for R/Bioconductor-powered RNA-seq analyses

SPEAQeasy provides a user-friendly, scalable RNA-seq pipeline that simplifies data processing and connects to R/Bioconductor tools for downstream analysis.

The Regulatory Evolution of the Primate Fine-Motor System

The paper compares open chromatin regions in motor cortex subdivisions across primates and rodents to identify gene regulatory programs involved in the evolution of fine motor skills.

dotdotdot: an automated approach to quantify multiplex single molecule fluorescent in situ hybridization (smFISH) images in complex tissues

The paper introduces dotdotdot, a software tool for quantifying smFISH images in complex tissues, demonstrating its use in mouse neurons and human brain tissue with autofluorescence masking and machine learning for cell type prediction.

Dissecting transcriptomic signatures of neuronal differentiation and maturation using iPSCs

The paper uses hiPSC transcriptomics to study neuronal differentiation and maturation across multiple conditions and develops a tool to estimate neuronal maturity.

BDNF-TrkB signaling in oxytocin neurons contributes to maternal behavior

This study shows that BDNF from promoters I and II is essential for maternal behavior in female mice by regulating oxytocin expression and signaling through TrkB in oxytocin neurons.