Articles tagged with Nanopore Sequencing
MARTi enables rapid taxonomic classification and abundance analysis of microorganisms in various settings, including agriculture, environmental monitoring, and clinical environments. The tool provides immediate analysis results, allowing for quick identification and targeted treatments of pathogen infections.
Recent studies using portable nanopore sequencing technologies document and sequence Amazonian wildlife, increasing representation of Peruvian species in global genetic libraries. This initiative empowers conservationists to generate their own data, making informed decisions to combat species extinction.
Researchers demonstrated CycloneSEQ's ability to sequence complete bacterial genomes with long-read data and hybrid assembly methods. This work has improved our understanding of microbial functions by closing gaps in genomic assemblies, particularly for complex bacterial communities.
A team of Singaporean scientists has released a comprehensive long-read RNA sequencing dataset, SG-NEx, to accelerate biomarker discovery and precision medicine. The dataset offers deeper biological insights into RNA complexity, enabling researchers to detect clinically relevant biomarkers and develop better treatments.
This special issue highlights novel applications of long-read sequencing technologies in biology and medicine, including human disease detection, rare disease diagnostics, and structural variation analysis. Several studies demonstrate the use of long-read sequencing data approaches to overcome challenges posed by repetitive regions, id...
A new study reveals that long-read sequencing can diagnose rare genetic diseases more accurately, quickly, and affordably. By analyzing longer stretches of DNA, this technology eliminates gaps and provides direct phasing data, improving the diagnostic yield of genetic sequencing.
Researchers have created a new circuit model that accounts for small changes to the sensor's behavior, allowing it to detect protein or DNA molecules from a sample. The device could lead to earlier diagnosis of diseases and more precise therapies tailored to each patient.
A new diagnostic test uses a unique molecular 'finger print' to detect different types of cancer, with near-perfect accuracy, and could lead to earlier detection and improved patient outcomes. The test targets ribosomal RNA molecules, which are modified differently in healthy and diseased tissues.
For the first time, researchers have demonstrated how mechanical forces affect gene expression by showing that RNAP polymerase remains on the DNA template and can be pulled to start a subsequent cycle of transcription. This force-directed recycling mechanism can change the relative abundance of adjacent genes.
Researchers at KAUST have developed NanoRanger, an accurate and rapid method for genetically diagnosing Mendelian genetic disorders. This breakthrough enables diagnosis in just 12 minutes, providing a detailed picture of the genomic disorder.
Researchers have successfully designed transmembrane β-barrel pores with custom shapes and properties, enabling miniaturization of sensing and sequencing applications into portable devices. The design method uses computational tools to control the shape and chemistry on a molecular level, resulting in stable and quiet signal generation.
A team of researchers used a rapid metagenomics technique to sequence viral RNA and DNA from blood-engorged mosquitoes collected in São Paulo city, identifying vectors, viruses, and hosts. The protocol has the potential to extend our understanding of insect genetic diversity and arbovirus transmission.
A new study reveals that different chromosomes have separate end-specific telomere-length distributions, challenging the scientific consensus. Researchers found that most telomeres were either the shortest or longest across all individuals, suggesting that specific chromosome ends may be the first to trigger stem-cell failure.
A new rapid test has been developed to identify hantavirus in South Korea, paving the way for early outbreak control. The Flongle sequencing-based diagnostic is cost-efficient and can detect HTNV genomes within 3 hours.
A novel contamination-detection method enables faster and safer T-cell therapy production, reducing the risk for patients and speeding up treatment. The method uses cutting-edge technology to identify harmful microorganisms within 24 hours.
A team of scientists developed a technique to rapidly detect genetic changes in malaria parasites using portable MinION sequencers. They demonstrated the first end-to-end, real-time pathogen monitoring from clinical blood samples in rural, resource-limited malaria hotspots.
Researchers at Cold Spring Harbor Laboratory discovered that bat genomes contain unique adaptations to defend against infection and cancer. The study highlights the interconnectedness of immunity and cancer response, revealing potential new treatments for human diseases.
Giovanni Maglia's breakthrough allows for simple handheld device protein sequencing with nanopore technology. Single-stranded proteins can be transported through the tiny hole in the same way as DNA strands.
A novel liquid biopsy technology developed by UCSC Assistant Professor Daniel Kim's lab leverages RNA 'dark matter' to enhance cancer diagnosis. The test detects both protein-coding and repetitive noncoding RNAs in the blood, showing improved sensitivity for early-stage cancer detection.
A new gene-editing technique combines peptide nucleic acids and prokaryotic Argonautes to introduce targeted breaks in the genome. The approach, called PNP editing, offers advantages over CRISPR-based methods, including improved specificity and targeting.
Researchers at Children's Hospital of Philadelphia developed TEQUILA-seq, a cost-effective technology for targeted long-read RNA sequencing. This innovation enables accurate accounting of all RNA molecules emanating from a single gene, crucial for understanding diseases like cancer.
A Duke University team has found that retrotransposons use the cell's DNA repair function to create a ring-like shape and then produce a matching double strand. This discovery challenges long-held theories about retrotransposons being byproducts of bad gene copying.
Researchers have developed a new method to control the movement of individual DNA molecules through a nanopore, allowing for higher accuracy in sequencing and analysis. This breakthrough has the potential to improve diagnostic and sequencing applications, including peptide sequencing.
Researchers developed a glycan identification method based on nanopore single-molecule sensing through derivatization strategy. The method identified different glycan isomers, varying lengths, and branched simple glycans. It revealed cation-π interactions contributing to sensing and paving the way for glycan sequencing
Researchers have developed a new technology to sequence individual mitochondria in single cells, allowing for unbiased analysis of full-length mtDNA. This has revealed complex patterns of pathogenic mtDNA mutations and the potential risks of off-target mutations in genetic editing strategies.
Researchers have developed a new method called Nano-tRNAseq to measure both the abundance and modification of tRNA molecules in a single step. This technology has significant advantages over conventional techniques, offering rapid, cost-effective, and high-throughput analysis with single-molecule resolution.
Researchers used long-read sequencing to identify novel mutational patterns and complex genomic rearrangements in cancer genomes, including those associated with liposarcoma. This approach offers a more comprehensive understanding of DNA mutations and their impact on cell function.
Scientists at the University of Freiburg have successfully characterized epigenetic modifications using nanopore analysis. The technique allows for rapid detection of protein fragments with varying levels of acetylation, enabling more accurate diagnosis and treatment of diseases like cancer.
Scientists at Kyoto University developed two methods to identify RNA modifications impacting gene regulation and disease. Their approach uses probability algorithms with high-throughput sequencing technology, distinguishing pseudouridine substitutions from other base changes.
A new prenatal test called STORK can determine if a fetus or embryo has the right number of chromosomes in under two hours, reducing time and cost. The test is about 10 times less expensive to process per sample and can improve treatment options for women trying to get pregnant.
A research team at Peking University developed SMOOTH-seq technology for sequencing single-cell genomes on third-generation sequencing platforms. They successfully assembled human genomes from just several individual cells, achieving megabase level contig N50 contigs.
Researchers used nanopore sequencing to detect specific genomic disorders in a fraction of the time it takes traditional testing. The study showed that diagnosis of larger chromosomal alterations could be made in one day, while smaller CNVs took two days.
Scientists have successfully sequenced an entire human genome, filling in gaps that were previously unknown or difficult to read. The achievement marks a major breakthrough in understanding the complexities of human genetics and has the potential to reveal new insights into evolution, disease, and adaptation.
Researchers at Rice University developed a new program called Variabel to accurately identify 'low-frequency' variants of the virus that causes COVID-19. By distinguishing true variants from sequencing errors, Variabel enables rapid characterization of within-host variation, which could aid in discovering future mutations.
A new DNA test has been developed to identify a range of hard-to-diagnose neurological and neuromuscular genetic diseases quicker and more accurately than existing tests. The test uses Nanopore sequencing technology to scan for abnormally long repeats within patients' genes, which are the hallmarks of disease.
Researchers at the University of Bristol have created new DNA parts that can shape the flow of cellular processes along DNA. This technology allows for the rapid assembly and testing of thousands of DNA parts in parallel, unlocking new tools for building sustainable biotechnologies.
Scientists at the University of Groningen have developed a nanopore-based method for protein identification and sequencing. They constructed a proteosome-nanopore system that can recognize proteins from peptide spectra and sequence entire proteins directly.
Researchers at Osaka University have developed a new method for detecting single DNA molecules directly from individual cells, eliminating the need for subsequent steps. The 3D-integrated nanopore allows for efficient delivery of released DNA molecules to the sensing zone, enabling robust detection and analysis.
Scientists have created a system dubbed "NanoporeTERs" allowing cells to express themselves in a whole new light. These new reporter proteins can detect multiple protein expression levels and shed new light on biological systems, enabling deeper analysis than before.
Researchers studied electrical conduction through membranes during Controlled Breakdown, a technique to fabricate single nanopores. They found that redox reactions occur at the membrane-electrolyte interface, allowing localization of pore formation using metal microelectrodes.
Researchers developed a new LEGO-like technique to assemble DNA molecules with protruding bumps, allowing precise measurement of DNA speed through nanopores. The study revealed a two-step process where DNA speed slows down before accelerating near the end of translocation.
A new technology has made it possible to quickly sequence the entire genome of plant pathogens, enabling faster diagnosis and identification of emerging pathogens. This breakthrough has great implications for the plant pathology field, allowing for more accurate identification of difficult-to-diagnose pathogens.
Researchers have developed a novel method for rapid and accurate glycan sequencing, reducing the time required from years to minutes. The technique utilizes a nanopore device and machine-learning software to identify sugar chains based on electrical signals generated as they pass through a tiny hole.
Researchers developed a simple barcoding system to reduce sequencing errors in Oxford Nanopore Technologies' MinION device, enabling accurate analysis of microorganisms like SARS-CoV-2. The new method achieves error rates below 0.005% and can process long stretches of DNA up to 10 times longer than conventional technologies.
Researchers at Tokyo University of Agriculture and Technology have developed a nanopore technique that can detect single-point mutations in circulating tumor DNA (ctDNA) with high accuracy. The method uses statistical analysis to identify the position of genetic mutations, paving the way for earlier and safer tumor detection.
Researchers have completed the first end-to-end assembly of a human X chromosome, exceeding the current human reference genome in continuity and accuracy. The breakthrough was made possible by new sequencing technologies that enable ultra-long reads, such as nanopore sequencing.
Researchers at UC Santa Cruz developed an efficient de novo human genome assembly algorithm using the Shasta toolkit, achieving high accuracy and scalability. The algorithm can assemble a complete human genome in under six hours and costs around $70, paving the way for pangenome research to represent true human diversity.
The Centre for Genomic Regulation has launched a new database to analyze COVID-19 data and compare different variations of the virus. Researchers can use this publicly available resource to study how SARS-CoV-2 grows, mutates, and replicates.
A new next-generation sequencing technique using real-time nanopore sequencing can analyze tiny amounts of microbial cell-free DNA, offering accurate diagnosis of sepsis-causing agents within hours. The technique achieved a 3.5-fold increase in sequencing throughput and allowed for pathogen identification within minutes.
Scientists successfully created a large synthetic nanopore made from DNA with a functional gating system for sensing and bio-sensing applications. The pore can translocate large protein-sized macromolecules between compartments separated by a lipid bilayer, enabling label-free real-time biosensing of trigger molecules.
Researchers used metagenomic nanopore sequencing to analyze 120 Lassa virus samples, implicating rodent contamination as the main driver of the outbreak. The technology provided rapid, real-time characterization of the pathogen, allowing for prompt public health responses and alleviating concerns about novel strains.
Researchers at Arizona State University have created a DNA walker that can rapidly traverse a track, significantly increasing speed and paving the way for new innovations in DNA nanotechnology. By optimizing DNA strand length and sequences, the device can cover ground up to 100 times faster than previous devices.
Researchers at the University of Groningen create a funnel-shaped nanopore that can detect polypeptides differing by one amino acid. The technology uses electro-osmotic flow to pull polypeptides into the pore, producing a unique 'fingerprint' for each.
Nanopore sequencing is a modern and promising technique that benefits from the potential advantages of label-free sequencing and long reads. This method analyzes DNA directly taken from cells, enhancing sequencing accuracy. Recent advances in solid-state nanopore sequencing are investigated in a review published in Recent Patents on Na...
Researchers at Harvard's Wyss Institute developed a new electronic DNA sequencing platform using biologically engineered nanopores, enabling highly scalable, accurate single-molecule DNA sequencing. The method can transform precision medicine by dramatically lowering the cost of sequencing while increasing accuracy.
Nottingham researchers demonstrate highly selective DNA sequencing method called Read Until, reducing time needed to analyze biological samples. The technique uses real-time nanopore sequencing and enables analysis of specific DNA strands with pre-determined signatures.
Researchers have developed a complete system to sequence DNA in nanopores electronically at single molecule level with single-base resolution. The system uses a protein nanopore array and polymer-tagged nucleotides to perform single molecule electronic DNA sequencing, enabling real-time and parallel sequencing of multiple DNA molecules.
A new open-source tool called NanoOK provides comprehensive alignment-based quality control and error profile analysis for the MinION platform. The tool is easily extensible through a Java programming interface and handles metagenomic sampling gracefully.
The MinION miniature DNA sequencing device has been evaluated by an international consortium, showing consistent good performance and accuracy across five laboratories. The data is freely available for re-analysis and innovation on F1000Research.
EPFL scientists have developed a method that improves the accuracy of DNA sequencing up to a thousand times by slowing down the process using nanopores and viscous liquids. This breakthrough paves the way for better and cheaper DNA sequencing, enabling scientists to detect mutations and identify different organisms with greater precision.