Genome Research

Article	Citations
The role of transposon activity in shapingcis-regulatory element evolution after whole-genome duplication	249
Dynamic dysregulation of retrotransposons in neurodegenerative diseases at the single-cell level	192
APOBEC3A drives deaminase mutagenesis in human gastric epithelium	101
Lake Malawi cichlid pangenome graph reveals extensive structural variation driven by transposable elements	96
De novo individualized disease modules reveal the synthetic penetrance of genes and inform personalized treatment regimens	90
A statistical physics approach for disease module detection	74
A chromosome-scale epigenetic map of theHydragenome reveals conserved regulators of cell state	72
Polishing copy number variant calls on exome sequencing data via deep learning	70
Unraveling the palindromic and nonpalindromic motifs of retroviral integration site sequences by statistical mixture models	69
Combinatorial microRNA activity is essential for the transition of pluripotent cells from proliferation into dormancy	67
De novo detection of somatic variants in high-quality long-read single-cell RNA sequencing data	64
Accurate fusion transcript identification from long- and short-read isoform sequencing at bulk or single-cell resolution	62
Measuring X-Chromosome inactivation skew for X-linked diseases with adaptive nanopore sequencing	62
Examining the dynamics of three-dimensional genome organization with multitask matrix factorization	59
Comparing genomic and epigenomic features across species using the WashU Comparative Epigenome Browser	59
De novo reconstruction of satellite repeat units from sequence data	58
Evolutionarily new genes in humans with disease phenotypes reveal functional enrichment patterns shaped by adaptive innovation and sexual selection	55
Comparative genomics ofCryptosporidium parvumreveals the emergence of an outbreak-associated population in Europe and its spread to the United States	54
Transposable element accumulation drives size differences among polymorphic Y Chromosomes in Drosophila	53
An efficient method to identify, date, and describe admixture events using haplotype information	52
Elasmobranch genome sequencing reveals evolutionary trends of vertebrate karyotype organization	52
Rapid SARS-CoV-2 surveillance using clinical, pooled, or wastewater sequence as a sensor for population change	50
A novel approach for in vivo DNA footprinting using short double-stranded cell-free DNA from plasma	50
Spatial Cellular Networks from omics data with SpaCeNet	49
Suv39h-catalyzed H3K9me3 is critical for euchromatic genome organization and the maintenance of gene transcription	48

Long-read genome assembly of the insect model organismTribolium castaneumreveals spread of satellite DNA in gene-rich regions by recurrent burst events	47
Ribosome decision graphs for the representation of eukaryotic RNA translation complexity	47
Functional assays inDrosophilafacilitate classification of variants of uncertain significance associated with rare diseases	46
Tissular chromatin-state cartography based on double-barcoded DNA arrays that capture unloaded PA-Tn5 transposase	46
An optimized toolkit for high-molecular-weight DNA extraction and ultra-long-read nanopore sequencing using glass beads and hexamminecobalt(III) chloride	46
Artificial intelligence and machine learning in cell-free-DNA-based diagnostics	46
Chromatin interaction maps identify oncogenic targets of enhancer duplications in cancer	45
Systematic identification of interchromosomal interaction networks supports the existence of specialized RNA factories	45
Advancing genomic technologies and clinical awareness accelerates discovery of disease-associated tandem repeat sequences	44
Density separation of petrous bone powders for optimized ancient DNA yields	44
Low-frequency somatic copy number alterations in normal human lymphocytes revealed by large-scale single-cell whole-genome profiling	44
Global compositional and functional states of the human gut microbiome in health and disease	42
Corrigendum: A sheep pangenome reveals the spectrum of structural variations and their effects on tail phenotypes	41
Transposable elements drive the evolution of metazoan zinc finger genes	41
Historical RNA expression profiles from the extinct Tasmanian tiger	40
Closing the gaps, and improving somatic structural variant analysis and benchmarking using CHM13-T2T	39
Batch correction methods used in single-cell RNA sequencing analyses are often poorly calibrated	37
Simulation of nanopore sequencing signal data with tunable parameters	37
KRAB zinc-finger proteins regulate endogenous retroviruses to sculpt germline transcriptomes and genome evolution	37
Chromatin structure influences rate and spectrum of spontaneous mutations inNeurospora crassa	37
Contrasting and combining transcriptome complexity captured by short and long RNA sequencing reads	36
Genome-wide oscillations in G + C density and sequence conservation	35
Long-read RNA sequencing of archival tissues reveals novel genes and transcripts associated with clear cell renal cell carcinoma recurrence and immune evasion	35
Genome biology of the darkedged splitfin, Girardinichthys multiradiatus, and the evolution of sex chromosomes and placentation	35
Target-enriched nanopore sequencing and de novo assembly reveals co-occurrences of complex on-target genomic rearrangements induced by CRISPR-Cas9 in human cells	34
Cross-species cell-type assignment from single-cell RNA-seq data by a heterogeneous graph neural network	34
Interactive visualization and interpretation of pangenome graphs by linear reference–based coordinate projection and annotation integration	34
Pathogenic variants inCRXhave distinctcis-regulatory effects on enhancers and silencers in photoreceptors	34
Phased nanopore assembly with Shasta and modular graph phasing with GFAse	33
PWAS Hub for exploring gene-based associations of common complex diseases	33
Large-scale genomic analysis of the domestic dog informs biological discovery	32
Challenges and considerations for reproducibility of STARR-seq assays	32
Nanopore strand-specific mismatch enables de novo detection of bacterial DNA modifications	31
Chromosome-specific telomere lengths and the minimal functional telomere revealed by nanopore sequencing	31
Human and rat skeletal muscle single-nuclei multi-omic integrative analyses nominate causal cell types, regulatory elements, and SNPs for complex traits	31
Three assays for in-solution enrichment of ancient human DNA at more than a million SNPs	30
Marker-free characterization of full-length transcriptomes of single live circulating tumor cells	30
Simultaneous profiling of host expression and microbial abundance by spatial metatranscriptome sequencing	30
Corrigendum: A mosquito small RNA genomics resource reveals dynamic evolution and host responses to viruses and transposons	30
Dynamic regulation of gonadal transposon control across the lifespan of the naturally short-lived African turquoise killifish	30
Aberrant landscapes of maternal meiotic crossovers contribute to aneuploidies in human embryos	29
KAS-ATAC reveals the genome-wide single-stranded accessible chromatin landscape of the human genome	28
Unexpectedly low recombination rates and presence of hotspots in termite genomes	28
Distal regulation, silencers, and a shared combinatorial syntax are hallmarks of animal embryogenesis	27
Cohesin organizes 3D DNA contacts surrounding active enhancers inC. elegans	27
MCHelper automatically curates transposable element libraries across eukaryotic species	26
3′-end ligation sequencing is a sensitive method to detect DNA nicks at potential sites of off-target activity induced by prime editors	26
Cell type–specific analysis by single-cell profiling identifies a stable mammalian tRNA–mRNA interface and increased translation efficiency in neurons	26
Mitochondrial DNA variation across 56,434 individuals in gnomAD	26
Whole-genome resequencing of temporally stratified samples reveals substantial loss of haplotype diversity in the highly inbred Scandinavian wolf population	26

Translation-dependent and -independent mRNA decay occur through mutually exclusive pathways defined by ribosome density during T cell activation	25
A temporal in vivo catalog of chromatin accessibility and expression profiles in pineoblastoma reveals a prevalent role for repressor elements	25
Motif conservation, stability, and host gene expression are the main drivers of snoRNA expression across vertebrates	25
Full-resolution HLA and KIR gene annotations for human genome assemblies	25
Hydrahas mammal-like mutation rates facilitating fast adaptation despite its nonaging phenotype	25
Transposon accumulation at xenobiotic gene family loci in aphids	25
Benchmarking small-variant genotyping in polyploids	25
Relative contributions of sex hormones, sex chromosomes, and gonads to sex differences in tissue gene regulation	25
Enhancer–silencer transitions in the human genome	24
Large-scale detection and characterization of interchromosomal rearrangements in normozoospermic bulls using massive genotype and phenotype data sets	24
Global identification of mammalian host and nested gene pairs reveal tissue-specific transcriptional interplay	24
QuadST identifies cell–cell interaction–changed genes in spatially resolved transcriptomics data	24
Colibactin leads to a bacteria-specific mutation pattern and self-inflicted DNA damage	24
Spatial transcriptomics reveals asymmetric cellular responses to injury in the regenerating spiny mouse (Acomys) ear	24
Accurate estimation of intraspecific microbial gene content variation in metagenomic data with MIDAS v3 and StrainPGC	24
Functional characterization of enhancer activity during a long terminal repeat's evolution	23
Differences in activity and stability drive transposable element variation in tropical and temperate maize	23
Efficient integration of spatial omics data for joint domain detection, matching, and alignment with stMSA	23
Hierarchical architecture of neo-sex chromosomes and accelerated adaptive evolution in tortricid moths	23
Chimeric mitochondrial RNA transcripts predict mitochondrial genome deletion mutations in mitochondrial genetic diseases and aging	23
Global mapping of RNA homodimers in living cells	23
Regeneration alters open chromatin andcis-regulatory landscape of erythroid precursors	23
Single-cell discovery of m6A RNA modifications in the hippocampus	23
Epigenetic drift score captures directional methylation variability and links aging to transcriptional, metabolic, and genetic alterations	23
Diversity, duplication, and genomic organization of homeobox genes in Lepidoptera	22
Accumulation and ineffective silencing of transposable elements on an avian W Chromosome	22
The SeqSplice multiplexed minigene splicing assay for characterization and quantitation of variant-induced BRCA1 and BRCA2 splice isoforms	22
Dynamic barriers modulate cohesin positioning and genome folding at fixed occupancy	22
A systematic review on the biochemical threshold of mitochondrial genetic variants	22
Rapid evolution and strain turnover in the infant gut microbiome	21
Genetics-driven risk predictions leveraging the Mendelian randomization framework	21
Dissecting and improving gene regulatory network inference using single-cell transcriptome data	21
Precise genotyping of circular mobile elements from metagenomic data uncovers human-associated plasmids with recent common ancestors	21
Diffusion-based generation of gene regulatory networks from scRNA-seq data with DigNet	21
Alu insertion variants alter gene transcript levels	21
Proving sequence aligners can guarantee accuracy in almostO(mlogn) time through an average-case analysis of the seed-chain-extend heuristic	21
Applications of single-cell genomics and computational strategies to study common disease and population-level variation	20
Molecular and genetic landscapes of retina and brain microglia in neurodegenerative diseases	20
Post-transcriptional cross- and auto-regulation buffer expression of the human RNA helicasesDDX3XandDDX3Y	20
Long-read sequencing of 111 rice genomes reveals significantly larger pan-genomes	20
Discovery of an unusually high number of de novo mutations in sperm of older men using duplex sequencing	20
Implications of the first complete human genome assembly	20
Variations in antibody repertoires correlate with vaccine responses	20
Gaps and complex structurally variant loci in phased genome assemblies	19
Optical genome mapping enables accurate testing of large repeat expansions	19
Integrated single-cell multiome analysis reveals muscle fiber-type gene regulatory circuitry modulated by endurance exercise	19
Proteome-wide structural analysis quantifies structural conservation across distant species	19
Sequencing of individual barcoded cDNAs using Pacific Biosciences and Oxford Nanopore Technologies reveals platform-specific error patterns	19
Profiling the quantitative occupancy of myriad transcription factors across conditions by modeling chromatin accessibility data	19
Pangenome-based genome inference using integer programming	19
MYC overexpression leads to increased chromatin interactions at super-enhancers and MYC binding sites	19
A new framework for exploratory network mediator analysis in omics data	19
Fast inference of genetic recombination rates in biobank scale data	19
Erratum: A butterfly pan-genome reveals that a large amount of structural variation underlies the evolution of chromatin accessibility	19
Long reads decipher genomes and transcriptomes and offer novel insights into biology and diseases	18
Protein domain embeddings for fast and accurate similarity search	18
A scalable adaptive quadratic kernel method for interpretable epistasis analysis in complex traits	18
Complete genomes of Asgard archaea reveal diverse integrated and mobile genetic elements	18
Genomic environments scale the activities of diverse core promoters	18
Streamlined spatial and environmental expression signatures characterize the minimalist duckweedWolffia australiana	17
Rearrangements of viral and human genomes at human papillomavirus integration events and their allele-specific impacts on cancer genome regulation	17
A curated collection of Klebsiella metabolic models reveals variable substrate usage and gene essentiality	17
Corrigendum: An association test of the spatial distribution of rare missense variants within protein structures identifies Alzheimer's disease–related patterns	17
Learning probabilistic protein–DNA recognition codes from DNA-binding specificities using structural mappings	17
A butterfly pan-genome reveals that a large amount of structural variation underlies the evolution of chromatin accessibility	17
Thousands of human mutation clusters are explained by short-range template switching	17
Assessing DNA methylation detection for primary human tissue using Nanopore sequencing	17
Characterization of human transcription factor function and patterns of gene regulation in HepG2 cells	17
Comprehensive identification of genomic and environmental determinants of phenotypic plasticity in maize	17
Revisiting chromatin packaging in mouse sperm	17
Accurate genotyping of three major respiratory bacterial pathogens with ONT R10.4.1 long-read sequencing	17
Meta-analysis of activated neurons reveals dynamic regulation of diverse classes of alternative splicing	16
Automated annotation of human centromeres with HORmon	16
De novo transcriptome assembly of mouse male germ cells reveals novel genes, stage-specific bidirectional promoter activity, and noncoding RNA expression	16
Building better genome annotations across the tree of life	16
Epigenomic translocation of H3K4me3 broad domains over oncogenes following hijacking of super-enhancers	16
Identifying cell state–associated alternative splicing events and their coregulation	16
Construction and evaluation of a new rat reference genome assembly, GRCr8, from long reads and long-range scaffolding	16
The predicted RNA-binding protein regulome of axonal mRNAs	16
ZSWIM8 destabilizes many murine microRNAs and is required for proper embryonic growth and development	16

Rtt109 promotes nucleosome replacement ahead of the replication fork	16
Modeling and predicting cancer clonal evolution with reinforcement learning	16
Parameter-efficient fine-tuning on large protein language models improves signal peptide prediction	16
Diverse tumorigenic consequences of human papillomavirus integration in primary oropharyngeal cancers	16
Long-read genome sequencing and variant reanalysis increase diagnostic yield in neurodevelopmental disorders	15
Generation and analysis of a mouse multitissue genome annotation atlas	15
Long-read transcriptome sequencing of CLL and MDS patients uncovers molecular effects ofSF3B1mutations	15
Nucleosome binding by TP53, TP63, and TP73 is determined by the composition, accessibility, and helical orientation of their binding sites	15
Mitotic chromosomes harbor cell type– and species-specific structural features within a universal loop array conformation	15
A Bayesian framework for inferring dynamic intercellular interactions from time-series single-cell data	15
Revolutionizing genomics and medicine—one long molecule at a time	15
Size-based expectation maximization for characterizing nucleosome positions and subtypes	15
Large haplotypes highlight a complex age structure within the maize pan-genome	15
Corrigendum: Cre-dependent Cas9-expressing pigs enable efficient in vivo genome editing	15
Clustered and diverse transcription factor binding underlies cell type specificity of enhancers for housekeeping genes	15
Accurate integration of multiple heterogeneous single-cell RNA-seq data sets by learning contrastive biological variation	15
CoRAL accurately resolves extrachromosomal DNA genome structures with long-read sequencing	15
Commoncis-regulatory variation modifies the penetrance of pathogenicSHROOM3variants in craniofacial microsomia	15
The genetics and epigenetics of satellite centromeres	14
miRNA-like secondary structures in maize (Zea mays) genes and transposable elements correlate with small RNAs, methylation, and expression	14
Machine learning identifies activation of RUNX/AP-1 as drivers of mesenchymal and fibrotic regulatory programs in gastric cancer	14
Assessing and mitigating privacy risks of sparse, noisy genotypes by local alignment to haplotype databases	14
Corrigendum: Human primitive brain displays negative mitochondrial-nuclear expression correlation of respiratory genes	14
Enhancing nanopore adaptive sampling for PromethION using readfish at scale	14
Cytosolic and mitochondrial translation elongation are coordinated through the molecular chaperone TRAP1 for the synthesis and import of mitochondrial proteins	14
Corrigendum: Enhancer–silencer transitions in the human genome	14
The paradox of R-loops: guardians of the genome or drivers of disease?	14
Listeria monocytogenes genes supporting growth under standard laboratory cultivation conditions and during macrophage infection	14
Biosurfer for systematic tracking of regulatory mechanisms leading to protein isoform diversity	14
Plant genome evolution in the genusEucalyptusis driven by structural rearrangements that promote sequence divergence	14
Theoretical framework for the difference of two negative binomial distributions and its application in comparative analysis of sequencing data	14
Navigating the landscape of epitranscriptomics and host immunity	14
Optimizing nanopore adaptive sampling for pneumococcal serotype surveillance in complex samples using the graph-based GNASTy algorithm	14