Genome Research

Article	Citations
Dynamic dysregulation of retrotransposons in neurodegenerative diseases at the single-cell level	278
Polishing copy number variant calls on exome sequencing data via deep learning	107
Unraveling the palindromic and nonpalindromic motifs of retroviral integration site sequences by statistical mixture models	92
APOBEC3A drives deaminase mutagenesis in human gastric epithelium	74
Evolutionarily new genes in humans with disease phenotypes reveal functional enrichment patterns shaped by adaptive innovation and sexual selection	74
Accurate fusion transcript identification from long- and short-read isoform sequencing at bulk or single-cell resolution	71
The role of transposon activity in shapingcis-regulatory element evolution after whole-genome duplication	71
A chromosome-scale epigenetic map of theHydragenome reveals conserved regulators of cell state	69
Lake Malawi cichlid pangenome graph reveals extensive structural variation driven by transposable elements	65
De novo reconstruction of satellite repeat units from sequence data	64
A statistical physics approach for disease module detection	64
Combinatorial microRNA activity is essential for the transition of pluripotent cells from proliferation into dormancy	61
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 detection of somatic variants in high-quality long-read single-cell RNA sequencing data	59
Elasmobranch genome sequencing reveals evolutionary trends of vertebrate karyotype organization	55
An efficient method to identify, date, and describe admixture events using haplotype information	55
Transposable element accumulation drives size differences among polymorphic Y Chromosomes in Drosophila	55
De novo individualized disease modules reveal the synthetic penetrance of genes and inform personalized treatment regimens	54
Measuring X-Chromosome inactivation skew for X-linked diseases with adaptive nanopore sequencing	52
Comparative genomics ofCryptosporidium parvumreveals the emergence of an outbreak-associated population in Europe and its spread to the United States	50
Rapid SARS-CoV-2 surveillance using clinical, pooled, or wastewater sequence as a sensor for population change	49
Suv39h-catalyzed H3K9me3 is critical for euchromatic genome organization and the maintenance of gene transcription	48
Spatial Cellular Networks from omics data with SpaCeNet	48
Tissular chromatin-state cartography based on double-barcoded DNA arrays that capture unloaded PA-Tn5 transposase	48

Ribosome decision graphs for the representation of eukaryotic RNA translation complexity	48
Functional assays inDrosophilafacilitate classification of variants of uncertain significance associated with rare diseases	47
Chromatin interaction maps identify oncogenic targets of enhancer duplications in cancer	47
An optimized toolkit for high-molecular-weight DNA extraction and ultra-long-read nanopore sequencing using glass beads and hexamminecobalt(III) chloride	47
Systematic identification of interchromosomal interaction networks supports the existence of specialized RNA factories	46
Density separation of petrous bone powders for optimized ancient DNA yields	45
Corrigendum: A sheep pangenome reveals the spectrum of structural variations and their effects on tail phenotypes	45
Global compositional and functional states of the human gut microbiome in health and disease	44
Historical RNA expression profiles from the extinct Tasmanian tiger	44
Artificial intelligence and machine learning in cell-free-DNA-based diagnostics	42
A novel approach for in vivo DNA footprinting using short double-stranded cell-free DNA from plasma	42
Long-read genome assembly of the insect model organismTribolium castaneumreveals spread of satellite DNA in gene-rich regions by recurrent burst events	42
Advancing genomic technologies and clinical awareness accelerates discovery of disease-associated tandem repeat sequences	40
Batch correction methods used in single-cell RNA sequencing analyses are often poorly calibrated	39
Transposable elements drive the evolution of metazoan zinc finger genes	39
Low-frequency somatic copy number alterations in normal human lymphocytes revealed by large-scale single-cell whole-genome profiling	39
Pathogenic variants inCRXhave distinctcis-regulatory effects on enhancers and silencers in photoreceptors	38
KRAB zinc-finger proteins regulate endogenous retroviruses to sculpt germline transcriptomes and genome evolution	38
Genome biology of the darkedged splitfin, Girardinichthys multiradiatus, and the evolution of sex chromosomes and placentation	36
Large-scale genomic analysis of the domestic dog informs biological discovery	36
Simultaneous profiling of host expression and microbial abundance by spatial metatranscriptome sequencing	36
Nanopore strand-specific mismatch enables de novo detection of bacterial DNA modifications	36
Target-enriched nanopore sequencing and de novo assembly reveals co-occurrences of complex on-target genomic rearrangements induced by CRISPR-Cas9 in human cells	35
PWAS Hub for exploring gene-based associations of common complex diseases	35
Contrasting and combining transcriptome complexity captured by short and long RNA sequencing reads	34
Simulation of nanopore sequencing signal data with tunable parameters	34
Long-read RNA sequencing of archival tissues reveals novel genes and transcripts associated with clear cell renal cell carcinoma recurrence and immune evasion	33
Challenges and considerations for reproducibility of STARR-seq assays	33
Human and rat skeletal muscle single-nuclei multi-omic integrative analyses nominate causal cell types, regulatory elements, and SNPs for complex traits	33
Three assays for in-solution enrichment of ancient human DNA at more than a million SNPs	33
Chromatin structure influences rate and spectrum of spontaneous mutations inNeurospora crassa	32
Dynamic regulation of gonadal transposon control across the lifespan of the naturally short-lived African turquoise killifish	32
Cross-species cell-type assignment from single-cell RNA-seq data by a heterogeneous graph neural network	32
Phased nanopore assembly with Shasta and modular graph phasing with GFAse	31
Closing the gaps, and improving somatic structural variant analysis and benchmarking using CHM13-T2T	30
Interactive visualization and interpretation of pangenome graphs by linear reference–based coordinate projection and annotation integration	30
Corrigendum: A mosquito small RNA genomics resource reveals dynamic evolution and host responses to viruses and transposons	28
Unexpectedly low recombination rates and presence of hotspots in termite genomes	28
Whole-genome resequencing of temporally stratified samples reveals substantial loss of haplotype diversity in the highly inbred Scandinavian wolf population	27
Marker-free characterization of full-length transcriptomes of single live circulating tumor cells	27
Cell type–specific analysis by single-cell profiling identifies a stable mammalian tRNA–mRNA interface and increased translation efficiency in neurons	27
3′-end ligation sequencing is a sensitive method to detect DNA nicks at potential sites of off-target activity induced by prime editors	27
Aberrant landscapes of maternal meiotic crossovers contribute to aneuploidies in human embryos	27
Cohesin organizes 3D DNA contacts surrounding active enhancers inC. elegans	26
Distal regulation, silencers, and a shared combinatorial syntax are hallmarks of animal embryogenesis	26
KAS-ATAC reveals the genome-wide single-stranded accessible chromatin landscape of the human genome	26
Relative contributions of sex hormones, sex chromosomes, and gonads to sex differences in tissue gene regulation	26
Motif conservation, stability, and host gene expression are the main drivers of snoRNA expression across vertebrates	26
Transposon accumulation at xenobiotic gene family loci in aphids	26
Epigenetic drift score captures directional methylation variability and links aging to transcriptional, metabolic, and genetic alterations	25

Mitochondrial DNA variation across 56,434 individuals in gnomAD	25
Spatial transcriptomics reveals asymmetric cellular responses to injury in the regenerating spiny mouse (Acomys) ear	25
A temporal in vivo catalog of chromatin accessibility and expression profiles in pineoblastoma reveals a prevalent role for repressor elements	25
MCHelper automatically curates transposable element libraries across eukaryotic species	25
Translation-dependent and -independent mRNA decay occur through mutually exclusive pathways defined by ribosome density during T cell activation	25
Hydrahas mammal-like mutation rates facilitating fast adaptation despite its nonaging phenotype	25
Global identification of mammalian host and nested gene pairs reveal tissue-specific transcriptional interplay	24
Colibactin leads to a bacteria-specific mutation pattern and self-inflicted DNA damage	24
Differences in activity and stability drive transposable element variation in tropical and temperate maize	24
Accurate estimation of intraspecific microbial gene content variation in metagenomic data with MIDAS v3 and StrainPGC	24
Regeneration alters open chromatin andcis-regulatory landscape of erythroid precursors	24
QuadST identifies cell–cell interaction–changed genes in spatially resolved transcriptomics data	24
Accumulation and ineffective silencing of transposable elements on an avian W Chromosome	24
Functional characterization of enhancer activity during a long terminal repeat's evolution	24
Enhancer–silencer transitions in the human genome	23
Chimeric mitochondrial RNA transcripts predict mitochondrial genome deletion mutations in mitochondrial genetic diseases and aging	23
Single-cell discovery of m6A RNA modifications in the hippocampus	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
Full-resolution HLA and KIR gene annotations for human genome assemblies	22
Dissecting and improving gene regulatory network inference using single-cell transcriptome data	22
Global mapping of RNA homodimers in living cells	22
Benchmarking small-variant genotyping in polyploids	22
A systematic review on the biochemical threshold of mitochondrial genetic variants	22
Large-scale detection and characterization of interchromosomal rearrangements in normozoospermic bulls using massive genotype and phenotype data sets	22
The SeqSplice multiplexed minigene splicing assay for characterization and quantitation of variant-induced BRCA1 and BRCA2 splice isoforms	22
Gaps and complex structurally variant loci in phased genome assemblies	21
Diffusion-based generation of gene regulatory networks from scRNA-seq data with DigNet	21
Precise genotyping of circular mobile elements from metagenomic data uncovers human-associated plasmids with recent common ancestors	21
Long-read sequencing of 111 rice genomes reveals significantly larger pan-genomes	21
Alu insertion variants alter gene transcript levels	21
Genetics-driven risk predictions leveraging the Mendelian randomization framework	21
MYC overexpression leads to increased chromatin interactions at super-enhancers and MYC binding sites	21
Post-transcriptional cross- and auto-regulation buffer expression of the human RNA helicasesDDX3XandDDX3Y	21
Proving sequence aligners can guarantee accuracy in almostO(mlogn) time through an average-case analysis of the seed-chain-extend heuristic	21
Optical genome mapping enables accurate testing of large repeat expansions	20
A new framework for exploratory network mediator analysis in omics data	20
Variations in antibody repertoires correlate with vaccine responses	20
Discovery of an unusually high number of de novo mutations in sperm of older men using duplex sequencing	20
Proteome-wide structural analysis quantifies structural conservation across distant species	20
Diversity, duplication, and genomic organization of homeobox genes in Lepidoptera	20
Molecular and genetic landscapes of retina and brain microglia in neurodegenerative diseases	20
Sequencing of individual barcoded cDNAs using Pacific Biosciences and Oxford Nanopore Technologies reveals platform-specific error patterns	20
Rapid evolution and strain turnover in the infant gut microbiome	19
Pangenome-based genome inference using integer programming	19
Long reads decipher genomes and transcriptomes and offer novel insights into biology and diseases	19
Complete genomes of Asgard archaea reveal diverse integrated and mobile genetic elements	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
Implications of the first complete human genome assembly	19
Learning probabilistic protein–DNA recognition codes from DNA-binding specificities using structural mappings	19
Dynamic barriers modulate cohesin positioning and genome folding at fixed occupancy	19
Profiling the quantitative occupancy of myriad transcription factors across conditions by modeling chromatin accessibility data	19
Protein domain embeddings for fast and accurate similarity search	19
A scalable adaptive quadratic kernel method for interpretable epistasis analysis in complex traits	19
Streamlined spatial and environmental expression signatures characterize the minimalist duckweedWolffia australiana	18
Genomic environments scale the activities of diverse core promoters	18
A gene regulatory element modulates myosin expression and controls cardiomyocyte response to stress	18
Integrated single-cell multiome analysis reveals muscle fiber-type gene regulatory circuitry modulated by endurance exercise	18
Rearrangements of viral and human genomes at human papillomavirus integration events and their allele-specific impacts on cancer genome regulation	18
Comprehensive identification of genomic and environmental determinants of phenotypic plasticity in maize	18
A butterfly pan-genome reveals that a large amount of structural variation underlies the evolution of chromatin accessibility	18
Characterization of human transcription factor function and patterns of gene regulation in HepG2 cells	18
Corrigendum: An association test of the spatial distribution of rare missense variants within protein structures identifies Alzheimer's disease–related patterns	18
Construction and evaluation of a new rat reference genome assembly, GRCr8, from long reads and long-range scaffolding	17
Modeling and predicting cancer clonal evolution with reinforcement learning	17
Meta-analysis of activated neurons reveals dynamic regulation of diverse classes of alternative splicing	17
Integrative chromatin state annotation of 234 human ENCODE4 cell types using Segway	17
Automated annotation of human centromeres with HORmon	17
Building better genome annotations across the tree of life	17
Thousands of human mutation clusters are explained by short-range template switching	17
De novo transcriptome assembly of mouse male germ cells reveals novel genes, stage-specific bidirectional promoter activity, and noncoding RNA expression	16
Revisiting chromatin packaging in mouse sperm	16
Long-read genome sequencing and variant reanalysis increase diagnostic yield in neurodevelopmental disorders	16
ZSWIM8 destabilizes many murine microRNAs and is required for proper embryonic growth and development	16
Parameter-efficient fine-tuning on large protein language models improves signal peptide prediction	16
The predicted RNA-binding protein regulome of axonal mRNAs	16
Accurate genotyping of three major respiratory bacterial pathogens with ONT R10.4.1 long-read sequencing	16
Epigenomic translocation of H3K4me3 broad domains over oncogenes following hijacking of super-enhancers	16
Diverse tumorigenic consequences of human papillomavirus integration in primary oropharyngeal cancers	16

A Bayesian framework for inferring dynamic intercellular interactions from time-series single-cell data	16
Assessing DNA methylation detection for primary human tissue using Nanopore sequencing	16
Rtt109 promotes nucleosome replacement ahead of the replication fork	16
A curated collection of Klebsiella metabolic models reveals variable substrate usage and gene essentiality	16
Identifying cell state–associated alternative splicing events and their coregulation	16
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
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
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
Commoncis-regulatory variation modifies the penetrance of pathogenicSHROOM3variants in craniofacial microsomia	15
Plant genome evolution in the genusEucalyptusis driven by structural rearrangements that promote sequence divergence	15
Nucleosome binding by TP53, TP63, and TP73 is determined by the composition, accessibility, and helical orientation of their binding sites	15
Size-based expectation maximization for characterizing nucleosome positions and subtypes	15
Machine learning identifies activation of RUNX/AP-1 as drivers of mesenchymal and fibrotic regulatory programs in gastric cancer	15
Mitotic chromosomes harbor cell type– and species-specific structural features within a universal loop array conformation	15
Revolutionizing genomics and medicine—one long molecule at a time	15
Corrigendum: Human primitive brain displays negative mitochondrial-nuclear expression correlation of respiratory genes	14
Corrigendum: Enhancer–silencer transitions in the human genome	14
Enhancing nanopore adaptive sampling for PromethION using readfish at scale	14
Assessing and mitigating privacy risks of sparse, noisy genotypes by local alignment to haplotype databases	14
Biosurfer for systematic tracking of regulatory mechanisms leading to protein isoform diversity	14
Optimizing nanopore adaptive sampling for pneumococcal serotype surveillance in complex samples using the graph-based GNASTy algorithm	14
CoRAL accurately resolves extrachromosomal DNA genome structures with long-read sequencing	14
Navigating the landscape of epitranscriptomics and host immunity	14
The genetics and epigenetics of satellite centromeres	14
Resolving the chromatin impact of mosaic variants with targeted Fiber-seq	13
miRNA-like secondary structures in maize (Zea mays) genes and transposable elements correlate with small RNAs, methylation, and expression	13
An organism-wide ATAC-seq peak catalog for the bovine and its use to identify regulatory variants	13
Theoretical framework for the difference of two negative binomial distributions and its application in comparative analysis of sequencing data	13
Cytosolic and mitochondrial translation elongation are coordinated through the molecular chaperone TRAP1 for the synthesis and import of mitochondrial proteins	13
Ultrafast genome-wide inference of pairwise coalescence times	13
De novo genome assemblies of two cryptodiran turtles with ZZ/ZW and XX/XY sex chromosomes provide insights into patterns of genome reshuffling and uncover novel 3D genome folding in amniotes	13
Listeria monocytogenes genes supporting growth under standard laboratory cultivation conditions and during macrophage infection	13
Genome skimming with nanopore sequencing precisely determines global and transposon DNA methylation in vertebrates	13
Diverse evolutionary trajectories of mitocoding DNA in mammalian and avian nuclear genomes	13
Synergistic regulation by H3K36 and H3K27 methylation defines the chromatin landscape to control virulence and secondary metabolism in a fungal pathogen	13
A national long-read sequencing study on chromosomal rearrangements uncovers hidden complexities	13
A novel multislice framework for precision 3D spatial domain reconstruction and disease pathology analysis	13
The paradox of R-loops: guardians of the genome or drivers of disease?	13
Estimating the size of long tandem repeat expansions from short reads with ScatTR	13
RNA Pol II–dependent transcription efficiency fine-tunes A-to-I editing levels	13
Genomic analysis of Rad26 and Rad1–Rad10 reveals differences in their dependence on Mediator and RNA polymerase II	13
RefSeq Functional Elements as experimentally assayed nongenic reference standards and functional interactions in human and mouse	13
Continuous infiltration and evolutionary trajectory of nuclear organelle DNA inOryza	13
Genome-wide transcript and protein analysis highlights the role of protein homeostasis in the aging mouse heart	13
A deconvolution framework that uses single-cell sequencing plus a small benchmark data set for accurate analysis of cell type ratios in complex tissue samples	13
Wnt signaling activation induces CTCF binding and loop formation at cis-regulatory elements of target genes	12
Haplotype and population structure inference using neural networks in whole-genome sequencing data	12
Endonucleolytic cleavage is the primary mechanism of decay elicited byC. elegansnonsense-mediated mRNA decay	12
A statistical learning method for simultaneous copy number estimation and subclone clustering with single-cell sequencing data	12
Analytical validation of germline small variant detection using long-read HiFi genome sequencing	12
Matching queried single-cell open-chromatin profiles to large pools of single-cell transcriptomes and epigenomes for reference supported analysis	12
Copy number variation alters local and global mutational tolerance	12
Unveiling the functional fate of duplicated genes through expression profiling and structural analysis	12
Deriving confidence intervals for mutation rates across a wide range of evolutionary distances using FracMinHash	12
Highly accurate assembly polishing with DeepPolisher	12
Phylogenetic relatedness rather than aquatic habitat fosters horizontal transfer of transposable elements in animals	12
Tn5 tagments and transposes oligos to single-stranded DNA for strand-specific RNA sequencing	12
Identification of the male-specific region on the guppy Y Chromosome from a haplotype-resolved assembly	12
The rate of de novo structural variation is increased in in vitro–produced offspring and preferentially affects the paternal genome	12
Interspecies regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes	12
Reference-informed prediction of alternative splicing and splicing-altering mutations from sequences	12
Multiscale network modeling reveals the gene regulatory landscape driving cancer prognosis in 32 cancer types	12
High temporal resolution RNA-seq time course data reveals widespread synchronous activation between mammalian lncRNAs and neighboring protein-coding genes	12
Vertebrates show coordinated elevated expression of mitochondrial and nuclear genes after birth	12
Systematic identification and characterization of exon–intron circRNAs	12
Individualized VDJ recombination predisposes the available Ig sequence space	11
An atlas of fish genome evolution reveals delayed rediploidization following the teleost whole-genome duplication	11
FocalSV enables target region–based structural variant assembly and refinement using single-molecule long-read sequencing data	11
Whole-genome long-read sequencing downsampling and its effect on variant-calling precision and recall	11
Genetic regulation of nascent RNA maturation revealed by direct RNA nanopore sequencing	11
Genetic control of the dynamic transcriptional response to immune stimuli and glucocorticoids at single-cell resolution	11
The fine-scale recombination rate variation and associations with genomic features in a butterfly	10
Efficient taxa identification using a pangenome index	10
Genome-wide promoter assembly in E. coli measured at single-base resolution	10
Defining the separation landscape of topological domains for decoding consensus domain organization of the 3D genome	10
Telomere-to-telomere assembly by preserving contained reads	10
Interpretable phenotype decoding from multicondition sequencing data with ALPINE	10
Multisite long-read sequencing reveals the early contributions of somatic structural variations to HBV-related hepatocellular carcinoma tumorigenesis	10
Characterization of transcript enrichment and detection bias in single-nucleus RNA-seq for mapping of distinct human adipocyte lineages	10
tRNA-derived small RNAs are embedded in the gene regulatory network instructingDrosophilametamorphosis	10
Assessing transcriptomic reidentification risks using discriminative sequence models	10
Genetic effects on chromatin accessibility uncover mechanisms of liver gene regulation and quantitative traits	10
Developmental transcriptomics inPristionchusreveals the environmental responsiveness of a plasticity gene-regulatory network	10
Single-nucleus CUT&RUN elucidates the function of intrinsic and genomics-driven epigenetic heterogeneity in head and neck cancer progression	10
MPRAbase a Massively Parallel Reporter Assay database	10
SWATH-MS-based proteogenomic analysis reveals the involvement of alternative splicing in poplar upon lead stress	10
Genome-wide relaxation of selection and the evolution of the island syndrome in Orkney voles	10
Dynamic DNAN6-adenine methylation (6mA) governs the encystment process, showcased in the unicellular eukaryotePseudocohnilembus persalinus	10
Loss of epigenetic suppression of retrotransposons with oncogenic potential in aging mammary luminal epithelial cells	10
High-fidelity, large-scale targeted profiling of microsatellites	10
Chromatin interaction–aware gene regulatory modeling with graph attention networks	10
Transposable element variants and their potential adaptive impact in urban populations of the malaria vector Anopheles coluzzii	9