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Sequenced simultaneously
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Circulating tumour DNA (ctDNA) detection and monitoring have enormous potential clinical utility in oncology. We describe here a fast, flexible and cost-effective method to profile multiple genes simultaneously in low input cell-free DNA (cfDNA).
14p
vibransone
28-03-2024
5
2
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Populations of closely related microbial strains can be simultaneously present in bacterial communities such as the human gut microbiome. We recently developed a de novo genome assembly approach that uses read cloud sequencing to provide more complete microbial genome drafts, enabling precise differentiation and tracking of strain-level dynamics across metagenomic samples.
17p
vibransone
28-03-2024
9
1
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Circulating tumor DNA (ctDNA) offers minimally invasive means to repeatedly interrogate tumor genomes, providing opportunities to monitor clonal dynamics induced by metastasis and therapeutic selective pressures. In metastatic cancers, ctDNA profiling allows for simultaneous analysis of both local and distant sites of recurrence. Despite the promise of ctDNA sampling, its utility in real-time genetic monitoring remains largely unexplored.
17p
vibransone
28-03-2024
3
2
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Metagenomic next-generation sequencing (mNGS) of body fluids is an emerging approach to identify occult pathogens in undiagnosed patients. We hypothesized that metagenomic testing can be simultaneously used to detect malignant neoplasms in addition to infectious pathogens.
11p
vibransone
28-03-2024
2
1
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We developed a sensitive sequencing approach that simultaneously profiles microsatellite instability, chromosomal instability, and subclonal structure in cancer. We assessed diverse repeat motifs across 225 microsatellites on colorectal carcinomas.
18p
vibransone
28-03-2024
2
2
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The aim of this study was to sequence fulllength p72 gene of a field strain of ASFV causing typical ASF in Dong Nai province in 2020 and fuse this p72 gene with VSV G gene to generate a recombinant fusion gene G-p72 that could simultaneously express both proteins and stimulate a better host immune response than p72 expression alone.
10p
vimichaelfaraday
28-12-2023
7
3
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The rapid development of sequencing technology and simultaneously the availability of large quantities of sequence data has facilitated the identification of rare variant associated with quantitative traits. However, existing statistical methods depend on certain assumptions and thus lacking uniform power.
9p
vihagrid
30-01-2023
10
3
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Measuring gene expression of tumor clones at single-cell resolution links functional consequences to somatic alterations. Without scalable methods to simultaneously assay DNA and RNA from the same single cell, parallel single-cell DNA and RNA measurements from independent cell populations must be mapped for genome-transcriptome association.
12p
vigalileogalilei
27-02-2022
12
1
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Single-cell RNA sequencing (scRNA-seq) offers new opportunities to study gene expression of tens of thousands of single cells simultaneously. We present DeepImpute, a deep neural network-based imputation algorithm that uses dropout layers and loss functions to learn patterns in the data, allowing for accurate imputation.
14p
vielonmusk
30-01-2022
10
0
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The interaction between a pathogen and a host is a highly dynamic process in which both agents activate complex programs. Here, we introduce a single-cell RNA-sequencing method, scDual-Seq, that simultaneously captures both host and pathogen transcriptomes.
8p
vialfrednobel
29-01-2022
9
0
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We propose a probabilistic method, CancerLocator, which exploits the diagnostic potential of cell-free DNA by determining not only the presence but also the location of tumors. CancerLocator simultaneously infers the proportions and the tissue-of-origin of tumor-derived cell-free DNA in a blood sample using genome-wide DNA methylation data.
12p
vialfrednobel
29-01-2022
10
0
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To expand the repertoire of Cas9s available for genome targeting, we present a new in vitro method for the simultaneous examination of guide RNA and protospacer adjacent motif (PAM) requirements. The method relies on the in vitro cleavage of plasmid libraries containing a randomized PAM as a function of Cas9-guide RNA complex concentration.
13p
viaristotle
29-01-2022
12
0
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Long-read sequencing is promising for the comprehensive discovery of structural variations (SVs). However, it is still non-trivial to achieve high yields and performance simultaneously due to the complex SV signatures implied by noisy long reads.
24p
viarchimedes
26-01-2022
15
0
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It is a major challenge to integrate single-cell sequencing data across experiments, conditions, batches, time points, and other technical considerations. New computational methods are required that can integrate samples while simultaneously preserving biological information.
21p
viarchimedes
26-01-2022
14
0
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Single-cell sequencing technologies are revolutionizing biology, but they are limited by the need to dissociate live samples. Here, we present ACME (ACetic-MEthanol), a dissociation approach for single-cell transcriptomics that simultaneously fixes cells. ACME-dissociated cells have high RNA integrity, can be cryopreserved multiple times, and are sortable and permeable.
34p
viarchimedes
26-01-2022
13
0
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The integration of a viral genome into the host genome has a major impact on the trajectory of the infected cell. Integration location and variation within the associated viral genome can influence both clonal expansion and persistence of infected cells.
24p
viarchimedes
26-01-2022
12
0
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Advances in transcriptome sequencing allow for simultaneous interrogation of differentially expressed genes from multiple species originating from a single RNA sample, termed dual or multi-species transcriptomics.
23p
viarchimedes
26-01-2022
11
1
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The third multiplex PCR reaction includes the 5 extended STS sY153, sY160, sY82, sY143, and sY83 and the 2 control sequences SRY and ZFX/Y. Six basic primer sequences and eleven extended primer sequences are redesigned to simultaneously pair and amplify STS in the same multiplex reaction: set of 8 primers for 6 basic STS: 6 basic STS + 2 (SRY, ZFX/Y), 8 extension primers set E1: 6 extended STS + 2 (SRY, ZFX/Y), and 7 extension primers set E2: 5 extended STS + 2 (SRY, ZFX/Y).
8p
princessmononoke
29-11-2021
15
1
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In this study we hypothesize that variants in some functional classes, such as splice site regions, coding regions, DNA methylated regions and long noncoding RNA will explain more variance in complex traits than others. Two variance component approaches were used to test this hypothesis – the first determines if variants in a functional class capture a greater proportion of the variance, than expected by chance, the second uses the proportion of variance explained when variants in all annotations are fitted simultaneously.
16p
vilarryellison
29-10-2021
11
0
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Understanding the underlying genetic structure of human populations is of fundamental interest to both biological and social sciences. Advances in high-throughput genotyping technology have markedly improved our understanding of global patterns of human genetic variation. The most widely used methods for collecting variant information at the DNA-level include whole genome sequencing, which remains costly, and the more economical solution of array-based techniques, as these are capable of simultaneously genotyping a pre-selected set of variable DNA sites in the human genome.
13p
vitzuyu2711
29-09-2021
14
1
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