Search Results - "Sun, Yanni"

CHEER: HierarCHical taxonomic classification for viral mEtagEnomic data via deep leaRning by Shang, Jiayu, Sun, Yanni

“…•Our model organizes multiple CNN-based classifiers for taxonomic classification.•It is designed and tested for assigning taxonomic groups for reads from new…”
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miR-PREFeR: an accurate, fast and easy-to-use plant miRNA prediction tool using small RNA-Seq data by Lei, Jikai, Sun, Yanni

“…Plant microRNA prediction tools that use small RNA-sequencing data are emerging quickly. These existing tools have at least one of the following problems: (i)…”
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Predicting the hosts of prokaryotic viruses using GCN-based semi-supervised learning by Shang, Jiayu, Sun, Yanni

“…Prokaryotic viruses, which infect bacteria and archaea, are the most abundant and diverse biological entities in the biosphere. To understand their regulatory…”
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Phage family classification under Caudoviricetes : A review of current tools using the latest ICTV classification framework by Zhu, Yilin, Shang, Jiayu, Peng, Cheng, Sun, Yanni

“…Bacteriophages, which are viruses infecting bacteria, are the most ubiquitous and diverse entities in the biosphere. There is accumulating evidence revealing…”
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De novo haplotype reconstruction in viral quasispecies using paired-end read guided path finding by Chen, Jiao, Zhao, Yingchao, Sun, Yanni

“…Abstract Motivation RNA virus populations contain different but genetically related strains, all infecting an individual host. Reconstruction of the viral…”
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Reconstructing 16S rRNA genes in metagenomic data by Yuan, Cheng, Lei, Jikai, Cole, James, Sun, Yanni

“…Metagenomic data, which contains sequenced DNA reads of uncultured microbial species from environmental samples, provide a unique opportunity to thoroughly…”
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Fast and accurate microRNA search using CNN by Tang, Xubo, Sun, Yanni

“…There are many different types of microRNAs (miRNAs) and elucidating their functions is still under intensive research. A fundamental step in functional…”
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Current knowledge of COVID-19 and infection prevention and control strategies in healthcare settings: A global analysis by Islam, M Saiful, Rahman, Kazi M, Sun, Yanni, Qureshi, Mohammed O, Abdi, Ikram, Chughtai, Abrar A, Seale, Holly

“…In the current absence of a vaccine for COVID-19, public health responses aim to break the chain of infection by focusing on the mode of transmission. We…”
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VirStrain: a strain identification tool for RNA viruses by Liao, Herui, Cai, Dehan, Sun, Yanni

“…Viruses change constantly during replication, leading to high intra-species diversity. Although many changes are neutral or deleterious, some can confer on the…”
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Ribosomal Database Project: data and tools for high throughput rRNA analysis by Cole, James R, Wang, Qiong, Fish, Jordan A, Chai, Benli, McGarrell, Donna M, Sun, Yanni, Brown, C Titus, Porras-Alfaro, Andrea, Kuske, Cheryl R, Tiedje, James M

“…Ribosomal Database Project (RDP; http://rdp.cme.msu.edu/) provides the research community with aligned and annotated rRNA gene sequence data, along with tools…”
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Air-stable all-inorganic perovskite quantum dot inks for multicolor patterns and white LEDs by Zhihai, Wu, Jiao, Wei, Yanni, Sun, Jun, Wu, Yafei, Hou, Pan, Wang, Nengping, Wang, Zhenfu, Zhao

“…Recently, all-inorganic perovskite quantum dots (QDs) (CsPbX 3 , X = Cl, Br, I) as the emerging semiconductor materials have been intensively studied owing to…”
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Improving protein domain classification for third-generation sequencing reads using deep learning by Du, Nan, Shang, Jiayu, Sun, Yanni

“…With the development of third-generation sequencing (TGS) technologies, people are able to obtain DNA sequences with lengths from 10s to 100s of kb. These long…”
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HMM-FRAME: accurate protein domain classification for metagenomic sequences containing frameshift errors by Zhang, Yuan, Sun, Yanni

“…Protein domain classification is an important step in metagenomic annotation. The state-of-the-art method for protein domain classification is profile…”
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High-resolution strain-level microbiome composition analysis from short reads by Liao, Herui, Ji, Yongxin, Sun, Yanni

“…Abstract Background Bacterial strains under the same species can exhibit different biological properties, making strain-level composition analysis an important…”
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Improving the impact of non-pharmaceutical interventions during COVID-19: examining the factors that influence engagement and the impact on individuals by Seale, Holly, Dyer, Clare E F, Abdi, Ikram, Rahman, Kazi M, Sun, Yanni, Qureshi, Mohammed O, Dowell-Day, Alexander, Sward, Jonathon, Islam, M Saiful

“…During an evolving outbreak or pandemic, non-pharmaceutical interventions (NPIs) including physical distancing, isolation, and mask use may flatten the peak in…”
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FunGene: the functional gene pipeline and repository by Fish, Jordan A, Chai, Benli, Wang, Qiong, Sun, Yanni, Brown, C Titus, Tiedje, James M, Cole, James R

“…Ribosomal RNA genes have become the standard molecular markers for microbial community analysis for good reasons, including universal occurrence in cellular…”
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MAKER-P: A Tool Kit for the Rapid Creation, Management, and Quality Control of Plant Genome Annotations by Campbell, Michael S., Law, MeiYee, Holt, Carson, Stein, Joshua C., Moghe, Gaurav D., Hufnagel, David E., Lei, Jikai, Achawanantakun, Rujira, Jiao, Dian, Lawrence, Carolyn J., Ware, Doreen, Shiu, Shin-Han, Childs, Kevin L., Sun, Yanni, Jiang, Ning, Yandell, Mark

“…We have optimized and extended the widely used annotation engine MAKER in order to better support plant genome annotation efforts. New features include better…”
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Impact of Multidrug Resistance on Tuberculosis Recurrence and Long-Term Outcome in China by Sun, Yanni, Harley, David, Vally, Hassan, Sleigh, Adrian

“…Little is known about the impact of drug resistance on recurrence in TB. We conducted a cohort study to measure the impact of multi-drug resistance (MDR) on TB…”
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Accelerating de novo SINE annotation in plant and animal genomes by Liao, Herui, Sun, Yanni, Ou, Shujun

“…Genome annotation is an important but challenging task. Accurate identification of short interspersed nuclear elements (SINEs) is particularly difficult due to…”
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The insect-phase gRNA transcriptome in Trypanosoma brucei by Koslowsky, Donna, Sun, Yanni, Hindenach, Jordan, Theisen, Terence, Lucas, Jasmin

“…One of the most striking examples of small RNA regulation of gene expression is the process of RNA editing in the mitochondria of trypanosomes. In these…”
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