A fully open access, peer-reviewed journal published jointly by Oxford University Press and the International Society for Computational Biology.
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🦠 Just published in Bioinformatics Advances: "Identification and characterization of bacterial repeat-in-toxin adhesins using long-read genome analysis"
Find it here: doi.org/10.1093/bioadv/vbag2…
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A long-read pipeline with MMseqs2 clustering, InterProScan, and AlphaFold3 modeling identified 35 RTX adhesin isoforms across 16 loci in seven bacterial pathogens. Ligand-binding domains include carbohydrate-binding modules and von Willebrand Factor A-like domains in mix-and-match arrangements.
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⚙️ LoRē, the in-house workflow orchestrator software used to run this pipeline, is available at doi.org/10.5281/zenodo.21615…
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📐 New in Bioinformatics Advances: "pykarambola: Minkowski tensor morphometry of 3D structures"
Read it here: doi.org/10.1093/bioadv/vbag2…
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pykarambola is a pure-Python reimplementation of C++ karambola, computing Minkowski tensors—rotation-aware descriptors of elongation, curvature, and topology—from NumPy arrays or 3D label images. It reproduces all 121 karambola features to near floating-point agreement and is up to 2.8x faster.
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🧰 pykarambola is available at github.com/Ishihara-SynthMor…
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🧫 New paper in Bioinformatics Advances: "CDS-BART: A BART-based foundation model for mRNA sequence analysis"
Find it at doi.org/10.1093/bioadv/vbag2…
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It was fine-tuned and evaluated across six mRNA property benchmarks covering protein expression, stability, and RNA degradation.
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💻 CDS-BART is available at github.com/mogam-ai/CDS-BART and archived at zenodo.org (DOI: 10.5281/zenodo.21502775).
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🍄 New paper in Bioinformatics Advances: "CentroFinder: A multi-feature framework for de novo prediction of fungal regional centromeres"
Read it here: doi.org/10.1093/bioadv/vbag2…
Authors include: @mostafarahnama
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CentroFinder integrates six long-read–derived features—TE density, tandem-repeat density, CpG methylation deviation, gene depletion, GC depletion, and read-depth anomaly—into a weighted scoring model to predict fungal regional centromeres. Benchmarked on three species, 27 of 28 predicted intervals overlapped experimentally mapped centromeres (96.4% sensitivity).
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🔬 New research in Bioinformatics Advances: "Central Dogma Transformer II: An AI microscope for understanding cellular regulatory mechanisms"
Read it here: doi.org/10.1093/bioadv/vbag2…
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On five held-out genes, it achieved per-gene mean r = 0.84, recovered the GFI1B regulatory network (6.6-fold enrichment), and concentrated cross-attention on ENCODE regulatory elements including CTCF sites.
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💻 Source code is available at github.com/nobusama/CDT2
Pre-computed embeddings, training data, and model weights are at huggingface.co/datasets/nobu…
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We lost a giant of our field this March and we are happy to be able to share this tribute: "Phil Bourne (1953–2026): From small molecules to big data—the journey of a multifaceted visionary".
Read the tribute here: doi.org/10.1093/bioadv/vbag2…
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He's remembered by colleagues for his generosity and humility, for believing knowledge should belong to everyone, and for treating everyone he met with the same openness.
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