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Cell Biology And Disease Mechanisms

Reprogramming macrophage mechanosensation via TRPV4 modulating mechano-immunotherapy controls fibrotic encapsulation of biomaterial implants. Bioactive materials
Nanotechnology-mediated podocyte injury repair: mechanistic exploration and therapeutic prospects. Renal failure
Neoplastic CD3⁺ B cells remodel the DLBCL tumor microenvironment via single-cell and spatial transcriptomics. Cancer biology & therapy
Integrative single-cell and spatial transcriptomic approaches to decipher the tumor microenvironment and therapeutic resistance in pancreatic cancer. Cancer biology & therapy
POU2F2 as a dual oncogenic and immunomodulatory driver in kidney renal clear cell carcinoma. Cell adhesion & migration
Multi-omics profiling identifies CDK1 as a key mediator of mitosis through the PTN pathway in bladder cancer. Future science OA
Persistence of tobacco-mutated alveolar progenitor cells after smoking cessation mirrors long term risk of lung adenocarcinoma biorxiv.org
Single-cell RNA-seq reveals conserved and divergent cellular states across wound types and species biorxiv.org
Lineage plasticity driven by GATA6 loss fuels colorectal cancer metastasis cell.com
Patient-derived organoids reveal ductal dysfunction and CFTR-modulator responses in chronic pancreatitis cell.com
A tissue-scale strategy for sensing threats in barrier organs cell.com
Capturing the dynamics of STAT6 macrophage polarization using bioluminescence temporal signatures cell.com
Human macrophages encode stimulus-specific information of prior exposures through trained immunity cell.com
Quantitative cytokine profiling of primary human macrophages reveals distinct single-cell modes of trained immunity cell.com
Decoding the spatiotemporal development of human meninges cell.com
Excessive epithelial mechanosensation drives nociceptive innervation and chronic bladder pain via the PIEZO1-SLC7A11-glutamate axis cell.com

Plant Stress Responses And Signaling

Oryza sativa heavy metal ATPase (OsHMA) transporter-mediated cadmium uptake in rice: functional insights for low-Cd breeding. Food chemistry. Molecular sciences
Jasmonate, salicylate, and ethylene-responsive transcriptomics discovery in spikelets of three wheat genotypes reveals a rapid and conserved response for jasmonate signaling. Plant signaling & behavior
AtGATA5 contributes to ABA-mediated seed germination by promoting NCED3 and ABI4 expression in Arabidopsis thaliana. Plant signaling & behavior
Plant cell wall-plasma membrane attachments mediate stress resilience through cellulose synthase complexes and remorins cell.com
Molecular integration of seasonal temperature signals in flowering time control nature.com

Neurodegenerative Disease Genetics

Cortical transcriptomic dysregulation in Autism spectrum disorder: A conceptual synthesis. IBRO neuroscience reports
DNA Methylation and Proteomic Profiling of Postmortem Brain Tissue Reveals Epigenetic Dysregulation and Neuroinflammatory in Fragile X-associated Tremor/Ataxia Syndrome (FXTAS) biorxiv.org
Schizophrenia-associated DNA methylation differences in the cortex are neuron-specific biorxiv.org
Nuclear proteome reveals microtubule-associated protein regulating fate and disease cell.com
An emergent disease-associated motor neuron state precedes cell death in ALS cell.com
Arc mediates intercellular tau transmission via extracellular vesicles cell.com
Recurrent patterns of TOP1-mediated neuronal genomic damage shared by major neurodegenerative disorders cell.com
Revisiting retinal and macular degeneration in the genomics era nature.com
Challenges and future directions for multiple sclerosis after the 2024 McDonald diagnostic criteria nature.com

Transcriptomic Data Analysis

Cross-study analysis identifies estrogen depletion and exposure duration as key determinants of bisphenol A transcriptomic potency in MCF-7 cells. Toxicology reports
MOLA: a novel topological data analysis framework for analyzing multiomic loops in precision medicine biorxiv.org
MKMC enables reference-free transcriptomic analysis using k-mer representations biorxiv.org
The Blood RNA Stability Atlas: defining temporal structure and trait-state programs in the human whole-blood transcriptome biorxiv.org
BulkFormer: A large-scale foundation model for bulk transcriptomes cell.com

Genetic Basis Of Disease

Integrative multi-omics Mendelian randomization reveals key lipid metabolism genes as therapeutic targets for diabetic nephropathy pathogenesis. Renal failure
Relationship between major depressive disorder and venous thromboembolism: a five-ancestry genetic analysis. Hematology (Amsterdam, Netherlands)
CATaN maps gene regulatory programs that shape genetic risk across complex diseases biorxiv.org
Detecting domain-level organization in genome-wide association study summary statistics using frequency-impact-reliability profiles biorxiv.org
Why linkage disequilibrium measures disagree: Fisher geometry of rare common haplotype structure biorxiv.org
Current challenges in GWAS integration and fine-mapping for variant interpretation biorxiv.org
LDSC regression-based heritability estimates can be biased when summary statistics are obtained from meta-analysis or imputed variants biorxiv.org
Interaction-finder: automated literature-based discovery of biological entity associations with quote-level provenance biorxiv.org
Kernelized approach enables explainable gene prioritizations for complex traits biorxiv.org
A Genetic Atlas of Direct and Inverse Neuropsychiatric-Cancer Comorbidity biorxiv.org

Cancer Microenvironment And Therapy

Decoding the microbiome: artificial intelligence-targeted gut microenvironment breakthroughs in personalized cancer therapy. Gut microbes
Gut microbiome drives glycodeoxycholic acid-mediated attenuation of hypertension. Gut microbes
Is Fusobacterium nucleatum the key mediator between oral infections and systemic diseases? Mechanistic insights and therapeutic implications. Gut microbes
Immune regulatory mechanisms and potential microbiota-associated targets in Kawasaki disease: an integrative multi-omics and network pharmacology study. Artificial cells, nanomedicine, and biotechnology
Iron drives protease-independent cleavage of gasdermin D in allergic airway diseases cell.com
Author Correction: Sustained nitric oxide production by engineered <i>E. coli</i> remodels the tumor microenvironment and potentiates immunotherapy nature.com

Cellular Immunotherapy And Gene Therapy

Preclinical translation of Neurofibromatosis type 1 (NF1) exon 17 skipping using targeted U7-SnRNA packaged into engineered AAV serotypes. biorxiv.org
FDA-approved fulvestrant-induced CAR phase separation enables precise control of CAR T antitumor function cell.com
The critical role of the endogenous immune compartment after CAR T cell therapy in recurrent GBM cell.com
Cuproptosis-immunity crosstalk informs strategy to overcome immunotherapy resistance cell.com
Expansion and CAR engineering of granulocyte-monocyte progenitors for cellular immunotherapy cell.com
Efficient targeting of human glial progenitor cells in vivo with engineered AAV vectors and glymphatic delivery nature.com
An AAV vector for glial cells nature.com
Anti-LAG-3 with or without anti-PD-1 in recurrent glioblastoma: a phase 1 trial nature.com
A second chance for gene therapy to restore natural hearing nature.com
Human embryonic stem cell-derived dopaminergic cells for Parkinson’s disease: a phase 1/2 open-label trial nature.com
KRAS-G12D inhibitor HRS-4642 plus chemotherapy in advanced <i>KRAS</i><sup>G12D</sup>-mutant pancreatic cancer: a phase 1b/2 trial nature.com

Population Genetics And Evolution

Recommendations for the ethical and accurate use of population descriptors: a trainee-led survey of early-career researchers biorxiv.org
A Lake Charr Pangenome Reveals Highly Conserved Ohnologs as Drivers of Phenotypic Diversity biorxiv.org
Metabarcoding replicate detection frequency tracks ddPCR copy number for cod and herring eDNA in ancient marine sediments biorxiv.org
Integrating Bottleneck Size into Selection Tests for Biological Diversity Data biorxiv.org
Harnessing citizen science to contextualize adaptation mechanism discovery cell.com
The traffic concentration effects of urban navigation services nature.com
Genetic origins and constraints of evolutionary innovation nature.com
How evolution builds three morphs from one genome nature.com
When the real world becomes the trial nature.com

Primate And Human Developmental Genetics

GAMETE maps the genetic architecture of chromatin accessibility in rice pollen at single-nucleus resolution biorxiv.org
Locus-Level Transposable Element Profiling Resolves Division-Coupled Transcriptional Dynamics During Human Endoderm Specification biorxiv.org
Interactome Specialization Predicts Genome-Wide Binding-Site Degeneracy in Drosophila melanogaster Transcription Factors biorxiv.org
Generation of spermatogonia from human and non-human primate pluripotent stem cells cell.com
Continuous modeling of primate embryogenesis from totipotency to early organogenesis cell.com
Two distinct causes contribute to the low efficiency of human pre-implantation development cell.com
Reconstituting human primitive streak formation through extra-embryonic cell coordination cell.com

Computational Biology And Protein Function

MAERM: Predicting Enzyme-Reaction Matching Relationships with a Mixed-Attention Model biorxiv.org
Safeguarding open-weight genomic foundation models through weight locking biorxiv.org
Glycine molecule radical: Predicted properties and dipeptide formation biorxiv.org
Metagenomic contextualization of proteins with state space models biorxiv.org
AGPI: An AI-Powered Genomic Pathogen Intelligence Platform for Integrated Classification, Visualization, and Therapeutic Targeting biorxiv.org
AptViralDB: A Repository of Experimentally Validated Antiviral Aptamers biorxiv.org
onsite: An Integrated Framework for Phosphosite Localization and False Localization Rate Estimation biorxiv.org
PKProbDesign: RNA inverse folding including pseudoknots by optimizing thermodynamic folding probability biorxiv.org
ProtAug: An Empirical Investigation of pLM-Guided Data Augmentation for Protein Sequence Prediction Tasks biorxiv.org
ProtPen combines sequence- and structure-based approaches to facilitate protein function predictions on a proteome-wide scale biorxiv.org
Active RNA synthesis patterns nuclear condensates cell.com
Deep learning of functional perturbations from condensate morphology cell.com
A viral ORFeome library for systems-level genetic dissection of host-pathogen interactions cell.com
Systematic discovery of pathogen effector functions across human pathogens and pathways cell.com
High-quality phage assembly from metagenomes with PALACE nature.com

Crispr Screens And Mutational Analysis

Transformer models of mutation risk at base-pair resolution identify non-coding hotspot cancer driver mutations biorxiv.org
Multidimensional mutational phenotypes of MMR deficiency in human cancer cells biorxiv.org
Somatic mutation inference from single-cell transcriptomics: A survey in the esophagus biorxiv.org
Isoform-level resolution in single-cell CRISPR screens reveals hidden functional consequences of gene perturbation biorxiv.org
Joint analysis of multiply perturbed cells improves statistical power and cost efficiency in Perturb-seq biorxiv.org
Deciphering protein mutation-phenotype linkages from CRISPR-based tiling mutagenesis screens cell.com
Uncovering spatially resolved functional genomics with CRISPR screen sequencing cell.com
Single-cell four-omics with CHARM nature.com

Neuroscience Data And Architecture

Multiscale harmonization and semantic integration of biomedical data enable biological insights through immersive exploration biorxiv.org
Multipair phase-modulated temporal interference electrical stimulation combined with fMRI cell.com
Physiological brain clearance architecture revealed by neuronal protein tracing cell.com
Shared neural geometries for bilingual semantic representations in human hippocampal neurons cell.com
Multimodal imaging of gene expression, morphology, and activity of the same neuron cell.com
Geometric constraints on the architecture of mammalian cortical connectomes cell.com
Map of spiking activity underlying change detection in the mouse visual system cell.com
Health system learning enables generalist neuroimaging models nature.com

Spatial Tissue And Cell Biology

Spatial mitochondrial lineage tracing uncovers a premetastatic niche and microenvironment programmed fate switching in osteosarcoma biorxiv.org
Digital decoding tissue microenvironment heterogeneity from spatial proteomics through graph-enhanced transfer learning cell.com
Multiscale integration of tissue and chromatin context converts cell heterogeneity into stable intestinal patterning cell.com
Four-dimensional molecular mapping from a spatial snapshot reveals the dynamics of hair follicle organogenesis cell.com

Quantum Physics And Photonics

Whole-cell particle-based digital twin simulations from 4D lattice light-sheet microscopy data cell.com
Gapless fracton quantum spin liquid and emergent photons in a 2D spin-1 model nature.com
Mesoscale ordered assembly of Er<sup>3+</sup>-doped quantum dots enables efficient 1.55 µm electroluminescence nature.com
Chip-integrated metasurface-enabled single-photon skyrmion sources nature.com

Nature Biotech

Engineered ADARs enable precision A-to-G base editing of DNA nature.com
Efficient in vivo cytosine base editing using virus-like particles with uracil DNA glycosylase inhibition nature.com
Biotech’s digital twin dilemma nature.com
Frontier AI companies as biotech acquirers nature.com

Arxiv Genetics

Driver-independent lexAop-tdTomato.nls reporter signal in the adult Drosophila proventriculus biorxiv.org
A genetically buffered helicase network promotes tolerance of G-quadruplex stabilization in Saccharomyces cerevisiae biorxiv.org
Shifts in Genetic Diversity of Porcine Reproductive and Respiratory Syndrome Virus 2 in Vietnam Before and After African Swine Fever: Increased Diversity and Novel Sub-lineages biorxiv.org
Drosophila beanbag (beba) encodes a novel insect receptor tyrosine kinase associated with reproductive niche organisation biorxiv.org
The Drosophila FET orthologue Cabeza is an essential cofactor for ETV4-mediated activation of GGAA microsatellite neoenhancers biorxiv.org
Knock-in = knock-out: differential fitness effects of cardinal mutations in Anopheles stephensi biorxiv.org
Modeling population control via tunable sex ratio distorter gene drives in Aedes aegypti biorxiv.org
Genetic Variation in Drosophila melanogaster Aggression biorxiv.org
Two-tower models for genomic prediction of reproductive outcomes and sex-specific fertility liabilities: simulation insights biorxiv.org
Genome-wide meQTL mapping in cattle blood reveals cis and trans regulation of DNA methylation biorxiv.org
Functional surrogacy enables Vascular Ehlers-Danlos Syndrome modelling in zebrafish in the absence of a COL3A1 ortholog biorxiv.org
Assessment of homing gene drive efficiency using multiplexed sgRNAs targeting doublesex in the global crop pest Drosophila suzukii biorxiv.org
Enhancing predictive accuracy of yield traits in cassava through multi-trait genomic prediction biorxiv.org
Model of naturally occurring refractive error (NORE) in mice biorxiv.org
The Effect of Depriving the Aedes aegypti Mosquito of Natural Levels of Radiation biorxiv.org
Pangenome-based human genome analysis improves trait association and genomic prediction biorxiv.org
Towards genetic indicators in ectomycorrhizal fungi: estimating the effective population size biorxiv.org
Paralogs of the <em>Candida albicans TLO</em> gene family form interconnected functional networks with incomplete redundancy biorxiv.org
Effects of Deficient Glycosylation and Deglycosylation on Sperm Condition in Zebrafish (Danio rerio) biorxiv.org
The impact of P-Element-induced hybrid dysgenesis on the male germline in Drosophila simulans biorxiv.org
Female genetic variation controlling timing of mating plug ejection in Drosophila melanogaster biorxiv.org

Cell Sys

The molecular landscape of cellular metal ion biology cell.com
High-throughput DNA engineering by mating bacteria cell.com
Living bacterial reservoir computers for information processing and sensing cell.com
A data-driven modeling framework for mapping genotypes to synthetic microbial community functions cell.com
Glycoform engineering of a mammalian platform to sculpt a humanized recombinant bioscavenger cell.com
Scalable enumeration and sampling of minimal metabolic pathways for organisms and communities cell.com
Targeted genomic editing of human gut Bacteroides species based on CRISPR-associated transposases cell.com
Integrated control of redox and energy metabolism by the membrane-bound and soluble transhydrogenases of Pseudomonas putida across metabolic regimes cell.com
High-throughput machine learning-aided antibody discovery for cell surface antigens cell.com
Pooled combinatorial screening identifies transcription factor sets that drive hematopoietic progenitor-like cell fate cell.com
Widespread transcriptional memory shapes heritable states and functional heterogeneity in cancer and stem cells cell.com
Discovering what is possible: How synthetic biology illuminates development cell.com
The tree labeling polytope: A unified approach to ancestral reconstruction problems cell.com
Multiplex genome engineering: Methodologies and applications cell.com

Cell

Co-option of lysosomal machinery shapes the evolution of the intracellular photosymbiosis supporting coral reefs cell.com
Structural basis for host membrane binding and remodeling by invading malaria parasites cell.com
Chloroplast sunscreening by protein condensates confers high-light tolerance cell.com
Mechanism of lipid transfer by bridge-like protein VPS13A and the scramblase XK cell.com
Complete biosynthesis of the anticancer cephalotaxinone and homoerythratine cell.com
Prion-based protein self-assembly tunes mutagenesis to enable rapid adaptation cell.com
mRNA 3′ UTRs chaperone intrinsically disordered regions to control protein activity cell.com
Xenophagocytosis blockade enhances interspecies chimerism cell.com
Replaying germinal center evolution on a quantified affinity landscape cell.com
Deep-sea megafauna co-opts microbial energy metabolism genes to withstand ultra-long starvation cell.com
TPPP/p25 amyloid seeding activity as a specific biomarker for multiple system atrophy cell.com
Genome instability triggers intercellular DNA transfer between human cells cell.com

Nat Rev Gen

Genetic analysis of imaging-derived phenotypes nature.com
RBPscan measures protein–RNA interactions in living cells nature.com
Advancing the applications of liquid biopsies in oncology nature.com

Nat Med

Biological aging clocks in health and disease nature.com

Nat Comm

Atmospheric CO₂-to-acetaldehyde artificial photosynthesis in metallo hydrogen-bonded organic frameworks nature.com
Pervasive summertime nitrous oxide undersaturation in U.S. lakes and reservoirs nature.com
Efficiency-weighted cooling degree days reveal opposing temperature and humidity effects on energy demand nature.com
Phage portal proteins counteract stringent-response–mediated restriction nature.com

Arxiv Genomics

Comparative Analysis of Transposable Elements in Hermetia illucens biorxiv.org
Characterizing the Small Non-Coding RNA Pathways in the Invasive Zebra Mussel (Dreissena polymorpha) biorxiv.org
First-Trimester Non-Invasive Prediction of Preterm Birth Using Cell-Free DNA Fragmentomics biorxiv.org
Gene model for the ortholog of raptor in Drosophila grimshawi biorxiv.org
Evolutionary dynamics of Aegilops revealed through comparative genome assembly of all 25 species biorxiv.org
An endogenous retrovirus insertion disrupting bovine ALKBH8 causes a failure-to-thrive syndrome with immunodeficiency associated with juvenile mortality in Brown Swiss cattle biorxiv.org
Concerted evolution and unorthodox recombination of human subtelomeres biorxiv.org
A near-complete genome assembly of the Fusarium oxysporum keratitis isolate MRL8996 biorxiv.org
Semantic fragment representations for coordinate-free analysis of genomics data biorxiv.org
Programmable CRISPRtune dissects the transcriptional repressive activity of MeCP2 biorxiv.org
Chromosome organization of Entamoeba histolytica and Entamoeba dispar biorxiv.org
Chromosome-level Genome Assembly of the Potato Leafhopper Empoasca fabae (Hemiptera: Cicadellidae) biorxiv.org
A Comprehensive DNA Methylome BodyMap across 12 Organs/Tissues from Spaceflight Mice biorxiv.org
COMPARATIVE GENOMIC ANALYSIS OF CORE AND ACCESSORY GENES IN RUST FUNGI REVEALS PATHOGENICITY-ASSOCIATED GENE FAMILIES IN Phakopsora pachyrhizi biorxiv.org
The Encyclopedia of DNA Elements biorxiv.org
A chromosome-level reference genome of the largest cervid species - the European moose (Alces alces; Linnaeus, 1758) biorxiv.org

Europepmc Genomics

Dual β-lactam therapy against high-risk Pseudomonas aeruginosa isolates: a dynamic in-vitro infection model study integrating population genomics with quantitative systems pharmacology modelling and simulations. The Lancet. Microbe
Interactive effects of temperature and water activity on growth, mycotoxin production, and transcriptomic profiles of Aspergillus flavus, Aspergillus parasiticus, and Fusarium verticillioides. Food microbiology
Comparative genomics and phenotypes of Listeria monocytogenes isolated from enoki mushrooms in South Korea and China. Food microbiology
Cross-feeding and stress response are the basis of increased fruitiness and leavening capacity of a new consortium of the sourdough microorganisms Companilactobacillus crustorum and Wickerhamomyces anomalus. Food microbiology
iNOS/NO-Induced autophagy primes PANoptosis as the central driver of streptococcal toxic shock-like syndrome in zoonotic Streptococcus suis infection. Emerging microbes & infections
Advances in SEC61G research: from ER translocon subunit to emerging pan-cancer oncogenic roles. Cancer biology & therapy
Population genomics reveals a long-term increase in azole resistance associated with the emerging cluster AZR among Candida tropicalis causing invasive infections. Emerging microbes & infections
Synthetic biology of oncolytic bacteria: Comparative microbial chassis and precise killing strategies. Toxicology reports
Metabolic engineering of Vibrio natriegens for the efficient biosynthesis of ergothioneine from sucrose using non-sterile fed-batch fermentation. Synthetic and systems biotechnology
Progresses of transposon research in Saccharomyces cerevisiae. Synthetic and systems biotechnology
A four-gene signature for diagnosis of acute kidney injury following kidney transplantation. Renal failure
Beyond pesticides: next-generation genetic biocontrol technologies for sustainable population suppression of agricultural insect pests. Fly
Engineered bacteria in disease diagnosis and therapy: A synthetic biology perspective. Synthetic and systems biotechnology
Transposon-based genome editing of industrial microorganisms: advances, challenges, and prospects. Synthetic and systems biotechnology
A CRISPR-driven aptasensor for colorimetric monitoring of lead (II) ion assisted by rolling circle amplification process: Effective in controlling food and health safety. Spectrochimica acta. Part A, Molecular and biomolecular spectroscopy
Development and clinical validation of a multiplex visual POCT platform based on RT-RAA-CRISPR/Cas12a for porcine diarrheal viruses. Synthetic and systems biotechnology
Multi-omics integration reveals convergent extracellular matrix remodelling and lipid metabolic reprogramming as central axes of adipocyte differentiation from mouse embryonic stem cells. Adipocyte
The RNA-binding activity of the Drosophila Brat protein is necessary for viability and mRNA regulation. RNA biology
In situ continuous evolution of native transporter HGT1 unlocks xylose utilization in Kluyveromyces lactis. Synthetic and systems biotechnology
OmniEdit: A unified CRISPR/Cas9 platform for precise genome engineering and strain optimization of the Cordyceps militaris cell factory. Synthetic and systems biotechnology
The epigenetic archaeology of human-dog companionship. Epigenetics
Chromosome-level genome and transcriptome analysis of Trichophyton verrucosum reveals pathogenicity mechanisms and antifungal response. Virulence
Statement of Retraction: Easy efficient HDR-based targeted knock-in in Saccharomyces cerevisiae genome using CRISPR-Cas9 system. Bioengineered

Arxiv Bfx

High resolution Streptococcus pyogenes core genome MLST and LIN coding scheme for outbreak detection biorxiv.org
ArthroVerse: mapping protein family diversity across arthropod-associated microbiomes biorxiv.org
M6AFormer Prioritizes Unannotated Functional m6A Candidate Sites in the Human m6A Epitranscriptome biorxiv.org
Panomap: Unbiased Nanopore Signal Mapping with Pangenome Variation Graphs biorxiv.org
GBZ-base and GAF-base: Indexed pangenome file formats biorxiv.org
SPARC: A Graph-based Optimization Framework for Directional Trajectory Reconstruction Across Ordered Single-Cell Conditions biorxiv.org
Structure-guided computational design and mechanistic understanding of the p95HER2-targeting NAZ-mAb antibody and its variants biorxiv.org
AtlasLens: Metadata-centric exploration and analysis of single-cell atlases biorxiv.org
Improved 3D Radial Phyllotaxis Trajectories for Uniform Density Distribution of Readout Directions and Sequential Binning biorxiv.org
Evaluating the cross-species transferability and scaling of sequence-to-function predictions in AlphaGenome biorxiv.org
Comparative Modelling of Actin-Tropomyosin Interfaces biorxiv.org
Benchmarking AI-Driven PTIm-mAb Across Eleven FDA-Approved Bispecific Antibodies: A Cross-Tool Validation Study biorxiv.org
MARiO: predicting cancer variant pathogenicity by integrating in silico evaluation and patient-level mutational contexts biorxiv.org

Cell Stem

SPACE-seq integrates spatial transcriptomics and lineage tracing in native tissues cell.com