FAIRsharing.fex4c8; Last edited: Feb. 13, 2020, 3:34 p.m.; Last accessed: Jan 03 2022 7:07 p.m.

metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:13.116598

rfam
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:13.116598

Other names: rfam

The Rfam database is a collection of RNA families, each represented by multiple sequence alignments, consensus secondary structures and covariance models (CMs). The families in Rfam break down into three broad functional classes: non-coding RNA genes, structured cis-regulatory elements and self-splicing RNAs. Typically these functional RNAs often have a conserved secondary structure which may be better preserved than the RNA sequence.

Webpage:

http://rfam.xfam.org/

Licence:

Name: EMBL-EBI Terms of Use
URL: http://www.ebi.ac.uk/about/terms-of-use

Publications:

Publications
More detailed information about this field from each metasource.

Rfam 12.0: updates to the RNA families database
PMID: 25392425
metasource: Fairsharing.org
version: FAIRsharing.org: Rfam; Rfam; DOI: https://doi.org/10.25504/FAIRsharing.fex4c8; Last edited: Feb. 13, 2020, 3:34 p.m.; Last accessed: Jan 03 2022 7:07 p.m.

Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families
PMID: 29112718
metasource: Fairsharing.org
version: FAIRsharing.org: Rfam; Rfam; DOI: https://doi.org/10.25504/FAIRsharing.fex4c8; Last edited: Feb. 13, 2020, 3:34 p.m.; Last accessed: Jan 03 2022 7:07 p.m.

http://dx.doi.org/10.1093/nar/gkaa1047
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

http://dx.doi.org/10.1093/nar/gkx1038
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:13.116598

http://dx.doi.org/10.1093/nar/gku1063
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:13.116598

Rfam 12.0: updates to the RNA families database PubMed citations: 495.

495 articles citing: Rfam 12.0: updates to the RNA families database

Incipient Sympatric Speciation and Evolution of Soil Bacteria Revealed by Metagenomic and Structured Non-Coding RNAs Analysis. PMID:35892966
Features and Colonization Strategies of Enterococcus faecalis in the Gut of Bombyx mori. PMID:35814682
Meta-omics approaches reveal unique small RNAs exhibited by the uncultured microorganisms dwelling deep-sea hydrothermal sediment in Guaymas Basin. PMID:35792953
Comparative Genomic Analyses Provide Insight Into the Pathogenicity of Metschnikowia bicuspidata LNES0119. PMID:35770163
Characterization of the pathogenicity of a Bacillus cereus isolate from the Mariana Trench. PMID:35733351
Halomonas jincaotanensis sp. nov., isolated from the Pamir Plateau degrading polycyclic aromatic hydrocarbon. PMID:35710957
In vitro anti-tuberculosis effect of probiotic Lacticaseibacillus rhamnosus PMC203 isolated from vaginal microbiota. PMID:35585245
Chromosome-level assembly, annotation and phylome of Pelobates cultripes, the western spadefoot toad. PMID:35583263
Genomic insights into the diversity of non-coding RNAs in Bacillus cereus sensu lato. PMID:35552506
miRNA/mRNA co-profiling identifies the miR-200 family as a central regulator of SMC quiescence. PMID:35465051
Admixture of divergent genomes facilitates hybridization across species in the family Brassicaceae. PMID:35403705
Genome Sequence and Description of Paracoccus denitrificans Strain R-1, Isolated from Activated Sludge. PMID:35343764
Genomic Analysis of Stropharia rugosoannulata Reveals Its Nutritional Strategy and Application Potential in Bioremediation. PMID:35205916
Genome assembly of the JD17 soybean provides a new reference genome for comparative genomics. PMID:35188189
Complete Genome Sequencing and Comparative Analysis of the Clinically-Derived Apiotrichum mycotoxinivorans Strain GMU1709. PMID:35186802
Integration of Small RNA and Transcriptome Sequencing Reveal the Roles of miR395 and ATP Sulfurylase in Developing Seeds of Chinese Kale. PMID:35185948
Haloterrigena gelatinilytica sp. nov., a new extremely halophilic archaeon isolated from salt-lake. PMID:35166931
Length-Dependent Deep Learning Model for RNA Secondary Structure Prediction. PMID:35164295
Integrated Analysis of mRNA-Seq and MiRNA-Seq Reveals the Molecular Mechanism of the Intestinal Immune Response in Marsupenaeus japonicus Under Decapod Iridescent Virus 1 Infection. PMID:35116034
Heteroresistance to Amikacin in Carbapenem-Resistant Klebsiella pneumoniae Strains. PMID:35035381
Transcriptome Dynamics of Human Neuronal Differentiation From iPSC. PMID:34970540
Small RNA sequencing reveals various microRNAs involved in piperine biosynthesis in black pepper (Piper nigrum L.). PMID:34794378
Potential of sperm small non-coding RNAs as biomarkers of testicular toxicity in a doxorubicin-induced mouse model. PMID:34729424
Genomic Changes and Genetic Divergence of Vibrio alginolyticus Under Phage Infection Stress Revealed by Whole-Genome Sequencing and Resequencing. PMID:34671325
Three chromosome-scale Papaver genomes reveal punctuated patchwork evolution of the morphinan and noscapine biosynthesis pathway. PMID:34654815
Prediction of RNA secondary structure including pseudoknots for long sequences. PMID:34601552
Complete genome sequence of Microbulbifer sp. YPW1 from mangrove sediments in Yanpu harbor, China. PMID:34585272
Elevated transcription of transposable elements is accompanied by het-siRNA-driven de novo DNA methylation in grapevine embryogenic callus. PMID:34544372
ncDLRES: a novel method for non-coding RNAs family prediction based on dynamic LSTM and ResNet. PMID:34544356
Avian Neo-Sex Chromosomes Reveal Dynamics of Recombination Suppression and W Degeneration. PMID:34542640
The stem rust fungus Puccinia graminis f. sp. tritici induces centromeric small RNAs during late infection that are associated with genome-wide DNA methylation. PMID:34526021
ViMIC: a database of human disease-related virus mutations, integration sites and cis-effects. PMID:34500462
Characterization of Martelella soudanensis sp. nov., Isolated from a Mine Sediment. PMID:34442814
Temporal Gene Expression Signature of Plasma Extracellular Vesicles-MicroRNAs from Post-Smolt Coho Salmon Challenged with Piscirickettsia salmonis. PMID:34390423
Identification of differentially expressed microRNAs in primary esophageal achalasia by next-generation sequencing. PMID:34377051
Haplotype-resolved genome assembly and allele-specific gene expression in cultivated ginger. PMID:34354050
Uncovering Transcriptional Regulators and Targets of sRNAs Using an Integrative Data-Mining Approach: H-NS-Regulated RseX as a Case Study. PMID:34327153
Genomic Analysis and Stability Evaluation of the Phenol-Degrading Bacterium Acinetobacter sp. DW-1 During Water Treatment. PMID:34326823
Draft Genome of the Mirrorwing Flyingfish (Hirundichthys speculiger). PMID:34306036
Metagenomic and metatranscriptomic profiling of Lactobacillus casei Zhang in the human gut. PMID:34210980
Reproductive developmental transcriptome analysis of Tripidium ravennae (Poaceae). PMID:34182921
Chromosome-Scale Genome Assembly of the Resurrection Plant Acanthochlamys bracteata (Velloziaceae). PMID:34165527
A map of the SARS-CoV-2 RNA structurome. PMID:34046592
DRAGoM: Classification and Quantification of Noncoding RNA in Metagenomic Data. PMID:34025724
Molecular mechanisms of mutualistic and antagonistic interactions in a plant-pollinator association. PMID:34002050
Polyploidy underlies co-option and diversification of biosynthetic triterpene pathways in the apple tribe. PMID:33986115
Extensive Reannotation of the Genome of the Model Streptomycete Streptomyces lividans TK24 Based on Transcriptome and Proteome Information. PMID:33935985
Use of RNA Sequencing to Perform Comprehensive Analysis of Long Noncoding RNA Expression Profiles in Macrophages Infected with Trichosporon asahii. PMID:33877524
A chromosome-level reference genome of the hazelnut, Corylus heterophylla Fisch. PMID:33871007
Classification of seed members of five riboswitch families as short sequences based on the features extracted by Block Location-Based Feature Extraction (BLBFE) method. PMID:33842280
PANDORA-seq expands the repertoire of regulatory small RNAs by overcoming RNA modifications. PMID:33820973
Metagenomic analysis exploring taxonomic and functional diversity of bacterial communities of a Himalayan urban fresh water lake. PMID:33764980
Identification of 11 candidate structured noncoding RNA motifs in humans by comparative genomics. PMID:33750298
The complete mitochondrial genome of the lobe coral Porites lobata (Anthozoa: Scleractinia) sequenced using ezRAD. PMID:33644352
Chromosome-scale assembly of the genome of Salix dunnii reveals a male-heterogametic sex determination system on chromosome 7. PMID:33609314
The long noncoding RNA NARL regulates immune responses via microRNA-mediated NOD1 downregulation in teleost fish. PMID:33581111
Machine learning a model for RNA structure prediction. PMID:33575634
RNA secondary structure prediction using deep learning with thermodynamic integration. PMID:33574226
Chromosome-level reference genome of the soursop (Annona muricata): A new resource for Magnoliid research and tropical pomology. PMID:33569882
A telomere-to-telomere assembly of Oscheius tipulae and the evolution of rhabditid nematode chromosomes. PMID:33561231
MicroRNA Profiles in Monocyte-Derived Macrophages Generated by Interleukin-27 and Human Serum: Identification of a Novel HIV-Inhibiting and Autophagy-Inducing MicroRNA. PMID:33525571
Microbial dynamics of elevated carbon flux in the open ocean's abyss. PMID:33479184
A Comprehensive Analysis of cis-Acting RNA Elements in the SARS-CoV-2 Genome by a Bioinformatics Approach. PMID:33424918
Development and Optimization of Chromosomally-Integrated Fluorescent Mycobacterium tuberculosis Reporter Constructs. PMID:33362741
Comparative genomics of Klebsiella michiganensis BD177 and related members of Klebsiella sp. reveal the symbiotic relationship with Bactrocera dorsalis. PMID:33339499
RefSeq: expanding the Prokaryotic Genome Annotation Pipeline reach with protein family model curation. PMID:33270901
Genome-wide identification of Azospirillum brasilense Sp245 small RNAs responsive to nitrogen starvation and likely involvement in plant-microbe interactions. PMID:33228533
Rfam 14: expanded coverage of metagenomic, viral and microRNA families. PMID:33211869
Ensembl 2021. PMID:33137190
Quorum Sensing System in Bacteroides thetaiotaomicron Strain Identified by Genome Sequence Analysis. PMID:33134713
Comparative Genome Analysis Reveals Natural Variations in the Genomes of Erwinia pyrifoliae, a Black Shoot Blight Pathogen in Apple and Pear. PMID:33082727
snR30/U17 Small Nucleolar Ribonucleoprotein: A Critical Player during Ribosome Biogenesis. PMID:33003357
A survey of RNA secondary structural propensity encoded within human herpesvirus genomes: global comparisons and local motifs. PMID:32974099
Expanded genome-wide comparisons give novel insights into population structure and genetic heterogeneity of Leishmania tropica complex. PMID:32946436
Cell Plasticity and Genomic Structure of a Novel Filterable Rhizobiales Bacterium that Belongs to a Widely Distributed Lineage. PMID:32906802
rboAnalyzer: A Software to Improve Characterization of Non-coding RNAs From Sequence Database Search Output. PMID:32849767
Improved reference genome of the arboviral vector Aedes albopictus. PMID:32847630
Comprehensive Analysis of Non-coding RNA Profiles of Exosome-Like Vesicles From the Protoscoleces and Hydatid Cyst Fluid of Echinococcus granulosus. PMID:32793506
PRIME-3D2D is a 3D2D model to predict binding sites of protein-RNA interaction. PMID:32678300
The Genome Sequence of the Octocoral Paramuricea clavata - A Key Resource To Study the Impact of Climate Change in the Mediterranean. PMID:32660973
Quality Matters: Biocuration Experts on the Impact of Duplication and Other Data Quality Issues in Biological Databases. PMID:32652120
HiPR: High-throughput probabilistic RNA structure inference. PMID:32637050
The regulatory landscape of early maize inflorescence development. PMID:32631399
Genome assembly of the basket willow, Salix viminalis, reveals earliest stages of sex chromosome expansion. PMID:32605573
MicroRNAs signatures, bioinformatics analysis of miRNAs, miRNA mimics and antagonists, and miRNA therapeutics in osteosarcoma. PMID:32565738
Dissecting the genome of star fruit (Averrhoa carambola L.). PMID:32528706
Regulation of hepatic microRNAs in response to early stage Echinococcus multilocularis egg infection in C57BL/6 mice. PMID:32442168
Temporal transcriptional patterns of cyanophage genes suggest synchronized infection of cyanobacteria in the oceans. PMID:32430017
Identification and Integrated Analysis of MicroRNA and mRNA Expression Profiles During Agonistic Behavior in Chinese Mitten Crab (Eriocheir sinensis) Using a Deep Sequencing Approach. PMID:32391050
Comparative Metatranscriptomics of Periodontitis Supports a Common Polymicrobial Shift in Metabolic Function and Identifies Novel Putative Disease-Associated ncRNAs. PMID:32328037
The functions of ocu-miR-205 in regulating hair follicle development in Rex rabbits. PMID:32321445
Genome-Wide Identification and Characterization of Drought Stress Responsive microRNAs in Tibetan Wild Barley. PMID:32316632
Knockout of glutathione peroxidase 5 down-regulates the piRNAs in the caput epididymidis of aged mice. PMID:32270769
Different Genetic Sources Contribute to the Small RNA Population in the Arbuscular Mycorrhizal Fungus Gigaspora margarita. PMID:32231650
Genes and novel sRNAs involved in PAHs degradation in marine bacteria Rhodococcus sp. P14 revealed by the genome and transcriptome analysis. PMID:32206489
De novo assembly of the cattle reference genome with single-molecule sequencing. PMID:32191811
Hepatic transcriptome of the freeze-tolerant Cope's gray treefrog, Dryophytes chrysoscelis: responses to cold acclimation and freezing. PMID:32164545
Organization of the Addax Major Histocompatibility Complex Provides Insights Into Ruminant Evolution. PMID:32161588
An Integrated Metagenome Catalog Reveals New Insights into the Murine Gut Microbiome. PMID:32130896
Comparative Insights Into the Complete Genome Sequence of Highly Metal Resistant Cupriavidus metallidurans Strain BS1 Isolated From a Gold-Copper Mine. PMID:32117100
Assessing the accuracy of direct-coupling analysis for RNA contact prediction. PMID:32115426
Comparison of Arachis monticola with Diploid and Cultivated Tetraploid Genomes Reveals Asymmetric Subgenome Evolution and Improvement of Peanut. PMID:32099754
Comparative genomics applied to Mucor species with different lifestyles. PMID:32039703
Identification of Novel and Recurrent RMRP Variants in a Series of Brazilian Patients with Cartilage-Hair Hypoplasia: McKusick Syndrome. PMID:32021596
Integrated mRNA and miRNA transcriptome analysis reveals a regulatory network for tuber expansion in Chinese yam (Dioscorea opposita). PMID:32013881
Total RNA sequencing reveals multilevel microbial community changes and functional responses to wood ash application in agricultural and forest soil. PMID:32009159
Whole-genome and time-course dual RNA-Seq analyses reveal chronic pathogenicity-related gene dynamics in the ginseng rusty root rot pathogen Ilyonectria robusta. PMID:32005849
RNAconTest: comparing tools for noncoding RNA multiple sequence alignment based on structural consistency. PMID:32005745
miRNAs and lncRNAs in Echinococcus and Echinococcosis. PMID:31979099
RNAmountAlign: Efficient software for local, global, semiglobal pairwise and multiple RNA sequence/structure alignment. PMID:31978147
Microbial composition of Kombucha determined using amplicon sequencing and shotgun metagenomics. PMID:31957879
A draft genome sequence of the elusive giant squid, Architeuthis dux. PMID:31942620
The genome sequence of celery (Apium graveolens L.), an important leaf vegetable crop rich in apigenin in the Apiaceae family. PMID:31934340
Development of a new oligonucleotide block location-based feature extraction (BLBFE) method for the classification of riboswitches. PMID:31901978
Draft Genomes of Two Artocarpus Plants, Jackfruit (A. heterophyllus) and Breadfruit (A. altilis). PMID:31878322
miR-10a-5p and miR-29b-3p as Extracellular Vesicle-Associated Prostate Cancer Detection Markers. PMID:31877768
The Pseudomonas aeruginosa accessory genome elements influence virulence towards Caenorhabditis elegans. PMID:31823826
Genome sequence of the model rice variety KitaakeX. PMID:31775618
Evolution of small RNA expression following hybridization and allopolyploidization: insights from Spartina species (Poaceae, Chloridoideae). PMID:31748889
Genome-wide analysis of small RNAs from Odontoglossum ringspot virus and Cymbidium mosaic virus synergistically infecting Phalaenopsis. PMID:31724809
Conservation and Divergence in the Meiocyte sRNAomes of Arabidopsis, Soybean, and Cucumber. PMID:31719152
Comparative Analysis of Whole-Genome and Methylome Profiles of a Smooth and a Rough Mycobacterium abscessus Clinical Strain. PMID:31719113
Mapping the RNA structural landscape of viral genomes. PMID:31711930
Multiomics analysis of tolerant interaction of potato with potato virus Y. PMID:31673114
The architecture of the Plasmodiophora brassicae nuclear and mitochondrial genomes. PMID:31673019
Unstable TTTTA/TTTCA expansions in MARCH6 are associated with Familial Adult Myoclonic Epilepsy type 3. PMID:31664039
The Genome Sequence of the Eastern Woodchuck (Marmota monax) - A Preclinical Animal Model for Chronic Hepatitis B. PMID:31645421
RNA 3D structure prediction guided by independent folding of homologous sequences. PMID:31640563
Serial horizontal transfer of vitamin-biosynthetic genes enables the establishment of new nutritional symbionts in aphids' di-symbiotic systems. PMID:31624345
A high-quality cucumber genome assembly enhances computational comparative genomics. PMID:31620884
Genome-wide association mapping of date palm fruit traits. PMID:31615981
The sequencing and de novo assembly of the Larimichthys crocea genome using PacBio and Hi-C technologies. PMID:31575853
The sequence and de novo assembly of Takifugu bimaculatus genome using PacBio and Hi-C technologies. PMID:31570724
Rhopalocnemis phalloides has one of the most reduced and mutated plastid genomes known. PMID:31565552
Characterization and Whole Genome Sequencing of AR23, a Highly Toxic Bacillus thuringiensis Strain Isolated from Lebanese Soil. PMID:31563972
Identification and Temporal Expression Analysis of Conserved and Novel MicroRNAs in the Leaves of Winter Wheat Grown in the Field. PMID:31552091
Comprehensive Profiles of mRNAs and miRNAs Reveal Molecular Characteristics of Multiple Organ Physiologies and Development in Pigs. PMID:31552085
Reference gene and small RNA data from multiple tissues of Davidia involucrata Baill. PMID:31551451
Genetic Characteristic and RNA-Seq Analysis in Transparent Mutant of Carp-Goldfish Nucleocytoplasmic Hybrid. PMID:31547242
Transposons played a major role in the diversification between the closely related almond and peach genomes: results from the almond genome sequence. PMID:31529539
Comparative genomic analysis of six Glossina genomes, vectors of African trypanosomes. PMID:31477173
The improved assembly of 7DL chromosome provides insight into the structure and evolution of bread wheat. PMID:31471988
On the emergence of structural complexity in RNA replicators. PMID:31467146
Evolutionary characteristics of intergenic transcribed regions indicate rare novel genes and widespread noisy transcription in the Poaceae. PMID:31431676
Genome-wide analysis of the transcriptional response to drought stress in root and leaf of common bean. PMID:31429863
Multilayered Tuning of Dosage Compensation and Z-Chromosome Masculinization in the Wood White (Leptidea sinapis) Butterfly. PMID:31400207
Functional genetic variants can mediate their regulatory effects through alteration of transcription factor binding. PMID:31375681
Small RNA discovery in the interaction between barley and the powdery mildew pathogen. PMID:31345162
Regulation of terpenoid biosynthesis by miRNA in Persicaria minor induced by Fusarium oxysporum. PMID:31311515
Genome Sequencing of Pleurozium schreberi: The Assembled and Annotated Draft Genome of a Pleurocarpous Feather Moss. PMID:31285273
Genome-wide identification and comparative analysis of drought-related microRNAs in two maize inbred lines with contrasting drought tolerance by deep sequencing. PMID:31276526
Nanopore Sequencing Significantly Improves Genome Assembly of the Protozoan Parasite Trypanosoma cruzi. PMID:31218350
Comparative genomics of Mycobacterium mucogenicum and Mycobacterium neoaurum clade members emphasizing tRNA and non-coding RNA. PMID:31215393
RNA-Seq analysis of soft rush (Juncus effusus): transcriptome sequencing, de novo assembly, annotation, and polymorphism identification. PMID:31195970
Structural prediction of RNA switches using conditional base-pair probabilities. PMID:31188853
Genomic insights into a robust gamma-aminobutyric acid-producer Lactobacillus brevis CD0817. PMID:31127390
Computational approaches for the discovery of splicing regulatory RNA structures. PMID:31048028
Identification and Characterization of Salt-Responsive MicroRNAs in Vicia faba by High-Throughput Sequencing. PMID:30999691
reactIDR: evaluation of the statistical reproducibility of high-throughput structural analyses towards a robust RNA structure prediction. PMID:30925857
Genome-wide discovery of structured noncoding RNAs in bacteria. PMID:30902049
SSS-test: a novel test for detecting positive selection on RNA secondary structure. PMID:30898084
Unraveling RNA dynamical behavior of TPP riboswitches: a comparison between Escherichia coli and Arabidopsis thaliana. PMID:30862893
In silico analysis of fungal small RNA accumulation reveals putative plant mRNA targets in the symbiosis between an arbuscular mycorrhizal fungus and its host plant. PMID:30832582
Genome-wide discovery and characterization of flower development related long non-coding RNAs in Prunus mume. PMID:30744565
miPIE: NGS-based Prediction of miRNA Using Integrated Evidence. PMID:30733467
Kelpie: generating full-length 'amplicons' from whole-metagenome datasets. PMID:30723610
The genomic basis for colonizing the freezing Southern Ocean revealed by Antarctic toothfish and Patagonian robalo genomes. PMID:30715292
Aerobic prokaryotes do not have higher GC contents than anaerobic prokaryotes, but obligate aerobic prokaryotes have. PMID:30691392
Tumor stem-like cell-derived exosomal RNAs prime neutrophils for facilitating tumorigenesis of colon cancer. PMID:30683126
Virulence Characteristics and an Action Mode of Antibiotic Resistance in Multidrug-Resistant Pseudomonas aeruginosa. PMID:30679735
Meiocyte-Specific and AtSPO11-1-Dependent Small RNAs and Their Association with Meiotic Gene Expression and Recombination. PMID:30674694
Iso-Seq Allows Genome-Independent Transcriptome Profiling of Grape Berry Development. PMID:30642874
Identification of Microbial Dark Matter in Antarctic Environments. PMID:30619224
Discovery and profiling of small RNAs from Puccinia triticina by deep sequencing and identification of their potential targets in wheat. PMID:30618015
A pan-transcriptome analysis shows that disease resistance genes have undergone more selection pressure during barley domestication. PMID:30616511
MicroRNA expression profile in chronic nonbacterial prostatitis revealed by next-generation small RNA sequencing. PMID:30604696
Characterization of siRNAs clusters in Arabidopsis thaliana galls induced by the root-knot nematode Meloidogyne incognita. PMID:30563458
The Integrator complex regulates differential snRNA processing and fate of adult stem cells in the highly regenerative planarian Schmidtea mediterranea. PMID:30557303
The draft genomes of five agriculturally important African orphan crops. PMID:30535374
Divergent evolution in the genomes of closely related lacertids, Lacerta viridis and L. bilineata, and implications for speciation. PMID:30535196
Complete Genome Sequence of the Endophytic Bacterium Chryseobacterium indologenes PgBE177, Isolated from Panax quinquefolius. PMID:30533712
The Transcriptional landscape of Streptococcus pneumoniae TIGR4 reveals a complex operon architecture and abundant riboregulation critical for growth and virulence. PMID:30517198
Genome sequence of the opportunistic human pathogen Magnusiomyces capitatus. PMID:30456648
Uncovering full-length transcript isoforms of sugarcane cultivar Khon Kaen 3 using single-molecule long-read sequencing. PMID:30397543
Genomic discovery of the hypsin gene and biosynthetic pathways for terpenoids in Hypsizygus marmoreus. PMID:30382831
Analysis of impact metrics for the Protein Data Bank. PMID:30325351
acI Actinobacteria Assemble a Functional Actinorhodopsin with Natively Synthesized Retinal. PMID:30315080
Rare variants of the FMN riboswitch class in Clostridium difficile and other bacteria exhibit altered ligand specificity. PMID:30287481
Extremophiles as a Model of a Natural Ecosystem: Transcriptional Coordination of Genes Reveals Distinct Selective Responses of Plants Under Climate Change Scenarios. PMID:30283484
Genome-scale analysis of Acetobacterium bakii reveals the cold adaptation of psychrotolerant acetogens by post-transcriptional regulation. PMID:30249742
The draft genome sequence of Clostridium sp. strain LJ4 with high furan and phenolic derivates' tolerances occurring from lignocellulosic hydrolysates. PMID:30237953
ANNOgesic: a Swiss army knife for the RNA-seq based annotation of bacterial/archaeal genomes. PMID:30169674
Challenges and approaches to predicting RNA with multiple functional structures. PMID:30143552
Identification and characterization of miRNAs in the gills of the mud crab (Scylla paramamosain) in response to a sudden drop in salinity. PMID:30107782
A Freeloader? The Highly Eroded Yet Large Genome of the Serratia symbiotica Symbiont of Cinara strobi. PMID:30102395
Accelerated RNA secondary structure design using preselected sequences for helices and loops. PMID:30097542
Whole Genome Sequencing, de Novo Assembly and Phenotypic Profiling for the New Budding Yeast Species Saccharomyces jurei. PMID:30097472
A glutamine riboswitch is a key element for the regulation of glutamine synthetase in cyanobacteria. PMID:30085248
Full-length transcriptome of Misgurnus anguillicaudatus provides insights into evolution of genus Misgurnus. PMID:30076392
siRNAs regulate DNA methylation and interfere with gene and lncRNA expression in the heterozygous polyploid switchgrass. PMID:30061930
Functional annotation and distribution overview of RNA families in 27 Streptococcus agalactiae genomes. PMID:30055586
Small Non-coding RNA Expression and Vertebrate Anoxia Tolerance. PMID:30042786
Genome-Guided Characterization of Ochrobactrum sp. POC9 Enhancing Sewage Sludge Utilization-Biotechnological Potential and Biosafety Considerations. PMID:30013002
MicroRNA expression profiling of goat peripheral blood mononuclear cells in response to peste des petits ruminants virus infection. PMID:30012212
Examination of novel Aureobasidium pullulans isolates dominating apple microflora and assessing their potential for apple juice spoilage. PMID:29998388
Identification of receptors for UNCG and GNRA Z-turns and their occurrence in rRNA. PMID:29986118
Trends in the development of miRNA bioinformatics tools. PMID:29982332
Pain-Associated Transcriptome Changes in Synovium of Knee Osteoarthritis Patients. PMID:29973527
Small non-coding RNA landscape is modified by GPAT2 silencing in MDA-MB-231 cells. PMID:29963267
Draft Genome Sequence of the Antimicrobial-Producing Strain Paenibacillus elgii AC13. PMID:29954895
Transcriptome analysis demonstrates that long noncoding RNA is involved in the hypoxic response in Larimichthys crocea. PMID:29948448
The High-Quality Genome Sequence of the Oceanic Island Endemic Species Drosophila guanche Reveals Signals of Adaptive Evolution in Genes Related to Flight and Genome Stability. PMID:29947749
Non-Coding RNA Analysis Using the Rfam Database. PMID:29927072
Integrated microRNA and mRNA expression profiling reveals a complex network regulating pomegranate (Punica granatum L.) seed hardness. PMID:29915181
Poly(3-hydroxybutyrate-co-3-hydroxyvalerate) co-produced with L-isoleucine in Corynebacterium glutamicum WM001. PMID:29907151
Identification of microRNAs involved in drought stress responses in early-maturing cotton by high-throughput sequencing. PMID:29892798
Parallels between experimental and natural evolution of legume symbionts. PMID:29891837
Stage-dependent piRNAs in chicken implicated roles in modulating male germ cell development. PMID:29859049
Group I introns are widespread in archaea. PMID:29788499
Loci under selection and markers associated with host plant and host-related strains shape the genetic structure of Brazilian populations of Spodoptera frugiperda (Lepidoptera, Noctuidae). PMID:29787608
Genome Sequencing and Analysis of the Peanut B-Genome Progenitor (Arachis ipaensis). PMID:29774047
Core non-coding RNAs of Piscirickettsia salmonis. PMID:29768466
bpRNA: large-scale automated annotation and analysis of RNA secondary structure. PMID:29746666
Plastid genome analysis of three Nemaliophycidae red algal species suggests environmental adaptation for iron limited habitats. PMID:29738547
SPORTS1.0: A Tool for Annotating and Profiling Non-coding RNAs Optimized for rRNA- and tRNA-derived Small RNAs. PMID:29730207
GLASSgo - Automated and Reliable Detection of sRNA Homologs From a Single Input Sequence. PMID:29719549
Innovative assembly strategy contributes to understanding the evolution and conservation genetics of the endangered Solenodon paradoxus from the island of Hispaniola. PMID:29718205
Development of a new sequential block finding strategy for detection of conserved sequences in riboswitches. PMID:29713598
Genome-centric metatranscriptomes and ecological roles of the active microbial populations during cellulosic biomass anaerobic digestion. PMID:29713376
miRToolsGallery: a tag-based and rankable microRNA bioinformatics resources database portal. PMID:29688355
FishTEDB: a collective database of transposable elements identified in the complete genomes of fish. PMID:29688350
Genome sequence of Planktotalea frisia type strain (SH6-1T), a representative of the Roseobacter group isolated from the North Sea during a phytoplankton bloom. PMID:29682168
Origin, Evolution, and Loss of Bacterial Small RNAs. PMID:29623872
Cell-wall synthesis and ribosome maturation are co-regulated by an RNA switch in Mycobacterium tuberculosis. PMID:29618088
An Evaluation of Function of Multicopy Noncoding RNAs in Mammals Using ENCODE/FANTOM Data and Comparative Genomics. PMID:29617896
De novo draft assembly of the Botrylloides leachii genome provides further insight into tunicate evolution. PMID:29615780
Phylogenomic and comparative analysis of the distribution and regulatory patterns of TPP riboswitches in fungi. PMID:29615754
Unexpected conservation of the RNA splicing apparatus in the highly streamlined genome of Galdieria sulphuraria. PMID:29606099
Comparative genome-wide analysis of extracellular small RNAs from the mucormycosis pathogen Rhizopus delemar. PMID:29588481
miR-126-5p by direct targeting of JNK-interacting protein-2 (JIP-2) plays a key role in Theileria-infected macrophage virulence. PMID:29570727
CMV: visualization for RNA and protein family models and their comparisons. PMID:29554223
Pervasive Regulatory Functions of mRNA Structure Revealed by High-Resolution SHAPE Probing. PMID:29551268
A Glycine Riboswitch in Streptococcus pyogenes Controls Expression of a Sodium:Alanine Symporter Family Protein Gene. PMID:29527194
Complete avian malaria parasite genomes reveal features associated with lineage-specific evolution in birds and mammals. PMID:29500236
Genome-reconstruction for eukaryotes from complex natural microbial communities. PMID:29496730
Identification and characterization of microRNAs in the intestinal tissues of sheep (Ovis aries). PMID:29489866
Deep sequencing and in silico analysis of small RNA library reveals novel miRNA from leaf Persicaria minor transcriptome. PMID:29479512
Polymorphism in Mitochondrial Group I Introns among Cryptococcus neoformans and Cryptococcus gattii Genotypes and Its Association with Drug Susceptibility. PMID:29467729
StructRNAfinder: an automated pipeline and web server for RNA families prediction. PMID:29454313
Culture-Facilitated Comparative Genomics of the Facultative Symbiont Hamiltonella defensa. PMID:29452355
Identification and characterization of microRNA in the lung tissue of pigs with different susceptibilities to PCV2 infection. PMID:29448950
Draft Genome Sequence of Cyanobacterium sp. Strain HL-69, Isolated from a Benthic Microbial Mat from a Magnesium Sulfate-Dominated Hypersaline Lake. PMID:29439050
Using RNA Sequence and Structure for the Prediction of Riboswitch Aptamer: A Comprehensive Review of Available Software and Tools. PMID:29403526
Genome-scale analysis of Methicillin-resistant Staphylococcus aureus USA300 reveals a tradeoff between pathogenesis and drug resistance. PMID:29396540
Multiple Roots of Fruiting Body Formation in Amoebozoa. PMID:29378020
Identification and Characterization of 5' Untranslated Regions (5'UTRs) in Zymomonas mobilis as Regulatory Biological Parts. PMID:29375488
Transcriptome sequencing of the human pathogen Corynebacterium diphtheriae NCTC 13129 provides detailed insights into its transcriptional landscape and into DtxR-mediated transcriptional regulation. PMID:29370758
Structural divergence creates new functional features in alphavirus genomes. PMID:29361131
The Small RNA ncS35 Regulates Growth in Burkholderia cenocepacia J2315. PMID:29359187
Know Your Enemy: Successful Bioinformatic Approaches to Predict Functional RNA Structures in Viral RNAs. PMID:29354101
Salicylic Acid Perturbs sRNA-Gibberellin Regulatory Network in Immune Response of Potato to Potato virus Y Infection. PMID:29312421
The complete and fully assembled genome sequence of Aeromonas salmonicida subsp. pectinolytica and its comparative analysis with other Aeromonas species: investigation of the mobilome in environmental and pathogenic strains. PMID:29304740
RNAseq analysis of α-proteobacterium Gluconobacter oxydans 621H. PMID:29304737
Effective computational detection of piRNAs using n-gram models and support vector machine. PMID:29297285
DotAligner: identification and clustering of RNA structure motifs. PMID:29284541
Isolation and characterization of a N4-like lytic bacteriophage infecting Vibrio splendidus, a pathogen of fish and bivalves. PMID:29284014
New specific primers for amplification of the Internal Transcribed Spacer region in Clitellata (Annelida). PMID:29238565
Differential Expression of Serum MicroRNAs Supports CD4⁺ T Cell Differentiation into Th2/Th17 Cells in Severe Equine Asthma. PMID:29231896
RNAStructuromeDB: A genome-wide database for RNA structural inference. PMID:29222504
LeishDB: a database of coding gene annotation and non-coding RNAs in Leishmania braziliensis. PMID:29220437
A comprehensive profile of circulating RNAs in human serum. PMID:29219730
High-quality draft genome sequence of Aquidulcibacter paucihalophilus TH1-2T isolated from cyanobacterial aggregates in a eutrophic lake. PMID:29213356
RNA-seq-based genome annotation and identification of long-noncoding RNAs in the grapevine cultivar 'Riesling'. PMID:29197332
Alignment-free comparative genomic screen for structured RNAs using coarse-grained secondary structure dot plots. PMID:29197323
The fungal snoRNAome. PMID:29196413
Increased Biosynthetic Gene Dosage in a Genome-Reduced Defensive Bacterial Symbiont. PMID:29181447
Sugar Metabolism of the First Thermophilic Planctomycete Thermogutta terrifontis: Comparative Genomic and Transcriptomic Approaches. PMID:29163426
Identification of drought-responsive miRNAs and physiological characterization of tea plant (Camellia sinensis L.) under drought stress. PMID:29157225
Swellix: a computational tool to explore RNA conformational space. PMID:29157200
The discovery potential of RNA processing profiles. PMID:29155959
Differential RNA Sequencing Implicates Sulfide as the Master Regulator of S0 Metabolism in Chlorobaculum tepidum and Other Green Sulfur Bacteria. PMID:29150516
Complete Genome Sequence of Bacillus cereus C1L, a Plant Growth-Promoting Rhizobacterium from the Rhizosphere of Formosa Lily in Taiwan. PMID:29146835
Functional annotation of structural ncRNAs within enhancer RNAs in the human genome: implications for human disease. PMID:29138457
Improving E. coli growth performance by manipulating small RNA expression. PMID:29137641
Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families. PMID:29112718
Ensembl Genomes 2018: an integrated omics infrastructure for non-vertebrate species. PMID:29092050
Minimal and RNA-free RNase P in Aquifex aeolicus. PMID:29073018
RNArchitecture: a database and a classification system of RNA families, with a focus on structural information. PMID:29069520
EBI Metagenomics in 2017: enriching the analysis of microbial communities, from sequence reads to assemblies. PMID:29069476
Synbiological systems for complex natural products biosynthesis. PMID:29062947
Repertoire of noncoding RNAs in corpus luteum of early pregnancy in buffalo (Bubalus bubalis). PMID:29062204
Determination of the Genome and Primary Transcriptome of Syngas Fermenting Eubacterium limosum ATCC 8486. PMID:29057933
Long-read sequencing of the coffee bean transcriptome reveals the diversity of full-length transcripts. PMID:29048540
Origin and Spread of Spliceosomal Introns: Insights from the Fungal Clade Zymoseptoria. PMID:29048531
Global Analysis of Small RNA Dynamics during Seed Development of Picea glauca and Arabidopsis thaliana Populations Reveals Insights on their Evolutionary Trajectories. PMID:29046688
Towards a balanced view of the bacterial tree of life. PMID:29041958
Analysis of the genome of the New Zealand giant collembolan (Holacanthella duospinosa) sheds light on hexapod evolution. PMID:29041914
Transcript expression plasticity as a response to alternative larval host plants in the speciation process of corn and rice strains of Spodoptera frugiperda. PMID:29037161
ITSoneDB: a comprehensive collection of eukaryotic ribosomal RNA Internal Transcribed Spacer 1 (ITS1) sequences. PMID:29036529
TurboFold II: RNA structural alignment and secondary structure prediction informed by multiple homologs. PMID:29036420
Mirnovo: genome-free prediction of microRNAs from small RNA sequencing data and single-cells using decision forests. PMID:29036314
Integrated analysis of coding genes and non-coding RNAs during hair follicle cycle of cashmere goat (Capra hircus). PMID:29020916
Non-coding RNAs and Their Roles in Stress Response in Plants. PMID:29017967
Detection of 224 candidate structured RNAs by comparative analysis of specific subsets of intergenic regions. PMID:28977401
Integrating transcriptome and microRNA analysis identifies genes and microRNAs for AHO-induced systemic acquired resistance in N. tabacum. PMID:28970509
A Genome-Wide Prediction and Identification of Intergenic Small RNAs by Comparative Analysis in Mesorhizobium huakuii 7653R. PMID:28943874
Apophysomyces variabilis: draft genome sequence and comparison of predictive virulence determinants with other medically important Mucorales. PMID:28923009
Integrative and conjugative elements and their hosts: composition, distribution and organization. PMID:28911112
Molecular Resources from Transcriptomes in the Brassicaceae Family. PMID:28900436
Catalog of Differentially Expressed Long Non-Coding RNA following Activation of Human and Mouse Innate Immune Response. PMID:28900427
Genomic and transcriptomic analysis of the toluene degrading black yeast Cladophialophora immunda. PMID:28900256
Small RNAs in vancomycin-resistant Enterococcus faecium involved in daptomycin response and resistance. PMID:28894187
Efficient approximations of RNA kinetics landscape using non-redundant sampling. PMID:28882001
A miRNA catalogue and ncRNA annotation of the short-living fish Nothobranchius furzeri. PMID:28874118
Comparative genomics and phylogenomic analyses of lysine riboswitch distributions in bacteria. PMID:28873470
mRNA pseudouridylation affects RNA metabolism in the parasite Toxoplasma gondii. PMID:28851751
Prediction of bacterial small RNAs in the RsmA (CsrA) and ToxT pathways: a machine learning approach. PMID:28830349
Draft Genome Sequence of Methylocaldum sp. SAD2, a Methanotrophic Strain That Can Convert Raw Biogas to Methanol in the Presence of Hydrogen Sulfide. PMID:28798172
nRC: non-coding RNA Classifier based on structural features. PMID:28785313
RNA folding kinetics using Monte Carlo and Gillespie algorithms. PMID:28780735
Modeling RNA Secondary Structure with Sequence Comparison and Experimental Mapping Data. PMID:28735622
Complete Genome Sequence of Burkholderia stabilis FERMP-21014. PMID:28729264
Identification of Conserved and Novel MicroRNAs in Blueberry. PMID:28713413
Genome-Wide Transcriptional Dynamics in the Companion Bacterial Symbionts of the Glassy-Winged Sharpshooter (Cicadellidae: Homalodisca vitripennis) Reveal Differential Gene Expression in Bacteria Occupying Multiple Host Organs. PMID:28705905
The yeast noncoding RNA interaction network. PMID:28701522
Comparative genomic analysis of Acinetobacter strains isolated from murine colonic crypts. PMID:28697749
sRNA and cis-antisense sRNA identification in Staphylococcus aureus highlights an unusual sRNA gene cluster with one encoding a secreted peptide. PMID:28676719
Identification and Characterization of miRNA Transcriptome in Asiatic Cotton (Gossypium arboreum) Using High Throughput Sequencing. PMID:28663752
Towards a Consistent, Quantitative Evaluation of MicroRNA Evolution. PMID:28637930
The RNA workbench: best practices for RNA and high-throughput sequencing bioinformatics in Galaxy. PMID:28582575
High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development. PMID:28581499
Genome annotation for clinical genomic diagnostics: strengths and weaknesses. PMID:28558813
Numerical integration methods and layout improvements in the context of dynamic RNA visualization. PMID:28558664
A MILI-independent piRNA biogenesis pathway empowers partial germline reprogramming. PMID:28530707
The Whole-Genome and Transcriptome of the Manila Clam (Ruditapes philippinarum). PMID:28505302
The identification and functional annotation of RNA structures conserved in vertebrates. PMID:28487280
Optimization of RNA 3D structure prediction using evolutionary restraints of nucleotide-nucleotide interactions from direct coupling analysis. PMID:28482022
Widespread adenine N6-methylation of active genes in fungi. PMID:28481340
Comparative transcriptomics in human and mouse. PMID:28479595
The EBI search engine: EBI search as a service-making biological data accessible for all. PMID:28472374
Transcriptomic analysis of maternally provisioned cues for phenotypic plasticity in the annual killifish, Austrofundulus limnaeus. PMID:28439397
Iron-regulated small RNA expression as Neisseria gonorrhoeae FA 1090 transitions into stationary phase growth. PMID:28431495
Noumeavirus replication relies on a transient remote control of the host nucleus. PMID:28429720
RNA-Seq Validation of RNAi Identifies Additional Gene Connectivity in Tribolium castaneum (Coleoptera: Tenebrionidae). PMID:28423418
A Genome-Wide Search for Ionizing-Radiation-Responsive Elements in Deinococcus radiodurans Reveals a Regulatory Role for the DNA Gyrase Subunit A Gene's 5' Untranslated Region in the Radiation and Desiccation Response. PMID:28411225
Emergence of New sRNAs in Enteric Bacteria is Associated with Low Expression and Rapid Evolution. PMID:28405712
Genome assembly with in vitro proximity ligation data and whole-genome triplication in lettuce. PMID:28401891
Ensembl core software resources: storage and programmatic access for DNA sequence and genome annotation. PMID:28365736
Revision and reannotation of the Halomonas elongata DSM 2581T genome. PMID:28349658
Transcriptomic analysis of staphylococcal sRNAs: insights into species-specific adaption and the evolution of pathogenesis. PMID:28348860
Towards the complete small RNome of Acinetobacter baumannii. PMID:28348845
Comparative genomics of microsporidian genomes reveals a minimal non-coding RNA set and new insights for transcription in minimal eukaryotic genomes. PMID:28338834
The primary transcriptome of Neisseria meningitidis and its interaction with the RNA chaperone Hfq. PMID:28334889
RNAscClust: clustering RNA sequences using structure conservation and graph based motifs. PMID:28334186
Theory and Modeling of RNA Structure and Interactions with Metal Ions and Small Molecules. PMID:28301768
A Small Regulatory RNA Contributes to the Preferential Colonization of Escherichia coli O157:H7 in the Large Intestine in Response to a Low DNA Concentration. PMID:28289405
Search for 5'-leader regulatory RNA structures based on gene annotation aided by the RiboGap database. PMID:28279853
Identification and characterization of differentially expressed miRNAs in subcutaneous adipose between Wagyu and Holstein cattle. PMID:28272430
Genomic Analysis of Caldithrix abyssi, the Thermophilic Anaerobic Bacterium of the Novel Bacterial Phylum Calditrichaeota. PMID:28265262
Bioinformatic analysis of riboswitch structures uncovers variant classes with altered ligand specificity. PMID:28265071
Highly Conserved Elements and Chromosome Structure Evolution in Mitochondrial Genomes in Ciliates. PMID:28264444
De novo transcriptome assembly reveals high transcriptional complexity in Pisum sativum axillary buds and shows rapid changes in expression of diurnally regulated genes. PMID:28253862
Differentiation of ncRNAs from small mRNAs in Escherichia coli O157:H7 EDL933 (EHEC) by combined RNAseq and RIBOseq - ryhB encodes the regulatory RNA RyhB and a peptide, RyhP. PMID:28245801
De novo assembly of the sea trout (Salmo trutta m. trutta) skin transcriptome to identify putative genes involved in the immune response and epidermal mucus secretion. PMID:28212382
Global transcriptome analysis reveals extensive gene remodeling, alternative splicing and differential transcription profiles in non-seed vascular plant Selaginella moellendorffii. PMID:28198676
Computational identification of the selenocysteine tRNA (tRNASec) in genomes. PMID:28192430
The first complete genome sequences of the acI lineage, the most abundant freshwater Actinobacteria, obtained by whole-genome-amplification of dilution-to-extinction cultures. PMID:28186143
Reconstruction of ancestral RNA sequences under multiple structural constraints. PMID:28185557
Large-scale analysis of microRNA expression, epi-transcriptomic features and biogenesis. PMID:28180281
Genome-Wide Transcriptional Start Site Mapping and sRNA Identification in the Pathogen Leptospira interrogans. PMID:28154810
De novo hybrid assembly of the rubber tree genome reveals evidence of paleotetraploidy in Hevea species. PMID:28150702
Plasmodium malariae and P. ovale genomes provide insights into malaria parasite evolution. PMID:28117441
Transposable elements (TEs) contribute to stress-related long intergenic noncoding RNAs in plants. PMID:28106309
Massive Effect on LncRNAs in Human Monocytes During Fungal and Bacterial Infections and in Response to Vitamins A and D. PMID:28094339
Mutation effects predicted from sequence co-variation. PMID:28092658
A novel bifunctional transcriptional regulator of riboflavin metabolism in Archaea. PMID:28073944
miRDis: a Web tool for endogenous and exogenous microRNA discovery based on deep-sequencing data analysis. PMID:28073746
The 24th annual Nucleic Acids Research database issue: a look back and upcoming changes. PMID:28053160
Design of RNAs: comparing programs for inverse RNA folding. PMID:28049135
Non-Coding RNAs in Lung Cancer: Contribution of Bioinformatics Analysis to the Development of Non-Invasive Diagnostic Tools. PMID:28035947
Identification of miRNAs Affecting the Establishment of Brassica Alboglabra Seedling. PMID:28018366
Complete genome sequence analysis of chicken astrovirus isolate from India. PMID:28012117
Integrated Strategy Improves the Prediction Accuracy of miRNA in Large Dataset. PMID:28002428
Global repositioning of transcription start sites in a plant-fermenting bacterium. PMID:27982035
New tools to analyze overlapping coding regions. PMID:27964762
Tools for Sequence-Based miRNA Target Prediction: What to Choose? PMID:27941681
Expression profiling and functional annotation of noncoding genes across 11 distinct organs in rat development. PMID:27934932
Small RNAs from Bemisia tabaci Are Transferred to Solanum lycopersicum Phloem during Feeding. PMID:27933079
Adaptation of Propionibacterium freudenreichii to long-term survival under gradual nutritional shortage. PMID:27931189
Comparison of Small RNA Profiles of Glycine max and Glycine soja at Early Developmental Stages. PMID:27929436
A Novel Transcriptional Regulator Related to Thiamine Phosphate Synthase Controls Thiamine Metabolism Genes in Archaea. PMID:27920295
Piecemeal Buildup of the Genetic Code, Ribosomes, and Genomes from Primordial tRNA Building Blocks. PMID:27918435
WormBase ParaSite - a comprehensive resource for helminth genomics. PMID:27899279
The genome, transcriptome, and proteome of the nematode Steinernema carpocapsae: evolutionary signatures of a pathogenic lifestyle. PMID:27876851
Identification of urinary exosomal noncoding RNAs as novel biomarkers in chronic kidney disease. PMID:27872161
The genome of the crustacean Parhyale hawaiensis, a model for animal development, regeneration, immunity and lignocellulose digestion. PMID:27849518
Robust statistical modeling improves sensitivity of high-throughput RNA structure probing experiments. PMID:27819660
A statistical test for conserved RNA structure shows lack of evidence for structure in lncRNAs. PMID:27819659
Characterization of a male reproductive transcriptome for Peromyscus eremicus (Cactus mouse). PMID:27812417
RNAcentral: a comprehensive database of non-coding RNA sequences. PMID:27794554
Small Open Reading Frames, Non-Coding RNAs and Repetitive Elements in Bradyrhizobium japonicum USDA 110. PMID:27788207
Draft genome sequence of the marine Rhodobacteraceae strain O3.65, cultivated from oil-polluted seawater of the Deepwater Horizon oil spill. PMID:27777651
The state of play in higher eukaryote gene annotation. PMID:27773922
RNAdualPF: software to compute the dual partition function with sample applications in molecular evolution theory. PMID:27756204
Accurate Classification of RNA Structures Using Topological Fingerprints. PMID:27755571
Complete Sequence and Analysis of Coconut Palm (Cocos nucifera) Mitochondrial Genome. PMID:27736909
Draft Genome Sequence of Bacillus litoralis C44, Isolated from Chinese Scholar Tree (Sophora japonica) Forest Soil. PMID:27688317
MicroRNA regulatory pathway analysis identifies miR-142-5p as a negative regulator of TGF-β pathway via targeting SMAD3. PMID:27683030
Identification and comparative analysis of the microRNA transcriptome in roots of two contrasting tobacco genotypes in response to cadmium stress. PMID:27667199
Identification of Non-Coding RNAs in the Candida parapsilosis Species Group. PMID:27658249
COOLAIR Antisense RNAs Form Evolutionarily Conserved Elaborate Secondary Structures. PMID:27653675
A method for identification of highly conserved elements and evolutionary analysis of superphylum Alveolata. PMID:27645252
Avoidance of stochastic RNA interactions can be harnessed to control protein expression levels in bacteria and archaea. PMID:27642845
Snapshots of a shrinking partner: Genome reduction in Serratia symbiotica. PMID:27599759
The genome sequence of allopolyploid Brassica juncea and analysis of differential homoeolog gene expression influencing selection. PMID:27595476
Genome-based insights into the resistome and mobilome of multidrug-resistant Aeromonas sp. ARM81 isolated from wastewater. PMID:27590015
A path-based measurement for human miRNA functional similarities using miRNA-disease associations. PMID:27585796
Genome-wide identification and characterization of long non-coding RNAs in developmental skeletal muscle of fetal goat. PMID:27550073
Well-characterized sequence features of eukaryote genomes and implications for ab initio gene prediction. PMID:27536341
Co-evolution of SNF spliceosomal proteins with their RNA targets in trans-splicing nematodes. PMID:27450547
A Genomic Analysis of Factors Driving lincRNA Diversification: Lessons from Plants. PMID:27440919
A computational strategy for the search of regulatory small RNAs in Actinobacillus pleuropneumoniae. PMID:27402897
The draft genome of MD-2 pineapple using hybrid error correction of long reads. PMID:27374615
Genome sequence of the olive tree, Olea europaea. PMID:27346392
NCBI prokaryotic genome annotation pipeline. PMID:27342282
RNAlien - Unsupervised RNA family model construction. PMID:27330139
The Genome of the Self-Fertilizing Mangrove Rivulus Fish, Kryptolebias marmoratus: A Model for Studying Phenotypic Plasticity and Adaptations to Extreme Environments. PMID:27324916
Studying RNA Homology and Conservation with Infernal: From Single Sequences to RNA Families. PMID:27322404
Toward reliable biomarker signatures in the age of liquid biopsies - how to standardize the small RNA-Seq workflow. PMID:27317696
Comparative Bioinformatics and Experimental Analysis of the Intergenic Regulatory Regions of Bacillus cereus hbl and nhe Enterotoxin Operons and the Impact of CodY on Virulence Heterogeneity. PMID:27252687
Genome-Wide Detection of Predicted Non-coding RNAs Related to the Adhesion Process in Vibrio alginolyticus Using High-Throughput Sequencing. PMID:27199948
Single-Cell (Meta-)Genomics of a Dimorphic Candidatus Thiomargarita nelsonii Reveals Genomic Plasticity. PMID:27199933
Isolation and Characterization of the First Xylanolytic Hyperthermophilic Euryarchaeon Thermococcus sp. Strain 2319x1 and Its Unusual Multidomain Glycosidase. PMID:27199905
In Vitro and In Vivo Enzyme Activity Screening via RNA-Based Fluorescent Biosensors for S-Adenosyl-l-homocysteine (SAH). PMID:27191512
Reinventing the Wheel and Making It Round Again: Evolutionary Convergence in Buchnera-Serratia Symbiotic Consortia between the Distantly Related Lachninae Aphids Tuberolachnus salignus and Cinara cedri. PMID:27190007
RNA motif search with data-driven element ordering. PMID:27188396
incaRNAfbinv: a web server for the fragment-based design of RNA sequences. PMID:27185893
tRF2Cancer: A web server to detect tRNA-derived small RNA fragments (tRFs) and their expression in multiple cancers. PMID:27179031
Complete Genome Sequence of Staphylococcus aureus MCRF184, a Necrotizing Fasciitis-Causing Methicillin-Sensitive Sequence Type 45 Staphylococcus Strain. PMID:27174283
The repetitive DNA element BncDNA, enriched in the B chromosome of the cichlid fish Astatotilapia latifasciata, transcribes a potentially noncoding RNA. PMID:27169573
ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules. PMID:27166375
Comparative transcriptomics across the prokaryotic tree of life. PMID:27154273
Parallel computation of genome-scale RNA secondary structure to detect structural constraints on human genome. PMID:27153986
RNA-Seq analysis reveals new evidence for inflammation-related changes in aged kidney. PMID:27153548
Identification and Characterization of Two Novel RNA Viruses from Anopheles gambiae Species Complex Mosquitoes. PMID:27138938
Term-seq reveals abundant ribo-regulation of antibiotics resistance in bacteria. PMID:27120414
Maximum margin classifier working in a set of strings. PMID:27118908
Companion: a web server for annotation and analysis of parasite genomes. PMID:27105845
Combining structure probing data on RNA mutants with evolutionary information reveals RNA-binding interfaces. PMID:27095200
3D RNA and Functional Interactions from Evolutionary Couplings. PMID:27087444
Draft Genome Sequence of Zymomonas mobilis ZM481 (ATCC 31823). PMID:27056218
Designing synthetic RNAs to determine the relevance of structural motifs in picornavirus IRES elements. PMID:27053355
Genome sequence of Shimia str. SK013, a representative of the Roseobacter group isolated from marine sediment. PMID:27042262
Genomic Insight into the Host-Endosymbiont Relationship of Endozoicomonas montiporae CL-33(T) with its Coral Host. PMID:27014194
ncRNA orthologies in the vertebrate lineage. PMID:26980512
Functional elucidation of the non-coding RNAs of Kluyveromyces marxianus in the exponential growth phase. PMID:26923790
Analysis of five complete genome sequences for members of the class Peribacteria in the recently recognized Peregrinibacteria bacterial phylum. PMID:26844018
U6 snRNA intron insertion occurred multiple times during fungi evolution. PMID:26828373
Identification of Novel and Conserved miRNAs in Leaves of In vitro Grown Citrus reticulata "Lugan" Plantlets by Solexa Sequencing. PMID:26779240
An evaluation of the accuracy and speed of metagenome analysis tools. PMID:26778510
A Factor Graph Approach to Automated GO Annotation. PMID:26771463
Discovery and profiling of small RNAs responsive to stress conditions in the plant pathogen Pectobacterium atrosepticum. PMID:26753530
Probing-directed identification of novel structured RNAs. PMID:26732206
The European Bioinformatics Institute in 2016: Data growth and integration. PMID:26673705
Promoter-based identification of novel non-coding RNAs reveals the presence of dicistronic snoRNA-miRNA genes in Arabidopsis thaliana. PMID:26607788
The UCSC Genome Browser database: 2016 update. PMID:26590259
Progress and Current Challenges in Modeling Large RNAs. PMID:26585404
antaRNA--Multi-objective inverse folding of pseudoknot RNA using ant-colony optimization. PMID:26581440
GREENC: a Wiki-based database of plant lncRNAs. PMID:26578586
RNA Thermodynamic Structural Entropy. PMID:26555444
Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation. PMID:26553804
The essential gene set of a photosynthetic organism. PMID:26508635
sRNATarBase 3.0: an updated database for sRNA-target interactions in bacteria. PMID:26503244
Network Properties of the Ensemble of RNA Structures. PMID:26488894
Predicting Large RNA-Like Topologies by a Knowledge-Based Clustering Approach. PMID:26478223
The Genome and Methylome of a Beetle with Complex Social Behavior, Nicrophorus vespilloides (Coleoptera: Silphidae). PMID:26454014
Gene-pseudogene evolution: a probabilistic approach. PMID:26449131
Identification and characterization of a minisatellite contained within a novel miniature inverted-repeat transposable element (MITE) of Porphyromonas gingivalis. PMID:26448788
MicroRNAs in the oriental fruit fly, Bactrocera dorsalis: extending Drosophilid miRNA conservation to the Tephritidae. PMID:26438165
Direct-Coupling Analysis of nucleotide coevolution facilitates RNA secondary and tertiary structure prediction. PMID:26420827
Selective small-molecule inhibition of an RNA structural element. PMID:26416753
Linking aptamer-ligand binding and expression platform folding in riboswitches: prospects for mechanistic modeling and design. PMID:26361734
Noncanoncial signal recognition particle RNAs in a major eukaryotic phylum revealed by purification of SRP from the human pathogen Cryptococcus neoformans. PMID:26275773
MultiSETTER: web server for multiple RNA structure comparison. PMID:26264783
Anaerobic biosynthesis of the lower ligand of vitamin B12. PMID:26246619
An Efficient Minimum Free Energy Structure-Based Search Method for Riboswitch Identification Based on Inverse RNA Folding. PMID:26230932
The Large Mitochondrial Genome of Symbiodinium minutum Reveals Conserved Noncoding Sequences between Dinoflagellates and Apicomplexans. PMID:26199191
Metal Ion-Mediated Nucleobase Recognition by the ZTP Riboswitch. PMID:26144884
Identifying novel sequence variants of RNA 3D motifs. PMID:26130723
R3D-2-MSA: the RNA 3D structure-to-multiple sequence alignment server. PMID:26048960
Genome-wide analyses of small non-coding RNAs in streptococci. PMID:26042151
RNAiFold 2.0: a web server and software to design custom and Rfam-based RNA molecules. PMID:26019176
Conservation and losses of non-coding RNAs in avian genomes. PMID:25822729
Key challenges for the creation and maintenance of specialist protein resources. PMID:25820941
Annotating RNA motifs in sequences and alignments. PMID:25520192
Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families PubMed citations: 368.

368 articles citing: Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families

Isolation and Characterization of a Lytic Vibrio parahaemolyticus Phage vB_VpaP_GHSM17 from Sewage Samples. PMID:35893666
Equilibrated evolution of the mixed auto-/allopolyploid haplotype-resolved genome of the invasive hexaploid Prussian carp. PMID:35835759
Chromosome-scale assembly and annotation of the perennial ryegrass genome. PMID:35831814
Genome Assembly and Analysis of the Flavonoid and Phenylpropanoid Biosynthetic Pathways in Fingerroot Ginger (Boesenbergia rotunda). PMID:35806276
Genome structure and evolutionary history of frankincense producing Boswellia sacra. PMID:35789857
Unprecedented frequency of mitochondrial introns in colonial bilaterians. PMID:35764672
A genome and gene catalog of glacier microbiomes. PMID:35760913
A miRNAs catalogue from third-stage larvae and extracellular vesicles of Anisakis pegreffii provides new clues for host-parasite interplay. PMID:35690629
Chromosome-Scale, Haplotype-Resolved Genome Assembly of Non-Sex-Reversal Females of Swamp Eel Using High-Fidelity Long Reads and Hi-C Data. PMID:35669182
SSRTool: A web tool for evaluating RNA secondary structure predictions based on species-specific functional interpretability. PMID:35664227
Ms1 RNA Interacts With the RNA Polymerase Core in Streptomyces coelicolor and Was Identified in Majority of Actinobacteria Using a Linguistic Gene Synteny Search. PMID:35633709
Genomic Survey and Resources for the Boring Giant Clam Tridacna crocea. PMID:35627288
The Construction and Exploration of a Comprehensive MicroRNA Centered Regulatory Network in Foxtail Millet (Setaria italica L.). PMID:35599893
Testicular miRNAs and tsRNAs provide insight into gene regulation during overwintering and reproduction of Onychostoma macrolepis. PMID:35595880
Revealing the novel complexity of plant long non-coding RNA by strand-specific and whole transcriptome sequencing for evolutionarily representative plant species. PMID:35590257
RNA-Seq, Bioinformatic Identification of Potential MicroRNA-like Small RNAs in the Edible Mushroom Agaricus bisporus and Experimental Approach for Their Validation. PMID:35563314
Genomic insights into the diversity of non-coding RNAs in Bacillus cereus sensu lato. PMID:35552506
Chromosome-level genome assembly for the horned-gall aphid provides insights into interactions between gall-making insect and its host plant. PMID:35475184
The Broad Host Range Phage vB_CpeS_BG3P Is Able to Inhibit Clostridium perfringens Growth. PMID:35458406
Sex-Biased miRNAs in the Gonads of Adult Chinese Alligator (Alligator sinensis) and Their Potential Roles in Sex Maintenance. PMID:35432471
The bacterial yjdF riboswitch regulates translation through its tRNA-like fold. PMID:35427649
Identifying miRNAs in the modulation of gene regulation associated with ammonia toxicity in catfish, Clarias magur (Linnaeus, 1758). PMID:35399140
SHAPE-guided RNA structure homology search and motif discovery. PMID:35361788
Disentangle genus microdiversity within a complex microbial community by using a multi-distance long-read binning method: example of Candidatus Accumulibacter. PMID:35315560
Distinct Expansion of Group II Introns During Evolution of Prokaryotes and Possible Factors Involved in Its Regulation. PMID:35295308
Genome-Wide Identification of Novel sRNAs in Streptococcus mutans. PMID:35285723
Secondary structural ensembles of the SARS-CoV-2 RNA genome in infected cells. PMID:35236847
Informative RNA base embedding for RNA structural alignment and clustering by deep representation learning. PMID:35211670
Comparison of structural variants in the whole genome sequences of two Medicago truncatula ecotypes: Jemalong A17 and R108. PMID:35193491
Genome-wide profiling of long non-coding RNA of the rice blast fungus Magnaporthe oryzae during infection. PMID:35168559
A Peroxide-Responding sRNA Evolved from a Peroxidase mRNA. PMID:35084505
LncRNAs Are Differentially Expressed between Wildtype and Cell Line Strains of African Trypanosomes. PMID:35076577
Analysis of the complete genome sequence of a rhizosphere-derived Pseudomonas sp. HN3-2 leads to the characterization of a cyclic lipopeptide-type antibiotic bananamide C. PMID:35070625
Genome-scale analysis of genetic regulatory elements in Streptomyces avermitilis MA-4680 using transcript boundary information. PMID:35062881
Differential microRNA expression, microRNA arm switching, and microRNA:long noncoding RNA interaction in response to salinity stress in soybean. PMID:35057741
Small RNA populations reflect the complex dialogue established between heterograft partners in grapevine. PMID:35048109
The reference genome of camellia chekiangoleosa provides insights into camellia evolution and tea oil biosynthesis. PMID:35039868
Comprehensive Annotation and Functional Exploration of MicroRNAs in Lettuce. PMID:35003165
Rhinoceros Serum microRNAs: Identification, Characterization, and Evaluation of Potential Iron Overload Biomarkers. PMID:34977204
Genome-wide analysis uncovers tomato leaf lncRNAs transcriptionally active upon Pseudomonas syringae pv. tomato challenge. PMID:34972834
Plasma Exosomal Mir-423-5p Is Involved in the Occurrence and Development of Bicuspid Aortopathy via TGF-β/SMAD2 Pathway. PMID:34955881
Integrating cultivation and metagenomics for a multi-kingdom view of skin microbiome diversity and functions. PMID:34952941
A high-quality genome and comparison of short- versus long-read transcriptome of the palaearctic duck Aythya fuligula (tufted duck). PMID:34927191
Distinct small non-coding RNA landscape in the axons and released extracellular vesicles of developing primary cortical neurons and the axoplasm of adult nerves. PMID:34882524
CoCoNet-boosting RNA contact prediction by convolutional neural networks. PMID:34871451
The oxidative stress response of pathogenic Leptospira is controlled by two peroxide stress regulators which putatively cooperate in controlling virulence. PMID:34855911
Genome Survey Sequencing of an Iconic 'Trophy' Sportfish, the Roosterfish Nematistius pectoralis: Genome Size, Repetitive Elements, Nuclear RNA Gene Operon, and Microsatellite Discovery. PMID:34828317
MicroRNA-222 Transferred From Semen Extracellular Vesicles Inhibits Sperm Apoptosis by Targeting BCL2L11. PMID:34820370
A viral RNA hijacks host machinery using dynamic conformational changes of a tRNA-like structure. PMID:34793227
Multispecies Populations of Methanotrophic Methyloprofundus and Cultivation of a Likely Dominant Species from the Iheya North Deep-Sea Hydrothermal Field. PMID:34788070
Chromosome-scale assembly reveals asymmetric paleo-subgenome evolution and targets for the acceleration of fungal resistance breeding in the nut crop, pecan. PMID:34778752
Putative MicroRNA-mRNA Networks Upon Mdfi Overexpression in C2C12 Cell Differentiation and Muscle Fiber Type Transformation. PMID:34738011
Sex without crossing over in the yeast Saccharomycodes ludwigii. PMID:34732243
Prokaryotic Genome Annotation. PMID:34718997
sRNA-mediated regulation of gal mRNA in E. coli: Involvement of transcript cleavage by RNase E together with Rho-dependent transcription termination. PMID:34710092
Genomic insights into biocontrol potential of Bacillus stercoris LJBS06. PMID:34692367
RNAlign2D: a rapid method for combined RNA structure and sequence-based alignment using a pseudo-amino acid substitution matrix. PMID:34656080
Three chromosome-level duck genome assemblies provide insights into genomic variation during domestication. PMID:34635656
SINEUPs: a novel toolbox for RNA therapeutics. PMID:34623427
Insertions and deletions in the RNA sequence-structure map. PMID:34610259
Analysis of 11,430 recombinant protein production experiments reveals that protein yield is tunable by synonymous codon changes of translation initiation sites. PMID:34610008
Differential Expression Pattern of Goat Uterine Fluids Extracellular Vesicles miRNAs during Peri-Implantation. PMID:34571957
The first chromosome-level genome assembly of a green lacewing Chrysopa pallens and its implication for biological control. PMID:34549894
Phenotype Bias Determines How Natural RNA Structures Occupy the Morphospace of All Possible Shapes. PMID:34542628
The GRAS gene family and its roles in seed development in litchi (Litchi chinensis Sonn). PMID:34535087
Genome-Wide Identification and Functional Characterization of Noncoding RNAs (ncRNAs) Differentially Expressed During Insect Development. PMID:34495502
Insights into 6S RNA in lactic acid bacteria (LAB). PMID:34479493
Interplay between Non-Coding RNA Transcription, Stringent/Relaxed Phenotype and Antibiotic Production in Streptomyces ambofaciens. PMID:34438997
The genome of the thin-necked bladder worm Taenia hydatigena reveals evolutionary strategies for helminth survival. PMID:34429506
tRNAscan-SE 2.0: improved detection and functional classification of transfer RNA genes. PMID:34417604
ZmFAR1 and ZmABCG26 Regulated by microRNA Are Essential for Lipid Metabolism in Maize Anther. PMID:34360681
The Genome of the Haptophyte Diacronema lutheri (Pavlova lutheri, Pavlovales): A Model for Lipid Biosynthesis in Eukaryotic Algae. PMID:34343248
The enigmatic RNase MRP of kinetoplastids. PMID:34308760
Multiomic analysis of Schistosoma mansoni reveals unique expression profiles in cercarial heads and tails. PMID:34253841
RNA landscape of the emerging cancer-associated microbe Fusobacterium nucleatum. PMID:34239075
An Integrated Database of Small RNAs and Their Interplay With Transcriptional Gene Regulatory Networks in Corynebacteria. PMID:34220744
Insights into Autotrophic Activities and Carbon Flow in Iron-Rich Pelagic Aggregates (Iron Snow). PMID:34201891
The Chromosome-Level Genome of Triplophysa dalaica (Cypriniformes: Cobitidae) Provides Insights into Its Survival in Extremely Alkaline Environment. PMID:34185063
Methyltransferase-directed orthogonal tagging and sequencing of miRNAs and bacterial small RNAs. PMID:34158037
A standardized archaeal taxonomy for the Genome Taxonomy Database. PMID:34155373
Identification of long noncoding natural antisense transcripts (lncNATs) correlated with drought stress response in wild rice (Oryza nivara). PMID:34103003
Identification of over 200-fold more hairpin ribozymes than previously known in diverse circular RNAs. PMID:34096583
Regulation of Glycine Cleavage and Detoxification by a Highly Conserved Glycine Riboswitch in Burkholderia spp. PMID:34076709
Chromosome-level genome assembly of the Chinese longsnout catfish Leiocassis longirostris. PMID:34075735
Identification of miRNAs and Their Targets Involved in Flower and Fruit Development across Domesticated and Wild Capsicum Species. PMID:34064462
A map of the SARS-CoV-2 RNA structurome. PMID:34046592
Complete Genome Sequences of One Prodigiosin-Producing Serratia marcescens Strain ZPG19. PMID:34046401
A human respiratory tract-associated bacterium with an extremely small genome. PMID:34040152
Multiple cellular compartments engagement in Nicotiana benthamiana-peanut stunt virus-satRNA interactions revealed by systems biology approach. PMID:34028582
DOE JGI Metagenome Workflow. PMID:34006627
Accessing Livestock Resources in Ensembl. PMID:33995484
Next-Generation Sequencing Identification and Characterization of MicroRNAs in Dwarfed Citrus Trees Infected With Citrus Dwarfing Viroid in High-Density Plantings. PMID:33995303
Whole genome sequencing of a snailfish from the Yap Trench (~7,000 m) clarifies the molecular mechanisms underlying adaptation to the deep sea. PMID:33983934
Genome-Wide Changes of Regulatory Non-Coding RNAs Reveal Pollen Development Initiated at Ecodormancy in Peach. PMID:33968979
Transcriptional and epi-transcriptional dynamics of SARS-CoV-2 during cellular infection. PMID:33961822
Elucidating the Regulatory Elements for Transcription Termination and Posttranscriptional Processing in the Streptomyces clavuligerus Genome. PMID:33947798
Large-Scale Annotation and Evolution Analysis of MiRNA in Insects. PMID:33905491
Chloroplast acquisition without the gene transfer in kleptoplastic sea slugs, Plakobranchus ocellatus. PMID:33902812
Identification of polycistronic transcriptional units and non-canonical introns in green algal chloroplasts based on long-read RNA sequencing data. PMID:33892645
Genomic insights into the origin, domestication and genetic basis of agronomic traits of castor bean. PMID:33874982
An Atlas of Genomic Resources for Studying Rosaceae Fruits and Ornamentals. PMID:33868343
Comparative genomics identifies thousands of candidate structured RNAs in human microbiomes. PMID:33845850
Vestiges of the Bacterial Signal Recognition Particle-Based Protein Targeting in Mitochondria. PMID:33837778
Modeling and Predicting RNA Three-Dimensional Structures. PMID:33835435
The reference genome and transcriptome of the limestone langur, Trachypithecus leucocephalus, reveal expansion of genes related to alkali tolerance. PMID:33832502
An expanded class of histidine-accepting viral tRNA-like structures. PMID:33811147
Differential MicroRNA Expression Involved in Endometrial Receptivity of Goats. PMID:33810054
MicroRNA-mediated regulation of glucose and lipid metabolism. PMID:33772227
Identification of virulence associated milRNAs and their bidirectional targets in Rhizoctonia solani and maize during infection. PMID:33771101
Evolutionary conservation of RNA sequence and structure. PMID:33754485
The chromosome-level genome of dragon fruit reveals whole-genome duplication and chromosomal co-localization of betacyanin biosynthetic genes. PMID:33750805
The SARS-CoV-2 subgenome landscape and its novel regulatory features. PMID:33713597
Genome sequence and genetic diversity analysis of an under-domesticated orphan crop, white fonio (Digitaria exilis). PMID:33710327
Mitochondrial Genome Evolution in Pelagophyte Algae. PMID:33675661
An African tick flavivirus forming an independent clade exhibits unique exoribonuclease-resistant RNA structures in the genomic 3'-untranslated region. PMID:33649491
The genome of Magnolia biondii Pamp. provides insights into the evolution of Magnoliales and biosynthesis of terpenoids. PMID:33642574
In vivo structural characterization of the SARS-CoV-2 RNA genome identifies host proteins vulnerable to repurposed drugs. PMID:33636127
Full-length annotation with multistrategy RNA-seq uncovers transcriptional regulation of lncRNAs in cotton. PMID:33631798
Relative Information Gain: Shannon entropy-based measure of the relative structural conservation in RNA alignments. PMID:33615214
The Genome of Banana Leaf Blight Pathogen Fusarium sacchari str. FS66 Harbors Widespread Gene Transfer From Fusarium oxysporum. PMID:33613610
Identification of a non-coding RNA and its putative involvement in the regulation of tetanus toxin synthesis in Clostridium tetani. PMID:33603121
Brassica carinata genome characterization clarifies U's triangle model of evolution and polyploidy in Brassica. PMID:33599732
Gene Annotation in High Schools: Successful Student Pipeline and Teacher Professional Development in Bioscience Using GENI-ACT. PMID:33584559
RNA secondary structure prediction using deep learning with thermodynamic integration. PMID:33574226
IsRNA1: De Novo Prediction and Blind Screening of RNA 3D Structures. PMID:33560836
Genomic and transcriptomic resources for candidate gene discovery in the Ranunculids. PMID:33552749
BSGatlas: a unified Bacillus subtilis genome and transcriptome annotation atlas with enhanced information access. PMID:33539279
Amynthas corticis genome reveals molecular mechanisms behind global distribution. PMID:33514865
De Novo Profiling of Long Non-Coding RNAs Involved in MC-LR-Induced Liver Injury in Whitefish: Discovery and Perspectives. PMID:33477898
Dicer-independent snRNA/snoRNA-derived nuclear RNA 3 regulates tumor-associated macrophage function by epigenetically repressing inducible nitric oxide synthase transcription. PMID:33455092
Computationally reconstructing cotranscriptional RNA folding from experimental data reveals rearrangement of non-native folding intermediates. PMID:33453165
Chromosome-level genome assembly of Ophiorrhiza pumila reveals the evolution of camptothecin biosynthesis. PMID:33452249
rfaRm: An R client-side interface to facilitate the analysis of the Rfam database of RNA families. PMID:33449976
Identification of microRNA-Associated-ceRNA Networks Regulating Crop Milk Production in Pigeon (Columba livia). PMID:33396684
Integrative analysis of long extracellular RNAs reveals a detection panel of noncoding RNAs for liver cancer. PMID:33391469
Genome survey sequencing of the Caribbean spiny lobster Panulirus argus: Genome size, nuclear rRNA operon, repetitive elements, and microsatellite discovery. PMID:33362980
Integrative characterization of the near-minimal bacterium Mesoplasma florum. PMID:33331123
A chromosome-scale genome assembly of a diploid alfalfa, the progenitor of autotetraploid alfalfa. PMID:33328470
Chromosome-level genome assembly of the aphid parasitoid Aphidius gifuensis using Oxford Nanopore sequencing and Hi-C technology. PMID:33314728
RNA structure-wide discovery of functional interactions with multiplexed RNA motif library. PMID:33293523
Symbiotic and Nonsymbiotic Members of the Genus Ensifer (syn. Sinorhizobium) Are Separated into Two Clades Based on Comparative Genomics and High-Throughput Phenotyping. PMID:33283865
DBCOVP: A database of coronavirus virulent glycoproteins. PMID:33276297
The Tetracentron genome provides insight into the early evolution of eudicots and the formation of vessel elements. PMID:33267872
Remote homology search with hidden Potts models. PMID:33253143
Discovery and characterization of a fourth class of guanidine riboswitches. PMID:33237283
The UCSC Genome Browser database: 2021 update. PMID:33221922
Rfam 14: expanded coverage of metagenomic, viral and microRNA families. PMID:33211869
Advances in RNA 3D Structure Modeling Using Experimental Data. PMID:33193680
Insertions of codons encoding basic amino acids in H7 hemagglutinins of influenza A viruses occur by recombination with RNA at hotspots near snoRNA binding sites. PMID:33188057
Deep learning predicts short non-coding RNA functions from only raw sequence data. PMID:33175836
A genomic catalog of Earth's microbiomes. PMID:33169036
Multi-omics analysis reveals that natural hibernation is crucial for oocyte maturation in the female Chinese alligator. PMID:33167853
Identification and analysis of miRNAs in IR56 rice in response to BPH infestations of different virulence levels. PMID:33154527
Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research. PMID:33147627
Characterizing Transcriptional Regulatory Sequences in Coronaviruses and Their Role in Recombination. PMID:33146390
RNANet: an automatically built dual-source dataset integrating homologous sequences and RNA structures. PMID:33135044
RNA structure prediction using positive and negative evolutionary information. PMID:33125376
gcType: a high-quality type strain genome database for microbial phylogenetic and functional research. PMID:33119759
RNAcentral 2021: secondary structure integration, improved sequence search and new member databases. PMID:33106848
CoBold: a method for identifying different functional classes of transient RNA structure features that can impact RNA structure formation in vivo. PMID:33095878
Complementary Tendencies in the Use of Regulatory Elements (Transcription Factors, Sigma Factors, and Riboswitches) in Bacteria and Archaea. PMID:33077635
Genome Sequencing of Paecilomyces Penicillatus Provides Insights into Its Phylogenetic Placement and Mycoparasitism Mechanisms on Morel Mushrooms. PMID:33065983
Cultivable marine fungi from the Arctic Archipelago of Svalbard and their antibacterial activity. PMID:33062384
The mole genome reveals regulatory rearrangements associated with adaptive intersexuality. PMID:33033216
The transcriptional response of pathogenic Leptospira to peroxide reveals new defenses against infection-related oxidative stress. PMID:33021995
Complete Genome Sequencing and Transcriptome Analysis of Nitrogen Metabolism of Succinivibrio dextrinosolvens Strain Z6 Isolated From Dairy Cow Rumen. PMID:33013723
Structural diversity and phylogenetic distribution of valyl tRNA-like structures in viruses. PMID:33008837
R-chie: a web server and R package for visualizing cis and trans RNA-RNA, RNA-DNA and DNA-DNA interactions. PMID:32976561
A survey of RNA secondary structural propensity encoded within human herpesvirus genomes: global comparisons and local motifs. PMID:32974099
Genome-wide screen and functional analysis in Xanthomonas reveal a large number of mRNA-derived sRNAs, including the novel RsmA-sequester RsmU. PMID:32969159
Nanopore Sequencing of the Fungal Intergenic Spacer Sequence as a Potential Rapid Diagnostic Assay. PMID:32967904
Systematics for types and effects of RNA variations. PMID:32951567
Small RNA deep sequencing reveals novel miRNAs in peripheral blood mononuclear cells from patients with IgA nephropathy. PMID:32945407
Premeiotic, 24-Nucleotide Reproductive PhasiRNAs Are Abundant in Anthers of Wheat and Barley But Not Rice and Maize. PMID:32917771
The shift from early to late types of ribosomes in zebrafish development involves changes at a subset of rRNA 2'-O-Me sites. PMID:32912962
Parallel analysis of miRNAs and mRNAs suggests distinct regulatory networks in Crassostrea gigas infected by Ostreid herpesvirus 1. PMID:32912133
TBDB: a database of structurally annotated T-box riboswitch:tRNA pairs. PMID:32882008
Identification of protein-protected mRNA fragments and structured excised intron RNAs in human plasma by TGIRT-seq peak calling. PMID:32876046
A database of flavivirus RNA structures with a search algorithm for pseudoknots and triple base interactions. PMID:32866223
Chromosome-level genome assembly of the female western mosquitofish (Gambusia affinis). PMID:32852039
Characterization of microRNAs during Embryonic Skeletal Muscle Development in the Shan Ma Duck. PMID:32823859
The Existence and Localization of Nuclear snoRNAs in Arabidopsis thaliana Revisited. PMID:32806552
Supersized Ribosomal RNA Expansion Segments in Asgard Archaea. PMID:32785681
Riboflow: Using Deep Learning to Classify Riboswitches With ∼99% Accuracy. PMID:32760712
αβDCA method identifies unspecific binding but specific disruption of the group I intron by the StpA chaperone. PMID:32747608
Analysis of conserved miRNAs in cynomolgus macaque genome using small RNA sequencing and homology searching. PMID:32728489
H/ACA snoRNA levels are regulated during stem cell differentiation. PMID:32710630
Improved Reference Genome for Cyclotella cryptica CCMP332, a Model for Cell Wall Morphogenesis, Salinity Adaptation, and Lipid Production in Diatoms (Bacillariophyta). PMID:32709619
A unified catalog of 204,938 reference genomes from the human gut microbiome. PMID:32690973
A novel riboswitch classification based on imbalanced sequences achieved by machine learning. PMID:32687488
Analysis of Transcriptome and miRNAome in the Muscle of Bamei Pigs at Different Developmental Stages. PMID:32679676
Degradome, small RNAs and transcriptome sequencing of a high-nicotine cultivated tobacco uncovers miRNA's function in nicotine biosynthesis. PMID:32678207
A high-resolution transcriptome map identifies small RNA regulation of metabolism in the gut microbe Bacteroides thetaiotaomicron. PMID:32678091
Extracellular vesicles from Heligmosomoides bakeri and Trichuris muris contain distinct microRNA families and small RNAs that could underpin different functions in the host. PMID:32659276
A database for ITS2 sequences from nematodes. PMID:32650716
A chromosome-scale reference genome of Aquilegia oxysepala var. kansuensis. PMID:32637141
Dual RNA-seq of Orientia tsutsugamushi informs on host-pathogen interactions for this neglected intracellular human pathogen. PMID:32620750
Draft Genome Sequence of the Bacterium Paraburkholderia aromaticivorans AR20-38, a Gram-Negative, Cold-Adapted Degrader of Aromatic Compounds. PMID:32616634
SEQU-INTO: Early detection of impurities, contamination and off-targets (ICOs) in long read/MinION sequencing. PMID:32612757
miRNAs involved in transcriptome remodeling during pollen development and heat stress response in Solanum lycopersicum. PMID:32612181
Competing Endogenous RNAs, Non-Coding RNAs and Diseases: An Intertwined Story. PMID:32605220
Abundant expression of maternal siRNAs is a conserved feature of seed development. PMID:32541052
FARFAR2: Improved De Novo Rosetta Prediction of Complex Global RNA Folds. PMID:32531203
IRESbase: A Comprehensive Database of Experimentally Validated Internal Ribosome Entry Sites. PMID:32512182
An in silico map of the SARS-CoV-2 RNA Structurome. PMID:32511381
RNA genome conservation and secondary structure in SARS-CoV-2 and SARS-related viruses. PMID:32511306
The nuclear and mitochondrial genomes of Frieseomelitta varia - a highly eusocial stingless bee (Meliponini) with a permanently sterile worker caste. PMID:32493270
A decade of research on the second messenger c-di-AMP. PMID:32472931
Complete Mitochondrial Genome of a Gymnosperm, Sitka Spruce (Picea sitchensis), Indicates a Complex Physical Structure. PMID:32449750
Discovery of new group I-D introns leads to creation of subtypes and link to an adaptive response of the mitochondrial genome in fungi. PMID:32449459
Discovery of 20 novel ribosomal leader candidates in bacteria and archaea. PMID:32448158
A Reference Genome of Bursaphelenchus mucronatus Provides New Resources for Revealing Its Displacement by Pinewood Nematode. PMID:32438771
Genome-wide identification and characterization of microRNAs by small RNA sequencing for low nitrogen stress in potato. PMID:32428011
RNA genome conservation and secondary structure in SARS-CoV-2 and SARS-related viruses: a first look. PMID:32398273
The First Draft Genome of the Plasterer Bee Colletes gigas (Hymenoptera: Colletidae: Colletes). PMID:32386319
The Protector within: Comparative Genomics of APSE Phages across Aphids Reveals Rampant Recombination and Diverse Toxin Arsenals. PMID:32386316
RNA-Puzzles Round IV: 3D structure predictions of four ribozymes and two aptamers. PMID:32371455
Wheat chromatin architecture is organized in genome territories and transcription factories. PMID:32349780
A framework for the computational prediction and analysis of non-coding RNAs in microbial environmental populations and their experimental validation. PMID:32346084
Footprints of a Singular 22-Nucleotide RNA Ring at the Origin of Life. PMID:32344921
A comprehensive annotation and differential expression analysis of short and long non-coding RNAs in 16 bat genomes. PMID:32289119
Evaluating DCA-based method performances for RNA contact prediction by a well-curated data set. PMID:32276988
Small Non-Coding RNA Profiling Identifies miR-181a-5p as a Mediator of Estrogen Receptor Beta-Induced Inhibition of Cholesterol Biosynthesis in Triple-Negative Breast Cancer. PMID:32260128
Streptomyces spp. From the Marine Sponge Antho dichotoma: Analyses of Secondary Metabolite Biosynthesis Gene Clusters and Some of Their Products. PMID:32256483
The sterlet sturgeon genome sequence and the mechanisms of segmental rediploidization. PMID:32231327
Genomic and Transcriptomic Analysis Identified Novel Putative Cassava lncRNAs Involved in Cold and Drought Stress. PMID:32231066
An Evolutionary Trace method defines functionally important bases and sites common to RNA families. PMID:32208421
PPanGGOLiN: Depicting microbial diversity via a partitioned pangenome graph. PMID:32191703
The honeysuckle genome provides insight into the molecular mechanism of carotenoid metabolism underlying dynamic flower coloration. PMID:32187685
Complete Genome Insights into Lactococcus petauri CF11 Isolated from a Healthy Human Gut Using Second- and Third-Generation Sequencing. PMID:32174973
Riboregulation in Nitrogen-Fixing Endosymbiotic Bacteria. PMID:32164262
Response of transgenic tobacco overexpressing the CchGLP gene to cadmium and aluminium: phenotypic and microRNAs expression changes. PMID:32158116
High Contiguity De Novo Genome Sequence Assembly of Trifoliate Yam (Dioscorea dumetorum) Using Long Read Sequencing. PMID:32143301
Molecular Mechanisms Underpinning Aggregation in Acidiphilium sp. C61 Isolated from Iron-Rich Pelagic Aggregates. PMID:32106516
Chromosomal-level assembly of Juglans sigillata genome using Nanopore, BioNano, and Hi-C analysis. PMID:32101299
Whole genome sequencing and comparative genomic analysis of oleaginous red yeast Sporobolomyces pararoseus NGR identifies candidate genes for biotechnological potential and ballistospores-shooting. PMID:32093624
Transcriptomics at Maize Embryo/Endosperm Interfaces Identifies a Transcriptionally Distinct Endosperm Subdomain Adjacent to the Embryo Scutellum. PMID:32086366
Animal, Fungi, and Plant Genome Sequences Harbor Different Non-Canonical Splice Sites. PMID:32085510
Whole-genome sequencing and analysis of the Chinese herbal plant Gelsemium elegans. PMID:32082980
Chromosome-level assemblies of multiple Arabidopsis genomes reveal hotspots of rearrangements with altered evolutionary dynamics. PMID:32080174
Differential Gene Expression between Fungal Mating Types Is Associated with Sequence Degeneration. PMID:32058544
Transcriptome profiling of differentially expressed genes in cytoplasmic male-sterile line and its fertility restorer line in pigeon pea (Cajanus cajan L.). PMID:32054447
Chromatin-enriched RNAs mark active and repressive cis-regulation: An analysis of nuclear RNA-seq. PMID:32040509
HAMAP as SPARQL rules-A portable annotation pipeline for genomes and proteomes. PMID:32034905
Keth-seq for transcriptome-wide RNA structure mapping. PMID:32015521
RNAconTest: comparing tools for noncoding RNA multiple sequence alignment based on structural consistency. PMID:32005745
Classification of Riboswitch Families Using Block Location-Based Feature Extraction (BLBFE) Method. PMID:32002367
Complete Genome Sequence of XaF13, a Novel Bacteriophage of Xanthomonas vesicatoria from Mexico. PMID:32001564
Giant virus diversity and host interactions through global metagenomics. PMID:31968354
Defining lncRNAs Correlated with CHO Cell Growth and IgG Productivity by RNA-Seq. PMID:31962234
Computational screening of miRNAs and their targets in leaves of Hypericum spp. by transcriptome-mining: a pilot study. PMID:31938871
Characterizing the ribosomal tandem repeat and its utility as a DNA barcode in lichen-forming fungi. PMID:31906844
Translation of the intrinsically disordered protein α-synuclein is inhibited by a small molecule targeting its structured mRNA. PMID:31900363
Small noncoding RNA discovery and profiling with sRNAtools based on high-throughput sequencing. PMID:31885040
Analysis of Soybean Long Non-Coding RNAs Reveals a Subset of Small Peptide-Coding Transcripts. PMID:31882456
Fast and accurate microRNA search using CNN. PMID:31881831
Accurate inference of the full base-pairing structure of RNA by deep mutational scanning and covariation-induced deviation of activity. PMID:31872260
Regulatory context drives conservation of glycine riboswitch aptamers. PMID:31860665
Tissue-specific transposon-associated small RNAs in the gymnosperm tree, Norway spruce. PMID:31856707
TRANSNAP: a web database providing comprehensive information on Japanese pear transcriptome. PMID:31831861
Genome-wide evolution of wobble base-pairing nucleotides of branchpoint motifs with increasing organismal complexity. PMID:31814500
GraphClust2: Annotation and discovery of structured RNAs with scalable and accessible integrative clustering. PMID:31808801
De Novo Genome Assembly of Populus simonii Further Supports That Populus simonii and Populus trichocarpa Belong to Different Sections. PMID:31806765
RNA-Puzzles toolkit: a computational resource of RNA 3D structure benchmark datasets, structure manipulation, and evaluation tools. PMID:31799609
A Bioinformatic Method For Identifying Group II Introns In Organella Genomes. PMID:31798632
Whole-genome comparison between the type strain of Halobacterium salinarum (DSM 3754T ) and the laboratory strains R1 and NRC-1. PMID:31797576
Computational search for UV radiation resistance strategies in Deinococcus swuensis isolated from Paramo ecosystems. PMID:31790419
Hybrid de novo transcriptome assembly of poinsettia (Euphorbia pulcherrima Willd. Ex Klotsch) bracts. PMID:31775622
Comparative analysis of small RNAs released by the filarial nematode Litomosoides sigmodontis in vitro and in vivo. PMID:31770367
Identification and Evaluation of Long Noncoding RNAs in Response to Handling Stress in Red Cusk-Eel (Genypterus chilensis) via RNA-seq. PMID:31748906
RNA base-pairing complexity in living cells visualized by correlated chemical probing. PMID:31744869
Structural basis of amino acid surveillance by higher-order tRNA-mRNA interactions. PMID:31740854
SyntDB: defining orthologues of human long noncoding RNAs across primates. PMID:31728519
Mapping the RNA structural landscape of viral genomes. PMID:31711930
MGnify: the microbiome analysis resource in 2020. PMID:31696235
Ensembl 2020. PMID:31691826
PDBe: improved findability of macromolecular structure data in the PDB. PMID:31691821
An Integrated Pipeline for Annotation and Visualization of Metagenomic Contigs. PMID:31681429
MaGenDB: a functional genomics hub for Malvaceae plants. PMID:31665439
Recurrent noncoding U1 snRNA mutations drive cryptic splicing in SHH medulloblastoma. PMID:31664194
Transcriptome-wide identification and characterization of the Sox gene family and microsatellites for Corbicula fluminea. PMID:31660260
A unicellular relative of animals generates a layer of polarized cells by actomyosin-dependent cellularization. PMID:31647412
A semi-supervised machine learning framework for microRNA classification. PMID:31639051
Long noncoding RNAs sustain high expression levels of exogenous octamer-binding protein 4 by sponging regulatory microRNAs during cellular reprogramming. PMID:31624145
Integrated Analysis of Small RNA, Transcriptome and Degradome Sequencing Provides New Insights into Floral Development and Abscission in Yellow Lupine (Lupinus luteus L.). PMID:31623090
Identification of Long Non-Coding RNA-Associated Competing Endogenous RNA Network in the Differentiation of Chicken Preadipocytes. PMID:31614854
Differential expression of miR-4492 and IL-10 is involved in chronic rhinosinusitis with nasal polyps. PMID:31611936
Continuous salt stress-induced long non-coding RNAs and DNA methylation patterns in soybean roots. PMID:31606033
snoDB: an interactive database of human snoRNA sequences, abundance and interactions. PMID:31598696
A rhlI 5' UTR-Derived sRNA Regulates RhlR-Dependent Quorum Sensing in Pseudomonas aeruginosa. PMID:31594819
Draft genome sequence of Solanum aethiopicum provides insights into disease resistance, drought tolerance, and the evolution of the genome. PMID:31574156
The Transcription Unit Architecture of Streptomyces lividans TK24. PMID:31555254
Emergence of Hierarchical Modularity in Evolving Networks Uncovered by Phylogenomic Analysis. PMID:31523127
ShaKer: RNA SHAPE prediction using graph kernel. PMID:31510707
New perspectives on the plant PARP family: Arabidopsis PARP3 is inactive, and PARP1 exhibits predominant poly (ADP-ribose) polymerase activity in response to DNA damage. PMID:31426748
Dual RNA-seq in Streptococcus pneumoniae Infection Reveals Compartmentalized Neutrophil Responses in Lung and Pleural Space. PMID:31409659
A conserved RNA structural motif for organizing topology within picornaviral internal ribosome entry sites. PMID:31399592
Characterization of novel small RNAs (sRNAs) contributing to the desiccation response of Salmonella enterica serovar Typhimurium. PMID:31390935
Multi-view Co-training for microRNA Prediction. PMID:31358877
Predicting functional long non-coding RNAs validated by low throughput experiments. PMID:31345106
De novo assembly of a chromosome-level reference genome of red-spotted grouper (Epinephelus akaara) using nanopore sequencing and Hi-C. PMID:31325912
Discovering and Constructing ceRNA-miRNA-Target Gene Regulatory Networks during Anther Development in Maize. PMID:31311189
De novo assembly of the goldfish (Carassius auratus) genome and the evolution of genes after whole-genome duplication. PMID:31249862
Using Rosetta for RNA homology modeling. PMID:31239046
Identification and Characterization of microRNAs and Their Predicted Functions in Biomineralization in the Pearl Oyster (Pinctada fucata). PMID:31212990
Whole-Genome Sequence of Brucella melitensis Strain B7, Isolated from a Blood Sample of a Brucellosis Patient from Hulunbuir, Inner Mongolia, China. PMID:31196914
RNA-align: quick and accurate alignment of RNA 3D structures based on size-independent TM-scoreRNA. PMID:31161212
Recompleting the Caenorhabditis elegans genome. PMID:31123080
A chromosome-level sequence assembly reveals the structure of the Arabidopsis thaliana Nd-1 genome and its gene set. PMID:31112551
Bacterial Community Succession, Transmigration, and Differential Gene Transcription in a Controlled Vertebrate Decomposition Model. PMID:31057499
The genome of cultivated peanut provides insight into legume karyotypes, polyploid evolution and crop domestication. PMID:31043757
rPredictorDB: a predictive database of individual secondary structures of RNAs and their formatted plots. PMID:31032840
Comparative Transcriptomic Profiling of Yersinia enterocolitica O:3 and O:8 Reveals Major Expression Differences of Fitness- and Virulence-Relevant Genes Indicating Ecological Separation. PMID:31020044
The EMBL-EBI search and sequence analysis tools APIs in 2019. PMID:30976793
How to benchmark RNA secondary structure prediction accuracy. PMID:30951834
Increased versatility despite reduced molecular complexity: evolution, structure and function of metazoan splicing factor PRPF39. PMID:30949712
Nucleomorph Small RNAs in Cryptophyte and Chlorarachniophyte Algae. PMID:30949682
The sncRNA Zoo: a repository for circulating small noncoding RNAs in animals. PMID:30937442
Phylogenetic Analysis with Improved Parameters Reveals Conservation in lncRNA Structures. PMID:30890332
Refining the Pneumococcal Competence Regulon by RNA Sequencing. PMID:30885934
A reference-grade wild soybean genome. PMID:30872580
Multiple Genome Sequences of Lactobacillus pentosus Strains Isolated from Biofilms on the Skin of Fermented Green Table Olives. PMID:30834370
Automated, customizable and efficient identification of 3D base pair modules with BayesPairing. PMID:30828711
Origin and evolution of the octoploid strawberry genome. PMID:30804557
A new genomic blueprint of the human gut microbiota. PMID:30745586
Genome structure and evolution of Antirrhinum majus L. PMID:30692677
Tissue-Specific Transcriptome Analysis Reveals Candidate Genes for Terpenoid and Phenylpropanoid Metabolism in the Medicinal Plant Ferula assafoetida. PMID:30679248
A High-quality Draft Genome Assembly of Sinella curviseta: A Soil Model Organism (Collembola). PMID:30668671
The Role of UV-B light on Small RNA Activity During Grapevine Berry Development. PMID:30647106
Expanding the miRNA Repertoire in Atlantic Salmon; Discovery of IsomiRs and miRNAs Highly Expressed in Different Tissues and Developmental Stages. PMID:30641951
The 26th annual Nucleic Acids Research database issue and Molecular Biology Database Collection. PMID:30626175
The structure of the SAM/SAH-binding riboswitch. PMID:30590743
Design and application of a novel two-amplicon approach for defining eukaryotic microbiota. PMID:30572961
The chromosome-level quality genome provides insights into the evolution of the biosynthesis genes for aroma compounds of Osmanthus fragrans. PMID:30479779
Hidden diversity of soil giant viruses. PMID:30451857
IRSOM, a reliable identifier of ncRNAs based on supervised self-organizing maps with rejection. PMID:30423081
RNAcentral: a hub of information for non-coding RNA sequences. PMID:30395267
Knock-Down of a Novel snoRNA in Tetrahymena Reveals a Dual Role in 5.8S rRNA Processing and Generation of a 26S rRNA Fragment. PMID:30380771
The Distinctive Regulation of Cyanobacterial Glutamine Synthetase. PMID:30373240
GENCODE reference annotation for the human and mouse genomes. PMID:30357393
Identification of a Novel Small RNA srvg23535 in Vibrio alginolyticus ZJ-T and Its Characterization With Phenotype MicroArray Technology. PMID:30349521
MGH: a genome hub for the medicinal plant maca (Lepidium meyenii). PMID:30339215
IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes. PMID:30289528
Expression Profile of Glossina pallidipes MicroRNAs During Symptomatic and Asymptomatic Infection With Glossina pallidipes Salivary Gland Hypertrophy Virus (Hytrosavirus). PMID:30233523
Challenges and approaches to predicting RNA with multiple functional structures. PMID:30143552
Complete genome of streamlined marine actinobacterium Pontimonas salivibrio strain CL-TW6T adapted to coastal planktonic lifestyle. PMID:30134835
Deep genome annotation of the opportunistic human pathogen Streptococcus pneumoniae D39. PMID:30107613
The State of Long Non-Coding RNA Biology. PMID:30103474
Comparative transcriptomics of limb regeneration: Identification of conserved expression changes among three species of Ambystoma. PMID:30092345
Genomic and Biotechnological Characterization of the Heavy-Metal Resistant, Arsenic-Oxidizing Bacterium Ensifer sp. M14. PMID:30060533
High-throughput determination of RNA structures. PMID:30054568
Transgenic microRNA-14 rice shows high resistance to rice stem borer. PMID:30044049
Examination of novel Aureobasidium pullulans isolates dominating apple microflora and assessing their potential for apple juice spoilage. PMID:29998388
A comprehensive review of web-based resources of non-coding RNAs for plant science research. PMID:29989090
aliFreeFold: an alignment-free approach to predict secondary structure from homologous RNA sequences. PMID:29949960
Non-Coding RNA Analysis Using the Rfam Database. PMID:29927072
RNA Framework: an all-in-one toolkit for the analysis of RNA structures and post-transcriptional modifications. PMID:29893890
Group I introns are widespread in archaea. PMID:29788499
De novo genome assembly of the red silk cotton tree (Bombax ceiba). PMID:29757382
Structural biology data archiving - where we are and what lies ahead. PMID:29749603
Draft Genome Sequences of Six Lactobacillus pentosus Strains Isolated from Brines of Traditionally Fermented Spanish-Style Green Table Olives. PMID:29724847
Complete Genome Sequence of the Heavy-Metal-Tolerant Endophytic Type Strain of Salinicola tamaricis. PMID:29674561
Complete Genome Sequence of Agrobacterium tumefaciens 1D1609. PMID:29674541
Surprising Sequence Effects on GU Closure of Symmetric 2 × 2 Nucleotide RNA Internal Loops. PMID:29570276
CMV: visualization for RNA and protein family models and their comparisons. PMID:29554223
A Genomic View of Alternative Splicing of Long Non-coding RNAs during Rice Seed Development Reveals Extensive Splicing and lncRNA Gene Families. PMID:29467783
The 2018 Nucleic Acids Research database issue and the online molecular biology database collection. PMID:29316735
The European Bioinformatics Institute in 2017: data coordination and integration. PMID:29186510
http://dx.doi.org/10.1093/nar/gkaa1047
http://dx.doi.org/10.1093/nar/gkx1038
http://dx.doi.org/10.1093/nar/gku1063

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More detailed information about this field from each metasource.

cis element
metasource: Fairsharing.org
version: FAIRsharing.org: Rfam; Rfam; DOI: https://doi.org/10.25504/FAIRsharing.fex4c8; Last edited: Feb. 13, 2020, 3:34 p.m.; Last accessed: Jan 03 2022 7:07 p.m.

curated information
metasource: Fairsharing.org
version: FAIRsharing.org: Rfam; Rfam; DOI: https://doi.org/10.25504/FAIRsharing.fex4c8; Last edited: Feb. 13, 2020, 3:34 p.m.; Last accessed: Jan 03 2022 7:07 p.m.

multiple sequence alignment
metasource: Fairsharing.org
version: FAIRsharing.org: Rfam; Rfam; DOI: https://doi.org/10.25504/FAIRsharing.fex4c8; Last edited: Feb. 13, 2020, 3:34 p.m.; Last accessed: Jan 03 2022 7:07 p.m.

non-coding rna
metasource: Fairsharing.org
version: FAIRsharing.org: Rfam; Rfam; DOI: https://doi.org/10.25504/FAIRsharing.fex4c8; Last edited: Feb. 13, 2020, 3:34 p.m.; Last accessed: Jan 03 2022 7:07 p.m.

rna splicing
metasource: Fairsharing.org
version: FAIRsharing.org: Rfam; Rfam; DOI: https://doi.org/10.25504/FAIRsharing.fex4c8; Last edited: Feb. 13, 2020, 3:34 p.m.; Last accessed: Jan 03 2022 7:07 p.m.

regulatory region
metasource: Fairsharing.org
version: FAIRsharing.org: Rfam; Rfam; DOI: https://doi.org/10.25504/FAIRsharing.fex4c8; Last edited: Feb. 13, 2020, 3:34 p.m.; Last accessed: Jan 03 2022 7:07 p.m.

ribonucleic acid
metasource: Fairsharing.org
version: FAIRsharing.org: Rfam; Rfam; DOI: https://doi.org/10.25504/FAIRsharing.fex4c8; Last edited: Feb. 13, 2020, 3:34 p.m.; Last accessed: Jan 03 2022 7:07 p.m.

rna sequence databases
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

functional, regulatory and non-coding rna
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:13.116598

gene and protein families
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:13.116598

rna
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:13.116598

cis element multiple sequence alignment non-coding rna rna splicing regulatory region rna rna sequence functional, regulatory and non-coding rna gene and protein families rna

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Pfam

RNAcentral

ncRNAs database

RMBase

lncRNAdb

NONCODE

RNArchitecture

Dfam

cncRNAdb

PANDIT

The RNA Modification Database (RNAMDB)

RNA SSTRAND

RNALocate

Nucleic Acid Phylogenetic Profile

ConsRM

Database of small human non-coding RNAs

Non-coding RNA Ontology

LNCipedia

RAID

snOPY