Genome Research

Papers
(The TQCC of Genome Research is 14. 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 2021-07-01 to 2025-07-01.)
ArticleCitations
The role of transposon activity in shapingcis-regulatory element evolution after whole-genome duplication178
Dynamic dysregulation of retrotransposons in neurodegenerative diseases at the single-cell level167
De novo individualized disease modules reveal the synthetic penetrance of genes and inform personalized treatment regimens137
A statistical physics approach for disease module detection123
De novo reconstruction of satellite repeat units from sequence data91
Accurate fusion transcript identification from long- and short-read isoform sequencing at bulk or single-cell resolution84
Measuring X-Chromosome inactivation skew for X-linked diseases with adaptive nanopore sequencing81
Lake Malawi cichlid pangenome graph reveals extensive structural variation driven by transposable elements80
Examining the dynamics of three-dimensional genome organization with multitask matrix factorization79
Comparing genomic and epigenomic features across species using the WashU Comparative Epigenome Browser71
Evolutionarily new genes in humans with disease phenotypes reveal functional enrichment patterns shaped by adaptive innovation and sexual selection71
Unraveling the palindromic and nonpalindromic motifs of retroviral integration site sequences by statistical mixture models67
Comparative genomics ofCryptosporidium parvumreveals the emergence of an outbreak-associated population in Europe and its spread to the United States66
De novo detection of somatic variants in high-quality long-read single-cell RNA sequencing data66
Combinatorial microRNA activity is essential for the transition of pluripotent cells from proliferation into dormancy64
A ChIP-exo screen of 887 Protein Capture Reagents Program transcription factor antibodies in human cells61
Elasmobranch genome sequencing reveals evolutionary trends of vertebrate karyotype organization61
Transposable element accumulation drives size differences among polymorphic Y Chromosomes in Drosophila57
Polishing copy number variant calls on exome sequencing data via deep learning56
A chromosome-scale epigenetic map of theHydragenome reveals conserved regulators of cell state53
Systematic identification of interchromosomal interaction networks supports the existence of specialized RNA factories52
An efficient method to identify, date, and describe admixture events using haplotype information52
An optimized toolkit for high-molecular-weight DNA extraction and ultra-long-read nanopore sequencing using glass beads and hexamminecobalt(III) chloride52
Ribosome decision graphs for the representation of eukaryotic RNA translation complexity49
Advancing genomic technologies and clinical awareness accelerates discovery of disease-associated tandem repeat sequences49
Functional assays inDrosophilafacilitate classification of variants of uncertain significance associated with rare diseases48
Suv39h-catalyzed H3K9me3 is critical for euchromatic genome organization and the maintenance of gene transcription48
Rapid SARS-CoV-2 surveillance using clinical, pooled, or wastewater sequence as a sensor for population change47
A novel approach for in vivo DNA footprinting using short double-stranded cell-free DNA from plasma47
Likelihood-based deconvolution of bulk gene expression data using single-cell references47
Chromatin interaction maps identify oncogenic targets of enhancer duplications in cancer47
Low-frequency somatic copy number alterations in normal human lymphocytes revealed by large-scale single-cell whole-genome profiling45
Spatial Cellular Networks from omics data with SpaCeNet44
Artificial intelligence and machine learning in cell-free-DNA-based diagnostics44
Long-read genome assembly of the insect model organismTribolium castaneumreveals spread of satellite DNA in gene-rich regions by recurrent burst events44
Ligand-induced native G-quadruplex stabilization impairs transcription initiation43
Global compositional and functional states of the human gut microbiome in health and disease43
Historical RNA expression profiles from the extinct Tasmanian tiger43
Density separation of petrous bone powders for optimized ancient DNA yields43
Closing the gaps, and improving somatic structural variant analysis and benchmarking using CHM13-T2T42
Transposable elements drive the evolution of metazoan zinc finger genes42
Tissular chromatin-state cartography based on double-barcoded DNA arrays that capture unloaded PA-Tn5 transposase42
Interactive visualization and interpretation of pangenome graphs by linear reference–based coordinate projection and annotation integration41
Contrasting and combining transcriptome complexity captured by short and long RNA sequencing reads41
Nanopore strand-specific mismatch enables de novo detection of bacterial DNA modifications41
KRAB zinc-finger proteins regulate endogenous retroviruses to sculpt germline transcriptomes and genome evolution40
Genome biology of the darkedged splitfin, Girardinichthys multiradiatus, and the evolution of sex chromosomes and placentation40
Genome-wide oscillations in G + C density and sequence conservation39
Cross-species cell-type assignment from single-cell RNA-seq data by a heterogeneous graph neural network38
Pathogenic variants inCRXhave distinctcis-regulatory effects on enhancers and silencers in photoreceptors38
Target-enriched nanopore sequencing and de novo assembly reveals co-occurrences of complex on-target genomic rearrangements induced by CRISPR-Cas9 in human cells37
Dynamic regulation of gonadal transposon control across the lifespan of the naturally short-lived African turquoise killifish37
Large-scale genomic analysis of the domestic dog informs biological discovery36
Simultaneous profiling of host expression and microbial abundance by spatial metatranscriptome sequencing35
Chromatin structure influences rate and spectrum of spontaneous mutations inNeurospora crassa35
Chromosome-specific telomere lengths and the minimal functional telomere revealed by nanopore sequencing35
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 GFAse32
Human and rat skeletal muscle single-nuclei multi-omic integrative analyses nominate causal cell types, regulatory elements, and SNPs for complex traits32
Simulation of nanopore sequencing signal data with tunable parameters32
PWAS Hub for exploring gene-based associations of common complex diseases32
Three assays for in-solution enrichment of ancient human DNA at more than a million SNPs32
Challenges and considerations for reproducibility of STARR-seq assays32
KAS-ATAC reveals the genome-wide single-stranded accessible chromatin landscape of the human genome31
Aberrant landscapes of maternal meiotic crossovers contribute to aneuploidies in human embryos31
Corrigendum: A mosquito small RNA genomics resource reveals dynamic evolution and host responses to viruses and transposons31
Motif conservation, stability, and host gene expression are the main drivers of snoRNA expression across vertebrates30
Marker-free characterization of full-length transcriptomes of single live circulating tumor cells30
Transposon accumulation at xenobiotic gene family loci in aphids30
Distal regulation, silencers, and a shared combinatorial syntax are hallmarks of animal embryogenesis30
Cell type–specific analysis by single-cell profiling identifies a stable mammalian tRNA–mRNA interface and increased translation efficiency in neurons30
Unexpectedly low recombination rates and presence of hotspots in termite genomes30
Relative contributions of sex hormones, sex chromosomes, and gonads to sex differences in tissue gene regulation29
Cohesin organizes 3D DNA contacts surrounding active enhancers inC. elegans29
MCHelper automatically curates transposable element libraries across eukaryotic species29
Whole-genome resequencing of temporally stratified samples reveals substantial loss of haplotype diversity in the highly inbred Scandinavian wolf population29
Mitochondrial DNA variation across 56,434 individuals in gnomAD29
Hydrahas mammal-like mutation rates facilitating fast adaptation despite its nonaging phenotype28
A temporal in vivo catalog of chromatin accessibility and expression profiles in pineoblastoma reveals a prevalent role for repressor elements28
Benchmarking small-variant genotyping in polyploids27
Chimeric mitochondrial RNA transcripts predict mitochondrial genome deletion mutations in mitochondrial genetic diseases and aging27
Global identification of mammalian host and nested gene pairs reveal tissue-specific transcriptional interplay26
Accurate estimation of intraspecific microbial gene content variation in metagenomic data with MIDAS v3 and StrainPGC26
Hierarchical architecture of neo-sex chromosomes and accelerated adaptive evolution in tortricid moths26
Regeneration alters open chromatin andcis-regulatory landscape of erythroid precursors26
Enhancer–silencer transitions in the human genome25
Spatial transcriptomics reveals asymmetric cellular responses to injury in the regenerating spiny mouse (Acomys) ear25
Colibactin leads to a bacteria-specific mutation pattern and self-inflicted DNA damage25
Translation-dependent and -independent mRNA decay occur through mutually exclusive pathways defined by ribosome density during T cell activation24
Differences in activity and stability drive transposable element variation in tropical and temperate maize24
Single-cell discovery of m6A RNA modifications in the hippocampus24
Accumulation and ineffective silencing of transposable elements on an avian W Chromosome24
QuadST identifies cell-cell interaction-changed genes in spatially resolved transcriptomics data24
Global mapping of RNA homodimers in living cells24
Functional characterization of enhancer activity during a long terminal repeat's evolution24
Full-resolution HLA and KIR gene annotations for human genome assemblies23
Diversity, duplication, and genomic organization of homeobox genes in Lepidoptera23
Large-scale detection and characterization of interchromosomal rearrangements in normozoospermic bulls using massive genotype and phenotype data sets23
A systematic review on the biochemical threshold of mitochondrial genetic variants23
Diffusion-based generation of gene regulatory networks from scRNA-seq data with DigNet22
Implications of the first complete human genome assembly22
Genetics-driven risk predictions leveraging the Mendelian randomization framework22
Post-transcriptional cross- and auto-regulation buffer expression of the human RNA helicasesDDX3XandDDX3Y22
Dissecting and improving gene regulatory network inference using single-cell transcriptome data22
A new framework for exploratory network mediator analysis in omics data22
Discovery of an unusually high number of de novo mutations in sperm of older men using duplex sequencing22
Sequencing of individual barcoded cDNAs using Pacific Biosciences and Oxford Nanopore Technologies reveals platform-specific error patterns22
Alu insertion variants alter gene transcript levels21
Long-read sequencing of 111 rice genomes reveals significantly larger pan-genomes21
Gaps and complex structurally variant loci in phased genome assemblies21
Variations in antibody repertoires correlate with vaccine responses21
Proteome-wide structural analysis quantifies structural conservation across distant species21
Proving sequence aligners can guarantee accuracy in almostO(mlogn) time through an average-case analysis of the seed-chain-extend heuristic21
MYC overexpression leads to increased chromatin interactions at super-enhancers and MYC binding sites21
Optical genome mapping enables accurate testing of large repeat expansions21
Precise genotyping of circular mobile elements from metagenomic data uncovers human-associated plasmids with recent common ancestors21
Applications of single-cell genomics and computational strategies to study common disease and population-level variation21
Erratum: A butterfly pan-genome reveals that a large amount of structural variation underlies the evolution of chromatin accessibility20
Fast inference of genetic recombination rates in biobank scale data20
Characterization of human transcription factor function and patterns of gene regulation in HepG2 cells20
Complete genomes of Asgard archaea reveal diverse integrated and mobile genetic elements20
A butterfly pan-genome reveals that a large amount of structural variation underlies the evolution of chromatin accessibility20
Rapid evolution and strain turnover in the infant gut microbiome20
Profiling the quantitative occupancy of myriad transcription factors across conditions by modeling chromatin accessibility data20
Learning probabilistic protein–DNA recognition codes from DNA-binding specificities using structural mappings20
Integrated single-cell multiome analysis reveals muscle fiber-type gene regulatory circuitry modulated by endurance exercise19
Long reads decipher genomes and transcriptomes and offer novel insights into biology and diseases19
Comprehensive identification of genomic and environmental determinants of phenotypic plasticity in maize19
A scalable adaptive quadratic kernel method for interpretable epistasis analysis in complex traits19
Protein domain embeddings for fast and accurate similarity search19
Rearrangements of viral and human genomes at human papillomavirus integration events and their allele-specific impacts on cancer genome regulation19
Streamlined spatial and environmental expression signatures characterize the minimalist duckweedWolffia australiana19
Genomic environments scale the activities of diverse core promoters19
Inferring genes that escape X-Chromosome inactivation reveals important contribution of variable escape genes to sex-biased diseases19
Construction and evaluation of a new rat reference genome assembly, GRCr8, from long reads and long-range scaffolding18
Assessing DNA methylation detection for primary human tissue using Nanopore sequencing18
Diverse tumorigenic consequences of human papillomavirus integration in primary oropharyngeal cancers18
Thousands of human mutation clusters are explained by short-range template switching18
Modeling and predicting cancer clonal evolution with reinforcement learning18
Epigenomic translocation of H3K4me3 broad domains over oncogenes following hijacking of super-enhancers18
Long-read genome sequencing and variant reanalysis increase diagnostic yield in neurodevelopmental disorders18
Sequence-based correction of barcode bias in massively parallel reporter assays18
Corrigendum: An association test of the spatial distribution of rare missense variants within protein structures identifies Alzheimer's disease–related patterns18
A curated collection of Klebsiella metabolic models reveals variable substrate usage and gene essentiality18
The predicted RNA-binding protein regulome of axonal mRNAs18
Accurate genotyping of three major respiratory bacterial pathogens with ONT R10.4.1 long-read sequencing17
ZSWIM8 destabilizes many murine microRNAs and is required for proper embryonic growth and development17
Parameter-efficient fine-tuning on large protein language models improves signal peptide prediction17
Identifying cell state–associated alternative splicing events and their coregulation17
Rtt109 promotes nucleosome replacement ahead of the replication fork17
Revisiting chromatin packaging in mouse sperm17
Building better genome annotations across the tree of life17
Meta-analysis of activated neurons reveals dynamic regulation of diverse classes of alternative splicing17
Automated annotation of human centromeres with HORmon17
De novo transcriptome assembly of mouse male germ cells reveals novel genes, stage-specific bidirectional promoter activity, and noncoding RNA expression17
Enhancing nanopore adaptive sampling for PromethION using readfish at scale16
Clustered and diverse transcription factor binding underlies cell type specificity of enhancers for housekeeping genes16
Revolutionizing genomics and medicine—one long molecule at a time16
Generation and analysis of a mouse multitissue genome annotation atlas16
Hydroxycarbamide effects on DNA methylation and gene expression in myeloproliferative neoplasms15
Size-based expectation maximization for characterizing nucleosome positions and subtypes15
Long-read transcriptome sequencing of CLL and MDS patients uncovers molecular effects ofSF3B1mutations15
Transposable elements and their KZFP controllers are drivers of transcriptional innovation in the developing human brain15
Plant genome evolution in the genusEucalyptusis driven by structural rearrangements that promote sequence divergence15
Corrigendum: Cre-dependent Cas9-expressing pigs enable efficient in vivo genome editing15
CoRAL accurately resolves extrachromosomal DNA genome structures with long-read sequencing15
Mitotic chromosomes harbor cell type and species-specific structural features within a universal loop array conformation15
Accurate integration of multiple heterogeneous single-cell RNA-seq data sets by learning contrastive biological variation15
Nucleosome binding by TP53, TP63, and TP73 is determined by the composition, accessibility, and helical orientation of their binding sites15
Commoncis-regulatory variation modifies the penetrance of pathogenicSHROOM3variants in craniofacial microsomia15
Large haplotypes highlight a complex age structure within the maize pan-genome15
A Bayesian framework for inferring dynamic intercellular interactions from time-series single-cell data15
Machine learning identifies activation of RUNX/AP-1 as drivers of mesenchymal and fibrotic regulatory programs in gastric cancer15
The genetics and epigenetics of satellite centromeres15
Assessing and mitigating privacy risks of sparse, noisy genotypes by local alignment to haplotype databases14
Resolving the chromatin impact of mosaic variants with targeted Fiber-seq14
RNA Pol II–dependent transcription efficiency fine-tunes A-to-I editing levels14
Optimizing nanopore adaptive sampling for pneumococcal serotype surveillance in complex samples using the graph-based GNASTy algorithm14
miRNA-like secondary structures in maize (Zea mays) genes and transposable elements correlate with small RNAs, methylation, and expression14
Diverse evolutionary trajectories of mitocoding DNA in mammalian and avian nuclear genomes14
A national long-read sequencing study on chromosomal rearrangements uncovers hidden complexities14
Ultrafast genome-wide inference of pairwise coalescence times14
Corrigendum: Human primitive brain displays negative mitochondrial-nuclear expression correlation of respiratory genes14
Genomic analysis of Rad26 and Rad1–Rad10 reveals differences in their dependence on Mediator and RNA polymerase II14
Continuous infiltration and evolutionary trajectory of nuclear organelle DNA inOryza14
Theoretical framework for the difference of two negative binomial distributions and its application in comparative analysis of sequencing data14
Cytosolic and mitochondrial translation elongation are coordinated through the molecular chaperone TRAP1 for the synthesis and import of mitochondrial proteins14
Listeria monocytogenes genes supporting growth under standard laboratory cultivation conditions and during macrophage infection14
Navigating the landscape of epitranscriptomics and host immunity14
Corrigendum: Enhancer–silencer transitions in the human genome14
RefSeq Functional Elements as experimentally assayed nongenic reference standards and functional interactions in human and mouse14
Genome-wide transcript and protein analysis highlights the role of protein homeostasis in the aging mouse heart14
An organism-wide ATAC-seq peak catalog for the bovine and its use to identify regulatory variants14
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