Investigation Of Experimental And Computational Approaches To Optimize The Bacterial Three Hybrid Assay

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Investigation of Experimental and Computational Approaches to Optimize the Bacterial Three-Hybrid Assay

Author : Linh Nguyen
Publisher :
ISBN 13 :
Total Pages : 0 pages
Book Rating : 4.:/5 (135 download)

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Book Synopsis Investigation of Experimental and Computational Approaches to Optimize the Bacterial Three-Hybrid Assay by : Linh Nguyen

Download or read book Investigation of Experimental and Computational Approaches to Optimize the Bacterial Three-Hybrid Assay written by Linh Nguyen and published by . This book was released on 2022 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Post-transcriptional gene regulation by non-coding small regulatory RNAs (sRNAs) plays an important role in bacterial stress responses and virulence. In many bacteria, the binding of sRNAs to their target mRNAs at or near the ribosome binding sites is often facilitated by protein chaperones such as Hfq or ProQ. In order to elucidate the molecular mechanisms of RNA-protein interactions, an in vivo genetic approach, the bacterial three-hybrid (B3H) assay, was developed to detect the binding of RNA with multiple RNA chaperones by connecting the strength of an RNA-protein interaction to the expression of a reporter gene. Despite the promise of the B3H system and its success in detecting many high-affinity interactions, low signal-to-noise for other RNA-protein interactions currently limits the broader utility of the assay. My study aims to optimize the hybrid RNA component of the assay to improve the breadth of detectable B3H interactions. To this end, I have focused on designing new hybrid RNA constructs with the addition of a GC-clamp - a short insert of guanines (G) and cytosines (C) flanking a region of interest - to promote proper folding and optimal display of RNA. My results demonstrate the potential of the short GC-clamp in improving the B3H detection of a broader range of sRNA-Hfq interactions. I have also explored the contributions of different components of the hybrid mRNA construct, including a stop codon, a short GC clamp and a trpA terminator, to mRNA expression level with the hope to understand how mRNA degradation might hinder the B3H detection of mRNA-Hfq interactions. To prioritize future experimental optimization, it is also imperative to understand this genetic toolbox from a systematic perspective. Using COPASI, a software package specializing in setting up and analyzing kinetic models, I have created a mathematical model of the B3H system and used the information from model simulations to predict the signal for RNA-protein interactions and guide further optimizing strategies. The work I present here represents significant progress towards increasing the sensitivity and generalizability of the B3H assay to study bacterial RNA-protein interactions which are implicated in many important processes in bacteria such as adaptation to stress, biofilm formation, virulence, and antibiotic resistance.

Computational Intelligence Paradigms for Optimization Problems Using MATLAB®/SIMULINK®

Author : S. Sumathi
Publisher : CRC Press
ISBN 13 : 1498743714
Total Pages : 601 pages
Book Rating : 4.4/5 (987 download)

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Book Synopsis Computational Intelligence Paradigms for Optimization Problems Using MATLAB®/SIMULINK® by : S. Sumathi

Download or read book Computational Intelligence Paradigms for Optimization Problems Using MATLAB®/SIMULINK® written by S. Sumathi and published by CRC Press. This book was released on 2018-09-03 with total page 601 pages. Available in PDF, EPUB and Kindle. Book excerpt: Considered one of the most innovative research directions, computational intelligence (CI) embraces techniques that use global search optimization, machine learning, approximate reasoning, and connectionist systems to develop efficient, robust, and easy-to-use solutions amidst multiple decision variables, complex constraints, and tumultuous environments. CI techniques involve a combination of learning, adaptation, and evolution used for intelligent applications. Computational Intelligence Paradigms for Optimization Problems Using MATLAB®/ Simulink® explores the performance of CI in terms of knowledge representation, adaptability, optimality, and processing speed for different real-world optimization problems. Focusing on the practical implementation of CI techniques, this book: Discusses the role of CI paradigms in engineering applications such as unit commitment and economic load dispatch, harmonic reduction, load frequency control and automatic voltage regulation, job shop scheduling, multidepot vehicle routing, and digital image watermarking Explains the impact of CI on power systems, control systems, industrial automation, and image processing through the above-mentioned applications Shows how to apply CI algorithms to constraint-based optimization problems using MATLAB® m-files and Simulink® models Includes experimental analyses and results of test systems Computational Intelligence Paradigms for Optimization Problems Using MATLAB®/ Simulink® provides a valuable reference for industry professionals and advanced undergraduate, postgraduate, and research students.

Novel Approaches in Microbiome Analyses and Data Visualization

Author : Jessica Galloway-Peña
Publisher : Frontiers Media SA
ISBN 13 : 2889456536
Total Pages : 186 pages
Book Rating : 4.8/5 (894 download)

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Book Synopsis Novel Approaches in Microbiome Analyses and Data Visualization by : Jessica Galloway-Peña

Download or read book Novel Approaches in Microbiome Analyses and Data Visualization written by Jessica Galloway-Peña and published by Frontiers Media SA. This book was released on 2019-02-06 with total page 186 pages. Available in PDF, EPUB and Kindle. Book excerpt: High-throughput sequencing technologies are widely used to study microbial ecology across species and habitats in order to understand the impacts of microbial communities on host health, metabolism, and the environment. Due to the dynamic nature of microbial communities, longitudinal microbiome analyses play an essential role in these types of investigations. Key questions in microbiome studies aim at identifying specific microbial taxa, enterotypes, genes, or metabolites associated with specific outcomes, as well as potential factors that influence microbial communities. However, the characteristics of microbiome data, such as sparsity and skewedness, combined with the nature of data collection, reflected often as uneven sampling or missing data, make commonly employed statistical approaches to handle repeated measures in longitudinal studies inadequate. Therefore, many researchers have begun to investigate methods that could improve incorporating these features when studying clinical, host, metabolic, or environmental associations with longitudinal microbiome data. In addition to the inferential aspect, it is also becoming apparent that visualization of high dimensional data in a way which is both intelligible and comprehensive is another difficult challenge that microbiome researchers face. Visualization is crucial in both the analysis and understanding of metagenomic data. Researchers must create clear graphic representations that give biological insight without being overly complicated. Thus, this Research Topic seeks to both review and provide novels approaches that are being developed to integrate microbiome data and complex metadata into meaningful mathematical, statistical and computational models. We believe this topic is fundamental to understanding the importance of microbial communities and provides a useful reference for other investigators approaching the field.

Issues in Computation: 2011 Edition

Author :
Publisher : ScholarlyEditions
ISBN 13 : 146496453X
Total Pages : 1318 pages
Book Rating : 4.4/5 (649 download)

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Book Synopsis Issues in Computation: 2011 Edition by :

Download or read book Issues in Computation: 2011 Edition written by and published by ScholarlyEditions. This book was released on 2012-01-09 with total page 1318 pages. Available in PDF, EPUB and Kindle. Book excerpt: Issues in Computation / 2011 Edition is a ScholarlyEditions™ eBook that delivers timely, authoritative, and comprehensive information about Computation. The editors have built Issues in Computation: 2011 Edition on the vast information databases of ScholarlyNews.™ You can expect the information about Computation in this eBook to be deeper than what you can access anywhere else, as well as consistently reliable, authoritative, informed, and relevant. The content of Issues in Computation / 2011 Edition has been produced by the world’s leading scientists, engineers, analysts, research institutions, and companies. All of the content is from peer-reviewed sources, and all of it is written, assembled, and edited by the editors at ScholarlyEditions™ and available exclusively from us. You now have a source you can cite with authority, confidence, and credibility. More information is available at http://www.ScholarlyEditions.com/.

Multi-objective Swarm Intelligence

Author : Satchidananda Dehuri
Publisher : Springer
ISBN 13 : 3662463091
Total Pages : 209 pages
Book Rating : 4.6/5 (624 download)

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Book Synopsis Multi-objective Swarm Intelligence by : Satchidananda Dehuri

Download or read book Multi-objective Swarm Intelligence written by Satchidananda Dehuri and published by Springer. This book was released on 2015-03-10 with total page 209 pages. Available in PDF, EPUB and Kindle. Book excerpt: The aim of this book is to understand the state-of-the-art theoretical and practical advances of swarm intelligence. It comprises seven contemporary relevant chapters. In chapter 1, a review of Bacteria Foraging Optimization (BFO) techniques for both single and multiple criterions problem is presented. A survey on swarm intelligence for multiple and many objectives optimization is presented in chapter 2 along with a topical study on EEG signal analysis. Without compromising the extensive simulation study, a comparative study of variants of MOPSO is provided in chapter 3. Intractable problems like subset and job scheduling problems are discussed in chapters 4 and 7 by different hybrid swarm intelligence techniques. An attempt to study image enhancement by ant colony optimization is made in chapter 5. Finally, chapter 7 covers the aspect of uncertainty in data by hybrid PSO.

Natural Computing in Computational Finance

Author : Anthony Brabazon
Publisher : Springer Science & Business Media
ISBN 13 : 3540774769
Total Pages : 298 pages
Book Rating : 4.5/5 (47 download)

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Book Synopsis Natural Computing in Computational Finance by : Anthony Brabazon

Download or read book Natural Computing in Computational Finance written by Anthony Brabazon and published by Springer Science & Business Media. This book was released on 2008-05-09 with total page 298 pages. Available in PDF, EPUB and Kindle. Book excerpt: Natural Computing in Computational Finance is a innovative volume containing fifteen chapters which illustrate cutting-edge applications of natural computing or agent-based modeling in modern computational finance. Following an introductory chapter the book is organized into three sections. The first section deals with optimization applications of natural computing demonstrating the application of a broad range of algorithms including, genetic algorithms, differential evolution, evolution strategies, quantum-inspired evolutionary algorithms and bacterial foraging algorithms to multiple financial applications including portfolio optimization, fund allocation and asset pricing. The second section explores the use of natural computing methodologies such as genetic programming, neural network hybrids and fuzzy-evolutionary hybrids for model induction in order to construct market trading, credit scoring and market prediction systems. The final section illustrates a range of agent-based applications including the modeling of payment card and financial markets. Each chapter provides an introduction to the relevant natural computing methodology as well as providing a clear description of the financial application addressed. The book was written to be accessible to a wide audience and should be of interest to practitioners, academics and students, in the fields of both natural computing and finance.

Practice of Optimisation Theory in Geotechnical Engineering

Author : Zhen-Yu Yin
Publisher : Springer
ISBN 13 : 9811334080
Total Pages : 356 pages
Book Rating : 4.8/5 (113 download)

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Book Synopsis Practice of Optimisation Theory in Geotechnical Engineering by : Zhen-Yu Yin

Download or read book Practice of Optimisation Theory in Geotechnical Engineering written by Zhen-Yu Yin and published by Springer. This book was released on 2019-04-25 with total page 356 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents the development of an optimization platform for geotechnical engineering, which is one of the key components in smart geotechnics. The book discusses the fundamentals of the optimization algorithm with constitutive models of soils. Helping readers easily understand the optimization algorithm applied in geotechnical engineering, this book first introduces the methodology of the optimization-based parameter identification, and then elaborates the principle of three newly developed efficient optimization algorithms, followed by the ideas of a variety of laboratory tests and formulations of constitutive models. Moving on to the application of optimization methods in geotechnical engineering, this book presents an optimization-based parameter identification platform with a practical and concise interface based on the above theories. The book is intended for undergraduate and graduate-level teaching in soil mechanics and geotechnical engineering and other related engineering specialties. It is also of use to industry practitioners, due to the inclusion of real-world applications, opening the door to advanced courses on both modeling and algorithm development within the industrial engineering and operations research fields.

Handbook of Research on Soft Computing and Nature-Inspired Algorithms

Author : Shandilya, Shishir K.
Publisher : IGI Global
ISBN 13 : 1522521291
Total Pages : 649 pages
Book Rating : 4.5/5 (225 download)

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Book Synopsis Handbook of Research on Soft Computing and Nature-Inspired Algorithms by : Shandilya, Shishir K.

Download or read book Handbook of Research on Soft Computing and Nature-Inspired Algorithms written by Shandilya, Shishir K. and published by IGI Global. This book was released on 2017-03-10 with total page 649 pages. Available in PDF, EPUB and Kindle. Book excerpt: Soft computing and nature-inspired computing both play a significant role in developing a better understanding to machine learning. When studied together, they can offer new perspectives on the learning process of machines. The Handbook of Research on Soft Computing and Nature-Inspired Algorithms is an essential source for the latest scholarly research on applications of nature-inspired computing and soft computational systems. Featuring comprehensive coverage on a range of topics and perspectives such as swarm intelligence, speech recognition, and electromagnetic problem solving, this publication is ideally designed for students, researchers, scholars, professionals, and practitioners seeking current research on the advanced workings of intelligence in computing systems.

RNA Tagging

Author : Manfred Heinlein
Publisher : Humana
ISBN 13 : 9781071607145
Total Pages : 490 pages
Book Rating : 4.6/5 (71 download)

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Book Synopsis RNA Tagging by : Manfred Heinlein

Download or read book RNA Tagging written by Manfred Heinlein and published by Humana. This book was released on 2021-08-08 with total page 490 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides a compendium of state-of-the-art methods for the labeling, detection, and purification of RNA and RNA-protein complexes and thereby constitutes an important toolbox for researchers interested in understanding the complex roles of RNA molecules in development, signaling, and disease. Beginning with a section on in situ detection of RNA molecules using FISH techniques, the volume continues with parts exploring in vivo imaging of RNA transport and localization, imaging and analysis of RNA uptake and transport between cells, identification and analysis of RNA-binding proteins, guide RNAs in genome editing, as well as other specific analytical techniques. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, RNA Tagging: Methods and Protocols serves as a vital reference for researchers looking to further the increasingly important research in RNA biology.

Integrative Structural Biology with Hybrid Methods

Author : Haruki Nakamura
Publisher : Springer
ISBN 13 : 9811322007
Total Pages : 272 pages
Book Rating : 4.8/5 (113 download)

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Book Synopsis Integrative Structural Biology with Hybrid Methods by : Haruki Nakamura

Download or read book Integrative Structural Biology with Hybrid Methods written by Haruki Nakamura and published by Springer. This book was released on 2019-01-08 with total page 272 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents a new emerging concept of "Integrative Structural Biology". It covers current trends of the molecular and cellular structural biology, providing new methods to observe, validate, and keep the structural models of the large cellular machines with recent scientific results. Structures of very large macromolecular machines in cells are being determined by combining observations from complementary experimental methods. Thus, this volume presents the each methods such as X-ray crystallography, NMR spectroscopy, 3DEM, small-angle scattering (SAS), FRET, crosslinking, and enables the readers to understand the hybrid methods. This book discusses how those integrative models should be represented, validated and archived. A unique highlight of this book is discussion of the data validation and archive, which are big problems in this filed along with the progress of this field. The researchers in biology will be interested in this book as a guide book for learning the current structure biology, but also those in structure biology may use this book as a comprehensive reference to cover broad topics.

Handbook of Research on Swarm Intelligence in Engineering

Author : Bhattacharyya, Siddhartha
Publisher : IGI Global
ISBN 13 : 1466682922
Total Pages : 770 pages
Book Rating : 4.4/5 (666 download)

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Book Synopsis Handbook of Research on Swarm Intelligence in Engineering by : Bhattacharyya, Siddhartha

Download or read book Handbook of Research on Swarm Intelligence in Engineering written by Bhattacharyya, Siddhartha and published by IGI Global. This book was released on 2015-04-30 with total page 770 pages. Available in PDF, EPUB and Kindle. Book excerpt: Swarm Intelligence has recently emerged as a next-generation methodology belonging to the class of evolutionary computing. As a result, scientists have been able to explain and understand real-life processes and practices that previously remained unexplored. The Handbook of Research on Swarm Intelligence in Engineering presents the latest research being conducted on diverse topics in intelligence technologies such as Swarm Intelligence, Machine Intelligence, Optical Engineering, and Signal Processing with the goal of advancing knowledge and applications in this rapidly evolving field. The enriched interdisciplinary contents of this book will be a subject of interest to the widest forum of faculties, existing research communities, and new research aspirants from a multitude of disciplines and trades.

Advances in Metaheuristics

Author : Timothy Ganesan
Publisher : CRC Press
ISBN 13 : 1315297647
Total Pages : 234 pages
Book Rating : 4.3/5 (152 download)

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Book Synopsis Advances in Metaheuristics by : Timothy Ganesan

Download or read book Advances in Metaheuristics written by Timothy Ganesan and published by CRC Press. This book was released on 2016-11-28 with total page 234 pages. Available in PDF, EPUB and Kindle. Book excerpt: Advances in Metaheuristics: Applications in Engineering Systems provides details on current approaches utilized in engineering optimization. It gives a comprehensive background on metaheuristic applications, focusing on main engineering sectors such as energy, process, and materials. It discusses topics such as algorithmic enhancements and performance measurement approaches, and provides insights into the implementation of metaheuristic strategies to multi-objective optimization problems. With this book, readers can learn to solve real-world engineering optimization problems effectively using the appropriate techniques from emerging fields including evolutionary and swarm intelligence, mathematical programming, and multi-objective optimization. The ten chapters of this book are divided into three parts. The first part discusses three industrial applications in the energy sector. The second focusses on process optimization and considers three engineering applications: optimization of a three-phase separator, process plant, and a pre-treatment process. The third and final part of this book covers industrial applications in material engineering, with a particular focus on sand mould-systems. It also includes discussions on the potential improvement of algorithmic characteristics via strategic algorithmic enhancements. This book helps fill the existing gap in literature on the implementation of metaheuristics in engineering applications and real-world engineering systems. It will be an important resource for engineers and decision-makers selecting and implementing metaheuristics to solve specific engineering problems.

Foundations of Computational Intelligence Volume 3

Author : Ajith Abraham
Publisher : Springer Science & Business Media
ISBN 13 : 3642010849
Total Pages : 531 pages
Book Rating : 4.6/5 (42 download)

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Book Synopsis Foundations of Computational Intelligence Volume 3 by : Ajith Abraham

Download or read book Foundations of Computational Intelligence Volume 3 written by Ajith Abraham and published by Springer Science & Business Media. This book was released on 2009-04-27 with total page 531 pages. Available in PDF, EPUB and Kindle. Book excerpt: Global optimization is a branch of applied mathematics and numerical analysis that deals with the task of finding the absolutely best set of admissible conditions to satisfy certain criteria / objective function(s), formulated in mathematical terms. Global optimization includes nonlinear, stochastic and combinatorial programming, multiobjective programming, control, games, geometry, approximation, algorithms for parallel architectures and so on. Due to its wide usage and applications, it has gained the attention of researchers and practitioners from a plethora of scientific domains. Typical practical examples of global optimization applications include: Traveling salesman problem and electrical circuit design (minimize the path length); safety engineering (building and mechanical structures); mathematical problems (Kepler conjecture); Protein structure prediction (minimize the energy function) etc. Global Optimization algorithms may be categorized into several types: Deterministic (example: branch and bound methods), Stochastic optimization (example: simulated annealing). Heuristics and meta-heuristics (example: evolutionary algorithms) etc. Recently there has been a growing interest in combining global and local search strategies to solve more complicated optimization problems. This edited volume comprises 17 chapters, including several overview Chapters, which provides an up-to-date and state-of-the art research covering the theory and algorithms of global optimization. Besides research articles and expository papers on theory and algorithms of global optimization, papers on numerical experiments and on real world applications were also encouraged. The book is divided into 2 main parts.

Protein Microarray Technology

Author : Dev Kambhampati
Publisher : John Wiley & Sons
ISBN 13 : 3527605215
Total Pages : 276 pages
Book Rating : 4.5/5 (276 download)

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Book Synopsis Protein Microarray Technology by : Dev Kambhampati

Download or read book Protein Microarray Technology written by Dev Kambhampati and published by John Wiley & Sons. This book was released on 2006-03-06 with total page 276 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book is the first of its kind in the field of protein microarrays and addresses novel strategies for constructing highly functional and biocompatible microarrays for screening proteins. The list of authors consisting of world leading experts provide a roadmap for solving the complex challenges that are currently faced while monitoring protein-protein interactions over a wide range of microarray platforms. In doing so, they also offer a comprehensive overview of microarray surface chemistry, detection technologies, fabrication options for array development, and data analysis of numerous types of protein interactions. Topics covered include: -Types of biomolecular interactions -Surface chemistry -Detection technologies -Spotting technologies -Bioinformatics/data analysis. While primarily intended to serve as a reference for researchers and students embarking on the exciting fields of proteomics, drug discovery and clinical diagnostics, this technology is also expected to potentially impact the areas of food diagnostics, environmental monitoring and national security.

RNA-protein Interactions

Author : Kiyoshi Nagai
Publisher : Oxford University Press, USA
ISBN 13 :
Total Pages : 302 pages
Book Rating : 4.3/5 (91 download)

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Book Synopsis RNA-protein Interactions by : Kiyoshi Nagai

Download or read book RNA-protein Interactions written by Kiyoshi Nagai and published by Oxford University Press, USA. This book was released on 1994 with total page 302 pages. Available in PDF, EPUB and Kindle. Book excerpt: The study of RNA-protein interactions is crucial to understanding the mechanisms and control of gene expression and protein synthesis. The realization that RNAs are often far more biologically active than was previously appreciated has stimulated a great deal of new research in this field. Uniquely, in this book, the world's leading researchers have collaborated to produce a comprehensive and current review of RNA-protein interactions for all scientists working in this area. Timely, comprehensive, and authoritative, this new Frontiers title will be invaluable for all researchers in molecular biology, biochemistry and structural biology.

Computational Systems Biology of Cancer

Author : Emmanuel Barillot
Publisher : CRC Press
ISBN 13 : 1439831459
Total Pages : 461 pages
Book Rating : 4.4/5 (398 download)

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Book Synopsis Computational Systems Biology of Cancer by : Emmanuel Barillot

Download or read book Computational Systems Biology of Cancer written by Emmanuel Barillot and published by CRC Press. This book was released on 2012-08-25 with total page 461 pages. Available in PDF, EPUB and Kindle. Book excerpt: The future of cancer research and the development of new therapeutic strategies rely on our ability to convert biological and clinical questions into mathematical models-integrating our knowledge of tumour progression mechanisms with the tsunami of information brought by high-throughput technologies such as microarrays and next-generation sequencin

Next Steps for Functional Genomics

Author : National Academies of Sciences, Engineering, and Medicine
Publisher : National Academies Press
ISBN 13 : 0309676738
Total Pages : 201 pages
Book Rating : 4.3/5 (96 download)

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Book Synopsis Next Steps for Functional Genomics by : National Academies of Sciences, Engineering, and Medicine

Download or read book Next Steps for Functional Genomics written by National Academies of Sciences, Engineering, and Medicine and published by National Academies Press. This book was released on 2020-12-18 with total page 201 pages. Available in PDF, EPUB and Kindle. Book excerpt: One of the holy grails in biology is the ability to predict functional characteristics from an organism's genetic sequence. Despite decades of research since the first sequencing of an organism in 1995, scientists still do not understand exactly how the information in genes is converted into an organism's phenotype, its physical characteristics. Functional genomics attempts to make use of the vast wealth of data from "-omics" screens and projects to describe gene and protein functions and interactions. A February 2020 workshop was held to determine research needs to advance the field of functional genomics over the next 10-20 years. Speakers and participants discussed goals, strategies, and technical needs to allow functional genomics to contribute to the advancement of basic knowledge and its applications that would benefit society. This publication summarizes the presentations and discussions from the workshop.