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Bioinformatics Advances @bioinfoadv.bsky.social · 15h

🤖 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

🎯 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

🌡️ 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

🦠 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

📐 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

🧫 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

🍄 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

🔬 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

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/vbag239

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

🧬 New paper in Bioinformatics Advances: "Loopcity: An R package for the detection of chromatin loop communities from Hi-C data" Read it here: doi.org/10.1093/bioadv/vbag269 Authors include: @jpflores.rbind.io

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Bioinformatics Advances @bioinfoadv.bsky.social · 17/09/2026

🦠 Just published in Bioinformatics Advances: "ClinIAN: Clinically Informed Attention Network” Access it here: doi.org/10.1093/bioadv/vbag254

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Bioinformatics Advances @bioinfoadv.bsky.social · 17/09/2026

🗺️ New paper in Bioinformatics Advances: "ScGeo reveals non-canonical trajectories beyond RNA velocity in radiation-induced hematopoietic recovery" Read it here: doi.org/10.1093/bioadv/vbag266

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Bioinformatics Advances @bioinfoadv.bsky.social · 16/09/2026

🔬 New research in Bioinformatics Advances: "A little longer, a lot better: Simulation-guided exploration of extended-length single-end barcoded reads for structural variant detection" Read it here: doi.org/10.1093/bioadv/vbag267

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Bioinformatics Advances @bioinfoadv.bsky.social · 16/09/2026

🧬 New paper in Bioinformatics Advances: "MosaicLev: Modified Levenshtein distance for mobile element-aware genome comparison" Read it here: doi.org/10.1093/bioadv/vbag261

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Bioinformatics Advances @bioinfoadv.bsky.social · 15/09/2026

🧬 New study in Bioinformatics Advances: "Theoretical estimates on the expected number of mutations needed to reconstruct clonal lineage trees" Find it at doi.org/10.1093/bioadv/vbag264

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Bioinformatics Advances @bioinfoadv.bsky.social · 15/09/2026

☁️ New paper in Bioinformatics Advances: "Fedflow: Cloud orchestration for federated learning with the FeatureCloud platform" See it here: doi.org/10.1093/bioadv/vbag255 Authors include: @janbaumbach

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Bioinformatics Advances @bioinfoadv.bsky.social · 14/09/2026

🔬 Latest research in Bioinformatics Advances: "SHISMA: SHape-driven Inference of significant celltype-specific Subnetworks from tiMe series single-cell trAnscriptomics" Read it here: doi.org/10.1093/bioadv/vbag258

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Bioinformatics Advances @bioinfoadv.bsky.social · 14/09/2026

🧪 New paper in Bioinformatics Advances: "EnzymeSifter: A tool for discovery of industrial enzymes from metagenomes" Available at: doi.org/10.1093/bioadv/vbag262 Authors include: @mattbashton.bsky.social

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Bioinformatics Advances @bioinfoadv.bsky.social · 11/09/2026

🦠 New study in Bioinformatics Advances: "MultiVirusConsensus: An accurate and efficient open-source pipeline for identification and consensus sequence generation of multiple viruses from mixed samples" Read more: doi.org/10.1093/bioadv/vbag256 Authors include: @niema.net

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Bioinformatics Advances @bioinfoadv.bsky.social · 11/09/2026

🧬 New research in Bioinformatics Advances: "annoreport: An interactive tool for metagenome annotation" Read it here: doi.org/10.1093/bioadv/vbag257

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Bioinformatics Advances @bioinfoadv.bsky.social · 10/09/2026

⏱️ Just published in Bioinformatics Advances: "MeTime: An R package for reproducible longitudinal metabolomics data analysis" See it here: doi.org/10.1093/bioadv/vbag252

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Bioinformatics Advances @bioinfoadv.bsky.social · 10/09/2026

🧬 Recently published in Bioinformatics Advances: "Derivation of oligonucleotide barcodes that are absent from natural sequences" Explore the paper: doi.org/10.1093/bioadv/vbag251

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

📚 New paper in Bioinformatics Advances: "QPL-enabled HTSlib library: Accelerating sequence file compression using Intel IAA" Read more: doi.org/10.1093/bioadv/vbag250 Authors include: @niema.net

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

🗺️ New in Bioinformatics Advances: "A FAIR gold-standard benchmark for geographic entity recognition in cancer genomics literature for biomedical NLP" Access it here: doi.org/10.1093/bioadv/vbag225

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Bioinformatics Advances @bioinfoadv.bsky.social · 08/09/2026

📊 Latest research in Bioinformatics Advances: "Leveraging uncertainty estimates for drug response prediction in cancer cell lines" Find it here: doi.org/10.1093/bioadv/vbag246 Authors include: @pascivers.bsky.social

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Bioinformatics Advances @bioinfoadv.bsky.social · 08/09/2026

🔬 New in Bioinformatics Advances: "GRIDGENE: Guided Region Identification based on density of GENEs – a transcript density-based approach to characterize tissues by spatial transcriptomics" Explore the paper: doi.org/10.1093/bioadv/vbag249 Authors include: @nfdemiranda.bsky.social

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Bioinformatics Advances @bioinfoadv.bsky.social · 04/09/2026

📊 New in Bioinformatics Advances: "survkl: An R package for transfer-learning-based integrated Cox models" See it here: doi.org/10.1093/bioadv/vbag234

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Bioinformatics Advances @bioinfoadv.bsky.social · 04/09/2026

🔭 Recently published in Bioinformatics Advances: "Pseudotime-conditioned diffusion models for imputing time-series single-cell data" Read more: doi.org/10.1093/bioadv/vbag248

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Bioinformatics Advances @bioinfoadv.bsky.social · 03/09/2026

🔬 New paper in Bioinformatics Advances: "NeuraGraph: A visual workflow framework for reproducible biomedical text mining with LLM-agents" Available at: doi.org/10.1093/bioadv/vbag240

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Bioinformatics Advances @bioinfoadv.bsky.social · 03/09/2026

⚗️ New research in Bioinformatics Advances: "GlycoTraitR: An R package for characterizing structural heterogeneity in N-linked glycoproteomics data" Read it here: doi.org/10.1093/bioadv/vbag244

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Reposted by Bioinformatics Advances

Sofia Kirke Forslund-Startceva @inanna-nalytica.bsky.social · 01/09/2026

Happy to see this out, thanks to extensive development, benchmarking and perseverance step after step by @mrollivander.bsky.social ! We've used versions of this tech for several years and now can offer it more easily to others along with concrete data on the advantages offered.

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Bioinformatics Advances @bioinfoadv.bsky.social · 02/09/2026

🦠 Just published in Bioinformatics Advances: "ViTax-RAG: A retrieval-augmented language modeling tool for viral contig taxonomic classification" Read more: doi.org/10.1093/bioadv/vbag247

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Bioinformatics Advances @bioinfoadv.bsky.social · 02/09/2026

📈 New paper in Bioinformatics Advances: "BiDRA: Bayesian inference as a robust alternative to non-linear regression for dose-response efficiency metrics assessment" Explore the paper: doi.org/10.1093/bioadv/vbag245 Authors include: @bhaibeka.bsky.social

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Bioinformatics Advances @bioinfoadv.bsky.social · 01/09/2026

🔬 Latest research in Bioinformatics Advances: "metadeconfoundR: Covariate analysis of high-dimensional cross-sectional omics data" See it here: doi.org/10.1093/bioadv/vbag242 Authors include: @mrollivander.bsky.social, @vhjarquind.bsky.social, @inanna-nalytica.bsky.social

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Bioinformatics Advances @bioinfoadv.bsky.social · 01/09/2026

💊 Recently published in Bioinformatics Advances: "ZSCAN-DDIE: An interpretable zero-shot learning method for the prediction of drug-drug interaction events using biomedical text". Access it here: doi.org/10.1093/bioadv/vbag243

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Bioinformatics Advances @bioinfoadv.bsky.social · 31/08/2026

🧩 New research in Bioinformatics Advances: "AINR: Attention-guided Implicit Neural Representations for spatial domain identification in spatial transcriptomics" Find the full paper at: doi.org/10.1093/bioadv/vbag241

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Bioinformatics Advances @bioinfoadv.bsky.social · 31/08/2026

📈 New in Bioinformatics Advances: "pared: Model selection using multi-objective optimization" Read it here: doi.org/10.1093/bioadv/vbag211

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Bioinformatics Advances @bioinfoadv.bsky.social · 28/08/2026

🔬 Latest research in Bioinformatics Advances: "Inductive bias influences the spatial scale of biological features learned from images" Read more: doi.org/10.1093/bioadv/vbag238

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Bioinformatics Advances @bioinfoadv.bsky.social · 27/08/2026

🦠 Recently published in Bioinformatics Advances: "DeepVIC: Modular prediction and classification of bacterial virulence factors using protein language model embeddings" Explore the paper: doi.org/10.1093/bioadv/vbag237

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Bioinformatics Advances @bioinfoadv.bsky.social · 26/08/2026

🔎 New paper in Bioinformatics Advances: "Interpretable prediction of nucleic acid-binding proteins using a protein language model" See it here: doi.org/10.1093/bioadv/vbag235

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Bioinformatics Advances @bioinfoadv.bsky.social · 25/08/2026

🔬 New research in Bioinformatics Advances: "T-SMmOTE: Tweaked Synthetic Majority minority Oversampling Technique for data scarcity issue in multi omics studies" Access it here: doi.org/10.1093/bioadv/vbag236

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Bioinformatics Advances @bioinfoadv.bsky.social · 24/08/2026

🧬 Recently published in Bioinformatics Advances: "Spatially varying gene regulation network inference from spatial transcriptomics" Find it here: doi.org/10.1093/bioadv/vbag230 Authors include: @haohanwang.bsky.social

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Bioinformatics Advances @bioinfoadv.bsky.social · 21/08/2026

🌽 New in Bioinformatics Advances: "MaizeGDB Phylostrata Tool: Exploring evolutionary origins of maize proteins" Read it here: doi.org/10.1093/bioadv/vbag216

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Bioinformatics Advances @bioinfoadv.bsky.social · 21/08/2026

🦠 New paper in Bioinformatics Advances: "microbiONT: An AI-assisted, privacy-focused platform for local Nanopore 16S and 18S amplicon analysis" Available at: doi.org/10.1093/bioadv/vbag229

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Bioinformatics Advances @bioinfoadv.bsky.social · 20/08/2026

🧬 New study in Bioinformatics Advances: "MAJA: Multivariate Bayesian model for discovery of shared epigenetic pathways across human phenotypes" Read it here: doi.org/10.1093/bioadv/vbag231

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Bioinformatics Advances @bioinfoadv.bsky.social · 20/08/2026

🔬 Latest research in Bioinformatics Advances: "Benchmarking antibody modeling tools across structure prediction, docking, and paratope–epitope interface analysis" Available at: doi.org/10.1093/bioadv/vbag223

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Bioinformatics Advances @bioinfoadv.bsky.social · 19/08/2026

⏱️ New paper in Bioinformatics Advances: "TimeTraits: Extracting functional traits from biological time-series in R" Find it here: doi.org/10.1093/bioadv/vbag226

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Bioinformatics Advances @bioinfoadv.bsky.social · 19/08/2026

🌐 Recently published in Bioinformatics Advances: "Usage and impact of global biodata resources" Read it here: doi.org/10.1093/bioadv/vbag219

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Bioinformatics Advances @bioinfoadv.bsky.social · 18/08/2026

🧪 New research in Bioinformatics Advances: "tidyexposomics: Integrated exposure-omics analysis powered by tidy principles" Available at: doi.org/10.1093/bioadv/vbag220

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Bioinformatics Advances @bioinfoadv.bsky.social · 18/08/2026

🌿 Just published in Bioinformatics Advances: "AmpliPhy improves gene trees by adding homologous sequences without affecting alignments" Find it here: doi.org/10.1093/bioadv/vbag222 Authors include: @dongwookkim.bsky.social, @dessimoz.bsky.social

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