Huge amounts of genotype data are being produced with recent technological advances, both from increasingly comprehensive and inexpensive genome-wide SNP microarrays and from ever more accessible whole-genome and whole-exome sequencing methods
engr.case.edu - In this report we provide an overview of known techniques for discovery of patterns of biological sequences (DNA and proteins). We also provide biological motivation, and methods of biological verification of such patterns. Finally we list publicly...
Horizontal gene transfer (HGT), the “non-sexual movement of genetic material between two organisms” , is relatively common in prokaryotes and single-celled eukaryotes, but a number of factors combine to make it far rarer in...
The study of Protein–Protein Interactions (PPIs) has a crucial role in biology, medicine and the pharmaceutical industry. PPIs can be investigated from two aspects: The interaction partners of a specific protein and the amino acid residues...
github.com - This document contains instructions on how to use the MITObim pipeline described in Hahn et al. 2013. The full article can be found here. Kindly cite the article if you are using MITObim in your work. The pipeline was originally developed...
github.com - The mmgenome toolbox enables reproducible extraction of individual genomes from metagenomes. It builds on the multi-metagenome concept, but wraps most of the process of extracting genomes in simple R functions. Thereby making the whole...
the sequenced reads can be mapped to the organism’s genes to assess how differently the genes are expressed under the experimental circumstances as opposed to the control scenario. This is known as differential expression (DE) analysis
evirusbioinfc.notion.site - Bioinformatics tools play a crucial role in studying viruses, enabling researchers to analyze their genetic makeup, structure, function, and evolution. Here are some commonly used bioinformatics tools for virus...
Fungal research is a rapidly growing field with vast implications for medicine, agriculture, and industry. For bioinformaticians, the availability of specialized resources—databases, tools, and community platforms—opens doors to innovative...
The study of biological pathways is a key to understand the different processes inside a cell: proteins exert their function not in isolation but in a tightly controlled network of interactions and reactions. Activation of a pathway typically leads...