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Items: 14

1.

Reproducible big data science: A case study in continuous FAIRness.

Madduri R, Chard K, D'Arcy M, Jung SC, Rodriguez A, Sulakhe D, Deutsch E, Funk C, Heavner B, Richards M, Shannon P, Glusman G, Price N, Kesselman C, Foster I.

PLoS One. 2019 Apr 11;14(4):e0213013. doi: 10.1371/journal.pone.0213013. eCollection 2019.

2.

Exploring the functional impact of alternative splicing on human protein isoforms using available annotation sources.

Sulakhe D, D'Souza M, Wang S, Balasubramanian S, Athri P, Xie B, Canzar S, Agam G, Gilliam TC, Maltsev N.

Brief Bioinform. 2018 Jun 21. doi: 10.1093/bib/bby047. [Epub ahead of print]

PMID:
29931155
3.

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

D'Souza M, Sulakhe D, Wang S, Xie B, Hashemifar S, Taylor A, Dubchak I, Conrad Gilliam T, Maltsev N.

Methods Mol Biol. 2017;1613:85-99. doi: 10.1007/978-1-4939-7027-8_5.

PMID:
28849559
4.

A case study for cloud based high throughput analysis of NGS data using the globus genomics system.

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

Comput Struct Biotechnol J. 2014 Nov 7;13:64-74. doi: 10.1016/j.csbj.2014.11.001. eCollection 2015.

5.

Lynx: a knowledge base and an analytical workbench for integrative medicine.

Sulakhe D, Xie B, Taylor A, D'Souza M, Balasubramanian S, Hashemifar S, White S, Dave UJ, Agam G, Xu J, Wang S, Gilliam TC, Maltsev N.

Nucleic Acids Res. 2016 Jan 4;44(D1):D882-7. doi: 10.1093/nar/gkv1257. Epub 2015 Nov 20.

6.

An integrative computational approach for prioritization of genomic variants.

Dubchak I, Balasubramanian S, Wang S, Cem M, Sulakhe D, Poliakov A, Börnigen D, Xie B, Taylor A, Ma J, Paciorkowski AR, Mirzaa GM, Dave P, Agam G, Xu J, Al-Gazali L, Mason CE, Ross ME, Maltsev N, Gilliam TC.

PLoS One. 2014 Dec 15;9(12):e114903. doi: 10.1371/journal.pone.0114903. eCollection 2014. Erratum in: PLoS One. 2015;10(4):e0124700. Meyden, Cem [corrected to Meydan, Cem].

7.

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

Madduri RK, Sulakhe D, Lacinski L, Liu B, Rodriguez A, Chard K, Dave UJ, Foster IT.

Concurr Comput. 2014 Sep 10;26(13):2266-2279.

8.

Lynx web services for annotations and systems analysis of multi-gene disorders.

Sulakhe D, Taylor A, Balasubramanian S, Feng B, Xie B, Börnigen D, Dave UJ, Foster IT, Gilliam TC, Maltsev N.

Nucleic Acids Res. 2014 Jul;42(Web Server issue):W473-7. doi: 10.1093/nar/gku517. Epub 2014 Jun 19.

9.

High-throughput translational medicine: challenges and solutions.

Sulakhe D, Balasubramanian S, Xie B, Berrocal E, Feng B, Taylor A, Chitturi B, Dave U, Agam G, Xu J, Börnigen D, Dubchak I, Gilliam TC, Maltsev N.

Adv Exp Med Biol. 2014;799:39-67. doi: 10.1007/978-1-4614-8778-4_3. Review.

PMID:
24292961
10.

Lynx: a database and knowledge extraction engine for integrative medicine.

Sulakhe D, Balasubramanian S, Xie B, Feng B, Taylor A, Wang S, Berrocal E, Dave U, Xu J, Börnigen D, Gilliam TC, Maltsev N.

Nucleic Acids Res. 2014 Jan;42(Database issue):D1007-12. doi: 10.1093/nar/gkt1166. Epub 2013 Nov 21.

11.

CaGrid Workflow Toolkit: a Taverna based workflow tool for cancer grid.

Tan W, Madduri R, Nenadic A, Soiland-Reyes S, Sulakhe D, Foster I, Goble CA.

BMC Bioinformatics. 2010 Nov 2;11:542. doi: 10.1186/1471-2105-11-542.

12.

Interoperability of GADU in using heterogeneous grid resources for bioinformatics applications.

Sulakhe D, Rodriguez A, Wilde M, Foster I, Maltsev N.

IEEE Trans Inf Technol Biomed. 2008 Mar;12(2):241-6. doi: 10.1109/TITB.2007.897783.

PMID:
18348953
13.

PUMA2--grid-based high-throughput analysis of genomes and metabolic pathways.

Maltsev N, Glass E, Sulakhe D, Rodriguez A, Syed MH, Bompada T, Zhang Y, D'Souza M.

Nucleic Acids Res. 2006 Jan 1;34(Database issue):D369-72.

14.

GNARE: automated system for high-throughput genome analysis with grid computational backend.

Sulakhe D, Rodriguez A, D'Souza M, Wilde M, Nefedova V, Foster I, Maltsev N.

J Clin Monit Comput. 2005 Oct;19(4-5):361-9.

PMID:
16328950

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