benchmarking

Voluntary engagement predicts recovery across rehabilitation time points after experimental spinal cord injury

This study identifies factors influencing rehabilitation effectiveness after spinal cord injury, finding that voluntary engagement promotes recovery while forced training may reduce benefits.

CRAIC: interactive interrogation of multiple sequence alignment uncertainty

CRAIC provides tools to inspect and curate multiple sequence alignment uncertainty using posterior probabilities from pair-HMM models.

Transcriptomics of independent CRISPR-edited cell lines reveal ciliary-specific ARL13B dependent changes

The paper uses CRISPR-edited cell lines to identify genes whose expression changes with loss and restoration of ciliary ARL13B.

tangermeme: A toolkit for understanding cis-regulatory logic using deep learning models

tangermeme provides tools to interpret deep learning models for cis-regulatory analysis, extracting human-readable insights from genomic predictions.

Characterizing and Mitigating Protocol-Dependent Gene Expression Bias in 3' and 5' Single-Cell RNA Sequencing

This study identifies and mitigates protocol-dependent gene expression bias between 3' and 5' scRNA-seq by focusing on a small set of biased genes rather than applying broad normalization.

Careers in Scientific Editing: Results from the 2024 Scientific Editors Network (ScENe) Survey

This study presents findings from a 2024 survey of 132 scientific editors, revealing demographic homogeneity and variability in career paths, with implications for integrating scientific editing roles into research development.

Hybrid Mechanistic-Neural Modeling of Concentration-Time Dynamics Generalizes Human Pharmacokinetics Prediction Across Unseen Chemical Space

PK-MUSE improves pharmacokinetics prediction by combining mechanistic models with neural corrections, achieving better performance across unseen chemical structures.

RNA3D-Decoy: A Large-Scale Benchmark Dataset of AI-Generated RNA Structure Models for Quality Assessment

The paper introduces RNA3D-Decoy, a benchmark dataset of AI-generated RNA structure models, to evaluate quality assessment methods for RNA structure prediction.

Reduced carbon emissions and chain elongation during mixotrophic fermentation of a biomass feedstock

This study tests mixotrophic fermentation of biomass and syngas, finding reduced CO2 emissions and increased production of C4 and C6 carboxylates.

scStable: assessing scRNA-seq analysis stability under bulk-derived between-sample variation

scStable evaluates scRNA-seq analysis stability by generating synthetic samples with between-sample variation, showing better performance than existing methods in gastric cancer data.

mzQC: a versatile way to communicate quality information for biological mass spectrometry

The paper introduces mzQC, a standard for representing quality control metrics in mass spectrometry, enabling interoperable and machine-readable QC reporting.

Cross-cohort Mamography]{Representation-dependent domain adaptation for cross-cohort generalization of mammography diagnostic models

This study evaluates cross-cohort generalization of mammography diagnostic models using different image representations and domain-adversarial learning, finding that MedSigLIP embeddings provide the best transferability.

Information regimes in population-graph neuroimaging: cohort context and implementation-dependent evaluation sensitivity

The paper evaluates how population-graph models' performance varies with evaluation context, showing implementation-dependent differences in AUC across splits.

Uncharacterized unicellular relatives reveal key gaps in sampling diversity for reconstructing animal origins

The paper identifies uncharacterized lineages within Holozoa and Opisthokonta, highlighting gaps in sampling diversity for understanding animal origins.

Nation-scale recovery of complete environmental plasmids pushes the boundaries of plasmid diversity through long-read sequencing

The paper expands plasmid diversity by analyzing long-read metagenomes, identifying novel plasmid lineages and providing tools for plasmid discovery.

CryoCodex: learning discrete structural representations for cryo-EM map post-processing

CryoCodex improves cryo-EM map quality by jointly enhancing density, estimating local quality, and masking molecules, outperforming existing methods on experimental maps.

Accurate Hippocampal Electric Field Modeling for Electroconvulsive Therapy: Numerical Accuracy and Convergence

The paper evaluates numerical accuracy and convergence of hippocampal electric field modeling across three methods in ECT patients, finding significant discrepancies at low resolutions.

Seascape genomics reveals shared spatial genetic structure in three co-occurring sea snakes

The paper uses genomic data to reveal shared and distinct genetic structures among three sea snake species across different geographic regions, highlighting conservation implications.

Machine learning-assisted directed evolution yields dramatic improvement on novel AAV engineering task

This study shows ML-assisted directed evolution improves AAV capsid manufacturing efficiency 41-fold compared to directed evolution alone.

Separating biological signal from statistical artifact in trait trade-off inference

The paper identifies and corrects for statistical artifacts in trait trade-off inference, showing that apparent trade-offs may be spurious but genuine biological signals can still be recovered.

Altered Aperiodic EEG Activity in Adolescents with Neurofibromatosis Type 1

This study finds that adolescents with Neurofibromatosis Type 1 have higher aperiodic EEG activity, consistent with increased inhibitory tone, but no cognitive performance differences.

Biomimetic scaffolds mimic human subretinal debris for preclinical testing of prosthetic vision

This paper develops biomimetic scaffolds to mimic human subretinal debris in animal models, improving the accuracy of preclinical testing for subretinal prostheses.

Evolutionary rates in "living fossils" across the Tree of Life

This study examines evolutionary rates in living-fossil lineages and finds reduced morphological but not molecular rates, suggesting morphological conservatism is a key feature.

Making Biorisk Measurable: A Bayesian Framework for Laboratory Risk Management

This paper introduces a Bayesian framework for laboratory risk management that quantifies biosafety risk using a log-risk scale and incorporates WHO Risk Group classifications and incident escalation models.

Modeling aroma release during in vivo food oral processing using digimouth

This study develops a modular Python framework called digimouth to model aroma release during food oral processing, validated with experimental data from 30 subjects.

How to design 1000-plex mass tags using the differential mass defect

This paper explores designing high-plex mass tags using differential mass defect to enable large-scale multiplexing in proteomics.

Super Bloom: Fast and precise filter for streaming k-mer queries

The paper introduces Super Bloom, a Bloom filter variant for streaming k-mer queries, which improves cache efficiency and reduces false positives.

Unified Network Spectroscopy: Inferring Reduced Biological Dynamics from Fluctuations under Structured Noise and Broken Ergodicity

This paper introduces Unified Network Spectroscopy (UNS), a method to infer biological dynamics from fluctuations, addressing issues with noise structure and ergodicity.

Informatics Methods to Enhance Bacterial Peptide Detection

The paper develops and benchmarks an in silico spectral library workflow to detect low-abundance bacterial peptides in human-dominated samples, finding it has complementary performance to conventional database searches.

How many crystal structures do you need to trust your docking results?

The paper evaluates how many crystal structures are needed for accurate pose prediction in drug discovery, finding that five structures per scaffold often suffice.