Related papers: Ab initio identification of putative human transcr…
Transcription factor binding sites vary in their specificity, both within and between species. Binding specificity has a strong impact on the evolution of gene expression, because it determines how easily regulatory interactions are gained…
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…
Network motifs, the recurring regulatory structural patterns in networks, are able to self-organize to produce networks. Three major motifs, feedforward loop, single input modules and bi-fan are found in gene regulatory networks. The large…
In vertebrates, olfactory sensory neurons choose only one olfactory receptor to produce out of ~2000 possibilities. The mechanism for how this singular receptor expression occurs is unknown. Here we propose a mechanism that can…
It is tempting to believe that we now own the genome. The ability to read and re-write it at will has ushered in a stunning period in the history of science. Nonetheless, there is an Achilles heel exposed by all of the genomic data that has…
Unraveling the co-expression of genes across studies enhances the understanding of cellular processes. Inferring gene co-expression networks from transcriptome data presents many challenges, including spurious gene correlations, sample…
The expression of one gene might be regulated by its corresponding protein, which is called autoregulation. Although gene regulation is a central topic in biology, autoregulation is much less studied. In general, it is extremely difficult…
Cis-regulatory elements (CREs), such as promoters and enhancers, are relatively short DNA sequences that directly regulate gene expression. The fitness of CREs, measured by their ability to modulate gene expression, highly depends on the…
Turnover of regulatory sequence and function is an important part of molecular evolution. But what are the modes of sequence evolution leading to rapid formation and loss of regulatory sites? Here, we show that a large fraction of…
Finding repeated patterns or motifs in a time series is an important unsupervised task that has still a number of open issues, starting by the definition of motif. In this paper, we revise the notion of motif support, characterizing it as…
Representation of intracellular signaling networks as directed graphs allows for the identification of regulatory motifs. Regulatory motifs are groups of nodes with the same connectivity structure, capable of processing information. The…
Transcription regulation is largely governed by the profile and the dynamics of transcription factors' binding to DNA. Stochastic effects are intrinsic to this dynamics and the binding to functional sites must be controled with a certain…
Inferring genetic networks from gene expression data is one of the most challenging work in the post-genomic era, partly due to the vast space of possible networks and the relatively small amount of data available. In this field, Gaussian…
The structure and dynamics of a typical biological system are complex due to strong and inhomogeneous interactions between its constituents. The investigation of such systems with classical mathematical tools, such as differential equations…
Background: The identification of transcription factor binding sites (TFBSs) and cis-regulatory modules (CRMs) is a crucial step in studying gene expression, but the computational method attempting to distinguish CRMs from NCNRs still…
Causal discovery, the task of inferring causal structure from data, has the potential to uncover mechanistic insights from biological experiments, especially those involving perturbations. However, causal discovery algorithms over larger…
One of the fundamental tasks in understanding genomics is the problem of predicting Transcription Factor Binding Sites (TFBSs). With more than hundreds of Transcription Factors (TFs) as labels, genomic-sequence based TFBS prediction is a…
The problem of motif detection can be formulated as the construction of a discriminant function to separate sequences of a specific pattern from background. In computational biology, motif detection is used to predict DNA binding sites of a…
Biophysicists are modeling conformations of interphase chromosomes, often basing the strengths of interactions between segments distant on the genetic map on contact frequencies determined experimentally. Here, instead, we develop a…
Current models for the folding of the human genome see a hierarchy stretching down from chromosome territories, through A/B compartments and TADs (topologically-associating domains), to contact domains stabilized by cohesin and CTCF.…