benchmarking

Two decades of Novel Ecosystems: Literature analysis of topics, trends and connectivity

This paper analyzes the development and application of the Novel Ecosystems Concept over two decades using bibliometric and linguistic methods, finding it remains focused on restoration rather than broader conservation.

Recalculated CNV penetrance: what it does and does not change for counselling

The paper recalculates CNV penetrance for intellectual disability, showing lower estimates due to methodological differences, and recommends phenotype-specific risk reporting.

Lack of adoption of computational gene-panel-selection tools in targeted spatial transcriptomics

This study examines the low adoption of computational gene-panel-selection tools in targeted spatial transcriptomics, finding that most researchers still use manual or vendor panels.

Exploring the role of multivariate associations between brain networks and gut microbiota in (food) value-based decision-making

The paper uses a supervised method to integrate gut microbiota and brain network data, identifying a multimodal component linked to food valuation and choice in a healthy population.

HSF1 inhibition potentiates the antifungal activity and proteome instability induced by the fungal Hsp110 inhibitor 2H

This study shows that combining HSF1 inhibition with Hsp110 inhibitor 2H enhances antifungal activity by increasing proteome instability in fungal pathogens.

Criticality-related dynamics accompany long-term functional decline in primary cortical MEA cultures

This study tracks long-term electrophysiological changes in rat cortical cultures, identifying criticality metrics as predictors of network survival and decline.

Long-read sequencing and benchmarking of saliva against blood for genomic variant detection in autism

This study benchmarks saliva-derived DNA against blood for long-read sequencing in autism, showing comparable variant detection despite nonhuman DNA contamination.

Variation in CURE instruction and limitations of CURE studies undermine what can be concluded about CURE effects on student outcomes

This study examines CURE instruction variation and limitations in CURE studies, finding that inconsistent design and reporting hinder conclusions about their effects on student outcomes.

An epigenetic palimpsest: the King penguin's blood methylome reveals conserved hematopoietic ageing

This study identifies conserved ageing-associated genes in King penguins using methylome data and shows their relevance to human epigenetic age prediction.

A multimodal foundation model to integrate histology with spatial molecular programs

SQUALL integrates histology and spatial transcriptomics to enable virtual spatial gene expression profiling and clinical prediction across cancers and platforms.

Deciphering auditory neuroprogenitor stemness for large-scale neuronal screening

The paper characterizes the molecular and metabolic changes in auditory neuroprogenitors induced by CHIR-DS treatment and demonstrates their utility in neuronal screening.

Mapping Synthetic Circuit Design Space through Massively Parallel Measurement of Single-Cell Dynamics

The paper uses a high-throughput platform to measure single-cell dynamics of gene-regulatory circuits and maps their design space by testing robustness and identifying key interactions.

PanTEon: a cross-kingdom framework to guide the design of transposable element classifiers

PanTEon provides a cross-kingdom framework for reproducible TE classification, benchmarking machine learning methods and highlighting performance variations across TE superfamilies and lineages.

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.

GENIE: a multi-agent system for closed-loop autonomous microscopy

GENIE creates an autonomous microscopy system that translates natural language goals into executable experiments and statistical analyses.

When label-free morphology is sufficient for targeted cellular measurements

The paper evaluates whether label-free morphology can replace targeted cellular measurements by analyzing paired phase-reporter data across gene knockouts and screens.

Interlaboratory benchmarking of differential scanning fluorimetry reveals sources of variability in protein thermal stability parameters

This study benchmarks DSF across labs, showing variability in thermal stability parameters due to instruments, workflows, and fluorescence readouts, with harmonization and centralized analysis improving consistency.

Sexual reproduction impacts vertebrate organ aging

This study shows that lifelong mating in killifish affects liver aging in a sex-specific manner and is associated with younger transcriptomic and proteomic ages in humans.

Do LLM Proposers Improve Budgeted Search for Ionizable Lipids?

This study evaluates if language models improve combinatorial molecular search for ionizable lipids compared to classical methods under budget constraints, finding no significant improvement.

A national ecosystem for long-read genome sequencing: Integrating population genomics and rare disease diagnostics in Sweden

This paper evaluates the clinical use of long-read genome sequencing in Sweden, showing it provides molecular diagnoses and reduces diagnostic costs.

ALBIS: simulation of multi-resolution and multi-dimensional spatial transcriptomics data

ALBIS generates synthetic spatial transcriptomics data across multiple resolutions and dimensions to enable benchmarking of computational methods.

Predicting cyanobacterial oxic diazotrophy and prioritizing candidate protein families beyond known Nif proteins

The paper predicts cyanobacterial diazotrophy using protein-family content and prioritizes candidate protein families for experimental validation.

Beyond the attractor: closed-loop stimulation design for learning multistable neural dynamics

This paper introduces PALDI, a method for active closed-loop stimulation to identify neural dynamics, showing improved performance in noisy and biased observation scenarios.

Surrogate variables and the risk of overfitting in neuropsychiatric gene expression analyses

This study shows that surrogate variable analysis (SVA) can lead to overfitting and reduced cross-cohort reproducibility in neuropsychiatric gene expression analyses.

Active teaching-learning methodology in a non-formal teaching environment as a tool to mitigate the "plant awareness disparity" in public school students.

This study tests if active teaching methods in a non-formal setting can reduce plant awareness disparity among students using digital games and qualitative assessments.

'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.

Efficient approximate Bayesian inference for large, heterogeneous biological datasets

The paper introduces an adaptive minibatch approach for approximate Bayesian inference, improving speed-precision tradeoffs for large, heterogeneous biological datasets.

Quantifying the genetic separability of disease subtypes

This paper introduces GenSep, a framework to quantify genetic separability of disease subtypes, showing current PRSs fall short of theoretical limits.

Sparse Stimulus Generation Improves Reverse Correlation Efficiency and Interpretability

This paper introduces a method for generating sparse stimuli to improve reverse correlation efficiency and interpretability, showing benefits in reconstruction quality, sample size efficiency, and subjective interpretability.

AnnZarro: scalable, interactive exploration of cell-by-cell and gene-by-gene relationships in single-cell data

AnnZarro enables interactive exploration of cell-by-cell and gene-by-gene relationships in single-cell data through a browser-based viewer linked to AnnData objects.