MicroRNA profiling analysis throughout tomato fruit development and ripening reveals potential regulatory role of RIN on microRNAs accumulation

Identification of microRNA targets in tomato fruit development using high-throughput sequencing and degradome analysis

(2013) Rumyana Karlova et al.   JOURNAL OF EXPERIMENTAL BOTANY

Single-base resolution methylomes of tomato fruit development reveal epigenome modifications associated with ripening

(2013) Silin Zhong et al.   NATURE BIOTECHNOLOGY

SRNAome parsing yields insights into tomato fruit ripening control

(2013) Jinhua Zuo et al.   PHYSIOLOGIA PLANTARUM

A Large-Scale Identification of Direct Targets of the Tomato MADS Box Transcription Factor RIPENING INHIBITOR Reveals the Regulation of Fruit Ripening

(2013) M. Fujisawa et al.   PLANT CELL

ETHYLENE-INSENSITIVE3 Is a Senescence-Associated Gene That Accelerates Age-Dependent Leaf Senescence by Directly Repressing miR164 Transcription in Arabidopsis

(2013) Z. Li et al.   PLANT CELL

Biogenesis, Turnover, and Mode of Action of Plant MicroRNAs

(2013) K. Rogers et al.   PLANT CELL

Sculpting the maturation, softening and ethylene pathway: The influences of microRNAs on tomato fruits

(2012) Jinhua Zuo et al.   BMC GENOMICS

Transcriptome analysis of rin mutant fruit and in silico analysis of promoters of differentially regulated genes provides insight into LeMADS-RIN-regulated ethylene-dependent as well as ethylene-independent aspects of ripening in tomato

(2012) Rahul Kumar et al.   MOLECULAR GENETICS AND GENOMICS

The tomato genome sequence provides insights into fleshy fruit evolution

(2012)   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

The Tomato FRUITFULL Homologs TDR4/FUL1 and MBP7/FUL2 Regulate Ethylene-Independent Aspects of Fruit Ripening

(2012) M. Bemer et al.   PLANT CELL

MicroRNA regulation of plant innate immune receptors

(2012) F. Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identification of potential target genes for the tomato fruit-ripening regulator RIN by chromatin immunoprecipitation

(2011) Masaki Fujisawa et al.   BMC PLANT BIOLOGY

Function and Evolution of a MicroRNA That Regulates a Ca2+-ATPase and Triggers the Formation of Phased Small Interfering RNAs in Tomato Reproductive Growth

(2011) Ying Wang et al.   PLANT CELL

Transcriptome and Metabolite Profiling Show That APETALA2a Is a Major Regulator of Tomato Fruit Ripening

(2011) R. Karlova et al.   PLANT CELL

Unraveling the regulatory network of the MADS box transcription factor RIN in fruit ripening

(2011) Guozheng Qin et al.   PLANT JOURNAL

Profiling of short RNAs during fleshy fruit development reveals stage-specific sRNAome expression patterns

(2011) Irina Mohorianu et al.   PLANT JOURNAL

Combined transcriptome, genetic diversity and metabolite profiling in tomato fruit reveals that the ethylene response factor SlERF6 plays an important role in ripening and carotenoid accumulation

(2011) Je Min Lee et al.   PLANT JOURNAL

The Tomato MADS-Box Transcription Factor RIPENING INHIBITOR Interacts with Promoters Involved in Numerous Ripening Processes in a COLORLESS NONRIPENING-Dependent Manner

(2011) C. Martel et al.   PLANT PHYSIOLOGY

Systems Biology of Tomato Fruit Development: Combined Transcript, Protein, and Metabolite Analysis of Tomato Transcription Factor ( nor, rin ) and Ethylene Receptor ( Nr ) Mutants Reveals Novel Regulatory Interactions

(2011) Sonia Osorio et al.   PLANT PHYSIOLOGY

Direct targets of the tomato-ripening regulator RIN identified by transcriptome and chromatin immunoprecipitation analyses

(2011) Masaki Fujisawa et al.   PLANTA

MiRNA Control of Vegetative Phase Change in Trees

(2011) Jia-Wei Wang et al.   PLoS Genetics

Orchestration of the Floral Transition and Floral Development in Arabidopsis by the Bifunctional Transcription Factor APETALA2

(2010) L. Yant et al.   PLANT CELL

A tomato (Solanum lycopersicum) APETALA2/ERF gene, SlAP2a, is a negative regulator of fruit ripening

(2010) Mi-Young Chung et al.   PLANT JOURNAL

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

SOAP2: an improved ultrafast tool for short read alignment

(2009) R. Li et al.   BIOINFORMATICS

The Sequential Action of miR156 and miR172 Regulates Developmental Timing in Arabidopsis

(2009) Gang Wu et al.   CELL

High throughput sequencing technology reveals that the taxoid elicitor methyl jasmonate regulates microRNA expression in Chinese yew (Taxus chinensis)

(2009) Deyou Qiu et al.   GENE

Identification of novel stress-regulated microRNAs from Oryza sativa L.

(2009) Xinyu Jian et al.   GENOMICS

Genetic analysis of reproductive development in tomato

(2009) Rafael Lozano et al.   INTERNATIONAL JOURNAL OF DEVELOPMENTAL BIOLOGY

TOMATO AGAMOUS-LIKE 1 is a component of the fruit ripening regulatory network

(2009) Maxim Itkin et al.   PLANT JOURNAL

Genome-wide survey of rice microRNAs and microRNA–target pairs in the root of a novel auxin-resistant mutant

(2009) Yijun Meng et al.   PLANTA

Comparative analysis of the small RNA transcriptomes of Pinus contorta and Oryza sativa

(2008) R. D. Morin et al.   GENOME RESEARCH

Deep sequencing of tomato short RNAs identifies microRNAs targeting genes involved in fruit ripening

(2008) S. Moxon et al.   GENOME RESEARCH

DNA-binding specificity, transcriptional activation potential, and therinmutation effect for the tomato fruit-ripening regulator RIN

(2008) Yasuhiro Ito et al.   PLANT JOURNAL

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY