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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