Related references
Note: Only part of the references are listed.Rfam 11.0: 10 years of RNA families
Sarah W. Burge et al.
NUCLEIC ACIDS RESEARCH (2013)
Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis
Andrea Pauli et al.
GENOME RESEARCH (2012)
Long non-coding antisense RNA controls Uchl1 translation through an embedded SINEB2 repeat
Claudia Carrieri et al.
NATURE (2012)
Reference genome sequence of the model plant Setaria
Jeffrey L. Bennetzen et al.
NATURE BIOTECHNOLOGY (2012)
Genome sequence of foxtail millet (Setaria italica) provides insights into grass evolution and biofuel potential
Gengyun Zhang et al.
NATURE BIOTECHNOLOGY (2012)
Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
Cole Trapnell et al.
NATURE PROTOCOLS (2012)
Emerging functional and mechanistic paradigms of mammalian long non-coding RNAs
Victoria A. Moran et al.
NUCLEIC ACIDS RESEARCH (2012)
Genome-Wide Analysis Uncovers Regulation of Long Intergenic Noncoding RNAs in Arabidopsis
Jun Liu et al.
PLANT CELL (2012)
A novel function for a redox-related LEA protein (SAG21/AtLEA5) in root development and biotic stress responses
Faezah Mohd Salleh et al.
PLANT CELL AND ENVIRONMENT (2012)
Effects of Drought on Gene Expression in Maize Reproductive and Leaf Meristem Tissue Revealed by RNA-Seq
Akshay Kakumanu et al.
PLANT PHYSIOLOGY (2012)
Computational Identification and Functional Predictions of Long Noncoding RNA in Zea mays
Susan Boerner et al.
PLOS ONE (2012)
A long noncoding RNA regulates photoperiod-sensitive male sterility, an essential component of hybrid rice
Jihua Ding et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2012)
Widespread dynamic DNA methylation in response to biotic stress
Robert H. Dowen et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2012)
Repeat associated small RNAs vary among parents and following hybridization in maize
Wesley T. Barber et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2012)
Long noncoding RNA: unveiling hidden layer of gene regulatory networks
Eun-Deok Kim et al.
TRENDS IN PLANT SCIENCE (2012)
Quality control and preprocessing of metagenomic datasets
Robert Schmieder et al.
BIOINFORMATICS (2011)
Functional annotation of the transcriptome of Sorghum bicolor in response to osmotic stress and abscisic acid
Diana V. Dugas et al.
BMC GENOMICS (2011)
Identification and characterization of wheat long non-protein coding RNAs responsive to powdery mildew infection and heat stress by using microarray analysis and SBS sequencing
Mingming Xin et al.
BMC PLANT BIOLOGY (2011)
Conserved Function of lincRNAs in Vertebrate Embryonic Development despite Rapid Sequence Evolution
Igor Ulitsky et al.
CELL (2011)
Long non-coding RNAs and chromatin regulation
Filomena De Lucia et al.
CURRENT OPINION IN PLANT BIOLOGY (2011)
Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses
Moran N. Cabili et al.
GENES & DEVELOPMENT (2011)
Setaria viridis and Setaria italica, model genetic systems for the Panicoid grasses
Pinghua Li et al.
JOURNAL OF EXPERIMENTAL BOTANY (2011)
lincRNAs act in the circuitry controlling pluripotency and differentiation
Mitchell Guttman et al.
NATURE (2011)
An siRNA pathway prevents transgenerational retrotransposition in plants subjected to stress
Hidetaka Ito et al.
NATURE (2011)
Gramene database in 2010: updates and extensions
Ken Youens-Clark et al.
NUCLEIC ACIDS RESEARCH (2011)
PlantTFDB 2.0: update and improvement of the comprehensive plant transcription factor database
He Zhang et al.
NUCLEIC ACIDS RESEARCH (2011)
miRBase: integrating microRNA annotation and deep-sequencing data
Ana Kozomara et al.
NUCLEIC ACIDS RESEARCH (2011)
Comparative analysis of drought-responsive transcriptome in Indica rice genotypes with contrasting drought tolerance
Sangram K. Lenka et al.
PLANT BIOTECHNOLOGY JOURNAL (2011)
Changes in 24-nt siRNA levels in Arabidopsis hybrids suggest an epigenetic contribution to hybrid vigor
Michael Groszmann et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)
Vernalization-Mediated Epigenetic Silencing by a Long Intronic Noncoding RNA
Jae Bok Heo et al.
SCIENCE (2011)
Comparative transcriptome analysis of differentially expressed genes in foxtail millet (Setaria italica L.) during dehydration stress
Charu Lata et al.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS (2010)
DEGseq: an R package for identifying differentially expressed genes from RNA-seq data
Likun Wang et al.
BIOINFORMATICS (2010)
BEDTools: a flexible suite of utilities for comparing genomic features
Aaron R. Quinlan et al.
BIOINFORMATICS (2010)
Small RNAs, DNA methylation and transposable elements in wheat
Dario Cantu et al.
BMC GENOMICS (2010)
Long Noncoding RNAs with Enhancer-like Function in Human Cells
Ulf Andersson Orom et al.
CELL (2010)
Function annotation of the rice transcriptome at single-nucleotide resolution by RNA-seq
Tingting Lu et al.
GENOME RESEARCH (2010)
Widespread transcription at neuronal activity-regulated enhancers
Tae-Kyung Kim et al.
NATURE (2010)
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
Cole Trapnell et al.
NATURE BIOTECHNOLOGY (2010)
The developmental dynamics of the maize leaf transcriptome
Pinghua Li et al.
NATURE GENETICS (2010)
APPLICATIONS OF NEXT-GENERATION SEQUENCING Sequencing technologies - the next generation
Michael L. Metzker
NATURE REVIEWS GENETICS (2010)
Establishing, maintaining and modifying DNA methylation patterns in plants and animals
Julie A. Law et al.
NATURE REVIEWS GENETICS (2010)
Survey of the transcriptome of Aspergillus oryzae via massively parallel mRNA sequencing
Bin Wang et al.
NUCLEIC ACIDS RESEARCH (2010)
Time of day shapes Arabidopsis drought transcriptomes
Olivia Wilkins et al.
PLANT JOURNAL (2010)
ABO3, a WRKY transcription factor, mediates plant responses to abscisic acid and drought tolerance in Arabidopsis
Xiaozhi Ren et al.
PLANT JOURNAL (2010)
Genome-wide transcriptome analysis of two maize inbred lines under drought stress
Jun Zheng et al.
PLANT MOLECULAR BIOLOGY (2010)
Long Noncoding RNA as Modular Scaffold of Histone Modification Complexes
Miao-Chih Tsai et al.
SCIENCE (2010)
Proline: a multifunctional amino acid
Laszlo Szabados et al.
TRENDS IN PLANT SCIENCE (2010)
Transcriptome pathways unique to dehydration tolerant relatives of modern wheat
Neslihan Z. Ergen et al.
FUNCTIONAL & INTEGRATIVE GENOMICS (2009)
Novel long non-protein coding RNAs involved in Arabidopsis differentiation and stress responses
Besma Ben Amor et al.
GENOME RESEARCH (2009)
Cold-induced silencing by long antisense transcripts of an Arabidopsis Polycomb target
Szymon Swiezewski et al.
NATURE (2009)
Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals
Mitchell Guttman et al.
NATURE (2009)
Long non-coding RNAs: insights into functions
Tim R. Mercer et al.
NATURE REVIEWS GENETICS (2009)
RNA-Seq: a revolutionary tool for transcriptomics
Zhong Wang et al.
NATURE REVIEWS GENETICS (2009)
A guide to using MapMan to visualize and compare Omics data in plants: a case study in the crop species, Maize
Bjoern Usadel et al.
PLANT CELL AND ENVIRONMENT (2009)
An abiotic stress-responsive bZIP transcription factor from wild and cultivated tomatoes regulates stress-related genes
Monica Yanez et al.
PLANT CELL REPORTS (2009)
Stress-induced changes in the Arabidopsis thaliana transcriptome analyzed using whole-genome tiling arrays
Georg Zeller et al.
PLANT JOURNAL (2009)
Transcriptional Regulatory Networks in Response to Abiotic Stresses in Arabidopsis and Grasses
Kazuo Nakashima et al.
PLANT PHYSIOLOGY (2009)
Toggle involving cis-interfering noncoding RNAs controls variegated gene expression in yeast
Stacie L. Bumgarner et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2009)
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
Ben Langmead et al.
GENOME BIOLOGY (2009)
The common function of a novel subfamily of B-box zinc finger proteins with reference to circadian-associated events in Arabidopsis thaliana
Takeshi Kumagai et al.
BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY (2008)
cDNA-AFLP Analysis Reveals Differential Gene Expression in Response to Salt Stress in Foxtail Millet (Setaria italica L.)
Ananthi Jayaraman et al.
MOLECULAR BIOTECHNOLOGY (2008)
Arabidopsis transcriptome analysis under drought, cold, high-salinity and ABA treatment conditions using a tiling array
Akihiro Matsui et al.
PLANT AND CELL PHYSIOLOGY (2008)
Distinct size distribution of endogenous siRNAs in maize: Evidence from deep sequencing in the mop1-1 mutant
Kan Nobuta et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2008)
The role of small RNAs in abiotic stress
Jonathan R. Phillips et al.
FEBS LETTERS (2007)
Small RNAs as big players in plant abiotic stress responses and nutrient deprivation
Ramanjulu Sunkar et al.
TRENDS IN PLANT SCIENCE (2007)
CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine
Lei Kong et al.
NUCLEIC ACIDS RESEARCH (2007)
Role of hydroxyproline-rich glycoproteins in resistance of pearl millet against downy mildew pathogen Sclerospora graminicola
Shantharaj Deepak et al.
PLANTA (2007)
An expression atlas of rice mRNAs and small RNAs
Kan Nobuta et al.
NATURE BIOTECHNOLOGY (2007)
Global genome expression analysis of rice in response to drought and high-salinity stresses in shoot, flag leaf, and panicle
Junli Zhou et al.
PLANT MOLECULAR BIOLOGY (2007)
The true story of the HD-Zip family
Federico D. Ariel et al.
TRENDS IN PLANT SCIENCE (2007)
WEGO: a web tool for plotting GO annotations
Jia Ye et al.
NUCLEIC ACIDS RESEARCH (2006)
Functional analysis of an Arabidopsis transcription factor, DREB2A, involved in drought-responsive gene expression
Y Sakuma et al.
PLANT CELL (2006)
Senescence- and drought-related changes in peroxidase and superoxide dismutase isoforms in leaves of Ramonda serbica
Sonja Veljovic-Jovanovic et al.
JOURNAL OF EXPERIMENTAL BOTANY (2006)
Endogenous siRNAs derived from a pair of natural cis-antisense transcripts regulate salt tolerance in Arabidopsis
O Borsani et al.
CELL (2005)
Blast2GO:: a universal tool for annotation, visualization and analysis in functional genomics research
A Conesa et al.
BIOINFORMATICS (2005)
Hahb-4, a sunflower homeobox-leucine zipper gene, is a developmental regulator and confers drought tolerance to Arabidopsis thaliana plants
CA Dezar et al.
TRANSGENIC RESEARCH (2005)
Genome-wide profiling of stored mRNA in Arabidopsis thaliana seed germination:: epigenetic and genetic regulation of transcription in seed
K Nakabayashi et al.
PLANT JOURNAL (2005)
Organization of cis-acting regulatory elements in osmotic- and cold-stress-responsive promoters
K Yamaguchi-Shinozaki et al.
TRENDS IN PLANT SCIENCE (2005)
Rational siRNA design for RNA interference
A Reynolds et al.
NATURE BIOTECHNOLOGY (2004)
Role of transposable elements in heterochromatin and epigenetic control
Z Lippman et al.
NATURE (2004)
Plant PP2C phosphatases: emerging functions in stress signaling
A Schweighofer et al.
TRENDS IN PLANT SCIENCE (2004)
ABF2, an ABRE-binding bZIP factor, is an essential component of glucose signaling and its overexpression affects multiple stress tolerance
S Kim et al.
PLANT JOURNAL (2004)
Regulatory network of gene expression in the drought and cold stress responses
K Shinozaki et al.
CURRENT OPINION IN PLANT BIOLOGY (2003)
The evolution of CONSTANS-like gene families in barley, rice, and Arabidopsis
S Griffiths et al.
PLANT PHYSIOLOGY (2003)
OsDREB genes in rice, Oryza sativa L., encode transcription activators that function in drought-, high-salt- and cold-responsive gene expression
JG Dubouzet et al.
PLANT JOURNAL (2003)
Transcription factors in plant defense and stress responses
KB Singh et al.
CURRENT OPINION IN PLANT BIOLOGY (2002)
Monitoring the expression profiles of 7000 Arabidopsis genes under drought, cold and high-salinity stresses using a full-length cDNA microarray
M Seki et al.
PLANT JOURNAL (2002)
The cell wall hydroxyproline-rich glycoprotein RSH is essential for normal embryo development in Arabidopsis
Q Hall et al.
PLANT CELL (2002)
Functional importance of conserved domains in the flowering-time gene CONSTANS demonstrated by analysis of mutant alleles and transgenic plants
F Robson et al.
PLANT JOURNAL (2001)
Analysis of relative gene expression data using real-time quantitative PCR and the 2-ΔΔCT method
KJ Livak et al.
METHODS (2001)
Regulation of drought tolerance by gene manipulation of 9-cis-epoxycarotenoid dioxygenase, a key enzyme in abscisic acid biosynthesis in Arabidopsis
S Iuchi et al.
PLANT JOURNAL (2001)
Arabidopsis basic leucine zipper transcription factors involved in an abscisic acid-dependent signal transduction pathway under drought and high-salinity conditions
Y Uno et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2000)
Involvement of CDSP 32, a drought-induced thioredoxin, in the response to oxidative stress in potato plants
M Broin et al.
FEBS LETTERS (2000)