84 citations · 123 across the 7 of their papers we have counts for
8 papers
Epigenetic factor competition reshapes the EMT landscape
M. Ali Al-Radhawi, Shubham Tripathi, Yun Zhang +2
The emergence of and transitions between distinct phenotypes in isogenic cells can be attributed to the intricate interplay of epigenetic marks, external signals, and gene regulato…
Towards decoding the coupled decision-making of metabolism and epithelial-mesenchymal transition in cancer
Dongya Jia, Jun Hyoung Park, Harsimran Kaur +9
Cancer cells have the plasticity to adjust their metabolic phenotypes for survival and metastasis. During metastasis, a developmental program known as the epithelial-mesenchymal tr…
Biological Regulatory Networks are Minimally Frustrated
Shubham Tripathi, David A. Kessler, Herbert Levine
Characterization of the differences between biological and random networks can reveal the design principles that enable the robust realization of crucial biological functions inclu…
Mathematical Modeling of Plasticity and Heterogeneity in EMT
Shubham Tripathi, Jianhua Xing, Herbert Levine +1
Epithelial-Mesenchymal Transition (EMT), and the corresponding reverse process, Mesenchymal-Epithelial Transition (MET), are dynamic and reversible cellular programs orchestrated b…
Quantifying cancer epithelial-mesenchymal plasticity and its association with stemness and immune response
Dongya Jia, Xuefei Li, Federico Bocci +5
Cancer cells can acquire a spectrum of stable hybrid epithelial/mesenchymal (E/M) states during epithelial-mesenchymal transition (EMT). Cells in these hybrid E/M phenotypes often…
The standard genetic code facilitates exploration of the space of functional nucleotide sequences
Shubham Tripathi, Michael W. Deem
The standard genetic code is well known to be optimized for minimizing the phenotypic effects of single nucleotide substitutions, a property that was likely selected for during the…
Analysis of hierarchical organization in gene expression networks reveals underlying principles of collective tumor cell dissemination and metastatic aggressiveness of inflammatory breast cancer
Shubham Tripathi, Mohit Kumar Jolly, Wendy A. Woodward +2
Clusters of circulating tumor cells (CTCs), although rare, may account for more than 95% of metastases. Inflammatory breast cancer (IBC) is a highly aggressive subtype that chiefly…
Hierarchy in Gene Expression is Predictive for Adult Acute Myeloid Leukemia
Shubham Tripathi, Michael W. Deem
Cancer progresses with a change in the structure of the gene network in normal cells. We define a measure of organizational hierarchy in gene networks of affected cells in adult ac…