Reconstructing the single-cell lineages and diversity in fates during epithelial-to-mesenchymal transition.
Cheng Y-C, Zhang Y, Tripathi S, Harshavardhan BV, Jolly MK, Schiebinger G, Levine H, McDonald T, Michor F (2023). bioRxiv: 558325

Mutually exclusive teams-like patterns of gene expression characterize phenotypic heterogeneity along the noradrenergic-mesenchymal axis in neuroblastoma.
Sehgal M, Nayak SP, Sahoo S, Somarelli J, Jolly MK (2023). bioRxiv: 556132

Low dimensionality of phenotypic space as an emergent property of coordinated teams in biological regulatory networks.
Hari K, Harlapur P, Saxena A, Haldar K, Girish A, Malpani T, Levine H, Jolly MK (2023). bioRxiv: 556132

Characterizing heterogeneity along EMT and metabolic axes in colorectal cancer reveals underlying consensus molecular subtype-specific trends.
Sehgal M, Soundharya R, Vaz JM, Yogeshwar RG, Muralidharan S, Venkatraghavan S, Jolly MK (2023). bioRxiv: 551165

An integrative phenotype-structured partial differential equation model for the population dynamics of epithelial-mesenchymal transition.
Sehgal M, Soundharya R, Vaz JM, Yogeshwar RG, Muralidharan S, Venkatraghavan S, Jolly MK (2023). aRxiv: 2309.09569

Spatial heterogeneity in tumor adhesion qualifies collective cell migration.
Prasanna CVS, Jolly MK#, Bhat R# (2023). bioRxiv: 559967

Lineage-specific dynamics of erasure of X-upregulation during inactive-X reactivation.
Naik HC, Chandel D, Majumdar S, Arava M, Baro R, Harshavardhan BV, Hari K, Parichitra, Avinchal, Jolly MK, Gayen S (2023). bioRxiv: 424181

Synthetic gene circuits combining CRISPR interference and CRISPR activation in E.coli: importance of equal guide RNA binding affinities to avoid context-dependent effects.
Barbier I, Kusumawadhani H#, Chauhan L#, Harlapur PV, Jolly MK, Schaerli Y (2023). bioRxiv: 544730

GPX4-VIM equates a proliferating DTP state in TNBC subtypes with converged vulnerabilities to autophagy and glutathione inhibition.
Chaudhury N, Choudhary BS, Patra S, Malvankar S, Shivashankar A, Jog E, Kailje VV, Khanna S, Manna S, Sahoo S, Soundharya R, Jolly MK, Dalal SN, Verma N (2023). bioRxiv: 541287

Cell-autonomous BMP signaling plays a key role in the maintenance of tumour cell EMT and migration programs in human ovarian carcinoma.
Joun G, Zolghadr F, Chakraborty P, Yen LLT, Chong JJH, Bowtell D, DeFazio A, Jolly MK, Seyedasli N (2023). bioRxiv: 538847

Melanocytes exhibit distinct cell states governed by a gene regulatory network under stochastic influence.
Aggarwal A, Nasreen A, Sahoo S, Faruq M, Pandey R, Jolly MK, Singh A, Gokhale RS, Natarajan T (2023). bioRxiv: 540111

Dual role of CASP8AP2/FLASH in regulating epithelial-to-mesenchymal transition (EMT).
Catalanotto M, Vaz JM*, Abshire C, Youngblood R, Chu M, Levine H, Jolly MK, Dragoi AM (2023). bioRxiv:  532282

Acquisition of hybrid EMT phenotype associated with increased migration, drug resistance and stemness is mediated by reduced miR-18a levels in ER-negative breast cancer.
Nair MG, Apoorva D, Chandrakala M, Snijesh VP, Anupama CE, Rajarajan S, Sahoo S, Mohan G, Jayakumar VS, Ramesh RS, Srinath BS, Jolly MK, Maliekal TT, Nakshatri H, Prabhu JS (2022). bioRxiv: 505398

Emergence of planar cell polarity from the interplay of asymmetric interaction and tissue-level gradients.
Singh D, Jolly MK#, Rizvi MS# (2021). bioRxiv: 468750

Continuum theory for planar cell polarity.
Rizvi MS#, Singh D, Jolly MK# (2021). bioRxiv: 468758

Lattice-based microenvironmental uncertainty driven phenotypic decision-making: a comparison with Notch-Delta-Jagged signaling.
Pujar AA, Barua A, Singh D, Roy U, Jolly MK#, Hatzikirou H# (2021). bioRxiv: 468748

Mechanistic modeling of the SARS-CoV-2 and immune system interplay unravels design principles for diverse clinicopathological outcomes.
Sahoo S, Hari K, Jhunjhunwala S, Jolly MK (2020). bioRxiv: 097238P

AMPK-Fyn signaling promotes Notch1 stability to potentiate hypoxia-induced breast cancer stemness and drug resistance.
Lahiry M, Kumar S, Hari K, Chedere A, Jolly MK, Rangarajan A (2020). bioRxiv: 458489

Feedback loops involving AMPK, ERK and TFEB in matrix detached leads to non-genetic heterogeneity.
Kumar S, Hari K, Jolly MK, Rangarajan A (2019). bioRxiv: 736546