Publications
-
Lineage structure of the human antibody repertoire in response to influenza vaccination.
Jiang N,
He J, Weinstein JA, Penland L, Sasaki S, He XS, Dekker CL, Zheng NY, Huang M, Sullivan M, Wilson PC, Greenberg HB, Davis MM, Fisher DS, Quake SR.
Sci Transl Med.
2013;
5
(171):
171ra19
-
Microfluidic serial digital to analog pressure converter for arbitrary pressure generation and contamination-free flow control.
Yu F,
Horowitz MA, Quake SR.
Lab Chip.
2013;
13
(10):
1911-8
-
Proteome-wide protein interaction measurements of bacterial proteins of unknown function.
Meier M,
Sit RV, Quake SR.
Proc Natl Acad Sci U S A.
2013;
110
(2):
477-82
-
Simultaneous measurement of amyloid fibril formation by dynamic light scattering and fluorescence reveals complex aggregation kinetics.
Streets AM,
Sourigues Y, Kopito RR, Melki R, Quake SR.
PLoS One.
2013;
8
(1):
e54541
-
Clonal evolution of preleukemic hematopoietic stem cells precedes human acute myeloid leukemia.
Jan M,
Snyder TM, Corces-Zimmerman MR, Vyas P, Weissman IL, Quake SR, Majeti R.
Sci Transl Med.
2012;
4
(149):
149ra118
-
DNA sequencing: clinical applications of new DNA sequencing technologies.
Dewey FE,
Pan S, Wheeler MT, Quake SR, Ashley EA.
Circulation.
2012;
125
(7):
931-44
-
Digital PCR provides absolute quantitation of viral load for an occult RNA virus.
White RA,
Quake SR, Curr K.
J Virol Methods.
2012;
179
(1):
45-50
-
Genome-wide single-cell analysis of recombination activity and de novo mutation rates in human sperm.
Wang J,
Fan HC, Behr B, Quake SR.
Cell.
2012;
150
(2):
402-12
-
High throughput automated chromatin immunoprecipitation as a platform for drug screening and antibody validation.
Wu AR,
Kawahara TL, Rapicavoli NA, van Riggelen J, Shroff EH, Xu L, Felsher DW, Chang HY, Quake SR.
Lab Chip.
2012;
12
(12):
2190-8
-
Identification of a cKit(+) colonic crypt base secretory cell that supports Lgr5(+) stem cells in mice.
Rothenberg ME,
Nusse Y, Kalisky T, Lee JJ, Dalerba P, Scheeren F, Lobo N, Kulkarni S, Sim S, Qian D, Beachy PA, Pasricha PJ, Quake SR, Clarke MF.
Gastroenterology.
2012;
142
(5):
1195-1205.e6
-
Microfluidic single-cell real-time PCR for comparative analysis of gene expression patterns.
Sanchez-Freire V,
Ebert AD, Kalisky T, Quake SR, Wu JC.
Nat Protoc.
2012;
7
(5):
829-38
-
Microfluidic very large scale integration (mVLSI) with integrated micromechanical valves.
Araci IE,
Quake SR.
Lab Chip.
2012;
12
(16):
2803-6
-
Non-invasive prenatal measurement of the fetal genome.
Fan HC,
Gu W, Wang J, Blumenfeld YJ, El-Sayed YY, Quake SR.
Nature.
2012;
487
(7407):
320-4
-
Quantitative analysis of the human airway microbial ecology reveals a pervasive signature for cystic fibrosis.
Blainey PC,
Milla CE, Cornfield DN, Quake SR.
Sci Transl Med.
2012;
4
(153):
153ra130
-
Single cell profiling of circulating tumor cells: transcriptional heterogeneity and diversity from breast cancer cell lines.
Powell AA,
Talasaz AH, Zhang H, Coram MA, Reddy A, Deng G, Telli ML, Advani RH, Carlson RW, Mollick JA, Sheth S, Kurian AW, Ford JM, Stockdale FE, Quake SR, Pease RF, Mindrinos MN, Bhanot G, Dairkee SH, Davis RW, Jeffrey SS.
PLoS One.
2012;
7
(5):
e33788
-
Single-cell sequencing provides clues about the host interactions of segmented filamentous bacteria (SFB).
Pamp SJ,
Harrington ED, Quake SR, Relman DA, Blainey PC.
Genome Res.
2012;
22
(6):
1107-19
-
Sizing up cell-free DNA.
Quake S,
Clin Chem.
2012;
58
(3):
489-90
-
Systematic reconstruction of RNA functional motifs with high-throughput microfluidics.
Martin L,
Meier M, Lyons SM, Sit RV, Marzluff WF, Quake SR, Chang HY.
Nat Methods.
2012;
9
(12):
1192-4
-
An information theoretic, microfluidic-based single cell analysis permits identification of subpopulations among putatively homogeneous stem cells.
Glotzbach JP,
Januszyk M, Vial IN, Wong VW, Gelbard A, Kalisky T, Thangarajah H, Longaker MT, Quake SR, Chu G, Gurtner GC.
PLoS One.
2011;
6
(6):
e21211
-
Determinism and stochasticity during maturation of the zebrafish antibody repertoire.
Jiang N,
Weinstein JA, Penland L, White RA, Fisher DS, Quake SR.
Proc Natl Acad Sci U S A.
2011;
108
(13):
5348-53
-
Digital MDA for enumeration of total nucleic acid contamination.
Blainey PC,
Quake SR.
Nucleic Acids Res.
2011;
39
(4):
e19
-
Dynamic chromatin localization of Sirt6 shapes stress- and aging-related transcriptional networks.
Kawahara TL,
Rapicavoli NA, Wu AR, Qu K, Quake SR, Chang HY.
PLoS Genet.
2011;
7
(6):
e1002153
-
Genome of a low-salinity ammonia-oxidizing archaeon determined by single-cell and metagenomic analysis.
Blainey PC,
Mosier AC, Potanina A, Francis CA, Quake SR.
PLoS One.
2011;
6
(2):
e16626
-
Genomic analysis at the single-cell level.
Kalisky T,
Blainey P, Quake SR.
Annu Rev Genet.
2011:
45
431-45
-
Single-cell dissection of transcriptional heterogeneity in human colon tumors.
Dalerba P,
Kalisky T, Sahoo D, Rajendran PS, Rothenberg ME, Leyrat AA, Sim S, Okamoto J, Johnston DM, Qian D, Zabala M, Bueno J, Neff NF, Wang J, Shelton AA, Visser B, Hisamori S, Shimono Y, van de Wetering M, Clevers H, Clarke MF, Quake SR.
Nat Biotechnol.
2011;
29
(12):
1120-7
-
Single-cell genomics.
Kalisky T,
Quake SR.
Nat Methods.
2011;
8
(4):
311-4
-
The RootChip: an integrated microfluidic chip for plant science.
Grossmann G,
Guo WJ, Ehrhardt DW, Frommer WB, Sit RV, Quake SR, Meier M.
Plant Cell.
2011;
23
(12):
4234-40
-
Tracking single hematopoietic stem cells in vivo using high-throughput sequencing in conjunction with viral genetic barcoding.
Lu R,
Neff NF, Quake SR, Weissman IL.
Nat Biotechnol.
2011;
29
(10):
928-33
-
Universal noninvasive detection of solid organ transplant rejection.
Snyder TM,
Khush KK, Valantine HA, Quake SR.
Proc Natl Acad Sci U S A.
2011;
108
(15):
6229-34
-
Whole-genome molecular haplotyping of single cells.
Fan HC,
Wang J, Potanina A, Quake SR.
Nat Biotechnol.
2011;
29
(1):
51-7
-
A microfluidic oligonucleotide synthesizer.
Lee CC,
Snyder TM, Quake SR.
Nucleic Acids Res.
2010;
38
(8):
2514-21
-
Analysis of the size distributions of fetal and maternal cell-free DNA by paired-end sequencing.
Fan HC,
Blumenfeld YJ, Chitkara U, Hudgins L, Quake SR.
Clin Chem.
2010;
56
(8):
1279-86
-
Biocompatibility and Reduced Drug Absorption of Sol-Gel-Treated Poly(dimethyl siloxane) for Microfluidic Cell Culture Applications.
Gomez-Sjoberg R,
Leyrat AA, Houseman BT, Shokat K, Quake SR.
Anal Chem.
2010
-
Clinical assessment incorporating a personal genome.
Ashley EA,
Butte AJ, Wheeler MT, Chen R, Klein TE, Dewey FE, Dudley JT, Ormond KE, Pavlovic A, Morgan AA, Pushkarev D, Neff NF, Hudgins L, Gong L, Hodges LM, Berlin DS, Thorn CF, Sangkuhl K, Hebert JM, Woon M, Sagreiya H, Whaley R, Knowles JW, Chou MF, Thakuria JV, Rosenbaum AM, Zaranek AW, Church GM, Greely HT, Quake SR, Altman RB.
Lancet.
2010;
375
(9725):
1525-35
-
Colloidal lenses allow high-temperature single-molecule imaging and improve fluorophore photostability.
Schwartz JJ,
Stavrakis S, Quake SR.
Nat Nanotechnol.
2010;
5
(2):
127-32
-
Ostwald ripening of clusters during protein crystallization.
Streets AM,
Quake SR.
Phys Rev Lett.
2010;
104
(17):
178102
-
Sensitivity of noninvasive prenatal detection of fetal aneuploidy from maternal plasma using shotgun sequencing is limited only by counting statistics.
Fan HC,
Quake SR.
PLoS One.
2010;
5
(5):
e10439
-
Single-cell NF-kappaB dynamics reveal digital activation and analogue information processing.
Tay S,
Hughey JJ, Lee TK, Lipniacki T, Quake SR, Covert MW.
Nature.
2010;
466
(7303):
267-71
-
An in vitro microfluidic approach to generating protein-interaction networks.
Gerber D,
Maerkl SJ, Quake SR.
Nat Methods.
2009;
6
(1):
71-4
-
Association of reactive oxygen species levels and radioresistance in cancer stem cells.
Diehn M,
Cho RW, Lobo NA, Kalisky T, Dorie MJ, Kulp AN, Qian D, Lam JS, Ailles LE, Wong M, Joshua B, Kaplan MJ, Wapnir I, Dirbas FM, Somlo G, Garberoglio C, Paz B, Shen J, Lau SK, Quake SR, Brown JM, Weissman IL, Clarke MF.
Nature.
2009;
458
(7239):
780-3
-
Automated microfluidic chromatin immunoprecipitation from 2,000 cells.
Wu AR,
Hiatt JB, Lu R, Attema JL, Lobo NA, Weissman IL, Clarke MF, Quake SR.
Lab Chip.
2009;
9
(10):
1365-70
-
Digital PCR provides sensitive and absolute calibration for high throughput sequencing.
White RA,
Blainey PC, Fan HC, Quake SR.
BMC Genomics.
2009:
10
116
-
Experimental determination of the evolvability of a transcription factor.
Maerkl SJ,
Quake SR.
Proc Natl Acad Sci U S A.
2009;
106
(44):
18650-5
-
High-throughput sequencing of the zebrafish antibody repertoire.
Weinstein JA,
Jiang N, White RA, Fisher DS, Quake SR.
Science.
2009;
324
(5928):
807-10
-
In vitro embryo culture in defined, sub-microliter volumes.
Melin J,
Lee A, Foygel K, Leong DE, Quake SR, Yao MW.
Dev Dyn.
2009;
238
(4):
950-5
-
Microfluidic digital PCR enables rapid prenatal diagnosis of fetal aneuploidy.
Fan HC,
Blumenfeld YJ, El-Sayed YY, Chueh J, Quake SR.
Am J Obstet Gynecol.
2009;
200
(5):
543.e1-7
-
Single molecule measurement of the "speed limit" of DNA polymerase.
Schwartz JJ,
Quake SR.
Proc Natl Acad Sci U S A.
2009;
106
(48):
20294-9
-
Single-molecule sequencing of an individual human genome.
Pushkarev D,
Neff NF, Quake SR.
Nat Biotechnol.
2009;
27
(9):
847-50
-
A synthetic Escherichia coli predator-prey ecosystem.
Balagaddé FK,
Song H, Ozaki J, Collins CH, Barnet M, Arnold FH, Quake SR, You L.
Mol Syst Biol.
2008:
4
187
-
Discovery of a hepatitis C target and its pharmacological inhibitors by microfluidic affinity analysis.
Einav S,
Gerber D, Bryson PD, Sklan EH, Elazar M, Maerkl SJ, Glenn JS, Quake SR.
Nat Biotechnol.
2008;
26
(9):
1019-27
-
Noninvasive diagnosis of fetal aneuploidy by shotgun sequencing DNA from maternal blood.
Fan HC,
Blumenfeld YJ, Chitkara U, Hudgins L, Quake SR.
Proc Natl Acad Sci U S A.
2008;
105
(42):
16266-71
-
At the interface of physics and biology.
Quake S,
Biotechniques.
2007;
43
(1):
19
-
Detection of aneuploidy with digital polymerase chain reaction.
Fan HC,
Quake SR.
Anal Chem.
2007;
79
(19):
7576-9
-
Dissecting biological "dark matter" with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth.
Marcy Y,
Ouverney C, Bik EM, Lösekann T, Ivanova N, Martin HG, Szeto E, Platt D, Hugenholtz P, Relman DA, Quake SR.
Proc Natl Acad Sci U S A.
2007;
104
(29):
11889-94
-
Lola regulates Drosophila olfactory projection neuron identity and targeting specificity.
Spletter ML,
Liu J, Liu J, Su H, Giniger E, Komiyama T, Quake S, Luo L.
Neural Dev.
2007:
2
14
-
Microfluidic large-scale integration: the evolution of design rules for biological automation.
Melin J,
Quake SR.
Annu Rev Biophys Biomol Struct.
2007:
36
213-31
-
Nanoliter reactors improve multiple displacement amplification of genomes from single cells.
Marcy Y,
Ishoey T, Lasken RS, Stockwell TB, Walenz BP, Halpern AL, Beeson KY, Goldberg SM, Quake SR.
PLoS Genet.
2007;
3
(9):
1702-8
-
Solvent resistant microfluidic DNA synthesizer.
Huang Y,
Castrataro P, Lee CC, Quake SR.
Lab Chip.
2007;
7
(1):
24-6
-
Versatile, fully automated, microfluidic cell culture system.
Gómez-Sjöberg R,
Leyrat AA, Pirone DM, Chen CS, Quake SR.
Anal Chem.
2007;
79
(22):
8557-63
-
A microfluidic rectifier: anisotropic flow resistance at low Reynolds numbers.
Groisman A,
Quake SR.
Phys Rev Lett.
2004;
92
(9):
094501
-
A nanoliter-scale nucleic acid processor with parallel architecture.
Hong JW,
Studer V, Hang G, Anderson WF, Quake SR.
Nat Biotechnol.
2004;
22
(4):
435-9
-
Microfluidic device reads up to four consecutive base pairs in DNA sequencing-by-synthesis.
Kartalov EP,
Quake SR.
Nucleic Acids Res.
2004;
32
(9):
2873-9
-
Solvent-resistant photocurable liquid fluoropolymers for microfluidic device fabrication [corrected].
Rolland JP,
Van Dam RM, Schorzman DA, Quake SR, DeSimone JM.
J Am Chem Soc.
2004;
126
(8):
2322-3
-
Systematic investigation of protein phase behavior with a microfluidic formulator.
Hansen CL,
Sommer MO, Quake SR.
Proc Natl Acad Sci U S A.
2004;
101
(40):
14431-6
-
Tip-enhanced fluorescence microscopy at 10 nanometer resolution.
Gerton JM,
Wade LA, Lessard GA, Ma Z, Quake SR.
Phys Rev Lett.
2004;
93
(18):
180801
-
Behavior of complex knots in single DNA molecules.
Bao XR,
Lee HJ, Quake SR.
Phys Rev Lett.
2003;
91
(26 Pt 1):
265506
-
Integrated nanoliter systems.
Hong JW,
Quake SR.
Nat Biotechnol.
2003;
21
(10):
1179-83
-
Microfabricated fountain pens for high-density DNA arrays.
Reese MO,
van Dam RM, Scherer A, Quake SR.
Genome Res.
2003;
13
(10):
2348-52
-
Microfluidic memory and control devices.
Groisman A,
Enzelberger M, Quake SR.
Science.
2003;
300
(5621):
955-8
-
Microfluidics in structural biology: smaller, faster em leader better.
Hansen C,
Quake SR.
Curr Opin Struct Biol.
2003;
13
(5):
538-44
-
Polyelectrolyte surface interface for single-molecule fluorescence studies of DNA polymerase.
Kartalov EP,
Unger MA, Quake SR.
Biotechniques.
2003;
34
(3):
505-10
-
Quantifying double-strand breaks and clustered damages in DNA by single-molecule laser fluorescence sizing.
Filippova EM,
Monteleone DC, Trunk JG, Sutherland BM, Quake SR, Sutherland JC.
Biophys J.
2003;
84
(2 Pt 1):
1281-90
-
Sequence information can be obtained from single DNA molecules.
Braslavsky I,
Hebert B, Kartalov E, Quake SR.
Proc Natl Acad Sci U S A.
2003;
100
(7):
3960-4
-
Solving the "world-to-chip" interface problem with a microfluidic matrix.
Liu J,
Hansen C, Quake SR.
Anal Chem.
2003;
75
(18):
4718-23
-
A nanoliter rotary device for polymerase chain reaction.
Liu J,
Enzelberger M, Quake S.
Electrophoresis.
2002;
23
(10):
1531-6
-
A robust and scalable microfluidic metering method that allows protein crystal growth by free interface diffusion.
Hansen CL,
Skordalakes E, Berger JM, Quake SR.
Proc Natl Acad Sci U S A.
2002;
99
(26):
16531-6
-
An integrated microfabricated cell sorter.
Fu AY,
Chou HP, Spence C, Arnold FH, Quake SR.
Anal Chem.
2002;
74
(11):
2451-7
-
Gene expression analysis with universal n-mer arrays.
van Dam RM,
Quake SR.
Genome Res.
2002;
12
(1):
145-52
-
Identification and confirmation of a module of coexpressed genes.
Thompson HG,
Harris JW, Wold BJ, Quake SR, Brody JP.
Genome Res.
2002;
12
(10):
1517-22
-
Microfluidic large-scale integration.
Thorsen T,
Maerkl SJ, Quake SR.
Science.
2002;
298
(5593):
580-4
-
Number, density, and surface/cytoplasmic distribution of GABA transporters at presynaptic structures of knock-in mice carrying GABA transporter subtype 1-green fluorescent protein fusions.
Chiu CS,
Jensen K, Sokolova I, Wang D, Li M, Deshpande P, Davidson N, Mody I, Quick MW, Quake SR, Lester HA.
J Neurosci.
2002;
22
(23):
10251-66
-
Significance and statistical errors in the analysis of DNA microarray data.
Brody JP,
Williams BA, Wold BJ, Quake SR.
Proc Natl Acad Sci U S A.
2002;
99
(20):
12975-8
-
Velocity-independent microfluidic flow cytometry.
Eyal S,
Quake SR.
Electrophoresis.
2002;
23
(16):
2653-7
-
Dynamic pattern formation in a vesicle-generating microfluidic device.
Thorsen T,
Roberts RW, Arnold FH, Quake SR.
Phys Rev Lett.
2001;
86
(18):
4163-6
-
Single-molecule measurements calibrate green fluorescent protein surface densities on transparent beads for use with 'knock-in' animals and other expression systems.
Chiu CS,
Kartalov E, Unger M, Quake S, Lester HA.
J Neurosci Methods.
2001;
105
(1):
55-63
-
Femtonewton force spectroscopy of single extended DNA molecules.
Meiners JC,
Quake SR.
Phys Rev Lett.
2000;
84
(21):
5014-7
-
From micro- to nanofabrication with soft materials.
Quake SR,
Scherer A.
Science.
2000;
290
(5496):
1536-40
-
Monolithic microfabricated valves and pumps by multilayer soft lithography.
Unger MA,
Chou HP, Thorsen T, Scherer A, Quake SR.
Science.
2000;
288
(5463):
113-6
-
A microfabricated device for sizing and sorting DNA molecules.
Chou HP,
Spence C, Scherer A, Quake S.
Proc Natl Acad Sci U S A.
1999;
96
(1):
11-3
-
A microfabricated fluorescence-activated cell sorter.
Fu AY,
Spence C, Scherer A, Arnold FH, Quake SR.
Nat Biotechnol.
1999;
17
(11):
1109-11
-
Single-molecule fluorescence observed with mercury lamp illumination.
Unger M,
Kartalov E, Chiu CS, Lester HA, Quake SR.
Biotechniques.
1999;
27
(5):
1008-14
-
The dynamics of partially extended single molecules of DNA.
Quake SR,
Babcock H, Chu S.
Nature.
1997;
388
(6638):
151-4
-
Fast Monte Carlo algorithms for knotted polymers.
Quake SR,
Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics.
1995;
52
(1):
1176-1180
-
Relaxation of a single DNA molecule observed by optical microscopy.
Perkins TT,
Quake SR, Smith DE, Chu S.
Science.
1994;
264
(5160):
822-6
-
Topological effects of knots in polymers.
Quake SR,
Phys Rev Lett.
1994;
73
(24):
3317-3320
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