PubMed Mentions

The links below are to publications on PubMed referring to TAPIR. This list is gathered weekly from PubMed automatically.

Publication/References
Diversity, expression and mRNA targeting abilities of Argonaute-targeting miRNAs among selected vascular plants. Description: Jagtap, Soham, et al. Diversity, expression and mRNA targeting abilities of Argonaute-targeting miRNAs among selected vascular plants. ''BMC Genomics''. 2014 Dec 2; '''15''': 1049
B-HIT - A Tool for Harvesting and Indexing Biodiversity Data. Description: Kelbert, Patricia, et al. B-HIT - A Tool for Harvesting and Indexing Biodiversity Data. ''PLoS One''. 2015; '''10''' (11):e0142240
Dicer-Dependent Biogenesis of Small RNAs and Evidence for MicroRNA-Like RNAs in the Penicillin Producing Fungus Penicillium chrysogenum. Description: Dahlmann, Tim A, et al. Dicer-Dependent Biogenesis of Small RNAs and Evidence for MicroRNA-Like RNAs in the Penicillin Producing Fungus Penicillium chrysogenum. ''PLoS One''. 2015; '''10''' (5):e0125989
Endogenous target mimics down-regulate miR160 mediation of ARF10, -16, and -17 cleavage during somatic embryogenesis in Dimocarpus longan Lour. Description: Lin, Yuling, et al. Endogenous target mimics down-regulate miR160 mediation of ARF10, -16, and -17 cleavage during somatic embryogenesis in Dimocarpus longan Lour. ''Front Plant Sci''. 2015; '''6''': 956
GraP: platform for functional genomics analysis of Gossypium raimondii. Description: Zhang, Liwei, et al. GraP: platform for functional genomics analysis of Gossypium raimondii. ''Database (Oxford)''. 2015; '''2015''': bav047
Identification and analysis of unitary loss of long-established protein-coding genes in Poaceae shows evidences for biased gene loss and putatively functional transcription of relics. Description: Zhao, Yi, et al. Identification and analysis of unitary loss of long-established protein-coding genes in Poaceae shows evidences for biased gene loss and putatively functional transcription of relics. ''BMC Evol Biol''. 2015 Apr 18; '''15''': 66
An integrative approach to identify hexaploid wheat miRNAome associated with development and tolerance to abiotic stress. Description: Agharbaoui, Zahra, et al. An integrative approach to identify hexaploid wheat miRNAome associated with development and tolerance to abiotic stress. ''BMC Genomics''. 2015 Apr 24; '''16''': 339
microRNAs and the evolution of complex multicellularity: identification of a large, diverse complement of microRNAs in the brown alga Ectocarpus. Description: Tarver, James E, et al. microRNAs and the evolution of complex multicellularity: identification of a large, diverse complement of microRNAs in the brown alga Ectocarpus. ''Nucleic Acids Res''. 2015 Jul 27; '''43''' (13):6384-98
Small RNAs from the wheat stripe rust fungus (Puccinia striiformis f.sp. tritici). Description: Mueth, Nicholas A, et al. Small RNAs from the wheat stripe rust fungus (Puccinia striiformis f.sp. tritici). ''BMC Genomics''. 2015 Sep 21; '''16''': 718
Small RNAs in Plant Responses to Abiotic Stresses: Regulatory Roles and Study Methods. Description: Ku, Yee-Shan, et al. Small RNAs in Plant Responses to Abiotic Stresses: Regulatory Roles and Study Methods. ''Int J Mol Sci''. 2015 Oct 15; '''16''' (10):24532-54
Phylogenomic methods outperform traditional multi-locus approaches in resolving deep evolutionary history: a case study of formicine ants. Description: Blaimer, Bonnie B, et al. Phylogenomic methods outperform traditional multi-locus approaches in resolving deep evolutionary history: a case study of formicine ants. ''BMC Evol Biol''. 2015 Dec 4; '''15''': 271
Identification of MicroRNA Targets of Capsicum spp. Using MiRTrans-a Trans-Omics Approach. Description: Zhang, Lu, et al. Identification of MicroRNA Targets of Capsicum spp. Using MiRTrans-a Trans-Omics Approach. ''Front Plant Sci''. 2017; '''8''': 495
Experience With Direct-to-Patient Recruitment for Enrollment Into a Clinical Trial in a Rare Disease: A Web-Based Study. Description: Krischer, Jeffrey, et al. Experience With Direct-to-Patient Recruitment for Enrollment Into a Clinical Trial in a Rare Disease: A Web-Based Study. ''J Med Internet Res''. 2017 Feb 28; '''19''' (2):e50
Transcriptome assembly in Suaeda aralocaspica to reveal the distinct temporal gene/miRNA alterations between the dimorphic seeds during germination. Description: Wang, Lei, et al. Transcriptome assembly in Suaeda aralocaspica to reveal the distinct temporal gene/miRNA alterations between the dimorphic seeds during germination. ''BMC Genomics''. 2017 Oct 19; '''18''' (1):806
A 3D two-point method for whole-brain water content and relaxation time mapping: Comparison with gold standard methods. Description: Schall, Melissa, et al. A 3D two-point method for whole-brain water content and relaxation time mapping: Comparison with gold standard methods. ''PLoS One''. 2018; '''13''' (8):e0201013
Noise and biases in genomic data may underlie radically different hypotheses for the position of Iguania within Squamata. Description: Mongiardino Koch, Nicolas, et al. Noise and biases in genomic data may underlie radically different hypotheses for the position of Iguania within Squamata. ''PLoS One''. 2018; '''13''' (8):e0202729
MiRNA160 is associated with local defense and systemic acquired resistance against Phytophthora infestans infection in potato. Description: Natarajan, Bhavani, et al. MiRNA160 is associated with local defense and systemic acquired resistance against Phytophthora infestans infection in potato. ''J Exp Bot''. 2018 Apr 9; '''69''' (8):2023-2036
Genome-wide identification and characterization of long non-coding RNAs involved in the early somatic embryogenesis in Dimocarpus longan Lour. Description: Chen, Yan, et al. Genome-wide identification and characterization of long non-coding RNAs involved in the early somatic embryogenesis in Dimocarpus longan Lour. ''BMC Genomics''. 2018 Nov 6; '''19''' (1):805
Analysis of miRNAs in Two Wheat Cultivars Infected With Puccinia striiformis f. sp. tritici. Description: Ramachandran, Sowmya R, et al. Analysis of miRNAs in Two Wheat Cultivars Infected With Puccinia striiformis f. sp. tritici. ''Front Plant Sci''. 2019; '''10''': 1574
Mining Magnaporthe oryzae sRNAs With Potential Transboundary Regulation of Rice Genes Associated With Growth and Defense Through Expression Profile Analysis of the Pathogen-Infected Rice. Description: Zhang, Hao, et al. Mining Magnaporthe oryzae sRNAs With Potential Transboundary Regulation of Rice Genes Associated With Growth and Defense Through Expression Profile Analysis of the Pathogen-Infected Rice. ''Front Genet''. 2019; '''10''': 296
Transcriptome and Phytochemical Analyses Provide New Insights Into Long Non-Coding RNAs Modulating Characteristic Secondary Metabolites of Oolong Tea (Camellia sinensis) in Solar-Withering. Description: Zhu, Chen, et al. Transcriptome and Phytochemical Analyses Provide New Insights Into Long Non-Coding RNAs Modulating Characteristic Secondary Metabolites of Oolong Tea (Camellia sinensis) in Solar-Withering. ''Front Plant Sci''. 2019; '''10''': 1638
Identification and characterization of pineapple leaf lncRNAs in crassulacean acid metabolism (CAM) photosynthesis pathway. Description: Bai, Youhuang, et al. Identification and characterization of pineapple leaf lncRNAs in crassulacean acid metabolism (CAM) photosynthesis pathway. ''Sci Rep''. 2019 Apr 30; '''9''' (1):6658
Discovering and Constructing ceRNA-miRNA-Target Gene Regulatory Networks during Anther Development in Maize. Description: Li, Ziwen, et al. Discovering and Constructing ceRNA-miRNA-Target Gene Regulatory Networks during Anther Development in Maize. ''Int J Mol Sci''. 2019 Jul 15; '''20''' (14):
Genome-wide exploration and characterization of miR172/euAP2 genes in Brassica napus L. for likely role in flower organ development. Description: Wang, Tengyue, et al. Genome-wide exploration and characterization of miR172/euAP2 genes in Brassica napus L. for likely role in flower organ development. ''BMC Plant Biol''. 2019 Aug 1; '''19''' (1):336
miR828 and miR858 regulate VvMYB114 to promote anthocyanin and flavonol accumulation in grapes. Description: Tirumalai, Varsha, et al. miR828 and miR858 regulate VvMYB114 to promote anthocyanin and flavonol accumulation in grapes. ''J Exp Bot''. 2019 Sep 24; '''70''' (18):4775-4792
Characteristics of a cohort of high-risk men who have sex with men on pre-exposure prophylaxis reporting transgender sexual partners. Description: Hassan, Adiba, et al. Characteristics of a cohort of high-risk men who have sex with men on pre-exposure prophylaxis reporting transgender sexual partners. ''Medicine (Baltimore)''. 2019 Dec; '''98''' (50):e18232
SIGS vs HIGS: a study on the efficacy of two dsRNA delivery strategies to silence Fusarium FgCYP51 genes in infected host and non-host plants. Description: Koch, Aline, et al. SIGS vs HIGS: a study on the efficacy of two dsRNA delivery strategies to silence Fusarium FgCYP51 genes in infected host and non-host plants. ''Mol Plant Pathol''. 2019 Dec; '''20''' (12):1636-1644
Pesticide application has little influence on coding and non-coding gene expressions in rice. Description: Muhammad, Sajid, et al. Pesticide application has little influence on coding and non-coding gene expressions in rice. ''BMC Genomics''. 2019 Dec 23; '''20''' (1):1009
Comprehensive Atlas of Wheat (Triticum aestivum L.) AUXIN RESPONSE FACTOR Expression During Male Reproductive Development and Abiotic Stress. Description: Xu, Lei, et al. Comprehensive Atlas of Wheat (Triticum aestivum L.) AUXIN RESPONSE FACTOR Expression During Male Reproductive Development and Abiotic Stress. ''Front Plant Sci''. 2020; '''11''': 586144
Comparative Analysis of miRNA Expression Profiles Between Heat-Tolerant and Heat-Sensitive Genotypes of Flowering Chinese Cabbage Under Heat Stress Using High-Throughput Sequencing. Description: Ahmed, Waqas, et al. Comparative Analysis of miRNA Expression Profiles Between Heat-Tolerant and Heat-Sensitive Genotypes of Flowering Chinese Cabbage Under Heat Stress Using High-Throughput Sequencing. ''Genes (Basel)''. 2020 Feb 28; '''11''' (3):
A novel approach to conducting clinical trials in the community setting: utilizing patient-driven platforms and social media to drive web-based patient recruitment. Description: Applequist, Janelle, et al. A novel approach to conducting clinical trials in the community setting: utilizing patient-driven platforms and social media to drive web-based patient recruitment. ''BMC Med Res Methodol''. 2020 Mar 13; '''20''' (1):58
Oomycete small RNAs bind to the plant RNA-induced silencing complex for virulence. Description: Dunker, Florian, et al. Oomycete small RNAs bind to the plant RNA-induced silencing complex for virulence. ''Elife''. 2020 May 22; '''9''':
Plant-pathogen interactions: MicroRNA-mediated trans-kingdom gene regulation in fungi and their host plants. Description: Mathur, Monika, et al. Plant-pathogen interactions: MicroRNA-mediated trans-kingdom gene regulation in fungi and their host plants. ''Genomics''. 2020 Sep; '''112''' (5):3021-3035
Gene regulatory effects of a large chromosomal inversion in highland maize. Description: Crow, Taylor, et al. Gene regulatory effects of a large chromosomal inversion in highland maize. ''PLoS Genet''. 2020 Dec; '''16''' (12):e1009213
Computational Identification of miRNAs and Temperature-Responsive lncRNAs From Mango (Mangifera indica L.). Description: Moh, Nann Miky Moh, et al. Computational Identification of miRNAs and Temperature-Responsive lncRNAs From Mango (Mangifera indica L.). ''Front Genet''. 2021; '''12''': 607248
Fusarium graminearum DICER-like-dependent sRNAs are required for the suppression of host immune genes and full virulence. Description: Werner, Bernhard Timo, et al. Fusarium graminearum DICER-like-dependent sRNAs are required for the suppression of host immune genes and full virulence. ''PLoS One''. 2021; '''16''' (8):e0252365
Interplay between miRNAs and lncRNAs: Mode of action and biological roles in plant development and stress adaptation. Description: Meng, Xiangxiang, et al. Interplay between miRNAs and lncRNAs: Mode of action and biological roles in plant development and stress adaptation. ''Comput Struct Biotechnol J''. 2021; '''19''': 2567-2574
The long noncoding RNA FRILAIR regulates strawberry fruit ripening by functioning as a noncanonical target mimic. Description: Tang, Yajun, et al. The long noncoding RNA FRILAIR regulates strawberry fruit ripening by functioning as a noncanonical target mimic. ''PLoS Genet''. 2021 Mar; '''17''' (3):e1009461
Phytohormone and integrated mRNA and miRNA transcriptome analyses and differentiation of male between hermaphroditic floral buds of andromonoecious Diospyros kaki Thunb. Description: Li, Huawei, et al. Phytohormone and integrated mRNA and miRNA transcriptome analyses and differentiation of male between hermaphroditic floral buds of andromonoecious Diospyros kaki Thunb. ''BMC Genomics''. 2021 Mar 23; '''22''' (1):203
Investigation of long non-coding RNAs as regulatory players of grapevine response to powdery and downy mildew infection. Description: Bhatia, Garima, et al. Investigation of long non-coding RNAs as regulatory players of grapevine response to powdery and downy mildew infection. ''BMC Plant Biol''. 2021 Jun 8; '''21''' (1):265
Waterlogging-Stress-Responsive LncRNAs, Their Regulatory Relationships with miRNAs and Target Genes in Cucumber (Cucumis sativus L.). Description: Keska, Kinga, et al. Waterlogging-Stress-Responsive LncRNAs, Their Regulatory Relationships with miRNAs and Target Genes in Cucumber (Cucumis sativus L.). ''Int J Mol Sci''. 2021 Jul 30; '''22''' (15):
Robust optimization of SWATH-MS workflow for human blood serum proteome analysis using a quality by design approach. Description: Serrano-Blesa, Edith, et al. Robust optimization of SWATH-MS workflow for human blood serum proteome analysis using a quality by design approach. ''Clin Proteomics''. 2021 Aug 12; '''18''' (1):20
Retrotransposons as pathogenicity factors of the plant pathogenic fungus Botrytis cinerea. Description: Porquier, Antoine, et al. Retrotransposons as pathogenicity factors of the plant pathogenic fungus Botrytis cinerea. ''Genome Biol''. 2021 Aug 16; '''22''' (1):225
Genome-Wide Discovery of miRNAs with Differential Expression Patterns in Responses to Salinity in the Two Contrasting Wheat Cultivars. Description: Zeeshan, Muhammad, et al. Genome-Wide Discovery of miRNAs with Differential Expression Patterns in Responses to Salinity in the Two Contrasting Wheat Cultivars. ''Int J Mol Sci''. 2021 Nov 21; '''22''' (22):
Genome-wide investigation of microRNAs and expression profiles during rhizome development in ginger (Zingiber officinale Roscoe). Description: Xing, Haitao, et al. Genome-wide investigation of microRNAs and expression profiles during rhizome development in ginger (Zingiber officinale Roscoe). ''BMC Genomics''. 2022 Jan 13; '''23''' (1):49
Degradome comparison between wild and cultivated rice identifies differential targeting by miRNAs. Description: Swetha, Chenna, et al. Degradome comparison between wild and cultivated rice identifies differential targeting by miRNAs. ''BMC Genomics''. 2022 Jan 14; '''23''' (1):53
Comparative Small RNA and Degradome Sequencing Provides Insights into Antagonistic Interactions in the Biocontrol Fungus Clonostachys rosea. Description: Piombo, Edoardo, et al. Comparative Small RNA and Degradome Sequencing Provides Insights into Antagonistic Interactions in the Biocontrol Fungus Clonostachys rosea. ''Appl Environ Microbiol''. 2022 Jul 12; '''88''' (13):e0064322
Genome-Wide Identification and Characterization of the NF-YA Gene Family and Its Expression in Response to Different Nitrogen Forms in Populus x canescens. Description: Zhou, Jing, et al. Genome-Wide Identification and Characterization of the NF-YA Gene Family and Its Expression in Response to Different Nitrogen Forms in Populus x canescens. ''Int J Mol Sci''. 2022 Sep 23; '''23''' (19):
miR482f and miR482c-5p from edible plant-derived foods inhibit the expression of pro-inflammatory genes in human THP-1 macrophages. Description: Diez-Sainz, Ester, et al. miR482f and miR482c-5p from edible plant-derived foods inhibit the expression of pro-inflammatory genes in human THP-1 macrophages. ''Front Nutr''. 2023; '''10''': 1287312
Viral synergism suppresses R gene-mediated resistance by impairing downstream defense mechanisms in soybean. Description: Alazem, Mazen, et al. Viral synergism suppresses R gene-mediated resistance by impairing downstream defense mechanisms in soybean. ''Plant Physiol''. 2023 Aug 3; '''192''' (4):3088-3105
Concurrent, Convergent, and Discriminant Validity of the DSM-5 Section III Psychopathy Specifier. Description: Fuller, Erin K, et al. Concurrent, Convergent, and Discriminant Validity of the DSM-5 Section III Psychopathy Specifier. ''Assessment''. 2023 Sep; '''30''' (6):1790-1810
TAPIR: a T-cell receptor language model for predicting rare and novel targets. Description: Fast, Ethan, et al. TAPIR: a T-cell receptor language model for predicting rare and novel targets. ''bioRxiv''. 2023 Sep 15;
Integrated microRNA and whole-transcriptome sequencing reveals the involvement of small and long non-coding RNAs in the fiber growth of ramie plant. Description: Fu, Yafen, et al. Integrated microRNA and whole-transcriptome sequencing reveals the involvement of small and long non-coding RNAs in the fiber growth of ramie plant. ''BMC Genomics''. 2023 Oct 9; '''24''' (1):599
The Identification and Comparative Analysis of Non-Coding RNAs in Spores and Mycelia of Penicillium expansum. Description: Lai, Tongfei, et al. The Identification and Comparative Analysis of Non-Coding RNAs in Spores and Mycelia of Penicillium expansum. ''J Fungi (Basel)''. 2023 Oct 9; '''9''' (10):
Genome-wide identification, stress- and hormone-responsive expression characteristics, and regulatory pattern analysis of Scutellaria baicalensis SbSPLs. Description: Wu, Jia-Wen, et al. Genome-wide identification, stress- and hormone-responsive expression characteristics, and regulatory pattern analysis of Scutellaria baicalensis SbSPLs. ''Plant Mol Biol''. 2024 Feb 16; '''114''' (2):20
Argonaute and Dicer are essential for communication between Trichoderma atroviride and fungal hosts during mycoparasitism. Description: Enriquez-Felix, Eli Efrain, et al. Argonaute and Dicer are essential for communication between Trichoderma atroviride and fungal hosts during mycoparasitism. ''Microbiol Spectr''. 2024 Apr 2; '''12''' (4):e0316523
Mutation mapping of a variegated EMS tomato reveals an FtsH-like protein precursor potentially causing patches of four phenotype classes in the leaves with distinctive internal morphology. Description: Dechkrong, Punyavee, et al. Mutation mapping of a variegated EMS tomato reveals an FtsH-like protein precursor potentially causing patches of four phenotype classes in the leaves with distinctive internal morphology. ''BMC Plant Biol''. 2024 Apr 10; '''24''' (1):265
MicroRNAs from edible plants reach the human gastrointestinal tract and may act as potential regulators of gene expression. Description: Diez-Sainz, Ester, et al. MicroRNAs from edible plants reach the human gastrointestinal tract and may act as potential regulators of gene expression. ''J Physiol Biochem''. 2024 Aug; '''80''' (3):655-670
RNA silencing is a key regulatory mechanism in the biocontrol fungus Clonostachys rosea-wheat interactions. Description: Piombo, Edoardo, et al. RNA silencing is a key regulatory mechanism in the biocontrol fungus Clonostachys rosea-wheat interactions. ''BMC Biol''. 2024 Sep 30; '''22''' (1):219
MYB transcription factors, their regulation and interactions with non-coding RNAs during drought stress in Brassica juncea. Description: Balhara, Rinku, et al. MYB transcription factors, their regulation and interactions with non-coding RNAs during drought stress in Brassica juncea. ''BMC Plant Biol''. 2024 Oct 24; '''24''' (1):999
Mechanism of zju-miR156c-mediated network in regulating witches' broom symptom of Chinese jujube. Description: Wang, Yunjie, et al. Mechanism of zju-miR156c-mediated network in regulating witches' broom symptom of Chinese jujube. ''Mol Plant Pathol''. 2024 Nov; '''25''' (11):e70031
Yerba mate (Ilex paraguariensis) genome provides new insights into convergent evolution of caffeine biosynthesis. Description: Vignale, Federico A, et al. Yerba mate (Ilex paraguariensis) genome provides new insights into convergent evolution of caffeine biosynthesis. ''Elife''. 2025 Jan 8; '''14''':
Transcriptional regulation of miR528-PPO module by miR156 targeted SPLs orchestrates chilling response in banana. Description: Kong, Xiangjin, et al. Transcriptional regulation of miR528-PPO module by miR156 targeted SPLs orchestrates chilling response in banana. ''Mol Hortic''. 2025 Jan 10; '''5''' (1):2