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Higher-order chromosomal organization for transcription regulation is poorly understood in eukaryotes. Using genome-wide Chromatin Interaction Analysis with Paired-End-Tag sequencing (ChIA-PET), we mapped long-range chromatin interactions associated with RNA polymerase II in human cells and uncovered widespread promoter-centered intragenic, extragenic, and(More)
The development of crowdsourced query processing systems has recently attracted a significant attention in the database community. A variety of crowdsourced queries have been investigated. In this paper, we focus on the crowdsourced join query which aims to utilize humans to find all pairs of matching objects from two collections. As a human-only solution(More)
In this paper, we study the problem of effective keyword search over XML documents. We begin by introducing the notion of Valuable Lowest Common Ancestor (VLCA) to accurately and effectively answer keyword queries over XML documents. We then propose the concept of Compact VLCA (CVLCA) and compute the meaningful compact connected trees rooted as CVLCAs as(More)
Traditional information systems return answers after a user submits a complete query. Users often feel "left in the dark" when they have limited knowledge about the underlying data, and have to use a try-and-see approach for finding information. A recent trend of supporting autocomplete in these systems is a first step towards solving this problem. In this(More)
In multicellular organisms, transcription regulation is one of the central mechanisms modelling lineage differentiation and cell-fate determination. Transcription requires dynamic chromatin configurations between promoters and their corresponding distal regulatory elements. It is believed that their communication occurs within large discrete foci of(More)
A proposed supercomputer-on-a-chip with optical interconnections between processing elements will require development of new lower-energy optical components and new circuit architectures that match electrical datapaths to complementary optical interfaces. ABSTRACT | We present a computing microsystem that uniquely leverages the bandwidth, density, and(More)
As two important operations in data cleaning, similarity join and similarity search have attracted much attention recently. Existing methods to support similarity join usually adopt a prefix-filtering-based framework. They select a prefix of each object and prune object pairs whose prefixes have no overlap. We have an observation that prefix lengths have(More)
Mammalian genomes are viewed as functional organizations that orchestrate spatial and temporal gene regulation. CTCF, the most characterized insulator-binding protein, has been implicated as a key genome organizer. However, little is known about CTCF-associated higher-order chromatin structures at a global scale. Here we applied chromatin interaction(More)
Chromatin interaction analysis with paired-end tag sequencing (ChIA-PET) is a new technology to study genome-wide long-range chromatin interactions bound by protein factors. Here we present ChIA-PET Tool, a software package for automatic processing of ChIA-PET sequence data, including linker filtering, mapping tags to reference genomes, identifying protein(More)
A string similarity join finds similar pairs between two collections of strings. It is an essential operation in many applications , such as data integration and cleaning, and has attracted significant attention recently. In this paper, we study string similarity joins with edit-distance constraints. Existing methods usually employ a filter-and-refine(More)