Abstract：
:Using second-generation sequencing (SGS) RNA-Seq strategies, extensive alterative splicing prediction is impractical and high variability of isoforms expression quantification is inevitable in organisms without true reference dataset. we report the development of a novel analysis method, termed hybrid sequencing and map finding (HySeMaFi) which combines the specific strengths of third-generation sequencing (TGS) (PacBio SMRT sequencing) and SGS (Illumina Hi-Seq/MiSeq sequencing) to effectively decipher gene splicing and to reliably estimate the isoforms abundance. Error-corrected long reads from TGS are capable of capturing full length transcripts or as large partial transcript fragments. Both true and false isoforms, from a particular gene, as well as that containing all possible exons, could be generated by employing different assembly methods in SGS. We first develop an effective method which can establish the mapping relationship between the error-corrected long reads and the longest assembled contig in every corresponding gene. According to the mapping data, the true splicing pattern of the genes was reliably detected, and quantification of the isoforms was also effectively determined. HySeMaFi is also the optimal strategy by which to decipher the full exon expression of a specific gene when the longest mapped contigs were chosen as the reference set.
journal_name
Sci Repjournal_title
Scientific reportsauthors
Ning G,Cheng X,Luo P,Liang F,Wang Z,Yu G,Li X,Wang D,Bao Mdoi
10.1038/srep43793subject
Has Abstractpub_date
2017-03-08 00:00:00pages
43793issn
2045-2322pii
srep43793journal_volume
7pub_type
杂志文章abstract：:Mathematical modelling has been widely used to predict the effects of perturbations to brain networks. An important example is epilepsy surgery, where the perturbation in question is the removal of brain tissue in order to render the patient free of seizures. Different dynamical models have been proposed to represent ...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-019-43871-7
更新日期：2019-05-14 00:00:00
abstract：:Vaginal microbiota is an important early source of bacterial colonization for newborns. However, only a few small studies have investigated the composition of vaginal microbiota during labor. In this work, we analyzed vaginal swabs collected at 36 weeks gestation and at the onset of labor from 256 women participating ...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-017-17972-0
更新日期：2017-12-14 00:00:00
abstract：:Memristors, memcapacitors, and meminductors represent an innovative generation of circuit elements whose properties depend on the state and history of the system. The hysteretic behavior of one of their constituent variables, is their distinctive fingerprint. This feature endows them with the ability to store and proc...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/srep46736
更新日期：2017-04-24 00:00:00
abstract：:The extended Hückel (eH) tight-binding method has historically been prized for its computational ease and intuitive chemical clarity. However, its lack of quantitative predictiveness has prevented the eH method from being used as a tool for rapidly screening materials for desired electronic properties. In this work, w...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-018-28864-2
更新日期：2018-07-12 00:00:00
abstract：:A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has been fixed in the paper. ...
journal_title：Scientific reports
pub_type： 已发布勘误
doi：10.1038/s41598-019-39022-7
更新日期：2019-05-03 00:00:00
abstract：:With Motor imagery (MI), movements are mentally rehearsed without overt actions; this procedure has been adopted in motor rehabilitation, primarily in brain-damaged patients. Here we rather tested the clinical potentials of MI in purely orthopaedic patients who, by definition, should maximally benefit of mental exerci...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-020-65820-5
更新日期：2020-06-02 00:00:00
abstract：:The recent past has seen impressive progress in the treatment of various malignancies using immunotherapy. One of the most promising approaches involves immune checkpoint inhibitors. However, the clinical results with these agents have demonstrated variability in the response. Pancreatic cancer, in particular, has pro...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-019-41251-9
更新日期：2019-03-18 00:00:00
abstract：:A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has not been fixed in the paper. ...
journal_title：Scientific reports
pub_type： 已发布勘误
doi：10.1038/s41598-018-23047-5
更新日期：2018-03-12 00:00:00
abstract：:Stryphnodendron adstringens is a medicinal plant belonging to the Leguminosae family, and it is commonly found in the southeastern savannas, endemic to the Cerrado biome. The goal of this study was to assemble and annotate the chloroplast genome of S. adstringens and to compare it with previously known genomes of the ...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-019-50620-3
更新日期：2019-10-02 00:00:00
abstract：:Sex-dependent effects of mismatched prenatal-postnatal maternal conditions are predicted by combining two evolutionary hypotheses: that foetal conditions provide a forecast of likely postnatal environments (Predictive Adaptive Response), and that the female foetus is better adapted than the male to maternal adversity ...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-019-39513-7
更新日期：2019-02-21 00:00:00
abstract：:Diatoms are known for their intricate, silicified cell walls (frustules). Silica polymerization occurs in a compartment called the silica deposition vesicle (SDV) and it was proposed that the cytoskeleton influences silica patterning through the SDV membrane (silicalemma) via interactions with transmembrane proteins. ...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-017-13613-8
更新日期：2017-10-18 00:00:00
abstract：:Microfluidic paper-based analytical devices (µPADs) have provided a breakthrough in portable and low-cost point-of-care diagnostics. Despite their significant scope, the complexity of fabrication and reliance on expensive and sophisticated tools, have limited their outreach and possibility of commercialization. Herein...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-019-44455-1
更新日期：2019-05-27 00:00:00
abstract：:Fungi play a key role in the functioning of soil in terrestrial ecosystems, and in particular in the remediation of degraded soils. The contribution of fungi to carbon and nutrient cycles, along with their capability to mobilise soil trace elements, is well-known. However, the importance of life history strategy for t...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-020-63194-2
更新日期：2020-04-15 00:00:00
abstract：:Algorithms in bioinformatics use textual representations of genetic information, sequences of the characters A, T, G and C represented computationally as strings or sub-strings. Signal and related image processing methods offer a rich source of alternative descriptors as they are designed to work in the presence of no...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-018-38197-9
更新日期：2019-02-15 00:00:00
abstract：:Understanding ethanol-induced stresses and responses in biofuel-producing bacteria at systems level has significant implications in engineering more efficient biofuel producers. We present a computational study of transcriptomic and genomic data of both ethanol-stressed and ethanol-adapted E. coli cells with computati...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/srep44150
更新日期：2017-03-16 00:00:00
abstract：:Obesity, often represented by higher body mass index (BMI), is not yet fully understood as a potential risk factor for poor clinical outcomes of prostate cancer (PCa) after radical prostatectomy (RP). This study aimed to evaluate the relationship between BMI and biochemical recurrence (BCR)-free survival in RP patient...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-018-30473-y
更新日期：2018-08-10 00:00:00
abstract：:In this paper, a multi-band metal-insulator-metal (MIM) perfect absorber with refractive index sensing capability has been investigated in near-infrared region. The proposed structure has been studied for biomedical applications such as detection of solution of glucose in water, diagnosis of different stages of malari...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-020-63459-w
更新日期：2020-04-14 00:00:00
abstract：:Nowadays, increasing awareness of environment and fossil fuels protection stimulates intensive research on clean and renewable sources of energy. Production of hydrogen from water through solar-driven splitting reactions is one of the most promising approaches in the field of photoelectrochemistry (PEC). In this work ...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-018-29247-3
更新日期：2018-07-18 00:00:00
abstract：:Mayaro virus (MAYV) is endemic in South American countries where it is responsible for sporadic outbreaks of acute febrile illness. The hallmark of MAYV infection is a highly debilitating and chronic arthralgia. Although MAYV emergence is a potential threat, there are no specific therapies or licensed vaccine. In this...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-020-62084-x
更新日期：2020-03-24 00:00:00
abstract：:There is considerable interest in how early life experiences shape behavioural development. For example, the socialisation of unfamiliar pigs pre-weaning has been suggested to decrease aggression during later life. However, the behavioural mechanisms behind this socialisation effect remain unexplored. We allowed 12 li...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-019-40980-1
更新日期：2019-03-12 00:00:00
abstract：:Various types of fluid expulsion features (mud volcanoes, pockmarks, authigenic carbonate mounds and associated gas pipes, etc.) are often found above subduction zones, which have the highest seismic potential on Earth. Faults potentially control the liberation of deep-seated greenhouse gases into the feeder systems o...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-019-47686-4
更新日期：2019-08-05 00:00:00
abstract：:Genome-wide association studies (GWAS) have uncovered numerous variants associated with body mass index (BMI), waist circumference, and waist-to-hip ratio. Our study aims to investigate how these variants are linked to fat distribution. We genotyped 56 validated variants of BMI, waist circumference, and waist-to-hip r...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/srep20691
更新日期：2016-02-05 00:00:00
abstract：:Parasitic lice (order Phthiraptera) infest birds and mammals. The typical animal mitochondrial (mt) genome organization, which consists of a single chromosome with 37 genes, was found in chewing lice in the suborders Amblycera and Ischnocera. The sucking lice (suborder Anoplura) known, however, have fragmented mt geno...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/srep17389
更新日期：2015-11-30 00:00:00
abstract：:The recent combination of ultra-intense lasers and laser-accelerated electron beams is enabling the development of a new generation of compact x-ray light sources, the coherence of which depends directly on electron beam emittance. Although the emittance of accelerated electron beams can be low, it can grow due to the...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/srep24622
更新日期：2016-04-19 00:00:00
abstract：:In recent years it has been shown that the therapeutic benefits of human mesenchymal stem/stromal cells (hMSCs) in the Central Nervous System (CNS) are mainly attributed to their secretome. The implementation of computer-controlled suspension bioreactors has shown to be a viable route for the expansion of these cells ...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/srep27791
更新日期：2016-06-15 00:00:00
abstract：:Highly selective hydrogenative carbon-carbon bond scission of biomass-derived platform oxygenates was achieved with a cerium oxide-supported ruthenium nanoparticle catalyst in water. The present catalyst enabled the selective cleavage of carbon-carbon σ bonds adjacent to carboxyl, ester, and hydroxymethyl groups, open...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-017-14373-1
更新日期：2017-10-25 00:00:00
abstract：:End stage renal disease (ESRD) patients depend on hemodialysis (HD) as a life-sustaining treatment, but HD membrane properties play a critical role in blood activation during HD and can lead to severe patient outcomes. This study reports on a series of investigations on the common clinical HD membranes available in Ca...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-020-71755-8
更新日期：2020-09-09 00:00:00
abstract：:Micron-scale droplets isolated by an immiscible liquid can provide miniaturised reaction vessels which can be manipulated in microfluidic networks, and has seen a rapid growth in development. In many experiments, the precise volume of these microdroplets is a critical parameter which can be influenced by many external...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-017-11254-5
更新日期：2017-09-05 00:00:00
abstract：:We report a non-iterative localization algorithm that utilizes the scaling of a three-dimensional (3D) image in the axial direction and focuses on evaluating the radial symmetry center of the scaled image to achieve the desired single-particle localization. Using this approach, we analyzed simulated 3D particle images...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/srep02462
更新日期：2013-01-01 00:00:00
abstract：:Controlling and reducing the formation of pathogenic biofilm on tooth surface is the key to the prevention and treatment of the biofilm-associated oral diseases. Antimicrobial peptides (AMPs), considered as possible future alternatives for conventional antibiotics, have been extensively studied for the control of bact...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/srep38410
更新日期：2016-12-02 00:00:00
