Finding function in the unknown

Kelly Boyd; Emma Highland; Amanda Misch; Amber Hu; Sushma Reddy; Catherine Putonti

doi:10.1109/BIBM.2015.7359834

Finding function in the unknown

Kelly Boyd, Emma Highland, Amanda Misch, Amber Hu, Sushma Reddy, Catherine Putonti

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Abstract

Through high-throughput RNA sequencing (RNAseq), transcriptomes for a single cell, tissue, or organism(s) can be ascertained at a high resolution. While a number of bioinformatic tools have been developed for transcriptome analyses, significant challenges exist for studies of non-model organisms. Without a reference sequence available, raw reads must first be assembled de novo followed by the tedious task of BLAST searches and data mining for functional information. We have created a pipeline, PyRanger, to automate this process. The pipeline includes functionality to assess a single transcriptome and also facilitate comparative transcriptomic studies.

Original language	English (US)
Title of host publication	Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015
Editors	lng. Matthieu Schapranow, Jiayu Zhou, Xiaohua Tony Hu, Bin Ma, Sanguthevar Rajasekaran, Satoru Miyano, Illhoi Yoo, Brian Pierce, Amarda Shehu, Vijay K. Gombar, Brian Chen, Vinay Pai, Jun Huan
Publisher	Institute of Electrical and Electronics Engineers Inc.
Pages	1098-1099
Number of pages	2
ISBN (Electronic)	9781467367981
DOIs	https://doi.org/10.1109/BIBM.2015.7359834
State	Published - Dec 16 2015
Externally published	Yes
Event	IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015 - Washington, United States Duration: Nov 9 2015 → Nov 12 2015

Publication series

Name	Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015

Other

Other	IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015
Country/Territory	United States
City	Washington
Period	11/9/15 → 11/12/15

Bibliographical note

Publisher Copyright:
© 2015 IEEE.

Keywords

RNA-seq
comparative gene expression
de novo transcriptomics

Publisher link

10.1109/BIBM.2015.7359834

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Boyd, K., Highland, E., Misch, A., Hu, A., Reddy, S., & Putonti, C. (2015). Finding function in the unknown. In L. M. Schapranow, J. Zhou, X. T. Hu, B. Ma, S. Rajasekaran, S. Miyano, I. Yoo, B. Pierce, A. Shehu, V. K. Gombar, B. Chen, V. Pai, & J. Huan (Eds.), Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015 (pp. 1098-1099). Article 7359834 (Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/BIBM.2015.7359834

Finding function in the unknown. / Boyd, Kelly; Highland, Emma; Misch, Amanda et al.
Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015. ed. / lng. Matthieu Schapranow; Jiayu Zhou; Xiaohua Tony Hu; Bin Ma; Sanguthevar Rajasekaran; Satoru Miyano; Illhoi Yoo; Brian Pierce; Amarda Shehu; Vijay K. Gombar; Brian Chen; Vinay Pai; Jun Huan. Institute of Electrical and Electronics Engineers Inc., 2015. p. 1098-1099 7359834 (Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Boyd, K, Highland, E, Misch, A, Hu, A, Reddy, S & Putonti, C 2015, Finding function in the unknown. in LM Schapranow, J Zhou, XT Hu, B Ma, S Rajasekaran, S Miyano, I Yoo, B Pierce, A Shehu, VK Gombar, B Chen, V Pai & J Huan (eds), Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015., 7359834, Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015, Institute of Electrical and Electronics Engineers Inc., pp. 1098-1099, IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015, Washington, United States, 11/9/15. https://doi.org/10.1109/BIBM.2015.7359834

Boyd K, Highland E, Misch A, Hu A, Reddy S, Putonti C. Finding function in the unknown. In Schapranow LM, Zhou J, Hu XT, Ma B, Rajasekaran S, Miyano S, Yoo I, Pierce B, Shehu A, Gombar VK, Chen B, Pai V, Huan J, editors, Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015. Institute of Electrical and Electronics Engineers Inc. 2015. p. 1098-1099. 7359834. (Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015). doi: 10.1109/BIBM.2015.7359834

Boyd, Kelly ; Highland, Emma ; Misch, Amanda et al. / Finding function in the unknown. Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015. editor / lng. Matthieu Schapranow ; Jiayu Zhou ; Xiaohua Tony Hu ; Bin Ma ; Sanguthevar Rajasekaran ; Satoru Miyano ; Illhoi Yoo ; Brian Pierce ; Amarda Shehu ; Vijay K. Gombar ; Brian Chen ; Vinay Pai ; Jun Huan. Institute of Electrical and Electronics Engineers Inc., 2015. pp. 1098-1099 (Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015).

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abstract = "Through high-throughput RNA sequencing (RNAseq), transcriptomes for a single cell, tissue, or organism(s) can be ascertained at a high resolution. While a number of bioinformatic tools have been developed for transcriptome analyses, significant challenges exist for studies of non-model organisms. Without a reference sequence available, raw reads must first be assembled de novo followed by the tedious task of BLAST searches and data mining for functional information. We have created a pipeline, PyRanger, to automate this process. The pipeline includes functionality to assess a single transcriptome and also facilitate comparative transcriptomic studies.",

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AU - Misch, Amanda

AU - Hu, Amber

AU - Reddy, Sushma

AU - Putonti, Catherine

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A2 - Rajasekaran, Sanguthevar

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Finding function in the unknown

Abstract

Publication series

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Bibliographical note

Keywords

Publisher link

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