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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
Subfield
neurodegeneration. Spatial omics imaging methods include multiple techniques combining spatial information with omics data. They include spatial transcriptomics (Nature
Spatial_biology
Technology for examining cells
and sequencing together. Spatial transcriptomics, spatial epigenomics, and spatial proteomics are prominent examples of spatial technologies that have provided
Spatial DNA methylation profiling
Spatial_DNA_methylation_profiling
Techniques to study geometric data
also applied to genomics, as in transcriptomics data, but is primarily for spatial data. Complex issues arise in spatial analysis, many of which are neither
Spatial_analysis
Distribution property in ecology
heterogeneity in spatial data using the HTA index with applications to spatial transcriptomics and imaging, Bioinformatics, Volume 37, Issue 21, November 2021
Spatial_heterogeneity
DNA barcoding technique
simultaneous spatial transcriptomic and proteomic analysis of a tissue sample. DBiT-seq improves upon previous spatial transcriptomics applications such
Deterministic Barcoding in Tissue for Spatial Omics Sequencing
Deterministic_Barcoding_in_Tissue_for_Spatial_Omics_Sequencing
Multidisciplinary research project
in the late 1990s by VEP collaborators of the first system for Spatial transcriptomics. Other areas that VEP researchers pioneered include early web technologies
Visible_Embryo_Project
Chinese-American computational biologist
computational biologist whose work spans cancer genomics, single-cell transcriptomics, and computational oncology. He is a tenured professor in the Department
Ken Chen (computational biologist)
Ken_Chen_(computational_biologist)
Autoimmune disease of skin and muscle
Muñoz-Braceras S, Wigerblad G, Dell'Orso S, et al. (5 March 2026), "Spatial transcriptomics reveals mechanism of autoimmunity driven by internalized autoantibodies"
Dermatomyositis
American biotechnology company
months later, 10x Genomics acquired Spatial Transcriptomics, a biotechnology company working in the field of spatial genomics. In November 2018, 10x Genomics
10x_Genomics
Machine learning framework
stress-strain fields in materials, classifying complex data like spatial transcriptomics, predicting multiphase flow in porous media, and carbon dioxide
Neural_operators
Molecular biology technique
and mitochondrial DNA mutations using commercially available spatial transcriptomics platforms. Laser capture microdissection coupled to ATAC-seq (LCM-ATAC-seq)
ATAC-seq
American biostatistician and data scientist
development of open-source software for genomics, epigenomics, and spatial transcriptomics, and applications involving single-cell sequencing. She is an associate
Stephanie_Hicks
Computational methods in biology
complexity. Integration of spatial transcriptomics with scRNAseq can help overcome these limitations by supporting the spatial deconvolution of low-resolution
Single-cell multi-omics integration
Single-cell_multi-omics_integration
Biological analysis approach
biology Single-cell multi-omics integration Single-cell transcriptomics Spatial transcriptomics Systems Biology Bersanelli, Matteo; Mosca, Ettore; Remondini
Multiomics
Chinese genome sequencing company
sequencer. In 2021, BGI developed Stereo-seq, its genome wide Spatial transcriptomics technology and released the first research findings from a consortium
BGI_Group
Different genetic causes for the same disease
interact. Emerging modalities like imaging mass cytometry and spatial transcriptomics integrate molecular data with high-resolution tissue architecture
Genetic_heterogeneity
Muscular inflammatory disease of unknown origin
Margherita; Ellezam, Benjamin; Laverny, Gilles (2026-03-05). "Spatial transcriptomics reveals mechanism of autoimmunity driven by internalized autoantibodies"
Inflammatory_myopathy
Histopathologist
Marion de Proce S, Aitman T, Chandran S, Smith C. (2020). Spatial transcriptomics identifies spatially dysregulated expression of GRM3 and USP47 in ALS. Neuropathology
Jenna_Gregory
File formats for microscopy data
spatial transcriptomics, which adds challenges from the transcriptomics to those of bioimaging also benefit from modern file formats, such as SpatialData
Microscopy_file_formats
American technology firm
work at Eolas, to create new technologies ranging from Spatial Genomics/Spatial transcriptomics, Code signing, transient-key cryptography, and blockchain
Eolas
Iranian-American computational biologist and biomedical engineer
deep generative model for integrating spatial transcriptomics with histological imaging characterizes spatial niches involving metabolic reprogramming
Elham_Azizi
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
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
Indian American scientist
immune-tissue crosstalk in regeneration and repair processes, spatial transcriptomics for stratification of psoriasis severity, and approaches in regenerative
Shruti_Naik
Embryonic Stem Cells
cellular complexity of gastruloids at the level of single cell and spatial transcriptomics, reveals that they contain representatives of the three germ layers
Gastruloid
Mammalian protein found in Homo sapiens
upregulated in hypertrophic (HCM) and dilated cardiomyopathy (DCM). Spatial transcriptomics and single cell studies reveal the expression of Osteopontin via
Osteopontin
Genome browser hosted by the University of California, Santa Cruz
platform designed to handle single-cell sequencing datasets and spatial transcriptomics. The browser has also integrated data from the Genotype-Tissue
UCSC_Genome_Browser
Methodology for biomedical research
Cleary, B; Farhi, SL (2025). "Simultaneous CRISPR screening and spatial transcriptomics reveal intracellular, intercellular, and functional transcriptional
Optical_pooled_screening
Suffix in biology
as genomics, proteomics, metabolomics, metagenomics, phenomics and transcriptomics. The related suffix -ome is used to address the objects of study of
Omics
American computer scientist
to include single cell sequencing, with a particular focus on spatial transcriptomics. She also has work on Bayesian experimental design using contextual
Barbara_Engelhardt
has conducted influential studies in whole-tissue and single-cell transcriptomics. He received his PhD from the University of Cambridge in Applied Mathematics
John_Marioni
German neurobiologist
different: Baier’s team employs single-cell RNA sequencing and spatial transcriptomics to develop catalogs of neuronal cell types in the retina, tectum
Herwig_Baier
Set of all RNA molecules in one cell or a population of cells
fields of life sciences and technology. As such, transcriptome and transcriptomics were one of the first words to emerge along with genome and proteome
Transcriptome
American immunologist
subsets in both mice and humans using single-cell RNA sequencing and spatial transcriptomics. Her research explores cross-species homology among mononuclear
Claudia_V._Jakubzick
Academic journal
1038/s41592-019-0703-5. Marx, Vivien (2021). "Method of the Year: spatially resolved transcriptomics". Nature Methods. 18 (1): 9–14. doi:10.1038/s41592-020-01033-y
Nature_Methods
Robot-assisted surgery Safety engineering — Sleep medicine — Soft tissue — Spatial transcriptomics — Speech-language pathology — Structural biology — Stem cell —
Index of biomedical engineering articles
Index_of_biomedical_engineering_articles
Study of biochemical processes in an individual cell
analysis and subcellular analysis refer to the study of genomics, transcriptomics, proteomics, metabolomics, and cell–cell interactions at the level
Single-cell_analysis
Joint biomedical research center of the Czech Academy of Sciences and Charles University
Dohnálek Provides transcriptomic services for academic and commercial users, including bulk, single-cell, and spatial transcriptomic analysis. Services
BIOCEV
Single cell RNA sequencing method
(OPS), which utilizes high-throughput imaging rather than transcriptomics to capture spatial and morphological phenotypes under genetic perturbation. The
Perturb-seq
Database of human proteins
including antibody-based imaging, mass spectrometry-based proteomics, transcriptomics and systems biology. All the data in the knowledge resource is open
Human_Protein_Atlas
Cellular biology lab technique
of information for the same cell by combining both proteomics and transcriptomics data. For phenotyping, this method has been shown to be as accurate
CITE-Seq
Environmental factor to which a person is exposed
Advances in high-throughput -omics technologies such as genomics, transcriptomics, proteomics, and metabolomics, have revolutionized our ability to measure
Exposome
Medical condition
Temple-Oberle C, Rosin N, Gabriel V, Biernaskie J (August 2024). "Spatial and Single-Cell Transcriptomics Reveal that Oncofetal Reprogramming of Fibroblasts Is Associated
Marjolin's_ulcer
Veres A, Li V, et al. (May 2015). "Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells". Cell. 161 (5): 1187–1201. Bibcode:2015Cell
List of single cell omics methods
List_of_single_cell_omics_methods
Species of beetle
as compared to other arthropod species. Using community annotation, transcriptomics, and genome sequencing, they uncovered that Colorado Potato beetles
Colorado_potato_beetle
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
Species of crayfish
utilized by yabbies through their antennas, allowing them to create a spatial configuration of the world around them during the night and in visually
Common_yabby
Laboratory technique
unknown GPCR-linked proteins. Proximity labeling has also been used for transcriptomics and interactomics. In 2019, Alice Ting and the Ting lab have used APEX
Proximity_labeling
Large part of the brain containing the cerebral cortex
cerebral cortex has three layers. Molecular studies using single-cell transcriptomics have confirmed that all cortices of modern reptiles share a three-layered
Cerebrum
The transcriptome is distinct from the exome and the translatome. transcriptomics The study of the transcriptome of a particular genome, cell, or organism
Glossary of cellular and molecular biology (M–Z)
Glossary_of_cellular_and_molecular_biology_(M–Z)
atlas, and the spatial myocardial infarction atlas, just to cite a few. These atlases integrate single-cell transcriptomics, spatial data, and clinical
Disease_Cell_Atlas
Scientific study of chemical processes involving metabolites
sample, such as a single organism. The word was coined in analogy with transcriptomics and proteomics; like the transcriptome and the proteome, the metabolome
Metabolomics
Mathematics researcher
parallel single-cell transcriptomic and epigenomic profiles. Genome Biology, 21(1):25, 2020 Cang Z and Q. Nie. Inferring spatial and signaling relationships
Qing_Nie
American neuroscientist (born 1979)
Chun-Chen; Suk, Ho-Jun (2021-01-29). "Expansion sequencing: Spatially precise in situ transcriptomics in intact biological systems". Science. 371 (6528) eaax2656
Edward_Boyden
Class of arthropods
Mirte; Ylstra, Bauke; Van Straalen, Nico M.; Roelofs, Dick (2009). "Transcriptomics reveals extensive inducible biotransformation in the soil-dwelling
Springtail
Chinese-American biostatistician, integrates statistics with genomics and transcriptomics Mingyao Li, Chinese-American biostatistician and statistical geneticist
List_of_women_in_statistics
Indian-American statistician
to high-dimensional biological data such as genomics, epigenomics, transcriptomics, and proteomics. His work also extends to neuro- and cancer-imaging
Veera_Baladandayuthapani
Large-scale study of proteins
first dedicated proteomics laboratory in 1995. After genomics and transcriptomics, proteomics is the next step in the study of biological systems. It
Proteomics
Examines sequence information from individual cells
Cell Atlas Single-cell analysis Single cell epigenomics Single-cell transcriptomics Single-cell multi-omics integration Tcr-seq Whole genome sequencing
Single-cell_sequencing
Branch of ecology
of complex functional diversity are only effective in a small range of spatial scales. However, by defining the functional trait probability density as
Functional_ecology
Virus that infects bacteria
Chen C, Shen W, Huang G, Le S, Lu S, et al. (January 2016). "Global Transcriptomic Analysis of Interactions between Pseudomonas aeruginosa and Bacteriophage
Bacteriophage
Species of crustacean
architecture may create an ecological trap for it. According to comparative transcriptomics, vital genes involved in phototransduction are down-regulated in the
Oratosquilla_oratoria
Branch of machine learning
Thas, O; Bender, A; Göhlmann, H. W.; Hochreiter, S (2015). "Using transcriptomics to guide lead optimization in drug discovery projects: Lessons learned
Deep_learning
Organ central to the nervous system
pallium, hippocampus, and cortical cell types revealed by single-cell transcriptomics in reptiles". Science. 360 (6391): 881–888. Bibcode:2018Sci...360.
Brain
Measurable indicator
inflammation and tumor growth. MRI has the advantages of having very high spatial resolution and is very adept at morphological imaging and functional imaging
Biomarker_(medicine)
Greek-born computational biologist
Meibalan, Elamaran; Mantero, Julio C.; Renfro, Ashley (2024). "Transcriptomic and spatial dissection of human ex vivo right atrial tissue reveals proinflammatory
Manolis_Kellis
predictive in silico computational models such as QSAR and omics such as transcriptomics technologies among other techniques. By using these human-derived biological
New_approach_methodologies
Family of spiders
(2018). "Phylogenomics, diversification dynamics, and comparative transcriptomics across the spider tree of life". Current Biology. 28 (9): 1489–1497
Orb-weaver_spider
Predatory cartilaginous fishes
release them. Species appropriate to home aquaria represent considerable spatial and financial investments as they generally approach adult lengths of 3
Shark
Utilizing polymers to examine small biological samples
H.; Boyden, Edward S. (2021). "Expansion sequencing: Spatially precise in situ transcriptomics in intact biological systems". Science. 371 (6528) eaax2656
Expansion_microscopy
Methods for diagnosing tuberculosis
Whelan A, Deeks JJ, et al. (June 2001). "Enhanced contact tracing and spatial tracking of Mycobacterium tuberculosis infection by enumeration of antigen-specific
Diagnosis_of_tuberculosis
Family of birds
and sites in high-elevation hummingbirds revealed by comparative transcriptomics". Genome Biology and Evolution. 11 (6): 1573–1585. doi:10.1093/gbe/evz101
Hummingbird
Neuroscientist
PMID 24695228. Marx, Vivien (January 2021). "Method of the Year: spatially resolved transcriptomics". Nature Methods. 18 (1): 9–14. doi:10.1038/s41592-020-01033-y
Hongkui_Zeng
Database of biological information
to document spatial/geographical distribution of 1,371 bird species in China, as existing databases had been severely lacking in spatial distribution
Biological_database
Central organ of the human nervous system
Mathias (June 15, 2015). "Defining the human brain proteome using transcriptomics and antibody-based profiling with a focus on the cerebral cortex".
Human_brain
Family of shellfish, many edible
fast and slow muscles in scallops revealed through proteomics and transcriptomics". BMC Genomics. 19 (1): 377. doi:10.1186/s12864-018-4770-2. PMC 5963113
Scallop
Species of fish
outlined in detail in the following Reproduction and Migration section. Spatially, the naked carp is benthopelagic, found between bottom and midwater zones
Schizopygopsis_przewalskii
Genus of coniferous trees
Velasco-Bautista, Efraín; Andrés, Flores (2018). "Current and Potential Spatial Distribution of Six Endangered Pine Species of Mexico: Towards a Conservation
Pine
Structure in the midbrain
primates, however, the superior colliculus is also involved in generating spatially directed head turns, arm-reaching movements, and shifts in attention that
Superior_colliculus
(2008-01-01). "Linking gene regulation and the exo-metabolome: A comparative transcriptomics approach to identify genes that impact on the production of volatile
Exometabolomics
Med. 2020. 201(10):1277-1291. (Senior author; IF = 24.7) Dheda K, et al. Spatial Network Mapping of Pulmonary Multidrug-Resistant Tuberculosis Cavities
Keertan_Dheda
Common ancestor evolutionary evidence
extinct. Richard Dawkins says that ring species "are only showing us in the spatial dimension something that must always happen in the time dimension". The
Evidence_of_common_descent
Medical condition
Shichao; Yang, Chaoyong (2024-06-01). "The dawn of spatiotemporal transcriptomics". Biomedical Analysis. 1 (2): 154–161. doi:10.1016/j.bioana.2024.06
FOXG1_syndrome
Topical clustering method
1145/2133806.2133826. S2CID 753304. Cao, Liangliang, and Li Fei-Fei. "Spatially coherent latent topic model for concurrent segmentation and classification
Topic_model
Medium-sized toothed whale species
January 2024. Watt, C. A.; Orr, J. R.; Ferguson, S. H. (January 2017). "Spatial distribution of narwhal (Monodon monoceros) diving for Canadian populations
Narwhal
PMID 12850333. Battich N, Stoeger T, Pelkmans L (October 2013). "Image-based transcriptomics in thousands of single human cells at single-molecule resolution".
High-content_screening
German physician and neuroscientist
dialogue between the synapse and the nucleus. His work highlighted the spatial aspects of calcium signals and in particular the importance of nuclear
Hilmar_Bading
Single-celled alga with a silica cell wall
(2009). "Update of the Diatom EST Database: A new tool for digital transcriptomics". Nucleic Acids Research. 37 (Database issue): D1001–5. doi:10.1093/nar/gkn905
Diatom
Study of DNA modifications that do not change its sequence
Holliday defined epigenetics as "the study of the mechanisms of temporal and spatial control of gene activity during the development of complex organisms."
Epigenetics
Type of fully automated microscopy
Johannes; Marcus, Katrin; Schubert, Walter (March 2008). "Interlocking transcriptomics, proteomics and toponomics technologies for brain tissue analysis in
Imaging_cycler_microscopy
Global health science project
building detailed maps of the human body, using cutting-edge single cell and spatial genomics methods at massive scale, combined with powerful computing and
Human_Cell_Atlas
Collection of microscopic DNA spots attached to a solid surface
terms Protocol (natural sciences) Biology portal Technology portal Transcriptomics technologies Serial analysis of gene expression RNA-Seq MAGIChip Microarray
DNA_microarray
single-cell sequencing technique allowing one to simultaneously obtain both transcriptomic and genomic data from single cells, allowing for direct comparison of
G&T-seq
Microbial community assemblage and activity
multi-labeled probing has improved visualization of the microbiome and transcriptomics and proteomics have been applied to examine host–microbiome interactions
Microbiome
Tiny lifeforms floating and drifting in the air, carried by the wind
fungal, bacterial, and viral biodiversity, and targeted genomics and transcriptomics towards ribosomal genes has supported earlier findings about the maintenance
Aeroplankton
Grouping a set of objects by similarity
artificial phylogenies clusters of organisms that share similar attributes. Transcriptomics Clustering is used to build groups of genes with related expression
Cluster_analysis
Protein-coding gene in humans
Gao Y, Liang G, Huang L, Wang J, Yang X, et al. (February 2020). "Transcriptomics of Gabra4 knockout mice reveals common NMDAR pathways underlying autism
GABRA4
Biological term
"Revisiting hematopoiesis: applications of the bulk and single-cell transcriptomics dissecting transcriptional heterogeneity in hematopoietic stem cells"
Hematopoietic_stem_cell_niche
Organ covering the outside of the human body
(February 2015). "Expression of human skin-specific genes defined by transcriptomics and antibody-based profiling". The Journal of Histochemistry and Cytochemistry
Human_skin
SPATIAL TRANSCRIPTOMICS
SPATIAL TRANSCRIPTOMICS
Girl/Female
Bengali, Indian, Telugu
Special
Girl/Female
Arabic, Muslim
Royal
Boy/Male
Tamil
Saisnigda | ஸாஈஸà¯à®¨à¯€à®•à¯à®¤à®¾
Special
Saisnigda | ஸாஈஸà¯à®¨à¯€à®•à¯à®¤à®¾
Girl/Female
Muslim
Royal
Girl/Female
Arabic, Bengali, Gujarati, Hindu, Indian, Kannada, Malayalam, Marathi, Muslim, Sindhi, Tamil, Telugu
Special
Girl/Female
Greek, Indian, Marathi, Turkish
Special
Girl/Female
Hindu, Indian, Tamil
Special
Girl/Female
Bengali, Indian, Modern
Special
Girl/Female
Hindu, Indian, Tamil
Special
Girl/Female
Indian
Special
Girl/Female
Indian, Telugu
Crystal; Pure
Girl/Female
Hindu
Crystal clear
Boy/Male
Hindu
Special
Boy/Male
Tamil
Special
Girl/Female
Bengali, Indian, Telugu
Special
Boy/Male
Arabic
Arab River
Girl/Female
Tamil
Special
Girl/Female
Indian
Special
Girl/Female
Indian, Telugu
Special
Boy/Male
Gujarati, Hindu, Indian, Kannada, Malayalam, Marathi, Punjabi, Sikh, Telugu
Protector
SPATIAL TRANSCRIPTOMICS
SPATIAL TRANSCRIPTOMICS
Male
English
English unisex name derived from a Middle English and Old French byname for a fair-minded person, JUSTICE means "equity, justice."
Girl/Female
Tamil
Chanasya | சநாஸà¯à®¯à®¾
Delighting, Pleasant, Wonderful
Boy/Male
Hindu, Indian, Punjabi, Sanskrit, Sikh, Telugu
Complete; Knowledge about Everything
Boy/Male
Tamil
Boy/Male
British, English
Famous
Boy/Male
Tamil
Lord Brahma
Girl/Female
Australian, French
The One Desired; Similar to Desiree; Desired; Longed for
Girl/Female
Hindu
Goddess of wealth or Goddess Laxmi or fortunate or
Boy/Male
Hindu, Indian, Marathi
Diamond Like
Boy/Male
Muslim/Islamic
One who presents
SPATIAL TRANSCRIPTOMICS
SPATIAL TRANSCRIPTOMICS
SPATIAL TRANSCRIPTOMICS
SPATIAL TRANSCRIPTOMICS
SPATIAL TRANSCRIPTOMICS
v. t.
To follow like a spaniel.
a.
Limited in range; confined to a definite field of action, investigation, or discussion; as, a special dictionary of commercial terms; a special branch of study.
a.
Furnished with a spathe; as, spathal flowers.
a.
Particular; peculiar; different from others; extraordinary; uncommon.
n.
One appointed for a special service or occasion.
n.
Of, pertaining to, or affecting, a part only; not general or universal; not total or entire; as, a partial eclipse of the moon.
a.
Appropriate; designed for a particular purpose, occasion, or person; as, a special act of Parliament or of Congress; a special sermon.
n.
A particular.
n.
An implement shaped like a knife, flat, thin, and somewhat flexible, used for spreading paints, fine plasters, drugs in compounding prescriptions, etc. Cf. Palette knife, under Palette.
pl.
of Spatha
a.
Of or pertaining to a species; constituting a species or sort.
n.
Inclined to favor one party in a cause, or one side of a question, more then the other; baised; not indifferent; as, a judge should not be partial.
a.
Of or pertaining to space.
a.
Pertaining to bodies at rest or in equilibrium.
a.
Resting; acting by mere weight without motion; as, statical pressure; static objects.
a.
See Spatial.
n.
A patrial noun. Thus Romanus, a Roman, and Troas, a woman of Troy, are patrial nouns, or patrials.
n.
Pertaining to a subordinate portion; as, a compound umbel is made up of a several partial umbels; a leaflet is often supported by a partial petiole.
a.
Chief in excellence.