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"paper_count": 899}], "paper_count": 4305}], "facets": [{"name": "Organism / system", "tags": ["human", "mouse", "other vertebrate", "invertebrate", "plant", "microbe", "virus", "cell-free / in vitro"]}, {"name": "Biological scale", "tags": ["molecule", "cell", "tissue / organ", "organism", "population", "ecosystem"]}, {"name": "Data type", "tags": ["sequence", "omics profile", "image", "structure", "physiological signal", "clinical record"]}, {"name": "Contribution form", "tags": ["new method/technology", "biological mechanism", "resource/atlas", "therapeutic/clinical result", "software/model", "review/perspective"]}], "heuristics": ["Pick the primary node by the paper's main methodological contribution, not the organism or disease it studies (a new spatial atlas of the tumour microenvironment is Transcriptomics > Spatial transcriptomics).", "A paper that introduces a new assay, instrument or reagent belongs under the technique it advances; papers that only use routine assays take their primary node from the method that drives the discovery.", "Combined computational-experimental papers: choose Computational or AI only when the model drives the discovery; otherwise the experimental method is primary and the computation is secondary.", "Perturbation plus readout (e.g. Perturb-seq): the perturbation branch is primary when the screen is the contribution; the readout branch is secondary.", "Clinical papers take their node from the study design (trial, cohort, Mendelian randomization); the disease belongs in the Application Tree.", "Use the Application Tree (and the organism facet) for what the work is for; keep the Method Tree for how the work was done."], "methods": {"1000 Genomes": {"title": "A global reference for human genetic variation", "year": 2015, "url": "https://doi.org/10.1038/nature15393"}, "3D bioprinting review": {"title": "3D bioprinting of tissues and organs", "year": 2014, "url": "https://doi.org/10.1038/nbt.2958"}, "AAV-PHP.B capsid evolution": {"title": "Cre-dependent selection yields AAV variants for widespread gene transfer to the adult brain", "year": 2016, "url": "https://doi.org/10.1038/nbt.3440"}, "ATAC-seq": {"title": "Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position", "year": 2013, "url": "https://doi.org/10.1038/nmeth.2688"}, "AlphaFold 3": {"title": "Accurate structure prediction of biomolecular interactions with AlphaFold 3", "year": 2024, "url": "https://doi.org/10.1038/s41586-024-07487-w"}, "AlphaFold2": {"title": "Highly accurate protein structure prediction with AlphaFold", "year": 2021, "url": "https://doi.org/10.1038/s41586-021-03819-2"}, "AlphaMissense": {"title": "Accurate proteome-wide missense variant effect prediction with AlphaMissense", "year": 2023, "url": "https://doi.org/10.1126/science.adg7492"}, "BLAST": {"title": "Basic local alignment search tool", "year": 1990, "url": 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for Sequence-Specific Control of Gene Expression", "year": 2013, "url": "https://doi.org/10.1016/j.cell.2013.02.022"}, "CUT&RUN": {"title": "An efficient targeted nuclease strategy for high-resolution mapping of DNA binding sites", "year": 2017, "url": "https://doi.org/10.7554/eLife.21856"}, "Cas13 RNA editing (Cox et al.)": {"title": "RNA editing with CRISPR-Cas13", "year": 2017, "url": "https://doi.org/10.1126/science.aaq0180"}, "Cellpose": {"title": "Cellpose: a generalist algorithm for cellular segmentation", "year": 2021, "url": "https://doi.org/10.1038/s41592-020-01018-x"}, "ChIP-seq (Johnson et al.)": {"title": "Genome-Wide Mapping of in Vivo Protein-DNA Interactions", "year": 2007, "url": "https://doi.org/10.1126/science.1141319"}, "Cytosine base editor (Komor et al.)": {"title": "Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage", "year": 2016, "url": "https://doi.org/10.1038/nature17946"}, "DREADDs (Armbruster et al.)": {"title": "Evolving the lock to fit the key to create a family of G protein-coupled receptors potently activated by an inert ligand", "year": 2007, "url": "https://doi.org/10.1073/pnas.0700293104"}, "Deep learning antibiotic discovery (Stokes et al.)": {"title": "A Deep Learning Approach to Antibiotic Discovery", "year": 2020, "url": "https://doi.org/10.1016/j.cell.2020.01.021"}, "Deep mutational scanning review": {"title": "Deep mutational scanning: a new style of protein science", "year": 2014, "url": "https://doi.org/10.1038/nmeth.3027"}, "DeepLabCut": {"title": "DeepLabCut: markerless pose estimation of user-defined body parts with deep learning", "year": 2018, "url": "https://doi.org/10.1038/s41593-018-0209-y"}, "Dermatologist-level classification": {"title": "Dermatologist-level classification of skin cancer with deep neural networks", "year": 2017, "url": "https://doi.org/10.1038/nature21056"}, "Drop-seq": {"title": "Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets", "year": 2015, "url": "https://doi.org/10.1016/j.cell.2015.05.002"}, "ESM-2 / ESMFold": {"title": "Evolutionary-scale prediction of atomic-level protein structure with a language model", "year": 2023, "url": "https://doi.org/10.1126/science.ade2574"}, "Enformer": {"title": "Effective gene expression prediction from sequence by integrating long-range interactions", "year": 2021, "url": "https://doi.org/10.1038/s41592-021-01252-x"}, "Epigenetic clock (Horvath)": {"title": "DNA methylation age of human tissues and cell types", "year": 2013, "url": "https://doi.org/10.1186/gb-2013-14-10-r115"}, "Expansion microscopy (Chen et al.)": {"title": "Expansion microscopy", "year": 2015, "url": "https://doi.org/10.1126/science.1260088"}, "FlyWire connectome": {"title": "Neuronal wiring diagram of an adult brain", "year": 2024, "url": "https://doi.org/10.1038/s41586-024-07558-y"}, "GCaMP6": {"title": "Ultrasensitive fluorescent proteins for imaging neuronal activity", "year": 2013, "url": "https://doi.org/10.1038/nature12354"}, "GFP as a marker (Chalfie et al.)": {"title": "Green Fluorescent Protein as a Marker for Gene Expression", "year": 1994, "url": "https://doi.org/10.1126/science.8303295"}, "Geneformer": {"title": "Transfer learning enables predictions in network biology", "year": 2023, "url": "https://doi.org/10.1038/s41586-023-06139-9"}, "Genetic toggle switch": {"title": "Construction of a genetic toggle switch in Escherichia coli", "year": 2000, "url": "https://doi.org/10.1038/35002131"}, "Genome-scale CRISPR screen (Shalem et al.)": {"title": "Genome-Scale CRISPR-Cas9 Knockout Screening in Human Cells", "year": 2014, "url": "https://doi.org/10.1126/science.1247005"}, "Hi-C": {"title": "Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome", "year": 2009, "url": "https://doi.org/10.1126/science.1181369"}, "Human Cell Atlas": {"title": "The Human Cell Atlas", "year": 2017, "url": "https://doi.org/10.7554/eLife.27041"}, "Human Microbiome Project": {"title": "Structure, function and diversity of the healthy human microbiome", "year": 2012, "url": "https://doi.org/10.1038/nature11234"}, "Human pangenome reference": {"title": "A draft human pangenome reference", "year": 2023, "url": "https://doi.org/10.1038/s41586-023-05896-x"}, "Illumina SBS (Bentley et al.)": {"title": "Accurate whole human genome sequencing using reversible terminator chemistry", "year": 2008, "url": "https://doi.org/10.1038/nature07517"}, "Intestinal organoids (Sato et al.)": {"title": "Single Lgr5 stem cells build crypt-villus structures in vitro without a mesenchymal niche", "year": 2009, "url": "https://doi.org/10.1038/nature07935"}, "LD score regression": {"title": "LD Score regression distinguishes confounding from polygenicity in genome-wide association studies", "year": 2015, "url": "https://doi.org/10.1038/ng.3211"}, "Lattice light-sheet microscopy": {"title": "Lattice light-sheet microscopy: Imaging molecules to embryos at high spatiotemporal resolution", "year": 2014, "url": "https://doi.org/10.1126/science.1257998"}, "Lung-on-a-chip (Huh et al.)": {"title": "Reconstituting Organ-Level Lung Functions on a Chip", "year": 2010, "url": "https://doi.org/10.1126/science.1188302"}, "MERFISH": {"title": "Spatially resolved, highly multiplexed RNA profiling in single cells", "year": 2015, "url": "https://doi.org/10.1126/science.aaa6090"}, "MS-based proteomics (Aebersold & Mann)": {"title": "Mass spectrometry-based proteomics", "year": 2003, "url": "https://doi.org/10.1038/nature01511"}, "Mass cytometry (Bendall et al.)": {"title": "Single-Cell Mass Cytometry of Differential Immune and Drug Responses Across a Human Hematopoietic Continuum", "year": 2011, "url": "https://doi.org/10.1126/science.1198704"}, "Med-PaLM (Singhal et al.)": {"title": "Large language models encode clinical knowledge", "year": 2023, "url": "https://doi.org/10.1038/s41586-023-06291-2"}, "Multiplex CRISPR editing (Cong et al.)": {"title": "Multiplex Genome Engineering Using CRISPR/Cas Systems", "year": 2013, "url": "https://doi.org/10.1126/science.1231143"}, "Mutational signatures (Alexandrov et al.)": {"title": "Signatures of mutational processes in human cancer", "year": 2013, "url": "https://doi.org/10.1038/nature12477"}, "Neandertal genome": {"title": "A Draft Sequence of the Neandertal Genome", "year": 2010, "url": "https://doi.org/10.1126/science.1188021"}, "Neuropixels": {"title": "Fully integrated silicon probes for high-density recording of neural activity", "year": 2017, "url": "https://doi.org/10.1038/nature24636"}, "Nuclear periphery cryo-ET (Mahamid et al.)": {"title": "Visualizing the molecular sociology at the HeLa cell nuclear periphery", "year": 2016, "url": "https://doi.org/10.1126/science.aad8857"}, "Optogenetics (Boyden et al.)": {"title": "Millisecond-timescale, genetically targeted optical control of neural activity", "year": 2005, "url": "https://doi.org/10.1038/nn1525"}, "PACE (Esvelt et al.)": {"title": "A system for the continuous directed evolution of biomolecules", "year": 2011, "url": "https://doi.org/10.1038/nature09929"}, "PALM (Betzig et al.)": {"title": "Imaging Intracellular Fluorescent Proteins at Nanometer Resolution", "year": 2006, "url": "https://doi.org/10.1126/science.1127344"}, "Perturb-seq": {"title": "Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens", "year": 2016, "url": "https://doi.org/10.1016/j.cell.2016.11.038"}, "Prime editing (Anzalone et al.)": {"title": "Search-and-replace genome editing without double-strand breaks or donor DNA", "year": 2019, "url": "https://doi.org/10.1038/s41586-019-1711-4"}, "ProteinMPNN": {"title": "Robust deep learning–based protein sequence design using ProteinMPNN", "year": 2022, "url": "https://doi.org/10.1126/science.add2187"}, "RFdiffusion": {"title": "De novo design of protein structure and function with RFdiffusion", "year": 2023, "url": "https://doi.org/10.1038/s41586-023-06415-8"}, "RNA velocity": {"title": "RNA velocity of single cells", "year": 2018, "url": "https://doi.org/10.1038/s41586-018-0414-6"}, "RNA-seq (Mortazavi et al.)": {"title": "Mapping and quantifying mammalian transcriptomes by RNA-Seq", "year": 2008, "url": "https://doi.org/10.1038/nmeth.1226"}, "RNAi (Fire et al.)": {"title": "Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans", "year": 1998, "url": "https://doi.org/10.1038/35888"}, "Repressilator": {"title": "A synthetic oscillatory network of transcriptional regulators", "year": 2000, "url": "https://doi.org/10.1038/35002125"}, "Resolution revolution (Kühlbrandt)": {"title": "The Resolution Revolution", "year": 2014, "url": "https://doi.org/10.1126/science.1251652"}, "Ribosome profiling (Ingolia et al.)": {"title": "Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling", "year": 2009, "url": "https://doi.org/10.1126/science.1168978"}, "SHERLOCK": {"title": "Nucleic acid detection with CRISPR-Cas13a/C2c2", "year": 2017, "url": "https://doi.org/10.1126/science.aam9321"}, "SMRT sequencing (Eid et al.)": {"title": "Real-Time DNA Sequencing from Single Polymerase Molecules", "year": 2009, "url": "https://doi.org/10.1126/science.1162986"}, "STARR-seq": {"title": "Genome-Wide Quantitative Enhancer Activity Maps Identified by STARR-seq", "year": 2013, "url": "https://doi.org/10.1126/science.1232542"}, "STORM (Rust et al.)": {"title": "Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM)", "year": 2006, "url": "https://doi.org/10.1038/nmeth929"}, "Seurat integration": {"title": "Comprehensive Integration of Single-Cell Data", "year": 2019, "url": "https://doi.org/10.1016/j.cell.2019.05.031"}, "Spatial transcriptomics (Ståhl et al.)": {"title": "Visualization and analysis of gene expression in tissue sections by spatial transcriptomics", "year": 2016, "url": "https://doi.org/10.1126/science.aaf2403"}, "T2T-CHM13": {"title": "The complete sequence of a human genome", "year": 2022, "url": "https://doi.org/10.1126/science.abj6987"}, "TRPV1 cryo-EM structure": {"title": "Structure of the TRPV1 ion channel determined by electron cryo-microscopy", "year": 2013, "url": "https://doi.org/10.1038/nature12822"}, "TurboID": {"title": "Efficient proximity labeling in living cells and organisms with TurboID", "year": 2018, "url": "https://doi.org/10.1038/nbt.4201"}, "UK Biobank plasma proteomics": {"title": "Plasma proteomic associations with genetics and health in the UK Biobank", "year": 2023, "url": "https://doi.org/10.1038/s41586-023-06592-6"}, "UK Biobank resource": {"title": "The UK Biobank resource with deep phenotyping and genomic data", "year": 2018, "url": "https://doi.org/10.1038/s41586-018-0579-z"}, "Ultra-large library docking": {"title": "Ultra-large library docking for discovering new chemotypes", "year": 2019, "url": "https://doi.org/10.1038/s41586-019-0917-9"}, "Ultra-long nanopore reads (Jain et al.)": {"title": "Nanopore sequencing and assembly of a human genome with ultra-long reads", "year": 2018, "url": "https://doi.org/10.1038/nbt.4060"}, "Zoonomia": {"title": "A comparative genomics multitool for scientific discovery and conservation", "year": 2020, "url": "https://doi.org/10.1038/s41586-020-2876-6"}, "gnomAD constraint": {"title": "The mutational constraint spectrum quantified from variation in 141,456 humans", "year": 2020, "url": "https://doi.org/10.1038/s41586-020-2308-7"}, "iPSCs (Takahashi & Yamanaka)": {"title": "Induction of Pluripotent Stem Cells from Mouse Embryonic and Adult Fibroblast Cultures by Defined Factors", "year": 2006, "url": "https://doi.org/10.1016/j.cell.2006.07.024"}, "scGPT": {"title": "scGPT: toward building a foundation model for single-cell multi-omics using generative AI", "year": 2024, "url": "https://doi.org/10.1038/s41592-024-02201-0"}}}