Scientific Computing and Data Management

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Benchmarking large-scale single-cell RNA-seq analysis
bioRxiv · 16 Oct 2026 · Preprint
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https://jclub.com.au/a/10.1101/2025.10.28.681564
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ddkg.skill: A Compositional Agent Skill for Translating Biomedical and Bioinformatics Questions into Cypher for the Data Distillery Knowledge Graph
bioRxiv · 7 Oct 2026 · Preprint
ddkg.skill enables accurate biomedical and bioinformatics queries on the NIH DDKG with 38 files and 239 routing relationships, achieving correct results in 5 of 7 tests.
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https://jclub.com.au/a/10.64898/2026.09.26.754400
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Democratizing protein language model training, sharing and collaboration.
Nature Biotechnology · 1 Oct 2026 · Journal Article
SaprotHub's ColabSaprot framework enables accessible training and sharing of large-scale protein language models via Google Colab.
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https://jclub.com.au/a/41136773
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Byte-exact, format-aware compression for FASTA, FASTQ, BED and VCF files
bioRxiv · 1 Oct 2026 · Preprint
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https://jclub.com.au/a/10.64898/2026.03.16.712193
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Reproducibility in biomedical research.
Nature Medicine · 1 Oct 2026 · Review
Reproducibility in biomedical research remains inconsistently implemented despite widespread awareness and policies, risking resource waste and patient safety.
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https://jclub.com.au/a/42811190
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The Vizitig pangenome and pantranscriptome explorer
bioRxiv · 30 Sept 2026 · Preprint
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https://jclub.com.au/a/10.1101/2025.04.19.649656
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Reimagining research papers as interactive and reliable AI agents.
Nature · 16 Sept 2026 · Journal Article
Paper2Agent converts research papers into interactive AI agents, enabling complex scientific queries and collaboration with over 80% accuracy in reproducing original results.
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https://jclub.com.au/a/42749808
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Apollo 3: Multi-Species Genome Curation
bioRxiv · 10 Sept 2026 · Preprint
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https://jclub.com.au/a/10.64898/2026.06.08.730970
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Challenges in the Computational Reproducibility of Linear Regression Analyses: An Empirical Study
medRxiv · 6 Sept 2026 · Preprint
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https://jclub.com.au/a/10.64898/2026.04.07.26350286
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In Search of Ethical Procedures for LLM-Assisted Systematic Review Production: A Proof-of-Concept Evaluation of Selected Review Components
medRxiv · 2 Sept 2026 · Preprint
LLMs can effectively assist in specific, well-defined tasks within systematic review processes, achieving up to 86.2% agreement with human decisions when criteria are carefully reworded.
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https://jclub.com.au/a/10.64898/2026.02.18.26346559
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Reproducibility in the era of large language models.
Nature Computational Science · 1 Sept 2026 · Editorial
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https://jclub.com.au/a/42773254
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The missing data for intelligent scientific instruments.
Nature Methods · 1 Sept 2026 · Journal Article
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https://jclub.com.au/a/41476115
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Benchmarking biomedical foundation models.
Nature Methods · 1 Sept 2026 · Review
Benchmarking foundation models in biomedicine reveals significant challenges in testing their limitations and evaluating their utility.
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https://jclub.com.au/a/42697996
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NeuroFLAME: A Scalable, Privacy-Preserving Federated Framework for Secure, Reproducible, and Multi-Site Neuroimaging Analysis
bioRxiv · 27 Aug 2026 · Preprint
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https://jclub.com.au/a/10.64898/2026.04.30.721881
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