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A Robust Methodology for Assessing Differential Homeolog Contributions to the Transcriptomes of Allopolyploids.

Boatwright JL, McIntyre LM, Morse AM, Chen S, Yoo MJ, Koh J, Soltis PS, Soltis DE, Barbazuk WB.

Genetics. 2018 Nov;210(3):883-894. doi: 10.1534/genetics.118.301564. Epub 2018 Sep 13.


The maize W22 genome provides a foundation for functional genomics and transposon biology.

Springer NM, Anderson SN, Andorf CM, Ahern KR, Bai F, Barad O, Barbazuk WB, Bass HW, Baruch K, Ben-Zvi G, Buckler ES, Bukowski R, Campbell MS, Cannon EKS, Chomet P, Dawe RK, Davenport R, Dooner HK, Du LH, Du C, Easterling KA, Gault C, Guan JC, Hunter CT, Jander G, Jiao Y, Koch KE, Kol G, Köllner TG, Kudo T, Li Q, Lu F, Mayfield-Jones D, Mei W, McCarty DR, Noshay JM, Portwood JL 2nd, Ronen G, Settles AM, Shem-Tov D, Shi J, Soifer I, Stein JC, Stitzer MC, Suzuki M, Vera DL, Vollbrecht E, Vrebalov JT, Ware D, Wei S, Wimalanathan K, Woodhouse MR, Xiong W, Brutnell TP.

Nat Genet. 2018 Sep;50(9):1282-1288. doi: 10.1038/s41588-018-0158-0. Epub 2018 Jul 30.


Population genomics of the eastern cottonwood (Populus deltoides).

Fahrenkrog AM, Neves LG, Resende MFR Jr, Dervinis C, Davenport R, Barbazuk WB, Kirst M.

Ecol Evol. 2017 Oct 10;7(22):9426-9440. doi: 10.1002/ece3.3466. eCollection 2017 Nov.


Genome Sequences of Mycobacteriophages Findley, Hurricane, and TBond007.

Saha S, Yan W, Washington JM, Davis WB, Barbazuk WB, Medellin R, Mendez A, Ramos JR, Sadana R, Edmonds M, Feng G, Ilyas M, Kaiser J, Monroe SJ, Pham TV, Cresawn SG, Garlena RA, Stoner TH, Russell DA, Pope WH, Jacobs-Sera D, Hatfull GF.

Genome Announc. 2017 Nov 9;5(45). pii: e01123-17. doi: 10.1128/genomeA.01123-17.


Evolutionarily Conserved Alternative Splicing Across Monocots.

Mei W, Boatwright L, Feng G, Schnable JC, Barbazuk WB.

Genetics. 2017 Oct;207(2):465-480. doi: 10.1534/genetics.117.300189. Epub 2017 Aug 24.


Identification and analysis of alternative splicing events in Phaseolus vulgaris and Glycine max.

Iñiguez LP, Ramírez M, Barbazuk WB, Hernández G.

BMC Genomics. 2017 Aug 22;18(1):650. doi: 10.1186/s12864-017-4054-2.


A Comprehensive Analysis of Alternative Splicing in Paleopolyploid Maize.

Mei W, Liu S, Schnable JC, Yeh CT, Springer NM, Schnable PS, Barbazuk WB.

Front Plant Sci. 2017 May 10;8:694. doi: 10.3389/fpls.2017.00694. eCollection 2017.


Evolution of the 3R-MYB Gene Family in Plants.

Feng G, Burleigh JG, Braun EL, Mei W, Barbazuk WB.

Genome Biol Evol. 2017 Apr 20. doi: 10.1093/gbe/evx056. [Epub ahead of print]


Detecting alternatively spliced transcript isoforms from single-molecule long-read sequences without a reference genome.

Liu X, Mei W, Soltis PS, Soltis DE, Barbazuk WB.

Mol Ecol Resour. 2017 Nov;17(6):1243-1256. doi: 10.1111/1755-0998.12670. Epub 2017 Jun 5.


Aberrant splicing in maize rough endosperm3 reveals a conserved role for U12 splicing in eukaryotic multicellular development.

Gault CM, Martin F, Mei W, Bai F, Black JB, Barbazuk WB, Settles AM.

Proc Natl Acad Sci U S A. 2017 Mar 14;114(11):E2195-E2204. doi: 10.1073/pnas.1616173114. Epub 2017 Feb 27.


Genome-wide association study reveals putative regulators of bioenergy traits in Populus deltoides.

Fahrenkrog AM, Neves LG, Resende MF Jr, Vazquez AI, de Los Campos G, Dervinis C, Sykes R, Davis M, Davenport R, Barbazuk WB, Kirst M.

New Phytol. 2017 Jan;213(2):799-811. doi: 10.1111/nph.14154. Epub 2016 Sep 6.


A Comparative Analysis of Gene Expression Profiles during Skin Regeneration in Mus and Acomys.

Brant JO, Lopez MC, Baker HV, Barbazuk WB, Maden M.

PLoS One. 2015 Nov 25;10(11):e0142931. doi: 10.1371/journal.pone.0142931. eCollection 2015.


Cellular events during scar-free skin regeneration in the spiny mouse, Acomys.

Brant JO, Yoon JH, Polvadore T, Barbazuk WB, Maden M.

Wound Repair Regen. 2016 Jan-Feb;24(1):75-88. doi: 10.1111/wrr.12385. Epub 2016 Jan 19.


MarkerMiner 1.0: A new application for phylogenetic marker development using angiosperm transcriptomes.

Chamala S, García N, Godden GT, Krishnakumar V, Jordon-Thaden IE, De Smet R, Barbazuk WB, Soltis DE, Soltis PS.

Appl Plant Sci. 2015 Apr 6;3(4). pii: apps.1400115. doi: 10.3732/apps.1400115. eCollection 2015 Apr.


Genome-wide identification of evolutionarily conserved alternative splicing events in flowering plants.

Chamala S, Feng G, Chavarro C, Barbazuk WB.

Front Bioeng Biotechnol. 2015 Mar 26;3:33. doi: 10.3389/fbioe.2015.00033. eCollection 2015.


Caffeine exposure alters cardiac gene expression in embryonic cardiomyocytes.

Fang X, Mei W, Barbazuk WB, Rivkees SA, Wendler CC.

Am J Physiol Regul Integr Comp Physiol. 2014 Dec 15;307(12):R1471-87. doi: 10.1152/ajpregu.00307.2014. Epub 2014 Oct 29.


Primers for low-copy nuclear genes in Metrosideros and cross-amplification in Myrtaceae.

Pillon Y, Johansen J, Sakishima T, Chamala S, Barbazuk WB, Stacy EA.

Appl Plant Sci. 2014 Oct 2;2(10). pii: apps.1400049. doi: 10.3732/apps.1400049. eCollection 2014 Oct.


Adaptive expansion of the maize maternally expressed gene (Meg) family involves changes in expression patterns and protein secondary structures of its members.

Xiong Y, Mei W, Kim ED, Mukherjee K, Hassanein H, Barbazuk WB, Sung S, Kolaczkowski B, Kang BH.

BMC Plant Biol. 2014 Aug 1;14:204. doi: 10.1186/s12870-014-0204-8.


Effects on specific promoter DNA methylation in zebrafish embryos and larvae following benzo[a]pyrene exposure.

Corrales J, Fang X, Thornton C, Mei W, Barbazuk WB, Duke M, Scheffler BE, Willett KL.

Comp Biochem Physiol C Toxicol Pharmacol. 2014 Jun;163:37-46. doi: 10.1016/j.cbpc.2014.02.005. Epub 2014 Feb 24.


Assembly and validation of the genome of the nonmodel basal angiosperm Amborella.

Chamala S, Chanderbali AS, Der JP, Lan T, Walts B, Albert VA, dePamphilis CW, Leebens-Mack J, Rounsley S, Schuster SC, Wing RA, Xiao N, Moore R, Soltis PS, Soltis DE, Barbazuk WB.

Science. 2013 Dec 20;342(6165):1516-7. doi: 10.1126/science.1241130.


A high-density gene map of loblolly pine (Pinus taeda L.) based on exome sequence capture genotyping.

Neves LG, Davis JM, Barbazuk WB, Kirst M.

G3 (Bethesda). 2014 Jan 10;4(1):29-37. doi: 10.1534/g3.113.008714.


Validation of reference transcripts in strawberry (Fragaria spp.).

Clancy MA, Rosli HG, Chamala S, Barbazuk WB, Civello PM, Folta KM.

Mol Genet Genomics. 2013 Dec;288(12):671-81. doi: 10.1007/s00438-013-0780-6. Epub 2013 Sep 24.


Primers for low-copy nuclear genes in the Hawaiian endemic Clermontia (Campanulaceae) and cross-amplification in Lobelioideae.

Pillon Y, Johansen J, Sakishima T, Chamala S, Barbazuk WB, Stacy EA.

Appl Plant Sci. 2013 May 16;1(6). pii: apps.1200450. doi: 10.3732/apps.1200450. eCollection 2013 Jun.


Whole-exome targeted sequencing of the uncharacterized pine genome.

Neves LG, Davis JM, Barbazuk WB, Kirst M.

Plant J. 2013 Jul;75(1):146-156. doi: 10.1111/tpj.12193. Epub 2013 May 7.


Potential use of low-copy nuclear genes in DNA barcoding: a comparison with plastid genes in two Hawaiian plant radiations.

Pillon Y, Johansen J, Sakishima T, Chamala S, Barbazuk WB, Roalson EH, Price DK, Stacy EA.

BMC Evol Biol. 2013 Feb 9;13:35. doi: 10.1186/1471-2148-13-35.


Next-generation sequencing and genome evolution in allopolyploids.

Buggs RJ, Renny-Byfield S, Chester M, Jordon-Thaden IE, Viccini LF, Chamala S, Leitch AR, Schnable PS, Barbazuk WB, Soltis PS, Soltis DE.

Am J Bot. 2012 Feb;99(2):372-82. doi: 10.3732/ajb.1100395. Epub 2012 Jan 20. Review.


Rapid, repeated, and clustered loss of duplicate genes in allopolyploid plant populations of independent origin.

Buggs RJ, Chamala S, Wu W, Tate JA, Schnable PS, Soltis DE, Soltis PS, Barbazuk WB.

Curr Biol. 2012 Feb 7;22(3):248-52. doi: 10.1016/j.cub.2011.12.027. Epub 2012 Jan 19.


Transcriptomic shock generates evolutionary novelty in a newly formed, natural allopolyploid plant.

Buggs RJ, Zhang L, Miles N, Tate JA, Gao L, Wei W, Schnable PS, Barbazuk WB, Soltis PS, Soltis DE.

Curr Biol. 2011 Apr 12;21(7):551-6. doi: 10.1016/j.cub.2011.02.016. Epub 2011 Mar 17.


Silencing of soybean seed storage proteins results in a rebalanced protein composition preserving seed protein content without major collateral changes in the metabolome and transcriptome.

Schmidt MA, Barbazuk WB, Sandford M, May G, Song Z, Zhou W, Nikolau BJ, Herman EM.

Plant Physiol. 2011 May;156(1):330-45. doi: 10.1104/pp.111.173807. Epub 2011 Mar 10.


SNP discovery by transcriptome pyrosequencing.

Barbazuk WB, Schnable PS.

Methods Mol Biol. 2011;729:225-46. doi: 10.1007/978-1-61779-065-2_15.


Functional analysis of the activation domain of RF2a, a rice transcription factor.

Ordiz MI, Yang J, Barbazuk WB, Beachy RN.

Plant Biotechnol J. 2010 Sep;8(7):835-44. doi: 10.1111/j.1467-7652.2010.00520.x. Epub 2010 Apr 7.


Characterization of duplicate gene evolution in the recent natural allopolyploid Tragopogon miscellus by next-generation sequencing and Sequenom iPLEX MassARRAY genotyping.

Buggs RJ, Chamala S, Wu W, Gao L, May GD, Schnable PS, Soltis DE, Soltis PS, Barbazuk WB.

Mol Ecol. 2010 Mar;19 Suppl 1:132-46. doi: 10.1111/j.1365-294X.2009.04469.x.


Changes in protein abundance during powdery mildew infection of leaf tissues of Cabernet Sauvignon grapevine (Vitis vinifera L.).

Marsh E, Alvarez S, Hicks LM, Barbazuk WB, Qiu W, Kovacs L, Schachtman D.

Proteomics. 2010 May;10(10):2057-64. doi: 10.1002/pmic.200900712.


Repeat subtraction-mediated sequence capture from a complex genome.

Fu Y, Springer NM, Gerhardt DJ, Ying K, Yeh CT, Wu W, Swanson-Wagner R, D'Ascenzo M, Millard T, Freeberg L, Aoyama N, Kitzman J, Burgess D, Richmond T, Albert TJ, Barbazuk WB, Jeddeloh JA, Schnable PS.

Plant J. 2010 Jun 1;62(5):898-909. doi: 10.1111/j.1365-313X.2010.04196.x. Epub 2010 Mar 4.


The B73 maize genome: complexity, diversity, and dynamics.

Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, Pasternak S, Liang C, Zhang J, Fulton L, Graves TA, Minx P, Reily AD, Courtney L, Kruchowski SS, Tomlinson C, Strong C, Delehaunty K, Fronick C, Courtney B, Rock SM, Belter E, Du F, Kim K, Abbott RM, Cotton M, Levy A, Marchetto P, Ochoa K, Jackson SM, Gillam B, Chen W, Yan L, Higginbotham J, Cardenas M, Waligorski J, Applebaum E, Phelps L, Falcone J, Kanchi K, Thane T, Scimone A, Thane N, Henke J, Wang T, Ruppert J, Shah N, Rotter K, Hodges J, Ingenthron E, Cordes M, Kohlberg S, Sgro J, Delgado B, Mead K, Chinwalla A, Leonard S, Crouse K, Collura K, Kudrna D, Currie J, He R, Angelova A, Rajasekar S, Mueller T, Lomeli R, Scara G, Ko A, Delaney K, Wissotski M, Lopez G, Campos D, Braidotti M, Ashley E, Golser W, Kim H, Lee S, Lin J, Dujmic Z, Kim W, Talag J, Zuccolo A, Fan C, Sebastian A, Kramer M, Spiegel L, Nascimento L, Zutavern T, Miller B, Ambroise C, Muller S, Spooner W, Narechania A, Ren L, Wei S, Kumari S, Faga B, Levy MJ, McMahan L, Van Buren P, Vaughn MW, Ying K, Yeh CT, Emrich SJ, Jia Y, Kalyanaraman A, Hsia AP, Barbazuk WB, Baucom RS, Brutnell TP, Carpita NC, Chaparro C, Chia JM, Deragon JM, Estill JC, Fu Y, Jeddeloh JA, Han Y, Lee H, Li P, Lisch DR, Liu S, Liu Z, Nagel DH, McCann MC, SanMiguel P, Myers AM, Nettleton D, Nguyen J, Penning BW, Ponnala L, Schneider KL, Schwartz DC, Sharma A, Soderlund C, Springer NM, Sun Q, Wang H, Waterman M, Westerman R, Wolfgruber TK, Yang L, Yu Y, Zhang L, Zhou S, Zhu Q, Bennetzen JL, Dawe RK, Jiang J, Jiang N, Presting GG, Wessler SR, Aluru S, Martienssen RA, Clifton SW, McCombie WR, Wing RA, Wilson RK.

Science. 2009 Nov 20;326(5956):1112-5. doi: 10.1126/science.1178534. Erratum in: Science. 2012 Aug 31;337(6098):1040.


Maize inbreds exhibit high levels of copy number variation (CNV) and presence/absence variation (PAV) in genome content.

Springer NM, Ying K, Fu Y, Ji T, Yeh CT, Jia Y, Wu W, Richmond T, Kitzman J, Rosenbaum H, Iniguez AL, Barbazuk WB, Jeddeloh JA, Nettleton D, Schnable PS.

PLoS Genet. 2009 Nov;5(11):e1000734. doi: 10.1371/journal.pgen.1000734. Epub 2009 Nov 20.


High-throughput genetic mapping of mutants via quantitative single nucleotide polymorphism typing.

Liu S, Chen HD, Makarevitch I, Shirmer R, Emrich SJ, Dietrich CR, Barbazuk WB, Springer NM, Schnable PS.

Genetics. 2010 Jan;184(1):19-26. doi: 10.1534/genetics.109.107557. Epub 2009 Nov 2.


On the origins of species: does evolution repeat itself in polyploid populations of independent origin?

Soltis DE, Buggs RJ, Barbazuk WB, Schnable PS, Soltis PS.

Cold Spring Harb Symp Quant Biol. 2009;74:215-23. doi: 10.1101/sqb.2009.74.007. Epub 2009 Aug 17. Review.


Alternative splicing of anciently exonized 5S rRNA regulates plant transcription factor TFIIIA.

Fu Y, Bannach O, Chen H, Teune JH, Schmitz A, Steger G, Xiong L, Barbazuk WB.

Genome Res. 2009 May;19(5):913-21. doi: 10.1101/gr.086876.108. Epub 2009 Feb 10.


Genome-wide analyses of alternative splicing in plants: opportunities and challenges.

Barbazuk WB, Fu Y, McGinnis KM.

Genome Res. 2008 Sep;18(9):1381-92. doi: 10.1101/gr.053678.106. Epub 2008 Jul 30. Review.


Novel and nodulation-regulated microRNAs in soybean roots.

Subramanian S, Fu Y, Sunkar R, Barbazuk WB, Zhu JK, Yu O.

BMC Genomics. 2008 Apr 10;9:160. doi: 10.1186/1471-2164-9-160.


The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants.

Rensing SA, Lang D, Zimmer AD, Terry A, Salamov A, Shapiro H, Nishiyama T, Perroud PF, Lindquist EA, Kamisugi Y, Tanahashi T, Sakakibara K, Fujita T, Oishi K, Shin-I T, Kuroki Y, Toyoda A, Suzuki Y, Hashimoto S, Yamaguchi K, Sugano S, Kohara Y, Fujiyama A, Anterola A, Aoki S, Ashton N, Barbazuk WB, Barker E, Bennetzen JL, Blankenship R, Cho SH, Dutcher SK, Estelle M, Fawcett JA, Gundlach H, Hanada K, Heyl A, Hicks KA, Hughes J, Lohr M, Mayer K, Melkozernov A, Murata T, Nelson DR, Pils B, Prigge M, Reiss B, Renner T, Rombauts S, Rushton PJ, Sanderfoot A, Schween G, Shiu SH, Stueber K, Theodoulou FL, Tu H, Van de Peer Y, Verrier PJ, Waters E, Wood A, Yang L, Cove D, Cuming AC, Hasebe M, Lucas S, Mishler BD, Reski R, Grigoriev IV, Quatrano RS, Boore JL.

Science. 2008 Jan 4;319(5859):64-9. Epub 2007 Dec 13.


SNP discovery via 454 transcriptome sequencing.

Barbazuk WB, Emrich SJ, Chen HD, Li L, Schnable PS.

Plant J. 2007 Sep;51(5):910-8. Epub 2007 Jul 27.


Natural variation for alleles under epigenetic control by the maize chromomethylase zmet2.

Makarevitch I, Stupar RM, Iniguez AL, Haun WJ, Barbazuk WB, Kaeppler SM, Springer NM.

Genetics. 2007 Oct;177(2):749-60. Epub 2007 Jul 29.


SNP Mining from Maize 454 EST Sequences.

Barbazuk WB, Emrich S, Schnable PS.

CSH Protoc. 2007 Jul 1;2007:pdb.prot4786. doi: 10.1101/pdb.prot4786.


Gene discovery and annotation using LCM-454 transcriptome sequencing.

Emrich SJ, Barbazuk WB, Li L, Schnable PS.

Genome Res. 2007 Jan;17(1):69-73. Epub 2006 Nov 9.


Evolution of sensory complexity recorded in a myxobacterial genome.

Goldman BS, Nierman WC, Kaiser D, Slater SC, Durkin AS, Eisen JA, Ronning CM, Barbazuk WB, Blanchard M, Field C, Halling C, Hinkle G, Iartchuk O, Kim HS, Mackenzie C, Madupu R, Miller N, Shvartsbeyn A, Sullivan SA, Vaudin M, Wiegand R, Kaplan HB.

Proc Natl Acad Sci U S A. 2006 Oct 10;103(41):15200-5. Epub 2006 Oct 2. Erratum in: Proc Natl Acad Sci U S A. 2006 Dec 19;103(51):19605. Eisen, J [corrected to Eisen, J A].


Uneven chromosome contraction and expansion in the maize genome.

Bruggmann R, Bharti AK, Gundlach H, Lai J, Young S, Pontaroli AC, Wei F, Haberer G, Fuks G, Du C, Raymond C, Estep MC, Liu R, Bennetzen JL, Chan AP, Rabinowicz PD, Quackenbush J, Barbazuk WB, Wing RA, Birren B, Nusbaum C, Rounsley S, Mayer KF, Messing J.

Genome Res. 2006 Oct;16(10):1241-51. Epub 2006 Aug 10.


The TIGR Maize Database.

Chan AP, Pertea G, Cheung F, Lee D, Zheng L, Whitelaw C, Pontaroli AC, SanMiguel P, Yuan Y, Bennetzen J, Barbazuk WB, Quackenbush J, Rabinowicz PD.

Nucleic Acids Res. 2006 Jan 1;34(Database issue):D771-6.

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