Abhishek Tiwari › Comments

A new class of small RNA (~45 bases long) is identified in gram positive and negative bacteria. These tssRNAs are associated with RNA polymerase pausing some 45 bases downstream of the transcription start site and show global changes in expression during the growth cycle. - Abhishek Tiwari

Live-cell imaging and mathematical modelling of the type-I interferon response to viral infection reveal that multiple layers of the cellular response are stochastic events in individual cells, while paracrine propagation of the IFN signal results in reliable antiviral protection. - Abhishek Tiwari

Comparative RNA-seq analysis of two related pathogenic and non-pathogenic bacterial strains reveals a hidden layer of divergence in the non-coding genome as well as conserved, widespread regulatory structures called ‘Excludons’, which mediate regulation through long non-coding antisense RNAs. - Abhishek Tiwari

The spindle position checkpoint (SPOC) is an important surveillance mechanism in the budding yeast cell cycle. An integrated approach, combining quantitative experimental cell biology with mathematical modeling, reveals how the SPOC inhibits mitotic exit at the molecular level. - Abhishek Tiwari

Many characterized metabolic enzymes currently lack associated gene and protein sequences. Here, pathway and genomic neighbour data are used to assign genes to these ‘orphan enzymes,’ and the predictions are validated with experimental assays and genome-scale metabolic modelling. - Abhishek Tiwari

A large set of high-content RNAi screens investigating mammalian virus infection and multiple cellular activities is analysed to reveal the impact of population context on phenotypic variability and to identify indirect RNAi effects. - Abhishek Tiwari

An intuitive formalism for reconstructing cellular networks from empirical data is presented, and used to build a comprehensive yeast MAP kinase network. The accompanying rxncon software tool can convert networks to a range of standard graphical formats and mathematical models. - Abhishek Tiwari

A common regulatory motif, where a heterodimeric transcriptional regulator positively autoregulates only one of its components, is found to have particular properties that enable precise and robust control of cellular responses to environmental stimuli, providing an explanation for the prevalence of this motif in evolved regulatory networks. - Abhishek Tiwari

Repetitive stretches of DNA that contain transcription factor (TF) binding sites can act as decoys that sequester TFs. This study shows that these decoy sites can have important indirect effects on transcriptional regulation by altering the dose–response between a TF and its target promoter. - Abhishek Tiwari

Proteomic analysis of T cells emerging from quiescence identifies dynamic network-level changes in key cellular processes. Disruption of two such processes, ribosome biogenesis and RNA splicing, reveals that the programs controlling cell growth and cell-cycle entry are separable. - Abhishek Tiwari

Recent findings are incorporated into a new mathematical model of the plant circadian clock, revealing a complex circuit structure comprised of multiple negative feedback loops, and predicting a repressive role for a key regulator, TOC1, which the authors confirm experimentally. - Abhishek Tiwari

Most cell cycle-regulated genes adopt non-optimal codon usage, namely, their translation involves wobbly matching codons. Here, the authors show that tRNA expression is cyclic and that codon usage, therefore, can give rise to cell-cycle regulation of proteins. - Abhishek Tiwari

The effect of kinase, phosphatase and N-acetyltransferase deletions on proteome phosphorylation and acetylation was investigated in Mycoplasma pneumoniae. Bi-directional cross-talk between post-transcriptional modifications suggests an underlying regulatory molecular code in prokaryotes. - Abhishek Tiwari

A genome-wide microRNA (miRNome) screen coupled with high-throughput monitoring of protein levels reveals complex, modular miRNA regulation of the EGFR-driven cell-cycle network, and identifies new miRNAs that can suppress breast cancer cell proliferation. - Abhishek Tiwari

Viral infection depends on a complex interplay between host and viral factors. Here, the authors link host susceptibility to viral infection to a network encompassing sulfur metabolism, tRNA modification, competitive binding, and programmed ribosomal frameshifting. - Abhishek Tiwari

Data-driven modeling was used to analyze the complex signaling dynamics that connect DNA repair with cell survival, cell-cycle arrest, or apoptosis. This analysis revealed an unexpected role for Erk in G1/S arrest and apoptotic cell death following - Abhishek Tiwari

Environmental light regulates and optimizes plant growth and development. Genomic profiling of polysome-associated mRNA reveals that light stimulates dramatic changes in translational regulation, which contribute more to light-induced gene expression changes than transcriptional regulation. - Abhishek Tiwari

Simulations of the evolution of simple gene regulatory networks reveal that fluctuating environmental selection can lead to the emergence of bistability under certain conditions where fluctuation and mutational rates are in tune. - Abhishek Tiwari

Protein and genetic interaction maps have typically been generated under a single condition, providing a static view of the interactome. Recent studies employing differential analysis, however, have revealed that widespread re-wiring of the interactome underlies key biological responses. - Abhishek Tiwari

Overloaded enzymatic processes are shown to create indirect coupling between upstream components in cellular networks. This has important implications for the design of synthetic biology devices and for our understanding of currently inexplicable links within endogenous biological systems. - Abhishek Tiwari

Inflammatory gene activation must be rigorously controlled to ensure a rapid, but transient, response. In this work, a regulatory circuit is revealed that governs the destabilization of inflammatory mRNAs and plays an essential role in re-establishing immune homeostasis after inflammatory stimulus. - Abhishek Tiwari

Measurement of metabolic and physiological parameters in replicated crosses of Drosophila melanogaster inbred lines reveals that environmental and genetic perturbations uncover substantially different networks of metabolic regulation. - Abhishek Tiwari

Strand-specific RNA sequencing of S. pombe reveals a highly structured programme of ncRNA expression at over 600 loci. Functional investigations show that this extensive ncRNA landscape controls the complex programme of sexual differentiation in S. pombe. - Abhishek Tiwari

A genetic tug-of-war system is used to explore the sensitivity of the fission yeast cell cycle to changes in gene dosage, revealing a deeply conserved fragile core. A mathematical model can reproduce the robustness of the cell cycle, and points to currently unknown regulatory mechanisms. - Abhishek Tiwari

An important cell fate decision in Bacillus subtilis is shown to be the result of a ‘molecular race’ between competing differentiation programs. The programs controlling competence initiation and spore formation progress independently, and without cross-talk, before cell fate choice. - Abhishek Tiwari

Genome-scale analysis of the DNA binding properties of the protein complex that regulates yeast sulfur metabolism identifies a specific DNA motif that directs the recruitment of key non-DNA-binding cofactors, revealing a powerful mechanism for selective target gene regulation. - Abhishek Tiwari

Proteomic analyses, literature mining, and structural data were combined to generate an extensive signaling network linked to the visual G protein-coupled receptor rhodopsin. Network analysis suggests novel signaling routes to cytoskeleton dynamics and vesicular trafficking. - Abhishek Tiwari

An in-depth proteomic comparison of human-induced pluripotent stem cells, and their parent fibroblast cells, with embryonic stem cells shows that the reprogramming process comprehensively remodels protein expression levels, creating cells that closely resemble natural stem cells. - Abhishek Tiwari

Experimental analysis of TFB family proteins in a halophilic archaeon reveals complex environment-dependent fitness contributions. Gene conversion events among these proteins can generate novel niche adaptation capabilities, a process that may have contributed to archaeal adaptation to extreme environments. - Abhishek Tiwari

Kinetic modeling, phase diagrams analysis, and quantitative single-cell experiments are combined to investigate how multiple factors, including the XIAP:caspase-3 ratio and ligand concentration, regulate receptor-mediated apoptosis. - Abhishek Tiwari