M. K. Jolly

Anoikis resistance and metastasis of ovarian cancer can be overcome by CDK8/19 Mediator kinase inhibition.

This study shows CDK8/19 inhibition can reverse anoikis resistance and metastasis in ovarian cancer by altering transcriptional programs.

Collective heterogeneity of mitochondrial potential in contact inhibition of proliferation

This paper reveals a density-dependent collective metabolic heterogeneity in epithelial cells during contact inhibition of proliferation, showing distinct metabolic patterns in different stages.

Mutually exclusive teams-like patterns of gene regulation characterize phenotypic heterogeneity along the noradrenergic-mesenchymal axis in neuroblastoma

The paper identifies mutually exclusive gene regulation patterns between noradrenergic and mesenchymal states in neuroblastoma, linking them to phenotypic plasticity and therapy resistance.

Characterizing heterogeneity along EMT and metabolic axes in colorectal cancer reveals underlying consensus molecular subtype-specific trends

The paper analyzes CRC subtypes to show how EMT and metabolic axes vary across CMS subtypes, revealing subtype-specific metabolic and mesenchymal correlations.

p53 amyloid pathology with cancer grades and p53 mutations

The paper shows p53 amyloid load correlates with cancer grades and shows both mutant and wild-type p53 form amyloids in cancer tissues.

GPX4-VIM equates a proliferating DTP state in TNBC subtypes with converged vulnerabilities to autophagy and glutathione inhibition.

The paper identifies a proliferating DTP state in TNBC subtypes that is vulnerable to autophagy and glutathione inhibition, linking GPX4-VIM expression to survival outcomes.

Melanocytes Exhibit Distinct Cell States Governed by A Gene Regulatory Network Under Stochastic Influence

The paper identifies distinct melanocyte states and shows stochastic gene expression and epigenetic modification enable their co-existence and response to environmental cues.

A synthetic lethal screen for Snail-induced enzalutamide resistance identifies JAK/STAT signaling as a therapeutic vulnerability in prostate cancer

The paper identifies JAK/STAT signaling as a therapeutic target for Snail-induced enzalutamide-resistant prostate cancer through synthetic lethal screens and validation in a resistant cell model.

Cell-autonomous BMP signalling plays a key role in the maintenance of tumour cell EMT and migration programs in human ovarian carcinoma

This study investigates the role of BMP signaling in maintaining EMT and migration in ovarian cancer cells, showing that inhibiting BMP reduces EMT and migration.

Dual role of CASP8AP2/FLASH in regulating epithelial-to-mesenchymal (EMT) plasticity

This study identifies FLASH as a regulator of EMT plasticity, showing it influences hybrid E/M states through its effects on EMT-TFs and cell junction proteins.

Androgen Receptor driven gene score identifies tumors with Epithelial to Mesenchymal Transition features in triple negative breast cancer

The paper develops an AR-driven gene score to identify tumors with EMT features in triple-negative breast cancer, finding AR high tumors have better clinical outcomes and higher EMT marker expression.

Population Dynamics of EMT Elucidates the Timing and Distribution of Phenotypic Intra-tumoral Heterogeneity

This paper develops a computational framework to infer and predict EMT-related trajectories from single-cell RNA sequencing data, revealing population dynamics and timing of phenotypic intra-tumoral heterogeneity.

Dynamical modelling of proliferative-invasive plasticity and IFN-gamma signaling in melanoma reveals mechanisms of PD-L1 expression heterogeneity

This study uses dynamical modeling to uncover how IFN-gamma signaling and proliferative-invasive transitions shape PD-L1 expression heterogeneity in melanoma, with experimental validation in cell lines and datasets.

Emergent dynamics of underlying regulatory network links EMT and androgen receptor-dependent resistance in prostate cancer

The paper models a regulatory network linking EMT and AR resistance in prostate cancer, identifying four phenotypes and showing stochastic switching between states.

Effects of microRNA-mediated negative feedback on gene expression noise

This study develops a mathematical model to show how miRNA-mediated negative feedback affects gene expression noise and creates bimodal mRNA distributions near an expression threshold.

Spatio-temporal Pattern Formation due to Host-Circuit Interplay in Gene Expression Dynamics

The paper investigates spatio-temporal pattern formation in a cellular array with non-cooperative positive feedback, analyzing stability and spatial distribution under varying diffusion conditions.

PD-L1 activity is associated with partial EMT and metabolic reprogramming in carcinomas

The paper identifies a link between PD-L1 activity, partial EMT, and metabolic reprogramming in carcinomas using transcriptomic data and single-cell RNA-seq.

Acquisition of hybrid E/M phenotype associated with increased migration, drug resistance and stemness is mediated by reduced miR-18a levels in ER-negative breast cancer

This study shows that low miR-18a levels in ER-negative breast cancer drive hybrid E/M cell traits linked to migration, drug resistance, and stemness.

Epigenetic memory acquired during long-term EMTinduction governs the recovery to the epithelial state

The paper shows that long-term EMT induction in MCF10A cells can be reversible with longer timescales, and epigenetic memory via miR-200 silencing by ZEB slows recovery to the epithelial state.

Partial EMT and associated changes in cellular plasticity in oncovirus-positive samples

The paper analyzes transcriptomics data to identify common gene regulatory features in oncovirus-positive samples, revealing partial EMT and metabolic changes linked to immune checkpoint molecules.

The ELF3 transcription factor is associated with an epithelial phenotype and represses epithelial-mesenchymal transition

The paper identifies ELF3 as an epithelial-associated transcription factor that inhibits EMT and stabilizes hybrid E/M phenotypes, with potential prognostic implications in solid tumors.

Spatiotemporal patterning enabled by gene regulatory networks

The paper investigates how spatiotemporal patterns emerge from synthetic gene regulatory networks with diffusion in 1D and 2D space, analyzing stability and diffusion effects.

Mapping phenotypic heterogeneity in melanoma onto the epithelial-hybrid-mesenchymal axis

This study maps phenotypic heterogeneity in melanoma onto the epithelial-hybrid-mesenchymal axis, showing a biphasic mesenchymal response during de-differentiation and metabolic shifts.

P4HA2: A link between tumor-intrinsic hypoxia, partial EMT and collective migration

This study identifies P4HA2 as a central regulator linking tumor-intrinsic hypoxia, partial EMT, and collective migration using microtumor models and differential gene expression analysis.

Cell geometry distinguishes migration-associated heterogeneity in two-dimensional systems

The paper develops an analytical pipeline to identify and characterize functional migratory subsets from 2D time-lapse migration data, revealing previously unappreciated heterogeneity in non-migratory cells.

Quantifying the patterns of metabolic plasticity and heterogeneity along the epithelial-hybrid-mesenchymal spectrum in cancer

The paper analyzes metabolic pathway associations with EMT status across cancer datasets, revealing both general trends and heterogeneity in metabolic plasticity.

Continuum Theory for Planar Cell Polarity

This paper develops a continuum model to explain how planar cell polarity (PCP) proteins localize asymmetrically on cell membranes and how tissue-level expression gradients stabilize PCP.

Lattice-based microenvironmental uncertainty driven phenotypic decision-making: a comparison with Notch-Delta-Jagged signaling

The paper develops a lattice-based agent model driven by microenvironmental uncertainty to study multicellular phenotypic decision-making, comparing it with Notch-Delta-Jagged signaling.

Computational analysis reveals similarities and differences between SCLC subtypes

The paper analyzes SCLC subtypes using gene expression data to determine their similarities and differences, identifying co-expressed modules and classifying cell lines into clusters.

KLF4 induces Mesenchymal-Epithelial Transition (MET) by suppressing multiple EMT-inducing transcription factors

This study shows KLF4 suppresses EMT-inducing transcription factors and promotes MET, acting as a potential MET-TF with implications for cancer survival.