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Alignment-free sequence comparison: benefits, applications, and tools

Genome Biology, 2017-10, Vol.18 (1), p.186-186, Article 186

2017

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NERD, a Plant-Specific GW Protein, Defines an Additional RNAi-Dependent Chromatin-Based Pathway in Arabidopsis

Molecular cell, 2012-10, Vol.48 (1), p.121-132

2012

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Dual Role of the Histone Variant H2A.Z in Transcriptional Regulation of Stress-Response Genes

The Plant cell, 2017-04, Vol.29 (4), p.791-807

2017

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Benchmarking of alignment-free sequence comparison methods

Genome Biology, 2019-07, Vol.20 (1), p.144-144, Article 144

2019

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TaWAK6 encoding wall-associated kinase is involved in wheat resistance to leaf rust similar to adult plant resistance

PloS one, 2020-01, Vol.15 (1), p.e0227713-e0227713

2020

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tRNA-Cys gene clusters exhibit high variability in Arabidopsis thaliana

BMC plant biology, 2023-12, Vol.23 (1), p.623-623, Article 623

2023

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MicroRNA172b-5p/trehalose-6-phosphate synthase module stimulates trehalose synthesis and microRNA172b-3p/AP2-like module accelerates flowering in barley upon drought stress

Frontiers in plant science, 2023-03, Vol.14, p.1124785-1124785

2023

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Sequence Dynamics of Pre-mRNA G-Quadruplexes in Plants

Frontiers in plant science, 2019-06, Vol.10, p.812

2019

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Annotation and profiling of barley GLYCOGEN SYNTHASE3/Shaggy-like genes indicated shift in organ-preferential expression

PloS one, 2018-06, Vol.13 (6), p.e0199364-e0199364

2018

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Comparative analysis of the receptor-like kinase family in Arabidopsis and rice

The Plant cell, 2004-05, Vol.16 (5), p.1220-1234

2004

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5SRNAdb: an information resource for 5S ribosomal RNAs

Nucleic acids research, 2016-01, Vol.44 (D1), p.D180-D183

2016

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Silencing of HvGSK1.1 -A GSK3/SHAGGY-Like Kinase-Enhances Barley ( Hordeum vulgare L.) Growth in Normal and in Salt Stress Conditions

International journal of molecular sciences, 2020-09, Vol.21 (18), p.6616

2020

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The identification of differentially expressed genes in male and female gametophytes of simple thalloid liverwort Pellia endiviifolia sp. B using an RNA-seq approach

Planta, 2020-07, Vol.252 (2), p.21-21, Article 21

2020

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liverwort Pellia endiviifolia shares microtranscriptomic traits that are common to green algae and land plants

The New phytologist, 2015-04, Vol.206 (1), p.352-367

2015

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Local Duplication of TIR-NBS-LRR Gene Marks Clubroot Resistance in Brassica napus cv. Tosca

Frontiers in plant science, 2021-04, Vol.12, p.639631-639631

2021

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Excess nitrogen responsive HvMADS27 transcription factor controls barley root architecture by regulating abscisic acid level

Frontiers in plant science, 2022-09, Vol.13, p.950796-950796

2022

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The plant s1-like nuclease family has evolved a highly diverse range of catalytic capabilities

Plant and cell physiology, 2013-07, Vol.54 (7), p.1064-1078

2013

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Sequence composition and genome organization of maize

Proceedings of the National Academy of Sciences - PNAS, 2004-10, Vol.101 (40), p.14349-14354

2004

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Is Polymorphism in the Apoptosis and Inflammatory Pathway Genes Associated With a Primary Response to Anti-TNF Therapy in Crohn’s Disease Patients?

Frontiers in pharmacology, 2020-08, Vol.11, p.1207-1207

2020

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Promoter-based identification of novel non-coding RNAs reveals the presence of dicistronic snoRNA-miRNA genes in Arabidopsis thaliana

BMC genomics, 2015-11, Vol.16 (1), p.1009-1009, Article 1009

2015

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Efficiency of PacBio long read correction by 2nd generation Illumina sequencing

Genomics (San Diego, Calif.), 2019-01, Vol.111 (1), p.43-49

2019

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mirEX: a platform for comparative exploration of plant pri-miRNA expression data

Nucleic acids research, 2012-01, Vol.40 (Database issue), p.D191-D197

2012

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Taxonomically Restricted Genes in Bacillus may Form Clusters of Homologs and Can be Traced to a Large Reservoir of Noncoding Sequences

Genome biology and evolution, 2023-03, Vol.15 (3)

2023

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TRGdb: a universal resource for the exploration of taxonomically restricted genes in bacteria

Database : the journal of biological databases and curation, 2023-08, Vol.2023

2023

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StarSeeker: an automated tool for mature duplex microRNA sequence identification based on secondary structure modeling of precursor molecule

Journal of biological research (Thessalonikē, Greece), 2018-06, Vol.25 (1), p.1-5, Article 11

2018

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Alignment-free sequence comparison: benefits, applications, and tools

NERD, a Plant-Specific GW Protein, Defines an Additional RNAi-Dependent Chromatin-Based Pathway in Arabidopsis

Dual Role of the Histone Variant H2A.Z in Transcriptional Regulation of Stress-Response Genes

Benchmarking of alignment-free sequence comparison methods

TaWAK6 encoding wall-associated kinase is involved in wheat resistance to leaf rust similar to adult plant resistance

tRNA-Cys gene clusters exhibit high variability in Arabidopsis thaliana

MicroRNA172b-5p/trehalose-6-phosphate synthase module stimulates trehalose synthesis and microRNA172b-3p/AP2-like module accelerates flowering in barley upon drought stress

Sequence Dynamics of Pre-mRNA G-Quadruplexes in Plants

Annotation and profiling of barley GLYCOGEN SYNTHASE3/Shaggy-like genes indicated shift in organ-preferential expression

Comparative analysis of the receptor-like kinase family in Arabidopsis and rice

5SRNAdb: an information resource for 5S ribosomal RNAs

Silencing of HvGSK1.1 -A GSK3/SHAGGY-Like Kinase-Enhances Barley ( Hordeum vulgare L.) Growth in Normal and in Salt Stress Conditions

The identification of differentially expressed genes in male and female gametophytes of simple thalloid liverwort Pellia endiviifolia sp. B using an RNA-seq approach

liverwort Pellia endiviifolia shares microtranscriptomic traits that are common to green algae and land plants

Local Duplication of TIR-NBS-LRR Gene Marks Clubroot Resistance in Brassica napus cv. Tosca

Excess nitrogen responsive HvMADS27 transcription factor controls barley root architecture by regulating abscisic acid level

The plant s1-like nuclease family has evolved a highly diverse range of catalytic capabilities

Sequence composition and genome organization of maize

Is Polymorphism in the Apoptosis and Inflammatory Pathway Genes Associated With a Primary Response to Anti-TNF Therapy in Crohn’s Disease Patients?

Promoter-based identification of novel non-coding RNAs reveals the presence of dicistronic snoRNA-miRNA genes in Arabidopsis thaliana

Efficiency of PacBio long read correction by 2nd generation Illumina sequencing

mirEX: a platform for comparative exploration of plant pri-miRNA expression data

Taxonomically Restricted Genes in Bacillus may Form Clusters of Homologs and Can be Traced to a Large Reservoir of Noncoding Sequences

TRGdb: a universal resource for the exploration of taxonomically restricted genes in bacteria

StarSeeker: an automated tool for mature duplex microRNA sequence identification based on secondary structure modeling of precursor molecule

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