Siddharth S. Dey

This study shows that matrix stiffness and stress relaxation influence osteogenesis by regulating histone demethylases KDM4B and KDM6B through mechanotransduction signaling.

The paper uses optogenetics in human gastruloids to show that precise spatiotemporal WNT signaling controls germ-layer patterning.

scSTAMP-seq enables spatially resolved single-cell transcriptomics and epigenomics by using photolabile oligonucleotides and light gradients to capture cell positions before sequencing.

The paper introduces scMHT-seq, a single-cell method to profile 5mC, 5hmC, and transcriptomes, revealing DNA methylation erasure mechanisms in human primordial germ cell maturation.

This study shows that Sp1 mechanotransduction enhances breast cancer cell invasion in response to combined ECM cues like stiffness, stress relaxation, and collagen density.

This study shows that YAP overactivation in HCM mutant cardiomyocytes drives hypertrophy via CCN2 secretion and TGFβ uptake.

The paper introduces Dyad-seq to quantify 5mC and 5hmC at CpG dyads and combines it with transcriptome data (scDyad&T-seq) to show how DNMT1 fidelity depends on methylation density and histone modifications in mouse cells.

EMBR-seq+ efficiently depletes rRNA in diverse bacterial species and co-cultures, enabling accurate transcriptome analysis of non-model microbial systems.

This study uses optogenetic control of the ISR to show proportional encoding of stress inputs and reveals a stress memory landscape through an ODE model.

The paper introduces scMAT-seq, a single-cell multiomics method, to study epigenetic regulation during human gastrulation and germ cell development in 3D organoids, revealing insights into DNA methylation and accessibility dynamics.

The paper introduces a single-cell methylomics method to study DNA demethylation dynamics in early mammalian development and finds distinct active and passive demethylation modes in mouse and human embryos.

The paper introduces EMBR-seq, a method for efficient and cost-effective bacterial mRNA sequencing by depleting rRNA, enabling deeper transcriptome analysis from low input samples.

This paper introduces scPECLR, a probabilistic algorithm that reconstructs cellular lineage trees at single-cell division resolution using 5-hydroxymethylcytosine sequencing in mouse embryos.

This paper introduces a method to simultaneously measure protein-DNA contacts and transcriptomes in single cells, revealing how chromatin states and genome organization influence gene expression.