239 citations · 412 across the 24 of their papers we have counts for
8 papers · 1 filter
Network Inference in Systems Biology: Recent Developments, Challenges, and Applications
Michael M. Saint-Antoine, Abhyudai Singh
One of the most interesting, difficult, and potentially useful topics in computational biology is the inference of gene regulatory networks (GRNs) from expression data. Although re…
Evaluating Pruning Methods in Gene Network Inference
Michael M. Saint-Antoine, Abhyudai Singh
One challenge in gene network inference is distinguishing between direct and indirect regulation. Some algorithms, including ARACNE and Phixer, approach this problem by using pruni…
Cell-cycle coupled expression minimizes random fluctuations in gene product levels
Mohammad Soltani, Abhyudai Singh
Expression of many genes varies as a cell transitions through different cell-cycle stages. How coupling between stochastic expression and cell cycle impacts cell-to-cell variabilit…
Gene expression noise is affected differentially by feedback in burst frequency and burst size
Pavol Bokes, Abhyudai Singh
Inside individual cells, expression of genes is stochastic across organisms ranging from bacterial to human cells. A ubiquitous feature of stochastic expression is burst-like synth…
Optimal regulation of protein degradation to schedule cellular events with precision
Khem Raj Ghusinga, Abhyudai Singh
An important occurrence in many cellular contexts is the crossing of a prescribed threshold by a regulatory protein. The timing of such events is stochastic as a consequence of the…
Decomposing variability in protein levels from noisy expression, genome duplication and partitioning errors during cell-divisions
Mohammad Soltani, Cesar Augusto Vargas-Garcia, Duarte Antunes +1
Inside individual cells, expression of genes is inherently stochastic and manifests as cell-to-cell variability or noise in protein copy numbers. Since proteins half-lives can be c…
Stochastic Analysis Of An Incoherent Feedforward Genetic Motif
Thierry Platini, Mohammad Soltani, Abhyudai Singh
Gene products (RNAs, proteins) often occur at low molecular counts inside individual cells, and hence are subject to considerable random fluctuations (noise) in copy number over ti…
Transcriptional bursting in gene expression: analytical results for general stochastic models
Niraj Kumar, Abhyudai Singh, Rahul V. Kulkarni
Gene expression in individual cells is highly variable and sporadic, often resulting in the synthesis of mRNAs and proteins in bursts. Bursting in gene expression is known to impac…