Multi-objective genetic algorithm for pseudoknotted RNA sequence design by Akito eTaneda

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A Hybrid Model for Assessing Student Mathematical Skills by Michael Voskoglou

Subjects: “…‎rectangular fuzzy assessment model (rfam)‎…”
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Shape based indexing for faster search of RNA family databases by Reeder Jens, Janssen Stefan, Giegerich Robert

“…<p>Abstract</p> <p>Background</p> <p>Most non-coding RNA families exert their function by means of a conserved, common secondary structure. The Rfam data base contains more than five hundred structurally annotated RNA families. …”
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Computational discovery and RT-PCR validation of novel <it>Burkholderia </it>conserved and <it>Burkholderia pseudomallei </it>unique sRNAs by Khoo Jia-Shiun, Chai Shiao-Fei, Mohamed Rahmah, Nathan Sheila, Firdaus-Raih Mohd

“…This integrated approach identified 29 <it>B. pseudomallei </it>sRNA genes - of which 21 have Rfam homologs and 8 are novel.</p>…”

Federated Learning for Precoding Design in Cell-Free Massive MIMO Systems by Dong Wang, Meixia Tao, Xing Zeng, Jing Liang

“…In the HFL-based precoding method, we design a low-cost residual global channel state information (CSI) feature acquisition mechanism called RFAM at each AP to create local datasets. RFAM eliminates the need for point-to-point CSI exchange between APs, resulting in reduced communication overhead. …”
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Evolutionary modeling and prediction of non-coding RNAs in Drosophila. by Robert K Bradley, Andrew V Uzilov, Mitchell E Skinner, Yuri R Bendaña, Lars Barquist, Ian Holmes

“…Some of our predictions are colocated with larger putative unannotated genes: for example, 17 of our predictions showing homology to the RFAM family snoR28 appear in a tandem array on the X chromosome; the 4.5 Kbp spanned by the predicted tandem array is contained within a FlyBase-annotated cDNA.…”
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In silico prediction and qPCR validation of novel sRNAs in Propionibacterium acnes KPA171202 by Praveen P. Balgir, Shobha R. Dhiman, Puneet Kaur

“…A total of eight potential candidate sRNAs were predicted using SIPHT, one was found to have a Rfam homolog and seven were novel. Out of these seven predicted sRNAs, five were validated by reverse transcriptase-polymerase chain reaction (RT-PCR) and sequencing. …”
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Predicting RNA secondary structure by a neural network: what features may be learned? by Elizaveta I. Grigorashvili, Zoe S. Chervontseva, Mikhail S. Gelfand

“…On the other hand, it successfully predicted pseudoknots. t-SNE clusters of embeddings of RNA sequences created by PredPair tend to contain embeddings from particular Rfam families, supporting the predictions of PredPair being in line with biological classification.…”
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Underwater Target Detection Based on Parallel High-Resolution Networks by Zhengwei Bao, Ying Guo, Jiyu Wang, Linlin Zhu, Jun Huang, Shu Yan

“…Finally, a receptive field augmentation module (RFAM) is constructed to obtain sufficient semantic information and rich detail information to further enhance the robustness and discrimination of features and improve the detection capability of the model for multi-scale underwater targets. …”
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Identification and characterization of microRNAs in channel catfish (Ictalurus punctatus) by using Solexa sequencing technology. by Zhiqiang Xu, Jiaping Chen, Xuguang Li, Jiachun Ge, Jianlin Pan, Xiaofeng Xu

“…After comparing the small RNA sequences with the RFam database, 4,542,396 reads that represent 25,538 unique sequences were mapped to the genome sequence of zebrafish to perform distribution analysis and to screen for candidate miRNA genes. …”
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Identification and Characterization of Non-Protein Coding RNA Homologs in Citrobacter rodentium by Comparative Genomics by Kishan Raj Selva Raju, Agilandeswarie Kavin Selvam

“…Secondly, screening the homolog npcRNA identified from previous step (BLASTn) through Rfam (RNA family) to identify unannotated homologs. …”
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Identification of novel growth phase- and media-dependent small non-coding RNAs in <it>Streptococcus pyogenes</it> M49 using intergenic tiling arrays by Patenge Nadja, Billion André, Raasch Peter, Normann Jana, Wisniewska-Kucper Aleksandra, Retey Julia, Boisguérin Valesca, Hartsch Thomas, Hain Torsten, Kreikemeyer Bernd

“…Some of the newly-identified sRNAs belonged to one of the common non-coding RNA families described in the Rfam database. Comparison of the results of our screen with the outcome of two recently published bioinformatics tools showed a low level of overlap between putative sRNA genes. …”
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Structator: fast index-based search for RNA sequence-structure patterns by Meyer, Fernando, Kurtz, Stefan, Backofen, Rolf, Will, Sebastian, Beckstette, Michael

“…In benchmark experiments on the Rfam database, our method runs up to two orders of magnitude faster than previous methods. …”
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In silico genome wide mining of conserved and novel miRNAs in the brain and pineal gland of Danio rerio using small RNA sequencing data by Suyash Agarwal, Naresh Sahebrao Nagpure, Prachi Srivastava, Basdeo Kushwaha, Ravindra Kumar, Manmohan Pandey, Shreya Srivastava

“…Other ncRNAs, such as tRNA, rRNA and snoRNA, were curated against Rfam. Using GRCz10 as reference, the subsequent bioinformatic analyses identified 25, 19 and 9 novel miRNAs from the brain, pineal gland (dark treatment) and pineal gland (light treatment), respectively. …”
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