benchmark study

Bioprocess Modeling Made Easy With Hybrax

Hybrax simplifies hybrid bioprocess modeling by providing a framework that automates model setup and data handling, enabling reproducible and reusable models.

GLESKit: an MCP-based system for gene-level biomedical investigation and evidence synthesis

GLESKit is a gene-centered system that synthesizes biomedical evidence by integrating multiple data types, achieving high report quality and performance in benchmark tasks.

Salmonid science on the move: Twenty years of research through the lens of early career researchers

This review analyzes 20 years of salmonid research through early-career researchers' contributions, identifying trends, gaps, and future directions in the field.

Beyond Delta Masses: MS Andrea Directly Resolves Combinatorial Peptide Modifications in Open Searches

MS Andrea, a tag-filtered open search engine, scores and localizes up to four Unimod modifications per peptide-spectrum match, with identification counts competitive with MSFragger and Sage.

Beyond Better Models: Barriers and a Path Forward in Generalisable TCR Antigen Specificity Prediction

This paper identifies barriers to generalisable TCR:pMHC prediction and proposes solutions through data analysis, evaluation setup, and metric alignment.

vardictcpp: A C++ reimplementation of VarDict variant caller

An AI-assisted C++17 port of VarDictJava gives byte-identical calls on five exome samples while running 3.7-4.8 times faster on one core and needing 8-17 times less memory.

Reliable and Efficient Agentic Protein Design with Toolset Harnessing

Chaperone, a DataFrame-based framework and agent harness for protein design tools, cut tokens 86% and GPU-hours 64% while raising pass rate from 6% to 12%.

PeakLocus: A transcript-aware toolkit for RNA-Centric Genomic Annotation

PeakLocus assigns RNA features to transcript intervals with high accuracy, outperforming existing tools in benchmark tests across multiple species.

MetAR: A semi-automated meta-analysis of skeletal muscle androgen receptors association with age

This study uses a novel R-based pipeline, MetAR, to analyze RNA-seq datasets and finds that androgen receptor expression declines with age in human skeletal muscle.

A Framework for Comparing Mouse Neoantigen Immunogenicity

Experimental pMHC melting-temperature stability ranked in vivo CD8+ T cell responses of 25 mouse neoantigens better than affinity assays or nine in silico predictors.

'broadSeq', a benchmarking tool to contrast differential gene expression methods and identify when genomic neighbourhood matters

broadSeq benchmarks differential gene expression methods and shows DELocal identifies distinct genes by considering genomic neighbourhood, particularly for highly expressed genes.

MtbAIM: AI/ML-guided endpoint-specific prediction of small-molecule activity across drug-susceptible and drug-resistant Mycobacterium tuberculosis

Tree models on RDKit/Morgan features predict M.tb activity and MIC endpoints for drug-susceptible and resistant isolates, slightly beating pretrained embeddings; released as a Colab tool.

TurbOmics: a web-based platform for the analysis of metabolomics data using a multi-omics integrative approach

TurbOmics is a web-based platform that enables multi-omics integration of metabolomics, proteomics, and transcriptomics data, addressing limitations in metabolomics annotation and accessibility.

Illuminating dark genes and dark metabolites: calibrated functional association across kingdoms with autoencoders and correlation

VaLPAS pairs a bi-directional autoencoder with correlation for omics guilt-by-association with calibrated confidence; in L. starkeyi its autoencoder linked 176 unidentified metabolites to known-function proteins at ≥50% confidence.

SpatialOmicsLab: an integrated research environment for AI co-scientists in spatial transcriptomics

SpatialOmicsLab provides an integrated environment with AI tools for spatial transcriptomics analysis, outperforming expert workflows in multiple tasks.

Joint protein, mRNA and DNA sequence design and optimization with nucleotide-level Potts models

A structure-conditioned nucleotide-level Potts model designs protein and coding sequences jointly, enabling tRNA adaptation and RNA motif embedding beyond synonymous codons with designability comparable to Caliby.

Accurate ab initio gene prediction in eukaryotes with Tiberius in multiple clades

Extended Tiberius models outscore Helixer and ANNEVO on all 33 genomes from the five clades all three tools cover, and approach BRAKER3 accuracy in four clades without extrinsic evidence.

Predicted Effector Gene Aggregation, Standards and Unified Schema (PEGASUS): A Community Framework for Effector Gene Reporting

PEGASUS defines a community reporting standard for GWAS predicted effector genes: a metadata record, a full locus-by-gene evidence matrix, and a derived author-prioritised gene list.

GROMTools: scalable individual-level GReX imputation for mega-biobank-scale cohorts

GROMTools, a sparse-weight C++/R engine streaming PLINK2 genotypes, reproduces PrediXcan and PLINK2 GReX imputations with about 100-fold less CPU time and 33-fold less peak memory.

PEtab Select: specification standard and supporting software for automated model selection

PEtab Select provides a standardized format and software for automated model selection in systems biology, supporting diverse modeling frameworks and enabling efficient evaluation of large model spaces.

vep-rs: high-throughput Rust variant annotation with population-scale concordance to Ensembl VEP

vep-rs is a Rust reimplementation of Ensembl VEP with high concordance and significantly improved throughput for variant annotation.

PanVasc Research for AI assisted evidence analysis in panvascular intervention

The paper evaluates an AI framework for evidence analysis in panvascular intervention using clinical trial data and NLI4CT tasks, showing improved accuracy with checklist prompts over generic ones.

AnnoAudit: a marker-based protocol for auditing single-cell atlas annotations reveals systematic, state-dependent annotation failure in a widely used traumatic brain injury resource

A marker audit finds 97.9% of CEREBRI's 45,051 official 'glutamatergic neuron' cells are not glutamatergic (four-check composite 82.6%), creating false ion-channel and OXPHOS signals; true neurons show acute KCNC3 up-regulation.

Accessing Enzyme Kinetic Data and Prediction Methods at Scale

OpenKinetics Predictor unifies thirteen enzyme kinetic predictors behind one interface and API; on E. coli iML1515, eight kcat predictors correlate pairwise at r 0.08 to 0.67.

sfate: Schur-free, target-conditioned absorption probabilities for scalable single-cell fate analysis

sfate computes annotation-targeted absorption probabilities by column-wise GMRES on a latent kNN graph, skipping Schur decomposition; a 74,984-cell mouse microglia analysis peaked at 1.76 GiB.

Coevolutionary mining of prokaryotic non-coding elements with a genome language model

Minerva extracts RNA base-pairing, protein-contact and repeat maps from a genome language model without alignments, flagging unannotated structured loci and a phage ncRNA array reverse-transcribed into short cDNAs.

An RNA Language Model trained on sequence alone reveals the structural logic of Internal Ribosome Entry Sites

Continued pretraining of an RNA language model on picornaviral 5′ UTRs alone predicts IRES base pairs with median precision 0.80 versus 0.47 for Infernal, and reveals a Type II subclass.

MAT-classifier: A memory-efficient pipeline for accurate genus level profiling from ancient metagenomic data

Per-genus Bowtie2 or BWA-aln alignments in place of MALT cut alignment-stage memory from about 140 GB (aMeta) to about 7 GB and gave higher simulated-data AUC (0.87 vs 0.79).

Incomplete references leave bulk deconvolution targets non-identifiable, but identification has a computable precision price

With an incomplete deconvolution reference, operator history changes estimates and associations, and the target is not point-identified; fitdrop scores remedies on shrinkage, coverage, certification and false certification, and prices measurements.

Benchmarking of bulk transcriptomic harmonization tools in a multi-platform B-cell lymphoma cohort identifies feature-specific quantile normalization and surrogate variable analysis as top-performing methods

Across 7,174 multi-platform lymphoma transcriptomes, only surrogate variable analysis and feature-specific quantile normalization corrected batch effects while keeping subtype and normal B-cell differences; top-scoring MNN erased biomarker correlations.