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Analysis technique of genes
Single-cell transcriptomics refers to the quantification and analysis of the transcriptomes of individual cells. Single-cell transcriptomics makes it possible
Single-cell_transcriptomics
Range of methods designed for assigning cell types
Spatial transcriptomics, or spatially resolved transcriptomics, is a method that captures positional context of transcriptional activity within intact
Spatial_transcriptomics
Examines sequence information from individual cells
sequencing Human Cell Atlas Disease Cell Atlas Single-cell analysis Single-cell epigenomics Single-cell transcriptomics Single-cell multi-omics integration
Single-cell_sequencing
Set of all RNA molecules in one cell or a population of cells
Transcription can also be studied at the level of individual cells by single-cell transcriptomics. Single-cell RNA sequencing (scRNA-seq) is a recently developed
Transcriptome
Topics referred to by the same term
sequencing Single cell epigenomics Single-cell transcriptomics, a technique in molecular biology Single-cell thunderstorm, a pulse storm Single Cell (comic)
Single_cell
Computational technique
technique used in single-cell transcriptomics to determine the pattern of a dynamic process experienced by cells and then arrange cells based on their progression
Trajectory_inference
Study of biochemical processes in an individual cell
cell biology, single-cell analysis and subcellular analysis refer to the study of genomics, transcriptomics, proteomics, metabolomics, and cell–cell interactions
Single-cell_analysis
Accessory cell of the mammalian immune system
DG, Bueno R, Levantini E, Pittet MJ, Klein AM (April 2019). "Single-Cell Transcriptomics of Human and Mouse Lung Cancers Reveals Conserved Myeloid Populations
Dendritic_cell
Medical procedure to replace blood or immune stem cells
applications of the bulk and single-cell transcriptomics dissecting transcriptional heterogeneity in hematopoietic stem cells". Briefings in Functional Genomics
Hematopoietic stem cell transplantation
Hematopoietic_stem_cell_transplantation
Study of RNA transcripts
captures a snapshot in time of the total transcripts present in a cell. Transcriptomics technologies provide a broad account of which cellular processes
Transcriptomics_technologies
Chinese-American computational biologist
a computational biologist whose work spans cancer genomics, single-cell transcriptomics, and computational oncology. He is a tenured professor in the
Ken Chen (computational biologist)
Ken_Chen_(computational_biologist)
specific phases of the cell cycle. Cell sorting Single-cell analysis Single-cell multi-omics integration Single-cell transcriptomics Habibi, Iman; Cheong
Single-cell_variability
Subtype of white blood cell
applications of the bulk and single-cell transcriptomics dissecting transcriptional heterogeneity in hematopoietic stem cells". Briefings in Functional Genomics
Lymphocyte
Immune cell found in connective tissue
Dwyer DF (October 2022). "Defining mast cell differentiation and heterogeneity through single-cell transcriptomics analysis". The Journal of Allergy and
Mast_cell
Type of cells of the immunological system
applications of the bulk and single-cell transcriptomics dissecting transcriptional heterogeneity in hematopoietic stem cells". Briefings in Functional Genomics
White_blood_cell
Computational methods in biology
frequencies of each cell type Cell sorting List of single cell omics methods Multiomics Single-cell analysis Single-cell transcriptomics Single-cell variability
Single-cell multi-omics integration
Single-cell_multi-omics_integration
Bioinformatician
2026. Shalek, Alex K. (2013). "Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells". Nature. 498: 236–240. doi:10
Aviv_Regev
Type of cell found in pancreatic islets
nutrients by inhibiting gastric emptying. Recent single-cell transcriptomic profiling during pancreatic beta-cell regeneration in zebrafish models has identified
Beta_cell
South Korean-born American chemist and physicist
Z. Levin, H. Park, A. Regev, "Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells," Nature **498** (2013): 236–240
Hongkun_Park
infarction atlas, just to cite a few. These atlases integrate single-cell transcriptomics, spatial data, and clinical metadata to elucidate disease mechanisms
Disease_Cell_Atlas
Marioni has conducted influential studies in whole-tissue and single-cell transcriptomics. He received his PhD from the University of Cambridge in Applied
John_Marioni
Stem cells that give rise to other blood cells
applications of the bulk and single-cell transcriptomics dissecting transcriptional heterogeneity in hematopoietic stem cells". Briefings in Functional Genomics
Hematopoietic_stem_cell
applications of the bulk and single-cell transcriptomics dissecting transcriptional heterogeneity in hematopoietic stem cells". Briefings in Functional Genomics
List_of_immune_cells
American scientist, inventor and entrepreneur (born 1969)
formed the basis of the first technologies to automate single-cell genomics and transcriptomics. A central theme of Quake's genomics work is diagnostics
Stephen_Quake
American entrepreneur
on Tangram, a deep-learning framework for spatially resolved single-cell transcriptomics. In 2022, Sanger co-founded Anysphere with Michael Truell, Sualeh
Aman_Sanger
Biological analysis approach
List of omics topics in biology Single-cell multi-omics integration Single-cell transcriptomics Spatial transcriptomics Systems Biology Bersanelli, Matteo;
Multiomics
Formation of blood cellular components
applications of the bulk and single-cell transcriptomics dissecting transcriptional heterogeneity in hematopoietic stem cells". Briefings in Functional Genomics
Haematopoiesis
Oval eosinophilic histiocytes
of Hofbauer cells in these processes. According to a systems level single-cell transcriptomics based study of human placental cell-cell communication
Hofbauer_cell
Describes how neurons transmit electric signals
A. (2022-08-09). "Single-neuron models linking electrophysiology, morphology, and transcriptomics across cortical cell types". Cell Reports. 40 (6) 111176
Hodgkin–Huxley_model
Large part of the brain containing the cerebral cortex
the cerebral cortex has three layers. Molecular studies using single-cell transcriptomics have confirmed that all cortices of modern reptiles share a three-layered
Cerebrum
Subfield
growing consensus has settled on usage of "spatial transcriptomics" or "spatially resolved transcriptomics." Spatial proteomics measures the localization
Spatial_biology
Subsystem of the immune system
Snyder ME, Senda T, Yuan J, et al. (October 2019). "Single-cell transcriptomics of human T cells reveals tissue and activation signatures in health and
Adaptive_immune_system
Organs that make blood cells
applications of the bulk and single-cell transcriptomics dissecting transcriptional heterogeneity in hematopoietic stem cells". Briefings in Functional Genomics
Haematopoietic_system
Lab technique in cellular biology
PMID 28604674. Sandberg R (January 2014). "Entering the era of single-cell transcriptomics in biology and medicine". Nature Methods. 11 (1): 22–4. doi:10
RNA-Seq
Medical condition
Rosin N, Gabriel V, Biernaskie J (August 2024). "Spatial and Single-Cell Transcriptomics Reveal that Oncofetal Reprogramming of Fibroblasts Is Associated
Marjolin's_ulcer
Immunity strategy in living beings
applications of the bulk and single-cell transcriptomics dissecting transcriptional heterogeneity in hematopoietic stem cells". Briefings in Functional Genomics
Innate_immune_system
Cellular biology lab technique
sequenced. Thus, proteomics and transcriptomics data can be obtained from a single sequencing run. Analysis of single-cell sequencing presents many challenges
CITE-Seq
Species of fish
Petzold A, Dahl A, Zhang Y, Kizil C (April 2019). "Single-Cell Transcriptomics Analyses of Neural Stem Cell Heterogeneity and Contextual Plasticity in a Zebrafish
Zebrafish
Inactivation of copies of X chromosome
"Parental haplotype-specific single-cell transcriptomics reveal incomplete epigenetic reprogramming in human female germ cells". Nature Communications. 9
X-inactivation
Single-Cell RNA-Sequencing Method
"Droplet Barcoding for Single-Cell Transcriptomics Applied to Embryonic Stem Cells". Cell. 161 (5): 1187–1201. doi:10.1016/j.cell.2015.04.044. PMC 4441768
Drop-Seq
Species of bacteria
number providing a defence against bacteriophages. Single-cell transcriptomics using single-cell RNA-Seq gave the complete transcriptome of H. pylori
Helicobacter_pylori
Immune system deterioration brought on by aging
applications of the bulk and single-cell transcriptomics dissecting transcriptional heterogeneity in hematopoietic stem cells". Briefings in Functional Genomics
Immunosenescence
Species of protozoan parasite
development of new molecular and genomic approaches, such as single-cell transcriptomics and proteomics, should be useful to those in the field working
Toxoplasma_gondii
Global health science project
Consortium; et al. (May 2022). "The Tabula Sapiens: A multiple-organ, single-cell transcriptomic atlas of humans". Science. 376 (6594) eabl4896. doi:10.1126/science
Human_Cell_Atlas
System of communication
Cell signaling (cell signalling in British English) is the biological process by which a cell interacts with itself, with other cells, and with the environment
Cell_signaling
barcoding for single-cell transcriptomics applied to embryonic stem cells". Cell. 161 (5): 1187–1201. Bibcode:2015Cell..161.1187K. doi:10.1016/j.cell.2015.04
List of single cell omics methods
List_of_single_cell_omics_methods
Greek-born computational biologist
genetic differences and disease phenotypes, including the first single-cell transcriptomic analysis of Alzheimer's disease (Nature, 2019). Kellis is a member
Manolis_Kellis
Type of white blood cell
Pfirschke C, Savova V, Zemmour D, Saatcioglu HD, et al. (May 2019). "Single-Cell Transcriptomics of Human and Mouse Lung Cancers Reveals Conserved Myeloid Populations
Neutrophil
Cell type in the exocrine pancreas
Butler L, Odeberg J, Dusart P, Edfors F (2021-07-28). "A single–cell type transcriptomics map of human tissues". Science advances. 7 (31). Retrieved
Acinar_cell
Subtype of leukocytes
applications of the bulk and single-cell transcriptomics dissecting transcriptional heterogeneity in hematopoietic stem cells". Briefings in Functional Genomics
Monocyte
Genetic testing technique
standard analysis scheme of FISH datasets in a similar way to single-cell transcriptomics analysis. Often parents of children with a developmental disability
Fluorescence in situ hybridization
Fluorescence_in_situ_hybridization
Organ central to the nervous system
"Evolution of pallium, hippocampus, and cortical cell types revealed by single-cell transcriptomics in reptiles". Science. 360 (6391): 881–888. Bibcode:2018Sci
Brain
Oldest cultured human cell line (1951)
an immortalized cell line used in scientific research. It is the oldest human cell line and one of the most commonly used. HeLa cells are durable and
HeLa
Class of protozoans
Alastair (2021). "Multigene phylogenetics of euglenids based on single-cell transcriptomics of diverse phagotrophs". Molecular Phylogenetics and Evolution
Euglenid
New Zealand cardiologist
also used large-scale human plasma proteomics and single-cell resolution unbiased cardiac transcriptomics to prioritize candidate protein candidate markers
A._Mark_Richards
Medical researcher (born 1975)
Defining inflammatory cell states in rheumatoid arthritis joint synovial tissues by integrating single-cell transcriptomics and mass cytometry. Nat
Soumya_Raychaudhuri
Single cell RNA sequencing method
CRISP-seq and CROP-seq) refers to a high-throughput method of performing single cell RNA sequencing (scRNA-seq) on pooled genetic perturbation screens. Perturb-seq
Perturb-seq
Concept in molecular biology
Aheyon; Gerstein, Mark; Zhang, Jing (2022-12-02). "DeepVelo: Single-cell transcriptomic deep velocity field learning with neural ordinary differential
RNA_velocity
Molecular biology technique
transcription factor-target expression from transcriptomic data to construct gene regulatory networks from single-cell and spatial multiomics data. ATAC-seq
ATAC-seq
analysis of epigenomics and transcriptomics data. BBrowser a platform for analyzing public and in-house single-cell transcriptomics data CLC Genomics Workbench
List of RNA-Seq bioinformatics tools
List_of_RNA-Seq_bioinformatics_tools
Kantarci, A.; Wu, D. (January 2024). "Single-Cell Transcriptomic Analysis of Dental Pulp and Periodontal Ligament Stem Cells". Journal of Dental Research. 103
Periodontal ligament stem cells
Periodontal_ligament_stem_cells
DNA barcoding technique
provides a spatial transcriptomics map of the tissue. While this is not a single-cell methodology, the 10 uM channels capture only 1-2 cells per square, generating
Deterministic Barcoding in Tissue for Spatial Omics Sequencing
Deterministic_Barcoding_in_Tissue_for_Spatial_Omics_Sequencing
Biological term
applications of the bulk and single-cell transcriptomics dissecting transcriptional heterogeneity in hematopoietic stem cells". Briefings in Functional Genomics
Hematopoietic_stem_cell_niche
Canadian researcher and molecular biologist
and cancer metabolism. Marignani combines technologies such as single-cell transcriptomics and machine learning to interrogate disease processes and discover
Paola_Marignani
Biomedical engineer
Shalek, A. K. et al. (2013). “Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells.” Nature 498: 236–240. "Alex Shalek
Alex_K._Shalek
Malaysian dermatologist and immunologist
Natasha; Tucci, Andrea; Chen, Xi (February 2019). "Single-Cell Transcriptomics of Regulatory T Cells Reveals Trajectories of Tissue Adaptation". Immunity
Muzlifah_Haniffa
Laboratory technique in electrophysiology
currents of single ion channel molecules for the first time, which improved understanding of the involvement of channels in fundamental cell processes such
Patch_clamp
Genus of single-celled organisms
A.; Suttle, C. A.; Keeling, P. J.; Leander, B. S. (2015). "Single-cell transcriptomics using spliced leader PCR: Evidence for multiple losses of photosynthesis
Polykrikos
Blood production outside of the bone marrow
applications of the bulk and single-cell transcriptomics dissecting transcriptional heterogeneity in hematopoietic stem cells". Briefings in Functional Genomics
Extramedullary_hematopoiesis
Laboratory technique
Allon M.; Sabatini, Bernardo L. (January 2018). "Single-cell analysis of experience-dependent transcriptomic states in the mouse visual cortex". Nature Neuroscience
Patch-sequencing
Canadian neuroscientist and science communicator
quiescence of neural stem cells and the fate specification of their progeny using clonal lineage tracing and single cell transcriptomics strategies. Yammine
Samantha_Yammine
Hungarian-American nephrologist
generated the first unbiased, comprehensive kidney cell-type atlas using single cell transcriptomics. She identified that specific renal phenotypes are
Katalin_Susztak
principles with biological data analysis, particularly in genomics and transcriptomics. Li has won several awards, including the Overton Prize from the International
Jingyi_Jessica_Li
Protein-coding gene in the species Homo sapiens
Arauzo-Bravo M, Carlo S, Zucchi I, Reinbold RA (June 2024). "Single-cell transcriptomic analysis to identify endomembrane regulation of metalloproteins
TMEM230
Belgian biologist
co-regulators. Using single cell transcriptomics, Deplancke's team discovered the previously unknown adipogenesis-regulatory cells (Aregs), which are endowed
Bart_Deplancke
American biotechnology company
use in scientific research, with a focus on product development for single-cell and spatial omics. 10x Genomics was founded in 2012 by Serge Saxonov
10x_Genomics
Technology for RNA sequencing
technological advances in single-cell transcriptomics, where sample barcoding made the early multiplexing of hundreds to thousands of single cells possible. Sample
BRB-seq
Suffix in biology
tRNA, and other non-coding RNA, produced in one or a population of cells. Transcriptomics: Study of transcriptomes, their structures and functions. The metabolome
Omics
Set of computational techniques
k} cell types known to be presented in the samples. These references can be derived by exploring external single-cell epigenomics or transcriptomics datasets
Cellular_deconvolution
Cancer of plasma cells
myeloma (MM), also known as plasma cell myeloma and simply myeloma, is a cancer of plasma cells, a type of white blood cell that normally produces antibodies
Multiple_myeloma
Developmental history of a tissue or organ
Chieh; Bar-Joseph, Ziv (2020). "Single-cell lineage tracing by integrating CRISPR-Cas9 mutations with transcriptomic data". Nature Communications. 11
Cell_lineage
Italian scientist (born 1965)
engineering to cell‑based therapies. Stassi's work has allowed the acquisition of multi-omics platforms (genomics, bulk and single cell transcriptomics, epigenomics
Giorgio_Stassi
American-Israeli biomedical scientist
T., Feder, M., Levin, M., Hall, B. K. & Yanai, I. Spatiotemporal transcriptomics reveals the evolutionary history of the endoderm germ layer. Nature
Itai_Yanai
Group of flagellates
(June 2021). "Multigene phylogenetics of euglenids based on single-cell transcriptomics of diverse phagotrophs". Molecular Phylogenetics and Evolution
Anisonemia
Turkish neuroscientist and geneticist (born 1981)
Association, April 23, 2019 Cosacak, M. I. (2019). "Single-Cell Transcriptomics Analyses of Neural Stem Cell Heterogeneity and Contextual Plasticity in a Zebrafish
Çağhan_Kızıl
Heuristic for distinct words in a document
Michele; Osella, Matteo (2023). "Emergent statistical laws in single-cell transcriptomic data". Physical Review E. 107 (4) 044403: 2021–06.16.448706. bioRxiv 10
Heaps's_law
Group of flagellates
et al. (2021). "Multigene phylogenetics of euglenids based on single-cell transcriptomics of diverse phagotrophs". Molecular Phylogenetics and Evolution
Peranemid
technique allowing one to simultaneously obtain both transcriptomic and genomic data from single cells, allowing for direct comparison of gene expression
G&T-seq
Probability distribution
Osella, Matteo (27 April 2023). "Emergent statistical laws in single-cell transcriptomic data". Physical Review E. 107 (4) 044403. Bibcode:2023PhRvE.107d4403L
Zipf's_law
Dutch biophysicist and systems biologist
Lennart; Alexander (2014). "Validation of noise models for single-cell transcriptomics". Nature Methods. 11 (6): 637–640. doi:10.1038/nmeth.2930. PMID 24747814
Alexander_van_Oudenaarden
Genus of flagellates
et al. (2021). "Multigene phylogenetics of euglenids based on single-cell transcriptomics of diverse phagotrophs". Molecular Phylogenetics and Evolution
Neometanema
Arauzo-Bravo M, Carlo S, Zucchi I, Reinbold RA (June 2024). "Single-cell transcriptomic analysis to identify endomembrane regulation of metalloproteins
Vasculogenic_mimicry
Group of flagellates with flexible cells
et al. (2021). "Multigene phylogenetics of euglenids based on single-cell transcriptomics of diverse phagotrophs". Molecular Phylogenetics and Evolution
Spirocuta
Chromatin remodeling complex
Schüller, Ulrich; Kerl, Kornelius (22 March 2022). "Single-cell transcriptomics identifies potential cells of origin of MYC rhabdoid tumors". Nature Communications
Mammalian SWI/SNF (BAF) complex
Mammalian_SWI/SNF_(BAF)_complex
Y, Yabukami H, et al. (November 2019). "Single-cell transcriptomics reveals expansion of cytotoxic CD4 T cells in supercentenarians". Proceedings of the
Timeline_of_aging_research
Genus of flagellates
Simpson AGB (2021). "Multigene phylogenetics of euglenids based on single-cell transcriptomics of diverse phagotrophs". Molecular Phylogenetics and Evolution
Urceolus
British immunologist and academic
Deborah K Dunn-Walters (18 March 2021). "Single-Cell Transcriptomic Analyses Define Distinct Peripheral B Cell Subsets and Discrete Development Pathways"
Deborah_Dunn-Walters
Novel human gene
"Pediatric T-cell acute lymphoblastic leukemia blast signature and MRD associated immune environment changes defined by single cell transcriptomics analysis"
ARMH1
Culture of cells from fresh tissues
Primary cell culture is the ex vivo culture of cells freshly obtained from a multicellular organism, as opposed to the culture of immortalized cell lines
Primary_cell_culture
American biostatistician and data scientist
software for genomics, epigenomics, and spatial transcriptomics, and applications involving single-cell sequencing. She is an associate professor at Johns
Stephanie_Hicks
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