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Items: 37

1.

Noncoding deletions reveal a gene that is critical for intestinal function.

Oz-Levi D, Olender T, Bar-Joseph I, Zhu Y, Marek-Yagel D, Barozzi I, Osterwalder M, Alkelai A, Ruzzo EK, Han Y, Vos ESM, Reznik-Wolf H, Hartman C, Shamir R, Weiss B, Shapiro R, Pode-Shakked B, Tatarskyy P, Milgrom R, Schvimer M, Barshack I, Imai DM, Coleman-Derr D, Dickel DE, Nord AS, Afzal V, van Bueren KL, Barnes RM, Black BL, Mayhew CN, Kuhar MF, Pitstick A, Tekman M, Stanescu HC, Wells JM, Kleta R, de Laat W, Goldstein DB, Pras E, Visel A, Lancet D, Anikster Y, Pennacchio LA.

Nature. 2019 Jul;571(7763):107-111. doi: 10.1038/s41586-019-1312-2. Epub 2019 Jun 19.

PMID:
31217582
2.

OrthoVenn2: a web server for whole-genome comparison and annotation of orthologous clusters across multiple species.

Xu L, Dong Z, Fang L, Luo Y, Wei Z, Guo H, Zhang G, Gu YQ, Coleman-Derr D, Xia Q, Wang Y.

Nucleic Acids Res. 2019 Jul 2;47(W1):W52-W58. doi: 10.1093/nar/gkz333.

3.

Strong succession in arbuscular mycorrhizal fungal communities.

Gao C, Montoya L, Xu L, Madera M, Hollingsworth J, Purdom E, Hutmacher RB, Dahlberg JA, Coleman-Derr D, Lemaux PG, Taylor JW.

ISME J. 2019 Jan;13(1):214-226. doi: 10.1038/s41396-018-0264-0. Epub 2018 Aug 31.

4.

Exploring the Root Microbiome: Extracting Bacterial Community Data from the Soil, Rhizosphere, and Root Endosphere.

Simmons T, Caddell DF, Deng S, Coleman-Derr D.

J Vis Exp. 2018 May 2;(135). doi: 10.3791/57561.

PMID:
29782021
5.

Drought delays development of the sorghum root microbiome and enriches for monoderm bacteria.

Xu L, Naylor D, Dong Z, Simmons T, Pierroz G, Hixson KK, Kim YM, Zink EM, Engbrecht KM, Wang Y, Gao C, DeGraaf S, Madera MA, Sievert JA, Hollingsworth J, Birdseye D, Scheller HV, Hutmacher R, Dahlberg J, Jansson C, Taylor JW, Lemaux PG, Coleman-Derr D.

Proc Natl Acad Sci U S A. 2018 May 1;115(18):E4284-E4293. doi: 10.1073/pnas.1717308115. Epub 2018 Apr 16. Erratum in: Proc Natl Acad Sci U S A. 2018 May 14;:.

6.

Drought Stress and Root-Associated Bacterial Communities.

Naylor D, Coleman-Derr D.

Front Plant Sci. 2018 Jan 9;8:2223. doi: 10.3389/fpls.2017.02223. eCollection 2017. Review.

7.

Drought and host selection influence bacterial community dynamics in the grass root microbiome.

Naylor D, DeGraaf S, Purdom E, Coleman-Derr D.

ISME J. 2017 Dec;11(12):2691-2704. doi: 10.1038/ismej.2017.118. Epub 2017 Jul 28.

8.

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.

9.

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.

PMID:
27485442
10.

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.

PMID:
27153733
11.

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.

12.

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.

13.

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.

14.

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.

15.

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.

16.

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.

17.

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.

18.

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.

19.

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.

20.

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.

PMID:
23250988
21.

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.

22.

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.

23.

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.

24.

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.

25.

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.

PMID:
19707805
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.

PMID:
19483776
27.

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.

28.

The complete chloroplast genome sequence of Brachypodium distachyon: sequence comparison and phylogenetic analysis of eight grass plastomes.

Bortiri E, Coleman-Derr D, Lazo GR, Anderson OD, Gu YQ.

BMC Res Notes. 2008 Jul 31;1:61. doi: 10.1186/1756-0500-1-61.

29.

The nuclear genome of Brachypodium distachyon: analysis of BAC end sequences.

Huo N, Lazo GR, Vogel JP, You FM, Ma Y, Hayden DM, Coleman-Derr D, Hill TA, Dvorak J, Anderson OD, Luo MC, Gu YQ.

Funct Integr Genomics. 2008 May;8(2):135-47. Epub 2007 Nov 6.

PMID:
17985162
30.

Rapid evolution and complex structural organization in genomic regions harboring multiple prolamin genes in the polyploid wheat genome.

Gao S, Gu YQ, Wu J, Coleman-Derr D, Huo N, Crossman C, Jia J, Zuo Q, Ren Z, Anderson OD, Kong X.

Plant Mol Biol. 2007 Sep;65(1-2):189-203. Epub 2007 Jul 16.

PMID:
17629796
31.

New insights into Oryza genome evolution: high gene colinearity and differential retrotransposon amplification.

Zhang S, Gu YQ, Singh J, Coleman-Derr D, Brar DS, Jiang N, Lemaux PG.

Plant Mol Biol. 2007 Jul;64(5):589-600. Epub 2007 May 30.

PMID:
17534720
32.

Construction and characterization of two BAC libraries from Brachypodium distachyon, a new model for grass genomics.

Huo N, Gu YQ, Lazo GR, Vogel JP, Coleman-Derr D, Luo MC, Thilmony R, Garvin DF, Anderson OD.

Genome. 2006 Sep;49(9):1099-108.

PMID:
17110990
33.

Types and rates of sequence evolution at the high-molecular-weight glutenin locus in hexaploid wheat and its ancestral genomes.

Gu YQ, Salse J, Coleman-Derr D, Dupin A, Crossman C, Lazo GR, Huo N, Belcram H, Ravel C, Charmet G, Charles M, Anderson OD, Chalhoub B.

Genetics. 2006 Nov;174(3):1493-504. Epub 2006 Oct 8.

34.

EST sequencing and phylogenetic analysis of the model grass Brachypodium distachyon.

Vogel JP, Gu YQ, Twigg P, Lazo GR, Laudencia-Chingcuanco D, Hayden DM, Donze TJ, Vivian LA, Stamova B, Coleman-Derr D.

Theor Appl Genet. 2006 Jul;113(2):186-95. Epub 2006 May 18.

PMID:
16791686
35.

Hybsweeper: a resource for detecting high-density plate gridding coordinates.

Lazo GR, Lui N, Gu YQ, Kong X, Coleman-Derr D, Anderson OD.

Biotechniques. 2005 Sep;39(3):320, 322, 324. No abstract available.

36.

Rapid genome evolution revealed by comparative sequence analysis of orthologous regions from four triticeae genomes.

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

Plant Physiol. 2004 May;135(1):459-70. Epub 2004 Apr 30.

37.

Genomic organization of the complex alpha-gliadin gene loci in wheat.

Gu YQ, Crossman C, Kong X, Luo M, You FM, Coleman-Derr D, Dubcovsky J, Anderson OD.

Theor Appl Genet. 2004 Aug;109(3):648-57. Epub 2004 Apr 22.

PMID:
15103408

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