Genome Research

Article	Citations
Accurate and efficient detection of gene fusions from RNA sequencing data	277
Enzymatic methyl sequencing detects DNA methylation at single-base resolution from picograms of DNA	253
Rapid and accurate alignment of nucleotide conversion sequencing reads with HISAT-3N	155
Advances in spatial transcriptomic data analysis	134
Accessing NCBI data using the NCBI Sequence Viewer and Genome Data Viewer (GDV)	130
Characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomic data with nonuniform cellular densities	105
A single-cell tumor immune atlas for precision oncology	100
A graph neural network model to estimate cell-wise metabolic flux using single-cell RNA-seq data	86
Low-pass sequencing increases the power of GWAS and decreases measurement error of polygenic risk scores compared to genotyping arrays	75
TSA-seq reveals a largely conserved genome organization relative to nuclear speckles with small position changes tightly correlated with gene expression changes	73
Data structures based on k-mers for querying large collections of sequencing data sets	72
Nondestructive enzymatic deamination enables single-molecule long-read amplicon sequencing for the determination of 5-methylcytosine and 5-hydroxymethylcytosine at single-base resolution	69
Longitudinal linked-read sequencing reveals ecological and evolutionary responses of a human gut microbiome during antibiotic treatment	68
Evolution of genome structure in theDrosophila simulansspecies complex	68
Semisupervised adversarial neural networks for single-cell classification	67
Deep metagenomics examines the oral microbiome during dental caries, revealing novel taxa and co-occurrences with host molecules	67
Ligand-induced native G-quadruplex stabilization impairs transcription initiation	64
Decoding the function of bivalent chromatin in development and cancer	64
Mitochondrial DNA variation across 56,434 individuals in gnomAD	63
Cellular plasticity balances the metabolic and proliferation dynamics of a regenerating liver	61
Post-transcriptional circadian regulation in macrophages organizes temporally distinct immunometabolic states	59
Meta-analysis of human and mouse ALS astrocytes reveals multi-omic signatures of inflammatory reactive states	59
A machine learning method for the discovery of minimum marker gene combinations for cell type identification from single-cell RNA sequencing	58
Contamination detection in sequencing studies using the mitochondrial phylogeny	56
Blood-derived mitochondrial DNA copy number is associated with gene expression across multiple tissues and is predictive for incident neurodegenerative disease	55

Genome and time-of-day transcriptome of Wolffia australiana link morphological minimization with gene loss and less growth control	55
Chromatin architecture transitions from zebrafish sperm through early embryogenesis	54
Structural variants are a major source of gene expression differences in humans and often affect multiple nearby genes	54
The loss of heterochromatin is associated with multiscale three-dimensional genome reorganization and aberrant transcription during cellular senescence	51
Characteristics, origin, and potential for cancer diagnostics of ultrashort plasma cell-free DNA	51
The Enterprise, a massive transposon carrying Spok meiotic drive genes	51
Multimodal single-cell/nucleus RNA sequencing data analysis uncovers molecular networks between disease-associated microglia and astrocytes with implications for drug repurposing in Alzheimer's diseas	50
Bayesian estimation of cell type–specific gene expression with prior derived from single-cell data	48
Acute depletion of METTL3 implicates N6-methyladenosine in alternative intron/exon inclusion in the nascent transcriptome	48
Subgenomic RNA identification in SARS-CoV-2 genomic sequencing data	48
Zebrafish transposable elements show extensive diversification in age, genomic distribution, and developmental expression	47
Three assays for in-solution enrichment of ancient human DNA at more than a million SNPs	46
The human ribosomal DNA array is composed of highly homogenized tandem clusters	46
A single-cell atlas reveals unanticipated cell type complexity in Drosophila ovaries	46
Thermal stress accelerates Arabidopsis thaliana mutation rate	46
Advancing genomic technologies and clinical awareness accelerates discovery of disease-associated tandem repeat sequences	45
A minimally destructive protocol for DNA extraction from ancient teeth	45
Targeted regulation of transcription in primary cells using CRISPRa and CRISPRi	44
Polycomb-dependent differential chromatin compartmentalization determines gene coregulation in Arabidopsis	44
Effective sequence similarity detection with strobemers	44
A joint deep learning model enables simultaneous batch effect correction, denoising, and clustering in single-cell transcriptomics	43
Genome-wide mapping reveals R-loops associated with centromeric repeats in maize	43
An atlas of fish genome evolution reveals delayed rediploidization following the teleost whole-genome duplication	42
A sheep pangenome reveals the spectrum of structural variations and their effects on tail phenotypes	42
Topologically associating domains and their role in the evolution of genome structure and function inDrosophila	42
Extensive protein dosage compensation in aneuploid human cancers	42
MAnorm2 for quantitatively comparing groups of ChIP-seq samples	42
CTCF looping is established during gastrulation in medaka embryos	41
Characterization of transcript enrichment and detection bias in single-nucleus RNA-seq for mapping of distinct human adipocyte lineages	40
A flexible repertoire of transcription factor binding sites and a diversity threshold determines enhancer activity in embryonic stem cells	40
Tracking pre-mRNA maturation across subcellular compartments identifies developmental gene regulation through intron retention and nuclear anchoring	39
Human and rat skeletal muscle single-nuclei multi-omic integrative analyses nominate causal cell types, regulatory elements, and SNPs for complex traits	39
Evolutionary rewiring of the wheat transcriptional regulatory network by lineage-specific transposable elements	38
The genetics and epigenetics of satellite centromeres	38
Genomic analyses provide insights into peach local adaptation and responses to climate change	37
MYC overexpression leads to increased chromatin interactions at super-enhancers and MYC binding sites	37
Interpretation of allele-specific chromatin accessibility using cell state–aware deep learning	36
Temperature dependence of spontaneous mutation rates	36
Precision environmental health monitoring by longitudinal exposome and multi-omics profiling	36
A new emu genome illuminates the evolution of genome configuration and nuclear architecture of avian chromosomes	36
Transcript assembly improves expression quantification of transposable elements in single-cell RNA-seq data	35
Spatial organization of chromosomes leads to heterogeneous chromatin motion and drives the liquid- or gel-like dynamical behavior of chromatin	35
Allelic diversification after transposable element exaptation promotedgsdfas the master sex determining gene of sablefish	35
Profiling chromatin accessibility in formalin-fixed paraffin-embedded samples	35
Genomic environments scale the activities of diverse core promoters	35
Multi–cell type gene coexpression network analysis reveals coordinated interferon response and cross–cell type correlations in systemic lupus erythematosus	34
SARS-CoV-2 genomic diversity and the implications for qRT-PCR diagnostics and transmission	34
Chromosome-specific telomere lengths and the minimal functional telomere revealed by nanopore sequencing	33
Plasma cell-free RNA characteristics in COVID-19 patients	33
Assembly of a pangenome for global cattle reveals missing sequences and novel structural variations, providing new insights into their diversity and evolutionary history	33

Enhancers with tissue-specific activity are enriched in intronic regions	33
Transposable elements and their KZFP controllers are drivers of transcriptional innovation in the developing human brain	33
Conserved noncoding sequences provide insights into regulatory sequence and loss of gene expression in maize	33
Analysis of alternative polyadenylation from single-cell RNA-seq using scDaPars reveals cell subpopulations invisible to gene expression	32
A systematic analysis of Trypanosoma brucei chromatin factors identifies novel protein interaction networks associated with sites of transcription initiation and termination	32
Epstein–Barr virus nuclear antigen 2 extensively rewires the human chromatin landscape at autoimmune risk loci	32
Inferring genes that escape X-Chromosome inactivation reveals important contribution of variable escape genes to sex-biased diseases	32
Sequence analysis in Bos taurus reveals pervasiveness of X–Y arms races in mammalian lineages	31
A mosquito small RNA genomics resource reveals dynamic evolution and host responses to viruses and transposons	31
Long-read assembly and comparative evidence-based reanalysis of Cryptosporidium genome sequences reveal expanded transporter repertoire and duplication of entire chromosome ends including subte	30
Accurate and robust inference of microbial growth dynamics from metagenomic sequencing reveals personalized growth rates	30
Dosage-sensitive functions in embryonic development drove the survival of genes on sex-specific chromosomes in snakes, birds, and mammals	30
Transporter genes in biosynthetic gene clusters predict metabolite characteristics and siderophore activity	30
Direct detection of natural selection in Bronze Age Britain	29
Haplotype diversity and sequence heterogeneity of human telomeres	28
Alu insertion variants alter gene transcript levels	28
Long-read RNA sequencing reveals widespread sex-specific alternative splicing in threespine stickleback fish	28
Active enhancers strengthen insulation by RNA-mediated CTCF binding at chromatin domain boundaries	28
The Drosophila brain on cocaine at single-cell resolution	27
Automated quality control and cell identification of droplet-based single-cell data using dropkick	27
Cancer-associated dynamics and potential regulators of intronic polyadenylation revealed by IPAFinder using standard RNA-seq data	27
Systematic detection of brain protein-coding genes under positive selection during primate evolution and their roles in cognition	27
ZNF91 deletion in human embryonic stem cells leads to ectopic activation of SVA retrotransposons and up-regulation of KRAB zinc finger gene clusters	27
BRAKER3: Fully automated genome annotation using RNA-seq and protein evidence with GeneMark-ETP, AUGUSTUS, and TSEBRA	27
Diverse tumorigenic consequences of human papillomavirus integration in primary oropharyngeal cancers	27
The contributions from the progenitor genomes of the mesopolyploid Brassiceae are evolutionarily distinct but functionally compatible	26
Likelihood-based deconvolution of bulk gene expression data using single-cell references	26
AP-1 subunits converge promiscuously at enhancers to potentiate transcription	26
DNA methylation epitypes highlight underlying developmental and disease pathways in acute myeloid leukemia	26
Rapid evolution and strain turnover in the infant gut microbiome	25
Selection and thermostability suggest G-quadruplexes are novel functional elements of the human genome	25
Mutability of mononucleotide repeats, not oxidative stress, explains the discrepancy between laboratory-accumulated mutations and the natural allele-frequency spectrum inC. elegans	25
Genetic features and genomic targets of human KRAB-zinc finger proteins	25
A chromosome-scale epigenetic map of theHydragenome reveals conserved regulators of cell state	25
Intergenic ORFs as elementary structural modules of de novo gene birth and protein evolution	25
Relative contributions of sex hormones, sex chromosomes, and gonads to sex differences in tissue gene regulation	25
Panoramic transcriptome analysis and functional screening of long noncoding RNAs in mouse spermatogenesis	24
Genomic analyses of wild argali, domestic sheep, and their hybrids provide insights into chromosome evolution, phenotypic variation, and germplasm innovation	24
Transcriptional activity and epigenetic regulation of transposable elements in the symbiotic fungus Rhizophagus irregularis	24
The role of insulators and transcription in 3D chromatin organization of flies	23
ATAC-STARR-seq reveals transcription factor–bound activators and silencers within chromatin-accessible regions of the human genome	23
Profiling neural editomes reveals a molecular mechanism to regulate RNA editing during development	22
The origin and evolution of a distinct mechanism of transcription initiation in yeasts	22
The genomic basis of evolutionary differentiation among honey bees	22
Enhancer–silencer transitions in the human genome	22
Third-generation sequencing revises the molecular karyotype for Toxoplasma gondii and identifies emerging copy number variants in sexual recombinants	22
Cis-acting variation is common across regulatory layers but is often buffered during embryonic development	22
A framework to score the effects of structural variants in health and disease	22
Targeted single-cell RNA sequencing of transcription factors enhances the identification of cell types and trajectories	21
Efficient computation of Faith's phylogenetic diversity with applications in characterizing microbiomes	21
Tagmentation-based single-cell genomics	21
Crossover-active regions of the wheat genome are distinguished by DMC1, the chromosome axis, H3K27me3, and signatures of adaptation	21
Low-input RNase footprinting for simultaneous quantification of cytosolic and mitochondrial translation	21
Genomic architecture constrained placental mammal X Chromosome evolution	21
Cellular abundance shapes function in piRNA-guided genome defense	21
Evolution of transcription factor binding through sequence variations and turnover of binding sites	21
An efficient method to identify, date, and describe admixture events using haplotype information	21
Single worm transcriptomics identifies a developmental core network of oscillating genes with deep conservation across nematodes	20
Allele-specific alternative splicing and its functional genetic variants in human tissues	20
Greater strength of selection and higher proportion of beneficial amino acid changing mutations in humans compared with mice and Drosophila melanogaster	20
Reevaluation of the Toxoplasma gondii and Neospora caninum genomes reveals misassembly, karyotype differences, and chromosomal rearrangements	20
Short arms of human acrocentric chromosomes and the completion of the human genome sequence	20
Functional noncoding SNPs in human endothelial cells fine-map vascular trait associations	20
Competition for DNA binding between paralogous transcription factors determines their genomic occupancy and regulatory functions	19
Profiling single-cell histone modifications using indexing chromatin immunocleavage sequencing	19
Sequencing of individual barcoded cDNAs using Pacific Biosciences and Oxford Nanopore Technologies reveals platform-specific error patterns	19
A platform for curated products from novel open reading frames prompts reinterpretation of disease variants	19
Snake venom gene expression is coordinated by novel regulatory architecture and the integration of multiple co-opted vertebrate pathways	19
Fast decoding cell type–specific transcription factor binding landscape at single-nucleotide resolution	19
Coordination of zygotic genome activation entry and exit by H3K4me3 and H3K27me3 in porcine early embryos	19
Positive selection in noncoding genomic regions of vocal learning birds is associated with genes implicated in vocal learning and speech functions in humans	19
Sir3 mediates long-range chromosome interactions in budding yeast	18
Individualized VDJ recombination predisposes the available Ig sequence space	18
Pooled protein tagging, cellular imaging, and in situ sequencing for monitoring drug action in real time	18
An efficient genotyper and star-allele caller for pharmacogenomics	18
Comprehensive determination of transcription start sites derived from all RNA polymerases using ReCappable-seq	18
ceRNA crosstalk mediated by ncRNAs is a novel regulatory mechanism in fish sex determination and differentiation	18
Ultrafast functional profiling of RNA-seq data for nonmodel organisms	18
A hidden layer of structural variation in transposable elements reveals potential genetic modifiers in human disease-risk loci	18
Three-dimensional missense tolerance ratio analysis	18

Mapping the regulatory landscape of auditory hair cells from single-cell multi-omics data	18
KDM1A maintains genome-wide homeostasis of transcriptional enhancers	18
A novel fragmented mitochondrial genome in the protist pathogen Toxoplasma gondii and related tissue coccidia	18
Effects of transcriptional noise on estimates of gene and transcript expression in RNA sequencing experiments	17
Scalable and model-free detection of spatial patterns and colocalization	17
Generation of mouse conditional knockout alleles in one step using the i-GONAD method	17
Extensive sampling of Saccharomyces cerevisiae in Taiwan reveals ecology and evolution of predomesticated lineages	17
Global loss of cellular m6A RNA methylation following infection with different SARS-CoV-2 variants	17
Chromosome-scale assemblies of Acanthamoeba castellanii genomes provide insights into Legionella pneumophila infection–related chromatin reorganization	17
Distinct roles for RSC and SWI/SNF chromatin remodelers in genomic excision repair	17
Mutagenesis of human genomes by endogenous mobile elements on a population scale	17
H3K36 dimethylation shapes the epigenetic interaction landscape by directing repressive chromatin modifications in embryonic stem cells	17
A KMT2A-AFF1 gene regulatory network highlights the role of core transcription factors and reveals the regulatory logic of key downstream target genes	17
Gaps and complex structurally variant loci in phased genome assemblies	17
Accumulation and ineffective silencing of transposable elements on an avian W Chromosome	17
Cross-species cell-type assignment from single-cell RNA-seq data by a heterogeneous graph neural network	17
Transposable elements drive the evolution of metazoan zinc finger genes	17
Variation in mutation, recombination, and transposition rates inDrosophila melanogasterandDrosophila simulans	17
Characterizing nucleotide variation and expansion dynamics in human-specific variable number tandem repeats	16
Long-range promoter–enhancer contacts are conserved during evolution and contribute to gene expression robustness	16
Domain-adaptive neural networks improve cross-species prediction of transcription factor binding	16
Transcription initiation mapping in 31 bovine tissues reveals complex promoter activity, pervasive transcription, and tissue-specific promoter usage	16
Ruminant-specific retrotransposons shape regulatory evolution of bovine immunity	16
Reactivation of transposable elements following hybridization in fission yeast	16
Robust analysis of prokaryotic pangenome gene gain and loss rates with Panstripe	16
Genome-wide analysis of plant miRNA action clarifies levels of regulatory dynamics across developmental contexts	16
Ultra-long-range interactions between active regulatory elements	16
TP53-inducible putative long noncoding RNAs encode functional polypeptides that suppress cell proliferation	16
Somatic structural variant formation is guided by and influences genome architecture	15
Copy number variation underlies complex phenotypes in domestic dog breeds and other canids	15
Gene prediction in the immunoglobulin loci	15
A butterfly pan-genome reveals that a large amount of structural variation underlies the evolution of chromatin accessibility	15
Applications of single-cell genomics and computational strategies to study common disease and population-level variation	15
The structure, function, and evolution of plant centromeres	15
Transcriptional milestones in Dictyostelium development	15
The fine-scale recombination rate variation and associations with genomic features in a butterfly	15
Global quantification exposes abundant low-level off-target activity by base editors	15
Dynamics of broad H3K4me3 domains uncover an epigenetic switch between cell identity and cancer-related genes	15
Tissue-specific reprogramming of host tRNA transcriptome by the microbiome	14
Cell type–specific analysis by single-cell profiling identifies a stable mammalian tRNA–mRNA interface and increased translation efficiency in neurons	14
De novo mutation rates at the single-mutation resolution in a human HBB gene region associated with adaptation and genetic disease	14
Spatially resolved whole transcriptome profiling in human and mouse tissue using Digital Spatial Profiling	14
Long-read sequencing of 111 rice genomes reveals significantly larger pan-genomes	14
Resetting of the 24-nt siRNA landscape in rice zygotes	14
Identification and characterization of centromeric sequences in Xenopus laevis	14
Fixation of allelic gene expression landscapes and expression bias pattern shape the transcriptome of the clonal Amazon molly	14
Mosaic loss of Chromosome Y in aged human microglia	14
Variations in antibody repertoires correlate with vaccine responses	14
Modeling molecular development of breast cancer in canine mammary tumors	14
Tissue-specific patterns of regulatory changes underlying gene expression differences among Ficedula flycatchers and their naturally occurring F1 hybrids	14
Non-Mendelian inheritance patterns and extreme deviation rates of CGG repeats in autism	14
Genomic context sensitivity of insulator function	14
Latent feature extraction with a prior-based self-attention framework for spatial transcriptomics	14
A single-cell transcriptome atlas of the maturing zebrafish telencephalon	13
Haplotype and population structure inference using neural networks in whole-genome sequencing data	13
Predicting unrecognized enhancer-mediated genome topology by an ensemble machine learning model	13
Genome biology of the darkedged splitfin, Girardinichthys multiradiatus, and the evolution of sex chromosomes and placentation	13
Population genomics reveals mechanisms and dynamics of de novo expressed open reading frame emergence inDrosophila melanogaster	13
Diversity, duplication, and genomic organization of homeobox genes in Lepidoptera	13
Linear-time cluster ensembles of large-scale single-cell RNA-seq and multimodal data	13
Cancer cell states and emergent properties of the dynamic tumor system	13
Automated annotation of human centromeres with HORmon	13
Loss of histone H3.3 results in DNA replication defects and altered origin dynamics in C. elegans	13
Chromatin interaction–aware gene regulatory modeling with graph attention networks	13
Embryonic LTR retrotransposons supply promoter modules to somatic tissues	13
Shared evolutionary trajectories of three independent neo-sex chromosomes in Drosophila	13
Lossless indexing with counting de Bruijn graphs	13
Analyses of 600+ insect genomes reveal repetitive element dynamics and highlight biodiversity-scale repeat annotation challenges	13
Discovery of an unusually high number of de novo mutations in sperm of older men using duplex sequencing	12
Small RNA expression and miRNA modification dynamics in human oocytes and early embryos	12
Efficient and accurate KIR and HLA genotyping with massively parallel sequencing data	12
Genome-wide identification of tandem repeats associated with splicing variation across 49 tissues in humans	12
De novo reconstruction of satellite repeat units from sequence data	12
Local nucleosome dynamics and eviction following a double-strand break are reversible by NHEJ-mediated repair in the absence of DNA replication	12
A Bayesian inference transcription factor activity model for the analysis of single-cell transcriptomes	12
Global patterns of enhancer activity during sea urchin embryogenesis assessed by eRNA profiling	12
Positive selective sweeps of epigenetic mutations regulating specialized metabolites in plants	12
Epigenomic translocation of H3K4me3 broad domains over oncogenes following hijacking of super-enhancers	12
Extremely fast construction and querying of compacted and colored de Bruijn graphs with GGCAT	12
Debiased personalized gene coexpression networks for population-scale scRNA-seq data	12
Systematic transcriptome analysis associated with physiological and chronological aging inCaenorhabditis elegans	12
NicE-C efficiently reveals open chromatin–associated chromosome interactions at high resolution	12
The motif composition of variable number tandem repeats impacts gene expression	12
Epigenomic analysis reveals prevalent contribution of transposable elements to cis-regulatory elements, tissue-specific expression, and alternative promoters in zebrafish	12
A harmonized public resource of deeply sequenced diverse human genomes	12
RefSeq Functional Elements as experimentally assayed nongenic reference standards and functional interactions in human and mouse	11
The western redcedar genome reveals low genetic diversity in a self-compatible conifer	11
Genome-wide profiling reveals functional interplay of DNA sequence composition, transcriptional activity, and nucleosome positioning in driving DNA supercoiling and helix destabilization in C. eleg	11
Listeria monocytogenes genes supporting growth under standard laboratory cultivation conditions and during macrophage infection	11
Genome-wide variability in recombination activity is associated with meiotic chromatin organization	11
Large palindromes on the primate X Chromosome are preserved by natural selection	11
Integration site–dependent HIV-1 promoter activity shapes host chromatin conformation	11
Gene expression imputation and cell-type deconvolution in human brain with spatiotemporal precision and its implications for brain-related disorders	11
Recent, full-length gene retrocopies are common in canids	11
Modeling expression ranks for noise-tolerant differential expression analysis of scRNA-seq data	11