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Conserved and nuanced hierarchy of gene regulatory response to hypoxia.

Lee TA, Bailey-Serres J.

New Phytol. 2020 Jan 18. doi: 10.1111/nph.16437. [Epub ahead of print] Review.


The Dynamic Kaleidoscope of RNA Biology in Plants.

Bailey-Serres J, Zhai J, Seki M.

Plant Physiol. 2020 Jan;182(1):1-9. doi: 10.1104/pp.19.01558. No abstract available.


Reprogramming of root cells during nitrogen-fixing symbiosis involves dynamic polysome association of coding and non-coding RNAs.

Traubenik S, Reynoso MA, Hobecker KV, Lancia M, Hummel M, Rosen B, Town C, Bailey-Serres J, Blanco FA, Zanetti ME.

Plant Cell. 2019 Nov 20. pii: tpc.00647.2019. doi: 10.1105/tpc.19.00647. [Epub ahead of print]


Genetic strategies for improving crop yields.

Bailey-Serres J, Parker JE, Ainsworth EA, Oldroyd GED, Schroeder JI.

Nature. 2019 Nov;575(7781):109-118. doi: 10.1038/s41586-019-1679-0. Epub 2019 Nov 6. Review.


Evolutionary flexibility in flooding response circuitry in angiosperms.

Reynoso MA, Kajala K, Bajic M, West DA, Pauluzzi G, Yao AI, Hatch K, Zumstein K, Woodhouse M, Rodriguez-Medina J, Sinha N, Brady SM, Deal RB, Bailey-Serres J.

Science. 2019 Sep 20;365(6459):1291-1295. doi: 10.1126/science.aax8862.


Integrative Analysis from the Epigenome to Translatome Uncovers Patterns of Dominant Nuclear Regulation during Transient Stress.

Lee TA, Bailey-Serres J.

Plant Cell. 2019 Nov;31(11):2573-2595. doi: 10.1105/tpc.19.00463. Epub 2019 Sep 13.


Ethylene-mediated nitric oxide depletion pre-adapts plants to hypoxia stress.

Hartman S, Liu Z, van Veen H, Vicente J, Reinen E, Martopawiro S, Zhang H, van Dongen N, Bosman F, Bassel GW, Visser EJW, Bailey-Serres J, Theodoulou FL, Hebelstrup KH, Gibbs DJ, Holdsworth MJ, Sasidharan R, Voesenek LACJ.

Nat Commun. 2019 Sep 5;10(1):4020. doi: 10.1038/s41467-019-12045-4.


Searching for a Match: Structure, Function and Application of Sequence-Specific RNA-Binding Proteins.

Dedow LK, Bailey-Serres J.

Plant Cell Physiol. 2019 Sep 1;60(9):1927-1938. doi: 10.1093/pcp/pcz072. Review.


After The Deluge: Plant Revival Post-Flooding.

Yeung E, Bailey-Serres J, Sasidharan R.

Trends Plant Sci. 2019 May;24(5):443-454. doi: 10.1016/j.tplants.2019.02.007. Epub 2019 Mar 9. Review.


A stress recovery signaling network for enhanced flooding tolerance in Arabidopsis thaliana.

Yeung E, van Veen H, Vashisht D, Sobral Paiva AL, Hummel M, Rankenberg T, Steffens B, Steffen-Heins A, Sauter M, de Vries M, Schuurink RC, Bazin J, Bailey-Serres J, Voesenek LACJ, Sasidharan R.

Proc Natl Acad Sci U S A. 2018 Jun 26;115(26):E6085-E6094. doi: 10.1073/pnas.1803841115. Epub 2018 Jun 11.


The Dynamic Plant: Capture, Transformation, and Management of Energy.

Bailey-Serres J, Pierik R, Ruban A, Wingler A.

Plant Physiol. 2018 Feb;176(2):961-966. doi: 10.1104/pp.18.00041. No abstract available.


Profiling of Accessible Chromatin Regions across Multiple Plant Species and Cell Types Reveals Common Gene Regulatory Principles and New Control Modules.

Maher KA, Bajic M, Kajala K, Reynoso M, Pauluzzi G, West DA, Zumstein K, Woodhouse M, Bubb K, Dorrity MW, Queitsch C, Bailey-Serres J, Sinha N, Brady SM, Deal RB.

Plant Cell. 2018 Jan;30(1):15-36. doi: 10.1105/tpc.17.00581. Epub 2017 Dec 11.


The Next Generation of Training for Arabidopsis Researchers: Bioinformatics and Quantitative Biology.

Friesner J, Assmann SM, Bastow R, Bailey-Serres J, Beynon J, Brendel V, Buell CR, Bucksch A, Busch W, Demura T, Dinneny JR, Doherty CJ, Eveland AL, Falter-Braun P, Gehan MA, Gonzales M, Grotewold E, Gutierrez R, Kramer U, Krouk G, Ma S, Markelz RJC, Megraw M, Meyers BC, Murray JAH, Provart NJ, Rhee S, Smith R, Spalding EP, Taylor C, Teal TK, Torii KU, Town C, Vaughn M, Vierstra R, Ware D, Wilkins O, Williams C, Brady SM.

Plant Physiol. 2017 Dec;175(4):1499-1509. doi: 10.1104/pp.17.01490. No abstract available.


Polysomes, Stress Granules, and Processing Bodies: A Dynamic Triumvirate Controlling Cytoplasmic mRNA Fate and Function.

Chantarachot T, Bailey-Serres J.

Plant Physiol. 2018 Jan;176(1):254-269. doi: 10.1104/pp.17.01468. Epub 2017 Nov 20. Review. No abstract available.


Rice SUB1A constrains remodelling of the transcriptome and metabolome during submergence to facilitate post-submergence recovery.

Locke AM, Barding GA Jr, Sathnur S, Larive CK, Bailey-Serres J.

Plant Cell Environ. 2018 Apr;41(4):721-736. doi: 10.1111/pce.13094. Epub 2017 Nov 27.


Global analysis of ribosome-associated noncoding RNAs unveils new modes of translational regulation.

Bazin J, Baerenfaller K, Gosai SJ, Gregory BD, Crespi M, Bailey-Serres J.

Proc Natl Acad Sci U S A. 2017 Nov 14;114(46):E10018-E10027. doi: 10.1073/pnas.1708433114. Epub 2017 Oct 30.


Nuclear Transcriptomes at High Resolution Using Retooled INTACT.

Reynoso MA, Pauluzzi GC, Kajala K, Cabanlit S, Velasco J, Bazin J, Deal R, Sinha NR, Brady SM, Bailey-Serres J.

Plant Physiol. 2018 Jan;176(1):270-281. doi: 10.1104/pp.17.00688. Epub 2017 Sep 27.


Lighting the shadows: methods that expose nuclear and cytoplasmic gene regulatory control.

Lee TA, Bailey-Serres J.

Curr Opin Biotechnol. 2018 Feb;49:29-34. doi: 10.1016/j.copbio.2017.07.010. Epub 2017 Aug 16. Review.


Noncanonical Alternative Polyadenylation Contributes to Gene Regulation in Response to Hypoxia.

de Lorenzo L, Sorenson R, Bailey-Serres J, Hunt AG.

Plant Cell. 2017 Jun;29(6):1262-1277. doi: 10.1105/tpc.16.00746. Epub 2017 May 30.


Plant biology: An immunity boost combats crop disease.

Bailey-Serres J, Ma W.

Nature. 2017 May 25;545(7655):420-421. doi: 10.1038/nature22497. Epub 2017 May 17. No abstract available.


Community recommendations on terminology and procedures used in flooding and low oxygen stress research.

Sasidharan R, Bailey-Serres J, Ashikari M, Atwell BJ, Colmer TD, Fagerstedt K, Fukao T, Geigenberger P, Hebelstrup KH, Hill RD, Holdsworth MJ, Ismail AM, Licausi F, Mustroph A, Nakazono M, Pedersen O, Perata P, Sauter M, Shih MC, Sorrell BK, Striker GG, van Dongen JT, Whelan J, Xiao S, Visser EJW, Voesenek LACJ.

New Phytol. 2017 Jun;214(4):1403-1407. doi: 10.1111/nph.14519. Epub 2017 Mar 9. No abstract available.


Bioorthogonal Noncanonical Amino Acid Tagging (BONCAT) Enables Time-Resolved Analysis of Protein Synthesis in Native Plant Tissue.

Glenn WS, Stone SE, Ho SH, Sweredoski MJ, Moradian A, Hess S, Bailey-Serres J, Tirrell DA.

Plant Physiol. 2017 Mar;173(3):1543-1553. doi: 10.1104/pp.16.01762. Epub 2017 Jan 19.


Analysis of Ribosome-Associated mRNAs in Rice Reveals the Importance of Transcript Size and GC Content in Translation.

Zhao D, Hamilton JP, Hardigan M, Yin D, He T, Vaillancourt B, Reynoso M, Pauluzzi G, Funkhouser S, Cui Y, Bailey-Serres J, Jiang J, Buell CR, Jiang N.

G3 (Bethesda). 2017 Jan 5;7(1):203-219. doi: 10.1534/g3.116.036020.


Transcriptomes of Eight Arabidopsis thaliana Accessions Reveal Core Conserved, Genotype- and Organ-Specific Responses to Flooding Stress.

van Veen H, Vashisht D, Akman M, Girke T, Mustroph A, Reinen E, Hartman S, Kooiker M, van Tienderen P, Schranz ME, Bailey-Serres J, Voesenek LA, Sasidharan R.

Plant Physiol. 2016 Oct;172(2):668-689. Epub 2016 May 15.


Flexible Ion Barrier.

Pauluzzi G, Bailey-Serres J.

Cell. 2016 Jan 28;164(3):345-6. doi: 10.1016/j.cell.2016.01.005.


Redundant ERF-VII Transcription Factors Bind to an Evolutionarily Conserved cis-Motif to Regulate Hypoxia-Responsive Gene Expression in Arabidopsis.

Gasch P, Fundinger M, Müller JT, Lee T, Bailey-Serres J, Mustroph A.

Plant Cell. 2016 Jan;28(1):160-80. doi: 10.1105/tpc.15.00866. Epub 2015 Dec 14.


Flooding stress signaling through perturbations in oxygen, ethylene, nitric oxide and light.

Voesenek LA, Sasidharan R, Visser EJ, Bailey-Serres J.

New Phytol. 2016 Jan;209(1):39-43. doi: 10.1111/nph.13775. No abstract available.


Proteomic LC-MS analysis of Arabidopsis cytosolic ribosomes: Identification of ribosomal protein paralogs and re-annotation of the ribosomal protein genes.

Hummel M, Dobrenel T, Cordewener JJ, Davanture M, Meyer C, Smeekens SJ, Bailey-Serres J, America TA, Hanson J.

J Proteomics. 2015 Oct 14;128:436-49. doi: 10.1016/j.jprot.2015.07.004. Epub 2015 Jul 29.


Emerging roles of long non-coding RNA in root developmental plasticity and regulation of phosphate homeostasis.

Bazin J, Bailey-Serres J.

Front Plant Sci. 2015 Jun 9;6:400. doi: 10.3389/fpls.2015.00400. eCollection 2015. Review.


Mechanism of cytoplasmic mRNA translation.

Browning KS, Bailey-Serres J.

Arabidopsis Book. 2015 Apr 24;13:e0176. doi: 10.1199/tab.0176. eCollection 2015.


Rapid immunopurification of ribonucleoprotein complexes of plants.

Sorenson R, Bailey-Serres J.

Methods Mol Biol. 2015;1284:209-19. doi: 10.1007/978-1-4939-2444-8_10.


Translating Ribosome Affinity Purification (TRAP) followed by RNA sequencing technology (TRAP-SEQ) for quantitative assessment of plant translatomes.

Reynoso MA, Juntawong P, Lancia M, Blanco FA, Bailey-Serres J, Zanetti ME.

Methods Mol Biol. 2015;1284:185-207. doi: 10.1007/978-1-4939-2444-8_9.


Ribosome profiling: a tool for quantitative evaluation of dynamics in mRNA translation.

Juntawong P, Hummel M, Bazin J, Bailey-Serres J.

Methods Mol Biol. 2015;1284:139-73. doi: 10.1007/978-1-4939-2444-8_7.


Genetic mechanisms of abiotic stress tolerance that translate to crop yield stability.

Mickelbart MV, Hasegawa PM, Bailey-Serres J.

Nat Rev Genet. 2015 Apr;16(4):237-51. doi: 10.1038/nrg3901. Epub 2015 Mar 10. Review.


Flood adaptive traits and processes: an overview.

Voesenek LA, Bailey-Serres J.

New Phytol. 2015 Apr;206(1):57-73. doi: 10.1111/nph.13209. Epub 2015 Jan 7. Review.


A trehalose-6-phosphate phosphatase enhances anaerobic germination tolerance in rice.

Kretzschmar T, Pelayo MA, Trijatmiko KR, Gabunada LF, Alam R, Jimenez R, Mendioro MS, Slamet-Loedin IH, Sreenivasulu N, Bailey-Serres J, Ismail AM, Mackill DJ, Septiningsih EM.

Nat Plants. 2015 Aug 24;1:15124. doi: 10.1038/nplants.2015.124.


Hypoxia and development: Air conditional.

Voesenek LA, Bailey-Serres J.

Nat Plants. 2015 Jul 7;1:15095. doi: 10.1038/nplants.2015.95. No abstract available.


A trihelix DNA binding protein counterbalances hypoxia-responsive transcriptional activation in Arabidopsis.

Giuntoli B, Lee SC, Licausi F, Kosmacz M, Oosumi T, van Dongen JT, Bailey-Serres J, Perata P.

PLoS Biol. 2014 Sep 16;12(9):e1001950. doi: 10.1371/journal.pbio.1001950. eCollection 2014 Sep.


Plant tolerance of flooding stress--recent advances.

Bailey-Serres J, Colmer TD.

Plant Cell Environ. 2014 Oct;37(10):2211-5. doi: 10.1111/pce.12420. Epub 2014 Aug 22. No abstract available.


Hairy root transformation using Agrobacterium rhizogenes as a tool for exploring cell type-specific gene expression and function using tomato as a model.

Ron M, Kajala K, Pauluzzi G, Wang D, Reynoso MA, Zumstein K, Garcha J, Winte S, Masson H, Inagaki S, Federici F, Sinha N, Deal RB, Bailey-Serres J, Brady SM.

Plant Physiol. 2014 Oct;166(2):455-69. doi: 10.1104/pp.114.239392. Epub 2014 May 27.


Profiling of translatomes of in vivo-grown pollen tubes reveals genes with roles in micropylar guidance during pollination in Arabidopsis.

Lin SY, Chen PW, Chuang MH, Juntawong P, Bailey-Serres J, Jauh GY.

Plant Cell. 2014 Feb;26(2):602-18. doi: 10.1105/tpc.113.121335. Epub 2014 Feb 14.


Selective mRNA sequestration by OLIGOURIDYLATE-BINDING PROTEIN 1 contributes to translational control during hypoxia in Arabidopsis.

Sorenson R, Bailey-Serres J.

Proc Natl Acad Sci U S A. 2014 Feb 11;111(6):2373-8. doi: 10.1073/pnas.1314851111. Epub 2014 Jan 27.


Characterization of distinct root and shoot responses to low-oxygen stress in Arabidopsis with a focus on primary C- and N-metabolism.

Mustroph A, Barding GA Jr, Kaiser KA, Larive CK, Bailey-Serres J.

Plant Cell Environ. 2014 Oct;37(10):2366-80. doi: 10.1111/pce.12282. Epub 2014 Mar 12.


Translational dynamics revealed by genome-wide profiling of ribosome footprints in Arabidopsis.

Juntawong P, Girke T, Bazin J, Bailey-Serres J.

Proc Natl Acad Sci U S A. 2014 Jan 7;111(1):E203-12. doi: 10.1073/pnas.1317811111. Epub 2013 Dec 23.


Two Rumex species from contrasting hydrological niches regulate flooding tolerance through distinct mechanisms.

van Veen H, Mustroph A, Barding GA, Vergeer-van Eijk M, Welschen-Evertman RA, Pedersen O, Visser EJ, Larive CK, Pierik R, Bailey-Serres J, Voesenek LA, Sasidharan R.

Plant Cell. 2013 Nov;25(11):4691-707. doi: 10.1105/tpc.113.119016. Epub 2013 Nov 27.


Flooding tolerance: O2 sensing and survival strategies.

Voesenek LA, Bailey-Serres J.

Curr Opin Plant Biol. 2013 Oct;16(5):647-53. doi: 10.1016/j.pbi.2013.06.008. Epub 2013 Jul 5. Review.


Cold shock protein 1 chaperones mRNAs during translation in Arabidopsis thaliana.

Juntawong P, Sorenson R, Bailey-Serres J.

Plant J. 2013 Jun;74(6):1016-28. doi: 10.1111/tpj.12187. Epub 2013 May 6.


Linking genes of unknown function with abiotic stress responses by high-throughput phenotype screening.

Luhua S, Hegie A, Suzuki N, Shulaev E, Luo X, Cenariu D, Ma V, Kao S, Lim J, Gunay MB, Oosumi T, Lee SC, Harper J, Cushman J, Gollery M, Girke T, Bailey-Serres J, Stevenson RA, Zhu JK, Mittler R.

Physiol Plant. 2013 Jul;148(3):322-33. doi: 10.1111/ppl.12013. Epub 2013 Mar 20.


Microgenomics: genome-scale, cell-specific monitoring of multiple gene regulation tiers.

Bailey-Serres J.

Annu Rev Plant Biol. 2013;64:293-325. doi: 10.1146/annurev-arplant-050312-120035. Epub 2013 Feb 28. Review.


Isolation and analysis of mRNAs from specific cell types of plants by ribosome immunopurification.

Mustroph A, Zanetti ME, Girke T, Bailey-Serres J.

Methods Mol Biol. 2013;959:277-302. doi: 10.1007/978-1-62703-221-6_19.


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