The Impact of Accurate Quantification on Proteomic and Genetic Analysis and Research

Editor: Yu Liu, PhD


Published. Available now.
Pub Date: March 5, 2014
Hardback Price: $159.95 US
Hard ISBN: 9781771880190
E-Book ISBN: 9781482246629
Pages: 412pp
Binding Type: hardbound

This title includes a number of Open Access chapters.

This book provides a valuable and informative overview of the field of bioinformatics and statistical methodology. The chapters show various approaches to bias correction and error estimation, as well as quantitative methods for genome and proteome analysis. The book covers RNA-Seq, microarrays, various genome-wide association studies, and proteomics.

The book:
• introduces bioinformatic and statistical methodology
• shows approaches to bias correction and error estimation
• presents quantitative methods for genome and proteome analysis

Part I: RNA-Seq
Chapter 1. The Bench Scientist's Guide to Statistical Analysis of RNA-Seq Data

Craig R. Yendrek, Elizabeth A. Ainsworth, and Jyothi Thimmapuram

Chapter 2. Assembly of Non-Unique Insertion Content Using Next-Generation Sequencing

Nathaniel Parrish, Farhad Hormozdiari, and Eleazar Eskin

Chapter 3. RSEM: Accurate Transcript Quantification from RNA-Seq Data With or Without a Reference Genome

Bo Li and Colin N. Dewey
Part II: Microarray

Chapter 4. A Regression System for Estimation of Errors Introduced by Confocal Imaging into Gene Expression Data In Situ

Ekaterina Myasnikova, Svetlana Surkova, Grigory Stein, Andrei Pisarev, and Maria Samsonova

Chapter 5. SPACE: An Algorithm to Predict and Quantify Alternatively Spliced Isoforms Using Microarrays

Miguel A. Anton, Dorleta Gorostiaga, Elizabeth Guruceaga, Victor Segura, Pedro Carmona-Saez, Alberto Pascual-Montano, Ruben Pio, Luis M. Montuenga, and Angel Rubio

Chapter 6. Link-Based Quantitative Methods to Identify Differentially Coexpressed Genes and Gene Pairs

Hui Yu, Bao-Hong Liu, Zhi-Qiang Ye, Chun Li, Yi-Xue Li, and Yuan-Yuan Li

Chapter 7. Dimension Reduction with Gene Expression Data Using Targeted Variable Importance Measurement

Hui Wang and Mark J. van der Laan

Chapter 8. Genome-Wide Association Study of Stevens-Johnson Syndrome and Toxic Epidermal Necrolysis in Europe

Emmanuelle Génin, Martin Schumacher, Jean-Claude Roujeau, Luigi Naldi,Yvonne Liss, Rémi Kazma, Peggy Sekula, Alain Hovnanian, and Maja Mockenhaupt

Chapter 9. Genotyping Common and Rare Variation Using Overlapping Pool Sequencing

Dan He, Noah Zaitlen, Bogdan Pasaniuc, Eleazar Eskin, and Eran Halperin

Chapter 10. Learning Genetic Epistasis Using Bayesian Network Scoring Criteria

Xia Jiang, Richard E. Neapolitan, M. Michael Barmada, and Shyam Visweswaran

Chapter 11. Combined Analysis of Three Genome-Wide Association Studies on vWF and FVIII Plasma Levels

Guillemette Antoni, Tiphaine Oudot-Mellakh, Apostolos Dimitromanolakis, Marine Germain, William Cohen, Philip Wells, Mark Lathrop, France Gagnon, Pierre-Emmanuel Morange, and David-Alexandre Tregouet
Part IV: Proteomics

Chapter 12. Statistical Methods for Quantitative Mass Spectrometry Proteomic Experiments with Labeling

Ann L. Oberg and Douglas W. Mahoney

Chapter 13. MRCQuant: An Accurate LC-MS Relative Isotopic Quantification Algorithm on TOF Instruments

William E. Haskins, Konstantinos Petritis, and Jianqiu Zhang


About the Authors / Editors:
Editor: Yu Liu, PhD
Senior Research Associate, Center for Proteomics and Bioinformatics, Case Western Reserve University, Cleveland, Ohio

As a bioinformatician, Dr. Yu Liu’s research has been centered on the development and application of computational tools for study of complex diseases. He is familiar with data generated from microarray, next generation sequencing, and high-resolution mass spectrometry, and he has extensive experience for developing bioinformatics tools and system biology approaches to study complex diseases, such as sleep apnea, neurodegenerative diseases, and cancers. More recently, he has developed a systems biology approach that enables the discovery of high-level disease mechanisms and provides testing hypotheses for further research. Currently, he is a senior research associate in Center for Proteomics and Bioinformatics of Case Western Reserve University, Cleveland, Ohio. He received his PhD in Bioinformatics from Montreal University, Montreal, Canada, and had postdoc training in University of Toronto, Canada.

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