Plant Systems Biology UCSD/SALK

IGERT trainees PUBLICATIONS

1. *Barrera DJ, Rosenberg JN, Chiu JG, Chang YN, Debatis M, Ngoi SM, Chang JT, Shoemaker CB, Oyler GA, Mayfield SP. (2015). Algal chloroplast produced camelid VH H antitoxins are capable of neutralizing botulinum neurotoxin. Plant Biotechnol Journal 13(1):117-24.

2. *Castellana NE, Shen Z, He Y, Walley JW, Cassidy CJ, Briggs SP, Bafna V. (2014). An automated proteogenomic method uses mass spectrometry to reveal novel genes in Zea mays. Molecular and Cellular Proteomics; 13(1):157-67.

3. Matos DA, *Cole BJ, Whitney IP, MacKinnon KJ, Kay SA, Hazen SP. (2014). Daily changes in temperature, not the circadian clock, regulate growth rate in Brachypodium distachyon. PLoS One 9(6):e100072.  doi: 10.1371/journal.pone.0100072. eCollection.

4. Mendoza-Cózatl DG, Xie Q, Akmakjian GZ, *Jobe TO, Patel A, Stacey MG, Song L, Demoin DW, Jurisson SS, Stacey G, Schroeder JI. (2014). OPT3 is a component of the iron-signaling network between leaves and roots and misregulation of OPT3 leads to an over-accumulation of cadmium in seeds. Molecular Plant 7(9):1455-69. doi: 10.1093/mp/ssu067.

5. Ma H, Morey R, O'Neil RC, He Y, Daughtry B, *Schultz MD, Hariharan M, Nery JR, Castanon R, Sabatini K, Thiagarajan RD, Tachibana M, Kang E, Tippner-Hedges R, Ahmed R, Gutierrez NM, Van Dyken C, Polat A, Sugawara A, Sparman M, Gokhale S, Amato P, Wolf DP, Ecker JR, Laurent LC, Mitalipov S. (2014). Abnormalities in human pluripotent cells due to reprogramming mechanisms. Nature 511(7508):177-83. doi: 10.1038/nature13551.

6. Buganim Y, Markoulaki S, van Wietmarschen N, Hoke H, Wu T, Ganz K, Akhtar-Zaidi B, He Y, Abraham BJ, Porubsky D, Kulenkampff E, Faddah DA, Shi L, Gao Q, Sarkar S, Cohen M, Goldmann J, Nery JR, *Schultz MD, Ecker JR, Xiao A, Young RA, Lansdorp PM, Jaenisch R. (2014). The developmental potential of iPSCs is greatly influenced by reprogramming factor selection. Cell Stem Cell 15(3):295-309. doi: 10.1016/j.stem.2014.07.003.

7. Rasala BA, Chao SS, Pier M, *Barrera DJ, Mayfield SP. (2014). PLoS One: 9(4):e94028.

8. *Barrera D, Gimpel J, Mayfield S. (2014). Rapid screening for the robust expression of recombinant proteins in algal plastids. Methods Molecular Biology;1132:391-9.

9. Sutimantanapi D, *Pater D, Smith LG. (2014). Divergent roles for maize PAN1 and PAN2 receptor-like proteins in cytokinesis and cell morphogenesis. Plant Physiology 164(4): 1905-17.

10. Roadmap Epigenomics Consortium, et al., *Schultz MD, et al., Kellis M. (2015). Integrative analysis of 111 reference human epigenomes. Nature 518:317-30. doi: 10.1038/nature14248.

11. Woo S, Cha SW, Merrihew G, He Y, *Castellana N, Guest C, MacCoss M, Bafna V. (2014). Proteogenomic database construction driven from large scale RNA-seq data. Journal of Proteome Research; 13(1):21-8.

12. Schmitz, R.J., *Schultz,M.D., Urich, M.A., Nery, J.R., Pelizzola, M., O. Libiger, Alix, A., McCosh, R.B., Chen, H., Schork, N.J.& Ecker, J.R. (2013). Patterns of population epigenomic diversity. Nature 495:193-198.

13. Huffaker A, Pearce G, Veyrat N, Erb M, Turlings TC, *Sartor R, Shen Z, Briggs SP, Vaughan MM, Alborn HT, Teal PE, Schmelz EA. (2013). Plant elicitor peptides are conserved signals regulating direct and indirect antiherbivore defense. Proceedings of the National Academy of Sciences of United States of America; 110(14):5707-12.

14. Jung HS, Crisp PA, Estavillo GM, *Cole BJ, Hong F, Mockler TC, Pogson BJ, Chory J.(2013). Subset of heat-shock transcription factors required for the early response of Arabidopsis to excess light. Proceedings of the National Academy of Sciences of United States of America; 110(35):14474-9.

15. Xie W, *Schultz MD, Lister R, Hou Z, Rajagopal N, Ray P, Whitaker JW, Tian S, Hawkins RD, Leung D, Yang H, Wang T, Lee AY, Swanson SA, Zhang J, Zhu Y, Kim A, Nery JR, Urich MA, Kuan S, Yen CA, Klugman S, Yu P, Suknuntha K, Propson NE, Chen H, Edsall LE, Wagner U, Li Y, Ye Z, Kulkarni A, Xuan Z, Chung WY, Chi NC, Antosiewicz-Bourget JE, Slukvin I, Stewart R, Zhang MQ, Wang W, Thomson JA, Ecker JR, Ren B. (2013). Epigenomic analysis of multilineage differentiation of embryonic stem cells. Cell.;153(5):1134-48.

16. O'Brien EJ, Lerman JA, *Chang RL, Hyduke DR, Palsson BO. (2013). Genome-scale models of metabolism and gene expression extend and refine growth phenotype prediction. Molecular Systems Biology; 9: 693.

17. Pencík A, Simonovik B, Petersson SV, Henyková E, Simon S, *Greenham K, Zhang Y, Kowalczyk M, Estelle M, Zazímalová E, Novák O, Sandberg G, Ljung K. (2013). Regulation of auxin homeostasis and gradients in Arabidopsis roots through the formation of the indole-3-acetic acid catabolite 2-oxindole-3-acetic acid. Plant Cell; 25(10):3858-70.

18. *Chang RL, Andrews K, Kim D, Li Z, Godzik A, Palsson BO. (2013). Structural systems biology evaluation of metabolic thermotolerance in Escherichia coli. Science; 340(6137):1220-3.

19. *Chang RL, Xie L, Bourne PE, Palsson BO. (2013). Antibacterial mechanisms identified through structural systems pharmacology. Systems Biology; 7:102.

20. Tran M, Van C, *Barrera DJ, Pettersson PL, Peinado CD, Bui J, Mayfield SP. (2013). Production of unique immunotoxin cancer therapeutics in algal chloroplasts. Proceedings of the National Academy of Sciences of United States of America; 110(1): E15-22.

21. Lister R, Mukamel EA, Nery JR, Urich M, Puddifoot CA, Johnson ND, Lucero J, Huang Y, Dwork AJ, *Schultz MD, Yu M, Tonti-Filippini J, Heyn H, Hu S, Wu JC, Rao A, Esteller M, He C, Haghighi FG, Sejnowski TJ, Behrens MM, Ecker JR. (2013). Global epigenomic reconfiguration during development. Science; 341(6146):1237905.

22. Rasala BA, *Barrera DJ, Ng J, Plucinak TM, Rosenberg JN, Weeks DP, Oyler GA, Peterson TC, Haerizadeh F, Mayfield SP. (2013). Expanding the spectral palette of fluorescent proteins for the green microalga Chlamydomonas reinhardtii. Plant Journal 74(4):545-56.

23. *Chang KN, Zhong S, Weirauch MT, Hon G, Pelizzola M, Li H, Huang SS, Schmitz RJ, Urich MA, Kuo D, Nery JR, Qiao H, Yang A, Jamali A, Chen H, Ideker T, Ren B, Bar-Joseph Z, Hughes TR, Ecker JR. (2013). Temporal transcriptional response to ethylene gas drives growth hormone cross-regulation in Arabidopsis. eLife. 2013 Jun 11; 2:e00675.

24. Hua Z, Pool JE, Schmitz RJ, *Schultz MD, Shiu SH, Ecker JR, Vierstra RD. (2013). Epigenomic programming contributes to the genomic drift evolution of the F-Box protein superfamily in Arabidopsis. Proceedings of the National Academy of Sciences of United States of America; 110(42):16927-32.

25. Walley JW, Shen Z, *Sartor R, Wu KJ, Osborn J, Smith LG, Briggs SP. (2013). Reconstruction of protein networks from an atlas of maize seed proteotypes. Proceedings of the National Academy of Sciences of United States of America; 110(49):E4808-17.

26. Li L, Ljung K, Breton G, Schmitz RJ, Pruneda-Paz J, Cowing-Zitron C, *Cole BJ, Ivans LJ, Pedmale UV, Jung HS, Ecker JR, Kay SA, Chory J. (2012). Linking photoreceptor excitation to changes in plant architecture. Genes Development 26(8): 785-790.

27. *Lewis, N.E., Nagarajan, H., Palsson, B.Ø. (2012). Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods. Nature Reviews Microbiology 10:291-305.

28. Chapman EJ, *Greenham K, Castillejo C, *Sartor R, Bialy A, Sun TP, Estelle M. (2012). Hypocotyl Transcriptome Reveals Auxin Regulation of Growth-Promoting Genes through GA-Dependent and -Independent Pathways. PLoS One 7(5).

29. *Jobe, T. O., Sung, D.-Y., Akmakjian, G., Pham, A., Komives, E. A., Mendoza-Cózatl, D. G. and Schroeder, J. I. (2012). Feedback inhibition by thiols outranks glutathione depletion: a luciferase-based screen reveals glutathione-deficient γ-ECS and glutathione synthetase mutants impaired in cadmium-induced sulfate assimilation. Plant Journal 70(5): 783-795.

30. Kurihara Y, Schmitz RJ, Nery JR, *Schultz MD et al. (2012), Surveillance of 3′ Noncoding Transcripts Requires FIERY1 and XRN3 in Arabidopsis. G3 Genes/Genomes/Genetics 2:487-498.

31. *Greenham K, Santner A, Castillejo C, Mooney S, Sairanen I, Ljung K, Estelle M. (2012). The AFB4 auxin receptor is a negative regulator of auxin signaling in seedlings. Current Biology. 21(6): 520-525.

32. *Cole B, Kay SA, Chory J. (2011). Automated analysis of hypocotyl growth dynamics during shade avoidance in Arabidopsis. Plant Journal 65(6): 991-1000.

33. *Chang RL, Ghamsari L, Manichaikul A, Hom EF, Balaji S, Fu W, Shen Y, Hao T, Palsson BØ, Salehi-Ashtiani K, Papin JA. (2011). Metabolic network reconstruction of Chlamydomonas offers insight into light-driven algal metabolism. Molecular Systems Biology; 7:518.

34. Schellenberger, J., Que, R., Fleming, R.T., Thiele, I., Orth, J., Feist, A.M., Zielinski , D.C., Bordbar, A., *Lewis, N.E., Rahmanian, S., Kang, J., Hyduke, D., Palsson, B.Ø. (2011). Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0. Nature Protocols 6:1290-307.

35. Mendoza-Cózatl, D.G., *Jobe, T.O., Hauser, F. and Schroeder, J.I. Long-distance transport, vacuolar sequestration, tolerance, and transcriptional responses induced by cadmium and arsenic. Current Opinion in Plant Biology 14: 554-562 (2011).

36. Johnson DB, Xu J, Shen Z, Takimoto JK, *Schultz MD, Schmitz RJ, Xiang Z, Ecker JR, Briggs SP, Wang L. (2011). RF1 knockout allows ribosomal incorporation of unnatural amino acids at multiple sites. Nature Chemical Biology 7(11): 779-86.

37. Schmitz RJ, *Schultz MD, Lewsey MG, O'Malley RC, Urich MA, Libiger O, Schork NJ, Ecker JR. (2011). Transgenerational epigenetic instability is a source of novel methylation variants. Science 334:369-73.

38. Schellenberger, J., *Lewis, N.E., Palsson, B.Ø. (2011). Elimination of thermodynamically infeasible loops in steady state metabolic models. Biophysical Journal, 100:544-53.

39. *Castellana NE, McCutcheon K, Pham VC, Harden K, Nguyen A, Young J, Adams C, Schroeder K, Arnott D, Bafna V, Grogan JL, Lill JR. (2011). Resurrection of a clinical antibody: template proteogenomic de novo proteomic sequencing and reverse engineering of an anti-lymphotoxin-antibody. Proteomics 11: 395-405.

40. *Greenham, K., Santner, A., Castillejo, C., Mooney, S., Sairanen, I., Ljung, K., and Estelle, M. (2011). The AFB4 Auxin Receptor Is a Negative Regulator of Auxin Signaling in Seedlings. Current Biology 21: 1-6.

41. *Cole B., Kay,S., Chory J. (2011). Automated analysis of hypocotyl growth dynamics during shade avoidance in Arabidopsis. Plant Journal 65: 991-1000.

42. Bar-Even, A., Noor, E., *Lewis, N.E., Milo, R. (2010). Design and analysis of synthetic carbon fixation pathways. Proceedings of the National Academy of Sciences of United States of America; 107:8889-8894.

43. *Lewis, N.E., Hixson, K.K., Conrad, T.M., Lerman, J.A., Charusanti, P., Polpitiya, A.D., Adkins, J.N., Schramm, G., Purvine, S.O., Lopez-Ferrer, D., Weitz, K.K., Eils, R., König, R., Smith, R.D., Palsson, B.Ø. (2010). Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models. Molecular Systems Biology, 6:390.

44. Portnoy, V.A., Scott, D.A., *Lewis, N.E., Tarasova, Y., Osterman, A.L., Palsson, B.Ø. (2010). Deletion of genes encoding cytochrome oxidases and quinol monooxygenase blocks the aerobic-anaerobic shift in Escherichia coli K-12 MG1655. Applied and Environmental Microbiology, 76:6529-40.

45. Bordbar, A., *Lewis, N.E., Schellenberger, J. Palsson, B.Ø., Jamshidi, N. (2010). Insight into human alveolar macrophage and M. tuberculosis interactions via metabolic reconstructions. Molecular Systems Biology 6:422.

46. Conrad, T.C., Frazier, M., Joyce, A.R., Cho, B. K., Knight, E. M., *Lewis, N.E., Landick, R, Palsson, B.Ø. (2010). RNA polymerase mutants found through adaptive evolution re-program Escherichia coli K-12 MG1655 for optimal growth in minimal media. Proceedings of the National Academy of Sciences of United States of America; 107:20500-5.

47. *Lewis, N.E., Schramm, G., Bordbar, A., Schellenberger, J., Andersen, M.P., Cheng, J.K., Patel, N., Yee, A., Lewis, R.A., Eils, R., König, R., Palsson, B.Ø. (2010). Large-scale in silico modeling of metabolic interactions between cell types in the human brain. Nature Biotechnology, 28:1279-1285.

48. *Chang RL, Xie L, Xie L, Bourne PE, Palsson BO. (2010). Drug off-target effects predicted using structural analysis in the context of a metabolic network model. PLoS Computational Biology 6(9).

49. Brinza D, *Schultz M, Tesler G, Bafna V. (2010). RAPID detection of gene-gene interactions in genome-wide association studies. Bioinformatics 26: 2856-62.

50. Kahan, B., Magliocca, J., Merriam, F., Treff, N., Budde, M., *Nelson, J., Browning, V., Ziehr, B., Odorico, J. (2010). Elimination of tumorigenic stem cells from differentiated progeny and selection of definitive endoderm reveals a Pdx1(+) foregut endoderm stem cell lineage. Stem Cell Research 6:143-57.

51. Mendoza-Cozatl, D.G., Zhai, Z., *Jobe, T.O., Akmakjian, G.Z., Song, W.Y., Limbo, O., Russell, M.R., Kozlovskyy, V.I., Martinoia, E., Vatamaniuk, O.K., Russell, P., Schroeder, J.I. (2010). Tonoplast-localized Abc2 Transporter Mediates Phytochelatin Accumulation in Vacuoles and Confers Cadmium Tolerance. The Journal of Biological Chemistry.

52. *Castellana NE, V Pham, D Arnott, JR Lill, V Bafna. (2010). Template Proteogenomics: sequencing whole proteins using an imperfect database. Molecular & Cellular Proteomics.

53. *Smith ZR, Long JA. (2010). Control of Arabidopsis apical-basal embryo polarity by antagonistic transcription factors. Nature 464: 423-426 .

54. Yamada M, *Greenham K, Prigge MJ, Jensen PJ, Estelle M. (2009). The Transport Inhibitor Response2 Gene Is Required for Auxin Synthesis and Diverse Aspects of Plant Development. Plant Physiology 151: 1-12.

55. Surzycki, R., *Greenham, K., Wagner, R.E. and Surzycki, S. (2009). Factors effecting expression of vaccines in microalgae. Biologicals: Journal of International Association of Biological Standardization; 37:133-138.

56. Manichaikul A, Ghamsari L, Hom EF, Lin C, Murray RR, *Chang RL, Balaji S, Hao T, Shen Y, Chavali AK, Thiele I, Yang X, Fan C, Mello E, Hill DE, Vidal M, Salehi-Ashtiani K, Papin JA. (2009). Metabolic network analysis integrated with transcript verification for sequenced genomes Nature Methods 6(8):589-594.

57. Qiao, H., *Chang, K. N., Yazaki, J., & Ecker, J. R. (2009).Interplay between ethylene, ETP1.ETP2 F-box proteins, and degradation of EIN2 triggers ethylene responses in Arabidopsis. Genes Development: 23, 512-521.

58. *Castellana, N.E., *Payne, S.H., Shen, Z., Stanke, M., Bafna, V., Briggs, S.P. (2008) Discovery and revision of Arabidopsis genes by proteogenomics. Proceedings of the National Academy of Sciences of United States of America; 105(52):21034-8.

59. *Tanner S, Agarwal P. (2008). Gene Vector Analysis (Geneva): a unified method to detect differentially-regulated gene sets and similar microarray experiments. BMC Bioinformatics 22;9:348.

60. *Payne SH, Yau M, Smolka MB, *Tanner S, Zhou H, Bafna V. (2008). Phosphorylation-specific MS/MS scoring for rapid and accurate phosphoproteome analysis. Journal of Proteome Research; 7(8):3373-81.

61. Frank AM, Bandeira N, Shen Z, *Tanner S, Briggs SP, Smith RD, Pevzner PA. (2008). Clustering millions of tandem mass spectra. Journal of Proteome Research; 7(1):113-22.

62. *Tanner S, *Payne SH, Dasari S, Shen Z, Wilmarth PA, David LL, Loomis WF, Briggs SP, Bafna V. (2008). Accurate annotation of peptide modifications through unrestrictive database search. Journal of Proteome Research; 7(1):170-81.

63. Rana BK, Insel PA, *Payne SH, Abel K, Beutler E, Ziegler MG, Schork NJ, O'Connor DT. (2007) Population-based sample reveals gene-gender interactions in blood pressure in White Americans. Hypertension. 49(1):96-106.

64. Gupta N, *Tanner S, Jaitly N, Adkins JN, Lipton M, Edwards R, Romine M, Osterman A, Bafna V, Smith RD, Pevzner PA. (2007). Whole proteome analysis of post-translational modifications: applications of mass-spectrometry for proteogenomic annotation. Genome Research;17(9):1362-77.

65. Patricelli MP, Szardenings AK, Liyanage M, Nomanbhoy TK, Wu M, Weissig H, Aban A, Chun D, *Tanner S, Kozarich JW. (2007). Functional interrogation of the kinome using nucleotide acyl phosphates. Biochemistry; 46(2):350-8.

66. *Tanner S, Shen Z, Ng J, Florea L, Guigó R, Briggs SP, Bafna V. (2007). Improving gene annotation using peptide mass spectrometry. Genome Research ;17(2):231-9.

67. Hirose S, *Payne SH, Loomis WF. (2006). cis-Acting site controlling bidirectional transcription at the growth-differentiation transition in Dictyostelium discoideum. Eukaryotic Cell; 5(7):1104-10.

68. *Tanner S, Pevzner PA, Bafna V. (2006). Unrestrictive identification of post-translational modifications through peptide mass spectrometry. Nature Protocols; 1(1):67-72.

69. Wilmarth, P A.; *Tanner, Stephen W.; Dasari, S; Riviere, M A.; Bafna, Vineet; Pevzner, Pavel A.; and David, L L. (2006) Age-Related Changes in Human Crystallins Determined from Comparative Analysis of Post-Translational Modifications in Young and Aged Lens: Does Deamidation Contribute to Cristallin Insolubility?, Journal of Proteome Research, 5(10), 2554-2556.

70. *Payne SH, Loomis WF. (2006). Retention and loss of amino acid biosynthetic pathways based on analysis of whole-genome sequences. Eukaryotic Cell; 5(2):272-6.

71. Tsur D, *Tanner S, Zandi E, Bafna V, Pevzner PA. (2005). Identification of post-translational modifications by blind search of mass spectra. Nature Biotechnology; 23(12):1562-7.

72. Frank A, *Tanner S, Bafna V, Pevzner P. (2005). Peptide sequence tags for fast database search in mass-spectrometry. Journal of Proteome Research; 4(4):1287-95.

73. *Tanner S, Shu H, Frank A, Wang LC, Zandi E, Mumby M, Pevzner PA, Bafna V. (2005). InsPecT: identification of posttranslationally modified peptides from tandem mass spectra. Analytical Chemistry; 77(14):4626-39.