Mohit Kumar Jolly

Decoding stress-induced adaptation of cancer cells in spatial confinement by integrating live-cell imaging and mathematical modeling

This study combines live-cell imaging and mathematical modeling to show how cancer cells adapt to stress in spatially confined environments, revealing cooperative and competitive strategies influenced by spatial organization and microenvironment dynamics.

MHC-I downregulation is associated with immune-evasion in breast cancers with heterogeneous activation of epithelial-mesenchymal plasticity

The paper shows that in mixed E-qM breast tumors, qM cancer cells create immunosuppressive niches leading to MHC-I downregulation and immune evasion.

Cyclic Hypoxia drives Wnt5a-ROR1 stroma-tumor crosstalk promoting breast cancer growth

This study shows cyclic hypoxia promotes breast cancer growth through WNT5A-ROR1 signaling between stromal and tumor cells in a co-culture model.

Malignant and stromal partial EMT programmes and cetuximab outcome in head and neck cancer

The paper identifies malignant and stromal partial EMT programs in head and neck cancer and shows that malignant measures correlate with better cetuximab outcomes.

Impact of oxygen fluctuation and consumption on the dynamics of a reduced go-or-grow model for tumor cell invasion

This study shows that rapid oxygen fluctuations alter tumor growth dynamics in a go-or-grow model, with the full model outperforming a reduced version under these conditions.

A Nanomechanical Fingerprint of Centromeric Methylation Co-Localization in TNBC Chromosomal Instability

This study maps 5mC and H3K9me3 co-localization on individual chromosomes using AFM, revealing mechanical stiffness differences between cancer and non-tumorigenic cells.

Endosomal pH Triggers Amyloid β Oligomerization and Maladaptive Phenotypic Plasticity in Alzheimers Disease

This paper models endosomal pH dysregulation in Alzheimer's disease, showing how NHE6 loss leads to hyperacidification, maladaptive plasticity, and Aβ oligomerization.

Regulatory stochasticity drives opposing phenotypic outcomes in cell-fate decision networks

The paper shows how regulatory noise affects cell-fate decisions by altering phenotype occupancy in gene regulatory networks.

Gene Regulatory Networks that support Multi-Fate Cellular Decisions

This study identifies network structures that support multi-fate cellular decisions by analyzing gene regulatory networks using monotone Boolean models.

Weak form Scientific Machine Learning for Systems Biology: A Tutorial on WENDy

This paper introduces WENDy, a method for parameter estimation in systems biology models using weak-form regression, demonstrating its application on real experimental data for glycolytic oscillators and cell-state transitions.

Traveling Wave Analysis of a Go-or-Grow Invasion Model with ECM-Regulated Phenotypic Switching

The paper analyzes a go-or-grow invasion model with ECM-regulated phenotypic switching, showing that the reduced model captures the dynamics and deriving the minimum traveling wave speed.

Distinct geometrical landscapes distinguish between modes of tristability in gene regulatory networks

The paper identifies distinct geometrical landscapes for two gene regulatory motifs that exhibit tristability and shows how these landscapes can model cell fate transitions in cancer.

Hepatobiliary Progenitor-like Reprogramming in Liver Metastases

This study identifies hepatobiliary progenitor-like reprogramming in liver metastases, driven by TGF-β and hypoxia, and shows its association with poor survival.

Systems-level analysis identifies IRF6 as an inhibitor of epithelial-mesenchymal transition

The paper identifies IRF6 as an inhibitor of epithelial-mesenchymal transition (EMT) through integrated computational and experimental analysis.

Feedback loops involving AMPK, ERK and TFEB in matrix detachment leads to non-genetic heterogeneity

The paper identifies a feedback loop between AMPK, ERK, and TFEB in matrix-detached cancer cells that generates non-genetic heterogeneity, affecting autophagy and cell survival.

Endocrine therapy-specific lineage and partial epithelial-mesenchymal reprogramming defines divergent resistant cell-states in ER+ breast cancer

This study identifies drug-specific resistance mechanisms in ER+ breast cancer by analyzing multi-omic data, revealing distinct transcriptional and chromatin states associated with SERM, SERD, and ESR1 mutant resistance.

Ecological Dynamics of Pro-tumor and Anti-tumor Teams in the Tumor Microenvironment

The paper models tumor-immune interactions as a two-team ecosystem using a generalized Lotka-Volterra framework to predict ecological outcomes in the tumor microenvironment.

CD4+ T-cells sensitize quasi-mesenchymal breast tumors lacking CD73 to anti-CTLA4 immune checkpoint blockade therapy

This study shows that targeting CD73 in quasi-mesenchymal breast tumors enhances their response to anti-CTLA4 therapy through CD4+ T-cell dependence.

Bidirectional coupling among EMT, AXL-RB1 signaling and lineage switch drives resistance to osimertinib and worse clinical outcomes in NSCLC

Time-dependent memory of hypoxia exposure influences tumor invasion dynamics

The paper shows hypoxic memory in cancer cells affects tumor invasion dynamics through time-dependent changes in cell state and spatial oxygen dynamics.

A Unified Control of Cellular Differentiation: From Temporal Multistability to Spatial Pattern Formation in Gene Regulatory Networks

This paper analyzes gene regulatory networks to show how cell fate transitions and spatial pattern formation arise from temporal multistability and network topology.

Androgen receptor activation stabilizes a hybrid epithelial/mesenchymal phenotype in presence of Notch-Jagged signaling

The paper develops a mathematical model showing that Androgen Receptor stabilizes a hybrid epithelial/mesenchymal phenotype in prostate cancer cells with Notch-Jagged signaling, correlating with worse patient outcomes.

Regulatory network and spatial modeling reveal cooperative mechanisms of resistance and immune escape in ER+ breast cancer

This study models regulatory networks and spatial dynamics in ER+ breast cancer to show how resistance and immune escape co-occur and how combination therapies can counteract these mechanisms.

Hierarchical organization in sparse gene regulatory networks shapes structural coherence and emergent regulatory coordination

The paper introduces a coherence matrix to analyze directional regulatory coordination in gene regulatory networks, showing how hierarchical structures mitigate scaling penalties in sparse networks.

Early detection of sudden transitions in Notch signalling

This study identifies sudden transitions in Notch signaling using early warning signals and analyzes how system parameters influence these transitions in one- and two-cell models.

A phenotype-structured PDE framework for investigating the role of hypoxic memory on tumor invasion under cyclic hypoxia

This paper develops a PDE framework to model hypoxic memory's impact on tumor invasion under cyclic hypoxia, showing enhanced invasion without reduced tumor volume.

Multi-omics investigation reveals molecular determinants of cancer cell evolution on soft extracellular matrix

The paper investigates how cancer cells adapt to soft extracellular matrix by analyzing multi-omics data to identify molecular mechanisms underlying fitness differences.

Repurposing statins in combination therapy for effective ablation of metastatic breast cancer

This study evaluates lovastatin's efficacy in combination with chemotherapy to ablate chemoresistant metastatic breast cancer cells by targeting Macc1 overexpression.

ONCOchannelome: A computational framework for investigating altered ion channels across tumor types

ONCOchannelome identifies altered ion channels in tumors using transcriptomic data, revealing their correlation with metastasis and biological changes.

Interconnected axes of phenotypic plasticity drive coordinated cellular behaviour and worse clinical outcomes in breast cancer

The paper shows that interconnected axes of phenotypic plasticity in breast cancer drive coordinated cellular behavior and influence clinical outcomes through mutual inhibition between two teams of plasticity-related nodes.