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A guide through present computational approaches for the identification of mammalian microRNA targets

Nature methods, 2006-11, Vol.3 (11), p.881-886

2006

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MicroRNAs Exhibit High Frequency Genomic Alterations in Human Cancer

Proceedings of the National Academy of Sciences - PNAS, 2006-06, Vol.103 (24), p.9136-9141

2006

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Genomic and epigenetic alterations deregulate microRNA expression in human epithelial ovarian cancer

Proceedings of the National Academy of Sciences - PNAS, 2008-05, Vol.105 (19), p.7004-7009

2008

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Frequency and fate of microRNA editing in human brain

Nucleic acids research, 2008-09, Vol.36 (16), p.5270-5280

2008

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Paired-End Analysis of Transcription Start Sites in Arabidopsis Reveals Plant-Specific Promoter Signatures

The Plant cell, 2014-07, Vol.26 (7), p.2746-2760

2014

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protein expression landscape of the Arabidopsis root

Proceedings of the National Academy of Sciences - PNAS, 2012-05, Vol.109 (18), p.6811-6818

2012

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Environmental Stresses Modulate Abundance and Timing of Alternatively Spliced Circadian Transcripts in Arabidopsis

Molecular plant, 2015-02, Vol.8 (2), p.207-227

2015

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miRGen 2.0: a database of microRNA genomic information and regulation

Nucleic acids research, 2010-01, Vol.38 (Database issue), p.D137-D141

2010

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MicroRNA promoter element discovery in Arabidopsis

RNA (Cambridge), 2006-09, Vol.12 (9), p.1612-1619

2006

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Metabolomics analysis reveals both plant variety and choice of hormone treatment modulate vinca alkaloid production in Catharanthus roseus

Plant direct, 2020-09, Vol.4 (9), p.e00267-n/a

2020

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RNA-Seq analysis of genes affected by Cyclophilin A/DIAGEOTROPICA (DGT) in tomato root development [version 1; peer review: 2 approved]

F1000 research, 2020, Vol.9, p.1175-1175

2020

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Alternative splicing in plants: directing traffic at the crossroads of adaptation and environmental stress

Current opinion in plant biology, 2015-04, Vol.24, p.125-135

2015

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IndeCut evaluates performance of network motif discovery algorithms

Bioinformatics, 2018-05, Vol.34 (9), p.1514-1521

2018

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miRGen: a database for the study of animal microRNA genomic organization and function

Nucleic acids research, 2007-01, Vol.35 (Database issue), p.D149-D155

2007

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Identification of transcription factors from NF-Y, NAC, and SPL families responding to osmotic stress in multiple tomato varieties

Plant science (Limerick), 2018-09, Vol.274, p.441-450

2018

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Editing of Epstein-Barr Virus-encoded BART6 MicroRNAs Controls Their Dicer Targeting and Consequently Affects Viral Latency

The Journal of biological chemistry, 2010-10, Vol.285 (43), p.33358-33370

2010

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NanoCAGE-XL: An Approach to High-Confidence Transcription Start Site Sequencing

Methods in molecular biology (Clifton, N.J.), 2018, Vol.1830, p.225

2018

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A stele‐enriched gene regulatory network in the Arabidopsis root

Molecular systems biology, 2011-01, Vol.7 (1)

2011

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NanoCAGE-XL and CapFilter: an approach to genome wide identification of high confidence transcription start sites

BMC genomics, 2015-08, Vol.16 (1), p.597-597, Article 597

2015

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TIPR: transcription initiation pattern recognition on a genome scale

Bioinformatics (Oxford, England), 2015-12, Vol.31 (23), p.3725-3732

2015

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Quality control and evaluation of plant epigenomics data

The Plant cell, 2022-01, Vol.34 (1), p.503-513

2022

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Small Genetic Circuits and MicroRNAs: Big Players in Polymerase II Transcriptional Control in Plants

The Plant cell, 2016-02, Vol.28 (2), p.286-303

2016

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The cyclophilin A DIAGEOTROPICA gene affects auxin transport in both root and shoot to control lateral root formation

Development (Cambridge), 2015-02, Vol.142 (4), p.712-721

2015

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comparative study of ripening among berries of the grape cluster reveals an altered transcriptional programme and enhanced ripening rate in delayed berries

Journal of experimental botany, 2014-11, Vol.65 (20), p.5889-5902

2014

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DNase I SIM: A Simplified In-Nucleus Method for DNase I Hypersensitive Site Sequencing

Methods in molecular biology (Clifton, N.J.), 2017, Vol.1629, p.141

2017

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A guide through present computational approaches for the identification of mammalian microRNA targets

MicroRNAs Exhibit High Frequency Genomic Alterations in Human Cancer

Genomic and epigenetic alterations deregulate microRNA expression in human epithelial ovarian cancer

Frequency and fate of microRNA editing in human brain

Paired-End Analysis of Transcription Start Sites in Arabidopsis Reveals Plant-Specific Promoter Signatures

protein expression landscape of the Arabidopsis root

Environmental Stresses Modulate Abundance and Timing of Alternatively Spliced Circadian Transcripts in Arabidopsis

miRGen 2.0: a database of microRNA genomic information and regulation

MicroRNA promoter element discovery in Arabidopsis

Metabolomics analysis reveals both plant variety and choice of hormone treatment modulate vinca alkaloid production in Catharanthus roseus

RNA-Seq analysis of genes affected by Cyclophilin A/DIAGEOTROPICA (DGT) in tomato root development [version 1; peer review: 2 approved]

Alternative splicing in plants: directing traffic at the crossroads of adaptation and environmental stress

IndeCut evaluates performance of network motif discovery algorithms

miRGen: a database for the study of animal microRNA genomic organization and function

Identification of transcription factors from NF-Y, NAC, and SPL families responding to osmotic stress in multiple tomato varieties

Editing of Epstein-Barr Virus-encoded BART6 MicroRNAs Controls Their Dicer Targeting and Consequently Affects Viral Latency

NanoCAGE-XL: An Approach to High-Confidence Transcription Start Site Sequencing

A stele‐enriched gene regulatory network in the Arabidopsis root

NanoCAGE-XL and CapFilter: an approach to genome wide identification of high confidence transcription start sites

TIPR: transcription initiation pattern recognition on a genome scale

Quality control and evaluation of plant epigenomics data

Small Genetic Circuits and MicroRNAs: Big Players in Polymerase II Transcriptional Control in Plants

The cyclophilin A DIAGEOTROPICA gene affects auxin transport in both root and shoot to control lateral root formation

comparative study of ripening among berries of the grape cluster reveals an altered transcriptional programme and enhanced ripening rate in delayed berries

DNase I SIM: A Simplified In-Nucleus Method for DNase I Hypersensitive Site Sequencing

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