Publications

Recent Press

 Amazon Web Services and Globus Genomics

Amazon Web Services  |  February 2014

AWS talking with Ravi Madduri

 Large-Scale Data Management for Reproducible Life Science Research

BioIT World Expo 2014  |  February 2014

Vivien Marx

 Genomics in the clouds

Nature Methods, 10(10):942-4  |  October 2013

Cloud computing can help busy genomics labs. But researchers will want to be cautious shoppers as they scan the skies for the cloud best suited to their needs.

2015

 

2014

Liu B., Madduri R. K., Sotomayor B., Chard K., Lacinski L., Dave U.J., Li J., Liu C., Foster I.T.

Cloud-based bioinformatics workflow platform for large-scale next-generation sequencing analyses

Journal of Biomedical Informatics  |  Elsevier  |  2014  |  Download paper

Trubetskoy V., Rodriguez A., Dave U., Campbell N., Crawford E.L., Cook E.H., Sutcliffe J.S., Foster I., Madduri R., Cox N.J. and Davis L.K.

Consensus Genotyper for Exome Sequencing (CGES): Improving the Quality of Exome Variant Genotypes

Oxford Journal of Bioinformatics  |  2014  |  Download paper

Krithika Bhuvaneshwar, Dinanath Sulakhe, Robinder Gauba, Alex Ro-Driguez, Ravi Madduri, Utpal Dave, Lukasz Lacinski, Ian Foster, Yuriy Gusev, Subha Madhavan, Gusev Yuriy, Madhavan Subha

A case study for cloud based high throughput analysis of NGS data using the Globus Genomics system

Computational and Structural Biotechnology Journal  |  November 2014

J. S. Sutcliffe, N. G. Campbell, E. L. Crawford, V. Trubetskoy, A. Rodriguez, R. Madduri, B. Li, L. K. Davis, N. J. Cox, E. H. Cook

 Leveraging Hyperserotonemia and Whole Exome Sequencing in Autism Spectrum Disorder Families to Tackle Genetic Heterogeneity

2014 International Meeting for Autism Research  |  May 2014

Guffanti G, Gaudi S, DeCrescenzo P, Mangalam H, Rodriguez A, Madduri R, Pato C, Macciardi F

 The role of the genomic architecture of transposable elements in the formation of copy number variants: evidence from one schizophrenia family

American Society of Human Genetics Annual Meeting  |  San Diego, CA  |  October 2014

Macciardi F, Guffanti G, DeCrescenzo P, Pato C, Mangalam H, Rodriguez A, Madduri R, Gaudi S

 Inherited and de novo Transposable Elements in schizophrenia

American Society of Human Genetics Annual Meeting  |  San Diego, CA  |  October 2014

Dinanath Sulakhe, A. Rodriguez, K. Bhuvaneshwar, Y. Gusev, R. Madduri, L. Lacinski, U. Dave, I. Foster, S. Madhavan

 A case study for high throughput analysis of NGS data for translational research using Globus Genomics

64th Annual Meeting of The American Society of Human Genetics  |  San Diego, CA  |  October 2014

2013

Madduri, R. K., Sulakhe, D., Liu, B., Dave, P., Lacinski, L., Foster, I. T.

 Experiences in building a next-generation sequencing analysis service using Galaxy, Globus Online and Amazon Web Services

Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery  |  ACM, p. 34  |  2013

Maheshwari K., Rodriguez A., Kelly D., Madduri R.K., Wozniak J. M., Wilde M., and Foster I.

 Extending the Galaxy portal with parallel and distributed execution capability

The 4th International Workshop on Data-Intensive Computing in the Clouds (DataCloud at SC13)  |  Denver, Colorado  |  IEEE/ACM  |  2013  |  Download paper

Maheshwari K., Rodriguez A., Kelly D., Madduri R.K., Wozniak J. M., Wilde M., and Foster I.

 Enabling Multi-task computation on Galaxy-based Gateways using Swift

Science Gateway Institute Workshop (SGIW at Cluster'13)  |  Indianapolis, Indiana  |  IEEE Computer Society  |  2013  |  Download paper

Sulakhe, D., Rodriguez, A., Prozorovsky, N., Kavthekar, N., Parikh, A., Lacinski, L., Madduri, R., Dave, P., Foster, I. T.

 Distributed Tools Deployment and Management for Multiple Galaxy Instances in Globus Genomics

Proceedings of the 8th Workshop on Workflows in Support of Large-scale Science  |  ACM  |  2013

Foster, I. T., Madduri, R. K.

 Science as a Service: How on-demand computing can accelerate discovery

Proceedings of the 4th ACM workshop on Scientific Cloud Computing  |  ACM, p. 1-2  |  2013

Madduri R., Sulakhe, D., Liu, B., Chard, K., Dave P., Foster I.T.

 Experiences Building Globus Genomics: A Next-Generation Sequencing Analysis Service using Galaxy, Globus, and Amazon Web Services

Special Issue submission to Concurrency and Computation: Practice and Experience  |  2013  |  Download paper

Sulakhe D., Paciorkowski A., Mirzaa G., Madduri R., Zhang Q., Aldinger K., Bennett J., Lacinski L., Dave P., Dobyns B.

 Globus Genomics: Enabling high-throughput analysis and management of NGS data for neurodevelopment disorders; (1633T)

63rd Annual Meeting of The American Society of Human Genetics  |  October 24, 2013  |  Boston, MA

Trubetskoy V., Madduri R., Rodriguez A., Scharf J., Dave P., Foster I.T., Cox N., Davis L.

 Consensus Genotyper for Exome Sequencing: Improving the Quality of Exome Variant Genotypes

63rd Annual Meeting of The American Society of Human Genetics  |  October 24, 2013  |  Boston, MA  |  Download poster

Madduri R. K., Rodriguez A., Trubetskoy V., Davis L, K., Dave P. J., Cox N., Foster I. T.

 Implementing a High Performance, Reusable Consensus Calling Pipeline for Next Generation Sequencing using Globus Genomics; (1530W)

63rd Annual Meeting of The American Society of Human Genetics  |  October 24, 2013  |  Boston, MA  |  Download poster

2012

Liu, B., Sotomayor, B., Madduri, R., Chard, K., & Foster, I.

 Deploying Bioinformatics Workflows on Clouds with Galaxy and Globus Provision

High Performance Computing, Networking, Storage and Analysis  |  2012 SC Companion, IEEE, p. 1087-1095  |  2012

Sulakhe, D., Kettimuthu, R., Dave, U.

 High-performance data management for genome sequencing centers using Globus Online: A case study

E-Science (e-Science)  |  2012 IEEE 8th International Conference on eScience  |  IEEE, p. 1-6  |  2012

2011

Foster, I.

 Globus Online: Accelerating and democratizing science through cloud-based services

Internet Computing  |  IEEE, 15(3), p. 70-73.  |  2011