Book Image

Bioinformatics with Python Cookbook - Second Edition

By : Tiago Antao
Book Image

Bioinformatics with Python Cookbook - Second Edition

By: Tiago Antao

Overview of this book

Bioinformatics is an active research field that uses a range of simple-to-advanced computations to extract valuable information from biological data. This book covers next-generation sequencing, genomics, metagenomics, population genetics, phylogenetics, and proteomics. You'll learn modern programming techniques to analyze large amounts of biological data. With the help of real-world examples, you'll convert, analyze, and visualize datasets using various Python tools and libraries. This book will help you get a better understanding of working with a Galaxy server, which is the most widely used bioinformatics web-based pipeline system. This updated edition also includes advanced next-generation sequencing filtering techniques. You'll also explore topics such as SNP discovery using statistical approaches under high-performance computing frameworks such as Dask and Spark. By the end of this book, you'll be able to use and implement modern programming techniques and frameworks to deal with the ever-increasing deluge of bioinformatics data.
Table of Contents (16 chapters)
Title Page
About Packt
Contributors
Preface
Index

Contributors

About the author

Tiago Antao is a bioinformatician currently working in the field of genomics. He was originally a computer scientist but he crossed over to computational biology with an MSc in Bioinformatics from the Faculty of Sciences at the University of Porto, Portugal, and a PhD on the spread of drug-resistant malaria from the Liverpool School of Tropical Medicine in the UK. He is one of the co-authors of Biopython, a major bioinformatics package written in Python.

In his post-doctoral career, he has worked with human datasets at the University of Cambridge (UK) and with mosquito whole genome sequence data at the University of Oxford (UK). He is currently working as a research scientist at the University of Montana.

 

 

About the reviewers

Cho-Yi Chen is an Assistant Professor of Biomedical Informatics at the National Yang-Ming University. While growing up, he was an active athlete, with a passion for science and technology, which led him to become an Olympic swimmer and later a scientist in genomics and systems biology. He received his BSc, MSc, and PhD from the National Taiwan University and Academia Sinica, and finished his postdoctoral training at the Dana-Farber Cancer Institute and Harvard University. He is a founding member of Taiwan's Society of Evolution and Computational Biology, and is a recipient of the MOST Young Scholar Fellowship for his dedication to biomedical research. He and his group strive to advance our understanding of cancer and other human diseases.

Pin-Jou Wu is a research assistant in Dr. Cho-Yi Chen's laboratory at the Institute of Biomedical Informatics at National Yang-Ming University, Taiwan. Her research interests lie in circadian rhythm and its relation to human aging and diseases. She enjoys multi-omics data mining by using statistics and machine learning approaches and enjoys discovering a new insight into chronobiology.

She was a research assistant at Tainan District Agriculture Research and Extension Station. She completed her Master's degree in Plant Pathology and Microbiology at National Taiwan University and also completed a full-year exchange program doing a Master's of Science degree at University College Dublin, Ireland.

Yao-Chung Chen is a bioinformatician with a background in molecular biology. After receiving his MS from National Taiwan University, he participated in a transcriptome analysis research project on immune systems in commercial fishes at National Pingtung University of Science and Technology. Previous research experience makes him believe that biologists should know more about programming, especially those who aim to work in bioinformatics.

Aiming to be a pioneer, he wishes to interpret bioinformatics in a more biology-friendly way and encourage more biologists to join this field. Currently, he works as a research assistant and studies chronobiology at the Institute of Biomedical Informatics, National Yang-Ming University.

 

 

 

 

 

 

 

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