Bioinformatics

Clinical evidence, research, and medical intelligence in Bioinformatics.

HiFiTaxa pipeline improves PacBio 16S and ITS taxonomic assignment

HiFiTaxa standardizes PacBio HiFi 16S and ITS analysis with versioned references and classifier choices, then benchmarks accuracy on mocks and holdouts.

By Dr. A. Nikhil Krishnan, MBBS · Nov 5, 2026 · 5 min read

Bioinformatics·bioRxiv

gcat and its_a_scam streamline single-cell QC beyond proprietary pipelines

Two open-source tools aim to replace proprietary single-cell workflows with modular processing, alignment-level QC, and count matrix generation.

Nov 5, 2026

Bioinformatics·bioRxiv

Hybrid ODE Mixture Models Map Disease Progression Trajectories

A new hybrid modeling framework links short-term physiology to long-term disease progression and outperforms neural methods in synthetic…

Nov 3, 2026

Bioinformatics·bioRxiv

AlphaFold 3 interaction confidence performs on par with BANDOCK+ in drug ranking

A preprint finds AlphaFold 3 interaction confidence can prioritize approved drugs across human proteins with disease ranking performance…

Oct 27, 2026

Bioinformatics·bioRxiv

MetaKG uses self-supervised learning to improve metabolite prediction

A metabolite-centric knowledge graph, MetaKG, outperformed existing models and surfaced new biochemical links in preclinical datasets.

Oct 27, 2026

Bioinformatics·bioRxiv

Single-Cell Perturbation Benchmarking Audit Exposes Calibration Flaws

An audit of single-cell perturbation benchmarks finds identity ceilings, split leakage, and context-dependent calibration failures across datasets and…

Oct 26, 2026

Bioinformatics·bioRxiv

DCAF framework improves single-cell perturbation simulation benchmarking

DCAF proposes a unified framework for single-cell perturbation simulation, aligning data validity, evaluation validity, and predictive modeling across…

Oct 26, 2026

Bioinformatics·bioRxiv

Genetic perturbation prediction models falter under OOD benchmark

EL-PERTURB benchmark finds 20 genetic perturbation models lose accuracy out of distribution, with complex embeddings offering no clear…

Oct 26, 2026

Bioinformatics·bioRxiv

RiboGRAM maps non-coding RNA grammar for structure and regulation

RiboGRAM identifies multi-scale non-coding RNA grammar, improving structure and binding inference across species, RNA families, and cell types.

Oct 25, 2026

Bioinformatics·bioRxiv

CAPO automates protein-model tuning with compute-aware gating

CAPO adds compute-aware gating to protein-model adaptation, reducing wasted GPU time while improving task-specific performance across three benchmarks.

Oct 24, 2026

Bioinformatics

Clinical evidence, research, and medical intelligence in Bioinformatics.

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Rapid guidance broadens empiric antibiotics for suspected sepsis.