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Bioinformatics Advances @bioinfoadv.bsky.social · 2h

In A549 lung carcinoma cells, it identified known and candidate novel RBPs enriched for RNA-binding functions.

Bioinformatics Advances @bioinfoadv.bsky.social · 2h

OOPSIE normalizes peptide-level OOPS proteomics data against glycoproteins, a cross-link-independent reference, then flags differential RNA-binding occupancy using robust regression with abundance-dependent prediction intervals.

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Bioinformatics Advances @bioinfoadv.bsky.social · 2h

🧪 New in Bioinformatics Advances: "OOPSIE (OOPS Informatics Extension)" Read it here: doi.org/10.1093/bioadv/vbag278

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Bioinformatics Advances @bioinfoadv.bsky.social · 05/10/2026

Across 39 verified datasets the pipeline reached 99.65% precision and 93.75% recall (F1 96.17%).

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Bioinformatics Advances @bioinfoadv.bsky.social · 05/10/2026

The workflow runs Gemini 3 Pro through a two-step pipeline: scanning articles for dataset deposits, then extracting structured metadata from curated repository landing pages. Human reviewers accept, edit, or delete each suggestion in the fredato system.

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Bioinformatics Advances @bioinfoadv.bsky.social · 05/10/2026

🏷️ New paper in Bioinformatics Advances: "Accelerating metadata annotation in collaborative research centers: A hybrid AI workflow for biomedical entities" Find it here: doi.org/10.1093/bioadv/vbag283

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Bioinformatics Advances @bioinfoadv.bsky.social · 02/10/2026

On a 10-million-variant benchmark, it ran 5.5x faster than CMplot for linear plots and completed three-track circular Manhattan plots in 81 seconds versus 323 seconds for CMplot's multi-track mode.

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Bioinformatics Advances @bioinfoadv.bsky.social · 02/10/2026

pycmplot generates multi-track Circos-style circular and linear Manhattan plots in Python, using density-aware sub-sampling to cut memory and runtime.

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Bioinformatics Advances @bioinfoadv.bsky.social · 02/10/2026

📊 Latest research in Bioinformatics Advances: "pycmplot: Fast, low-memory multi-track circular and linear Manhattan plotting in Python" See it here: doi.org/10.1093/bioadv/vbag281 Authors include: @cesarforteslima.bsky.social

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Bioinformatics Advances @bioinfoadv.bsky.social · 01/10/2026

🧬 Enrichment analysis confirmed mutations cluster non-randomly near functional sites (q < 0.05), with protein-protein interfaces showing the strongest signal. Bacterial blight resistance was the most common associated trait, linked to 37 of the 102 mutations.

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Bioinformatics Advances @bioinfoadv.bsky.social · 01/10/2026

Thirty-nine mutations fell within 5 Å of predicted functional sites, including protein-protein interfaces, ligand-binding, and allosteric sites, and six were predicted to enhance binding affinity with partner proteins.

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Bioinformatics Advances @bioinfoadv.bsky.social · 01/10/2026

This study maps 102 GWAS-linked stress mutations onto 76 high-quality AlphaFold/TED-derived rice protein domains to assess structural and functional impact.

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Bioinformatics Advances @bioinfoadv.bsky.social · 01/10/2026

🌾 New study in Bioinformatics Advances: "Employing AlphaFold and TED to explore the structural impacts of stress-associated mutations in rice" Read it here: doi.org/10.1093/bioadv/vbag275

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Bioinformatics Advances @bioinfoadv.bsky.social · 30/09/2026

In testing by 25 users across 157 prompts, the system scored highest on summarization tasks, and longer response times correlated with lower perceived quality.

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Bioinformatics Advances @bioinfoadv.bsky.social · 30/09/2026

Llemy is an agentic LLM system that pulls elements, reactions, and annotations from the MINERVA API to answer natural-language queries about pathway diagrams with literature references.

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Bioinformatics Advances @bioinfoadv.bsky.social · 30/09/2026

🤖 New research in Bioinformatics Advances: "User-driven development and evaluation of an agentic framework for analysis of large pathway diagrams" Explore the paper: doi.org/10.1093/bioadv/vbag277 Authors include: @egonw.mastodon.social.ap.brid.gy

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Bioinformatics Advances @bioinfoadv.bsky.social · 29/09/2026

Lab-validated qPCR assays for Mpox, SARS-CoV-2, M. tuberculosis, and C. albicans matched or exceeded CDC reference assay sensitivity.

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Bioinformatics Advances @bioinfoadv.bsky.social · 29/09/2026

TAPPR uses alignment-free k-mer set operations to find conserved marker regions across genome-scale datasets, bypassing the alignment bottleneck of traditional primer design tools.

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Bioinformatics Advances @bioinfoadv.bsky.social · 29/09/2026

🎯 New study in Bioinformatics Advances: "TAPPR PCR assay design — Targeted, Automated, Primer and Probe Retrieval for scalable molecular assay design" Explore the paper: doi.org/10.1093/bioadv/vbag274

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Bioinformatics Advances @bioinfoadv.bsky.social · 28/09/2026

RBApy 3.0 now models eukaryotic cell architecture, including organelle compartmentalization and multi-organelle protein localization. Applied to Arabidopsis thaliana and Escherichia coli, models accurately predicted growth across 10–46°C against published data.

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Bioinformatics Advances @bioinfoadv.bsky.social · 28/09/2026

🌡️ Just published in Bioinformatics Advances: "RBApy: Extending resource allocation modeling to eukaryotes in complex environments" Find it here: doi.org/10.1093/bioadv/vbag276

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Bioinformatics Advances @bioinfoadv.bsky.social · 25/09/2026

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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Bioinformatics Advances @bioinfoadv.bsky.social · 25/09/2026

🦠 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/vbag272 Authors include: @guo-lab.bsky.social

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Bioinformatics Advances @bioinfoadv.bsky.social · 24/09/2026

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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Bioinformatics Advances @bioinfoadv.bsky.social · 24/09/2026

📐 New in Bioinformatics Advances: "pykarambola: Minkowski tensor morphometry of 3D structures" Read it here: doi.org/10.1093/bioadv/vbag273 Authors include: @ishiharaksk.bsky.social

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Bioinformatics Advances @bioinfoadv.bsky.social · 23/09/2026

It was fine-tuned and evaluated across six mRNA property benchmarks covering protein expression, stability, and RNA degradation.

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Bioinformatics Advances @bioinfoadv.bsky.social · 23/09/2026

CDS-BART combines SentencePiece BPE tokenization with BART's denoising seq2seq architecture, pre-trained on 60 million CDSs from nine NCBI RefSeq taxonomic groups to handle sequences up to ~4 kb.

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Bioinformatics Advances @bioinfoadv.bsky.social · 23/09/2026

🧫 New paper in Bioinformatics Advances: "CDS-BART: A BART-based foundation model for mRNA sequence analysis" Find it at doi.org/10.1093/bioadv/vbag259

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Bioinformatics Advances @bioinfoadv.bsky.social · 22/09/2026

Benchmarked on three species, 27 of 28 predicted intervals overlapped experimentally mapped centromeres (96.4% sensitivity).

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Bioinformatics Advances @bioinfoadv.bsky.social · 22/09/2026

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.

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Bioinformatics Advances @bioinfoadv.bsky.social · 22/09/2026

🍄 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/vbag270

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Bioinformatics Advances @bioinfoadv.bsky.social · 21/09/2026

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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Bioinformatics Advances @bioinfoadv.bsky.social · 21/09/2026

CDT-II mirrors the central dogma with DNA self-attention, RNA self-attention, and DNA-to-RNA cross-attention, trained on K562 CRISPRi data to predict perturbation effects.

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Bioinformatics Advances @bioinfoadv.bsky.social · 21/09/2026

🔬 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/vbag268

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Bioinformatics Advances @bioinfoadv.bsky.social · 18/09/2026

Thank you for tagging your co-author! We were unable to find them when searching!

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Bioinformatics Advances @bioinfoadv.bsky.social · 18/09/2026

His influence endures through the databases, journals, and open-science movements he built, and through the countless scientists he mentored along the way.

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Bioinformatics Advances @bioinfoadv.bsky.social · 18/09/2026

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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Bioinformatics Advances @bioinfoadv.bsky.social · 18/09/2026

...and championed the FAIR principles that now underpin open science. As founding dean, he built UVA's School of Data Science from the ground up.

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Bioinformatics Advances @bioinfoadv.bsky.social · 18/09/2026

Phil Bourne was a prolific member of the bioinformatics community. He helped build the Protein Data Bank into structural biology's global archive, co-founded PLOS Computational Biology—starting the “Ten Simple Rules” series—and FORCE11 (cont'd)

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