Related papers: AmpliconHunter: A Scalable Tool for PCR Amplicon P…
Summary: We present AmpliconHunter2 (AHv2), a highly scalable in silico PCR engine written in C that can handle degenerate primers and uses a highly accurate melting temperature model. AHv2 implements a bit-mask IUPAC matcher with AVX2 SIMD…
Thermalcycler were extensively used machine for amplify DNA sample. One of the major problems in the working time was that it spent most of time for cooling and heating. In order to improve the efficient, this study presented a novel method…
A critical problem in the emerging high-throughput genotyping protocols is to minimize the number of polymerase chain reaction (PCR) primers required to amplify the single nucleotide polymorphism loci of interest. In this paper we study PCR…
We developed a low-cost, high-throughput microbiome profiling method that uses combinatorial sequence tags attached to PCR primers that amplify the rRNA V6 region. Amplified PCR products are sequenced using an Illumina paired-end protocol…
Recent advances in next-generation sequencing have revolutionized genomic research. 16S rRNA amplicon sequencing using paired-end sequencing on the MiSeq platform from Illumina, Inc., is being used to characterize the composition and…
Summary: Microbiome HiFi Amplicon Sequence Simulator (MHASS) creates realistic synthetic PacBio HiFi amplicon sequencing datasets for microbiome studies, by integrating genome-aware abundance modeling, realistic dual-barcoding strategies,…
The high throughput and cost-effectiveness afforded by short-read sequencing technologies, in principle, enable researchers to perform 16S rRNA profiling of complex microbial communities at unprecedented depth and resolution. Existing…
Antibody therapeutics has been extensively studied in drug discovery and development within the past decades. One increasingly popular focus in the antibody discovery pipeline is the optimization step for therapeutic leads. Both traditional…
Microbial communities play important roles in the function and maintenance of various biosystems, ranging from human body to the environment. Current methods for analysis of microbial communities are typically based on taxonomic…
DETR-like methods have significantly increased detection performance in an end-to-end manner. The mainstream two-stage frameworks of them perform dense self-attention and select a fraction of queries for sparse cross-attention, which is…
Deep learning research has generated widespread interest leading to emergence of a large variety of technological innovations and applications. As significant proportion of deep learning research focuses on vision based applications, there…
Training next-generation code generation models requires high-quality datasets, yet existing datasets face difficulty imbalance, format inconsistency, and data quality problems. We address these challenges through systematic data processing…
Metagenomics is the study of environments through genetic sampling of their microbiota. Metagenomic studies produce large datasets that are estimated to grow at a faster rate than the available computational capacity. A key step in the…
Understanding neuronal communication is fundamental in neuroscience but there are few methodologies offering detailed analysis for well-controlled conditions. By interfacing microElectrode arrays with microFluidics ({\mu}EF devices), it is…
Conventional scanning tunneling microscopy (STM) is limited to a bandwidth of circa 1kHz around DC. Here, we develop, build and test a novel amplifier circuit capable of measuring the tunneling current in the MHz regime while simultaneously…
Astrocytes are critical glial cells whose altered morphology and density are hallmarks of many neurological disorders. However, their intricate branching and stain dependent variability make automated detection of histological images a…
Ad relevance modeling plays a critical role in online advertising systems including Microsoft Bing. To leverage powerful transformers like BERT in this low-latency setting, many existing approaches perform ad-side computations offline.…
Targeted amplicon panels are widely used in oncology diagnostics, but providing per-gene performance guarantees for copy number variant (CNV) detection remains challenging due to amplification artifacts, process-mismatch heterogeneity, and…
The primary step in search of the gene prediction is an identification of the coding region from genomic DNA sequence. Gene structure in the case of a eukaryotic organism is composed of promoter, intron, start codon, exons, stop codon, etc.…
An approach for multiplex qualitative and quantitative microarray-based PCR analysis has been proposed. The characteristics of PCR executed on a gel-based oligonucleotide microarray with immobilized forward primers and a single common…