Abhishek Tiwari

Harmful epistatic (genetic) interactions not only occur between mutations, but also when genes change in expression. Gene expression dynamics in yeast suggests that this ‘epigenetic’ epistasis constrains evolution, with the tight regulation of network hubs promoting a robust, ‘canalized’ phenotype. - Abhishek Tiwari

PySB is a framework for creating biological models as Python programs using a high-level, action-oriented vocabulary that promotes transparency, extensibility and reusability. PySB interoperates with many existing modeling tools and supports distributed model development. - Abhishek Tiwari

Escherichia coli cells were evolved over 500 generations and profiled in four abiotic stressors to observe several cases of emerging cross-stress behavior whereby adaptation to one stressful environment provided fitness advantage when exposed to a second stressor. - Abhishek Tiwari

A Bayesian framework is used to calibrate a mass-action model of receptor-mediated apoptosis. Despite parameter non-identifiability and model ‘sloppiness’, Bayes factor analysis discriminates between two alternative models of mitochondrial outer membrane permeabilization. - Abhishek Tiwari

By comparative analysis of RNA polymerase II and FOXO3 ChIP-sequencing, combined with 4C-sequencing and ChIPs on histone modifications, general mechanisms of FOXO3-mediated target gene regulation are identified. - Abhishek Tiwari

This review provides an overview of methodologies and technologies enabling genome-scale engineering, focusing on the design, construction, and testing of modified genomes in a variety of organisms. Future applications for systems and synthetic biology are discussed. - Abhishek Tiwari

Human brain transcriptome analysis revealed widespread age-related splicing changes in the prefrontal cortex and cerebellum. While most of the splicing changes take place in development, approximately one-third of them extends into aging. - Abhishek Tiwari

Escherichia coli were engineered to enable programmed motility, sensing and phenotypic response to the density of epidermal growth factor receptor expressed on the surface of cancer cells. - Abhishek Tiwari

A new quantitative strategy has generated a comprehensive rate control map for protein synthesis in exponentially growing yeast cells. This analysis reveals the modularity of the system as well as highly non-stoichiometric relationships between components. - Abhishek Tiwari

Precise analysis of systematic errors shows suitability of immunofluorescence protocols to quantify gene expression means, variances, and cross-correlations. Application to Drosophila gap genes enables reconstructing expression level dynamics and the progression of positional accuracy. - Abhishek Tiwari

Phosphorylation sites of human proteins are frequently mutated in cancer. Statistical analysis of phosphorylation-associated single nucleotide variants (pSNVs) predicts novel cancer drivers and phospho-mutation mechanisms in known cancer genes. - Abhishek Tiwari

A simple, parameterless mathematical model, in combination with real-time monitoring of promoter activities, shows how control of gene expression in bacteria is shared between transcription factors and global physiological effects. - Abhishek Tiwari

Genome sequencing technologies have advanced rapidly, dramatically decreasing cost and increasing throughput. But beyond faster and cheaper, these advances have also stimulated the development of innovative new experimental approaches, and are opening new doors in human medicine and health. - Abhishek Tiwari