Mikhail G. Dozmorov

Structure-guided targeting of the GATAD2A-CHD4 interaction within the MBD2-NuRD complex results in high levels of HbF in adult erythroid cells

This paper identifies critical interaction domains in the GATAD2A-CHD4 complex within the MBD2-NuRD complex that, when disrupted, increase fetal hemoglobin (HbF) expression in adult erythroid cells.

Beyond Blacklists: A Critical Assessment of Exclusion Set Generation Strategies and Alternative Approaches

The paper evaluates exclusion set generation strategies in short-read sequencing, finding that pre-generated Blacklists are hard to reproduce and proposes sponge sequences as an alternative to reduce artifacts.

Daraxonrasib (RMC-6236) is an effective targeted therapy for RAS-mutant neuroblastoma

This study shows that Daraxonrasib (RMC-6236) effectively targets RAS-mutant neuroblastoma by inhibiting MAPK signaling and enhancing cell death.

EpiTADformer: A Transformer-Based Model for High-Resolution TAD Boundary Detection Using Epigenomic Signal Embeddings

EpiTADformer uses epigenomic signal embeddings to detect TAD boundaries with higher resolution than Hi-C-based methods.

Targeting of SUMOylation leads to cBAF complex stabilization and disruption of the SS18::SSX transcriptome in Synovial Sarcoma

This study shows that inhibiting SUMOylation with TAK-981 stabilizes cBAF complexes and disrupts the SS18::SSX-driven transcriptome in synovial sarcoma, leading to tumor inhibition.

Tumor cell dissemination is facilitated through regulatory T cell-driven extracellular matrix remodeling

This study shows Treg cells remodel the tumor ECM to promote metastasis, with matrisome signatures linked to poor survival in breast cancer.

Glycomics Profiling Reveals a Stromal Chondroitin-4-sulfate State that Shapes Platinum Response in Ovarian Cancer

This study identifies stromal chondroitin-4-sulfate as a determinant of platinum response in ovarian cancer through glycomics profiling and functional validation.

scHiCcompare: an R package for differential analysis of single-cell Hi-C data

The paper introduces scHiCcompare, an R package for differential analysis of single-cell Hi-C data, improving detection of chromatin interactions across various conditions.

RNA-sequencing Strain-specific Genome Alignment Increases Differential Expression Findings in Comparison of C57BL/6J and DBA/2J Nucleus Accumbens

The paper shows that aligning RNA-seq data to strain-specific genomes increases the number of differentially expressed genes and exons detected when comparing C57BL/6J and DBA/2J mice.

Ablation of LRP6 in alpha-smooth muscle actin-expressing cells abrogates lung inflammation and fibrosis upon bleomycin-induced lung injury

This study shows that deleting LRP6 in SMA-expressing cells prevents lung inflammation and fibrosis caused by bleomycin.

Inducible deletion of Ezh2 in CD4+ T cells inhibits kidney T cell infiltration and prevents interstitial nephritis in MRL/lpr lupus-prone mice

Genomic and Transcriptomic Analysis of Ninein Alternative Splicing Between C57BL/6J and DBA/2J Mice

The paper identifies strain-specific alternative splicing differences in the Ninein gene between C57BL/6J and DBA/2J mice, linking these differences to ethanol anxiolytic effects.

A novel multi-omics mendelian randomization method for gene set enrichment and its application to psychiatric disorders

This paper introduces MR-GSE, a multi-omics Mendelian randomization method for gene set enrichment in psychiatric disorders, showing increased detection of significant gene sets compared to non-MR methods.

matchRanges: Generating null hypothesis genomic ranges via covariate-matched sampling

The paper introduces matchRanges, a tool for generating covariate-matched null genomic ranges to facilitate comparative genomic analyses.

bootRanges: Flexible generation of null sets of genomic ranges for hypothesis testing

bootRanges generates null genomic ranges for hypothesis testing, improving reliability by preserving genomic correlation structure through block bootstrap methods.

Expanding the HDAC druggable landscape beyond enzymatic activity

This paper identifies a non-enzymatic HDAC inhibitor with anti-tumor and anti-psychedelic effects, showing reduced gene modulation compared to enzymatic inhibitors.

excluderanges: exclusion sets for T2T-CHM13, GRCm39, and other genome assemblies

The paper provides exclusion region sets for T2T-CHM13, GRCm39, and other genomes through an R/Bioconductor package and API, offering unified access to curated genomic ranges.

preciseTAD: A transfer learning framework for 3D domain boundary prediction at base-pair resolution

preciseTAD predicts 3D domain boundaries at base-pair resolution using transfer learning, supported by experimental evidence and applicable without Hi-C data.

Histone acetylation at the sulfotransferase 1a1 gene is associated with its hepatic expression in normal aging

The paper examines age-related epigenetic changes in Sult1a1 and Ugt1a6 genes in mice, finding significant loss of DNA methylation and increased H3K9ac at Sult1a1, with H3K9ac positively correlating with gene expression.

Yin Yang 1 sets up the stage for cerebellar astrocyte maturation

This study identifies YY1's role in regulating cerebellar astrocyte maturation and maintenance in adult mice through single-cell RNA-seq analysis.

Chromatin conformation capture (Hi-C) sequencing of patient-derived xenografts: analysis guidelines

This study evaluates the impact of mouse read removal and library preparation on Hi-C data quality in patient-derived xenografts, finding that library strategy has the largest effect.

Assessing the role of long-noncoding RNA in nucleus accumbens in subjects with alcohol dependence

The paper profiles lncRNA and protein coding gene expression in nucleus accumbens from alcohol-dependent and control subjects, identifying differentially expressed genes and their functional roles in alcohol dependence.

SpectralTAD: an R package for defining a hierarchy of Topologically Associated Domains using spectral clustering

SpectralTAD detects hierarchical TAD structures from Hi-C data, outperforming existing tools and showing biological relevance of shared TAD boundaries.

DYRK1A regulates the recruitment of 53BP1 to the sites of DNA damage in part through interaction with RNF169

This paper identifies DYRK1A's role in DNA repair by regulating RNF169-mediated 53BP1 recruitment to DSB sites, with implications for DNA damage therapy response.

HiCcompare: a method for joint normalization of Hi-C datasets and differential chromatin interaction detection

HiCcompare normalizes multiple Hi-C datasets and detects differential chromatin interactions, outperforming single-dataset normalization methods in identifying true interaction changes.

Sexually divergent DNA methylation programs with hippocampal aging

This study identifies sexually divergent DNA methylation changes in mouse and human hippocampus with aging, revealing sex as a key factor in epigenomic aging.