Genome Research

Papers
(The TQCC of Genome Research is 13. The table below lists those papers that are above that threshold based on CrossRef citation counts [max. 250 papers]. The publications cover those that have been published in the past four years, i.e., from 2021-09-01 to 2025-09-01.)
ArticleCitations
The role of transposon activity in shapingcis-regulatory element evolution after whole-genome duplication213
Dynamic dysregulation of retrotransposons in neurodegenerative diseases at the single-cell level187
Combinatorial microRNA activity is essential for the transition of pluripotent cells from proliferation into dormancy129
De novo detection of somatic variants in high-quality long-read single-cell RNA sequencing data98
Accurate fusion transcript identification from long- and short-read isoform sequencing at bulk or single-cell resolution91
Measuring X-Chromosome inactivation skew for X-linked diseases with adaptive nanopore sequencing89
Comparing genomic and epigenomic features across species using the WashU Comparative Epigenome Browser79
Examining the dynamics of three-dimensional genome organization with multitask matrix factorization73
Transposable element accumulation drives size differences among polymorphic Y Chromosomes in Drosophila71
Evolutionarily new genes in humans with disease phenotypes reveal functional enrichment patterns shaped by adaptive innovation and sexual selection70
A chromosome-scale epigenetic map of theHydragenome reveals conserved regulators of cell state69
Elasmobranch genome sequencing reveals evolutionary trends of vertebrate karyotype organization66
Comparative genomics ofCryptosporidium parvumreveals the emergence of an outbreak-associated population in Europe and its spread to the United States62
Polishing copy number variant calls on exome sequencing data via deep learning60
De novo reconstruction of satellite repeat units from sequence data58
Lake Malawi cichlid pangenome graph reveals extensive structural variation driven by transposable elements56
Unraveling the palindromic and nonpalindromic motifs of retroviral integration site sequences by statistical mixture models52
An efficient method to identify, date, and describe admixture events using haplotype information51
APOBEC3A drives deaminase mutagenesis in human gastric epithelium51
A statistical physics approach for disease module detection51
De novo individualized disease modules reveal the synthetic penetrance of genes and inform personalized treatment regimens50
Tissular chromatin-state cartography based on double-barcoded DNA arrays that capture unloaded PA-Tn5 transposase49
Systematic identification of interchromosomal interaction networks supports the existence of specialized RNA factories49
Functional assays inDrosophilafacilitate classification of variants of uncertain significance associated with rare diseases49
An optimized toolkit for high-molecular-weight DNA extraction and ultra-long-read nanopore sequencing using glass beads and hexamminecobalt(III) chloride49
Chromatin interaction maps identify oncogenic targets of enhancer duplications in cancer49
A novel approach for in vivo DNA footprinting using short double-stranded cell-free DNA from plasma46
Historical RNA expression profiles from the extinct Tasmanian tiger46
Rapid SARS-CoV-2 surveillance using clinical, pooled, or wastewater sequence as a sensor for population change45
Density separation of petrous bone powders for optimized ancient DNA yields45
Artificial intelligence and machine learning in cell-free-DNA-based diagnostics45
Spatial Cellular Networks from omics data with SpaCeNet45
Low-frequency somatic copy number alterations in normal human lymphocytes revealed by large-scale single-cell whole-genome profiling44
Long-read genome assembly of the insect model organismTribolium castaneumreveals spread of satellite DNA in gene-rich regions by recurrent burst events44
Ribosome decision graphs for the representation of eukaryotic RNA translation complexity44
Advancing genomic technologies and clinical awareness accelerates discovery of disease-associated tandem repeat sequences43
Suv39h-catalyzed H3K9me3 is critical for euchromatic genome organization and the maintenance of gene transcription43
Global compositional and functional states of the human gut microbiome in health and disease41
Transposable elements drive the evolution of metazoan zinc finger genes40
Nanopore strand-specific mismatch enables de novo detection of bacterial DNA modifications39
Closing the gaps, and improving somatic structural variant analysis and benchmarking using CHM13-T2T39
Simultaneous profiling of host expression and microbial abundance by spatial metatranscriptome sequencing38
Pathogenic variants inCRXhave distinctcis-regulatory effects on enhancers and silencers in photoreceptors37
Genome-wide oscillations in G + C density and sequence conservation37
Interactive visualization and interpretation of pangenome graphs by linear reference–based coordinate projection and annotation integration37
Large-scale genomic analysis of the domestic dog informs biological discovery36
Challenges and considerations for reproducibility of STARR-seq assays35
Chromatin structure influences rate and spectrum of spontaneous mutations inNeurospora crassa35
Long-read RNA sequencing of archival tissues reveals novel genes and transcripts associated with clear cell renal cell carcinoma recurrence and immune evasion35
Phased nanopore assembly with Shasta and modular graph phasing with GFAse34
Contrasting and combining transcriptome complexity captured by short and long RNA sequencing reads34
PWAS Hub for exploring gene-based associations of common complex diseases33
Genome biology of the darkedged splitfin, Girardinichthys multiradiatus, and the evolution of sex chromosomes and placentation33
Chromosome-specific telomere lengths and the minimal functional telomere revealed by nanopore sequencing32
Batch correction methods used in single-cell RNA sequencing analyses are often poorly calibrated32
Target-enriched nanopore sequencing and de novo assembly reveals co-occurrences of complex on-target genomic rearrangements induced by CRISPR-Cas9 in human cells32
KRAB zinc-finger proteins regulate endogenous retroviruses to sculpt germline transcriptomes and genome evolution32
Dynamic regulation of gonadal transposon control across the lifespan of the naturally short-lived African turquoise killifish32
Simulation of nanopore sequencing signal data with tunable parameters32
Cross-species cell-type assignment from single-cell RNA-seq data by a heterogeneous graph neural network31
Human and rat skeletal muscle single-nuclei multi-omic integrative analyses nominate causal cell types, regulatory elements, and SNPs for complex traits31
Three assays for in-solution enrichment of ancient human DNA at more than a million SNPs31
Corrigendum: A mosquito small RNA genomics resource reveals dynamic evolution and host responses to viruses and transposons30
Aberrant landscapes of maternal meiotic crossovers contribute to aneuploidies in human embryos30
KAS-ATAC reveals the genome-wide single-stranded accessible chromatin landscape of the human genome29
Distal regulation, silencers, and a shared combinatorial syntax are hallmarks of animal embryogenesis29
Unexpectedly low recombination rates and presence of hotspots in termite genomes29
Motif conservation, stability, and host gene expression are the main drivers of snoRNA expression across vertebrates29
Relative contributions of sex hormones, sex chromosomes, and gonads to sex differences in tissue gene regulation28
Marker-free characterization of full-length transcriptomes of single live circulating tumor cells27
Transposon accumulation at xenobiotic gene family loci in aphids27
Cell type–specific analysis by single-cell profiling identifies a stable mammalian tRNA–mRNA interface and increased translation efficiency in neurons27
3′-end ligation sequencing is a sensitive method to detect DNA nicks at potential sites of off-target activity induced by prime editors27
Cohesin organizes 3D DNA contacts surrounding active enhancers inC. elegans27
Mitochondrial DNA variation across 56,434 individuals in gnomAD26
MCHelper automatically curates transposable element libraries across eukaryotic species26
Enhancer–silencer transitions in the human genome25
Whole-genome resequencing of temporally stratified samples reveals substantial loss of haplotype diversity in the highly inbred Scandinavian wolf population25
Hydrahas mammal-like mutation rates facilitating fast adaptation despite its nonaging phenotype25
Full-resolution HLA and KIR gene annotations for human genome assemblies25
A temporal in vivo catalog of chromatin accessibility and expression profiles in pineoblastoma reveals a prevalent role for repressor elements25
Regeneration alters open chromatin andcis-regulatory landscape of erythroid precursors24
Large-scale detection and characterization of interchromosomal rearrangements in normozoospermic bulls using massive genotype and phenotype data sets24
Single-cell discovery of m6A RNA modifications in the hippocampus24
Efficient integration of spatial omics data for joint domain detection, matching, and alignment with stMSA24
Functional characterization of enhancer activity during a long terminal repeat's evolution24
Differences in activity and stability drive transposable element variation in tropical and temperate maize24
Chimeric mitochondrial RNA transcripts predict mitochondrial genome deletion mutations in mitochondrial genetic diseases and aging23
Global identification of mammalian host and nested gene pairs reveal tissue-specific transcriptional interplay23
QuadST identifies cell–cell interaction–changed genes in spatially resolved transcriptomics data23
Benchmarking small-variant genotyping in polyploids23
Hierarchical architecture of neo-sex chromosomes and accelerated adaptive evolution in tortricid moths23
Translation-dependent and -independent mRNA decay occur through mutually exclusive pathways defined by ribosome density during T cell activation23
Global mapping of RNA homodimers in living cells23
Epigenetic drift score captures directional methylation variability and links aging to transcriptional, metabolic, and genetic alterations23
Accurate estimation of intraspecific microbial gene content variation in metagenomic data with MIDAS v3 and StrainPGC23
Colibactin leads to a bacteria-specific mutation pattern and self-inflicted DNA damage23
Accumulation and ineffective silencing of transposable elements on an avian W Chromosome23
A new framework for exploratory network mediator analysis in omics data22
Dynamic barriers modulate cohesin positioning and genome folding at fixed occupancy22
A systematic review on the biochemical threshold of mitochondrial genetic variants22
Implications of the first complete human genome assembly22
Spatial transcriptomics reveals asymmetric cellular responses to injury in the regenerating spiny mouse (Acomys) ear22
Applications of single-cell genomics and computational strategies to study common disease and population-level variation21
Dissecting and improving gene regulatory network inference using single-cell transcriptome data21
Proteome-wide structural analysis quantifies structural conservation across distant species21
Sequencing of individual barcoded cDNAs using Pacific Biosciences and Oxford Nanopore Technologies reveals platform-specific error patterns21
Genetics-driven risk predictions leveraging the Mendelian randomization framework21
Alu insertion variants alter gene transcript levels21
Precise genotyping of circular mobile elements from metagenomic data uncovers human-associated plasmids with recent common ancestors21
Post-transcriptional cross- and auto-regulation buffer expression of the human RNA helicasesDDX3XandDDX3Y21
Proving sequence aligners can guarantee accuracy in almostO(mlogn) time through an average-case analysis of the seed-chain-extend heuristic21
Molecular and genetic landscapes of retina and brain microglia in neurodegenerative diseases20
Diffusion-based generation of gene regulatory networks from scRNA-seq data with DigNet20
Discovery of an unusually high number of de novo mutations in sperm of older men using duplex sequencing20
Variations in antibody repertoires correlate with vaccine responses20
Diversity, duplication, and genomic organization of homeobox genes in Lepidoptera20
The SeqSplice multiplexed minigene splicing assay for characterization and quantitation of variant-induced BRCA1 and BRCA2 splice isoforms20
Gaps and complex structurally variant loci in phased genome assemblies20
Rapid evolution and strain turnover in the infant gut microbiome19
Erratum: A butterfly pan-genome reveals that a large amount of structural variation underlies the evolution of chromatin accessibility19
Long reads decipher genomes and transcriptomes and offer novel insights into biology and diseases19
Optical genome mapping enables accurate testing of large repeat expansions19
MYC overexpression leads to increased chromatin interactions at super-enhancers and MYC binding sites19
Fast inference of genetic recombination rates in biobank scale data19
Genomic environments scale the activities of diverse core promoters19
Long-read sequencing of 111 rice genomes reveals significantly larger pan-genomes19
Profiling the quantitative occupancy of myriad transcription factors across conditions by modeling chromatin accessibility data19
Streamlined spatial and environmental expression signatures characterize the minimalist duckweedWolffia australiana18
A butterfly pan-genome reveals that a large amount of structural variation underlies the evolution of chromatin accessibility18
A scalable adaptive quadratic kernel method for interpretable epistasis analysis in complex traits18
Complete genomes of Asgard archaea reveal diverse integrated and mobile genetic elements18
Protein domain embeddings for fast and accurate similarity search18
Integrated single-cell multiome analysis reveals muscle fiber-type gene regulatory circuitry modulated by endurance exercise17
Pangenome-based genome inference using integer programming17
Construction and evaluation of a new rat reference genome assembly, GRCr8, from long reads and long-range scaffolding17
Learning probabilistic protein–DNA recognition codes from DNA-binding specificities using structural mappings17
Characterization of human transcription factor function and patterns of gene regulation in HepG2 cells17
Corrigendum: An association test of the spatial distribution of rare missense variants within protein structures identifies Alzheimer's disease–related patterns17
Comprehensive identification of genomic and environmental determinants of phenotypic plasticity in maize17
Rearrangements of viral and human genomes at human papillomavirus integration events and their allele-specific impacts on cancer genome regulation17
Modeling and predicting cancer clonal evolution with reinforcement learning17
Rtt109 promotes nucleosome replacement ahead of the replication fork16
Diverse tumorigenic consequences of human papillomavirus integration in primary oropharyngeal cancers16
Assessing DNA methylation detection for primary human tissue using Nanopore sequencing16
Meta-analysis of activated neurons reveals dynamic regulation of diverse classes of alternative splicing16
Identifying cell state–associated alternative splicing events and their coregulation16
De novo transcriptome assembly of mouse male germ cells reveals novel genes, stage-specific bidirectional promoter activity, and noncoding RNA expression16
Accurate genotyping of three major respiratory bacterial pathogens with ONT R10.4.1 long-read sequencing16
The predicted RNA-binding protein regulome of axonal mRNAs16
Building better genome annotations across the tree of life15
Long-read genome sequencing and variant reanalysis increase diagnostic yield in neurodevelopmental disorders15
Thousands of human mutation clusters are explained by short-range template switching15
Revolutionizing genomics and medicine—one long molecule at a time15
Plant genome evolution in the genusEucalyptusis driven by structural rearrangements that promote sequence divergence15
Revisiting chromatin packaging in mouse sperm15
ZSWIM8 destabilizes many murine microRNAs and is required for proper embryonic growth and development15
Automated annotation of human centromeres with HORmon15
Commoncis-regulatory variation modifies the penetrance of pathogenicSHROOM3variants in craniofacial microsomia15
The genetics and epigenetics of satellite centromeres15
Epigenomic translocation of H3K4me3 broad domains over oncogenes following hijacking of super-enhancers15
A curated collection of Klebsiella metabolic models reveals variable substrate usage and gene essentiality15
Parameter-efficient fine-tuning on large protein language models improves signal peptide prediction15
Generation and analysis of a mouse multitissue genome annotation atlas15
Accurate integration of multiple heterogeneous single-cell RNA-seq data sets by learning contrastive biological variation15
Clustered and diverse transcription factor binding underlies cell type specificity of enhancers for housekeeping genes15
CoRAL accurately resolves extrachromosomal DNA genome structures with long-read sequencing14
Enhancing nanopore adaptive sampling for PromethION using readfish at scale14
Genomic analysis of Rad26 and Rad1–Rad10 reveals differences in their dependence on Mediator and RNA polymerase II14
Mitotic chromosomes harbor cell type– and species-specific structural features within a universal loop array conformation14
Navigating the landscape of epitranscriptomics and host immunity14
Large haplotypes highlight a complex age structure within the maize pan-genome14
Corrigendum: Enhancer–silencer transitions in the human genome14
Nucleosome binding by TP53, TP63, and TP73 is determined by the composition, accessibility, and helical orientation of their binding sites14
Machine learning identifies activation of RUNX/AP-1 as drivers of mesenchymal and fibrotic regulatory programs in gastric cancer14
Corrigendum: Cre-dependent Cas9-expressing pigs enable efficient in vivo genome editing14
Long-read transcriptome sequencing of CLL and MDS patients uncovers molecular effects ofSF3B1mutations14
Size-based expectation maximization for characterizing nucleosome positions and subtypes14
Corrigendum: Human primitive brain displays negative mitochondrial-nuclear expression correlation of respiratory genes14
A Bayesian framework for inferring dynamic intercellular interactions from time-series single-cell data14
Continuous infiltration and evolutionary trajectory of nuclear organelle DNA inOryza13
Assessing and mitigating privacy risks of sparse, noisy genotypes by local alignment to haplotype databases13
Biosurfer for systematic tracking of regulatory mechanisms leading to protein isoform diversity13
RNA Pol II–dependent transcription efficiency fine-tunes A-to-I editing levels13
Genome skimming with nanopore sequencing precisely determines global and transposon DNA methylation in vertebrates13
Optimizing nanopore adaptive sampling for pneumococcal serotype surveillance in complex samples using the graph-based GNASTy algorithm13
miRNA-like secondary structures in maize (Zea mays) genes and transposable elements correlate with small RNAs, methylation, and expression13
A novel multislice framework for precision 3D spatial domain reconstruction and disease pathology analysis13
Diverse evolutionary trajectories of mitocoding DNA in mammalian and avian nuclear genomes13
Listeria monocytogenes genes supporting growth under standard laboratory cultivation conditions and during macrophage infection13
Theoretical framework for the difference of two negative binomial distributions and its application in comparative analysis of sequencing data13
Resolving the chromatin impact of mosaic variants with targeted Fiber-seq13
RefSeq Functional Elements as experimentally assayed nongenic reference standards and functional interactions in human and mouse13
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