Reposted by Sukhwan ParkbioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 19/09/2026BFVD v3-UniProt-complete, improved viral protein structure predictions www.biorxiv.org/content/10.64898/20… 092
Reposted by Sukhwan ParkKatharina Hoff @katharinahoff.bsky.social · 31/08/2026A revolution in annotating protein coding genes in eukaryotes: Richard Krieg, Joscha Diehl & @masta.bsky.social developed Vipsania, a genome foundation model with integrated HMM-layer: www.biorxiv.org/content/10.6... 🎉💐 So impressive work! Congratulations!biorxiv.org 11513
Reposted by Sukhwan ParkDongwook Kim @dongwookkim.bsky.social · 10/08/2026AmpliPhy is now reviewed and published in @bioinfoadv.bsky.social! AmpliPhy improves your gene trees by adding homologs with a single command, based on the observations from a quantitative benchmark design. More details in quoted 🧵 📄 doi.org/10.1093/bioadv/vbag222 💾 github.com/DessimozLab/ampliphydoi.orgAmpliPhy improves gene trees by adding homologous sequences without affecting alignmentsAbstractMotivation. In phylogenomics, gene tree reconstruction depends on multiple sequence alignment and tree inference, and ongoing work continues to imp 074
Reposted by Sukhwan ParkKieran Didi @kdidi.bsky.social · 01/08/2026Fast MSAs are coming to nucleic acids! Riboseek has been super helpful for some of my own work, very excited to see what people do with this cool new tool! Amazing collaboration as always with @milot.bsky.social @martinsteinegger.bsky.social and co, led by @sukhwanpark.bsky.social! 072
Reposted by Sukhwan ParkMartin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 01/08/2026Riboseek is a fast RNA/DNA search. More sensitive than nhmmer at 250x speed. Structure-aware realignment produces MSAs approaching rMSA quality. Plus 1.7M precomputed RNA MSAs, and an API to search your own 📄 www.biorxiv.org/content/10.6... 💾 github.com/steineggerla... 🌐 search.foldseek.com/riboseek 217975
Reposted by Sukhwan ParkDongwook Kim @dongwookkim.bsky.social · 03/06/2025Unicore is now published on GBE 🚀 Unicore rapidly identifies structural single-copy core genes from input species proteomes for phylogenetic analysis. Powered by Foldseek and ProstT5, Unicore enables linear-scale structure-based phylogeny of any given set of taxa. 🧵1/n 📃 doi.org/10.1093/gbe/evaf109 36831
Reposted by Sukhwan ParkbioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 23/12/2024Unicore enables scalable and accurate phylogenetic reconstruction with structural core genes www.biorxiv.org/content/10.1101/202… 053
Reposted by Sukhwan ParkMartin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 23/12/2024Unicore identifies single-copy protein structures across genomes using Foldseek, bypassing slow structure predictions by utilizing 3Di predictions from ProstT5, enabling rapid phylogenetic inference at the tree-of-life scale. 1/n 📄 www.biorxiv.org/content/10.1... 💾 github.com/steineggerla... 212256
Reposted by Sukhwan ParkKarolin Luger @nucleosomepolice.bsky.social · 14/12/2024this is now published y'all #giantvirus academic.oup.com/nar/advance-...academic.oup.comBFVD—a large repository of predicted viral protein structuresAbstract. The AlphaFold Protein Structure Database (AFDB) is the largest repository of accurately predicted structures with taxonomic labels. Despite provi 15613
Reposted by Sukhwan Parkrecombseq.bsky.social @recombseq.bsky.social · 11/12/2024🚨 Call for Papers: RECOMB-seq 2025 🚨 🗓️ Dates: April 24-25, 2025 📍 Location: Seoul, South Korea Key deadlines: 🔹 Abstract registration: Jan 24, 2025 🔹 Submission: Jan 31, 2025 More details: recomb-seq.github.io/papers/recomb-seq.github.ioCall for PapersRECOMB-seq is the RECOMB Satellite Conference on Biological Sequence Analysis 01215
Reposted by Sukhwan ParkWayne Maddison @waynemaddison.bsky.social · 06/12/2024A new method for trimming alignments in #phylogenomics — PhyIN. It identifies and trims regions with high phylogenetic discord. Able to trim well even on single loci — an advantage for gene tree/species tree studies. #evolbiol #phylogeny 🧪http://doi.org/10.7717/peerj.18504 Some backstory... 🧵doi.orgPhyIN: trimming alignments by phylogenetic incompatibilities among neighbouring sitesIn phylogenomics, regions of low alignment reliability and high noise are typically trimmed from multiple sequence alignments before they are used in phylogenetic inference. I introduce a new trimming... 513250
Reposted by Sukhwan ParkRob Patro @robp.bsky.social · 04/12/2024Very cool work from Yang Lu et al. demonstrating miscalibration of BLASTP’s E-values and generating well-calibrated values via a knockoff-based approach (cc @mikelove.bsky.social) - academic.oup.com/bioinformati...! More analyses could benefit from knockoff-based approaches.academic.oup.comA BLAST from the past: revisiting blastp’s E-valueAbstractMotivation. The Basic Local Alignment Search Tool, BLAST, is an indispensable tool for genomic research. BLAST established itself as the canonical 23722
Reposted by Sukhwan ParkMilot Mirdita @milot.bsky.social · 27/11/2024MMseqs2 Release 16 Highlights: GPU-accelerated search📄, ORF or new 6-frame translated search modes, contig taxonomy always keeps the longest ORF, bug fixes (reduced memory and higher sensitivity) and relicensed as MIT 📄 biorxiv.org/content/10.1... 💾 mmseqs.com and 🐍Bioconda 🖥️🧬🧶 011443
Reposted by Sukhwan ParkMartin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 28/11/2024Interested in bioinformatics method development for proteins, structures or metagenomic analysis? Please check out my lab’s starter pack! 🔗 go.bsky.app/VJhXcSs 35611
