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Items: 44

1.

Genome-wide association study (GWAS) of leaf cuticular wax components in Camelina sativa identifies genetic loci related to intracellular wax transport.

Luo Z, Tomasi P, Fahlgren N, Abdel-Haleem H.

BMC Plant Biol. 2019 May 7;19(1):187. doi: 10.1186/s12870-019-1776-0.

2.

Antiviral ARGONAUTEs Against Turnip Crinkle Virus Revealed by Image-Based Trait Analysis.

Zheng X, Fahlgren N, Abbasi A, Berry JC, Carrington JC.

Plant Physiol. 2019 Jul;180(3):1418-1435. doi: 10.1104/pp.19.00121. Epub 2019 May 1.

3.

Genetic Diversity and Population Structure of a Camelina sativa Spring Panel.

Luo Z, Brock J, Dyer JM, Kutchan T, Schachtman D, Augustin M, Ge Y, Fahlgren N, Abdel-Haleem H.

Front Plant Sci. 2019 Feb 20;10:184. doi: 10.3389/fpls.2019.00184. eCollection 2019.

4.

An automated, high-throughput method for standardizing image color profiles to improve image-based plant phenotyping.

Berry JC, Fahlgren N, Pokorny AA, Bart RS, Veley KM.

PeerJ. 2018 Oct 4;6:e5727. doi: 10.7717/peerj.5727. eCollection 2018.

5.

Components of Water Use Efficiency Have Unique Genetic Signatures in the Model C4 Grass Setaria.

Feldman MJ, Ellsworth PZ, Fahlgren N, Gehan MA, Cousins AB, Baxter I.

Plant Physiol. 2018 Oct;178(2):699-715. doi: 10.1104/pp.18.00146. Epub 2018 Aug 9.

6.

Raspberry Pi-powered imaging for plant phenotyping.

Tovar JC, Hoyer JS, Lin A, Tielking A, Callen ST, Elizabeth Castillo S, Miller M, Tessman M, Fahlgren N, Carrington JC, Nusinow DA, Gehan MA.

Appl Plant Sci. 2018 Mar 31;6(3):e1031. doi: 10.1002/aps3.1031. eCollection 2018 Mar.

7.

PlantCV v2: Image analysis software for high-throughput plant phenotyping.

Gehan MA, Fahlgren N, Abbasi A, Berry JC, Callen ST, Chavez L, Doust AN, Feldman MJ, Gilbert KB, Hodge JG, Hoyer JS, Lin A, Liu S, Lizárraga C, Lorence A, Miller M, Platon E, Tessman M, Sax T.

PeerJ. 2017 Dec 1;5:e4088. doi: 10.7717/peerj.4088. eCollection 2017.

8.

Plant scientists: GM technology is safe.

Fahlgren N, Bart R, Herrera-Estrella L, Rellán-Álvarez R, Chitwood DH, Dinneny JR.

Science. 2016 Feb 19;351(6275):824. doi: 10.1126/science.351.6275.824-a. Epub 2016 Feb 18. No abstract available.

PMID:
26912883
9.

Preparation of Multiplexed Small RNA Libraries From Plants.

Gilbert KB, Fahlgren N, Kasschau KD, Chapman EJ, Carrington JC, Carbonell A.

Bio Protoc. 2014 Nov 5;4(21). pii: e1275.

10.

CG gene body DNA methylation changes and evolution of duplicated genes in cassava.

Wang H, Beyene G, Zhai J, Feng S, Fahlgren N, Taylor NJ, Bart R, Carrington JC, Jacobsen SE, Ausin I.

Proc Natl Acad Sci U S A. 2015 Nov 3;112(44):13729-34. doi: 10.1073/pnas.1519067112. Epub 2015 Oct 19.

11.

P-SAMS: a web site for plant artificial microRNA and synthetic trans-acting small interfering RNA design.

Fahlgren N, Hill ST, Carrington JC, Carbonell A.

Bioinformatics. 2016 Jan 1;32(1):157-8. doi: 10.1093/bioinformatics/btv534. Epub 2015 Sep 17.

12.

A Versatile Phenotyping System and Analytics Platform Reveals Diverse Temporal Responses to Water Availability in Setaria.

Fahlgren N, Feldman M, Gehan MA, Wilson MS, Shyu C, Bryant DW, Hill ST, McEntee CJ, Warnasooriya SN, Kumar I, Ficor T, Turnipseed S, Gilbert KB, Brutnell TP, Carrington JC, Mockler TC, Baxter I.

Mol Plant. 2015 Oct 5;8(10):1520-35. doi: 10.1016/j.molp.2015.06.005. Epub 2015 Jun 20.

13.

Highly specific gene silencing in a monocot species by artificial microRNAs derived from chimeric miRNA precursors.

Carbonell A, Fahlgren N, Mitchell S, Cox KL Jr, Reilly KC, Mockler TC, Carrington JC.

Plant J. 2015 Jun;82(6):1061-75. doi: 10.1111/tpj.12835. Epub 2015 May 20.

14.

Roles and programming of Arabidopsis ARGONAUTE proteins during Turnip mosaic virus infection.

Garcia-Ruiz H, Carbonell A, Hoyer JS, Fahlgren N, Gilbert KB, Takeda A, Giampetruzzi A, Garcia Ruiz MT, McGinn MG, Lowery N, Martinez Baladejo MT, Carrington JC.

PLoS Pathog. 2015 Mar 25;11(3):e1004755. doi: 10.1371/journal.ppat.1004755. eCollection 2015 Mar.

15.

Correction. Arabidopsis RNA-dependent RNA polymerases and dicer-like proteins in antiviral defense and small interfering RNA biogenesis during Turnip mosaic virus infection.

Garcia-Ruiz H, Takeda A, Chapman EJ, Sullivan CM, Fahlgren N, Brempelis KJ, Carrington JC.

Plant Cell. 2015 Mar;27(3):944-5. doi: 10.1105/tpc.15.00204. Epub 2015 Mar 17. No abstract available.

16.

Lights, camera, action: high-throughput plant phenotyping is ready for a close-up.

Fahlgren N, Gehan MA, Baxter I.

Curr Opin Plant Biol. 2015 Apr;24:93-9. doi: 10.1016/j.pbi.2015.02.006. Epub 2015 Feb 27. Review.

17.

New generation of artificial MicroRNA and synthetic trans-acting small interfering RNA vectors for efficient gene silencing in Arabidopsis.

Carbonell A, Takeda A, Fahlgren N, Johnson SC, Cuperus JT, Carrington JC.

Plant Physiol. 2014 May;165(1):15-29. doi: 10.1104/pp.113.234989. Epub 2014 Mar 19.

18.

Parallel analysis of RNA ends enhances global investigation of microRNAs and target RNAs of Brachypodium distachyon.

Jeong DH, Schmidt SA, Rymarquis LA, Park S, Ganssmann M, German MA, Accerbi M, Zhai J, Fahlgren N, Fox SE, Garvin DF, Mockler TC, Carrington JC, Meyers BC, Green PJ.

Genome Biol. 2013 Dec 24;14(12):R145. doi: 10.1186/gb-2013-14-12-r145.

19.

Phytophthora have distinct endogenous small RNA populations that include short interfering and microRNAs.

Fahlgren N, Bollmann SR, Kasschau KD, Cuperus JT, Press CM, Sullivan CM, Chapman EJ, Hoyer JS, Gilbert KB, Grünwald NJ, Carrington JC.

PLoS One. 2013 Oct 21;8(10):e77181. doi: 10.1371/journal.pone.0077181. eCollection 2013.

20.

Functional analysis of three Arabidopsis ARGONAUTES using slicer-defective mutants.

Carbonell A, Fahlgren N, Garcia-Ruiz H, Gilbert KB, Montgomery TA, Nguyen T, Cuperus JT, Carrington JC.

Plant Cell. 2012 Sep;24(9):3613-29. doi: 10.1105/tpc.112.099945. Epub 2012 Sep 28.

21.

The Caenorhabditis elegans RDE-10/RDE-11 complex regulates RNAi by promoting secondary siRNA amplification.

Zhang C, Montgomery TA, Fischer SE, Garcia SM, Riedel CG, Fahlgren N, Sullivan CM, Carrington JC, Ruvkun G.

Curr Biol. 2012 May 22;22(10):881-90. doi: 10.1016/j.cub.2012.04.011. Epub 2012 Apr 26.

22.

The ERI-6/7 helicase acts at the first stage of an siRNA amplification pathway that targets recent gene duplications.

Fischer SE, Montgomery TA, Zhang C, Fahlgren N, Breen PC, Hwang A, Sullivan CM, Carrington JC, Ruvkun G.

PLoS Genet. 2011 Nov;7(11):e1002369. doi: 10.1371/journal.pgen.1002369. Epub 2011 Nov 10.

23.

The Arabidopsis lyrata genome sequence and the basis of rapid genome size change.

Hu TT, Pattyn P, Bakker EG, Cao J, Cheng JF, Clark RM, Fahlgren N, Fawcett JA, Grimwood J, Gundlach H, Haberer G, Hollister JD, Ossowski S, Ottilar RP, Salamov AA, Schneeberger K, Spannagl M, Wang X, Yang L, Nasrallah ME, Bergelson J, Carrington JC, Gaut BS, Schmutz J, Mayer KF, Van de Peer Y, Grigoriev IV, Nordborg M, Weigel D, Guo YL.

Nat Genet. 2011 May;43(5):476-81. doi: 10.1038/ng.807. Epub 2011 Apr 10.

24.

Evolution and functional diversification of MIRNA genes.

Cuperus JT, Fahlgren N, Carrington JC.

Plant Cell. 2011 Feb;23(2):431-42. doi: 10.1105/tpc.110.082784. Epub 2011 Feb 11. Review.

25.

mut-16 and other mutator class genes modulate 22G and 26G siRNA pathways in Caenorhabditis elegans.

Zhang C, Montgomery TA, Gabel HW, Fischer SE, Phillips CM, Fahlgren N, Sullivan CM, Carrington JC, Ruvkun G.

Proc Natl Acad Sci U S A. 2011 Jan 25;108(4):1201-8. doi: 10.1073/pnas.1018695108. Epub 2011 Jan 18.

26.

Unique functionality of 22-nt miRNAs in triggering RDR6-dependent siRNA biogenesis from target transcripts in Arabidopsis.

Cuperus JT, Carbonell A, Fahlgren N, Garcia-Ruiz H, Burke RT, Takeda A, Sullivan CM, Gilbert SD, Montgomery TA, Carrington JC.

Nat Struct Mol Biol. 2010 Aug;17(8):997-1003. doi: 10.1038/nsmb.1866. Epub 2010 Jun 18.

27.

MicroRNA gene evolution in Arabidopsis lyrata and Arabidopsis thaliana.

Fahlgren N, Jogdeo S, Kasschau KD, Sullivan CM, Chapman EJ, Laubinger S, Smith LM, Dasenko M, Givan SA, Weigel D, Carrington JC.

Plant Cell. 2010 Apr;22(4):1074-89. doi: 10.1105/tpc.110.073999. Epub 2010 Apr 20.

28.

Arabidopsis RNA-dependent RNA polymerases and dicer-like proteins in antiviral defense and small interfering RNA biogenesis during Turnip Mosaic Virus infection.

Garcia-Ruiz H, Takeda A, Chapman EJ, Sullivan CM, Fahlgren N, Brempelis KJ, Carrington JC.

Plant Cell. 2010 Feb;22(2):481-96. doi: 10.1105/tpc.109.073056. Epub 2010 Feb 26. Erratum in: Plant Cell. 2015 Mar;27(3):944-5.

29.

Genome-wide profiling of populus small RNAs.

Klevebring D, Street NR, Fahlgren N, Kasschau KD, Carrington JC, Lundeberg J, Jansson S.

BMC Genomics. 2009 Dec 20;10:620. doi: 10.1186/1471-2164-10-620.

30.

Identification of MIR390a precursor processing-defective mutants in Arabidopsis by direct genome sequencing.

Cuperus JT, Montgomery TA, Fahlgren N, Burke RT, Townsend T, Sullivan CM, Carrington JC.

Proc Natl Acad Sci U S A. 2010 Jan 5;107(1):466-71. doi: 10.1073/pnas.0913203107. Epub 2009 Dec 14.

31.

miRNA Target Prediction in Plants.

Fahlgren N, Carrington JC.

Methods Mol Biol. 2010;592:51-7. doi: 10.1007/978-1-60327-005-2_4.

PMID:
19802588
32.

Distinct argonaute-mediated 22G-RNA pathways direct genome surveillance in the C. elegans germline.

Gu W, Shirayama M, Conte D Jr, Vasale J, Batista PJ, Claycomb JM, Moresco JJ, Youngman EM, Keys J, Stoltz MJ, Chen CC, Chaves DA, Duan S, Kasschau KD, Fahlgren N, Yates JR 3rd, Mitani S, Carrington JC, Mello CC.

Mol Cell. 2009 Oct 23;36(2):231-44. doi: 10.1016/j.molcel.2009.09.020. Epub 2009 Oct 1.

33.

Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans.

Haas BJ, Kamoun S, Zody MC, Jiang RH, Handsaker RE, Cano LM, Grabherr M, Kodira CD, Raffaele S, Torto-Alalibo T, Bozkurt TO, Ah-Fong AM, Alvarado L, Anderson VL, Armstrong MR, Avrova A, Baxter L, Beynon J, Boevink PC, Bollmann SR, Bos JI, Bulone V, Cai G, Cakir C, Carrington JC, Chawner M, Conti L, Costanzo S, Ewan R, Fahlgren N, Fischbach MA, Fugelstad J, Gilroy EM, Gnerre S, Green PJ, Grenville-Briggs LJ, Griffith J, Grünwald NJ, Horn K, Horner NR, Hu CH, Huitema E, Jeong DH, Jones AM, Jones JD, Jones RW, Karlsson EK, Kunjeti SG, Lamour K, Liu Z, Ma L, Maclean D, Chibucos MC, McDonald H, McWalters J, Meijer HJ, Morgan W, Morris PF, Munro CA, O'Neill K, Ospina-Giraldo M, Pinzón A, Pritchard L, Ramsahoye B, Ren Q, Restrepo S, Roy S, Sadanandom A, Savidor A, Schornack S, Schwartz DC, Schumann UD, Schwessinger B, Seyer L, Sharpe T, Silvar C, Song J, Studholme DJ, Sykes S, Thines M, van de Vondervoort PJ, Phuntumart V, Wawra S, Weide R, Win J, Young C, Zhou S, Fry W, Meyers BC, van West P, Ristaino J, Govers F, Birch PR, Whisson SC, Judelson HS, Nusbaum C.

Nature. 2009 Sep 17;461(7262):393-8. doi: 10.1038/nature08358. Epub 2009 Sep 9.

PMID:
19741609
34.

Computational and analytical framework for small RNA profiling by high-throughput sequencing.

Fahlgren N, Sullivan CM, Kasschau KD, Chapman EJ, Cumbie JS, Montgomery TA, Gilbert SD, Dasenko M, Backman TW, Givan SA, Carrington JC.

RNA. 2009 May;15(5):992-1002. doi: 10.1261/rna.1473809. Epub 2009 Mar 23.

35.

AGO1-miR173 complex initiates phased siRNA formation in plants.

Montgomery TA, Yoo SJ, Fahlgren N, Gilbert SD, Howell MD, Sullivan CM, Alexander A, Nguyen G, Allen E, Ahn JH, Carrington JC.

Proc Natl Acad Sci U S A. 2008 Dec 23;105(51):20055-62. doi: 10.1073/pnas.0810241105. Epub 2008 Dec 9.

36.

PRG-1 and 21U-RNAs interact to form the piRNA complex required for fertility in C. elegans.

Batista PJ, Ruby JG, Claycomb JM, Chiang R, Fahlgren N, Kasschau KD, Chaves DA, Gu W, Vasale JJ, Duan S, Conte D Jr, Luo S, Schroth GP, Carrington JC, Bartel DP, Mello CC.

Mol Cell. 2008 Jul 11;31(1):67-78. doi: 10.1016/j.molcel.2008.06.002. Epub 2008 Jun 19.

37.

Specificity of ARGONAUTE7-miR390 interaction and dual functionality in TAS3 trans-acting siRNA formation.

Montgomery TA, Howell MD, Cuperus JT, Li D, Hansen JE, Alexander AL, Chapman EJ, Fahlgren N, Allen E, Carrington JC.

Cell. 2008 Apr 4;133(1):128-41. doi: 10.1016/j.cell.2008.02.033. Epub 2008 Mar 13.

38.

Update of ASRP: the Arabidopsis Small RNA Project database.

Backman TW, Sullivan CM, Cumbie JS, Miller ZA, Chapman EJ, Fahlgren N, Givan SA, Carrington JC, Kasschau KD.

Nucleic Acids Res. 2008 Jan;36(Database issue):D982-5. Epub 2007 Nov 13.

39.

Repression of AUXIN RESPONSE FACTOR10 by microRNA160 is critical for seed germination and post-germination stages.

Liu PP, Montgomery TA, Fahlgren N, Kasschau KD, Nonogaki H, Carrington JC.

Plant J. 2007 Oct;52(1):133-46. Epub 2007 Aug 2.

40.

Genome-wide analysis of the RNA-DEPENDENT RNA POLYMERASE6/DICER-LIKE4 pathway in Arabidopsis reveals dependency on miRNA- and tasiRNA-directed targeting.

Howell MD, Fahlgren N, Chapman EJ, Cumbie JS, Sullivan CM, Givan SA, Kasschau KD, Carrington JC.

Plant Cell. 2007 Mar;19(3):926-42. Epub 2007 Mar 30.

41.

High-throughput sequencing of Arabidopsis microRNAs: evidence for frequent birth and death of MIRNA genes.

Fahlgren N, Howell MD, Kasschau KD, Chapman EJ, Sullivan CM, Cumbie JS, Givan SA, Law TF, Grant SR, Dangl JL, Carrington JC.

PLoS One. 2007 Feb 14;2(2):e219.

42.

Genome-wide profiling and analysis of Arabidopsis siRNAs.

Kasschau KD, Fahlgren N, Chapman EJ, Sullivan CM, Cumbie JS, Givan SA, Carrington JC.

PLoS Biol. 2007 Mar;5(3):e57.

43.

Regulation of AUXIN RESPONSE FACTOR3 by TAS3 ta-siRNA affects developmental timing and patterning in Arabidopsis.

Fahlgren N, Montgomery TA, Howell MD, Allen E, Dvorak SK, Alexander AL, Carrington JC.

Curr Biol. 2006 May 9;16(9):939-44.

44.

Expression of Arabidopsis MIRNA genes.

Xie Z, Allen E, Fahlgren N, Calamar A, Givan SA, Carrington JC.

Plant Physiol. 2005 Aug;138(4):2145-54. Epub 2005 Jul 22.

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