Vivekanandan Ramalingam

Architectural chromatin interactions provide a framework for context-dependent gene regulation

The paper develops an integrative framework to classify and interpret promoter-centric chromatin interactions by combining Hi-C, ChIA-PET, and functional genomic data, identifying a distinct class of architectural promoter-enhancer interactions with context-dependent regulatory roles.

Thermodynamic principles link in vitro transcription factor affinities to single-molecule chromatin states in cells

This study links in vitro transcription factor affinities to in vivo single-molecule chromatin states using thermodynamic models and experimental data for KLF1.

An updated compendium and reevaluation of the evidence for nuclear transcription factor occupancy over the mitochondrial genome

The paper updates and reevaluates evidence for nuclear transcription factor occupancy over the mitochondrial genome using expanded ChIP-seq data and deep learning models.

An Expanded Registry of Candidate cis-Regulatory Elements for Studying Transcriptional Regulation

The paper expands the ENCODE Registry of candidate cis-regulatory elements (cCREs) to include 2.35 million human and 927 thousand mouse cCREs, revealing novel regulatory functions and identifying KLF1 as a causal gene for red blood cell traits.

Comparative atlas of genome-wide chromatin-associated protein co-occupancy

The paper identifies cell type-specific and shared chromatin-associated protein co-association modules using ChIP-Seq and machine learning in K562 and HepG2 cells.

The dynseq genome browser track enables visualization of context-specific, dynamic DNA sequence features at single nucleotide resolution

The paper introduces a genome browser track for visualizing dynamic DNA sequence features at single nucleotide resolution using machine learning-derived scores.

Lola-I is a developmentally regulated promoter pioneer factor

The paper shows that Lola-I, a Drosophila zinc finger transcription factor, regulates promoter accessibility and paused Pol II during development, similar to enhancer regulation by pioneer factors.

Acquisition of Innate Odor Preference Depends on Spontaneous and Experiential Activities During Critical Period

This study shows that innate odor preference in mice requires both spontaneous neural activity and sensory experience during a critical period, with ectopic projections altering odor valence.

TATA and paused promoters active in differentiated tissues have distinct expression characteristics

The paper compares TATA and paused promoters in Drosophila embryos, finding that TATA promoters show Pol II occupancy only when active, while paused promoters have consistent Pol II levels regardless of gene expression.