Difference between revisions of "Journal Club"

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

CD4+ T cell activation distinguishes response to anti-PD-L1+anti-CTLA4 therapy from anti-PD-L1 monotherapy

Single-cell and spatial profiling identify three response trajectories to pembrolizumab and radiation therapy in triple negative breast cancer

A TCF4-dependent gene regulatory network confers resistance to immunotherapy in melanoma

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

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

[https://doi.org/10.1101/2024.06.04.597354 Cell-Graph Compass: Modeling Single Cells with Graph Structure Foundation Model

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

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

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

Large-scale foundation model on single-cell transcriptomics

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

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

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.

Genomic Correlates of Immune-Cell Infiltrates in Colorectal Carcinoma.

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

Pan-cancer Immunogenomic Analyses Reveal Genotype-Immunophenotype Relationships and Predictors of Response to Checkpoint Blockade.

Systemic Immunity Is Required for Effective Cencer Immunotherapy.

Linking the Human Gut Microbiome to Inflammatory Cytokine Production Capacity.

Host and Environmental Factors Influencing Individual Human Cytokine Responses.

A Functional Genomics Approach to Understand Variation in Cytokine Production in Humans.

Pooled CRISPR screening with single-cell transcriptome readout.

Dissecting Immune Circuits by Linking CRISPR-Pooled Screens with Single-Cell RNA-Seq.

Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens.

Wishbone identifies bifurcating developmental trajectories from single-cell data.

Reversed graph embedding resolves complex single-cell developmental trajectories.

Single-cell mRNA quantification and differential analysis with Census.

Single-Cell Transcriptomic Analysis Defines Heterogeneity and Transcriptional Dynamics in the Adult Neural Stem Cell Lineage.

Single-Cell Network Analysis Identifies DDIT3 as a Nodal Lineage Regulator in Hematopoiesis.

Single-cell analysis of mixed-lineage states leading to a binary cell fate choice.

Dissecting direct reprogramming from fibroblast to neuron using single-cell RNA-seq.

Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq.

Single-cell mRNA sequencing identifies subclonal heterogeneity in anti-cancer drug responses of lung adenocarcinoma cells.

A Comprehensive Characterization of the Function of LincRNAs in Transcriptional Regulation Through Long-Range Chromatin Interactions.

Epigenomic Deconvolution of Breast Tumors Reveals Metabolic Coupling between Constituent Cell Types.

Convergence of dispersed regulatory mutations predicts driver genes in prostate cancer.

Chromatin structure-based prediction of recurrent noncoding mutations in cancer.

Somatic Mutations and Neoepitope Homology in Melanomas Treated with CTLA-4 Blockade.

Chemotherapy weakly contributes to predicted neoantigen expression in ovarian cancer.

Microbiota Diurnal Rhythmicity Programs Host Transcriptome Oscillations.

Transcriptional Landscape of Human Tissue Lymphocytes Unveils Uniqueness of Tumor-Infiltrating T Regulatory Cells.

Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C

CHiCAGO: robust detection of DNA looping interactions in Capture Hi-C data.

ZIFA: Dimensionality reduction for zero-inflated single-cell gene expression analysis

Single-cell messenger RNA sequencing reveals rare intestinal cell types

Decoding the regulatory network of early blood development from single-cell gene expression measurements.

Single-Cell RNA-Seq with Waterfall Reveals Molecular Cascades underlying Adult Neurogenesis.

The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells.

Classification of low quality cells from single-cell RNA-seq data.

Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells.

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets.

Causal Mechanistic Regulatory Network for Glioblastoma Deciphered Using Systems Genetics Network Analysis.

Comprehensive analyses of tumor immunity: implications for cancer immunotherapy.

Widespread parainflammation in human cancer

Analysis of protein-coding genetic variation in 60,706 humans

Functional characterization of somatic mutations in cancer using network-based inference of protein activity pubmed fulltext

Exploiting single-cell expression to characterize co-expression replicability.

Clonal neoantigens elicit T cell immunoreactivity and sensitivity to immune checkpoint blockade

A Computational Drug Repositioning Approach for Targeting Oncogenic Transcription Factors

The landscape of accessible chromatin in mammalian preimplantation embryos

Enhancer-promoter interactions are encoded by complex genomic signatures on looping chromatin

Personalized Immunomonitoring Uncovers Molecular Networks that Stratify Lupus Patients

Integration of summary data from GWAS and eQTL studies predicts complex trait gene targets

Identification of transcriptional regulators in the mouse immune system

Mapping the effects of drugs on the immune system

Elucidating compound mechanism of action by network perturbation analysis

Integrative approaches for large-scale transcriptome-wide association studies

Tissue-specific regulatory circuits reveal variable modular perturbations across complex diseases

Survey of variation in human transcription factors reveals prevalent DNA binding changes

Large-scale identification of sequence variants influencing human transcription factor occupancy in vivo

Predicting Cancer-specific vulnerability via data-driven detection of synthetic lethality

Dynamic regulatory network controlling Th17 cell differentiation

Characterization of the immunophenotypes and antigenomes of colorectal cancers reveals distinct tumor escape mechanisms and novel targets for immunotherapy

Regulators of genetic risk of breast cancer identified by integrative network analysis

A predictive computational framework for direct reprogramming between human cell types

CellNet: Network biology applied to stem cell engineering

Improved exome prioritization of disease genes through cross-species phenotype comparison.

Phevor combines multiple biomedical ontologies for accurate identification of disease-causing alleles in single individuals and small nuclear families.

eXtasy: variant prioritization by genomic data fusion.

A probabilistic disease-gene finder for personal genomes.

Systematic analysis of noncoding somatic mutations and gene expression alterations across 14 tumor types.

GREAT improves functional interpretation of cis-regulatory regions.

Functional annotation of noncoding sequence variants.

FunSeq2: A framework for prioritizing noncoding regulatory variants in cancer.

Selecting causal genes from genome-wide association studies via functionally coherent subnetworks.

Biological interpretation of genome-wide association studies using predicted gene functions.

Human symptoms-disease network.

A nondegenerate code of deleterious variants in Mendelian loci contributes to complex disease risk.

Uncovering disease-disease relationships through the incomplete interactome.

The discovery of integrated gene networks for autism and related disorders.

Integrated systems analysis reveals a molecular network underlying autism spectrum disorders.

Dissecting neural differentiation regulatory networks through epigenetic footprinting.

Cell-of-origin chromatin organization shapes the mutational landscape of cancer.

Integrative analysis of 111 reference human epigenomes.

Genome-wide analysis of local chromatin packing in Arabidopsis thaliana.

A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping.

Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data.

Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells.

Cupid: simultaneous reconstruction of microRNA-target and ceRNA networks.

Characterization of the neural stem cell gene regulatory network identifies OLIG2 as a multifunctional regulator of self-renewal.

Decoding the regulatory network of early blood development from single-cell gene expression measurements.

Computational and analytical challenges in single-cell transcriptomics.

Extensive Strain-Level Copy-Number Variation across Human Gut Microbiome Species.

Richness of human gut microbiome correlates with metabolic markers.

A metagenome-wide association study of gut microbiota in type 2 diabetes.

Practical guidelines for the comprehensive analysis of ChIP-seq data.

Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions.

Rapid neurogenesis through transcriptional activation in human stem cells.

Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation.

Integrating multiple genomic data to predict disease-causing nonsynonymous single nucleotide variants in exome sequencing studies.

The Genotype-Tissue Expression (GTEx) project.

Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution.

Principles of regulatory information conservation between mouse and human.

Conservation of trans-acting circuitry during mammalian regulatory evolution.

Genetic and epigenetic fine mapping of causal autoimmune disease variants.

A general framework for estimating the relative pathogenicity of human genetic variants.

A probabilistic model to predict clinical phenotypic traits from genome sequencing.

Relating the metatranscriptome and metagenome of the human gut.

Alterations of the human gut microbiome in liver cirrhosis.

An integrated catalog of reference genes in the human gut microbiome.

Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes.

Computational meta'omics for microbial community studies.

Functional profiling of the gut microbiome in disease-associated inflammation.

Biodiversity and functional genomics in the human microbiome.

Chapter 12: Human Microbiome Analysis.

Conducting a Microbiome Study.

Small RNA changes en route to distinct cellular states of induced pluripotency.

Genome-wide characterization of the routes to pluripotency.

Divergent reprogramming routes lead to alternative stem-cell states.

Global view of enhancer-promoter interactome in human cells.

Combining Hi-C data with phylogenetic correlation to predict the target genes of distal regulatory elements in human genome.

Super-enhancers in the control of cell identity and disease.

Master transcription factors and mediator establish super-enhancers at key cell identity genes.

Unraveling the biology of a fungal meningitis pathogen using chemical genetics.

A proteome-scale map of the human interactome network.

The role of the interactome in the maintenance of deleterious variability in human populations.

Integrative annotation of variants from 1092 humans: application to cancer genomics.

Mapping functional transcription factor networks from gene expression data.

In pursuit of design principles of regulatory sequences.

Epigenomics of human embryonic stem cells and induced pluripotent stem cells: insights into pluripotency and implications for disease.

Developmental fate and cellular maturity encoded in human regulatory DNA landscapes.

The 'dnet' approach promotes emerging research on cancer patient survival.

Determination and inference of eukaryotic transcription factor sequence specificity.

Transcription factors interfering with dedifferentiation induce cell type-specific transcriptional profiles.

Dissecting engineered cell types and enhancing cell fate conversion via CellNet.

CellNet: network biology applied to stem cell engineering.

Predicting Cancer-Specific Vulnerability via Data-Driven Detection of Synthetic Lethality.

Phen-Gen: combining phenotype and genotype to analyze rare disorders.

A community effort to assess and improve drug sensitivity prediction algorithms.

Multi-tiered genomic analysis of head and neck cancer ties TP53 mutation to 3p loss.

Network-based stratification of tumor mutations.

Synonymous mutations frequently act as driver mutations in human cancers.

VarWalker: Personalized Mutation Network Analysis of Putative Cancer Genes from Next-Generation Sequencing Data.

DriverNet: uncovering the impact of somatic driver mutations on transcriptional networks in cancer.

Integrated analysis of recurrent properties of cancer genes to identify novel drivers.

Improving the prediction of the functional impact of cancer mutations by baseline tolerance transformation.

A network module-based method for identifying cancer prognostic signatures.

Realizing the promise of cancer predisposition genes.

Assessing the clinical utility of cancer genomic and proteomic data across tumor types.

Mutational landscape and significance across 12 major cancer types.

Signatures of mutational processes in human cancer.

Discovery and saturation analysis of cancer genes across 21 tumour types.

Comprehensive identification of mutational cancer driver genes across 12 tumor types.

IntOGen-mutations identifies cancer drivers across tumor types.

Computational approaches to identify functional genetic variants in cancer genomes.

Mutational heterogeneity in cancer and the search for new cancer-associated genes.

Cancer genomes: discerning drivers from passengers

The Cancer Genome Atlas Pan-Cancer analysis project.

Cancer genome landscapes.

Distinguishing driver and passenger mutations in an evolutionary history categorized by interference.

A promoter-level mammalian expression atlas.

An atlas of active enhancers across human cell types and tissues.