Research Interests and Accomplishments

Konstantinos Krampis' research interests are focused on algorithmic designs using cloud and high performance computing frameworks for solving computational bottlenecks in data analysis of large-scale genomic datasets. He has a M.Sc. in Molecular Biology from the University of Athens in Greece, and a Ph.D. in Bioinformatics and Computational Biology from Virginia Tech.

While at Virginia Tech Dr. Krampis was a member of an interdisciplinary scientific research team, and was responsible for implementing a terabyte-scale relational database hosting microarray datasets, and statistical procedures for in silico polymorphism discovery using gene expression data. Furthermore, he designed algorithms for metabolic graph intersection and identification of new biological pathway modules conferring disease resistance, while  developing automated genome analysis pipelines using web service workflows. At JCVI he has written NSF and NIH research proposals on bioinformatics computing using cloud infrastructures, both as Principal Investigator (PI) and co-PI. In addition, he has coordinated deployment and manages a compute cluster at JCVI running the Eucalyptus open-source cloud platform and Hadoop/MapReduce parallel programming framework, has book chapters and peer-reviewed papers on cloud computing applications for bioinformatics, and has presented workshops at JCVI, national and international conferences on cloud-based, scalable implementations of bioinformatics algorithms.

Dr. Krampis has initiated and has been the lead developer for the JCVI Cloud Biolinux project, a bioinformatics Virtual Machine (VM) with more than 100 pre-configured genome analysis software tools coupled with an intuitive graphical interface. The software included with Cloud Biolinux runs on a practically unlimited pool of high capacity VM servers that can be allocated on-demand using cloud computing platforms. A diverse community of researchers from both the US (Massachusetts General Hospital, Harvard School of Public Health, Emory University) and Europe (National Environmental Research Center, King's College London, Denmark Technical University, Netherlands Wageninghen University) has been already established around the project, and members of the community have agreed to use Cloud Biolinux as the basis for porting bioinformatics software the compute cloud.

Konstantinos Krampis' research on cloud computing infrastructures for bioinformatics is driven by the belief that the cloud can democratize access to computational resources for genomic data analysis for underrepresented research laboratories independently of institutional, economic or national boundaries, and consecutively support the wider adoption of genome sequencing technology for biological and medical research. 

Select Publications

Krampis K., Booth T., Chapman B., Tiwari B., Bicak M., Field D. and Nelson K.E. (2011) BMC Bioinformatics (in press), “Cloud BioLinux: pre-configured and on-demand bioinformatics computing for the genomics community”

Madupu R., Rogers Y.H., Rusch D., Miller J., Krampis K. and Nelson K. (2011) Chapter in Encyclopedia of Molecular Cell Biology and Molecular Medicine, Wiley Science (in press), “Microbiomes”

Zhou L., Mideros S.X., Bao L., Hanlon R., Arredondo F., Tripathy S., Krampis K. et al. (2009) BMC Genomics 26(10): 49.  "Infection and genotype remodel the entire Soybean transcriptome". PMCID: PMC2662884

Prassinos C., Haralampidis K., Milioni D., Samakovli D., Krampis K. and Hatzopoulos P. (2008) Plant Mol Biol. 67(4): 323. “Complexity of Hsp90 in organelle targeting”

Krampis, K. (2007) VBI e-connections 2(3): 2. “Bioinformatics and the Semantic Web: distilling knowledge by mining heterogeneous data”

Tyler B. M., Tripathy S., Zhang X., Dehal P., Jiang R. H., Aerts A., Arredondo F.D., Baxter L., Bensasson D., Beynon J.L., Chapman J., Damasceno C.M., Dorrance A.E., Dou D.,  Dickerman A.W., Dubchak I.L., Garbelotto M., Gijzen M., Gordon S.G., Govers F., Grunwald, N.J., Huang W., Ivors K.L., Jones R.W., Kamoun S., Krampis K., et al.  (2006) Science 313(5791): 1261. "Phytophthora genome sequences uncover evolutionary origins and mechanisms of pathogenesis."

Krampis K., Tyler B. M. and Boore J.L. (2006) Mol Plant Microbe Interact 19(12): 1329. "Extensive variation in nuclear mitochondrial DNA content between the genomes of P. sojae and P. ramorum"

Prasinos C., Krampis K., Samakovli D. and Hatzopoulos P.  (2005)  J Exp Bot  56(412): 633. "Tight regulation of expression of two Arabidopsis cytosolic Hsp90 genes during embryo development."