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Cells must coordinate adjustments in genome expression to accommodate changes in their environment. We hypothesized that the amount of transcriptome change is proportional to the amount of environmental change. To capture the effects of…
How adaptive evolution to one environmental stress improves or suppresses adaptation to another is an important problem in evolutionary biology. For instance, in microbiology, the evolution of bacteria to be resistant to different…
Cells adapt to different conditions by altering a vast number of components, which is measurable using transcriptome analysis. Given that a cell undergoing steady growth is constrained to sustain each of its internal components, the…
Evolution of gene regulation is crucial for our understanding of the phenotypic differences between species, populations and individuals. Sequence-specific binding of transcription factors to the regulatory regions on the DNA is a key…
One of the outstanding challenges in comparative genomics is to interpret the evolutionary importance of regulatory variation between species. Rigorous molecular evolution-based methods to infer evidence for natural selection from…
Genes are connected in complex networks of interactions where often the product of one gene is a transcription factor that alters the expression of another. Many of these networks are based on a few fundamental motifs leading to switches…
The baseline level of transcription, which is variable and difficult to quantify, seriously complicates the normalization of comparative transcriptomic data, but its biological importance remains unappreciated. We show that this currently…
Genetically identical cells in the same population can take on phenotypically variable states, leading to differentiated responses to external signals, such as nutrients and drug-induced stress. Many models and experiments have focused on a…
Transcriptomic analysis are characterized by being not directly quantitative and only providing relative measurements of expression levels up to an unknown individual scaling factor. This difficulty is enhanced for differential expression…
Transcription is a fundamental cellular process, and the first step of gene expression. In human cells, it depends on the binding to chromatin of various proteins, including RNA polymerases and numerous transcription factors (TFs).…
Many cellular responses to surrounding cues require temporally concerted transcriptional regulation of multiple genes. In prokaryotic cells, a single-input-module motif with one transcription factor regulating multiple target genes can…
The different cell types in a living organism acquire their identity through the process of cell differentiation in which the multipotent progenitor cells differentiate into distinct cell types. Experimental evidence and analysis of…
Due to recent breakthroughs in state-of-the-art DNA sequencing technology, genomics data sets have become ubiquitous. The emergence of large-scale data sets provides great opportunities for better understanding of genomics, especially gene…
Bacterial plant pathogens rely on a battalion of transcription factors to fine-tune their response to changing environmental conditions and marshal the genetic resources required for successful pathogenesis. Prediction of transcription…
Bacterial chemotaxis systems are as diverse as the environments that bacteria inhabit, but how much environmental variation can cells tolerate with a single system? Diversification of a single chemotaxis system could serve as an…
In recent times whole-genome gene expression analysis has turned out to be a highly important tool to study the coordinated function of a very large number of genes within their corresponding cellular environment, especially in relation to…
Cells continuously sense their surroundings to detect modifications and generate responses. Very often changes in extracellular concentrations initiate signaling cascades that eventually result in changes in gene expression. Increasing…
Cells often exhibit different and stable phenotypes from the same DNA sequence. Robustness and plasticity of such cellular states are controlled by diverse transcriptional and epigenetic mechanisms, among them the modification of…
Understanding functional organization of genetic information is a major challenge in modern biology. Following the initial publication of the human genome sequence in 2001, advances in high-throughput measurement technologies and efficient…
Large language models (LLMs) have shown strong ability in generating rich representations across domains such as natural language processing and generation, computer vision, and multimodal learning. However, their application in biomedical…