Genome Research

Article	Citations
The role of transposon activity in shapingcis-regulatory element evolution after whole-genome duplication	188
Dynamic dysregulation of retrotransposons in neurodegenerative diseases at the single-cell level	185
De novo individualized disease modules reveal the synthetic penetrance of genes and inform personalized treatment regimens	127
A statistical physics approach for disease module detection	95
Combinatorial microRNA activity is essential for the transition of pluripotent cells from proliferation into dormancy	87
Unraveling the palindromic and nonpalindromic motifs of retroviral integration site sequences by statistical mixture models	86
Comparative genomics ofCryptosporidium parvumreveals the emergence of an outbreak-associated population in Europe and its spread to the United States	82
De novo detection of somatic variants in high-quality long-read single-cell RNA sequencing data	74
Accurate fusion transcript identification from long- and short-read isoform sequencing at bulk or single-cell resolution	72
Measuring X-Chromosome inactivation skew for X-linked diseases with adaptive nanopore sequencing	70
De novo reconstruction of satellite repeat units from sequence data	68
A ChIP-exo screen of 887 Protein Capture Reagents Program transcription factor antibodies in human cells	66
Polishing copy number variant calls on exome sequencing data via deep learning	66
Examining the dynamics of three-dimensional genome organization with multitask matrix factorization	61
Comparing genomic and epigenomic features across species using the WashU Comparative Epigenome Browser	61
Transposable element accumulation drives size differences among polymorphic Y Chromosomes in Drosophila	58
Lake Malawi cichlid pangenome graph reveals extensive structural variation driven by transposable elements	58
An efficient method to identify, date, and describe admixture events using haplotype information	55
A chromosome-scale epigenetic map of theHydragenome reveals conserved regulators of cell state	54
Elasmobranch genome sequencing reveals evolutionary trends of vertebrate karyotype organization	53
Evolutionarily new genes in humans with disease phenotypes reveal functional enrichment patterns shaped by adaptive innovation and sexual selection	51
An optimized toolkit for high-molecular-weight DNA extraction and ultra-long-read nanopore sequencing using glass beads and hexamminecobalt(III) chloride	50
Systematic identification of interchromosomal interaction networks supports the existence of specialized RNA factories	50
Tissular chromatin-state cartography based on double-barcoded DNA arrays that capture unloaded PA-Tn5 transposase	49
Historical RNA expression profiles from the extinct Tasmanian tiger	48

Chromatin interaction maps identify oncogenic targets of enhancer duplications in cancer	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	46
A novel approach for in vivo DNA footprinting using short double-stranded cell-free DNA from plasma	46
Global compositional and functional states of the human gut microbiome in health and disease	45
Rapid SARS-CoV-2 surveillance using clinical, pooled, or wastewater sequence as a sensor for population change	45
Density separation of petrous bone powders for optimized ancient DNA yields	45
Suv39h-catalyzed H3K9me3 is critical for euchromatic genome organization and the maintenance of gene transcription	44
Spatial Cellular Networks from omics data with SpaCeNet	44
Low-frequency somatic copy number alterations in normal human lymphocytes revealed by large-scale single-cell whole-genome profiling	44
Transposable elements drive the evolution of metazoan zinc finger genes	43
Long-read genome assembly of the insect model organismTribolium castaneumreveals spread of satellite DNA in gene-rich regions by recurrent burst events	43
Closing the gaps, and improving somatic structural variant analysis and benchmarking using CHM13-T2T	43
Advancing genomic technologies and clinical awareness accelerates discovery of disease-associated tandem repeat sequences	43
Artificial intelligence and machine learning in cell-free-DNA-based diagnostics	43
Ligand-induced native G-quadruplex stabilization impairs transcription initiation	43
Nanopore strand-specific mismatch enables de novo detection of bacterial DNA modifications	42
Simultaneous profiling of host expression and microbial abundance by spatial metatranscriptome sequencing	41
KRAB zinc-finger proteins regulate endogenous retroviruses to sculpt germline transcriptomes and genome evolution	41
Interactive visualization and interpretation of pangenome graphs by linear reference–based coordinate projection and annotation integration	38
Chromosome-specific telomere lengths and the minimal functional telomere revealed by nanopore sequencing	38
Dynamic regulation of gonadal transposon control across the lifespan of the naturally short-lived African turquoise killifish	37
Pathogenic variants inCRXhave distinctcis-regulatory effects on enhancers and silencers in photoreceptors	37
Genome-wide oscillations in G + C density and sequence conservation	37
Large-scale genomic analysis of the domestic dog informs biological discovery	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	35
Cross-species cell-type assignment from single-cell RNA-seq data by a heterogeneous graph neural network	35
Challenges and considerations for reproducibility of STARR-seq assays	34
Contrasting and combining transcriptome complexity captured by short and long RNA sequencing reads	34
Chromatin structure influences rate and spectrum of spontaneous mutations inNeurospora crassa	34
Long-read RNA sequencing of archival tissues reveals novel genes and transcripts associated with clear cell renal cell carcinoma recurrence and immune evasion	34
Simulation of nanopore sequencing signal data with tunable parameters	32
PWAS Hub for exploring gene-based associations of common complex diseases	32
Batch correction methods used in single-cell RNA sequencing analyses are often poorly calibrated	32
Genome biology of the darkedged splitfin, Girardinichthys multiradiatus, and the evolution of sex chromosomes and placentation	32
Human and rat skeletal muscle single-nuclei multi-omic integrative analyses nominate causal cell types, regulatory elements, and SNPs for complex traits	32
Phased nanopore assembly with Shasta and modular graph phasing with GFAse	32
Three assays for in-solution enrichment of ancient human DNA at more than a million SNPs	32
Corrigendum: A mosquito small RNA genomics resource reveals dynamic evolution and host responses to viruses and transposons	32
Aberrant landscapes of maternal meiotic crossovers contribute to aneuploidies in human embryos	31
Unexpectedly low recombination rates and presence of hotspots in termite genomes	31
KAS-ATAC reveals the genome-wide single-stranded accessible chromatin landscape of the human genome	30
Whole-genome resequencing of temporally stratified samples reveals substantial loss of haplotype diversity in the highly inbred Scandinavian wolf population	30
Cohesin organizes 3D DNA contacts surrounding active enhancers inC. elegans	30
Motif conservation, stability, and host gene expression are the main drivers of snoRNA expression across vertebrates	30
MCHelper automatically curates transposable element libraries across eukaryotic species	29
Mitochondrial DNA variation across 56,434 individuals in gnomAD	29
Relative contributions of sex hormones, sex chromosomes, and gonads to sex differences in tissue gene regulation	28
Distal regulation, silencers, and a shared combinatorial syntax are hallmarks of animal embryogenesis	28
Cell type–specific analysis by single-cell profiling identifies a stable mammalian tRNA–mRNA interface and increased translation efficiency in neurons	27

Transposon accumulation at xenobiotic gene family loci in aphids	27
Marker-free characterization of full-length transcriptomes of single live circulating tumor cells	27
Hydrahas mammal-like mutation rates facilitating fast adaptation despite its nonaging phenotype	26
A temporal in vivo catalog of chromatin accessibility and expression profiles in pineoblastoma reveals a prevalent role for repressor elements	26
Differences in activity and stability drive transposable element variation in tropical and temperate maize	26
Enhancer–silencer transitions in the human genome	26
Benchmarking small-variant genotyping in polyploids	26
Chimeric mitochondrial RNA transcripts predict mitochondrial genome deletion mutations in mitochondrial genetic diseases and aging	25
Full-resolution HLA and KIR gene annotations for human genome assemblies	25
Functional characterization of enhancer activity during a long terminal repeat's evolution	25
Regeneration alters open chromatin andcis-regulatory landscape of erythroid precursors	25
Hierarchical architecture of neo-sex chromosomes and accelerated adaptive evolution in tortricid moths	24
Global identification of mammalian host and nested gene pairs reveal tissue-specific transcriptional interplay	24
Accumulation and ineffective silencing of transposable elements on an avian W Chromosome	24
Accurate estimation of intraspecific microbial gene content variation in metagenomic data with MIDAS v3 and StrainPGC	24
Translation-dependent and -independent mRNA decay occur through mutually exclusive pathways defined by ribosome density during T cell activation	24
Spatial transcriptomics reveals asymmetric cellular responses to injury in the regenerating spiny mouse (Acomys) ear	23
Global mapping of RNA homodimers in living cells	23
Colibactin leads to a bacteria-specific mutation pattern and self-inflicted DNA damage	23
Epigenetic drift score captures directional methylation variability and links aging to transcriptional, metabolic, and genetic alterations	23
QuadST identifies cell-cell interaction-changed genes in spatially resolved transcriptomics data	23
Single-cell discovery of m6A RNA modifications in the hippocampus	23
Large-scale detection and characterization of interchromosomal rearrangements in normozoospermic bulls using massive genotype and phenotype data sets	22
A systematic review on the biochemical threshold of mitochondrial genetic variants	22
Discovery of an unusually high number of de novo mutations in sperm of older men using duplex sequencing	22
A new framework for exploratory network mediator analysis in omics data	22
Genetics-driven risk predictions leveraging the Mendelian randomization framework	22
Implications of the first complete human genome assembly	22
Proteome-wide structural analysis quantifies structural conservation across distant species	22
Dissecting and improving gene regulatory network inference using single-cell transcriptome data	21
Post-transcriptional cross- and auto-regulation buffer expression of the human RNA helicasesDDX3XandDDX3Y	21
Precise genotyping of circular mobile elements from metagenomic data uncovers human-associated plasmids with recent common ancestors	21
Proving sequence aligners can guarantee accuracy in almostO(mlogn) time through an average-case analysis of the seed-chain-extend heuristic	21
Variations in antibody repertoires correlate with vaccine responses	21
Applications of single-cell genomics and computational strategies to study common disease and population-level variation	21
Sequencing of individual barcoded cDNAs using Pacific Biosciences and Oxford Nanopore Technologies reveals platform-specific error patterns	21
Rapid evolution and strain turnover in the infant gut microbiome	21
Profiling the quantitative occupancy of myriad transcription factors across conditions by modeling chromatin accessibility data	20
Optical genome mapping enables accurate testing of large repeat expansions	20
Diffusion-based generation of gene regulatory networks from scRNA-seq data with DigNet	20
MYC overexpression leads to increased chromatin interactions at super-enhancers and MYC binding sites	20
Fast inference of genetic recombination rates in biobank scale data	20
Diversity, duplication, and genomic organization of homeobox genes in Lepidoptera	20
Alu insertion variants alter gene transcript levels	20
Long reads decipher genomes and transcriptomes and offer novel insights into biology and diseases	20
Erratum: A butterfly pan-genome reveals that a large amount of structural variation underlies the evolution of chromatin accessibility	20
Gaps and complex structurally variant loci in phased genome assemblies	20
Long-read sequencing of 111 rice genomes reveals significantly larger pan-genomes	20
Comprehensive identification of genomic and environmental determinants of phenotypic plasticity in maize	19
A butterfly pan-genome reveals that a large amount of structural variation underlies the evolution of chromatin accessibility	19
Protein domain embeddings for fast and accurate similarity search	19
Complete genomes of Asgard archaea reveal diverse integrated and mobile genetic elements	19
Rearrangements of viral and human genomes at human papillomavirus integration events and their allele-specific impacts on cancer genome regulation	19
Learning probabilistic protein–DNA recognition codes from DNA-binding specificities using structural mappings	19
Integrated single-cell multiome analysis reveals muscle fiber-type gene regulatory circuitry modulated by endurance exercise	19
Characterization of human transcription factor function and patterns of gene regulation in HepG2 cells	19
A scalable adaptive quadratic kernel method for interpretable epistasis analysis in complex traits	19
Genomic environments scale the activities of diverse core promoters	19
Streamlined spatial and environmental expression signatures characterize the minimalist duckweedWolffia australiana	19
Corrigendum: An association test of the spatial distribution of rare missense variants within protein structures identifies Alzheimer's disease–related patterns	18
Rtt109 promotes nucleosome replacement ahead of the replication fork	18
Construction and evaluation of a new rat reference genome assembly, GRCr8, from long reads and long-range scaffolding	18
Modeling and predicting cancer clonal evolution with reinforcement learning	18
Inferring genes that escape X-Chromosome inactivation reveals important contribution of variable escape genes to sex-biased diseases	18
Thousands of human mutation clusters are explained by short-range template switching	18
The predicted RNA-binding protein regulome of axonal mRNAs	17
Identifying cell state–associated alternative splicing events and their coregulation	17
Epigenomic translocation of H3K4me3 broad domains over oncogenes following hijacking of super-enhancers	17
De novo transcriptome assembly of mouse male germ cells reveals novel genes, stage-specific bidirectional promoter activity, and noncoding RNA expression	17
Meta-analysis of activated neurons reveals dynamic regulation of diverse classes of alternative splicing	17
Assessing DNA methylation detection for primary human tissue using Nanopore sequencing	17
Diverse tumorigenic consequences of human papillomavirus integration in primary oropharyngeal cancers	17
ZSWIM8 destabilizes many murine microRNAs and is required for proper embryonic growth and development	16
Building better genome annotations across the tree of life	16
Long-read genome sequencing and variant reanalysis increase diagnostic yield in neurodevelopmental disorders	16
Parameter-efficient fine-tuning on large protein language models improves signal peptide prediction	16
A curated collection of Klebsiella metabolic models reveals variable substrate usage and gene essentiality	16
Revisiting chromatin packaging in mouse sperm	16
Plant genome evolution in the genusEucalyptusis driven by structural rearrangements that promote sequence divergence	15
A Bayesian framework for inferring dynamic intercellular interactions from time-series single-cell data	15

Clustered and diverse transcription factor binding underlies cell type specificity of enhancers for housekeeping genes	15
Commoncis-regulatory variation modifies the penetrance of pathogenicSHROOM3variants in craniofacial microsomia	15
Large haplotypes highlight a complex age structure within the maize pan-genome	15
Long-read transcriptome sequencing of CLL and MDS patients uncovers molecular effects ofSF3B1mutations	15
Enhancing nanopore adaptive sampling for PromethION using readfish at scale	15
Accurate genotyping of three major respiratory bacterial pathogens with ONT R10.4.1 long-read sequencing	15
Generation and analysis of a mouse multitissue genome annotation atlas	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
Size-based expectation maximization for characterizing nucleosome positions and subtypes	15
Nucleosome binding by TP53, TP63, and TP73 is determined by the composition, accessibility, and helical orientation of their binding sites	15
Automated annotation of human centromeres with HORmon	15
Revolutionizing genomics and medicine—one long molecule at a time	15
Corrigendum: Cre-dependent Cas9-expressing pigs enable efficient in vivo genome editing	15
Machine learning identifies activation of RUNX/AP-1 as drivers of mesenchymal and fibrotic regulatory programs in gastric cancer	15
Genome skimming with nanopore sequencing precisely determines global and transposon DNA methylation in vertebrates	14
An organism-wide ATAC-seq peak catalog for the bovine and its use to identify regulatory variants	14
Mitotic chromosomes harbor cell type– and species-specific structural features within a universal loop array conformation	14
Corrigendum: Enhancer–silencer transitions in the human genome	14
Navigating the landscape of epitranscriptomics and host immunity	14
RefSeq Functional Elements as experimentally assayed nongenic reference standards and functional interactions in human and mouse	14
Theoretical framework for the difference of two negative binomial distributions and its application in comparative analysis of sequencing data	14
Diverse evolutionary trajectories of mitocoding DNA in mammalian and avian nuclear genomes	14
The genetics and epigenetics of satellite centromeres	14
Corrigendum: Human primitive brain displays negative mitochondrial-nuclear expression correlation of respiratory genes	14
Ultrafast genome-wide inference of pairwise coalescence times	14
Biosurfer for systematic tracking of regulatory mechanisms leading to protein isoform diversity	14
Cytosolic and mitochondrial translation elongation are coordinated through the molecular chaperone TRAP1 for the synthesis and import of mitochondrial proteins	14
Assessing and mitigating privacy risks of sparse, noisy genotypes by local alignment to haplotype databases	14
Transposable elements and their KZFP controllers are drivers of transcriptional innovation in the developing human brain	14
Genomic analysis of Rad26 and Rad1–Rad10 reveals differences in their dependence on Mediator and RNA polymerase II	14
Optimizing nanopore adaptive sampling for pneumococcal serotype surveillance in complex samples using the graph-based GNASTy algorithm	14
Listeria monocytogenes genes supporting growth under standard laboratory cultivation conditions and during macrophage infection	13
Continuous infiltration and evolutionary trajectory of nuclear organelle DNA inOryza	13
Tn5 tagments and transposes oligos to single-stranded DNA for strand-specific RNA sequencing	13
A national long-read sequencing study on chromosomal rearrangements uncovers hidden complexities	13
RNA Pol II–dependent transcription efficiency fine-tunes A-to-I editing levels	13
A novel multislice framework for precision 3D spatial domain reconstruction and disease pathology analysis	13
miRNA-like secondary structures in maize (Zea mays) genes and transposable elements correlate with small RNAs, methylation, and expression	13
Resolving the chromatin impact of mosaic variants with targeted Fiber-seq	13
Genome-wide transcript and protein analysis highlights the role of protein homeostasis in the aging mouse heart	13
Identification of the male-specific region on the guppy Y Chromosome from a haplotype-resolved assembly	12
Copy number variation alters local and global mutational tolerance	12
Whole-genome long-read sequencing downsampling and its effect on variant-calling precision and recall	12
The fine-scale recombination rate variation and associations with genomic features in a butterfly	12
Embryonic LTR retrotransposons supply promoter modules to somatic tissues	12
High temporal resolution RNA-seq time course data reveals widespread synchronous activation between mammalian lncRNAs and neighboring protein-coding genes	12
Multiscale network modeling reveals the gene regulatory landscape driving cancer prognosis in 32 cancer types	12
Interspecies regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes	12
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	12
Matching queried single-cell open-chromatin profiles to large pools of single-cell transcriptomes and epigenomes for reference supported analysis	12
MPRAbase a Massively Parallel Reporter Assay database	12
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
Analytical validation of germline small variant detection using long-read HiFi genome sequencing	12
A statistical learning method for simultaneous copy number estimation and subclone clustering with single-cell sequencing data	12
The rate of de novo structural variation is increased in in vitro–produced offspring and preferentially affects the paternal genome	12
Effective sequence similarity detection with strobemers	12
Variational inference using approximate likelihood under the coalescent with recombination	12
Genetic regulation of nascent RNA maturation revealed by direct RNA nanopore sequencing	12
Systematic identification and characterization of exon–intron circRNAs	12
Highly accurate assembly polishing with DeepPolisher	12
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	12
Vertebrates show coordinated elevated expression of mitochondrial and nuclear genes after birth	12
Individualized VDJ recombination predisposes the available Ig sequence space	11
Single-nucleus CUT&RUN elucidates the function of intrinsic and genomics-driven epigenetic heterogeneity in head and neck cancer progression	11
Deriving confidence intervals for mutation rates across a wide range of evolutionary distances using FracMinHash	11
Characterization of transcript enrichment and detection bias in single-nucleus RNA-seq for mapping of distinct human adipocyte lineages	11
A general framework for identifying oligogenic combinations of rare variants in complex disorders	11
tRNA-derived small RNAs are embedded in the gene regulatory network instructingDrosophilametamorphosis	11
Multisite long-read sequencing reveals the early contributions of somatic structural variations to HBV-related hepatocellular carcinoma tumorigenesis	11
Reference-informed prediction of alternative splicing and splicing-altering mutations from sequences	11
An atlas of fish genome evolution reveals delayed rediploidization following the teleost whole-genome duplication	11
Telomere-to-telomere assembly by preserving contained reads	11
Genome-wide relaxation of selection and the evolution of the island syndrome in Orkney voles	11
Endonucleolytic cleavage is the primary mechanism of decay elicited byC. elegansnonsense-mediated mRNA decay	11
SWATH-MS-based proteogenomic analysis reveals the involvement of alternative splicing in poplar upon lead stress	11
Chromatin interaction–aware gene regulatory modeling with graph attention networks	11
Genetic control of the dynamic transcriptional response to immune stimuli and glucocorticoids at single-cell resolution	11
High-fidelity, large-scale targeted profiling of microsatellites	11
Efficient taxa identification using a pangenome index	11
CGC1, a new reference genome for Caenorhabditis elegans	10
Genetic effects on chromatin accessibility uncover mechanisms of liver gene regulation and quantitative traits	10
Population genomics reveals mechanisms and dynamics of de novo expressed open reading frame emergence inDrosophila melanogaster	10
Long-read genomics reveal extensive nuclear-specific evolution and allele-specific expression in a dikaryotic fungus	10
A sheep pangenome reveals the spectrum of structural variations and their effects on tail phenotypes	10
De novo antibody identification in human blood from full-length single B cell transcriptomics and matching haplotype-resolved germline assemblies	10
Developmental transcriptomics inPristionchusreveals the environmental responsiveness of a plasticity gene-regulatory network	10
The human ribosomal DNA array is composed of highly homogenized tandem clusters	10
Defining the separation landscape of topological domains for decoding consensus domain organization of the 3D genome	10
Atypical epigenetic and small RNA control of degenerated transposons and their fragments in clonally reproducingSpirodela polyrhiza	10
Locus-resolution analysis of L1 regulation and retrotransposition potential in mouse embryonic development	10
Genome-scale targeted mutagenesis inBrassica napususing a pooled CRISPR library	9
Seamless, rapid, and accurate analyses of outbreak genomic data using splitk-mer analysis	9
Long-read Ribo-STAMP simultaneously measures transcription and translation with isoform resolution	9