Professor research guide
Lee Otterson Professor of Bioengineering and Professor of Applied Physics · Bioengineering and Applied Physics
Stephen Quake develops microfluidic and sequencing approaches to single cells, individual molecules, and nucleic acids in blood. This independent guide distinguishes his lab contributions from collaborations and consortium resources.
Official profile ↗Independent educational guide. Not affiliated with or endorsed by the universities, professors or laboratories described here. This collection reflects the material currently mapped on Socratic Learn.
Research develops biological measurement tools and applies them to single-cell genomics, genomic diagnostics, microbial ecology, and quantitative biological analysis. This independent primer distinguishes historical lab contributions, collaborative and consortium results, current research, and clinical screening from diagnosis.
6 lessons · ~29 minutes
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Research primer
6 lessons · ~29 minutes
New measurement tools reveal individual cells, human cell atlases, molecular traces in blood, immune clones, and microbial ecosystems. A video-first introduction to genomics and bioengineering.
Interpret fragmented extracellular DNA as a molecular mixture.
Explain why cfRNA can carry expression information but source inference needs assumptions.
Distinguish genome, transcriptome and bulk versus single-cell information.
Use cell-atlas reference profiles while accounting for sampling and capture bias.
Interpret immune clone counts without inferring antigen or complete tissue coverage.
Explain how microfluidic scale, isolation and valves change what can be measured.
Separate microbial DNA detection from viability, infection and causal ecology.
Relate counting noise, placental DNA and donor DNA to scoped screening and monitoring principles.
Describe reference-based mixture deconvolution, validation and identifiability limits.
Interpret RNA matrices, cell types and states without equating clusters with biological identities.
Distinguish individual-molecule measurements from averages and sole-invention claims.
Explain the consortium atlas and cross-tissue diversity within its donor and tissue scope.
Science · 2000
Unger MA, Chou HP, Thorsen T, Scherer A, Quake SR
Why this matters: HISTORICAL QUAKE-LAB PRIMARY RESULT: multilayer valves and pumps enable parallel biological measurements.
DOI: 10.1126/science.288.5463.113
Science · 2002
Thorsen T, Maerkl SJ, Quake SR
Why this matters: HISTORICAL QUAKE-LAB PRIMARY RESULT: integrated chambers and valves automate many measurements.
DOI: 10.1126/science.1076996
PNAS · 2003
Braslavsky I, Hebert B, Kartalov E, Quake SR
Why this matters: HISTORICAL QUAKE-LAB PRIMARY RESULT: demonstrated sequence fingerprints up to five bases; not sole invention of all sequencing.
DOI: 10.1073/pnas.0230489100
Nat Biotechnol · 2009
Pushkarev D, Neff NF, Quake SR
Why this matters: HISTORICAL QUAKE-LAB PRIMARY RESULT: individual human genome sequencing with the then-current single-molecule platform.
DOI: 10.1038/nbt.1561
Science · 2006
Ottesen EA, Hong JW, Quake SR, Leadbetter JR
Why this matters: COLLABORATIVE PRIMARY RESULT: Leadbetter-led multigene measurements of individual environmental bacteria.
DOI: 10.1126/science.1131370
PNAS · 2006
Warren L, Bryder D, Weissman IL, Quake SR
Why this matters: COLLABORATIVE PRIMARY RESULT: digital RT-PCR profiles individual hematopoietic progenitors.
DOI: 10.1073/pnas.0608512103
Nature · 2014
Treutlein B, Brownfield DG, Wu AR, et al., Krasnow MA, Quake SR
Why this matters: COLLABORATIVE PRIMARY RESULT: 198 cells across four developmental stages of mouse lung; not every human lung state.
DOI: 10.1038/nature13173
PNAS · 2015
Darmanis S, Sloan SA, Zhang Y, et al., Barres BA, Quake SR
Why this matters: COLLABORATIVE PRIMARY RESULT: 466 adult and fetal human brain cells reveal transcriptomic diversity.
DOI: 10.1073/pnas.1507125112
Nat Med · 2020
Wang W, Vilella F, Alama P, Moreno I, Mignardi M, Isakova A, Pan W, Simon C, Quake SR
Why this matters: COLLABORATIVE PRIMARY RESULT: endometrial cell states across the menstrual cycle; measured RNA is not direct protein measurement.
DOI: 10.1038/s41591-020-1040-z
Science · 2022
The Tabula Sapiens Consortium (Jones RC, Karkanias J, Krasnow MA, Pisco AO, Quake SR, Salzman J, Yosef N, et al.)
Why this matters: CONSORTIUM PRIMARY RESULT: 483,152 cells from 24 tissues/organs, 475 annotated types and 15 donors. Sampling and dissociation limit coverage.
DOI: 10.1126/science.abl4896
bioRxiv · 2024
The Tabula Sapiens Consortium
Why this matters: CURRENT PREPRINT / CONSORTIUM: source audit dated 7 October 2026 identifies the 27 August 2025 version as not peer reviewed; nine new donors and 28 tissues. Not an exhaustive human census.
DOI: 10.1101/2024.12.03.626516
Nat Biotechnol · 2026
Isakova A, et al., Quake SR
Why this matters: CURRENT QUAKE-LAB PRIMARY RESULT: published TotalX measures coding and noncoding RNA at single-cell scale in evaluated samples.
DOI: 10.1038/s41587-026-03068-6
PNAS · 2008
Fan HC, Blumenfeld YJ, Chitkara U, Hudgins L, Quake SR
Why this matters: SMALL EARLY STUDY: 18 pregnancies including nine T21, two T18 and one T13 cases. Historical title uses diagnosis; contemporary application is prenatal screening, not diagnostic confirmation.
DOI: 10.1073/pnas.0808319105
PLoS One · 2010
Fan HC, Quake SR
Why this matters: QUAKE-LAB PRIMARY RESULT: counting-statistics model after GC-bias correction; larger counts reduce random error, not every biological or technical bias.
DOI: 10.1371/journal.pone.0010439
PNAS · 2011
Snyder TM, Khush KK, Valantine HA, Quake SR
Why this matters: QUAKE-LAB PRIMARY RESULT: donor cfDNA associated with biopsy-established heart transplant rejection; does not replace every biopsy.
DOI: 10.1073/pnas.1013924108
Sci Transl Med · 2014
De Vlaminck I, Valantine HA, Snyder TM, et al., Quake SR, Khush KK
Why this matters: PROSPECTIVE PRIMARY RESULT: 65 patients, 565 samples and AUC 0.83; monitoring performance is scoped to the cohort and clinical context.
DOI: 10.1126/scitranslmed.3007803
PNAS · 2015
De Vlaminck I, Martin L, Kertesz M, et al., Khush KK, Quake SR
Why this matters: QUAKE-LAB PRIMARY RESULT: lung-transplant monitoring of rejection and infection; DNA detection alone does not prove viable organisms caused disease.
DOI: 10.1073/pnas.1517494112
PNAS · 2014
Koh W, Pan W, Gawad C, Fan HC, Kerchner GA, Wyss-Coray T, Blumenfeld YJ, El-Sayed YY, Quake SR
Why this matters: QUAKE-LAB PRIMARY RESULT: tissue-associated cfRNA expression and longitudinal pregnancy measurements.
DOI: 10.1073/pnas.1405528111
Science · 2018
Ngo TTM, Moufarrej MN, Rasmussen MH, et al., Melbye M, Quake SR
Why this matters: PILOT / EARLY STUDY: 31 women for gestational age and 38 elevated-risk women for preterm delivery, including 15 preterm. Requires larger blinded clinical validation.
DOI: 10.1126/science.aar3819
Nature · 2022
Moufarrej MN, Vorperian SK, Wong RJ, et al., Stevenson DK, Quake SR
Why this matters: RESEARCH VALIDATION: 404 samples from 199 mothers; an 18-gene panel at 5–16 weeks with independent validation. Possible test basis, not universal clinical readiness.
DOI: 10.1038/s41586-022-04410-z
Nat Biotechnol · 2022
Vorperian SK, Moufarrej MN, Tabula Sapiens Consortium, Quake SR
Why this matters: CONSORTIUM / COLLABORATIVE PRIMARY RESULT: Tabula Sapiens reference-based nu-SVR validated on bulk tissues. Similar and missing signatures limit identifiability.
DOI: 10.1038/s41587-021-01188-9
Sci Transl Med · 2013
Jiang N, He J, Weinstein JA, et al., Davis MM, Fisher DS, Quake SR
Why this matters: COLLABORATIVE PRIMARY RESULT: vaccination-associated antibody lineages; sequence expansion does not automatically reveal antigen specificity.
DOI: 10.1126/scitranslmed.3004794
PNAS · 2017
de Bourcy CFA, Angel CJL, Vollmers C, Dekker CL, Davis MM, Quake SR
Why this matters: COLLABORATIVE PRIMARY RESULT: aging-associated repertoire specialization and reduced plasticity, not a complete immunity census.
DOI: 10.1073/pnas.1617959114
PNAS · 2025
Cvijović I, Swift M, Quake SR
Why this matters: CURRENT QUAKE-LAB PRIMARY RESULT: six donors and four immune-rich tissues demonstrate limits of blood-only repertoire monitoring.
DOI: 10.1073/pnas.2406474122
PNAS · 2017
Kowarsky M, Camunas-Soler J, Kertesz M, et al., Wolfe ND, Quake SR
Why this matters: QUAKE-LAB PRIMARY RESULT: 1,351 blood samples from 188 patients; 7,190 contigs including 3,761 novel. Sequence detection is distinct from viability and causal infection.
DOI: 10.1073/pnas.1707009114
eLife · 2017
Yu FB, Blainey PC, Schulz F, Woyke T, Horowitz MA, Quake SR
Why this matters: QUAKE-LAB PRIMARY RESULT: two Yellowstone samples, 96 subsamples of 5–10 cells, 29 genomes; scoped environmental sampling.
DOI: 10.7554/eLife.26580
PLoS Pathog · 2026
Kowarsky M, et al., Quake SR
Why this matters: CURRENT ASSOCIATION STUDY: 42 plasma samples from 14 people living with HIV; host and microbial correlates do not establish causation.
DOI: 10.1371/journal.ppat.1014066