I am hiring a postdoc (bioinformatician or computer scientist) or scientific programmer at GIS Singapore. Join us to develop a T2T haploid aware genome assembler based on Raven github.com/lbcb-sci/raven and AI. More on sikic-lab.github.io/Postdoctoral/. DM or email me

After many months, I'm proud to share our work on untangling genome assembly graphs with GNNs. Or, GNNome Assembly (sorry not sorry)🧬 Paper: arxiv.org/abs/2206.00668 Code/Data: github.com/lvrcek/GNNome-… with Xavier Bresson, T. Laurent, Martin Schmitz, and Mile Sikic. Read more in 🧵

We present de novo genome assembly, based on Layout phase trained using GNNs, which outperforms the classical approach (removal of transitive edges, bubble popping, tips, unitigs,...) arxiv.org/abs/2206.00668 w/ Lovro Vrček Xavier Bresson T. Laurent, and Martin Schmitz

Excited to present deep learning for genome assembly ! A new project at the intersection of genomics, graph neural networks and combinatorial optimization. Data, code, arxiv available below. My recent talk on this topic dropbox.com/s/evox8758tsit…

Long reads metagenome benchmark is out. Highlights. 1. In most cases Kraken, 2. minimap2/ram for slightly higher accuracy. 3. The right database is of huge importance 4. Check taxonomy files carefully. bmcbioinformatics.biomedcentral.com/articles/10.11… w/Niranjan Nagarajan Krešimir Križanović @jmaricb Sylvain

Happy to present an initial draft of a telomere-to-telomere diploid Indian genome. A joint effort of Jianjun Liu's and my lab spearheaded by Prasadms and Josipa Lipovac github.com/lbcb-sci/I002C or github.com/LHG-GG/I002C

Happy to present RiNALMO - our RNA large language model arxiv.org/abs/2403.00043 w/ Rafael Josip Penić Tin Vlasic Yue Wan and Roland Huber. RiNALMo is the largest RNA language model to date, with 650 million parameters pre-trained on 36 million non-coding RNA sequences. 1/2

Our new paper is out! We made a lot of progress on our GNN-based de novo genome assembly paradigm and here we present all our findings and progress 🧬🥳 Code: github.com/lbcb-sci/GNNome Paper: biorxiv.org/content/10.110… See details of GNNome below 👇🧵

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]