Let's start looking for classic citations at the EuropePMC database.Once more, we will use naive definitions of citation classics.
- Classics are all cited more than 150 times.
- Big classics: more than 500 citations
- Medium classics: at least 300 citations, less than 500
- Small classics: at least 150 citations, less than 300
Currently, we have 133 classics that meet the criteria above:
- Butler A et al, Integrating single-cell transcriptomic data across different conditions, technologies, and species.
- Tirosh I et al, Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq.
- Klein AM et al, Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells.
- Macosko EZ et al, Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets.
- Satija R et al, Spatial reconstruction of single-cell gene expression data.
- Zeisel A et al, Brain structure. Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq.
- Jaitin DA et al, Massively parallel single-cell RNA-seq for marker-free decomposition of tissues into cell types.
- Lavin Y et al, Tissue-resident macrophage enhancer landscapes are shaped by the local microenvironment.
- Patel AP et al, Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma.
- Picelli S et al, Full-length RNA-seq from single cells using Smart-seq2.
- Trapnell C et al, The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells.
- Treutlein B et al, Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq.
- Shalek AK et al, Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells.
- Yan L et al, Single-cell RNA-Seq profiling of human preimplantation embryos and embryonic stem cells.
- Ramsköld D et al, Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells.
- Afgan E et al, The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update.
- Thorsson V et al, The Immune Landscape of Cancer.
- Keren-Shaul H et al, A Unique Microglia Type Associated with Restricting Development of Alzheimer's Disease.
- Ott PA et al, An immunogenic personal neoantigen vaccine for patients with melanoma.
- Villani AC et al, Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors.
- Conesa A et al, A survey of best practices for RNA-seq data analysis.
- Massagué J et al, Metastatic colonization by circulating tumour cells.
- Tasic B et al, Adult mouse cortical cell taxonomy revealed by single cell transcriptomics.
- Buenrostro JD et al, Single-cell chromatin accessibility reveals principles of regulatory variation.
- Erny D et al, Host microbiota constantly control maturation and function of microglia in the CNS.
- Levine JH et al, Data-Driven Phenotypic Dissection of AML Reveals Progenitor-like Cells that Correlate with Prognosis.
- Stegle O et al, Computational and analytical challenges in single-cell transcriptomics.
- Usoskin D et al, Unbiased classification of sensory neuron types by large-scale single-cell RNA sequencing.
- Bendall SC et al, Single-cell trajectory detection uncovers progression and regulatory coordination in human B cell development.
- Deng Q et al, Single-cell RNA-seq reveals dynamic, random monoallelic gene expression in mammalian cells.
- Islam S et al, Quantitative single-cell RNA-seq with unique molecular identifiers.
- Kharchenko PV et al, Bayesian approach to single-cell differential expression analysis.
- Lara-Astiaso D et al, Immunogenetics. Chromatin state dynamics during blood formation.
- Risso D et al, Normalization of RNA-seq data using factor analysis of control genes or samples.
- Shalek AK et al, Single-cell RNA-seq reveals dynamic paracrine control of cellular variation.
- Takashima Y et al, Resetting transcription factor control circuitry toward ground-state pluripotency in human.
- Theunissen TW et al, Systematic identification of culture conditions for induction and maintenance of naive human pluripotency.
- Wu AR et al, Quantitative assessment of single-cell RNA-sequencing methods.
- Wu H et al, Reversing DNA methylation: mechanisms, genomics, and biological functions.
- Blaschke K et al, Vitamin C induces Tet-dependent DNA demethylation and a blastocyst-like state in ES cells.
- Brennecke P et al, Accounting for technical noise in single-cell RNA-seq experiments.
- Hackett JA et al, Germline DNA demethylation dynamics and imprint erasure through 5-hydroxymethylcytosine.
- Xue Z et al, Genetic programs in human and mouse early embryos revealed by single-cell RNA sequencing.
- Buganim Y et al, Single-cell expression analyses during cellular reprogramming reveal an early stochastic and a late hierarchic phase.
- Hashimshony T et al, CEL-Seq: single-cell RNA-Seq by multiplexed linear amplification.
- Islam S et al, Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq.
- Kalsotra A et al, Functional consequences of developmentally regulated alternative splicing.
- Shi S et al, Association of Cardiac Injury With Mortality in Hospitalized Patients With COVID-19 in Wuhan, China.
- Xu H et al, High expression of ACE2 receptor of 2019-nCoV on the epithelial cells of oral mucosa.
- Stuart T et al, Comprehensive Integration of Single-Cell Data.
- Binnewies M et al, Understanding the tumor immune microenvironment (TIME) for effective therapy.
- Zeisel A et al, Molecular Architecture of the Mouse Nervous System.
- Birey F et al, Assembly of functionally integrated human forebrain spheroids.
- Cao J et al, Comprehensive single-cell transcriptional profiling of a multicellular organism.
- Haber AL et al, A single-cell survey of the small intestinal epithelium.
- Hulsmans M et al, Macrophages Facilitate Electrical Conduction in the Heart.
- Kiselev VY et al, SC3: consensus clustering of single-cell RNA-seq data.
- Lavin Y et al, Innate Immune Landscape in Early Lung Adenocarcinoma by Paired Single-Cell Analyses.
- Lim WA et al, The Principles of Engineering Immune Cells to Treat Cancer.
- Mackenzie KJ et al, cGAS surveillance of micronuclei links genome instability to innate immunity.
- McCarthy DJ et al, Scater: pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in R.
- Puram SV et al, Single-Cell Transcriptomic Analysis of Primary and Metastatic Tumor Ecosystems in Head and Neck Cancer.
- Qiu X et al, Reversed graph embedding resolves complex single-cell trajectories.
- Qiu X et al, Single-cell mRNA quantification and differential analysis with Census.
- Regev A et al, The Human Cell Atlas.
- Shaffer SM et al, Rare cell variability and drug-induced reprogramming as a mode of cancer drug resistance.
- Stoeckius M et al, Simultaneous epitope and transcriptome measurement in single cells.
- Wang Q et al, Tumor Evolution of Glioma-Intrinsic Gene Expression Subtypes Associates with Immunological Changes in the Microenvironment.
- Ziegenhain C et al, Comparative Analysis of Single-Cell RNA Sequencing Methods.
- Adamson B et al, A Multiplexed Single-Cell CRISPR Screening Platform Enables Systematic Dissection of the Unfolded Protein Response.
- Baron M et al, A Single-Cell Transcriptomic Map of the Human and Mouse Pancreas Reveals Inter- and Intra-cell Population Structure.
- Dixit A et al, Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens.
- Goldmann T et al, Origin, fate and dynamics of macrophages at central nervous system interfaces.
- Hashimshony T et al, CEL-Seq2: sensitive highly-multiplexed single-cell RNA-Seq.
- Kiehn O. et al, Decoding the organization of spinal circuits that control locomotion.
- Lake BB et al, Neuronal subtypes and diversity revealed by single-nucleus RNA sequencing of the human brain.
- Lun AT et al, Pooling across cells to normalize single-cell RNA sequencing data with many zero counts.
- Malladi S et al, Metastatic Latency and Immune Evasion through Autocrine Inhibition of WNT.
- Marques S et al, Oligodendrocyte heterogeneity in the mouse juvenile and adult central nervous system.
- Mass E et al, Specification of tissue-resident macrophages during organogenesis.
- McKenna A et al, Whole-organism lineage tracing by combinatorial and cumulative genome editing.
- Nowakowski TJ et al, Expression Analysis Highlights AXL as a Candidate Zika Virus Entry Receptor in Neural Stem Cells.
- Petropoulos S et al, Single-Cell RNA-Seq Reveals Lineage and X Chromosome Dynamics in Human Preimplantation Embryos.
- Petryszak R et al, Expression Atlas update--an integrated database of gene and protein expression in humans, animals and plants.
- Schmitz SU et al, Mechanisms of long noncoding RNA function in development and disease.
- Scotti MM et al, RNA mis-splicing in disease.
- Segerstolpe Å et al, Single-Cell Transcriptome Profiling of Human Pancreatic Islets in Health and Type 2 Diabetes.
- Setty M et al, Wishbone identifies bifurcating developmental trajectories from single-cell data.
- Sharma U et al, Biogenesis and function of tRNA fragments during sperm maturation and fertilization in mammals.
- Shekhar K et al, Comprehensive Classification of Retinal Bipolar Neurons by Single-Cell Transcriptomics.
- Spitzer MH et al, Mass Cytometry: Single Cells, Many Features.
- Sweeney MD et al, Pericytes of the neurovascular unit: key functions and signaling pathways.
- Tirosh I et al, Single-cell RNA-seq supports a developmental hierarchy in human oligodendroglioma.
- Tremblay R et al, GABAergic Interneurons in the Neocortex: From Cellular Properties to Circuits.
- Wang J et al, Clonal evolution of glioblastoma under therapy.
- Zheng GX et al, Haplotyping germline and cancer genomes with high-throughput linked-read sequencing.
- Alizadeh AA et al, Toward understanding and exploiting tumor heterogeneity.
- Anahtar MN et al, Cervicovaginal bacteria are a major modulator of host inflammatory responses in the female genital tract.
- Bond AM et al, Adult Mammalian Neural Stem Cells and Neurogenesis: Five Decades Later.
- Camp JG et al, Human cerebral organoids recapitulate gene expression programs of fetal neocortex development.
- Chan CK et al, Identification and specification of the mouse skeletal stem cell.
- Cusanovich DA et al, Multiplex single cell profiling of chromatin accessibility by combinatorial cellular indexing.
- Dey SS et al, Integrated genome and transcriptome sequencing of the same cell.
- Finak G et al, MAST: a flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data.
- Gaublomme JT et al, Single-Cell Genomics Unveils Critical Regulators of Th17 Cell Pathogenicity.
- Grow EJ et al, Intrinsic retroviral reactivation in human preimplantation embryos and pluripotent cells.
- Lee JW et al, Deep Sequencing in Microdissected Renal Tubules Identifies Nephron Segment-Specific Transcriptomes.
- Parnas O et al, A Genome-wide CRISPR Screen in Primary Immune Cells to Dissect Regulatory Networks.
- Pollen AA et al, Molecular identity of human outer radial glia during cortical development.
- Rotem A et al, Single-cell ChIP-seq reveals cell subpopulations defined by chromatin state.
- Shin J et al, Single-Cell RNA-Seq with Waterfall Reveals Molecular Cascades underlying Adult Neurogenesis.
- Trapnell C. et al, Defining cell types and states with single-cell genomics.
- Vaughan AE et al, Lineage-negative progenitors mobilize to regenerate lung epithelium after major injury.
- Wang Y et al, Advances and applications of single-cell sequencing technologies.
- Wilson NK et al, Combined Single-Cell Functional and Gene Expression Analysis Resolves Heterogeneity within Stem Cell Populations.
- Benayoun BA et al, H3K4me3 breadth is linked to cell identity and transcriptional consistency.
- Boroviak T et al, The ability of inner-cell-mass cells to self-renew as embryonic stem cells is acquired following epiblast specification.
- Hogan BL et al, Repair and regeneration of the respiratory system: complexity, plasticity, and mechanisms of lung stem cell function.
- Kotton DN et al, Lung regeneration: mechanisms, applications and emerging stem cell populations.
- Kumar RM et al, Deconstructing transcriptional heterogeneity in pluripotent stem cells.
- Macaulay IC et al, Single cell genomics: advances and future perspectives.
- Marinov GK et al, From single-cell to cell-pool transcriptomes: stochasticity in gene expression and RNA splicing.
- Pollen AA et al, Low-coverage single-cell mRNA sequencing reveals cellular heterogeneity and activated signaling pathways in developing cerebral cortex.
- Saliba AE et al, Single-cell RNA-seq: advances and future challenges.
- Smith ZD et al, DNA methylation dynamics of the human preimplantation embryo.
- Ting DT et al, Single-cell RNA sequencing identifies extracellular matrix gene expression by pancreatic circulating tumor cells.
- Guo H et al, Single-cell methylome landscapes of mouse embryonic stem cells and early embryos analyzed using reduced representation bisulfite sequencing.
- Leitch HG et al, Naive pluripotency is associated with global DNA hypomethylation.
- Shyh-Chang N et al, Lin28: primal regulator of growth and metabolism in stem cells.
- Tang F et al, Tracing the derivation of embryonic stem cells from the inner cell mass by single-cell RNA-Seq analysis.
- Tang F et al, RNA-Seq analysis to capture the transcriptome landscape of a single cell.
October 29, 2020