Communications Biology

Article	Citations
DeepEMhancer: a deep learning solution for cryo-EM volume post-processing	523
BrainSpace: a toolbox for the analysis of macroscale gradients in neuroimaging and connectomics datasets	265
A comprehensive review on plasmonic-based biosensors used in viral diagnostics	255
Single-cell and spatial transcriptomics enables probabilistic inference of cell type topography	248
Single-cell transcriptomes of the human skin reveal age-related loss of fibroblast priming	230
Second-generation lung-on-a-chip with an array of stretchable alveoli made with a biological membrane	160
pH-responsive high stability polymeric nanoparticles for targeted delivery of anticancer therapeutics	158
Identification of 3-chymotrypsin like protease (3CLPro) inhibitors as potential anti-SARS-CoV-2 agents	150
Activation of mitochondrial TUFM ameliorates metabolic dysregulation through coordinating autophagy induction	150
Ionization and structural properties of mRNA lipid nanoparticles influence expression in intramuscular and intravascular administration	147
Mapping the immune environment in clear cell renal carcinoma by single-cell genomics	135
SARS-CoV-2 infection induces a pro-inflammatory cytokine response through cGAS-STING and NF-κB	124
Extended pharmacodynamic responses observed upon PROTAC-mediated degradation of RIPK2	124
Towards organoid culture without Matrigel	123
Role of sleep deprivation in immune-related disease risk and outcomes	121
Identification of SARS-CoV-2 inhibitors targeting Mpro and PLpro using in-cell-protease assay	115
The antimicrobial potential of cannabidiol	112
Amplification-free RNA detection with CRISPR–Cas13	112
Deep ocean metagenomes provide insight into the metabolic architecture of bathypelagic microbial communities	105
Sex differences in SARS-CoV-2 infection rates and the potential link to prostate cancer	104
Human ACE2 receptor polymorphisms and altered susceptibility to SARS-CoV-2	102
Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants	102
NetTCR-2.0 enables accurate prediction of TCR-peptide binding by using paired TCRα and β sequence data	100
Tetracycline-inactivating enzymes from environmental, human commensal, and pathogenic bacteria cause broad-spectrum tetracycline resistance	95
Comparative ACE2 variation and primate COVID-19 risk	94

Cells grown in three-dimensional spheroids mirror in vivo metabolic response of epithelial cells	90
Fatty-acid-induced FABP5/HIF-1 reprograms lipid metabolism and enhances the proliferation of liver cancer cells	89
Evolution of antibiotic resistance at low antibiotic concentrations including selection below the minimal selective concentration	89
Interaction of SHP-2 SH2 domains with PD-1 ITSM induces PD-1 dimerization and SHP-2 activation	88
Newly discovered Synechococcus sp. PCC 11901 is a robust cyanobacterial strain for high biomass production	87
Climate-change-driven growth decline of European beech forests	87
Temporal sequences of brain activity at rest are constrained by white matter structure and modulated by cognitive demands	86
Genomic and transcriptomic variation defines the chromosome-scale assembly of Haemonchus contortus, a model gastrointestinal worm	86
Molecular basis for the disruption of Keap1–Nrf2 interaction via Hinge & Latch mechanism	84
The genetic architecture of appendicular lean mass characterized by association analysis in the UK Biobank study	83
Telomere-to-telomere gapless chromosomes of banana using nanopore sequencing	82
Human ACE2 peptide-mimics block SARS-CoV-2 pulmonary cells infection	82
Brains and algorithms partially converge in natural language processing	82
SARS-CoV-2 specific antibody and neutralization assays reveal the wide range of the humoral immune response to virus	81
Large-scale integration of single-cell transcriptomic data captures transitional progenitor states in mouse skeletal muscle regeneration	81
From whole-mount to single-cell spatial assessment of gene expression in 3D	81
Improved designs for pET expression plasmids increase protein production yield in Escherichia coli	80
Temporal association between human upper respiratory and gut bacterial microbiomes during the course of COVID-19 in adults	80
Training instance segmentation neural network with synthetic datasets for crop seed phenotyping	79
Robust estimation of bacterial cell count from optical density	79
Simple and effective serum-free medium for sustained expansion of bovine satellite cells for cell cultured meat	79
PD-1 derived CA-170 is an oral immune checkpoint inhibitor that exhibits preclinical anti-tumor efficacy	78
Met-Flow, a strategy for single-cell metabolic analysis highlights dynamic changes in immune subpopulations	76
Inhibition of the CCL2 receptor, CCR2, enhances tumor response to immune checkpoint therapy	76
Integration of substrate- and flow-derived stresses in endothelial cell mechanobiology	73
ExoSTING, an extracellular vesicle loaded with STING agonists, promotes tumor immune surveillance	72
Prioritization of candidate causal genes for asthma in susceptibility loci derived from UK Biobank	72
Single-cell analysis supports a luminal-neuroendocrine transdifferentiation in human prostate cancer	70
A framework for identifying the recent origins of mobile antibiotic resistance genes	69
A genome-wide meta-analysis yields 46 new loci associating with biomarkers of iron homeostasis	69
A miRNA-based diagnostic model predicts resectable lung cancer in humans with high accuracy	68
Accelerating antibiotic discovery through artificial intelligence	68
A haplotype-led approach to increase the precision of wheat breeding	68
Cryo-EM structure of type 1 IP3R channel in a lipid bilayer	67
Tipiracil binds to uridine site and inhibits Nsp15 endoribonuclease NendoU from SARS-CoV-2	66
Multiple impacts of microplastics can threaten marine habitat-forming species	66
Maize GOLDEN2-LIKE genes enhance biomass and grain yields in rice by improving photosynthesis and reducing photoinhibition	65
Type I toxin-antitoxin systems contribute to the maintenance of mobile genetic elements in Clostridioides difficile	65
High frequency acoustic cell stimulation promotes exosome generation regulated by a calcium-dependent mechanism	64
Cyanobacterial blooms contribute to the diversity of antibiotic-resistance genes in aquatic ecosystems	63
Exploring the evidence for epigenetic regulation of environmental influences on child health across generations	63
Climate change threatens Chinook salmon throughout their life cycle	63
IFN signaling and neutrophil degranulation transcriptional signatures are induced during SARS-CoV-2 infection	63
Design and optimisation of dendrimer-conjugated Bcl-2/xL inhibitor, AZD0466, with improved therapeutic index for cancer therapy	62
Features and applications of haplotypes in crop breeding	62
A combined approach for single-cell mRNA and intracellular protein expression analysis	61
Microglial metabolism is a pivotal factor in sexual dimorphism in Alzheimer’s disease	61
Optogenetic therapy: high spatiotemporal resolution and pattern discrimination compatible with vision restoration in non-human primates	60
Gut mycobiota alterations in patients with COVID-19 and H1N1 infections and their associations with clinical features	59
When dormancy fuels tumour relapse	58

The brain and its time: intrinsic neural timescales are key for input processing	58
Applying deep learning to single-trial EEG data provides evidence for complementary theories on action control	58
Understanding the synergistic effect of physicochemical properties of nanoparticles and their cellular entry pathways	57
The gut mycobiome of healthy mice is shaped by the environment and correlates with metabolic outcomes in response to diet	56
Gut microbiome diversity is an independent predictor of survival in cervical cancer patients receiving chemoradiation	56
A time-dependent diffusion MRI signature of axon caliber variations and beading	56
Tumor microbiome contributes to an aggressive phenotype in the basal-like subtype of pancreatic cancer	56
Biomolecular condensates as arbiters of biochemical reactions inside the nucleus	56
Sand flies: Basic information on the vectors of leishmaniasis and their interactions with Leishmania parasites	56
Wnt signaling in lung development, regeneration, and disease progression	56
Increasing atmospheric CO2 concentrations correlate with declining nutritional status of European forests	56
Detritivore conversion of litter into faeces accelerates organic matter turnover	55
Targeting the interaction between RNA-binding protein HuR and FOXQ1 suppresses breast cancer invasion and metastasis	55
A normative modelling approach reveals age-atypical cortical thickness in a subgroup of males with autism spectrum disorder	55
A novel canine reference genome resolves genomic architecture and uncovers transcript complexity	55
Parameter tuning differentiates granule cell subtypes enriching transmission properties at the cerebellum input stage	54
Transcriptomic signatures of brain regional vulnerability to Parkinson’s disease	53
β-amyloid and tau drive early Alzheimer’s disease decline while glucose hypometabolism drives late decline	53
The multiple mechanisms of MCL1 in the regulation of cell fate	53
Genome-resolved metagenomics suggests a mutualistic relationship between Mycoplasma and salmonid hosts	53
A spatial regime shift from predator to prey dominance in a large coastal ecosystem	52
Bacterial diets differentially alter lifespan and healthspan trajectories in C. elegans	51
Adaptive laboratory evolution enhances methanol tolerance and conversion in engineered Corynebacterium glutamicum	51
Full structural ensembles of intrinsically disordered proteins from unbiased molecular dynamics simulations	51
Omental macrophages secrete chemokine ligands that promote ovarian cancer colonization of the omentum via CCR1	51
Epigenetic landscape of pancreatic neuroendocrine tumours reveals distinct cells of origin and means of tumour progression	51
An algorithm to quantify intratumor heterogeneity based on alterations of gene expression profiles	50
Control of protein palmitoylation by regulating substrate recruitment to a zDHHC-protein acyltransferase	50
High resolution DNA barcode library for European butterflies reveals continental patterns of mitochondrial genetic diversity	50
Spatial and temporal tracking of cardiac exosomes in mouse using a nano-luciferase-CD63 fusion protein	50
Author Correction: Cycloalkane-modified amphiphilic polymers provide direct extraction of membrane proteins for CryoEM analysis	50
Anion-exchange chromatography mass spectrometry provides extensive coverage of primary metabolic pathways revealing altered metabolism in IDH1 mutant cells	50
Ecosystem-wide metagenomic binning enables prediction of ecological niches from genomes	50
Large-scale shift in the structure of a kelp forest ecosystem co-occurs with an epizootic and marine heatwave	49
Dead or alive: sediment DNA archives as tools for tracking aquatic evolution and adaptation	49
NEBULA is a fast negative binomial mixed model for differential or co-expression analysis of large-scale multi-subject single-cell data	49
Global patterns in genomic diversity underpinning the evolution of insecticide resistance in the aphid crop pest Myzus persicae	48
Tet2 at the interface between cancer and immunity	48
Pan-cancer molecular analysis of the RB tumor suppressor pathway	48
A multi-ethnic meta-analysis identifies novel genes, including ACSL5, associated with amyotrophic lateral sclerosis	48
Metagenome-assembled genomes and gene catalog from the chicken gut microbiome aid in deciphering antibiotic resistomes	48
Uptake of osteoblast-derived extracellular vesicles promotes the differentiation of osteoclasts in the zebrafish scale	48
The feather degradation mechanisms of a new Streptomyces sp. isolate SCUT-3	47
Ten emerging SARS-CoV-2 spike variants exhibit variable infectivity, animal tropism, and antibody neutralization	47
Mash-based analyses of Escherichia coli genomes reveal 14 distinct phylogroups	47
Comparative analysis of 1152 African-American and European-American men with prostate cancer identifies distinct genomic and immunological differences	46
Surfactant-assisted one-pot sample preparation for label-free single-cell proteomics	46
Integrative omics analysis of the termite gut system adaptation to Miscanthus diet identifies lignocellulose degradation enzymes	46
High temperatures alter cross-over distribution and induce male meiotic restitution in Arabidopsis thaliana	46
Genome editing in plants using CRISPR type I-D nuclease	46
The kinetics of humoral response and its relationship with the disease severity in COVID-19	46
Mitochondrial stress-activated cGAS-STING pathway inhibits thermogenic program and contributes to overnutrition-induced obesity in mice	45
Temporal hierarchy of intrinsic neural timescales converges with spatial core-periphery organization	45
A high-throughput Galectin-9 imaging assay for quantifying nanoparticle uptake, endosomal escape and functional RNA delivery	45
The structural basis of function and regulation of neuronal cotransporters NKCC1 and KCC2	45
Trodusquemine displaces protein misfolded oligomers from cell membranes and abrogates their cytotoxicity through a generic mechanism	44
The Rnf complex is a Na+ coupled respiratory enzyme in a fermenting bacterium, Thermotoga maritima	44
Restoring indigenous names in taxonomy	44
Clinical evolution of ST11 carbapenem resistant and hypervirulent Klebsiella pneumoniae	44
Ancient Jomon genome sequence analysis sheds light on migration patterns of early East Asian populations	44
Lactobacillus spp. attenuate antibiotic-induced immune and microbiota dysregulation in honey bees	44
Inside-out chicken enteroids with leukocyte component as a model to study host–pathogen interactions	44
Development of a CRISPR/Cas9n-based tool for metabolic engineering of Pseudomonas putida for ferulic acid-to-polyhydroxyalkanoate bioconversion	43
Prediction of 3D Cardiovascular hemodynamics before and after coronary artery bypass surgery via deep learning	43
The lexicon of antimicrobial peptides: a complete set of arginine and tryptophan sequences	43
A large-scale genome-wide cross-trait analysis reveals shared genetic architecture between Alzheimer’s disease and gastrointestinal tract disorders	43
Real-time synthesis of imagined speech processes from minimally invasive recordings of neural activity	43
DNA methylation reprogramming during seed development and its functional relevance in seed size/weight determination in chickpea	43
Genome-wide analysis of DNA G-quadruplex motifs across 37 species provides insights into G4 evolution	43
Artificial light during the polar night disrupts Arctic fish and zooplankton behaviour down to 200 m depth	43
Optimizing spectral quality with quantum dots to enhance crop yield in controlled environments	43
Climate and seasonality drive the richness and composition of tropical fungal endophytes at a landscape scale	42
Biocompatible nucleus-targeted graphene quantum dots for selective killing of cancer cells via DNA damage	42
Co-delivery of resolvin D1 and antibiotics with nanovesicles to lungs resolves inflammation and clears bacteria in mice	42
Cell-autonomous immune gene expression is repressed in pulmonary neuroendocrine cells and small cell lung cancer	42
Deciphering tissue structure and function using spatial transcriptomics	42
BMP-2 and VEGF-A modRNAs in collagen scaffold synergistically drive bone repair through osteogenic and angiogenic pathways	42
High-resolution cryo-EM structure of photosystem II reveals damage from high-dose electron beams	42
Subtyping analysis reveals new variants and accelerated evolution of Clostridioides difficile toxin B	41
Liposomal nanotheranostics for multimode targeted in vivo bioimaging and near‐infrared light mediated cancer therapy	41

Single-cell transcriptomics following ischemic injury identifies a role for B2M in cardiac repair	41
More than half of data deficient species predicted to be threatened by extinction	41
The cardiolipin-binding peptide elamipretide mitigates fragmentation of cristae networks following cardiac ischemia reperfusion in rats	41
Immunological considerations and challenges for regenerative cellular therapies	41
MYB repressors and MBW activation complex collaborate to fine-tune flower coloration in Freesia hybrida	40
Bridgehead effect and multiple introductions shape the global invasion history of a termite	40
DNA–protein crosslink proteases in genome stability	40
Growth and rapid succession of methanotrophs effectively limit methane release during lake overturn	40
High-content fluorescence imaging with the metabolic flux assay reveals insights into mitochondrial properties and functions	40
The genome of pest Rhynchophorus ferrugineus reveals gene families important at the plant-beetle interface	40
Fast automated detection of COVID-19 from medical images using convolutional neural networks	40
An intact C-terminal end of albumin is required for its long half-life in humans	40
Wuschel2 enables highly efficient CRISPR/Cas-targeted genome editing during rapid de novo shoot regeneration in sorghum	40
Passive eDNA collection enhances aquatic biodiversity analysis	39
Secreted midbody remnants are a class of extracellular vesicles molecularly distinct from exosomes and microparticles	39
Molecular and phenotypic analysis of rodent models reveals conserved and species-specific modulators of human sarcopenia	39
Identification of a pathway for electron uptake in Shewanella oneidensis	39
Insights into the genomic evolution of insects from cricket genomes	39
Highly efficient gene transfer in the mouse gut microbiota is enabled by the Incl2 conjugative plasmid TP114	39
Droplet-based microfluidic platform for high-throughput screening of Streptomyces	39
Menstrual flow as a non-invasive source of endometrial organoids	39
Spatiotemporal identification of druggable binding sites using deep learning	39
Loss of consciousness reduces the stability of brain hubs and the heterogeneity of brain dynamics	39
The interplay between membrane topology and mechanical forces in regulating T cell receptor activity	39
Cell response analysis in SARS-CoV-2 infected bronchial organoids	39
3D tumor spheroid microarray for high-throughput, high-content natural killer cell-mediated cytotoxicity	39
Igf2bp3 maintains maternal RNA stability and ensures early embryo development in zebrafish	39
Anti-HIV agent azidothymidine decreases Tet(X)-mediated bacterial resistance to tigecycline in Escherichia coli	39
A generic approach to study the kinetics of liquid–liquid phase separation under near-native conditions	38
Large genome-wide association study identifies three novel risk variants for restless legs syndrome	38
Breakdown of supersaturation barrier links protein folding to amyloid formation	38
Wolfberry genomes and the evolution of Lycium (Solanaceae)	38
Reconstituted cell-free protein synthesis using in vitro transcribed tRNAs	38
Adaptation by copy number variation increases insecticide resistance in the fall armyworm	38
Biohydrogen production beyond the Thauer limit by precision design of artificial microbial consortia	38
Whole-genome sequence analysis unveils different origins of European and Asiatic mouflon and domestication-related genes in sheep	38
Vector competence of Aedes albopictus populations for chikungunya virus is shaped by their demographic history	38
ImmuneBuilder: Deep-Learning models for predicting the structures of immune proteins	38
Pre-innervated tissue-engineered muscle promotes a pro-regenerative microenvironment following volumetric muscle loss	38
Single-cell RNA sequencing reveals a heterogeneous response to Glucocorticoids in breast cancer cells	38
Immunoreactive peptide maps of SARS-CoV-2	38
Volatile organic compound patterns predict fungal trophic mode and lifestyle	38
Antibodies exhibit multiple paratope states influencing VH–VL domain orientations	37
SARS-CoV-2 Omicron variant is attenuated for replication in a polarized human lung epithelial cell model	37
A single day of TGF-β1 exposure activates chondrogenic and hypertrophic differentiation pathways in bone marrow-derived stromal cells	37
A modular two yeast species secretion system for the production and preparative application of unspecific peroxygenases	37
Decoding the transcriptome of calcified atherosclerotic plaque at single-cell resolution	37
The anesthetic sevoflurane induces tau trafficking from neurons to microglia	37
Stony coral tissue loss disease decimated Caribbean coral populations and reshaped reef functionality	37
Spatio-molecular domains identified in the mouse subthalamic nucleus and neighboring glutamatergic and GABAergic brain structures	37
Analysis of genetically independent phenotypes identifies shared genetic factors associated with chronic musculoskeletal pain conditions	37
Structural definition of a pan-sarbecovirus neutralizing epitope on the spike S2 subunit	37
The surprising role of the default mode network in naturalistic perception	37
Fungal mycelium classified in different material families based on glycerol treatment	37
Deep splicing plasticity of the human adenovirus type 5 transcriptome drives virus evolution	37
Cancer-associated hypersialylated MUC1 drives the differentiation of human monocytes into macrophages with a pathogenic phenotype	36
Predicting clinical resistance prevalence using sewage metagenomic data	36
Sedimentary DNA tracks decadal-centennial changes in fish abundance	36
Drosophila melanogaster behaviour changes in different social environments based on group size and density	36
Genomic epidemiology of animal-derived tigecycline-resistant Escherichia coli across China reveals recent endemic plasmid-encoded tet(X4) gene	36
Structure and function of a malaria transmission blocking vaccine targeting Pfs230 and Pfs230-Pfs48/45 proteins	36
Identifying behavioral structure from deep variational embeddings of animal motion	36
Targeted intracellular degradation of SARS-CoV-2 via computationally optimized peptide fusions	36
Structural basis of coronavirus E protein interactions with human PALS1 PDZ domain	36
LIVE-PAINT allows super-resolution microscopy inside living cells using reversible peptide-protein interactions	36
A multi-ethnic genome-wide association study implicates collagen matrix integrity and cell differentiation pathways in keratoconus	36
Genome-wide association studies and heritability analysis reveal the involvement of host genetics in the Japanese gut microbiota	36
Multi-species and multi-tissue methylation clocks for age estimation in toothed whales and dolphins	36
An alternative pathway for membrane protein biogenesis at the endoplasmic reticulum	36
Naphthoquinone-derivative as a synthetic compound to overcome the antibiotic resistance of methicillin-resistant S. aureus	36
The reliability and heritability of cortical folds and their genetic correlations across hemispheres	36
Sulforaphane exhibits antiviral activity against pandemic SARS-CoV-2 and seasonal HCoV-OC43 coronaviruses in vitro and in mice	36
Outer-membrane-acting peptides and lipid II-targeting antibiotics cooperatively kill Gram-negative pathogens	36
Cell-free biogenesis of bacterial division proto-rings that can constrict liposomes	36
Tau affects P53 function and cell fate during the DNA damage response	35
Osteopontin binds ICOSL promoting tumor metastasis	35
Phylogenetic inference enables reconstruction of a long-overlooked outbreak of almond leaf scorch disease (Xylella fastidiosa) in Europe	35
Genome-wide bioinformatic analyses predict key host and viral factors in SARS-CoV-2 pathogenesis	35
Harmonizing hybridization dissonance in conservation	35
Crowding-induced opening of the mechanosensitive Piezo1 channel in silico	35
A gene prioritization method based on a swine multi-omics knowledgebase and a deep learning model	35
Organisational and neuromodulatory underpinnings of structural-functional connectivity decoupling in patients with Parkinson’s disease	34
Dorsal and ventral striatal functional connectivity shifts play a potential role in internet gaming disorder	34
Molecular bases for HOIPINs-mediated inhibition of LUBAC and innate immune responses	34
Floral transcriptomes reveal gene networks in pineapple floral growth and fruit development	34
The cancer glycocalyx mediates intravascular adhesion and extravasation during metastatic dissemination	34
The challenge of intracellular antibiotic accumulation, a function of fluoroquinolone influx versus bacterial efflux	34
Zebrafish xenografts as a fast screening platform for bevacizumab cancer therapy	34
NAD+/NADH redox alterations reconfigure metabolism and rejuvenate senescent human mesenchymal stem cells in vitro	34
Multivalent nanoparticle-based vaccines protect hamsters against SARS-CoV-2 after a single immunization	34
Maximizing transcription of nucleic acids with efficient T7 promoters	34
An automated platform to monitor long-term behavior and healthspan in Caenorhabditis elegans under precise environmental control	34
Pheromone components affect motivation and induce persistent modulation of associative learning and memory in honey bees	34
Cryo-EM structure of the volume-regulated anion channel LRRC8D isoform identifies features important for substrate permeation	34
SARS-CoV-2 spike opening dynamics and energetics reveal the individual roles of glycans and their collective impact	34