Sequencing Methods & Technologies

Issue 432

Particles of echovirus 18 open to release their genomes in vivo

Issue 431

Identification of a conserved gene family with an essential role in Leishmania parasite–insect vector adhesion

Issue 430

Environmental phylogenetics supports a steady diversification of crown eukaryotes starting from the mid-Proterozoic

Issue 426

ProtoCloud: A prototypical self-explaining model for single-cell analysis

Issue 425

Bayesian inference of tissue-migration histories in metastatic cancer from cell-lineage tracing data

Issue 424

A protein interactome for the last eukaryotic common ancestor illuminates the biochemical basis of modern genetic diseases

Issue 421

Pre-existing cell states predict resistance to multiple treatments

Issue 420

Genetic diversity and regulatory features of human-specific NOTCH2NL duplications

Issue 419

The Single-Cell Pediatric Cancer Atlas: Data portal and open-source tools for single-cell transcriptomics of pediatric tumors

Issue 418

Translating genome-wide association studies at multiple scales: Drug target prioritization, cellular architectures, and organ imaging

Issue 414

Long-term stability and performance of Cas9/guide RNA-based gene drives in anopheline mosquitoes

Issue 411

A scalable, dividing cell model for the robust propagation and quantification of human sporadic Creutzfeldt–Jakob disease prions

Issue 407

SLC11A2 withholds divalent metals from Salmonella in the gut epithelium

Issue 403

Homologous recombination deficiency-driven genomic instability in ovarian cancer as an indicator of BRCA1 and BRCA2 variant pathogenicity

Issue 401

De novo variants in LDB1 are linked to distinct neurodevelopmental phenotypes determined by variant location and differing pathomechanisms

Issue 400

Complete chromosome 21 centromere sequencing of families with Down syndrome

Issue 399

Genome-wide analysis implicates inner ear development in Ménière disease

Issue 397

SciPhy: A Bayesian phylogenetic framework using sequential genetic lineage tracing data

Issue 390

DNA-intercalating antiphage molecules trigger abortive infection through mutual destruction and synergize with bacterial immunity

Issue 388

mRNA‑laden LNP‑enabled in situ CAR‑macrophage alleviates liver fibrosis via inhibiting activated HSCs and modulating the immune microenvironment

Issue 383

Multi-cohort proteogenomic analyses reveal genetic effects across the proteome and diseasome

Issue 380

A multiplex, prime editing framework for identifying drug resistance variants at scale

Issue 379

Long-read genome sequencing improves detection and functional interpretation of structural and repeat variants in autism

Issue 375

Biallelic loss-of-function variants in DSCAM cause a neurodevelopmental syndrome with nystagmus and retinal dysfunction

Issue 374

DNA-guided CRISPR–Cas12a effectors for programmable RNA recognition and cleavage

Issue 373

Identification of a non-canonical ciliate nuclear genetic code where UAA and UAG code for different amino acids

Issue 366

Regulation of antiviral and antitumor immunity by the BRCA1 pseudogene in human cancers

Issue 365

CRISPR base editor screening identifies spectrum of MEN1 mutations impacting menin inhibitors in clinical trials

Issue 361

Chiral inversion mutagenesis identifies geometrically constrained residues within self - associating low - complexity domains

Issue 359

Computational design of an ultrapotent deltacoronavirus miniprotein inhibitor

Issue 358

Biallelic variants in CHCHD4 are associated with combined OXPHOS defect leading to mitochondrial disease

Issue 354

Cohesin acetylation and ATPase activity control cohesion and loop architecture through distinct mechanisms

Issue 349

Structural basis of transcription -coupled RNA damage by incorporation of oxidized ribonucleotides

Issue 348

A plasma - based DNA test for quantification of disease burden in acute myeloid leukemia patients undergoing bone marrow transplantation

Issue 342

Using a modular massively parallel reporter assay to discover context-dependent regulatory activity in type 2 diabetes-linked noncoding regions

Issue 340

Alternative microexon splicing code for a four - amino acid peptide of PTPRD governs behavioral development

Issue 338

Bi-allelic WDHD1 variants cause microcephalic primordial dwarfism

Issue 331

Bi-allelic variants in NDUFA5 cause a mitochondriopathy with complex I deficiency

Issue 327

Bi-allelic ATG12 variants impair autophagy and cause a neurodevelopmental disorder

Issue 324

The E3 ubiquitin ligase mechanism specifying targeted microRNA degradation

Issue 318

Biallelic Variants in RNU6ATAC Result in a Minor Spliceopathy Characterized by Transcriptome-Wide Minor Intron Retention Events and Short Stature with Variable Multisystem Manifestations

Issue 317

Overlap between COPD genetic association results and transcriptional quantitative trait loci

Issue 315

Capturing dynamic phage–pathogen coevolution by clinical surveillance

Issue 311

When alternative becomes essential: The role of mitochondrial glycerol-3-phosphate dehydrogenase

Issue 309

A reference panel for linkage disequilibrium and genotype imputation using whole-genome sequencing data from 2,680 participants across India

Issue 306

Loss-of-function variants in SAXO6, encoding a microtubule inner protein of photoreceptor cilia, cause a late-onset retinal dystrophy

Issue 305

Functional dissection of complex trait variants at single-nucleotide resolution

Issue 300

Population-scale sequencing resolves determinants of persistent EBV DNA

Issue 298

Bi-allelic variants in FSD1L cause retinitis pigmentosa with or without neurological involvement

Issue 297

Bi-allelic variants in FSD1L cause a neurodevelopmental disorder overlapping with L1 syndrome

Issue 295

Cystic fibrosis risk variants confer protection against inflammatory bowel disease

Issue 294

The splice of life: how alternative splicing shapes regulatory and phenotypic evolution

Issue 288

Molecular assemblies and pharmacology of cerebellar GABAA receptors

Issue 287

EPOP and MTF2 activate PRC2 activity through DNA-sequence specificity

Issue 284

Integrative functional genomics analysis identifies pleiotropic genes for vascular diseases

Issue 281

Molecular genotype-phenotype correlation in ACTB- and ACTG1-related non-muscle actinopathies

Issue 277

MDGA2 homozygous loss-of-function variants cause developmental and epileptic encephalopathy

Issue 275

Genomic analysis of 11,555 probands identifies 60 dominant congenital heart disease genes

Issue 274

RPE- specific MCT2 expression promotes cone survival in models of retinitis pigmentosa

Issue 273

Horizontal transfer of nuclear DNA in transmissible cancer

Issue 272

The activity and expression of adenylosuccinate lyase were reduced during modern human evolution, affecting brain and behavior

Issue 270

Mechanistic basis for relaxation of DNA supercoils by human topoisomerase IIIα–RMI1–RMI2

Issue 262

Human epidermal Langerhans cells induce tolerance and hamper T cell function upon tick-borne pathogen transmission

Issue 259

Oligomerisation of Ku from Mycobacterium tuberculosis promotes DNA synapsis

Issue 255

Impact of anionic lipids on the energy landscape of conformational transition in anion exchanger 1 (AE1)

Issue 254

Rescuing the bacterial replisome at a nick requires recombinational repair and helicase reloading

Issue 252

Genetic evolution of keratinocytes to cutaneous squamous cell carcinoma

Issue 251

Loss of cell-autonomously secreted laminin-α2 drives muscle stem cell dysfunction in LAMA2-related muscular dystrophy

Issue 250

The CIP2A-TOPBP1 axis facilitates mitotic DNA repair via MiDAS and MMEJ

Issue 247

Genome graphs reveal the importance of structural variation in Mycobacterium tuberculosis evolution and drug resistance

Issue 246

Structural pharmacology of SV2A reveals an allosteric modulation mechanism in the major facilitator superfamily

Issue 241

Insights into natural neocentromere evolution from a cattle T2T X chromosome

Issue 238

Germline polymorphisms in the immunoglobulin kappa and lambda loci underpinning antibody light chain repertoire variability

Issue 237

Using metagenomics and whole-genome sequencing to characterize enteric pathogens across various sources in Africa

Issue 235

Maternal histone methyltransferases antagonistically regulate autosomal random monoallelic expression (aRMAE) in C. elegans

Issue 233

Mechanistic insights into histone recognition and H3K14 acetylation by the NuA3 histone acetyltransferase complex

Issue 230

A de novo missense variant in MIDEAS results in increased deacetylase activity of the MiDAC HDAC complex causing a neurodevelopmental syndrome

Issue 228

Characterization of two non-competing antibodies to influenza H3N2 hemagglutinin stem reveals its evolving antigenicity

Issue 221

An allele-resolved nanopore-guided tour of the human placental methylome

Issue 220

The AML cellular state space unveils NPM1 immune evasion subtypes with distinct clinical outcomes

Issue 219

Multi-omic analysis reveals lipid dysregulation associated with mitochondrial dysfunction in Parkinson’s disease brain

Issue 216

53BP1-RIF1 and DNA-PKcs show distinct genetic interactions with diverse chromosomal break repair outcomes

Issue 212

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Issue 210

Tumour-reactive heterotypic CD8 T cell clusters from clinical samples

Issue 209

Prime editing-installed suppressor tRNAs for disease-agnostic genome editing

Issue 207

Semantic design of functional de novo genes from a genomic language model

Issue 204

StealTHY: An immunogen-free CRISPR platform to expose concealed metastasis regulators in immunocompetent models

Issue 199

Loss-of-function mutations in PLD4 lead to systemic lupus erythematosus

Issue 196

Impact of disease-associated chromatin accessibility QTLs across immune cell types and contexts

Issue 190

Single-cell mRNA-regulation analysis reveals cell type-specific mechanisms of type 2 diabetes

Issue 190

Single-cell mRNA-regulation analysis reveals cell type-specific mechanisms of type 2 diabetes

Issue 188

Issue 167

Single-cell and spatial detection of senescent cells using DeepScence

Issue 162

Spatially resolved microRNA expression in tissues: technologies, challenges, and opportunities

Issue 160

Single-cell omics sequencing technologies: the long-read generation

Issue 160

Single-cell omics sequencing technologies: the long-read generation

Issue 159

The untapped potential of short-read sequencing in biodiversity research

Issue 156

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Issue 155

A cardiovascular, craniofacial, and neurodevelopmental disorder caused by loss-of-function variants in the eIF3 complex component genes EIF3A and EIF3B

Issue 152

Hereditary Alpha Tryptasemia: Validation of a Single-Well Multiplex Digital Droplet PCR Assay in a Cohort of Symptomatic Patients

Issue 148

Systematic Minigene-Based Splicing Analysis and Tentative Clinical Classification of 52 CHEK2 Splice-Site Variants

Issue 147

Comprehensive Annotation of Complete ABO Alleles and Resolution of ABO Variants by an Improved Full-Length ABO Haplotype Sequencing

Issue 146

Automated and Decentralized Genomic Profiling of Plasma Cell-Free DNA for Identification of Targetable and Resistance Alterations in Advanced Solid Tumors

Issue 145

A Validated Highly Sensitive Microsatellite Instability Assay Accurately Identifies Individuals Harboring Biallelic Germline PMS2 Pathogenic Variants in Constitutional Mismatch Repair Deficiency

Issue 142

Specifications of the ACMG/AMP variant curation guidelines for the analysis of germline PALB2 sequence variants

Issue 141

RetiGene, a comprehensive gene atlas for inherited retinal diseases

Issue 140

Landscapes of missense variant impact for human superoxide dismutase 1

Issue 139

MosCoverY: A method to estimate mosaic loss of Y chromosome from sequencing coverage data

Issue 136

Gene context drift identifies drug targets to mitigate cancer treatment resistance

Issue 134

Single-cell analysis of Barrett’s esophagus and carcinoma reveals cell types conferring risk via genetic predisposition

Issue 133

Culture-independent meta-pangenomics enabled by long-read metagenomics reveals associations with pediatric undernutrition

Issue 131

A cryptic plasmid is among the most numerous genetic elements in the human gut

Issue 130

Combining evidence from human genetic and functional screens to identify pathways altering obesity and fat distribution

Issue 129

Structural variation, selection, and diversification of the NPIP gene family from the human pangenome

Issue 128

LINE-1 retrotransposons mediate cis-acting transcriptional control in human pluripotent stem cells and regulate early brain development

Issue 126

Molecular and developmental deficits in Smith-Magenis syndrome human stem cell-derived cortical neural models

Issue 123

Dominant negative ATP5F1A variants disrupt oxidative phosphorylation causing neurological disorders

Issue 120

Rare variants in BMAL1 are associated with a neurodevelopmental syndrome

Issue 116

Cell type–specific purifying selection of synonymous mitochondrial DNA variation

Issue 115

A transcriptomic, proteomic, and functional genetic atlas dissects neurofibromin function in the peripheral nervous system

Issue 114

One-hour extraction-free loop-mediated isothermal amplification HPV DNA assay for point-of-care testing in Maputo, Mozambique

Issue 113

Joint, multifaceted genomic analysis enables diagnosis of diverse, ultra-rare monogenic presentations

Issue 110

Whole-exome sequencing analysis identifies risk genes for schizophrenia

Issue 106

Transcriptomic decoding of surface-based imaging phenotypes and its application to pharmacotranscriptomics

Issue 105

Genome-level selection in tumors as a universal marker of resistance to therapy

Issue 104

Issue 100

Epigenomic diagnosis and prognosis of Acute Myeloid Leukemia

Issue 099

NXT2 is a key component of the RNA nuclear export factor complex in the human testis and essential for spermatogenesis

Issue 098

Cell Marker Accordion: interpretable single-cell and spatial omics annotation in healthand disease

Issue 096

Issue 092

Loss of CFHR5 function reduces the risk for age-related macular degeneration

Issue 091

A genome-wide association study in 10,000 individuals links plasma N-glycome to liver disease and anti-inflammatory proteins

Issue 084

Variants in NR6A1 cause a novel oculo vertebral renal syndrome

Issue 083

Single-cell analysis of dup15q syndrome reveals developmental and postnatal molecular changes in autism

Issue 082

JAK2 inhibition mediates clonal selection of RAS pathway mutations in myeloproliferative neoplasms

Issue 080

Genome sequencing is critical for forecasting outcomes following congenital cardiacsurgery

Issue 079

Cross-population GWAS and proteomics improve risk prediction and reveal mechanisms in atrial fibrillation

Issue 078

Interactions between TTYH2 and APOE facilitate endosomal lipid transfer

Issue 075

The role of metabolism in shaping enzyme structures over 400 million years

Issue 074

Benchmarking of T cell receptor-epitope predictors with ePytope-TCR

Issue 073

Assessing family history and approaches for identifying dementia patients with diagnostically significant genetic findings

Issue 071

ELFN1 Deficiency: the mechanistic basis and phenotypic spectrum of a neurodevelopmental disorder with epilepsy

Issue 069

Three independent approaches identify IGF2BP2 as a top SDL target of PLK1

Issue 062

BRCA2 reversion mutation–independent resistance to PARP inhibition through impaired DNA prereplication complex function

Issue 061

Issue 054

Temporal multi-omics analysis of COVID-19 in end-stage kidney disease

Issue 052

Human genetic variation reveals FCRL3 is a lymphocyte receptor for Yersinia pestis

Issue 049

Environmental DNA adsorption to chitin can promote horizontal gene transfer by natural transformation

Issue 046

tRNA modifications tune m6A-dependent mRNA decay

Issue 044

The proofreading mechanism of the human leading-strand DNA polymerase ε holoenzyme

Issue 043

Personalized molecular signatures of insulin resistance and type 2 diabetes

Issue 040

SLC7A11 is an unconventional H+ transporter in lysosomes

Issue 038

The recency and geographical origins of the bat viruses ancestral to SARS-CoV and SARS-CoV-2

Issue 037

Prioritizing disease-associated missense variants with chemoproteomic-detected amino acids

Issue 036

Bi-allelic variants in POPDC2 cause an autosomal recessive syndrome presenting with cardiac conduction defects and hypertrophic cardiomyopathy

Issue 035

Tracing the evolutionary history of the CCR5delta32 deletion via ancient and modern genomes

Issue 033

Mis-splicing-derived neoantigens and cognate TCRs in splicing factor mutant leukemias

Issue 028

scPrediXcan integrates deep learning methods and single-cell data into a cell-type-specific transcriptome-wide association study framework

Issue 027

Engineered nucleocytosolic vehicles for loading of programmable editors

Issue 026

Reannotation of cancer mutations based on expressed RNA transcripts reveals functional non-coding mutations in melanoma

Issue 021

High-throughput screening of human genetic variants by pooled prime editing

Issue 017

The structure of human sweetness

Issue 013

Human de novo mutation rates from a four-generation pedigree reference

Issue 008

A structural variation reference for medical and population genetics

Issue 004

CXCL12 drives natural variation in coronary artery anatomy across diverse populations