(Q28833186)

1

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Justin Preece

2

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Justin Elser

3

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Denise Nemeth

4

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Gina Bono

5

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Kenny Wu

describes a project that uses

6

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language of work or name

English

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publication date

29 May 2013

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published in

Rice

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volume

6

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page(s)

14

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issue

1

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Cytoscape

object named as

Cytoscape

2 references

Europe PubMed Central

9 June 2022

https://europepmc.org/search?query=(METHODS:'Cytoscape')

inferred from PubMed Central ID database lookup

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

exact match

https://scigraph.springernature.com/pub.10.1186/1939-8433-6-14

0 references

cites work

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WikiPathways: building research communities on biological pathways

16 March 2017

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The genome of woodland strawberry (Fragaria vesca)

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Gramene database in 2010: updates and extensions

16 March 2017

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InParanoid 7: new algorithms and tools for eukaryotic orthology analysis

16 March 2017

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Presenting and exploring biological pathways with PathVisio

16 March 2017

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WikiPathways: pathway editing for the people

16 March 2017

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Gramene: a bird's eye view of cereal genomes

16 March 2017

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It's time to flower: the genetic control of flowering time

16 March 2017

1 reference

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BIND: the Biomolecular Interaction Network Database

16 March 2017

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Orchestrated transcription of key pathways in Arabidopsis by the circadian clock

7 April 2017

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GrameneMart: the BioMart data portal for the Gramene project

7 April 2017

1 reference

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Genetic dissection of the biotic stress response using a genome-scale gene network for rice.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4883732

Identification of genes associated with nitrogen-use efficiency by genome-wide transcriptional analysis of two soybean genotypes

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4883732

Systematic prediction of gene function in Arabidopsis thaliana using a probabilistic functional gene network

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4883732

Global profiling of rice and poplar transcriptomes highlights key conserved circadian-controlled pathways and cis-regulatory modules

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4883732

Deep sequencing reveals the complex and coordinated transcriptional regulation of genes related to grain quality in rice cultivars

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4883732

Field transcriptome revealed critical developmental and physiological transitions involved in the expression of growth potential in japonica rice

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4883732

Creation of a genome-wide metabolic pathway database for Populus trichocarpa using a new approach for reconstruction and curation of metabolic pathways for plants

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4883732

Comparative genomics of flowering time pathways using Brachypodium distachyon as a model for the temperate grasses

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4883732

Global analysis of gene activity during Arabidopsis seed development and identification of seed-specific transcription factors

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4883732

An expanding universe of circadian networks in higher plants

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4883732

Allelic diversities in rice starch biosynthesis lead to a diverse array of rice eating and cooking qualities

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4883732

The syncytium-specific expression of the Orysa;KRP3 CDK inhibitor: implication of its involvement in the cell cycle control in the rice (Oryza sativa L.) syncytial endosperm

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4883732

Arabidopsis circadian clock and photoperiodism: time to think about location

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4883732

Characterization of a new rice glutelin gene GluD-1 expressed in the starchy endosperm

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4883732

Flowering time regulation produces much fruit

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4883732

Expression pattern and activity of six glutelin gene promoters in transgenic rice

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4883732

The Rice Annotation Project Database (RAP-DB): 2008 update

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4883732

An "Electronic Fluorescent Pictograph" browser for exploring and analyzing large-scale biological data sets

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4883732

Using genomics to study legume seed development

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4883732

Transcriptional profiling of Arabidopsis heat shock proteins and transcription factors reveals extensive overlap between heat and non-heat stress response pathways

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4883732

Mining iron: iron uptake and transport in plants

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4883732

F-box proteins in rice. Genome-wide analysis, classification, temporal and spatial gene expression during panicle and seed development, and regulation by light and abiotic stress

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4883732

Functional conservation of MADS-box factors controlling floral organ identity in rice and Arabidopsis.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4883732

New insights into the complex and coordinated transcriptional regulation networks underlying rice seed development through cDNA chip-based analysis

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4883732

Rice plant development: from zygote to spikelet

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4883732

A snapshot of the low temperature stress transcriptome of developing rice seedlings (Oryza sativa L.) via ESTs from subtracted cDNA library

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4883732

A network of rice genes associated with stress response and seed development

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4883732

The TIGR rice genome annotation resource: annotating the rice genome and creating resources for plant biologists

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4883732

Expression profile matrix of Arabidopsis transcription factor genes suggests their putative functions in response to environmental stresses.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4883732

MADS-box gene evolution beyond flowers: expression in pollen, endosperm, guard cells, roots and trichomes.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4883732

Population genomics of the Arabidopsis thaliana flowering time gene network.

3 June 2018

1 reference

https://api.crossref.org/works/10.1186%2F1939-8433-6-14

Compensation and interaction between RISBZ1 and RPBF during grain filling in rice.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1939-8433-6-14

EGENES: transcriptome-based plant database of genes with metabolic pathway information and expressed sequence tag indices in KEGG.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1939-8433-6-14

The DIURNAL project: DIURNAL and circadian expression profiling, model-based pattern matching, and promoter analysis.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1939-8433-6-14

Contrapuntal networks of gene expression during Arabidopsis seed filling.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1939-8433-6-14

A novel factor FLOURY ENDOSPERM2 is involved in regulation of rice grain size and starch quality

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1939-8433-6-14

Arabidopsis reactome: a foundation knowledgebase for plant systems biology

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1939-8433-6-14

Reactome knowledgebase of human biological pathways and processes.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4883732

Identification of a maize kernel stress-related protein and its effect on aflatoxin accumulation

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4883732

Improved biomass productivity and water use efficiency under water deficit conditions in transgenic wheat constitutively expressing the barley HVA1 gene

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4883732

Technical advance: transcript profiling in rice (Oryza sativa L.) seedlings using serial analysis of gene expression (SAGE)

26 November 2018

1 reference

12 December 2020

KEGG bioinformatics resource for plant genomics research

1 reference

12 December 2020

Cytoscape: a community-based framework for network modeling

1 reference

12 December 2020

Gramene database: a hub for comparative plant genomics

1 reference

12 December 2020

Evidence for a Cytoskeleton-Associated Binding Site Involved in Prolamine mRNA Localization to the Protein Bodies in Rice Endosperm Tissue

1 reference

12 December 2020

Identifiers

DOI

10.1186/1939-8433-6-14

1 reference

Dimensions Publication ID

1482186

1020516742

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1482186

1 reference

1 reference

1 reference