Related papers: Characterizing virulence differences in a parasito…
Phenotype of biological systems needs to be robust against mutation in order to sustain themselves between generations. On the other hand, phenotype of an individual also needs to be robust against fluctuations of both internal and external…
Learning latent expression themes that best express complex patterns in a sample is a central problem in data mining and scientific research. For example, in computational biology we seek a set of salient gene expression themes that explain…
Coevolution is expected to follow two alternative dynamics, often called trench warfare and arms races in plant-pathogen systems. Trench warfare situations are stable cycles of allele frequencies at the coevolving loci of both host and…
Noise in gene expression, either due to inherent stochasticity or to varying inter- and intracellular environment, can generate significant cell-to-cell variability of protein levels in clonal populations. We present a theoretical…
In this paper, we consider two stochastic models of gene expression in prokaryotic cells. In the first model, sixteen biochemical reactions involved in transcription, translation and transcriptional regulation in the presence of inducer…
Much of the work on modeling the spread of viral infections utilized partial differential equa- tions. Traveling-wave solutions to these PDEs are typically concentrated on velocities and their dependence on the various parameters. Most of…
We report on a diffusive analysis of the motion of flagellate protozoa species. These parasites are the etiological agents of neglected tropical diseases: leishmaniasis caused by Leishmania amazonensis and Leishmania braziliensis, African…
Ecological and evolutionary dynamics have been historically regarded as unfolding at broadly separated timescales. However, these two types of processes are nowadays well documented to much more tightly than traditionally assumed,…
This work analyses the transcriptional effects of some biochemical mechanisms proposed in previous literature which attempts to explain the differential spatial expression of Hedgehog target genes involved in Drosophila development.…
Transcription is regulated through interplay between transcription factors, an RNA polymerase(RNAP), and a promoter. Even for a simple repressive transcription factor that disturbs promoter activity at the initial binding of RNAP, its…
MOTIVATION: A central goal of postgenomic biology is the elucidation of the regulatory relationships among all cellular constituents that together comprise the 'genetic network' of a cell or microorganism. Experimental manipulation of gene…
Much recent work has explored molecular and population-genetic constraints on the rate of protein sequence evolution. The best predictor of evolutionary rate is expression level, for reasons which have remained unexplained. Here, we…
Identifying variables responsible for changes to a biological system enables applications in drug target discovery and cell engineering. Given a pair of observational and interventional datasets, the goal is to isolate the subset of…
Inspired by DNA data of the human cytomegalovirus we propose a model of a two-type parasite population distributed over its hosts. The parasite is capable to persist in its host till the host dies, and to reinfect other hosts. To maintain…
Precise temporal coordination of gene expression is crucial for many developmental processes. One central question in developmental biology is how such coordinated expression patterns are robustly controlled. During embryonic development of…
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has a variable clinical presentation that ranges from asymptomatic, to severe disease with cytokine storm. The mortality rates also differ across the globe, ranging from 0.5-13%.…
The depletion interaction mediated by non-adsorbing polymers promotes condensation and assembly of repulsive colloidal particles into diverse higher-order structures and materials. One example, with particularly rich emergent behaviors, is…
We investigate the phase retrieval problem perturbed by dense bounded noise and sparse outliers that can change an adversarially chosen $s$-fraction of the measurement vector. The adversarial sparse outliers may exhibit dependence on both…
We introduce a general class of branching Markov processes for the modelling of a parasite infection in a cell population. Each cell contains a quantity of parasites which evolves as a diffusion with positive jumps. The growth rate,…
Sporulation in Bacillus subtilis serves as a paradigm for the development of two different cell types (mother cell and prespore) from a single cell. The mechanism by which the two different developmental programs are initiated has been much…