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Detecting repeating patterns of different lengths in time series, also called variable-length motifs, has received a great amount of attention by researchers and practitioners. Despite the significant progress that has been made in recent…
Causal discovery in multi-omic datasets is crucial for understanding the bigger picture of gene regulatory mechanisms, but remains challenging due to high dimensionality, differentiation of direct from indirect relationships, and hidden…
The mutation and selection of regulatory DNA sequences is presented as an ideal model system of molecular evolution where genotype, phenotype, and fitness can be explicitly and independently characterized. In this theoretical study, we…
One of the most important concepts in biological network analysis is that of network motifs, which are patterns of interconnections that occur in a given network at a frequency higher than expected in a random network. In this work we are…
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…
Gene regulatory networks arise in all living cells, allowing the control of gene expression patterns. The study of their topology has revealed that certain subgraphs of interactions or "motifs" appear at anomalously high frequencies. We ask…
From the response to external stimuli to cell division and death, the dynamics of living cells is based on the expression of specific genes at specific times. The decision when to express a gene is implemented by the binding and unbinding…
We discuss a simple and powerful approach for the ab initio identification of cis-regulatory motifs involved in transcriptional regulation. The method we present integrates several elements: human-mouse comparison, statistical analysis of…
Studying the topology of so-called real networks, that is networks obtained from sociological or biological data for instance, has become a major field of interest in the last decade. One way to deal with it is to consider that networks are…
Gene regulation is a complex process involving the role of several genomic elements which work in concert to drive spatio-temporal expression. The experimental characterization of gene regulatory elements is a very complex and…
Motifs are the fundamental components of complex systems. The topological structure of networks representing complex systems and the frequency and distribution of motifs in these networks are intertwined. The complexities associated with…
Motif extraction is an important task in motif based molecular representation learning. Previously, machine learning approaches employing either rule-based or string-based techniques to extract motifs. Rule-based approaches may extract…
The mining of graphs in terms of their local substructure is a well-established methodology to analyze networks. It was hypothesized that motifs - subgraph patterns which appear significantly more often than expected at random - play a key…
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…
Most cellular phenotypes are genetically complex. Identifying the set of genes that are most closely associated with a specific cellular state is still an open question in many cases. Here we study the transcriptional profile of cellular…
A blood cell lineage consists of several consecutive developmental stages from the pluri- or multipotent stem cell to a state of terminal differentiation. Despite their importance for human biology, the regulatory pathways and gene networks…
Studying the topology of so-called {\em real networks}, that is networks obtained from sociological or biological data for instance, has become a major field of interest in the last decade. One way to deal with it is to consider that…
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…
In microarray experiments, it is often of interest to identify genes which have a pre-specified gene expression profile with respect to time. Methods available in the literature are, however, typically not stringent enough in identifying…
Motivation: Modules in gene coexpression networks (GCN) can be regarded as gene groups with individual relationships. No studies have optimized module detection methods to extract diverse gene groups from GCN, especially for data from…