BIOINFORMATICS & GENOMICS

Nanopore sequencing of DNA-barcoded probes for highly multiplexed detection of microRNA, proteins and small biomarkers

Escherichia coli non-coding regulatory regions are highly conserved

LncRNA NEAT1 controls the lineage fates of BMSCs during skeletal aging by impairing mitochondrial function and pluripotency maintenance

Translation of non-canonical open reading frames as a cancer cell survival mechanism in childhood medulloblastoma

Advancing microRNA Target Site Prediction with Transformer and Base-Pairing Patterns

MILIP Binding to tRNAs Promotes Protein Synthesis to Drive Triple-Negative Breast Cancer

Super Enhancer–Regulated LncRNA LINC01089 Induces Alternative Splicing of DIAPH3 to Drive Hepatocellular Carcinoma Metastasis

A circular RNA activated by TGFβ promotes tumor metastasis through enhancing IGF2BP3-mediated PDPN mRNA stability

Genome-scale pan-cancer interrogation of lncRNA dependencies using CasRx

LncRNA MIR200CHG inhibits EMT in gastric cancer by stabilizing miR-200c from target-directed miRNA degradation

Expression of novel long noncoding RNAs defines virus-specific effector and memory CD8+ T cells

Systematic annotation of orphan RNAs reveals blood-accessible molecular barcodes of cancer identity and cancer-emergent oncogenic drivers

Genetic drivers of heterogeneity in type 2 diabetes pathophysiology

The frequency of pathogenic variation in the All of Us cohort reveals ancestry-driven disparities

Selection, optimization and validation of ten chronic disease polygenic risk scores for clinical implementation in diverse US populations

Computational prediction and experimental validation identify functionally conserved lncRNAs from zebrafish to human

Genomic data in the All of Us Research Program

Domain generalization enables general cancer cell annotation in single-cell and spatial transcriptomics

Clustering single-cell RNA-seq data with a model-based deep learning approach

Enhancing CRISPR-Cas9 gRNA efficiency prediction by data integration and deep learning

Modeling CRISPR-Cas13d on-target and off-target effects using machine learning approaches

A universal deep neural network for in-depth cleaning of single-cell RNA-Seq data

Ultra-fast deep-learned CNS tumour classification during surgery

Genome-wide CRISPR off-target prediction and optimization using RNA-DNA interaction fingerprints

From function to translation: Decoding genetic susceptibility to human diseases via artificial intelligence

Cue: a deep-learning framework for structural variant discovery and genotyping

scBERT as a large-scale pretrained deep language model for cell type annotation of single-cell RNA-seq data

Unambiguous discrimination of all 20 proteinogenic amino acids and their modifications by nanopore

Illuminating protein space with a programmable generative model

scGPT: Towards building a foundation model for single-cell multi-omics using generative AI

SVision: a deep learning approach to resolve complex structural variants

Modeling and predicting cancer clonal evolution with reinforcement learning

Genetic and chemotherapeutic influences on germline hypermutation

The construction of cross-population polygenic risk scores using transfer learning

Long-read sequencing of 3,622 Icelanders provides insight into the role of structural variants in human diseases and other traits

Whole genome sequence analysis of blood lipid levels in >66,000 individuals

Exploring the Role of Contactins across Psychological, Psychiatric and Cardiometabolic Traits within UK Biobank

Pan-cancer and cross-population genome-wide association studies dissect shared genetic backgrounds underlying carcinogenesis

A saturated map of common genetic variants associated with human height

A genome-wide association study for extremely high intelligence

Genome-wide study on 72,298 individuals in Korean biobank data for 76 traits

A draft human pangenome reference

Deficit of homozygosity among 1.52 million individuals and genetic causes of recessive lethality

Analysis of rare genetic variation underlying cardiometabolic diseases and traits among 200,000 individuals in the UK Biobank

Mobile element variation contributes to population-specific genome diversification, gene regulation and disease risk

Parent-of-Origin inference for biobanks

Lung adenocarcinoma promotion by air pollutants

Non-coding de novo mutations in chromatin interactions are implicated in autism spectrum disorder

High-coverage whole-genome sequencing of the expanded 1000 Genomes Project cohort including 602 trios

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

The sequences of 150,119 genomes in the UK Biobank

Precise modulation of transcription factor levels identifies features underlying dosage sensitivity

An atlas of genetic scores to predict multi-omics traits

Sensitive and powerful single-cell RNA sequencing using mcSCRB-seq

Polony gels enable amplifiable DNA stamping and spatial transcriptomics of chromic pain

Somatic mutation landscapes at single-molecule resolution

Nano3P-seq: transcriptome-wide analysis of gene expression and tail dynamics using end-capture nanopore cDNA sequencing

A highly scalable method for joint whole-genome sequencing and gene-expression profiling of single cells

DiMeLo-seq: a long-read, single-molecule method for mapping protein-DNA interactions genome wide

Targeted long-read sequencing identifies missing disease-causing variation

Transcriptional recording by CRISPR spacer acquisition from RNA

MIPP-Seq: ultra-sensitive rapid detection and validation of low-frequency mosaic mutations

Locus-specific expression of transposable elements in single cells with CELLO-seq

Identifying synergistic high-order 3D chromatin conformations from genome-scale nanopore concatemer sequencing

Mapping phosphorylation post-translational modifications along single peptides with nanopores

Cost-efficient whole genome-sequencing using novel mostly natural sequencing-by-synthesis chemistry and open fluidics platform

Targeted profiling of human extrachromosomal DNA by CRISPR-CATCH

Accelerated identification of disease-causing variants with ultra-rapid nanopore genome sequencing

Engineering circular RNA for enhanced protein production

High-plex imaging of RNA and proteins at subcellular resolution in fixed tissue by spatial molecular imaging

Live-seq enables temporal transcriptomic recording of single cells

Integrated analysis of multimodal single-cell data

CRISPR/Cas13 effectors have differing extents of off-target effects that limit their utility in eukaryotic cells

Exploring the cellular landscape of circular RNAs using full length single-cell RNA sequencing

Patterns and distribution of de novo mutations in multiplex Middle Eastern families

De novo protein design by deep network hallucination

The sequences of 150,119 genomes in the UK Biobank

Massively parallel characterization of engineered transcript isoforms using direct RNA sequencing

The NASA Twins Study: A multidimensional analysis of a year-long human spaceflight

Trajectory-based differential expression analysis for single-cell sequencing data

Engineered miniature CRISPR-Cas system for mammalian genome regulation and editing

Telomerase regulation by the long non-coding RNA H19 in human acute promyelocytic leukemia cells

High-fidelity KKH variant of Staphylococcus aureus Cas9 nucleases with improved base mismatch discrimination

Circular RNA vaccines against SARS-CoV-2 and emerging variants

De novo structural mutation rates and gamete-of-origin biases revealed through genome sequencing of 2,396 families

Highly accurate protein structure prediction with AlphaFold

The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species

SNHG15 is a bifunctional MYC-regulated noncoding locus encoding a lncRNA that promotes cell proliferation, invasion and drug resistance in colorectal cancer by interacting with AIF

m6A RNA modifications are measured at single-base resolution across the mammalian transcriptome

Human transcription factor protein interaction networks

Cas11 enables genome engineering in human cells with compact CRISPR-Cas3 systems

Spatial genomics enables multi-modal study of clonal heterogenity in tissues

Chromatin-state barriers enforce an irreversible mammalian cell fate decision

Clump sequencing exposes the spatial expression programs of intestinal secretory cells

Mammalian circular RNAs result largely from splicing errors

Differences in the number of de novo mutations between individuals are due to small family-specific effects and stochasticity

Genome-wide de novo risk score implicates promoter variation in autism spectrum disorder

Small RNAs are modified with N-glycans and displayed on the surface of living cells

Translational tuning optimizes nascent protein folding in cells

Multiple rereads of single proteins at single–amino acid resolution using nanopores

Defining the genetic and evolutionary architecture of alternative splicing in response to infection

Efficient C•G-to-G•C base editors developed using CRISPRi screens, target-library analysis, and machine learning

Single-cell analysis of human non-small cell lung cancer lesions refines tumor classification and patient stratification

An unsupervised method for physical cell interaction profiling of complex tissues

Migration through a small pore disrupts inactive chromatin organization in neutrophil-like cells

Expression and regulation of intergenic long noncoding RNAs during T cell development and differentiation

Patterns of de novo tandem repeat mutations and their role in autism

Profiling of Small Ribosomal Subunits Reveals Modes and Regulation of Translation Initiation

Geometric deep learning of RNA structure

RNA m6A modification orchestrates a LINE-1–host interaction that facilitates retrotransposition and contributes to long gene vulnerability

The coding and long noncoding single-cell atlas of the developing human fetal striatum

Haplotype-resolved diverse human genomes and integrated analysis of structural variation

Characterizing the tumor microenvironment of metastatic ovarian cancer by single-cell transcriptomics

Programmed DNA destruction by miniature CRISPR-Cas14 enzymes

Multimodal Analysis of Composition and Spatial Architecture in Human Squamous Cell Carcinoma

DNA of neutrophil extracellular traps promotes cancer metastatis via CCDC25

Co-evolution of tumor and immune cells during progression of multiple myeloma

Dynamics of genome architecture and chromatin function during human B cell differentiation and neoplastic transformation

Pan-cancer proteomgenomic analysis reveals long and circular noncoding RNAs encoding peptides

De novo structural mutation rates and gamete-of-origin biases revealed through genome sequencing of 2,396 families

The Ccr4-Not complex monitors the translating ribosome for codon optimality

Comprehensive profiling of circular RNAs with nanopore sequencing and CIRI-long

Splicing-associated chromatin signatures: a combinatorial and position-dependent role for histone marks in splicing definition

Predicting the efficiency of prime editing guide RNAs in human cells

Single-Cell Multiomics Sequencing Reveals Prevalent Genomic Alterations in Tumor Stromal Cells of Human Colorectal Cancer

Benchmarking Computational Doublet-Detection Methods for Single-Cell RNA Sequencing Data,

Expression of novel long noncoding RNAs defines virus-specific effector and memory CD8+ T cells

A macrophage-specific lncRNA regulates apoptosis and atherosclerosis by tethering HuR in the nucleus

Single-cell analysis reveals transcriptomic remodellings in distinct cell types that contribute to human prostate cancer progression

Detection of simple and complex de novo mutations with multiple reference sequences

Translation of the circular RNA circb-catenin promotes liver cancer cell growth through activation of the Wnt pathway

The ZSWIM8 ubiquitin ligase mediates target-directed microRNA degradation

Simultaneous profiling of chromatin accessibility and methylation on human cell lines with nanopore sequencing

High throughput error corrected Nanopore single cell transcriptome sequencing

Search and replace genome editing without double strand breaks or donor DNA

Transcriptional kinetics and molecular functions of long non-coding RNAs

scds : computational annotation of doublets in single-cell RNA sequencing data

A pan-cancer blueprint of the heterogeneous tumor microenvironment revealed by single-cell profiling

Structural cells are key regulators of organ-specific immune responses

A robust benchmark for dectection of germline large deletions and insertions

Modulation of circRNA Metabolism by m 6 A Modification

XPO5 promotes primary miRNA processing independently of RanGTP

A Unified Model for the Function of YTHDF Proteins in Regulating m6A-Modified mRNA

Distinct Processing of lncRNAs Contributes to Nonconserved Functions in Stem Cells

Prediction of the sequence-specific cleavage activity of Cas9 variants

Single-Cell Analyses Inform Mechanisms of Myeloid-Targeted Therapies in Colon Cancer

Mapping the physical network of cellular interactions

Single-cell Long Non-coding RNA Landscape of T Cells in Human Cancer Immunity

Pan-cancer characterization of immune-related lncRNAs identifies potential oncogenic biomarkers

A single-cell landscape of high-grade serous ovarian cancer

Ribosome profiling at isoform level reveals evolutionary conserved impacts of differential splicing on the proteome

Identification of de novo mutations in prenatal neurodevelopment-associated genes in schizophrenia in two Han Chinese patient-sibling family-based cohorts

Single-Cell Alternative Splicing Analysis with Expedition Reveals Splicing Dynamics during Neuron Differentiation

Deep exploration networks for rapid engineering of functional DNA sequences

Direct detection of RNA modifications and structure using single molecule nanopore sequencing

High-throughput analysis of the activities of xCas9, SpCas9-NG and SpCas9 at matched and mismatched target sequences in human cells

Lineage-dependent gene expression programs influence the immune landscape of colorectal cancer

QAPA: a new method for the systematic analysis of alternative polyadenylation from RNA-seq data

Single-Cell Transcriptional Profiling Reveals Cellular Diversity and Intercommunication in the Mouse Heart

hnRNP C Tetramer Measures RNA Length to Classify RNA Polymerase II Transcripts for Export

SYNTHESIZER: Rethinking Self-Attention in Transformer Models

Deciphering human macrophage development at single-cell resolution

Single-cell RNA sequencing demonstrates the molecular and cellular reprogramming of metastatic lung adenocarcinoma

A functional screen of translated pancreatic lncRNAs identifies a microprotein-independent role for LINC00261 in endocrine cell differentiation

Comprehensive identification of alternative back-splicing in human tissue transcriptomes

Comparative Analysis for the Performance of Variant Calling Pipelines on Detecting the de novo Mutations in Humans

Unconstrained genome targeting with near-PAMless engineered CRISPR-Cas9 variants

Single-cell full-length total RNA sequencing uncovers dynamics of recursive splicing and enhancer RNAs

DoubletFinder: Doublet Detection in Single-Cell RNA Sequencing Data Using Artificial Nearest Neighbors

Benchmarking single-cell RNA-sequencing protocols for cell atlas projects

Direct full-length RNA sequencing reveals unexpected transcriptome complexity during Caenorhabditis elegans developmen

Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris

Pan-cancer characterization of immune-related lncRNAs identifies potential oncogenic biomarkers

Pervasive functional translation of non canonical human open reading frames

Pan-cancer analysis of whole genomes The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium

Accurate quantification of circular RNAs identifies extensive circular isoform switching events

Patterns of somatic structural variation in human cancer genomes

Time-Resolved Small RNA Sequencing Unravels the Molecular Principles of MicroRNA Homeostasis

Limits in the detection of m6A changes using MeRIP/m6A-seq

Universal Alternative Splicing of Noncoding Exons

High-throughput analysis of the activities of xCas9, SpCas9-NG and SpCas9 at matched and mismatched target sequences in human cells

Tumor Cell Biodiversity Drives Microenvironmental Reprogramming in Liver Cancer

APASdb: a database describing alternative poly(A) sites and selection of heterogeneous cleavage sites downstream of poly(A) signals

Phenotype molding of stromal cells in the lung tumor microenvironment

Global Positioning System: Understanding Long Noncoding RNAs through Subcellular Localization

Accurate annotation of human protein-coding small open reading frames

Patterns and mechanisms of structural variations in human cancer

Neutrophils escort circulating tumour cells to enable cell cycle progression