Genome Research

Article	Citations
HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads	419
Accurate and efficient detection of gene fusions from RNA sequencing data	213
Enzymatic methyl sequencing detects DNA methylation at single-base resolution from picograms of DNA	167
Rapid and accurate alignment of nucleotide conversion sequencing reads with HISAT-3N	106
Advances in spatial transcriptomic data analysis	100
Functional annotation of human long noncoding RNAs via molecular phenotyping	99
Comprehensive analyses of 723 transcriptomes enhance genetic and biological interpretations for complex traits in cattle	95
Accessing NCBI data using the NCBI Sequence Viewer and Genome Data Viewer (GDV)	95
Single-cell analysis of human embryos reveals diverse patterns of aneuploidy and mosaicism	93
Single-cell-resolution transcriptome map of human, chimpanzee, bonobo, and macaque brains	93
Mapping genome variation of SARS-CoV-2 worldwide highlights the impact of COVID-19 super-spreaders	85
A single-cell tumor immune atlas for precision oncology	84
Characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomic data with nonuniform cellular densities	77
Genome variation and population structure among 1142 mosquitoes of the African malaria vector species Anopheles gambiae and Anopheles coluzzii	74
Transcriptome-wide sites of collided ribosomes reveal principles of translational pausing	72
Comprehensive analysis of structural variants in breast cancer genomes using single-molecule sequencing	71
Ultralow-input single-tube linked-read library method enables short-read second-generation sequencing systems to routinely generate highly accurate and economical long-range sequencing information	66
Cross-species analysis of enhancer logic using deep learning	65
Low-pass sequencing increases the power of GWAS and decreases measurement error of polygenic risk scores compared to genotyping arrays	64
Nondestructive enzymatic deamination enables single-molecule long-read amplicon sequencing for the determination of 5-methylcytosine and 5-hydroxymethylcytosine at single-base resolution	63
Detection and characterization of jagged ends of double-stranded DNA in plasma	61
Characterizing and inferring quantitative cell cycle phase in single-cell RNA-seq data analysis	61
Data structures based on k-mers for querying large collections of sequencing data sets	59
Semisupervised adversarial neural networks for single-cell classification	56
A graph neural network model to estimate cell-wise metabolic flux using single-cell RNA-seq data	56

Quantitative analysis of Y-Chromosome gene expression across 36 human tissues	56
Sequencing identifies multiple early introductions of SARS-CoV-2 to the New York City region	56
Accurate reconstruction of bacterial pan- and core genomes with PEPPAN	56
Longitudinal linked-read sequencing reveals ecological and evolutionary responses of a human gut microbiome during antibiotic treatment	55
Binding specificities of human RNA-binding proteins toward structured and linear RNA sequences	55
Evolution of genome structure in theDrosophila simulansspecies complex	55
Deep metagenomics examines the oral microbiome during dental caries, revealing novel taxa and co-occurrences with host molecules	54
Genome and time-of-day transcriptome of Wolffia australiana link morphological minimization with gene loss and less growth control	53
Blood-derived mitochondrial DNA copy number is associated with gene expression across multiple tissues and is predictive for incident neurodegenerative disease	51
Redundant and specific roles of cohesin STAG subunits in chromatin looping and transcriptional control	51
TSA-seq reveals a largely conserved genome organization relative to nuclear speckles with small position changes tightly correlated with gene expression changes	50
Cellular plasticity balances the metabolic and proliferation dynamics of a regenerating liver	50
Post-transcriptional circadian regulation in macrophages organizes temporally distinct immunometabolic states	50
High-throughput single-cell functional elucidation of neurodevelopmental disease–associated genes reveals convergent mechanisms altering neuronal differentiation	49
Decoding the function of bivalent chromatin in development and cancer	49
Parallel bimodal single-cell sequencing of transcriptome and chromatin accessibility	49
Chromatin architecture transitions from zebrafish sperm through early embryogenesis	48
Mitochondrial DNA variation across 56,434 individuals in gnomAD	47
Dynamic effects of interacting genes underlying rice flowering-time phenotypic plasticity and global adaptation	47
Meta-analysis of human and mouse ALS astrocytes reveals multi-omic signatures of inflammatory reactive states	47
Subgenomic RNA identification in SARS-CoV-2 genomic sequencing data	46
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	46
Paternal age in rhesus macaques is positively associated with germline mutation accumulation but not with measures of offspring sociability	46
Molecular barcoding of native RNAs using nanopore sequencing and deep learning	45
Contamination detection in sequencing studies using the mitochondrial phylogeny	45
Structural variants are a major source of gene expression differences in humans and often affect multiple nearby genes	45
Ligand-induced native G-quadruplex stabilization impairs transcription initiation	45
The Enterprise, a massive transposon carrying Spok meiotic drive genes	43
A machine learning method for the discovery of minimum marker gene combinations for cell type identification from single-cell RNA sequencing	43
Characteristics, origin, and potential for cancer diagnostics of ultrashort plasma cell-free DNA	42
Distinct contributions of DNA methylation and histone acetylation to the genomic occupancy of transcription factors	40
Thermal stress accelerates Arabidopsis thaliana mutation rate	39
Bayesian estimation of cell type–specific gene expression with prior derived from single-cell data	38
A single-cell atlas reveals unanticipated cell type complexity in Drosophila ovaries	37
Characterization of transcript enrichment and detection bias in single-nucleus RNA-seq for mapping of distinct human adipocyte lineages	37
A joint deep learning model enables simultaneous batch effect correction, denoising, and clustering in single-cell transcriptomics	37
Effective sequence similarity detection with strobemers	37
Complete characterization of the human immune cell transcriptome using accurate full-length cDNA sequencing	36
The loss of heterochromatin is associated with multiscale three-dimensional genome reorganization and aberrant transcription during cellular senescence	36
Acute depletion of METTL3 implicates N6-methyladenosine in alternative intron/exon inclusion in the nascent transcriptome	36
Genome-wide mapping reveals R-loops associated with centromeric repeats in maize	36
Sex differences in human adipose tissue gene expression and genetic regulation involve adipogenesis	36
CTCF looping is established during gastrulation in medaka embryos	35
A flexible repertoire of transcription factor binding sites and a diversity threshold determines enhancer activity in embryonic stem cells	35
Advancing genomic technologies and clinical awareness accelerates discovery of disease-associated tandem repeat sequences	35
Characterization of colibactin-associated mutational signature in an Asian oral squamous cell carcinoma and in other mucosal tumor types	35
Polycomb-dependent differential chromatin compartmentalization determines gene coregulation in Arabidopsis	35
RNA-Bloom enables reference-free and reference-guided sequence assembly for single-cell transcriptomes	34
PR-DUB maintains the expression of critical genes through FOXK1/2- and ASXL1/2/3-dependent recruitment to chromatin and H2AK119ub1 deubiquitination	34
An atlas of fish genome evolution reveals delayed rediploidization following the teleost whole-genome duplication	34

Rapid evolution of piRNA-mediated silencing of an invading transposable element was driven by abundant de novo mutations	34
The human ribosomal DNA array is composed of highly homogenized tandem clusters	34
Topologically associating domains and their role in the evolution of genome structure and function inDrosophila	34
Chromatin activation as a unifying principle underlying pathogenic mechanisms in multiple myeloma	34
Interpretation of allele-specific chromatin accessibility using cell state–aware deep learning	33
Arabidopsis retrotransposon virus-like particles and their regulation by epigenetically activated small RNA	33
A minimally destructive protocol for DNA extraction from ancient teeth	32
Distinctive regulatory architectures of germline-active and somatic genes in C. elegans	32
MAnorm2 for quantitatively comparing groups of ChIP-seq samples	32
Human and rat skeletal muscle single-nuclei multi-omic integrative analyses nominate causal cell types, regulatory elements, and SNPs for complex traits	31
Transcript assembly improves expression quantification of transposable elements in single-cell RNA-seq data	31
Targeted regulation of transcription in primary cells using CRISPRa and CRISPRi	31
ADAR-deficiency perturbs the global splicing landscape in mouse tissues	31
Tracking pre-mRNA maturation across subcellular compartments identifies developmental gene regulation through intron retention and nuclear anchoring	30
Large tandem duplications affect gene expression, 3D organization, and plant–pathogen response	30
Genome-wide CRISPR screening reveals genes essential for cell viability and resistance to abiotic and biotic stresses in Bombyx mori	30
Genomic analyses provide insights into peach local adaptation and responses to climate change	30
Untangling the effects of cellular composition on coexpression analysis	30
A systematic analysis of Trypanosoma brucei chromatin factors identifies novel protein interaction networks associated with sites of transcription initiation and termination	30
A long-read RNA-seq approach to identify novel transcripts of very large genes	29
Conserved noncoding sequences provide insights into regulatory sequence and loss of gene expression in maize	29
Widespread intron retention impairs protein homeostasis in C9orf72 ALS brains	29
Comparative transcriptomics of primary cells in vertebrates	29
Long-read sequencing for non-small-cell lung cancer genomes	29
Zebrafish transposable elements show extensive diversification in age, genomic distribution, and developmental expression	29
SARS-CoV-2 genomic diversity and the implications for qRT-PCR diagnostics and transmission	29
Temperature dependence of spontaneous mutation rates	28
A new emu genome illuminates the evolution of genome configuration and nuclear architecture of avian chromosomes	28
Extensive protein dosage compensation in aneuploid human cancers	28
Evolutionary rewiring of the wheat transcriptional regulatory network by lineage-specific transposable elements	28
Native molecule sequencing by nano-ID reveals synthesis and stability of RNA isoforms	28
Sequence analysis in Bos taurus reveals pervasiveness of X–Y arms races in mammalian lineages	28
High precision Neisseria gonorrhoeae variant and antimicrobial resistance calling from metagenomic Nanopore sequencing	28
LCM-seq reveals unique transcriptional adaptation mechanisms of resistant neurons and identifies protective pathways in spinal muscular atrophy	27
Plasma cell-free RNA characteristics in COVID-19 patients	27
A mosquito small RNA genomics resource reveals dynamic evolution and host responses to viruses and transposons	27
Spatial organization of chromosomes leads to heterogeneous chromatin motion and drives the liquid- or gel-like dynamical behavior of chromatin	27
Transposable elements and their KZFP controllers are drivers of transcriptional innovation in the developing human brain	26
Prevalence of alternative AUG and non-AUG translation initiators and their regulatory effects across plants	26
Precision environmental health monitoring by longitudinal exposome and multi-omics profiling	26
Three assays for in-solution enrichment of ancient human DNA at more than a million SNPs	26
Dosage-sensitive functions in embryonic development drove the survival of genes on sex-specific chromosomes in snakes, birds, and mammals	25
Genomic environments scale the activities of diverse core promoters	25
Systematic detection of brain protein-coding genes under positive selection during primate evolution and their roles in cognition	25
Inferring genes that escape X-Chromosome inactivation reveals important contribution of variable escape genes to sex-biased diseases	25
Multi–cell type gene coexpression network analysis reveals coordinated interferon response and cross–cell type correlations in systemic lupus erythematosus	25
Long-read assembly and comparative evidence-based reanalysis of Cryptosporidium genome sequences reveal expanded transporter repertoire and duplication of entire chromosome ends including subte	25
A limited set of transcriptional programs define major cell types	25
Epstein–Barr virus nuclear antigen 2 extensively rewires the human chromatin landscape at autoimmune risk loci	24
Dynamic transcriptional and chromatin accessibility landscape of medaka embryogenesis	24
The evolution of sex-biased gene expression in the Drosophila brain	24
MYC overexpression leads to increased chromatin interactions at super-enhancers and MYC binding sites	24
Allelic diversification after transposable element exaptation promotedgsdfas the master sex determining gene of sablefish	24
Transporter genes in biosynthetic gene clusters predict metabolite characteristics and siderophore activity	24
Simple and efficient profiling of transcription initiation and transcript levels with STRIPE-seq	24
Alu insertion variants alter gene transcript levels	24
Analysis of alternative polyadenylation from single-cell RNA-seq using scDaPars reveals cell subpopulations invisible to gene expression	24
Long-read RNA sequencing reveals widespread sex-specific alternative splicing in threespine stickleback fish	24
Translation initiation downstream from annotated start codons in human mRNAs coevolves with the Kozak context	23
Automated quality control and cell identification of droplet-based single-cell data using dropkick	23
Noncoding regions underpin avian bill shape diversification at macroevolutionary scales	23
Accurate and robust inference of microbial growth dynamics from metagenomic sequencing reveals personalized growth rates	23
The genetics and epigenetics of satellite centromeres	23
Genome-wide dynamics of RNA synthesis, processing, and degradation without RNA metabolic labeling	22
Mutability of mononucleotide repeats, not oxidative stress, explains the discrepancy between laboratory-accumulated mutations and the natural allele-frequency spectrum inC. elegans	22
ZNF91 deletion in human embryonic stem cells leads to ectopic activation of SVA retrotransposons and up-regulation of KRAB zinc finger gene clusters	22
The contributions from the progenitor genomes of the mesopolyploid Brassiceae are evolutionarily distinct but functionally compatible	22
Intragenic repeat expansion in the cell wall protein gene HPF1 controls yeast chronological aging	21
Complex mosaic structural variations in human fetal brains	21
Chromosome-specific telomere lengths and the minimal functional telomere revealed by nanopore sequencing	21
The Drosophila brain on cocaine at single-cell resolution	21
Enhancers with tissue-specific activity are enriched in intronic regions	21
HDA6-dependent histone deacetylation regulates mRNA polyadenylation in Arabidopsis	21
Intergenic ORFs as elementary structural modules of de novo gene birth and protein evolution	20
Transcriptional activity and epigenetic regulation of transposable elements in the symbiotic fungus Rhizophagus irregularis	20
A sheep pangenome reveals the spectrum of structural variations and their effects on tail phenotypes	20
CRISPR-Cas9-mediated pinpoint microbial genome editing aided by target-mismatched sgRNAs	20
Polymorphic centromere locations in the pathogenic yeast Candida parapsilosis	20
DNA methylation epitypes highlight underlying developmental and disease pathways in acute myeloid leukemia	20
Rapid evolution and strain turnover in the infant gut microbiome	20

Panoramic transcriptome analysis and functional screening of long noncoding RNAs in mouse spermatogenesis	20
Selection and thermostability suggest G-quadruplexes are novel functional elements of the human genome	20
Metabolic labeling of RNA using multiple ribonucleoside analogs enables the simultaneous evaluation of RNA synthesis and degradation rates	19
Diverse tumorigenic consequences of human papillomavirus integration in primary oropharyngeal cancers	19
Pan-cancer multi-omics analysis and orthogonal experimental assessment of epigenetic driver genes	19
Leveraging mouse chromatin data for heritability enrichment informs common disease architecture and reveals cortical layer contributions to schizophrenia	19
A chromosome-scale epigenetic map of theHydragenome reveals conserved regulators of cell state	19
Cis-acting variation is common across regulatory layers but is often buffered during embryonic development	19
Haplotype diversity and sequence heterogeneity of human telomeres	19
Cancer-associated dynamics and potential regulators of intronic polyadenylation revealed by IPAFinder using standard RNA-seq data	19
Targeted single-cell RNA sequencing of transcription factors enhances the identification of cell types and trajectories	18
Relative contributions of sex hormones, sex chromosomes, and gonads to sex differences in tissue gene regulation	18
Diploid genome architecture revealed by multi-omic data of hybrid mice	18
Reevaluation of the Toxoplasma gondii and Neospora caninum genomes reveals misassembly, karyotype differences, and chromosomal rearrangements	18
Fast decoding cell type–specific transcription factor binding landscape at single-nucleotide resolution	18
Direct detection of natural selection in Bronze Age Britain	18
An efficient method to identify, date, and describe admixture events using haplotype information	18
Crossover-active regions of the wheat genome are distinguished by DMC1, the chromosome axis, H3K27me3, and signatures of adaptation	18
Global fitness landscapes of the Shine-Dalgarno sequence	18
The origin and evolution of a distinct mechanism of transcription initiation in yeasts	18
The genomic basis of evolutionary differentiation among honey bees	18
Enhancer–silencer transitions in the human genome	17
Xylem systems genetics analysis reveals a key regulator of lignin biosynthesis in Populus deltoides	17
Somatic structural variation targets neurodevelopmental genes and identifies SHANK2 as a tumor suppressor in neuroblastoma	17
Tagmentation-based single-cell genomics	17
Transposon expression in the Drosophila brain is driven by neighboring genes and diversifies the neural transcriptome	17
Single worm transcriptomics identifies a developmental core network of oscillating genes with deep conservation across nematodes	17
Profiling neural editomes reveals a molecular mechanism to regulate RNA editing during development	17
A platform for curated products from novel open reading frames prompts reinterpretation of disease variants	17
The role of insulators and transcription in 3D chromatin organization of flies	17
Third-generation sequencing revises the molecular karyotype for Toxoplasma gondii and identifies emerging copy number variants in sexual recombinants	17
Individualized VDJ recombination predisposes the available Ig sequence space	17
Generation of mouse conditional knockout alleles in one step using the i-GONAD method	17
A novel fragmented mitochondrial genome in the protist pathogen Toxoplasma gondii and related tissue coccidia	17
Likelihood-based deconvolution of bulk gene expression data using single-cell references	17
Allele-specific alternative splicing and its functional genetic variants in human tissues	17
Cellular abundance shapes function in piRNA-guided genome defense	16
Mutagenesis of human genomes by endogenous mobile elements on a population scale	16
Profiling single-cell histone modifications using indexing chromatin immunocleavage sequencing	16
Determining the impact of uncharacterized inversions in the human genome by droplet digital PCR	16
Profiling chromatin accessibility in formalin-fixed paraffin-embedded samples	16
Efficient computation of Faith's phylogenetic diversity with applications in characterizing microbiomes	16
Identification of determinants of differential chromatin accessibility through a massively parallel genome-integrated reporter assay	16
A KMT2A-AFF1 gene regulatory network highlights the role of core transcription factors and reveals the regulatory logic of key downstream target genes	16
Genomic architecture constrained placental mammal X Chromosome evolution	16
Mapping the regulatory landscape of auditory hair cells from single-cell multi-omics data	16
Greater strength of selection and higher proportion of beneficial amino acid changing mutations in humans compared with mice and Drosophila melanogaster	16
Assembly of a pangenome for global cattle reveals missing sequences and novel structural variations, providing new insights into their diversity and evolutionary history	16
Genome-wide analysis of plant miRNA action clarifies levels of regulatory dynamics across developmental contexts	16
Positive selection in noncoding genomic regions of vocal learning birds is associated with genes implicated in vocal learning and speech functions in humans	16
ceRNA crosstalk mediated by ncRNAs is a novel regulatory mechanism in fish sex determination and differentiation	15
Low-input RNase footprinting for simultaneous quantification of cytosolic and mitochondrial translation	15
Characterizing nucleotide variation and expansion dynamics in human-specific variable number tandem repeats	15
Sir3 mediates long-range chromosome interactions in budding yeast	15
Ultrafast functional profiling of RNA-seq data for nonmodel organisms	15
Long-range promoter–enhancer contacts are conserved during evolution and contribute to gene expression robustness	15
TransBorrow: genome-guided transcriptome assembly by borrowing assemblies from different assemblers	15
Distinct roles for RSC and SWI/SNF chromatin remodelers in genomic excision repair	15
Single-cell strand sequencing of a macaque genome reveals multiple nested inversions and breakpoint reuse during primate evolution	15
Three-dimensional missense tolerance ratio analysis	15
KDM1A maintains genome-wide homeostasis of transcriptional enhancers	14
V(DD)J recombination is an important and evolutionarily conserved mechanism for generating antibodies with unusually long CDR3s	14
Dissecting the regulatory activity and sequence content of loci with exceptional numbers of transcription factor associations	14
ATAC-STARR-seq reveals transcription factor–bound activators and silencers within chromatin-accessible regions of the human genome	14
Ultrafast and scalable variant annotation and prioritization with big functional genomics data	14
AP-1 subunits converge promiscuously at enhancers to potentiate transcription	14
Competition for DNA binding between paralogous transcription factors determines their genomic occupancy and regulatory functions	14
Snake venom gene expression is coordinated by novel regulatory architecture and the integration of multiple co-opted vertebrate pathways	14
Long-read sequencing of 111 rice genomes reveals significantly larger pan-genomes	13
Reactivation of transposable elements following hybridization in fission yeast	13
A hidden layer of structural variation in transposable elements reveals potential genetic modifiers in human disease-risk loci	13
Comprehensive determination of transcription start sites derived from all RNA polymerases using ReCappable-seq	13
Sequencing of individual barcoded cDNAs using Pacific Biosciences and Oxford Nanopore Technologies reveals platform-specific error patterns	13
Global quantification exposes abundant low-level off-target activity by base editors	13
Domain-adaptive neural networks improve cross-species prediction of transcription factor binding	13
Evolution of transcription factor binding through sequence variations and turnover of binding sites	13
A framework to score the effects of structural variants in health and disease	13
Effects of transcriptional noise on estimates of gene and transcript expression in RNA sequencing experiments	13
The multicomparative 2-n-way genome suite	13
Active enhancers strengthen insulation by RNA-mediated CTCF binding at chromatin domain boundaries	13
Whole-genome analysis of noncoding genetic variations identifies multiscale regulatory element perturbations associated with Hirschsprung disease	13
Dynamics of broad H3K4me3 domains uncover an epigenetic switch between cell identity and cancer-related genes	13
Pooled protein tagging, cellular imaging, and in situ sequencing for monitoring drug action in real time	12
Resetting of the 24-nt siRNA landscape in rice zygotes	12
Predicting unrecognized enhancer-mediated genome topology by an ensemble machine learning model	12
H3K36 dimethylation shapes the epigenetic interaction landscape by directing repressive chromatin modifications in embryonic stem cells	12
Suppressor mutations in Mecp2-null mice implicate the DNA damage response in Rett syndrome pathology	12
Accumulation and ineffective silencing of transposable elements on an avian W Chromosome	12
Modeling molecular development of breast cancer in canine mammary tumors	12
Identification and characterization of centromeric sequences in Xenopus laevis	12
Short arms of human acrocentric chromosomes and the completion of the human genome sequence	12
Linear-time cluster ensembles of large-scale single-cell RNA-seq and multimodal data	12
Background-suppressed live visualization of genomic loci with an improved CRISPR system based on a split fluorophore	12
Tissue-specific patterns of regulatory changes underlying gene expression differences among Ficedula flycatchers and their naturally occurring F1 hybrids	12
Genomic context sensitivity of insulator function	12