Relevant Publications from the GRASSIUS Team

Schmitz, R.J., Grotewold, E., and Stam, E. (2021)
Cis-regulatory sequences in plants: their importance, discovery and future challenges.
Plant Cell, 34: 718-741.
PMID: 34918159

Yang, F., Li, W., Jiang, N., Yu, H., Morohashi, K., Ouma, W.Z., Morales-Mantilla, D., Gomez-Cano, F., Mukundi, E., Prada-Salcedo, L.D., Alers Velazquez, R., Valentin, J., Mejía-Guerra, M.K., Gray, J., Doseff, A.I., and Grotewold, E. (2017).
A maize gene regulatory network for phenolic metabolism.
Mol Plant, 10: 489-515.
PMID: 27871810

Mukundi, E., Gomez-Cano, F., Ouma, W.Z., and Grotewold, E. (2017)
Design of knowledge bases for plant gene regulatory networks.
Methods Mol Biol, 1629: 207-223.
PMID: 28623588

Mejía-Guerra, K.M., Li, W., Galeano, N.F., Vidal, M., Gray, J., Doseff, A.I., and Grotewold, E. (2015)
Core promoter plasticity between maize tissues and genotypes contrasts with predominance of sharp transcription initiation sites.
Plant Cell, 27: 3309-3320.
PMID: 26628745

Gray, J., Burdo, B., Goetting-Minesky, M. P., Wittler, B., Hunt, M., Li, T., Velliquette, D., Thomas, J., Agarwal, T., Key, K., Gentzel, I., Brito, M. d., Mejía-Guerra, M. K., Connolly, L. N., Qaisi, D., Li, W., Casas, M. I., Doseff, A. I. and Grotewold, E. (2015).
Protocol for the generation of a transcription factor open reading frame collection (TFome).
Bio-protocol, 5: e1547.

Burdo, B., Gray, J., Goetting-Minesky, M.P., Wittler, B., Hunt, M., Li, T., Velliquette, D., Thomas, J., Gentzel, I., Brito, M.D., Mejía-Guerra, M.K., Connolly, L.N., Qaisi, D., Li, W., Casas, M.I., Doseff, A.I., and Grotewold, E. (2014)
The Maize TFome - Development of a transcription factor open reading frame collection for functional genomics.
Plant J. 80: 356-366.
PMID: 25053252

Gray, J., Bevan, M., Brutnell, T., Buell, R., Cone, K., Hake, S., Jackson, D., Kellogg, E.A., Lawrence, C., McCouch, S., Mockler, T., Moose, S.P., Paterson, A., Peterson, T., Rokshar, D., Souza, G.M., Springer, N., Stein, N., Timmermans, M.C., Wang, G.-L., and Grotewold, E. (2009)
A recommendation for naming transcription factor proteins in the grasses.
Plant Physiol, 149: 4-6.
PMID: 19126689

Yilmaz, A., Nishiyama, M.Y., Garcia-Fuentes, B., Souza, G.M., Janies, D., Gray, J. and Grotewold, E. (2009)
GRASSIUS: A platform for comparative regulatory genomics across the grasses.
Plant Physiol, 149: 171-180.
PMID: 18987217

Morohashi K, Casas MI, Falcone Ferreyra ML, Falcone Ferreyra L, Mejía-Guerra MK, Pourcel L, Yilmaz A, Feller A, Carvalho B, Emiliani J, Rodriguez E, Pellegrinet S, McMullen M, Casati P, Grotewold E.
A genome-wide regulatory framework identifies maize pericarp color1 controlled genes.
Plant Cell. 2012 Jul;24(7):2745-64.
PMID: 22822204

Bolduc N, Yilmaz A, Mejia-Guerra MK, Morohashi K, O'Connor D, Grotewold E, Hake S.
Unraveling the KNOTTED1 regulatory network in maize meristems.
Genes Dev. 2012 Aug 1;26(15):1685-90.
PMID: 22855831

Eveland AL, Goldshmidt A, Pautler M, Morohashi K, Liseron-Monfils C, Lewis MW, Kumari S, Hiraga S, Yang F, Unger-Wallace E, Olson A, Hake S, Vollbrecht E, Grotewold E, Ware D, Jackson D.
Regulatory modules controlling maize inflorescence architecture.
Genome Res. 2014 Mar;24(3):431-43.
PMID: 24307553

Pautler M, Eveland AL, LaRue T, Yang F, Weeks R, Lunde C, Je BI, Meeley R, Komatsu M, Vollbrecht E, Sakai H, Jackson D.
FASCIATED EAR4 encodes a bZIP transcription factor that regulates shoot meristem size in maize.
Plant Cell. 2015 Jan;27(1):104-20.
PMID: 25616871

Li C, Qiao Z, Qi W, Wang Q, Yuan Y, Yang X, Tang Y, Mei B, Lv Y, Zhao H, Xiao H, Song R.
Genome-wide characterization of cis-acting DNA targets reveals the transcriptional regulatory framework of opaque2 in maize.
Plant Cell. 2015 Mar;27(3):532-45.
PMID: 25691733

Plant Transcription Factor Databases

The Plant Transcription Factor Database (PlantTFDB) is a comprehensive plant transcription factor (TF) database including about 20 species.

PlnTFDB (3.0) is a public database arising from efforts to identify and catalogue all Plant genes involved in transcriptional control.

Maize Links

MaizeGDB is the community database for biological information about the crop plant Zea mays ssp. mays. Genetic, genomic, sequence, gene product, functional characterization, literature reference, and person/organization contact information are among the datatypes accessible through this site.

The Maize Full Length cDNA Project
This project uses genomics tools to understand a fundamental biological process through identificaion of genes expressed during maize reproduction and in somatic tissues responding to abiotic perturbations such as heat, cold, salt, UV-B, drought, and lack of light.

Maize Genetics Nomenclature Committee

Rice Links

TIGR Rice Genome
The TIGR Rice Genome Annotation Database and Resource is a National Science Foundation project and provides sequence and annotation data for the rice genome.

RiceTFDB is a public database arising from efforts to identify and catalogue all Oryza sativa genes involved in transcriptional control.

Sugarcane Links

The SUCEST-FUN Project aims to associate function to the genes identified by the Sugarcane EST Project (SUCEST). With this purpose several groups have joined efforts to study the sugarcane transcriptome

Sorghum Links

Sorghum genome at Phytozome
Sorghum genome browser, BLAST and download Sorghum bicolor sequences.

Comparative Genomic Resources

The Arabidopsis Gene Regulatory Information Server (AGRIS) is a information resource for Arabidopsis promoter sequences, transcription factors and their target genes.

Copyright © 2023 | Last updated: 2023-06-26