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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)…
Single-cell RNA-Sequencing (scRNA-Seq) is a revolutionary technique for discovering and describing cell types in heterogeneous tissues, yet its measurement of expression often suffers from large systematic bias. A major source of this bias…
Background: Small interfering RNA (siRNA) is a promising therapeutic agent due to its ability to silence disease-related genes via RNA interference. While traditional machine learning and early deep learning methods have made progress in…
RNA secondary structures of increasing complexity are probed combining single molecule stretching experiments and stochastic unfolding/refolding simulations. We find that force-induced unfolding pathways cannot usually be interpretated by…
MicroRNAs are small non-coding nucleotide sequences that regulate target protein expression at post-transcriptional levels. Biogenesis of microRNA is a highly regulated multi-step pathway. Regulation of miRNA biogenesis can be caused…
Homeostasis of protein concentrations in cells is crucial for their proper functioning, and this requires concentrations (at their steady-state levels) to be stable to fluctuations. Since gene expression is regulated by proteins such as…
Small open reading frames are understudied as they have been historically excluded from genome annotations. However, evidence for the functional significance of small proteins in various cellular processes accumulates. Proteins with less…
Modeling gene regulatory networks (GRNs) is an important topic in systems biology. Although there has been much work focusing on various specific systems, the generic behavior of GRNs with continuous variables is still elusive. In…
Single-cell RNA-seq data allow the quantification of cell type differences across a growing set of biological contexts. However, pinpointing a small subset of genomic features explaining this variability can be ill-defined and…
The intricate network of interactions observed in RNA three-dimensional structures is often described in terms of a multitude of geometrical properties, including helical parameters, base pairing/stacking, hydrogen bonding and backbone…
Tight regulation of messenger RNA (mRNA) stability is essential to ensure accurate gene expression in response to developmental and environmental cues. mRNA stability is controlled by mRNA decay pathways, which have traditionally been…
Sequencing costs currently prohibit the application of single-cell mRNA-seq to many biological and clinical analyses. Targeted single-cell mRNA-sequencing reduces sequencing costs by profiling reduced gene sets that capture biological…
Corynebacterium glutamicum is a Gram-positive bacterium found in soil where the condition changes demand plasticity of the regulatory machinery. The study of such machinery at the global scale has been challenged by the lack of data…
Single-cell RNA sequencing has transformed biology by enabling the measurement of gene expression at cellular resolution, providing information for cell types, states, and disease contexts. Recently, single-cell foundation models have…
RNA function is deeply intertwined with its conformational dynamics. In this review, we survey recent advances in the use of atomistic molecular dynamics simulations to characterize RNA dynamics in diverse contexts, including isolated…
Central to the functioning of a living cell is its ability to control the readout or expression of information encoded in the genome. In many cases, a single transcription factor protein activates or represses the expression of many genes.…
Features of the CRISPR-Cas system, in which bacteria integrate small segments of phage genome (spacers) into their DNA to neutralize future attacks, suggest that its effect is not limited to individual bacteria but may control the fate and…
MicroRNAs are extensively known for post-transcriptional gene regulation and pattern formation in the embryonic developmental stage. We explore the origin of these spatio-temporal patterns mathematically, considering three different motifs…
Gene regulatory networks typically have low in-degrees, whereby any given gene is regulated by few of the genes in the network. They also tend to have broad distributions for the out-degree. What mechanisms might be responsible for these…
Identification and quantification of condition-specific transcripts using RNA-Seq is vital in transcriptomics research. While initial efforts using mathematical or statistical modeling of read counts or per-base exonic signal have been…