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Preprint on "BWT construction and search at the terabase scale". We can compress 100 human genomes to 11GB in 21 hours, find SMEMs with it, do affine-gap alignment and retrieve similar local haplotypes. 7.3Tb commonly sequenced bacterial genomes ⇒ 30GB arxiv.org/abs/2409.00613

Thrilled to have our study on microbiome changes in Asian octogenerians published recently! I tweeted previously about the key results (x.com/NiranjanTW/sta…) but not about the 3+ years of struggle under review ... here are some key lessons (1/4) nature.com/articles/s4146…

Strainy is finally out! It enables assembly of individual strains from ONT and Pacbio metagenomes. The secret ingredient is multi-allelic phasing algorithm that does not make assumptions about number and abundance of haplotypes. Unpaywalled link - rdcu.be/dVakX

Published in 2009, bwa-aln is one of the oldest short-read aligners. It remains a popular choice for aligning ancient DNA reads. The following blog post explains the algorithmic reasons. lh3.github.io/2024/09/28/why…

🚀 We're #Hiring #PhD students at MLBio Lab at EPFL through the EDIC Program! 📅 Deadline: Dec 15 Are you passionate about generative AI, unsupervised learning and solving problems in biomedicine? 🧬 Apply & mention your interest in your application. 💥 We're part of

Hifiasm 0.21.0 has been released. It now has a beta module for direct assembly of ONT R10 simplex reads. Initial tests with regular simplex reads show very promising results! github.com/chhylp123/hifi…

Ivona Martinović Bryan Hooi Selection of the best-predicted structures using Rosetta and ARES. The correlation between trRosettaRNA (trRNA) and Rosetta is not surprising, but look at Alfafold3 and ARES !! #ai #RNA #structure #prediction

Tech Alert! 🚀🧬 We can now determine the sequence of DNA with non-canonical bases in a direct and high-throughput manner with Nanopore sequencing. Check out our preprint for details: biorxiv.org/content/10.110…

A comparative approach that predicts any modifications in RNA (or DNA) using raw Oxford Nanopore signals. Although simple, It outperforms the current SOTA. academic.oup.com/nar/advance-ar… w/ Ivan Vujaklija Siniša Biđin, Marin Volarić, Sara Bakić, Zhe Li, Jianjun Liu and Roger Foo

Our hitchhiking paper is out at genomebiology.biomedcentral.com/articles/10.11… - a great collaborative effort with Prasadms Josipa Lipovac, FilipTomas13 JJ Liu. Briefly, Oxford Nanopore is enough for high-quality human genomes. Recently, HERRO showed that even UL is sufficient. 1/3

The paper explores more details about the coverages required. This project extends the work we began in 2016 - when we were among the first to demonstrate that nanopore can produce decent assembly academic.oup.com/bioinformatics… 2/3

So our paper is finally out! 🥳 Our findings aim to guide researchers on balancing cost, data, and quality in population-level human genome assembly projects. Check it here: rdcu.be/d36pr

miniprot-0.14 was released two weeks ago. It now supports chromosomes longer than 2Gb.

longcallD is a new variant caller for genomic long reads. It jointly calls phased small and structural variants. Single binary, one command line for the whole process. Comparable accuracy to mainstream callers. Great work by Yan Gao. github.com/yangao07/longc…

Looking for a Pi position in genomics , especilly for related to Ai or computational biology. Join us at the Genome Institute of Singapore. Great environment, abundance of data and stable funding!

wow, turns out even investors want Laravel for JS. We had to sprinkle a bit of AI story on top to make them buy it, but it worked 🤞 Joke aside, Martin Sosic and I are beyond excited to share this news. We still can't believe we get to build the next-generation full-stack web

Join our team - Mile Sikic, Lovro Vrček, Ivona Martinović, Tin Vlašić - at the AI for nucleic acids workshop happening next Monday 28 April at Singapore Expo. Check out: ai4na-workshop.github.io

GNNome was published in Genome Research! This is a novel paradigm for de novo genome assembly based on GNNs. Without explicitly implementing any simplification strategies, it can achieve results comparable or higher than other SOTA tools. Paper, code, and overview are 👇 [1/8]

Our publication in  Genome Research presents a new paradigm in genome de novo assembly - using AI instead of classical algorithms. Here, we replace the Layout phase with Graph Neural Networks

I am happy to share our new preprint introducing MADRe - a pipeline for Metagenomic Assembly-Driven Database Reduction, enabling accurate and computationally efficient strain-level metagenomic classification. Mile Sikic, Riccardo Vicedomini, Krešimir Križanović 🔗biorxiv.org/content/10.110… 1/9