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Items: 1 to 50 of 62

1.

Assembly, annotation, and comparison of Macrophomina phaseolina isolates from strawberry and other hosts.

Burkhardt AK, Childs KL, Wang J, Ramon ML, Martin FN.

BMC Genomics. 2019 Nov 4;20(1):802. doi: 10.1186/s12864-019-6168-1.

2.

Allelic Variation in the Chloroplast Division Gene FtsZ2-2 Leads to Natural Variation in Chloroplast Size.

Kadirjan-Kalbach DK, Turmo A, Wang J, Smith BC, Chen C, Porter KJ, Childs KL, DellaPenna D, Osteryoung KW.

Plant Physiol. 2019 Nov;181(3):1059-1074. doi: 10.1104/pp.19.00841. Epub 2019 Sep 5.

3.

Evolutionary characteristics of intergenic transcribed regions indicate rare novel genes and widespread noisy transcription in the Poaceae.

Lloyd JP, Bowman MJ, Azodi CB, Sowers RP, Moghe GD, Childs KL, Shiu SH.

Sci Rep. 2019 Aug 20;9(1):12122. doi: 10.1038/s41598-019-47797-y.

4.

Transcriptional Regulation of the Glucose-6-Phosphate/Phosphate Translocator 2 Is Related to Carbon Exchange Across the Chloroplast Envelope.

Weise SE, Liu T, Childs KL, Preiser AL, Katulski HM, Perrin-Porzondek C, Sharkey TD.

Front Plant Sci. 2019 Jun 27;10:827. doi: 10.3389/fpls.2019.00827. eCollection 2019.

5.

Genome Sequencing and Transcriptome Analysis of the Hop Downy Mildew Pathogen Pseudoperonospora humuli Reveal Species-Specific Genes for Molecular Detection.

Rahman A, Góngora-Castillo E, Bowman MJ, Childs KL, Gent DH, Martin FN, Quesada-Ocampo LM.

Phytopathology. 2019 Aug;109(8):1354-1366. doi: 10.1094/PHYTO-11-18-0431-R. Epub 2019 Jun 26.

PMID:
30939079
6.

Corrigendum: Transcriptomics Identifies Modules of Differentially Expressed Genes and Novel Cyclotides in Viola pubescens.

Sternberger AL, Bowman MJ, Kruse CPS, Childs KL, Ballard HE, Wyatt SE.

Front Plant Sci. 2019 Mar 18;10:278. doi: 10.3389/fpls.2019.00278. eCollection 2019.

7.

Author Correction: Origin and evolution of the octoploid strawberry genome.

Edger PP, Poorten TJ, VanBuren R, Hardigan MA, Colle M, McKain MR, Smith RD, Teresi SJ, Nelson ADL, Wai CM, Alger EI, Bird KA, Yocca AE, Pumplin N, Ou S, Ben-Zvi G, Brodt A, Baruch K, Swale T, Shiue L, Acharya CB, Cole GS, Mower JP, Childs KL, Jiang N, Lyons E, Freeling M, Puzey JR, Knapp SJ.

Nat Genet. 2019 Apr;51(4):765. doi: 10.1038/s41588-019-0380-4.

PMID:
30842601
8.

Transcriptomics Identifies Modules of Differentially Expressed Genes and Novel Cyclotides in Viola pubescens.

Sternberger AL, Bowman MJ, Kruse CPS, Childs KL, Ballard HE, Wyatt SE.

Front Plant Sci. 2019 Feb 15;10:156. doi: 10.3389/fpls.2019.00156. eCollection 2019. Erratum in: Front Plant Sci. 2019 Mar 18;10:278.

9.

Origin and evolution of the octoploid strawberry genome.

Edger PP, Poorten TJ, VanBuren R, Hardigan MA, Colle M, McKain MR, Smith RD, Teresi SJ, Nelson ADL, Wai CM, Alger EI, Bird KA, Yocca AE, Pumplin N, Ou S, Ben-Zvi G, Brodt A, Baruch K, Swale T, Shiue L, Acharya CB, Cole GS, Mower JP, Childs KL, Jiang N, Lyons E, Freeling M, Puzey JR, Knapp SJ.

Nat Genet. 2019 Mar;51(3):541-547. doi: 10.1038/s41588-019-0356-4. Epub 2019 Feb 25. Erratum in: Nat Genet. 2019 Apr;51(4):765.

PMID:
30804557
10.

Isoprene Acts as a Signaling Molecule in Gene Networks Important for Stress Responses and Plant Growth.

Zuo Z, Weraduwage SM, Lantz AT, Sanchez LM, Weise SE, Wang J, Childs KL, Sharkey TD.

Plant Physiol. 2019 May;180(1):124-152. doi: 10.1104/pp.18.01391. Epub 2019 Feb 13.

11.

Haplotype-phased genome and evolution of phytonutrient pathways of tetraploid blueberry.

Colle M, Leisner CP, Wai CM, Ou S, Bird KA, Wang J, Wisecaver JH, Yocca AE, Alger EI, Tang H, Xiong Z, Callow P, Ben-Zvi G, Brodt A, Baruch K, Swale T, Shiue L, Song GQ, Childs KL, Schilmiller A, Vorsa N, Buell CR, VanBuren R, Jiang N, Edger PP.

Gigascience. 2019 Mar 1;8(3). pii: giz012. doi: 10.1093/gigascience/giz012.

12.

Single-molecule sequencing and optical mapping yields an improved genome of woodland strawberry (Fragaria vesca) with chromosome-scale contiguity.

Edger PP, VanBuren R, Colle M, Poorten TJ, Wai CM, Niederhuth CE, Alger EI, Ou S, Acharya CB, Wang J, Callow P, McKain MR, Shi J, Collier C, Xiong Z, Mower JP, Slovin JP, Hytönen T, Jiang N, Childs KL, Knapp SJ.

Gigascience. 2018 Feb 1;7(2):1-7. doi: 10.1093/gigascience/gix124.

13.

Dual impact of elevated temperature on plant defence and bacterial virulence in Arabidopsis.

Huot B, Castroverde CDM, Velásquez AC, Hubbard E, Pulman JA, Yao J, Childs KL, Tsuda K, Montgomery BL, He SY.

Nat Commun. 2017 Nov 27;8(1):1808. doi: 10.1038/s41467-017-01674-2.

14.

A modified GC-specific MAKER gene annotation method reveals improved and novel gene predictions of high and low GC content in Oryza sativa.

Bowman MJ, Pulman JA, Liu TL, Childs KL.

BMC Bioinformatics. 2017 Nov 25;18(1):522. doi: 10.1186/s12859-017-1942-z.

15.

Comparative genomics of Spiraeoideae-infecting Erwinia amylovora strains provides novel insight to genetic diversity and identifies the genetic basis of a low-virulence strain.

Zeng Q, Cui Z, Wang J, Childs KL, Sundin GW, Cooley DR, Yang CH, Garofalo E, Eaton A, Huntley RB, Yuan X, Schultes NP.

Mol Plant Pathol. 2018 Jul;19(7):1652-1666. doi: 10.1111/mpp.12647. Epub 2018 Mar 6.

16.

Extensive gene tree discordance and hemiplasy shaped the genomes of North American columnar cacti.

Copetti D, Búrquez A, Bustamante E, Charboneau JLM, Childs KL, Eguiarte LE, Lee S, Liu TL, McMahon MM, Whiteman NK, Wing RA, Wojciechowski MF, Sanderson MJ.

Proc Natl Acad Sci U S A. 2017 Nov 7;114(45):12003-12008. doi: 10.1073/pnas.1706367114. Epub 2017 Oct 23.

17.

Subgenome Dominance in an Interspecific Hybrid, Synthetic Allopolyploid, and a 140-Year-Old Naturally Established Neo-Allopolyploid Monkeyflower.

Edger PP, Smith R, McKain MR, Cooley AM, Vallejo-Marin M, Yuan Y, Bewick AJ, Ji L, Platts AE, Bowman MJ, Childs KL, Washburn JD, Schmitz RJ, Smith GD, Pires JC, Puzey JR.

Plant Cell. 2017 Sep;29(9):2150-2167. doi: 10.1105/tpc.17.00010. Epub 2017 Aug 16.

18.

Correction: Genome, Functional Gene Annotation, and Nuclear Transformation of the Heterokont Oleaginous Alga Nannochloropsis oceanica CCMP1779.

Vieler A, Wu G, Tsai CH, Bullard B, Cornish AJ, Harvey C, Reca IB, Thornburg C, Achawanantakun R, Buehl CJ, Campbell MS, Cavalier D, Childs KL, Clark TJ, Deshpande R, Erickson E, Armenia Ferguson A, Handee W, Kong Q, Li X, Liu B, Lundback S, Peng C, Roston RL, Sanjaya, Simpson JP, TerBush A, Warakanont J, Zäuner S, Farre EM, Hegg EL, Jiang N, Kuo MH, Lu Y, Niyogi KK, Ohlrogge J, Osteryoung KW, Shachar-Hill Y, Sears BB, Sun Y, Takahashi H, Yandell M, Shiu SH, Benning C.

PLoS Genet. 2017 May 23;13(5):e1006802. doi: 10.1371/journal.pgen.1006802. eCollection 2017 May.

19.
20.

Identification, characterization, and gene expression analysis of nucleotide binding site (NB)-type resistance gene homologues in switchgrass.

Frazier TP, Palmer NA, Xie F, Tobias CM, Donze-Reiner TJ, Bombarely A, Childs KL, Shu S, Jenkins JW, Schmutz J, Zhang B, Sarath G, Zhao B.

BMC Genomics. 2016 Nov 8;17(1):892.

21.

Draft Assembly of Elite Inbred Line PH207 Provides Insights into Genomic and Transcriptome Diversity in Maize.

Hirsch CN, Hirsch CD, Brohammer AB, Bowman MJ, Soifer I, Barad O, Shem-Tov D, Baruch K, Lu F, Hernandez AG, Fields CJ, Wright CL, Koehler K, Springer NM, Buckler E, Buell CR, de Leon N, Kaeppler SM, Childs KL, Mikel MA.

Plant Cell. 2016 Nov;28(11):2700-2714. Epub 2016 Nov 1.

22.

Fine mapping of the stem rust resistance gene SrTA10187.

Wiersma AT, Brown LK, Brisco EI, Liu TL, Childs KL, Poland JA, Sehgal SK, Olson EL.

Theor Appl Genet. 2016 Dec;129(12):2369-2378. Epub 2016 Aug 31.

PMID:
27581540
23.

Analysis of salt-induced physiological and proline changes in 46 switchgrass (Panicum virgatum) lines indicates multiple response modes.

Kim J, Liu Y, Zhang X, Zhao B, Childs KL.

Plant Physiol Biochem. 2016 Aug;105:203-212. doi: 10.1016/j.plaphy.2016.04.020. Epub 2016 Apr 13.

PMID:
27111258
24.

Genome-guided investigation of plant natural product biosynthesis.

Kellner F, Kim J, Clavijo BJ, Hamilton JP, Childs KL, Vaillancourt B, Cepela J, Habermann M, Steuernagel B, Clissold L, McLay K, Buell CR, O'Connor SE.

Plant J. 2015 May;82(4):680-92. doi: 10.1111/tpj.12827. Epub 2015 Apr 11. Erratum in: Plant J. 2019 May;98(4):760.

25.

Automated update, revision, and quality control of the maize genome annotations using MAKER-P improves the B73 RefGen_v3 gene models and identifies new genes.

Law M, Childs KL, Campbell MS, Stein JC, Olson AJ, Holt C, Panchy N, Lei J, Jiao D, Andorf CM, Lawrence CJ, Ware D, Shiu SH, Sun Y, Jiang N, Yandell M.

Plant Physiol. 2015 Jan;167(1):25-39. doi: 10.1104/pp.114.245027. Epub 2014 Nov 10.

26.

A root-expressed L-phenylalanine:4-hydroxyphenylpyruvate aminotransferase is required for tropane alkaloid biosynthesis in Atropa belladonna.

Bedewitz MA, Góngora-Castillo E, Uebler JB, Gonzales-Vigil E, Wiegert-Rininger KE, Childs KL, Hamilton JP, Vaillancourt B, Yeo YS, Chappell J, DellaPenna D, Jones AD, Buell CR, Barry CS.

Plant Cell. 2014 Sep;26(9):3745-62. doi: 10.1105/tpc.114.130534. Epub 2014 Sep 16.

27.

Nucleotide polymorphism and copy number variant detection using exome capture and next-generation sequencing in the polyploid grass Panicum virgatum.

Evans J, Kim J, Childs KL, Vaillancourt B, Crisovan E, Nandety A, Gerhardt DJ, Richmond TA, Jeddeloh JA, Kaeppler SM, Casler MD, Buell CR.

Plant J. 2014 Sep;79(6):993-1008. doi: 10.1111/tpj.12601. Epub 2014 Aug 11.

28.

An improved genome release (version Mt4.0) for the model legume Medicago truncatula.

Tang H, Krishnakumar V, Bidwell S, Rosen B, Chan A, Zhou S, Gentzbittel L, Childs KL, Yandell M, Gundlach H, Mayer KF, Schwartz DC, Town CD.

BMC Genomics. 2014 Apr 27;15:312. doi: 10.1186/1471-2164-15-312.

29.

Phenotypic and Transcriptional Analysis of Divergently Selected Maize Populations Reveals the Role of Developmental Timing in Seed Size Determination.

Sekhon RS, Hirsch CN, Childs KL, Breitzman MW, Kell P, Duvick S, Spalding EP, Buell CR, de Leon N, Kaeppler SM.

Plant Physiol. 2014 Jun;165(2):658-669. Epub 2014 Apr 7.

30.

MAKER-P: a tool kit for the rapid creation, management, and quality control of plant genome annotations.

Campbell MS, Law M, Holt C, Stein JC, Moghe GD, Hufnagel DE, Lei J, Achawanantakun R, Jiao D, Lawrence CJ, Ware D, Shiu SH, Childs KL, Sun Y, Jiang N, Yandell M.

Plant Physiol. 2014 Feb;164(2):513-24. doi: 10.1104/pp.113.230144. Epub 2013 Dec 4.

31.

Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data.

Kawahara Y, de la Bastide M, Hamilton JP, Kanamori H, McCombie WR, Ouyang S, Schwartz DC, Tanaka T, Wu J, Zhou S, Childs KL, Davidson RM, Lin H, Quesada-Ocampo L, Vaillancourt B, Sakai H, Lee SS, Kim J, Numa H, Itoh T, Buell CR, Matsumoto T.

Rice (N Y). 2013 Feb 6;6(1):4. doi: 10.1186/1939-8433-6-4.

32.

Development of transcriptomic resources for interrogating the biosynthesis of monoterpene indole alkaloids in medicinal plant species.

Góngora-Castillo E, Childs KL, Fedewa G, Hamilton JP, Liscombe DK, Magallanes-Lundback M, Mandadi KK, Nims E, Runguphan W, Vaillancourt B, Varbanova-Herde M, Dellapenna D, McKnight TD, O'Connor S, Buell CR.

PLoS One. 2012;7(12):e52506. doi: 10.1371/journal.pone.0052506. Epub 2012 Dec 26.

33.

Genome, functional gene annotation, and nuclear transformation of the heterokont oleaginous alga Nannochloropsis oceanica CCMP1779.

Vieler A, Wu G, Tsai CH, Bullard B, Cornish AJ, Harvey C, Reca IB, Thornburg C, Achawanantakun R, Buehl CJ, Campbell MS, Cavalier D, Childs KL, Clark TJ, Deshpande R, Erickson E, Armenia Ferguson A, Handee W, Kong Q, Li X, Liu B, Lundback S, Peng C, Roston RL, Sanjaya, Simpson JP, Terbush A, Warakanont J, Zäuner S, Farre EM, Hegg EL, Jiang N, Kuo MH, Lu Y, Niyogi KK, Ohlrogge J, Osteryoung KW, Shachar-Hill Y, Sears BB, Sun Y, Takahashi H, Yandell M, Shiu SH, Benning C.

PLoS Genet. 2012;8(11):e1003064. doi: 10.1371/journal.pgen.1003064. Epub 2012 Nov 15. Erratum in: PLoS Genet. 2017 May 23;13(5):e1006802.

34.

Transcriptional and metabolic analysis of senescence induced by preventing pollination in maize.

Sekhon RS, Childs KL, Santoro N, Foster CE, Buell CR, de Leon N, Kaeppler SM.

Plant Physiol. 2012 Aug;159(4):1730-44. doi: 10.1104/pp.112.199224. Epub 2012 Jun 25.

35.

Expression profiling of Cucumis sativus in response to infection by Pseudoperonospora cubensis.

Adhikari BN, Savory EA, Vaillancourt B, Childs KL, Hamilton JP, Day B, Buell CR.

PLoS One. 2012;7(4):e34954. doi: 10.1371/journal.pone.0034954. Epub 2012 Apr 24.

36.

The Biofuel Feedstock Genomics Resource: a web-based portal and database to enable functional genomics of plant biofuel feedstock species.

Childs KL, Konganti K, Buell CR.

Database (Oxford). 2012 Jan 15;2012:bar061. doi: 10.1093/database/bar061. Print 2012.

37.

The transcriptome of the reference potato genome Solanum tuberosum Group Phureja clone DM1-3 516R44.

Massa AN, Childs KL, Lin H, Bryan GJ, Giuliano G, Buell CR.

PLoS One. 2011;6(10):e26801. doi: 10.1371/journal.pone.0026801. Epub 2011 Oct 28.

38.

Gene coexpression network analysis as a source of functional annotation for rice genes.

Childs KL, Davidson RM, Buell CR.

PLoS One. 2011;6(7):e22196. doi: 10.1371/journal.pone.0022196. Epub 2011 Jul 22.

39.

A stereoselective hydroxylation step of alkaloid biosynthesis by a unique cytochrome P450 in Catharanthus roseus.

Giddings LA, Liscombe DK, Hamilton JP, Childs KL, DellaPenna D, Buell CR, O'Connor SE.

J Biol Chem. 2011 May 13;286(19):16751-7. doi: 10.1074/jbc.M111.225383. Epub 2011 Mar 24.

40.

Genome-wide atlas of transcription during maize development.

Sekhon RS, Lin H, Childs KL, Hansey CN, Buell CR, de Leon N, Kaeppler SM.

Plant J. 2011 May;66(4):553-63. doi: 10.1111/j.1365-313X.2011.04527.x. Epub 2011 Mar 9.

41.

Bovine Genome Database: integrated tools for genome annotation and discovery.

Childers CP, Reese JT, Sundaram JP, Vile DC, Dickens CM, Childs KL, Salih H, Bennett AK, Hagen DE, Adelson DL, Elsik CG.

Nucleic Acids Res. 2011 Jan;39(Database issue):D830-4. doi: 10.1093/nar/gkq1235. Epub 2010 Dec 1.

42.

Bovine Genome Database: supporting community annotation and analysis of the Bos taurus genome.

Reese JT, Childers CP, Sundaram JP, Dickens CM, Childs KL, Vile DC, Elsik CG.

BMC Genomics. 2010 Nov 19;11:645. doi: 10.1186/1471-2164-11-645.

43.

Hymenoptera Genome Database: integrated community resources for insect species of the order Hymenoptera.

Munoz-Torres MC, Reese JT, Childers CP, Bennett AK, Sundaram JP, Childs KL, Anzola JM, Milshina N, Elsik CG.

Nucleic Acids Res. 2011 Jan;39(Database issue):D658-62. doi: 10.1093/nar/gkq1145. Epub 2010 Nov 10.

44.

Genomewide SNP variation reveals relationships among landraces and modern varieties of rice.

McNally KL, Childs KL, Bohnert R, Davidson RM, Zhao K, Ulat VJ, Zeller G, Clark RM, Hoen DR, Bureau TE, Stokowski R, Ballinger DG, Frazer KA, Cox DR, Padhukasahasram B, Bustamante CD, Weigel D, Mackill DJ, Bruskiewich RM, Rätsch G, Buell CR, Leung H, Leach JE.

Proc Natl Acad Sci U S A. 2009 Jul 28;106(30):12273-8. doi: 10.1073/pnas.0900992106. Epub 2009 Jul 13.

45.

Plant genome annotation methods.

Ouyang S, Thibaud-Nissen F, Childs KL, Zhu W, Buell CR.

Methods Mol Biol. 2009;513:263-82. doi: 10.1007/978-1-59745-427-8_14.

PMID:
19347655
46.

Genomic and genetic database resources for the grasses.

Childs KL.

Plant Physiol. 2009 Jan;149(1):132-6. doi: 10.1104/pp.108.129593. Review. No abstract available.

47.

Identification and characterization of lineage-specific genes within the Poaceae.

Campbell MA, Zhu W, Jiang N, Lin H, Ouyang S, Childs KL, Haas BJ, Hamilton JP, Buell CR.

Plant Physiol. 2007 Dec;145(4):1311-22. Epub 2007 Oct 19.

48.

Computational and transcriptional evidence for microRNAs in the honey bee genome.

Weaver DB, Anzola JM, Evans JD, Reid JG, Reese JT, Childs KL, Zdobnov EM, Samanta MP, Miller J, Elsik CG.

Genome Biol. 2007;8(6):R97.

49.

The TIGR Plant Transcript Assemblies database.

Childs KL, Hamilton JP, Zhu W, Ly E, Cheung F, Wu H, Rabinowicz PD, Town CD, Buell CR, Chan AP.

Nucleic Acids Res. 2007 Jan;35(Database issue):D846-51. Epub 2006 Nov 6.

50.

Community annotation: procedures, protocols, and supporting tools.

Elsik CG, Worley KC, Zhang L, Milshina NV, Jiang H, Reese JT, Childs KL, Venkatraman A, Dickens CM, Weinstock GM, Gibbs RA.

Genome Res. 2006 Nov;16(11):1329-33. Epub 2006 Oct 25.

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