Jennifer E. Phillips‐Cremins

Exploring transcriptomic and genomic latent variable correction approaches in differential expression analysis.

This paper evaluates combining expression-based surrogate variables and genotype-based principal components in differential expression analysis, finding the combined approach improves replicability and biological recall in ALS datasets.

Persistent chromatin alterations and gene expression reprogramming follow widespread DNA damage in glioblastoma

This study shows that DNA damage in glioblastoma cells leads to long-term chromatin changes and gene expression reprogramming, affecting cellular function and tumor outcomes.

Integrative spatial profiling of 3D genome organization and gene expression in tissue

This paper introduces Spatial Hi-C-RNA, a spatial multi-omics technology that co-maps chromatin conformation and transcriptome in tissue, revealing spatially coherent domains and new insights into gene regulation.

An integrated view of the structure and function of the human 4D nucleome

The paper integrates 4D Nucleome data to analyze 3D genome structure and function in human cells, revealing chromatin domains, loops, and interactions, and showing how genetic variants affect genome folding.

Autism spectrum disorder risk genes have convergent effects on transcription and neuronal firing patterns in primary neurons

The paper tests nine ASD-linked transcription regulators in neurons, finding shared gene expression disruptions and firing pattern changes.

Learning induces persistent chromatin loops underlying robust gene expression during memory recall

The paper identifies persistent chromatin loops in hippocampal neurons after fear conditioning that correlate with gene expression changes during memory recall.

Persistent chromatin loops shape gene expression plasticity upon stimulation and restimulation of human neurons

The paper shows that persistent chromatin loops in human neurons influence gene expression plasticity during and after stimulation, with some loops maintaining repression or activation for up to five days.

FISHnet: Detecting chromatin domains in single-cell sequential Oligopaints imaging data

FISHnet detects chromatin domains in single-cell sequential Oligopaints imaging data using graph theory and network modularity optimization.

Mosaic H3K9me3 at BREACHes predicts synaptic gene expression associated with fragile X syndrome cognitive severity

The paper identifies H3K9me3 variation at BREACHes in FXS patients and shows it improves prediction of cognitive metrics when combined with FMRP and BREACH gene mRNA levels.

B cell stimulation changes the structure and higher-order organization of the inactive X chromosome

This study investigates how B cell stimulation affects the structure and organization of the inactive X chromosome, revealing dynamic changes in TAD boundaries and Xi compaction.

Polygenic burden of short tandem repeat expansions promote risk for Alzheimer's disease

The paper assesses the role of short tandem repeat (STR) expansions in Alzheimer's disease risk by analyzing genome-wide STR data from 2,981 individuals.

Cell type-specific loops linked to RNA polymerase II elongation in human neural differentiation

The paper identifies cell-specific DNA loops linked to RNA polymerase II elongation during human neural differentiation and shows their role in gene expression changes.

MASTR-seq: Multiplexed Analysis of Short Tandem Repeats with sequencing

MASTR-seq enables cost-effective, high-throughput, and accurate measurement of STR length and DNA methylation at single-allele resolution using nanopore sequencing.

The chromatin conformation landscape of Alzheimer's disease

The paper investigates chromatin conformation changes in Alzheimer's disease, finding loss of genomic loops and CTCF dysfunction linked to neurodegeneration.

A multi-looping chromatin signature predicts dysregulated gene expression in neurons with familial Alzheimer's disease mutations

The paper identifies multi-loop chromatin miswiring in FAD-mutant neurons that correlates with gene expression changes and DLX transcription factor activity.

High-throughput Oligopaint screen identifies druggable regulators of genome folding

The paper develops HiDRO, a high-throughput imaging pipeline, to screen the human druggable genome and identifies >300 factors regulating chromatin folding, including GSK3A as a regulator of TAD interactions.

Schizophrenia-associated somatic copy number variants from 12,834 cases reveal contribution to risk and recurrent, isoform-specific NRXN1 disruptions

This study identifies somatic copy number variants (sCNVs) in schizophrenia cases, revealing their contribution to risk and specific NRXN1 disruptions.

Remodeling and compaction of the inactive X is regulated by Xist during female B cell activation

This study shows that Xist regulates Xi compaction and TAD boundaries in B cells, impacting XCI maintenance and X-linked gene expression.

Cohesin-mediated loop anchors confine the location of human replication origins

This study shows that cohesin-mediated loops in G1 phase determine the genomic location of replication origins in S phase by anchoring replication initiation zones.

Reliance of neuronal gene expression on cohesin scales with chromatin loop length

The paper shows that cohesin's role in neuronal gene expression depends on chromatin loop length, with longer loops requiring cohesin for full gene expression.

Cell environment shapes TDP-43 function: implications in neuronal and muscle disease

The paper compares TDP-43's transcriptional and splicing effects in muscle and neuronal cells, showing tissue-specific roles in disease.

Acetylated Chromatin Domains Link Chromosomal Organization to Cell- and Circuit-level Dysfunction in Schizophrenia and Bipolar Disorder

The paper identifies acetylated chromatin domains associated with dysfunction in schizophrenia and bipolar disorder by analyzing histone modifications in prefrontal cortex samples.

Stress-induced epigenetic regulation of transcription in neocortical excitatory neurons drives depression-like behavior

The paper identifies epigenetic changes in neocortical excitatory neurons under chronic stress that contribute to depression-like behaviors in mice.

Spatially coordinated heterochromatinization of distal short tandem repeats in fragile X syndrome

The paper shows that in fragile X syndrome, long-range heterochromatinization of distal synaptic genes with STR instability is reversible by overexpression of a pre-mutation-length CGG tract.

Genome-Wide Meta-Analysis of Late-Onset Alzheimer's Disease Using Rare Variant Imputation in 324,809 Subjects Identifies Novel Rare Variant Locus NCK2: The International Genomics of Alzheimer's Project (IGAP)

3DeFDR: Identifying cell type-specific looping interactions with empirical false discovery rate guided thresholding

3DeFDR identifies cell type-specific looping interactions from 5C data by using empirical false discovery rate guided thresholding to reduce false positives.

Promoter-anchored chromatin interactions predicted from genetic analysis of epigenomic data

This study predicts promoter-anchored chromatin interactions using DNA methylation QTL data from a human cohort, finding overlaps with experimental data and associations with complex traits.

Postmortem Cortex Samples Identify Distinct Molecular Subtypes of ALS: Retrotransposon Activation, Oxidative Stress, and Activated Glia

The paper uses unsupervised machine learning to identify three molecular subtypes in ALS cortex samples, associated with oxidative stress, retrotransposon activation, and glial activation.

LADL: Light-activated dynamic looping for endogenous gene expression control

This paper introduces LADL, a light-activated system to dynamically control chromatin looping, showing it can redirect enhancer-promoter interactions and alter gene expression within four hours.

Re-configuration of Chromatin Structure During the Mitosis-G1 Phase Transition

The paper examines how chromatin structures re-establish after mitosis using Hi-C, showing rapid compartment formation and dynamics of CTCF and cohesin binding.