Related papers: A race model for singular olfactory receptor expre…
The relationship between a neuron's complex inputs and its spiking output defines the neuron's coding strategy. This is frequently and effectively modeled phenomenologically by one or more linear filters that extract the components of the…
Morphogenesis is central to biology but remains largely unexplored in chemistry. Reaction-diffusion (RD) mechanisms are, however, essential to understand how shape emerges in the living world. While numerical methods confirm the incredible…
Gene expression levels in a population vary extensively across tissues. Such heterogeneity is caused by genetic variability and environmental factors, and is expected to be linked to disease development. The abundance of experimental data…
Background: Differential expression analysis of (individual) genes is often used to study their roles in diseases. However, diseases such as cancer are a result of the combined effect of multiple genes. Gene products such as proteins seldom…
Single-cell gene expression measurements offer opportunities in deriving mechanistic understanding of complex diseases, including cancer. However, due to the complex regulatory machinery of the cell, gene regulatory network (GRN) model…
In many organisms the expression levels of each gene are controlled by the activation levels of known "Transcription Factors" (TF). A problem of considerable interest is that of estimating the "Transcription Regulation Networks" (TRN)…
Living cells must control the reading out or "expression" of information encoded in their genomes, and this regulation often is mediated by transcription factors--proteins that bind to DNA and either enhance or repress the expression of…
We identify a set of 575 human genes that are expressed in all conditions tested in a publicly available database of microarray results. Based on this common occurrence, the set is expected to be rich in "housekeeping" genes, showing…
Transcription of genes is the focus of most forms of regulation of gene expression. Even though careful biochemical experimentation has revealed the molecular mechanisms of transcription initiation for a number of different promoters in…
Motivated by applications to word-of-mouth advertising, we consider a game-theoretic scenario in which competing advertisers want to target initial adopters in a social network. Each advertiser wishes to maximize the resulting cascade of…
Motivation: Predicting the metastatic potential of primary malignant tissues has direct bearing on choice of therapy. Several microarray studies yielded gene sets whose expression profiles successfully predicted survival (Ramaswamy et al…
In the principal cells of the insect mushroom body, the Kenyon cells (KC), olfactory information is represented by a spatially and temporally sparse code. Each odor stimulus will activate only a small portion of neurons and each stimulus…
Gene regulatory networks typically have low in-degrees, whereby any given gene is regulated by few of the genes in the network. What mechanisms might be responsible for these low in-degrees? Starting with an accepted framework of the…
The reshaping and decorrelation of similar activity patterns by neuronal networks can enhance their discriminability, storage, and retrieval. How can such networks learn to decorrelate new complex patterns, as they arise in the olfactory…
Olfactory systems use a small number of broadly sensitive receptors to combinatorially encode a vast number of odors. We propose a method of decoding such distributed representations by exploiting a statistical fact: receptors that do not…
Single-cell RNA-seq data are challenging because of the sparseness of the read counts, the tiny expression of many relevant genes, and the variability in the efficiency of RNA extraction for different cells. We consider a simple…
Gene regulatory networks, i.e. DNA segments in a cell which interact with each other indirectly through their RNA and protein products, lie at the heart of many important intracellular signal transduction processes. In this paper we analyse…
Multicellular organisms contain a wide variety of highly specialized cell types. The consistency and robustness of developmental trajectories suggest that complex gene regulatory networks effectively act as low-dimensional cell fate…
Single-cell gene expression measurements encode variability spanning molecular noise, cell-to-cell heterogeneity, and technical artifacts. Mechanistic stochastic models provide powerful approaches to disentangle these sources, yet inferring…
Many biological systems approach physical limits to their performance, motivating the idea that their behavior and underlying mechanisms could be determined by such optimality. Nevertheless, optimization as a predictive principle has only…