Sukhwan Park
@sukhwanpark.bsky.social
Reposted by Sukhwan Park
Unicore 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
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
June 3, 2025 at 6:55 AM
Unicore 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
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
Reposted by Sukhwan Park
Unicore enables scalable and accurate phylogenetic reconstruction with structural core genes https://www.biorxiv.org/content/10.1101/2024.12.22.629535v1
December 23, 2024 at 3:51 AM
Unicore enables scalable and accurate phylogenetic reconstruction with structural core genes https://www.biorxiv.org/content/10.1101/2024.12.22.629535v1
Reposted by Sukhwan Park
Unicore 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...
📄 www.biorxiv.org/content/10.1...
💾 github.com/steineggerla...
December 23, 2024 at 4:39 PM
Unicore 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...
📄 www.biorxiv.org/content/10.1...
💾 github.com/steineggerla...
Reposted by Sukhwan Park
🚨 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/
🗓️ 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/
Call for Papers
RECOMB-seq is the RECOMB Satellite Conference on Biological Sequence Analysis
recomb-seq.github.io
December 11, 2024 at 11:18 AM
🚨 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/
🗓️ 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/
Reposted by Sukhwan Park
A 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... 🧵
PhyIN: trimming alignments by phylogenetic incompatibilities among neighbouring sites
In 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...
doi.org
December 6, 2024 at 12:56 AM
A 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... 🧵
Reposted by Sukhwan Park
Very 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.
A BLAST from the past: revisiting blastp’s E-value
AbstractMotivation. The Basic Local Alignment Search Tool, BLAST, is an indispensable tool for genomic research. BLAST established itself as the canonical
academic.oup.com
December 4, 2024 at 5:26 PM
Very 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.
Reposted by Sukhwan Park
MMseqs2 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 🖥️🧬🧶
📄 biorxiv.org/content/10.1...
💾 mmseqs.com and 🐍Bioconda 🖥️🧬🧶
November 27, 2024 at 9:08 AM
MMseqs2 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 🖥️🧬🧶
📄 biorxiv.org/content/10.1...
💾 mmseqs.com and 🐍Bioconda 🖥️🧬🧶
Reposted by Sukhwan Park
Interested in bioinformatics method development for proteins, structures or metagenomic analysis? Please check out my lab’s starter pack!
🔗 go.bsky.app/VJhXcSs
🔗 go.bsky.app/VJhXcSs
November 28, 2024 at 12:36 PM
Interested in bioinformatics method development for proteins, structures or metagenomic analysis? Please check out my lab’s starter pack!
🔗 go.bsky.app/VJhXcSs
🔗 go.bsky.app/VJhXcSs