Publications - 2012
Arnison PG, Bibb MJ, Bierbaum G, Bowers AA, Bulaj G, Camarero JA, Campopiano DJ, Clardy J, Cotter PD, Craik DJ, Dittmann E, Donadio S, Dorrestein PC, Entian KD, Fischbach MA, Garavelli JS, Göransson U, Gruber CW, Haft DH, Hemscheidt TK, Hertweck C, Hill C, Horswill AR, Jaspars M, Kelly WL, Klinman JP, Kuipers OP, Link AJ, Liu W, Marahiel MA, Mitchell DA, Moll GN, Moore BS, Nair SK, Nes IF, Norris GE, Olivera BM, Onaka H, Patchett ML, Reaney MJT, Rebuffat S, Ross RP, Sahl HG, Schmidt EW, Selsted ME, Severinov K, Shen B, Sivonen K, Smith L, Stein T, Süssmuth RE, Tagg JR, Tang GL, Vederas JC, Walsh CT, Walton JD, Willey JM and van der Donk WA (2012) Ribosomally synthesized and post-translationally modified peptide natural products: Overview and recommendations for a universal nomenclature. Nat Prod Rep In press.
Attaran E, He SY (2012) The long-sought-after salicylic acid receptors. Mol Plant 5:971-3.
Aung K and Hu J (2012) Differential roles of Arabidopsis dynamin-related proteins DRP3A, DRP3B, and DRP5B in organelle division. J Integr Plant Biol 54 (11):921-931.
Avila CA, Arévalo-Soliz LM, Jia L, Navarre DA, Chen Z, Howe GA, Meng QW, Smith JE, Goggin FL (2012) Loss of function of FATTY ACID DESATURASE7 in tomato enhances basal aphid resistance in a salicylate-dependent manner. Plant Physiol 158(4):2028-41. Epub 2012 Jan 30. Abstract
Awad S, Panchy N, Ng SK, Chen J (2012) Inferring the Regulatory Interaction Models of Transcription Factors in Transcriptional Regulatory Networks. J Bioinform Comput Biol 10(5):1250012 (TRIM website) .
Banerjee G, Car S, Liu T, Williams DL, López Meza S, Walton JD and Hodge DB (2012) Scale-up and integration of alkaline hydrogen peroxide pretreatment, enzymatic hydrolysis, and ethanolic fermentation. Biotechnol Bioeng 109:922-931.
Chen J, Lalonde S, Obrdlik P, Vatani AN, Parsa SA, Vilarino V, Revuelta JL, Frommer WB, Rhee SY (2012) Uncovering Arabidopsis membrane protein interactome enriched in transporters using mating-based split ubiquitin assays and classification models. Front Plant Physiol 3:124.
Chen Y, Brandizzi F (2012) AtIRE1 and AGB1 independently control two essential unfolded protein response pathways in plants. Plant J 69:266-277. Abstract
Du W, Tamura K and Brandizzi F (2012) ARF-GEF diversity underlies Arabidopsis Golgi integrity at specific stages of cell growth. Mol Plant In press.
Du W, Tamura K, Stefano G, and Brandizzi F (2012) The Integrity of the Plant Golgi Apparatus Depends on Cell Growth-Controlled Activity of Gnl1. Mol Plant In press.
Ducat D, Avelar-Rivas JA, Way J, Silver P (2012) Re-routing carbon flux to enhance photosynthetic efficiency. Appl Environ Microbiol 78(8):2660-8.
Ducat D, Silver P (2012) Improving Carbon Fixation Pathways. Curr Opin Chem Biol 16(3-4):337-44.
Erb M, Meldau S, Howe GA (2012) Role of phytohormones in insect-specific plant reactions. Trends Plant Sci Feb 1 (Epub ahead of print). Abstract
Gärtner K, Lechno-Yossef S, Cornish A, Wolk CP, Hegg EL (2012) Expression of Shewanella oneidensis MR-1 [FeFe]-hydrogenase genes in Anabaena sp. strain PCC 7120. Appl Env Microbiol 78: 8579-8586.
Hu J, Baker A, Bartel B, Linka N, Mullen R, Reumann S, and Zolman B (2012) Plant peroxisomes: biogenesis and function. Plant Cell 24:2279-2303.
Hu P, Lang J, Wawrousek K, Yu J, Maness P, Chen J (2012) Draft genome sequence of Rubrivivax gelatinosus CBS. J Bacteriol In press. (SEQUENCES)
Huang P, Liu CJ, Xiao L, Chen J (2012) Wireless Spectrum Occupancy Prediction Based on Partial Periodic Pattern Mining. Proceedings of IEEE / ACM 20th Intl Workshop on Quality of Service (IWQoS), Coimbra, Portugal.
Ioannidis NE, Cruz JA, Kotzabasis K, Kramer DM (2012) Evidence that Putrescine Modulates the Higher Plant Photosynthetic Proton Circuit. PLoS ONE 7(1): e29864. doi:10.1371/journal.pone.0029864 Abstract
Jensen JK, Schultink A, Keegstra K, Wilkerson CG, Pauly M (2012) RNA-Seq analysis of developing nasturtium seeds (Tropaeolum majus): Identification and characterization of an additional galactosyltransferase involved in xyloglucan biosynthesis. Mol Plant 5:984-992.
Jiao Y, Rosa BA, Oh S, Montgomery B, Qin W, Chen J (2012) Detection and Decomposition: Treatment-induced Cyclic Gene Expression Disruption in High-throughput Time-series Datasets. J Bioinform Comput Biol In press (Critical Comments Paper).
Kohzuma K, Dal Bosco C, Kanazawa A, Dhingra A, Nitschke W, Meurer J, Kramer DM (2012) Thioredoxin-insensitive plastid ATP synthase that performs moonlighting functions. Proc Natl Acad Sci In press.
Koo AJK and Howe GA (2012) Catabolism and deactivation of the lipid-derived hormone jasmonoyl-isoleucine. Front Plant Sci 3:19. doi:10.3389/fpls.2012.00019 Abstract
Lawson T, Kramer DM, Raines CA (2012) Improving yield by exploiting mechanisms underlying natural variation of photosynthesis. Curr Opin Biotech In press Abstract
Lee CM, Thomashow MF (2012) Photoperiodic regulation of the C-repeat binding factor (CBF) cold acclimation pathway and freezing tolerance in Arabidopsis thaliana. Proc Natl Acad Sci USA 109:15054-15059.
López-Igual R, Lechno-Yossef S, Fan Q, Herrero A, Flores E, Wolk CP (2012) A major facilitator superfamily protein, HepP, is involved in formation of the heterocyst envelope polysaccharide in the cyanobacterium Anabaena sp. strain PCC 7120. J Bacteriol 194:4677-4687.
Luo H, Hallen-Adams HE, Scott-Craig JS and Walton JD (2012) Ribosomal biosynthesis of -amanitin in Galerina marginata. Fung Genet Biol 49:123-129.
Moreno AA, Mukhtar MS, Blanco F, Boatwright JL, Moreno I, Jordan MR, Chen Y, Brandizzi F, Dong X, Orellana A, Pajerowska-Mukhtar KM (2012) IRE1/bZIP60-Mediated Unfolded Protein Response Plays Distinct Roles in Plant Immunity and Abiotic Stress Responses. PLoS One 7(2):e31944. Epub 2012 Feb 16 Abstract
Paper JM, Scott-Craig JS, Cavalier D, Faik A, Wiemels RE, Borrusch MS, Bongers M and Walton JD (2012) Fucosidases with different substrate specificities from two species of Fusarium. Appl Microbiol Biotechnol In press.
Pattanaik B, Whitaker MJ, Montgomery BL. (2012) Light quantity affects the regulation of cell shape in Fremyella diplosiphon. Front Microbiol 3:170.
Peng J, Chen J, Wang Y (2012) Identifying Cross-category Relations in Gene Ontology and Constructing Genome-specific Term Association Networks. BMC Bioinformatics (special issue for selected papers presented at the 11th Asia-Pacific Bioinformatics Conference) In press.
Rosa B, Jiao Y, Oh S, Montgomery B, Qin W, Chen J (2012) Frequency-based time-series gene expression recomposition using PRIISM. BMC Systems Biology 6:69.
Rosa BA, Zhang J, Major I, Qin W and Chen J (2012) Knowledge‐based Optimal Timepoint Sampling in High‐Throughput Temporal Experiments. Bioinformatics In press.
Shyu C, Figueroa P, DePew CL, Cooke TF, Sheard LB, Morena JE, Katsir L, Zheng N, Browse J, Howe GA (2012) JAZ8 Lacks a Canonical Degron and has an EAR Motif that Mediates Transcriptional Repression of Jasmonate Responses in Arabidopsis. Plant Cell (Epub ahead of print) doi:10.1105/tpc.111.093005 Abstract
Singh SP, Montgomery BL (2012) Reactive oxygen species are involved in the morphology-determining mechanism of Fremyella diplosiphon cells during complementary chromatic adaptation. Microbiology In press.
Sparkes I, Brandizzi F (2012) Fluorescent protein-based technologies: shedding new light on the plant endomembrane system. Plant J In press.
Srivastava M, Chen Y, Deng Y, Brandizzi F and Howell SH (2012) Critical elements in bZIP28 mediate its organelle-to-organelle movement under ER stress conditions. Plant J 70:1033-1042. Abstract
Stefano G, Renna L, Brandizzi F (2012) Next generation sequencing for the fast identification of EMS mutations in forward genetics screens. J Visual Experim In press.
Stefano G, Renna L, Moss TJ, McNew JA and Brandizzi F (2012) In Arabidopsis, the spatial and dynamic organization of the endoplasmic reticulum and Golgi apparatus largely relies on a non-essential GTPase, RHD3. Plant J 69:957-966.
Tan X, Liang W, Hu J, and Zhang D (2012) MTR1 encodes a secretory fasciclin glycoprotein required for male reproductive development in rice. Developmental Cell 22:1127-1137.
Walton JD, Luo H and Hallen-Adams H (2012) Ribosomally encoded cyclic peptide toxins from mushrooms. Meth Enzymol 516, part B (D.A. Hopwood, ed.), pp. 63-77.
Wang Y, Alonso AP, Wilkerson CG, Keegstra K (2012) Deep EST profiling of developing fenugreek endosperm to investigate glactomannan biosynthesis and its regulation. Plant Mol Biol 79:243-258.
Wang Y, Mortimer JC, Davis J, DuPree P, Keegstra K (2012) Identification of an additional protein involved in mannan biosynthesis. Plant J doi:10.1111/tpj.12019.
Withers J, Yao J, Mecey C, Howe GA, Melotto M, He SY (2012) Transcription factor-dependent nuclear localization of a transcriptional repressor in jasmonate hormone signaling. Proc Natl Acad Sci USA 109: 20148-20153.
Yang DL, Yao J, Mei CS, Tong XH, Zeng LJ, Li Q, Xiao LT, Sun TP, Li J, Deng XW, Lee CM, Thomashow MF, Yang Y, He Z, He SY (2012) Plant hormone jasmonate prioritizes defense over growth by interfering with gibberellin signaling cascade. Proc Natl Acad Sci USA 109:E1192-200.
Zabotina OA, Avci U, Cavalier D, Pattathil S, Chou Y-H, Eberhard S, Danhof, L, Keegstra K, Hahn MG (2012) Mutations in multiple XXT genes of Arabidopsis reveal the complexity of xyloglucan biosynthesis. Plant Physiol 159:1367-1384.
Zheng XY, Spivey NW, Zeng W, Liu PP, Fu ZQ, Klessig DF, He SY, Dong X (2012) Coronatine Promotes Pseudomonas syringae Virulence in Plants by Activating a Signaling Cascade that Inhibits Salicylic Acid Accumulation. Cell Host & Microbe 11:587-96. Abstract
