Related papers: Barcoding-free BAC Pooling Enables Combinatorial S…

In order to overcome the limitations imposed by DNA barcoding when multiplexing a large number of samples in the current generation of high-throughput sequencing instruments, we have recently proposed a new protocol that leverages advances…

Genome assembly from the high-throughput sequencing (HTS) reads is a fundamental yet challenging computational problem. An intrinsic challenge is the uncertainty caused by the widespread repetitive elements. Here we get around the…

Detection of rare variants by resequencing is important for the identification of individuals carrying disease variants. Rapid sequencing by new technologies enables low-cost resequencing of target regions, although it is still prohibitive…

In this paper we describe a new technique for the comparison of populations of DNA strands. Comparison is vital to the study of ecological systems, at both the micro and macro scales. Existing methods make use of DNA sequencing and cloning,…

De novo genome assembly is challenging in highly repetitive regions; however, reference-guided assemblers often suffer from bias. We propose a framework for pangenome-guided sequence assembly, which can resolve short-read data in complex…

Decoding sequences that stem from multiple transmissions of a codeword over an insertion, deletion, and substitution channel is a critical component of efficient deoxyribonucleic acid (DNA) data storage systems. In this paper, we consider a…

We study the amount of reliable information that can be stored in a DNA-based storage system with noisy sequencing, where each codeword is composed of short DNA molecules. We analyze a concatenated coding scheme, where the outer code is…

The high-throughput short-reads RNA-seq protocols often produce paired-end reads, with the middle portion of the fragments being unsequenced. We explore if the full-length fragments can be computationally reconstructed from the sequenced…

Combinatorial pooling schemes have enabled the measurement of thousands of experiments in a small number of reactions. This efficiency is achieved by distributing the items to be measured across multiple reaction units called pools.…

We propose a novel semantic segmentation algorithm by learning a deconvolution network. We learn the network on top of the convolutional layers adopted from VGG 16-layer net. The deconvolution network is composed of deconvolution and…

This paper studies sequencing and mapping methods that rely solely on pooling and shotgun sequencing of clones. First, we scrutinize and improve the recently proposed Clone-Array Pooled Shotgun Sequencing (CAPSS) method, which delivers a…

In this paper, we present an optimal metric function on average, which leads to a significantly low decoding computation while maintaining the superiority of the polarization-adjusted convolutional (PAC) codes' error-correction performance.…

Polarization-adjusted convolutional (PAC) codes have recently emerged as a promising class of error-correcting codes, achieving near-capacity performance particularly in the short block-length regime. In this paper, we propose an enhanced…

Composite DNA is a recent novel method to increase the information capacity of DNA-based data storage above the theoretical limit of 2 bits/symbol. In this method, every composite symbol does not store a single DNA nucleotide but a mixture…

We propose a new family of polar coding which realizes high coding gain, low complexity, and high throughput by introducing a protograph-based design. The proposed technique called as quasi-cyclic (QC) polar codes can be highly parallelized…

Background: The short reads output by first- and second-generation DNA sequencing instruments cannot completely reconstruct microbial chromosomes. Therefore, most genomes have been left unfinished due to the significant resources required…

New algorithms for efficient decoding of polar codes (which may be CRC-augmented), transmitted over either a binary erasure channel (BEC) or an additive white Gaussian noise channel (AWGNC), are presented. We start by presenting a new…

A weakly-supervised semantic segmentation framework with a tied deconvolutional neural network is presented. Each deconvolution layer in the framework consists of unpooling and deconvolution operations. 'Unpooling' upsamples the input…

Convolution operations dominate the overall execution time of Convolutional Neural Networks (CNNs). This paper proposes an easy yet efficient technique for both Convolutional Neural Network training and testing. The conventional convolution…

Genome assembly using high throughput data with short reads, arguably, remains an unresolvable task in repetitive genomes, since when the length of a repeat exceeds the read length, it becomes difficult to unambiguously connect the flanking…