Related papers: A read-filtering algorithm for high-throughput mar…
In this work we present a flexible, probabilistic and reference-free method of error correction for high throughput DNA sequencing data. The key is to exploit the high coverage of sequencing data and model short sequence outputs as…
High-throughput phenotyping refers to the non-destructive and efficient evaluation of plant phenotypes. In recent years, it has been coupled with machine learning in order to improve the process of phenotyping plants by increasing…
Metagenomics characterizes the taxonomic diversity of microbial communities by sequencing DNA directly from an environmental sample. One of the main challenges in metagenomics data analysis is the binning step, where each sequenced read is…
Advances in gene sequencing have enabled in silico analyses of microbial genomes and have led to the revision of concepts of microbial taxonomy and evolution. We explore deficiencies in existing multiple sequence global alignment algorithms…
Read mapping is a fundamental, yet computationally-expensive step in many genomics applications. It is used to identify potential matches and differences between fragments (called reads) of a sequenced genome and an already known genome…
Real-world data contains various kinds of errors. Before analyzing data, one usually needs to process the raw data. However, traditional data processing based on exactly match often misses lots of valid information. To get high-quality…
Iterating with new and improved OCR solutions enforces decision making when it comes to targeting the right candidates for reprocessing. This especially applies when the underlying data collection is of considerable size and rather diverse…
Quantum computers require high-fidelity measurement of many qubits to achieve a quantum advantage. Traditional approaches suffer from readout crosstalk for a neutral-atom quantum processor with a tightly spaced array. Although classical…
We now need more than ever to make genome analysis more intelligent. We need to read, analyze, and interpret our genomes not only quickly, but also accurately and efficiently enough to scale the analysis to population level. There currently…
Today, machine learning tools, particularly artificial neural networks, have become crucial for diverse applications. However, current digital computing tools to train and deploy artificial neural networks often struggle with massive data…
DNA sequencing is the physical/biochemical process of identifying the location of the four bases (Adenine, Guanine, Cytosine, Thymine) in a DNA strand. As semiconductor technology revolutionized computing, modern DNA sequencing technology…
This paper presents an accurate short-read mapper for next-generation sequencing data which is widely used in the 1000 Genomes Project, and human clinical and other species genome studies.
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…
Recent emergence of next-generation DNA sequencing technology has enabled acquisition of genetic information at unprecedented scales. In order to determine the genetic blueprint of an organism, sequencing platforms typically employ…
With recent high-throughput technology we can synthesize large heterogeneous collections of DNA structures, and also read them all out precisely in a single procedure. Can we use these tools, not only to do things faster, but also to devise…
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…
Recurrent neural networks are powerful tools for handling incomplete data problems in computer vision, thanks to their significant generative capabilities. However, the computational demand for these algorithms is too high to work in real…
High throughput sequencing (HTS) continues to expand our understanding of microbial communities, despite insufficient sequencing depths to detect all rare taxa. These low abundance taxa are not accounted for in existing methods for…
High-quality system-level message flow specifications are necessary for comprehensive validation of system-on-chip (SoC) designs. However, manual development and maintenance of such specifications are daunting tasks. We propose a disruptive…
The ever-growing deep learning technologies are making revolutionary changes for modern life. However, conventional computing architectures are designed to process sequential and digital programs, being extremely burdened with performing…