A Cell Biologist S Guide To Modeling And Bioinformatics

Author : Raquell M. Holmes
Publisher : John Wiley & Sons
Page : 224 pages
File Size : 40,6 Mb
Release : 2008-02-13
Category : Science
ISBN : 047013934X

Get Book

A Cell Biologist's Guide to Modeling and Bioinformatics by Raquell M. Holmes Pdf

A step-by-step guide to using computational tools to solve problems in cell biology Combining expert discussion with examples that can be reproduced by the reader, A Cell Biologist's Guide to Modeling and Bioinformatics introduces an array of informatics tools that are available for analyzing biological data and modeling cellular processes. You learn to fully leverage public databases and create your own computational models. All that you need is a working knowledge of algebra and cellular biology; the author provides all the other tools you need to understand the necessary statistical and mathematical methods. Coverage is divided into two main categories: Molecular sequence database chapters are dedicated to gaining an understanding of tools and strategies—including queries, alignment methods, and statistical significance measures—needed to improve searches for sequence similarity, protein families, and putative functional domains. Discussions of sequence alignments and biological database searching focus on publicly available resources used for background research and the characterization of novel gene products. Modeling chapters take you through all the steps involved in creating a computational model for such basic research areas as cell cycle, calcium dynamics, and glycolysis. Each chapter introduces a new simulation tooland is based on published research. The combination creates a rich context for ongoing skill and knowledge development in modeling biological research systems. Students and professional cell biologists can develop the basic skills needed to learn computational cell biology. This unique text, with its step-by-step instruction, enables you to test and develop your new bioinformatics and modeling skills. References are provided to help you take advantage of more advanced techniques, technologies, and training.

Author : William Cohen,Charles Cohen
Publisher : Springer
Page : 0 pages
File Size : 49,9 Mb
Release : 2024-08-17
Category : Science
ISBN : 3031559061

Get Book

A Computer Scientist's Guide to Cell Biology by William Cohen,Charles Cohen Pdf

Unlike the structured world of computer science, biology is complex, evolving, and often lacks clean abstract models. This book aims to serve as a guide for computer scientists who need to understand cell biology, breaking the field into three parts: biological mechanics, experimental methods, and language/nomenclature. While biological mechanics, which investigates cellular-level details, is covered by many texts, this book also focuses on experimental methods – how biologists conduct experiments and gather data - and on helping the reader understand the language and terminology of biology, which is rich but challenging for non-biologists. A Computer Scientist's Guide to Cell Biology uses a metaphor of biology as a strange land with an unfamiliar language and customs. The goal of the book is to provide a high-level introduction to cell biology, simplifying concepts and relating them to familiar ideas from computer science, so that working computer scientists can more effectively understand read recent research papers and results. This Second Edition contains a number of updates, including discussions of CRISPR, advances in DNA Sequencing, and mRNA vaccines. It serves as an easy-to-read travel guide for computer scientists navigating the intricate and sometimes perplexing terrain of cell biology, offering insights into experimental methods and helping bridge the gap between the structured world of computer science and the complexities of biological systems.

Author : Christopher P. Fall,Eric S. Marland,John M. Wagner
Publisher : Unknown
Page : 492 pages
File Size : 40,7 Mb
Release : 2014-01-15
Category : Electronic
ISBN : 147577706X

Get Book

Computational Cell Biology by Christopher P. Fall,Eric S. Marland,John M. Wagner Pdf

Author : Edward Curry
Publisher : CRC Press
Page : 298 pages
File Size : 44,6 Mb
Release : 2020-11-02
Category : Science
ISBN : 9781351015301

Get Book

Introduction to Bioinformatics with R by Edward Curry Pdf

In biological research, the amount of data available to researchers has increased so much over recent years, it is becoming increasingly difficult to understand the current state of the art without some experience and understanding of data analytics and bioinformatics. An Introduction to Bioinformatics with R: A Practical Guide for Biologists leads the reader through the basics of computational analysis of data encountered in modern biological research. With no previous experience with statistics or programming required, readers will develop the ability to plan suitable analyses of biological datasets, and to use the R programming environment to perform these analyses. This is achieved through a series of case studies using R to answer research questions using molecular biology datasets. Broadly applicable statistical methods are explained, including linear and rank-based correlation, distance metrics and hierarchical clustering, hypothesis testing using linear regression, proportional hazards regression for survival data, and principal component analysis. These methods are then applied as appropriate throughout the case studies, illustrating how they can be used to answer research questions. Key Features: · Provides a practical course in computational data analysis suitable for students or researchers with no previous exposure to computer programming. · Describes in detail the theoretical basis for statistical analysis techniques used throughout the textbook, from basic principles · Presents walk-throughs of data analysis tasks using R and example datasets. All R commands are presented and explained in order to enable the reader to carry out these tasks themselves. · Uses outputs from a large range of molecular biology platforms including DNA methylation and genotyping microarrays; RNA-seq, genome sequencing, ChIP-seq and bisulphite sequencing; and high-throughput phenotypic screens. · Gives worked-out examples geared towards problems encountered in cancer research, which can also be applied across many areas of molecular biology and medical research. This book has been developed over years of training biological scientists and clinicians to analyse the large datasets available in their cancer research projects. It is appropriate for use as a textbook or as a practical book for biological scientists looking to gain bioinformatics skills.

Author : Zoltan Neufeld
Publisher : Unknown
Page : 300 pages
File Size : 53,7 Mb
Release : 2013-06-30
Category : Computers
ISBN : 1848169019

Get Book

Introduction to Systems Bology by Zoltan Neufeld Pdf

This book is a comprehensive guide to applications of mathematical and computational approaches to cell biology. It provides an accessible entry route into this interdisciplinary field for students and researchers from various specialized backgrounds in biology, mathematics, physics, engineering or computer science. It gives a balanced presentation of the methodology (differential equations, dynamical systems analysis, stochastic processes, networks and optimization) and new, emerging modeling approaches, illustrated through a structured collection of case studies in which the use of mathematical and computational methods combined with experiments leads to new insights into the biological phenomena. At the end of each chapter, this is complemented with a brief overview of the relevant systems biology literature, providing links to reviews and key research publications in the particular area for further reading. In addition to the modeling approaches, the book also describes the relevant mathematical and systems biology software tools, including a set of problems and computational exercises through which the reader can gain a practical knowledge of the wide range of computational tools and model databases currently available.

Author : Wallace F. Marshall
Publisher : Biota Publishing
Page : 60 pages
File Size : 52,5 Mb
Release : 2017-07-20
Category : Science
ISBN : 9781615046690

Get Book

Introduction to Quantitative Cell Biology by Wallace F. Marshall Pdf

For the past decade or more, much of cell biology research has been focused on determining the key molecules involved in different cellular processes, an analytical problem that has been amenable to biochemical and genetic approaches. Now, we face an integrative problem of understanding how all of these molecules work together to produce living cells, a challenge that requires using quantitative approaches to model the complex interactions within a cell, and testing those models with careful quantitative measurements. This book is an introductory overview of the various approaches, methods, techniques, and models employed in quantitative cell biology, which are reviewed in greater detail in the other volumes in this e-book series. Particular emphasis is placed on the goals and purpose of quantitative analysis and modeling, and the special challenges that cell biology holds for understanding life at the physical level.

Author : Masao Nagasaki,Ayumu Saito,Atsushi Doi,Hiroshi Matsuno,Satoru Miyano
Publisher : Springer Science & Business Media
Page : 155 pages
File Size : 42,6 Mb
Release : 2009-04-21
Category : Science
ISBN : 9781848820234

Get Book

Foundations of Systems Biology by Masao Nagasaki,Ayumu Saito,Atsushi Doi,Hiroshi Matsuno,Satoru Miyano Pdf

Today, as hundreds of genomes have been sequenced and thousands of proteins and more than ten thousand metabolites have been identi?ed, navigating safely through this wealth of information without getting completely lost has become crucial for research in, and teaching of, molecular biology. Consequently, a considerable number of tools have been developed and put on the market in the last two decades that describe the multitude of potential/putative interactions between genes, proteins, metabolites, and other biologically relevant compounds in terms of metabolic, genetic, signaling, and other networks, their aim being to support all sorts of explorations through bio-data bases currently called Systems Biology. As a result, navigating safely through this wealth of information-processing tools has become equally crucial for successful work in molecular biology. To help perform such navigation tasks successfully, this book starts by providing an extremely useful overview of existing tools for ?nding (or designing) and inv- tigating metabolic, genetic, signaling, and other network databases, addressing also user-relevant practical questions like • Is the database viewable through a web browser? • Is there a licensing fee? • What is the data type (metabolic, gene regulatory, signaling, etc. )? • Is the database developed/maintained by a curator or a computer? • Is there any software for editing pathways? • Is it possible to simulate the pathway? It then goes on to introduce a speci?c such tool, that is, the fabulous “Cell - lustrator 3. 0” tool developed by the authors.

Author : Lan K. Nguyen
Publisher : Springer Nature
Page : 387 pages
File Size : 44,9 Mb
Release : 2023-04-19
Category : Science
ISBN : 9781071630082

Get Book

Computational Modeling of Signaling Networks by Lan K. Nguyen Pdf

This volume focuses on the computational modeling of cell signaling networks and the application of these models and model-based analysis to systems and personalized medicine. Chapters guide readers through various modeling approaches for signaling networks, new methods and techniques that facilitate model development and analysis, and new applications of signaling network modeling towards systems and personalized treatment of cancer. Written in the format of the highly successful Methods in Molecular Biology series, each chapter includes an introduction to the topic, lists necessary materials and methods, includes tips on troubleshooting and known pitfalls, and step-by-step, readily reproducible protocols. Authoritative and cutting-edge, Computational Modeling of Signaling Networks aims to benefit a wide spectrum of readers including researchers from the biological as well as computational systems biology communities.

Author : Andrea Cabibbo,Richard P. Grant,Manuela Helmer Citterich
Publisher : Taylor & Francis
Page : 392 pages
File Size : 55,5 Mb
Release : 2002-08-12
Category : Medical
ISBN : UOM:39015051577636

Get Book

The Internet for Cellular and Molecular Biologists by Andrea Cabibbo,Richard P. Grant,Manuela Helmer Citterich Pdf

None available yet.

Author : Nataša Jonoska,Masahico Saito
Publisher : Springer Science & Business Media
Page : 524 pages
File Size : 40,9 Mb
Release : 2013-12-23
Category : Computers
ISBN : 9783642401930

Get Book

Discrete and Topological Models in Molecular Biology by Nataša Jonoska,Masahico Saito Pdf

Theoretical tools and insights from discrete mathematics, theoretical computer science, and topology now play essential roles in our understanding of vital biomolecular processes. The related methods are now employed in various fields of mathematical biology as instruments to "zoom in" on processes at a molecular level. This book contains expository chapters on how contemporary models from discrete mathematics – in domains such as algebra, combinatorics, and graph and knot theories – can provide perspective on biomolecular problems ranging from data analysis, molecular and gene arrangements and structures, and knotted DNA embeddings via spatial graph models to the dynamics and kinetics of molecular interactions. The contributing authors are among the leading scientists in this field and the book is a reference for researchers in mathematics and theoretical computer science who are engaged with modeling molecular and biological phenomena using discrete methods. It may also serve as a guide and supplement for graduate courses in mathematical biology or bioinformatics, introducing nontraditional aspects of mathematical biology.

Author : Dominik Wodarz,Natalia L. Komarova
Publisher : World Scientific
Page : 268 pages
File Size : 42,5 Mb
Release : 2005
Category : Science
ISBN : 9789812560278

Get Book

Computational Biology of Cancer by Dominik Wodarz,Natalia L. Komarova Pdf

- Provides an introduction to computational methods in cancer biology - Follows a multi-disciplinary approach

Author : Marina Sirota
Publisher : Unknown
Page : 0 pages
File Size : 54,9 Mb
Release : 2014
Category : Bioinformatics
ISBN : 1936113228

Get Book

A Bioinformatics Guide for Molecular Biologists by Marina Sirota Pdf

Informatics can vastly assist progress in research and development in cell and molecular biology and biomedicine. However, many investigators are either unaware of the ways in which informatics can improve their research or find it inaccessible due to a feeling of "informatics anxiety." This sense of apprehension results from improper communication of the principles behind these approaches and of the value of the many tools available. In fact, many researchers are inherently distrustful of these tools. A more complete understanding of bioinformatics offered in A Bioinformatics Guide for Molecular Biologists will allow the reader to become comfortable with these techniques, encouraging their use-thus helping to make sense of the vast accumulation of data. To make these concepts more accessible, the editors approach the field of bioinformatics from the viewpoint of a molecular biologist, (1) arming the biologist with a basic understanding of the fundamental concepts in the field, (2) presenting approaches for using the tools from the standpoint of the data for which they are created, and (3) showing how the field of informatics is quickly adapting to the advancements in biology and biomedical technologies. All concepts are paired with recommendations for the appropriate programming environment and tools best suited to solve the particular problem at hand. It is a must-read for those interested in learning informatics techniques required for successful research and development in the laboratory.

Author : Xuhua Xia
Publisher : Springer Science & Business Media
Page : 350 pages
File Size : 45,6 Mb
Release : 2007-04-24
Category : Science
ISBN : 9780387713373

Get Book

Bioinformatics and the Cell by Xuhua Xia Pdf

The many books that have been published on bioinformatics tend toward either of two extremes: those that feature computational details with a great deal of mathematics, for computational scientists and mathematicians; and those that treat bioinformatics as a giant black box, for biologists. This is the first book using comprehensive numerical illustration of mathematical techniques and computational algorithms used in bioinformatics that converts molecular data into organized biological knowledge.

Author : Frederick Marcus
Publisher : Springer Science & Business Media
Page : 296 pages
File Size : 44,7 Mb
Release : 2008-07-22
Category : Science
ISBN : 9783540783534

Get Book

Bioinformatics and Systems Biology by Frederick Marcus Pdf

Collaborative research in bioinformatics and systems biology is a key element of modern biology and health research. This book highlights and provides access to many of the methods, environments, results and resources involved, including integral laboratory data generation and experimentation and clinical activities. Collaborative projects embody a research paradigm that connects many of the top scientists, institutions, their resources and research worldwide, resulting in first-class contributions to bioinformatics and systems biology. Central themes include describing processes and results in collaborative research projects using computational biology and providing a guide for researchers to access them. The book is also a practical guide on how science is managed. It shows how collaborative researchers are putting results together in a way accessible to the entire biomedical community.

Author : Marek Kimmel,David E. Axelrod
Publisher : Springer Science & Business Media
Page : 242 pages
File Size : 44,6 Mb
Release : 2006-05-26
Category : Mathematics
ISBN : 9780387216393

Get Book

Branching Processes in Biology by Marek Kimmel,David E. Axelrod Pdf

This book introduces biological examples of Branching Processes from molecular and cellular biology as well as from the fields of human evolution and medicine and discusses them in the context of the relevant mathematics. It provides a useful introduction to how the modeling can be done and for what types of problems branching processes can be used.