benchmarking

Claustrum Morphometry Reveals Spatially Heterogeneous Alterations in 22q11DS

The paper uses surface-based morphometry to analyze claustrum structure in 22q11DS, finding age-related shape changes and reduced deformation in the syndrome.

World Wide Eyes: Social Media-Assisted Wildlife Research. Assessing Supplementary Feeding Areas for Eastern Australian Humpback Whales as a Case Study.

This study uses social media data to identify supplementary feeding areas for Eastern Australian humpback whales, finding three recurrent candidate areas and supporting the idea of recurrent supplementary feeding.

Who contributes to whom: following the evidence behind protein language-model predictions of backbone variability

ESMfluc predicts local backbone variability in proteins using attention-based evidence decomposition, showing how sequence positions contribute to predictions of single or multi-PB states.

Comparative evaluation of sample preparation and enrichment methods for culture and molecular detection of Burkholderia pseudomallei in naturally contaminated soils from Thailand over one year.

This study compares culture and molecular detection methods for B. pseudomallei in Thai soil samples, finding that qPCR with ACER enrichment detects more positives than culture alone.

Antimicrobial peptide databases and prediction tools: Toward a standard evaluation framework

The paper evaluates antimicrobial peptide prediction tools and proposes a standardized evaluation framework to improve comparability and reproducibility.

Genus replacement and weak spatial structure characterize phytoplankton beta diversity in rain-fed dryland waterpans of Kenya

The paper examines phytoplankton beta diversity in Kenyan waterpans across seasons and land use, finding that genus replacement and weak spatial structure drive diversity patterns, with nutrient levels and cyanobacteria playing key roles in the dry season.

Community performance curves predict temporal stability despite interaction effects

The paper shows that community performance curves predict temporal stability of ecological communities despite species interactions.

Predictive consequences of alternative representations of metabolic measurements: A controlled synthetic study of categories, longitudinal information and transition preservation

The paper evaluates predictive performance of different metabolic measurement representations in synthetic data, finding that some representations outperform others in specific scenarios.

NK-RCPP: a receptor-conditioned computational workflow for prioritizing neurokinin-receptor peptide candidates

The paper introduces NK-RCPP, a workflow for prioritizing neurokinin-receptor peptide candidates using receptor-matched scores and structural-neighbour comparisons.

The past and potential antagonistic effects of fishing ban against nutrient loading control on eutrophication restoration in Lake Hongze

This study evaluates how fishing bans may counteract nutrient control efforts in Lake Hongze, showing increased nutrient levels and reduced biodiversity under continued bans.

Conserved genes, discordant structure: a pangenomic view of plant mitochondrial genome evolution

This study analyzes over 300 plant mitochondrial genomes to show that gene content is conserved but structural complexity varies, driven by repeat proliferation and recombination rather than intergenomic DNA transfer.

Mutation breeding for quantitative traits in the era of genomic selection

This study evaluates how genomic selection can capture polygenic variation from mutation breeding in wheat and tomato, showing improved predictive ability when mutations are shared among lines.

LDscnR: LD-aware complexity reduction for genome scans

LDscnR reduces genome scan tests by grouping correlated markers using LD decay, improving precision while maintaining recall, and showing structure can explain outlier regions.

'Somebody to find an answer, so I can sleep at night': Diverse Perspectives on Genomic Research for Rare Disease

This study explores equitable strategies for participant engagement in rare disease genomic research through interviews with underrepresented individuals and clinicians.

Flexible compression of sensory evidence makes human decisions more resilient to noisy neural computations

The paper shows humans make more accurate decisions by compressing sensory evidence into decision categories, and RNNs trained on the same task exhibit similar resilience to noisy computations.

MALER: a web server to build, evaluate, and apply machine learning models for numerical biomedical data analysis

Widespread Presence of Catalytic RNAs in All Domains of Life

The paper identifies millions of self-cleaving ribozymes in humans and other species, revealing a much larger ribozyme-ome than previously thought and their potential roles in gene regulation and biotechnology.

According to a large citizen science dataset, UK farmland bird indicator species and other bird groups, are more likely to be found on farms with shoots than on otherwise similar farms

The paper analyzes a citizen science dataset to show that UK farmland bird species richness is higher on farms with gamebird shoots compared to similar farms without shoots.

Leukemic fitness predicts treatment-free remission and guides adaptive therapy in chronic myeloid leukemia

This paper develops a minimal mathematical model to predict treatment-free remission in chronic myeloid leukemia using leukemic fitness, and proposes adaptive therapy strategies based on this parameter.

Cross-family learning transfers thermal adaptation between enzymes

This paper shows that thermal adaptation can be transferred between unrelated enzymes using a generative framework, improving thermostability without evolutionary homology.

Human-calibrated automated intelligibility evaluation of speech neuroprostheses

This paper fine-tunes an ASR model on human-transcribed synthesized speech to better align its word error rate with human perception, achieving higher correlation than zero-shot ASR.

Ecological context shapes the interpretation of biodiversity intactness metrics

The paper evaluates how ecological context affects the interpretation of Mean Species Abundance (MSA) as a biodiversity intactness metric across different biomes and taxonomic groups.

Absolute Quantification of Tissue Composition by Raman Spectroscopy

This paper introduces a method to quantify tissue composition using Raman spectroscopy, validated on cartilage with high accuracy compared to biochemical assays.

Reference normalizations of Effort-To-Compress across length, alphabet size, and composition

The paper introduces normalized versions of Effort-To-Compress (ETC) to enable fair comparisons of symbolic complexity across different sequence lengths, alphabet sizes, and compositions.

On the feasibility of temporal interference stimulation of human brains using two arrays of electrodes

This paper evaluates two-array temporal interference stimulation for deep brain modulation, showing it achieves similar focality to multi-pair TI with faster optimization and fewer electrodes.

Predictive adequacy and measurement dependence of metabolic representations in controlled synthetic systems

The paper evaluates metabolic representations in synthetic systems, finding that adequacy, compactness, and responsiveness are distinct properties, and adequacy certification does not guarantee predictive accuracy.

Defining and measuring proximity to criticality

The paper develops a method to measure proximity to criticality in complex systems using a temporal renormalization group and information theory, applying it to brain activity data to show shifts in criticality during wakefulness and sleep.

TransPepMS: A Tool to Verify Peptides Absent from Reference Proteomes

TransPepMS verifies peptides not in reference proteomes by resolving ambiguities in mass-spectrometry data to distinguish genuine non-canonical peptides from false positives.

Thyra: Bridging Mass Spectrometry Imaging and SpatialData for Unified Multi-Modal Analysis

Thyra converts Mass Spectrometry Imaging data into the SpatialData format to improve interoperability and enable multi-modal spatial analysis.

Long-Term Dynamics of Esca Disease in Western Switzerland

This study analyzes long-term esca disease incidence in Western Switzerland from 2001 to 2022, identifying water balance as a key climatic driver and observing a slight decreasing trend linked to drier conditions.