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Items: 1 to 20 of 30


PIECE 2.0: an update for the plant gene structure comparison and evolution database.

Wang Y, Xu L, Thilmony R, You FM, Gu YQ, Coleman-Derr D.

Nucleic Acids Res. 2017 Jan 4;45(D1):1015-1020. doi: 10.1093/nar/gkw935. Epub 2016 Oct 13.


MetaCoMET: a web platform for discovery and visualization of the core microbiome.

Wang Y, Xu L, Gu YQ, Coleman-Derr D.

Bioinformatics. 2016 Nov 15;32(22):3469-3470. Epub 2016 Aug 2.


GSP: a web-based platform for designing genome-specific primers in polyploids.

Wang Y, Tiwari VK, Rawat N, Gill BS, Huo N, You FM, Coleman-Derr D, Gu YQ.

Bioinformatics. 2016 Aug 1;32(15):2382-3. doi: 10.1093/bioinformatics/btw134. Epub 2016 Mar 9.


The Cacti Microbiome: Interplay between Habitat-Filtering and Host-Specificity.

Fonseca-García C, Coleman-Derr D, Garrido E, Visel A, Tringe SG, Partida-Martínez LP.

Front Microbiol. 2016 Feb 12;7:150. doi: 10.3389/fmicb.2016.00150. eCollection 2016.


High-resolution phylogenetic microbial community profiling.

Singer E, Bushnell B, Coleman-Derr D, Bowman B, Bowers RM, Levy A, Gies EA, Cheng JF, Copeland A, Klenk HP, Hallam SJ, Hugenholtz P, Tringe SG, Woyke T.

ISME J. 2016 Aug;10(8):2020-32. doi: 10.1038/ismej.2015.249. Epub 2016 Feb 9.


Plant compartment and biogeography affect microbiome composition in cultivated and native Agave species.

Coleman-Derr D, Desgarennes D, Fonseca-Garcia C, Gross S, Clingenpeel S, Woyke T, North G, Visel A, Partida-Martinez LP, Tringe SG.

New Phytol. 2016 Jan;209(2):798-811. doi: 10.1111/nph.13697. Epub 2015 Oct 15.


OrthoVenn: a web server for genome wide comparison and annotation of orthologous clusters across multiple species.

Wang Y, Coleman-Derr D, Chen G, Gu YQ.

Nucleic Acids Res. 2015 Jul 1;43(W1):W78-84. doi: 10.1093/nar/gkv487. Epub 2015 May 11.


Gill bacteria enable a novel digestive strategy in a wood-feeding mollusk.

O'Connor RM, Fung JM, Sharp KH, Benner JS, McClung C, Cushing S, Lamkin ER, Fomenkov AI, Henrissat B, Londer YY, Scholz MB, Posfai J, Malfatti S, Tringe SG, Woyke T, Malmstrom RR, Coleman-Derr D, Altamia MA, Dedrick S, Kaluziak ST, Haygood MG, Distel DL.

Proc Natl Acad Sci U S A. 2014 Nov 25;111(47):E5096-104. doi: 10.1073/pnas.1413110111. Epub 2014 Nov 10.


Building the crops of tomorrow: advantages of symbiont-based approaches to improving abiotic stress tolerance.

Coleman-Derr D, Tringe SG.

Front Microbiol. 2014 Jun 6;5:283. doi: 10.3389/fmicb.2014.00283. eCollection 2014.


Natural soil microbes alter flowering phenology and the intensity of selection on flowering time in a wild Arabidopsis relative.

Wagner MR, Lundberg DS, Coleman-Derr D, Tringe SG, Dangl JL, Mitchell-Olds T.

Ecol Lett. 2014 Jun;17(6):717-26. doi: 10.1111/ele.12276. Epub 2014 Apr 4. Erratum in: Ecol Lett. 2015 Feb;18(2):218-20.


A near complete snapshot of the Zea mays seedling transcriptome revealed from ultra-deep sequencing.

Martin JA, Johnson NV, Gross SM, Schnable J, Meng X, Wang M, Coleman-Derr D, Lindquist E, Wei CL, Kaeppler S, Chen F, Wang Z.

Sci Rep. 2014 Mar 31;4:4519. doi: 10.1038/srep04519.


The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin.

Zemach A, Kim MY, Hsieh PH, Coleman-Derr D, Eshed-Williams L, Thao K, Harmer SL, Zilberman D.

Cell. 2013 Mar 28;153(1):193-205. doi: 10.1016/j.cell.2013.02.033.


DNA methylation, H2A.Z, and the regulation of constitutive expression.

Coleman-Derr D, Zilberman D.

Cold Spring Harb Symp Quant Biol. 2012;77:147-54. doi: 10.1101/sqb.2012.77.014944. Epub 2012 Dec 18. Review.


Deposition of histone variant H2A.Z within gene bodies regulates responsive genes.

Coleman-Derr D, Zilberman D.

PLoS Genet. 2012;8(10):e1002988. doi: 10.1371/journal.pgen.1002988. Epub 2012 Oct 11.


Nucleotide diversity maps reveal variation in diversity among wheat genomes and chromosomes.

Akhunov ED, Akhunova AR, Anderson OD, Anderson JA, Blake N, Clegg MT, Coleman-Derr D, Conley EJ, Crossman CC, Deal KR, Dubcovsky J, Gill BS, Gu YQ, Hadam J, Heo H, Huo N, Lazo GR, Luo MC, Ma YQ, Matthews DE, McGuire PE, Morrell PL, Qualset CO, Renfro J, Tabanao D, Talbert LE, Tian C, Toleno DM, Warburton ML, You FM, Zhang W, Dvorak J.

BMC Genomics. 2010 Dec 14;11:702. doi: 10.1186/1471-2164-11-702.


Structural and transcriptional analysis of plant genes encoding the bifunctional lysine ketoglutarate reductase saccharopine dehydrogenase enzyme.

Anderson OD, Coleman-Derr D, Gu YQ, Heath S.

BMC Plant Biol. 2010 Jun 16;10:113. doi: 10.1186/1471-2229-10-113.


Genome comparisons reveal a dominant mechanism of chromosome number reduction in grasses and accelerated genome evolution in Triticeae.

Luo MC, Deal KR, Akhunov ED, Akhunova AR, Anderson OD, Anderson JA, Blake N, Clegg MT, Coleman-Derr D, Conley EJ, Crossman CC, Dubcovsky J, Gill BS, Gu YQ, Hadam J, Heo HY, Huo N, Lazo G, Ma Y, Matthews DE, McGuire PE, Morrell PL, Qualset CO, Renfro J, Tabanao D, Talbert LE, Tian C, Toleno DM, Warburton ML, You FM, Zhang W, Dvorak J.

Proc Natl Acad Sci U S A. 2009 Sep 15;106(37):15780-5. doi: 10.1073/pnas.0908195106. Epub 2009 Aug 26.


Conserved globulin gene across eight grass genomes identify fundamental units of the loci encoding seed storage proteins.

Gu YQ, Wanjugi H, Coleman-Derr D, Kong X, Anderson OD.

Funct Integr Genomics. 2010 Mar;10(1):111-22. doi: 10.1007/s10142-009-0135-x. Epub 2009 Aug 26.


Rapid development of PCR-based genome-specific repetitive DNA junction markers in wheat.

Wanjugi H, Coleman-Derr D, Huo N, Kianian SF, Luo MC, Wu J, Anderson O, Gu YQ.

Genome. 2009 Jun;52(6):576-87. doi: 10.1139/g09-033.


Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks.

Zilberman D, Coleman-Derr D, Ballinger T, Henikoff S.

Nature. 2008 Nov 6;456(7218):125-9. doi: 10.1038/nature07324. Epub 2008 Sep 24.

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