benchmarking

When are population connectome harmonics adequate representations of individual brains?

The paper evaluates how well population-level connectome harmonics represent individual brains across different dimensions and finds they can be useful despite not perfectly matching individual data.

A clinically annotated proteomic and histological resource of 1,000 colorectal cancers

Deep proteomics of 997 treatment-naïve colorectal cancers defines six subgroups, splitting chromosomally unstable tumors into three and revealing a rare adverse subgroup, with H&E slide benchmarks.

Calibration of AlphaGenome Variant Impact and SpliceAI2 scores as PP3/BP4 evidence for missense, non-coding, and synonymous variants

The paper calibrates AlphaGenome Variant Impact (AVI) and SpliceAI2 scores for variant classification, showing their performance across different variant classes and comparison methods.

BeatRatePy - Automated High-Throughput Python-Based Beat Rate Quantification and Generation of Speed and Contraction Traces

BeatRatePy quantifies beat rate, contraction, and speed from label-free cardiac imaging data, showing consistent performance across different systems and datasets.

A critical assessment of LGN segmentation quality based on volume, contour, and location

This study benchmarks seven automated methods and manual segmentation for LGN delineation, finding HIPS-THOMAS and DeepThalamus perform best, while manual segmentation remains precise but variable.

Different, same, or arrhythmic: an empirically informed benchmark of differential rhythmicity methods

The paper benchmarks 12 differential rhythmicity methods using synthetic RNA-seq data to guide method selection for time series analysis.

Single-Cell Sequencing in Pediatric Acute Leukemia: A Systematic Review of Biologic Insights and Translational Potential

This review evaluates single-cell sequencing findings in pediatric acute leukemia, highlighting insights into clonal evolution, chemoresistance, and immune dynamics, while noting limitations in study design and bias.

Signal Associa: hot tumors elicit field-spanning NK cell coordination linked to their recruitment

Signal Associa identifies coupling regimes in NK cell dynamics across tumor microenvironments, showing hot tumors elicit more integrated NK cell networks.

An integrated semantic publishing workflow for taxonomy: a review of the Afrotropical dung beetle genus Amietina (Coleoptera: Scarabaeinae)

The paper introduces a semantic publishing workflow for taxonomic studies, applying it to describe four new species of dung beetles and update taxonomic data.

Accretion of novel genetic elements reverses genome erosion and enables host-switching in the deep sea

This study shows that genome erosion in deep-sea bacterial symbionts can be reversed through horizontal gene transfer and mobile genetic elements, enabling host-switching.

Early-life core microbiota are associated with postlarval survival of Penaeus vannamei: A meta-analysis

This study identifies core microbiota associated with postlarval survival in shrimp through a meta-analysis of 16S rRNA gene datasets.

Averaging in gene perturbation benchmarks hides perturbation-strength variation: Consequences for model evaluation

The paper evaluates how averaging perturbation responses in gene perturbation benchmarks affects the ability to assess perturbation-strength variation, finding that current models fail to reliably recover perturbation identity.

Projected Gradient Descent for Hallucination-Based Protein Binder Design

This paper evaluates projected gradient descent (PGD) for hallucination-based protein binder design, finding it improves design efficiency and diversity compared to softmax-based methods.

2C-RT Quantifies Genome-Wide DNA Replication Perturbations and Redefines RIF1-CDC7 Regulation of Replication Timing

Sorting S-phase cells by Cyclin A2 rather than DNA content exposes a uniform genome-wide delay after CDC7 inhibition and a broad replication timing advance in RIF1 knockout.

Whole-genome sequencing reveals tumor T-cell infiltration associated with immunotherapy outcomes

The paper develops a DNA-based T-cell infiltration score from whole-genome sequencing to predict immunotherapy response and survival.

A global assessment reveals widespread co-benefits for forest protection

This study assesses the global impacts of avoided forest conversion on well-being, biodiversity, and ecosystem services, finding widespread co-benefits across 29,038 studies.

When word order matters: human brains represent sentence meaning differently from large language models

This study compares how human brains and large language models represent sentence meaning, finding that transformers poorly match brain representations despite capturing some structural aspects.

Pediatric brain charts reveal ADHD biotypes with distinct developmental, molecular, and therapeutic profiles

The paper identifies two distinct ADHD biotypes using brain imaging and transcriptomic data, showing different developmental, molecular, and treatment responses.

NAD metabolism mediates a sex-specific protection against early life infections

This study identifies NAD metabolism as a sex-dependent factor influencing early-life infection outcomes, showing sex-specific effects of NAD precursor supplementation in mice and humans.

Information contracts determine what inverse perturbation benchmarks measure

The paper introduces InverseBench and FSTN to evaluate inverse perturbation benchmarks, showing varying accuracy across tasks and highlighting the importance of endpoint construction.

Robust and accessible in situ sequencing with an open-source automated sequencer

The paper introduces Seq-o-Matic, an open-source automated in situ sequencer that reduces hands-on time and improves sequencing consistency across tissue sections.

Sample preparation for direct nanopore based protein identification via tryptic peptide recognition

This paper introduces a sample preparation workflow (SP3) that enables nanopore-based protein identification by decoupling proteolysis from interfering components, demonstrating its effectiveness with tryptic digests of myelin basic protein.

Towards forecasting antimicrobial resistance evolution: concordance of in vitro and in vivo studies

This study compares in vitro and in vivo antimicrobial resistance evolution data to show that experimental data can predict in vivo resistance emergence.

Insomnia and the genetic overlap of sleep with depression and anxiety: a genomic structural equation modelling study

This study uses genomic structural equation modelling to assess the genetic overlap between insomnia, depression, and anxiety, finding insomnia is the best-supported location of the genetic overlap.

Acute scalp EEG signatures of anterior thalamic DBS in epilepsy:reproducible gamma power enhancement within an aperiodic spectral-state shift

The paper identifies consistent acute scalp EEG signatures of anterior thalamic DBS in epilepsy, showing gamma power enhancement and aperiodic parameter changes across multiple sessions.

Contact heterogeneity in network reconstruction: evaluating synthetic graph generators for rabies transmission modeling

This study evaluates synthetic graph generators for rabies transmission modeling, finding that the degree-corrected stochastic block model best reproduces empirical contact networks and outbreak dynamics for short-infectious-window pathogens.

Development of Neonatal Functional Brain Network Organisation and Its Association with Childhood Neurodevelopmental Outcomes

This study examines neonatal functional brain network organisation using fMRI and links it to childhood neurodevelopmental outcomes, finding associations with later difficulties in 4-6 year olds.

Active Learning framework for Antibody Binding Affinity Prediction

This paper benchmarks a Gaussian process active learning framework for antibody-antigen binding affinity prediction, showing significant improvements over random selection.

A Quarter-Power Law for Translating Human Development intoEquivalent Mouse and Rat Ages

The paper develops a quarter-power law to translate human developmental age into equivalent mouse and rat ages, finding it outperforms other models in cross-validation.

A pilot computer-vision model trained to identify slide-mounted scale insect pests from the family Rhizoecidae

The paper trains a computer-vision model to identify 16 species of root mealybugs using high-resolution images from museum specimens, achieving 79% F1 score.