@article{babaoglu_dutta_2014, title={A GENI Meso-Scale Experiment of a Verification Service}, DOI={10.1109/gree.2014.13}, abstractNote={In this work, we demonstrate the real world results of a verification service that verifies the performance of a set of network providers by measuring the user flows, using GENI experimental facility. We first give an overview of the architectural components and their interactions to enable such a verification capability. We then give the experiment setup details followed by the numerical results for various network measurement metrics and the evaluation of these results.}, journal={2014 THIRD GENI RESEARCH AND EDUCATIONAL EXPERIMENT WORKSHOP (GREE)}, author={Babaoglu, Ahmet Can and Dutta, Rudra}, year={2014}, pages={65–68} }
 @article{howard_hu_babaoglu_chandra_borghi_tan_he_winter-sederoff_gassmann_veronese_et al._2013, title={High-Throughput RNA Sequencing of Pseudomonas-Infected Arabidopsis Reveals Hidden Transcriptome Complexity and Novel Splice Variants}, volume={8}, ISSN={["1932-6203"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84885077606&partnerID=MN8TOARS}, DOI={10.1371/journal.pone.0074183}, abstractNote={We report the results of a genome-wide analysis of transcription in Arabidopsis thaliana after treatment with Pseudomonas syringae pathovar tomato. Our time course RNA-Seq experiment uses over 500 million read pairs to provide a detailed characterization of the response to infection in both susceptible and resistant hosts. The set of observed differentially expressed genes is consistent with previous studies, confirming and extending existing findings about genes likely to play an important role in the defense response to Pseudomonas syringae. The high coverage of the Arabidopsis transcriptome resulted in the discovery of a surprisingly large number of alternative splicing (AS) events – more than 44% of multi-exon genes showed evidence for novel AS in at least one of the probed conditions. This demonstrates that the Arabidopsis transcriptome annotation is still highly incomplete, and that AS events are more abundant than expected. To further refine our predictions, we identified genes with statistically significant changes in the ratios of alternative isoforms between treatments. This set includes several genes previously known to be alternatively spliced or expressed during the defense response, and it may serve as a pool of candidate genes for regulated alternative splicing with possible biological relevance for the defense response against invasive pathogens.}, number={10}, journal={PLOS ONE}, author={Howard, Brian E. and Hu, Qiwen and Babaoglu, Ahmet Can and Chandra, Manan and Borghi, Monica and Tan, Xiaoping and He, Luyan and Winter-Sederoff, Heike and Gassmann, Walter and Veronese, Paola and et al.}, year={2013}, month={Oct} }
 @inproceedings{babaoglu_dutta_2011, title={Benefits of multi wavelength approach to converter placement to support broadcast with available wavelengths}, DOI={10.1109/glocom.2011.6134393}, abstractNote={Optical networks are widely used in communication systems. Finding optimal converter placement for broadcast on optical networks has been an important area of research. In this problem, the free wavelengths on different links of a optical network are used to support network-wide broadcast, which is useful as a control channel or other OAM tasks. Previous work has articulated the essential difficulty of this problem. In this work, we recognize that bandwidth minimization is not an appropriate goal for this problem, and by using multiple wavelengths, and replicating some transmissions, it is possible to reduce the number of converters. We show example schemas to show that the difference in the optimal number of converters can be arbitrarily large, that adopting multiple wavelength paths whose union contains cycles can strictly reduce the optimal number, and then present a heuristic algorithm for broadcast path assignment to minimize converters under the new model.}, booktitle={2011 ieee global telecommunications conference (globecom 2011)}, author={Babaoglu, A. C. and Dutta, Rudra}, year={2011} }