Genome Research

Article	Citations
Cell-type- and chromosome-specific chromatin landscapes and DNA replication programs of Drosophila testis tumor stem cell–like cells	522
Examining the dynamics of three-dimensional genome organization with multitask matrix factorization	136
Dynamic metabolic and molecular changes during seasonal shrinking in Sorex araneus	135
Dynamic dysregulation of retrotransposons in neurodegenerative diseases at the single-cell level	114
Evolutionarily new genes in humans with disease phenotypes reveal functional enrichment patterns shaped by adaptive innovation and sexual selection	86
Unraveling the palindromic and nonpalindromic motifs of retroviral integration site sequences by statistical mixture models	80
De novo detection of somatic variants in high-quality long-read single-cell RNA sequencing data	80
APOBEC3A drives deaminase mutagenesis in human gastric epithelium	76
Lake Malawi cichlid pangenome graph reveals extensive structural variation driven by transposable elements	75
A chromosome-scale epigenetic map of the Hydra genome reveals conserved regulators of cell state	74
De novo reconstruction of satellite repeat units from sequence data	72
Combinatorial microRNA activity is essential for the transition of pluripotent cells from proliferation into dormancy	67
Simultaneous modeling of chromatin conformation changes from multiple single-cell interaction maps with ChromMovie	66
Lignature provides a curated resource of ligand-induced transcriptomic signatures for signaling inference	65
Comparing genomic and epigenomic features across species using the WashU Comparative Epigenome Browser	63
Accurate fusion transcript identification from long- and short-read isoform sequencing at bulk or single-cell resolution	61
Elasmobranch genome sequencing reveals evolutionary trends of vertebrate karyotype organization	59
Comparative genomics of Cryptosporidium parvum reveals the emergence of an outbreak-associated population in Europe and its spread to the United States	58
A statistical physics approach for disease module detection	57
An efficient method to identify, date, and describe admixture events using haplotype information	54
The role of transposon activity in shapingcis-regulatory element evolution after whole-genome duplication	54
Polishing copy number variant calls on exome sequencing data via deep learning	53
Suv39h-catalyzed H3K9me3 is critical for euchromatic genome organization and the maintenance of gene transcription	52
Measuring X-Chromosome inactivation skew for X-linked diseases with adaptive nanopore sequencing	52
Ribosome decision graphs for the representation of eukaryotic RNA translation complexity	52

Transposable element small RNAs and large RNAs in aging brains and implications in Huntington's and Parkinson's disease	52
Long-read genome assembly of the insect model organism Tribolium castaneum reveals spread of satellite DNA in gene-rich regions by recurrent burst events	51
Tissular chromatin-state cartography based on double-barcoded DNA arrays that capture unloaded PA-Tn5 transposase	48
Transposable elements drive the evolution of metazoan zinc finger genes	47
An optimized toolkit for high-molecular-weight DNA extraction and ultra-long-read nanopore sequencing using glass beads and hexamminecobalt(III) chloride	47
Rapid SARS-CoV-2 surveillance using clinical, pooled, or wastewater sequence as a sensor for population change	45
Spatial Cellular Networks from omics data with SpaCeNet	43
Historical RNA expression profiles from the extinct Tasmanian tiger	42
Systematic identification of interchromosomal interaction networks supports the existence of specialized RNA factories	42
Functional assays inDrosophilafacilitate classification of variants of uncertain significance associated with rare diseases	41
Corrigendum: A sheep pangenome reveals the spectrum of structural variations and their effects on tail phenotypes	41
Cultivation-independent high-quality microbial genome reconstruction from environmental samples with midi-metagenomics	40
Global compositional and functional states of the human gut microbiome in health and disease	38
The superpowers of imprinting control regions	37
Isoform- and pathway-specific regulation of post-transcriptional RNA processing in human cells	37
A novel approach for in vivo DNA footprinting using short double-stranded cell-free DNA from plasma	35
Density separation of petrous bone powders for optimized ancient DNA yields	35
Chromatin interaction maps identify oncogenic targets of enhancer duplications in cancer	34
Artificial intelligence and machine learning in cell-free-DNA-based diagnostics	33
Herbaria provide a valuable resource for obtaining informative mRNA	33
Batch correction methods used in single-cell RNA sequencing analyses are often poorly calibrated	32
Functional genomics analysis of developing zebrafish and human endoderm reveals highly conserved cis -regulatory modules acting during vertebrate organog	32
Nanopore strand-specific mismatch enables de novo detection of bacterial DNA modifications	32
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
Interactive visualization and interpretation of pangenome graphs by linear reference–based coordinate projection and annotation integration	31
Whole-genome variant detection in long-read sequencing data from ultra-low input patient samples	31
Phased nanopore assembly with Shasta and modular graph phasing with GFAse	31
Cross-species cell-type assignment from single-cell RNA-seq data by a heterogeneous graph neural network	31
Three assays for in-solution enrichment of ancient human DNA at more than a million SNPs	30
KRAB zinc-finger proteins regulate endogenous retroviruses to sculpt germline transcriptomes and genome evolution	30
Simulation of nanopore sequencing signal data with tunable parameters	29
Closing the gaps, and improving somatic structural variant analysis and benchmarking using CHM13-T2T	29
Pathogenic variants in CRX have distinct cis -regulatory effects on enhancers and silencers in photorecept	29
PWAS Hub for exploring gene-based associations of common complex diseases	29
Challenges and considerations for reproducibility of STARR-seq assays	28
Dynamic regulation of gonadal transposon control across the lifespan of the naturally short-lived African turquoise killifish	28
Large-scale genomic analysis of the domestic dog informs biological discovery	28
Long-read RNA sequencing of archival tissues reveals novel genes and transcripts associated with clear cell renal cell carcinoma recurrence and immune evasion	28
Contrasting and combining transcriptome complexity captured by short and long RNA sequencing reads	28
Simultaneous profiling of host expression and microbial abundance by spatial metatranscriptome sequencing	28
Chromatin structure influences rate and spectrum of spontaneous mutations in Neurospora crassa	28
A genome-wide survey reveals that a diverse array of enhancers coordinates the Drosophila innate immune response	28
Marker-free characterization of full-length transcriptomes of single live circulating tumor cells	27
Corrigendum: A mosquito small RNA genomics resource reveals dynamic evolution and host responses to viruses and transposons	27
A systems view on DNA damage response kinetics in Tetrahymena	27
KAS-ATAC reveals the genome-wide single-stranded accessible chromatin landscape of the human genome	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
Unexpectedly low recombination rates and presence of hotspots in termite genomes	26
Automated chromatin profiling with spa-ChIP-seq uncovers the impacts of condition variations	26
Early feature extraction drives model performance in high-resolution chromatin accessibility prediction	26

Evidence for negative selection against somatic mutations induced in normal fibroblasts by N -ethyl- N -ni	25
Motif conservation, stability, and host gene expression are the main drivers of snoRNA expression across vertebrates	25
MCHelper automatically curates transposable element libraries across eukaryotic species	25
Aberrant landscapes of maternal meiotic crossovers contribute to aneuploidies in human embryos	25
Transposon accumulation at xenobiotic gene family loci in aphids	25
QuadST identifies cell–cell interaction–changed genes in spatially resolved transcriptomics data	24
A temporal in vivo catalog of chromatin accessibility and expression profiles in pineoblastoma reveals a prevalent role for repressor elements	24
Polycomb misregulation in enterocytes drives tissue decline in the aging Drosophila intestine	24
Cohesin organizes 3D DNA contacts surrounding active enhancers in C. elegans	24
Hydrahas mammal-like mutation rates facilitating fast adaptation despite its nonaging phenotype	24
Colibactin leads to a bacteria-specific mutation pattern and self-inflicted DNA damage	24
Allele-specific splicing modulates protein isoforms and Alzheimer's disease risk	24
Spatial transcriptomics reveals asymmetric cellular responses to injury in the regenerating spiny mouse (Acomys) ear	23
Single-cell discovery of m 6 A RNA modifications in the hippocampus	23
Chimeric mitochondrial RNA transcripts predict mitochondrial genome deletion mutations in mitochondrial genetic diseases and aging	23
Epigenetic drift score captures directional methylation variability and links aging to transcriptional, metabolic, and genetic alterations	23
Dynamic A-to-I RNA editing in response to gut microbiome in honeybees	23
Translation-dependent and -independent mRNA decay occur through mutually exclusive pathways defined by ribosome density during T cell activation	23
Global identification of mammalian host and nested gene pairs reveal tissue-specific transcriptional interplay	23
Hierarchical architecture of neo-sex chromosomes and accelerated adaptive evolution in tortricid moths	23
Large-scale detection and characterization of interchromosomal rearrangements in normozoospermic bulls using massive genotype and phenotype data sets	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
Tissue-specific mRNA m 6 A reprogramming unveils vitamin-driven post-transcriptional regulation in mice	22
Efficient integration of spatial omics data for joint domain detection, matching, and alignment with stMSA	22
Regeneration alters open chromatin andcis-regulatory landscape of erythroid precursors	22
Functional characterization of enhancer activity during a long terminal repeat's evolution	22
The SynMall resource for characterizing the functional impact of synonymous variation	21
Full-resolution HLA and KIR gene annotations for human genome assemblies	21
Post-transcriptional cross- and auto-regulation buffer expression of the human RNA helicases DDX3X and DDX3Y	21
MHC in newts illuminates the evolutionary dynamics of complex regions in giant genomes	21
DNA conformational flexibility descriptors improve transcription factor binding prediction across diverse transcription factor families	21
Transcription and potential functions of a novel XIST isoform in male peripheral glia	21
The SeqSplice multiplexed minigene splicing assay for characterization and quantitation of variant-induced BRCA1 and BRCA2 splice isoforms	21
A systematic review on the biochemical threshold of mitochondrial genetic variants	20
Proteome-wide structural analysis quantifies structural conservation across distant species	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
A new framework for exploratory network mediator analysis in omics data	20
Dynamic barriers modulate cohesin positioning and genome folding at fixed occupancy	20
Diversity, duplication, and genomic organization of homeobox genes in Lepidoptera	20
Dissecting and improving gene regulatory network inference using single-cell transcriptome data	20
Diffusion-based generation of gene regulatory networks from scRNA-seq data with DigNet	20
Optical genome mapping enables accurate testing of large repeat expansions	20
Genetics-driven risk predictions leveraging the Mendelian randomization framework	20
A gene regulatory element modulates myosin expression and controls cardiomyocyte response to stress	19
Streamlined spatial and environmental expression signatures characterize the minimalist duckweedWolffia australiana	19
A scalable adaptive quadratic kernel method for interpretable epistasis analysis in complex traits	19
Statistically rigorous and computationally efficient chromatin stripe detection with Quagga	19
Long reads decipher genomes and transcriptomes and offer novel insights into biology and diseases	19
Gaps and complex structurally variant loci in phased genome assemblies	19
Protein domain embeddings for fast and accurate similarity search	19
Hash functions in nucleotide sequence analysis	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
Learning probabilistic protein–DNA recognition codes from DNA-binding specificities using structural mappings	18
Characterization of human transcription factor function and patterns of gene regulation in HepG2 cells	18
Integrated single-cell multiome analysis reveals muscle fiber-type gene regulatory circuitry modulated by endurance exercise	18
Fast inference of genetic recombination rates in biobank scale data	18
A butterfly pan-genome reveals that a large amount of structural variation underlies the evolution of chromatin accessibility	18
Pangenome-based genome inference using integer programming	18
Accurate genotyping of three major respiratory bacterial pathogens with ONT R10.4.1 long-read sequencing	17
Genome evolution in parthenogenetic nematodes shaped by chromosome rearrangements and introgression	17
Building better genome annotations across the tree of life	17
Modeling and predicting cancer clonal evolution with reinforcement learning	17
Assessing DNA methylation detection for primary human tissue using Nanopore sequencing	17
Corrigendum: An association test of the spatial distribution of rare missense variants within protein structures identifies Alzheimer's disease–related patterns	17
Meta-analysis of activated neurons reveals dynamic regulation of diverse classes of alternative splicing	17
Parameter-efficient fine-tuning on large protein language models improves signal peptide prediction	17
De novo transcriptome assembly of mouse male germ cells reveals novel genes, stage-specific bidirectional promoter activity, and noncoding RNA expression	17
Erratum: A butterfly pan-genome reveals that a large amount of structural variation underlies the evolution of chromatin accessibility	17
Revisiting chromatin packaging in mouse sperm	17
Complete genomes of Asgard archaea reveal diverse integrated and mobile genetic elements	17
ZSWIM8 destabilizes many murine microRNAs and is required for proper embryonic growth and development	16
The predicted RNA-binding protein regulome of axonal mRNAs	16
Identifying cell state–associated alternative splicing events and their coregulation	16
Construction and evaluation of a new rat reference genome assembly, GRCr8, from long reads and long-range scaffolding	16
A transcriptome-wide systematic search does not detect A-to-I RNA editing in cis -antisense RNA duplexes	16
Integrative chromatin state annotation of 234 human ENCODE4 cell types using Segway	16
Long-read genome sequencing and variant reanalysis increase diagnostic yield in neurodevelopmental disorders	16

Corrigendum: Cre-dependent Cas9-expressing pigs enable efficient in vivo genome editing	16
Thousands of human mutation clusters are explained by short-range template switching	16
Dynamics and consequences of differential RNA isoform production during cardiomyocyte fate determination and early-stage maturation	16
Strain-level metagenomic profiling using pangenome graphs with PanTax	16
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
Generation and analysis of a mouse multitissue genome annotation atlas	15
Mitotic chromosomes harbor cell type– and species-specific structural features within a universal loop array conformation	15
Size-based expectation maximization for characterizing nucleosome positions and subtypes	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
Commoncis-regulatory variation modifies the penetrance of pathogenicSHROOM3variants in craniofacial microsomia	14
Navigating the landscape of epitranscriptomics and host immunity	14
Machine learning identifies activation of RUNX/AP-1 as drivers of mesenchymal and fibrotic regulatory programs in gastric cancer	14
Plant genome evolution in the genus Eucalyptus is driven by structural rearrangements that promote sequence divergence	14
Long-read transcriptome sequencing of CLL and MDS patients uncovers molecular effects of SF3B1 mutations	14
CoRAL accurately resolves extrachromosomal DNA genome structures with long-read sequencing	14
Large haplotypes highlight a complex age structure within the maize pan-genome	14
Nucleosome binding by TP53, TP63, and TP73 is determined by the composition, accessibility, and helical orientation of their binding sites	14
Corrigendum: Enhancer–silencer transitions in the human genome	14
Enhancing nanopore adaptive sampling for PromethION using readfish at scale	14
An organism-wide ATAC-seq peak catalog for the bovine and its use to identify regulatory variants	13
Cytosolic and mitochondrial translation elongation are coordinated through the molecular chaperone TRAP1 for the synthesis and import of mitochondrial proteins	13
Synergistic regulation by H3K36 and H3K27 methylation defines the chromatin landscape to control virulence and secondary metabolism in a fungal pathogen	13
Resolving the chromatin impact of mosaic variants with targeted Fiber-seq	13
RNA Pol II–dependent transcription efficiency fine-tunes A-to-I editing levels	13
Stable genome structures in living fossil fishes	13
Biosurfer for systematic tracking of regulatory mechanisms leading to protein isoform diversity	13
Theoretical framework for the difference of two negative binomial distributions and its application in comparative analysis of sequencing data	13
OMKar automates genome karyotyping using optical maps to identify constitutional abnormalities	13
Estimating the size of long tandem repeat expansions from short reads with ScatTR	13
miRNA-like secondary structures in maize ( Zea mays ) genes and transposable elements correlate with small RNAs, methylation, and expression	13
Diverse evolutionary trajectories of mitocoding DNA in mammalian and avian nuclear genomes	13
Assessing and mitigating privacy risks of sparse, noisy genotypes by local alignment to haplotype databases	13
Continuous infiltration and evolutionary trajectory of nuclear organelle DNA inOryza	13
Listeria monocytogenes genes supporting growth under standard laboratory cultivation conditions and during macrophage infection	13
Tn5 tagments and transposes oligos to single-stranded DNA for strand-specific RNA sequencing	12
A comprehensive single-cell atlas of monoallelic expression across various tissues in zebrafish	12
Optimizing nanopore adaptive sampling for pneumococcal serotype surveillance in complex samples using the graph-based GNASTy algorithm	12
A novel multislice framework for precision 3D spatial domain reconstruction and disease pathology analysis	12
Modest increase in the de novo single-nucleotide mutation rate in house mice born by assisted reproduction	12
Highly accurate assembly polishing with DeepPolisher	12
Matching queried single-cell open-chromatin profiles to large pools of single-cell transcriptomes and epigenomes for reference supported analysis	12
The rate of de novo structural variation is increased in in vitro–produced offspring and preferentially affects the paternal genome	12
Unveiling the functional fate of duplicated genes through expression profiling and structural analysis	12
Ultrafast genome-wide inference of pairwise coalescence times	12
Genomic analysis of Rad26 and Rad1–Rad10 reveals differences in their dependence on Mediator and RNA polymerase II	12
Corrigendum: Human primitive brain displays negative mitochondrial-nuclear expression correlation of respiratory genes	12
Wnt signaling activation induces CTCF binding and loop formation at cis-regulatory elements of target genes	12
Identification of the male-specific region on the guppy Y Chromosome from a haplotype-resolved assembly	12
Graph-based deep reinforcement learning for haplotype assembly with Ralphi	12
Haplotype and population structure inference using neural networks in whole-genome sequencing data	12
A national long-read sequencing study on chromosomal rearrangements uncovers hidden complexities	12
Genome skimming with nanopore sequencing precisely determines global and transposon DNA methylation in vertebrates	12
Enabling efficient and robust analysis of tandem repeats in genomic data using Wavefront-based String Decomposer	12
The paradox of R-loops: guardians of the genome or drivers of disease?	12
High temporal resolution RNA-seq time course data reveals widespread synchronous activation between mammalian lncRNAs and neighboring protein-coding genes	12
A statistical learning method for simultaneous copy number estimation and subclone clustering with single-cell sequencing data	12
Interspecies regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes	11
Integration of high-throughput proteomic data and complementary omics layers with PriOmics	11
FocalSV enables target region–based structural variant assembly and refinement using single-molecule long-read sequencing data	11
Genetic regulation of nascent RNA maturation revealed by direct RNA nanopore sequencing	11
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	11
Copy number variation alters local and global mutational tolerance	11
Multiscale network modeling reveals the gene regulatory landscape driving cancer prognosis in 32 cancer types	11
Characterizing cytosine methylation of polymorphic transposable element insertions using the human pangenome resources	11
Reference-informed prediction of alternative splicing and splicing-altering mutations from sequences	11
SWATH-MS-based proteogenomic analysis reveals the involvement of alternative splicing in poplar upon lead stress	11
The fine-scale recombination rate variation and associations with genomic features in a butterfly	11
Dynamics of intronic polyadenylation in the hematopoietic lineage and its regulation by DNA methylation	11
Phylogenetic relatedness rather than aquatic habitat fosters horizontal transfer of transposable elements in animals	11
A spectral component approach leveraging identity-by-descent graphs to address recent population structure in genomic analysis	11
Systematic identification and characterization of exon–intron circRNAs	11
Interpretable phenotype decoding from multicondition sequencing data with ALPINE	11
MPRAbase a Massively Parallel Reporter Assay database	11
Multisite long-read sequencing reveals the early contributions of somatic structural variations to HBV-related hepatocellular carcinoma tumorigenesis	11
Joint imputation and deconvolution of gene expression across spatial transcriptomics platforms	11
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	11
Vertebrates show coordinated elevated expression of mitochondrial and nuclear genes after birth	11
Analytical validation of germline small variant detection using long-read HiFi genome sequencing	11
The grasshopper genome reveals long-term gene content conservation of the X Chromosome and temporal variation in X Chromosome evolution	10
Kinetic measurement of gene-specific RNA polymerase II transcription elongation rates	10
De novo antibody identification in human blood from full-length single B cell transcriptomics and matching haplotype-resolved germline assemblies	10
Population genomics reveals mechanisms and dynamics of de novo expressed open reading frame emergence in Drosophila melanogaster	10
Genome-wide relaxation of selection and the evolution of the island syndrome in Orkney voles	10
An atlas of fish genome evolution reveals delayed rediploidization following the teleost whole-genome duplication	10
Locus-resolution analysis of L1 regulation and retrotransposition potential in mouse embryonic development	10
Developmental transcriptomics inPristionchusreveals the environmental responsiveness of a plasticity gene-regulatory network	10
Haplotype-resolved telomere-to-telomere genome of Aphelenchus avenae implicates P5CS in nematode desiccati	10
Genetic effects on chromatin accessibility uncover mechanisms of liver gene regulation and quantitative traits	10
Single-nucleus CUT&RUN elucidates the function of intrinsic and genomics-driven epigenetic heterogeneity in head and neck cancer progression	10
Telomere-to-telomere assembly by preserving contained reads	10
Epigenomic analysis reveals prevalent contribution of transposable elements to cis-regulatory elements, tissue-specific expression, and alternative promoters in zebrafish	10
tRNA-derived small RNAs are embedded in the gene regulatory network instructingDrosophilametamorphosis	10
Efficient taxa identification using a pangenome index	10