Difference between revisions of "Journal Club"

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

Prediction of single-cell RNA expression profiles in live cells by Raman microscopy with Raman2RNA

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

Predicting RNA-seq coverage from DNA sequence as a unifying model of gene regulation

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

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 metagenomes of Asian octogenarians reveal metabolic potential expansion and distinct microbial species associated with aging phenotypes

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