simulation

Thermodynamic Quality Control Reshapes Spatially Resolved Metabolic Flux Predictions in Prostate Cancer

Quality-controlled, cycle-certified E-Flux Human-GEM models of twelve regions from one prostate tumor curb implementation-driven flux inflation and show predicted metabolic similarity tracks spatial region, not histology.

Synaptotagmin-mediated plasma membrane homeostasis is required to recruit the endocytic machinery during cold stress

This study shows that SYT1 and SYT3 are essential for maintaining endocytosis during cold stress in Arabidopsis by preserving membrane composition and TPC subunit association.

Latent-Factor Stability Is Not Sufficient: Evaluating SABLE-MO in Simulated and Cancer Multi-Omics Data

The paper evaluates SABLE-MO's performance in identifying shared factors in multi-omics data, finding that stricter retention reduces errors but does not eliminate them.

Sequence-dependent conformational and mechanical landscapes of double-stranded nucleic acids

This study introduces cgNA+, a model predicting sequence-dependent mechanical properties of dsNAs with high accuracy, revealing hidden regulatory layers in nucleic acid mechanics.

A Sense of Direction: Detecting Natural Selection Across Non-Stationary Genomes

dFEL extends FEL to model lineage-specific GC/AT drift as per-branch mixtures of three shared regime matrices, correcting selection calls at 1%–4% of boundary codons.

Ancestral State Reconstruction under Localized Evolutionary Change: Error Patterns and Their Control by Tree Partitioning

This study examines how localized evolutionary changes affect ancestral state reconstruction and shows that tree partitioning can reduce errors in these reconstructions.

Gene Regulatory Network Inference reveals tcf4 as a key a player in neuroblastoma gene expression circuitry

Mechanistic stochastic gene regulatory network inference on neuroblastoma tumoroid scRNA-seq predicts TCF4 as a hub whose loss slows chromaffin-to-sympathoblast progression, supported by JQ1 treatment ex vivo.

Positive selection and structural disruption of KCNA5 by mutation in colorectal cancer

The paper identifies KCNA5 mutations under positive selection in colorectal cancer and shows they disrupt channel structure and function, affecting tumor pathways.

Cancer-associated mutations reconfigure dynamical responses in EGFR kinase

This study uses D-NEMD simulations to show how cancer mutations in EGFR alter allosteric communication networks and signal propagation within the kinase domain.

Senescence-associated KRAS upregulation in peripheral T cells links to premature coronary artery disease

The paper identifies KRAS upregulation in senescent CD8+ T cells as linked to premature coronary artery disease through single-cell and bulk transcriptomic analyses.

Folding-Driven Control of the Functional PP1 Complex via Multiscale Modeling

The paper develops a multiscale model to study how conformational dynamics regulate the PP1-GADD34-eIF2 complex, showing folding-dependent assembly enhances biochemical function.

Navigating between global robustness and fine-scale resolution: the potential of demographic inference based on identical-by-descent segments.

This study evaluates two IBD-based methods for estimating effective density and dispersal variance, finding that IBD-Analysis performs better under spatially homogeneous conditions while MAPS captures spatial patterns but introduces noise in uniform landscapes.

Metabolic-Epigenetic Coupling in Cellular Senescence: In Silico Cristae Remodeling Depletes Alpha-Ketoglutarate to Drive KDM4/6 Inhibition and SASP Amplification

The paper develops a computational systems biology framework to model metabolic-epigenetic coupling in cellular senescence, showing how mitochondrial remodeling and alpha-ketoglutarate depletion inhibit KDM4/KDM6 and amplify SASP.

stably: error-controlled stability selection for biomarker panel discovery

stably (Python) applies error-controlled stability selection to DIA-NN output; its 17-protein pancreatic cancer panel reached held-out AUC 0.93 versus 0.82 for a published two-protein panel rescored on the same data.

RNAPII and XPC remodel the 3D genome for UV repair

This study shows that RNAPII and XPC remodel chromatin loops and domains during UV repair, enhancing lesion recognition and repair efficiency.

Revisiting bacterial division control with likelihood inference: limited identifiability of simple models

Likelihood comparison on six E. coli mother-machine datasets finds sizer, adder, and log-foldchange division rules only weakly separable, while a neural conditional cycle-duration model fits best.

Stepping-stone population structure and widespread clonality of the mesophotic octocoral Swiftia exserta in the Warm Temperate Northwest Atlantic

This study uses population genomics and larval dispersal modeling to show that Swiftia exserta relies on clonal propagation within mesophotic banks and episodic larval exchange between them.

Climate-driven niche tracking and genomic resilience shape future distribution of a widespread agricultural weed

The paper examines how blackgrass adapts to climate change by tracking its ecological niche and showing polygenic adaptation, suggesting resilience in agricultural systems.

Revealing the abiotic and biotic drivers of past and future local adaptation in a coastal dogwhelk

The paper identifies abiotic and biotic drivers of local adaptation in dogwhelks and predicts future evolutionary responses to environmental changes.

CpG islands act as topological sinks for transcription-induced DNA supercoiling

The paper shows CpG islands act as topological sinks for transcription-induced DNA supercoiling by focusing torsional stress and promoting DNA melting.

Differential Effects of Incomplete Lineage Sorting and Gene Tree Estimation Error on Gene Tree Distributions and Species Tree Inference

This study compares the effects of incomplete lineage sorting and gene tree estimation error on species tree inference using simulated and real datasets.

Metabolites form a globally connected chemical network across protein families

The paper analyzes protein-ligand interactions to show that ancient metabolites form a globally connected network across protein families, while non-ancient metabolites expand this network without disrupting its connectivity.

Inferring disruption of directed graphs using LIKA reveals altered protein phosphorylation networks in schizophrenia

LIKA, a likelihood model over many-to-many kinase-substrate networks, beats KSEA in simulations with shared substrates, recovers EGFR and ABL1 in cell lines, and ranks MAPK3 first in schizophrenia cortex.

A Cluster-Specific First-principles Network Pharmacology Framework for Molecular-Level Mechanism Deduction: Application to the HL-60-Selective Cytotoxicity of 3-Deoxycardiobutanolide

This paper introduces a network pharmacology framework to generate molecular-level hypotheses for drug mechanisms, applying it to explain the selective cytotoxicity of 3-deoxycardiobutanolide in HL-60 cells.

Cohesin loading at regulatory elements shapes 3D genome folding during erythropoiesis

The paper identifies 'matchmaker' cis-regulatory elements in erythropoiesis that strengthen loops between neighboring elements and are linked to gene expression and cohesin loading.

The gut microbiome of infants with hypoplastic left heart syndrome is enriched in pathobionts and exhibits altered responses to nutritional intervention

This study examines gut microbiome differences in infants with congenital heart disease, finding HLHS-specific pathobiont enrichment and functional shifts that respond to nutritional interventions.

Omega-seq: ultra-low-background RNA sequencing with faithful molecular counting and precise transcript-end capture

USER-excisable uracil TSOs, a uracil-intolerant polymerase and excess primer confine UMI incorporation to reverse transcription, minimizing background and UMI inflation; a separate Omega-shaped dT primer captures stranded transcript ends.

Anticodon nucleotide modifications affect translational tuning by the ribosomal CAR surface

The paper investigates how anticodon nucleotide modifications affect translational tuning via interactions at the ribosomal CAR site.

Recombination on 'non-recombining' sex chromosomes: empirical insights from the blackspotted stickleback

The paper identifies a recombination event within a non-recombining sex chromosome in blackspotted sticklebacks, challenging the notion that recombination suppression is irreversible.

Inferring and simulating a gene regulatory network for the sympathoadrenal differentiation from single-cell transcriptomics in human.

The paper infers and simulates a gene regulatory network for sympathoadrenal differentiation using single-cell RNA-seq data from human cells, identifying a 97-gene network that drives the transition from Schwann cell precursors to chromaffin cells and sympathoblasts.