Related papers: Modelling chromosome-wide target search
The study of gene regulation and expression is often discussed in quantitative terms. In particular, the expression of genes is regularly characterized with respect to how much, how fast, when and where. Whether discussing the level of gene…
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…
High-dimensional data are commonly seen in modern statistical applications, variable selection methods play indispensable roles in identifying the critical features for scientific discoveries. Traditional best subset selection methods are…
Whole and targeted sequencing of human genomes is a promising, increasingly feasible tool for discovering genetic contributions to risk of complex diseases. A key step is calling an individual's genotype from the multiple aligned short read…
Predicting how genetic perturbations change cellular state is a core problem for building controllable models of gene regulation. Perturbations targeting the same gene can produce different transcriptional responses depending on their…
Stereo matching, a critical step of 3D reconstruction, has fully shifted towards deep learning due to its strong feature representation of remote sensing images. However, ground truth for stereo matching task relies on expensive airborne…
Cohesive subgraph mining is a fundamental problem in graph theory with numerous real-world applications, such as social network analysis and protein-protein interaction modeling. Among various cohesive subgraphs, the $\gamma$-quasi-clique…
A self-organizing approach is proposed for gene finding based on the model of codon usage for coding regions and positional preference for noncoding regions. The symmetry between the direct and reverse coding regions is adopted for reducing…
Technology progress in DNA sequencing boosts the genomic database growth at faster and faster rate. Compression, accompanied with random access capabilities, is the key to maintain those huge amounts of data. In this paper we present an…
In this work, we describe a computational framework for the genome-wide identification and characterization of mixed transcriptional/post-transcriptional regulatory circuits in humans. We concentrated in particular on feed-forward loops…
Understanding the three-dimensional (3D) structure of the genome is essential for elucidating vital biological processes and their links to human disease. To determine how the genome folds within the nucleus, chromosome conformation capture…
The variation in DNA copy number carries information on the modalities of genome evolution and misregulation of DNA replication in cancer cells; its study can be helpful to localize tumor suppressor genes, distinguish different populations…
Coexpression of genes or, more generally, similarity in the expression profiles poses an unsurmountable obstacle to inferring the gene regulatory network (GRN) based solely on data from DNA microarray time series. Clustering of genes with…
Genome organization in eukaryotes during interphase stems from the delicate balance between non-random correlations present in the DNA polynucleotide linear sequence and the physico/chemical reactions which shape continuously the form and…
Next-generation sequencing technologies generate millions of short sequence reads, which are usually aligned to a reference genome. In many applications, the key information required for downstream analysis is the number of reads mapping to…
We model the transcription factor based regulation network of yeast using a content-based network model that mimicks the recognition of binding motifs on the regulatory regions of the genes. We are thereby able to faithfully reproduce many…
Genomic selection (GS), as a critical crop breeding strategy, plays a key role in enhancing food production and addressing the global hunger crisis. The predominant approaches in GS currently revolve around employing statistical methods for…
Increasing evidence suggests that chromosome folding and genetic expression are intimately connected. For example, the co-expression of a large number of genes can benefit from their spatial co-localization in the cellular space.…
Following recent discoveries of colocalization of downstream-regulating genes in living cells, the impact of the spatial distance between such genes on the kinetics of gene product formation is increasingly recognized. We here show from…
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…