Nacho Molina

This study compares cell-cycle gene expression dynamics and mRNA kinetics across mouse and human pluripotent systems, revealing species-specific differences in transcriptional complexity and oscillatory control.

This study shows androgen receptor signaling maintains skeletal muscle stem cell quiescence and regenerative capacity, and its loss leads to premature activation and stem cell depletion.

The paper investigates the dynamic behavior of RNA polymerase II and its initiation factors during transcription activation in live cells, revealing distinct kinetic behaviors and a quantitative model for PIC assembly.

The paper develops SpaceCycle to infer cell-cycle phases and oscillatory gene expression from spatial transcriptomic data, revealing spatial and temporal patterns of proliferation in tumors.

The paper uses SMF and live imaging to study promoter dynamics, showing Tat influences nucleosome removal and polymerase activity.

The paper uses single-cell transcriptomics to study EEC lineage dynamics and gene regulatory networks during intestinal development in mice and humans, finding that most EECs are specified during development independently of crypt-villus structures and microbiota.

The paper identifies three types of megabase-scale heterochromatin domains in C. elegans using single-molecule tracing and shows their developmental dynamics and structural differences.

The paper uses single-cell multiomics to analyze mRNA metabolism and chromatin accessibility dynamics during the cell cycle, revealing oscillatory patterns and regulatory mechanisms.

The paper introduces HiddenFoot, a probabilistic model to infer TF, nucleosome, and Pol II occupancy from single-molecule data, revealing binding dynamics and heterogeneity in mouse, Drosophila, and human cells.

The paper shows that TIP60 depletion alters transcription and is offset by changes in RNA export and stability, revealing gene-specific transcript buffering mechanisms.

The paper refactors plant circadian clock models to absolute units, predicts high clock protein levels in Arabidopsis, and identifies discrepancies in DNA-binding constants.

The paper measures RNA Polymerase II occupancy at promoters in mouse and Drosophila, finding lower occupancy and higher turnover in mammals.

FateCompass identifies lineage-specific transcription factors during cell differentiation using single-cell RNA-seq data, revealing known and novel regulators in mouse islet cell development and beta-like cell protocols.

The paper uses scRNA-seq and deep learning to map cell cycle gene regulation dynamics in mouse and human cells, identifying key transcription waves and transitions.

This paper introduces GP-FBM, a computational framework for analyzing chromatin diffusion dynamics, and shows similar diffusion properties in interphase and mitosis in mouse embryonic stem cells.

The paper develops a mathematical model to correct for cell-cycle desynchronization and identifies a core gene regulatory network and potential mitotic bookmarking factors involved in transcription reactivation post-mitosis.

The paper uses single molecule footprinting to study transcription factor co-occupancy and cooperativity in mouse cis-regulatory elements, finding that high DNA co-occupancy can occur without direct physical interaction.

The paper characterizes the transcriptional response to TNF-α using single-cell analysis, showing heterogeneous gene expression with prompt and sharp population-level dynamics driven by 'first responders'.

The paper uses bulk and single-cell RNA sequencing to study Drosophila hemocyte heterogeneity across developmental stages and immune challenges, identifying novel cell types and functional states.

This study identifies Rfx6 as a key regulator of enteroendocrine cell differentiation, promoting peptidergic cells while repressing serotonin-producing cells.

The paper investigates how stochastic gene switching and negative feedback influence gene expression dynamics, showing they can produce pulsed activity and specific time distributions.