Publications

  1. Gehan MA, Fahlgren N, Abbasi A, Berry JC, Callen ST, Chavez L, Doust AN, Feldman MJ, Gilbert KB, Hodge JG, Steen Hoyer J, Lin A, Liu S, Lizárraga C, Lorence A, Miller M, Platon E, Tessman M, Sax T. 2017. PlantCV v2.0: Image analysis software for high-throughput plant phenotyping. PeerJ Preprints 5:e3225v1. DOI: 10.7287/peerj.preprints.3225v1.
  2. Tovar J, Hoyer JS, Lin A, Tielking A, Callen S, Castillo E, Miller M, Tessman M, Fahlgren N, Carrington J, Nusinow D, Gehan MA. 2017. Raspberry Pi powered imaging for plant phenotyping. bioRxiv:183822. DOI: 10.1101/183822.
  3. Abbasi A, Fahlgren N. 2016. Naive Bayes pixel-level plant segmentation. In: 2016 IEEE Western New York Image and Signal Processing Workshop (WNYISPW). 1–4. DOI: 10.1109/WNYIPW.2016.7904790.
  4. Fahlgren N, Bart R, Herrera-Estrella L, Rellán-Álvarez R, Chitwood DH, Dinneny JR. 2016. Plant scientists: GM technology is safe. Science 351:824. DOI: 10.1126/science.351.6275.824-a.
  5. Wang H, Beyene G, Zhai J, Feng S, Fahlgren N, Taylor NJ, Bart R, Carrington JC, Jacobsen SE, Ausin I. 2015. 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 112:13729–13734. DOI: 10.1073/pnas.1519067112.
  6. Fahlgren N, Hill ST, Carrington JC, Carbonell A. 2016. 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.
  7. 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. 2015. A versatile phenotyping system and analytics platform reveals diverse temporal responses to water availability in Setaria. Molecular Plant 8:1520–1535. DOI: 10.1016/j.molp.2015.06.005.
  8. Fahlgren N, Gehan MA, Baxter I. 2015. Lights, camera, action: high-throughput plant phenotyping is ready for a close-up. Current Opinion in Plant Biology 24:93–99. DOI: 10.1016/j.pbi.2015.02.006.
  9. 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. 2015. Roles and programming of Arabidopsis ARGONAUTE proteins during Turnip mosaic virus infection. PLoS Pathogens 11:e1004755. DOI: 10.1371/journal.ppat.1004755.
  10. Carbonell A, Fahlgren N, Mitchell S, Cox KL Jr., Reilly KC, Mockler TC, Carrington JC. 2015. Highly specific gene silencing in a monocot species by artificial microRNAs derived from chimeric miRNA precursors. The Plant Journal 82:1061–1075. DOI: 10.1111/tpj.12835.
  11. Gilbert KB, Fahlgren N, Kasschau KD, Chapman EJ, Carrington JC, Carbonell A. 2014. Preparation of Multiplexed Small RNA Libraries From Plants. Bio-protocol 4:e1275. DOI: 10.21769/BioProtoc.1275.
  12. Carbonell A, Takeda A, Fahlgren N, Johnson SC, Cuperus JT, Carrington JC. 2014. New generation of artificial MicroRNA and synthetic trans-acting small interfering RNA vectors for efficient gene silencing in Arabidopsis. Plant Physiology 165:15–29. DOI: 10.1104/pp.113.234989.
  13. Fahlgren N, Bollmann SR, Kasschau KD, Cuperus JT, Press CM, Sullivan CM, Chapman EJ, Hoyer JS, Gilbert KB, Grünwald NJ, Carrington JC. 2013. Phytophthora have distinct endogenous small RNA populations that include short interfering and microRNAs. PLoS ONE 8:e77181. DOI: 10.1371/journal.pone.0077181.
  14. Jeong D-H, 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. 2013. Parallel analysis of RNA ends enhances global investigation of microRNAs and target RNAs of Brachypodium distachyon. Genome Biology 14:R145. DOI: 10.1186/gb-2013-14-12-r145.
  15. Carbonell A, Fahlgren N, Garcia-Ruiz H, Gilbert KB, Montgomery TA, Nguyen T, Cuperus JT, Carrington JC. 2012. Functional analysis of three Arabidopsis ARGONAUTES using slicer-defective mutants. The Plant Cell 24:3613–3629. DOI: 10.1105/tpc.112.099945.
  16. Zhang C, Montgomery TA, Fischer SEJ, Garcia SMDA, Riedel CG, Fahlgren N, Sullivan CM, Carrington JC, Ruvkun G. 2012. The Caenorhabditis elegans RDE-10/RDE-11 complex regulates RNAi by promoting secondary siRNA amplification. Current Biology 22:881–890. DOI: 10.1016/j.cub.2012.04.011.
  17. Cuperus JT, Fahlgren N, Carrington JC. 2011. Evolution and functional diversification of MIRNA genes. The Plant Cell 23:431–442. DOI: 10.1105/tpc.110.082784.
  18. Fischer SEJ, Montgomery TA, Zhang C, Fahlgren N, Breen PC, Hwang A, Sullivan CM, Carrington JC, Ruvkun G. 2011. The ERI-6/7 helicase acts at the first stage of an siRNA amplification pathway that targets recent gene duplications. PLoS Genetics 7:e1002369. DOI: 10.1371/journal.pgen.1002369.
  19. Zhang C, Montgomery TA, Gabel HW, Fischer SEJ, Phillips CM, Fahlgren N, Sullivan CM, Carrington JC, Ruvkun G. 2011. 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 108:1201–1208. DOI: 10.1073/pnas.1018695108.
  20. Hu TT, Pattyn P, Bakker EG, Cao J, Cheng J-F, 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 KFX, Van de Peer Y, Grigoriev IV, Nordborg M, Weigel D, Guo Y-L. 2011. The Arabidopsis lyrata genome sequence and the basis of rapid genome size change. Nature Genetics 43:476–481. DOI: 10.1038/ng.807.
  21. International Brachypodium Initiative. 2010. Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature 463:763–768. DOI: 10.1038/nature08747.
  22. Fahlgren N, Jogdeo S, Kasschau KD, Sullivan CM, Chapman EJ, Laubinger S, Smith LM, Dasenko M, Givan SA, Weigel D, Carrington JC. 2010. MicroRNA gene evolution in Arabidopsis lyrata and Arabidopsis thalianaThe Plant Cell 22:1074–1089. DOI: 10.1105/tpc.110.073999.
  23. Cuperus JT, Carbonell A, Fahlgren N, Garcia-Ruiz H, Burke RT, Takeda A, Sullivan CM, Gilbert SD, Montgomery TA, Carrington JC. 2010. Unique functionality of 22-nt miRNAs in triggering RDR6-dependent siRNA biogenesis from target transcripts in Arabidopsis. Nature Structural & Molecular Biology 17:997–1003. DOI: 10.1038/nsmb.1866.
  24. Cuperus JT, Montgomery TA, Fahlgren N, Burke RT, Townsend T, Sullivan CM, Carrington JC. 2010. 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 107:466–471. DOI: 10.1073/pnas.0913203107.
  25. Fahlgren N, Carrington JC. 2010. miRNA Target Prediction in Plants. In: Meyers BC, Green PJ eds. Plant MicroRNAs. Methods in Molecular Biology. Totowa, NJ: Humana Press, 51–57. DOI: 10.1007/978-1-60327-005-2_4.
  26. Garcia-Ruiz H, Takeda A, Chapman EJ, Sullivan CM, Fahlgren N, Brempelis KJ, Carrington JC. 2010. 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 22:481–496. DOI: 10.1105/tpc.109.073056.
  27. Fahlgren N, Sullivan CM, Kasschau KD, Chapman EJ, Cumbie JS, Montgomery TA, Gilbert SD, Dasenko M, Backman TWH, Givan SA, Carrington JC. 2009. Computational and analytical framework for small RNA profiling by high-throughput sequencing. RNA 15:992–1002. DOI: 10.1261/rna.1473809.
  28. Haas BJ, Kamoun S, Zody MC, Jiang RHY, Handsaker RE, Cano LM, Grabherr M, Kodira CD, Raffaele S, Torto-Alalibo T, Bozkurt TO, Ah-Fong AMV, Alvarado L, Anderson VL, Armstrong MR, Avrova A, Baxter L, Beynon J, Boevink PC, Bollmann SR, Bos JIB, 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 C-H, Huitema E, Jeong D-H, Jones AME, Jones JDG, Jones RW, Karlsson EK, Kunjeti SG, Lamour K, Liu Z, Ma L, Maclean D, Chibucos MC, McDonald H, McWalters J, Meijer HJG, 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 PJI, Phuntumart V, Wawra S, Weide R, Win J, Young C, Zhou S, Fry W, Meyers BC, van West P, Ristaino J, Govers F, Birch PRJ, Whisson SC, Judelson HS, Nusbaum C. 2009. Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans. Nature 461:393–398. DOI: 10.1038/nature08358.
  29. Gu W, Shirayama M, Conte D Jr., Vasale J, Batista PJ, Claycomb JM, Moresco JJ, Youngman EM, Keys J, Stoltz MJ, Chen C-CG, Chaves DA, Duan S, Kasschau KD, Fahlgren N, Yates JR 3rd, Mitani S, Carrington JC, Mello CC. 2009. Distinct argonaute-mediated 22G-RNA pathways direct genome surveillance in the C. elegans germline. Molecular Cell 36:231–244. DOI: 10.1016/j.molcel.2009.09.020.
  30. Klevebring D, Street NR, Fahlgren N, Kasschau KD, Carrington JC, Lundeberg J, Jansson S. 2009. Genome-wide profiling of populus small RNAs. BMC Genomics 10:620. DOI: 10.1186/1471-2164-10-620.
  31. Montgomery TA, Howell MD, Cuperus JT, Li D, Hansen JE, Alexander AL, Chapman EJ, Fahlgren N, Allen E, Carrington JC. 2008. Specificity of ARGONAUTE7-miR390 interaction and dual functionality in TAS3 trans-acting siRNA formation. Cell 133:128–141. DOI: 10.1016/j.cell.2008.02.033.
  32. Montgomery TA, Yoo SJ, Fahlgren N, Gilbert SD, Howell MD, Sullivan CM, Alexander A, Nguyen G, Allen E, Ahn JH, Carrington JC. 2008. AGO1-miR173 complex initiates phased siRNA formation in plants. Proceedings of the National Academy of Sciences of the United States of America 105:20055–20062. DOI: 10.1073/pnas.0810241105.
  33. Backman TWH, Sullivan CM, Cumbie JS, Miller ZA, Chapman EJ, Fahlgren N, Givan SA, Carrington JC, Kasschau KD. 2008. Update of ASRP: the Arabidopsis Small RNA Project database. Nucleic Acids Research 36:D982–5. DOI: 10.1093/nar/gkm997.
  34. 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. 2008. PRG-1 and 21U-RNAs interact to form the piRNA complex required for fertility in C. elegans. Molecular Cell 31:67–78. DOI: 10.1016/j.molcel.2008.06.002.
  35. Liu P-P, Montgomery TA, Fahlgren N, Kasschau KD, Nonogaki H, Carrington JC. 2007. Repression of AUXIN RESPONSE FACTOR10 by microRNA160 is critical for seed germination and post-germination stages. The Plant Journal 52:133–146. DOI: 10.1111/j.1365-313X.2007.03218.x.
  36. Howell MD, Fahlgren N, Chapman EJ, Cumbie JS, Sullivan CM, Givan SA, Kasschau KD, Carrington JC. 2007. 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 19:926–942. DOI: 10.1105/tpc.107.050062.
  37. Kasschau KD, Fahlgren N, Chapman EJ, Sullivan CM, Cumbie JS, Givan SA, Carrington JC. 2007. Genome-wide profiling and analysis of Arabidopsis siRNAs. PLoS Biology 5:e57. DOI: 10.1371/journal.pbio.0050057.
  38. Fahlgren N, Howell MD, Kasschau KD, Chapman EJ, Sullivan CM, Cumbie JS, Givan SA, Law TF, Grant SR, Dangl JL, Carrington JC. 2007. High-throughput sequencing of Arabidopsis microRNAs: evidence for frequent birth and death of MIRNA genes. PLoS ONE 2:e219. DOI: 10.1371/journal.pone.0000219.
  39. Fahlgren N, Montgomery TA, Howell MD, Allen E, Dvorak SK, Alexander AL, Carrington JC. 2006. Regulation of AUXIN RESPONSE FACTOR3 by TAS3 ta-siRNA affects developmental timing and patterning in Arabidopsis. Current Biology: CB 16:939–944. DOI: 10.1016/j.cub.2006.03.065.
  40. Xie Z, Allen E, Fahlgren N, Calamar A, Givan SA, Carrington JC. 2005. Expression of Arabidopsis MIRNA genes. Plant Physiology 138:2145–2154. DOI: 10.1104/pp.105.062943.
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