Rewiring the altered tryptophan metabolism as a novel therapeutic strategy in inflammatory bowel diseases

C Michaudel, C Danne, A Agus, A Magniez… - Gut, 2023 - gut.bmj.com
Objective The extent to which tryptophan (Trp) metabolism alterations explain or influence
the outcome of inflammatory bowel diseases (IBDs) is still unclear. However, several Trp …

Landscape of epithelial–mesenchymal plasticity as an emergent property of coordinated teams in regulatory networks

K Hari, V Ullanat, A Balasubramanian, A Gopalan… - Elife, 2022 - elifesciences.org
Elucidating the design principles of regulatory networks driving cellular decision-making has
fundamental implications in mapping and eventually controlling cell-fate decisions. Despite …

Universal structures for adaptation in biochemical reaction networks

RP Araujo, LA Liotta - Nature Communications, 2023 - nature.com
At the molecular level, the evolution of life is driven by the generation and diversification of
adaptation mechanisms. A universal description of adaptation-capable chemical reaction …

Topological signatures in regulatory network enable phenotypic heterogeneity in small cell lung cancer

L Chauhan, U Ram, K Hari, MK Jolly - Elife, 2021 - elifesciences.org
Phenotypic (non-genetic) heterogeneity has significant implications for the development and
evolution of organs, organisms, and populations. Recent observations in multiple cancers …

Network topology and interaction logic determine states it supports

T Gedeon - NPJ Systems Biology and Applications, 2024 - nature.com
In this review paper we summarize a recent progress on the problem of describing range of
dynamics supported by a network. We show that there is natural connection between …

KLF4 induces mesenchymal–epithelial transition (MET) by suppressing multiple EMT-inducing transcription factors

AR Subbalakshmi, S Sahoo, I McMullen, AN Saxena… - Cancers, 2021 - mdpi.com
Simple Summary Cancer is expected to be the leading cause of death due to
noncommunicable diseases in the 21st century. Cancer-related mortality is largely due to …

Hybrid E/M phenotype (s) and stemness: a mechanistic connection embedded in network topology

S Pasani, S Sahoo, MK Jolly - Journal of Clinical Medicine, 2020 - mdpi.com
Metastasis remains an unsolved clinical challenge. Two crucial features of metastasizing
cancer cells are (a) their ability to dynamically move along the epithelial–hybrid …

Dynamics of T-helper cell differentiation and plasticity: How have computational models improved our understanding?

P Harlapur, AS Duddu, MK Jolly - Current Opinion in Systems Biology, 2024 - Elsevier
Naïve CD4+ T cells can polarize into diverse functionally distinct effector cell types such as
Th1, Th2, Th17 and Treg. These cell types can also interconvert among one another. The …

Dynamics of hepatocyte-cholangiocyte cell-fate decisions during liver development and regeneration

S Sahoo, A Mishra, AM Diehl, MK Jolly - Iscience, 2022 - cell.com
The immense regenerative potential of the liver is attributed to the ability of its two key cell
types–hepatocytes and cholangiocytes–to trans-differentiate to one another either directly or …

Modular, robust, and extendible multicellular circuit design in yeast

A Carignano, C Mallory, RC Wright, G Seelig, E Klavins - Elife, 2022 - elifesciences.org
Division of labor between cells is ubiquitous in biology but the use of multicellular consortia
for engineering applications is only beginning to be explored. A significant advantage of …