Communications Biology

Article	Citations
DeepEMhancer: a deep learning solution for cryo-EM volume post-processing	715
A comprehensive review on plasmonic-based biosensors used in viral diagnostics	308
Single-cell and spatial transcriptomics enables probabilistic inference of cell type topography	295
Ionization and structural properties of mRNA lipid nanoparticles influence expression in intramuscular and intravascular administration	194
Role of sleep deprivation in immune-related disease risk and outcomes	185
Second-generation lung-on-a-chip with an array of stretchable alveoli made with a biological membrane	181
Mapping the immune environment in clear cell renal carcinoma by single-cell genomics	179
Towards organoid culture without Matrigel	173
Activation of mitochondrial TUFM ameliorates metabolic dysregulation through coordinating autophagy induction	169
Identification of 3-chymotrypsin like protease (3CLPro) inhibitors as potential anti-SARS-CoV-2 agents	165
Amplification-free RNA detection with CRISPR–Cas13	142
SARS-CoV-2 infection induces a pro-inflammatory cytokine response through cGAS-STING and NF-κB	141
Identification of SARS-CoV-2 inhibitors targeting Mpro and PLpro using in-cell-protease assay	140
The antimicrobial potential of cannabidiol	140
NetTCR-2.0 enables accurate prediction of TCR-peptide binding by using paired TCRα and β sequence data	133
The genetic architecture of appendicular lean mass characterized by association analysis in the UK Biobank study	129
Brains and algorithms partially converge in natural language processing	128
Deep ocean metagenomes provide insight into the metabolic architecture of bathypelagic microbial communities	128
Climate-change-driven growth decline of European beech forests	124
Simple and effective serum-free medium for sustained expansion of bovine satellite cells for cell cultured meat	122
Human ACE2 receptor polymorphisms and altered susceptibility to SARS-CoV-2	117
Fatty-acid-induced FABP5/HIF-1 reprograms lipid metabolism and enhances the proliferation of liver cancer cells	114
Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants	111
Telomere-to-telomere gapless chromosomes of banana using nanopore sequencing	105
Genomic and transcriptomic variation defines the chromosome-scale assembly of Haemonchus contortus, a model gastrointestinal worm	104

Inhibition of the CCL2 receptor, CCR2, enhances tumor response to immune checkpoint therapy	100
Accelerating antibiotic discovery through artificial intelligence	100
Large-scale integration of single-cell transcriptomic data captures transitional progenitor states in mouse skeletal muscle regeneration	99
Comparative ACE2 variation and primate COVID-19 risk	98
Single-cell analysis supports a luminal-neuroendocrine transdifferentiation in human prostate cancer	98
Integration of substrate- and flow-derived stresses in endothelial cell mechanobiology	97
Temporal association between human upper respiratory and gut bacterial microbiomes during the course of COVID-19 in adults	95
Molecular basis for the disruption of Keap1–Nrf2 interaction via Hinge & Latch mechanism	95
Prioritization of candidate causal genes for asthma in susceptibility loci derived from UK Biobank	94
A genome-wide meta-analysis yields 46 new loci associating with biomarkers of iron homeostasis	93
Human ACE2 peptide-mimics block SARS-CoV-2 pulmonary cells infection	93
From whole-mount to single-cell spatial assessment of gene expression in 3D	90
Cryo-EM structure of type 1 IP3R channel in a lipid bilayer	90
ExoSTING, an extracellular vesicle loaded with STING agonists, promotes tumor immune surveillance	88
Sand flies: Basic information on the vectors of leishmaniasis and their interactions with Leishmania parasites	88
The brain and its time: intrinsic neural timescales are key for input processing	88
PD-1 derived CA-170 is an oral immune checkpoint inhibitor that exhibits preclinical anti-tumor efficacy	87
SARS-CoV-2 specific antibody and neutralization assays reveal the wide range of the humoral immune response to virus	86
ImmuneBuilder: Deep-Learning models for predicting the structures of immune proteins	85
Multiple impacts of microplastics can threaten marine habitat-forming species	83
Exploring the evidence for epigenetic regulation of environmental influences on child health across generations	81
Microglial metabolism is a pivotal factor in sexual dimorphism in Alzheimer’s disease	80
A framework for identifying the recent origins of mobile antibiotic resistance genes	80
Climate change threatens Chinook salmon throughout their life cycle	79
Tipiracil binds to uridine site and inhibits Nsp15 endoribonuclease NendoU from SARS-CoV-2	77
Type I toxin-antitoxin systems contribute to the maintenance of mobile genetic elements in Clostridioides difficile	77
A haplotype-led approach to increase the precision of wheat breeding	76
Features and applications of haplotypes in crop breeding	76
Optogenetic therapy: high spatiotemporal resolution and pattern discrimination compatible with vision restoration in non-human primates	76
Temporal hierarchy of intrinsic neural timescales converges with spatial core-periphery organization	76
A novel canine reference genome resolves genomic architecture and uncovers transcript complexity	75
Cyanobacterial blooms contribute to the diversity of antibiotic-resistance genes in aquatic ecosystems	75
When dormancy fuels tumour relapse	73
High frequency acoustic cell stimulation promotes exosome generation regulated by a calcium-dependent mechanism	72
More than half of data deficient species predicted to be threatened by extinction	72
NEBULA is a fast negative binomial mixed model for differential or co-expression analysis of large-scale multi-subject single-cell data	71
Wnt signaling in lung development, regeneration, and disease progression	71
IFN signaling and neutrophil degranulation transcriptional signatures are induced during SARS-CoV-2 infection	71
Tumor microbiome contributes to an aggressive phenotype in the basal-like subtype of pancreatic cancer	69
The multiple mechanisms of MCL1 in the regulation of cell fate	69
Genome-resolved metagenomics suggests a mutualistic relationship between Mycoplasma and salmonid hosts	69
Gut microbiome diversity is an independent predictor of survival in cervical cancer patients receiving chemoradiation	68
Design and optimisation of dendrimer-conjugated Bcl-2/xL inhibitor, AZD0466, with improved therapeutic index for cancer therapy	68
A combined approach for single-cell mRNA and intracellular protein expression analysis	68
Large-scale shift in the structure of a kelp forest ecosystem co-occurs with an epizootic and marine heatwave	67
Surfactant-assisted one-pot sample preparation for label-free single-cell proteomics	67
Biomolecular condensates as arbiters of biochemical reactions inside the nucleus	66
The gut mycobiome of healthy mice is shaped by the environment and correlates with metabolic outcomes in response to diet	66
Gut mycobiota alterations in patients with COVID-19 and H1N1 infections and their associations with clinical features	65
Bacterial diets differentially alter lifespan and healthspan trajectories in C. elegans	64

High resolution DNA barcode library for European butterflies reveals continental patterns of mitochondrial genetic diversity	63
Detritivore conversion of litter into faeces accelerates organic matter turnover	63
Epigenetic landscape of pancreatic neuroendocrine tumours reveals distinct cells of origin and means of tumour progression	62
Topologically associating domain boundaries are required for normal genome function	62
Biocompatible nucleus-targeted graphene quantum dots for selective killing of cancer cells via DNA damage	61
A high-throughput Galectin-9 imaging assay for quantifying nanoparticle uptake, endosomal escape and functional RNA delivery	60
Immunological considerations and challenges for regenerative cellular therapies	60
Author Correction: Cycloalkane-modified amphiphilic polymers provide direct extraction of membrane proteins for CryoEM analysis	59
Full structural ensembles of intrinsically disordered proteins from unbiased molecular dynamics simulations	59
Tet2 at the interface between cancer and immunity	59
Mash-based analyses of Escherichia coli genomes reveal 14 distinct phylogroups	58
Decoding the transcriptome of calcified atherosclerotic plaque at single-cell resolution	58
SARS-CoV-2 Omicron variant is attenuated for replication in a polarized human lung epithelial cell model	57
Deciphering tissue structure and function using spatial transcriptomics	57
Real-time synthesis of imagined speech processes from minimally invasive recordings of neural activity	57
Metagenome-assembled genomes and gene catalog from the chicken gut microbiome aid in deciphering antibiotic resistomes	57
Identifying behavioral structure from deep variational embeddings of animal motion	56
Clinical evolution of ST11 carbapenem resistant and hypervirulent Klebsiella pneumoniae	56
Global patterns in genomic diversity underpinning the evolution of insecticide resistance in the aphid crop pest Myzus persicae	55
Prediction of 3D Cardiovascular hemodynamics before and after coronary artery bypass surgery via deep learning	55
BMP-2 and VEGF-A modRNAs in collagen scaffold synergistically drive bone repair through osteogenic and angiogenic pathways	54
Stony coral tissue loss disease decimated Caribbean coral populations and reshaped reef functionality	54
Comparative analysis of 1152 African-American and European-American men with prostate cancer identifies distinct genomic and immunological differences	53
A large-scale genome-wide cross-trait analysis reveals shared genetic architecture between Alzheimer’s disease and gastrointestinal tract disorders	53
Inside-out chicken enteroids with leukocyte component as a model to study host–pathogen interactions	53
Discovery of stripe rust resistance with incomplete dominance in wild emmer wheat using bulked segregant analysis sequencing	52
The structural basis of function and regulation of neuronal cotransporters NKCC1 and KCC2	52
Large genome-wide association study identifies three novel risk variants for restless legs syndrome	52
High stability and metabolic capacity of bacterial community promote the rapid reduction of easily decomposing carbon in soil	52
Whole-genome sequence analysis unveils different origins of European and Asiatic mouflon and domestication-related genes in sheep	52
Optimizing spectral quality with quantum dots to enhance crop yield in controlled environments	52
Genome-wide analysis of DNA G-quadruplex motifs across 37 species provides insights into G4 evolution	51
A multi-ethnic genome-wide association study implicates collagen matrix integrity and cell differentiation pathways in keratoconus	51
High-resolution cryo-EM structure of photosystem II reveals damage from high-dose electron beams	51
Passive eDNA collection enhances aquatic biodiversity analysis	51
Genome editing in plants using CRISPR type I-D nuclease	51
Wuschel2 enables highly efficient CRISPR/Cas-targeted genome editing during rapid de novo shoot regeneration in sorghum	51
Cell-autonomous immune gene expression is repressed in pulmonary neuroendocrine cells and small cell lung cancer	51
Restoring indigenous names in taxonomy	51
DNA–protein crosslink proteases in genome stability	50
AlphaFold2 reveals commonalities and novelties in protein structure space for 21 model organisms	50
The interplay between membrane topology and mechanical forces in regulating T cell receptor activity	50
Loss of consciousness reduces the stability of brain hubs and the heterogeneity of brain dynamics	49
Integrating cell morphology with gene expression and chemical structure to aid mitochondrial toxicity detection	49
Menstrual flow as a non-invasive source of endometrial organoids	49
The lexicon of antimicrobial peptides: a complete set of arginine and tryptophan sequences	49
Insights into the genomic evolution of insects from cricket genomes	49
Molecular and phenotypic analysis of rodent models reveals conserved and species-specific modulators of human sarcopenia	49
Co-delivery of resolvin D1 and antibiotics with nanovesicles to lungs resolves inflammation and clears bacteria in mice	49
Sulforaphane exhibits antiviral activity against pandemic SARS-CoV-2 and seasonal HCoV-OC43 coronaviruses in vitro and in mice	49
Wolfberry genomes and the evolution of Lycium (Solanaceae)	49
Volatile organic compound patterns predict fungal trophic mode and lifestyle	49
Secreted midbody remnants are a class of extracellular vesicles molecularly distinct from exosomes and microparticles	48
Adaptation by copy number variation increases insecticide resistance in the fall armyworm	48
The kinetics of humoral response and its relationship with the disease severity in COVID-19	48
Ten emerging SARS-CoV-2 spike variants exhibit variable infectivity, animal tropism, and antibody neutralization	48
Spatiotemporal identification of druggable binding sites using deep learning	48
Predicting clinical resistance prevalence using sewage metagenomic data	47
DeepBacs for multi-task bacterial image analysis using open-source deep learning approaches	47
Dynamic relationships between spontaneous and evoked electrophysiological activity	47
Climate and seasonality drive the richness and composition of tropical fungal endophytes at a landscape scale	47
Structural definition of a pan-sarbecovirus neutralizing epitope on the spike S2 subunit	47
The surprising role of the default mode network in naturalistic perception	47
Engineering of ultraID, a compact and hyperactive enzyme for proximity-dependent biotinylation in living cells	46
Identification of a pathway for electron uptake in Shewanella oneidensis	46
Annotation of chromatin states in 66 complete mouse epigenomes during development	46
Single-cell transcriptomics following ischemic injury identifies a role for B2M in cardiac repair	46
Cell response analysis in SARS-CoV-2 infected bronchial organoids	46
Fast automated detection of COVID-19 from medical images using convolutional neural networks	46
Integrated molecular characterisation of the MAPK pathways in human cancers reveals pharmacologically vulnerable mutations and gene dependencies	45
An alternative pathway for membrane protein biogenesis at the endoplasmic reticulum	45
Droplet-based microfluidic platform for high-throughput screening of Streptomyces	45
SARS-CoV-2 spike opening dynamics and energetics reveal the individual roles of glycans and their collective impact	45
Cerebrospinal fluid metabolomics identifies 19 brain-related phenotype associations	44
A modular two yeast species secretion system for the production and preparative application of unspecific peroxygenases	44
Real-time structure search and structure classification for AlphaFold protein models	44
Reduced C9orf72 function leads to defective synaptic vesicle release and neuromuscular dysfunction in zebrafish	44
Photoreceptor metabolic reprogramming: current understanding and therapeutic implications	44
Bridgehead effect and multiple introductions shape the global invasion history of a termite	44
A global microbiome survey of vineyard soils highlights the microbial dimension of viticultural terroirs	43

Engineered marble-like bovine fat tissue for cultured meat	43
OxPhos defects cause hypermetabolism and reduce lifespan in cells and in patients with mitochondrial diseases	43
A generic approach to study the kinetics of liquid–liquid phase separation under near-native conditions	43
The cancer glycocalyx mediates intravascular adhesion and extravasation during metastatic dissemination	43
A chromosome-level genome sequence of Chrysanthemum seticuspe, a model species for hexaploid cultivated chrysanthemum	43
A single day of TGF-β1 exposure activates chondrogenic and hypertrophic differentiation pathways in bone marrow-derived stromal cells	43
Crowding-induced opening of the mechanosensitive Piezo1 channel in silico	43
A deeper look at carrier proteome effects for single-cell proteomics	43
3D tumor spheroid microarray for high-throughput, high-content natural killer cell-mediated cytotoxicity	43
Phylogenetic inference enables reconstruction of a long-overlooked outbreak of almond leaf scorch disease (Xylella fastidiosa) in Europe	42
Impact of sleep duration on executive function and brain structure	42
Cancer-associated hypersialylated MUC1 drives the differentiation of human monocytes into macrophages with a pathogenic phenotype	42
Characterization of phage resistance and phages capable of intestinal decolonization of carbapenem-resistant Klebsiella pneumoniae in mice	42
Dorsal and ventral striatal functional connectivity shifts play a potential role in internet gaming disorder	42
Targeted intracellular degradation of SARS-CoV-2 via computationally optimized peptide fusions	42
Structural basis of coronavirus E protein interactions with human PALS1 PDZ domain	42
Elevated microglial oxidative phosphorylation and phagocytosis stimulate post-stroke brain remodeling and cognitive function recovery in mice	42
Long-term field-realistic exposure to a next-generation pesticide, flupyradifurone, impairs honey bee behaviour and survival	41
Global population genomic signature of Spodoptera frugiperda (fall armyworm) supports complex introduction events across the Old World	41
Breakdown of supersaturation barrier links protein folding to amyloid formation	41
Genome-wide association studies and heritability analysis reveal the involvement of host genetics in the Japanese gut microbiota	41
A pictorial account of the human embryonic heart between 3.5 and 8 weeks of development	41
NAD+/NADH redox alterations reconfigure metabolism and rejuvenate senescent human mesenchymal stem cells in vitro	41
Simple sequence repeats drive genome plasticity and promote adaptive evolution in penaeid shrimp	41
Towards a comprehensive evaluation of dimension reduction methods for transcriptomic data visualization	41
LPMO-oxidized cellulose oligosaccharides evoke immunity in Arabidopsis conferring resistance towards necrotrophic fungus B. cinerea	41
Multivalent nanoparticle-based vaccines protect hamsters against SARS-CoV-2 after a single immunization	40
Moisture modulates soil reservoirs of active DNA and RNA viruses	40
Organisational and neuromodulatory underpinnings of structural-functional connectivity decoupling in patients with Parkinson’s disease	40
Chemokine mediated signalling within arteries promotes vascular smooth muscle cell recruitment	40
Multi-species and multi-tissue methylation clocks for age estimation in toothed whales and dolphins	40
Development of deep learning algorithms for predicting blastocyst formation and quality by time-lapse monitoring	40
Osteopontin binds ICOSL promoting tumor metastasis	40
Immunoreactive peptide maps of SARS-CoV-2	40
Three-dimensional spatial transcriptomics uncovers cell type localizations in the human rheumatoid arthritis synovium	40
Human TRPC5 structures reveal interaction of a xanthine-based TRPC1/4/5 inhibitor with a conserved lipid binding site	40
Non-linear machine learning models incorporating SNPs and PRS improve polygenic prediction in diverse human populations	40
Matrigel 3D bioprinting of contractile human skeletal muscle models recapitulating exercise and pharmacological responses	40
R–R–T (resistance–resilience–transformation) typology reveals differential conservation approaches across ecosystems and time	40
Distortion of the bilayer and dynamics of the BAM complex in lipid nanodiscs	39
p38-MAPK-mediated translation regulation during early blastocyst development is required for primitive endoderm differentiation in mice	39
Phenotypic analysis of catastrophic childhood epilepsy genes	39
The C-terminal tail of α-synuclein protects against aggregate replication but is critical for oligomerization	39
Outer-membrane-acting peptides and lipid II-targeting antibiotics cooperatively kill Gram-negative pathogens	39
Structural insights into photoactivation of plant Cryptochrome-2	39
A reference-grade genome identifies salt-tolerance genes from the salt-secreting mangrove species Avicennia marina	39
Antibodies exhibit multiple paratope states influencing VH–VL domain orientations	39
Live cell dynamics of production, explosive release and killing activity of phage tail-like weapons for Pseudomonas kin exclusion	39
Methamphetamine induces cardiomyopathy by Sigmar1 inhibition-dependent impairment of mitochondrial dynamics and function	39
Multiple memories can be simultaneously reactivated during sleep as effectively as a single memory	38
NTRK kinase domain mutations in cancer variably impact sensitivity to type I and type II inhibitors	38
The anesthetic sevoflurane induces tau trafficking from neurons to microglia	38
Enhancing carbohydrate repartitioning into lipid and carotenoid by disruption of microalgae starch debranching enzyme	38
Plants grown in Apollo lunar regolith present stress-associated transcriptomes that inform prospects for lunar exploration	38
An investigation of the cognitive and neural correlates of semantic memory search related to creative ability	38
Artemisinin resistance in the malaria parasite, Plasmodium falciparum, originates from its initial transcriptional response	38
Genome-wide bioinformatic analyses predict key host and viral factors in SARS-CoV-2 pathogenesis	38
Causal contributors to tissue stiffness and clinical relevance in urology	38
Human encroachment into wildlife gut microbiomes	38
Sedimentary DNA tracks decadal-centennial changes in fish abundance	38
Combination of antiviral drugs inhibits SARS-CoV-2 polymerase and exonuclease and demonstrates COVID-19 therapeutic potential in viral cell culture	38
Evidence for continuity of interstitial spaces across tissue and organ boundaries in humans	37
Bovine host genome acts on rumen microbiome function linked to methane emissions	37
The metabolic network of the last bacterial common ancestor	37
The hierarchy of root branching order determines bacterial composition, microbial carrying capacity and microbial filtering	37
Hyperthermophilic methanogenic archaea act as high-pressure CH4 cell factories	37
Post-correlation on-lamella cryo-CLEM reveals the membrane architecture of lamellar bodies	37
The ribosome modulates folding inside the ribosomal exit tunnel	37
Phytoplankton responses to changing temperature and nutrient availability are consistent across the tropical and subtropical Atlantic	37
Partial inhibition of mitochondrial complex I ameliorates Alzheimer’s disease pathology and cognition in APP/PS1 female mice	37
High-frequency burst spiking in layer 5 thick-tufted pyramids of rat primary somatosensory cortex encodes exploratory touch	37
Genomic profiling reveals heterogeneous populations of ductal carcinoma in situ of the breast	37
A synthetic RNA editing factor edits its target site in chloroplasts and bacteria	37
Characterisation of PDGF-BB:PDGFRβ signalling pathways in human brain pericytes: evidence of disruption in Alzheimer’s disease	36
Identification of a missense variant in SPDL1 associated with idiopathic pulmonary fibrosis	36
Single cell analysis of spondyloarthritis regulatory T cells identifies distinct synovial gene expression patterns and clonal fates	36
Intracellular thermometry uncovers spontaneous thermogenesis and associated thermal signaling	36
Light environment drives evolution of color vision genes in butterflies and moths	36
Decorin-mediated suppression of tumorigenesis, invasion, and metastasis in inflammatory breast cancer	36
Fluorescence lifetime DNA-PAINT for multiplexed super-resolution imaging of cells	36
Time-resolved structure-function coupling in brain networks	36
Squalenoyl siRNA PMP22 nanoparticles are effective in treating mouse models of Charcot-Marie-Tooth disease type 1 A	36
Automated amplification-free digital RNA detection platform for rapid and sensitive SARS-CoV-2 diagnosis	36
Microbial dysbiosis reflects disease resistance in diverse coral species	35
High concentrations of dissolved biogenic methane associated with cyanobacterial blooms in East African lake surface water	35
Claudin-2 promotes colorectal cancer liver metastasis and is a biomarker of the replacement type growth pattern	35
Accessory proteins of the RAS-MAPK pathway: moving from the side line to the front line	35
IL36 is a critical upstream amplifier of neutrophilic lung inflammation in mice	35
Active maintenance of proton motive force mediates starvation-induced bacterial antibiotic tolerance in Escherichia coli	35
Pharmacological inactivation of the prion protein by targeting a folding intermediate	35
Components of a Neanderthal gut microbiome recovered from fecal sediments from El Salt	35
Sensitive quantification of carbon monoxide in vivo reveals a protective role of circulating hemoglobin in CO intoxication	35
Environmental DNA provides higher resolution assessment of riverine biodiversity and ecosystem function via spatio-temporal nestedness and turnover partitioning	35
SARS-CoV-2 ORF6 disrupts nucleocytoplasmic trafficking to advance viral replication	35
Preclinical validation of a live attenuated dermotropic Leishmania vaccine against vector transmitted fatal visceral leishmaniasis	35