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Gramene Database: Navigating Plant Comparative Genomics Resources.

Gupta P, Naithani S, Tello-Ruiz MK, Chougule K, D'Eustachio P, Fabregat A, Jiao Y, Keays M, Lee YK, Kumari S, Mulvaney J, Olson A, Preece J, Stein J, Wei S, Weiser J, Huerta L, Petryszak R, Kersey P, Stein LD, Ware D, Jaiswal P.

Curr Plant Biol. 2016 Nov;7-8:10-15. doi: 10.1016/j.cpb.2016.12.005.


Improved maize reference genome with single-molecule technologies.

Jiao Y, Peluso P, Shi J, Liang T, Stitzer MC, Wang B, Campbell MS, Stein JC, Wei X, Chin CS, Guill K, Regulski M, Kumari S, Olson A, Gent J, Schneider KL, Wolfgruber TK, May MR, Springer NM, Antoniou E, McCombie WR, Presting GG, McMullen M, Ross-Ibarra J, Dawe RK, Hastie A, Rank DR, Ware D.

Nature. 2017 Jun 22;546(7659):524-527. doi: 10.1038/nature22971. Epub 2017 Jun 12.


Fate and transport of hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) and its degradation products in sedimentary and volcanic rocks, Los Alamos, New Mexico.

Heerspink BP, Pandey S, Boukhalfa H, Ware DS, Marina O, Perkins G, Vesselinov VV, WoldeGabriel G.

Chemosphere. 2017 Sep;182:276-283. doi: 10.1016/j.chemosphere.2017.04.149. Epub 2017 May 2.


Draft Genome Sequence of a Chromium-Reducing Strain, Pseudomonas fluorescens S613, Isolated from a Chromium-Contaminated Aquifer in Los Alamos, New Mexico.

Wang D, Boukhalfa H, Ware DS, Daligault HE.

Genome Announc. 2017 Apr 20;5(16). pii: e00241-17. doi: 10.1128/genomeA.00241-17.


Colloid-Facilitated Plutonium Transport in Fractured Tuffaceous Rock.

Wolfsberg A, Dai Z, Zhu L, Reimus P, Xiao T, Ware D.

Environ Sci Technol. 2017 May 16;51(10):5582-5590. doi: 10.1021/acs.est.7b00968. Epub 2017 Apr 24.


Paracentral acute middle maculopathy as a finding in patients with severe vision loss following phacoemulsification cataract surgery.

Creese K, Ong D, Sandhu SS, Ware D, Alex Harper C, Al-Qureshi SH, Wickremasinghe SS.

Clin Exp Ophthalmol. 2017 Mar 13. doi: 10.1111/ceo.12945. [Epub ahead of print]


DNA methylation and gene expression regulation associated with vascularization in Sorghum bicolor.

Turco GM, Kajala K, Kunde-Ramamoorthy G, Ngan CY, Olson A, Deshphande S, Tolkunov D, Waring B, Stelpflug S, Klein P, Schmutz J, Kaeppler S, Ware D, Wei CL, Etchells JP, Brady SM.

New Phytol. 2017 May;214(3):1213-1229. doi: 10.1111/nph.14448. Epub 2017 Feb 10.


High-throughput interpretation of gene structure changes in human and nonhuman resequencing data, using ACE.

Majoros WH, Campbell MS, Holt C, DeNardo EK, Ware D, Allen AS, Yandell M, Reddy TE.

Bioinformatics. 2017 May 15;33(10):1437-1446. doi: 10.1093/bioinformatics/btw799.


Towards an open grapevine information system.

Adam-Blondon AF, Alaux M, Pommier C, Cantu D, Cheng ZM, Cramer GR, Davies C, Delrot S, Deluc L, Di Gaspero G, Grimplet J, Fennell A, Londo JP, Kersey P, Mattivi F, Naithani S, Neveu P, Nikolski M, Pezzotti M, Reisch BI, Töpfer R, Vivier MA, Ware D, Quesneville H.

Hortic Res. 2016 Nov 23;3:16056. eCollection 2016. Review.


Biostimulation and microbial community profiling reveal insights on RDX transformation in groundwater.

Wang D, Boukhalfa H, Marina O, Ware DS, Goering TJ, Sun F, Daligault HE, Lo CC, Vuyisich M, Starkenburg SR.

Microbiologyopen. 2017 Apr;6(2). doi: 10.1002/mbo3.423. Epub 2016 Nov 17.


Plant Reactome: a resource for plant pathways and comparative analysis.

Naithani S, Preece J, D'Eustachio P, Gupta P, Amarasinghe V, Dharmawardhana PD, Wu G, Fabregat A, Elser JL, Weiser J, Keays M, Fuentes AM, Petryszak R, Stein LD, Ware D, Jaiswal P.

Nucleic Acids Res. 2017 Jan 4;45(D1):D1029-D1039. doi: 10.1093/nar/gkw932. Epub 2016 Oct 30.


A Sorghum Mutant Resource as an Efficient Platform for Gene Discovery in Grasses.

Jiao Y, Burke J, Chopra R, Burow G, Chen J, Wang B, Hayes C, Emendack Y, Ware D, Xin Z.

Plant Cell. 2016 Jul;28(7):1551-62. doi: 10.1105/tpc.16.00373. Epub 2016 Jun 27.


Unveiling the complexity of the maize transcriptome by single-molecule long-read sequencing.

Wang B, Tseng E, Regulski M, Clark TA, Hon T, Jiao Y, Lu Z, Olson A, Stein JC, Ware D.

Nat Commun. 2016 Jun 24;7:11708. doi: 10.1038/ncomms11708.


Lighting up sugars: fluorescent BODIPY-gluco-furanose and -septanose conjugates linked by direct B-O-C bonds.

Liu B, Novikova N, Simpson MC, Timmer MS, Stocker BL, Söhnel T, Ware DC, Brothers PJ.

Org Biomol Chem. 2016 Jun 21;14(23):5205-9. doi: 10.1039/c6ob00726k. Epub 2016 May 20.


Large-scale atlas of microarray data reveals the distinct expression landscape of different tissues in Arabidopsis.

He F, Yoo S, Wang D, Kumari S, Gerstein M, Ware D, Maslov S.

Plant J. 2016 Jun;86(6):472-80. doi: 10.1111/tpj.13175.


The iPlant Collaborative: Cyberinfrastructure for Enabling Data to Discovery for the Life Sciences.

Merchant N, Lyons E, Goff S, Vaughn M, Ware D, Micklos D, Antin P.

PLoS Biol. 2016 Jan 11;14(1):e1002342. doi: 10.1371/journal.pbio.1002342. eCollection 2016 Jan.


Air Toxics Under the Big Sky: Examining the Effectiveness of Authentic Scientific Research on High School Students' Science Skills and Interest.

Ward TJ, Delaloye N, Adams ER, Ware D, Vanek D, Knuth R, Hester CL, Marra NN, Holian A.

Int J Sci Educ. 2016;38(6):905-921. doi: 10.1080/09500693.2016.1167984. Epub 2016 Apr 28.


An ultra-high-density map as a community resource for discerning the genetic basis of quantitative traits in maize.

Liu H, Niu Y, Gonzalez-Portilla PJ, Zhou H, Wang L, Zuo T, Qin C, Tai S, Jansen C, Shen Y, Lin H, Lee M, Ware D, Zhang Z, Lübberstedt T, Pan G.

BMC Genomics. 2015 Dec 21;16:1078. doi: 10.1186/s12864-015-2242-5.


Genome Sequence of a Chromium-Reducing Strain, Bacillus cereus S612.

Wang D, Boukhalfa H, Ware DS, Reimus PW, Daligault HE, Gleasner CD, Johnson SL, Li PE.

Genome Announc. 2015 Dec 10;3(6). pii: e01392-15. doi: 10.1128/genomeA.01392-15.


Higher Incidence of Pulmonary Hypertension in Antiphospholipid Antibody Positive Lupus.

Ware D, Sharma V, Kalekar L, Kamble A, Mahajan A, Gokhale Y.

J Assoc Physicians India. 2015 Apr;63(4):17-20.


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