Genome Research

Article	Citations
Evolutionarily new genes in humans with disease phenotypes reveal functional enrichment patterns shaped by adaptive innovation and sexual selection	317
The role of transposon activity in shapingcis-regulatory element evolution after whole-genome duplication	217
Combinatorial microRNA activity is essential for the transition of pluripotent cells from proliferation into dormancy	167
Dynamic dysregulation of retrotransposons in neurodegenerative diseases at the single-cell level	126
De novo individualized disease modules reveal the synthetic penetrance of genes and inform personalized treatment regimens	122
Transposable element accumulation drives size differences among polymorphic Y Chromosomes in Drosophila	117
Comparing genomic and epigenomic features across species using the WashU Comparative Epigenome Browser	111
A statistical physics approach for disease module detection	83
Unraveling the palindromic and nonpalindromic motifs of retroviral integration site sequences by statistical mixture models	80
Lake Malawi cichlid pangenome graph reveals extensive structural variation driven by transposable elements	78
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	78
The genomic basis of evolutionary differentiation among honey bees	70
Measuring X-Chromosome inactivation skew for X-linked diseases with adaptive nanopore sequencing	68
Examining the dynamics of three-dimensional genome organization with multitask matrix factorization	67
Accurate fusion transcript identification from long- and short-read isoform sequencing at bulk or single-cell resolution	66
De novo detection of somatic variants in high-quality long-read single-cell RNA sequencing data	66
Polishing copy number variant calls on exome sequencing data via deep learning	63
Elasmobranch genome sequencing reveals evolutionary trends of vertebrate karyotype organization	63
A ChIP-exo screen of 887 Protein Capture Reagents Program transcription factor antibodies in human cells	61
A chromosome-scale epigenetic map of theHydragenome reveals conserved regulators of cell state	61
De novo reconstruction of satellite repeat units from sequence data	59
Comparative genomics ofCryptosporidium parvumreveals the emergence of an outbreak-associated population in Europe and its spread to the United States	59
An efficient method to identify, date, and describe admixture events using haplotype information	57
Rapid SARS-CoV-2 surveillance using clinical, pooled, or wastewater sequence as a sensor for population change	56
Systematic identification of interchromosomal interaction networks supports the existence of specialized RNA factories	55

Chromatin interaction maps identify oncogenic targets of enhancer duplications in cancer	53
Suv39h-catalyzed H3K9me3 is critical for euchromatic genome organization and the maintenance of gene transcription	53
An optimized toolkit for high-molecular-weight DNA extraction and ultra-long-read nanopore sequencing using glass beads and hexamminecobalt(III) chloride	52
Historical RNA expression profiles from the extinct Tasmanian tiger	51
Likelihood-based deconvolution of bulk gene expression data using single-cell references	49
Global compositional and functional states of the human gut microbiome in health and disease	48
Artificial intelligence and machine learning in cell-free-DNA-based diagnostics	48
A novel approach for in vivo DNA footprinting using short double-stranded cell-free DNA from plasma	47
Spatial Cellular Networks from omics data with SpaCeNet	47
Long-read genome assembly of the insect model organismTribolium castaneumreveals spread of satellite DNA in gene-rich regions by recurrent burst events	46
Density separation of petrous bone powders for optimized ancient DNA yields	46
Ribosome decision graphs for the representation of eukaryotic RNA translation complexity	45
Advancing genomic technologies and clinical awareness accelerates discovery of disease-associated tandem repeat sequences	45
Transposable elements drive the evolution of metazoan zinc finger genes	44
Low-frequency somatic copy number alterations in normal human lymphocytes revealed by large-scale single-cell whole-genome profiling	44
Closing the gaps, and improving somatic structural variant analysis and benchmarking using CHM13-T2T	42
Challenges and considerations for reproducibility of STARR-seq assays	42
Ligand-induced native G-quadruplex stabilization impairs transcription initiation	42
Chromatin structure influences rate and spectrum of spontaneous mutations inNeurospora crassa	41
Positive selective sweeps of epigenetic mutations regulating specialized metabolites in plants	41
Human and rat skeletal muscle single-nuclei multi-omic integrative analyses nominate causal cell types, regulatory elements, and SNPs for complex traits	41
Cross-species cell-type assignment from single-cell RNA-seq data by a heterogeneous graph neural network	40
PWAS Hub for exploring gene-based associations of common complex diseases	40
Nanopore strand-specific mismatch enables de novo detection of bacterial DNA modifications	40
Simultaneous profiling of host expression and microbial abundance by spatial metatranscriptome sequencing	40
KRAB zinc-finger proteins regulate endogenous retroviruses to sculpt germline transcriptomes and genome evolution	39
Pathogenic variants inCRXhave distinctcis-regulatory effects on enhancers and silencers in photoreceptors	39
Simulation of nanopore sequencing signal data with tunable parameters	39
Large-scale genomic analysis of the domestic dog informs biological discovery	39
Purifying selection on noncoding deletions of human regulatory loci detected using their cellular pleiotropy	38
Interactive visualization and interpretation of pangenome graphs by linear reference–based coordinate projection and annotation integration	37
Dynamic regulation of gonadal transposon control across the lifespan of the naturally short-lived African turquoise killifish	37
Genome-wide oscillations in G + C density and sequence conservation	37
Target-enriched nanopore sequencing and de novo assembly reveals co-occurrences of complex on-target genomic rearrangements induced by CRISPR-Cas9 in human cells	37
Genome biology of the darkedged splitfin, Girardinichthys multiradiatus, and the evolution of sex chromosomes and placentation	37
Chromosome-specific telomere lengths and the minimal functional telomere revealed by nanopore sequencing	36
Long-read RNA sequencing of archival tissues reveals novel genes and transcripts associated with clear cell renal cell carcinoma recurrence and immune evasion	36
Contrasting and combining transcriptome complexity captured by short and long RNA sequencing reads	36
Distal regulation, silencers, and a shared combinatorial syntax are hallmarks of animal embryogenesis	35
Three assays for in-solution enrichment of ancient human DNA at more than a million SNPs	35
Phased nanopore assembly with Shasta and modular graph phasing with GFAse	35
Corrigendum: A mosquito small RNA genomics resource reveals dynamic evolution and host responses to viruses and transposons	33
Motif conservation, stability, and host gene expression are the main drivers of snoRNA expression across vertebrates	32
Cell type–specific analysis by single-cell profiling identifies a stable mammalian tRNA–mRNA interface and increased translation efficiency in neurons	32
Relative contributions of sex hormones, sex chromosomes, and gonads to sex differences in tissue gene regulation	32
Whole-genome resequencing of temporally stratified samples reveals substantial loss of haplotype diversity in the highly inbred Scandinavian wolf population	31
Cohesin organizes 3D DNA contacts surrounding active enhancers inC. elegans	31
KAS-ATAC reveals the genome-wide single-stranded accessible chromatin landscape of the human genome	30
Mitochondrial DNA variation across 56,434 individuals in gnomAD	30
Marker-free characterization of full-length transcriptomes of single live circulating tumor cells	30

Transposon accumulation at xenobiotic gene family loci in aphids	30
Unexpectedly low recombination rates and presence of hotspots in termite genomes	30
MCHelper automatically curates transposable element libraries across eukaryotic species	29
A temporal in vivo catalog of chromatin accessibility and expression profiles in pineoblastoma reveals a prevalent role for repressor elements	29
Acute depletion of METTL3 implicates N6-methyladenosine in alternative intron/exon inclusion in the nascent transcriptome	29
Aberrant landscapes of maternal meiotic crossovers contribute to aneuploidies in human embryos	29
Translation-dependent and -independent mRNA decay occur through mutually exclusive pathways defined by ribosome density during T cell activation	28
Global mapping of RNA homodimers in living cells	28
Hydrahas mammal-like mutation rates facilitating fast adaptation despite its nonaging phenotype	28
Global identification of mammalian host and nested gene pairs reveal tissue-specific transcriptional interplay	28
Functional characterization of enhancer activity during a long terminal repeat's evolution	28
Colibactin leads to a bacteria-specific mutation pattern and self-inflicted DNA damage	27
Single-cell discovery of m6A RNA modifications in the hippocampus	27
Benchmarking small-variant genotyping in polyploids	27
Differences in activity and stability drive transposable element variation in tropical and temperate maize	27
Spatial transcriptomics reveals asymmetric cellular responses to injury in the regenerating spiny mouse (Acomys) ear	26
Accumulation and ineffective silencing of transposable elements on an avian W Chromosome	26
Enhancer–silencer transitions in the human genome	26
Full-resolution HLA and KIR gene annotations for human genome assemblies	26
Accurate estimation of intraspecific microbial gene content variation in metagenomic data with MIDAS v3 and StrainPGC	25
Chimeric mitochondrial RNA transcripts predict mitochondrial genome deletion mutations in mitochondrial genetic diseases and aging	25
Large-scale detection and characterization of interchromosomal rearrangements in normozoospermic bulls using massive genotype and phenotype data sets	25
Hierarchical architecture of neo-sex chromosomes and accelerated adaptive evolution in tortricid moths	25
Proteome-wide structural analysis quantifies structural conservation across distant species	24
A systematic review on the biochemical threshold of mitochondrial genetic variants	24
Diffusion-based generation of gene regulatory networks from scRNA-seq data with DigNet	24
Diversity, duplication, and genomic organization of homeobox genes in Lepidoptera	24
A new framework for exploratory network mediator analysis in omics data	24
Proving sequence aligners can guarantee accuracy in almostO(mlogn) time through an average-case analysis of the seed-chain-extend heuristic	23
Sequencing of individual barcoded cDNAs using Pacific Biosciences and Oxford Nanopore Technologies reveals platform-specific error patterns	23
Implications of the first complete human genome assembly	23
Optical genome mapping enables accurate testing of large repeat expansions	22
Post-transcriptional cross- and auto-regulation buffer expression of the human RNA helicasesDDX3XandDDX3Y	22
Long-read sequencing of 111 rice genomes reveals significantly larger pan-genomes	22
Alu insertion variants alter gene transcript levels	22
Genetics-driven risk predictions leveraging the Mendelian randomization framework	22
MYC overexpression leads to increased chromatin interactions at super-enhancers and MYC binding sites	22
Dissecting and improving gene regulatory network inference using single-cell transcriptome data	22
Assessing conservation of alternative splicing with evolutionary splicing graphs	22
Precise genotyping of circular mobile elements from metagenomic data uncovers human-associated plasmids with recent common ancestors	22
Applications of single-cell genomics and computational strategies to study common disease and population-level variation	22
Discovery of an unusually high number of de novo mutations in sperm of older men using duplex sequencing	21
Rapid evolution and strain turnover in the infant gut microbiome	21
Fast inference of genetic recombination rates in biobank scale data	21
Gaps and complex structurally variant loci in phased genome assemblies	21
Streamlined spatial and environmental expression signatures characterize the minimalist duckweedWolffia australiana	21
Complete genomes of Asgard archaea reveal diverse integrated and mobile genetic elements	21
Variations in antibody repertoires correlate with vaccine responses	21
Erratum: A butterfly pan-genome reveals that a large amount of structural variation underlies the evolution of chromatin accessibility	21
Comprehensive identification of genomic and environmental determinants of phenotypic plasticity in maize	21
Protein domain embeddings for fast and accurate similarity search	20
Learning probabilistic protein–DNA recognition codes from DNA-binding specificities using structural mappings	20
Characterization of human transcription factor function and patterns of gene regulation in HepG2 cells	20
Profiling the quantitative occupancy of myriad transcription factors across conditions by modeling chromatin accessibility data	20
Long reads decipher genomes and transcriptomes and offer novel insights into biology and diseases	20
A butterfly pan-genome reveals that a large amount of structural variation underlies the evolution of chromatin accessibility	20
A scalable adaptive quadratic kernel method for interpretable epistasis analysis in complex traits	20
Rearrangements of viral and human genomes at human papillomavirus integration events and their allele-specific impacts on cancer genome regulation	20
Identifying cell state–associated alternative splicing events and their coregulation	19
Selection and thermostability suggest G-quadruplexes are novel functional elements of the human genome	19
A curated collection of Klebsiella metabolic models reveals variable substrate usage and gene essentiality	19
Inferring genes that escape X-Chromosome inactivation reveals important contribution of variable escape genes to sex-biased diseases	19
The predicted RNA-binding protein regulome of axonal mRNAs	19
Genomic environments scale the activities of diverse core promoters	19
Rtt109 promotes nucleosome replacement ahead of the replication fork	18
Modeling and predicting cancer clonal evolution with reinforcement learning	18
Sequence-based correction of barcode bias in massively parallel reporter assays	18
ZSWIM8 destabilizes many murine microRNAs and is required for proper embryonic growth and development	18
Long-read RNA sequencing reveals widespread sex-specific alternative splicing in threespine stickleback fish	18
Epigenomic translocation of H3K4me3 broad domains over oncogenes following hijacking of super-enhancers	18
Assessing DNA methylation detection for primary human tissue using Nanopore sequencing	18
Long-read genome sequencing and variant reanalysis increase diagnostic yield in neurodevelopmental disorders	18
Corrigendum: An association test of the spatial distribution of rare missense variants within protein structures identifies Alzheimer's disease–related patterns	18
De novo transcriptome assembly of mouse male germ cells reveals novel genes, stage-specific bidirectional promoter activity, and noncoding RNA expression	18
Construction and evaluation of a new rat reference genome assembly, GRCr8, from long reads and long-range scaffolding	18
Diverse tumorigenic consequences of human papillomavirus integration in primary oropharyngeal cancers	18
Revisiting chromatin packaging in mouse sperm	17
Parameter-efficient fine-tuning on large protein language models improves signal peptide prediction	17
Automated annotation of human centromeres with HORmon	17
Thousands of human mutation clusters are explained by short-range template switching	17

Meta-analysis of activated neurons reveals dynamic regulation of diverse classes of alternative splicing	17
Building better genome annotations across the tree of life	17
Nucleosome binding by TP53, TP63, and TP73 is determined by the composition, accessibility, and helical orientation of their binding sites	16
Revolutionizing genomics and medicine—one long molecule at a time	16
The genetics and epigenetics of satellite centromeres	16
Plant genome evolution in the genusEucalyptusis driven by structural rearrangements that promote sequence divergence	16
Hydroxycarbamide effects on DNA methylation and gene expression in myeloproliferative neoplasms	16
Enhancing nanopore adaptive sampling for PromethION using readfish at scale	16
Size-based expectation maximization for characterizing nucleosome positions and subtypes	16
Long-read transcriptome sequencing of CLL and MDS patients uncovers molecular effects ofSF3B1mutations	16
Generation and analysis of a mouse multitissue genome annotation atlas	16
CoRAL accurately resolves extrachromosomal DNA genome structures with long-read sequencing	16
Commoncis-regulatory variation modifies the penetrance of pathogenicSHROOM3variants in craniofacial microsomia	16
Clustered and diverse transcription factor binding underlies cell type specificity of enhancers for housekeeping genes	16
Machine learning identifies activation of RUNX/AP-1 as drivers of mesenchymal and fibrotic regulatory programs in gastric cancer	15
Accurate integration of multiple heterogeneous single-cell RNA-seq data sets by learning contrastive biological variation	15
Rapid and accurate alignment of nucleotide conversion sequencing reads with HISAT-3N	15
Genomic analysis of Rad26 and Rad1–Rad10 reveals differences in their dependence on Mediator and RNA polymerase II	15
Corrigendum: Enhancer–silencer transitions in the human genome	15
Large haplotypes highlight a complex age structure within the maize pan-genome	15
Theoretical framework for the difference of two negative binomial distributions and its application in comparative analysis of sequencing data	15
Navigating the landscape of epitranscriptomics and host immunity	15
Transposable elements and their KZFP controllers are drivers of transcriptional innovation in the developing human brain	15
A Bayesian framework for inferring dynamic intercellular interactions from time-series single-cell data	15
Corrigendum: Human primitive brain displays negative mitochondrial-nuclear expression correlation of respiratory genes	15
RNA Pol II–dependent transcription efficiency fine-tunes A-to-I editing levels	15
Genome skimming with nanopore sequencing precisely determines global and transposon DNA methylation in vertebrates	14
Assessing and mitigating privacy risks of sparse, noisy genotypes by local alignment to haplotype databases	14
RefSeq Functional Elements as experimentally assayed nongenic reference standards and functional interactions in human and mouse	14
miRNA-like secondary structures in maize (Zea mays) genes and transposable elements correlate with small RNAs, methylation, and expression	14
Cytosolic and mitochondrial translation elongation are coordinated through the molecular chaperone TRAP1 for the synthesis and import of mitochondrial proteins	14
Optimizing nanopore adaptive sampling for pneumococcal serotype surveillance in complex samples using the graph-based GNASTy algorithm	14
A national long-read sequencing study on chromosomal rearrangements uncovers hidden complexities	14
An organism-wide ATAC-seq peak catalog for the bovine and its use to identify regulatory variants	14
Continuous infiltration and evolutionary trajectory of nuclear organelle DNA inOryza	14
Resolving the chromatin impact of mosaic variants with targeted Fiber-seq	14
Ultrafast genome-wide inference of pairwise coalescence times	14
Biosurfer for systematic tracking of regulatory mechanisms leading to protein isoform diversity	14
Genome-wide transcript and protein analysis highlights the role of protein homeostasis in the aging mouse heart	14
Listeria monocytogenes genes supporting growth under standard laboratory cultivation conditions and during macrophage infection	13
Identification of the male-specific region on the guppy Y Chromosome from a haplotype-resolved assembly	13
Competition for DNA binding between paralogous transcription factors determines their genomic occupancy and regulatory functions	13
Interspecies regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes	13
Enzymatic methyl sequencing detects DNA methylation at single-base resolution from picograms of DNA	13
Embryonic LTR retrotransposons supply promoter modules to somatic tissues	13
Copy number variation alters local and global mutational tolerance	13
De novo genome assemblies of two cryptodiran turtles with ZZ/ZW and XX/XY sex chromosomes provide insights into patterns of genome reshuffling and uncover novel 3D genome folding in amniotes	13
Vertebrates show coordinated elevated expression of mitochondrial and nuclear genes after birth	13
High temporal resolution RNA-seq time course data reveals widespread synchronous activation between mammalian lncRNAs and neighboring protein-coding genes	13
Tn5 tagments and transposes oligos to single-stranded DNA for strand-specific RNA sequencing	13
Matching queried single-cell open-chromatin profiles to large pools of single-cell transcriptomes and epigenomes for reference supported analysis	13
The Drosophila brain on cocaine at single-cell resolution	12
Deriving confidence intervals for mutation rates across a wide range of evolutionary distances using FracMinHash	12
Variational inference using approximate likelihood under the coalescent with recombination	12
Distinct roles for RSC and SWI/SNF chromatin remodelers in genomic excision repair	12
Systematic identification and characterization of exon–intron circRNAs	12
Multiscale network modeling reveals the gene regulatory landscape driving cancer prognosis in 32 cancer types	12
Erratum: Ultralow-input single-tube linked-read library method enables short-read second-generation sequencing systems to routinely generate highly accurate and economical long-range sequencing inform	12
Reference-informed prediction of alternative splicing and splicing-altering mutations from sequences	12
Whole-genome long-read sequencing downsampling and its effect on variant-calling precision and recall	12
Effective sequence similarity detection with strobemers	12
A statistical learning method for simultaneous copy number estimation and subclone clustering with single-cell sequencing data	12
The rate of de novo structural variation is increased in in vitro–produced offspring and preferentially affects the paternal genome	12
Characterization of transcript enrichment and detection bias in single-nucleus RNA-seq for mapping of distinct human adipocyte lineages	12
MPRAbase a Massively Parallel Reporter Assay database	12
Multisite long-read sequencing reveals the early contributions of somatic structural variations to HBV-related hepatocellular carcinoma tumorigenesis	12
A deconvolution framework that uses single-cell sequencing plus a small benchmark data set for accurate analysis of cell type ratios in complex tissue samples	12
Analytical validation of germline small variant detection using long-read HiFi genome sequencing	12
Haplotype and population structure inference using neural networks in whole-genome sequencing data	12
SWATH-MS-based proteogenomic analysis reveals the involvement of alternative splicing in poplar upon lead stress	11
Genetic control of the dynamic transcriptional response to immune stimuli and glucocorticoids at single-cell resolution	11
Chromatin interaction–aware gene regulatory modeling with graph attention networks	11
Efficient taxa identification using a pangenome index	11
Assessing transcriptomic reidentification risks using discriminative sequence models	11
Genetic regulation of nascent RNA maturation revealed by direct RNA nanopore sequencing	11
Chromatin architecture transitions from zebrafish sperm through early embryogenesis	11
Single-nucleus CUT&RUN elucidates the function of intrinsic and genomics-driven epigenetic heterogeneity in head and neck cancer progression	11
Genome-wide relaxation of selection and the evolution of the island syndrome in Orkney voles	11
Defining the separation landscape of topological domains for decoding consensus domain organization of the 3D genome	11
High-fidelity, large-scale targeted profiling of microsatellites	11
Individualized VDJ recombination predisposes the available Ig sequence space	11
The fine-scale recombination rate variation and associations with genomic features in a butterfly	11
An atlas of fish genome evolution reveals delayed rediploidization following the teleost whole-genome duplication	11
Loss of epigenetic suppression of retrotransposons with oncogenic potential in aging mammary luminal epithelial cells	11
Three-dimensional missense tolerance ratio analysis	11
A machine learning method for the discovery of minimum marker gene combinations for cell type identification from single-cell RNA sequencing	10
Parental methylome reprogramming in human uniparental blastocysts reveals germline memory transition	10
De novo antibody identification in human blood from full-length single B cell transcriptomics and matching haplotype-resolved germline assemblies	10
Population genomics reveals mechanisms and dynamics of de novo expressed open reading frame emergence inDrosophila melanogaster	10
Characteristics, origin, and potential for cancer diagnostics of ultrashort plasma cell-free DNA	10
Epigenomic analysis reveals prevalent contribution of transposable elements to cis-regulatory elements, tissue-specific expression, and alternative promoters in zebrafish	10
A sheep pangenome reveals the spectrum of structural variations and their effects on tail phenotypes	10
A complete pedigree-based graph workflow for rare candidate variant analysis	10
Atypical epigenetic and small RNA control of degenerated transposons and their fragments in clonally reproducingSpirodela polyrhiza	10
tRNA-derived small RNAs are embedded in the gene regulatory network instructingDrosophilametamorphosis	10