A cellular atlas of Pitx2-dependent cardiac development

Hill MC et al. Development. 2019 Jun 14;146(12). pii: dev180398. doi: 10.1242/dev.180398. PMID: 31201182.

Single-cell transcriptomic analysis of Alzheimer’s disease

Mathys H et al. Nature. 2019 Jun;570(7761):332-337.. doi: 10.1038/s41586-019-1195-2. PMID: 31042697.
Single cell transcriptional profiling of > 80,000 cells revealed disease-linked gene expression changes that occur in different brain cell types.

The bone marrow microenvironment at single-cell resolution

Tikhonova AN et al. Nature. 2019 Apr 10; online. doi: 10.1038/s41586-019-1104-8. PMID: 30971824.
Mapped the transcriptional landscape of mouse bone marrow microenvironment both at homeostasis and under conditions of stress-induced haematopoiesis revealing previously unappreciated levels of cellular heterogeneity and considerable transcriptional remodelling under stress conditions

Spatiotemporal Dynamics of Molecular Pathology in Amyotrophic Lateral Sclerosis

Maniatis S et al. Science. 2019 Apr 5;364(6435):89-93. doi: 10.1126/science.aav9776. PMID: 30948552.
Used spatial RNA sequencing to define transcriptomic changes in different regions of the spinal cord of a mouse ALS model and a postmortem human ALS spinal cord. Identified disease-associated pathways and established the key steps in motor neuron degeneration observed in ALS.

Single-Cell Transcriptomics Uncovers Glial Progenitor Diversity and Cell Fate Determinants during Development and Gliomagenesis

Weng Q et al. Cell Stem Cell. 2019 Mar 23. pii: S1934-5909(19)30105-5. doi: 10.1016/j.stem.2019.03.006. PMID: 30982771.
Single cell transcriptional profiling uncovered distinct intermediate glial progenitors in the neonatal mouse brain and identified their malignant counterparts in mouse and human gliomas.

Memory CD4+ T cells are generated in the human fetal intestine

Li N et al. Nat Immunol. 2019 Jan 21; online. doi: 10.1038/s41590-018-0294-9. PMID: 30664737.
Characterize the CD4+ T cell compartment in the human fetal intestine and found evidence for the generation of memory-like CD4+ T cells in the human fetal intestine that is consistent with exposure to foreign antigens.

Gene expression variability across cells and species shapes innate immunity

Hagai T et al. Nature. 2018 Oct 24; online. doi: 10.1038/s41586-018-0657-2. PMID: 30356220.
Using single cell and bulk RNA sequencing, charted the evolutionary architecture of the innate immune response and found that genes that diverge rapidly between species show higher levels of cell-to-cell expression variability than genes that diverge more slowly.

Spatially Resolved Transcriptomics Enables Dissection of Genetic Heterogeneity in Stage III Cutaneous Malignant Melanoma

Thrane K et al. Cancer Res. 2018 Oct 15;78(20):5970-5979. doi: 10.1158/0008-5472.CAN-18-0747. PMID: 30154148.
Spatial Gene Expression assay was used to better understand melanoma lymph node metastases which revealed a complex transcriptional landscape in a localized context; may help in better understanding the multiple components of melanoma tumor progression and therapy outcome

Single-Cell Map of Diverse Immune Phenotypes in the Breast Tumor Microenvironment

Azizi E et al. Cell. 2018 Jun 28; online. doi: 10.1016/j.cell.2018.05.060. PMID: 29961579.
Performed single-cell transcriptional profiling combined with T cell receptor sequencing in 27K T cells and characterized populations with unique combinations of clonotypes.

Spatial maps of prostate cancer transcriptomes reveal an unexplored landscape of heterogeneity

Berglund E et al. Nat Commun. 2018 Jun 20;9(1):2419. doi: 10.1038/s41467-018-04724-5. PMID: 29925878.
Profiled gene expression in an unbiased manner using Spatial Transcriptomics technology in prostate cancer tissue. Extracted distinct expression profiles for various tissue components, including immune infiltrates and tumor

Classes and continua of hippocampal CA1 inhibitory neurons revealed by single-cell transcriptomics

Harris KD et al. PLoS Biol. 2018 Jun 18;16(6):e2006387. doi: 10.1371/journal.pbio.2006387. PMID: 29912866.
Studied the transcriptomes of 3,663 CA1 neurons, revealing 10 major GABAergic groups that divided into 49 fine-scale clusters. All previously known and several novel cell classes were identified.

Generalizable visualization of mega-scale single-cell data

Cho H et al. Res Comput Mol Biol. 2018 Apr;10812:251-253. PMID: 29725668.

Linked-Read sequencing resolves complex structural variants

Garcia S et al. 2017 Dec 8; Pre-print*.

Visualization and analysis of gene expression in tissue sections by spatial transcriptomics

Ståhl PL et al. Science. 2016 Jul 1;353(6294):78-82. doi: 10.1126/science.aaf2403. PMID: 27365449.
Analyzed patterns of RNA expression in mouse brain and human breast cancer enabling a new way of analyzing all gene expression while preserving tissue morphology with implications in diagnostics, research and novel target identification

Haplotypes drop by drop

Kitzman JO. Nat Biotechnol. 2016 Mar;34(3):296-8. doi: 10.1038/nbt.3500. PMID: 26963554.
*Pre-prints are available at BioRxiv.