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Automation in Proteomics and Genomics: An Engineering Case-Based Approach


Description: In the last decade DNA sequencing costs have decreased over a magnitude, largely because of increasing throughput by incremental advances in tools, technologies and process improvements. Further cost reductions in this and in related proteomics technologies are expected as a result of the development of new high-throughput techniques and the computational machinery needed to analyze data generated.

Automation in Proteomics & Genomics: An Engineering Case-Based Approach describes the automation technology currently in the areas of analysis, design, and integration, as well as providing basic biology concepts behind proteomics and genomics. The book also discusses the current technological limitations that can be viewed as an emerging market rather than a research bottleneck. Topics covered include:

- molecular biology fundamentals: from ‘blueprint’ (DNA) to ‘task list’ (RNA) to ‘molecular machine’ (protein); proteomics methods and technologies; modelling protein networks and interactions
- analysis via automation: DNA sequencing; microarrays and other parallelization technologies; protein characterization and identification; protein interaction and gene regulatory networks
- design via automation: DNA synthesis; RNA by design; building protein libraries; synthetic networks
- integration: multiple modalities; computational and experimental methods; trends in automation for genomics and proteomics
- new enabling technologies and future applications

Automation in Proteomics & Genomics: An Engineering Case-Based Approach is an essential guide to the current capabilities and challenges of high-throughput analysis of genes and proteins for bioinformaticians, engineers, chemists, and biologists interested in developing a cross-discipline problem-solving based approach to systems biology.


Contents: Preface.
List of Contributors.

SECTION 1: FUNDAMENTALS OF MOLECULAR AND CELLULAR BIOLOGY.

1. The Central Dogma: from DNA to RNA, and to Protein (Takashi Ohtsuki and Masahiko Sisido).

2. Genomes to Proteomes (Ellen A. Panisko, Igor Grigoriev, Don S. Daly, Bobbie-Jo Webb-Robertson and Scott E. Baker).

SECTION 2: ANALYSIS VIA AUTOMATION.

3. High-throughput DNA Sequencing (Tarjei Mikkelsen).

4. Modeling a regulatory network using temporal gene expression data: why and how (Sophie Lébre, Gaëlle Lelandais).

5. Automated Prediction of Protein Attributes and Its Impact to Biomedicine and Drug Discovery (Kuo-Chen Chou).

6. Molecular Interaction Networks: Topological and Functional Characterizations (Jake Chen and Xiaogang Wu).

SECTION 3: DESIGN VIA AUTOMATION.

7. DNA Synthesis (Jingdong Tian).

8. Computational and Experimental RNA Nanoparticle Design (Isil Severcan, Cody Geary, Luc Jaeger, Eckart Bindewald, Wojciech Kasprzak and Bruce A. Shapiro).

9. New Paradigms in Droplet Based Microfluidics and DNA Amplification (Michael Samuels, John Leamon, Jonathan Rothberg, Ronald Godiska, Thomas Schoenfeld and David Mead).

10. Synthetic Networks (Jongmin Kim).

SECTION 4: INTEGRATION.

11. Molecular Modeling of CYP Proteins and Its Implication for Personal Drug Design (Chengcheng Zhang, Jingyi Yan, Jingfang Wang, Kuo-Chen Chou and Dongqing Wei).

12. Recent Progress of Bioinformatics in Membrane Protein Structural Studies (Hong-Bin Shen, Jun-Feng Wang, Li-Xiu Yao, Jie Yang and Kuo-Chen Chou).

13. Trends in Automation for Genomics and Proteomics (Gil Alterovitz, Roseann Benson, Marco Ramoni and Dmitriy Sonkin).


Author Dr Gil Alterovitz Dr. Gil Alterovitz is a research fellow (and incoming faculty member) at the Harvard/MIT Health Sciences and Technology Division Children's Hospital Informatics Program (CHIP). He is also a research affiliate at the Department of Electrical Engineering and Computer Science at the Massachusetts Institute of Technology (MIT) and affiliated  with Harvard Medical School Partners' Center for Genetics and Genomics (HPCGG).  Roseann Benson Roseann Benson is a chemical engineer/MBA with eleven years of industrial automation experience and specializes in non-fiction writing.   Dr Marco Ramoni Dr. Marco Ramoni is an Assistant Professor of Pediatrics and Medicine at Harvard Medical School and the Harvard Partners Center for Genetics and Genomics Associate Director of Bioinformatics.


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