Genome Research

Article	Citations
A general framework for identifying oligogenic combinations of rare variants in complex disorders	281
Deep sequencing of 1320 genes reveals the landscape of protein-truncating variants and their contribution to psoriasis in 19,973 Chinese individuals	253
Accurate transcriptome-wide identification and quantification of alternative polyadenylation from RNA-seq data with APAIQ	179
Highly complete long-read genomes reveal pangenomic variation underlying yeast phenotypic diversity	134
Extensive protein dosage compensation in aneuploid human cancers	106
Combinatorial microRNA activity is essential for the transition of pluripotent cells from proliferation into dormancy	100
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	92
Allele-specific RNAN6-methyladenosine modifications reveal functional genetic variants in human tissues	75
A Bayesian framework to study tumor subclone–specific expression by combining bulk DNA and single-cell RNA sequencing data	69
Enabling tradeoffs in privacy and utility in genomic data Beacons and summary statistics	68
Gene by environment interaction mouse model reveals a functional role for 5-hydroxymethylcytosine in neurodevelopmental disorders	68
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	67
Reevaluation of the Toxoplasma gondii and Neospora caninum genomes reveals misassembly, karyotype differences, and chromosomal rearrangements	66
An efficient method to identify, date, and describe admixture events using haplotype information	64
Spatially resolved whole transcriptome profiling in human and mouse tissue using Digital Spatial Profiling	64
Defining the separation landscape of topological domains for decoding consensus domain organization of the 3D genome	63
Unraveling the palindromic and nonpalindromic motifs of retroviral integration site sequences by statistical mixture models	61
Characterizing the targets of transcription regulators by aggregating ChIP-seq and perturbation expression data sets	60
De novo individualized disease modules reveal the synthetic penetrance of genes and inform personalized treatment regimens	58
tRNA-derived small RNAs are embedded in the gene regulatory network instructingDrosophilametamorphosis	56
GenomeMUSter mouse genetic variation service enables multitrait, multipopulation data integration and analysis	55
Genome-wide promoter assembly in E. coli measured at single-base resolution	54
Comprehensive identification of genomic and environmental determinants of phenotypic plasticity in maize	54
A scalable adaptive quadratic kernel method for interpretable epistasis analysis in complex traits	51
Protein domain embeddings for fast and accurate similarity search	51

Designing realistic regulatory DNA with autoregressive language models	51
Erratum: A butterfly pan-genome reveals that a large amount of structural variation underlies the evolution of chromatin accessibility	50
Mosaic loss of Chromosome Y in aged human microglia	48
Parental methylome reprogramming in human uniparental blastocysts reveals germline memory transition	48
A joint deep learning model enables simultaneous batch effect correction, denoising, and clustering in single-cell transcriptomics	48
Erratum: Proving sequence aligners can guarantee accuracy in almostO(mlogn) time through an average-case analysis of the seed-chain-extend heuristic	48
High-throughput and genome-scale targeted mutagenesis using CRISPR in a nonmodel multicellular organism,Bombyx mori	47
Efficient taxa identification using a pangenome index	46
Profiling the quantitative occupancy of myriad transcription factors across conditions by modeling chromatin accessibility data	46
Genomic context sensitivity of insulator function	46
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	45
Epigenomic analysis reveals prevalent contribution of transposable elements to cis-regulatory elements, tissue-specific expression, and alternative promoters in zebrafish	45
A statistical physics approach for disease module detection	44
The pig pangenome provides insights into the roles of coding structural variations in genetic diversity and adaptation	44
Spatial organization of chromosomes leads to heterogeneous chromatin motion and drives the liquid- or gel-like dynamical behavior of chromatin	44
Characteristics, origin, and potential for cancer diagnostics of ultrashort plasma cell-free DNA	43
Population genomics reveals mechanisms and dynamics of de novo expressed open reading frame emergence inDrosophila melanogaster	43
Leveraging protein language models for accurate multiple sequence alignments	42
Genomic architecture constrained placental mammal X Chromosome evolution	42
Functional noncoding SNPs in human endothelial cells fine-map vascular trait associations	42
A framework to score the effects of structural variants in health and disease	41
Evaluation ofN6-methyldeoxyadenosine antibody-based genomic profiling in eukaryotes	40
A fast and scalable method for inferring phylogenetic networks from trees by aligning lineage taxon strings	40
Genome-wide analysis of plant miRNA action clarifies levels of regulatory dynamics across developmental contexts	39
Assessing transcriptomic reidentification risks using discriminative sequence models	39
Fast inference of genetic recombination rates in biobank scale data	39
Three-dimensional missense tolerance ratio analysis	38
Comparative genomics ofCryptosporidium parvumreveals the emergence of an outbreak-associated population in Europe and its spread to the United States	38
Genome-wide relaxation of selection and the evolution of the island syndrome in Orkney voles	37
Evaluation of strategies for evidence-driven genome annotation using long-read RNA-seq	36
Inferring ancestry with the hierarchical soft clustering approach tangleGen	36
Taurine pangenome uncovers a segmental duplication upstream ofKITassociated with depigmentation in white-headed cattle	36
Analyzing super-enhancer temporal dynamics reveals potential critical enhancers and their gene regulatory networks underlying skeletal muscle development	36
Accurate and efficient detection of gene fusions from RNA sequencing data	35
Probing the eukaryotic microbes of ruminants with a deep-learning classifier and comprehensive protein databases	35
Selection and thermostability suggest G-quadruplexes are novel functional elements of the human genome	35
Aberrant homeodomain-DNA cooperative dimerization underlies distinct developmental defects in two dominantCRXretinopathy models	35
A naturally occurring variant ofMBD4causes maternal germline hypermutation in primates	34
Genomic analyses provide insights into peach local adaptation and responses to climate change	34
Integration site–dependent HIV-1 promoter activity shapes host chromatin conformation	33
Multiple Pristionchus pacificus genomes reveal distinct evolutionary dynamics between de novo candidates and duplicated genes	33
Inferring genes that escape X-Chromosome inactivation reveals important contribution of variable escape genes to sex-biased diseases	33
Physiological intron retaining transcripts in the cytoplasm abound during human motor neurogenesis	33
The genome of the colonial hydroidHydractiniareveals that their stem cells use a toolkit of evolutionarily shared genes with all animals	33
Inferring and comparing metabolism across heterogeneous sets of annotated genomes using AuCoMe	33
Comparing genomic and epigenomic features across species using the WashU Comparative Epigenome Browser	33
Transposon wave remodeled the epigenomic landscape in the rapid evolution of X-Chromosome dosage compensation	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
Variation in mutation, recombination, and transposition rates inDrosophila melanogasterandDrosophila simulans	32
The genomic basis of evolutionary differentiation among honey bees	32

Transposable element accumulation drives size differences among polymorphic Y Chromosomes in Drosophila	32
The Enterprise, a massive transposon carrying Spok meiotic drive genes	31
De novo reconstruction of satellite repeat units from sequence data	30
Comprehensive characterization of tissue-specific chromatin accessibility in L2 Caenorhabditis elegans nematodes	30
The human ribosomal DNA array is composed of highly homogenized tandem clusters	30
The Chinese longsnout catfish genome provides novel insights into the feeding preference and corresponding metabolic strategy of carnivores	29
The grasshopper genome reveals long-term gene content conservation of the X Chromosome and temporal variation in X Chromosome evolution	28
Streamlined spatial and environmental expression signatures characterize the minimalist duckweedWolffia australiana	28
Dynamic dysregulation of retrotransposons in neurodegenerative diseases at the single-cell level	28
High-fidelity, large-scale targeted profiling of microsatellites	28
A ChIP-exo screen of 887 Protein Capture Reagents Program transcription factor antibodies in human cells	27
Complete genomes of Asgard archaea reveal diverse integrated and mobile genetic elements	27
Polishing copy number variant calls on exome sequencing data via deep learning	27
Global characterization of somatic mutations and DNA methylation changes during vegetative propagation in strawberries	27
A chromosome-scale epigenetic map of theHydragenome reveals conserved regulators of cell state	27
AGAPduplicons associate with structural diversity at Chromosome 10q11.22	27
Loss of epigenetic suppression of retrotransposons with oncogenic potential in aging mammary luminal epithelial cells	26
Learning probabilistic protein–DNA recognition codes from DNA-binding specificities using structural mappings	26
Sir3 mediates long-range chromosome interactions in budding yeast	26
Characterization of human transcription factor function and patterns of gene regulation in HepG2 cells	26
Complete sequencing of a cynomolgus macaque major histocompatibility complex haplotype	25
Elasmobranch genome sequencing reveals evolutionary trends of vertebrate karyotype organization	25
Genomic environments scale the activities of diverse core promoters	25
Genome enrichment of rare and unknown species from complicated microbiomes by nanopore selective sequencing	25
Analyses of 600+ insect genomes reveal repetitive element dynamics and highlight biodiversity-scale repeat annotation challenges	25
Corrigendum: Benchmark and integration of resources for the estimation of human transcription factor activities	25
Cancer-associated dynamics and potential regulators of intronic polyadenylation revealed by IPAFinder using standard RNA-seq data	24
Extremely fast construction and querying of compacted and colored de Bruijn graphs with GGCAT	24
Short arms of human acrocentric chromosomes and the completion of the human genome sequence	23
Dynamics of broad H3K4me3 domains uncover an epigenetic switch between cell identity and cancer-related genes	23
A machine learning method for the discovery of minimum marker gene combinations for cell type identification from single-cell RNA sequencing	22
Snake venom gene expression is coordinated by novel regulatory architecture and the integration of multiple co-opted vertebrate pathways	22
DNA methylation epitypes highlight underlying developmental and disease pathways in acute myeloid leukemia	22
A minimally destructive protocol for DNA extraction from ancient teeth	22
Single-nucleus transcriptomic mapping uncovers targets for traumatic brain injury	21
Analysis of a cell-free DNA-based cancer screening cohort links fragmentomic profiles, nuclease levels, and plasma DNA concentrations	21
Understanding isoform expression by pairing long-read sequencing with single-cell and spatial transcriptomics	21
Characterizing tandem repeat complexities across long-read sequencing platforms with TREAT andotter	21
Allele-specific alternative splicing and its functional genetic variants in human tissues	21
Telomere-to-telomere assembly by preserving contained reads	21
An optimized protocol for quality control of gene therapy vectors using nanopore direct RNA sequencing	21
Dynamic DNAN6-adenine methylation (6mA) governs the encystment process, showcased in the unicellular eukaryotePseudocohnilembus persalinus	21
Measuring X-Chromosome inactivation skew for X-linked diseases with adaptive nanopore sequencing	21
Factors impacting target-enriched long-read sequencing of resistomes and mobilomes	21
A sheep pangenome reveals the spectrum of structural variations and their effects on tail phenotypes	20
Rearrangements of viral and human genomes at human papillomavirus integration events and their allele-specific impacts on cancer genome regulation	20
A butterfly pan-genome reveals that a large amount of structural variation underlies the evolution of chromatin accessibility	20
Locus-resolution analysis of L1 regulation and retrotransposition potential in mouse embryonic development	20
Meta-analysis of human and mouse ALS astrocytes reveals multi-omic signatures of inflammatory reactive states	20
Diverse tumorigenic consequences of human papillomavirus integration in primary oropharyngeal cancers	19
Spatiotemporal kinetics of CAF-1-dependent chromatin maturation ensures transcription fidelity during S-phase	19
Conserved noncoding sequences provide insights into regulatory sequence and loss of gene expression in maize	19
Sequence-based correction of barcode bias in massively parallel reporter assays	19
Low-frequency somatic copy number alterations in normal human lymphocytes revealed by large-scale single-cell whole-genome profiling	19
Accelerated somatic mutation calling for whole-genome and whole-exome sequencing data from heterogenous tumor samples	19
Characterization of the distribution and dynamics of chromatin states in theC. elegansgermline reveals substantial H3K4me3 remodeling during oogenesis	19
A plug and play microfluidic platform for standardized sensitive low-input chromatin immunoprecipitation	19
Ribosome decision graphs for the representation of eukaryotic RNA translation complexity	18
ZNF91 deletion in human embryonic stem cells leads to ectopic activation of SVA retrotransposons and up-regulation of KRAB zinc finger gene clusters	18
SARS-CoV-2 genomic diversity and the implications for qRT-PCR diagnostics and transmission	18
A somatic hypermutation–based machine learning model stratifies individuals with Crohn's disease and controls	18
Widespread association of the Argonaute protein AGO2 with meiotic chromatin suggests a distinct nuclear function in mammalian male reproduction	18
Localizing unmapped sequences with families to validate the Telomere-to-Telomere assembly and identify new hotspots for genetic diversity	18
Automated annotation of human centromeres with HORmon	18
Profiling single-cell histone modifications using indexing chromatin immunocleavage sequencing	18
Probabilistic association of differentially expressed genes withcis-regulatory elements	18
The predicted RNA-binding protein regulome of axonal mRNAs	18
Multisample motif discovery and visualization for tandem repeats	18
A KMT2A-AFF1 gene regulatory network highlights the role of core transcription factors and reveals the regulatory logic of key downstream target genes	17
Graph-based self-supervised learning for repeat detection in metagenomic assembly	17
Accurate assembly of circular RNAs with TERRACE	17
A graph neural network model to estimate cell-wise metabolic flux using single-cell RNA-seq data	17
A novel approach for in vivo DNA footprinting using short double-stranded cell-free DNA from plasma	17
Parameter-efficient fine-tuning on large protein language models improves signal peptide prediction	17
Rtt109 promotes nucleosome replacement ahead of the replication fork	17
Deciphering D4Z4 CpG methylation gradients in fascioscapulohumeral muscular dystrophy using nanopore sequencing	17
Genome-wide patterns of selection–drift variation strongly associate with organismal traits across the green plant lineage	17
Spatial Cellular Networks from omics data with SpaCeNet	17
Ligand-induced native G-quadruplex stabilization impairs transcription initiation	17
Analyzing rare mutations in metagenomes assembled using long and accurate reads	17

Linking the dynamics of chromatin occupancy and transcription with predictive models	16
A Chinese indicine pangenome reveals a wealth of novel structural variants introgressed from otherBosspecies	16
A curated collection of Klebsiella metabolic models reveals variable substrate usage and gene essentiality	16
Corrigendum: An association test of the spatial distribution of rare missense variants within protein structures identifies Alzheimer's disease–related patterns	16
Joint actions of diverse transcription factor families establish neuron-type identities and promote enhancer selectivity	16
Global compositional and functional states of the human gut microbiome in health and disease	16
ZSWIM8 destabilizes many murine microRNAs and is required for proper embryonic growth and development	16
Historical RNA expression profiles from the extinct Tasmanian tiger	16
Enhancers with tissue-specific activity are enriched in intronic regions	16
Different trajectories of polyploidization shape the genomic landscape of theBrettanomyces bruxellensisyeast species	16
A complete pedigree-based graph workflow for rare candidate variant analysis	16
Genome-wide chromatin interaction profiling reveals a vital role of super-enhancers and rearrangements in host enhancer contacts during BmNPV infection	15
Transposable elements drive the evolution of metazoan zinc finger genes	15
Suv39h-catalyzed H3K9me3 is critical for euchromatic genome organization and the maintenance of gene transcription	15
Mendelian randomization analyses implicate biogenesis of translation machinery in human aging	15
Modeling expression ranks for noise-tolerant differential expression analysis of scRNA-seq data	15
Genome-scale targeted mutagenesis inBrassica napususing a pooled CRISPR library	15
Epigenomic translocation of H3K4me3 broad domains over oncogenes following hijacking of super-enhancers	15
Transcription initiation mapping in 31 bovine tissues reveals complex promoter activity, pervasive transcription, and tissue-specific promoter usage	15
De novo transcriptome assembly of mouse male germ cells reveals novel genes, stage-specific bidirectional promoter activity, and noncoding RNA expression	15
Third-generation sequencing revises the molecular karyotype for Toxoplasma gondii and identifies emerging copy number variants in sexual recombinants	14
A HIT-trapping strategy for rapid generation of reversible and conditional alleles using a universal donor	14
Large palindromes on the primate X Chromosome are preserved by natural selection	14
Efficient mapping of accurate long reads in minimizer space with mapquik	14
A novel quantitative trait locus implicatesMsh3in the propensity for genome-wide short tandem repeat expansions in mice	14
Revisiting chromatin packaging in mouse sperm	14
Characterizing nucleotide variation and expansion dynamics in human-specific variable number tandem repeats	14
Entropy predicts sensitivity of pseudorandom seeds	14
Modeling and predicting cancer clonal evolution with reinforcement learning	14
Transcriptional milestones in Dictyostelium development	14
H3K36 dimethylation shapes the epigenetic interaction landscape by directing repressive chromatin modifications in embryonic stem cells	14
Discordant calls across genotype discovery approaches elucidate variants with systematic errors	14
An association test of the spatial distribution of rare missense variants within protein structures identifies Alzheimer's disease–related patterns	14
Transposable element variants and their potential adaptive impact in urban populations of the malaria vector Anopheles coluzzii	13
Identifying cell state–associated alternative splicing events and their coregulation	13
Accurate and fast graph-based pangenome annotation and clustering with ggCaller	13
Tagmentation-based single-cell genomics	13
Transcriptome innovations in primates revealed by single-molecule long-read sequencing	13
Non-Mendelian inheritance patterns and extreme deviation rates of CGG repeats in autism	13
Long-read RNA sequencing reveals widespread sex-specific alternative splicing in threespine stickleback fish	13
Leveraging family data to design Mendelian randomization that is provably robust to population stratification	13
Simultaneous assessment of human genome and methylome data in a single experiment using limited deamination of methylated cytosine	13
Density separation of petrous bone powders for optimized ancient DNA yields	13
Comprehensive assessment of 11 de novo HiFi assemblers on complex eukaryotic genomes and metagenomes	13
Thousands of human mutation clusters are explained by short-range template switching	13
Comprehensive determination of transcription start sites derived from all RNA polymerases using ReCappable-seq	13
Improved redox homeostasis owing to the up-regulation of one-carbon metabolism and related pathways is crucial for yeast heterosis at high temperature	12
Partial alignment of multislice spatially resolved transcriptomics data	12
Candida albicansisolates contain frequent heterozygous structural variants and transposable elements within genes and centromeres	12
Rapid evolution of piRNA clusters in theDrosophila melanogasterovary	12
MYT1L is required for suppressing earlier neuronal development programs in the adult mouse brain	12
Targeted regulation of transcription in primary cells using CRISPRa and CRISPRi	12
Global loss of cellular m6A RNA methylation following infection with different SARS-CoV-2 variants	12
Plasma cell-free RNA characteristics in COVID-19 patients	12
Systematic identification of interchromosomal interaction networks supports the existence of specialized RNA factories	12
Advancing genomic technologies and clinical awareness accelerates discovery of disease-associated tandem repeat sequences	12
Targeted, programmable, and precise tandem duplication in the mammalian genome	12
Robust analysis of prokaryotic pangenome gene gain and loss rates with Panstripe	12
Likelihood-based deconvolution of bulk gene expression data using single-cell references	12
Fixation of allelic gene expression landscapes and expression bias pattern shape the transcriptome of the clonal Amazon molly	12
Seamless, rapid, and accurate analyses of outbreak genomic data using splitk-mer analysis	12
Gene prediction in the immunoglobulin loci	12
Incomplete erasure of histone marks during epigenetic reprogramming in medaka early development	12
Long-read genome sequencing and variant reanalysis increase diagnostic yield in neurodevelopmental disorders	11
Enhanced detection of RNA modifications and read mapping with high-accuracy nanopore RNA basecalling models	11
Long-read subcellular fractionation and sequencing reveals the translational fate of full-length mRNA isoforms during neuronal differentiation	11
The rate and spectrum of new mutations in mice inferred by long-read sequencing	11
C. Thomas Caskey (1938–2022)	11
Long-read Ribo-STAMP simultaneously measures transcription and translation with isoform resolution	11
Chromatin interaction maps identify oncogenic targets of enhancer duplications in cancer	11
Long-read genome assembly of the insect model organismTribolium castaneumreveals spread of satellite DNA in gene-rich regions by recurrent burst events	11
Construction and evaluation of a new rat reference genome assembly, GRCr8, from long reads and long-range scaffolding	11
Inferring disease progressive stages in single-cell transcriptomics using a weakly-supervised deep learning approach	11
Enhancers display constrained sequence flexibility and context-specific modulation of motif function	11
The chromatin tapestry as a framework for neurodevelopment	11
Rapid SARS-CoV-2 surveillance using clinical, pooled, or wastewater sequence as a sensor for population change	11
Extensive sampling of Saccharomyces cerevisiae in Taiwan reveals ecology and evolution of predomesticated lineages	11
Mutational bias in spermatogonia impacts the anatomy of regulatory sites in the human genome	11
Large haplotypes highlight a complex age structure within the maize pan-genome	11
Transposable elements and their KZFP controllers are drivers of transcriptional innovation in the developing human brain	10
Challenges and considerations for reproducibility of STARR-seq assays	10
Natural variation inC. elegansshort tandem repeats	10
Using long-read CAGE sequencing to profile cryptic-promoter-derived transcripts and their contribution to the immunopeptidome	10
Coordination of zygotic genome activation entry and exit by H3K4me3 and H3K27me3 in porcine early embryos	10
Haig H. Kazazian, Jr. (1937–2022)	10
Early embryonic mutations reveal dynamics of somatic and germ cell lineages in mice	10
GC-biased gene conversion drives accelerated evolution of ultraconserved elements in mammalian and avian genomes	10
Purifying selection on noncoding deletions of human regulatory loci detected using their cellular pleiotropy	10
A model-based constrained deep learning clustering approach for spatially resolved single-cell data	10
High resolution genomes of multipleXiphophorusspecies provide new insights into microevolution, hybrid incompatibility, and epistasis	10
Recent, full-length gene retrocopies are common in canids	10
De novo mutation rates at the single-mutation resolution in a human HBB gene region associated with adaptation and genetic disease	9
Haplotype diversity and sequence heterogeneity of human telomeres	9
Inferring the mode and strength of ongoing selection	9
Genome-wide oscillations in G + C density and sequence conservation	9