1st Edition
RNA-Seq in Drug Discovery and Development
The research and development process in modern drug discovery and development is a complex and challenging task. Using traditional biological test methods such as PCR to measure the expression levels or function of these genes is costly and time-consuming. RNA-seq can measure the expression patterns of thousands of genes simultaneously and provide insights into functional pathways or regulations in biological processes, which has revolutionized the way biological scientists examine gene functions. This book addresses the various aspects of the RNA-seq technique, especially its application in drug discovery and development.
Features
• One of the few books that focuses on the applications of the RNA-seq technique in drug discovery and development.
• Comprehensive and timely publication which relates RNA sequencing to drug targets, mechanisms of action, and resistance.
• The editor has extensive experience in the field of computational medicinal chemistry, computational biophysics, and bioinformatics.
• Chapter authors are at the frontline of the academic and industrial science in this particular area of RNA sequencing.
Preface.................................................................................................................vii
Editors................................................................................................................... ix
Contributors.......................................................................................................... xi
Chapter 1 Introduction to RNA Sequencing and Quality Control.................... 1
Robert Morris and Feng Cheng
Chapter 2 Read Alignment and Transcriptome Assembly............................. 35
Robert Morris and Feng Cheng
Chapter 3 Normalization and Downstream Analyses.................................... 61
Robert Morris and Feng Cheng
Chapter 4 Constitutive and Alternative Splicing Events................................101
Robert Morris and Feng Cheng
Chapter 5 The Role of Transcriptomics in Identifying Fusion Genes
and Chimeric RNAs in Cancer.................................................... 129
Robert Morris, Valeria Zuluaga, and Feng Cheng
Chapter 6 MiRNA and RNA-seq.................................................................. 153
Robert Morris and Feng Cheng
Chapter 7 Toxicogenomics and RNA-seq......................................................171
Robert Morris, Kyle Eckhoff, Rebecca Polsky, and Feng Cheng
Chapter 8 Herbal Medicine and RNA-seq.................................................... 205
Robert Morris and Feng Cheng
Chapter 9 Single-Cell RNA Sequencing...................................................... 233
Robert Morris and Feng Cheng
Index.................................................................................................................. 263
Biography
Feng Cheng
Dr. Cheng is a computational biologist. He received systematic training in bioinformatics at Chinese Academy of Science, University of Illinois at Urbana Champaign, Rice University, University of Virginia and Yale University. His researches mainly focus on applications of bioinformatics methods for the identifications of drug-drug interactions (DDIs) and for drug repositioning by analyzing Big Data from public resources. He is also interested in computer-aided drug design. Dr. Cheng has published over 50 research papers in prestigious journals including Nature, Neuron, J. Am. Chem. Soc, and Scientific Reports. His work has been cited more than 1,600 times. Presently, Dr. Cheng is an editor board member of Journal of Proteomics and Bioinformatics, and the Open Bioinformatics Journal. Dr. Cheng has been serving as a peer reviewer for more than ten journals.
Robert Morris
Mr. Morris is a computational biologist with an M.S in molecular biology and is currently working on his MPH in applied biostatistics. His research primarily is focused on using bioinformatic tools to identify drug-drug interactions as well as identify risk factors associated with elevated risk of adverse drug reactions including bradycardia and dysphagia using publicly available Big Data. He also is focused on elucidating drug mechanisms using bioinformatics and RNA sequencing techniques. He currently has 10 publications in a variety of journals including the Journal of Alzheimer’s Disease and Brain Science. Finally, he has recently served as a peer reviewer for the Drugs – Real World Outcomes (DRWO) journal.
