Systems Biology at Washington University

FIBR

Journal Publications

	Journal	Title and Authors	Remarks

	OMICS: A Journal of Integrative Biology, 2007,11:161-185 DOI: 10.1089/omi.2007.0013	A Light Regulated Network in Cyanobacteria , Aurora, R.,Hihara, Y., Singh, A.K. and Pakrasi, H.B.	Supplementary Information

	Current Opinion in Plant Biology 2007,10:182-189	Physcomitrella patens: mosses enter the genomic age , Quatrano R.S., McDaniel, S.F., Khandelwal, A., et al.

	Developmental Dynamics 236(8):2181-97, 2007	Systems Level Analysis of Osteoclastogenesis Reveals Intrinsic and Extrinsic Regulatory Interactions, Kiesel, J., Miller, C., Abu-Amer, Y. and Aurora, R.

	Proceedings of the National Academy of Science USA. 104:13337-13342	Moonlighting activity of presenilin in plants is independent of γ-secretase and evolutionarily conserved , Khandelwal, A., Chandu, D., Roe, M.D., Kopan, R. and Quatrano, R.S.

	Science, 4 January 2008 : Vol. 319. no. 5859, pp. 64 - 69	The Physcomitrella Genome Reveals Evolutionary Insights into the Conquest of Land by Plants , Rensing S.A. et al.	Supplementary Information, Supplementary Table

	J.Biol. Chem.,Vol. 283, Issue 23, 15762-15770	Identification of an atypical membrane protein involved in the formation of protein disulfide bonds in oxygenic photosynthetic organisms, Singh, A.K., Bhattacharyya-Pakrasi, M. and Pakrasi H.B.	Supplementary Information

	Plant Physiology, July 4, 2008	Integration of carbon and nitrogen metabolism with energy production is crucial to light acclimation in the cyanobacterium Synechocystis , Singh A.K., Elvitigala T.R., Bhattacharya-Pakrasi, M., Aurora, R., Ghosh, B.K. and Pakrasi, H.B.	Supplementary Information figures,table2

	Plant Cell Physiol. doi:10.1093/pcp/pcn139	Properties of Mutants of Synechocystis sp. PCC 6803 Lacking Carbon Sequestration Systems, Xu, M., Bernat, G., Singh, A.K., Mi, H., Rogner, M., Pakrasi, H.B., Ogawa, T.

	PNAS, Sept 23, 2008	The genome of Cyanothece 51142, a unicellular diazotrophic cyanobacterium important in the marine nitrogen cycle, Eric A. Welsh, et al.

	Plant Physiology, Vol. 148, Issue 4, Dec, 2008	Arabidopsis transcriptome reveals control circuits regulating redox homeostasis and the role of an AP2 transcription factor , Khandelwal, A., Elvitigala, T.R., Ghosh, B.K. and Quatrano, R.S.	Supplementary Information

	IEEEi/ACM Computational Biology and Bioinformatics, In press	Identification of Genes with Diurnal Oscillations from Microarray Time Series Data, Wang, W. Ghosh, B.K. and Pakrasi, H.B.

	BMC Genomics, Vol.10:226	Effect of continuous light on diurnal rhythms in Cyanothece sp. ATCC 51142, Elvitigala, T.R., Stockel, J., Ghosh, B.K., and Pakrasi, H.B.

	Plant Physiology, Sept, 2009	A systems level analysis of the effects of light quality on the metabolism of a cyanobacterium Singh, A.K., Bhattacharya-Pakrasi, M., Elvitigala, T., Ghosh, B.K., Aurora, R., and Pakrasi, H.B.

	Submitted	High Throughput Biological Data Analysis, A step towards understanding a living cell, Elvitigala T.R. Polpitiya, A.D., Wang, W., Stockel, J., Khandelwal, A., Pakrasi, H.B., and Ghosh B.K.

	In Preparation	Meta-transcriptome analyses reveal the organismal adaptations to environmental perturbations in photosynthetic organism, Singh A.K., Elvitigala T.R., Cameron, J.C., Bhattacharya-Pakrasi, M., Ghosh, B.K., Pakrasi, H.B



Conference Papers and Book Chapters

	Conference/Book	Title and Authors

	2nd CoE Workshop on Human Adaptive Mechatronics, Center of Excellence Project, Tokyo Denki University, Saitama, 2005	Light Induced Gene Expression Dynamics in Cyanobacteria, Ghosh B.K., Du X. and Polpitiya, A.D.

	Emerging Model Organism Project: Moss (P. patens)	The Moss, Physcomitrella patens (abstract), Cove, D. J., Perroud, P., Charron, A.J., McDaniel, S.F., Khandelwal, A. and Quatrano, R.S.

	10th International Conference on Control, Automation, Robotics and Vision, 2008.	Controlling diurnal rhythms by light, Ghosh, B.K., Pakrasi, H.B., and Elvitigala, T.R.

	American Control Conference, 2009	Modeling and Simulation of Diurnal Biological Processes in Cyanobacteria, Elvitigala, T.R., Pakrasi, H.B., and Ghosh, B.K.

	Foundations of Systems Biology in Engineering, 2009	Dynamical Systems Modeling of Interactions in Cyanobacteria Diurnal Genes, Elvitigala, T.R., Pakrasi, H.B., and Ghosh, B.K.

	Springer, In Press	Dynamic Network Modeling of Diurnal Genes in Cyanobacteria, Elvitigala, T.R., Pakrasi, H.B., and Ghosh, B.K.


Poster Presentations

	Event	Title and Authors

	7th Annual Fall symposium, Merging and Emerging Disciplines in Biology, Sep30- Oct1, 2005	Redox Regulation of Arabidopsis Transcriptome, Abha Khandelwal et al.

	International Conference for Systems Biology, 2005, Boston, USA	A Network of Genes Regulated by Light in Cyanobacteria, Rajeev Aurora et al.

	Experimental Biology, April 2006	The effect of experimental design on network inference, Rajeev Aurora et al.

	International Conference for Systems Biology, 2006, Yokahama, Japan	Genes and functions that regulate redox status in a photosynthetic organism, Rajeev Aurora et al.

	NSF, June 2006	A Systems Approach to Study Redox Regulation of Functions of Photosynthetic Organisms, Pakrasi H , et al.

	32nd Annual Midwest Photosynthesis Meeting, Oct 29th – 31st 2006	Identification of novel genes required for the maintenance of redox homeostasis in the oxygenic photosynthetic organisms ( poster ), Abhay Singh et al.

	Biology Research Symposium, Colgate University, NY	Genome-wide Comparison of Gene Expression in H₂O₂ Treated kap108Δ Yeast Mutants, Dima Tkachev

	Summer Undergraduate Research Symposium, Colgate University, NY	A Double NLS mutation in the S. cerevisiae Protein Nma111 Prevents Nuclear Localization, Travis OBrien

	Undergraduate Research Poster Session, April 2007, Colgate University, NY	Genome-wide Comparison of Gene Expression in H₂O₂ Treated kap108Δ Yeast Mutants, Dima Tkachev

	9th Cyanobacterial Workshop,June 6-10,2007,Wisconsin,USA	Recovery from photoinhibition requires a lumen localized peroxiredoxin-Q in Synechocystis 6803, Maitrayee Bhattacharyya-Pakrasi et al.

	9th Cyanobacterial Workshop,June 6-10,2007,Wisconsin,USA	A novel membrane-bound VKORC1/Dsb-like fusion protein involved in disulfide bond formation in oxygenic photosynthetic organisms ( poster ), Abhay Singh et al.

	9th Cyanobacterial Workshop,June 6-10,2007,Wisconsin,USA	The reduction-oxidation buffering system in Synechocystis sp. PCC 6803, Jeffrey Cameron et al.

	9th Cyanobacterial Workshop,June 6-10,2007,Wisconsin,USA	Response to redox stresses in Synechocystis 6803: information revealed from microarray experiments ( poster ), Thanura Elvitigala et al.

	Plant biology and Botany Joint congress 2007, July7-11, Chicago, USA	Redox homeostasis in plants: The Arabidopsis transcriptome in response to photosynthetic stress using high light and DCMU, ( poster ), Abha Khandelwal et al.

	8th International Conference on Systems Biology-2007, October 1-6, Long Beach, California, USA	Identification and Modeling of Co-Rhythmic Genes from Micro-array Time Series Data, ( poster ), Wenxue Wang et al.

	8th International Conference on Systems Biology-2007, October 1-6, Long Beach, California, USA	Computational Analysis of the Redox stress response in organisms, ( poster ), Thanura Elvitigala et al.

	8th International Conference on Systems Biology-2007, October 1-6, Long Beach, California, USA	Systems approach divulges redox regulation of Arabidopsis transcriptome, ( poster ), Abha Khandelwal et al.


Other Presentations

	Event	Title and Speaker

	Seminar Series, California state University, Long Beach, Oct 4, 2007	Systems Analysis of Redox Regulated Arabidopsis Transcriptome, Abha Khandelwal

	Danforth Plant Science Center (DDPSC), April 1, 2008	Glutathione metabolism and redox homeostasis in the cyanobacterium Synechocystis sp. PCC 6803, Jeff Cameron