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Noah Fahlgren, Ph.D. - Publications

Affiliations: 
2011 Oregon State University, Corvallis, OR 
Area:
Molecular Biology, Evolution and Development Biology, Botany Biology, Genetics
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44 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Ludwig E, Sumner J, Berry J, Polydore S, Ficor T, Agnew E, Haines K, Greenham K, Fahlgren N, Mockler TC, Gehan MA. Natural variation in Brachypodium distachyon responses to combined abiotic stresses. The Plant Journal : For Cell and Molecular Biology. PMID 37483133 DOI: 10.1111/tpj.16387  0.732
2021 Mansfeld BN, Boyher A, Berry JC, Wilson M, Ou S, Polydore S, Michael TP, Fahlgren N, Bart RS. Large structural variations in the haplotype-resolved African cassava genome. The Plant Journal : For Cell and Molecular Biology. PMID 34661327 DOI: 10.1111/tpj.15543  0.773
2019 Zheng X, Fahlgren N, Abbasi A, Berry JC, Carrington JC. Antiviral ARGONAUTEs Against Turnip Crinkle Virus Revealed by Image-based Trait Analysis. Plant Physiology. PMID 31043494 DOI: 10.1104/Pp.19.00121  0.651
2018 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. Raspberry Pi-powered imaging for plant phenotyping. Applications in Plant Sciences. 6: e1031. PMID 29732261 DOI: 10.1002/Aps3.1031  0.539
2016 Fahlgren N, Hill ST, Carrington JC, Carbonell A. P-SAMS: a web site for plant artificial microRNA and synthetic trans-acting small interfering RNA design. Bioinformatics (Oxford, England). 32: 157-8. PMID 26382195 DOI: 10.1093/Bioinformatics/Btv534  0.688
2015 Wang H, Beyene G, Zhai J, Feng S, Fahlgren N, Taylor NJ, Bart R, Carrington JC, Jacobsen SE, Ausin I. CG gene body DNA methylation changes and evolution of duplicated genes in cassava. Proceedings of the National Academy of Sciences of the United States of America. 112: 13729-34. PMID 26483493 DOI: 10.1073/Pnas.1519067112  0.565
2015 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, et al. A versatile phenotyping system and analytics platform reveals diverse temporal responses to water availability in Setaria. Molecular Plant. PMID 26099924 DOI: 10.1016/J.Molp.2015.06.005  0.548
2015 Carbonell A, Fahlgren N, Mitchell S, Cox KL, Reilly KC, Mockler TC, Carrington JC. Highly specific gene silencing in a monocot species by artificial microRNAs derived from chimeric miRNA precursors. The Plant Journal : For Cell and Molecular Biology. 82: 1061-1075. PMID 25809382 DOI: 10.1111/Tpj.12835  0.67
2015 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. Roles and programming of Arabidopsis ARGONAUTE proteins during Turnip mosaic virus infection. Plos Pathogens. 11: e1004755. PMID 25806948 DOI: 10.1371/Journal.Ppat.1004755  0.702
2015 Garcia-Ruiz H, Takeda A, Chapman EJ, Sullivan CM, Fahlgren N, Brempelis KJ, Carrington JC. Correction. Arabidopsis RNA-dependent RNA polymerases and dicer-like proteins in antiviral defense and small interfering RNA biogenesis during Turnip mosaic virus infection. The Plant Cell. 27: 944-5. PMID 25783032 DOI: 10.1105/tpc.15.00204  0.78
2015 Fahlgren N, Gehan MA, Baxter I. Lights, camera, action: high-throughput plant phenotyping is ready for a close-up. Current Opinion in Plant Biology. 24: 93-9. PMID 25733069 DOI: 10.1016/J.Pbi.2015.02.006  0.304
2015 Fahlgren N, Hill ST, Carrington JC, Carbonell A. P-SAMS: A web site for plant artificial microRNA and synthetic trans-acting small interfering RNA design Bioinformatics. 32: 157-158. DOI: 10.1093/bioinformatics/btv534  0.635
2014 Gilbert KB, Fahlgren N, Kasschau KD, Chapman EJ, Carrington JC, Carbonell A. Preparation of Multiplexed Small RNA Libraries From Plants. Bio-Protocol. 4. PMID 26661568 DOI: 10.21769/BIOPROTOC.1275  0.784
2014 Carbonell A, Takeda A, Fahlgren N, Johnson SC, Cuperus JT, Carrington JC. New generation of artificial MicroRNA and synthetic trans-acting small interfering RNA vectors for efficient gene silencing in Arabidopsis. Plant Physiology. 165: 15-29. PMID 24647477 DOI: 10.1104/Pp.113.234989  0.802
2013 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. Parallel analysis of RNA ends enhances global investigation of microRNAs and target RNAs of Brachypodium distachyon. Genome Biology. 14: R145. PMID 24367943 DOI: 10.1186/Gb-2013-14-12-R145  0.716
2013 Fahlgren N, Bollmann SR, Kasschau KD, Cuperus JT, Press CM, Sullivan CM, Chapman EJ, Hoyer JS, Gilbert KB, Grünwald NJ, Carrington JC. Phytophthora have distinct endogenous small RNA populations that include short interfering and microRNAs. Plos One. 8: e77181. PMID 24204767 DOI: 10.1371/Journal.Pone.0077181  0.83
2013 Fahlgren N, Bollmann SR, Kasschau KD, Cuperus JT, Press CM, Sullivan CM, Chapman EJ, Hoyer JS, Gilbert KB, Grünwald NJ, Carrington JC. Dcl , Rdr , Ago and MIRNA genes in three Phytophthora species. Plos One. DOI: 10.1371/Journal.Pone.0077181.T001  0.711
2013 Fahlgren N, Bollmann SR, Kasschau KD, Cuperus JT, Press CM, Sullivan CM, Chapman EJ, Hoyer JS, Gilbert KB, Grünwald NJ, Carrington JC. Computational and molecular characterization of Phytophthora MIRNA genes. Plos One. DOI: 10.1371/Journal.Pone.0077181.G006  0.703
2012 Carbonell A, Fahlgren N, Garcia-Ruiz H, Gilbert KB, Montgomery TA, Nguyen T, Cuperus JT, Carrington JC. Functional analysis of three Arabidopsis argonautes using slicer-defective mutants Plant Cell. 24: 3613-3629. PMID 23023169 DOI: 10.1105/Tpc.112.099945  0.839
2012 Zhang C, Montgomery TA, Fischer SE, Garcia SM, Riedel CG, Fahlgren N, Sullivan CM, Carrington JC, Ruvkun G. The Caenorhabditis elegans RDE-10/RDE-11 complex regulates RNAi by promoting secondary siRNA amplification. Current Biology : Cb. 22: 881-90. PMID 22542102 DOI: 10.1016/J.Cub.2012.04.011  0.805
2011 Fischer SE, Montgomery TA, Zhang C, Fahlgren N, Breen PC, Hwang A, Sullivan CM, Carrington JC, Ruvkun G. The ERI-6/7 helicase acts at the first stage of an siRNA amplification pathway that targets recent gene duplications. Plos Genetics. 7: e1002369. PMID 22102828 DOI: 10.1371/Journal.Pgen.1002369  0.807
2011 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, et al. The Arabidopsis lyrata genome sequence and the basis of rapid genome size change. Nature Genetics. 43: 476-81. PMID 21478890 DOI: 10.1038/Ng.807  0.585
2011 Cuperus JT, Fahlgren N, Carrington JC. Evolution and functional diversification of MIRNA genes. The Plant Cell. 23: 431-42. PMID 21317375 DOI: 10.1105/Tpc.110.082784  0.777
2011 Zhang C, Montgomery TA, Gabel HW, Fischer SE, Phillips CM, Fahlgren N, Sullivan CM, Carrington JC, Ruvkun G. mut-16 and other mutator class genes modulate 22G and 26G siRNA pathways in Caenorhabditis elegans. Proceedings of the National Academy of Sciences of the United States of America. 108: 1201-8. PMID 21245313 DOI: 10.1073/Pnas.1018695108  0.788
2010 Cuperus JT, Carbonell A, Fahlgren N, Garcia-Ruiz H, Burke RT, Takeda A, Sullivan CM, Gilbert SD, Montgomery TA, Carrington JC. Unique functionality of 22-nt miRNAs in triggering RDR6-dependent siRNA biogenesis from target transcripts in Arabidopsis Nature Structural and Molecular Biology. 17: 997-1003. PMID 20562854 DOI: 10.1038/Nsmb.1866  0.83
2010 Fahlgren N, Jogdeo S, Kasschau KD, Sullivan CM, Chapman EJ, Laubinger S, Smith LM, Dasenko M, Givan SA, Weigel D, Carrington JC. MicroRNA gene evolution in Arabidopsis lyrata and Arabidopsis thaliana. The Plant Cell. 22: 1074-89. PMID 20407027 DOI: 10.1105/Tpc.110.073999  0.792
2010 Garcia-Ruiz H, Takeda A, Chapman EJ, Sullivan CM, Fahlgren N, Brempelis KJ, Carrington JC. Arabidopsis RNA-dependent RNA polymerases and dicer-like proteins in antiviral defense and small interfering RNA biogenesis during Turnip mosaic virus infection Plant Cell. 22: 481-496. PMID 20190077 DOI: 10.1105/Tpc.109.073056  0.797
2010 Vogel JP, Garvin DF, Mockler TC, Schmutz J, Rokhsar D, Bevan MW, Barry K, Lucas S, Harmon-Smith M, Lail K, Tice H, Grimwood J, McKenzie N, Huo N, Gu YQ, ... ... Fahlgren N, et al. Genome sequencing and analysis of the model grass Brachypodium distachyon Nature. 463: 763-768. PMID 20148030 DOI: 10.1038/Nature08747  0.723
2010 Cuperus JT, Montgomery TA, Fahlgren N, Burke RT, Townsend T, Sullivan CM, Carrington JC. Identification of MIR390a precursor processing-defective mutants in Arabidopsis by direct genome sequencing. Proceedings of the National Academy of Sciences of the United States of America. 107: 466-71. PMID 20018656 DOI: 10.1073/Pnas.0913203107  0.798
2010 Fahlgren N, Carrington JC. miRNA Target Prediction in Plants. Methods in Molecular Biology (Clifton, N.J.). 592: 51-7. PMID 19802588 DOI: 10.1007/978-1-60327-005-2_4  0.673
2009 Klevebring D, Street NR, Fahlgren N, Kasschau KD, Carrington JC, Lundeberg J, Jansson S. Genome-wide profiling of populus small RNAs. Bmc Genomics. 10: 620. PMID 20021695 DOI: 10.1186/1471-2164-10-620  0.712
2009 Gu W, Shirayama M, Conte D, Vasale J, Batista PJ, Claycomb JM, Moresco JJ, Youngman EM, Keys J, Stoltz MJ, Chen CC, Chaves DA, Duan S, Kasschau KD, Fahlgren N, et al. Distinct argonaute-mediated 22G-RNA pathways direct genome surveillance in the C. elegans germline. Molecular Cell. 36: 231-44. PMID 19800275 DOI: 10.1016/J.Molcel.2009.09.020  0.7
2009 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, ... ... Fahlgren N, et al. Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans. Nature. 461: 393-8. PMID 19741609 DOI: 10.1038/Nature08358  0.585
2009 Fahlgren N, Sullivan CM, Kasschau KD, Chapman EJ, Cumbie JS, Montgomery TA, Gilbert SD, Dasenko M, Backman TW, Givan SA, Carrington JC. Computational and analytical framework for small RNA profiling by high-throughput sequencing. Rna (New York, N.Y.). 15: 992-1002. PMID 19307293 DOI: 10.1261/Rna.1473809  0.813
2008 Montgomery TA, Yoo SJ, Fahlgren N, Gilbert SD, Howell MD, Sullivan CM, Alexander A, Nguyen G, Allen E, Ahn JH, Carrington JC. AGO1-miR173 complex initiates phased siRNA formation in plants. Proceedings of the National Academy of Sciences of the United States of America. 105: 20055-62. PMID 19066226 DOI: 10.1073/Pnas.0810241105  0.79
2008 Batista PJ, Ruby JG, Claycomb JM, Chiang R, Fahlgren N, Kasschau KD, Chaves DA, Gu W, Vasale JJ, Duan S, Conte D, Luo S, Schroth GP, Carrington JC, Bartel DP, et al. PRG-1 and 21U-RNAs interact to form the piRNA complex required for fertility in C. elegans. Molecular Cell. 31: 67-78. PMID 18571452 DOI: 10.1016/J.Molcel.2008.06.002  0.684
2008 Montgomery TA, Howell MD, Cuperus JT, Li D, Hansen JE, Alexander AL, Chapman EJ, Fahlgren N, Allen E, Carrington JC. Specificity of ARGONAUTE7-miR390 interaction and dual functionality in TAS3 trans-acting siRNA formation. Cell. 133: 128-41. PMID 18342362 DOI: 10.1016/J.Cell.2008.02.033  0.803
2008 Backman TW, Sullivan CM, Cumbie JS, Miller ZA, Chapman EJ, Fahlgren N, Givan SA, Carrington JC, Kasschau KD. Update of ASRP: the Arabidopsis Small RNA Project database. Nucleic Acids Research. 36: D982-5. PMID 17999994 DOI: 10.1093/Nar/Gkm997  0.783
2007 Liu PP, Montgomery TA, Fahlgren N, Kasschau KD, Nonogaki H, Carrington JC. Repression of AUXIN RESPONSE FACTOR10 by microRNA160 is critical for seed germination and post-germination stages. The Plant Journal : For Cell and Molecular Biology. 52: 133-46. PMID 17672844 DOI: 10.1111/J.1365-313X.2007.03218.X  0.758
2007 Howell MD, Fahlgren N, Chapman EJ, Cumbie JS, Sullivan CM, Givan SA, Kasschau KD, Carrington JC. Genome-wide analysis of the RNA-DEPENDENT RNA POLYMERASE6/DICER-LIKE4 pathway in Arabidopsis reveals dependency on miRNA- and tasiRNA-directed targeting. The Plant Cell. 19: 926-42. PMID 17400893 DOI: 10.1105/Tpc.107.050062  0.834
2007 Fahlgren N, Howell MD, Kasschau KD, Chapman EJ, Sullivan CM, Cumbie JS, Givan SA, Law TF, Grant SR, Dangl JL, Carrington JC. High-throughput sequencing of Arabidopsis microRNAs: evidence for frequent birth and death of MIRNA genes. Plos One. 2: e219. PMID 17299599 DOI: 10.1371/Journal.Pone.0000219  0.789
2007 Kasschau KD, Fahlgren N, Chapman EJ, Sullivan CM, Cumbie JS, Givan SA, Carrington JC. Genome-wide profiling and analysis of Arabidopsis siRNAs. Plos Biology. 5: e57. PMID 17298187 DOI: 10.1371/Journal.Pbio.0050057  0.815
2006 Fahlgren N, Montgomery TA, Howell MD, Allen E, Dvorak SK, Alexander AL, Carrington JC. Regulation of AUXIN RESPONSE FACTOR3 by TAS3 ta-siRNA affects developmental timing and patterning in Arabidopsis. Current Biology : Cb. 16: 939-44. PMID 16682356 DOI: 10.1016/J.Cub.2006.03.065  0.8
2005 Xie Z, Allen E, Fahlgren N, Calamar A, Givan SA, Carrington JC. Expression of Arabidopsis MIRNA genes. Plant Physiology. 138: 2145-54. PMID 16040653 DOI: 10.1104/Pp.105.062943  0.704
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