相关论文: EndHiC: assemble large contigs into chromosomal-le…
Scaffolding is an important subproblem in "de novo" genome assembly in which mate pair data are used to construct a linear sequence of contigs separated by gaps. Here we present SLIQ, a set of simple linear inequalities derived from the…
Ensemble learning is a classical learning method utilizing a group of weak learners to form a strong learner, which aims to increase the accuracy of the model. Recently, brain-inspired hyperdimensional computing (HDC) becomes an emerging…
Long-range and highly accurate de novo assembly from short-read data is one of the most pressing challenges in genomics. Recently, it has been shown that read pairs generated by proximity ligation of DNA in chromatin of living tissue can…
Chromatin conformation capture technologies such as Hi-C have revealed that the genome is organized in a hierarchy of structures spanning multiple scales observed at different resolutions. Current algorithms often focus on specific…
Digital Computing-in-Memory (DCIM) is an innovative technology that integrates multiply-accumulation (MAC) logic directly into memory arrays to enhance the performance of modern AI computing. However, the need for customized memory cells…
Sounds, especially music, contain various harmonic components scattered in the frequency dimension. It is difficult for normal convolutional neural networks to observe these overtones. This paper introduces a multiple rates dilated causal…
(An updated version of this manuscript has been accepted to Scientific Reports in 2016, please refer to http://www.nature.com/articles/srep31900) The highly anticipated transition from next generation sequencing (NGS) to third generation…
Motivation: In this paper we present the latest release of EBIC, a next-generation biclustering algorithm for mining genetic data. The major contribution of this paper is adding support for big data, making it possible to efficiently run…
Just as in eukaryotes, high-throughput chromosome conformation capture (Hi-C) data have revealed nested organizations of bacterial chromosomes into overlapping interaction domains. In this chapter, we present a multiscale analysis framework…
Hi-C sequencing is widely used for analyzing chromosomal interactions. In this study, we propose "superimposed Hi-C" which features paired EcoP15I sites in a linker to facilitate sticky-end ligation with target DNAs. Superimposed Hi-C…
Hyperdimensional Computing (HDC) is a bio-inspired computing framework that has gained increasing attention, especially as a more efficient approach to machine learning (ML). This work introduces the \name{} compiler, the first open-source…
Metagenome assembly is the process of transforming a set of short, overlapping, and potentially erroneous DNA segments from environmental samples into the accurate representation of the underlying microbiomes's genomes. State-of-the-art…
With the increasing affordability and accessibility of genome sequencing data, de novo genome assembly is an important first step to a wide variety of downstream studies and analyses. Therefore, bioinformatics tools that enable the…
Currently, third-generation sequencing techniques, which allow to obtain much longer DNA reads compared to the next-generation sequencing technologies, are becoming more and more popular. There are many possibilities to combine data from…
Computational spectral imaging (CSI) achieves real-time hyperspectral imaging through co-designed optics and algorithms, but typical CSI methods suffer from a bulky footprint and limited fidelity. Therefore, Spectral Deconvolution imaging…
Lattice surgery is a leading approach for implementing fault-tolerant logical operations in surface code quantum computing, but compiling efficient lattice surgery layouts remains challenging. Existing compilers are largely circuit-centric…
Fine-pitch hybridisation processes are essential for next-generation pixel detectors and high-density microelectronic assemblies. Conventional bump-bonding techniques, although reliable, remain costly and difficult to implement for…
At the core of high throughput DNA sequencing platforms lies a bio-physical surface process that results in a random geometry of clusters of homogenous short DNA fragments typically hundreds of base pairs long - bridge amplification. The…
Motivation: Hi-C matrices are cornerstones for qualitative and quantitative studies of genome folding, from its territorial organization to compartments and topological domains. The high dynamic range of genomic distances probed in Hi-C…
To better understand DNA's 3D folding in cell nuclei, researchers developed chromosome capture methods such as Hi-C that measure the contact frequencies between all DNA segment pairs across the genome. As Hi-C data sets often are massive,…