Transient architecture of the embryonic pancreas determines endocrine mass biorxiv.org 2026-07-09 During organogenesis, epithelial tissues undergo extensive three-dimensional (3D) remodeling while simultaneously generating specialized cell types.
Guide-tree bias of whole genome alignment can mislead phylogenomic analyses biorxiv.org 2026-07-09 Whole-genome alignment (WGA) is widely used for genome-scale phylogenetic inference, and most scalable WGA pipelines rely on progressive alignment gui
Metabolic Rewiring in Triple-Negative Breast Cancer: Systems Analysis of TCGA-BRCA Transcriptome Reveals Prognostic Hub Genes biorxiv.org 2026-07-09 Triple Negative Breast Cancer (TNBC) is the deadliest and most aggressive subtype of breast cancer, with poor prognosis and high rates of metastasis.
Transcriptionally defined AML cell states associate with treatment response and microenvironmental remodeling biorxiv.org 2026-07-09 While therapy resistance in acute myeloid leukemia (AML) is often attributed to leukemic stem cells (LSCs), their functional properties are not fully
Head-to-head organized segmental paralogs AtOFP2 and AtOFP17 exhibit differential, spatio-temporal partitioning of function, and negative regulation of multiple developmental traits including seed-yield and root architecture biorxiv.org 2026-07-09 Ovate Family Proteins (OFPs) are a class of plant-specific, negative nuclear transcriptional regulators characterized by conserved C-terminal OVATE do
Novel quantitative trait loci conferring broad-based resistance to root-knot nematodes in lima bean (Phaseolus lunatus) biorxiv.org 2026-07-09 Lima bean (Phaseolus lunatus) is a broadly adapted, economically important leguminous crop and a susceptible host of root-knot nematodes (Meloidogyne
The MicroTron: a microfluidic platform for single cell studies in P. patens biorxiv.org 2026-07-09 O_LIThe effect of some bioactive compounds on living organisms is dependent on their concentration and gradients, as is the case of hormones and signa
Photoswitchable optoGPCRs for reversible control of Gs and arrestin signalling biorxiv.org 2026-07-09 OptoGPCRs are light-activatable G protein-coupled receptors (GPCRs) used for optogenetic control of physiological processes.
Regulation of RNA maturation by the family of human G-patch proteins biorxiv.org 2026-07-09 The family of human G-patch proteins comprises more than 20 members, each characterized by a glycine-rich G-patch implicated in mediating interactions
A Cross-Species Systems Genetics Framework Identifies Causal Genes in Diabetic Nephropathy biorxiv.org 2026-07-09 Diabetic nephropathy (DN) is the leading cause of kidney failure in the developed world, but the genetic architecture of DN susceptibility is not well
Biological Network Organization, Not Generic Graph Topology, Drives Graph-Based Gene Essentiality Prediction biorxiv.org 2026-07-09 Predicting gene essentiality across cellular contexts is a central challenge in computational biology, with implications for identifying cancer vulner
Trisomy 21 Impairs Development of Enteric Neural Crest-Derived Cells via SOD1-Mediated RET Dysregulation biorxiv.org 2026-07-09 Hirschsprung disease (HSCR) is a rare congenital disorder of the enteric nervous system (ENS), marked by the absence of enteric ganglia along variable
Rapid and efficient oligodendrocyte differentiation from human pluripotent stem cells via dual inhibition of BMP and Notch signaling biorxiv.org 2026-07-09 The protracted timing required for oligodendrocyte differentiation from human pluripotent stem cells (hPSCs) has limited their use in disease modeling
Smad1 and Smad5 differentially transduce BMP signaling during in vitro differentiation of mouse embryonic stem cells into dorsal interneurons biorxiv.org 2026-07-09 A central unresolved question in development biology is how systems of overwhelming complexity arise from relatively few families of growth factors.
SMAD4 MH2 Mutations Disrupt CREBBP/EP300 Recruitment and TGF-β-Induced Transcription in Colorectal Cancer biorxiv.org 2026-07-09 SMAD4 is a central transcriptional effector of the TGF-{beta} signaling pathway and a frequently inactivated tumor suppressor gene in various cancers.
NNMT Loss Drives Cancer Progression by enhancing SAM availability for mTORC1 Signaling and Chromatin Methylation biorxiv.org 2026-07-09 Aberrant epigenetic reprogramming together with dysregulated mTOR signaling are hallmarks of cancer, where altered chromatin methylation and nutrient-
Linker-Length Landscape Mapping Enables Coupling of Diverse Synthetic Chemically Induced Dimerization Systems to Molecular Readouts biorxiv.org 2026-07-09 Programmable molecular biology increasingly requires strategies for converting engineered recognition or proximity modules into measurable outputs, pa
Shield-4i: A Whole-mount Multiplexed Imaging Platform for Studying Multiscale Information Flow in 3D Multicellular Systems biorxiv.org 2026-07-09 Self-organization in multicellular systems emerges from reciprocal interactions across spatiotemporal scales.
Liver microbiome composition associates with histological severity and PNPLA3 genotype in metabolic dysfunction-associated steatotic liver disease biorxiv.org 2026-07-09 BACKGROUNDMetabolic dysfunction-associated steatotic liver disease (MASLD) is a systemic immunometabolic disorder rapidly increasing worldwide, affect
GIGYF2/4EHP-Mediated Translational Attenuation Maintains Cellular Homeostasis Following Ionizing Radiation biorxiv.org 2026-07-09 Translational regulation is a critical component of the cellular response to environmental stress.
Dfm1 promotes Ste24-dependent translocon quality control biorxiv.org 2026-07-09 Proteins stalled during endoplasmic reticulum translocation clog Sec61 channels and require translocon quality control (TQC) mechanisms for clearance.
Bacterial Hsp70 DnaK transiently samples the proteome to rapidly capture stress-induced misfolding biorxiv.org 2026-07-09 Protein-quality-control systems are essential for cells to maintain protein homeostasis during both steady-state growth and acute stress.
Late embryonic expansion of a novel bone ridge underlies the evolutionary transformation of cylindrically shaped forelimb bones into the flattened skeleton of the penguin flipper biorxiv.org 2026-07-09 The evolution of flippers for wing-powered diving in penguins is a striking example of tetrapod limb specialization.
Subfunctionalization of tbx2 paralogues during photoreceptor cell specification in zebrafish biorxiv.org 2026-07-09 Zebrafish possess three distinct sources of retinal progenitors that produce identical photoreceptor subtypes throughout life.
Cytogenomic signatures of hybridisation in the genus Carpobrotus reveal biased parental dominance biorxiv.org 2026-07-09 O_LIHybridisation is frequently associated with plant invasions; however, its consequences for genome organisation and chromosome evolution remain poo
Selective autophagy promotes bacterial immunity under warming through NBR1-dependent regulation of ABI5 biorxiv.org 2026-07-09 Elevated temperatures compromise plant immunity and increase susceptibility to bacterial pathogens through extensive reprogramming of hormone signalin
A Chemically Defined Synthetic Cell Capable Of Growth And Replication biorxiv.org 2026-07-09 Cells are the fundamental unit of life. Yet there is no natural cell for which all its life-essential functions are understood.
Dissecting human fetal cardiac repair using cardioids biorxiv.org 2026-07-09 Human cardiac injury responses are governed by dynamic interacting processes that are difficult to resolve.
Thematic Shifts in Early-High-Impact Cancer Genomics and Diagnostics Research: A Bibliometric and Semantic Analysis biorxiv.org 2026-07-09 Cancer genomics and diagnostics is a rapidly evolving field in which identifying which topics attract early citation prominence can inform laboratory
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