BertST: BERT-based Spatial Domain Identification in Patient Data biorxiv.org 2026-07-09 Spatial transcriptomics enables the study of gene expression within its native tissue context, providing critical insights into cellular organization
EZSolver: Template-free prediction of polar enzymatic mechanisms via bidirectional flow matching and search biorxiv.org 2026-07-09 Predicting enzymatic reaction mechanisms is critical for understanding enzyme function and for designing and dis-covering new enzymes.
LeafRank: A phylodynamic framework for inferring relative fitness from single-cell phylogenies in chromosomally unstable tumors biorxiv.org 2026-07-09 Tumors contain cancer cells with diverse growth potentials that shape evolutionary trajectories, yet this fitness diversity remains difficult to quant
Coding agents author interpretable single-cell embedding models from the literature biorxiv.org 2026-07-09 The single-cell literature catalogs cell states as validated marker-gene programs - a sparse, compositional prior.
Mind the Alignment Gap: A Spatial Transcriptomics Benchmark for Scientific Coding Agents biorxiv.org 2026-07-09 Scientific coding agents are difficult to benchmark because many research tasks require executable work yet produce ambiguous or hard-to-verify output
Rectangle: robust and scalable multiscale deconvolution informed by single-cell RNA sequencing data biorxiv.org 2026-07-09 Bulk RNA-seq enables effective profiling of large cohorts and complex experimental designs, but current single-cell-informed deconvolution methods inc
Gene Program Negotiation Defines Cellular Identity in Single-Cell Transcriptomes biorxiv.org 2026-07-09 Single-cell transcriptomics has transformed the characterization of cellular heterogeneity by enabling systematic analysis of biological gene programs
Coupling of tubulin acetylation to microtubule stabilization through molecular mimicry biorxiv.org 2026-07-09 Microtubules support diverse cellular functions through regulation by microtubule-associated proteins and tubulin post-translational modification, yet
A DMT1-dependent iron-endoplasmic reticulum-extracellular matrix axis regulates cancer cell invasion biorxiv.org 2026-07-09 Intracellular iron homeostasis is increasingly recognized as a regulator of cancer cell behavior, but how iron distribution influences extracellular m
Modeling the metabolic heterogeneity of high-grade serous ovarian cancer solid tumors in 3D Microphysiological systems biorxiv.org 2026-07-09 High-grade serous carcinoma (HGSOC) is the deadliest subtype of ovarian cancer, characterized by high metastatic rates.
Dopamine Abundance Uncouples Neurodegeneration and Lifespan in a C. elegans Model of Parkinson's Disease biorxiv.org 2026-07-09 The neuropathology of Parkinson's disease is characterized by -synuclein (-syn) aggregation and dopaminergic (DAergic) neurodegeneration.
High throughput chromatographic ultra-purification of virus-like particles for downstream viromics biorxiv.org 2026-07-09 Virus-like particles (VLPs) are an abundant component of microbiomes with critical ecological roles such as population control through viral predation
Targeting the 3 splice site by a decoy oligonucleotide attenuates U2AF1 splicing activity and inhibits leukemia biorxiv.org 2026-07-09 Mutations in spliceosomal genes are a hallmark of myeloid malignancies, yet leukemic cells remain dependent on residual splicing activity, exposing a
Circadian clock control of translation fidelity through MetRS-mediated methionine misincorporation biorxiv.org 2026-07-09 Translation fidelity is generally viewed as a constitutive process that deteriorates under stress and aging.
Phenotypic CRISPR screening identifies ZBTB10 as a novel regulator of human trophoblast differentiation biorxiv.org 2026-07-09 The human placenta is built by trophoblast cells that fuse together, secrete hormones, and invade the uterus, and defects in these processes contribut
Multiscale three-dimensional ultrastructural mapping of intestinal tissues and organoids biorxiv.org 2026-07-09 Understanding cell biology in native environments requires imaging of subcellular organization in three dimensions.
Solid-like PAR protein assemblies encode long-term spatial memory of cell polarity during suspended animation biorxiv.org 2026-07-09 During suspended animation, organisms must preserve cellular organization despite the collapse of the active biochemical processes that normally maint
Morphospace analysis reveals divergent cellular behaviours driving tissue internalisation during insect gastrulation biorxiv.org 2026-07-09 During gastrulation, embryonic epithelia undergo large-scale remodelling to internalise the mesoderm.
Transforming avian to mammalian modes of digit patterning biorxiv.org 2026-07-09 How a conserved embryonic organiser--the Sonic hedgehog (Shh)-expressing Zone of Polarising Activity (ZPA)--generates diverse limb architectures in am
The combination of nelfinavir and cisplatin drives lytic cell death through a caspase-8/caspase-3/GSDME axis in platinum-resistant ovarian cancer cells biorxiv.org 2026-07-09 PurposeCisplatin (CDDP) is the most active chemotherapy for ovarian cancer; primary or acquired resistance signals a poor prognosis.
Transgressive gene expression and methylation remodeling in an intraspecific hexaploid wheat hybrid biorxiv.org 2026-07-09 Intraspecific hybridization in allopolyploid plant genomes has the potential to induce non-additive changes in gene expression and DNA cytosine methyl
Dynamic Patterns of Nuclear Transcription Factor Abundance in Plant Basal Immunity Revealed by Spatial Proteomics of Arabidopsis Nuclei biorxiv.org 2026-07-09 O_LIThe control of amount of nuclear proteins is fundamental in regulating plant gene expression, but the mechanisms of quantitative dynamics of the n
NLR from soybean Rsv1 locus confers broad-spectrum resistance to soybean mosaic virus G1-G7 strains by recognizing viral P3 protein biorxiv.org 2026-07-09 Nucleotide-binding leucine-rich repeat (NLR) immune receptor genes are of significant value in disease resistance breeding and the control of viral di
A new genome-scale model enables prediction of cancer metabolic dependencies biorxiv.org 2026-07-09 Cancer cells rewire metabolism to support proliferation. Intriguingly, divergent metabolic choices are made to attain this common goal.
Connexin 30 mutation rescues high-frequency hearing, reduces gap junctional coupling and alters potassium currents in cochlear Deiters cells biorxiv.org 2026-07-09 The early-onset, high-frequency hearing loss phenotype of CD-1 mice is rescued by the A88V mutation of the connexin 30 gap-junctional protein, despite
Challenges and Solutions in Quantifying Brain β-Hydroxybutyrate (BHB) with 1H-MRS Following Oral Keto-Ester Consumption biorxiv.org 2026-07-09 Purpose: {beta}-hydroxybutyrate (BHB), a ketone body and alternative cerebral energy substrate, can be measured in vivo using J-difference edited prot
Hippocampal CA3 forms a two-layer network of molecularly distinct cell types in mice and humans biorxiv.org 2026-07-09 Associational memory is critically dependent on the CA3 recurrent circuit, at the centre of the hippocampal system.
Exposure to P. falciparum and common cold viruses shape vaccine responses in early life biorxiv.org 2026-07-09 Vaccine immunogenicity is consistently lower in low-income countries than in high-income settings, yet the factors driving this disparity remain incom
Ecological connectivity modelling with WebAssembly biorxiv.org 2026-07-09 Circuit theory has been successfully applied to ecological connectivity modelling, notably via the Circuitscape software, which is typically run local
Data-driven forecasts of regional arrivals of non-native vertebrates worldwide biorxiv.org 2026-07-09 Aim: To forecast near-future arrivals of non-native terrestrial and freshwater vertebrates at the regional level.