Your Passport to a Career in Bioinformatics

Description

This book which is the second edition of Your Passport to a Career in Bioinformatics, is intended for students who plan to work in bioinformatics. In addition to addressing the opportunities and challenges faced by today’s bioinformatics community, it demonstrates how bioinformatics is currently transitioning from research to vocation and avocation. Further, it extols the virtues of in silico for bioinformatics predictions, as it helps wet-lab biologists reduce the time needed for experiments. In turn, the book addresses career prospects and the Ten Commandments for becoming a bioinformatics professional; bioinformatics for developing countries; bioinformatics for schools; bioinformatics for markets; and the knowns and unknowns of bioinformatics. It also explores how bioinformatics interacts with various fields in terms of three Cs: consistency, continuity, and credibility. Foreword Acknowledgments Prologue Contents About the Editor Chapter 1: Whither Bioinformatics? 1.1 Bioinformatics ``Aging´´ in Systems Biology 1.2 Defining Systems Biology Through Omics: The Two Paradigms 1.3 Is Biology Explained Through Protein-Protein Interaction Networks Alone? 1.4 Systems Biology in Wet Laboratory 1.4.1 Metabolomics 1.5 Mitochondriomics 1.6 ``Omic´´ Challenges in Systems Biology 1.7 Are Interactions Based on the Nature of Binding? 1.8 Fundamental and Best Practiced Tools for Annotating Proteins and Genes 1.9 Can Bioinformatics Influence Animal Experimentation? 1.10 Addendum: Results of Poll @Bioinformatics.org 1.10.1 Opinion of Few Scientists on Bioinformatics Influencing Animal Experimentation References Chapter 2: Ten Reasons One Should Take Bioinformatics as a Career 2.1 Bioinformatics Is Challenging and One Is Free to Respect Open-Access 2.2 It Delves into Predictions but Bona Fidelity Is the Means for Predicting Genes 2.3 Intelligent and Efficient Storage of Data Is the Key 2.4 Development of Tools and Programs Making Wet Laboratory Biologists Ease Their Experiments 2.5 It Is Multifaceted and Brings Networking Among Cross Disciplinarians 2.6 It may Partly Influence Animal Experiments 2.7 Bioinformatics Curation, not Annotation Is the Key for Databases 2.8 Use of Bioinformatics Methods Propel Contract Research Organizations 2.9 Bringing Core Programmers Closer 2.10 It Is Dynamic and So Is Inviting to Be Entrepreneurial Chapter 3: Developing Bioinformatics Skills 3.1 Be Devoted 3.2 Be Determined 3.3 Bioinformatics and the Three Cs of Research 3.4 Consistency 3.5 Hate Wet Laboratory Work? 3.6 Coping the Pressure of Experimental Work 3.7 From ``Hands-on In Vitro´´ to ``Hands-on In Silico´´ 3.7.1 Correlating and Identifying Statistically Significant Causality Data 3.7.1.1 Problem 3.7.2 Brief Methods 3.7.2.1 Dataset 3.7.2.2 Statistical Analyses 3.7.3 Interpreting the Results Based on Preliminary Analyses Using PPA 3.7.4 Predicting the Antigens Immunizing the Groups 3.7.5 Conclusions 3.7.6 Bottom Line 3.8 Case Study on Nematome: Protein Interactions Specific to Parasitism in Nematodes 3.8.1 Methods 3.8.2 Interaction Analyses 3.8.3 Dry Laboratory/Bioinformatics 3.9 Tips and Traps in Writing a Research Article in Bioinformatics 3.10 Convert Ideas and Thoughts into Action for a Strong Problem Formulation 3.10.1 Address the Problem Well with Subheadings 3.10.1.1 Background 3.10.1.2 Introduction and Review of Literature 3.10.1.3 Problem Formulation and Objectives of the Study 3.10.1.4 Materials and Methods 3.10.1.5 Results and Discussion 3.10.1.6 Conclusions and Future Directions 3.10.1.7 References/Bibliography 3.10.2 Plan Your Next Steps and Always Give Plenty of Time 3.10.3 Discuss with your Peers 3.10.4 Accept Constructive Criticism 3.10.5 Publish or Perish Is the Key While Citing and Cross-Referring Other Articles of Interest 3.10.6 Peer Review Holds an Important Community Service References Chapter 4: The Esoteric of Bioinformatics 4.1 Bioinformatics Market: Hype or Hope? 4.2 Decoding Genes Using Genealogy: What Bioinformatics Can Do? 4.3 Communication Between Organelles and the Genes 4.4 Pull-Down Assays and the Role of Bioinformatics 4.5 Say ``Ome´´ Using Essential Bioinformatical Indicators 4.6 Ten Career Options to Opt Through Bioinformatics References Chapter 5: Common Minimum Standards: A Syllabus for Bioinformatics Practitioners Chapter 6: Colloquial Group Discussion on Bioinformatics: Grand Challenges 6.1 Opinion of Bioinformatics Practitioners Chapter 7: The Bioinforma ``TICKS´´: Frequently Asked Questions Chapter 8: Undergraduate Education in Bioinformatics-Progress and Lessons Learnt from an Engineering Degree References Chapter 9: Engineering Minds for Biologists 9.1 Why Bioinformatics Needs an Engineering Mind 9.2 The Importance of Data Handling 9.3 Scope 9.4 Naming and Standardization 9.5 Data Format 9.6 Timing of Updates 9.7 Modeling for Simulation 9.8 Conclusions References Chapter 10: Design Bioinformatics Curriculum Guidelines: Perspectives 10.1 Introduction 10.2 Curricular Goals and Learning Outcomes 10.3 Targeted Educational Level 10.3.1 High Schools Level 10.3.2 Undergraduate Level 10.3.3 Postgraduate Level 10.4 Targeted Specialization Needs 10.5 Designing and Running Course in Bioinformatics 10.6 Courses Design and Offering Issues 10.7 Recommendation 10.8 Conclusions References Chapter 11: Machine Learning for Bioinformatics 11.1 Introduction 11.2 Machine Learning Algorithms for Bioinformatics 11.3 Deep Learning Algorithms for Bioinformatics 11.4 Applications of Machine Learning (ML) in Bioinformatics 11.5 Conclusions References Bioinformatics Cross Word Epilogue References Web References