Difference between revisions of "Journal Club"

Bidirectional subsethood of shared marker profiles enables accurate virus classification

Self-supervised learning enables robust 1 microbiome predictions in data-limited and 2 cross-cohort settings

Microbiome-wide PheWAS links gut microbial SNVs to human health and exposures

BioLLM: A standardized framework for integrating and benchmarking single-cell foundation models

Predicting functions of uncharacterized gene products from microbial communities

OmniCellAgent: Towards AI Co-Scientists for Scientific Discovery in Precision Medicine

Autonomous chemical research with large language models

Systema: a framework for evaluating genetic perturbation response prediction beyond systematic variation

GLM-Prior: a nucleotide transformer model reveals prior knowledge as the driver of GRN inference performance

Yanomami skin microbiome complexity challenges prevailing concepts of healthy skin

Large-scale skin metagenomics reveals extensive prevalence, coordination, and functional adaptation of skin microbiome dermotypes across body sites

Generanno: A Genomic Foundation Model for Metagenomic Annotation

Inferring gene regulatory networks from single-cell multiome data using atlas-scale external data

Interpreting Attention Mechanisms in Genomic Transformer Models: A Framework for Biological Insights

A large-scale foundation model for bulk transcriptomes

xTrimoPGLM: unified 100-billion-parameter pretrained transformer for deciphering the language of proteins

Generalized biological foundation model with unified nucleic acid and protein language

AlphaGenome: advancing regulatory variant effect prediction with a unified DNA sequence model

Gut microbiome evolution from infancy to 8 years of age

Sliding Window Interaction Grammar (SWING): a generalized interaction language model for peptide and protein interactions

SSAlign: Ultrafast and Sensitive Protein Structure Search at Scale

Foundation Model Attributions Reveal Shared Inflammatory Program Across

Gut microbial GABA imbalance emerges as a metabolic signature in mild autism spectrum disorder linked to overrepresented Escherichia

Multi-omic analysis reveals transkingdom gut dysbiosis in metabolic dysfunction-associated steatotic liver disease

scNET: learning context-specific gene and cell embeddings by integrating single-cell gene expression data with protein–protein interactions

Fine-Tuning Protein Language Models Unlocks the Potential of Underrepresented Viral Proteomes

Orthology inference at scale with FastOMA

Lineage-specific microbial protein prediction enables large-scale exploration of protein ecology within the human gut

Cell2Sentence: Teaching Large Language Models the Language of Biology

High‑resolution strain‑level microbiome composition analysis from short reads

Gut metagenomes reveal interactions between dietary restriction, ageing and the microbiome in genetically diverse mice

A machine learning approach to leveraging electronic health records for enhanced omics analysis

Predicting transcriptional outcomes of novel multigene perturbations with GEARS

Nucleotide Transformer: building and evaluating robust foundation models for human genomics

Previously hidden intraspecies dynamics underlie the apparent stability of two important skin microbiome species

VIRGO2: Unveiling the Functional and Ecological Complexity of the Vaginal Microbiome with an Enhanced Non-Redundant Gene Catalog

Effects of gut microbiota on immune checkpoint inhibitors in multi-cancer and as microbial biomarkers for predicting therapeutic response

Highly accurate prophage island detection with PIDE

Genome modeling and design across all domains of life with Evo 2

Metagenome-informed metaproteomics of the human gut microbiome, host, and dietary exposome uncovers signatures of health and inflammatory bowel disease

A cell atlas foundation model for scalable search of similar human cells

geneRNIB: a living benchmark for gene regulatory network inference

GenomeOcean: An Efficient Genome Foundation Model Trained on Large-Scale Metagenomic Assemblies

SaprotHub: Making Protein Modeling Accessible to All Biologists

Disentanglement of single-cell data with biolord

Simulating 500 million years of evolution with a language model

Unveiling familial aggregation of nasopharyngeal carcinoma: Insights from oral microbiome dysbiosis

Predicting metabolite response to dietary intervention using deep learning

Ultra-fast and highly sensitive protein structure alignment with segment-level representations and block-sparse optimization

Integrating single-cell RNA and T cell/B cell receptor sequencing with mass cytometry reveals dynamic trajectories of human peripheral immune cells from birth to old age

GOPhage: protein function annotation for bacteriophages by integrating the genomic context

Fast, sensitive detection of protein homologs using deep dense retrieval

ImmuneLENS characterizes systemic immune dysregulation in aging and cancer

Mapping cells through time and space with moscot

Human gut microbiota subspecies carry implicit information for in-depth microbiome research

Intraspecies associations from strain-rich metagenome sample

Commonly used compositional data analysis implementations are not advantageous in microbial differential abundance analyses benchmarked against biological ground truth

Moving towards genome-wide data integration for patient stratification with Integrate Any Omics

Learning multi-cellular representations of single-cell transcriptomics data enables characterization of patient-level disease states

Emergence of community behaviors in the gut microbiota upon drug treatment

Prediction of strain level phage–host interactions across the Escherichia genus using only genomic information

Metagenomic estimation of absolute bacterial biomass in the mammalian gut through host-derived read normalization

De novo discovery of conserved gene clusters in microbial genomes with Spacedust

Rapid and Sensitive Protein Complex Alignment with Foldseek-Multimer

Single-cell RNA sequencing of human tissue supports successful drug targets

MGM as a large-scale pretrained foundation model for microbiome analyses in diverse contexts

Sequence modeling and design from molecular to genome scale with Evo

Human gut microbiome gene co-expression network reveals a loss in taxonomic and functional diversity in Parkinson’s disease

Quantifying Metagenomic Strain Associations from Microbiomes with Anpan

Evaluating the Utilities of Foundation Models in Single-cell Data Analysis

Accurate predictions on small data with a tabular foundation model

scEMB: Learning context representation of genes based on large-scale single-cell transcriptomics

TT3D: Leveraging precomputed protein 3D sequence models to predict protein–protein interactions

Topsy-Turvy: integrating a global view into sequence-based PPI prediction

D-SCRIPT translates genome to phenome with sequence-based, structure-aware, genome-scale predictions of protein-protein interactions

Quantized multi-task learning for context-specific representations of gene network dynamics

ANDES: a novel best-match approach for enhancing gene set analysis in embedding spaces

CellRank 2: unified fate mapping in multiview single-cell data

scPRINT: pre-training on 50 million cells allows robust gene network predictions

Bidirectional generation of structure and properties through a single molecular foundation model

MaAsLin 3: Refining and extending generalized multivariable linear models for meta-omic association discovery

Profiling lateral gene transfer events in the human microbiome using WAAFLE

ProTrek: Navigating the Protein Universe through Tri-Modal Contrastive Learning

The genetic diversity and populational specificity of the human gut virome at single nucleotide resolution

pan-Draft: automated reconstruction of species-representative metabolic models from multiple genomes

A core microbiome signature as an indicator of health

Using artificial intelligence to document the hidden RNA virosphere

Learning a deep language model for microbiomes: the power of large scale unlabeled microbiome data

Accurate proteome-wide missense variant effect prediction with AlphaMissense

A gut microbial signature for combination immune checkpoint blockade across cancer types

Fecal microbial marker panel for aiding diagnosis of autism spectrum disorders

Multikingdom and functional gut microbiota markers for autism spectrum disorder

A realistic benchmark for differential abundance testing and confounder adjustment in human microbiome studies

Microbial community-scale metabolic modelling predicts personalized short-chain fatty acid production profiles in the human gut

Gut microbiota wellbeing index predicts overall health in a cohort of 1000 infants

VirRep: a hybrid language representation learning framework for identifying viruses from human gut metagenomes

Ultrafast and accurate sequence alignment and clustering of viral genomes

The OMG dataset: An Open MetaGenomic corpus for mixed-modality genomic language modeling

Genomic language model predicts protein co-regulation and function

Protein Set 1 Transformer: A protein-based genome language model to power high diversity viromics

Prophage-DB: A comprehensive database to explore diversity,distribution, and ecology of prophages

Strain‑resolved de‑novo metagenomic assembly of viral genomes and microbial 16S rRNAs

Prokaryotic‑virus‑encoded auxiliary metabolic genes throughout the global oceans

Unexplored microbial diversity from 2,500 food metagenomes and links with the human microbiome

Pangenomes of Human Gut Microbiota Uncover Links Between Genetic Diversity and Stress Response

vClassifier: a toolkit for species-level classification of prokaryotic viruses

GRAViTy-V2: a grounded viral taxonomy application

Accurately predicting enzyme functions through geometric graph learning on ESMFold-predicted structures

Improved detection of microbiome-disease associations via population structure-aware generalized linear mixed effects models (microSLAM)

A blueprint for tumor-infiltrating B cells across human cancers

Systematic dissection of tumor-normal single-cell ecosystems across a thousand tumors of 30 cancer types

scDrugPrio: a framework for the analysis of single‑cell transcriptomics to address multiple problems in precision medicine in immune‑mediated inflammatory diseases

A visual-language foundation model for computational pathology

SLIDE: Significant Latent Factor Interaction Discovery and Exploration across biological domains

Clinical and molecular features of acquired resistance to immunotherapy in non-small cell lungcancer

Cell-Graph Compass: Modeling Single Cells with Graph Structure Foundation Model

Single-cell transcriptome landscape of circulating CD4+ T cell populations in autoimmune diseases

Population-level comparisons of gene regulatory networks modeled on highthroughput single-cell transcriptomics data

node2vec2rank: Large Scale and Stable Graph Differential Analysis via Multi-Layer Node Embeddings and Ranking

Unified cross-modality integration and analysis of T cell receptors and T cell transcriptomes by low-resource-aware representation learning

Contextual AI models for single-cell protein biology

Nicheformer: a foundation model for single-cell and spatial omics

Large Scale Foundation Model on Single-cell Transcriptomics

scGPT: toward building a foundation modelfor single-cell multi-omics using generative AI

Transfer learning enables predictions in network biology

The Web-Based Portal SpatialTME Integrates Histological Images with Single-Cell and Spatial Transcriptomics to Explore the Tumor Microenvironment

SEVtras delineates small extracellular vesicles at droplet resolution from single-cell transcriptomes

A relay velocity model infers cell-dependent RNA velocity

Pathway centric analysis for single-cell RNA-seq and spatial transcriptomics data with GSDensity

Dandelion uses the single-cell adaptive immune receptor repertoire to explore lymphocyte developmental origins

Automatic cell-type harmonization and integration across Human Cell Atlas datasets

Deep generative modeling of transcriptional dynamics for RNA velocity analysis in single cells

Gene signature extraction and cell identity recognition at the single-cell level with Cell-ID

Polygenic regression uncovers trait-relevant cellular contexts through pathway activation transformation of single-cell RNA sequencing data

Strain-specific gut microbial signatures in type 2 diabetes identified in a cross-cohort analysis of 8,117 metagenomes

Gut virome-wide association analysis identifes cross-population viral signatures for infammatory bowel disease

Efficient Low-rank Multimodal Fusion with Modality-Specific Factors

Tensor Fusion Network for Multimodal Sentiment Analysis

Gut symbionts alleviate MASH through a secondary bile acid biosynthetic pathway

Gut microbiota DPP4-like enzymes are increased in type-2 diabetes and contribute to incretin inactivation

Deep learning with multimodal representation for pancancer prognosis prediction

Pathomic Fusion: An Integrated Framework for Fusing Histopathology and Genomic Features for Cancer Diagnosis and Prognosis

Pan-cancer integrative histology-genomic analysis via multimodal deep learning

A metagenomics pipeline reveals insertion sequence-driven evolution of the microbiota

BiomedCLIP: a multimodal biomedical foundation model pretrained from fifteen million scientific image-text pairs

Learning Transferable Visual Models From Natural Language Supervision

BIONIC: biological network integration using convolutions

Protein remote homology detection and structural alignment using deep learning

Accurate structure prediction of biomolecular interactions with AlphaFold 3

Gut microbiome-metabolome interactions predict host condition

Microbiome confounders and quantitative profiling challenge predicted microbial targets in colorectal cancer development

A multi-kingdom collection of 33,804 reference genomes for the human vaginal microbiome

Efficient and accurate detection of viral sequences at single-cell resolution reveals putative novel viruses perturbing host gene expression

Compositional Differential Abundance Testing: Defining and Finding a New Type of Health-Microbiome Associations

Discovery of antimicrobial peptides in the global microbiome with machine learning

Custom scoring based on ecological topology of gut microbiota associated with cancer immunotherapy outcome

Paternal microbiome perturbations impact offspring fitness

Interactions-based classification of a single microbial sample

Accurate estimation of intraspecificmicrobial gene content variation inmetagenomic data with MIDAS v3 andStrainPGC

A pan-cancer analysis of the microbiome inmetastatic cancer

A specific enterotype derived from gut microbiomeof older individuals enables favorable responses toimmune checkpoint blockade therapy

Stratification of Fusobacterium nucleatum by localhealth status in the oral cavity defines its subspeciesdisease association

A universe of human gut-derived bacterialprophages: unveiling the hidden viral players inintestinal microecology

Robustness of cancer microbiome signals over a broad range of methodological variation

A distinct Fusobacterium nucleatum clade dominates the colorectal cancer niche

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

Gut microbiome and metabolome profiling in Framingham heart study reveals cholesterol-metabolizing bacteria

Fecal microbial load is a major determinant of gut microbiome variation and aconfounder for disease associations

A host-microbiota interactome reveals extensive transkingdom connectivity

Metagenomic estimation of dietary intake from human stool

A metagenomic catalog of the early-life human gut virome

Large-scale computational analyses of gut microbial CAZyme repertoires enabled by Cayman

Defining the biogeographical map and potential bacterial translocation of microbiome in human ‘surface organs’

Gut microbial structural variation associates with immune checkpoint inhibitor response

Fungal signature differentiates alcohol-associated liver disease from nonalcoholic fatty liver disease

Incorporating metabolic activity, taxonomy and community structure to improve microbiome based predictive models for host phenotype prediction

Disease-specific loss of microbial cross feeding interactions in the human gut

Multigroup analysis of compositions of microbiomes with covariate adjustments and repeated measures

Microdiversity of the vaginal microbiome is associated with preterm birth

Large language models improve annotation of prokaryotic viral proteins

Clinically relevant antibiotic resistance genes are linked to a limited set of taxa within gut microbiome worldwide

Visualizing ’omic feature rankings and log-ratios using Qurro

Establishing microbial composition measurement standards with reference frames

AnnoPRO: a strategy for protein function annotation based on multi-scale protein representation and a hybrid deep learning of dual-path encoding

Differential responses of the gut microbiome and resistome to antibiotic exposures in infants and adults

Effective binning of metagenomic contigs using contrastive multi-view representation learning

Polarization of microbial communities between competitive and cooperative metabolism

Metagenomic Insight into The Global Dissemination of The Antibiotic Resistome

Conjugative plasmids interact with insertion sequences to shape the horizontal transfer of antimicrobial resistance genes

Spatial transcriptomics reveal neuron–astrocyte synergy in long-term memory

scGNN is a novel graph neural network framework for single-cell RNA-Seq analyses

Spatial transcriptomics of planktonic and sessile bacterial populations at single-cell resolution

Human lung cancer harbors spatially organized stem-immunity hubs associated with response to immunotherapy

Single-cell transcriptomics captures features of human midbrain development and dopamine neuron diversity in brain organoids

Cell-type-specific responses to fungal infection in plants revealed by single-cell transcriptomics

The single-cell stereo-seq reveals region-specific cell subtypes and transcriptome profiling in Arabidopsis leaves

Single-cell and bulk transcriptome sequencing identifies two epithelial tumor cell states and refines the consensus molecular classification of colorectal cancer

Delineating mouse β-cell identity during lifetime and in diabetes with a single cell atlas

Multimodal spatiotemporal phenotyping of human retinal organoid development

Immune microniches shape intestinal Treg function

A single-cell analysis of the Arabidopsis vegetative shoot apex

Droplet-based high-throughput single microbe RNA sequencing by smRandom-seq

Single-cell massively-parallel multiplexed microbial sequencing (M3-seq) identifies rare bacterial populations and profiles phage infection

Spatial transcriptomics demonstrates the role of CD4 T cells in effector CD8 T cell differentiation during chronic viral infection

Spatial metatranscriptomics resolves host–bacteria–fungi interactomes

Dissecting the immune suppressive human prostate tumor microenvironment via integrated single-cell and spatial transcriptomic analyses

Single-nucleus genomics in outbred rats with divergent cocaine addiction-like behaviors reveals changes in amygdala GABAergic inhibition

Spatial transcriptomics reveals the distinct organization of mouse prefrontal cortex and neuronal subtypes regulating chronic pain

Spatial cellular architecture predicts prognosis in glioblastoma

Single-cell spatial transcriptomic and translatomic profiling of dopaminergic neurons in health, aging, and disease

Transcriptional adaptation of olfactory sensory neurons to GPCR identity and activity

Spatial deconvolution of HER2-positive breast cancer delineates tumor-associated cell type interactions

Single-Cell Analysis Reveals Cxcl14+ Fibroblast Accumulation in Regenerating Diabetic Wounds Treated by Hydrogel-Delivering Carbon Monoxide

Single-cell RNA sequencing provides a high-resolution roadmap for understanding the multicellular compartmentation of specialized metabolism

Single-cell spatial multi-omics and deep learning dissect enhancer-driven gene regulatory networks in liver zonation

Spatial transcriptomics landscape of lesions from non-communicable inflammatory skin diseases

Neuregulin 4 suppresses NASH-HCC development by restraining tumor-prone liver microenvironment

Single-nucleus multiregion transcriptomic analysis of brain vasculature in Alzheimer’s disease

Single-cell transcriptomic analysis deciphers heterogenous cancer stem-like cells in colorectal cancer and their organ-specific metastasis

Single cell sequencing identifies clonally expanded synovial CD4+ TPH cells expressing GPR56 in rheumatoid arthritis

Progenitor-like exhausted SPRY1+CD8+ T cells potentiate responsiveness to neoadjuvant PD-1 blockade in esophageal squamous cell carcinoma

Population-level integration of single-cell datasets enables multi-scale analysis across samples

scDiffCom: a tool for differential analysis of cell–cell interactions provides a mouse atlas of aging changes in intercellular communication

Modeling intercellular communication in tissues using spatial graphs of cells

Precise identification of cell states altered in disease using healthy single-cell references

Learning Individual Survival Models from PanCancer Whole Transcriptome Data

Dictys: dynamic gene regulatory network dissects developmental continuum with single-cell multiomics

Preexisting tumor-resident T cells with cytotoxic potential associate with response to neoadjuvant anti–PD-1 in head and neck cancer

MHC II immunogenicity shapes the neoepitope landscape in human tumors

Hallmarks of transcriptional intratumour heterogeneity across a thousand tumours

Pan-cancer classification of single cells in the tumour microenvironment

Single-cell mapping of combinatorial target antigens for CAR switches using logic gates

Comparative analysis of cell–cell communication at single-cell resolution

Phenotypic diversity of T cells in human primary and metastatic brain tumors revealed by multiomic interrogation

An integrated tumor, immune and microbiome atlas of colon cancer

Multi-omic single-cell velocity models epigenome–transcriptome interactions and improves cell fate prediction

Recruitment of epitope-specific T cell clones with a low-avidity threshold supports efficacy against mutational escape upon re-infection

Phages are unrecognized players in the ecology of the oral pathogen Porphyromonas gingivalis

A predicted CRISPR-mediated symbiosis between uncultivated archaea

Integrating compositional and functional content to describe vaginal microbiomes in health and disease

Contamination source modeling with SCRuB improves cancer phenotype prediction from microbiome data

Mapping the T cell repertoire to a complex gut bacterial community

Multi-view integration of microbiome data for identifying disease-associated modules

Phage-bacteria dynamics during the first years of life revealed by trans-kingdom marker gene analysis

Multi-level analysis of the gut–brain axis shows autism spectrum disorder-associated molecular and microbial profiles

Metagenomic Immunoglobulin Sequencing (MIG-Seq) Exposes Patterns of IgA Antibody Binding in the Healthy Human Gut Microbiome

Impact of dietary interventions on pre-diabetic oral and gut microbiome, metabolites and cytokines

Fast and robust metagenomic sequence comparison through sparse chaining with skani

Bacterial SNPs in the human gut microbiome associate with host BMI

Multimodal metagenomic analysis reveals microbial single nucleotide variants as superior biomarkers for early detection of colorectal cancer

Multi-kingdom gut microbiota analyses define bacterial-fungal interplay and microbial markers of pan-cancer immunotherapy across cohorts

Prior antibiotic administration disrupts anti-PD-1 responses in advanced gastric cancer by altering the gut microbiome and systemic immune response

Ultra-deep sequencing of Hadza hunter-gatherers recovers vanishing gut microbes

Altered infective competence of the human gut microbiome in COVID-19

Host-Variable-Embedding Augmented Microbiome-Based Simultaneous Detection of Multiple Diseases by Deep Learning

A data-driven approach for predicting the impact of drugs on the human microbiome

Activation of programmed cell death and counter-defense functions of phage accessory genes

Top-down identification of keystone taxa in the microbiome

Pitfalls of genotyping microbial communities with rapidly growing genome collections

Reconstruction of the last bacterial common ancestor from 183 pangenomes reveals a versatile ancient core genome

Generation of accurate, expandable phylogenomic trees with uDance

Phage display sequencing reveals that genetic, environmental, and intrinsic factors influence variation of human antibody epitope repertoire

Phage-display immunoprecipitation sequencing of the antibody epitope repertoire in inflammatory bowel disease reveals distinct antibody signatures

Consistency across multi-omics layers in a drug-perturbed gut microbial community

Identification of mobile genetic elements with geNomad

Microbiome-derived cobalamin and succinyl-CoA as biomarkers for improved screening of anal cancer

The airway microbiome mediates the interaction between environmental exposure and respiratory health in humans

Ordering taxa in image convolution networks improves microbiome-based machine learning accuracy

The defensome of complex bacterial communities

Dietary tryptophan metabolite released by intratumoral Lactobacillus reuteri facilitates immune checkpoint inhibitor treatment

Toward an improved definition of a healthy microbiome for healthy aging

Associations of the skin, oral and gut microbiome with aging, frailty and infection risk reservoirs in older adults

Statistical modeling of gut microbiota for personalized health status monitoring

Adjusting for age improves identification of gut microbiome alterations in multiple diseases

Centenarians have a diverse gut virome with the potential to modulate metabolism and promote healthy lifespan

Longitudinal comparison of the developing gut virome in infants and their mothers

Structure of the Mucosal and Stool Microbiome in Lynch Syndrome

Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases

Roles of oral microbiota and oral-gut microbial transmission in hypertension

Human gut microbiota stimulate defined innate immune responses that vary from phylum to strain

Gut microbial metabolism of 5-ASA diminishes its clinical efficacy in inflammatory bowel disease

Deficient butyrate-producing capacity in the gut microbiome is associated with bacterial network disturbances and fatigue symptoms in ME/CFS

Gut microbiota-mediated nucleotide synthesis attenuates the response to neoadjuvant chemoradiotherapy in rectal cancer

Multi-omics reveal microbial determinants impacting responses to biologic therapies in inflammatory bowel disease

Identification of trypsin-degrading commensals in the large intestine

Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies

Tissue-resident Lachnospiraceae family bacteria protect against colorectal carcinogenesis by promoting tumor immune surveillance

Pan-cancer analyses reveal cancer-type-specific fungal ecologies and bacteriome interactions

A pan-cancer mycobiome analysis reveals fungal involvement in gastrointestinal and lung tumors

Multi-kingdom microbiota analyses identify bacterial–fungal interactions and biomarkers of colorectal cancer across cohorts

The antitumour effects of caloric restriction are mediated by the gut microbiome

Variability of strain engraftment and predictability of microbiome composition after fecal microbiota transplantation across different diseases

Drivers and determinants of strain dynamics following fecal microbiota transplantation

Mobile genetic elements from the maternal microbiome shape infant gut microbial assembly and metabolism

Mother-to-infant microbiota transmission and infant microbiota development across multiple body sites

Population-level impacts of antibiotic usage on the human gut microbiome

Enterococci enhance Clostridioides difficile pathogenesis

Targeting keystone species helps restore the dysbiosis of butyrate‐producing bacteria in nonalcoholic fatty liver disease

Differential Oral Microbial Input Determines Two Microbiota Pneumo-Types Associated with Health Status

Gut microbiome of multiple sclerosis patients and paired household healthy controls reveal associations with disease risk and course

Decoupling the correlation between cytotoxic and exhausted T lymphocyte transcriptomic signatures enhances melanoma immunotherapy response prediction from tumor expression

Major data analysis errors invalidate cancer microbiome findings

A single-cell atlas of glioblastoma evolution under therapy reveals cell-intrinsic and cell-extrinsic therapeutic targets

Single-cell meta-analyses reveal responses of tumor-reactive CXCL13+ T cells to immune-checkpoint blockade

Estimation of tumor cell total mRNA expression in 15 cancer types predicts disease progression

DIALOGUE maps multicellular programs in tissue from single-cell or spatial transcriptomics data

Pan-cancer T cell atlas links a cellular stress response state to immunotherapy resistance

Self-supervised graph representation learning integrates multiple molecular networks and decodes gene-disease relationships

High-resolution single-cell atlas reveals diversity and plasticity of tissue-resident neutrophils in non-small cell lung cancer

Parallel single-cell and bulk transcriptome analyses reveal key features of the gastric tumor microenvironment

Mutated processes predict immune checkpoint inhibitor therapy benefit in metastatic melanoma

Temporal single-cell tracing reveals clonal revival and expansion of precursor exhausted T cells during anti-PD-1 therapy in lung cancer

Integrative single-cell analysis of cardiogenesis indentifies developmental trajectories and non-conding mutations in congenital heart disease

Supervised discovery of interpretable gene programs from single-cell data

Effect of the intratumoral microbiota on spatial and cellular heterogeneity in cancer

Cancer cell states recur across tumor types and form specific interactions with the tumor microenvironment

MetaTiME: Meta-components of the Tumor Immune Microenvironment

Pre-encoded responsiveness to type I interferon in the peripheral immune system defines outcome of PD1 blockade therapy

Integrated single-cell profiling dissects cell-state-specific enhancer landscapes of human tumor-infiltrating T cells

A T cell resilience model associated with response to immunotherapy in multiple tumor types

Single-nucleus and spatial transcriptome profiling of pancreatic cancer identifies multicellular dynamics associated with neoadjuvant treatment

Cross-tissue, single-cell stromal atlas identifies shared pathological fibroblast phenotypes in four chronic inflammatory diseases

Pan-cancer integrative histology-genomic analysis via multimodal deep learning

Tissue-resident memory and circulating T cells are early responders to pre-surgical cancer immunotherapy

Enterosignatures define common bacterial guilds in the human gut microbiome

PhyloMed: a phylogeny-based test of mediation effect in microbiome

The TaxUMAP atlas: Efficient display of large clinical microbiome data reveals ecological competition in protection against bacteremia

Measurement of bacterial replication rates in microbial communities

Skin microbiome diferentiates into distinct cutotypes with unique metabolic functions upon exposure to polycyclic aromatic hydrocarbons

Enrichment of oral-derived bacteria in inflamed colorectal tumors and distinct associations of Fusobacterium in the mesenchymal subtype

Profiling the human intestinal environment under physiological conditions

Genome-centric metagenomics reveals the host-driven dynamics and ecological role of CPR bacteria in an activated sludge system

Enhanced metagenomic deep learning for disease prediction and consistent signature recognition by restructured microbiome 2D representations

Gene fow and introgression are pervasive forces shaping the evolution of bacterial species

Alterations of oral microbiota and impact on the gut microbiome in type 1 diabetes mellitus revealed by integrated multi‑omic analyses

Deciphering microbial gene function using natural language processing

Rethinking bacterial relationships in light of their molecular abilities

The CD4+ T cell response to a commensal-derived epitope transitions from a tolerant to an inflammatory state in Crohn’s disease

Antigen discovery and specification of immunodominance hierarchies for MHCIIrestricted epitopes

Single Cell Transcriptomics Reveals the Hidden Microbiomes of Human Tissues

Stability of the human faecal microbiome in a cohort of adult men

Metatranscriptome of human faecal microbial communities in a cohort of adult men

Tumor microbiome links cellular programs and immunity in pancreatic cancer

Extensive gut virome variation and its associations with host and environmental factors in a population-level cohort

The person-to-person transmission landscape of the gut and oral microbiomes

BIRDMAn: A Bayesian differential abundance framework that enables robust inference of host-microbe associations

Phage–host coevolution in natural populations

A randomized controlled trial for response of microbiome network to exercise and diet intervention in patients with nonalcoholic fatty liver disease

Scalable power analysis and effect size exploration of microbiome community differences with Evident

Phanta: Phage-inclusive profiling of human gut metagenomes

Computational approach to modeling microbiome landscapes associated with chronic human disease progression

SCENIC+: single-cell multiomic inference of enhancers and gene regulatory networks

Representation learning of RNA velocity reveals robust cell transitions UniTVelo: temporally unified RNA velocity reinforces single-cell trajectory inference Mapping transcriptomic vector fields of single cells

Network-based machine learning approach to predict immunotherapy response in cancer patients

Modeling fragment counts improves single-cell ATAC-seq analysis

Extricating human tumour immune alterations from tissue inflammation

T cell receptor convergence is an indicator of antigen-specific T cell response in cancer immunotherapies

Identifying phenotype-associated subpopulations by integrating bulk and single-cell sequencing data

MIRA: Joint regulatory modeling of multimodal expression and chromatin accessibility in single cells

Immune phenotypic linkage between colorectal cancer and liver metastasis

Biologically informed deep learning to infer gene program activity in single cells

Cell type and gene expression deconvolution with BayesPrism enables Bayesian integrative analysis across bulk and single-cell RNA sequencing in oncology

Mapping single-cell data to reference atlases by transfer learning

Pan-cancer mapping of single T cell profiles reveals a TCF1:CXCR6-CXCL16 regulatory axis essential for effective anti-tumor immunity

Identifying disease-critical cell types and cellular processes across the human body by integration of single-cell profiles and human genetics

Metacells untangle large and complex single-cell transcriptome networks MetaCell: analysis of single-cell RNA-seq data using K-nn graph partitions Metacell‑2: a divide‑and‑conquer metacell algorithm for scalable scRNA‑seq analysis

Co-varying neighborhood analysis identifies cell populations associated with phenotypes of interest from single-cell transcriptomics

Integrating T cell receptor sequences and transcriptional profiles by clonotype neighbor graph analysis (CoNGA)

Hepatocellular carcinoma patients with high circulating cytotoxic T cells and intra-tumoral immune signature benefit from pembrolizumab: results from a single-arm phase 2 trial

Effect of imputation on gene network reconstruction from single-cell RNA-seq data

Diagnostic Evidence GAuge of Single cells (DEGAS): a flexible deep transfer learning framework for prioritizing cells in relation to disease

Integrating single-cell sequencing data with GWAS summary statistics reveals CD16+monocytes and memory CD8+T cells involved in severe COVID-19

Single cell T cell landscape and T cell receptor repertoire profiling of AML in context of PD-1 blockade therapy

Systematic investigation of cytokine signaling activity at the tissue and single-cell levels

Neoantigen-driven B cell and CD4 T follicular helper cell collaboration promotes anti-tumor CD8 T cell responses

MultiMAP: dimensionality reduction and integration of multimodal data

CellRank for directed single-cell fate mapping

Single-cell analyses reveal key immune cell subsets associated with response to PD-L1 blockade in triple-negative breast cancer

Chromatin and gene-regulatory dynamics of the developing human cerebral cortex at single-cell resolution

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

Pan-cancer single-cell landscape of tumor-infiltrating T cells

Atlas of clinically distinct cell states and ecosystems across human solid tumors

Single-cell ATAC and RNA sequencing reveal pre-existing and persistent cells associated with prostate cancer relapse

A novel in silico method employs chemical and protein similarity algorithms to accurately identify chemical transformations in the human gut microbiome

Inference of disease-associated microbial biomarkers based on metagenomic and metatranscriptomic data

Personalized microbiome-driven effects of non-nutritive sweeteners on human glucose tolerance

Identification of shared and disease-specific host gene–microbiome associations across human diseases using multi-omic integration

Caudovirales bacteriophages are associated with improved executive function and memory in flies, mice, and humans

SynTracker: a synteny based tool for tracking microbial strains

Identification of antimicrobial peptides from the human gut microbiome using deep learning

Discovery of bioactive microbial gene products in inflammatory bowel disease

Large-scale microbiome data integration enables robust biomarker identification

Predicting cancer prognosis and drug response from the tumor microbiome

Thousands of small, novel genes predicted in global phage genomes

MetaPop: a pipeline for macro- and microdiversity analyses and visualization of microbial and viral metagenome-derived populations

Biosynthetic potential of the global ocean microbiome

Compositionally Aware Phylogenetic Beta-Diversity Measures Better Resolve Microbiomes Associated with Phenotype

Tutorial: assessing metagenomics software with the CAMI benchmarking toolkit disease Critical Assessment of Metagenome Interpretation: the second round of challenges

Identification of Faecalibacterium prausnitzii strains for gut microbiome-based intervention in Alzheimer’s-type dementia

Microbiome and metabolome features of the cardiometabolic disease spectrum

Functional and genetic markers of niche partitioning among enigmatic members of the human oral microbiome

Integrating phylogenetic and functional data in microbiome studies

Pandora: nucleotide-resolution bacterial pan-genomics with reference graphs

Multivariable association discovery in population-scale meta-omics studies

Comprehensive Analysis Reveals the Evolution and Pathogenicity of Aeromonas, Viewed from Both Single Isolated Species and Microbial Communities

AGAMEMNON: an Accurate metaGenomics And MEtatranscriptoMics quaNtificatiON analysis suite

Metapangenomics of the oral microbiome provides insights into habitat adaptation and cultivar diversity

Microbiota of the prostate tumor environment investigated by whole-transcriptome profiling

Species-resolved sequencing of low-biomass or degraded microbiomes using 2bRAD-M

Microbial co-occurrence complicates associations of gut microbiome with US immigration, dietary intake and obesity

Gut microbial determinants of clinically important improvement in patients with rheumatoid arthritis

Gut microbiota modulates weight gain in mice after discontinued smoke exposure

The human microbiome encodes resistance to the antidiabetic drug acarbose

Commensal bacteria promote endocrine resistance in prostate cancer through androgen biosynthesis

The influence of the gut microbiome on BCG-induced trained immunity

Towards the biogeography of prokaryotic genes

ReprDB and panDB: minimalist databases with maximal microbial representation

Maast: genotyping thousands of microbial strains efficiently

MIDAS2: Metagenomic Intra-species Diversity Analysis System

Scalable microbial strain inference in metagenomic data using StrainFacts

StrainPanDA: linked reconstruction of strain composition and gene content profiles via pangenome-based decomposition of metagenomic data

Metagenomic strain detection with SameStr: identification of a persisting core gut microbiota transferable by fecal transplantation

Fast and accurate metagenotyping of the human gut microbiome with GT-Pro

inStrain profiles population microdiversity from metagenomic data and sensitively detects shared microbial strains

Longitudinal linked-read sequencing reveals ecological and evolutionary responses of a human gut microbiome during antibiotic treatment

Dispersal strategies shape persistence and evolution of human gut bacteria

The long-term genetic stability and individual specificity of the human gut microbiome

Analysis of 1321 Eubacterium rectale genomes from metagenomes uncovers complex phylogeographic population structure and subspecies functional adaptations

Evolutionary dynamics of bacteria in the gut microbiome within and across hosts

Extensive transmission of microbes along the gastrointestinal tract

Distinct Genetic and Functional Traits of Human Intestinal Prevotella copri Strains Are Associated with Different Habitual Diets

Strain-level microbial epidemiology and population genomics from shotgun metagenomics

Chromatin and gene-regulatory dynamics of the developing human cerebral cortex at single-cell resolution

Single-cell ATAC and RNA sequencing reveal pre-existing and persistent subpopulations of cells associated with relapse of prostate cancer

Integrated single-cell transcriptomics and epigenomics reveals strong germinal center-associated etiology of autoimmune risk loci

Functional Inference of Gene Regulation using Single-Cell Multi-Omics

Single-cell analyses reveal a continuum of cell state and composition changes in the malignant transformation of polyps to colorectal cancer

Single-cell sequencing links multiregional immune landscapes and tissue-resident T cells in ccRCC to tumor topology and therapy efficacy

Tumor and immune reprogramming during immunotherapy in advanced renal cell carcinoma

Single-cell chromatin accessibility landscape identifies tissue repair program in human regulatory T cells

Identification of resistance pathways and therapeutic targets in relapsed multiple myeloma patients through single-cell sequencing

A single-cell map of intratumoral changes during anti-PD1 treatment of patients with breast cancer

Single-cell landscape of the ecosystem in early-relapse hepatocellular carcinoma

Interpreting type 1 diabetes risk with genetics and single-cell epigenomics

Massive expansion of human gut bacteriophage diversity

The infant gut resistome associates with E. coli, environmental exposures, gut microbiome maturity, and asthma-associated bacterial composition

Methotrexate impacts conserved pathways in diverse human gut bacteria leading to decreased host immune activation

A metagenomic strategy for harnessing the chemical repertoire of the human microbiome

Predictive metabolomic profiling of microbial communities using amplicon or metagenomic sequences

Gut microbiome structure and metabolic activity in inflammatory bowel disease

Microbiome connections with host metabolism and habitual diet from 1,098 deeply phenotyped individuals

A predictive index for health status using species-level gut microbiome profiling

Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases

Gastrointestinal microbiota composition predicts peripheral inflammatory state during treatment of human tuberculosis

Structure of the Mucosal and Stool Microbiome in Lynch Syndrome

Cross-reactivity between tumor MHC class 1-restricted antigens and an enterococcal bacteriophage

Bifidobacterium bifidum strains synergize with immune checkpoint inhibitors to reduce tumour burden in mice

The gut microbiome modulates the protective association between a Mediterranean diet and cardiometabolic disease risk

Impact of commonly used drugs on the composition and metabolic function of the gut microbiota

Personalized Mapping of Drug Metabolism by the Human Gut Microbiome

Mining the Human Gut Microbiota for Immunomodulatory Organisms

Microbiome analyses of blood and tissues suggest cancer diagnostic approach

The human tumor microbiome is composed of tumor type-specific intracellular bacteria

Functional CRISPR dissection of gene networks controlling human regulatory T cell identity

Molecular Pathways of Colon Inflammation Induced by Cancer Immunotherapy

Single-cell epigenomic analyses implicate candidate causal variants at inherited risk loci for Alzheimer’s and Parkinson’s diseases

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

Genetic determinants of co-accessible chromatin regions in activated T cells across humans

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

Single-Cell Analysis of Crohn's Disease Lesions Identifies a Pathogenic Cellular Module Associated with Resistance to Anti-TNF Therapy

Multi-omic single-cell snapshots reveal multiple independent trajectories to drug tolerance in a melanoma cell line

Multi-omic single-cell snapshots reveal multiple independent trajectories to drug tolerance in a melanoma cell line

Dysfunctional CD8 T Cells Form a Proliferative, Dynamically Regulated Compartment Within Human Melanoma

A Cancer Cell Program Promotes T Cell Exclusion and Resistance to Checkpoint Blockade

Single-cell Transcriptional Diversity Is a Hallmark of Developmental Potential

Landscape and Dynamics of Single Immune Cells in Hepatocellular Carcinoma

Peripheral T Cell Expansion Predicts Tumour Infiltration and Clinical Response

Defining T Cell States Associated With Response to Checkpoint Immunotherapy in Melanoma

Rapid Non-Uniform Adaptation to Conformation-Specific KRAS(G12C) Inhibition

Targeted Therapy Guided by Single-Cell Transcriptomic Analysis in Drug-Induced Hypersensitivity Syndrome: A Case Report

Distinct Microbial and Immune Niches of the Human Colon

Massively Parallel Single-Cell Chromatin Landscapes of Human Immune Cell Development and Intratumoral T Cell Exhaustion

Single-cell Gene Expression Reveals a Landscape of Regulatory T Cell Phenotypes Shaped by the TCR

A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility

scAI: An Unsupervised Approach for the Integrative Analysis of Parallel Single-Cell Transcriptomic and Epigenomic Profiles

Single-cell Multiomic Analysis Identifies Regulatory Programs in Mixed-Phenotype Acute Leukemia

Obese Individuals with and without Type 2 Diabetes Show Different Gut Microbial Functional Capacity and Composition

Clustering co-abundant genes identifies components of the gut microbiome that are reproducibly associated with colorectal cancer and inflammatory bowel disease

Massively parallel single-cell chromatin landscapes of human immune cell development and intratumoral T cell exhaustion

Assessment of computational methods for the analysis of single-cell ATAC-seq data

Meta-Analysis Reveals Reproducible Gut Microbiome Alterations in Response to a High-Fat Diet

Tumor Microbiome Diversity and Composition Influence Pancreatic Cancer Outcomes

The accessible chromatin landscape of the murine hippocampus at single-cell resolution

Integrated Single-Cell Analysis Maps the Continuous Regulatory Landscape of Human Hematopoietic Differentiation

A sparse covarying unit that describes healthy and impaired human gut microbiota development

Large-Scale Analyses of Human Microbiomes Reveal Thousands of Small, Novel Genes

Intra- and Inter-cellular Rewiring of the Human Colon during Ulcerative Colitis

Multiplexed droplet single-cell RNA-sequencing using natural genetic variation

The Landscape of Genetic Content in the Gut and Oral Human Microbiome

Benchmarking Metagenomics Tools for Taxonomic Classification

Coexpression uncovers a unified single-cell transcriptomic landscape

Single-cell interactomes of the human brain reveal cell-type specific convergence of brain disorders

Proportionality: a valid alternative to correlation for relative data

propr: An R-package for Identifying Proportionally Abundant Features Using Compositional Data Analysis

Robust prediction of response to immune checkpoint blockade therapy in metastatic melanoma

A test metric for assessing single-cell RNA-seq batch correction

Comprehensive Integration of Single-Cell Data

Defining T Cell States Associated with Response to Checkpoint Immunotherapy in Melanoma

High-Dimensional Analysis Delineates Myeloid and Lymphoid Compartment Remodeling during Successful Immune-Checkpoint Cancer Therapy

A single-cell reference map for human blood and tissue T cell activation reveals functional states in health and disease

Dysfunctional CD8 T Cells Form a Proliferative, Dynamically Regulated Compartment within Human Melanoma

High-dimensional single-cell analysis predicts response to anti-PD-1 immunotherapy

A Cancer Cell Program Promotes T Cell Exclusion and Resistance to Checkpoint Blockade

COMPASS identifies T-cell subsets correlated with clinical outcomes.

Sensitive detection of rare disease-associated cell subsets via representation learning

Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer

Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation

Microbial network disturbances in relapsing refractory Crohn's disease.

New insights from uncultivated genomes of the global human gut microbiome

A new genomic blueprint of the human gut microbiota

Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle.

Dynamics of metatranscription in the inflammatory bowel disease gut microbiome.

Metatranscriptome of human faecal microbial communities in a cohort of adult men.

Post-Antibiotic Gut Mucosal Microbiome Reconstitution Is Impaired by Probiotics and Improved by Autologous FMT.

Personalized Gut Mucosal Colonization Resistance to Empiric Probiotics Is Associated with Unique Host and Microbiome Features.

Distinct Immune Cell Populations Define Response to Anti-PD-1 Monotherapy and Anti-PD-1/Anti-CTLA-4 Combined Therapy.

Subsets of exhausted CD8+ T cells differentially mediate tumor control and respond to checkpoint blockade.

Lineage tracking reveals dynamic relationships of T cells in colorectal cancer.

Single cell dissection of plasma cell heterogeneity in symptomatic and asymptomatic myeloma.

Single-cell profiling of breast cancer T cells reveals a tissue-resident memory subset associated with improved prognosis.

Global characterization of T cells in non-small-cell lung cancer by single-cell sequencing

Reference component analysis of single-cell transcriptomes elucidates cellular heterogeneity in human colorectal tumors.

Landscape of Infiltrating T Cells in Liver Cancer Revealed by Single-Cell Sequencing.

Phenotype molding of stromal cells in the lung tumor microenvironment.

A single-cell molecular map of mouse gastrulation and early organogenesis

The single-cell transcriptional landscape of mammalian organogenesis

Single-Cell Map of Diverse Immune Phenotypes in the Breast Tumor Microenvironment

Single-Cell Transcriptomic Analysis of Primary and Metastatic Tumor Ecosystems in Head and Neck Cancer

A Pan-Cancer Analysis of Enhancer Expression in Nearly 9000 Patient Samples.

Machine Learning Identifies Stemness Features Associated with Oncogenic Dedifferentiation.

Developmental and oncogenic programs in H3K27M gliomas dissected by single-cell RNA-seq.

Chemoresistance Evolution in Triple-Negative Breast Cancer Delineated by Single-Cell Sequencing.

Mapping human pluripotent stem cell differentiation pathways using high throughput single-cell RNA-sequencing.

A single-cell RNA-seq survey of the developmental landscape of the human prefrontal cortex.

Single-cell RNA sequencing identifies celltype-specific cis-eQTLs and co-expression QTLs.

FOCS: a novel method for analyzing enhancer and gene activity patterns infers an extensive enhancer-promoter map.

A Distinct Gene Module for Dysfunction Uncoupled from Activation in Tumor-Infiltrating T Cells.

A global transcriptional network connecting noncoding mutations to changes in tumor gene expression.

Inferring regulatory element landscapes and transcription factor networks from cancer methylomes.

Genomic and Transcriptomic Features of Response to Anti-PD-1 Therapy in Metastatic Melanoma.

Tumor aneuploidy correlates with markers of immune evasion and with reduced response to immunotherapy.

Landscape of tumor-infiltrating T cell repertoire of human cancers.

The landscape of T cell infiltration in human cancer and its association with antigen presenting gene expression.

A Distinct Gene Module for Dysfunction Uncoupled from Activation in Tumor-Infiltrating T Cells.

Identification of genetic determinants of breast cancer immune phenotypes by integrative genome-scale analysis.