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Learn how AI and data science are upending the worlds of biology and medicine
In Silico Dreams: How Artificial Intelligence and Biotechnology Will Create the Medicines of the Future delivers an illuminating and fresh perspective on the convergence of two powerful technologies: AI and biotech. Accomplished genomics expert, executive, and author Brian Hilbush offers readers a brilliant exploration of the most current work of pioneering tech giants and biotechnology startups who have already started disrupting healthcare. The book provides an in-depth understanding of the sources of innovation that are driving the shift in the pharmaceutical industry away from serendipitous therapeutic discovery and toward engineered medicines and curative therapies.
In this fascinating book, you'll discover:
Perfect for anyone with an interest in scientific topics and technology, In Silico Dreams also belongs on the bookshelves of decision-makers in a wide range of industries, including healthcare, technology, venture capital, and government.
BRIAN HILBUSH, PhD, is Director, IT Advanced Analytics and Data Solutions at Veranome Biosystems. He received his doctorate in Neuroscience from Stony Brook University and has over three decades of experience in computational biology, genomics, drug discovery, data science, and artificial intelligence.
Introduction xvii
Chapter 1 The Information Revolution’s Impact on Biology 1
A Biological Data Avalanche at Warp Speed 5
Tracking SARS-CoV-2 with Genomic Epidemiology 11
Biology’s Paradigm Shift Enables In Silico Biology 17
Transitions and Computation in Cancer Research 18
Structural Biology and Genomics 24
Sequencing the Human Genome 27
Computational Biology in the Twenty-First Century 33
Applications of Human Genome Sequencing 35
Analyzing Human Genome Sequence Information 37
Omics Technologies and Systems Biology 40
Chapter 2 A New Era of Artificial Intelligence 53
AI Steps Out of the Bronx 55
From Neurons and Cats Brains to Neural Networks 58
Machine Learning and the Deep Learning Breakthrough 66
Deep Learning Arrives for AI 73
Deep Neural Network Architectures 75
Deep Learning’s Beachhead on Medicine: Medical Imaging 78
Limitations on Artificial Intelligence 83
Chapter 3 The Long Road to New Medicines 91
Medicine’s Origins: The Role of Opium Since the Stone Age 96
Industrial Manufacturing of Medicines 102
Paul Ehrlich and the Birth of Chemotherapeutic Drug Discovery 108
The Pharmaceutical Industry: Drugs and War—New Medicines in the Twentieth Century 112
From Synthetic Antibiotics to the Search for New Drugs from the Microbial World 116
Developing Therapeutics for Cancer 119
Antifolates and the Emergence of DNA Synthesis Inhibitors 120
Antibiotics as Cancer Chemotherapeutic Drugs 123
Immunotherapy 125
The Pharmaceutical Business Model in the Twenty-First Century 126
R&D Productivity Challenges Within the Pharmaceutical Industry 131
Sources of Pharmaceutical Innovation: Biotechnology and New Therapeutic Modalities 135
Chapter 4 Gene Editing and the New Tools of Biotechnology 145
Molecular Biology and Biological Information Flow 150
Manipulating Gene Information with Recombinant DNA Technology 154
Genetics, Gene Discovery, and Drugs for Rare Human Diseases 160
Second-Generation Biotechnology Tools: CRISPR- Cas9 and Genome Editing Technologies 167
Human Genome Editing and Clinical Trials 171
Biotechnology to the Rescue: Vaccine Development Platforms Based on Messenger RNA 179
Chapter 5 Healthcare and the Entrance of the Technology Titans 189
Digital Health and the New Healthcare Investment Arena 191
Assessing the Tech Titans as Disruptors in Healthcare 195
Alphabet: Extending Its Tentacles Into Healthcare with Google and Other Bets 196
Apple Inc: Consumer Technology Meets Healthcare 200
Amazon: Taking Logistics to the Next Level for Delivering Healthcare 204
Echoes of the Final Frontier 207
Chapter 6 AI-Based Algorithms in Biology and Medicine 211
Recognizing the Faces of Cancer 217
Tumor Classification Using Deep Learning with Genomic Features 222
AI for Diseases of the Nervous System: Seeing and Changing the Brain 229
Regulatory Approval and Clinical Implementation: Twin Challenges for AI-Based Algorithms in Medicine 234
Chapter 7 AI in Drug Discovery and Development 245
A Brief Survey of In Silico Methods in Drug Discovery 247
Virtual Screening with Cheminformatics and HTS Technologies 250
AI Brings a New Toolset for Computational Drug Design 252
AI-Based Virtual Screening Tools 257
Generative Models for De Novo Drug Design 257
A New Base of Innovation for the Pharmaceutical Industry 259
Atomwise 261
Recursion Pharmaceuticals 262
Deep Genomics 262
Relay Therapeutics 263
Summary 265
Chapter 8 Biotechnology, AI, and Medicine’s Future 269
Building Tools to Decipher Molecular Structures and Biological Systems 272
AlphaFold: Going Deep in Protein Structure Prediction 274
Predicting Genome 3D Organization and Regulatory Elements 276
AI Approaches to Link Genetics-Based Targets to Disease 277
Quantum Computing for In Silico Chemistry and Biology 278
Neuroscience and AI: Modeling Brain and Behavior 280
Brain Information Processing and Modularity: Climbing a Granite Wall 283
Engineering Medicines with Biotechnology and AI 289
Glossary 295
Index 303
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