Genome-wide screening and characterization of long non-coding RNAs involved in flowering development of trifoliate orange (Poncirus trifoliata L. Raf.)

Identifying the genome-wide genetic variation between precocious trifoliate orange and its wild type and developing new markers for genetics research

(2016) Jin-Zhi Zhang et al.   DNA RESEARCH

COOLAIR Antisense RNAs Form Evolutionarily Conserved Elaborate Secondary Structures

(2016) Emily J. Hawkes et al.   Cell Reports

Global identification and analysis of long non-coding RNAs in diploid strawberry Fragaria vesca during flower and fruit development

(2015) Chunying Kang et al.   BMC GENOMICS

Long non-coding RNAs and their functions in plants

(2015) Julia A Chekanova   CURRENT OPINION IN PLANT BIOLOGY

RNA sequencing and functional analysis implicate the regulatory role of long non-coding RNAs in tomato fruit ripening

(2015) Benzhong Zhu et al.   JOURNAL OF EXPERIMENTAL BOTANY

CANTATAdb: A Collection of Plant Long Non-Coding RNAs

(2015) Michał W. Szcześniak et al.   PLANT AND CELL PHYSIOLOGY

Long Non-coding RNAs and Their Biological Roles in Plants

(2015) Xue Liu et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

PLEK: a tool for predicting long non-coding RNAs and messenger RNAs based on an improved k-mer scheme

(2014) Aimin Li et al.   BMC BIOINFORMATICS

A genome-wide association study of seed protein and oil content in soybean

(2014) Eun-Young Hwang et al.   BMC GENOMICS

Long Noncoding RNA Modulates Alternative Splicing Regulators in Arabidopsis

(2014) Florian Bardou et al.   DEVELOPMENTAL CELL

Genome-wide identification and functional prediction of novel and drought-responsive lincRNAs in Populus trichocarpa

(2014) Peng Shuai et al.   JOURNAL OF EXPERIMENTAL BOTANY

Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication

(2014) G Albert Wu et al.   NATURE BIOTECHNOLOGY

Characterization of stress-responsive lncRNAs inArabidopsis thalianaby integrating expression, epigenetic and structural features

(2014) Chao Di et al.   PLANT JOURNAL

Genome-Wide Classification and Evolutionary and Expression Analyses of Citrus MYB Transcription Factor Families in Sweet Orange

(2014) Xiao-Jin Hou et al.   PLoS One

Genome-wide discovery and characterization of maize long non-coding RNAs

(2014) Lin Li et al.   GENOME BIOLOGY

Long non-coding RNAs: new players in cell differentiation and development

(2013) Alessandro Fatica et al.   NATURE REVIEWS GENETICS

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

NONCODEv4: exploring the world of long non-coding RNA genes

(2013) Chaoyong Xie et al.   NUCLEIC ACIDS RESEARCH

Genome-Wide Identification, Classification, Expression Profiling, and SSR Marker Development of the MADS-Box Gene Family in Citrus

(2013) Xiao-Jin Hou et al.   PLANT MOLECULAR BIOLOGY REPORTER

Widespread Long Noncoding RNAs as Endogenous Target Mimics for MicroRNAs in Plants

(2013) H.-J. Wu et al.   PLANT PHYSIOLOGY

R-Loop Stabilization Represses Antisense Transcription at the Arabidopsis FLC Locus

(2013) Q. Sun et al.   SCIENCE

Genetic regulation of flowering time in annual and perennial plants

(2013) Muhammad Rehman Gul Khan et al.   Wiley Interdisciplinary Reviews-RNA

Modular regulatory principles of large non-coding RNAs

(2012) Mitchell Guttman et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

DNA helicase and helicase-nuclease enzymes with a conserved iron-sulfur cluster

(2012) Y. Wu et al.   NUCLEIC ACIDS RESEARCH

NGC: lossless and lossy compression of aligned high-throughput sequencing data

(2012) Niko Popitsch et al.   NUCLEIC ACIDS RESEARCH

Identification and Comparative Profiling of miRNAs in an Early Flowering Mutant of Trifoliate Orange and Its Wild Type by Genome-Wide Deep Sequencing

(2012) Lei-Ming Sun et al.   PLoS One

A long noncoding RNA regulates photoperiod-sensitive male sterility, an essential component of hybrid rice

(2012) J. Ding et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identification of novel transcripts in annotated genomes using RNA-Seq

(2011) A. Roberts et al.   BIOINFORMATICS

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

(2011) Mingming Xin et al.   BMC PLANT BIOLOGY

Identification of miRNAs and Their Target Genes Using Deep Sequencing and Degradome Analysis in Trifoliate Orange [Poncirus trifoliate (L.) Raf]

(2011) Jin-Zhi Zhang et al.   MOLECULAR BIOTECHNOLOGY

Molecular cloning and functional characterization of genes associated with flowering in citrus using an early-flowering trifoliate orange (Poncirus trifoliata L. Raf.) mutant

(2011) Jin-Zhi Zhang et al.   PLANT MOLECULAR BIOLOGY

Long noncoding RNA: unveiling hidden layer of gene regulatory networks

(2011) Eun-Deok Kim et al.   TRENDS IN PLANT SCIENCE

Manipulation of FASTQ data with Galaxy

(2010) D. Blankenberg et al.   BIOINFORMATICS

PtSVP, an SVP homolog from trifoliate orange (Poncirus trifoliata L. Raf.), shows seasonal periodicity of meristem determination and affects flower development in transgenic Arabidopsis and tobacco plants

(2010) Zhi-Min Li et al.   PLANT MOLECULAR BIOLOGY

Vernalization-Mediated Epigenetic Silencing by a Long Intronic Noncoding RNA

(2010) J. B. Heo et al.   SCIENCE

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals

(2009) Mitchell Guttman et al.   NATURE

Transcriptome analysis by strand-specific sequencing of complementary DNA

(2009) Dmitri Parkhomchuk et al.   NUCLEIC ACIDS RESEARCH

PtFLC homolog from trifoliate orange (Poncirus trifoliata) is regulated by alternative splicing and experiences seasonal fluctuation in expression level

(2009) Jin-Zhi Zhang et al.   PLANTA

Catalogues of mammalian long noncoding RNAs: modest conservation and incompleteness

(2009) Ana C Marques et al.   GENOME BIOLOGY

Noncoding Transcription by RNA Polymerase Pol IVb/Pol V Mediates Transcriptional Silencing of Overlapping and Adjacent Genes

(2008) Andrzej T. Wierzbicki et al.   CELL

Identification of flowering-related genes between early flowering trifoliate orange mutant and wild-type trifoliate orange (Poncirus trifoliata L. Raf.) by suppression subtraction hybridization (SSH) and macroarray

(2008) Jin-Zhi Zhang et al.   GENE

Novel long non-protein coding RNAs involved in Arabidopsis differentiation and stress responses

(2008) B. Ben Amor et al.   GENOME RESEARCH

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

Evidence for stage-specific modulation of specific microRNAs (miRNAs) and miRNA processing components in zygotic embryo and female gametophyte of loblolly pine (Pinus taeda)

(2008) Thomas J. Oh et al.   NEW PHYTOLOGIST