Related papers: Biological insights from RIL-seq in bacteria
The single-cell RNA sequencing (scRNA-seq) technology enables researchers to study complex biological systems and diseases with high resolution. The central challenge is synthesizing enough scRNA-seq samples; insufficient samples can impede…
Background: MicroRNAs (miRNAs) play multiple roles in tumor biology [1]. Interestingly, reports from multiple groups suggest that miRNA targets may be coupled through competitive stoichiometric sequestration [2]. Specifically, computational…
The transcriptional regulation of gene expression is orchestrated by complex networks of interacting genes. Increasing evidence indicates that these transcriptional regulatory networks (TRNs) in bacteria have an inherently hierarchical…
Despite the absence of a membrane-enclosed nucleus, the bacterial DNA is typically condensed into a compact body - the nucleoid. This compaction influences the localization and dynamics of many cellular processes including transcription,…
Single cell combinatorial indexing RNA sequencing (sci-RNA-seq) is a powerful method for recovering gene expression data from an exponentially scalable number of individual cells or nuclei. However, sci-RNA-seq is a complex protocol that…
MicroRNAs (miRNAs) are endogenous small non-coding RNAs that play an important role in post-transcriptional gene regulation. However, the experimental determination of miRNA sequence and structure is both expensive and time-consuming.…
The precise layout of gene expression patterns is a crucial step in development. Formation of a sharp boundary between high and low expression domains requires a genetic mechanism which is both sensitive and robust to fluctuations, a demand…
Non-conding RNAs play a key role in the post-transcriptional regulation of mRNA translation and turnover in eukaryotes. miRNAs, in particular, interact with their target RNAs through protein-mediated, sequence-specific binding, giving rise…
In recent years, the advances in single-cell RNA-seq techniques have enabled us to perform large-scale transcriptomic profiling at single-cell resolution in a high-throughput manner. Unsupervised learning such as data clustering has become…
Correct inference of genetic regulations inside a cell is one of the greatest challenges in post genomic era for the biologist and researchers. Several intelligent techniques and models were already proposed to identify the regulatory…
Gene regulatory networks (GRNs) represent the causal relationships between transcription factors (TFs) and target genes in single-cell RNA sequencing (scRNA-seq) data. Understanding these networks is crucial for uncovering disease…
We study genetic networks that produce many species of non-coding RNA molecules that are present at a moderate density, as typically exists in the cell. The associations of the many species of these RNA are modeled physically, taking into…
Single-cell RNA sequencing (scRNA-seq) has revolutionized the study of cellular heterogeneity, enabling detailed molecular profiling at the individual cell level. However, integrating high-dimensional single-cell data into causal mediation…
Gene regulatory network (GRN) refers to the complex network formed by regulatory interactions between genes in living cells. In this paper, we consider inferring GRNs in single cells based on single cell RNA sequencing (scRNA-seq) data. In…
Single-cell RNA sequencing (scRNA-seq) has transformed our ability to explore biological systems. Nevertheless, proficient expertise is essential for handling and interpreting the data. In this paper, we present scX, an R package built on…
In unicellular organisms such as bacteria the same acquired mutations beneficial in one environment can be restrictive in another. However, evolving Escherichia coli populations demonstrate remarkable flexibility in adaptation. The…
Cellular phenotypes are determined by the dynamical activity of networks of co-regulated genes. Elucidating such networks is crucial for the understanding of normal cell physiology as well as for the dissection of complex pathologic…
A bacterial colony may develop a small number of cells genetically identical to, but phenotypically different from other normally growing bacteria. These so-called persister cells keep themselves in a dormant state and thus are insensitive…
Functional or non-coding RNAs are attracting more attention as they are now potentially considered valuable resources in the development of new drugs intended to cure several human diseases. The identification of drugs targeting the…
In the past decades microRNAs (miRNA) have much attracted the attention of researchers at the interface between life and theoretical sciences for their involvement in post-transcriptional regulation and related diseases. Thanks to the…