Nature Methods
- xTrimoPGLM: unified 100-billion-parameter pretrained transformer for deciphering the language of proteins
- Scaling a foundational protein language model to 100 billion parameters
- The need to implement FAIR principles in biomolecular simulations
- Life beyond labels
- Sharing data from the Human Tumor Atlas Network through standards, infrastructure and community engagement
- Enabling global image data sharing in the life sciences
- Uncalled4 improves nanopore DNA and RNA modification detection via fast and accurate signal alignment
- Atomic context-conditioned protein sequence design using LigandMPNN
- Denoising Search doubles the number of metabolite and exposome annotations in human plasma using an Orbitrap Astral mass spectrometer
- Single-cell parallel analysis of DNA damage and transcriptome reveals selective genome vulnerability
- Simultaneous single-cell DNA damage profiling and RNA sequencing by Paired-Damage-seq
- Connectivity of single neurons classifies cell subtypes in mouse brains
- Marrying mechanics with spatial transcriptomics
Molecular Systems Biology
- Metabolic reaction fluxes as amplifiers and buffers of risk alleles for coronary artery disease
- Multi-epitope immunocapture of huntingtin reveals striatum-selective molecular signatures
- Mouse promoters are characterised by low occupancy and high turnover of RNA polymerase II
- Persistent epigenetic memory of SARS-CoV-2 mRNA vaccination in monocyte-derived macrophages
- Pulsed stimuli enable p53 phase resetting to synchronize single cells and modulate cell fate
- Circadian clock features define novel subtypes among breast cancer cells and shape drug sensitivity
- Abundant clock proteins point to missing molecular regulation in the plant circadian clock
- Refuse in order to resist: metabolic bottlenecks reduce antibiotic susceptibility
- Enhanced flux potential analysis links changes in enzyme expression to metabolic flux
- Leveraging prior knowledge to infer gene regulatory networks from single-cell RNA-sequencing data
- Hormone circuit explains why most HPA drugs fail for mood disorders and predicts the few that work
- Gemcitabine and ATR inhibitors synergize to kill PDAC cells by blocking DNA damage response
- Epigenetic modifications and metabolic gene mutations drive resistance evolution in response to stimulatory antibiotics
- Metabolic mutations reduce antibiotic susceptibility of E. coli by pathway-specific bottlenecks
Nature Genetics
- An eRNA transcription checkpoint for diverse signal-dependent enhancer activation programs
- A conserved checkpoint for ligand-dependent enhancer activation
- Psychiatric genetics in the diverse landscape of Latin American populations
- Spatially resolved transcriptomic analysis of the adult human prostate
- Quantitative characterization of tissue states using multiomics and ecological spatial analysis
- Borzoi decodes the complex DNA signals governing gene regulation
- The interplay between germline and somatic variants in alpha-1 anti-trypsin deficiency liver disease
- Collaborative genome-wide association analysis with cryptography
- The complexity of tobacco smoke-induced mutagenesis in head and neck cancer
- Causal machine learning for single-cell genomics
- The genome and GeneBank genomics of allotetraploid Nicotiana tabacum provide insights into genome evolution and complex trait regulation
- Author Correction: Origin and de novo domestication of sweet orange
- Rare loss-of-function variants in HECTD2 and AKAP11 confer risk of bipolar disorder
- Author Correction: Rare variant analyses in 51,256 type 2 diabetes cases and 370,487 controls reveal the pathogenicity spectrum of monogenic diabetes genes
- The landscape of N6-methyladenosine in localized primary prostate cancer
NSMB
- Heritable maintenance of chromatin modifications confers transcriptional memory of interferon-γ signaling
- Structural basis for membrane remodeling by the AP5–SPG11–SPG15 complex
- O-GlcNAc transferase is a key regulator of DNA methylation and transposon silencing
- Author Correction: DELE1 oligomerization promotes integrated stress response activation
- OGT prevents DNA demethylation and suppresses the expression of transposable elements in heterochromatin by restraining TET activity genome-wide
- Small-molecule glues selectively restrict deubiquitylase activity and inflammatory signaling
- Microtubule motors of opposite polarity cooperate rather than compete in cargo transport
- Conformational changes in heat- and proton-sensing ion channel in centipedes
- Thylakoid membrane remodeling by VIPP1 ESCRT-III-like filaments
- Molecular glues that inhibit deubiquitylase activity and inflammatory signaling
- A nuclear pore-anchored condensate enables germ granule organization and transgenerational epigenetic inheritance
- Mutant tau filaments from some inherited frontotemporal dementias show the Alzheimer fold
Nature ChemBiol
- Native top-down proteomics enables discovery in endocrine-resistant breast cancer
- TOPO-seq reveals DNA topology-induced off-target activity by Cas9 and base editors
- Single-step discovery of high-affinity RNA ligands by UltraSelex
- Post-transcriptional modular synthetic receptors
- Author Correction: Imaging the dynamics of messenger RNA with a bright and stable green fluorescent RNA
- Trans-splicing for gene regulation
- Reversible histone deacetylase activity catalyzes lysine acylation
- Pharmacological targeting of BMAL1 modulates circadian and immune pathways
- Guiding chemoenzymatic synthesis
- Phage-fueled defense system
- Learning from CoQ10 history
PLoS Genetics
- ClpP2 proteasomes and SpxA1 determine Listeria monocytogenes tartrolon B hyper-resistance
- Spindle integrity is regulated by a phospho-dependent interaction between the Ndc80 and Dam1 kinetochore complexes
- A phage-encoded counter-defense inhibits an NAD-degrading anti-phage defense system
- Identification of modifier gene variants overrepresented in familial hypomagnesemia with hypercalciuria and nephrocalcinosis patients with a more aggressive renal phenotype
- A Rfa1-MN–based system reveals new factors involved in the rescue of broken replication forks
- Correction: Histone variant H2A.Z is needed for efficient transcription-coupled NER and genome integrity in UV challenged yeast cells
- Doxifluridine promotes host longevity through bacterial metabolism
- Parental germline mosaicism in genome-wide phased de novo variants: Recurrence risk assessment and implications for precision genetic counselling
- Generation of prostate cancer assembloids modeling the patient-specific tumor microenvironment
- RatXcan: A framework for cross-species integration of genome-wide association and gene expression data
- Gene expression in soft-shell clam (Mya arenaria) transmissible cancer reveals survival mechanisms during host infection and seawater transfer
- Significant roles in RNA-binding for the amino-terminal regions of Drosophila Pumilio and Nanos
- Fluctuating reproductive isolation and stable ancestry structure in a fine-scaled mosaic of hybridizing Mimulus monkeyflowers
- Archaic introgression and the distribution of shared variation under stabilizing selection
- Human genetic evidence enriched for side effects of approved drugs
PLoS CompBio
- Molecular dynamics simulations of human cohesin subunits identify DNA binding sites and their potential roles in DNA loop extrusion
- Ten simple rules for getting started with knowledge mobilization
- TIPP3 and TIPP3-fast: Improved abundance profiling in metagenomics
- Logic-based modeling of biological networks with Netflux
- Segmentation of dense and multi-species bacterial colonies using models trained on synthetic microscopy images
- Seizure and redox rescue in a model of glucose transport deficiency
- Why the growth of arboviral diseases necessitates a new generation of global risk maps and future projections
- scTrans: Sparse attention powers fast and accurate cell type annotation in single-cell RNA-seq data
- Quantifying the impact of contact tracing interview prioritisation strategies on disease transmission: A modelling study
- CINner: Modeling and simulation of chromosomal instability in cancer at single-cell resolution
- Spatial structure facilitates evolutionary rescue by drug resistance
- Playbook workflow builder: Interactive construction of bioinformatics workflows
- Integrating multiple spatial transcriptomics data using community-enhanced graph contrastive learning
- Predicting and comparing transcription start sites in single cell populations
- SpaMask: Dual masking graph autoencoder with contrastive learning for spatial transcriptomics
Science Signalling
- RIPK3 coordinates RHIM domain–dependent antiviral inflammatory transcription in neurons | Science Signaling
- Poor sleep for pass-out drunks | Science Signaling
- A sensitive biosensor of endogenous Gαi activity enables the accurate characterization of endogenous GPCR agonist responses | Science Signaling
- A lupus-derived autoantibody that binds to intracellular RNA activates cGAS-mediated tumor immunity and can deliver RNA into cells | Science Signaling
- Treating neuroinflammation through the nose | Science Signaling
- The kinase PLK1 promotes Hedgehog signaling–dependent resistance to the antiandrogen enzalutamide in metastatic prostate cancer | Science Signaling
- Structural analysis reveals how tetrameric tyrosine-phosphorylated STAT1 is targeted by the rabies virus P-protein | Science Signaling
- Tales from the cryptic pocket | Science Signaling
- Myeloid sirtuin 6 deficiency causes obesity in mice by inducing norepinephrine degradation to limit thermogenic tissue function | Science Signaling
- NEMO is essential for directing the kinases IKKα and ATM to the sites of DNA damage | Science Signaling
- The NEMO/ATM/IKKα complex: A key player in colorectal cancer progression and treatment | Science Signaling
- Metabolic pressure from sensory neurons | Science Signaling
- The acetyltransferase GCN5 contributes to neuroinflammation in mice by acetylating and activating the NF-κB subunit p65 in microglia | Science Signaling
- Making sense of gastric cancer | Science Signaling
Cell Reports
- Cancer-cell-derived cGAMP limits the activity of tumor-associated CD8+ T cells
- Sex differences in DNMT3A-mutant clonal hematopoiesis and the effects of estrogen
- Insights into convergent evolution of cosexuality in liverworts from the Marchantia quadrata genome
- LAMP2A-mediated neuronal hyperexcitability by enhancing NKAβ1 degradation underlies depression-induced allodynia
- Circular RNAs exhibit exceptional stability in the aging brain and serve as reliable age and experience indicators
- Single-cell RNA-seq analysis identifies the atlas of lymph fluid and reveals a sepsis-related T cell subset
- A global collaboration for systematic analysis of broad-ranging antibodies against the SARS-CoV-2 spike protein
- A spatiotemporal cell atlas of cardiopulmonary progenitor cell allocation during development
- Ciliary marginal zone of the developing human retina maintains retinal progenitor cells until late gestational stages
- Hypoxia-induced PRMT1 methylates HIF2β to promote breast tumorigenesis via enhancing glycolytic gene transcription
- Targeting CXCR1 alleviates hyperoxia-induced lung injury through promoting glutamine metabolism
- Hi-C profiling in tissues reveals 3D chromatin-regulated breast tumor heterogeneity informing a looping-mediated therapeutic avenue
- The Exserohilum turcicum effector EtEC81 reprograms alternative splicing in maize and activates immunity
- Intestinal-region-specific functions of AHR in intrinsic enteric neurons during infections
- Identification of the core regulatory program driving NEUROD1-induced neuronal reprogramming
Molecular Cell
- STING mediates lysosomal quality control and recovery through its proton channel function and TFEB activation in lysosomal storage disorders
- An ultraconserved snoRNA-like element in long noncoding RNA CRNDE promotes ribosome biogenesis and cell proliferation
- Hypoxia-induced phase separation of ZHX2 alters chromatin looping to drive cancer metastasis
- Ultrastable and versatile multimeric ensembles of FoxP3 on microsatellites
- Pcf11/Spt5 condensates stall RNA polymerase II to facilitate termination and piRNA-guided heterochromatin formation
- Identification of molecular determinants of gene-specific bursting patterns by high-throughput imaging screens
- SLFN11-mediated ribosome biogenesis impairment induces TP53-independent apoptosis
- SUMO4 promotes SUMO deconjugation required for DNA double-strand-break repair
- A PARP2 active site helix melts to permit DNA damage-induced enzymatic activation
- Transcription elongation factor ELOF1 is required for efficient somatic hypermutation and class switch recombination
- Transcription-coupled AID deamination damage depends on ELOF1-associated RNA polymerase II
- A comprehensive Schizosaccharomyces pombe atlas of physical transcription factor interactions with proteins and chromatin
- Degradation of circular RNA by the ribonuclease DIS3
- Molecular basis of promiscuous chemokine binding and structural mimicry at the C-X-C chemokine receptor, CXCR2
- Nucleic-acid-induced ZCCHC3 condensation promotes broad innate immune responses