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• • Neel@neelam

  

  Neel bookmarked BakRep (Denglish blend of Bakterien & Repository) simplifies access to this data 205 days ago

  2,438,386 bacterial genomes at your fingertips consistently processed & characterized, enriched with metadata, accessible via a flexible search engine. BakRep (Denglish blend of Bakterien & Repository) simplifies access to this data. It...

  https://bakrep.computational.bio/
• • Neel@neelam

  

  Neel published a blog post 10 Books to Kickstart (and Level Up) Your Bioinformatics Journey 206 days ago

  If you’re starting out in bioinformatics or looking to sharpen your computational biology skills, having the right learning resources makes all the difference. Here’s my curated list of 10 must-read books — from beginner-friendly introductions to...
• • Abhi@abhinav

  

  Abhi published a blog post SNP Analysis: Unlocking the Secrets in Our DNA 233 days ago

  Single Nucleotide Polymorphisms (SNPs) are the most common type of genetic variation in humans—and many other organisms. A single base change in the DNA sequence (for example, an A instead of a G) can influence everything from our eye color to...
• • Abhi@abhinav

  

  Abhi published a blog post P-Value, FDR, q-score: What Do They Mean? A Simple Guide with Example 252 days ago

  In statistics and bioinformatics, you’ll often see results reported with p-values, FDR, and q-values (q-scores). But what do these terms mean, and how are they different? Let’s break them down with simple definitions and a step-by-step example.
• • Abhi@abhinav

  

  Abhi posted to the wire 257 days ago

  Convert #GFF2BED (base) [b@hn1 DUMP]$ awk 'BEGIN {OFS = "\t"};$3=="gene"{print $1,$4-1,$5}' genomic.gff > genes.bed
• • Abhi@abhinav

  

  Abhi published a blog post What is Data Science? — A Bioinformatics Perspective 263 days ago

  In today’s era of big biology, we’re generating more data than ever before—genomes, transcriptomes, proteomes, metabolomes, microbiomes… you name it. But raw biological data doesn’t speak for itself. Making sense of it requires more than...
• • LEGE@lege

  

  LEGE published a blog post Trust But Verify: Sequencing Your Cell Lines Might Reveal an Uninvited Guest 275 days ago

  High-throughput sequencing has become indispensable in cell biology, enabling detailed insights into chromatin structure, gene expression, and regulatory dynamics. Yet, when faced with unexpectedly low mapping rates to the human genome,...
• • LEGE@lege

  

  LEGE published a fun post A Bioinformatician’s Lament 281 days ago

  "I have a presentation tomorrow," they say, With hopeful eyes, like it’s all child's play. As if results bloom overnight, full-grown— Not wrangled from chaos, and error-prone.
• • LEGE@lege

  

  LEGE published a blog post Basics of DESeq2: Differential Expression Made Simple 281 days ago

  DESeq2 is a powerful and widely-used R package that identifies differentially expressed genes (DEGs) from RNA-seq data. Whether you're comparing treated vs untreated samples, disease vs healthy conditions, or wild-type vs mutant strains, DESeq2...
• • LEGE@lege

  

  LEGE published a blog post Magic Wormhole: The Easiest Way to Send Files Securely 281 days ago

  In a world increasingly dependent on digital data exchange, secure and user-friendly file transfer solutions are more important than ever. Enter Magic Wormhole, a deceptively simple yet powerful tool that makes it trivial to send files and...
• • LEGE@lege

  

  LEGE published a blog post Unlocking Evolutionary Secrets: A Dive into Comparative Genomics Methods 290 days ago

  Comparative genomics is the art and science of comparing genomes—across species, within species, or even among individuals—to unravel evolutionary relationships, functional elements, and genetic adaptations. As sequencing technologies have...
• • BioStar@biostar

  

  BioStar published a blog post HiBC: Human Intestinal Bacteria Collection 303 days ago

  The 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,...
• • BioStar@biostar

  

  BioStar published a blog post Kallisto vs Salmon: Choosing the Right Tool for RNA-Seq Quantification 307 days ago

  In the world of transcriptomics, quantifying gene and transcript expression accurately and efficiently is crucial. With the explosion of RNA-Seq data, researchers have turned to fast, alignment-free tools that streamline the quantification process...
• • BioStar@biostar

  

  BioStar published a blog post When Chromosomes Shift: Understanding Chromosome Rearrangement and Human Disease 329 days ago

  In the vast and complex world of genetics, our chromosomes are like carefully arranged bookshelves — each holding critical information that defines who we are. But what happens when those books are shuffled, inverted, or swapped? The answer lies...
• • LEGE@lege

  

  LEGE published a blog post Genomic architecture surrounding the fusion site of human chromosome 2 366 days ago

  This fusion event is a key evolutionary marker distinguishing humans from other great apes, as humans have 46 chromosomes while chimpanzees, gorillas, and orangutans possess 48. The fusion occurred through an end-to-end joining of two ancestral...
• • LEGE@lege

  

  LEGE published a blog post Genetic basis of tail-loss evolution 366 days ago

  The study suggests that a specific genetic mutation, involving the insertion of an Alu element (a type of transposable DNA sequence), played a critical role in the evolutionary transition from tailed primates to tailless hominoids.
• • BioStar@biostar

  

  BioStar published a blog post NVIDIA and Arc Institute Unveil Evo 2: A Breakthrough AI for DNA Design 377 days ago

  NVIDIA and the Arc Institute have introduced Evo 2, a groundbreaking AI model designed to understand, predict, and generate DNA sequences. This marks a major advancement in computational biology, offering scientists an unprecedented tool to decode...
• • LEGE@lege

  

  LEGE bookmarked TRITEX, a computational pipeline for chromosome-scale assembly of plant genomes 384 days ago

  This is the documentation of TRITEX, a computational pipeline for chromosome-scale assembly of plant genomes. It was developed in the research group Domestication Genomics at the Leibniz Institute of Plant Genetics and Crop Research (IPK)...

  https://tritexassembly.bitbucket.io/
• • BioStar@biostar

  

  BioStar published a blog post Genome Simulation with SLiM and msprime 398 days ago

  SLiM 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...
• • BioStar@biostar

  

  BioStar published a blog post Stay Connected and Productive: Unlock the Power of Screen, Tmux, and Mosh for Bioinformatics 408 days ago

  If you are a bioinformatician, chances are you have spent hours running long, complex analyses on remote servers only to lose your session because of an unstable connection. Frustrating, isnt it? Fear not! With tools like screen, tmux, and mosh,...

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