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Topic · Molecular Biology

Single-cell and spatial transcriptomics

Single-cell and spatial transcriptomics is a research topic within Molecular Biology. Science Explorer counts 23k research works in it since 1952. 9.9% of them reached the world's top 10% most cited for their field and year.

This cluster of papers focuses on the comprehensive integration and analysis of single-cell transcriptomic data, covering topics such as cell types, spatial profiling, lineage tracking, data integration, gene expression, and cell heterogeneity. The research explores various technologies and computational methods to study the transcriptomic landscape at the single-cell level.

  • Single-Cell
  • Transcriptomics
  • RNA-Seq
  • Cell Types
  • Spatial Profiling
  • Lineage Tracking
  • Data Integration
  • Gene Expression
  • Cell Heterogeneity
  • Droplet-based Sequencing
Research works
23k
fractional, since 1952
In the world top 10%
2.3k
per year above
Top-10% rate
9.9%
share of its works in the world top 10%
Growth, 2018-21 → 2022-25
+101%
the tick is no change
Largest producer
United States
39% of the 10 largest, 2022-now
Single-cell and spatial transcriptomics

Which countries lead Single-cell and spatial transcriptomics research?

By volume, the United States and China publish the most (4.2k and 3.9k works in 2022-now).

By volume, 2022-now

  1. 1 United States 4.2k works
  2. 2 China 3.9k works
  3. 3 Germany 616 works
  4. 4 United Kingdom 517 works
  5. 5 Japan 287 works
  6. 6 Canada 284 works
  7. 7 France 277 works
  8. 8 Australia 239 works
  9. 9 South Korea 228 works
  10. 10 Italy 208 works

How concentrated that is

The same countries as shares of everything the list above accounts for. A node where two countries do two thirds of the work and one spread evenly across twelve read alike as a ranking and not at all alike here.

United States: 39.0%China: 36.4%Germany: 5.7%United Kingdom: 4.8%6 others listed: 14.1%39%largest
United States4,202 · 39.0%China3,927 · 36.4%Germany616 · 5.7%United Kingdom517 · 4.8%6 others listed1,524 · 14.1%

Shares of the rows listed above, not of the whole node.

Which institutions lead Single-cell and spatial transcriptomics research?

By volume in 2022-now, Harvard University publishes the most Single-cell and spatial transcriptomics research, followed by Chinese Academy of Sciences and Sun Yat-sen University.

By volume, 2022-now

  1. 1 Harvard UniversityUnited States 276 works
  2. 2 Chinese Academy of SciencesChina 131 works
  3. 3 Sun Yat-sen UniversityChina 131 works
  4. 4 Shanghai Jiao Tong UniversityChina 125 works
  5. 5 Stanford UniversityUnited States 114 works
  6. 6 National Institutes of HealthUnited States 110 works
  7. 7 Peking UniversityChina 102 works
  8. 8 Fudan UniversityChina 90 works
  9. 9 Zhejiang UniversityChina 90 works
  10. 10 Johns Hopkins UniversityUnited States 80 works

Who are the leading researchers in Single-cell and spatial transcriptomics?

The most-cited researchers publishing on Single-cell and spatial transcriptomics include Eric S. Lander, Zhong Lin Wang and Yoshua Bengio.

  1. 1 Eric S. Lander United States 524k citations
  2. 2 Zhong Lin Wang United States 491k citations
  3. 3 Yoshua Bengio Canada 476k citations
  4. 4 Rob Knight United States 468k citations
  5. 5 George Davey Smith United Kingdom 435k citations
  6. 6 Richard M. Durbin United Kingdom 410k citations
  7. 7 Mark J. Daly United States 403k citations
  8. 8 Stacey L. Gabriel United States 402k citations
  9. 9 Robert John Tibshirani United States 396k citations
  10. 10 Guido Kroemer France 386k citations

Ranked by citations received across their whole record, among researchers with at least three works on this topic.

What are the most cited papers in Single-cell and spatial transcriptomics?

The most cited paper in Single-cell and spatial transcriptomics is "edgeR : a Bioconductor package for differential expression analysis of digital gene expression data" (Mark D. Robinson, Davis James McCarthy, Gordon K. Smyth, 2009), with 45,449 citations. Next come "Comprehensive Integration of Single-Cell Data" (17,471) and "GSVA: gene set variation analysis for microarray and RNA-Seq data" (17,089).

Most cited papers
#PaperReleasedCitations
1 edgeR : a Bioconductor package for differential expression analysis of digital gene expression data Mark D. Robinson, Davis James McCarthy, Gordon K. Smyth · Bioinformatics Open access 11 Nov 2009 45,449
2 Comprehensive Integration of Single-Cell Data Tim Stuart, Andrew W. Butler, Paul Hoffman et al. · Cell Open access Jun 2019 17,471
3 GSVA: gene set variation analysis for microarray and RNA-Seq data Sonja Hänzelmann, Robert Castelo, Justin Guinney · BMC Bioinformatics Open access 16 Jan 2013 17,089
4 Integrative genomics viewer James Theodore Robinson, Helga Thorvaldsdóttir, Wendy Winckler et al. · Nature Biotechnology Open access 2011 16,977
5 Integrated analysis of multimodal single-cell data Yuhan Hao et al. · Cell Open access 31 May 2021 16,879
All 100 most cited papers, with filters and sorting

Where is Single-cell and spatial transcriptomics research done?

The largest centres of Single-cell and spatial transcriptomics research in 2022-now are Beijing (China), Shanghai (China), Guangzhou (China) and New York (United States). Among places with at least 20 works in it, it is an unusually large share of all research in Delray Beach and Chevy Chase.

Largest cities, 2022-now

  1. 1 BeijingChina 579 works
  2. 2 ShanghaiChina 410 works
  3. 3 GuangzhouChina 304 works
  4. 4 New YorkUnited States 229 works
  5. 5 CambridgeUnited States 197 works
  6. 6 BostonUnited States 180 works
  7. 7 LondonUnited Kingdom 172 works
  8. 8 HangzhouChina 170 works
  9. 9 HoustonUnited States 151 works
  10. 10 ParisFrance 148 works

Where it is the local speciality

  1. Delray BeachUS · 25.3 works265×
  2. Chevy ChaseUS · 24.1 works22×
← less than its size predicts1×more →

Location quotient: how much more of its research is in Single-cell and spatial transcriptomics than the world average.

See Single-cell and spatial transcriptomics on the map

Where is the best place to study Single-cell and spatial transcriptomics?

Among universities, judged by research, Harvard University, Weizmann Institute of Science and Massachusetts Institute of Technology score highest, combining citation excellence, specialisation, size, growth and international reach. Research strength is one signal when choosing where to study; it does not measure teaching.

0%10%20%mean 16.59%fractional works in this field (log) →share of work in the world top 10% →Massachusetts Instit…Weizmann Institute o…Harvard UniversityStanford University
above the meannear itbelow it

One dot per university in the first ten of the table below, at the default weights. The upper left is the interesting corner: small places doing unusually strong work.

Citation excellenceshare of its work in the world top 10%, 2022-now and all time averaged
40%
Specialisationhow much of its work is in this field, counted up to 10× the world share
10%
Sizeits output in this field, on a log scale
30%
Growthoutput growth, counted from -20% to +20%
10%
Internationalshare of its work with a co-author abroad
10%
Each slider sets a weight; the share it gets of the score is beside it.
#UniversityScoreTop 10%SpecialisationWorksGrowth
1Harvard UniversityUnited States 85.517.2%8.0×276 +43.9%
2Weizmann Institute of ScienceIsrael 72.320.6%13.6×21 +44.0%
3Massachusetts Institute of TechnologyUnited States 69.321.7%4.4×34 +20.5%
4Stanford UniversityUnited States 69.215.1%7.1×114 +3.7%
5Peking UniversityChina 68.814.4%4.6×102 +129.5%
6Karolinska InstitutetSweden 68.512.9%9.3×57 +55.1%
7Kettering UniversityUnited States 63.323.3%22.0×9 +143.4%
8KU LeuvenBelgium 63.115.4%3.1×32 +91.0%
9Heidelberg UniversityGermany 62.513.6%6.5×54 +93.9%
10Johns Hopkins UniversityUnited States 61.611.7%4.8×80 +57.2%

Universities only. The score blends citation excellence (40%), size (30%), specialisation (10%), growth (10%), international reach (10%), 2022-now; growth compares 2018-21 with 2022-25 and counts up to +20%, since a jump from a small base is mostly noise.

Every institution in Single-cell and spatial transcriptomics, country by country

Is Single-cell and spatial transcriptomics research growing?

Output in 2022-2025 was 101% higher than in 2018-2021, peaking in 2025. The fastest-growing topics are Single-cell and spatial transcriptomics.

still counting19801990200020102020
grewheldshrank

The same series as a ribbon: one cell per year, darker for more. The line above answers how much; this answers when.

Its share of all research

Growing output can still be a shrinking share: all of science grows. This is Single-cell and spatial transcriptomics as a percentage of every work published that year, 0.042% in 2024.

still counting0.020%0.040%0.060%Single-cell and spatial transcriptomics0.056% in 202519801990200020102020

Fractional works of Single-cell and spatial transcriptomics over all fractional works that year. How the balance of science has shifted.

How much of it reaches the world top 10%

Year by year.

still counting5%10%15%Single-cell and spatial transcriptomics9.8% in 2025200020102020

Of each year's works in it, the share that reached the world's 10% most cited for their field and year. A field is the world for its own topics, so there is no other line to hold it against.

Which topics inside it are moving

Growth and decline on one axis around a shared zero. Two lists side by side hide the thing that matters: whether the growth dwarfs the decline, or the other way round.

Questions people ask

Who leads single-cell and spatial genomics research?

By volume in 2022-now, Harvard University publishes the most Single-cell and spatial transcriptomics research, followed by Chinese Academy of Sciences and Sun Yat-sen University. By volume, the United States and China publish the most (4.2k and 3.9k works in 2022-now).

All 1,273 questions in the Question Catalogue

Discussion

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