Genome Research

Article	Citations
APOBEC3A drives deaminase mutagenesis in human gastric epithelium	342
Dynamic dysregulation of retrotransposons in neurodegenerative diseases at the single-cell level	111
Polishing copy number variant calls on exome sequencing data via deep learning	103
Examining the dynamics of three-dimensional genome organization with multitask matrix factorization	88
Unraveling the palindromic and nonpalindromic motifs of retroviral integration site sequences by statistical mixture models	79
Comparing genomic and epigenomic features across species using the WashU Comparative Epigenome Browser	77
A statistical physics approach for disease module detection	69
Combinatorial microRNA activity is essential for the transition of pluripotent cells from proliferation into dormancy	68
Accurate fusion transcript identification from long- and short-read isoform sequencing at bulk or single-cell resolution	67
Evolutionarily new genes in humans with disease phenotypes reveal functional enrichment patterns shaped by adaptive innovation and sexual selection	66
Elasmobranch genome sequencing reveals evolutionary trends of vertebrate karyotype organization	64
Measuring X-Chromosome inactivation skew for X-linked diseases with adaptive nanopore sequencing	63
Dynamic metabolic and molecular changes during seasonal shrinking in Sorex araneus	61
Cell-type- and chromosome-specific chromatin landscapes and DNA replication programs of Drosophila testis tumor stem cell–like cells	60
De novo detection of somatic variants in high-quality long-read single-cell RNA sequencing data	58
Comparative genomics of Cryptosporidium parvum reveals the emergence of an outbreak-associated population in Europe and its spread to the United States	57
De novo reconstruction of satellite repeat units from sequence data	57
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	51
Lake Malawi cichlid pangenome graph reveals extensive structural variation driven by transposable elements	50
The role of transposon activity in shapingcis-regulatory element evolution after whole-genome duplication	50
A chromosome-scale epigenetic map of the Hydra genome reveals conserved regulators of cell state	50
Historical RNA expression profiles from the extinct Tasmanian tiger	49
A novel approach for in vivo DNA footprinting using short double-stranded cell-free DNA from plasma	48
Transposable elements drive the evolution of metazoan zinc finger genes	48

Artificial intelligence and machine learning in cell-free-DNA-based diagnostics	45
An optimized toolkit for high-molecular-weight DNA extraction and ultra-long-read nanopore sequencing using glass beads and hexamminecobalt(III) chloride	44
Tissular chromatin-state cartography based on double-barcoded DNA arrays that capture unloaded PA-Tn5 transposase	44
Chromatin interaction maps identify oncogenic targets of enhancer duplications in cancer	44
Systematic identification of interchromosomal interaction networks supports the existence of specialized RNA factories	43
Density separation of petrous bone powders for optimized ancient DNA yields	42
Corrigendum: A sheep pangenome reveals the spectrum of structural variations and their effects on tail phenotypes	42
Ribosome decision graphs for the representation of eukaryotic RNA translation complexity	41
Long-read genome assembly of the insect model organism Tribolium castaneum reveals spread of satellite DNA in gene-rich regions by recurrent burst events	41
Suv39h-catalyzed H3K9me3 is critical for euchromatic genome organization and the maintenance of gene transcription	40
The superpowers of imprinting control regions	39
Functional assays inDrosophilafacilitate classification of variants of uncertain significance associated with rare diseases	39
Global compositional and functional states of the human gut microbiome in health and disease	38
Spatial Cellular Networks from omics data with SpaCeNet	37
Rapid SARS-CoV-2 surveillance using clinical, pooled, or wastewater sequence as a sensor for population change	37
Nanopore strand-specific mismatch enables de novo detection of bacterial DNA modifications	36
Large-scale genomic analysis of the domestic dog informs biological discovery	36
Genome biology of the darkedged splitfin, Girardinichthys multiradiatus, and the evolution of sex chromosomes and placentation	35
Challenges and considerations for reproducibility of STARR-seq assays	35
Pathogenic variants in CRX have distinct cis -regulatory effects on enhancers and silencers in photorecept	35
Long-read RNA sequencing of archival tissues reveals novel genes and transcripts associated with clear cell renal cell carcinoma recurrence and immune evasion	34
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
Interactive visualization and interpretation of pangenome graphs by linear reference–based coordinate projection and annotation integration	34
Phased nanopore assembly with Shasta and modular graph phasing with GFAse	33
Simultaneous profiling of host expression and microbial abundance by spatial metatranscriptome sequencing	31
Dynamic regulation of gonadal transposon control across the lifespan of the naturally short-lived African turquoise killifish	31
PWAS Hub for exploring gene-based associations of common complex diseases	31
KRAB zinc-finger proteins regulate endogenous retroviruses to sculpt germline transcriptomes and genome evolution	31
Simulation of nanopore sequencing signal data with tunable parameters	31
Batch correction methods used in single-cell RNA sequencing analyses are often poorly calibrated	30
Chromatin structure influences rate and spectrum of spontaneous mutations in Neurospora crassa	30
Three assays for in-solution enrichment of ancient human DNA at more than a million SNPs	29
Closing the gaps, and improving somatic structural variant analysis and benchmarking using CHM13-T2T	29
Corrigendum: A mosquito small RNA genomics resource reveals dynamic evolution and host responses to viruses and transposons	28
Contrasting and combining transcriptome complexity captured by short and long RNA sequencing reads	28
Cross-species cell-type assignment from single-cell RNA-seq data by a heterogeneous graph neural network	28
Unexpectedly low recombination rates and presence of hotspots in termite genomes	27
Motif conservation, stability, and host gene expression are the main drivers of snoRNA expression across vertebrates	27
Aberrant landscapes of maternal meiotic crossovers contribute to aneuploidies in human embryos	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
KAS-ATAC reveals the genome-wide single-stranded accessible chromatin landscape of the human genome	27
Transposon accumulation at xenobiotic gene family loci in aphids	27
Relative contributions of sex hormones, sex chromosomes, and gonads to sex differences in tissue gene regulation	27
MCHelper automatically curates transposable element libraries across eukaryotic species	26
Hydrahas mammal-like mutation rates facilitating fast adaptation despite its nonaging phenotype	26
Mitochondrial DNA variation across 56,434 individuals in gnomAD	26
Automated chromatin profiling with spa-ChIP-seq uncovers the impacts of condition variations	26
Distal regulation, silencers, and a shared combinatorial syntax are hallmarks of animal embryogenesis	26
Whole-genome resequencing of temporally stratified samples reveals substantial loss of haplotype diversity in the highly inbred Scandinavian wolf population	26
Cohesin organizes 3D DNA contacts surrounding active enhancers in C. elegans	26

Marker-free characterization of full-length transcriptomes of single live circulating tumor cells	26
Epigenetic drift score captures directional methylation variability and links aging to transcriptional, metabolic, and genetic alterations	25
A temporal in vivo catalog of chromatin accessibility and expression profiles in pineoblastoma reveals a prevalent role for repressor elements	25
Chimeric mitochondrial RNA transcripts predict mitochondrial genome deletion mutations in mitochondrial genetic diseases and aging	24
QuadST identifies cell–cell interaction–changed genes in spatially resolved transcriptomics data	24
Regeneration alters open chromatin andcis-regulatory landscape of erythroid precursors	24
Full-resolution HLA and KIR gene annotations for human genome assemblies	24
Hierarchical architecture of neo-sex chromosomes and accelerated adaptive evolution in tortricid moths	24
Colibactin leads to a bacteria-specific mutation pattern and self-inflicted DNA damage	24
Large-scale detection and characterization of interchromosomal rearrangements in normozoospermic bulls using massive genotype and phenotype data sets	24
Polycomb misregulation in enterocytes drives tissue decline in the aging Drosophila intestine	23
Enhancer–silencer transitions in the human genome	23
Functional characterization of enhancer activity during a long terminal repeat's evolution	23
Global identification of mammalian host and nested gene pairs reveal tissue-specific transcriptional interplay	23
Single-cell discovery of m 6 A RNA modifications in the hippocampus	22
Accurate estimation of intraspecific microbial gene content variation in metagenomic data with MIDAS v3 and StrainPGC	22
Differences in activity and stability drive transposable element variation in tropical and temperate maize	22
Global mapping of RNA homodimers in living cells	22
Spatial transcriptomics reveals asymmetric cellular responses to injury in the regenerating spiny mouse (Acomys) ear	22
Translation-dependent and -independent mRNA decay occur through mutually exclusive pathways defined by ribosome density during T cell activation	22
A systematic review on the biochemical threshold of mitochondrial genetic variants	21
Efficient integration of spatial omics data for joint domain detection, matching, and alignment with stMSA	21
Proteome-wide structural analysis quantifies structural conservation across distant species	21
Implications of the first complete human genome assembly	21
The SeqSplice multiplexed minigene splicing assay for characterization and quantitation of variant-induced BRCA1 and BRCA2 splice isoforms	21
Molecular and genetic landscapes of retina and brain microglia in neurodegenerative diseases	21
Diffusion-based generation of gene regulatory networks from scRNA-seq data with DigNet	21
Accumulation and ineffective silencing of transposable elements on an avian W Chromosome	21
Genetics-driven risk predictions leveraging the Mendelian randomization framework	21
A new framework for exploratory network mediator analysis in omics data	21
Optical genome mapping enables accurate testing of large repeat expansions	20
Variations in antibody repertoires correlate with vaccine responses	20
Precise genotyping of circular mobile elements from metagenomic data uncovers human-associated plasmids with recent common ancestors	20
Proving sequence aligners can guarantee accuracy in almost O ( m log n	20
Discovery of an unusually high number of de novo mutations in sperm of older men using duplex sequencing	20
Dynamic barriers modulate cohesin positioning and genome folding at fixed occupancy	20
Post-transcriptional cross- and auto-regulation buffer expression of the human RNA helicases DDX3X and DDX3Y	20
MYC overexpression leads to increased chromatin interactions at super-enhancers and MYC binding sites	19
Long-read sequencing of 111 rice genomes reveals significantly larger pan-genomes	19
Rapid evolution and strain turnover in the infant gut microbiome	19
Complete genomes of Asgard archaea reveal diverse integrated and mobile genetic elements	19
The SynMall resource for characterizing the functional impact of synonymous variation	19
Dissecting and improving gene regulatory network inference using single-cell transcriptome data	19
Transcription and potential functions of a novel XIST isoform in male peripheral glia	19
Long reads decipher genomes and transcriptomes and offer novel insights into biology and diseases	19
Sequencing of individual barcoded cDNAs using Pacific Biosciences and Oxford Nanopore Technologies reveals platform-specific error patterns	19
Diversity, duplication, and genomic organization of homeobox genes in Lepidoptera	19
Erratum: A butterfly pan-genome reveals that a large amount of structural variation underlies the evolution of chromatin accessibility	19
Gaps and complex structurally variant loci in phased genome assemblies	19
Pangenome-based genome inference using integer programming	18
Fast inference of genetic recombination rates in biobank scale data	18
Streamlined spatial and environmental expression signatures characterize the minimalist duckweedWolffia australiana	18
Learning probabilistic protein–DNA recognition codes from DNA-binding specificities using structural mappings	18
Profiling the quantitative occupancy of myriad transcription factors across conditions by modeling chromatin accessibility data	18
Integrated single-cell multiome analysis reveals muscle fiber-type gene regulatory circuitry modulated by endurance exercise	18
A scalable adaptive quadratic kernel method for interpretable epistasis analysis in complex traits	18
Statistically rigorous and computationally efficient chromatin stripe detection with Quagga	17
Characterization of human transcription factor function and patterns of gene regulation in HepG2 cells	17
Meta-analysis of activated neurons reveals dynamic regulation of diverse classes of alternative splicing	17
Protein domain embeddings for fast and accurate similarity search	17
A butterfly pan-genome reveals that a large amount of structural variation underlies the evolution of chromatin accessibility	17
Rearrangements of viral and human genomes at human papillomavirus integration events and their allele-specific impacts on cancer genome regulation	17
The predicted RNA-binding protein regulome of axonal mRNAs	17
A gene regulatory element modulates myosin expression and controls cardiomyocyte response to stress	17
Comprehensive identification of genomic and environmental determinants of phenotypic plasticity in maize	17
Corrigendum: An association test of the spatial distribution of rare missense variants within protein structures identifies Alzheimer's disease–related patterns	17
Rtt109 promotes nucleosome replacement ahead of the replication fork	17
Long-read genome sequencing and variant reanalysis increase diagnostic yield in neurodevelopmental disorders	16
De novo transcriptome assembly of mouse male germ cells reveals novel genes, stage-specific bidirectional promoter activity, and noncoding RNA expression	16
Accurate genotyping of three major respiratory bacterial pathogens with ONT R10.4.1 long-read sequencing	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
Thousands of human mutation clusters are explained by short-range template switching	16
Modeling and predicting cancer clonal evolution with reinforcement learning	16
Automated annotation of human centromeres with HORmon	16
ZSWIM8 destabilizes many murine microRNAs and is required for proper embryonic growth and development	16
Assessing DNA methylation detection for primary human tissue using Nanopore sequencing	16
Building better genome annotations across the tree of life	16
Construction and evaluation of a new rat reference genome assembly, GRCr8, from long reads and long-range scaffolding	16
Integrative chromatin state annotation of 234 human ENCODE4 cell types using Segway	16

Revisiting chromatin packaging in mouse sperm	16
Parameter-efficient fine-tuning on large protein language models improves signal peptide prediction	16
Revolutionizing genomics and medicine—one long molecule at a time	15
Clustered and diverse transcription factor binding underlies cell type specificity of enhancers for housekeeping genes	15
Size-based expectation maximization for characterizing nucleosome positions and subtypes	15
Commoncis-regulatory variation modifies the penetrance of pathogenicSHROOM3variants in craniofacial microsomia	15
Nucleosome binding by TP53, TP63, and TP73 is determined by the composition, accessibility, and helical orientation of their binding sites	15
Generation and analysis of a mouse multitissue genome annotation atlas	15
A Bayesian framework for inferring dynamic intercellular interactions from time-series single-cell data	15
Accurate integration of multiple heterogeneous single-cell RNA-seq data sets by learning contrastive biological variation	15
Corrigendum: Cre-dependent Cas9-expressing pigs enable efficient in vivo genome editing	15
Long-read transcriptome sequencing of CLL and MDS patients uncovers molecular effects of SF3B1 mutations	15
Large haplotypes highlight a complex age structure within the maize pan-genome	15
Plant genome evolution in the genus Eucalyptus is driven by structural rearrangements that promote sequence divergence	15
Mitotic chromosomes harbor cell type– and species-specific structural features within a universal loop array conformation	14
Ultrafast genome-wide inference of pairwise coalescence times	14
Corrigendum: Enhancer–silencer transitions in the human genome	14
Theoretical framework for the difference of two negative binomial distributions and its application in comparative analysis of sequencing data	14
Corrigendum: Human primitive brain displays negative mitochondrial-nuclear expression correlation of respiratory genes	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
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
Navigating the landscape of epitranscriptomics and host immunity	14
Synergistic regulation by H3K36 and H3K27 methylation defines the chromatin landscape to control virulence and secondary metabolism in a fungal pathogen	14
Diverse evolutionary trajectories of mitocoding DNA in mammalian and avian nuclear genomes	14
CoRAL accurately resolves extrachromosomal DNA genome structures with long-read sequencing	14
The genetics and epigenetics of satellite centromeres	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
Continuous infiltration and evolutionary trajectory of nuclear organelle DNA inOryza	14
Enhancing nanopore adaptive sampling for PromethION using readfish at scale	14