相关论文: Digital PCR provides sensitive and absolute calibr…
Cheap high-throughput DNA sequencing may soon become routine not only for human genomes but also for practically anything requiring the identification of living organisms from their DNA: tracking of infectious agents, control of food…
The interpretation of count data originating from the current generation of DNA sequencing platforms requires special attention. In particular, the per-sample library sizes often vary by orders of magnitude from the same sequencing run, and…
A common approach to quantifying DNA involves repeated cycles of DNA amplification. This approach, employed by the polymerase chain reaction (PCR), produces outputs that are corrupted by amplification noise, making it challenging to…
Portable genome sequencing technology is revolutionizing genomic research by providing a faster, more flexible method of sequencing DNA and RNA [1, 2]. The unprecedented shift from bulky stand-alone benchtop equipment confined in a…
The determination of a patient's DNA sequence can, in principle, reveal an increased risk to fall ill with particular diseases [1,2] and help to design "personalized medicine" [3]. Moreover, statistical studies and comparison of genomes [4]…
Technologies for sequencing (reading) and synthesizing (writing) DNA have progressed on a Moore's law-like trajectory over the last three decades. This has motivated the idea of using DNA for data storage. Theoretically, DNA-based storage…
Motivation: Modern genomics laboratories generate massive volumes of sequencing data, often resulting in significant storage costs. Genomics storage consists of duplicate files, temporary processing files, and redundant intermediate data.…
Single-cell RNA sequencing (scRNA-seq) is powerful technology that allows researchers to understand gene expression patterns at the single-cell level. However, analysing scRNA-seq data is challenging due to issues and biases in data…
Motivation: Next generation methods of DNA sequencing produce relatively high rate of reading errors, which interfere with de novo genome assembly of newly sequenced organisms and particularly affect the quality of SNP detection important…
Deep sequencing has become one of the most popular tools for transcriptome profiling in biomedical studies. While an abundance of computational methods exists for "normalizing" sequencing data to remove unwanted between-sample variations…
DNA-encoded small molecule libraries (DELs) have enabled discovery of novel inhibitors for many distinct protein targets of therapeutic value through screening of libraries with up to billions of unique small molecules. We demonstrate a new…
With the rapid increase of available digital data, DNA storage is identified as a storage media with high density and capability of long-term preservation, especially for archival storage systems. However, the encoding density (i.e., how…
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…
Storing data in DNA is being explored as an efficient solution for archiving and in-object storage. Synthesis time and cost remain challenging, significantly limiting some applications at this stage. In this paper we investigate efficient…
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…
DNA has been considered a promising medium for storing digital information. As an essential step in the DNA-based data storage workflow, coding algorithms are responsible to implement functions including bit-to-base transcoding, error…
Identifying cell clusters is a critical step for single-cell transcriptomics study. Despite the numerous clustering tools developed recently, the rapid growth of scRNA-seq volumes prompts for a more (computationally) efficient clustering…
As transistor dimensions continue to shrink, binary devices are rapidly approaching their fundamental limits in power density. In response, multi-valued systems have attracted significant attention due to their enhanced information density.…
DNA-Encoded Library (DEL) technology has enabled significant advances in hit identification by enabling efficient testing of combinatorially-generated molecular libraries. DEL screens measure protein binding affinity though sequencing reads…
Purpose Nanopore-based molecular sensing and measurement, specifically Deoxyribonucleic acid (DNA) sequencing, is advancing at a fast pace. Some embodiments have matured from coarse particle counters to enabling full human genome assembly.…