Genome Research

Article	Citations
Cell-type- and chromosome-specific chromatin landscapes and DNA replication programs of Drosophila testis tumor stem cell–like cells	607
Examining the dynamics of three-dimensional genome organization with multitask matrix factorization	161
Dynamic dysregulation of retrotransposons in neurodegenerative diseases at the single-cell level	145
Elasmobranch genome sequencing reveals evolutionary trends of vertebrate karyotype organization	121
A statistical physics approach for disease module detection	91
The role of transposon activity in shapingcis-regulatory element evolution after whole-genome duplication	86
Unraveling the palindromic and nonpalindromic motifs of retroviral integration site sequences by statistical mixture models	85
APOBEC3A drives deaminase mutagenesis in human gastric epithelium	80
Combinatorial microRNA activity is essential for the transition of pluripotent cells from proliferation into dormancy	78
Simultaneous modeling of chromatin conformation changes from multiple single-cell interaction maps with ChromMovie	73
Lignature provides a curated resource of ligand-induced transcriptomic signatures for signaling inference	72
Evolutionarily new genes in humans with disease phenotypes reveal functional enrichment patterns shaped by adaptive innovation and sexual selection	71
Influence of cis -regulatory elements on expression divergence in human segmental duplications	67
The Topological Regulatory Logic of noncoding RNA–mediated gene expression	64
Measuring X-Chromosome inactivation skew for X-linked diseases with adaptive nanopore sequencing	60
Dynamic metabolic and molecular changes during seasonal shrinking in Sorex araneus	58
Lake Malawi cichlid pangenome graph reveals extensive structural variation driven by transposable elements	58
Comparing genomic and epigenomic features across species using the WashU Comparative Epigenome Browser	58
Transposable element small RNAs and large RNAs in aging brains and implications in Huntington's and Parkinson's disease	58
De novo reconstruction of satellite repeat units from sequence data	57
Accurate fusion transcript identification from long- and short-read isoform sequencing at bulk or single-cell resolution	56
Biobank-scale genotype similarity search and dynamic patient-matched cohort creation with GenoSiS	55
Comparative genomics of Cryptosporidium parvum reveals the emergence of an outbreak-associated population in Europe and its spread to the United States	55
A chromosome-scale epigenetic map of the Hydra genome reveals conserved regulators of cell state	49
Ribosome decision graphs for the representation of eukaryotic RNA translation complexity	48

De novo detection of somatic variants in high-quality long-read single-cell RNA sequencing data	48
Spatial Cellular Networks from omics data with SpaCeNet	46
The superpowers of imprinting control regions	45
Corrigendum: A sheep pangenome reveals the spectrum of structural variations and their effects on tail phenotypes	45
Chromatin interaction maps identify oncogenic targets of enhancer duplications in cancer	44
Density separation of petrous bone powders for optimized ancient DNA yields	44
Systematic identification of interchromosomal interaction networks supports the existence of specialized RNA factories	42
A novel approach for in vivo DNA footprinting using short double-stranded cell-free DNA from plasma	42
Tissular chromatin-state cartography based on double-barcoded DNA arrays that capture unloaded PA-Tn5 transposase	42
An optimized toolkit for high-molecular-weight DNA extraction and ultra-long-read nanopore sequencing using glass beads and hexamminecobalt(III) chloride	40
Herbaria provide a valuable resource for obtaining informative mRNA	39
Global compositional and functional states of the human gut microbiome in health and disease	37
Cultivation-independent high-quality microbial genome reconstruction from environmental samples with midi-metagenomics	36
Isoform- and pathway-specific regulation of post-transcriptional RNA processing in human cells	36
Artificial intelligence and machine learning in cell-free-DNA-based diagnostics	36
Historical RNA expression profiles from the extinct Tasmanian tiger	35
Functional assays inDrosophilafacilitate classification of variants of uncertain significance associated with rare diseases	35
Rapid SARS-CoV-2 surveillance using clinical, pooled, or wastewater sequence as a sensor for population change	34
Transposable elements drive the evolution of metazoan zinc finger genes	34
Suv39h-catalyzed H3K9me3 is critical for euchromatic genome organization and the maintenance of gene transcription	34
Long-read genome assembly of the insect model organism Tribolium castaneum reveals spread of satellite DNA in gene-rich regions by recurrent burst events	33
KRAB zinc-finger proteins regulate endogenous retroviruses to sculpt germline transcriptomes and genome evolution	33
Chromatin structure influences rate and spectrum of spontaneous mutations in Neurospora crassa	33
Nanopore strand-specific mismatch enables de novo detection of bacterial DNA modifications	32
Simulation of nanopore sequencing signal data with tunable parameters	32
Batch correction methods used in single-cell RNA sequencing analyses are often poorly calibrated	32
Simultaneous profiling of host expression and microbial abundance by spatial metatranscriptome sequencing	32
Cross-species cell-type assignment from single-cell RNA-seq data by a heterogeneous graph neural network	32
Pathogenic variants in CRX have distinct cis -regulatory effects on enhancers and silencers in photorecept	31
Target-enriched nanopore sequencing and de novo assembly reveals co-occurrences of complex on-target genomic rearrangements induced by CRISPR-Cas9 in human cells	31
A genome-wide survey reveals that a diverse array of enhancers coordinates the Drosophila innate immune response	31
Functional genomics analysis of developing zebrafish and human endoderm reveals highly conserved cis -regulatory modules acting during vertebrate organog	31
Dynamic regulation of gonadal transposon control across the lifespan of the naturally short-lived African turquoise killifish	30
Whole-genome variant detection in long-read sequencing data from ultralow input patient samples	30
Long-read RNA sequencing of archival tissues reveals novel genes and transcripts associated with clear cell renal cell carcinoma recurrence and immune evasion	30
PWAS Hub for exploring gene-based associations of common complex diseases	30
Interactive visualization and interpretation of pangenome graphs by linear reference–based coordinate projection and annotation integration	30
Challenges and considerations for reproducibility of STARR-seq assays	29
Contrasting and combining transcriptome complexity captured by short and long RNA sequencing reads	29
Large-scale genomic analysis of the domestic dog informs biological discovery	29
Phased nanopore assembly with Shasta and modular graph phasing with GFAse	29
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
A systems view on DNA damage response kinetics in Tetrahymena	28
Tracing genome size dynamics in sharks and rays with inclusive sequence analysis by the Squalomix Consortium	28
3′-end ligation sequencing is a sensitive method to detect DNA nicks at potential sites of off-target activity induced by prime editors	28
Marker-free characterization of full-length transcriptomes of single live circulating tumor cells	27
KAS-ATAC reveals the genome-wide single-stranded accessible chromatin landscape of the human genome	27
Evidence for negative selection against somatic mutations induced in normal fibroblasts by N -ethyl- N -ni	26

Motif conservation, stability, and host gene expression are the main drivers of snoRNA expression across vertebrates	26
Early feature extraction drives model performance in high-resolution chromatin accessibility prediction	26
Automated chromatin profiling with spa-ChIP-seq uncovers the impacts of condition variations	26
Aberrant landscapes of maternal meiotic crossovers contribute to aneuploidies in human embryos	26
Transposon accumulation at xenobiotic gene family loci in aphids	26
Allele-specific splicing modulates protein isoforms and Alzheimer's disease risk	25
MCHelper automatically curates transposable element libraries across eukaryotic species	25
ComicGTN infers disease-associated rare cell states from single-cell multiomic data using DNA sequence–augmented graph transformer networks	25
Moderated designs can balance between batch-effect mitigation and cell loss due to hashtag-assisted pooling in single-cell experiments	25
Unexpectedly low recombination rates and presence of hotspots in termite genomes	25
Dietary effects on cytosolic and mitochondrial tRNA abundance and modification patterns across mouse tissues	25
Hydrahas mammal-like mutation rates facilitating fast adaptation despite its nonaging phenotype	25
Cohesin organizes 3D DNA contacts surrounding active enhancers in C. elegans	25
A temporal in vivo catalog of chromatin accessibility and expression profiles in pineoblastoma reveals a prevalent role for repressor elements	25
Dynamic A-to-I RNA editing in response to gut microbiome in honeybees	24
QuadST identifies cell–cell interaction–changed genes in spatially resolved transcriptomics data	24
Tissue-specific mRNA m 6 A reprogramming unveils vitamin-driven post-transcriptional regulation in mice	24
Translation-dependent and -independent mRNA decay occur through mutually exclusive pathways defined by ribosome density during T cell activation	24
Large-scale detection and characterization of interchromosomal rearrangements in normozoospermic bulls using massive genotype and phenotype data sets	24
Efficient integration of spatial omics data for joint domain detection, matching, and alignment with stMSA	24
Polycomb misregulation in enterocytes drives tissue decline in the aging Drosophila intestine	24
Single-cell discovery of m 6 A RNA modifications in the hippocampus	23
Spatial transcriptomics reveals asymmetric cellular responses to injury in the regenerating spiny mouse (Acomys) ear	23
DNA conformational flexibility descriptors improve transcription factor binding prediction across diverse transcription factor families	23
Global identification of mammalian host and nested gene pairs reveal tissue-specific transcriptional interplay	23
Accurate estimation of intraspecific microbial gene content variation in metagenomic data with MIDAS v3 and StrainPGC	22
Epigenetic drift score captures directional methylation variability and links aging to transcriptional, metabolic, and genetic alterations	22
Hierarchical architecture of neo-sex chromosomes and accelerated adaptive evolution in tortricid moths	22
Colibactin leads to a bacteria-specific mutation pattern and self-inflicted DNA damage	22
Differences in activity and stability drive transposable element variation in tropical and temperate maize	22
Regeneration alters open chromatin andcis-regulatory landscape of erythroid precursors	21
A systematic review on the biochemical threshold of mitochondrial genetic variants	21
Genetics-driven risk predictions leveraging the Mendelian randomization framework	21
MHC in newts illuminates the evolutionary dynamics of complex regions in giant genomes	21
Chimeric mitochondrial RNA transcripts predict mitochondrial genome deletion mutations in mitochondrial genetic diseases and aging	21
Full-resolution HLA and KIR gene annotations for human genome assemblies	21
The SeqSplice multiplexed minigene splicing assay for characterization and quantitation of variant-induced BRCA1 and BRCA2 splice isoforms	21
Transcription and potential functions of a novel XIST isoform in male peripheral glia	21
Functional characterization of enhancer activity during a long terminal repeat's evolution	21
Dissecting and improving gene regulatory network inference using single-cell transcriptome data	21
Diversity, duplication, and genomic organization of homeobox genes in Lepidoptera	21
Diffusion-based generation of gene regulatory networks from scRNA-seq data with DigNet	21
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
A new framework for exploratory network mediator analysis in omics data	20
Gaps and complex structurally variant loci in phased genome assemblies	20
Proteome-wide structural analysis quantifies structural conservation across distant species	20
Optical genome mapping enables accurate testing of large repeat expansions	20
Proving sequence aligners can guarantee accuracy in almost O ( m log n	20
Molecular and genetic landscapes of retina and brain microglia in neurodegenerative diseases	20
Fast inference of genetic recombination rates in biobank scale data	19
Pangenome-based genome inference using integer programming	19
The SynMall resource for characterizing the functional impact of synonymous variation	19
Streamlined spatial and environmental expression signatures characterize the minimalist duckweedWolffia australiana	19
Hash functions in nucleotide sequence analysis	19
Statistically rigorous and computationally efficient chromatin stripe detection with Quagga	19
A gene regulatory element modulates myosin expression and controls cardiomyocyte response to stress	19
Long reads decipher genomes and transcriptomes and offer novel insights into biology and diseases	18
Learning probabilistic protein–DNA recognition codes from DNA-binding specificities using structural mappings	18
A scalable adaptive quadratic kernel method for interpretable epistasis analysis in complex traits	18
Erratum: A butterfly pan-genome reveals that a large amount of structural variation underlies the evolution of chromatin accessibility	18
Genome evolution in parthenogenetic nematodes shaped by chromosome rearrangements and introgression	18
Integrated single-cell multiome analysis reveals muscle fiber-type gene regulatory circuitry modulated by endurance exercise	18
A butterfly pan-genome reveals that a large amount of structural variation underlies the evolution of chromatin accessibility	17
Construction and evaluation of a new rat reference genome assembly, GRCr8, from long reads and long-range scaffolding	17
Dynamics and consequences of differential RNA isoform production during cardiomyocyte fate determination and early-stage maturation	17
Protein domain embeddings for fast and accurate similarity search	17
Meta-analysis of activated neurons reveals dynamic regulation of diverse classes of alternative splicing	17
Strain-level metagenomic profiling using pangenome graphs with PanTax	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
Rearrangements of viral and human genomes at human papillomavirus integration events and their allele-specific impacts on cancer genome regulation	17
Comprehensive identification of genomic and environmental determinants of phenotypic plasticity in maize	17
The predicted RNA-binding protein regulome of axonal mRNAs	17
A transcriptome-wide systematic search does not detect A-to-I RNA editing in cis -antisense RNA duplexes	17
Complete genomes of Asgard archaea reveal diverse integrated and mobile genetic elements	17
Telomere-driven replicative crisis is driven by large-scale changes in genomic architecture	16
Integrative chromatin state annotation of 234 human ENCODE4 cell types using Segway	16
Parameter-efficient fine-tuning on large protein language models improves signal peptide prediction	16
Building better genome annotations across the tree of life	16

Revisiting chromatin packaging in mouse sperm	16
Modeling and predicting cancer clonal evolution with reinforcement learning	16
An RNA polymerase III tissue and tumor atlas uncovers context-specific activities linked to 3D epigenome regulatory mechanisms	16
ZSWIM8 destabilizes many murine microRNAs and is required for proper embryonic growth and development	16
De novo transcriptome assembly of mouse male germ cells reveals novel genes, stage-specific bidirectional promoter activity, and noncoding RNA expression	15
Clustered and diverse transcription factor binding underlies cell type specificity of enhancers for housekeeping genes	15
Revolutionizing genomics and medicine—one long molecule at a time	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
Long-read transcriptome sequencing of CLL and MDS patients uncovers molecular effects of SF3B1 mutations	15
Machine learning identifies activation of RUNX/AP-1 as drivers of mesenchymal and fibrotic regulatory programs in gastric cancer	15
Corrigendum: Cre-dependent Cas9-expressing pigs enable efficient in vivo genome editing	15
Long-read genome sequencing and variant reanalysis increase diagnostic yield in neurodevelopmental disorders	15
Accurate genotyping of three major respiratory bacterial pathogens with ONT R10.4.1 long-read sequencing	15
Large haplotypes highlight a complex age structure within the maize pan-genome	15
Size-based expectation maximization for characterizing nucleosome positions and subtypes	15
Stable genome structures in living fossil fishes	14
Ultrafast genome-wide inference of pairwise coalescence times	14
Enhancing nanopore adaptive sampling for PromethION using readfish at scale	14
Mitotic chromosomes harbor cell type– and species-specific structural features within a universal loop array conformation	14
Navigating the landscape of epitranscriptomics and host immunity	14
Diverse evolutionary trajectories of mitocoding DNA in mammalian and avian nuclear genomes	14
Resolving the chromatin impact of mosaic variants with targeted Fiber-seq	14
Generation and analysis of a mouse multitissue genome annotation atlas	14
Plant genome evolution in the genus Eucalyptus is driven by structural rearrangements that promote sequence divergence	14
Estimating the size of long tandem repeat expansions from short reads with ScatTR	14
Commoncis-regulatory variation modifies the penetrance of pathogenicSHROOM3variants in craniofacial microsomia	14
Nucleosome binding by TP53, TP63, and TP73 is determined by the composition, accessibility, and helical orientation of their binding sites	14
CoRAL accurately resolves extrachromosomal DNA genome structures with long-read sequencing	14
RNA Pol II–dependent transcription efficiency fine-tunes A-to-I editing levels	13
A comprehensive single-cell atlas of monoallelic expression across various tissues in zebrafish	13
Modest increase in the de novo single-nucleotide mutation rate in house mice born by assisted reproduction	13
Cytosolic and mitochondrial translation elongation are coordinated through the molecular chaperone TRAP1 for the synthesis and import of mitochondrial proteins	13
Characterizing cytosine methylation of polymorphic transposable element insertions using the human pangenome resources	13
Tn5 tagments and transposes oligos to single-stranded DNA for strand-specific RNA sequencing	13
Synergistic regulation by H3K36 and H3K27 methylation defines the chromatin landscape to control virulence and secondary metabolism in a fungal pathogen	13
A novel multislice framework for precision 3D spatial domain reconstruction and disease pathology analysis	13
Enabling efficient and robust analysis of tandem repeats in genomic data using Wavefront-based String Decomposer	13
OMKar automates genome karyotyping using optical maps to identify constitutional abnormalities	13
An organism-wide ATAC-seq peak catalog for the bovine and its use to identify regulatory variants	13
Optimizing nanopore adaptive sampling for pneumococcal serotype surveillance in complex samples using the graph-based GNASTy algorithm	13
The paradox of R-loops: guardians of the genome or drivers of disease?	13
Phylogenetic relatedness rather than aquatic habitat fosters horizontal transfer of transposable elements in animals	13
miRNA-like secondary structures in maize ( Zea mays ) genes and transposable elements correlate with small RNAs, methylation, and expression	13
Resf1 is required for proper placental development and configuration of trophoblast cell–specific heterochromatin	13
Listeria monocytogenes genes supporting growth under standard laboratory cultivation conditions and during macrophage infection	13
Corrigendum: Human primitive brain displays negative mitochondrial-nuclear expression correlation of respiratory genes	13
A national long-read sequencing study on chromosomal rearrangements uncovers hidden complexities	13
Theoretical framework for the difference of two negative binomial distributions and its application in comparative analysis of sequencing data	13
Assessing and mitigating privacy risks of sparse, noisy genotypes by local alignment to haplotype databases	13
Multisource omic alignment and biological feature discovery with Performer encoder and triplet networks	13
Interspecies regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes	13
Genome skimming with nanopore sequencing precisely determines global and transposon DNA methylation in vertebrates	13
Continuous infiltration and evolutionary trajectory of nuclear organelle DNA inOryza	13
Biosurfer for systematic tracking of regulatory mechanisms leading to protein isoform diversity	13