Eleazar Eskin's Books

Hidden Treasures in Contemporary RNA Sequencing

By: Serghei Mangul,Harry Taegyun Yang,Eleazar Eskin,Noah Zaitlen

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Hidden Treasures in Contemporary RNA Sequencing

By: Serghei Mangul,Harry Taegyun Yang,Eleazar Eskin,Noah Zaitlen

Advances in RNA-sequencing (RNA-seq) technologies have provided an unprecedented opportunity to explore the gene expression landscape across individuals, tissues, and environments by efficiently profiling the RNA sequences present in the samples. When a reference genome sequence or a transcriptome of the sample is available, mapping-based RNA-seq analysis protocols align the RNA-seq reads to the reference sequences, identify novel transcripts, and quantify the abundance of expressed transcripts.The reads that fail to map to the human reference, known as unmapped reads, are a large and often overlooked output of standard RNA-seq analyses. Even in carefully executed experiments, the unmapped reads can comprise a considerable fraction of the complete set of reads produced, and can arise due to technical sequencing produced by low-quality and error-prone copies of the nascent RNA sequence being sampled. Reads can also remain unmapped due to unknown transcripts, recombined B and T cell receptor sequences, A-to-G mismatches from A-to-I RNA editing, trans-splicing, gene fusion, circular RNAs, and the presence of non-host RNA sequences (e.g. bacterial, fungal, and viral organisms). Unmapped reads represent a rich resource for the study of B and T cell receptor repertoires and the human microbiome system—without incurring the expense of additional targeted sequencing.This book introduces and describes the Read Origin Protocol (ROP), a tool that identifies the origin of both mapped and unmapped reads. The protocol first identifies human reads using a standard high-throughput algorithm to map them onto a reference genome and transcriptome. After alignment, reads are grouped into genomic (e.g. CDS, UTRs, introns) and repetitive (e.g. SINEs, LINEs, LTRs) categories. The rest of the ROP protocol characterizes the remaining unmapped reads, which failed to map to the human reference sequences.

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ISBN 10

3030139735

ISBN 13

9783030139735

Hidden Treasures in Contemporary RNA Sequencing

By: Serghei Mangul,Harry Taegyun Yang,Eleazar Eskin,Noah Zaitlen

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Hidden Treasures in Contemporary RNA Sequencing

By: Serghei Mangul,Harry Taegyun Yang,Eleazar Eskin,Noah Zaitlen

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3030139735

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9783030139735

Regulatory Genomics

RECOMB 2004 International Workshop, RRG 2004, San Diego, CA, USA, March 26-27, 2004, Revised Selected Papers

By: Eleazar Eskin,Chris Workman

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Regulatory Genomics

RECOMB 2004 International Workshop, RRG 2004, San Diego, CA, USA, March 26-27, 2004, Revised Selected Papers

By: Eleazar Eskin,Chris Workman

This book constitutes the thoroughly refereed post-proceedings of the RECOMB 2004 Satellite Workshop on Regulatory Genomics, RRG 2004, held in San Diego, CA, USA in March 2004. The 10 revised full papers presented were carefully reviewed and improved for inclusion in the book. The papers address a broad variety of aspects of regulatory genomics including classification, functional module detection, proteonomics, sampling, kernel methods, TF binding motifs, gene expression data analysis, regulatory network model learning, RNA regulatory sequence motifs, DNA regulatory sequence motifs, parameter landscape analysis, and biological network regulation.

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121

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Springer

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3540322809

ISBN 13

9783540322801

Book's by Eleazar Eskin

Hidden Treasures in Contemporary RNA Sequencing

Hidden Treasures in Contemporary RNA Sequencing

Hidden Treasures in Contemporary RNA Sequencing

Hidden Treasures in Contemporary RNA Sequencing

Regulatory Genomics

Regulatory Genomics

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