Publications

 Strategic Integration of Multiple Bioinformatics Resources for System Level Analysis of Biological Networks

Mark D’Souza, Dinanath Sulakhe, Sheng Wang, Bing Xie, Somaye Hashemifar, Andrew Taylor, Inna Dubchak, T Conrad Gilliam, Natalia Maltsev.

Biological Networks and Pathway Analysis  |  pp 85-99 (MIMB, volume 1613)  |  2017

 Developing a Framework for Digital Objects in the Big Data to Knowledge (BD2K) Commons: Report from the Commons Framework Pilots Workshop

Jagodnik KM., Koplev S., Jenkins S., Ohno-Machado L., Paten B., Schurer SC., Dumontier M., Verborgh R., Bui A., Ping P., McKenna NJ., Madduri R., Pillai A., Ma'ayan A.

J Biomed Inform  |  pii: S1532-0464(17)30101-6  |  2017

 Numerical and Implementation Issues in Food Quality Modeling for Human Diseases Prevention

Galletti1 A., Montella R., Marcellino L., Riccio A., Di Luccio D., Brizius A., Foster I.

In Proceedings of the 10th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2017)  |  Volume 5: HEALTHINF, pages 526-534  |  2017

 A novel MERTK mutation causing retinitis pigmentosa

Hasenin Al-khersan, Kaanan, P. Shah, Segun C. Jung, Alex Rodriguez, Ravi K. Madduri, Michael A. Grassi.

Graefe's Archive for Clinical and Experimental Ophthalmology  |  2017  |  Download paper

 Globus: A Case Study in So ware as a Service for Scientists

Bryce Allen, Rachana Ananthakrishnan, Kyle Chard, Ian Foster, Ravi Madduri, Jim Pruyne, Stephen Rosen, Steve Tuecke.

ScienceCloud ’17  |  2017  |  Download paper

 Development of Bioinformatics Infrastructure for Genomics Research in H3Africa

Mulder NJ, Adebiyi E, Adebiyi M, Adeyemi S, Ahmed A, Ahmed R, Akanle B, Alibi M, Armstrong DL, Aron S, Ashano E, Baichoo S, Benkahla A, Brown DK, Chimusa ER, Fadlelmola FM, Falola D, Fatumo S, Ghedira K, Ghouila A, Hazelhurst S, Isewon I, Jung S, Kassim SK, Kayondo JK, Mbiyavanga M, Meintjes A, Mohammed S, Mosaku A, Moussa A, Muhammd M, Mungloo-Dilmohamud Z, Nashiru O, Odia T, Okafor A, Oladipo O, Osamor V, Oyelade J, Sadki K, Salifu SP, Soyemi J, Panji S, Radouani F, Souiai O, Tastan Bishop Ö; H3ABioNet Consortium, as members of the H3Africa Consortium

Global Heart  |  2017  |  Download paper

 I'll take that to go: Big data bags and minimal identifiers for exchange of large, complex datasets

Kyle Chard, Mike D'Arcy, Ben Heavner, Ian Foster, Carl Kesselman, Ravi Madduri, Alexis Rodriguez, Stian Soiland-Reyes, Carole Goble, Kristi Clark, Eric W Deutsch, Ivo Dinov, Nathan Price, Arthur Toga.

Big Data (Big Data), 2016 IEEE International Conference on  | Washington, DC, USA | 2016  |  Download paper

 An automated tool profiling service for the cloud

Ryan Chard, Kyle Chard, Bryan Ng, Kris Bubendorfer, Alex Rodriguez, Ravi Madduri, and Ian Foster.

In the proceedings of the 16th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing (CCGrid)  | Cartagena, Colombia | 2016  |  Download paper

 Predictive Big Data Analytics: A Study of Parkinson's Disease Using Large, Complex, Heterogeneous, Incongruent, Multi-Source and Incomplete Observations

Ivo D. Dinov , Ben Heavner, Ming Tang, Gustavo Glusman, Kyle Chard, Mike Darcy, Ravi Madduri, Judy Pa, Cathie Spino, Carl Kesselman, Ian Foster, Eric W. Deutsch, Nathan D. Price, John D. Van Horn, Joseph Ames, Kristi Clark, Leroy Hood, Benjamin M. Hampstead, William Dauer, Arthur W. Toga.

PLoS One  |  2016  |  Download paper

 LINE1 insertions as a genomic risk factor for schizophrenia: Preliminary evidence from an affected family.

Guia Guffanti, Simona Gaudi, Torsten Klengel, James H. Fallon, Harry Mangalam, Ravi Madduri, Alex Rodriguez, Paula DeCrescenzo, Emily Glovienka, Janet Sobell, Claudia Klengel, Michele Pato, Kerry J. Ressler, Carlos Pato, Fabio Macciardi.

Am J Med Genet B Neuropsychiatr Genet.  |  2016  |  Download paper

 Models and Simulations as a Service: Exploring the Use of Galaxy for Delivering Computational Models.

Mark A. Walker, Ravi Madduri, Alex Rodriguez, Joseph L. Greenstein, Raimond L. Winslow.

Biophys J.  |  2016  |  Download paper

 Cost-Aware Elastic Cloud Provisioning for Scientific Workloads

Chard R., Chard K., Bubendorfer K., Lacinski L., Madduri R., Foster I.

In Cloud Computing (CLOUD), 2015 IEEE 8th International Conference, vol., no., pp.971-974  | June 27 - July 2, 2015  |  Download paper

 Cost-Aware Resource Provisioning for Cloud-based Scientific Workflows

Chard R., Chard K., Bubendorfer K., Lacinski L., Madduri R., Foster I.

11th IEEE International Conference on eScience (eScience)  | 2015  |  Download paper

 Big biomedical data as the key resource for discovery science.

Arthur W Toga, Ian Foster, Carl Kesselman, Ravi Madduri, Kyle Chard, Eric W Deutsch, Nathan D Price, Gustavo Glusman, Benjamin D Heavner, Ivo D Dinov, Joseph Ames, John Van Horn, Roger Kramer, Leroy Hood.

J Am Med Inform Assoc.  |  2015  |  Download paper

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

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.

Oxford Journal of Bioinformatics  |  2015  |  Download paper

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

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

Journal of Biomedical Informatics  |  Elsevier  |  2014  |  Download paper

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

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

Computational and Structural Biotechnology Journal  |  November 2014

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

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

2014 International Meeting for Autism Research  |  May 2014

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

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

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

 Inherited and de novo Transposable Elements in schizophrenia

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

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

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

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

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

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

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

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

 Extending the Galaxy portal with parallel and distributed execution capability

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

 Deploying Bioinformatics Workflows on Clouds with Galaxy and Globus Provision

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

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

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

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

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

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

Foster, I.

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

 EuPathDB: the eukaryotic pathogen genomics database resource

Aurrecoechea C., Barreto A., Basenko EY., Brestelli J., Brunk BP., Cade S., Crouch K., Doherty R., Falke D., Fischer S., Gajria B., Harb OS., Heiges M., Hertz-Fowler C., Hu S., Iodice J., Kissinger JC., Lawrence C., Li W., Pinney DF., Pulman JA., Roos DS., Shanmugasundram A., Silva-Franco F., Steinbiss S., Stoeckert CJ Jr2., Spruill D., Wang H., Warrenfeltz S., Zheng J.

Nucleic Acids Res.  |  45(D1):D581-D591  |  2017

 PEMapper and PECaller provide a simplified approach to whole-genome sequencing

Johnston HR., Chopra P., Wingo TS., Patel V.; International Consortium on Brain and Behavior in 22q11.2 Deletion Syndrome, Epstein MP., Mulle JG., Warren ST., Zwick ME., Cutler DJ.

Proc Natl Acad Sci U S A  |  114(10):E1923-E1932  |  2017

 Detection and quantification of viral RNA in human tumors using open source pipeline: viGEN

Bhuvaneshwar K., Song L., Madhavan S., Gusev Y.

bioRxiv  |  doi: https://doi.org/10.1101/099788  |  2017

 The Lair: a resource for exploratory analysis of published RNA-Seq data

Pimentel H., Sturmfels P., Bray N., Melsted P., Pachter L.

BMC Bioinformatics  |  1;17(1):490  |  2016

 Improving the Performance of Cloud-based Scientific Services

Chard R.

Victoria University of Wellington  |  Doctoral Theses  |  2016

 Respiratory infections with pneumococci establish multi-pronged heterotypic protection against pneumonia

Smith N.

Boston University School of Medicine  |  Doctoral Theses  |  2016