Workshop: Novel transcript reconstruction from paired-end RNA-Seq reads using fragment length distribution

Serghei Mangul; Adrian Caciula; Ion Mandoiu; Alex Zelikovsky

doi:10.1109/ICCABS.2012.6182673

Workshop: Novel transcript reconstruction from paired-end RNA-Seq reads using fragment length distribution

Serghei Mangul^*, Adrian Caciula, Ion Mandoiu, Alex Zelikovsky

^*Corresponding author for this work

Surgery, Thoracic Surgery Division

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

Abstract

Recent advances in DNA sequencing have made it possible to sequence the whole transcriptome by massively parallel sequencing, commonly referred as RNA-Seq. RNA-Seq is quickly becoming the technology of choice for transcriptome research and analyses. RNA-Seq allows to reduce the sequencing cost and significantly increase data throughput, but it is computationally challenging to use such RNA-Seq data for reconstructing of full length transcripts and accurately estimate their abundances across all cell types. The common computational problems include: gene and isoform expression level estimation [1], find transcriptome quantification, transcriptome discovery and reconstruction. To solve these problems it is required to have scalable computational tools.

Original language	English (US)
Title of host publication	2012 IEEE 2nd International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2012
DOIs	https://doi.org/10.1109/ICCABS.2012.6182673
State	Published - 2012
Event	2012 IEEE 2nd International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2012 - Las Vegas, NV, United States Duration: Feb 23 2012 → Feb 25 2012

Publication series

Name	2012 IEEE 2nd International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2012

Conference

Conference	2012 IEEE 2nd International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2012
Country/Territory	United States
City	Las Vegas, NV
Period	2/23/12 → 2/25/12

ASJC Scopus subject areas

Biomedical Engineering
Applied Mathematics

Access to Document

10.1109/ICCABS.2012.6182673

Cite this

Mangul, S., Caciula, A., Mandoiu, I., & Zelikovsky, A. (2012). Workshop: Novel transcript reconstruction from paired-end RNA-Seq reads using fragment length distribution. In 2012 IEEE 2nd International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2012 Article 6182673 (2012 IEEE 2nd International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2012). https://doi.org/10.1109/ICCABS.2012.6182673

Mangul, Serghei ; Caciula, Adrian ; Mandoiu, Ion et al. / Workshop : Novel transcript reconstruction from paired-end RNA-Seq reads using fragment length distribution. 2012 IEEE 2nd International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2012. 2012. (2012 IEEE 2nd International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2012).

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title = "Workshop: Novel transcript reconstruction from paired-end RNA-Seq reads using fragment length distribution",

abstract = "Recent advances in DNA sequencing have made it possible to sequence the whole transcriptome by massively parallel sequencing, commonly referred as RNA-Seq. RNA-Seq is quickly becoming the technology of choice for transcriptome research and analyses. RNA-Seq allows to reduce the sequencing cost and significantly increase data throughput, but it is computationally challenging to use such RNA-Seq data for reconstructing of full length transcripts and accurately estimate their abundances across all cell types. The common computational problems include: gene and isoform expression level estimation [1], find transcriptome quantification, transcriptome discovery and reconstruction. To solve these problems it is required to have scalable computational tools.",

author = "Serghei Mangul and Adrian Caciula and Ion Mandoiu and Alex Zelikovsky",

year = "2012",

doi = "10.1109/ICCABS.2012.6182673",

language = "English (US)",

isbn = "9781467313216",

series = "2012 IEEE 2nd International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2012",

booktitle = "2012 IEEE 2nd International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2012",

note = "2012 IEEE 2nd International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2012 ; Conference date: 23-02-2012 Through 25-02-2012",

}

Mangul, S, Caciula, A, Mandoiu, I & Zelikovsky, A 2012, Workshop: Novel transcript reconstruction from paired-end RNA-Seq reads using fragment length distribution. in 2012 IEEE 2nd International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2012., 6182673, 2012 IEEE 2nd International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2012, 2012 IEEE 2nd International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2012, Las Vegas, NV, United States, 2/23/12. https://doi.org/10.1109/ICCABS.2012.6182673

Workshop: Novel transcript reconstruction from paired-end RNA-Seq reads using fragment length distribution. / Mangul, Serghei; Caciula, Adrian; Mandoiu, Ion et al.
2012 IEEE 2nd International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2012. 2012. 6182673 (2012 IEEE 2nd International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2012).

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

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T1 - Workshop

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AU - Mangul, Serghei

AU - Caciula, Adrian

AU - Mandoiu, Ion

AU - Zelikovsky, Alex

PY - 2012

Y1 - 2012

N2 - Recent advances in DNA sequencing have made it possible to sequence the whole transcriptome by massively parallel sequencing, commonly referred as RNA-Seq. RNA-Seq is quickly becoming the technology of choice for transcriptome research and analyses. RNA-Seq allows to reduce the sequencing cost and significantly increase data throughput, but it is computationally challenging to use such RNA-Seq data for reconstructing of full length transcripts and accurately estimate their abundances across all cell types. The common computational problems include: gene and isoform expression level estimation [1], find transcriptome quantification, transcriptome discovery and reconstruction. To solve these problems it is required to have scalable computational tools.

AB - Recent advances in DNA sequencing have made it possible to sequence the whole transcriptome by massively parallel sequencing, commonly referred as RNA-Seq. RNA-Seq is quickly becoming the technology of choice for transcriptome research and analyses. RNA-Seq allows to reduce the sequencing cost and significantly increase data throughput, but it is computationally challenging to use such RNA-Seq data for reconstructing of full length transcripts and accurately estimate their abundances across all cell types. The common computational problems include: gene and isoform expression level estimation [1], find transcriptome quantification, transcriptome discovery and reconstruction. To solve these problems it is required to have scalable computational tools.

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T3 - 2012 IEEE 2nd International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2012

BT - 2012 IEEE 2nd International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2012

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Mangul S, Caciula A, Mandoiu I, Zelikovsky A. Workshop: Novel transcript reconstruction from paired-end RNA-Seq reads using fragment length distribution. In 2012 IEEE 2nd International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2012. 2012. 6182673. (2012 IEEE 2nd International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2012). doi: 10.1109/ICCABS.2012.6182673

Workshop: Novel transcript reconstruction from paired-end RNA-Seq reads using fragment length distribution

Abstract

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ASJC Scopus subject areas

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