statistical model

HLAResolver: A statistical framework for resolving HLA ambiguity in T-cell response data

HLAResolver improves HLA resolution in T-cell response data by integrating MIRA responses with NetMHCpan predictions, achieving higher sensitivity and fewer candidate HLAs.

Photoentrainment as Bayesian Inference: How the central circadian clock may weight and integrate the intensity and wavelength of natural light to estimate astronomical time

The paper proposes a Bayesian model explaining how the circadian clock integrates light intensity and wavelength to estimate astronomical time despite natural variability.

Follow-up availability and the robustness of immune transcriptomic recovery after myocardial infarction

The paper assesses the robustness of immune transcriptomic recovery after myocardial infarction by evaluating how missing data and assay availability affect inflammatory-response scores over time.

A Systems Theory of Cardiac-Autonomic Trajectories and Equilibria

This paper develops a theoretical framework to analyze cardiac-autonomic regulation using dynamical systems theory and demonstrates its properties through simulations.

A candidate HNRNPU-CHD2 RNA-processing axis in neurodevelopmental disease

The paper identifies a HNRNPU-CHD2 RNA-processing axis linked to neurodevelopmental disease by showing HNRNPU depletion causes splicing changes in CHD2 that may lead to nonsense-mediated decay.

Socio-demographic gradients in traumatic brain injury disability, severity and nutrition: a two-level analysis of the Global Burden of Disease Study 2023 and NHANES 2011-2014

This paper examines socio-demographic gradients in traumatic brain injury (TBI) disability, severity, and nutrition using global and US-based data, finding persistent disparities and nutritional risks among food-insecure TBI survivors.

Endogenous PROM1 activation redistributes liver cancer cells along a preexisting differentiation axis

The paper shows PROM1 activation in liver cancer cells shifts their state along a preexisting differentiation axis, suggesting CD133's role extends beyond being a stem-like marker.

Cell-lineage selection interacts with development and life history to shape the rates and identity of heritable mutations

The paper shows that mutation transmission is influenced by developmental and life-history traits, altering mutation rates and identities across species.

A Reproducible Pre-Transplant γδ T-cell Effector Signature Reveals Immune-Metabolic Programs Associated with Kidney Allograft Rejection

The paper identifies a pre-transplant γδ T-cell effector signature associated with kidney allograft rejection using multi-omics data from transplant recipients.

Intraspecific trait variation shapes macro-scale patterns ofniche breadth and range size

The paper shows that greater intraspecific morphological variation in bulbuls predicts broader ecological niches and larger geographic ranges.

Spatial transcriptomics of pediatric tuberculosis lymph nodes reveals a conserved hypoxia_SPP1 niche

This study uses spatial transcriptomics to identify a hypoxia-associated SPP1-enriched microenvironment in pediatric TB granulomas that may contribute to incomplete bacterial clearance.

The ecological niche and seasonality of Theileria equi in Portugal

This study identifies spatio-temporal dynamics and ecological niche factors influencing Theileria equi infection in Portugal using field-surveillance data and environmental variables.

DPYD links glial lipids and myelination to sleep duration

This study identifies DPYD's role in sleep regulation through glial lipid metabolism and myelination across species, linking genetic variants to oligodendrocyte-specific control.

Predicting cortical signal mixing in coarse-resolution fMRI: a forward-operator analysis of surface mapping and the conditional benefit of correction

This paper develops a forward-operator model to predict signal mixing in fMRI and shows that correcting for it improves coarse-resolution cortical mapping.

Ranging and territoriality in African Apes

The paper compares ranging and territoriality among African apes, finding that economic defendability does not fully explain interspecific variation in territorial behavior.

ANABOLIC FAILURE, NOT CATABOLIC ACTIVATION, UNDERLIES GLYCOGEN DEPLETION IN CERVICAL CARCINOGENESIS: A MULTI-COHORT TRANSCRIPTOMIC ANALYSIS

Sensory representation by non-equilibrium flows of neural activity at the mesoscale of cortex

This paper introduces a non-equilibrium theory of sensory perception using activity flows in cortical columns, showing that small-number fluctuations are essential for effective representation.

FoXSight: Facilitating Computational Hit Identification in Crystallographic Fragment Screening Experiments

FoXSight identifies weak binding events in crystallographic fragment screening by detecting target-specific density features in noisy electron density maps.

Ancient U/V sex chromosomes reveal slow expansion of recombination suppression in Polytrichaceae mosses.

This study analyzes ancient U/V sex chromosomes in Polytrichaceae mosses, showing that recombination suppression has limited SDR expansion and functional degeneration despite their 124 million-year-old origin.

Stochastic and Heritable Responses in Cell-Size Regulation and Survival to pH Stress in C. glutamicum

This study examines how C. glutamicum cells respond to pH stress by tracking cell size and survival, revealing stochastic and heritable differences in acid and alkaline stress survival.

Synthetic reaction-diffusion patterning in mammalian cells

This study designs synthetic reaction-diffusion circuits in mammalian cells to generate spatial patterns with controllable spatial scales.

NPlasmid-seq: Cas9-encoded terminal signatures enable molecule-level nanopore quality control of vector and IVT-template plasmids

NPlasmid-seq detects sub-percent contamination and sequence heterogeneity in plasmid preparations using Cas9-encoded terminal signatures, revealing structural variants missed by consensus-based methods.

Serum Calprotectin as predictor of Rheumatoid Arthritis disease severity and Mortality

This study evaluates serum calprotectin as a biomarker for disease activity, severity, cardiovascular risk, and mortality in inflammatory rheumatic diseases, finding it to be a better predictor than CRP in certain contexts.

Mapping and Probing the Substrate Scope of a Ketoamide-Forming Splicease by Computational Design

The paper uses computational methods to design and evaluate splicease variants for generating diverse ketoamide substrates, finding that top-scoring peptides are spliced more efficiently than single-point mutants.

GMP-Cor: Quantifying Transcriptional Dysregulation in Antibiotic Tolerance and Persistence

This study quantifies transcriptional dysregulation in antibiotic tolerance using single-cell RNA-seq and introduces GMP-Cor to analyze gene-gene correlations in disrupted growth-arrest states.

Metabolic complexity in the human brain supports metastable network dynamics and declines in normative ageing

This study investigates metabolic complexity in the human brain using PET and fMRI, finding that metabolic entropy correlates with network metastability and declines with age.

Stable large-scale network architecture and structured individual variability in the awake mouse brain

The paper introduces the Awake Mouse Connectome Project (AMCP), a dataset of 212 awake mice, and presents functional network atlases and analysis tools for studying brain connectivity and variability.

Prokaryotic Community Structures in the Bering and Chukchi Seas

The paper characterizes bacterial communities in the Bering and Chukchi Seas using 16S rRNA gene sequencing, finding that water mass, salinity, and bloom stage shape community structure.

Dissecting the genetic basis of DUS characters in Pakistani wheat varieties

This study identifies genomic regions associated with DUS traits in Pakistani wheat varieties using GWAS, aiming to improve varietal identification through molecular markers.

RNA accessibility sequencing reveals transcriptome-wide RBP binding and RNA structure

This paper introduces RAD-seq, a method to quantify RNA accessibility by protein binding, and shows it can detect RBP footprints and RNA structure changes under stress.