Genome Research

Article	Citations
A general framework for identifying oligogenic combinations of rare variants in complex disorders	253
Deep sequencing of 1320 genes reveals the landscape of protein-truncating variants and their contribution to psoriasis in 19,973 Chinese individuals	179
Accurate transcriptome-wide identification and quantification of alternative polyadenylation from RNA-seq data with APAIQ	134
Highly complete long-read genomes reveal pangenomic variation underlying yeast phenotypic diversity	106
Extensive protein dosage compensation in aneuploid human cancers	100
Combinatorial microRNA activity is essential for the transition of pluripotent cells from proliferation into dormancy	92
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	75
Allele-specific RNAN6-methyladenosine modifications reveal functional genetic variants in human tissues	68
A Bayesian framework to study tumor subclone–specific expression by combining bulk DNA and single-cell RNA sequencing data	68
Gene by environment interaction mouse model reveals a functional role for 5-hydroxymethylcytosine in neurodevelopmental disorders	67
Enabling tradeoffs in privacy and utility in genomic data Beacons and summary statistics	66
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	64
Reevaluation of the Toxoplasma gondii and Neospora caninum genomes reveals misassembly, karyotype differences, and chromosomal rearrangements	63
An efficient method to identify, date, and describe admixture events using haplotype information	61
Spatially resolved whole transcriptome profiling in human and mouse tissue using Digital Spatial Profiling	60
Defining the separation landscape of topological domains for decoding consensus domain organization of the 3D genome	58
Characterizing the targets of transcription regulators by aggregating ChIP-seq and perturbation expression data sets	54
Unraveling the palindromic and nonpalindromic motifs of retroviral integration site sequences by statistical mixture models	54
De novo individualized disease modules reveal the synthetic penetrance of genes and inform personalized treatment regimens	51
GenomeMUSter mouse genetic variation service enables multitrait, multipopulation data integration and analysis	51
tRNA-derived small RNAs are embedded in the gene regulatory network instructingDrosophilametamorphosis	51
Genome-wide promoter assembly in E. coli measured at single-base resolution	50
Designing realistic regulatory DNA with autoregressive language models	48
A scalable adaptive quadratic kernel method for interpretable epistasis analysis in complex traits	48
Comprehensive identification of genomic and environmental determinants of phenotypic plasticity in maize	48

Protein domain embeddings for fast and accurate similarity search	48
Erratum: A butterfly pan-genome reveals that a large amount of structural variation underlies the evolution of chromatin accessibility	47
A joint deep learning model enables simultaneous batch effect correction, denoising, and clustering in single-cell transcriptomics	46
Erratum: Proving sequence aligners can guarantee accuracy in almostO(mlogn) time through an average-case analysis of the seed-chain-extend heuristic	46
Mosaic loss of Chromosome Y in aged human microglia	46
Parental methylome reprogramming in human uniparental blastocysts reveals germline memory transition	45
High-throughput and genome-scale targeted mutagenesis using CRISPR in a nonmodel multicellular organism,Bombyx mori	45
Efficient taxa identification using a pangenome index	44
Genomic context sensitivity of insulator function	44
Profiling the quantitative occupancy of myriad transcription factors across conditions by modeling chromatin accessibility data	44
Epigenomic analysis reveals prevalent contribution of transposable elements to cis-regulatory elements, tissue-specific expression, and alternative promoters in zebrafish	43
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	43
A statistical physics approach for disease module detection	42
The pig pangenome provides insights into the roles of coding structural variations in genetic diversity and adaptation	42
Spatial organization of chromosomes leads to heterogeneous chromatin motion and drives the liquid- or gel-like dynamical behavior of chromatin	42
Population genomics reveals mechanisms and dynamics of de novo expressed open reading frame emergence inDrosophila melanogaster	41
Genomic architecture constrained placental mammal X Chromosome evolution	40
Characteristics, origin, and potential for cancer diagnostics of ultrashort plasma cell-free DNA	40
Leveraging protein language models for accurate multiple sequence alignments	39
A framework to score the effects of structural variants in health and disease	39
Functional noncoding SNPs in human endothelial cells fine-map vascular trait associations	39
Evaluation ofN6-methyldeoxyadenosine antibody-based genomic profiling in eukaryotes	38
A fast and scalable method for inferring phylogenetic networks from trees by aligning lineage taxon strings	38
Genome-wide analysis of plant miRNA action clarifies levels of regulatory dynamics across developmental contexts	37
Assessing transcriptomic reidentification risks using discriminative sequence models	36
Fast inference of genetic recombination rates in biobank scale data	36
Three-dimensional missense tolerance ratio analysis	36
Genome-wide relaxation of selection and the evolution of the island syndrome in Orkney voles	35
Inferring ancestry with the hierarchical soft clustering approach tangleGen	35
Comparative genomics ofCryptosporidium parvumreveals the emergence of an outbreak-associated population in Europe and its spread to the United States	35
Taurine pangenome uncovers a segmental duplication upstream ofKITassociated with depigmentation in white-headed cattle	35
Evaluation of strategies for evidence-driven genome annotation using long-read RNA-seq	34
Analyzing super-enhancer temporal dynamics reveals potential critical enhancers and their gene regulatory networks underlying skeletal muscle development	34
The genome of the colonial hydroidHydractiniareveals that their stem cells use a toolkit of evolutionarily shared genes with all animals	33
Selection and thermostability suggest G-quadruplexes are novel functional elements of the human genome	33
Physiological intron retaining transcripts in the cytoplasm abound during human motor neurogenesis	33
A naturally occurring variant ofMBD4causes maternal germline hypermutation in primates	33
Genomic analyses provide insights into peach local adaptation and responses to climate change	33
Inferring and comparing metabolism across heterogeneous sets of annotated genomes using AuCoMe	33
Probing the eukaryotic microbes of ruminants with a deep-learning classifier and comprehensive protein databases	33
Integration site–dependent HIV-1 promoter activity shapes host chromatin conformation	32
Positive selection in noncoding genomic regions of vocal learning birds is associated with genes implicated in vocal learning and speech functions in humans	32
Comparing genomic and epigenomic features across species using the WashU Comparative Epigenome Browser	32
Inferring genes that escape X-Chromosome inactivation reveals important contribution of variable escape genes to sex-biased diseases	32
Multiple Pristionchus pacificus genomes reveal distinct evolutionary dynamics between de novo candidates and duplicated genes	32
Variation in mutation, recombination, and transposition rates inDrosophila melanogasterandDrosophila simulans	30
Transposable element accumulation drives size differences among polymorphic Y Chromosomes in Drosophila	30
Transposon wave remodeled the epigenomic landscape in the rapid evolution of X-Chromosome dosage compensation	29
The Enterprise, a massive transposon carrying Spok meiotic drive genes	28
The human ribosomal DNA array is composed of highly homogenized tandem clusters	28

The genomic basis of evolutionary differentiation among honey bees	28
De novo reconstruction of satellite repeat units from sequence data	28
Comprehensive characterization of tissue-specific chromatin accessibility in L2 Caenorhabditis elegans nematodes	27
The Chinese longsnout catfish genome provides novel insights into the feeding preference and corresponding metabolic strategy of carnivores	27
The grasshopper genome reveals long-term gene content conservation of the X Chromosome and temporal variation in X Chromosome evolution	27
High-fidelity, large-scale targeted profiling of microsatellites	27
Streamlined spatial and environmental expression signatures characterize the minimalist duckweedWolffia australiana	27
AGAPduplicons associate with structural diversity at Chromosome 10q11.22	26
Dynamic dysregulation of retrotransposons in neurodegenerative diseases at the single-cell level	26
Complete genomes of Asgard archaea reveal diverse integrated and mobile genetic elements	26
Global characterization of somatic mutations and DNA methylation changes during vegetative propagation in strawberries	26
Polishing copy number variant calls on exome sequencing data via deep learning	25
Loss of epigenetic suppression of retrotransposons with oncogenic potential in aging mammary luminal epithelial cells	25
A ChIP-exo screen of 887 Protein Capture Reagents Program transcription factor antibodies in human cells	25
Learning probabilistic protein–DNA recognition codes from DNA-binding specificities using structural mappings	25
A chromosome-scale epigenetic map of theHydragenome reveals conserved regulators of cell state	25
Characterization of human transcription factor function and patterns of gene regulation in HepG2 cells	25
Sir3 mediates long-range chromosome interactions in budding yeast	24
Meta-analysis of human and mouse ALS astrocytes reveals multi-omic signatures of inflammatory reactive states	24
A butterfly pan-genome reveals that a large amount of structural variation underlies the evolution of chromatin accessibility	23
A sheep pangenome reveals the spectrum of structural variations and their effects on tail phenotypes	23
Analyses of 600+ insect genomes reveal repetitive element dynamics and highlight biodiversity-scale repeat annotation challenges	22
Genomic environments scale the activities of diverse core promoters	22
Locus-resolution analysis of L1 regulation and retrotransposition potential in mouse embryonic development	22
Complete sequencing of a cynomolgus macaque major histocompatibility complex haplotype	22
Extremely fast construction and querying of compacted and colored de Bruijn graphs with GGCAT	21
Short arms of human acrocentric chromosomes and the completion of the human genome sequence	21
Dynamics of broad H3K4me3 domains uncover an epigenetic switch between cell identity and cancer-related genes	21
Elasmobranch genome sequencing reveals evolutionary trends of vertebrate karyotype organization	21
Cancer-associated dynamics and potential regulators of intronic polyadenylation revealed by IPAFinder using standard RNA-seq data	21
Snake venom gene expression is coordinated by novel regulatory architecture and the integration of multiple co-opted vertebrate pathways	21
Corrigendum: Benchmark and integration of resources for the estimation of human transcription factor activities	21
Genome enrichment of rare and unknown species from complicated microbiomes by nanopore selective sequencing	21
A minimally destructive protocol for DNA extraction from ancient teeth	21
DNA methylation epitypes highlight underlying developmental and disease pathways in acute myeloid leukemia	21
Dynamic DNAN6-adenine methylation (6mA) governs the encystment process, showcased in the unicellular eukaryotePseudocohnilembus persalinus	20
A machine learning method for the discovery of minimum marker gene combinations for cell type identification from single-cell RNA sequencing	20
Characterizing tandem repeat complexities across long-read sequencing platforms with TREAT andotter	20
Single-nucleus transcriptomic mapping uncovers targets for traumatic brain injury	20
Measuring X-Chromosome inactivation skew for X-linked diseases with adaptive nanopore sequencing	19
Understanding isoform expression by pairing long-read sequencing with single-cell and spatial transcriptomics	19
An optimized protocol for quality control of gene therapy vectors using nanopore direct RNA sequencing	19
Proxy panels enable privacy-aware outsourcing of genotype imputation	19
Factors impacting target-enriched long-read sequencing of resistomes and mobilomes	19
Rearrangements of viral and human genomes at human papillomavirus integration events and their allele-specific impacts on cancer genome regulation	19
Telomere-to-telomere assembly by preserving contained reads	19
Analysis of a cell-free DNA–based cancer screening cohort links fragmentomic profiles, nuclease levels, and plasma DNA concentrations	18
Sequence-based correction of barcode bias in massively parallel reporter assays	18
Accelerated somatic mutation calling for whole-genome and whole-exome sequencing data from heterogenous tumor samples	18
Aberrant homeodomain–DNA cooperative dimerization underlies distinct developmental defects in two dominantCRXretinopathy models	18
Diverse tumorigenic consequences of human papillomavirus integration in primary oropharyngeal cancers	18
A plug and play microfluidic platform for standardized sensitive low-input chromatin immunoprecipitation	18
Identification of the shortest species-specific oligonucleotide sequences	18
Low-frequency somatic copy number alterations in normal human lymphocytes revealed by large-scale single-cell whole-genome profiling	18
Spatiotemporal kinetics of CAF-1-dependent chromatin maturation ensures transcription fidelity during S-phase	18
Characterization of the distribution and dynamics of chromatin states in theC. elegansgermline reveals substantial H3K4me3 remodeling during oogenesis	18
ZNF91 deletion in human embryonic stem cells leads to ectopic activation of SVA retrotransposons and up-regulation of KRAB zinc finger gene clusters	17
Localizing unmapped sequences with families to validate the Telomere-to-Telomere assembly and identify new hotspots for genetic diversity	17
Multisample motif discovery and visualization for tandem repeats	17
Widespread association of the Argonaute protein AGO2 with meiotic chromatin suggests a distinct nuclear function in mammalian male reproduction	17
Probabilistic association of differentially expressed genes withcis-regulatory elements	17
The predicted RNA-binding protein regulome of axonal mRNAs	17
SARS-CoV-2 genomic diversity and the implications for qRT-PCR diagnostics and transmission	17
Ribosome decision graphs for the representation of eukaryotic RNA translation complexity	17
Profiling single-cell histone modifications using indexing chromatin immunocleavage sequencing	17
A somatic hypermutation–based machine learning model stratifies individuals with Crohn's disease and controls	17
Automated annotation of human centromeres with HORmon	17
Conserved noncoding sequences provide insights into regulatory sequence and loss of gene expression in maize	17
Genome-wide patterns of selection–drift variation strongly associate with organismal traits across the green plant lineage	16
Accurate assembly of circular RNAs with TERRACE	16
Ligand-induced native G-quadruplex stabilization impairs transcription initiation	16
A KMT2A-AFF1 gene regulatory network highlights the role of core transcription factors and reveals the regulatory logic of key downstream target genes	16
Graph-based self-supervised learning for repeat detection in metagenomic assembly	16
Spatial Cellular Networks from omics data with SpaCeNet	16
A graph neural network model to estimate cell-wise metabolic flux using single-cell RNA-seq data	16
A novel approach for in vivo DNA footprinting using short double-stranded cell-free DNA from plasma	16
Parameter-efficient fine-tuning on large protein language models improves signal peptide prediction	16
Rtt109 promotes nucleosome replacement ahead of the replication fork	16
Deciphering D4Z4 CpG methylation gradients in fascioscapulohumeral muscular dystrophy using nanopore sequencing	16
Corrigendum: An association test of the spatial distribution of rare missense variants within protein structures identifies Alzheimer's disease–related patterns	15

Joint actions of diverse transcription factor families establish neuron-type identities and promote enhancer selectivity	15
A complete pedigree-based graph workflow for rare candidate variant analysis	15
Historical RNA expression profiles from the extinct Tasmanian tiger	15
A Chinese indicine pangenome reveals a wealth of novel structural variants introgressed from otherBosspecies	15
Global compositional and functional states of the human gut microbiome in health and disease	15
Analyzing rare mutations in metagenomes assembled using long and accurate reads	15
Linking the dynamics of chromatin occupancy and transcription with predictive models	15
Enhancers with tissue-specific activity are enriched in intronic regions	15
Genome-wide chromatin interaction profiling reveals a vital role of super-enhancers and rearrangements in host enhancer contacts during BmNPV infection	14
Transposable elements drive the evolution of metazoan zinc finger genes	14
De novo transcriptome assembly of mouse male germ cells reveals novel genes, stage-specific bidirectional promoter activity, and noncoding RNA expression	14
Different trajectories of polyploidization shape the genomic landscape of theBrettanomyces bruxellensisyeast species	14
Mendelian randomization analyses implicate biogenesis of translation machinery in human aging	14
Modeling expression ranks for noise-tolerant differential expression analysis of scRNA-seq data	14
Genome-scale targeted mutagenesis inBrassica napususing a pooled CRISPR library	14
Suv39h-catalyzed H3K9me3 is critical for euchromatic genome organization and the maintenance of gene transcription	14
A curated collection of Klebsiella metabolic models reveals variable substrate usage and gene essentiality	14
Epigenomic translocation of H3K4me3 broad domains over oncogenes following hijacking of super-enhancers	14
Transcription initiation mapping in 31 bovine tissues reveals complex promoter activity, pervasive transcription, and tissue-specific promoter usage	14
Nanopore-based consensus sequencing enables accurate multimodal tumor cell-free DNA profiling	14
ZSWIM8 destabilizes many murine microRNAs and is required for proper embryonic growth and development	14
An association test of the spatial distribution of rare missense variants within protein structures identifies Alzheimer's disease–related patterns	13
Large palindromes on the primate X Chromosome are preserved by natural selection	13
Entropy predicts sensitivity of pseudorandom seeds	13
Modeling and predicting cancer clonal evolution with reinforcement learning	13
A HIT-trapping strategy for rapid generation of reversible and conditional alleles using a universal donor	13
Revisiting chromatin packaging in mouse sperm	13
Characterizing nucleotide variation and expansion dynamics in human-specific variable number tandem repeats	13
Third-generation sequencing revises the molecular karyotype for Toxoplasma gondii and identifies emerging copy number variants in sexual recombinants	13
Discordant calls across genotype discovery approaches elucidate variants with systematic errors	13
Transcriptional milestones in Dictyostelium development	13
H3K36 dimethylation shapes the epigenetic interaction landscape by directing repressive chromatin modifications in embryonic stem cells	13
Efficient mapping of accurate long reads in minimizer space with mapquik	13
A novel quantitative trait locus implicatesMsh3in the propensity for genome-wide short tandem repeat expansions in mice	13