Abhyudai Singh
University of Delaware
GenePhysicsStatistical physicsStochastic modellingGene expressionNoiseBiological systemPopulationMathematicsComputer scienceMoment (mathematics)Noise (electronics)GeneticsControl theoryExpression (mathematics)Stochastic processCell divisionBiologyNegative feedbackCell biology
Publications 220
#1Abhyudai Singh (UD: University of Delaware)H-Index: 34
#2Brooks Emerick (KU: Kutztown University of Pennsylvania)H-Index: 4
Abstract null null Discrete-time models are the traditional approach for capturing population dynamics of insects living in the temperate regions of the world. We revisit classical discrete-time models of host–parasitoid population dynamics and provide novel results on the stability of the population dynamics. Discrete-time host–parasitoid models are characterized by update functions that connect the population densities from one year to the next, and a host escape response — the fraction of hos...
#1Shahla Nemati (UIdaho: University of Idaho)H-Index: 3
#2Abhyudai Singh (UD: University of Delaware)H-Index: 34
Last. Andreas E. Vasdekis (UIdaho: University of Idaho)H-Index: 17
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Single-cells grow by increasing their biomass and size. Here, we report that while mass and size accumulation rates of single Escherichia coli cells are exponential, their density fluctuates during growth. As such, the rates of mass and size accumulation of a single-cell are generally not the same, but rather cells differentiate into increasing one rate with respect to the other. This differentiation yields a previously unknown density homeostasis mechanism, which we support mathematically. Furt...
#1Paryad-Zanjani S (UD: University of Delaware)
#2Michael M. Saint-Antoine (UD: University of Delaware)H-Index: 3
Last. Abhyudai Singh (UD: University of Delaware)H-Index: 34
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One of the most difficult challenges in cancer therapy is the emergence of drug resistance within tumors. Sometimes drug resistance can emerge as the result of mutations and Darwinian selection. However, recently another phenomenon has been discovered, in which tumor cells switch back and forth between drug-sensitive and pre-resistant states. Upon exposure to the drug, sensitive cells die off, and pre-resistant cells become locked in to a state of permanent drug resistance. In this paper, we exp...
#1Andreas E. Vasdekis (UIdaho: University of Idaho)H-Index: 17
#2Abhyudai Singh (UD: University of Delaware)H-Index: 34
From the time a cell was first placed under the microscope, it became apparent that identifying two clonal cells that "look" identical is extremely challenging. Since then, cell-to-cell differences in shape, size, and protein content have been carefully examined, informing us of the ultimate limits that hinder two cells from occupying an identical phenotypic state. Here, we present recent experimental and computational evidence that similar limits emerge also in cellular metabolism. These limits...
1 CitationsSource
#1Candan Çelik (Comenius University in Bratislava)H-Index: 1
#2Pavol BokesH-Index: 11
Last. Abhyudai SinghH-Index: 34
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Chemical reaction networks involving molecular species at low copy numbers lead to stochasticity in protein levels in gene expression at the single-cell level. Mathematical modelling of this stochastic phenomenon enables us to elucidate the underlying molecular mechanisms quantitatively. Here we present a two-stage stochastic gene expression model that extends the standard model by an mRNA inactivation loop. The extended model exhibits smaller protein noise than the original two-stage model. Int...
#1José E. Pérez-Ortín (University of Valencia)H-Index: 38
#2Adriana Mena (University of Valencia)H-Index: 2
Last. José García-Martínez (University of Valencia)H-Index: 23
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The adjustment of transcription and translation rates to the changing needs of cells is of utmost importance for their fitness and survival. We have previously shown that the global transcription rate for RNA polymerase II in budding yeast Saccharomyces cerevisiae is regulated in relation to cell volume. Total mRNA concentration is constant with cell volume since global RNApol II-dependent nascent transcription rate (nTR) also keeps constant but mRNA stability increases with cell size. In this p...
1 CitationsSource
#1Niccolo Totis (Katholieke Universiteit Leuven)H-Index: 2
#2Cesar Nieto (University of Los Andes)H-Index: 2
Last. Steffen Waldherr (Katholieke Universiteit Leuven)H-Index: 4
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The dynamics of the size distribution in growing and dividing rod-shaped bacteria can change depending on the perspective through which the cell population is observed. From the perspective of single-cell lineages, only one descendant is followed after each division, while in population snapshots all of the offspring is considered. In this letter, we propose an analytical derivation of Population Balance Equations (PBEs) that can be used to compute the dynamics of the main statistics of the cell...
2 CitationsSource
#1Helen R. ClarkH-Index: 6
Last. Sergi Regot (JHUSOM: Johns Hopkins University School of Medicine)H-Index: 13
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To prevent damage to the host or its commensal microbiota, epithelial tissues must match the intensity of the immune response to the severity of a biological threat. Toll-like receptors allow epithelial cells to identify microbe associated molecular patterns. However, the mechanisms that mitigate biological noise in single cells to ensure quantitatively appropriate responses remain unclear. Here we address this question using single cell and single molecule approaches in mammary epithelial cells...
#1Yiyang Lu (UIUC: University of Illinois at Urbana–Champaign)H-Index: 3
#2Harpal Singh (UIUC: University of Illinois at Urbana–Champaign)H-Index: 2
Last. Roy D. Dar (UIUC: University of Illinois at Urbana–Champaign)H-Index: 14
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Summary Reactivation of human immunodeficiency virus 1 (HIV-1) from latently infected T cells is a critical barrier to cure patients. It remains unknown whether reactivation of individual latent cells occurs stochastically in response to latency reversal agents (LRAs), or is a deterministic outcome of an underlying cell state. To characterize these single-cell responses, we leverage the classical Luria-Delbruck fluctuation test where single-cells are isolated from a clonal population, and expose...
1 CitationsSource
#1Chen JiaH-Index: 11
#2Abhyudai Singh (UD: University of Delaware)H-Index: 34
Last. Ramon Grima (Edin.: University of Edinburgh)H-Index: 37
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Summary Recent advances in single-cell technologies have enabled time-resolved measurements of the cell size over several cell cycles. This data encodes information on how cells correct size aberrations so that they do not grow abnormally large or small. Here we formulate a piecewise deterministic Markov model describing the evolution of the cell size over many generations, for all three cell size homeostasis strategies (timer, sizer, and adder). The model is solved to obtain an analytical expre...