Live online courses on statistics with R based on this book, led by the author, are offered regularly; see this page for more information and dates.

The past decades have transformed the world of statistical data analysis, with new methods, new types of data, and new computational tools. The aim of Modern Statistics with R is to introduce you to key parts of the modern statistical toolkit. It teaches you:

• Data wrangling - importing, formatting, reshaping, merging, and filtering data in R.
• Exploratory data analysis - using visualisations and multivariate techniques to explore datasets.
• Statistical inference - modern methods for testing hypotheses and computing confidence intervals.
• Predictive modelling - regression models and machine learning methods for prediction, classification, and forecasting.
• Simulation - using simulation techniques for sample size computations and evaluations of statistical methods.
• Ethics in statistics - ethical issues and good statistical practice.
• R programming - writing code that is fast, readable, and (hopefully!) free from bugs.

The book includes plenty of examples and more than 200 exercises with worked solutions. The datasets used for the examples and the exercises can be downloaded here.

Address of the bookmark: https://www.modernstatisticswithr.com/

Structural variants presentation by

Jan Korbel

European Molecular Biology Laboratory (EMBL) Heidelberg Genome Biology Research Unit

Reference: 

https://www.genome.gov/pages/research/der/1000genomesprojecttutorials/structuralvariants-jankorbel.pdf

Address of the bookmark: https://www.nature.com/articles/srep20802

Caretta, a multiple structure alignment suite meant for homologous but sequentially divergent protein families which consistently returns accurate alignments with a higher coverage than current state-of-the-art tools. Caretta is available as a GUI and command-line application and additionally outputs an aligned structure feature matrix for a given set of input structures, which can readily be used in downstream steps for supervised or unsupervised machine learning. 

Address of the bookmark: http://www.bioinformatics.nl/caretta/

Address of the bookmark: http://www.mdpi.com/2073-4425/3/3/423

SiLiX adopts a graph-theoretical framework to interpret similarity pairs as edges of a network. A very efficient algorithm, based on the Disjoint Sets Data Structure, allows the computation of sequence families with low time and space requirements.

A parallel version of SiLiX, based on MPI, is also available in this package and has been proved to be scalable, so that its allows the study of very large datasets.

SiLiX is already included in the analysis pipeline for HOGENOM.

Address of the bookmark: http://lbbe.univ-lyon1.fr/SiLiX?lang=fr

What is HiBC?

The Human Intestinal Bacteria Collection (HiBC) is a comprehensive, high-quality reference repository of bacterial isolates derived from human fecal samples. It focuses on anaerobic and facultative anaerobic bacteria that play pivotal roles in digestion, immune modulation, vitamin synthesis, and pathogen resistance. The collection includes both culturable strains and genomic data from unculturable taxa, bridging the gap between culture-dependent and -independent microbiome studies.

Why is HiBC Important?

1. Understanding Microbiome-Host Interactions
   HiBC enables deeper insight into the functions of specific bacterial taxa in the gut. With well-characterized isolates, researchers can conduct mechanistic studies to explore how certain bacteria influence metabolism, inflammation, or mental health.

2. Precision Probiotics and Therapeutics
   By providing access to native human gut microbes, HiBC supports the development of next-generation probiotics, live biotherapeutic products (LBPs), and fecal microbiota transplantation (FMT) alternatives.

3. Standardization and Reproducibility
   With standardized cultivation and genomic protocols, HiBC ensures consistency across microbiome research studies, improving reproducibility and comparability of findings.

4. Antimicrobial Resistance (AMR) Surveillance
   HiBC includes metadata on antibiotic resistance genes (ARGs), helping track the spread of AMR in commensal gut bacteria and understanding its implications for human health.

Key Features of HiBC

• Culturable Bacteria Repository: A living collection of anaerobic and facultative strains isolated from healthy and diseased individuals worldwide.

• Metadata-rich Entries: Each isolate is annotated with host details (age, health status, diet), geographical origin, phenotypic traits, and antibiotic susceptibility profiles.

• Whole Genome Sequencing (WGS): High-quality genome assemblies for most strains to support functional and comparative genomics.

• Interactive Database Access: User-friendly search and filtering options for strain selection based on taxonomy, function, or clinical relevance.

• Cross-linking with Other Databases: Integration with NCBI, GOLD, and Human Microbiome Project (HMP) data for broader context and validation.

Applications of HiBC

• Microbiome-based diagnostics and biomarker discovery

• Host-microbe interaction studies in gnotobiotic mouse models

• Gut microbiome modulation through diet, drugs, or engineered bacteria

• Longitudinal studies of gut flora across age, geography, and lifestyle

• Environmental and evolutionary microbiology of human-associated bacteria

Accessing HiBC

Researchers and interested parties can explore the HiBC database through its official website: https://www.hibc.rwth-aachen.de/. The platform offers comprehensive information on bacterial isolates, including taxonomy, cultivation conditions, and genomic data, facilitating advanced research in human gut microbiome studies.

Final Thoughts

The HiBC is a cornerstone resource in the rapidly evolving field of microbiome research. As science moves toward personalized medicine and microbial therapeutics, having a reliable and diverse collection of human gut bacteria is not just useful — it's essential. Whether you're a microbiologist, clinician, computational biologist, or biotechnologist, HiBC offers tools to accelerate discovery and innovation in gut microbiome science.

" the microbes exist in very low concentrations, of around 1,000 microbes in every tea spoon full of rock, compared with billions or trillions of bacteria that would typically be found in the same amount of soil at Earth's surface."

Reference:

http://www.bbc.co.uk/news/science-environment-23855436

http://clark.cs.ucr.edu/Spaced/

Address of the bookmark: http://clark.cs.ucr.edu/Spaced/

http://www.extension.org/pages/67926/upcoming-webinar:-selective-sequencing-through-combinatorial-pooling#.UggsVuHyPqU