Rahul Nayak
A Bioinformatician
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Genome Simulation with SLiM and msprime
By BioStar 613 days agoSLiM and msprime are valuable tools for genome simulation, each serving distinct but complementary purposes in population genetics research. By leveraging the strengths of both simulators with slendr, researchers can conduct robust and efficient...PG2: Making Pangenome Graphs Easier to Understand
By Jitendra Narayan 49 days agoGenomics is moving beyond the traditional approach of studying DNA using a single reference genome. Today, researchers are increasingly using pangenomes, which represent genetic information from multiple genomes and capture a much broader range of...The Tree That Learned to Read Genomes
By BioStar 26 days agoA recent study by Webster and Chapman introduces Buscogeny, an open-source bioinformatics pipeline designed to make this process easier. The tool uses BUSCO (Benchmarking Universal Single-Copy Orthologs), which identifies conserved genes that are...Ancestral Genomes: a resource for reconstructed ancestral genes and genomes across the tree of life
By Abhimanyu Singh 2895 days agoancestralgenomes.org - Ancestral Genomes (http://ancestralgenomes.org) is a resource for comprehensive reconstructions of these ‘fossil genomes’. Comprehensive sets of protein-coding genes have been reconstructed for 78 genomes of now-extinct species...The Home Microbiome Project
By Abhimanyu Singh 4417 days agoThe Home Microbiome Project is an initiative aimed at uncovering the dynamic co-associations between people's bacteria and the bacteria found in their homes.The hope is that the data and project will show that routine monitoring of the microbial...GeneMates: an R package for Detecting Horizontal Gene Co-transfer between Bacteria Using Gene-gene...
By Rahul Nayak 2404 days agogithub.com - GeneMates is an R package implementing a network approach to identify horizontal gene co-transfer (HGcoT) between bacteria using whole-genome sequencing (WGS) data. It is particularly useful for investigating intra-species HGcoT, where...HiBC: Human Intestinal Bacteria Collection
By BioStar 517 days agoThe human gut is home to trillions of microorganisms, forming one of the most complex and dynamic microbial ecosystems known to science. The Human Intestinal Bacteria Collection (HiBC) is a pioneering initiative aimed at cataloging, preserving,...CLARK: Fast, accurate and versatile sequence classification system
By Jit 2425 days agoclark.cs.ucr.edu - CLARK, a method based on a supervised sequence classification using discriminative k-mers. Considering two distinct specific classification problems (see the article for details), namely (1) the taxonomic classification of metagenomic reads to...Public Databases for Bioinformatics !
By Jit 2023 days agomitra.stanford.edu - https://www.nature.com/articles/s41467-020-17155-yServer Infrastructure: File Server: dhara: Synology 3614 Storage Appliance 4 Core Xeon 108TB disk storage 10Gb ethernet to SCG3 Access atx: dhara:5000 Has btsync server (try it - its much...
