Post-2015 paradigm: scRNA-seq, spatial transcriptomics, multi-omics integration, single-cell ATAC-seq, RNA-velocity, trajectory inference, cell-type ontologies, cell-cell communication.
Single-Cell Biology
Smart-seq scRNA (Tang-Surani / Picelli)
Tang-Surani 2009 first-mouse-blastomere scRNA-seq → Picelli 2013 Smart-seq2 full-length transcripts. Random-priming + template-switching +…
Droplet scRNA (Drop-seq / 10x Chromium)
Macosko-Klein 2015 Drop-seq + Zheng-Terry 2017 10x-Chromium: inDrops-/STAMP-style cell+bead co-encapsulation with cell-barcode + UMI…
UMAP / t-SNE manifold embedding
van der Maaten-Hinton 2008 t-SNE / McInnes-Healy 2018 UMAP: nonlinear-manifold-learning for scRNA visualisation. t-SNE preserves…
RNA velocity (La Manno-Linnarsson)
La Manno-Linnarsson 2018: ratio of unspliced (intronic) / spliced (exonic) reads for each gene estimates dRNA/dt → projects future cell…
Trajectory inference (Monocle / Slingshot)
Trapnell-Cacchiarelli 2014 Monocle / Street 2018 Slingshot: order single cells along pseudotime trajectory by minimum-spanning-tree on…
Spatial transcriptomics (Visium / Stereo-seq / MERFISH)
Stahl-Lundeberg 2016 → 10x Visium 55 μm spots; Stereo-seq (Chen 2022) 220 nm DNA nanoball resolution; MERFISH (Chen-Zhuang 2015)…
Batch effect correction (Harmony / MNN / Scanorama)
Haghverdi-Lun-Marioni 2018 MNN / Korsunsky 2019 Harmony / Hie-Bryson-Berger 2019 Scanorama: remove technical-batch artefacts in scRNA…
Single-cell ATAC-seq (Buenrostro)
Buenrostro-Wu-Litzenburger 2015 / 10x Multiome 2020: Tn5 transposase tags accessible chromatin in single cells. Reveals cis-regulatory…
CITE-seq multimodal (Stoeckius)
Stoeckius 2017: oligonucleotide-conjugated antibodies stain cell-surface protein → counted alongside scRNA in the same cell. Enables joint…
Perturb-seq pooled CRISPR + scRNA (Dixit-Regev)
Dixit-Parnas-Adamson-Regev 2016 / CROP-seq Datlinger 2017: pool of CRISPR-perturbed cells → scRNA-seq with sgRNA capture. Reads out…
Cell-cell communication inference (CellChat / CellPhoneDB)
Jin-Plikus 2021 CellChat / Efremova 2020 CellPhoneDB: ligand-receptor pair databases score predicted intercellular signalling between…
Cell-type ontology (Human Cell Atlas / Cell Ontology)
Regev-Teichmann 2017 Human Cell Atlas: comprehensive reference of all human cell types via scRNA + scATAC + spatial + protein. Cell…
scRNA-seq (Tang 2009)
F Tang 2009 first scRNA-seq; modern 10x + Smart-seq3 + Drop-seq + Macosko 2015 + 10M+ cells profiled.
HCA (Regev 2017)
A Regev 2017 Human Cell Atlas; modern Tabula Sapiens + Tabula Muris; 1B-cell goal by 2030.
Trajectory inference (Wolf 2018)
Wolf 2018 PAGA + Trapnell 2014 Monocle pseudotime; modern RNA-velocity La Manno 2018; cell-fate transitions.
Spatial (Stahl 2016)
Stahl 2016 spatial-barcoded array; modern Visium + Slide-seq + MERFISH + Stereo-seq sub-cellular resolution.
Multi-omics (CITE-seq 2017)
Stoeckius-Smibert 2017 CITE-seq protein + RNA; modern multi-modal Seurat + ASAP-seq + 10x-Multiome.
Rare cell types (Grun 2015)
D Grun 2015 RaceID rare-cell discovery; modern Tabula-Muris-Atlas + 'novel cell-type' discoveries.