Genome Research

Article	Citations
De novo reconstruction of satellite repeat units from sequence data	303
Identification of the shortest species-specific oligonucleotide sequences	209
Proxy panels enable privacy-aware outsourcing of genotype imputation	161
Spatially resolved whole transcriptome profiling in human and mouse tissue using Digital Spatial Profiling	121
Comparative genomics ofCryptosporidium parvumreveals the emergence of an outbreak-associated population in Europe and its spread to the United States	113
Short arms of human acrocentric chromosomes and the completion of the human genome sequence	109
Erratum: A butterfly pan-genome reveals that a large amount of structural variation underlies the evolution of chromatin accessibility	87
Inferring and comparing metabolism across heterogeneous sets of annotated genomes using AuCoMe	81
Extremely fast construction and querying of compacted and colored de Bruijn graphs with GGCAT	77
Evaluation ofN6-methyldeoxyadenosine antibody-based genomic profiling in eukaryotes	76
A butterfly pan-genome reveals that a large amount of structural variation underlies the evolution of chromatin accessibility	76
Genome-wide analysis of plant miRNA action clarifies levels of regulatory dynamics across developmental contexts	67
Accurate fusion transcript identification from long- and short-read isoform sequencing at bulk or single-cell resolution	65
Evolutionarily new genes in humans with disease phenotypes reveal functional enrichment patterns shaped by adaptive innovation and sexual selection	64
The role of transposon activity in shapingcis-regulatory element evolution after whole-genome duplication	64
Ancient dog introgression into the Iberian wolf genome may have facilitated adaptation to human-dominated landscapes	62
Leveraging protein language models for accurate multiple sequence alignments	62
Atypical epigenetic and small RNA control of degenerated transposons and their fragments in clonally reproducingSpirodela polyrhiza	62
Allele-specific RNAN6-methyladenosine modifications reveal functional genetic variants in human tissues	60
GenomeMUSter mouse genetic variation service enables multitrait, multipopulation data integration and analysis	59
Accurate transcriptome-wide identification and quantification of alternative polyadenylation from RNA-seq data with APAIQ	58
A Bayesian framework to study tumor subclone–specific expression by combining bulk DNA and single-cell RNA sequencing data	57
Genomic architecture constrained placental mammal X Chromosome evolution	56
Gene by environment interaction mouse model reveals a functional role for 5-hydroxymethylcytosine in neurodevelopmental disorders	56
Genomic environments scale the activities of diverse core promoters	55

Aberrant homeodomain–DNA cooperative dimerization underlies distinct developmental defects in two dominantCRXretinopathy models	54
Telomere-to-telomere assembly by preserving contained reads	54
Dynamic dysregulation of retrotransposons in neurodegenerative diseases at the single-cell level	51
Complete genomes of Asgard archaea reveal diverse integrated and mobile genetic elements	51
High-fidelity, large-scale targeted profiling of microsatellites	50
Factors impacting target-enriched long-read sequencing of resistomes and mobilomes	49
A scalable adaptive quadratic kernel method for interpretable epistasis analysis in complex traits	48
Estrogen receptor 1 chromatin profiling in human breast tumors reveals high inter-patient heterogeneity with enrichment of risk SNPs and enhancer activity at most-conserved regions	48
Comprehensive identification of genomic and environmental determinants of phenotypic plasticity in maize	46
Measuring X-Chromosome inactivation skew for X-linked diseases with adaptive nanopore sequencing	46
An optimized protocol for quality control of gene therapy vectors using nanopore direct RNA sequencing	44
Mosaic loss of Chromosome Y in aged human microglia	44
Probing the eukaryotic microbes of ruminants with a deep-learning classifier and comprehensive protein databases	44
Defining the separation landscape of topological domains for decoding consensus domain organization of the 3D genome	43
Enabling tradeoffs in privacy and utility in genomic data Beacons and summary statistics	43
Single-nucleus transcriptomic mapping uncovers targets for traumatic brain injury	42
The genomic basis of evolutionary differentiation among honey bees	42
Integration site–dependent HIV-1 promoter activity shapes host chromatin conformation	42
Dynamic DNAN6-adenine methylation (6mA) governs the encystment process, showcased in the unicellular eukaryotePseudocohnilembus persalinus	42
Spatial organization of chromosomes leads to heterogeneous chromatin motion and drives the liquid- or gel-like dynamical behavior of chromatin	41
Designing realistic regulatory DNA with autoregressive language models	40
Multiple Pristionchus pacificus genomes reveal distinct evolutionary dynamics between de novo candidates and duplicated genes	40
The Chinese longsnout catfish genome provides novel insights into the feeding preference and corresponding metabolic strategy of carnivores	40
Inferring ancestry with the hierarchical soft clustering approach tangleGen	40
Unraveling the palindromic and nonpalindromic motifs of retroviral integration site sequences by statistical mixture models	39
A naturally occurring variant ofMBD4causes maternal germline hypermutation in primates	39
The genome of the colonial hydroidHydractiniareveals that their stem cells use a toolkit of evolutionarily shared genes with all animals	38
Genome-wide profiling reveals functional interplay of DNA sequence composition, transcriptional activity, and nucleosome positioning in driving DNA supercoiling and helix destabilization in C. eleg	38
Deep sequencing of 1320 genes reveals the landscape of protein-truncating variants and their contribution to psoriasis in 19,973 Chinese individuals	38
Genome-wide relaxation of selection and the evolution of the island syndrome in Orkney voles	37
Erratum: Proving sequence aligners can guarantee accuracy in almostO(mlogn) time through an average-case analysis of the seed-chain-extend heuristic	37
Streamlined spatial and environmental expression signatures characterize the minimalist duckweedWolffia australiana	37
Combinatorial microRNA activity is essential for the transition of pluripotent cells from proliferation into dormancy	37
Corrigendum: Benchmark and integration of resources for the estimation of human transcription factor activities	37
Protein domain embeddings for fast and accurate similarity search	36
Analyzing super-enhancer temporal dynamics reveals potential critical enhancers and their gene regulatory networks underlying skeletal muscle development	36
A machine learning method for the discovery of minimum marker gene combinations for cell type identification from single-cell RNA sequencing	36
AGAPduplicons associate with structural diversity at Chromosome 10q11.22	36
Comprehensive characterization of tissue-specific chromatin accessibility in L2 Caenorhabditis elegans nematodes	36
Global characterization of somatic mutations and DNA methylation changes during vegetative propagation in strawberries	35
Inferring genes that escape X-Chromosome inactivation reveals important contribution of variable escape genes to sex-biased diseases	34
Analysis of a cell-free DNA–based cancer screening cohort links fragmentomic profiles, nuclease levels, and plasma DNA concentrations	34
Rearrangements of viral and human genomes at human papillomavirus integration events and their allele-specific impacts on cancer genome regulation	34
The grasshopper genome reveals long-term gene content conservation of the X Chromosome and temporal variation in X Chromosome evolution	34
Examining dynamics of three-dimensional genome organization with multitask matrix factorization	34
Heterogeneous and novel transcript expression in single cells of patient-derived clear cell renal cell carcinoma organoids	32
De novo detection of somatic variants in high-quality long-read single-cell RNA sequencing data	32
Three-dimensional missense tolerance ratio analysis	31
Parental methylome reprogramming in human uniparental blastocysts reveals germline memory transition	30
Snake venom gene expression is coordinated by novel regulatory architecture and the integration of multiple co-opted vertebrate pathways	29

Positive selection in noncoding genomic regions of vocal learning birds is associated with genes implicated in vocal learning and speech functions in humans	29
Selection and thermostability suggest G-quadruplexes are novel functional elements of the human genome	29
De novo individualized disease modules reveal the synthetic penetrance of genes and inform personalized treatment regimens	29
Genomic context sensitivity of insulator function	28
Characterizing the targets of transcription regulators by aggregating ChIP-seq and perturbation expression data sets	28
Transposable element accumulation drives size differences among polymorphic Y Chromosomes in Drosophila	27
tRNA-derived small RNAs are embedded in the gene regulatory network instructingDrosophilametamorphosis	27
Efficient taxa identification using a pangenome index	27
Assessing transcriptomic reidentification risks using discriminative sequence models	27
Highly complete long-read genomes reveal pangenomic variation underlying yeast phenotypic diversity	27
The aberrant epigenome ofDNMT3B-mutated ICF1 patient iPSCs is amenable to correction, with the exception of a subset of regions with H3K4me3- and/or CTCF-based epigenetic memory	26
Polishing copy number variant calls on exome sequencing data via deep learning	26
Profiling the quantitative occupancy of myriad transcription factors across conditions by modeling chromatin accessibility data	26
Physiological intron retaining transcripts in the cytoplasm abound during human motor neurogenesis	26
Variation in mutation, recombination, and transposition rates inDrosophila melanogasterandDrosophila simulans	25
A general framework for identifying oligogenic combinations of rare variants in complex disorders	25
Transposon wave remodeled the epigenomic landscape in the rapid evolution of X-Chromosome dosage compensation	25
Elasmobranch genome sequencing reveals evolutionary trends of vertebrate karyotype organization	25
Comparing genomic and epigenomic features across species using the WashU Comparative Epigenome Browser	25
Learning probabilistic protein–DNA recognition codes from DNA-binding specificities using structural mappings	25
Characterization of human transcription factor function and patterns of gene regulation in HepG2 cells	24
Locus-resolution analysis of L1 regulation and retrotransposition potential in mouse embryonic development	24
Analyses of 600+ insect genomes reveal repetitive element dynamics and highlight biodiversity-scale repeat annotation challenges	24
Extensive protein dosage compensation in aneuploid human cancers	24
Loss of epigenetic suppression of retrotransposons with oncogenic potential in aging mammary luminal epithelial cells	24
Functional noncoding SNPs in human endothelial cells fine-map vascular trait associations	24
The pig pangenome provides insights into the roles of coding structural variations in genetic diversity and adaptation	24
A statistical physics approach for disease module detection	24
Fast inference of genetic recombination rates in biobank scale data	24
A chromosome-scale epigenetic map of theHydragenome reveals conserved regulators of cell state	24
Characterizing tandem repeat complexities across long-read sequencing platforms with TREAT andotter	24
Cancer-associated dynamics and potential regulators of intronic polyadenylation revealed by IPAFinder using standard RNA-seq data	23
Characteristics, origin, and potential for cancer diagnostics of ultrashort plasma cell-free DNA	22
Epigenomic analysis reveals prevalent contribution of transposable elements to cis-regulatory elements, tissue-specific expression, and alternative promoters in zebrafish	22
Reevaluation of the Toxoplasma gondii and Neospora caninum genomes reveals misassembly, karyotype differences, and chromosomal rearrangements	22
A fast and scalable method for inferring phylogenetic networks from trees by aligning lineage taxon strings	22
A ChIP-exo screen of 887 Protein Capture Reagents Program transcription factor antibodies in human cells	22
Genome-wide promoter assembly in E. coli measured at single-base resolution	22
Quality assessment of long read data in multisample lrRNA-seq experiments using SQANTI-reads	21
Complete sequencing of a cynomolgus macaque major histocompatibility complex haplotype	21
Population genomics reveals mechanisms and dynamics of de novo expressed open reading frame emergence inDrosophila melanogaster	21
De novo antibody identification in human blood from full-length single B cell transcriptomics and matching haplotype-resolved germline assemblies	21
Genome enrichment of rare and unknown species from complicated microbiomes by nanopore selective sequencing	21
High-throughput and genome-scale targeted mutagenesis using CRISPR in a nonmodel multicellular organism,Bombyx mori	21
A joint deep learning model enables simultaneous batch effect correction, denoising, and clustering in single-cell transcriptomics	21
An efficient method to identify, date, and describe admixture events using haplotype information	21
Evaluation of strategies for evidence-driven genome annotation using long-read RNA-seq	21
The Enterprise, a massive transposon carrying Spok meiotic drive genes	21
A framework to score the effects of structural variants in health and disease	21
Meta-analysis of human and mouse ALS astrocytes reveals multi-omic signatures of inflammatory reactive states	21
Epigenomic translocation of H3K4me3 broad domains over oncogenes following hijacking of super-enhancers	20
Taurine pangenome uncovers a segmental duplication upstream ofKITassociated with depigmentation in white-headed cattle	20
The human ribosomal DNA array is composed of highly homogenized tandem clusters	20
Understanding isoform expression by pairing long-read sequencing with single-cell and spatial transcriptomics	20
A sheep pangenome reveals the spectrum of structural variations and their effects on tail phenotypes	20
Dynamics of broad H3K4me3 domains uncover an epigenetic switch between cell identity and cancer-related genes	20
An association test of the spatial distribution of rare missense variants within protein structures identifies Alzheimer's disease–related patterns	19
Characterizing nucleotide variation and expansion dynamics in human-specific variable number tandem repeats	19
Rtt109 promotes nucleosome replacement ahead of the replication fork	19
Global loss of cellular m6A RNA methylation following infection with different SARS-CoV-2 variants	19
Extensive sampling of Saccharomyces cerevisiae in Taiwan reveals ecology and evolution of predomesticated lineages	19
Mendelian randomization analyses implicate biogenesis of translation machinery in human aging	19
Analyzing rare mutations in metagenomes assembled using long and accurate reads	19
Efficient mapping of accurate long reads in minimizer space with mapquik	18
Transposable element variants and their potential adaptive impact in urban populations of the malaria vector Anopheles coluzzii	18
A Chinese indicine pangenome reveals a wealth of novel structural variants introgressed from otherBosspecies	18
Localizing unmapped sequences with families to validate the Telomere-to-Telomere assembly and identify new hotspots for genetic diversity	18
Density separation of petrous bone powders for optimized ancient DNA yields	18
Corrigendum: An association test of the spatial distribution of rare missense variants within protein structures identifies Alzheimer's disease–related patterns	18
Accurate and fast graph-based pangenome annotation and clustering with ggCaller	18
A curated collection of Klebsiella metabolic models reveals variable substrate usage and gene essentiality	18
Discordant calls across genotype discovery approaches elucidate variants with systematic errors	18
A novel quantitative trait locus implicatesMsh3in the propensity for genome-wide short tandem repeat expansions in mice	18
Identifying cell state–associated alternative splicing events and their coregulation	18
Transcriptional milestones in Dictyostelium development	17
Graph-based self-supervised learning for repeat detection in metagenomic assembly	17
Accurate assembly of circular RNAs with TERRACE	17
Large palindromes on the primate X Chromosome are preserved by natural selection	17
Different trajectories of polyploidization shape the genomic landscape of theBrettanomyces bruxellensisyeast species	17
Historical RNA expression profiles from the extinct Tasmanian tiger	17

Long-read subcellular fractionation and sequencing reveals the translational fate of full-length mRNA isoforms during neuronal differentiation	17
Likelihood-based deconvolution of bulk gene expression data using single-cell references	17
Global compositional and functional states of the human gut microbiome in health and disease	17
The chromatin tapestry as a framework for neurodevelopment	16
Long-read genome assembly of the insect model organismTribolium castaneumreveals spread of satellite DNA in gene-rich regions by recurrent burst events	16
Joint actions of diverse transcription factor families establish neuron-type identities and promote enhancer selectivity	16
H3K36 dimethylation shapes the epigenetic interaction landscape by directing repressive chromatin modifications in embryonic stem cells	16
Multisample motif discovery and visualization for tandem repeats	16
Thousands of human mutation clusters are explained by short-range template switching	16
Construction and evaluation of a new rat reference genome assembly, GRCr8, from long reads and long-range scaffolding	15
Parameter-efficient fine-tuning on large protein language models improves signal peptide prediction	15
The predicted RNA-binding protein regulome of axonal mRNAs	15
Spatial Cellular Networks from omics data with SpaCeNet	15
Third-generation sequencing revises the molecular karyotype for Toxoplasma gondii and identifies emerging copy number variants in sexual recombinants	15
Inferring disease progression stages in single-cell transcriptomics using a weakly supervised deep learning approach	15
Leveraging family data to design Mendelian randomization that is provably robust to population stratification	15
Linking the dynamics of chromatin occupancy and transcription with predictive models	15
Chromatin interaction maps identify oncogenic targets of enhancer duplications in cancer	15
A KMT2A-AFF1 gene regulatory network highlights the role of core transcription factors and reveals the regulatory logic of key downstream target genes	15
Widespread association of the Argonaute protein AGO2 with meiotic chromatin suggests a distinct nuclear function in mammalian male reproduction	15
Entropy predicts sensitivity of pseudorandom seeds	15
Partial alignment of multislice spatially resolved transcriptomics data	15
Transcriptome innovations in primates revealed by single-molecule long-read sequencing	15
Long-read RNA sequencing reveals widespread sex-specific alternative splicing in threespine stickleback fish	15
Rapid evolution of piRNA clusters in theDrosophila melanogasterovary	14
Transposable elements drive the evolution of metazoan zinc finger genes	14
A prospective trial comparing programmable targeted long-read sequencing and short-read genome sequencing for genetic diagnosis of cerebellar ataxia	14
Rapid SARS-CoV-2 surveillance using clinical, pooled, or wastewater sequence as a sensor for population change	14
Long-read Ribo-STAMP simultaneously measures transcription and translation with isoform resolution	14
Probabilistic association of differentially expressed genes withcis-regulatory elements	14
A HIT-trapping strategy for rapid generation of reversible and conditional alleles using a universal donor	14
Unraveling the hidden complexity of cancer through long-read sequencing	14
A novel approach for in vivo DNA footprinting using short double-stranded cell-free DNA from plasma	14
The rate and spectrum of new mutations in mice inferred by long-read sequencing	14
Artificial intelligence and machine learning in cell-free-DNA-based diagnostics	14
Ribosome decision graphs for the representation of eukaryotic RNA translation complexity	14
Accelerated somatic mutation calling for whole-genome and whole-exome sequencing data from heterogenous tumor samples	14
A somatic hypermutation–based machine learning model stratifies individuals with Crohn's disease and controls	14
Conserved noncoding sequences provide insights into regulatory sequence and loss of gene expression in maize	14
Profiling single-cell histone modifications using indexing chromatin immunocleavage sequencing	14
Automated annotation of human centromeres with HORmon	14