相关论文: Using sequencing coverage statistics to identify s…
Understanding the behavior of laboratory animals is a key to find answers about diseases and neurodevelopmental disorders that also affects humans. One behavior of interest is the stopping, as it correlates with exploration, feeding and…
While bacterial chromosomes were long thought to be amorphous, recent experiments reveal pronounced organizational features. However, the extent of bacterial chromosome organization remains unclear. Here, we develop a fully data-driven…
Sequence classification has numerous applications in various fields. Despite extensive studies in the last decades, many challenges still exist, particularly in pattern-based methods. Existing pattern-based methods measure the…
Gender contains a wide range of information regarding to the characteristics difference between male and female. Successful gender recognition is essential and critical for many applications in the commercial domains such as applications of…
Nucleosome organization in eukaryotic genomes has a deep impact on gene function. Although progress has been recently made in the identification of various concurring factors influencing nucleosome positioning, it is still unclear whether…
As researchers collect increasingly large molecular data sets to reconstruct the Tree of Life, the heterogeneity of signals in the genomes of diverse organisms poses challenges for traditional phylogenetic analysis. A class of phylogenetic…
Genome-wide association studies (GWAS) have identified hundreds of loci at very stringent levels of statistical significance across many different human traits. However, it is now clear that very large samples (n~10^4-10^5) are needed to…
The detection of molecular signatures of selection is one of the major concerns of modern population genetics. A widely used strategy in this context is to compare samples from several populations, and to look for genomic regions with…
The introduction and persistence of novel sexually antagonistic alleles can depend upon factors that differ between males and females. Understanding the conditions for invasion in a two-locus model can elucidate these processes. For…
Understanding and predicting interactions between predators and prey and their environment are fundamental for understanding food web structure, dynamics, and ecosystem function in both terrestrial and marine ecosystems.Thus, estimating the…
Mapping between sequence and structure is currently an open problem in structural biology. Despite many experimental and computational efforts it is not clear yet how the structure is encoded in the sequence. Answering this question may…
Understanding the population structure and patterns of gene flow within species is of fundamental importance to the study of evolution. In the fields of population and evolutionary genetics, measures of genetic differentiation are commonly…
Genetic data are frequently categorical and have complex dependence structures that are not always well understood. For this reason, clustering and classification based on genetic data, while highly relevant, are challenging statistical…
The past decade and a half has seen the design and execution of several ground-based spectroscopic surveys, both Galactic and Extra-galactic. Additionally, new surveys are being designed that extend the boundaries of current surveys. In…
Segmental duplications (SDs), or low-copy repeats (LCR), are segments of DNA greater than 1 Kbp with high sequence identity that are copied to other regions of the genome. SDs are among the most important sources of evolution, a common…
Pathogenic chromosome abnormalities are very common among the general population. While numerical chromosome abnormalities can be quickly and precisely detected, structural chromosome abnormalities are far more complex and typically require…
Applying machine learning to biological sequences - DNA, RNA and protein - has enormous potential to advance human health, environmental sustainability, and fundamental biological understanding. However, many existing machine learning…
Estimating species and gene trees from sequence data is challenging. Gene tree estimation is often hampered by low phylogenetic signal in alignments, leading to inaccurate trees. Species tree estimation is complicated by incomplete lineage…
Motivation: Bisulphite sequencing enables the detection of cytosine methylation. The sequence of the methylation states of cytosines on any given read forms a methylation pattern that carries substantially more information than merely…
In this paper, I introduce a Sequence-based Multiscale Model (SeqMM) for the biomolecular data analysis. With the combination of spectral graph method, I reveal the essential difference between the global scale models and local scale ones…