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Phylogenetics, a hands-on introduction
This book introduces concepts of modern phylogenetics through hands-on examples, including how to construct, read and analyze phylogenetic trees in the command line and in R. The book targets undergraduate and graduate students in biology, bioinformatics, data science or related fields. Numerous examples and exercises are included throughout the book, mostly using data from the scientific literature. Phylogenies used in the examples/exercises span the entire tree of life including viruses, bacteria, archaea and eukaryotes. Prerequisites include basic familiarity with the command line (bash) and with R. References to the scientific literature are provided throughout for the interested reader. This book is suitable as reading material in related university courses as well as for self-teaching.
Introduction to Biological Data Analysis in Python
This book introduces computational data analysis in biology, using the free and popular programming language python 3. The book targets undergraduate and graduate students in biology with an interest in computational techniques, but could also be of interest to students in other scientific disciplines such as biochemistry, environmental sciences and physics. No prior programming experience is required -- this book is intended for the motivated novice! Readers will learn to load and analyze data and produce professional visualizations. The mathematical content is kept to a bare minimum. Examples and exercises are drawn from a wide spectrum across biology, such as epidemiology, ecology, conservation biology, neuroscience, evolution, genetics, genomics and microbiology. Many exercises use realistic datasets published in the scientific literature, such as bacterial genome sequences, animal GPS tracking data, population time series and biodiversity inventories. References to the scientific literature are provided throughout.
Dynamical Modeling of Biological Systems
This book introduces concepts and practical tools for dynamical mathematical modeling of biological systems. Dynamical models describe the behavior of a system over time as a result of internal feedback loops and external forcing, based on mathematically formulated dynamical laws, similarly to how Newton's laws describe the movement of celestial bodies. Dynamical models are increasingly popular in biology, as they tend to be more powerful than static regression models. This book is meant for undergraduate and graduate students in physics, applied mathematics and data science with an interest in biology, as well as students in biology with a strong interest in mathematical methods. The book c...
Extinctions
"A distinguished geologist and a popular science writer Charles Frankel turns his attention in his latest book to the mass extinctions on our planet, considering what the past can tell us about the future. Explaining Earth's past mass extinctions, Frankel suggests that, each time, a decrease in biodiversity created fragile conditions that eventuated into widespread and cataclysmic disappearances. The rise of mammals led to the rise of humans, who, over the past 200,000 years, have become their own geological force, forever affecting the bio-environment, from the massacre of megafauna in the Ice Age to the impoverishment of soils and pollution of waterways and air, to the unwitting transfer o...
Can Microbial Communities Regenerate?
"You take antibiotics to fight an infection. Unfortunately, the treatment also kills the community of bacteria in your gut microbiome; you now have digestion issues. You might start eating yogurt to reintroduce good bacteria. Or, if the bacterial community is more significantly disordered, you might need a "fecal microbiota transplant" - a doctor transfers stool from a healthy donor into your gut. The new bacteria community thrives, and you can again digest your food. If all the same types of bacteria are present in this new community, has your microbiome "regenerated"? What if the bacteria are completely different, but they perform the same function? How do the answers to these questions ch...
Microbiome Engineering
This reference book compiles the latest techniques and applications of microbiome engineering. Microbial communities interact dynamically with their hosts, creating a considerable impact on the host and their ecosystem. This book introduces readers to microbiomes and microbiome engineering. It covers topics like omics tools in microbial research, strategies to engineer human microbiomes, the application of synthetic biology to build smart microbes, and the future of microbiome engineering. It includes the application of microbiome engineering in improving human health, livestock, and agricultural productivity. The book is intended for researchers and students in the fields of microbiology and biotechnology.
Bioinformatic and Statistical Analysis of Microbiome Data
This unique book addresses the bioinformatic and statistical modelling and also the analysis of microbiome data using cutting-edge QIIME 2 and R software. It covers core analysis topics in both bioinformatics and statistics, which provides a complete workflow for microbiome data analysis: from raw sequencing reads to community analysis and statistical hypothesis testing. It includes real-world data from the authors’ research and from the public domain, and discusses the implementation of QIIME 2 and R for data analysis step-by-step. The data as well as QIIME 2 and R computer programs are publicly available, allowing readers to replicate the model development and data analysis presented in each chapter so that these new methods can be readily applied in their own research. Bioinformatic and Statistical Analysis of Microbiome Data is an ideal book for advanced graduate students and researchers in the clinical, biomedical, agricultural, and environmental fields, as well as those studying bioinformatics, statistics, and big data analysis.
Species, Science and Society
- presents an engaging and accessible examination of the role of systematic biology in species exploration and biodiversity conservation - clarifies misconceptions about systematic biology, reimagining it for the 21st Century - proposes an ambitious, planetary-scale project to inventory and make known every kind of plant, animal, and microbe on Earth - challenges the next and present generations of taxonomists to allow molecular data to assume it’s proper place alongside traditional data, to reembrace the fundamentally important mission of systematics - will be of great interest to those researching and working in systematics in botany and zoology, as well as professionals working in taxonomy and biodiversity conservation.
Microbes in Agri-Forestry Biotechnology
This book explores recent advances on the use of microbes for agri-forestry biotechnological applications. It provides technical concepts and discussions on the use of microorganisms for processes such as bioprocessing, bioremediation, soil enhancement, aquaponics advances, and plant-host symbiosis. The book provides an overview of the microbial approach to the tools and processes used in agriculture and forestry that make or modify products, improve plants for specific uses, and make use of livestock in agricultural systems. The authors discuss the main process conditions that enhance agri-forestry applications with the use of microbes and introduce the use of genetically modified (GM) microbes in agrobiotechnology. Finally, the authors explore the main technological advances in the production of secondary metabolites with potential applications in agri-forestry. This book is intended for biotechnologists, biologists, bioengineers, biochemists, microbiologists, food technologists, enzymologists, and related researchers.
Ethnolinguistic Prehistory
This volume provides the most up-to-date and holistic but compact account of the peopling of the world from the perspective of language, genes and material culture. The book provides detailed answers to the question of where we all came from.
