[https://doi.org/10.1101/2024.07.11.603044 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
[https://doi.org/10.1186/s40168-024-01904-y Strain‑resolved de‑novo metagenomic assembly of viral genomes and microbial 16S rRNAs]
[https://doi.org/10.1186/s40168-024-01876-z Prokaryotic‑virus‑encoded auxiliary metabolic genes throughout the global oceans]
[https://doi.org/10.1016/j.cell.2024.07.039 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
[https://doi.org/10.1038/s41467-024-52533-w Accurately predicting enzyme functions through geometric graph learning on ESMFold-predicted structures]
[https://doi.org/10.1101/2024.06.27.600934 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
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
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
Gastrointestinal microbiota composition predicts peripheral inflammatory state during treatment of human tuberculosis
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
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
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.
Identification of genetic determinants of breast cancer immune phenotypes by integrative genome-scale analysis.
Genomic Correlates of Immune-Cell Infiltrates in Colorectal Carcinoma.
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.
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.
2012
2011
Identifying relationships among genomic disease regions: predicting genes at pathogenic SNP associations and rare deletions
2010
Reference:SEA(Similarity Ensemble Approach)
