2013

  • Agostoni M, Koestler BJ, Waters CM, Williams BL, Montgomery BL (2013) Occurrence of cyclic di-GMP-modulating output domains in cyanobacteria: an illuminating perspective. MBio 4(4). pii: e00451-13. doi: 10.1128/mBio.00451-13. Abstract.

  • Awad S and Chen J (2013) Inferring Transcription Factor Collaborations in Gene Regulatory Networks. BMC Systems Biology. In press.

  • Bhosale R, Jewell JB, Hollunder J, Koo AJ, Vuylsteke M, Michoel T, Hilson P, Goossens A, Howe GA, Browse J, Maere S (2013) Predicting gene function from uncontrolled expression variation among individual wild-type Arabidopsis plants. Plant Cell Aug;25(8):2865-77. doi: 10.1105/tpc.113.112268. Epub 2013 Aug 13. PMID: 23943861. Abstract.

  • Brandizzi F, Barlowe C (2013) Organization of the ER-Golgi interface for membrane traffic control. Nat Rev Mol Cell Biol Jun;14(6):382-92. doi: 10.1038/nrm3588. Abstract

  • Brandizzi F, Wasteneys GO (2013) Cytoskeleton-Dependent Endomembrane Organization in Plant Cells: An Emerging Role for Microtubules. Plant J May 7. doi: 10.1111/tpj.12227. [Epub ahead of print]. Abstract

  • Cai F, Axen S and Kerfeld CA (2013) Evidence for the widespread CRISPR-Cas immunity system in the phylum Cyanobacteria. RNA Biology 10: 687-693. Abstract.

  • Cai F, Sutter M, Cameron J, Stanley D and Kerfeld CA (2013) Tandem BMC-domain proteins of carboxysomes form a subcompartment within a microcompartment. Journal of Biological Chemistry 288:16055-16063. Abstract.

  • Cameron JC, Wilson SC, Bernstein SL and Kerfeld CA (2013) Biogenesis of a Bacterial Organelle: The Carboxysome Assembly Pathway. Cell 155:1131-40. Abstract.

  • Chen Y, Aung K, Rol?ík J, Walicki K, Friml J, Brandizzi F (2013) Inter-regulation of the unfolded protein response and auxin signaling. Plant J doi: 10.1111/tpj.12373. Abstract.

  • Chen Y, Brandizzi F (2013) Analysis of unfolded protein response in Arabidopsis. Methods Mol Biol. 2013;1043:73-80. doi: 10.1007/978-1-62703-532-3_8. Abstract.

  • Chen Y, Brandizzi F (2013) IRE1: ER stress sensor and cell fate executor. Trends Cell Biol 23(11): 547-55. doi: 10.1016/j.tcb.2013.06.005. Abstract.

  • Du Y, Nomura Y, Satar G, Hu Z, Nauen R, He, SY, Zhorov BS, Dong K (2013) Molecular evidence for dual pyrethroid-receptor sites on a mosquito sodium channel. Proc Natl Acad Sci USA 110:11785-90. Abstract.

  • Herde M, Koo AJ, Howe GA (2013) Elicitation of jasmonate-mediated defense responses by mechanical wounding and insect herbivory. Methods Mol Biol 1011:51-61. Abstract.

  • Huang P, Liu CJ, Xiao L, Chen J (2013) Wireless Spectrum Occupancy Prediction with Partial Periodic Pattern Mining. IEEE Transactions on Parallel and Distributed Systems PP(99) 1-11. Abstract. 

  • Jiang S, Yao J, Ma KW, Zhou H, Song J, He SY, Ma W (2013)  Bacterial effector activates jasmonate signaling by directly targeting JAZ transcriptional repressors. PLOS Pathogens DOI: 10.1371/journal.ppat.1003715. Abstract.

  • Kaur N, Li J, Hu J (2013). Peroxisomes and photomorphogenesis. Subcell Biochem 69: 195-211.

  • Kaur N, Zhao Q, Xie Q and Hu J (2013) Arabidopsis RING peroxins are E3 ubiquitin ligases that interact with two homologous ubiquitin receptor proteins. J. Integr. Plant Biol. DOI: 10.1111/jipb.12014. Abstract.

  • Kerfeld CA (2013) Sequences and Consequences. Biochemistry and Molecular Biology Education 41:12-15. Article. 

  • Kirilovsky D and Kerfeld CA (2013) The Orange Carotenoid Protein: A blue-green light photoactive protein. Photochemistry and Photobiological Sciences 12:1135-1143. Abstract. 

  • Leikoski N, Liu L, Jokela J, Wahlsten M, Gugger M, Kerfeld CA, Calteau A, Permi P, Sivonen K and Fewer DP (2013) Genome mining expands the chemical diversity of the cyanobactin family to include highly modified linear peptides. Chemistry and Biology 20:1033-1043. Abstract.

  • Lozano-Durán R, Bourdais G, He SY, Robatzek S (2013) The bacterial effector HopM1 suppresses PAMP-triggered oxidative burst and stomatal immunity. New Phytol DOI: 10.1111/nph.12651. Abstract.

  • Lucker B, Kramer DM (2013) Regulation of cyclic electron flow in Chlamydomonas reinhardtii under fluctuating carbon availability. Photosynth Res 117(1-3): 449-59. Abstract.

  • Moreno JE, Shyu C, Campos ML, Patel L, Chung HS, Yao J, He SY, Howe GA (2013) Negative feedback control of jasmonate signaling by an alternative splice variant of JAZ10. Plant Physiol 162:1006-17. Abstract.

  • Nakata M, Mitsuda N, Herde M, Koo AJ, Moreno JE, Suzuki K, Howe GA, Ohme-Takagi M (2013) A bHLH-type transcription factor, ABA-INDUCIBLE BHLH-TYPE TRANSCRIPTION FACTOR/JA-ASSOCIATED MYC2-LIKE1, acts as a repressor to negatively regulate jasmonate signaling in arabidopsis. Plant Cell May;25(5):1641-56. doi: 10.1105/tpc.113.111112. Epub 2013 May 14.PMID: 23673982. Abstract.

  • Niu N, Liang W, Yang, X, Jin W, Wilson ZA, Hu J and Zhang D (2013) EAT1 promotes tapetal cell death by regulating aspartic proteases during male reproductive development in rice. Nat Commun 4:1445 doi:10.1038/ncomms2396. Abstract.

  • Oh S, Warnasooriya SN, Montgomery BL (2013) Downstream effectors of light- and phytochrome-dependent regulation of hypocotyl elongation in Arabidopsis thaliana. Plant Mol Biol 2013 March 1 (epub ahead of print). PMID: 23456246. Abstract.

  • Oh S, Montgomery BL (2013) Phytochromes Contribute to Light-Dependent SIG2 Expression and Anterograde Signaling-Dependent Plastid Gene Expression. Journal of Experimental Botany, 64(18): 5457–5472. Abstract. 

  • Park J-J, Lechno-Yossef S, Wolk CP, Vieille C (2013) Cell-specific gene expression in Anabaena variabilis grown phototrophically, mixotrophically, and heterotrophically. BMC Genomic 14:759. Abstract. 

  • Peng J, Chen J, Wang Y (2013) Identifying Cross-category Relations in Gene Ontology and Constructing Genome-specific Term Association Networks. BMC Bioinformatics 14(Suppl 2):S15. Abstract.

  • Peng J, Uygun S, Kim T, Wang Y, Rhee SY and Chen J (2013) NETSIM: A Novel Tool for Measuring Functional Similarities using Gene Ontology and Gene Co-Function Networks. Bioinformatics. In revision. 

  • Peng J, Wang Y and Chen J (2013) Towards Integrative Gene Functional Similarity Measurement. BMC Bioinformatics. In press.

  • Pourcel L, Irani NG, Koo AJ, Bohorquez-Restrepo A, Howe GA, Grotewold E (2013) A chemical complementation approach reveals genes and interactions of flavonoids with other pathways. Plant J May;74(3):383-97. doi: 10.1111/tpj.12129. Epub 2013 Mar 29. PMID: 23360095. Abstract.

  • Quan S, Yang P, Cassin-Ross G, Kaur N, Aung K, Switzenberg R, Li J, Hu J (2013) Proteome analysis identifies a peroxisomal protease involved in β-oxidation and development. Plant Physiol 163(4):1518-38. Abstract.

  • Rajeev L, Nunes da Rocha U, Klitgord NJ, Luning EG, Fortney J, Axen SD, Shih PM, Bouskill NJ, Bowen B, Kerfeld CA, Garcia-Pichel F, Brodie EL, Northen TR and Mukhopadhyay A (2013) Dynamic cyanobacterial response to hydration and dehydration in a desert biological soil crust. ISME Journal 7: 2178-91. Abstract.

  • Sanjaya, Miller R, Durrett TP, Kosma DK, Lydic TA, Muthan B, Koo AJ, Bukhman YV, Reid GE, Howe GA, Ohlrogge J, Benning C (2013) Altered lipid composition and enhanced nutritional value of Arabidopsis leaves following introduction of an algal diacylglycerol acyltransferase 2. Plant Cell 2013 Feb 15. PMID: 23417035. Abstract.

  • Shih PM, Wu D,Latifi A, Axen SD, Fewer DP, Talla E, Calteau A, Cai F, Tandeau de Marsac N, Rippka R, Herdman M, Sivonen K, Coursin T, Laurent T, Goodwin L, Nolan M, Davenport KW, Han CS, Rubin EM, Eisen JA, Woyke T, Gugger M and Kerfeld CA (2013) Improving the coverage of the cyanobacterial phylum using diversity-driven genome sequencing. Proceedings of the National Academy of Sciences, USA 110:1053-1058. Abstract. 

  • Singh SP, Miller HL, Montgomery BL (2013) Temporal dynamics of changes in reactive oxygen species (ROS) levels and cellular morphology are coordinated during complementary chromatic acclimation in Fremyella diplosiphon. Photosynth Res Oct 14. Abstract.

  • Singh SP, Montgomery BL (2013) Salinity impacts photosynthetic pigmentation and cellular morphology changes by distinct mechanisms in Fremyella diplosiphon. Biochem Biophys Res Commun 2013 Feb 27 (Epub ahead of print). PMID: 23454384. Abstract and article.

  • Stanley D, Raines CA and Kerfeld CA (2013) Comparative Analysis of 126 cyanobacterial genomes reveals evidence of functional diversity in the homologs of the redox regulated CP12 protein. Plant Physiology 161: 824-835. Abstract.

  • Sutter M, Wilson A, Leverenz R, Lopez-Igual R, Thurotte A, Salmeen A, Kirilovsky D and Kerfeld CA (2013) Crystal structure of the FRP and identification of the active site for modulation of OCP-mediated photoprotection in cyanobacteria. Proceedings of the National Academy of Sciences, USA 110: 10022-10027. Abstract.

  • Sutter M, Wilson SC, Deutsch S and Kerfeld CA (2013) Two new high-resolution crystal structures of carboxysome pentamer proteins reveal high structural conservation of CcmL orthologs among distantly related cyanobacterial species. Photosynthesis Research 118:9-16. Abstract. 

  • Tessmer OL, Jiao Y, Cruz JA, Kramer DM and Chen J (2013) Functional Approach to High-throughput Plant Growth Analysis. BMC Systems Biology 7(Suppl 6):S17. Abstract.

  • Walters KJ, Whitaker MJ, Singh SP, Montgomery BL (2013) Light Intensity and Reactive Oxygen Species are Centrally Involved in Photoregulatory Responses During Complementary Chromatic Adaptation in Fremyella diplosiphon. Communicative & Integrative Biology 6(5): e25005-1–e25005-5. Abstract.

  • Wight WD, Labuda R, Walton JD (2013) Conservation of the genes for HC-toxin biosynthesis in Alternaria jesenskae. BMC Microbiol 13:165. doi: 10.1186/1471-2180-13-165. Abstract. 

  • Xin X-F, Nomura K, Underwood W, He SY (2013) Induction and suppression of PEN3 focal accumulation during Pseudomonas syringae pv. tomato DC3000 infection of Arabidopsis. Mol Plant-Microbe Interact 26:861-7. Abstract.

  • Xin, XF, He SY (2013) Pseudomonas syringae pv. tomato DC3000 as a model for probing disease susceptibility and jasmonate signaling in plants. Annu Rev Phytopathol 51:473-98. Abstract.

  • Yao J, Withers J, He SY (2013) Pseudomonas syringae Infection assays in Arabidopsis. Methods Mol Biol 1011:63-81. doi: 10.1007/978-1-62703-414-2_6. Abstract.

  • Zarzycki J and Kerfeld CA (2013) The Crystal Structures of tri-functional Chlorofexus aurantiacus and bi-functional Rhodobacter sphaeroides Malyl-CoA Lyases and Comparison with CitE-like superfamily enzymes and Malate Synthases. BMC Structural Biology 13(1):28. Abstract. 

  • Zarzycki J, Axen SD, Kinney JN and Kerfeld CA (2013) Cyanobacterial-based Approaches to Improving Plant Photosynthesis. Journal of Experimental Botany 64:787-98. Abstract. 

  • Zhang H, Xu C, He Y, Hu J, Liang W and Zhang D (2013) A mutation in CSA creates a new photo-sensitive genic male sterile line applicable for hybrid rice seed production. Proc Natl Acad Sci USA doi:10.1073/pnas.1213041110. Abstract.