eLife

Article	Citations
Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3	1028
Atomic structures of respiratory complex III2, complex IV, and supercomplex III2-IV from vascular plants	616
Tracking excess mortality across countries during the COVID-19 pandemic with the World Mortality Dataset	338
DunedinPACE, a DNA methylation biomarker of the pace of aging	337
Effects of common mutations in the SARS-CoV-2 Spike RBD and its ligand, the human ACE2 receptor on binding affinity and kinetics	279
The connectome of the adult Drosophila mushroom body provides insights into function	273
N501Y mutation of spike protein in SARS-CoV-2 strengthens its binding to receptor ACE2	258
ACE2: Evidence of role as entry receptor for SARS-CoV-2 and implications in comorbidities	256
Sampling alternative conformational states of transporters and receptors with AlphaFold2	254
SARS-CoV-2 spike protein induces inflammation via TLR2-dependent activation of the NF-κB pathway	243
DNA damage—how and why we age?	221
Lytic transglycosylases mitigate periplasmic crowding by degrading soluble cell wall turnover products	216
Antimicrobial resistance and COVID-19: Intersections and implications	213
Cancer-associated fibroblasts and their influence on tumor immunity and immunotherapy	209
Standardizing workflows in imaging transcriptomics with the abagen toolbox	201
Colistin kills bacteria by targeting lipopolysaccharide in the cytoplasmic membrane	200
Sex differences in biological aging with a focus on human studies	194
A connectome of the Drosophila central complex reveals network motifs suitable for flexible navigation and context-dependent action selection	189
FRET-based dynamic structural biology: Challenges, perspectives and an appeal for open-science practices	183
Neuronal timescales are functionally dynamic and shaped by cortical microarchitecture	172
Microbiota-derived short chain fatty acids modulate microglia and promote Aβ plaque deposition	171
The OpenNeuro resource for sharing of neuroscience data	169
TRex, a fast multi-animal tracking system with markerless identification, and 2D estimation of posture and visual fields	166
A simple and effective F0 knockout method for rapid screening of behaviour and other complex phenotypes	162
Tumor stiffening reversion through collagen crosslinking inhibition improves T cell migration and anti-PD-1 treatment	162

SARS-CoV-2 requires cholesterol for viral entry and pathological syncytia formation	161
The genomic consequences of hybridization	158
Simultaneous trimodal single-cell measurement of transcripts, epitopes, and chromatin accessibility using TEA-seq	158
SpikeInterface, a unified framework for spike sorting	156
Mapping single-cell atlases throughout Metazoa unravels cell type evolution	153
Assembly of recombinant tau into filaments identical to those of Alzheimer’s disease and chronic traumatic encephalopathy	149
Mechanistic theory predicts the effects of temperature and humidity on inactivation of SARS-CoV-2 and other enveloped viruses	148
Viral load and contact heterogeneity predict SARS-CoV-2 transmission and super-spreading events	147
Association of Toll-like receptor 7 variants with life-threatening COVID-19 disease in males: findings from a nested case-control study	147
A Bayesian approach to single-particle electron cryo-tomography in RELION-4.0	146
An open-source, high-performance tool for automated sleep staging	143
The Spike D614G mutation increases SARS-CoV-2 infection of multiple human cell types	143
HP1 proteins compact DNA into mechanically and positionally stable phase separated domains	142
Reporting and misreporting of sex differences in the biological sciences	139
Single-cell multiomic profiling of human lungs reveals cell-type-specific and age-dynamic control of SARS-CoV2 host genes	137
Investigating the replicability of preclinical cancer biology	135
A versatile oblique plane microscope for large-scale and high-resolution imaging of subcellular dynamics	135
The mTORC1-mediated activation of ATF4 promotes protein and glutathione synthesis downstream of growth signals	133
A fully automated high-throughput workflow for 3D-based chemical screening in human midbrain organoids	132
Racial inequity in grant funding from the US National Institutes of Health	131
Effector membrane translocation biosensors reveal G protein and βarrestin coupling profiles of 100 therapeutically relevant GPCRs	131
Generation of vascularized brain organoids to study neurovascular interactions	131
Challenges for assessing replicability in preclinical cancer biology	127
An open label trial of anakinra to prevent respiratory failure in COVID-19	127
Genetic architecture of 11 organ traits derived from abdominal MRI using deep learning	127
Single-nucleus transcriptomic analysis of human dorsal root ganglion neurons	124
Metabolic biomarker profiling for identification of susceptibility to severe pneumonia and COVID-19 in the general population	124
Highly contiguous assemblies of 101 drosophilid genomes	124
The LOTUS initiative for open knowledge management in natural products research	123
Relationship between simultaneously recorded spiking activity and fluorescence signal in GCaMP6 transgenic mice	117
Modelling the impact of decidual senescence on embryo implantation in human endometrial assembloids	117
The Mouse Action Recognition System (MARS) software pipeline for automated analysis of social behaviors in mice	116
Modality-specific tracking of attention and sensory statistics in the human electrophysiological spectral exponent	115
SARS-CoV-2 entry into human airway organoids is serine protease-mediated and facilitated by the multibasic cleavage site	113
Diverse viral proteases activate the NLRP1 inflammasome	113
Information flow, cell types and stereotypy in a full olfactory connectome	113
Heterogeneity in transmissibility and shedding SARS-CoV-2 via droplets and aerosols	112
GENESPACE tracks regions of interest and gene copy number variation across multiple genomes	111
Diversity and asynchrony in soil microbial communities stabilizes ecosystem functioning	111
Simple biochemical features underlie transcriptional activation domain diversity and dynamic, fuzzy binding to Mediator	110
Patterns of within-host genetic diversity in SARS-CoV-2	110
Convalescent COVID-19 patients are susceptible to endothelial dysfunction due to persistent immune activation	108
Real-time, low-latency closed-loop feedback using markerless posture tracking	108
The diversity and function of sourdough starter microbiomes	106
Self-blinding citizen science to explore psychedelic microdosing	106
Topographic gradients of intrinsic dynamics across neocortex	105
Pathogenic mechanisms of post-acute sequelae of SARS-CoV-2 infection (PASC)	104
Single nuclei RNA-seq of mouse placental labyrinth development	104
Analysis of the immune response to sciatic nerve injury identifies efferocytosis as a key mechanism of nerve debridement	103
Quantifying the relationship between SARS-CoV-2 viral load and infectiousness	103

SARS-CoV-2 S protein:ACE2 interaction reveals novel allosteric targets	101
Transcriptional profiling of mouse peripheral nerves to the single-cell level to build a sciatic nerve ATlas (SNAT)	100
Viral persistence, reactivation, and mechanisms of long COVID	100
Standardized and reproducible measurement of decision-making in mice	99
DeepEthogram, a machine learning pipeline for supervised behavior classification from raw pixels	99
Plasma proteomic biomarker signature of age predicts health and life span	98
Individual variations in ‘brain age’ relate to early-life factors more than to longitudinal brain change	98
TCR meta-clonotypes for biomarker discovery with tcrdist3 enabled identification of public, HLA-restricted clusters of SARS-CoV-2 TCRs	98
Neural effects of propofol-induced unconsciousness and its reversal using thalamic stimulation	98
Plasmodium falciparum K13 mutations in Africa and Asia impact artemisinin resistance and parasite fitness	98
A cell atlas of the chick retina based on single-cell transcriptomics	95
Longitudinal high-throughput TCR repertoire profiling reveals the dynamics of T-cell memory formation after mild COVID-19 infection	95
Small molecule cognitive enhancer reverses age-related memory decline in mice	94
A lung-on-chip model of early Mycobacterium tuberculosis infection reveals an essential role for alveolar epithelial cells in controlling bacterial growth	94
Visualizing cellular and tissue ultrastructure using Ten-fold Robust Expansion Microscopy (TREx)	94
Ct threshold values, a proxy for viral load in community SARS-CoV-2 cases, demonstrate wide variation across populations and over time	93
Multi-omic rejuvenation of human cells by maturation phase transient reprogramming	92
GWAS of three molecular traits highlights core genes and pathways alongside a highly polygenic background	92
Virtual conferences raise standards for accessibility and interactions	91
The orchestrated cellular and molecular responses of the kidney to endotoxin define a precise sepsis timeline	91
Cortical astrocytes independently regulate sleep depth and duration via separate GPCR pathways	91
A transcriptomic taxonomy of Drosophila circadian neurons around the clock	91
Efficient chromatin accessibility mapping in situ by nucleosome-tethered tagmentation	90
GAF is essential for zygotic genome activation and chromatin accessibility in the early Drosophila embryo	90
Structural basis for SARM1 inhibition and activation under energetic stress	89
How subtle changes in 3D structure can create large changes in transcription	89
In vivo reconstitution finds multivalent RNA–RNA interactions as drivers of mesh-like condensates	88
Systematic examination of low-intensity ultrasound parameters on human motor cortex excitability and behavior	86
Broad geographic sampling reveals the shared basis and environmental correlates of seasonal adaptation in Drosophila	86
Single mosquito metatranscriptomics identifies vectors, emerging pathogens and reservoirs in one assay	86
Quantifying the relationship between genetic diversity and population size suggests natural selection cannot explain Lewontin’s Paradox	86
Visualizing anatomically registered data with brainrender	86
Spatiotemporal dynamics of PIEZO1 localization controls keratinocyte migration during wound healing	86
Structural basis for PRC2 decoding of active histone methylation marks H3K36me2/3	85
Fitness variation across subtle environmental perturbations reveals local modularity and global pleiotropy of adaptation	85
Functional specialization within the inferior parietal lobes across cognitive domains	85
HIV-1 uncoating by release of viral cDNA from capsid-like structures in the nucleus of infected cells	85
The brain in motion: How ensemble fluidity drives memory-updating and flexibility	84
Type 2 diabetes mellitus accelerates brain aging and cognitive decline: Complementary findings from UK Biobank and meta-analyses	83
Association of lipid-lowering drugs with COVID-19 outcomes from a Mendelian randomization study	83
Evidence for adaptive evolution in the receptor-binding domain of seasonal coronaviruses OC43 and 229e	83
A modular platform for automated cryo-FIB workflows	83
A high rate of COVID-19 vaccine hesitancy in a large-scale survey on Arabs	83
COVID-19 CG enables SARS-CoV-2 mutation and lineage tracking by locations and dates of interest	82
Selective sorting of microRNAs into exosomes by phase-separated YBX1 condensates	82
Quantitative proteomics reveals the selectivity of ubiquitin-binding autophagy receptors in the turnover of damaged lysosomes by lysophagy	81
HP1α is a chromatin crosslinker that controls nuclear and mitotic chromosome mechanics	81
Charting brain growth and aging at high spatial precision	81
Ral GTPases promote breast cancer metastasis by controlling biogenesis and organ targeting of exosomes	80
Global epistasis emerges from a generic model of a complex trait	80
Early postmortem mapping of SARS-CoV-2 RNA in patients with COVID-19 and the correlation with tissue damage	80
DNA methylation meta-analysis reveals cellular alterations in psychosis and markers of treatment-resistant schizophrenia	80
Bidirectional synaptic plasticity rapidly modifies hippocampal representations	80
Ferroptotic stress promotes the accumulation of pro-inflammatory proximal tubular cells in maladaptive renal repair	80
Profiling sensory neuron microenvironment after peripheral and central axon injury reveals key pathways for neural repair	79
Proteomic and transcriptomic profiling reveal different aspects of aging in the kidney	79
Cell types and neuronal circuitry underlying female aggression in Drosophila	79
A visual pathway for skylight polarization processing in Drosophila	79
Demographic history mediates the effect of stratification on polygenic scores	78
Common coupling map advances GPCR-G protein selectivity	78
Mouse aging cell atlas analysis reveals global and cell type-specific aging signatures	77
Single-cell analysis of the ventricular-subventricular zone reveals signatures of dorsal and ventral adult neurogenesis	77
Freshwater monitoring by nanopore sequencing	77
Protein phase separation and its role in tumorigenesis	77
Evidence for additive and synergistic action of mammalian enhancers during cell fate determination	76
Human airway cells prevent SARS-CoV-2 multibasic cleavage site cell culture adaptation	76
Single-cell transcriptomes of developing and adult olfactory receptor neurons in Drosophila	76
Brain endothelial cell TRPA1 channels initiate neurovascular coupling	75
Failures of nerve regeneration caused by aging or chronic denervation are rescued by restoring Schwann cell c-Jun	74
The molecular basis of coupling between poly(A)-tail length and translational efficiency	74
Regulatory roles of Escherichia coli 5' UTR and ORF-internal RNAs detected by 3' end mapping	74
An increase of inhibition drives the developmental decorrelation of neural activity	74
Respiration aligns perception with neural excitability	74
Generation of stress fibers through myosin-driven reorganization of the actin cortex	73
Anti-ferroptotic mechanism of IL4i1-mediated amino acid metabolism	72
Locating macromolecular assemblies in cells by 2D template matching with cisTEM	72
Iron derived from autophagy-mediated ferritin degradation induces cardiomyocyte death and heart failure in mice	72
Niche partitioning facilitates coexistence of closely related honey bee gut bacteria	72
High social status males experience accelerated epigenetic aging in wild baboons	71
Structural and mechanistic basis of the EMC-dependent biogenesis of distinct transmembrane clients	71

Mechanisms of distributed working memory in a large-scale network of macaque neocortex	71
Linking mPFC circuit maturation to the developmental regulation of emotional memory and cognitive flexibility	71
Microglial trogocytosis and the complement system regulate axonal pruning in vivo	70
Adult stem cell-derived complete lung organoid models emulate lung disease in COVID-19	70
To lie or not to lie: Super-relaxing with myosins	70
On the emergence of P-Loop NTPase and Rossmann enzymes from a Beta-Alpha-Beta ancestral fragment	70
High-resolution transcriptional and morphogenetic profiling of cells from micropatterned human ESC gastruloid cultures	70
The right time for senescence	70
Framework for rapid comparison of extracellular vesicle isolation methods	69
A survey of optimal strategy for signature-based drug repositioning and an application to liver cancer	69
Chemoreceptor co-expression in Drosophila melanogaster olfactory neurons	69
Sensory coding and the causal impact of mouse cortex in a visual decision	69
Distinct temporal difference error signals in dopamine axons in three regions of the striatum in a decision-making task	69
Single-cell transcriptomic profiling of the zebrafish inner ear reveals molecularly distinct hair cell and supporting cell subtypes	69
Walking Drosophila navigate complex plumes using stochastic decisions biased by the timing of odor encounters	69
Cohesin residency determines chromatin loop patterns	68
Activity-dependent modulation of synapse-regulating genes in astrocytes	68
The neural basis for a persistent internal state in Drosophila females	67
A Brownian ratchet model for DNA loop extrusion by the cohesin complex	67
Pupil diameter is not an accurate real-time readout of locus coeruleus activity	67
The global burden of yellow fever	67
Lapses in perceptual decisions reflect exploration	67
Cross-reactive antibodies after SARS-CoV-2 infection and vaccination	67
Sexual dimorphism in trait variability and its eco-evolutionary and statistical implications	67
An open-source device for measuring food intake and operant behavior in rodent home-cages	67
Heterogeneity of murine periosteum progenitors involved in fracture healing	66
Phenotypic and molecular evolution across 10,000 generations in laboratory budding yeast populations	66
Pre-existing bilayer stresses modulate triglyceride accumulation in the ER versus lipid droplets	66
3DeeCellTracker, a deep learning-based pipeline for segmenting and tracking cells in 3D time lapse images	66
The Arabidopsis active demethylase ROS1 cis-regulates defence genes by erasing DNA methylation at promoter-regulatory regions	66
Quantifying the impact of quarantine duration on COVID-19 transmission	66
The missing link between genetic association and regulatory function	66
A survey of early-career researchers in Australia	65
Multiple time-scales of decision-making in the hippocampus and prefrontal cortex	65
Massively multiplex single-molecule oligonucleosome footprinting	65
Regulation of immune receptor kinase plasma membrane nanoscale organization by a plant peptide hormone and its receptors	65
Identifying molecular features that are associated with biological function of intrinsically disordered protein regions	64
Ecological adaptation in Atlantic herring is associated with large shifts in allele frequencies at hundreds of loci	64
Reduction of elevated proton leak rejuvenates mitochondria in the aged cardiomyocyte	64
On the limits of fitting complex models of population history to f-statistics	64
Analysis of ultrasonic vocalizations from mice using computer vision and machine learning	64
Structure and function of axo-axonic inhibition	64
Single-cell transcriptome reveals insights into the development and function of the zebrafish ovary	63
Comprehensive fitness landscape of SARS-CoV-2 Mpro reveals insights into viral resistance mechanisms	63
MetaHiC phage-bacteria infection network reveals active cycling phages of the healthy human gut	63
An integrative study of five biological clocks in somatic and mental health	63
Autophagy in T cells from aged donors is maintained by spermidine and correlates with function and vaccine responses	63
Fixation can change the appearance of phase separation in living cells	63
Circuit and synaptic organization of forebrain-to-midbrain pathways that promote and suppress vocalization	63
Pharmacological rescue of impaired mitophagy in Parkinson’s disease-related LRRK2 G2019S knock-in mice	63
Metabolomic profiling of rare cell populations isolated by flow cytometry from tissues	63
High infectiousness immediately before COVID-19 symptom onset highlights the importance of continued contact tracing	63
Comprehension of computer code relies primarily on domain-general executive brain regions	63
Combined transient ablation and single-cell RNA-sequencing reveals the development of medullary thymic epithelial cells	63
Low-dimensional learned feature spaces quantify individual and group differences in vocal repertoires	63
Detecting adaptive introgression in human evolution using convolutional neural networks	62
The trajectory of cortical GABA across the lifespan, an individual participant data meta-analysis of edited MRS studies	62
Epigenetic reprogramming rewires transcription during the alternation of generations in Arabidopsis	62
Mesoscale phase separation of chromatin in the nucleus	62
Nutrient dominance governs the assembly of microbial communities in mixed nutrient environments	62
Decoding the physical principles of two-component biomolecular phase separation	62
Smoking, alcohol consumption, and 24 gastrointestinal diseases: Mendelian randomization analysis	62
Cytosolic aggregation of mitochondrial proteins disrupts cellular homeostasis by stimulating the aggregation of other proteins	61
Reconsidering the evidence for learning in single cells	61
Quantifying the impact of immune history and variant on SARS-CoV-2 viral kinetics and infection rebound: A retrospective cohort study	61
A pulse-chasable reporter processing assay for mammalian autophagic flux with HaloTag	61
Impaired adaptation of learning to contingency volatility in internalizing psychopathology	61
Cell non-autonomous regulation of health and longevity	61
The discriminatory power of the T cell receptor	61
ProteInfer, deep neural networks for protein functional inference	61
Understanding implicit sensorimotor adaptation as a process of proprioceptive re-alignment	61
Conformational dynamics and allosteric modulation of the SARS-CoV-2 spike	60
The structural connectome constrains fast brain dynamics	60
YAP and TAZ are transcriptional co-activators of AP-1 proteins and STAT3 during breast cellular transformation	60
Single-cell RNA-seq analysis reveals penaeid shrimp hemocyte subpopulations and cell differentiation process	60
Concerted action of kinesins KIF5B and KIF13B promotes efficient secretory vesicle transport to microtubule plus ends	60
Altered excitatory and inhibitory neuronal subpopulation parameters are distinctly associated with tau and amyloid in Alzheimer’s disease	60
Recovery of consciousness and cognition after general anesthesia in humans	60
A cross-sectional study of functional and metabolic changes during aging through the lifespan in male mice	60
Lives saved with vaccination for 10 pathogens across 112 countries in a pre-COVID-19 world	59
Longitudinal proteomic profiling of dialysis patients with COVID-19 reveals markers of severity and predictors of death	59
Molecular and anatomical characterization of parabrachial neurons and their axonal projections	59
Structure-based prediction of T cell receptor:peptide-MHC interactions	59
Pathogenic LRRK2 control of primary cilia and Hedgehog signaling in neurons and astrocytes of mouse brain	59
Right inferior frontal gyrus implements motor inhibitory control via beta-band oscillations in humans	58
Application of human liver organoids as a patient-derived primary model for HBV infection and related hepatocellular carcinoma	58
ATP and large signaling metabolites flux through caspase-activated Pannexin 1 channels	58
Systemic racial disparities in funding rates at the National Science Foundation	58
Competition between parallel sensorimotor learning systems	57
Regulatory T-cells inhibit microglia-induced pain hypersensitivity in female mice	57
Common cell type nomenclature for the mammalian brain	57
Mitochondrial phenotypes in purified human immune cell subtypes and cell mixtures	57
Single molecule microscopy reveals key physical features of repair foci in living cells	57
Convergence of cortical types and functional motifs in the human mesiotemporal lobe	57
Alpha-satellite RNA transcripts are repressed by centromere–nucleolus associations	57