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Translational Bioinformatics for Therapeutic Development

  • Book
  • © 2021

Overview

Editors:
  1. Joseph Markowitz

    1. Department of Cutaneous Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, USA

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  • Includes cutting-edge methods and protocols
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts

Part of the book series: Methods in Molecular Biology (MIMB, volume 2194)

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Table of contents (17 protocols)

  1. Front Matter

    Pages i-xv
    Download chapter PDF

  2. Development and Optimization of Clinical Informatics Infrastructure to Support Bioinformatics at an Oncology Center

    • Randa M. Perkins, Joseph Markowitz
    Pages 1-19

  3. Leveraging Pathology Informatics Concepts to Achieve Discrete Lab Data for Clinical Use and Translational Research

    • Mandy Flannery O’Leary
    Pages 21-33

  4. Cohort Identification for Translational Bioinformatics Studies

    • Tiffany A. Lin, Zeynep Eroglu, Rodrigo Carvajal, Joseph Markowitz
    Pages 35-44

  5. Transitioning Clinical Practice Guidelines into the Electronic Health Record through Clinical Pathways

    • Sharjeel M. Hooda, Karen K. Fields
    Pages 45-59

  6. Variable Selection for Time-to-Event Data

    • Ai Ni, Chi Song
    Pages 61-76

  7. Binary Classification for Failure Risk Assessment

    • Ali Foroughi Pour, Ian Loveless, Grzegorz Rempala, Maciej Pietrzak
    Pages 77-105

  8. Challenges and Opportunities of Genomic Approaches in Therapeutics Development

    • Jaimie S. Gray, Moray J. Campbell
    Pages 107-126

  9. Accessible Pipeline for Translational Research Using TCGA: Examples of Relating Gene Mechanism to Disease-Specific Outcomes

    • Anders E. Berglund, Ryan M. Putney, Jordan H. Creed, Garrick Aden-Buie, Travis A. Gerke, Robert J. Rounbehler
    Pages 127-142

  10. Statistical and Bioinformatics Analysis of Data from Bulk and Single-Cell RNA Sequencing Experiments

    • Xiaoqing Yu, Farnoosh Abbas-Aghababazadeh, Y. Ann Chen, Brooke L. Fridley
    Pages 143-175

  11. Investigating Inter- and Intrasample Diversity of Single-Cell RNA Sequencing Datasets

    • Meghan C. Ferrall-Fairbanks, Philipp M. Altrock
    Pages 177-186

  12. Managing a Large-Scale Multiomics Project: A Team Science Case Study in Proteogenomics

    • Paul A. Stewart, Eric A. Welsh, Bin Fang, Victoria Izumi, Tania Mesa, Chaomei Zhang et al.
    Pages 187-221

  13. Synergistic Drug Combination Prediction by Integrating Multiomics Data in Deep Learning Models

    • Tianyu Zhang, Liwei Zhang, Philip R. O. Payne, Fuhai Li
    Pages 223-238

  14. Introduction to Multiparametric Flow Cytometry and Analysis of High-Dimensional Data

    • James Sun, Jodi L. Kroeger, Joseph Markowitz
    Pages 239-253

  15. High-Dimensional Flow Cytometry Analysis of Regulatory Receptors on Human T Cells, NK Cells, and NKT Cells

    • Ryosuke Nakagawa, Jason Brayer, Nicole Restrepo, James J. Mulé, Adam W. Mailloux
    Pages 255-290

  16. Quantitative Analysis of Bile Acid with UHPLC-MS/MS

    • Yuan Tian, Jingwei Cai, Erik L. Allman, Philip B. Smith, Andrew D. Patterson
    Pages 291-300

  17. Sample Preparation and Data Analysis for NMR-Based Metabolomics

    • Tapas K. Mal, Yuan Tian, Andrew D. Patterson
    Pages 301-313

  18. Correction to: Development and Optimization of Clinical Informatics Infrastructure to Support Bioinformatics at an Oncology Center

    • Randa M. Perkins, Joseph Markowitz
    Pages C1-C1

  19. Back Matter

    Pages 315-317
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Keywords

About this book

This volume introduces Translational Bioinformatics as it relates to therapeutic development, and addresses the techniques needed to effectively translate large data sets to relevant biological networks. Chapters detail clinical informatics infrastructure, and leverage pathology, immunology, pharmacology, genomic, proteomic, and metabolomic informatics approaches.   Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, application details for both the expert and non-expert reader, and tips on troubleshooting and avoiding known pitfalls.

 

Authoritative and practical, Translational Bioinformatics for Therapeutic Development: Methods and Protocols aims to ensure success in the study of Translational Bioinformatics.

Editors and Affiliations

  • Department of Cutaneous Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, USA

    Joseph Markowitz

Bibliographic Information

  • Book Title: Translational Bioinformatics for Therapeutic Development

  • Editors: Joseph Markowitz

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-0716-0849-4

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media, LLC, part of Springer Nature 2021

  • Hardcover ISBN: 978-1-0716-0848-7Published: 15 September 2020

  • Softcover ISBN: 978-1-0716-0851-7Published: 16 September 2021

  • eBook ISBN: 978-1-0716-0849-4Published: 14 September 2020

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XV, 317

  • Number of Illustrations: 9 b/w illustrations, 66 illustrations in colour

  • Topics: Bioinformatics

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