相关论文: Joint Overlap Analysis of Multiple Genomic Interva…
Balanced search trees are widely used in computer science to efficiently maintain dynamic ordered data. To support efficient set operations (e.g., union, intersection, difference) using trees, the join-based framework is widely studied.…
Identification of functional elements of a genome often requires dividing a sequence of measurements along a genome into segments differing from adjacent segments. In many applications, the mean of the measured values at multiple genomic…
The ordered set is one of the most important data type in both theoretical algorithm design and analysis and practical programming. In this paper we study the set operations on two ordered sets, including Union, Intersect and Difference,…
Motivation: The comparison of diverse genomic datasets is fundamental to understanding genome biology. Researchers must explore many large datasets of genome intervals (e.g., genes, sequence alignments) to place their experimental results…
The lexical and syntactic disparities among different programming languages (e.g., Java and Python) pose significant challenges for multi-language software engineering tasks such as cross-language code clone detection and code retrieval,…
Finding spanning trees under various constraints is a classic problem with applications in many fields. Recently, a novel notion of "dense" ("sparse") tree, and in particular spanning tree (DST and SST respectively), is introduced as the…
The segment tree is an extremely versatile data structure. In this paper, a new heap based implementation of segment trees is proposed. In such an implementation of segment tree, the structural information associated with the tree nodes can…
Genome assembly is a fundamental problem in Bioinformatics, where for a given set of overlapping substrings of a genome, the aim is to reconstruct the source genome. The classical approaches to solving this problem use assembly graphs, such…
Integrative analysis of disparate data blocks measured on a common set of experimental subjects is one major challenge in modern data analysis. This data structure naturally motivates the simultaneous exploration of the joint and individual…
Given an elementary chain of vertex set V, seen as a labelling of V by the set {1, ...,n=|V|}, and another discrete structure over $V$, say a graph G, the problem of common intervals is to compute the induced subgraphs G[I], such that $I$…
Processing graphs with temporal information (the temporal graphs) has become increasingly important in the real world. In this paper, we study efficient solutions to temporal graph applications using new algorithms for Incremental Minimum…
Research in several fields now requires the analysis of data sets in which multiple high-dimensional types of data are available for a common set of objects. In particular, The Cancer Genome Atlas (TCGA) includes data from several diverse…
De novo genome assembly, i.e., rebuilding the sequence of an unknown genome from redundant and erroneous short sequences, is a key but computationally intensive step in many genomics pipelines. The exponential growth of genomic data is…
Merge trees, a type of topological descriptor, serve to identify and summarize the topological characteristics associated with scalar fields. They present a great potential for the analysis and visualization of time-varying data. First,…
Deploying multi-sequence magnetic resonance imaging (MRI) segmentation models to new clinical environments is challenging due to variations in scanners and acquisition protocols. Although existing TTA methods handle basic per-modality…
The interval graph for a set of intervals on a line consists of one vertex for each interval, and an edge for each intersecting pair of intervals. A probe interval graph is a variant that is motivated by an application to genomics, where…
Plant phenotyping is a central task in agriculture, as it describes plants' growth stage, development, and other relevant quantities. Robots can help automate this process by accurately estimating plant traits such as the number of leaves,…
Genomics has revolutionized biology, enabling the interrogation of whole transcriptomes, genome-wide binding sites for proteins, and many other molecular processes. However, individual genomic assays measure elements that interact in vivo…
Genomic regions represent features such as gene annotations, transcription factor binding sites and epigenetic modifications. Performing various genomic operations such as identifying overlapping/non-overlapping regions or nearest gene…
Genomic phenotypes, such as DNA methylation and chromatin accessibility, can be used to characterize the transcriptional and regulatory activity of DNA within a cell. Recent technological advances have made it possible to measure such…