Vijay Ramani

The paper maps tRNA dependencies in cancer cells across different environments, finding that tRNA dependencies are environmentally sensitive while some dependencies are shared across cell lines.

This study develops small molecules that activate the tumor suppressor kinase LKB1 and shows their therapeutic benefits in cancer cell lines.

The paper shows DNA sequence guides nucleosome rotation and positioning across species, with chromatin regulators navigating rather than overriding these settings.

The paper introduces LASSI, a method to measure nucleosome spacing in chromatin interactions, revealing fiber homotypy as a structural pattern influenced by genomic features and cohesin dynamics.

This study shows that FACT is essential for chromatin replication and transcription by disrupting and reassembling nucleosomes, preventing genome aggregation.

This study identifies methionine metabolism and the NOP2 methyltransferase as critical for MYC-driven liver tumorigenesis, suggesting NOP2 as a potential therapeutic target.

The paper investigates how two chromatin remodelers, ACF and RSC, affect chromatin condensation and dynamics, revealing distinct mesoscale effects on chromatin structure and function.

The paper investigates chromatin asymmetry on newly replicated DNA strands using yeast replisome reconstitution and single-molecule chromatin footprinting, revealing intrinsic asymmetry in nucleosome positioning between lagging and leading strands.

This study shows HMGB1 counteracts linker histone H1 by distorting nucleosomal DNA and contacting H1's C-terminal tail, enabling co-occupancy and dynamic chromatin states.

The paper identifies ELOA-dependent mechanisms regulating transcription maturation and links them to cellular senescence and aging through RNA processing defects and growth arrest.

The paper identifies ZZEF1 as a tRNA-specific transcription factor that suppresses breast cancer metastasis by regulating tRNA-LysUUU expression and affecting codon-specific translation.

The paper introduces IDLI, a method to map nucleosome structures and distortion patterns in mammalian chromatin, revealing widespread and regulated DNA accessibility across cell types.

This study introduces RASAM, a method to analyze nascent chromatin structure, finding that newly replicated chromatin is hyperaccessible and has unique organization features.

This study shows that neuronal DNA double-strand breaks, even when accumulated due to loss of C-NHEJ, do not drive brain aging or neurodegeneration in mice.

This study shows that macrophages transfer intact cancer cell surface proteins to their own surface after phagocytosis, which may affect their function and metabolism.

The paper introduces Mach-1, an RNA foundation model that predicts transcriptome architecture from DNA sequence, validated through experimental perturbations and CRISPR editing.

The paper trains bidirectional transformer models to predict RNA splicing using perturbative RNA data, achieving state-of-the-art performance in splice junction prediction.

The paper identifies PRC2.1's role in opposing G1 progression by regulating CCND1 and CCND2, showing its importance in cell proliferation across multiple cancer types.

SMRT-Tag enables low-input, single-molecule sequencing for simultaneous detection of genetic and epigenetic variations in human samples.

This study uses a single-molecule platform to show that SNF2h, a chromatin remodeler, regulates DNA accessibility based on nucleosome density in vitro and in vivo.

The paper integrates single-cell RNA-seq, ATAC-seq, and Hi-C data to study nuclear configuration and gene expression changes during stem cell differentiation and X inactivation, revealing discrete structural changes and delayed chromatin compaction.

This paper shows MLX and MondoA are essential for male fertility and tumor survival, with MLX regulating metabolism, stress, and germ cell development.

The paper introduces a single-molecule sequencing method to measure nucleosome positions on chromatin fibers and reveals heterogeneous patterns of oligonucleosome occupancy across epigenomic domains.

This paper applies and extends MMD-MA to align single-cell transcriptome and chromatin accessibility data from ~2000 cells, demonstrating its scalability and accuracy.

This study uses topic modeling on scHi-C data to identify cell type-specific chromatin structural patterns and compartment structures.

Sci-Hi-C is a single-cell Hi-C method that maps 3D genome organization in large numbers of single cells, enabling analysis of chromatin interactions and cellular variability.

The paper studies how nuclear architecture changes during human heart development using Hi-C, RNA-seq, and ATAC-seq, revealing dynamic chromosomal organization and gene regulation.

The paper shows Dxz4 orientation controls long-range contacts on the inactive X chromosome, maintaining its bipartite structure through CTCF motif direction.

This paper introduces sci-RNA-seq, a combinatorial indexing method for single-cell RNA sequencing, and applies it to profile 42,035 C. elegans cells, identifying 27 cell types and their specific genes.

This paper introduces combinatorial single cell Hi-C, a method for measuring chromosome conformation in single cells, and shows its ability to distinguish cell types and reveal chromosomal heterogeneity.